Germline Single Nucleotide Polymorphisms Research Articles

Genome-wide Meta-analysis Identifies Novel Genes Associated with Recurrence and Progression in Non–muscle-invasive Bladder Cancer

BackgroundNon–muscle-invasive bladder cancer (NMIBC) is characterized by frequent recurrences and a risk of progression in stage and grade. Increased knowledge of underlying biological mechanisms is needed. ObjectiveTo identify single nucleotide polymorphisms (SNPs) associated with recurrence-free (RFS) and progression-free (PFS) survival in NMIBC. Design, setting, and participantsWe analyzed outcome data from 3400 newly diagnosed NMIBC patients from the Netherlands, the UK, Canada, and Spain. We generated genome-wide germline SNP data using Illumina OmniExpress and Infinium Global Screening Array in combination with genotype imputation. Outcome measurements and statistical analysisCohort-specific genome-wide association studies (GWASs) for RFS and PFS were performed using a Cox proportional hazard model. Results were combined in a fixed-effect inverse-variance weighted meta-analysis. Candidate genes for the identified SNP associations were prioritized using functional annotation, gene-based analysis, expression quantitative trait locus analysis, and transcription factor binding site databases. Tumor expression levels of prioritized genes were tested for association with RFS and PFS in an independent NMIBC cohort. Results and limitationsThis meta-analysis revealed a genome-wide significant locus for RFS on chromosome 14 (lead SNP rs12885353, hazard ratio [HR] C vs T allele 1.55, 95% confidence interval [CI] 1.33–1.82, p = 4.0 × 10–8), containing genes G2E3 and SCFD1. Higher expression of SCFD1 was associated with increased RFS (HR 0.70, 95% CI 0.59–0.84, pFDR = 0.003). Twelve other loci were suggestively associated with RFS (p < 10–5), pointing toward 18 additional candidate genes. For PFS, ten loci showed suggestive evidence of association, indicating 36 candidate genes. Expression levels of ten of these genes were statistically significantly associated with PFS, of which four (IFT140, UBE2I, FAHD1, and NME3) showed directional consistency with our meta-analysis results and published literature. ConclusionsIn this first prognostic GWAS in NMIBC, we identified several novel candidate loci and five genes that showed convincing associations with recurrence or progression. Patient summaryIn this study, we searched for inherited DNA changes that affect the outcome of non–muscle-invasive bladder cancer (NMIBC). We identified several genes that are associated with disease recurrence and progression. The roles and mechanisms of these genes in NMIBC prognosis should be investigated in future studies.

Immunotherapy-Mediated Thyroid Dysfunction: Genetic Risk and Impact on Outcomes with PD-1 Blockade in Non-Small Cell Lung Cancer.

Genetic differences in immunity may contribute to toxicity and outcomes with immune checkpoint inhibitor (CPI) therapy, but these relationships are poorly understood. We examined the genetics of thyroid immune-related adverse events (irAE). In patients with non-small cell lung cancer (NSCLC) treated with CPIs at Memorial Sloan Kettering (MSK) and Vanderbilt University Medical Center (VUMC), we evaluated thyroid irAEs. We typed germline DNA using genome-wide single-nucleotide polymorphism (SNP) arrays and imputed genotypes. Germline SNP imputation was also performed in an independent Dana-Farber Cancer Institute (DFCI) cohort. We developed and validated polygenic risk scores (PRS) for hypothyroidism in noncancer patients using the UK and VUMC BioVU biobanks. These PRSs were applied to thyroid irAEs and CPI response in patients with NSCLC at MSK, VUMC, and DFCI. Among 744 patients at MSK and VUMC, thyroid irAEs occurred in 13% and were associated with improved outcomes [progression-free survival adjusted HR (PFS aHR) = 0.68; 95% confidence interval (CI), 0.52-0.88]. The PRS for hypothyroidism developed from UK Biobank predicted hypothyroidism in the BioVU dataset in noncancer patients [OR per standard deviation (SD) = 1.33, 95% CI, 1.29-1.37; AUROC = 0.6]. The same PRS also predicted development of thyroid irAEs in both independent cohorts of patients treated with CPIs (HR per SD = 1.34; 95% CI, 1.08-1.66; AUROC = 0.6). The results were similar in the DFCI cohort. However, PRS for hypothyroidism did not predict CPI benefit. Thyroid irAEs were associated with response to anti-PD-1 therapy. Genetic risk for hypothyroidism was associated with risk of developing thyroid irAEs. Additional studies are needed to determine whether other irAEs also have shared genetic risk with known autoimmune disorders and the association with treatment response.

