Whole-genome and transcriptome analysis enhances precision cancer treatment options.

BACKGROUND: Recent advances are enabling delivery of precision genomic medicine to cancer clinics. While the majority of approaches profile panels of selected genes or hotspot regions, comprehensive data provided by whole-genome and transcriptome sequencing and analysis (WGTA) present an opportunity to align a much larger proportion of patients to therapies. PATIENTS AND METHODS: Samples from 570 patients with advanced or metastatic cancer of diverse types enrolled in the Personalized OncoGenomics (POG) program underwent WGTA. DNA-based data, including mutations, copy number and mutation signatures, were combined with RNA-based data, including gene expression and fusions, to generate comprehensive WGTA profiles. A multidisciplinary molecular tumour board used WGTA profiles to identify and prioritize clinically actionable alterations and inform therapy. Patient responses to WGTA-informed therapies were collected. RESULTS: Clinically actionable targets were identified for 83% of patients, of which 37% of patients received WGTA-informed treatments. RNA expression data were particularly informative, contributing to 67% of WGTA-informed treatments; 25% of treatments were informed by RNA expression alone. Of a total 248 WGTA-informed treatments, 46% resulted in clinical benefit. RNA expression data were comparable to DNA-based mutation and copy number data in aligning to clinically beneficial treatments. Genome signatures also guided therapeutics including platinum, poly-ADP ribose polymerase inhibitors and immunotherapies. Patients accessed WGTA-informed treatments through clinical trials (19%), off-label use (35%) and as standard therapies (46%) including those which would not otherwise have been the next choice of therapy, demonstrating the utility of genomic information to direct use of chemotherapies as well as targeted therapies. CONCLUSIONS: Integrating RNA expression and genome data illuminated treatment options that resulted in 46% of treated patients experiencing positive clinical benefit, supporting the use of comprehensive WGTA profiling in clinical cancer care.

Acute toxicity and tissue distributions of malathion in Ambystoma tigrinum.

The kinetics of the bioaccumulation of malathion (O,O-dimethyl phosphorodithioate of diethyl mercaptosuccinate) and the biological impact of exposure for tiger salamanders, Ambystoma tigrinum, were assessed through exposure to soil surface contaminated with 50 microg/cm(2) or 100 microg/cm(2 )malathion and ingestion of an earthworm exposed to soil contaminated with 200 microg/cm(2) malathion. Malathion and malaoxon burdens in salamanders sampled at different times after exposure(s) were measured by gas chromatography in four tissue/organ subgroups: liver, epaxial muscle, pooled viscera (except the liver and brain), and pooled avisceral carcass (muscle, skin, and bone). The total tiger salamander xenobiotic burdens were calculated from these data. The malathion/malaoxon burden 1 day after exposure was greatest in the avisceral carcass and 2 days after exposure was greatest in the viscera. Bioconcentration and bioaccumulation factors remained less than unity throughout the experiment and did not support the hypothesis of bioaccumulation of malathion in the tiger salamander. Biological impact was assessed with a colorimetric brain cholinesterase microassay. Brain cholinesterase activities in salamanders exposed to malathion-contaminated soil (50 microg/cm(2) or 100 microg/cm(2 )malathion) were suppressed approximately 50-65% and 90%, respectively, compared to unexposed controls. The exposed animals did not exhibit overt clinical signs of malathion toxicosis.

Environmental uranium and human health.

Uranium from the environment enters the human body by ingestion with food and drink and by inhalation of respirable airborne uranium-containing dust particles or aerosols. Daily intake of uranium in food and water varies from approximately 1 to approximately 5 micrograms U/d daily in uncontaminated regions to 13-18 micrograms/d or more in uranium mining areas. A 70 kg, non-occupationally exposed 'Reference Man' living in Europe or in the United States has an estimated total body uranium content of about 22 micrograms. Uranium is absorbed from the intestine or the lungs, enters the bloodstream, and is rapidly deposited in the tissues, predominantly kidney and bone, or excreted in the urine. In the bloodstream, uranium is associated with red cells, and its clearance is relatively rapid. Renal toxicity is a major adverse effect of uranium, but the metal has toxic effects on the cardiovascular system, liver, muscle, and nervous system as well. Any possible direct risk of cancer or other chemical- or radiation-induced health detriments from uranium deposited in the human body is probably less than 0.005% in contrast to an expected indirect risk of 0.2% to 3% through inhaling the radioactive inert gas radon, which is produced by the decay of environmental uranium-238 in rocks and soil and is present in materials that are used to build dwellings and buildings where people live and work.

