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US Army Mycoplasma Fermentans
Incognitus Patent - Read It And Weep
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United States Patent 5,242,820
Lo September 7, 1993
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Pathogenic mycoplasma
Abstract
 
The invention relates to a novel pathogenic mycoplasma isolated from
patients with Acquired Immune Deficiency Syndrome (AIDS) and its use in
detecting antibodies in sera of AIDS patients, patients with AIDS-related
complex (ARC) or patients dying of diseases and symptoms resembling AIDS
diseases. The invention further relates to specific DNA sequences,
antibodies against the pathogenic mycoplasma, and their use in detecting
DNA or antigens of the pathogenic mycoplasma or other genetically and
serologically closely related mycoplasmas in infected tissue of patients
with AIDS or ARC or patients dying of symptoms resembling AIDS diseases.
The invention still further relates to a variety of different forms of
vaccine against mycoplasma infection in humans and/or animals.
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Inventors: Lo; Shyh-Ching (Potomac, MD)
Assignee: American Registry of Pathology (Washington, DC)
Appl. No.: 710361
Filed: June 6, 1991
 
Current U.S. Class: 435/252.1; 435/5; 435/872
Intern'l Class: C12N 005/00; C12N 005/02; C12N 001/00; C12Q 001/70
Field of Search: 435/870,5,872,240.2
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References Cited [Referenced By]
 
Other References
 
 
Marquart et al (1985) Mycoplasma-Like Structures . . . Eur J Clin Microbiol
4(1):73-74.
Lo et al (1989) A Novel Virus-like Infectious Agent . . . Am J Trop Med Hyg
40(2):213-226.
Lo et al (1989) Identification of M Incognitus . . . Am. J. Trop-Med. Hyg
41(5):601-616.
Lo et al (1989) Association of the Virus-like Agent . . . Am J Trop Med Hyg
41(3):364-376.
Lo et al (1989) Fatal Infection of Silvered Leaf Monkeys . . . Am. T Trop
Med Hyg 40(4):399-409.
Lo et al (1989) Virus-like Infectious Agent . . . Am J Trop Med Hyg
41(5):586-600.
Marquart et al (Feb. 1985) Abstract Only Eur J Clin Microbiol 4(1):73-74.
Hu et al (1990) Gene 93:67-72.
Primary Examiner: Nucker; Christine M.
Assistant Examiner: Preston; D. R.
Attorney, Agent or Firm: Venable, Baetjer, Howard & Civiletti
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Goverment Interests
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The invention described herein was made in the course of work under a grant
or award from the United States Department of the Army.
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Parent Case Text
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CROSS-REFERENCE TO RELATED APPLICATIONS
This is a continuation-in-part of U.S. patent application Ser. No. 265,920,
filed Nov. 2, 1988, now abandoned, which is a continuation-in-part of U.S.
patent application Ser. No. 875,535, filed Jun. 18, 1986, now abandoned.
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Claims
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What is claimed is:
1. A biologically pure mycoplasma isolated from tissues of patients with
AIDS comprising the mycoplasma produced by the cell line ATCC No. CRL 9127.
2. A biologically pure mycoplasma having the identifying characteristics of
M. fermentans incognitus, ATCC 53949.
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Description
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BACKGROUND OF THE INVENTION
 
1. Field of the Invention
 
The present invention relates to a novel strain of mycoplasma isolated from
a patient with AIDS. The mycoplasma is closely related to a species of
human mycoplasma, M. fermentans. Upon characterization of this mycoplasma,
it may be classified as a unique strain within the species M. fermentans
incognitus.
 
This novel strain of nycoplasma is referred to hereinafter as the
incognitus strain or M. fermentans incognitus.
 
The invention also relates to use of the mycoplasma M. fermentans
incognitus as well as all strains of M. fermentans in detecting specific
antibodies in sera of patients with AIDS or an acute fulminant systemic
disease and/or animals and its use as a vaccine against infection by the
mycoplasma. The invention further relates to incognitus strain-specific
antibodies and cross-reactive which later break up into individual cells
that are capable of passing through membrane filters of pore size 0.45
.mu.m or even 0.22 .mu.m.
 
A trilaminar cytoplasmic membrane contains sterols, phospholipid and
proteins. Therefore, the cells are generally susceptible to polyene
antibiotics and to lysis by digitonin.
 
Replication of the Mycoplasma genome may precede cytoplasmic division
resulting in multinucleate filaments before individual cells are delimited
by constriction. Budding can also occur.
Most Mycoplasma species are facultatively anaerobic, and all known species
are chemoorganotrophic. The fermentative species of Mycoplasma utilize
sugars such as glucose, while non-fermentative species can utilize
arginine.
 
Known mycoplasmas may be grown on complex media, such as Hayflick medium,
while fastidious mycoplasmas may be grown on diphasic SP-4 medium. The
colonies are usually of the "fried egg" type, i.e., an opaque, granular
central region, embedded in the agar, surrounded by non-granular surface
growth. The optimal growth temperature of mammalian strains is
36.degree.-37.degree. C.
Many species of Mycoplasma produce weak or clear haemolysis which appears
to be due to the secretion of H.sub.2 O.sub.2. This H.sub.2 O.sub.2
secretion is believed to be responsible for some aspects of the
mycoplasmas' pathogenicity. Known mycoplasmas are commonly sensitive to
chloramphenicol and
tetracyclines.
 
The Mycoplasma genus currently consists of more than 60 known species which
are differentiated on the basis of various tests, including utilization of
glucose and mannose, arginine hydrolysis, phosphatase production, the "film
and spots" reaction and haemadsorption. M. fermentans antibodies (i.e.
antibodies to homologous antigenic determinants), including monoclonal
antibodies of each, which are useful in detecting incognitus strain
antigens in infected tissue of patients or animals. The invention also
relates to incognitus strain-specific DNA probes which are useful in
detecting incognitus strain genetic materials in infected tissues of
patients or animals. Incognitus strain genetic materials may also be
detected in infected humans or animals by using specific incognitus strain
DNA sequences a homologous M. fermentans DNA sequences and the polymerase
chain reaction ("PCR") (U.S. Pat. No. 4,683,202 incorporated herein by
reference).
 
The ability to monitor AIDS or other acute fulminant systemic disease
status can be of great value. In addition to improving
prognostication,knowledge of the disease status allows the attending
physician to select the most appropriate therapy for the individual
patient, e.g. highly aggressive or less aggressive therapy regimens.
Because of patient distress caused by more aggressive therapy regimens, it
is desirable to distinguish those patients requiring such therapies. It has
been found that M. fermentans incognitus is more directly associated and
functional deficits of the infected organ systems and is capable of
distinguishing such patients.
 
Mycoplasma is a genus of cell wall-less sterol-requiring, catalase-negative
pathogens commonly found in the respiratory and urogenital tracts of man
and other animals. The cells of Mycoplasma are typically non-motile and
pleomorphic, ranging from spherical, ovoid or pear-shaped to branched
filamentous forms.
 
Filaments are the typical forms in young cultures under optimal conditions,
which subsequently transform into chains of coccoid cells
 
Mycoplasmas are the smallest and simplest free-living organisms known.
Mycoplasmas are not obligatory intracellular microorganisms and are usually
found extracellularly, but are often found intracellularly in the infected
tissues (Mycoplasma, Eds. Wolfgang, J. J., Willette, H. P., Amos, D. B.,
Wilfert, C. M., Zinsser Microbiology 19th Ed. 1988, Appleton and Lange,
617-623). The term mycoplasma apparently was first used by B. Frank in 1889
(Frank B., Dent. Bot. Ges., 7, 332 (1889) and Krass, C. J. et al., Int. J.
Syst. Bacteriol. 23, 62 (1973)). Frank, after careful microscopic
observation, began writing about invasion of plants (legume) by these
microorganisms and stated: "the changed character of the protoplasm in the
cortical cells arising from infection, I will designate as mycoplasma".
Later, he had more explicitly defined mycoplasma as a mixture of small
fungus-like microorganisms and cell protoplasm (Frank, B., Landwirt. Jahrb.
19, 523 (1890)). The description reflected the difficulty of
differentiating this unique microorganism from the infected host cells
morphologically.
 
Even today with electron microscopy, it is still often difficult to
differentiate the mycoplasmas from the cellular protoplasmic processes or
the subcellular organelles of the infected host, because ultrastructurally,
these microorganisms have protoplasm-like internal structures and are
bounded by only an outer limited membrane (unit membrane) without a cell
wall. Thus, there have been few electron microscopic studies of mycoplasmas
identified directly in the infected tissues of animals or humans.
 
It has been reported that ultrastructural examination of infected tissues
has failed to localize the microbe, even in tissues where very high titers
(>10.sup.9 /gm) of microorganisms were recovered in culture (Elizan, T. S.
et al., Pro. Soc. Exp. Biol. Med. 139, 52 (1972) and Schwartz, J. et al.,
Pro. Soc. Exp. Biol. Med. 139, 56 (1972)). Therefore, morphologically, the
microbe might be mimicking certain normal cellular or subcellular
structures in the infected host tissues and preventing direct
identification.
 
In addition to the natural difficulty of morphological differentiation
between the microorganisms and the protoplasm of infected cells, the often
poorly preserved formalin-fixed clinical materials present further
limitations to any attempt to directly visualize mycoplasma organisms in
the tissues.
 
 
DESCRIPTION OF THE BACKGROUND ART
 
Acquired Immune Deficiency Syndrome (AIDS) is a devastating disease that
has afflicted over 70,000 people worldwide (AIDS Weekly Surveillance
Report--United States, Centers for Disease Control, Aug. 29, 1988). The
disease is clinically characterized by a set of typical syndromes which
manifests itself by the development of opportunistic infections such as
pneumocystic carinii pneumonia (PCP), toxoplasmosis, atypical
mycobacteriosis and cytomegalovirus (CMV). Further characteristics of the
AIDS associated syndromes are the clinical manifestation of
neuropsychiatric abnormalities, of AIDS encephalopathy (Naura, B. A., et
at., Ann.Neuro 19, 517 (1986)), kidney failure of AIDS nephropathy, heart
failure of AIDS cardiomyopathy infections and certain uncommon malignancies
such as Kaposi's sarcoma or B-cell lymphoma (Durack, D. T., N.Eng.J.Med.
305, 1465 (1981); Reichert, C. M., et al., Am.J.Path. 112, 357 (1983);
Ziegler, J. L., et al., N.Eng.J.Med. 311, 565 (1984)).
 
Through co-cultivation of AIDS patients' peripheral blood cells with
mitogen-stimulated normal human lymphocytes or permanent human T-cell
lines, a number of laboratories have isolated T-cell-tropic human
retroviruses (HTLV-III/LAV), Barre-Sinoussi, F., et al., Science 220, 868
(1983); Gallo, R. C., et al., Science 224, 500 (1984). Epidemiologically,
the newly isolated retroviruses have been shown to be highly associated
with patients of AIDS and/or AIDS-related complex (ARC). Schupback, J., et
al., Science 224, 503 (1984); Sarngadharan, M. G., et al., Science 224, 506
(1984). In vitro studies with HTLV-III/LAV have demonstrated T-cell tropism
and cytopathic changes. Barre-Sinoussi, F., et al., supra; Popovic, M., et
al., Science 224, 497 (1984). HTLV-III/LAV is believed to be the causative
agent of AIDS.
 
However, the establishment of an animal model of AIDS by HTLV-III-LAV
injection has not been successful. Gajdusek, D.C., et al., Lancet I, 1415
(1984). The chimpanzee is the only primate other than man found to be
susceptible to infection by HTLV-III/LAV. However, overt AIDS manifested by
the development of opportunistic infections and/or unusual malignancies has
not yet been seen, despite evidence for persistent infection and/or viremia
in experiments on this species. Gajdusek, D.C., et al. Lancet I, 55 (1985).
Thus, the human retroviruses have not fulfilled Koch's postulates, i.e.,
producing transmissible AIDS-like diseases in experimental animals.
HTLV-III/LAV is not associated with the unusual malignancies such as B-cell
lymphoma and Kaposi's sarcoma, commonly found in patients with AIDS. Shaw,
G. M., et al., Science 226: 1165-1171, 1984; Delli Bovi, P. et al., Cancer
Research, 46: 6333-6338, 1986; Groopman, J. E., et al., Blood 67: 612-615,
1986. Furthermore, HIV infected patients often show a wide variation in
times of disease incubation and speed of disease progression. It is not
known whether any specific infectious agent other than HIV can be
responsible for the complex pathogenesis often seen in this disease. One
such candidate, initially identified as a virus or virus-like infectious
agent in parent application Ser. No. 265,920 has now been discovered to be
the mycoplasma M. fermentans (incognitus strain).
 
Although a viral etiology of developing these malignancies has long been
suggested, conventional approaches for isolating infectious viral agents
have not been fruitful. The presence of a transforming gene or transforming
genes (oncogenes) has been associated with Kaposi's sarcoma (Lo. S., et
al., Am. J. Path., 118, 7 (1985)). A transformant carrying the transforming
gene can cause tumors in mice.
 
However, there is no further characterization of this transforming gene
except for the presence of human repetitive DNA sequences. The transforming
gene has not been shown to be associated with any viral or virus-like
agent. An ongonege of AIDS Kaposi Sarcoma was similarly identified
following DNA transfection into NIH/3T3 cells and was later characterized
in detail (Delli Bovi O. et al., Proc Natl Acad Sci 84, 5660 (1987) and
Delli Bovi P. et al., 50, 729 (1987). The oncogene was found to be a
rearranged human protooncogene of the fibroblast growth factor (FGF)
family.
 
 
SUMMARY OF INVENTION
 
The present invention relates to a novel strain of the mycoplasma M.
fermentans which has been isolated from Kaposi's sarcoma of a patient with
AIDS. This novel strain of mycoplasama has been designated the incognitus
strain of M. fermentans or M. fermentans incognitus. The invention further
relates to the use of this incognitus strain of M. fermentans as well as
other strains of M. fermentans with homologous antigenic determinants for
the detection of specific antibodies in sera of human patients and animals,
and for vaccines against mycoplasmas. The invention also relates to
antibodies, including monoclonal antibodies, to M. fermentans incognitus
and to homologous antigenic determinants of M. fermentans and their use in
detecting M. fermentans incognitus antigens in the infected tissue of human
patients and animals. The invention further relates to sequencing the DNA
of the M. fermentans incognitus and the manufacture of DNA probes based on
such sequencing and homologous sequences of M. fermentans for use in the
direct detection of the unique DNA sequences in the tissues of human
patients and animals.
 