Inherited GATA3 genetic Variants Are Associated With Childhood BCR-ABL1-Like Acute Lymphoblastic Leukemia and Increased Risk Of Relapse

Recent genomic profiling of acute lymphoblastic leukemia (ALL) has identified a novel high-risk subtype with a gene expression signature similar to that of BCR-ABL1-positive (Ph+) ALL and a poor prognosis. This novel BCR-ABL1-like ALL subtype is characterized by genomic aberrations targeting lymphoid development, cytokine receptor, and tyrosine kinase signaling pathways, e.g., IKZF1 deletion, CRLF2 rearrangements, and JAK mutations. However, the role of the inherited genetic variation in the pathogenesis of BCR-ABL1-like ALL remains unknown.Taking a genome-wide association study (GWAS) approach, we sought to examine germline single-nucleotide polymorphisms (SNPs) for their association with the predisposition to BCR-ABL1-like ALL. In the discovery GWAS, we compared germline SNP genotype frequencies between ALL cases with (N=75) vs. without (N=436) the BCR-ABL1-like expression signature enrolled on the high risk Children's Oncology Group (COG) AALL0232 protocol, and between BCR-ABL1-like ALL (N=75) vs. non-ALL controls (N=6,661). BCR-ABL1-like ALL was identified by prediction analysis of microarrays. After adjusting for genetic ancestry, we observed a single susceptibility locus on 10p14 signified by two SNPs within the GATA3 gene with genome-wide significant association (P=1.05×10-8 and P=2.62×10-7 [BCR-ABL1-like ALL vs. non-BCR-ABL1-like ALL]; P=2.17×10-14 and P=4.94×10-12 [BCR-ABL1-like ALL vs. non-ALL controls]). In a replication cohort of high-risk ALL, namely COG P9906, the disease risk alleles at both GATA3 polymorphisms were consistently over-represented in BCR-ABL1-like ALL (N=32) compared with 139 non-BCR-ABL1-like ALL (P=0.01 and P=0.004, respectively) and compared with an independent set of 5,755 non-ALL controls (P=3.69×10-5 and P=0.0001, respectively). This GATA3 SNP was also associated with GATA3 expression in lymphoblastoid cell lines (N=56, P=0.034) and in primary ALL blasts (COG AALL0232, N=511, P=9.2×10-8; COG P9906, N=173, P=3.6×10-6), indicating that this variant may function as a cis-acting element regulating GATA3 transcription. Ectopic overexpression of GATA3 in ALL cell lines led to global changes in gene expression, with a particular enrichment of genes within the BCR-ABL1-like ALL expression signature.In the discovery cohort (COG AALL0232), the GATA3 SNP was also significantly associated with CRLF2 rearrangements (P=9.64×10-7), JAK mutations (P=2.06×10-5), and IKZF1 deletion (P=0.0002), which was validated in COG P9906 (P=0.08, 0.008, and 0.002, respectively) and in a third independent cohort, COG P9905 (P=0.009, 0.05, and 0.0002, respectively). The GATA3 risk allele was further enriched among patients with multiple “BCR-ABL1-like ALL-related” lesions concurrently, with the highest frequency observed in cases with three genomic lesions, followed by those with one or two lesions, and lowest among patients without any of the three lesions (COG AALL0232, P=6.09×10-5; COG P9906, P=0.0005; and COG P9905, P=7.6×10-5). Interestingly, the association of the GATA3 SNP with BCR-ABL1-likeness remained significant after adjusting for all three genomic lesions (P=0.001).We further examined the relationships between GATA3 SNP genotype and ALL relapse. In the COG P9906 cohort, the GATA3 allele linked to BCR-ABL1-like ALL was associated with a higher risk of relapse (N=222, P=0.002) and poor early treatment response as measured by minimal residual disease (N=193, P=9.8×10-5), which was validated in COG P9905 (N=777, P=0.007 and N=710, P=0.039, respectively). Of interest, the GATA3 allele associated with relapse and BCR-ABL1-like ALL was more frequent in Hispanics (40%) than in populations of European descent (12%), consistent with the inferior treatment outcome for Hispanic children with ALL.In conclusion, we have identified common GATA3 germline variants associated with BCR-ABL1-like ALL, somatic molecular lesions characteristic of this subtype, and importantly the risk of ALL relapse. These results suggest plausible interactions between host and tumor genomic variations in ALL pathogenesis and drug response. Disclosures:Evans:St. Jude: In accordance with institutional policy, St. Jude allocates a portion of the income it receives from licensing inventions and tangible research materials to those researchers responsible for creating this intellectual property. Patents & Royalties, Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics., Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Other. Relling:St. Jude: In accordance with institutional policy, St. Jude allocates a portion of the income it receives from licensing inventions and tangible research materials to those researchers responsible for creating this intellectual property. Patents & Royalties, Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics., Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Other.

