Germline Susceptibility Variants Research Articles

Germline Pathogenic Variants in Patients With Pancreatic and Periampullary Cancers.

Inherited cancer susceptibility is often not suspected in the absence of a significant cancer family history. Pathogenic germline variants in pancreatic cancer are well-studied, and routine genetic testing is recommended in the guidelines. However, data on rare periampullary cancers other than pancreatic cancer are insufficient. We compared the prevalence of germline susceptibility variants in patients with pancreatic cancer and nonpancreatic periampullary cancers. Six hundred and eight patients who had undergone pancreaticoduodenal resection at a tertiary referral hospital were studied, including 213 with pancreatic ductal adenocarcinoma, 172 with ampullary cancer, 154 with distal common bile duct cancer, and 69 with duodenal adenocarcinoma. Twenty cancer susceptibility and candidate susceptibility genes were sequenced, and variant interpretation was assessed by interrogating ClinVar and PubMed. Pathogenic or likely pathogenic, moderate- to high-penetrant germline variants were identified in 46 patients (7.7%), including a similar percentage of patients with pancreatic (8.5%) and nonpancreatic periampullary cancer (7.1%). Low-penetrant variants were identified in an additional 11 patients (1.8%). Eighty-nine percent of the moderate- to high-penetrant variants involved the major cancer susceptibility genes BRCA2, ATM, BRCA1, CDKN2A, MSH2/MLH1, and PALB2; the remaining 11% involved other cancer susceptibility genes such as BRIP1, BAP1, and MSH6. Almost all pathogenic variant carriers had a family history of cancer. Patients with pancreatic and nonpancreatic periampullary cancer have a similar prevalence of pathogenic cancer susceptibility variants. Germline susceptibility testing should be considered for patients with any periampullary cancer.

SNP rs9387478 at ROS1-DCBLD1 Locus is Significantly Associated with Lung Cancer Risk and Poor Survival in Indian Population.

Receptor tyrosine kinases (RTK) are relevant therapeutic targets in the treatment of lung cancer. Germline susceptibility variants that influence these RTKs may provide new insights into their regulation. rs9387478 is located in the genomic interval between two RTK-genes ROS1/DCBLD1, of which ROS1 alterations are implicated in lung carcinogenesis and treatment response while the latter remains poorly understood. Venous blood was drawn from 100 control and 231 case subjects. Genotype was scored by restriction fragment length polymorphism (RFLP), PCR amplification followed by HindIII digestion. Logistic regression was applied to compare the association between variables. Survival curve was plotted to draw a correlation between the genotype and overall survival. Also, eQTL and chromatin state changes were analyzed and correlated with the survival of patients using available datasets. In our population smoking correlated significantly with lung cancer [OR= 2.607] with the presence of the minor allele 'A' enhancing the nicotine dependence [CA (OR=3.23)]. Individuals with homozygous risk allele 'A' had a higher chance of developing lung cancer [OR=2.65] than individuals with CA/CC implying a recessive model of association. Patients with CC/CA genotype had better overall survival than patients with AA genotype [161 days/142 days vs 54 days, p=0.005]. The homozygous risk allele was significantly associated with increased DCBLD1 and ROS1 expression in lung cancer, with enriched active histone marks due to the polymorphism. Interestingly, increased DCBLD1 expression was associated with poor outcomes in lung cancer. Overall, our study provides strong evidence that rs9387478 is significantly associated with both nicotine dependence and lung cancer in our North Indian cohort. The association of the SNP with prognostic genes, DCBLD1 and ROS1 make rs9387478 a promising prognostic marker in the North Indian population. The results obtained are significant, however, the study needs to be performed in a larger sample size.

Synchronous primary cutaneous melanomas: a descriptive study of their clinical features, histology, genetic background of the patients and clinical outcomes.

Around 0.5% of cutaneous melanoma (CM) patients will present with synchronous melanomas when first seen. Moreover, 26-40% of patients with multiple primary melanomas present with synchronous lesions. To assess the prevalence, clinical and histopathological characteristics, germline mutations and outcome in patients with synchronous melanoma. Clinical and histopathological data from 4703 melanoma patients were included. Clinical, histological and genetic mutational status information was analysed. Kaplan-Meier curves were used to investigate survival outcomes. A total of 144 patients (3.06%) presented simultaneously with two or more primary melanomas. During follow-up, 25.7% of patients with synchronous melanoma developed a new primary melanoma compared to 8.6% of patients diagnosed with single melanoma (P < 0.001). Germinal CDKN2A mutations were identified in 10.7% of patients with synchronous melanomas and genetic variants in MC1R in 72%. No significant differences in all survival outcomes between patients with synchronous melanomas and single melanomas were found. Synchronous melanomas are more frequent than previously reported and are more frequent in older patients compared to single melanomas. Moreover, these patients have a higher risk of developing a new primary melanoma during follow-up and have higher rates of germline susceptibility variants. Nevertheless, these findings were not associated with worse outcomes.