Is recombinant human erythropoietin (rh-epo) more than just a treatment of anemia in cancer and chemotherapy?

Recombinant human eythropoietin (rh-epo) is a well established treatment for many kinds of anemia including the anemia of cancer with or without myelosuppressive chemotherapy. This review considers the effects of rh-epo in humans, tumour-bearing and healthy experimental animals treated with cisplatin with or without rh-epo, and proposes that the ability of rh-epo to improve the quality of life in cancer patients may also be due to interference with the prostaglandin pathways.

Prevalence of Bartonella henselae antibody in Florida panthers.

Serum samples from 28 free-ranging Florida panthers (Puma concolor coryi) and seven mountain lions from Texas (P. concolor stanleyana) living in south Florida (USA) between 1997 to 1998 were tested for antibodies to Bartonella henselae. Twenty percent (7/35) of the samples were reactive to B. henselae antisera with a subspecies prevalence of 18% (5/ 28) for Florida panthers and 28% (2/7) for cougars from Texas (USA). There was not a significant sex related difference in infection rates among the Florida panthers. Antibody prevalence was higher in panthers <2-yr of age (40%) compared to panthers >2-yr (13%). Compared to studies of antibody prevalence in mountain lions (P. concolor) from California (USA), overall seroprevalence was lower as was prevalence in panthers >2-yr-old. However, the seroprevalence in animals <2-yr from southern Florida was similar to prevalences reported in mountain lions or domestic felids in California.

Effects of malathion on disease susceptibility in Woodhouse's toads.

Adult male Woodhouse's toads (Bufo woodhousi) developed clinical disease, hepatomegaly, and died at a higher rate when externally exposed once to either a high or low sublethal dose (0.011 or 0.0011 mg malathion/g toad) of field grade malathion and challenged with a sublethal dose of Aeromonas hydrophila injected intraperintoneally (1.1 x 10(4) bacteria/g toad) when compared to toads not exposed to malathion but challenged with A. hydrophila (P < 0.007). Toads exposed to malathion (high or low dose) and challenged with A. hyydrophila had clinical disease, hepatomegaly, and died at a higher rate [9 (90%) of 10] than toads exposed to malathion alone (P < 0.002). Toads exposed to the high and low doses of malathion had a 22% and 17% decrease in brain cholinesterase levels, respectively, when they were compared to nonmalathion exposed toads (P < 0.025, P < 0.006). It appears that field grade malathion applied externally to adult Woodhouse's toads may cause increased disease susceptibility when challenged with a potentially pathogenic bacteria.

Hematologic effects of cytauxzoonosis in Florida panthers and Texas cougars in Florida.

Cytauxzoon felis is a long-recognized hemoparasite of free-ranging Florida panthers (Puma concolor coryi), but its prevalence and effect on the population has not been assessed. Red blood cell indices and white blood cell counts were compared between infected and noninfected Florida panthers and Texas cougars (Puma concolor stanleyana) from 1983-1997 in Florida (USA). The prevalence of cytauxzoonosis for both populations was 39% (11/28) for Texas cougars, 35% for Florida panthers (22/63) and 36% overall. Thirteen hematologic parameters were compared between C. felis positive and negative panthers and cougars. Florida panthers had significantly lower mean cell hemoglobin count (MCHC) and higher white blood cell (WBC), neutrophil, monocyte and eosinophil counts (P < or = 0.05) than Texas cougars. Infected Florida panthers had significantly lower mean cell hemoglobin (MCH) and monocyte counts and higher neutrophil and eosinophil counts than infected Texas cougars. Although statistically significant differences were measured for hematologic parameters in C. felis positive panthers and cougars, biologically significant differences were not likely because values were generally within expected reference ranges for healthy animals. Cytauxzoonosis does not appear to have a negative effect on the hematologic parameters of chronically infected panthers and cougars. Potential transient changes during initial infection were not evaluated.

Experimental exposure of Canadian toads to Basidiobolus ranarum.