Abstract 2991: Mutational screening of BRCA1/2 genes in 667 spontaneous canine tumors

Abstract BRCA1 and BRCA2 (Breast cancer susceptibility gene 1 and 2) are tumor suppressor genes that maintain genomic stability by repairing damaged DNA. The proteins coded by these genes are involved in complexes that activate the repair of double strand breaks (DSBs) and initiate homologous recombination (HR). BRCA mutations are common in various forms of human cancers, most notably breast cancer, and previously described in canine tumors. Tumors in canines and humans share many characteristics, including: inter-individual and intra-tumoral heterogeneity, biological behavior, similar tumor microenvironments, and similar genomic mutations. This study interrogates naturally-occuring cancers in dogs as a tool that can add valuable information to our understanding of similar tumors in people. A total of 667 tumors of various histologies were obtained from client-owned dogs and sequenced on the FidoCure® Next-generation sequencing (NGS) panel as part of their veterinary precision medicine platform. Mutations in BRCA1 and BRCA2 were among the 5 most common genetic mutations identified. BRCA1 or BRCA2 mutations were identified in 71.8% (479/667) of tumors overall; 36.4% (n=243) BRCA1 mutations, 33.7% (n=225) BRCA2 mutations, and 1.6% (n=11) BRCA1/2 co-mutations. Germline single-nucleotide polymorphisms (SNPs) represented 56% (136/243) and 61% (138/225) of BRCA1 and BRCA2 mutations, respectively. Removing SNPs and focusing on single-nucleotide variants (SNVs), 16.1% of cases (107/667) had BRCA1 mutations, 13.0% (87/667) had BRCA2 mutations, and 1.65% (11/667) had both BRCA1 and BRCA2 mutations. Utilizing Protein Variation Effect Analyzed (PROVEAN) and Sort Intolerant From Tolerant (SIFT) bioinformatic tools to assess the functional significance of BRCA1 and BRCA2 missense variants, 69.2% and 54.8% of mutations, respectively, were predicted as pathogenic/deleterious. Interestingly, a search of the 2017 MSK IMPACT dataset reveals a pan-cancer prevalence in humans of 2.0% BRCA1 variants (216/10,945 cases) and 3.6% BRCA2 variants (399/10,945 cases). Looking at cancer histologies in dogs, BRCA1 variants were identified in 14.1% of soft tissue sarcomas (STS), 11.4% of apocrine gland anal-sac adenocarcinomas (AGASACA), 11.1% of mast cell tumors (MCT), 10.9% of osteosarcomas (OSA), and 10% of thyroid carcinomas. BRCA2 mutations were identified in 33.3% of MCTs, 32.1% of STSs, 23.8% of histiocytic sarcomas, 17.2% of OSAs, and 16.3% of AGASACAs. This analysis of BRCA1/2 mutations in dogs highlights the value of companion animals as a model for human disease to better understand the contribution of these genes in tumorigenesis and for exploring different targeted therapeutic interventions. Further evaluation of the efficacy of PARP inhibitors, either with or without chemotherapy and/or radiotherapy, in tumors with BRCA1/2 mutations in dogs may reveal information that can then be used to benefit humans with similar malignancies. Citation Format: Benjamin Lewis, Gerry Post, Garrett Harvey, Lindsay Lambert, Aubrey Miller, Rilke Van Buren, Christina Lopes, Lucas Rodrigues. Mutational screening of BRCA1/2 genes in 667 spontaneous canine tumors [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 2991.