The present invention further relates to the detection of the presence of
M. fermentans incognitus in patients which are HIV-positive or have other
acute fulminant systemic disease as an indication of the prognosis of the
disease, which can be used to determine the appropriate therapy regimen.
The presence of M. fermentans incognitus is determined as described above.
 
The M. fermentans incognitus DNA is detected in the spleen, liver, brain,
lymph nodes, kidney, placenta, lungs, adrenal glands, heart and peripheral
blood mononuclear cells of patients with AIDS, or from Kaposi's sarcoma
tissue from patients with AIDS. The M. fermentans incognitus DNA is capable
of transfecting and transforming NIH/3T3 cells. M. fermentans incognitus is
a transmissible virus-like infectious agent in cell cultures, experimental
animals and humans. The DNA of the transformants does not contain human
repetitive DNA sequences. Two transformants are identified as Sb51 and
Kb43. These transformants are persistently infected by the M. fermentans
incognitus. M. fermentans incognitus is then isolated from the
transformants.
 
The majority of M. fermentans incognitus cells have a size of about 140 nm
to about 280 nm, with an overall range of 100-900 nm. Introduction of M.
fermentans incognitus into nude mice and immunocompetent mice (Balb/c)
results in a significant morbidity and mortality of the infected animals
and the manifestation of many symptoms such as B-cell tumor, spindle cell
tumor or immunodeficiency.
 
Similar diseases are transmitted from animal to animal by introduction of
infected tissues.
M. fermentans incognitus was also found to infect non-human primates
(monkeys). M. fermentans incognitus antigens were identified in the
infected monkey's sera, and M. fermentans incognitus DNA was found in DNA
isolated from tissues of the infected monkeys.
 
M. fermentans incognitus and other strains of M. fermentans having
homologous antigens are capable of detecting antibodies in sera of patients
with AIDS, ARC or non-AIDS patients with this mycoplasma infection. Any
method for detecting an antigen-antibody reaction may be utilized,
including enzyme-linked immunosorbent assay (ELISA), immunoradiometric
assay, direct and indirect immunofluorescent assay, Western blot technique,
and the like. In addition, M. fermentans incognitus-specific antibodies (as
well as antibodies to homologous antigens of other M. fermentans strains)
are raised in experimental animals or developed in monoclonal antibodies
which are capable of detecting M. fermentans incognitus- related antigens
in infected tissues. Furthermore, the probes having M. fermentans
incognitus-specific or homologous M. fermentans DNA sequences can be used
in the direct detection of M. fermentans incognitus DNA in infected
tissues, or specific M. fermentans incognitus or homologous M. fermentans
DNA sequences can be used in the polymerase chain reaction ("PCR") to
identify M. fermentans incognitus DNA in infected tissues. Since antibodies
or antisera are successfully raised against M. fermentans incognitus, the
M. fermentans incognitus or homologous antigens of M. fermentans antigens
can be utilized to prepare vaccines which may be used to protect animals,
including humans, against infection by M. fermentans incognitus or other
mycoplasmas.
 
 
BRIEF DESCRIPTION OF THE DRAWINGS
 
FIG. 1A shows an electron photomicrograph of M. fermentans incognitus.
FIG. 1B shows an electron photomicrograph of M. fermentans prototype strain
(PG18).
FIG. 1C shows the colony morphology of M. fermentans incognitus.
FIG. 1D shows the colony morphology of the prototype strain (PG18) of M.
fermentans.
FIG. 2A shows antigenic comparison of M. fermentans incognitus, M.
fermentans and other human mycoplasmas in immunoblots immunostained with
rabbit antiserum raised specifically against M. fermentans incognitus.
FIG. 2B shows mycoplasmas in immunoblots immunostained with mule antiserum
raised specifically against M. fermentans.
FIG. 3 shows a comparison of DNA homology and restriction patterns between
M. fermentans incognitus and other human mycoplasmas. The samples were
probed with A) pst-8.6, B) psb-2.2, C) RS48, D) MI-H 3.3, E) cDNA clone of
E. coli rRNA.
FIG. 4A shows direct immunofluorescence staining of M. fermentans
incognitus using FITC conjugated monoclonal antibody D81E7 (X900).
FIG. 4B shows direct immunofluorescence staining of M. fermentans using
FITC conjugated monoclonal antibody D81E7 (X900).
FIG. 5A shows the genetic map of a repetitive segment of a 2.2 Kb Eco RI
fragment of M. fermentans incognitus.
FIG. 5B shows the nucleotide sequence of a repetitive segment of a 2.2 Kb
Eco RI fragment of M. fermentans incognitus.
FIG. 5C shows the genetic map of a repetitive segment of a 2.2 Kb Eco RI
fragment of M. fermentans incognitus.
FIG. 6 shows the analysis of repetitive elements following probing with A)
psb-2.2 and B-K of FIG. 5A.
FIG. 7A shows detection of M. fermentans from urine specimens following PCR
stained with ethidium bromide.
FIG. 7B shows detection of M. fermentans from urine specimens following PCR
stained with Probe RU006.
FIG. 8A shows detection of M. fermentans incognitus from urine specimens
following PCR stained with ethidium bromide.
FIG. 8B shows detection of M. fermentans incognitus from urine specimens
following PCR stained with Probe RU006.
FIG. 9 shows analysis of genomic DNA from various strains or isolates of M.
fermentans.
FIG. 10A shows an electron micrograph of thin sections of M. fermentans
incognitus cells in the cytoplasm of degenerating Sb51 cells.
FIG. 10B shows an electron micrograph of membrane bound M. fermentans
incognitus.
FIG. 10C shows an electron micrograph of a partially disrupted M.
fermentans incognitus at high magnification.
FIG. 11 shows a graph of body weight of monkeys over time, after
innoculation with M. fermentans incognitus.
FIG. 12A shows immunocytochemical staining of Sb51 cells with non-AIDS serum.
FIG. 12B shows immunocytochemical staining of NIH/3T3 cells with AIDS serum.
FIG. 12C shows immunocytochemical staining of Sb51 cells with AIDS serum.
FIG. 13 shows the immunocytochemical staining of the subcapsular cortical
sinus of a lymph node from a patient with AIDS.
FIG. 14 shows the immunohistochemistry of the midbrain of the brain stem of
a patient with AIDS.
FIG. 15A shows blotted filters of DNA from Sb51 cells and control NIH/3T3
cells probed with psb-8.6.
FIG. 15B shows blotted filters of DNA from Sb51 cells and control NIH/3T3
cells probed with psb-2.2.
FIG. 16 shows blotted filters of digested DNA from Sb51 cells, control
NIH/3T3, cells, cell-free M. fermentans incognitus transmission in NIH/3T3
cells and DNA of partially purified M. fermentans incognitus probed with
psb-8.6.
FIG. 17A shows a sucrose gradient banding of M. fermentans incognitus.
FIG. 17B shows DNA and antigen dot blot analysis of sucrose gradient-banded
M. fermentans incognitus in which the blot was probed with .sup.32 P in a
labeled insert fragment of psb-8.6.
FIG. 18A shows DNA and antigen dot blot analysis of sucrose gradient-banded
M. fermentans incognitus in which immunochemical staining using
pre-immunized rabbit serum was performed.
FIG. 18B shows DNA and antigen dot blot analysis of sucrose gradient-banded
M. fermentans incognitus in which immunochemical staining using post-M.
fermentans incognitus immunization rabbit antisera was performed.
FIG. 19A shows Southern blot hybridizations to compare M. fermentans
incognitus DNA to DNA from known human herpes viruses, vaccinia virus, MCMV
and HVS. The samples were probed with A) HSV-1 pHSV-106.
FIG. 19B shows the Southern blot of FIG. 19A using B) VZV pEco A.
FIG. 19C shows the Southern blot of FIG. 19A using C) EBV pBam W.
FIG. 19D shows the Southern blot of FIG. 19A using D) CMV pCMH-35.
FIG. 19E shows the Southern blot of FIG. 19A using E) HBLV pZVH-70.
FIG. 19F shows the Southern blot of FIG. 19A using F) Vaccinia pEH-1.
FIG. 19G shows the Southern blot of FIG. 19A using G) MCMV pAMB-25.
FIG. 19H shows the Southern blot of FIG. 19A using H) HVS pT 7.4.
FIGS. 20A and 20B shows DNA amplification analysis of various tissue DNA
isolated from patients with AIDS and control subjects without AIDS.
FIG. 21A shows M. fermentans incognitus-induced histopathological changes
of fulminant necrosis in the spleen of a patient without AIDS dying of an
acute systemic disease.
FIG. 21B shows the advancing margin of FIG. 21A.
FIG. 21C shows M. fermentans incognitus-induced histopathological changes
of fulminant necrosis in the lymph node of a patient without AIDS dying of
an acute systemic disease.
FIG. 21D shows M. fermentans incognitus-induced histopathological changes
of fulminant necrosis in the adrenal gland of a patient without AIDS dying
of an acute systemic disease.
FIG. 22A shows the immunohistochemistry of M. fermentans incognitus-induced
necrotizing lesions in the spleen using M. fermentans incognitus-specific
rabbit antiserum.
FIG. 22B shows the margin of microsis of FIG. 22A.
FIG. 22C shows the immunohistochemistry of M. fermentans incognitus-induced
necrotizing lesions in the lymph node using M. fermentans
incognitus-specific rabbit antiserum.
FIG. 22D shows the peripheral zone of necrosis of FIG. 22C.
FIG. 22E shows the immunohistochemistry of M. fermentans incognitus-induced
necrotizing lesions in the adrenal gland using M. fermentans
incognitus-specific rabbit antiserum.
FIG. 23A shows in situ hybridization for M. fermentans incognitus nucleic
acids in the necrotizing lesions of splenic tissue in the peripheral zone
around necrosis.
FIG. 23B shows a higher magnification of FIG. 23A.
FIG. 23C shows an area of differing necrosis in splenic tissue.
FIG. 23D shows an area of differing necrosis in splenic tissue.
FIG. 24A.sub.1 shows an electron micrograph of the margin of necrosis of an
adrenal gland highly positive for M. fermentans incognitus-specific
antigens.
FIG. 24A.sub.2 is a higher magnification of FIG. 24A.sub.1.
FIG. 24B.sub.1 shows an electron photomicrograph of the peripheral zone of
necrosis in lymph node highly positive for M. fermentans
incognitus-specific antigens.
FIG. 24B.sub.2 shows an electron photomicrograph of the peripheral zone of
necrosis in lymph node highly positive for M. fermentans
incognitus-specific antigens.
FIG. 24B.sub.3 is higher magnification of FIG. 24B.sub.1.
FIG. 25A shows analysis and comparison of DNA restriction patterns of VLIA
and M. fermentans incognitus probed with psb-8.6.
FIG. 25B shows analysis and comparison of DNA restriction patterns of VLIA
and M. fermentans incognitus probed with psb-2.2.
FIG. 26A shows the immunohistochemistry of thymic tissues derived from
patients with AIDS.
FIG. 26B is a higher magnification of FIG. 26A.
FIG. 26C is a higher magnification of FIG. 26B.
FIG. 26D shows the immunohistochemistry of thymic tissues derived from
patients with AIDS.
FIG. 26E is a higher magnification of FIG. 26D.
FIG. 27A shows an electron micrograph of an AIDS thymus immunostained
positively for M. fermentans incognitus-specific antigens showing
mononuclear lymphohistiocytes.
FIG. 27B shows an electron micrograph of an AIDS thymus immunostained
positively for M. fermentans incognitus-specific antigens showing
mononuclear lymphohistiocytes.
FIG. 27C shows an electron micrograph of an AIDS thymus immunostained
positively for M. fermentans incognitus-specific antigens showing
mycoplasma-like particles.
FIG. 27D shows an electron micrograph of an AIDS thymus immunostained
positively for M. fermentans incognitus-specific antigens showing
mycoplasma-like particles.
FIG. 28A shows the immunohistochemistry of livers from patients with AIDS
using monoclonal antibody C42H10.
FIG. 28B shows the immunohistochemistry of livers from patients with AIDS
using monoclonal antibody C42H10.
FIG. 28C shows the immunohistochemistry of livers from patients with AIDS
using a non-specific monoclonal antibody.
FIG. 28D shows the immunohistochemistry of livers from patients with AIDS
using monoclonal antibody C42H10.
FIG. 29A shows an electron micrograph of AIDS liver immunostained
positively for M. fermentans incognitus-specific antigens at low
magnification.
FIG. 29B is a higher magnification of FIG. 29A.
FIG. 29C is a higher magnification of FIG. 29B.
FIG. 29D shows an electron micrograph of AIDS liver immunostained
positively for M. fermentans incognitus-specific antigens at low
magnification.
FIG. 29E is a higher magnification of FIG. 29D.
FIG. 30A shows the immunohistochemistry of a brain derived from a patient
with AIDS using monoclonal antibody C42H10.
FIG. 30B shows the immunohistochemistry of a brain derived from a patient
with AIDS using monoclonal antibody C42H10.
FIG. 30C shows the immunohistochemistry of a brain derived from a patient
with AIDS using a non-specific monoclonal antibody.
FIG. 30D shows the immunohistochemistry of a brain derived from a patient
with AIDS using monoclonal antibody C42H10.
FIG. 31A shows electron microscopy of CNS encephalopathy AIDS brains which
were histologically unremarkable but immunostained positively for M.
fermentans incognitus-specific antigens.
FIG. 31B is a higher magnification of FIG. 31A.
FIG. 31C is a higher magnification of FIG. 31B.
FIG. 31D is a higher magnification of FIG. 31C.
FIG. 32A shows the immunohistochemistry of a placenta delivered by a
patient with AIDS using monoclonal antibody C42H10.
FIG. 32B is a higher magnification of FIG. 32A.
FIG. 33A shows electron microscopy of an AIDS patient's placenta
immunostained positively for M. fermentans incognitus specific antigens
showing Hofbauer cell.
FIG. 33B shows electron microscopy of an AIDS patient's placenta
immunostained positively for M. fermentans incognitus specific antigens
showing Hofbauer cell.
FIG. 33C shows electron microscopy of an AIDS patient's placenta
immunostained positively for M. fermentans incognitus specific antigens
showing stronal connective tissue.
FIG. 33D shows electron microscopy of an AIDS patient's placenta
immunostained positively for M. fermentans incognitus specific antigens
showing stronal connective tissue.
FIG. 33E shows electron microscopy of an AIDS patient's placenta
immunostained positively for M. fermentans incognitus specific antigens
showing stronal connective tissue.
FIG. 34A shows in situ hybridization for M. fermentans incognitus nucleic
acid in liver from patients with AIDS.
FIG. 34B shows in situ hybridization for M. fermentans incognitus nucleic
acid in liver from patients with AIDS.
FIG. 34C shows in situ hybridization for M. fermentans incognitus nucleic
acid in spleen from patients with AIDS.
FIG. 34D shows in situ hybridization for M. fermentans incognitus nucleic
acid in spleen from patients with AIDS.
FIG. 35 shows the inhibition of HIV-1-induced syncytium formation by M.
fermentans incognitus.
FIG. 36A shows the augmentation of cytocidal effect and inhibition of RT
activity in HIV-1 infected A3.01 cells cultures by M. fermentans
incognitus.
FIG. 36B shows the inhibition of RT activity in HIV-1 infected A3.01 cell
cultures by M. fermentans incognitus.
FIG. 37A shows continued viral production of HIV-1 and M. fermentans
incognitus in culture supernatant by ELISA.
FIG. 37B shows continued viral production of HIV-1 and M. fermentans
incognitus in culture supernatant by electron micrograph.
 