Experimental transmission of the fungus Basidiobolus ranarum was induced in two treatment groups of Canadian toads (Bufo hemiophrys) and caused a fatal mycotic dermatitis. Seven of 10 (70%) toads that had their ventral skin mildly abraded and exposed to B. ranarum developed hyperemia, and sloughing of their ventral skin and died. Toads with abraded ventral skin or exposure to infected skin also were affected statistically at a higher rate than those with abraded skin and exposure to pure cultures of B. ranarum inoculated into their water source. Of toads showing clinical disease, B. ranarum was identified by both impression smears and histology in all cases, but not from toads that appeared clinically healthy. The organism was cultured from 5 of 7 (71%) toads with clinical disease but not from any toad that appeared clinically healthy (n = 28). This study documents methods of experimental transmission of B. ranarum, an organism responsible for causing a mycotic dermatitis that is fatal to toads.

Mortality of captive Canadian toads from Basidiobolus ranarum mycotic dermatitis.

Twenty-six adult free-ranging Canadian toads (Bufo hemiophrys) were collected from northeastern North Dakota (USA) during the last week of August 1994 and placed in captivity. During late December and January 1995, 21 Canadian toads died. Clinical signs included increased time sitting in water bowls, darkened dorsal skin, constant arching of their backs, and hyperemia and sloughing of ventral epidermis. The condition progressively worsened until death occurred within 5 to 7 days after onset of clinical disease. Mycotic dermatitis due to Basidiobolus ranarum was diagnosed in all toads and the fungus was isolated from 11 (52%) of 21 toads. Histology of the ventral skin and digits revealed numerous fungal spherules and occasional hyphae without significant inflammatory reaction. This condition clinically resembled red leg associated with Aeromonas hydrophila and many other bacterial organisms, and the diseases could be confused without appropriate diagnostic tests. This also is the first report of B. ranarum causing clinical disease in a toad species.

Hematologic, serologic values, histopathologic and fecal evaluations of bison from Yellowstone Park.

Hematologic and blood chemistry parameters were measured in 149 free-ranging American bison (Bison bison) from Yellowstone National Park, Wyoming (USA). Additionally, histopathologic evaluations of lung, liver, spleen, kidney, and mesenteric and bronchial lymph nodes were made from ten animals. Forty-five fecal samples were screened for the presence of helminth ova. Leukopenia and markedly low blood urea nitrogen concentrations were the most notable differences observed from other bison populations. All tissues examined were essentially normal; there was evidence of moderate intestinal parasite burdens.

Isolation of Pasteurella spp. from free-ranging American bison (Bison bison).

From November 1991 through March 1992, nasal and pharyngeal swab samples were collected from 45 bison (Bison bison) from Yellowstone National Park, Montana (USA) and cultured for Pasteurella spp. Thirteen isolates of Pasteurella spp. were recovered from 10 (22%) of the animals. Ten isolates were from pharyngeal samples in contrast to three isolates from nasal samples. Pasteurella haemolytica (six biotype T, two biotype A, and two biotype 3) was the predominant Pasteurella species. Five biotype T isolates were serotype 4 and the sixth agglutinated in antisera 3, 4, and 10. Both biotype A isolates were untypable with antisera to recognized type strains. Pasteurella multocida was isolated from the pharyngeal samples of one animal. Two isolates could not be identified to species.

Mucormycotic dermatitis in captive adult Wyoming toads.

During late May 1995, 50 adult captive endangered Wyoming toads (Bufo baxteri) were brought out of hibernation. Approximately 3 to 10 days after hibernation emergence, all toads were hormonally induced to breed, and paired. Each pair was placed in their own breeding tank. Four toads developed clinical signs of disease which included lethargy and multiple (4 to 12) small (2 mm) raised hyperemic nodules with white fuzzy caps on the ventral skin. The condition progressively worsened until death occurred, within 3 to 6 days. Mycotic dermatitis caused by Mucor sp. was diagnosed in the four toads through histology and isolation of the organism. This is the first case report of a Mucor sp. causing a fatal dermatitis in an amphibian without significant inflammatory response and without systemic involvement.

Safety of Brucella abortus strain RB51 in deer mice.