Abstract 2829: Identifying germline variants for metastatic risk assessment in sporadic colorectal carcinomas

Abstract Colorectal carcinoma (CRC) is the third highest incidence cancer and leading cause of cancer mortality worldwide. Metastasis to distal organ is the major cause of cancer mortality. This trend is expected to be exacerbated by an aging population in the developed world. Genetic predisposition plays a greater role in disease progression than disease etiology in sporadic CRC. However, the underlying genetic factors for metastasis are currently unclear. We identified germline single nucleotide polymorphism (SNP) variants contributing to metastasis risk from a case-case (metastasis-positive vs metastasis-negative) genome-wide association study (GWAS) comprising 3,000 sporadic Chinese CRC cases with definitive metastasis status. Metastasis-positive case is defined as one with distal-organ involvement attributable to primary CRC; metastasis-negative case is defined as metastasis-free with 5 years or more follow-up. By interrogating summarized SNP statistics from the case-case GWAS using the Functional Mapping and Annotation (FUMA) software, we identified 5 genomic risk loci and 74 disease-relevant genes based on gene set enrichment analysis and the Molecular Signatures Database. These genes are in various pathways implicated in different metastasis steps, from epithelial-mesenchymal transition (EMT) to implantation at distal organs. They are different from the risk variants identified by case-control GWAS for disease occurrence. We will expression-profile 250 metastasis-positive vs metastasis negative cases from the GWAS panel to validate the bioinformatics analysis by quantitative real-time PCR. We will focus first on the five genes implicated in glycolysis as this is a biochemical fingerprint of malignant cells that represents one of the ‘hallmarks of cancer'. Expression profile of these genes will be validated in a second independent panel. Kaplan Meier survival analysis as function of the median expression value will be performed to assess prognostic value of these genes. The ultimate goal is to improve metastasis risk assessment for secondary prevention to reduce cancer mortality and morbidity for individual patient as well as reducing public health expenditure. Citation Format: PehYean Cheah, Lai Fun Thean, Michelle Wong, Michelle Lo, Emile Tan, Choong Leong Tang. Identifying germline variants for metastatic risk assessment in sporadic colorectal carcinomas [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 2829.

Clinical and Germline Risk Factors for the Occurrence of Multiple Treatment Toxicities during Childhood Acute Lymphoblastic Leukemia (ALL) Therapy

Treatment-related toxicities can be severe, life-threatening events that impact on delivery of ALL therapy and impair quality of life. The occurrence of multiple (≥ 2) toxicities in any one individual is of particular clinical concern, due to cumulative short and long-term impacts on health and functioning. Few studies have examined the co-occurrence of and risk factors for multiple non-infectious, non hematological toxicities in children with ALL.We evaluated clinical factors and germline single nucleotide polymorphisms (SNPs), to determine the incidence of multiple toxicities and associated risk factors; and to provide insights into their pathogenesis and prevention. We hypothesized that susceptibility factors associated with a two-fold increased risk of multiple toxicity could be identified, and that these may serve as predictive biomarkers.A systematic retrospective review of 1251 Australian children (1-18 years) treated on consecutive ALL protocols, between 1998-2013, was performed. Selected toxicities were venous thromboembolism (VTE), insulin-requirement, bone toxicity (osteonecrosis and fractures); neurotoxicity (central and peripheral). Toxicities chosen were those with a reported incidence >5%, robustness of retrospective data capture and clinical significance. Multiple toxicities were defined as ≥2 selected toxicities occurring in the one patient during first-line ALL therapy. Multivariate logistic regression, Cox regression and Kaplan-Meier survival analyses were performed. Two-tailed P values <0.05 were considered significant. A genome-wide association study (GWAS) was conducted on 702 Caucasian individuals within the cohort, which included 64 cases (≥2 toxicities) and 638 controls (≤ 1 toxicity). Samples were genotyped on the Illumina Oncoarray platform and imputed to the 1000G reference set. Genome-wide significance levels for the GWAS were P < 5E-08.There were 1033 children treated on BFM-based protocols and 218 children on COG-based protocols (Table 1, “Baseline characteristics”). The median age of the cohort was 59 months (range 9-218 months) and median follow-up time was 78 months (range 3-186 months).Five-year overall survival (OS), event-free survival (EFS) and leukemia-free survival (LFS) were 92% ±0.8%, 83.8% ±1.1% and 85.6% ±1.1% respectively. Multiple (≥ 2) toxicities occurred in 133/1240 evaluable children (10.73%). There was no difference in survival for children who experienced multiple toxicities (n=133) compared to the rest of the cohort (n=1107) (P =0.138 for OS, P= 0.595 for EFS, P = 0.276 for LFS).Independent clinical risk factors in multivariate analysis were age ≥ 10 years, female sex, and high-risk ALL. Additional laboratory test risk factors in induction/consolidation were an elevated gamma glutamyl-transferase (GGT) > 5 x upper limit normal (ULN) and serum albumin <20g/L (Table 2). The analysis was adjusted for treatment platform (BFM vs COG), gender, age and immunophenotype (T vs B).An intronic SNP rs78342591 in the MUC16 locus reached genome-wide significance for multiple toxicity (P =2.42E-08, odds ratio 5.89, 95% confidence interval (CI) 3.23-10.74). This was an imputed SNP.Clinical and germline factors could identify children who may benefit from targeted supportive care and surveillance for acute toxicity following ALL therapy. Future research directions include replication, direct sequencing and subsequent functional validation, focusing on MUC16 expression and modulation of drug toxicity. Translation of this research may involve analysis of both risk and protective mechanisms associated with development of multiple toxicities in childhood ALL. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