 
DETAILED DESCRIPTION OF THE INVENTION
 
A. Definitions
 
In order to provide a clear and consistent understanding of the
specification and the claims, including the scope given to such terms, the
following terms as used herein are defined below.
 
The term "AIDS-like syndrome" is used to describe a set of physiologic
conditions or clinical presentations which are commonly used to identify
individuals who are suspected of having the disease AIDS, but who have not
had confirmation of the disease by blood test. The physiologic conditions
are those that are common to individuals with blood test-confirmed AIDS,
and include the development of opportunistic infections such as
pneumocystic carinii pneumonia (PCP), atypical mycobacterial infection,
toxoplasmosis and cytomegalovirus (CMV), the clinical manifestation of
progressive weight loss, persistent diarrhea, neuropsychiatric
abnormalities of AIDS encephalopathy, kidney failure of AIDS nepthropathy,
heart failure of AIDS cardiomyopathy, respiratory distress syndrome and
infections and uncommon malgnancies such as Kaposi's sarcoma or B-cell
lymphoma.
 
The term "substantial sequence homology" is used to describe substantial
functional and/or structural equivalence between sequences of nucleotides
or amino acids. Functional and/or structural differences between sequences
having substantial sequence homology will be de minimus.
 
 
B. Previous Related Applications
 
The present invention relates to a novel strain of infectious mycoplasma
(M. fermentans incognitus) isolated from patients with AIDS. The
recognition of this pathogen as a mycoplasma has been a slowly evolving
process as evidenced by the history of the present specification.
 
The predecessor patent applications (Ser. No. 875,535, filed Jun. 18, 1986
and Ser. No. 265,920, filed Nov. 2, 1988) identified the subject pathogen
as a virus and a virus-like infectious agent (VLIA), respectively. However,
continuing study of the pathogen has resulted in the present identification
of the pathogen as an infectious mycoplasma. Ser. Nos. 265,920 and 875,535
are incorporated herein by reference.
 
The presently identified mycoplasma like many other mycoplasmas has many of
the characteristics of a virus, which resulted in its identification as
such in the original patent application (Ser. No. 875,535, filed Jun. 18,
1986). Further research then showed characteristics which were not typical
of classic viruses, thus the characterization as a VLIA in Ser. No.
265,920, filed Nov. 2, 1988. Additional research has now revealed
characteristic traits of a mycoplasma as fully explained below.
 
 
C. Deposits
 
A mycoplasma (M. fermentans incognitus) according to the invention, in
persistently infected cells, is deposited with the American Type Culture
Collection under Deposit No. CRL 9127, deposited on Jun. 17, 1986. M.
fermentans incognitus, itself is also deposited with the American Type
Culture Collection under Deposit No. 53949, deposited on Sep. 29, 1989.
 
Deposit is for the purpose of completeness but is not intended to limit the
scope of the present invention to the materials deposited since the
description as further illustrated by the Examples fully enables the
practice of the instant invention. Access to the cultures will be available
during the pendency of the patent application to those determined by the
Commissioner of Patents and Trademarks to be entitled thereto. All
restrictions on availability of said cultures to the public will be removed
irrevocably upon the grant of the instant application and said cultures
will remain available permanently during the term of said patent 30 years
or five years after last request, whichever is longer. Should any culture
become nonviable or be destroyed, it will be replaced.
 
 
D. Physical Characteristics of M. fermentans incognitus
 
The M. fermentans incognitus cell is roughly spherical and about 140-200 nm
in diameter, has an outer limiting membrane (about 8 nm thick), and has a
buoyant density of about 1.17 g/ml to about 1.20 g/ml in a sucrose
gradient. Although M. fermentans incognitus could be identified in the
nuclei, mature M. fermentans incognitus cells are usually seen in the
cytoplasm or associated with the plasma membrane of disrupted cytolytic
cells.
 
Using Southern blot hybridization analysis, the M. fermentans incognitus
was distinct from all known members of human herpes virus. M. fermentans
incognitus was also distinct from vaccinia virus, monkey herpesvirus
saimiri (HVS) and mouse cytomegalovirus (MCMV). M. fermentans incognitus
can be transmitted from culture to culture by cell-free filtrate, after
0.22 micron filtration.
 
M. fermentans incognitus was also found to be distinct from any other known
strain of Mycoplasma. One unique feature of M. fermentans incognitus is its
ability to catabolize glucose both aerobically and anaerobically and also
to hydrolyze arginine. M. fermentans incognitus cannot hydrolyze urea in a
biochemical ssay. When grown in culture, M. fermentans incognitus produces
a prominent alkaline shift in pH after an initial brief acidic shift. The
only other human mycoplasma which is known to metabolize both glucose and
arginine is the rarely isolated M. fermentans.
 
However, the incognitus strain differs from M. fermentans in that it
appears to be is more fastidious in its cultivation requirements and has
only been grown in a cell-free modified SP-4 medium. M. fermentans also
grows in modified SP-4 medium, but at a much faster rate than M. fermentans
incognitus.
 
Furthermore, M. fermentans incognitus can be grown in a variety of commonly
used mycoplasma media, whereas M. fermentans incognitus cannot.
 
When grown in the modified SP-4 medium, M. fermentans incognitus displays
smaller spherical particle size than M. fermentans incognitus, and
occasional filamentous morphology which is not seen with M. fermentans
incognitus. Furthermore, M. fermentans incognitus forms only irregular and
very small colonies with diffuse edges when grown on agar plates. The M.
fermentans incognitus are cell wall-free and bound by a single triple
layered membrane. The average size of an M. fermentans incognitus cell is
about 180 nm, compared to an average size of about 460 nm for an M.
fermentans cell.
 
FIG. 1 shows electron photomicrographs and colony morphology of M.
fermentans incognitus and M. fermentans. Thin sections of concentrated M.
fermentans incognitus (A) and M. fermentans incognitus (B) reveal
pleophorphic microorganisms with trilaminar outer unit membrane as
designated by the arrows. The bars in 1A and 1B represent 100 nm. M.
fermentans incognitus (C) and M. fermentans (D) formed colonies of
apparently different size and morphology after 14 days and 10 days of
incubation, respectively. In these figures, the bar represents 50 .mu.m and
20 .mu.m, respectively.
 
 
E. Antigenic differentiation of M. fermentans incognitus and M. fermentans
 
Further differentiation of M. fermentans incognitus from prototype strain
of M. fermentans (PG18) was displayed by antigenic analysis using both
polyclonal and monoclonal antibodies, as well as DNA analysis of sequence
homology and restriction enzyme mapping. These analyses showed that the
incognitus strain is distinct from all other mycoplasmas, but is most
closely related to previously isolated M. fermentans strains.
 
M. fermentans incognitus was distinguished from M. fermentans (PG18 strain)
by comparing their specific antigenicity. Polyclonal rabbit antiserum
(raised originally against VLIA-sb51) was found to react with both M.
fermentans (PG18 strain) and M. fermentans incognitus, but not with any of
the other mycoplasmas tested. However, in the same assay a larger amount of
M. fermentans (PG18 strain) protein (>0.63 .mu.g) was required to elicit a
positive immunochemical response, and the positivity of the reaction
rapidly disappeared when the M. fermentans (PG18 strain) protein was
further diluted. In contrast, a 250-fold to 1000 fold lower concentration
of M. fermentans incognitus protein still carried a sufficient amount of
antigenic determinants to elicit positive reactions in the assay.
 
In a parallel assay, antiserum raised specifically against M. fermentans
(PG18 strain) also reacted intensely with M. fermentans incognitus. The M.
fermentans incognitus-specific antiserum reacted as effectively with the
antigens of M. fermentans incognitus as with the antigens of M. fermentans
(PG18 strain). There was approximately an equal amount of antigens which
could be recognized by the M. fermentans incognitus antiserum in each unit
of M. fermentans (PG18 strain) and M. fermentans incognitus proteins. Both
M. fermentans and M. fermentans incognitus proteins could be diluted to 40
ng per well and still elicit a positive reaction.
 
However, when M. fermentans incognitus proteins and M. fermentans (PG18
strain) proteins were reacted with monoclonal antibodies raisedspecifically
against M. fermentans incognitus, only M. fermentans incognitus proteins
reacted positively. Six M. fermentans incognitus monoclonal antibodies
(many with different isotypes) reacted with only M. fermentas incognitus,
but not with M. fermentans. Therefore, M. fermentans incognitus carries
additional specific antigens which can not be identified in the prototype
of M. fermentans (PG18 strain).
 
FIG. 2 shows antigenic comparison of M. fermentans incognitus, M.
fermentans and other human mycoplasmas in immunoblots. Upper blot (2A) was
immunostained with rabbit antiserum raised specifically against M.
fermentans incognitus. Lower blot (2B) was immunostained with mule
antiserum raised specifically against M. fermentans (PG18 strain). The
concentration of mycoplasma protein was dot-blotted decrementally (1:4
dilution) from lane 1 (10 .mu.g) to lane 12 (2.5 pg). Row A (M. arginini),
row B (A. laidlawii), row C (M. fermentans), row D (M. hominis), row E (M.
orale), row F (M. hyorhinis), row G (M. pneumonia), row H (M. fermentans
incognitus). In FIG. 2C row A, B, C, D and F were immunostained with
monoclonal antibodies D81E7, C69H3, F89H7, B109H8, F11C6 and C42H10,
respectively. The concentration of mycoplasma protein was dot-blotted
decrementally (1:10 dilution) from lane 1 (10 .mu.g) to lane 8 (1 pg). Row
a (M. fermentans incognitus) and Row b (M. fermentans).
 
 
F. DNA Homology
 
DNA was isolated from M. fermentans incognitus and ten other species of
mycoplasmas (M. orale), M. hyorhinis, M. pneumonia, M. arginini, M.
hominis, M. fermentans, M. genitalium, M. salivarium, U. urealyticum and A.
laidlawii) and analyzed on Southern blots, being probed with .sup.32
P-labeled cloned M. fermentans incognitus DNA (psb-8.6, psb 2.2) or
synthetic oligonucleotide RS48 (SEQ ID NO:1) a M. fermentans
incognitus-specific sequence. An additional molecular clone, carrying a 3.3
kilobase insert of M. fermentans incognitus DNA (MI-H 3.3) was also used as
a probe.
 
Although some homology with psb-2.2 was observed in the M. orale genome, no
homology with RS48 (the specific DNA sequences occurring at one terminal
end of psb-2.2) and no homology with psb-8.6 or MI-H 3.3 were identified in
the M. orale genome. Although DNA homology with psb-8.6, psb-2.2, RS48 and
MI-H 3.3 were all found in the M. fermentans (PG18 strain) genome, the
restriction patterns revealed by these probes were different between M.
fermentans (PG18 strain) and M. fermentans incognitus.
 
FIG. 3 shows a comparison of DNA homology and restriction patterns between
M. fermentans incognitus and other human mycoplasmas. The blots were probed
with .sup.32 P nick-translated psb-8.6 (3A) and psb-2.2 (3B), .sup.32 P
end-labeled RS48 (3C), .sup.32 P labeled MI-H 3.3 (3D) and .sup.32 P
end-labeled cDNA probe of E. coli ribosomal RNA (3E). Each lane contained
0.2 microgram of EcoRI enzyme pre-digested DNA from Acholeplasm laidlawii
(lane 1), M. arginini (lane 2), M. hominis (lane 3), M. hyorhinis (lane 4),
M. pneumoniae (lane 5), M. orale (lane 6), M. fermentans (PG18 strain)
(lane 7) and M. fermentans incognitus (lane 8). Arrows indicate the
positions of standard size marker 23, 9.4, 6.7, 4.4, 2.3, and 2.0 kb,
respectively.
 
Furthermore, there is significant homology between the ribosomal RNA
(r-RNA) genes of procaryotive mycoplasmas and those of Escherichia coli
bacterium. The same blot which was consecutively probed with RS48 and MI-H
33 was reprobed with .sup.32 P-labeled cDNA of E. coli or r-RNA, after
removing the previously incorporated probe by boiling the filter. The
analysis of r-RNA genes revealed both a difference in numbers and size of
the hybridization bands with each different species of mycoplasma tested.
The EcoRI restriction pattern of the r-RNA genes for M. fermentans
incognitus and M. fermentans (PG18 strain) appeared to be identical, but
were different from any other mycoplasma tested.
 
 
G. Immunofluorescence Staining
 
Further support for the conclusion that M. fermentans incognitus differs
from any other mycoplasma came from a study of direct immunofluorescence
staining. An FITC probe was conjugated to the purified M. fermentans
incognitus monoclonal antibodies, and again revealed positive staining only
in M. fermentans incognitus, but not in M. fermentans (PG18 strain) or six
other species of human mycoplasmas. FIG. 4 shows direct immunofluorescence
straining of M. fermentans incognitus (A) and M. fermentans (PG18 strain)
(B) using FITC conjugated monoclonal antibody D81E7 (X900).
 
