Abstract 3628: Comprehensive identification of lineage associated cancer genes in 122 histologies

Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor.

Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB > 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS.

Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P < 0.05) gene and lineage associations, and an additional 109 involving genes mutated at >10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages.

We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology.

Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.

Abstract 1752: BRCA-mediated tumorigenesis is origin and cell-type dependent

BRCA1 and BRCA2 mutations predispose to select cancers, yet the interplay between germline and somatic BRCA alterations in driving tumorigenesis and conferring drug sensitivity remain poorly understood. To determine which tumors are dependent on mutant BRCA, we integrated the prospective clinical sequencing of germline blood and matched tumor specimens from 17,152 advanced cancer patients with zygosity analysis, broader somatic molecular features, and treatment outcomes. Tumor lineage dictated BRCA dependence in cancers of both the 2.7% of carriers with germline pathogenic variants and the 1.8% of patients with somatic loss-of-function mutations in BRCA1 and BRCA2 across 38 affected cancer types. The rate of biallelic inactivation of mutant BRCA1/2 varied by mutational origin and tumor lineage. Consequently, BRCA-mediated phenotypes such as homologous recombination deficiency (HRD) were associated with BRCA1/2 mutations in a cell type- and zygosity-dependent manner. Phenotypic penetrance was greatest in tumors of high-risk cancer types and in tumors with biallelic inactivation of mutant BRCA, independent of its germline or somatic origin. Conversely, heterozygous BRCA mutations in other cancer types conferred no HRD phenotype. These lineage-specific differences among hallmarks of BRCA dependence also predicted differential response to PARP-inhibitor therapy. Collectively, only BRCA mutations in tumors of high BRCA penetrance had a strong selective pressure for somatic biallelic inactivation, conferred dose-dependent somatic phenotypic consequences, and PARP inhibitor sensitivity. In contrast, BRCA1/2-mutant patients with cancers not traditionally associated with BRCA susceptibility generally had tumorigenesis independent of mutant BRCA. Overall, mutant BRCA was a founding pathogenic event on which some tumors depended while in others it was likely a dispensable and biologically neutral passenger mutation unrelated to tumorigenesis. This difference was conditioned by lineage, mutational origin, and zygosity, an understanding of which requires integrated germline and somatic molecular characterization in cancer patients with implications for screening, disease pathogenesis, clinical trial design, and therapy.

Citation Format: Philip Jonsson, Michael L. Cheng, Chaitanya Bandlamudi, Preethi Srinivasan, Shweta S. Chavan, Noah D. Friedman, Ezra Y. Rosen, Allison L. Richards, Nancy Bouvier, S. Duygu Selcuklu, Craig Bielski, Wassim Abida, Ahmet Zehir, Nikolaus Schultz, Mark T. Donoghue, Jose Baselga, Kenneth Offit, Marc Ladanyi, Eileen M. O’Reilly, Howard I. Scher, Zsofia K. Stadler, Mark E. Robson, David M. Hyman, Michael F. Berger, David B. Solit, Barry S. Taylor. BRCA-mediated tumorigenesis is origin and cell-type dependent [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1752.

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background

Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.

Results

Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.

Conclusions

This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.

Ceftizoxime-induced hemolysis secondary to combined drug adsorption and immune-complex mechanisms

BACKGROUND

Immune hemolytic anemia has been associated with the administration of various antibiotics, including cephalosporins. Presented here is a patient who developed severe acute hemolysis while receiving ceftizoxime (Ceftizox, Fujisawa USA), a third-generation cephalosporin. This is the fourth reported case of hemolysis in association with ceftizoxime. In the previous cases, ceftizoxime was shown to induce hemolysis by the immune-complex mechanism. However, in one of those reports, the concentration of drug used to treat the target RBCs in vitro may not have been optimal.

CASE REPORT

The patient's antemortem blood samples were analyzed retrospectively for drug-dependent antibodies by the drug-adsorption and immune-complex methods. Antibody class and titer were evaluated.

RESULTS

The patient's sample agglutinated RBCs coated with ceftizoxime as well as uncoated RBCs in the presence of ceftizoxime. The antibodies to ceftizoxime were IgM and IgG.

CONCLUSION

This is the first report on both the immune-complex and drug-adsorption mechanisms of ceftizoxime-induced hemolysis. The differential diagnosis of a falling Hct in a patient receiving antibiotics should include drug-related hemolysis; once this diagnosis is considered, management includes the appropriate serologic workup, immediate cessation of the implicated drugs, and possible transfusion support.