MHC-I Antigen Presentation Role in Immune Escape of Acute Myeloid Leukemia with High Burden of Genomic Aberration

Background:MHC I antigen presentation is a key pathway in immune response against tumor. It involves degradation of tumor associated antigens, folding and loading of immune epitopes on MHC-I molecules and MHC-I associated presentation on tumor cell surface. Evidence suggests that solid and hematological tumors with high mutational burden or high load in newly tumor associated antigens needs to escape immune surveillance to develop. Acute myeloid leukemia (AML) is not usually believed to be an immunogenic tumor, but patients with complex karyotype, or patients with TP53 alterations have a hypothetical high load of mutation or genomic aberrations.Our study aims to check the entire genome of a large set of newly diagnosed AML to discover if alterations in MHC I antigen presentation could explain the immune escape of the small set of out-layer AML with a high neo-antigen load.Method:We collected 300 bone marrow samples of AML patients at diagnosis from 3 hematological Institutions. Affymetrix Cytoscan HD or 6.0 single nucleotide polymorphism (SNP) array was performed for every samples. Germline SNP array was performed in 114/300 patients, the remaining 186/300 were normalized with a reference pool of 222 healthy donors. Clinical data were collected retrospectively, TP53 , IDH1 , IDH2 , FLT3 , NPM1 , DNMT3A and RUNX1 mutations were tested at diagnosis according ordinary practice. We selected genes involved in MHC class I antigen presentation basing on Reactome pathway. For each patient, we considered MHC-I antigen presentation altered if pathway's alteration rate (altered genes in a pathway/gene in a pathway ratio) scored in the 4th quartile in the alterations rate of all pathways.Results:Twenty out of 300 patients (6.7%) had alteration in MHC I antigen presentation. Patients had alterations in one or more genes: overall 53 genes was founded altered in our set.Patients with alteration in MHC I antigen presentation (group A) did not have differences in age (figure 1a), and in white blood count at diagnosis (figure 1b) compared with other patients in our set (group B). Group A had a prevalence of complex karyotype (14/20 patients, p<.001), and isolated del(5q) (3/30) and abundance in patients harboring TP53 mutation (11/20 patients, p<.001). In group A, a patient harbored FLT3 ITD mutation, a patient IDH2 mutation and 3 patients out of 4 patients tested harbored RUNX1 mutation. In group B, 39/271 patients (13.9%, 9 patients had missing data) harbored TP53 mutation and 56/280 patients had a complex karyotype (29.0%, 9 patients had missing data). Patients in group A had a higher burden of alterations per pathway than patients in group B (0.08 vs 0.04, p<.001).Patients in group A had a median overall survival (OS) of 3.0 months, group B had an OS of 15.7 months (figure 1c, p<.001). MHC class I alteration did not result an essential factor in Cox-hazard ratio model with age, induction therapy, karyotype at diagnosis, TP53, FLT3 and NPM1 mutations.Conclusion:MHC I alteration conferred poor OS at patients in group A; as expected, dismal OS was not confirmed in a multivariable model. We demonstrate that MHC I alteration frequently co-occurred with TP53 mutations and complex karyotype. MHC I alteration was not proved to be a driver alteration in AML, but in the subset of AML with a high number of karyotype aberrations it could favor immune escape and be permissive toward leukemia development and maintenance. Furthermore our approach could be useful in identifying a cohort of patients that are unlikely to respond to immune check-point inhibitors or similar drugs for the dysfunctions in antigen presentation, and a second cohort of patients with TP53 alteration and/or complex karyotype in which these drugs could be administered.Acknowledgments: ELN, AIL, AIRC, project Regione-Università 2010-12 (L. Bolondi), FP7 NGS-PTL project, HARMONY project, Fondazione del Monte BO e RA project. [Display omitted] DisclosuresMartinelli:Amgen: Consultancy; Pfizer: Consultancy; Celgene: Consultancy; Ariad/Incyte: Consultancy; Johnson&Johnson: Consultancy; Roche: Consultancy.