 
H. M. fermentans incognitus Infection
 
A high prevalence of M. fermentans incognitus infection has been found in
patients with AIDS by using the polymerase chain reaction. The genetic
material specific for M. fermentans incognitus has been isolated from
spleens, Kaposi's sarcoma, livers, lymph nodes, peripheral blood
mononuclear cells and brains of patients with AIDS.
 
Furthermore, M. fermentans incognitus infection has been found in
previously healthy non-AIDS subjects with an acute fatal disease. The M.
fermentans incognitus infection in these patients was directly identified
in the necrotizing lesions in lymph nodes, spleens, livers, adrenal glands,
heart and brain.
The pathogensis of M. fermentans incognitus infection is unusual in that
despite fulminant tissue necrosis, there is lymphocyte depletion and an
apparent lack of cellular immune response or inflammatory reaction in the
infected tissues. It is believed that infection of M. fermentans incognitus
either has concomittantly caused damage to key components of the hosts'
immune system, or this pathogen has special biological properties which
enable it to elude immunosurveillance of the infected hosts.
 
Coinfection with Mycoplasma fermentans (incognitus strain) enhances the
ability of human immunodeficiency virus type-1 (HIV-1) to induce cytopathic
effects on human T lymphocytes in vitro. Syncytium formation of
HIV-infected T cells was essentially eliminated in the presence of M.
fermentans (incognitus strain), despite prominent cell death. However,
replication and production of HIV-1 particles continued during the
coinfection. Furthermore, the supernatant from cultures coinfected with
HIV-1 and mycoplasma may be involved in the pathogenesis of acquired
immunodeficiency syndrome (AIDS).
 
Abstract from Science 251, 1074 (1991). Since the presence of M. fermentans
incognitus is most often associated with AIDS and other acute fulminant
disease states and more profoundly affects the course of its disease, it
can be used to determine the prognosis of these diseases, which information
can be utilized for designing therapy regimes. Without being bound by any
proposed mechanism, it is believed that antibodies against ORF-1 (see
below) may react against CD4.sup.+ lymphocytes resulting in an
auto-antibody response against CD4 on T cells thus enhancing the cytopathic
effects of HIV-1 on T cells.
 
 
I. DNA Characteristics of M. fermentans incognitus
 
M. fermentans incognitus was originally isolated from Kaposi sarcoma tissue
of an AIDS patient. The DNA genome of the M. fermentans incognitus is
greater than 150 kilobase (kb) pairs and carries repetitive sequences. An
8.6 kb pair cloned probe (psb-8.6) and a 2.2 kb pair cloned probe (psb-2.2)
of M. fermentans incognitus detected specific sequences of DNA in Sb51
cells and M. fermentans incognitus infected cells, but not in DNA of
uninfected NIH/3T3 cells.
 
The cloned probes (psb-8.6 and psb-2.2) can be obtained from an EcoRI
partial digest of M. fermentans incognitus enriched DNA which is cloned
into bacteriophage lambda charon 28. The lambda-recombinant clones are
screened by differential plaque hybridization with .sup.32 P-labeled DNA
derived from gradient banded M. fermentans incognitus. The insert of the
phage clone is then recloned into the EcoRI site of Bluescript KS (M
13.sup.-) vector (Stratogene) to produce the cloned probes, psb-8.6 and
psb-2.2.
 
By nucleic acid analysis, the M. fermentans incognitus has been compared
with large DNA viruses of the herpes group such as herpes simplex virus
type I and II (HSV-I and II), human cytomegalovirus (CMV), Epstein-Barr
virus (EBV), Varicella-Zoster virus (VZV) and human B-lymphocytic virus
(HBLV) or human herpesvirus-6 (HHV-6), vaccinia virus, Herpesvirus saimiri
(HVS) of monkeys and mouse cytomegalovirus (MCMV). Part of the M.
fermentans incognitus genomic DNA has been molecularly cloned. The entire
sequence of a cloned M. fermentans incognitus psb-2.2 DNA has been obtained
and is shown as SEQ ID NO:2.
 
To obtain the genetic materials of M. fermentans incognitus, the Kaposi's
sarcoma tissue is minced into small pieces and treated with collagenase.
The tissue suspension is then treated with a proteinase, such as proteinase
K. Genetic materials are obtained after phenol extraction,
phenol/chloroform/ isoamylalcohol extraction, and chloroform/isoamylalcohol
extraction. High molecular weight DNA is visibly observed after ethanol
precipitation of the genetic materials. The genetic materials are dissolved
and contain high molecular weight DNA and RNA of various sizes.
 
The isolated genetic materials from Kaposi's sarcoma are utilized to
transfect NIH/3T3 cells or other proper recipient cells in accordance with
the procedure of Graham, F. L., et al., Virology 52, 456 (1973). In this
procedure, the nucleic acid is precipitated with calcium phosphate and
incubated with NIH/3T3 cells. The precipitated nucleic acid is removed and
the cells trypsinized. The trypsinized cells are reseeded and treated with
glycerol before splitting, as described by Copeland, N. G., et al., Cell
16, 347 (1979). The subcultures are fed with Dulbecco's medium with fetal
bovine serum (FBS) and re-fed at three- to four-day intervals.
 
Foci of morphologically transformed cells become evident in about two
weeks. The phenotypical transformation is characterized by rapid overgrowth
of the transfected cells which pile up in multilayers and form grossly
visible foci. Transformation efficiency is about 0.01-0.02 identifiable
foci per microgram of donor nucleic acid. Transformed colonies are
harvested after three weeks, and are cultured in monolayers.The DNA of
transformants contain human repetitive DNA sequences.
 
Genetic materials are isolated from the primary transfectants as previously
described, and used to transfect fresh NIH/3T3 cells. Transformation is
again seen using the genetic materials with a slightly higher
transformation efficiency. This demonstrates that the genetic materials
isolated from tissues of AIDS patients contain active transforming
elements. This is the first description ever of mycoplasmal DNAtransfecting
cells.
 
The nucleotide sequence of the M. fermentans incognitus EcoRI 2.2 kb DNA
(plasmid psb 2.2) is shown in SEQ ID NO:2. This plasmid has a segment of
unique sequences which occurs repeatedly in the M. fermentans incognitus
genome.
 
By sequence analysis, a genetic element of 1405 base pairs (SEQ ID NO:3)
with unique structural characteristics was identified. These unique
structural characteristics strongly resemble bacterial insertion sequence
(IS) elements. The IS-like element occurs repeatedly in the M. fermentans
incognitus genome.
 
In analyzing the M. fermentans incognitus EcoRI 2.2 kb DNA, one pair of
inverted repeats (IR) consisting of 29 bp with seven mismatches was found.
These IR are SEQ ID NO:4 (left IR) and SEQ ID NO:5 (right IR). Immediately
outside and flanking these 29-bp IR is a 3-bp direct repeat (DR), TTT. The
element framed by these two 29-bp IR contains 1405 bp (SEQ ID NO:3). Many
pairs of IR that have eight or more contiguous nucleotides are also found
within this 1405-bp element. There are two potential stem-and-loop (s&1)
structures, L and R, in the element (see FIG. 5) (SEQ ID NO:3).
L(.DELTA.G=-16.8 kcal/mol) is located exactly at the left terminus of the
element, while R (.DELTA.G=-14.4 kcal/mol) is located very near the right
terminus. Both of the potential s&1 structures are followed by a stretch of
T residues pointing toward the interior of the element. These s&1
structures with T resides strongly resemble transcription terminators
(Rosenberg and Court, Annu. Rev. Genet., 13 319 (1979), which would prevent
transcription from the outside into the element (Syvanen, Annu. Rev.
Genet., 18 271 (1984)). The structures may also be responsible for the
strong polarity of this element (Grindley and Reed, Annu. Rev. Biochem., 54
863 (1985)). Similar transcription terminators have been found at the
termini of several bacterial IS elements. These unique structures are
probably maintained for specific benefit of the IS elements and play an
important role in the regulation of transposition.
 
Mycoplasma DNAs are extremely rich in A and T. It has already been shown in
the codon usage of ribosomal protein genes of M. capricolum that synonymous
nucleotide substitution and conservative amino acid substitution can occur
(Muto et al., Nucleic Acids Res., 12 8209 (1984)). It has also been
reported that TGA, instead of being a stop codon, is a Trp codon in many
species of mycoplasma (Yamao et al., Proc. Natl. Acad. Sci. USA, 82 2306
(1985)); Inamine et al., J. Bacteriol., 172 504 (1990)). According to this
unique character of codon usages in mycoplasma, three potential ORFs,
ORF-1, ORF-2, and ORF-3 (SEQ ID NO:6, 7 and 8, respectively) have been
identified in the 2.2-kb DNA. ORF-1 and ORF-2 are located inside the
element and ORF-3 is located on the complementary strand 100-bp away from
the element.
 
ORF-1 (SEQ ID NO:6) begins immediately after the s&1 structure L at
nucleotide 176 and ends at nucleotide 604, and could encode a protein of
143 amino acids (SEQ ID NO:9). There is a possible Shine Delgarno (SD)
sequence, AAGGGG (nucleotides 161-166), which precedes the start codon of
ORF-1 by 9-bp, and is located inside the s&1 structure L (FIG. 5, SEQ ID
NO:2 and 3, respectively). There is no consensus sequence for the -10 and
-35 promoter regions, however, the left IR may provide a promoter function
which has been previously shown in the E. coli IS1 element (Machida et al.,
J. Mol. Biol., 177 229 (1984)).
 
ORF-2 (SEQ ID NO:7) begins at nucleotide 1149 and ends at nucleotide 1457,
immediately in front of the s&1 structure R, and could encode a protein of
103 amino acids (SEQ ID NO:10). There is a promoter-like region which has a
-35 region (TTGATT) at nucleotides 1090-1095 and a -10 region (TAGGTT) at
nucleotides 1114-1119 located upstream from ORF-2 (FIG. 5, SEQ ID NO:2 and
3, respectively). ORF-3 (SEQ ID NO:8), between nucleotide 1912 and 1637 (on
the complementary strand), could encode a 92-amino acids protein (SEQ ID
NO:11) (FIG. 5, SEQ ID NO:2 and 3, respectively).
 
A computer search of the National Biomedical Research Foundation (NBRF)
Protein Data Bank has revealed a 40% homology (49% with conservative
replacements) between a region of the deduced amino acid sequence of ORF-1
(SEQ ID NO:9; amino acid 101-140) and Streptococcus pyogenes Pep M5 protein
(amino acids 23-65). The biological function of antiphagocytosis in this
pathogenic bacteria is known to be associated with Pep M5 protein (Fox,
Bacteriol. Rev., 38 57 (1974)). The search also revealed that 75% of the
amino acids are identical between a region of the deduced amino acid
sequence of ORF-1 (SEQ ID NO:9, amino acid 117-128) and the sequence in the
extracelluar V4 domain of human T-cell surface glycoprotein CD4 molecule
(amino acid 319-329). Another extracellular domain (V1) of the same CD4
molecule is critical for recognition by HIV envelope glycoprotein (Arthos
et al., Cell, 57 469 (1989)). The significance of the homologies of ORF-1
with Pep M5 protein and the CD4 molecule on human T cells is not clear at
this time, but this 75% homology between the amino acid sequence of ORF-1
and CD4 is enough difference to result in the production of antibody to the
ORF-1 antigen. However, this antibody may then attack both the ORF-1
antigen and the CD4 receptors due to their similarity.
 
In a similar analysis, a 43% homology (55% with conservative replacements)
between a region of the deduced amino acid sequence of ORF-2 (SEQ ID NO:10,
amino acid 18-74) and the deduced amino acid sequence of the putative
transposase of E. coli IS3 (SEQ ID NO:12, amino acid 189-245) was found. In
addition, the ratio of basic to acidic amino acid in protein predicted by
ORF-2 is around 2. Thus, this basic protein encoded by ORF-2 highly
resembles the E. coli putative transposase which is believed to be
essential for transpositional recombination (Grindley and Reed, Annu. Rev.
Biochem., 54 863 (1985)). No significant homology was found between ORF-3
and sequences in the NBRF Protein Data Bank. Also there is no significant
homology between the nucleotide sequence of 2.2-kb DNA (SEQ ID NO:2) and
the nucleotide sequences in the GenBank database.
 
It has been shown that this cloned DNA (psb-2.2; ID SEQ NO:2) contains a
unique sequence which occurs more than ten times in the genome of M.
fermentans incognitus (Lo et al., Am. J. Trop. Med. Hyg., 40 213 (1989))
(also FIG. 6). To precisely define the boundary of this repetitive element,
a series of ten oligos, B through K, were synthesized and used as probes.
Each probe contained 20-24 nucleotides of a specific sequence from a
selected segment in 2.2-kb DNA (FIG. 5). The nt positions of the synthetic
oligo, B through K, used as serial probes to identify the boundary of the
IS-like repetitive element in the M. fermentans incognitus genome (see FIG.
4) as follows: B (1659-1678), C (1531-1550), D (1514-1533), E (1454-1477),
F (1228-1247), G (681-700), H (328-347), I (129-148), J (115-135), and K
(44-65) of SEQ ID NO:2. Among the ten oligos, D to I are a series of
representative sequences within the 1405-bp IS-like element, and I and D
represent sequences within the left and right terminal IR, respectively. B,
C, J, and K represent sequences outside the element. Both J and C represent
the sequence of the junction areas of the element and actually carry a part
of the sequence of the left and right IR, respectively. Each of these
synthetic oligo probes was end-labeled with .sup.32 P and used individually
to probe M. fermentans incognitus genomic DNA predigested with either EcoRI
or HindIII.
 
The hybridization patterns of multiple bands produced by probes D to I,
which carry representative sequences of the various segments in the IS-like
element, were essentially the same. In EcoRI digestion, there are eleven
identical bands with sizes ranging from 2.20 to 8.90 kb (FIG. 6, D-I, lanes
b). When using HindIII digestion, there are twelve identical bands with
sizes ranging from 1.95 to 9.10 kb (FIG. 6, D-I, lanes a, b). This pattern
of multiple hybridization bands matches exactly with that produced when
psb-2.2 DNA is nick-translated and used as a probe (FIG. 6A).
 