Brucella abortus strain RB51 is an approved brucellosis vaccine for use in cattle that may have potential as an oral vaccine for use in elk (Cervus elaphus) and/or bison (Bison bison). This study was designed to determine effects of strain RB51 on deer mice (Peromyscus maniculatus), a nontarget species that could have access to treated baits in a field situation. In February 1994, 90 mice were orally dosed or intraperitoneally injected with 1 x 10(8) colony forming units strain RB51 and 77 controls were similarly dosed with sterile saline. At weekly intervals through early April 1994, 4 to 6 mice from each group were euthanized, gross necropsies performed, spleens and uteruses cultured, and tissues examined histologically. All orally inoculated mice cleared the infection by 6 wk post-inoculation (PI). While most of the injected mice cleared the infection by 7 wk PI, a few required 9 wk. There were minimal adverse effects attributable to strain RB51. Apparently, strain RB51 would not negatively impact P. maniculatus populations if it were used in a field situation. Also, deer mice appear to be able to clear the vaccine in 6 to 9 wk, thus the probability of these mice transmitting the vaccine to other animals is low.

Causes of mortality of the Wyoming toad.

Wyoming toads (Bufo baxteri) that died from January 1989 to June 1996 were submitted to the Wyoming State Veterinary Laboratory (Laramie, Wyoming, USA) for postmortem evaluation. These consisted of 108 free-ranging toads and 170 animals from six captive populations. Ninety-seven (90%) of 108 free-ranging toad carcasses were submitted during September and October. From 1989 to 1992, 27 (77%) of 35 mortalities in the captive populations occurred in October, November, and December. From 1993 to 1996, mortality in captive toads occurred without a seasonal pattern and coincided with changes in hibernation protocols that no longer mimicked natural cycles. Cause of mortality was determined in 147 (53%) of the 278 cases. Mycotic dermatitis with secondary bacterial septicemia was the most frequent diagnosis in 104 (71%) of 147 toads. Basidiobolus ranarum was found by microscopic examination of skin sections in 100 (96%) of 104 of these mortalities. This fungus was isolated from 30 (56%) of 54 free-ranging and 24 (48%) of 50 captive toads. This research documents the causes of mortality for both free-ranging and captive endangered Wyoming toads over a 7 yr period.

Serologic survey for infectious pathogens in free-ranging American bison.

From November 1991 through March 1992, we evaluated 101 free-ranging American bison (Bison bison) from Yellowstone National Park, Wyoming (USA) for exposure to infectious organisms that commonly infect cattle. No titers were detected for bluetongue virus, bovine leukemia virus, or Campylobacter fetus in these 101 bison. Detectable antibodies occurred against Anaplasma marginale (eight of 76, 11%), bovine respiratory syncytial virus (31 of 101, 31%), bovine viral diarrhea (31 of 101, 31%), bovine herpesvirus 1 (29 of 76, 38%), Leptospira interrogans icterohaemorrhagiae (four of 101, 4%), L interrogans hardjo (seven of 101, 7%), L interrogans autumnalis (one of 101, 1%), L interrogans bratislava (seven of 101, 7%), L interrogans australis (one of 101, 1%), and parainfluenza 3 virus (27 of 75, 36%). The low antibody titers and the lack of gross lesions are evidence that while previous exposure to infectious organisms may have occurred, none appeared to have active infections.

Infectious keratoconjunctivitis in free-ranging mule deer (Odocoileus hemionus) from Zion National Park, Utah.

An epizootic of infectious keratoconjunctivitis (IK) was studied opportunistically in free-ranging mule deer (Odocoileus hemionus) from Zion National Park, Utah (USA), from November 1992 to March 1994. Moraxella sp. and Chlamydia sp. were isolated from the conjunctiva of two of seven deer. In addition, Thelazia californiensis occurred on the conjunctivas of six of seven deer. Based on field observations, adults appeared to be affected clinically at a higher incidence during both years as opposed to juveniles. Corneal opacity was the most apparent clinical sign from 1992 to 1993. However, in the following year, blepharospasm and epiphora were noted more often. We were also able to document the clinical recovery of three affected deer. In addition, Moraxella sp. was recovered from the eyes of a clinically unaffected deer 1 year after the epizootic occurred.

Atrial septal defects in Florida panthers.

