Abstract P4-03-03: Germline potentially pathogenic variants in breast cancer intrinsic molecular subtypes are not associated with somatic TMB

Background: Breast cancer (BC) is a heterogeneous disease. It is estimated that 5 to 10% of all BC to have a germline genetic predisposition. A 50-gene assay (PAM50) identifies 5 intrinsic molecular subtypes (IMS): Luminal A, Luminal B, HER2-enriched, Basal-like, and Normal-like. Basal-like breast cancers are enriched for BRCA1/2 germline mutations. Deleterious mutations in BRCA1/2 or other DNA-damage repair (DDR) genes may increase tumor mutational burden (TMB), a biomarker for response to checkpoint inhibition therapy. We sought to determine the spectrum of germline mutations in molecular BC subtypes (IMS), and their relation to somatic TMB. Methods: We performed a retrospective analysis of data from NantHealth database. RNAseq was used to classify breast tumors into IMS. Germline variants within putative driver genes (COSMIC v.76) were detected in analysis of 181 whole-genomes and 89 whole-exomes sequenced using Illumina chemistry. Classification of germline variants into potentially pathogenic variants (pPv) was determined using ClinVar database annotation. Patients were categorized as TMB-high by thresholding on >200 non-synonymous exonic somatic mutations as was previously reported. Results: A total of 270 BC patients with comprehensive omics profiling (germline DNAseq, somatic DNAseq, and somatic RNAseq) were available for this analysis. The mean age (±SD) was 56.4 (± 12.5) years (range 20.8-86.5). Forty-six patients (17.0%) were classified TMB-high. The IMS distribution was 40.7% Luminal A, 31.5% Luminal B, 5.9% HER2-enriched, 21.5% Basal-like, and 0.37% Normal-like. Over 200 unique germline variants were detected of which 98 were pPv according to ClinVar annotation. These pPv spanned 21 genes, 7 of which are directly related to DDR. One hundred and four patients had ≥1 pPv (78 had only 1 pPv, and 26 had >1 pPv). The most common pPv were APC (5.9%), BRCA2 (5.2%), TSC2 (4.4%), BRCA1 (3.7%), SDHB (3.3%), SDHD (3.3%), TSC1 (3.0%), PMS2 (3.0%), MUTYH (2.6%), MSH2 (1.5%) and MSH6 (1.5%). BRCA1 and especially BRCA2 pPv were mostly seen in the basal-like patients. Luminal B had distinctly more germline pPv in PMS2, BRCA1 & BRCA2 than Luminal A. TMB-high patients were not significantly enriched for germline pPv (OR 0.73, p=0.41), even when limited to pPv in DDR genes (OR 0.69, p=0.52). TMB-high patients were present in all 4 major IMS types; Her2-enriched 37.5%, Luminal B 23.5%, Basal-like 17.2%, and Luminal A 9.1%. Conclusion: We identified differential distribution of germline pPv in BC IMS. Of the pPv found, APC was the most commonly detected pPv across subtypes, while BRCA1/2 pPv were clustered in Basal-like subtype, and PMS2 in Luminal B subtype. 17% of all patients had a pPv within at least one DDR gene, that potentially may benefit from targeted therapy. Despite IMS types having distinct germline pPv profiles especially in DDR genes, there was no association with subsequent somatic TMB. This suggests that either 1. somatic events are the primary drivers of TMB, or 2. that germline variants with either unknown or benign significance need to be revisited. Future analysis in a larger demographically well-annotated dataset (commercial data, ExAC, other) or via functional studies should be considered.

Citation Format: Obeid E, Reddy SB, Goldstein LJ, Daly MB, Benz SC, Hall MJ, Szeto C. Germline potentially pathogenic variants in breast cancer intrinsic molecular subtypes are not associated with somatic TMB [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-03.

Diagnosis of herpes simplex virus-1 keratitis using Giemsa stain, immunofluorescence assay, and polymerase chain reaction assay on corneal scrapings

AIMS

To evaluate three tests used routinely for the diagnosis of herpes simplex virus (HSV) keratitis.