In contrast, the probes B, C, J and K produced a completely different
pattern with only a single hybridization band of 2.2-kb in EcoRI digestion
or a 1.95-kb fragment in HindIII digestion (FIG. 6B, C, J and K). Probes I
(20-mer) and J (21-mer) overlap 7 nucleotides within the left IR; the
former produced the typical pattern of multiple bands (FIG. 6I), however,
the latter only produced a single band (FIG. 6J).
It was also noted that probes D(20-mer) and C(20-mer) overlap by 3
nucleotides within the right IR; the former produced the typical pattern of
multiple bands (FIG. 6D), however, the latter only produced a single band
(FIG. 6C). Thus, the 1405-bp IS-like element (SEQ ID NO:3) which is located
between nucleotides 129 and 1533, is the repetitive element which occurs
more than ten times in the genome of M. fermentans incognitus. This finding
suggests that the IS-like element is a mobile element. Such mobility
suggests the use of this IS-like element as a means for inserting other
sequences into other cells (i.e. the IS-like-element can be used as a
cloning vector). The presence of mulitiple gene copies may result from
transposition.
 
The evidence which supports the conclusion that the 1405-bp element is an
IS-like element is: (1) the size of the element (1405-bp) being in the
range of previously identified bacterial IS elements (800-2500 bp); (2) the
presence of 29-bp IR, with seven mismatches located at both of the termini
of the element; (3) the presence of a 3-bp DR immediately flanking outside
both of the terminal IR; (4) two ORFs (ORF-1 and ORF-2) which could
potentially encode two basic proteins; part of the deduced amino acid
sequence of ORF-2 being homologous to part of the putative transposase of
IS3, and (5) the presence of multiple copies in the genome of M. fermentans
incognitus. Several other unique structural features found in the 1405-bp
element which are also present in bacterial IS elements are: (i) the s&1
structure located close to at least one terminus; (ii) the presence of a
large number of sequences with properties of IR, and (iii) part (9 bp) of
the sequence in one of the terminal IR found again as a repeat sequence
(either direct or indirect) near the other terminal IR (see SEQ ID NO:2 &
3).
 
 
J. Detection of M. fermentans incognitus DNA by PCR
 
A polymerase chain reaction (PCR) assay to detect M. fermentans was
designed on the basis of specific nucleotide (nt) sequences found at one
terminus of the cloned incognitus strain of M. fermentans DNA psb-2.2 (SEQ
ID NO:2). Primers (RS47 (SEQ ID NO:13) and RS49 (SEQ ID NO:14)) were chosen
to produce an amplified DNA fragment of 160 bp. (See Examples 16 and 19.)
The PCR assay detected very specifically the mycoplasmas of M. fermentans
species but not other human or hon-human mycoplasmas, bacteria or
eucaryotic cell DNA that we tested. However, this highly specific assay
using these primers failed to detect some mycoplasmas of the M. fermentans
species. Ten fg of DNA consistently yielded a positive 160 bp amplified
band in DNA isolated from the incognitus strain of M. fermentans, from a
strain (k7) previously islated from the bone marrow of a patient with
leukemia/lymphoma and from other M. fermentans strains (MT-2) isolated from
contaminated human lymphocyte cultures. A thousand fold higher amount of
DNA (10 pg) isolated from the prototype strain of M. fermentans (PG-18, and
ATCC #19989) as well as DNA from two recent clinical isolates from patients
with AIDS tested negative for the diagnostic DNA fragments. Thus, the
specific gene arrangement used in this PCR assay was apparently not
universally present in the DNA of all M. fermentans species.
 
A more sensitive PCR assay which is able to detect all the different
strains or clinical isolates of M. fermentans, yet remains highly selective
or specific, was then developed based on the presence of multiple copies of
an insertion sequence-like (IS-like) genetic element in M. fermentans. The
actual copy number of the IS-like element found in the genomes of different
strains or isolates of M. fermentans may vary and range from 5 to more than
10 copies. A new set of primers (RW004 (SEQ ID NO:15) and RW005 (SEQ ID
NO:16)) used to produce an amplified fragment of 206 bp in our new PCR
assay.
 
Using the new set of primers and RW006 (SEQ ID NO:17) as a probe, the
reaction consistently detected 1 fg of DNA in all M. fermentans species
tested (FIG. 7) including the prototype strain PG-18 and new clinical
isolates from patients with AIDS, whose DNA (up to 10-pg) tested negative
in the PCR reaction using the old set of primers. Sensitivity of this newly
developmed PCR assay was further verified by successfully detecting 1 fg of
the M. fermentans DNA in the presence of 1 ug of non-specific human
background DNA. Specificity of the reaction has also been examined by
attempting to amply the DNAs isolated from other human or non-human
mycoplasmas, common tissue culture contaminating mycoplasmas, Gram-positive
or Gram-negative bacteria, mouse, monkey and human cell culture and/or
tissue. The reaction does not produce the specific 206 bp DNA fragment.
 
The present study shows that we have developed a highly selective assay to
detect M. fermentans by PCR with remarkable sensitivity. The assay detects
all the different strains and the new clinical isolates of M. fermentans
that the previous PCR assay using primers RS47 and RS49 failed to detect
and appears to be 10 times more sensitive. The limitation of reaction
sensitivity per assay for our current PCR is 0.1 to 1 fg M. fermentans DNA
within a background of 1 ug of human DNA instead of 1 to 10 fg of microbe
DNA in our previous PCR assay. Thus, a molecular technique selectively
detecting a single microorganism of M. fermentans is available.
 
 
K. Infection and Transfection with M. fermentans incognitus
 
M. fermentans incognitus is isolated from the transformants, such as Sb51.
In general, Sb51 cell pellets are lysed by freezing and thawing to release
M. fermentans incognitus particles. The large M. fermentans incognitus
particles are pelleted through a sucrose barrier and banded in a sucrose
isopycnic gradient. The intact M. fermentans incognitus particles have a
density of about 1.17 to about 1.20.
 
M. fermentans incognitus can be introduced into mice. In general, the M.
fermentans incognitus isolated from 5.times.10.sup.6 Sb51 cells is injected
either intravenously or intraperitoneally into six-week-old mice. Nude mice
or immunocompetent mice can be infected. Infection of nude mice with M.
fermentans incognitus results in significant mortality of the infected
animals. Many symptoms similarly seen in patients with AIDS are induced by
the infected mice. Thus, at necropsy, the infected mice often showed
prominent systemic lymphadenopathy, neuropathy or lymphoid depletion with
varying degrees of plasmacytosis. Signs of immune deficiency with profound
cutaneous infection in some of the animals were noted. Disseminated
pruritic skin rashes were also common. There were proliferative lesions of
spindle cells in the cutaneous tissue and deep viscera. The immunocompetent
mice (Balb/c) infected by M. fermentans incognitus were found to be
subsequently infected by Pneumocystis carinii, which is evidence of the
immunnodeficient state of these infected animals.
 
Similar diseases are transmitted from animal to animal by injecting
filtrated lysates of spleen, lymph nodes or whole blood from the
diseasedanimals. M. fermentans incognitus is also identified in the
cytoplasm of the cytopathic cells. Some of the infected mice were found to
produce prominent antibody against M. fermentans incognitus.
 
When silver leaf monkeys are inoculated with M. fermentans incognitus, the
monkeys show wasting syndromes and die within seven to nine months after
inoculation. At necropsy, the monkeys do not show evidence of opportunistic
infections, acute inflammatory lesions or malignancy. M. fermentans
incognitus-specific DNA can be directly detected in necropsy tissues of the
monkeys, by use of polymerase chain reaction method. M. fermentans
incognitus infection can be identified in spleen tissue, liver tissue,
kidney tissue and brain tissue of the monkeys. Some of the infected monkeys
produced antibody to M. fermentans incognitus.
 
L. Detection of M. fermentans incognitus Antigens
 
The M. fermentans incognitus pathogen is useful for the detection of
antibodies in the sera of patients or animals infected with M. fermentans
incognitus. Some of these patients who are infected with M. fermentans
incognitus will be patients who have been diagnosed as having AIDS or
ARC,Cchronic Fatigue Syndrome, Wegener's Disease, Sarcoidosis, respiratory
distress syndrome, Kibuchi's disease, antoimmune diseases such as Collagen
Vascular Disease and Lupus and chronic debilitating diseases such as
Alzheimer's Disease. In one procedure, presistently M. fermentans
incognitus infected cells are grown in low cell density on sterile glass
slides. Sera from suspected patients, and normal subjects are examined in
an immunoperoxidase staining procedure such as that described by Hsu, S-M.,
et al., Am.J.Clin.Path. 80, 21 (1983). Using this assay, 23 of 24 sera from
AIDS patients showed strong positivity. Serum from the other AIDS patient
showed weak positivity. Twenty-six of 30 sera from non-AIDS normal subjects
showed no reactivity. The other four non-AIDS patients showed mild to weak
reactivity, but much weaker than that of AIDS patients. In addition, some
of the sera from experimentally infected animals, as described above, also
contained antibodies which reacted with the persistently M. fermentans
incognitus-infected cells in this assay procedure. Similarly, M. fermentans
infected cells can also be used in this procedure to detect antibodies in
sera of infected patients as a result of homologous antigens.
 
In addition to this procedure, any other procedure for detecting an
antigen-antibody reaction can be utilized to detect antibodies to M.
fermentans incognitus or M. fermentans in the sera of AIDS patients or
patients with ARC. Such procedures include, but are not limited to, ELISA,
Western-blot, direct or indirect immunofluorescent assay and
immunoradiometric assay. Such assay procedures for the detection of
antibodies in sera of AIDS patients or patients with ARC have been
described in U.S. Pat. No. 4,520,113, incorporated herein by reference,
which uses HTLV-III/LAV as the antigen. Similar procedures employing M.
fermentans incognitus or M. fermentans can be used. A diagnostic kit for
the detection of M. fermentans incognitus-specific or M.
fermentans-specific antibodies can be prepared in a conventional manner
using M. fermentans incognitus or M. fermentans. It is expected that assays
utilizing these techniques, especially Western-blot, will provide better
results, particularly fewer false-positives.
 
A final procedure for detecting the presence of M. fermentans incognitus or
other M. fermentans strains in suspected patients is by testing for DNA in
conventional methods, preferably using probes based on the sequence of the
IS-like element (SEQ ID NO:3). A preferred method is the PCR assay
described above.
 
 
M. Production of Antibodies to M. fermentans incognitus.
 
Antibodies against M. fermentans incognitus (or M. fermentans) can be
produced in experimental animals such as mice, rabbits and goats, using
standard techniques. Alternatively, monoclonal antibodies against M.
fermentans incognitus (or other strains of M. fermentans) antigens can be
prepared in a conventional manner. Homologous antibodies are useful for
detecting antigens to M. fermentans incognitus in infected tissues such as
lymph nodes, spleen, Kaposi's sarcoma, lymphoma tissue, brain and
peripheral blood cells, as well as sera, of patients with AIDS. Any
procedure useful for detecting an antigen-antibody reaction, such as those
described above, can be utilized to detect the M. fermentans incognitus
antigens in tissues of patients infected by the mycoplasma.
 
Rabbit antiserum has been prepared using M. fermentans incognitus. The
antiserum positively immune stains brain and lymph node tissue from AIDS
patients. To produce the antiserum, sucrose gradient banded M. fermentans
incognitus or any form of concentrated mycoplasma is used with complete
adjuvant and administered to rabbits by intraperitoneal and subcutaneous
injections at multiple sites. Serum collected from the rabbits is then
preabsorbed with NIH/3T3 cells, mouse liver powder and normal human
peripheral mononuclear cells isolated from Ficoll-Hypaque gradients.
Monoclonal antibodies may also be prepared by conventional procedures.
 
The antibodies are useful for detecting cells which have been infected by
M. fermentans incognitus. This capability is useful for the isolation of M.
fermentans incognitus from other tissues. For example, additional M.
fermentans incognitus can be isolated by co-cultivating infected tissue
from patients with AIDS and a suitable recipient cell line or cells, such
as lymphocytes. The infected cells are assayed or recognized by the
antibody, and M. fermentans incognitus can be obtained from the infected
cells as described above. An affinity column can also be prepared using the
antibodies and used to purify the M. fermentans incognitus from the
infected cell lysate.
 
 
N. Vaccines
 
The M. fermentans incognitus pathogen, antigens of M. fermentans incognitus
or homologous antigens of other M. fermentans strains can be utilized as a
vaccine in a conventional manner to induce the formation of protective
antibodies or cell-mediated immunity. The antigens can be isolated from M.
fermentans incognitus (or other strains) or can be produced by conventional
recombinant DNA techniques. The vaccines are prepared by usual procedures,
such as by in vitro cell cultures, by recombinant DNA techniques, and by
application of the usual and prescribed controls to eliminate bacterial
and/or viral contaminations, according to well known principles and
international standard requirements.
Preferably an inactivated, i.e., attenuated or killed, vaccine is utilized.
The M. fermentans incognitus pathogen is isolated from the infected cells
grown in monolayers. M. fermentans incognitus is killed by known procedures
or modifications thereof, e.g., by the addition of betapropiolactone,
Formalin or acetylethyleneimine, by ultraviolat radiation, or by treatment
with psoralen or psoralen derivatives and long-wavelength ultraviolet
light. Alternatively, M. fermentans incognitus is attenuated by
conventional techniques and isolated.
 
The vaccine of the invention may contain one or more suitable stabilizers,
preservatives, buffering salts and/or adjuvants. The vaccine may be
formulated for oral or parenteral administration. Compositions in the form
of an injectable solution contain a proper titer of M. fermentans
incognitus as the active ingredient, and may also contain one or more of a
pH adjuster, buffer, stabilizer, excipient and/or an additive for rendering
the solutions isotonic. The injectable solutions may be prepared to be
adapted for subcutaneous, intramuscular or intravenous injection by
conventional techniques. If desired, the solutions may be lyophilized in a
usual manner to prepare lyophilized injections.
 
The dosage of M. fermentans incognitus administered will, of course, depend
on the mode of administration and the interval of administration. An
optimal dose of the active ingredient and an optimal interval of
administration can easily be determined by routine preliminary tests known
in the art.
 
The antigens of mycoplasmas such as other strains of M. fermentans which
share antigenic determinants with M. fermentans incognitus can also be used
as vaccines to induce the formation of protective antibodies or
cell-mediated immunity to M. fermentans incognitus. It has been found that
antigens of other mycoplasmas share many antigenic determinants with M.
fermentans incognitus, but lack the pathogenicity of M. fermentans
incognitus. One such mycoplasma which can then be used in a vaccine against
M. fermentans incognitus is M. fermentans. Other mycoplasmas useful in
vaccines against M. fermentans incognitus can be determined using
conventional techniques for comparing nucleotide sequences for sequence
homology.
 