DCBLD1 is associated with the integrin signaling pathway and has prognostic value in non-small cell lung and invasive breast carcinoma

Germline single nucleotide polymorphisms in the promoter region of the DCBLD1 gene are associated with non-smoking cases of both non-small cell lung carcinoma (NSCLC) and human papillomavirus-negative head and neck cancer. However the clinical relevance and function of DCBLD1 remain unclear. This multicenter retrospective study was designed to evaluate the prognostic value and function of DCBLD1 in the four main solid cancers: NSCLC, invasive breast carcinoma, colorectal adenocarcinoma and prostate adenocarcinoma. We included the following cohorts: GSE81089 NSCLC, METABRIC invasive breast carcinoma, GSE14333 colorectal adenocarcinoma, GSE70770 prostate adenocarcinoma and The Cancer Genome Atlas (TCGA) Firehose Legacy cohorts of all four cancers. DCBLD1 gene expression was associated with a worse overall survival in multivariate analyses for both NSCLC cohorts (TCGA: P = 0.03 and GSE81089: P = 0.04) and both invasive breast carcinoma cohorts (TCGA: P = 0.02 and METABRIC: P < 0.001). Patients with high DCBLD1 expression showed an upregulation of the integrin signaling pathway in comparison to those with low DCBLD1 expression in the TCGA NSCLC cohort (FDR = 5.16 × 10–14) and TCGA invasive breast carcinoma cohort (FDR = 1.94 × 10–05).

Cumulative incidence and risk factors for radiation induced leukoencephalopathy in high grade glioma long term survivors

The incidence and risk factors associated with radiation-induced leukoencephalopathy (RIL) in long-term survivors of high-grade glioma (HGG) are still poorly investigated. We performed a retrospective research in our institutional database for patients with supratentorial HGG treated with focal radiotherapy, having a progression-free overall survival > 30 months and available germline DNA. We reviewed MRI scans for signs of leukoencephalopathy on T2/FLAIR sequences, and medical records for information on cerebrovascular risk factors and neurological symptoms. We investigated a panel of candidate single nucleotide polymorphisms (SNPs) to assess genetic risk. Eighty-one HGG patients (18 grade IV and 63 grade III, 50M/31F) were included in the study. The median age at the time of radiotherapy was 48 years old (range 18–69). The median follow-up after the completion of radiotherapy was 79 months. A total of 44 patients (44/81, 54.3%) developed RIL during follow-up. Twenty-nine of the 44 patients developed consistent symptoms such as subcortical dementia (n = 28), gait disturbances (n = 12), and urinary incontinence (n = 9). The cumulative incidence of RIL was 21% at 12 months, 42% at 36 months, and 48% at 60 months. Age > 60 years, smoking, and the germline SNP rs2120825 (PPARg locus) were associated with an increased risk of RIL. Our study identified potential risk factors for the development of RIL (age, smoking, and the germline SNP rs2120825) and established the rationale for testing PPARg agonists in the prevention and management of late-delayed radiation-induced neurotoxicity.