METHODS

Corneal scrapings from 28 patients with clinically typical dendritic corneal ulcer suggestive of HSV keratitis, and 30 patients with clinically non-viral corneal ulcers, were tested by (i) Giemsa stain for multinucleated giant cells, (ii) immunofluorescence assay (IFA) for HSV-1 antigen, and (iii) polymerase chain reaction (PCR) for HSV-1 DNA, by investigators masked to clinical diagnosis. The control subjects were also investigated by smears and cultures for bacteria, fungus, and Acanthamoeba.

RESULTS

The specificity and positive predictive values of all three tests for the diagnosis of HSV keratitis were between 95-100%. The sensitivity of IFA and PCR was 78.6% and 81.2%, respectively, and the difference was not significant; however, their sensitivity and negative predictive value were significantly higher than Giemsa stain.

CONCLUSIONS

While a combination of IFA and PCR constitute the choice of tests in clinically suspected cases of HSV keratitis, multinucleated giant cells in Giemsa stain can pre-empt testing by IFA and PCR in otherwise atypical cases of HSV keratitis.

Esophageal involvement in Wegener's granulomatosis: a case report and review of the literature

Wegener's granulomatosis is characterized by a granulomatous arteritis involving the upper and lower respiratory tracts, progressive glomerulonephritis and systemic symptoms attributable to small vessel vasculitis. Although multisystemic manifestations are frequent, involvement of the gastrointestinal tract is uncommon. Cases have been reported of intestinal perforation, ulceration and hemorrhage. A patient whose initial presentation of Wegener's granulomatosis was odynophagia secondary to esophageal vasculitis is described. Endoscopy revealed multiple punched out ulcerations in the esophagus, which resolved with standard therapy for systemic Wegener's granulomatosis. There are only two previous reports of symptomatic esophageal vasculitis in patients with Wegener's granulomatosis. These reports illustrate the need to consider odynophagia as a reflection of disease activity as opposed to complications of immunosuppressive therapy.

Acute complications of Crohn's disease

Crohn's disease can be acute. If proper diagnosis is not made and appropriate therapy instituted, morbidity and mortality can be high. A team approach with cooperation between gastroenterologists and surgeons is mandatory.

Hemolytic anemia following insertion of Ionescu-Shiley mitral valve bioprosthesis

Hemolytic anemia is a relatively common complication after the replacement of cardiac valves with mechanical prostheses; the prevalence rate varies from 38% to 85%, depending on the prosthesis implanted. However, cardiac valves fabricated from biologic material are associated with a reduced incidence of hemolytic anemia, and to the authors' knowledge this report is the first to document hemolytic anemia in a patient who had the mitral valve replaced with an Ionescu-Shiley valve. The anemia was not associated with evidence of hemodynamically important mitral regurgitation and was ultimately controlled by iron and folate supplements.

Response of male germ cells of mouse to acute and fractionated doses of 131I induced radiation

The effects of radioactive iodine in acute as well as fractionated doses on male germ cells were studied. 131I in four acute doses of 10, 15, 20 and 25 microCi was given intraperitoneally. For fractionated doses, 12.5 microCi was given twice with an interval of 24 h. A dose relationship was exhibited between the concentration of radionuclide and the survival fraction of type A spermatogonia, intermediate and type B spermatogonia and preleptotene spermatocytes. The maximum depletion was recorded after 25 microCi. The survival values for this dose group were 40.4, 51.4, and 25.0% for type A cells, intermediate and type B cells and preleptotene spermatocytes, respectively. Fractionated doses of radioiodine also reduced the survival rate of gonadal cells and are more effective than 20 microCi acute dose in decreasing the survival fraction of all types of gonadal cells.