 
O. Other Disease States in Which M. fermentans incognitus Has Been Implicated
 
In addition to AIDS, M. fermentans incognitus has been implicated in a
number of other Disease states including Chronic Fatigue Syndrome,Wegener's
Disease, Sarcoidosis, respiratory distress syndrome, Kikuchi's disease,
autoimmune diseases such as Collagen Vascular Disease and Lupus, and
chronic debilitating diseases such as Alzheimer's Disease. M. fermentans
incognitus may be either a causative agent of these diseases or a key
co-factor in these diseases.
 
 
P. Treatment of M. fermentans incognitus Infection
 
M. fermentans incognitus is known to be sensitive to a number of
antibiotics, including doxycycline, quinalones such as ciprofloxacin,
chloramphenicol and tetracycline. Therefore, effective treatment of any of
the above implicated diseases should include administration of antibiotics
to which M. fermentans incognitus is sensitive.
 
When using the effective antibiotics as the active ingredients of
pharmaceutical compositions, the pharmaceutical compositions may be
administered by a variety of routes including oral, intravenous, aerosol
and parenteral. The amount of active ingredient (antibiotic) necessary to
treat an M. fermentans incognitus infection will depend on the body weight
of the patient, but will usually be from about 0.001 to about 100 mg/kg of
body weight, two to four times daily.
 
 
Q. Enhancement of HIV-1 Cytocidal Effects in CD4.sup.+ Lymphocytes by M.
fermentans incognitus.
 
Coinfection with Mycoplasma fermentans (incognitus strain) enhances the
ability of human immunodeficiency virus type-1 (HIV-1) to induce cytopathic
effects on human T lymphocytes in vitro.
Syncytium formation of HIV-infected T cells was essentially eliminated in
the presence of M. fermentans (incognitus strain), despite prominent cell
death. However, replication and production of HIV-1 particles continued
during the coinfection. Furthermore, the supernatant from cultures
coinfected with HIV-1 and mycoplasma may be involved in the pathogenesis of
acquired immunodeficiency syndrome (AIDS).
 
Abstract from Science 251, 1074 (1991). Since the presence of M. fermentans
incognitus is most often associated with AIDS and other acute fulminant
disease states and more profoundly affects the course of its disease, it
can be used to determine the prognosis of these diseases, which information
can be utilized for designing therapy regimes.
 
The presence of M. fermentans incognitus in patient tissue or cell sample
is determined by conventional techniques such as immunoassays, PCR analysis
and DNA hybridizations as more fully described herein.
The present invention is further illustrated by reference to the following
examples. These examples are provided for illustrative purposes, and are in
no way intended to limit the scope of the invention.
 
 
EXAMPLE 1
 
Isolation of Genetic Materials from AIDS Patients and Cell Culture
 
Kaposi's sarcoma tissue was obtained from a patient with AIDS who died of
fulminant Pneumocystis carinii pneumonitis. At autopsy, extensive Kaposi's
sarcoma involving skin, both lungs, parietal pleura, gastrointestinal
tract, pancreas, liver, kidney and lymph nodes was found. The tissue used
to extract genetic material was derived from Kaposi's sarcoma in the
patient's retroperitoneal lymph nodes, five to six hours after death.
Permanent paraffin sections confirmed near-total effacement of lymph node
architecture by Kaposi's sarcoma.
 
Splenic tissue was obtained from a second patient with AIDS who also died
of P. carinii pneumonitis. No tumor (i.e., Kaposi's sarcoma or lymphoma)
was identified at autopsy. Paraffin sections of the splenic tissue used to
extract genetic material showed congestion and lymphocyte depletion.
 
The splenic or Kaposi's sarcoma tissue (1-2 g) was minced into small pieces
and treated with collagenase (5 mg/ml) in 1 ml phosphate-buffered saline
(PBS) at 37.degree. C. for 15 minutes. The tissue suspension was then
treated with proteinase K (250 g/ml) in 10X volume of 150 mM NaCl, 10 mM
Tris (pH 7.5), 0.4% SDS, at 65.degree. C. for 30 minutes and at 37.degree.
C. for ten hours. Phenol extraction (twice) followed by
phenol/chloroform/isoamylalcohol (25:24:1) and chloroform/isoamylalcohol
(24:1) extraction were used to purify genetic material. Grossly visible
high molecular weight DNA was easily observed after ethanol precipitation.
The genetic materials were redissolved in aqueous phase (1 mM Tris, 1 mM
EDTA) after overnight air-drying. The recovered genetic materials contained
high molecular weight DNA and 30-40% RNA of various size. The procedures of
isolating genetic materials from the cultures of the primary transformants
and normal human fibroblasts (ATCC, CRL-1521) were similar. The pellets of
10-20.times.10.sup.6 cells were mixed directly with 10X volume of
proteinase K (250 g/ml) in the same buffer without collagenase treatment.
 
 
EXAMPLE 2
 
Transfection of NIH/3T3 Cells
 
The transfection procedures were slightly modified from that of Graham et
al., supra. Approximately 30 micrograms of nucleic acid isolated from
Kaposi's sarcoma tissue, splenic tissue, normal human fibroblast, or salmon
sperm were precipitated with calcium phosphate in each 60 mm Petri dish
culture (containing about 5.times.10.sup.5 NIH/3T3 cells). The DNA
precipitate was removed after cells were incubated at 37.degree. C. for 12
hours. After an additional 24 hours, each plate of cells was trypsinized
and reseeded into four to five 60 mm Petri dishes. The cells received five
minutes of 15% glycerol treatment in 10% fetal bovine serum (FBS, Gibco)
Dulbecco's modified Eagle's medium (DMEM) before the splitting as described
by Copeland et al., supra. The subcultures were fed with Dulbecco's medium
with 5% FBS and re-fed with this medium at intervals of three to four days.
Foci of morphologically transformed cells became evident in two weeks.
Colonies were harvested after three weeks.
 
NIH/3T3 cells transfected with genetic material derived from both spleen
and Kaposi's sarcoma tissue of AIDS patients produced morphologically
transformed colonies which were visible within two weeks. The phenotypical
transformation was characterized by the rapid overgrowth of the transfected
cells which piled up in multilayers and formed grossly visible foci.
Transformation efficiency was approximately 0.01 to 0.02 identifiable foci
per microgram of donor nucleic acid. In contrast, no transformed foci were
identified in parallel cultures using DNA from salmon sperm or nucleic acid
from human fibroblasts. The transformants were recovered from these
phenotypically malignant foci after two weeks and cultured in monolayers.
Transformants retained their tendency of piling up in multilayers and
reached more than three-fold higher cellular density than normal NIH/3T3
fibroblasts.
 
 
EXAMPLE 3
 
Confirmation of NIH/3T3 Cell Transformation
 
To confirm that transformation of the NIH/3T3 cells was mediated by active
transforming genetic elements, the primary transformants' capacity to
transmit their malignant phenotypes of rapid cell growth and pile-up (lack
of cell-cell contact inhibition) in high cellular density in subsequent
cycles of transfection was examined. Thus, a second cycle of transfection,
as described above, was performed using genetic material which was isolated
as previously described from some of the primary transfectants. A higher
efficiency of transformation was observed in the second cycle of the
transfection assay (up to 0.05 foci per microgram of donor nucleic acid).
These results indicate that genetic materials isolated from spleen and
Kaposi's sarcoma tissues of the AIDS patients contained active transforming
elements that induce malignant transformation of rapid cell growth upon
transfection and retransfection of phenotypically normal cells. DNA from
first and second stages of transformation clones selected for further
studies were then characterized with respect to the presence of human DNA
repetitive sequences by probing with .sup.32 P nick-translated Blur
8-plasmid. No human repetitive DNA sequences were detected in these
transformants.
 
 
EXAMPLE 4
 
Analysis of Transformants
 
Normal NIH/3T3 and transformant clones were all routinely maintained in
monolayer cultures with 10% FBS-supplemented Dulbecco's media. Autoclavable
slides (Cell-line Asso. Inc.) were previously sterilized and overlaid with
trypsinized cell suspension (1.times.10.sup.5 cells/ml) in square petri
dishes. The cultures were incubated at 37.degree. C. in a 5% CO.sub.2
incubator for 48 to 72 hours. The culture slides were washed three times
with cold PBS, air-dried and stored at 4.degree. C. Immunocytochemistry was
performed within two to three days on these stored slides.
 
The monolayers were scraped directly from the cultures. The cells were
harvested by centrifugation of 1,000 rpm for 10 minutes. The cell pellets
were fixed overnight at 4.degree. C. in 2.5% glutaraldehyde in phosphate
buffer and post-fixed with 1% OsO.sub.4. The fixed tissues were then
processed by standard methods and embedded in Maraglass 655. The grids with
ultra-thin sections were double-stained with uranylacetate and lead
citrate. The specimens were then examined under an electron microscope with
60 kv or 100 kv voltage. Negative staining of the virus-like particles in
the culture supernatants was performed. Briefly, the particles in the
culture supernatant were pelleted through a 5 ml 20% sucrose barrier in
SW41 centrifugation tubes, at 40,000 rpm for one hour. The pellets were
then resuspended in 1/50 to 1/100 volume of Tris-normal saline (pH 7.4,
0.05M Tris). The suspensions were directly put on formvar coated grids and
negatively stained with 2% phosphotungstic acid (PTA) (pH 7.2).
 
Two of the transformants (Sb51 and Kb43, from different patients) were
studied in detail. These two transformants were obtained from the second
cycle transfections with genetic materials from Kaposi's sarcoma spleen and
tissues, respectively. Sb51 cells persistently infected with M. fermentans
incognitus were deposited with the ATCC under No. CRL 9127 under the
Budapest Treaty on Jun. 17, 1986. The cells grew in high cellular density
with no significant cytopathic changes. However, occasional lytic plaques,
with cells showing cytopathic changes, were noted after the transformants
reached saturated density.
 
Many physiologic factors, including incubation temperatures and culture
media, were found to affect the degree of lytic plaque formation. For
example, a reduction in the temperature to 32.degree. C. results in higher
lytic plaque formation. Sb51 cells tended to pile-up in a monolayer
culture. Foci of rapid cell overgrowth and pile-up into multicellular
layers can best be appreciated under low-power light microscopy with a dark
background. Cytopathic changes commonly occurred in the centers of the high
cell density foci. Detachment of the cytolytic cells in the center of
hyperplastic foci was evident. There were prominent cytopathic effects
among the densely-packed cells on the peripheral edges of the lytic plaque.
 
These cells rounded up and appeared smaller in size with a shrunken
configuration.
 
The monolayers of Sb51 and Kb43 which showed significant cytopathic changes
in at least 30% of cells were examined by electron microscopy.
 
In those cells undergoing cytopathic changes numerous M. fermentans
incognitus cells were seen, mainly in the cytoplasm of disrupted cells.
Early cytopathic changes showing nuclear chromatin condensation and
margination was seen at 15,000X magnification. Accumulation of M.
fermentans incognitus nucleocapsids within the nucleus is prominent.
Numerous M. fermentans incognitus particles of different maturation stages
were seen in the cytoplasm at 45,800X magnification. Most of the mature M.
fermentans incognitus cells in the cytoplasm are lined up along the plasma
membrane while others are free. The M. fermentans incognitus cells were
roughly spherical enveloped particles of heterogenous sizes. The majority
of mature M. fermentans incognitus cells were 140-280 nm, with an overall
range of 100-900 nm. The intact M. fermentans incognitus particle had a
well-defined outer limited membrane about 8 nm thick and tightly packed
internal nucleocapsids. Occasionally, the nucleocapsids were seen to
condense into compact cores inside the M. fermentans incognitus cell.
Although the M. fermentans incognitus outer envelope was well-defined and
thick, it was not rigid. Elongated, ovoid, and pleomorphic forms with
protrusions were not uncommonly identified among the M. fermentans
incognitus cells (at 45,800X magnification).
 
To further confirm the ultrastructure and morphology of M. fermentans
incognitus, the unsectioned M. fermentans incognitus were examined by
pelleting M. fermentans incognitus particles from Sb51 and Kb43 culture
supernatants through a 20% sucrose gradient barrier. The particles were
resuspended in Tris-normal saline at 1/100 of original volume. The
precipitated particles were directly examined under electron microscopy
following negative stainings with PTA. Some preparations of the intact M.
fermentans incognitus particles were briefly fixed with 0.5% Formalin to
preserve the M. fermentans incognitus morphology as well as to avoid
possible infectious problems in the laboratory. The negative staining
preparations of M. fermentans incognitus usually revealed more surface
detail together with their internal structure. There was some heterogeneity
in both particle size and shape. Some M. fermentans incognitus cells often
appeared to be elongated or had irregular bulging protrusions (when viewed
at 101,800X magnification. The internal component consisted of strands
arranged more or less parallel to each other and to the long axis of the
particle. The internal nucleocapsid strands appeared to be better preserved
in the particles fixed with low concentrations of Formalin. The
well-defined envelope revealed inconspicuous spikes on the external
surface. At high magnification (370,000X), M. fermentans incognitus
demonstrated complex membranous envelopes. The released nucleocapsids
appear to be uncoiled.
 
 
EXAMPLE 5
 
PCR Assay for M. fermentans incognitus
 
An assay of urine sediments prepared in Example 6 is illustrative of a PCR
assay. The amplification of selective DNA sequences was performed with
thermostable Taq DNA polymerase (Native Taq; Perkin Elmer Cetus, Norwalk,
Conn.) (10) in the automated Perkin-Elmer Cetus DNA thermal cycler
(Norwalk, Conn.). One ml of urine sediment prepared and filtered as
described in Example 6 was first centrifuged at 1,500 x g for 15 min.
Nine-hundred ul of the supernatant was removed. Proteinase K was added to
the remaining 100 ul sample (final concentration of 200 ug/ml) and the
sample was digested at 56.degree. C. for 2 hrs. Before PCR analysis the
digested samples were heated at 95.degree. C. for 10 min. Each 10 ul urine
sediment sample to amplified was adjusted to a total volume of 160 ul with
PCR buffer containing a final concentration of 50 mM KCl, 20 mM Tris-HCl
(pH 8.3), 1 mM MgCl.sub.2, 0.001% gelatin, each primer (RW004 (SEQ ID
NO:15) and RW005 (SEQ ID NO:16) (R. Y-H Wang et al., Abstr. Gen. Meet. Am.
Soc. Microbio. 1991, G-5, p. 134) at 0.5 uM, each dNTP at 250 uM and 2.5 U
of Taq DNA polymerase. It has been found that these primers are preferred
over the RS47 and RS49 primers used in PCR assays below (Example 16 and
19). The samples were overlaid with 3 drops of mineral oil (50 ul). Samples
were denatured at 94.degree. C. for 35 sec, annealing of primers at
56.degree. C. for 45 sec and extension at 72.degree. C. for 1 min. The
annealing time was increased by one sec/cycle during the amplification.
 