Ostium secundum atrial septal defects (ASDs) were observed in six (3 M, 3 F) of 33 (20 M, 13 F) (18%) Florida panthers (Puma concolor coryi) necropsied by veterinary pathologists between 1985 and 1998. A seventh ASD was found in a female panther necropsied in the field and is included in the pathological description but not the prevalence of ASDs in Florida panthers. One panther (FP205) with severe ASD also had tricuspid valve dysplasia (TVD). Atrial septal defects and/or TVD are believed to have caused or contributed to the deaths of three (9%) Florida panthers in this study. Mean diameter +/- SD of ASDs was 9.0 +/- 4.7 mm (range 3 to 15 mm). Gross pathological changes attributed to ASDs/TVD in severely affected panthers (ASD > or = 10 mm) (n = 4) included mild right ventricular dilatation (n = 3) and hypertrophy (n = 2), mild to severe right atrial dilatation (n = 2), and acute pulmonary edema (n = 3). Panthers with mild ASDs (ASD < or = 5 mm) (n = 3) had no other detectable gross pathological changes associated with the ASDs. Histological examination of lungs of three panthers with severe ASDs revealed mild to moderate dilatation with fibrosis and smooth muscle atrophy of the tunica media of medium to large caliber arteries (n = 2), interstitial and/or pleural fibrosis (n = 2), perivascular fibrosis (n = 1), and acute to chronic edema (n = 3). Twenty-six necropsied panthers were examined one or more times while living; medical records were retrospectively evaluated. Antemortem radiographic, electrocardiographic, and echocardiographic examinations were performed on two panthers with severe ASDs (FP20 and FP205). Thoracic radiographic abnormalities in both included right heart enlargement, and in FP205 (severe ASD and TVD), mild pulmonary overperfusion. Electrocardiographic examination of FP205 revealed a right ventricular hypertrophy pattern, while FP205 had a normal electrocardiogram. Echocardiographic examination of FP20 revealed marked right atrial dilatation; a bubble contrast study indicated regurgitation across the tricuspid valve. Echocardiographic abnormalities in FP20 included right atrial and ventricular lilatation, atrial septal drop-out, and severe tricuspid regurgitation; non-selective angiography revealed significant left to right shunting across the ASD. All panthers with severe ASDs ausculted (n = 3) had systolic right or left-sided grade I-V/VI murmurs loudest at the heart base. All male panthers with ASDs (n = 3) (100%) and 9 of 17 (53%) male panthers without ASDs in this study were cryptorchid.

Dissecting thoracoabdominal aortic aneurysm in a free-ranging Florida panther (felis concolor coryi).

A 12-yr-old female free-ranging Florida panther (Felis concolor coryi) was found dead in good flesh. The panther had a ruptured thoracoabdominal aneurysm and 0.5 L of unclotted blood in its thorax. Intimal plaques 6.0 x 3.0 x 3.0 cm and 4.0 x 3.0 x 1.0 cm were present in the thoracic and abdominal aorta extending below the bifurcation of the renal arteries. Histologic examination revealed necrohemorrhagic aortitis with a mixed inflammatory infiltrate of lymphocytes, macrophages, and neutrophils. Death was almost certainly due to exsanguination and hypovolemic shock secondary to the ruptured aneurysm, and the aortitis with the resultant aneurysm may have been secondary to an infectious or a toxic process. This is the first reported death of a free-ranging mammal from a ruptured aortic aneurysm.

Dermatophyte infections in free-ranging Florida panthers (Felis concolor coryi).

Three free-ranging Florida panthers (Felis concolor coryi) were diagnosed with clinical dermatophytosis; two were infected with Trichophyton mentagrophytes, and one was infected with Microsporum gypseum. Two of these panthers were juvenile males that were diagnosed with focal to focally coalescing dermatophytosis; one caused by M. gypseum and the other by T. mentagrophytes. These animals were not treated, and clinical signs resolved spontaneously over 6 mo. The third panther, an adult male from southern Florida, presented with a diffuse dermatophytosis due to T. mentagrophytes infection. Initially, the panther had alopecia, excoriations, ulcerations, and multifocal pyoderma of the head, ears, neck, rear limbs, and abdominal region that progressed to lichenification of the skin and loss of nails from two digits. When topical therapy applied in the field at 45-day intervals was ineffective in clearing the infection, the animal was placed in captivity for intensive oral therapy to prevent further development of dermal mycosis, loss of additional nails, and spread of infection to other panthers. The panther was treated orally with itraconazole (9.5 mg/ kg) in the food s.i.d. for 6 wk. After treatment, nail regrowth occurred but the multifocal areas of alopecia remained. The panther was released back into the wild after two skin biopsy cultures were negative for fungal growth. Temporary removal of a free-ranging animal of an endangered species from its habitat for systemic treatment of dermatophytosis requires consideration of factors such as age, reproductive potential, holding facilities, treatment regimen, and the potential for successful reintroduction of the animal.