Studies on the population kinetics of the Walker carcinoma by autoradiography and pulse cytophotometry

The proliferation parameters of the Walker carcinoma were estimated from both in vivo and in vitro measurements. tthe transplantable Walker carcinoma 256 was grown in male inbred BD1 rats. During exponential growth, 5--6 days after transplantation, a PLM curve was performed, yielding estimates of TC approximately equal to 18-0 hr, TS approximately equal to 6-4 hr, TG2+M approximately equal to 4-1 hr. With the double labelling technique in vitro under 2-2 atm oxygen we obtained: TC approximately equal to 18-2 hr, TS approximately equal to 8-2 hr, TG2+M approximately equal to 2-0 hr. From pulse cytophotometry DNA content histograms the fractions of cells in the cell cycle phases were calculated using a computer program: fG1 approximately equal to (47-6 +/- 1-1)%, fS approximately equal to (34-1 +/- 1-0)%, fG2+M approximately equal to (18-3 +/- 1-5)%. These fractions remained constant between the fifth and the twelfth day after transplantation. At that time the tumour growth had already slowed down appreciably. The growth fraction determined by repetitive labelling was 0.96 on the fifth and 0-93 on the seventh and eleventh day. The cell loss factor was phi approximately equal to 17% during exponential tumor growth and increased to about 100% between the tenth and twelfth day. The agreement of the cell kinetic data determined by autoradiography from solid tumours in vivo (PLM, continuous labelling) and autoradiography as well as pulse cytophotometry from in vitro experiments (excised material) was satisfactory.

A comparative study of four sublines of mouse fibroblast cells

Cell doubling time, DNA distribution pattern, frequency distribution of chromosome numbers per cell and degree of synchrony obtained after mitotic selection were studied in 4 different sublines of mouse fibroblast cells, NCTC L-929, in culture. The 4 sublines did not differ with respect to their cell kinetic data but showed changes of the chromosome pattern compared to the stemline and compared to each other suggesting that chromosome analysis provides a very sensitive means to detect evolutianary changes of a permanent cell line.

Dissecting aneurysm of the descending aorta. Improved surgical results in 91 patients

Dissecting aneurysm of the descending thoraic aorta (type iii) is a specific disease process whose pathogenesis, pathologic description, surgical treatment, and prognosis is different from dissections of the ascending arota (types l and ll). From 1964 through 1974, 91 patients underwent surgical correction of type iii dissection. The operative mortality was 21% and late mortality, up to ten years follow-up, was 13%. During the past four years, operative mortality has dropped to 6.5%. Mortality was determined by extent of the aneurysm and underlying cardiac disease. Antihypertensive and negative ionotropic drugs have not been used as definitive treatment but as adjuncts in perioperative support. Based on our present mortality of 6.5%, with no late mortality, we urge early surgical treatment of acute and chronic dissecting aneurysms of the descending thoracic aorta before extension, rupture, or massive enlargement of the aneurysm occurs.

Further aspects of the radioprotective mechanism of thiourea

Thiourea in three different concentrations ranging from 10-4-M to 10-2-M was employed in pre- and post-treatments to test whether it decreases the chromosomal fragment frequency induced by 1000 R of X-rays in the growing root tips of Hordeum vulgare. In pre-treatment experiments thiourea in 10-2-M concentration yielded the maximal protection of 28.9 percent against radiation- induced chromosomal fragments. In post-treatment approximately a similar rate of protection is secured. It is discussed that the test-chemical protected the chromosomes against X-rays by two different mechanisms. The recovery process by restitution of the broken chromosomal fragments and the protection against initial radiation damage were the possible protective mechanisms displayed by thiourea in this plant material.

A study on the radioprotective property of thiourea against radiation-induced chromosome damage

The protective ability of thiourea in five different concentrations ranging from 5 × 10−2M to 1 × 10−5M has been demonstrated on chromosome aberrations in root tips of Allium cepa exposed to 350r X-irradiation. It was shown that protection against radiation-induced chromosome fragments and anaphase bridges was attained when the germinating seeds had been treated with thiourea for 1 hour prior to irradiation.