After the final cycle, the annealing time was increased to 5 min, followed
by extension for 5 min. Twenty ul aliquots from each amplified sample were
removed and analyzed on a 6% polyacrylamide gel in 1.times.
Tris-borate-EDTA buffer (Maniatis et al., Molecular Cloning: a laboratory
manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1982)).
The gels were stained with ethidium bromide and the DNA visualized by UV
fluorescence. The fractionated DNA was electroblotted onto a Zeta-Probe
membrane (Bio-Rad, Richmond, Calif.) at 100 volts for 2 hrs., in 0.5.times.
Tris-acetate-EDTA buffer (Maniatis et al., supra), followed by denaturation
and fixation in 400 mM NaOH, 2 mM EDTA for 10 min. at room temperature. The
Zeta-Probe membrane was rinsed 3 times with 2.times. SSC in 20 mM Tris-HCl
(pH 7.5) and air dried for 10 min. Prehybridization was carried out in 30%
formamide, 4.times. SSC, 5.times. Denhardt's, 20 mM Tris-HCl, (pH 7.5), 2
mM EDTA, 1% SDS and 350 ug/ml of denatured salmon sperm DNA at 30.degree.
C. Hybridization was in the same mixture but contaiing the oligonucleotide
probe RW006 (SEQ ID NO:17) (Wang et al., Abstr. Gen. Meet. Am. Soc.
Microbiol. 1991, G-5. p. 134) which was 5'end labeled with .sup.32 P-ATP,
and was conducted overnight at 30.degree. C. After hybridization the
membrane was washed at 45.degree. C. in 2.times. SSC, 0.5% SDS four times
(30 min. each).
 
Forty-three urine sediments obtained from 40 HIV positive patients and 50
urine sediments obtained from HIV negative healthy control individuals were
tested for the presence of M. fermentans specific DNA sequences by using
the PCR assay. Primer pairs of synthetic oligonucleotides, designated RW004
(SEQ ID NO:15) and RW005 (SEQ ID NO:16) containing specific sequences
within the insertion sequence (IS)-like genetic element found in multiple
copies in M. fermentans mycoplasmas were used to amplify a 206 bp segment
of the IS-like DNA. Ten of 43 urine sediments obtained from HIV positive
patients with varying stages of AIDS disease, tested positive for the
presence of M. fermentans DNA. In contrast, none of the 50 urine sediments
obtained from HIV negative non-AIDS controls tested positive. FIG. 8 shows
the PCR results of representative samples from HIV negative controls (FIG.
8, lanes b and c) and HIV positive patients' urine sediments (FIG. 8, lanes
d-m). Lane n contained one femtogram M. fermentans incognitus DNA diluted
into one microgram of human placental DNA and lane o contained pUC18 DNA
digested with MspI, serving as size markers. A distinct band could be
observed in the ethidium bromide stained gel at a position corresponding to
the 206 bp fragment amplified in M. fermentans control DNA (FIG. 8A, lane
n), and in positively amplified AIDS patients' urine sediments (FIG. 8A,
lanes d-f, h, k and l). The RW006 (SEQ ID NO:17) probe hybridized strongly
to all positively amplified samples (FIG. 8B, lanes d-f, h, k, l, and n).
 
Using a similar procedure, M. fermentans species including the prototype
strain PG-18 and new clinical isolates from patients with AIDS, which had
tested negative in previous PCR reactions were analyzed in a PCR reaction
using RW004 (SEQ ID NO:15) and RW006 (SEQ ID NO:16) as primers. The assay
consistently deteted 1 fg of DNA in all species (FIG. 7). Specificity of
the reaction has also been examined by attempting to amply the DNAs
isolated from other human or non-human mycoplasmas, common tissue culture
contaminating mycoplasmas, Gram-positive or Gram-negative bacteria, mouse,
monkey and human cell culture and/or tissue. The reaction does not produce
the specific 206 bp DNA fragment
(Table 1).
 
TABLE 1
______________________________________
SPECIFICITY OF PCR FOR M. FERMENTANS
USING UNIQUE SEQUENCES WITHIN THE
IS-LIKE GENETIC ELEMENT
Concentration
of DNA
Sources tested Positivity
______________________________________
Mycoplasmas
M. fermentans
ATCC 19989 1 fg +
incognitus strain 1 fg +
PG-18 1 fg +
K-7 1 fg +
MT-2 1 fg +
and nine clinical isolates
1 fg +
M. hominis (ACTCC 15488)
1 ng -
M. orale (ATCC 23714)
1 ng -
and one clinical isolate
1 ng -
M. salivarium (ATCC 23064)
1 ng -
and two calinical isolates
1 ng -
M. buccale 1 ng -
M. pneumoniae (ATCC 15531)
1 ng -
M. genitalium (ATCC 33530)
1 ng -
M. arginini (ATCC 23838)
1 ng -
M. pirum 1 ng -
M. alvi 1 ng -
M. moatsii 1 ng -
M. sualvi 1 ng -
M. iowae 1 ng -
M. arthritidis 1 ng -
M. hyorhinis (ATCC 17981)
1 ng -
Acholeplasma laidlawii (ATCC 23206)
1 ng -
Ureaplasma urealyticum
1 ng -
(ATCC 27618)
Bacteria
E. coli 1 ug -
Streptococcus pneumoniae
1 ug -
Clostridium perfringens
1 ug -
Mouse
NIH/3T3 1 ug -
Spleen (Balb/c) 1 ug -
Liver (Balb/c) 1 ug -
Brain (Balb/c) 1 ug -
Monkey
Vero cells (ATCC CCL18)
1 ug -
Spleen (green monkey)
1 ug -
Liver (green monkey)
1 ug -
Brain (green monkey)
1 ug -
Human
CCRF-cem (ATCC CCL119)
1 ug -
Placenta (nl. delivery) 4X)
1 ug -
PBMC (nl. donor) 50X
1 ug -
______________________________________
 
 
EXAMPLE 6
 
Direct Isolation of AIDS-associated Myoplasma From Infected Tissues of AIDS
Patients
 
Urine was collected in sterile containers and concentrated 10-fold by
centrifugation (3000.times.g for 15 min. at 4.degree. C.) and resuspended
in 1/10 of the original urine. The resulting urine sediments were diluted
1:10 in modified SP-4 media (Lo et al. (1989(a), Am. J. Trop. Med. Hyg. 41:
586-600) and then filtered through a 0.22 um filter.
 
The filtered urine sediments (10 ml), previously diluted in modified SP-4
media, were cultured in 25 cm.sup.2 tissue culture flasks and also cultured
with a further 1:10 aerobically and in GasPak jars (BBL, Microbiology
Systems, Cockeysville, Md.) anaerobically. Flasks showing a color change
were subcultured to modified SP-4 agar to confirm the mycoplasma growth.
Speciation of various mycoplasma colonies obtained was assayed by
immunofluorescence of colonies on agar using species-specific
FITC-conjugated antibodies (Del Guidice et al. (1967), J. Bacteriol.
93:1205-1209).
 
Restriction endonuclease cleavage and Southern blot hybridization of
genomic DNA from prototype strains and new clinical isolates of M.
fermentans was carried out basically as previously described (Lo et al.
(1989a), supra; Lo et al. (1989b). Am. J. Trop. Med. Hyg. 41:213-226). DNA
was isolated from cultures of each isolate or strain of M. fermentans,
purified by standard methods, and digested with either EcoRI or HindIII
restriction enzymes (Gibco-BRL, Gaithersburg, Md.). The enzyme digests of
NDA, after electrophoresis in 1% agarose, were transferred to a Zeta-Probe
membrane by the Southern blot method. Each filter was prehybridized in 50%
formamide, 4 x SSC, 5 x Denhardts', 20 mM Tris-HCl (pH 7.5), 2 mM EDTA, 1%
SDS, and 250 ug/ml denatured salmon sperm DNA for at least 4 hrs at
42.degree. C. and hybridized with .sup.32 P nick-translated psb-2.2 DNA (Hu
et al. (1990). Gene 93:67-72) at 42.degree. C. in the prehybridization
solution as described, (Lo et al. (1989b), supra). After hybridization the
blots were washed at 55.degree. C. in x 2 SSC, 0.5% SDS, 10 mM Tris-HCl (pH
7.5) for 120 min. with 4 changes and then washed at 50.degree. C. in 0.5 x
SSC, 0.1% SDS for 60 min. with 2 changes before autoradiography (Lo et al.
(1989b), supra).
 
M. fermentans was isolated and grown in modiifed SP-4 media from 3 of the
AIDS patients' urine sediments which tested positive in the PCR assay of
Example 5. DNA was prepared from cultures of the new clinical isolates and
compared with that of representative M. fermentans strains in Southern blot
analysis. The DNASs were digested with EcoRI (a lanes) or HindIII (b
lanes), fractionated in an agarose gel and hybridized with .sup.32
P-labeled psb-2.2 (FIG. 9). Lane m is HindIII digested lambda phage DNA
used as marker of 23.1, 6.6, 4.4, 2.3 and 2.0 kb, respectively. The new
clinical isolates (FIG. 9, D and E) have similar but distinct restriction
enzyme patterns from K7 strain (FIG. 9,A) PG18 prototype strain (FIG. 9,B),
original M. fermentans incognitus (FIG. 9,C) which indicates that they are
indeed independent isolates.
M. fermentans mycoplasmas were successfully isolated and grwon in
mycoplasma culture from 3 urine sediments derived from 2 HIV positive
individuals (Table 1). Five Ureaplams Urealyticum and two M. hominis were
also isolated from the 43 cultures of AIDS patients' urine sediments. Fifty
urine sediments similarly prepared from age-matched HIV negative healthy
controls did not grow M. fermentans mycoplasmas. In this study, 23
Ureaplasma Urealyticum and M. hominis were isolated from the 50 control
urine sediments (Table 2).
 
 
TABLE 2
______________________________________
Isolation of Different Species of
Mycoplasma and Ureaplasma urealyticum
from Urine of HIV positive AIDS patients
and HIV negative non-AIDS controls
Source of Urine
HIV Positive HIV Negative
Species AIDS Patients
Controls
______________________________________
M. fermentans 3/43.sup.a (7.0%).sup.b
0/50 (0%)
M. fermentans 2/43 (4.7%) 1/50 (2.0%)
U. urealyticum
5/43 (11.6%) 23/50 (46.0)%
______________________________________
.sup.a Number of isolates over number of samples cultured
.sup.b Percentage of isolation
 
 
EXAMPLE 7
 
Isolation and Gradient Banding of M. fermentans incognitus
 
Sb51 cells grown as monolayers were briefly trypsinized and pelleted by
centrifugation at 1,000 rpm for 10 minutes. The cell pellet was resuspended
with an equal volume of Dulbecco's medium. The cells were lysed by five
cycles of freezing and thawing to release the cell-associated M. fermentans
incognitus particles. The particles were pelleted through a 20% sucrose
barrier in a SW41 centrifuge tube by centrifugation at 40,000 rpm for 45
minutes. The particles were resuspended in PBS and banded in a sucrose
isopycnic gradient (20% to 60%). Electron micrographs of the M. fermentans
incognitus cells in the cytoplasm of degenerating Sb51 cells is shown in
FIG. 10. The M. fermentans incognitus particles were localized at a density
of about 1.17 to about 1.20 (FIGS. 10(B) and 10(C)). The M. fermentans
incognitus particles were directly identified by electron microscopy with
PTA negative staining.
 
 
EXAMPLE 8
 
Production of Antibodies Against M. fermentans incognitus
 
M. fermentans incognitus particles were isolated as described in Example 7
from 5.times.10.sup.6 Sb51 cells, and mixed with Freund's adjuvant. Rabbits
were injected with the immunogen twice at a two- to three-month interval. A
good antibody response to M. fermentans incognitus was obtained after the
second immunization.
 
 
EXAMPLE 9
 
Infection of Mice by M. fermentans incognitus
 
M. fermentans incognitus was isolated as described in Example 7, from
5.times.10.sup.6 Sb51 cells, and resuspended in a small amount of PBS. The
M. fermentans incognitus suspension was injected into either a six-week-old
NIH (Nu) male mouse or a six-week-old Balb/c male mouse. The injection was
performed either intravenously or intraperitoneally. Sixty percent of the
nude mice who received intravenous or intraperitoneal injections of the M.
fermentans incognitus preparation showed evidence of skin rashes with areas
of erythematous changes and conjunctivitis in 10 to 12 days. One animal
also showed prominent periorbital edema. These signs disappeared after two
to three weeks. All the animals appeared to recover from the acute
infection. Two animals then developed pruritic skin rashes after six weeks.
These two animals and the other two animals died or became too sick, and
had to be sacrificed in three months. Therefore, 40% of the animals had
died in the first three months following injection. One animal which did
not develop recognizable skin lesions showed systemic lymphadenopathy and
paralysis. The animal appeared to be wasting and experienced complete
paralysis of its hind legs. One animal had several purplish skin lesions
which were slightly raised. At necropsy, all lymph nodes in these animals
showed lymphocyte depletion. Only very small lymph nodes were identified on
gross examination. In contrast, disseminated lymphadenopathy was seen in
the inguinal, axillary, cervical, mediastinal and mesentery lymph nodes.
The animal also developed hepatosplenomegaly. Histologic sections of the
lymph nodes revealed prominent plasmacytosis. Areas of sinus histiocytosis
were also noted. The plasma cell effaced normal lymph node architecture and
diffusely infiltrated the sinus. Lymph nodes in all the other animals
showed lymphocyte depletion. Only small lymph nodes could be identified
grossly.
 