Abstract 826: Large-scale genome-wide association study identifies multiple novel germline susceptibility variants associated with bladder cancer risk

Abstract Background: Genomic regions that confer susceptibility for bladder cancer have provided important insights into the mechanisms of this disease. Sixteen genomic regions harboring bladder cancer susceptibility loci have been reported to date. To identify additional loci associated with bladder cancer risk, we conducted a meta-analysis including data from previously published genome-wide association studies as well as unpublished data. Methods: Data from 32 studies including 13,790 bladder cancer cases and 343,502 controls of European ancestry were included. Stratified analyses by sex and smoking status, as well as heterogeneity in risk by muscle-invasiveness, were also conducted. We tested for multiplicative and additive interactions between cigarette smoking and susceptibility loci that achieved genome-wide significance. After genotyping, quality control, and imputation log-additive effects were calculated by study/array group using regression models adjusting for age and significant eigenvectors. Results were combined by meta-analysis using a fixed-effects model. Results: We report strengthened or independent signals in several previously published regions at 4p16.3 (TACC3, FGFR3), 5p15.33 (CLPTM1L, TERT) and 11p15.5 (TNNT3, LSP1), as well as nine novel loci. In addition, we observed the first evidence of effect modification by sex at the FGFR3 locus, with a stronger risk observed in women (pmultiplicative-interaction=0.002). Further, we confirmed an interaction between smoking and a susceptibility locus at 8p22 (NAT2), indicating an increased risk of bladder cancer among smokers with the NAT2 slow acetylation genotype/phenotype (pmultiplicative-interaction=0.001). We also identified additional multiplicative, as well as additive, interactions between several novel loci and cigarette smoking status. In addition, we are currently building a risk stratification model using the combined effects of smoking and genetic susceptibility to identify subgroups of individuals at higher and lower absolute risk of bladder cancer. Conclusions: This meta-analysis identified 3 novel loci in previously reported regions and 9 novel bladder cancer susceptibility loci in new regions. These results add to our knowledge of the genetic architecture of bladder cancer. In addition, observed gene-smoking interactions suggest that risk stratification models may have translational implications, informing future disease screening efforts. Citation Format: Stella Koutros, Lambertus A. Kiemeney, Roger L. Milne, Yuanqing Ye, Vijai Joseph, Jonine Figueroa, Nilanjan Chatterjee, Graham G. Giles, Michelle A. Hildebrandt, Lars Dyrskjot, Kenneth Offit, Manolis Kogevinas, Elisabete Weiderpass, Marjorie L. McCullough, Neal D. Freedman, Demetrius Albanes, Charles Kooperberg, Victoria Cortessis, Margaret R. Karagas, Dalsu Baris, Alison Johnson, Molly R. Schwenn, Helena Furberg, Dean F. Bajorin, Parichoy Pal Choudhury, Oscar Florez-Vargas, Olivier Cussenot, Geraldine Cancel-Tassin, Simone Benhamou, Peter Kraft, Stefano Porru, Mark P. Purdue, Katherine A. McGlynn, Cari M. Kitahara, Christopher A. Haiman, Mark H. Greene, Thorunn Rafnar, Stephen J. Chanock, Xifeng Wu, Francisco X. Real, Debra T. Silverman, Montserrat Garcia-Closas, Kari Stefansson, Ludmila Prokunina-Olsson, Nuria Malats, Nathaniel Rothman. Large-scale genome-wide association study identifies multiple novel germline susceptibility variants associated with bladder cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 826.

The Clinical Relevance of Frequent Germline Genetic Variants Detected by Targeted Sequencing in Patients With Rectal Adenocarcinoma (READ).

