Abstract P4-03-01: Pathway level complementarity of germline and somatic events in breast cancer
Authors: Qing T , Marczyk M , Wali V , Gunasekharan V , Patwardhan G , Pusztai L , Hatzis C 
Published: May 2019

Abstract
Background: Progression from a normal cell state to cancer requires multiple genomic hits in key regulatory pathways. In the case of hereditary cancer syndromes, some of these hits occur in the germline, but additional somatic mutations are required for malignant transformation. We hypothesize that this paradigm could be extended to sporadic cancers as well. What somatic mutation function as a cancer driver event may be determined by the constellation of germline variants a person is born with. We propose that even rare, non-recurrent, high functional impact germline variants in genes involved in cancer-related pathways could influence the biological impact of somatic mutations in other cancer-related genes. The goal of the current analysis was to examine associations between pathway alterations caused by high functional impact germline variants or somatic mutations in the “hallmarks of cancer” pathways in breast cancer.
Methods: We obtained germline DNA sequencing and copy number variation (CNV) data from the breast cancer TCGA cohort. After population clustering with the HapMap cohort, we selected a homogeneous group of 796 patients of Western European ancestry and downloaded the matching somatic mutations (SNVs and INDELs) that were available for 750 cases, that comprise the current study population. Germline CNVs were classified as recurrent or rare losses or gains. Potentially pathogenic germline variants (SNPs) were obtained from the PanCancer Altas project. All germline or somatic mutations were mapped at the gene level to the 50 Cancer Hallmarks pathway collection. We designated a pathway mutated if at least 1 gene had a germline or a somatic mutation. Complementarity between pathway alterations by germline and somatic events were evaluated using the Fisher exact test adjusted for multiple comparisons.
Results: At the germline level, 2,057 genes were affected by CNVs (mean 30, range 3-151 genes/patient), and a total of 43 genes carried germline pathogenic SNPs that affected 13.8% of the patients. At the somatic level, we detected 40,881 high functional impact mutations (mean 54.3, range 1-3889 mutations/patient) in 13,080 genes (mean 50.8, range 1-3166 genes/patient). The 50 Cancer Hallmark pathways contained 4386 genes (mean 146.5, range 32-200 genes/pathway), and were mutated in the majority of the patients (85% germline, 93% somatic). Several pathways, such as HEME_METABOLISM, INTERFERON_ALPHA_RESPONSE, and KRAS_SIGNALING, were frequently affected by germline alterations, while the somatic mutations were most frequently involved in the COMPLEMENT, E2F_TARGET, and UV_RESPONSE_UP. Interaction analysis revealed co-occurrence between MYC_TARGETS_V1 (germline) and UV_RESPONSE_DN (somatic) or MTORC1_SINGALING (somatic) (p&lt;0.01), and TNFA_SIGNALING_VIA_NFKB (germline) and IL6_JAK_STAT3_SIGNALING (germline) with E2F_TARGETS (somatic) (p&lt;0.01). We also observed an exclusive relationship between germline alterations in BILE_ACID_METABOLISM and somatic mutations in COMPLEMENT pathway (p&lt;0.01).
Conclusions: Our results highlight the importance of pathway-level analysis of germline alterations in breast cancer, which might help to understand the interrelationship between germline and somatic alterations in breast cancer.
Citation Format: Qing T, Marczyk M, Wali V, Gunasekharan V, Patwardhan G, Pusztai L, Hatzis C. Pathway level complementarity of germline and somatic events in breast cancer [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 P4-03-01.