Histologic sections of purplish skin lesions revealed spindle cell
proliferation. The spindle cells appeared to infiltrate cutaneous adipose
tissue as well as underlying muscles. Extravasation of red blood cells was
seen in some areas. Mitotic figures were identified, but not prominent.
Histologic examination of the liver of the animal also revealed spindle
cell proliferation in the periportal areas. The homogeneous tumor cells
exhibited more epithelioid appearance. Numerous red blood cells were
trapped in the intercellular slits.
 
Electron microscopic examination of the infiltrating spindle cells in the
skin lesions revealed cells with cytopathic changes. An accumulation of M.
fermentans incognitus nucleocapsids were seen in many of the nuclei, and
some in the cytoplasm. The morphology and the characters of these M.
fermentans incognitus nucleocapsids were similar to those observed in Sb51
cells previously described. Mature M. fermentans incognitus cells were also
identified in some of the disrupted cells. Both nucleocapsids and M.
fermentans incognitus cells were often seen in dilated cisternae of smooth
endoplasmic reticulum. Electron microscope studies of the periportal
spindle cell lesions in the liver similarly revealed prominent infection of
M. fermentans incognitus.
 
Balb/c mice infected with the M. fermentans incognitus also appeared to be
sensitive to the M. fermentans incognitus pathogen. Three of seven animals
died in the first three months following infection. Two more animals died
in the fourth month following infection. None of the control animals showed
any disease in four months. Clinical evaluation of skin rashes and
lymphadenopathy while these animals were alive was much more difficult. At
necropsy, all of the animals were found to be lymphocyte-depleted. The
animals had very small lymph nodes and spleens. Lymph nodes were often
unrecognizable grossly. The lungs of these animals were found to have
severe pneumonitis. M-Ag and toluene blue staining revealed P. carinii.
Therefore, these animals were believed to be severely immunodeficient. Two
of the animals who survived for more than four months were found to have
antibody in their sera which recognized Sb51 cells but not NIH/3T3 parental
cells. Immunoperoxidase reaction of the sera showed positive reactions in
both the nuclei and the cytoplasm of Sb51 cells indicating the presence of
M. fermentans incognitus.
 
 
EXAMPLE 10
 
Infection of Non-Human Primates with the M. fermentans incognitus
 
Four silver leaf monkeys (presbytis cristatus) were inoculated
(intraperitoneally) with partially purified M. fermentans incognitus (see
Example 7 above). All four monkeys displayed a wasting syndrome as shown in
FIG. 11, and died within seven to nine months. A control monkey which had
been inoculated with a preparation derived from normal NIH/3T3 cells did
not exhibit the wasting syndrome and did not die during the seven- to
nine-month period.
 
The monkeys were followed daily for signs of illness, and examined once
every two weeks for body weight, body temperature and general physical
condition. Serial blood samples were also collected every two weeks for
blood cell counts and antibody and antigen assays.
 
Two weeks after M. fermentans incognitus inoculation, one monkey showed
signs of a flu-like syndrome which persisted for six weeks. This same
monkey later developed facial/neck edema (between week 8 and week 12), poor
skin tones, and dermatities associated with alopecia (after week 18). This
was the first monkey to succumb, expiring at the 29th week after M.
fermentans incognitus inoculation. The animal had apparently been afebrile
throughout the whole course, except at the time of the 16th week after M.
fermentans incognitus inoculation.
 
Body weights of all M. fermentans incognitus inoculated monkeys fluctuated.
However, a progressive weight loss was noted among these animals in the
last 14 weeks of the experiment (FIG. 11). No diarrhea was detected for any
of the animals. Two of the monkeys also had transient lymphadenopathy at 4
to 14 weeks and 4 to 20 weeks after M. fermentans incognitus inoculation,
respectively. Three monkeys appeared to have persistent low grade fever in
the earlier course of the experiment, but no significant febrile response
could be detected in the later stages (the last month). The moribund
animals revealed paradoxical hypothermia in the final periods. One monkey
revealed signs of tremor, rigidity and imbalance in the terminal stage. The
clinical signs strongly suggested a neurological illness. Accurate
assessment, however, was hampered by the obvious physical weakness of the
animal which may have been due to the prominent weight loss.
 
At necropsy, no malignant tumor or opportunistic infection could be
identified in any M. fermentans incognitus inoculated animal.
Histopathology of the lymph nodes obtained from these monkeys revealed
features of lymphocyte depletion. There was spindle cell proliferation in
the perinodal areas, but typical diagnosis of Kaposi's sarcoma could not be
made.
 
One animal revealed persistent and significant leukocytosis that lasted for
about three months (between 16 to 28 weeks after inoculation). In contrast,
two other monkeys showed prominent leukopenia in the terminal stage.
Differential cell count revealed that their lymphocytes were 448, and 410
per microliter, respectively. Both red blood cell and platelet counts
fluctuated. Transient periods of low platelet counts were observed during
the course of the study for all animals. However, no animal was
thrombocytopenic in the terminal stage.
 
To study if the M. fermentans incognitus inoculated animals developed an
immune response and produced specific antibodies, the serum samples
obtained from serial bleedings during the course of the experiment were
examined. Sucrose gradient-banded M. fermentans incognitus was used as the
antigen in the Western blot antibody analysis. Seroconversions which were
defined by definite changes of the immunoreactive patterns and development
of new reactive bands on the blot strips after M. fermentans incognitus
inoculation, occurred unusually late. Only one monkey had a prominent
antibody response, which however, occurred as late as seven months after M.
fermentans incognitus inoculation. Another monkey had a transient antibody
response for two months (six months to eight months after M. fermentans
incognitus inoculation) which apparently disappeared in the terminal stage,
one month before the animal expired. The other two monkeys had a poor and
very late immune response which again only occurred in the terminal stage,
4 to 6 weeks before the animals expired. No antibody response could be
detected in the control monkey. Estimated molecular weights for the newly
developed major protein bands which revealed a positive reaction with the
first monkey's sera obtained seven months post M. fermentans incognitus
inoculation, were 97, 88, 84, 32.5 and 27.5 kilodaltons, respectively.
 
M. fermentans incognitus antigens in the animals' sera obtained during the
course of the experiment were also measured. By sandwiched radioimmunoassay
using rabbit antiserum raised against M. fermentans incognitus antigens,
periodic M. fermentans incognitus antigenemia was detected in the three
monkeys which failed to produce a prominent antibody response. The first
monkey to succumb showed the most prominent, early and persistent M.
fermentans incognitus antigenemia.
 
To further confirm that these animals inoculated with M. fermentans
incognitus suffered a fatal systemic infection by M. fermentans incognitus,
DNA obtained from various tissues taken at necropsy was directly examined.
In this study, the highly sensitive polymerase chain reaction (PCR) method
of selective DNA amplification was used. Primer pairs (RS47 (SEQ ID
NO:13)/RS49 (SEQ ID NO: 14)) of synthetic oligonucleotides with M.
fermentans incognitus-specific sequences and Taq DNA polymerase were used
for 35 reaction cycles of M. fermentans incognitus-specific DNA
amplification. The primer pairs RS47/RS49 were previously shown to span the
first 160 bp region at one terminal end of M. fermentans incognitus DNA of
psb-2.2 (SEQ ID NO:2). The presence of M. fermentans incognitus-specific
DNA in the amplified products was confirmed by blot hybridization using
synthetic oligonucleotide probe (RS48 (SEQ ID NO:1)) 5' end-labeled with
.sup.32 P. The typical positive hybridizations for M. fermentans
incognitus-specific DNA products revealed diagnostic 160 bp DNA fragments
with sequence homology to RS48 (SEQ ID NO:1) representing a central segment
of the intervening sequences between RS47 (SEQ ID NO:13) and RS49 (SEQ ID
NO:14). In the PCR, M. fermentans incognitus DNA was found in spleen,
liver, brain and kidney of the M. fermentans incognitus inoculated animals,
but not in the tissues of the control animal.
 
The necropsy tissues of two monkeys' livers as well as a monkey which
appeared to contain the most abundant amount of M. fermentans incognitus
DNA also stained positively with M. fermentans incognitus-specific rabbit
antiserum. Direct examination by electron microscopy of these tissues
revealed M. fermentans incognitus particles. Clusters of M. fermentans
incognitus particles could most frequently be found in the cytoplasm of
hepatocytes and degenerating Kuffer cells. The nearly spherical particles
were 140-280 nm in diameter, had well-defined outer limiting membranes and
a densely packed granular or thin tubular internal structure. Occasionally,
these M. fermentans incognitus particles were seen in the nuclei of cells
with prominent pathological changes. Some M. fermentans incognitus
particles were also noted in the extracellular tissue matrix. The necropsy
tissues of liver and apleen obtained from the control monkey which did not
contain M. fermentans incognitus DNA did not stain with M. fermentans
incognitus-specific antiserum and did not have similar M. fermentans
incognitus particles.
 
In an attempt to reisolate M. fermentans incognitus from M. fermentans
incognitus-inoculated monkeys, the peripheral blood mononuclear cells
obtained from the moribund monkeys were co-cultivated with normal human
peripheral blood mononuclear cells (PBMC), NIH/3T3 cells and monkey BSC
cells. Supernatants of the cultures were assayed for the presence of M.
fermentans incognitus-specific antigens and DNA once every week. The
cultures were maintained for three months without evidence of M. fermentans
incognitus growth. All the cultures were also examined for the presence of
reverse transcriptase enzyme activity representing growth of retroviruses.
Homogenates of necropsy tissues such as liver and spleen were also
inoculated into NIH/3T3 cells and monkey BSC cells. No M. fermentans
incognitus was successfully recovered in any of these attempts.
 
 
EXAMPLE 11
 
Detection of Antibodies Against M. fermentans incognitus
 
Sera from AIDS patients and from normal subjects were analyzed by the
immunoperioxidase straining procedure as described by Hsu et al., supra.
Briefly, persistently infected Sb51 cells or normal NIH/3T3 cells were
grown in low cell density on sterile glass slides. The culture slides were
fixed in acetone at room temperature for five minutes. After washing in
Tris-buffered saline (TBS), pH 7.6, 0.05M, the slides were first incubated
with 1% normal horse serum containing 100 g/ml avidin (Sigma) for 30
minutes, and then incubated with saturated solution of biotin (Sigma) in
TBS for an additional 15 minutes.
 
This initial step has been shown to minimize any nonspecific reaction
derived from avidin-biotin-peroxidase complex (ABC). The human antisera
from AIDS patients or normal subjects were then used at 1:200 dilution
followed by biotin- labelled goat anti-human immunoglobulin (Tago,
Burlingame, Calif.) at 1:200 dilutions and ABC (Vector Lab., Burlingame,
Calif.). Each incubation step was conducted for 30 minutes with extensive
washing between steps. The color reaction was developed in DAB-Ni-H.sub.2
O.sub.2 solution and counterstained with methyl green. Controls for the
technique were performed by omitting the secondary antibody.
 
Sera of patients with AIDS produced positive immunochemical reactions with
these infected cells, but not with normal NIH/3T3 cells (FIGS. 12(C) and
12(B), respectively). The reaction appeared to be positive in both nuclei
and cytoplasm of Sb51 cells. However, many of the nuclei stained
significantly stronger than the cytoplasm. A population of smaller round
cells with apparently fewer cellular processes were found to be most
heavily stained. Using this assay, 23 of 24 sera from AIDS patients,
whether they presented with Kaposi's sarcoma, Kaposi's sarcoma with
opportunistic infections, or opportunistic infections alone, were positive
(Table 3). Serum from only one AIDS patient, with both Kaposi's sarcoma and
opportunistic infections, showed weak positivity. Twenty-six of 30 non-AIDS
normal human sera showed no reactivity to the infected Sb51 cells. One such
negative reaction is shown in FIG. 12(A). The other four sera showed mild
reactivity to these cells. However, staining intensity was significantly
less than that seen in the reactions of AIDS patients' sera.
 
 
TABLE 3
______________________________________
Prevalence of Serum Antibodies to Sb51 Cells
in AIDS Patients with Various Clinical Presentations
Number
Risk Group Positive for
Male Antibodies
Homo- Total to SB.sub.51
Subjects sexual Other Number Cells**
______________________________________
Patients with
23 1* 24 23
AIDS
Kaposi's 8 8 8
sarcoma
Opportunistic
5 1* 6 6
infection
Kaposi's 10 10 9
sarcoma and
opportunistic
infections
Normal 30 0**
Controls
______________________________________
*Female, sexual partner of bisexual males.
**Four nonAids control sera showed mild reactivity; all the other control
sera did not elicit any reaction.
 
 
EXAMPLE 12
 
Identification of M. fermentans incognitus Infected Cells in Tissues of
AIDS Patients
 
Lymph node, spleen, Kaposi's sarcoma and brain tissues from AIDS patients
were fixed in Formalin and processed in paraffin sections. An
immunoperoxidase assay, such as described in Example 11, was performed
using antisera from mice or rabbits prepared as described in Example 8 in
place of the antisera from AIDS patients. M. fermentans incognitus infected
cells were identified in virtually all of the tissues examined. Electron
microscopy was performed to confirm the infection by M. fermentans
incognitus. Mature M. fermentans incognitus cells were also seen in some of
the cells of the infected tissues.
 
 
EXAMPLE 13
 
Transmission of Cell-Free M. fermentans incognitus
 
Sb51 cells (about 2.times.10.sup.7 cells) were harvested following
trypsinization. The cell pellet was resuspended in 2 ml of RPMI-1640 media
with 10% sorbitol (w/v). The suspension was then subjected to five cycles
of freezing and thawing followed by clarification of cell debris as
described above. Supernatant containing M. fermentans incognitus was
diluted in 20 ml of RPMI-1640 with 10% bovine calf serum and filtered
through a 0.22 micron filter. The filtered supernatant was added to four
75-cm.sup.2 tissue culture flasks containing 70% to 80% confluent normal
NIH/3T3 cells, human embryo fibroblasts or monkey BSC cells (about 5 ml of
filtered supernatant were added to each flask). The infected cultures were
split one week later and replenished with fresh media. The cultures were
kept for an additional week. At the end of two weeks, two flasks of cells
were used for the next cycle of cell-free, M. fermentans incognitus
transmission. The other two flasks were used for DNA extraction or antigen
determination. Equal numbers of normal NIH/3T3 cells, instead of Sb51
cells, were cultured in parallel through each cycle of cell-free M.
fermentans incognitus transmission as controls.
 
 
Part II

 
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