The progression of colorectal cancer (CRC) mainly stems from the occurrence of somatic mutation. However, there is little information that can be used to comprehensively analyse the importance of germline variants in CRC patients. The candidate germline variants between tumor relapse and cured rectal adenocarcinoma (READ) were firstly filtered by whole-exome sequencing (n=4), and validated by targeted sequencing and associated with clinical outcome in READ (n=48). We identified 9 pathogenic germline variants that were clinically associated with survival outcome in READ, including TIPIN, TLR1, TLR10, OR4D6, IGSF3, UBBP4, OR6J1, FAM208A and DISC1. Patients carrying these germline susceptibility variants had an increased risk of poor survival outcome compared to those without these variants. Not only the tumor genome, but also the germline sequence must be analysed to depict the overall genetic profile, providing potential therapeutic strategies for personalized medicine.

Sa1339 – Analysis of 1200 Cancer-Related Genes for Pancreatic Cancer Germline Susceptibility Variants and Patient Survival by Mutation Status

Sa1339 – Analysis of 1200 Cancer-Related Genes for Pancreatic Cancer Germline Susceptibility Variants and Patient Survival by Mutation Status

Germline susceptibility variants impact clinical outcome and therapeutic strategies for stage III colorectal cancer

Although somatic mutations are the main cause of cancer, underlying germline alterations may affect cancer outcome. There is little information on comprehensive analysis of germline genome sequencing for cancer healthcare strategy. Here we studied the implication of germline cancer-associated variants on cancer counselling and therapeutic strategies by germline whole genome and tumor targeted sequencing. Fifty-five gynecological and 104 colorectal cancer (CRC) patients were enrolled. We identified 22 germline pathogenic variants in 16 cancer-associated genes. Most of them are involved in DNA repair signaling, including MLH1, BRCA1/2, MUTYH, ATM, PMS2, MSH6, BAP1, and FANCA. About 6% of cancer patients presented the secondary findings of germline variants with non-oncogenic impact, mainly on the cardiovascular system which should be carefully monitored during chemotherapy. CRC patients carrying germline susceptibility variants had better disease-free survival than those without variants. Importantly, in the CRC model, the underlying germline alterations mold the tumor somatic alteration landscape. NOTCH1 mutation was the most common somatic mutation in recurrent CRC, implying a potential therapeutic target in adjuvant setting. In conclusion, both tumor genome and germline sequence data have to be analyzed to have a more complete picture of the overall genetic foundation of cancer.

A Tumor Suppressor Role for Bank1 in B-Cell Precursor Acute Lymphoblastic Leukemia

Introduction: Since the implementation of next generation sequencing techniques, inherited mutations in malignancy-associated susceptibility genes have become of major interest, to identify high-risk individuals, even before an actual disease onset. One challenge in this regard is that germline susceptibility variants often display incomplete or reduced penetrance, which can be influenced by genetic as well as environmental factors (Martin-Lorenzo A. et al., Cancer Discov, 2015), making it even harder to assess the complete spectrum of the predisposition. Here, we aimed to elucidate the variable penetrance of a family, which harbors the inherited B-cell precursor ALL (BCP-ALL) susceptibility variant PAX5 c.547G>A (Auer F et al., Leukemia, 2014).Methods: We generated a new in vivo model, namely double transgenic Bank1+/-+Pax5+/- mice. Next generation sequencing was used to determine candidate genes influencing the variable penetrance of PAX5 c.547G>A. Pax5+/-+Bank1+/-, as well as Arf-/-+Bank1+/- mouse models were utilized to assess the tumor suppressor potential of Bank1. Murine leukemias were characterized by immune-phenotyping, whole exome sequencing (WES) as well as expression analyses.Results: In a family, harboring PAX5 c.547G>A, 5 out of 7 analyzed children were shown to be mutation carriers, while only 3 out of 5 developed BCP-ALL. In order to assess this variable penetrance further, re-analysis of the WES data revealed an additional rare variant in the B-cell scaffold protein with ankyrin repeats (BANK1) (c.120G>C; rs35978636, minor allele frequency (MAF)<0.01), with a similar transmission spectrum like the heterozygous PAX5 susceptibility variant c.547G>A (Figure 1).BANK1 is primarily expressed in B-cells where it acts as an important adaptor that is involved in B-cell receptor (BCR) induced Ca2+ mobilization from intracellular stores (Yokoyama K et al., EMBO, 2002). Importantly, single nucleotide variants (SNVs) in BANK1 could be linked to confer a susceptibility to a variety of autoimmune diseases, including Systemic Lupus Erythematosus (SLE) (Kozyrev SV et al., Nat. Genet., 2008). The identified BANK1 variant c.120G>C is located in Exon2, the IP3R binding site of BANK1, in proximity to the previously described SLE susceptibility variant c.182G>A, and results in a predicted deleterious protein structure as calculated by SIFT and PolyPhen-2.To test whether Bank1 and Pax5 heterozygosity could cooperate to promote BCP-ALL development, we crossed Bank1+/- mice on a Pax5 heterozygous background and monitored the leukemia incidence of double transgenic Bank1+/-+Pax5+/- mice. Bank1+/-+Pax5+/- mice developed BCP-ALL with clonal blast infiltration in secondary lymphoid organs and an identical leukemia phenotype (CD19-B220+IgM-) and latency like Pax5+/- mice. However, we observed an increase in BCP-ALL disease incidence of 33% compared to the Pax5+/- cohort. These results suggest that Pax5 loss promotes an aberrant B-cell precursor compartment that is susceptible for leukemic transformation, while the combination with Bank1 heterozygosity causes a susceptibility increase in the pre-leukemic population. While these results reflect the variable BCP-ALL penetrance in the human family carrying both PAX5 c.547G>A and BANK1 c.120G>C, it also underlines the multifactorial nature of the disease.Since these results suggest a tumor suppressor function of BANK1 in BCP-ALL, we next explored the effect of Bank1 loss of function on the disease phenotype in a tumor-prone mouse model lacking BCP-ALL susceptibility. Therefore, Bank1-/- mice were crossed back on a p19Arf-deficient background, to obtain the mouse cohorts Bank1+/-p19Arf-/- and Bank1-/-p19Arf-/-. The additional Bank1-deficiency promoted a shift from a T- to mainly B-cell phenotype in the resulting p19Arf-deficient tumors, further supporting a specific tumor suppressor role of Bank1 in BCP-ALL.Conclusion: Taken together, our data underline a tumor suppressor role of Bank1 in the context of BCP-ALL development and supports its involvement in the variable penetrance of BCP-ALL in a family carrying PAX5 c.547G>A. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types. mRNA and miRNA expression profile frequently performed the best, followed by DNA methylation profile. Germline susceptibility variants displayed low prognostic performance consistently across cancer types. The integration of omic profiles with clinical variables can lead to substantially improved prognostic performance over the use of clinical variables alone in half of cancer types examined. Moreover, we showed that the kernel machine learning method consistently outperformed existing prognostic signatures, suggesting that including a large number of omic biomarkers may provide substantial improvement in prognostic assessment. Our study provides a comprehensive portrait of omic architecture for tumor prognosis across cancers, and highlights the prognostic value of genome-wide omic biomarker aggregation, which may facilitate refined prognostic assessment in the era of precision oncology.

Cooperation between somatic mutations and germline susceptibility variants in tumorigenesis – a dangerous liaison

ABSTRACTHigh-throughput genotyping and sequencing generate comprehensive catalogs of inherited genetic variations and acquired somatic mutations. However, their possible interactions and roles in tumorigenesis remain largely unexplored. We recently reported cooperation between the EWSR1-FLI1 (Ewing sarcoma breakpoint region 1 – Friend leukemia virus integration 1) fusion oncogene and a germline variant that regulates the EGR2 (early growth response 2) Ewing sarcoma susceptibility gene via a GGAA-microsatellite.

Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite.

Deciphering the ways in which somatic mutations and germline susceptibility variants cooperate to promote cancer is challenging. Ewing sarcoma is characterized by fusions between EWSR1 and members of the ETS gene family, usually EWSR1-FLI1, leading to the generation of oncogenic transcription factors that bind DNA at GGAA motifs. A recent genome-wide association study identified susceptibility variants near EGR2. Here we found that EGR2 knockdown inhibited proliferation, clonogenicity and spheroidal growth in vitro and induced regression of Ewing sarcoma xenografts. Targeted germline deep sequencing of the EGR2 locus in affected subjects and controls identified 291 Ewing-associated SNPs. At rs79965208, the A risk allele connected adjacent GGAA repeats by converting an interspaced GGAT motif into a GGAA motif, thereby increasing the number of consecutive GGAA motifs and thus the EWSR1-FLI1-dependent enhancer activity of this sequence, with epigenetic characteristics of an active regulatory element. EWSR1-FLI1 preferentially bound to the A risk allele, which increased global and allele-specific EGR2 expression. Collectively, our findings establish cooperation between a dominant oncogene and a susceptibility variant that regulates a major driver of Ewing sarcomagenesis.