Comprehensive Analysis of Multiple Cohort Datasets Deciphers the Utility of Germline Single-Nucleotide Polymorphisms in Prostate Cancer Diagnosis.

Prostate cancer susceptibility is a polygenic trait. We aimed to examine the controversial diagnostic utility of single-nucleotide polymorphisms (SNP) for prostate cancer. We analyzed two datasets collected from Europeans and one from Africans. These datasets were generated by the genome-wide association studies, that is, CGEMS, BPC3, and MEC-Africans, respectively. About 540,000 SNPs, including 61 risk markers that constitute a panel termed MK-61, were commonly genotyped. For each dataset, we augmented the MK-61 panel to generate an MK-61+ one by adding several thousands of SNPs that were moderately associated with prostate cancer occurrence in external dataset(s). We assessed the diagnostic utility of both panels by measuring their predictive strength for prostate cancer occurrence with AUC statistics. We calculated the theoretical AUCs using quantitative genetics model-based formulae and obtained the empirical estimates via 10-fold cross-validation using statistical and machine learning techniques. For the MK-61 panel, the 95% confidence intervals of the theoretical AUCs (AUC-CI.95) were 0.578-0.655, 0.596-0.656, and 0.539-0.596 in the CGEMS, BPC3, and MEC-Africans cohorts, respectively. For the MK-61+ panels, the corresponding AUC-CI.95 were 0.617-0.663, 0.527-0.736, and 0.547-0.565. The empirical AUCs largely fell within the theoretical interval. A promising result (AUC = 0.703, FNR = 0.354, FPR = 0.353) was obtained in the BPC3 cohort when the MK-61+ panel was used. In the CGEMS cohort, the MK-61+ panel complemented PSA in predicting the disease status of PSA ≥ 2.0 ng/mL samples. This study demonstrates that augmented risk SNP panels can enhance prostate cancer prediction for males of European ancestry, especially those with [Formula: see text]ng/mL. PREVENTION RELEVANCE: This study demonstrates that augmented risk SNP panels can enhance prostate cancer prediction for males of European ancestry, especially those with PSA ≥ 2 ng/mL.

Biomarkers Associated with Regorafenib First-Line Treatment Benefits in Metastatic Colorectal Cancer Patients: REFRAME Molecular Study.

Simple SummaryBiomarkers able to predict response and toxicity upon regorafenib therapy for colorectal cancer (CRC) are critical for treatment choice, particularly relevant in fragile patients. Here, we validated for the first time 18 distinct microRNAs (miRNAs) detected in serum and primary tumor samples, three germline single-nucleotide polymorphisms (SNPs) in vascular endothelial growth factor (VEGF) and vascular endothelial growth factor receptor (VEGFR) genes, and low levels of Notch 1 expression in the primary tumor as predictive biomarkers of different features. Specifically, these markers were associated with a favorable response to treatment, disease stage, and relapse, as well as the appearance of asthenia. Therefore, these markers can be potentially useful biomarkers for patient stratification and for providing a more personalized and effective therapeutic strategy in fragile patients, while limiting the appearance of adverse effects.First-line treatment with regorafenib in frail metastatic colorectal cancer (mCRC) patients has shown some benefit. To accurately identify such patients before treatment, we studied blood biomarkers and primary tumor molecules. We unveiled serum microRNAs (miRNAs), single-nucleotide polymorphisms (SNPs) in angiogenic-related genes, and Notch 1 expression as biomarkers associated with response or toxicity. MicroRNA array profiling and genotyping of selected SNPs were performed in the blood of fragile mCRC patients treated with regorafenib. Notch 1 and CRC-associated miRNA expression was also analyzed in tumors. High levels of miR-185-5p in serum, rs7993418 in the vascular endothelial growth factor receptor 1 (VEGFR1) gene, and Notch 1 expression in biopsies were associated with a favorable response to treatment. Serum levels of miR-126-3p and miR-152-3p and tumor expression of miR-92a-1-5p were associated with treatment toxicity, particularly interesting in patients exhibiting comorbidities, and high levels of miR-362-3p were associated with asthenia. Additionally, several miRNAs were associated with the presence of metastasis, local recurrence, and peritoneal metastasis. Besides, miRNAs determined in primary tumors were associated with tumor-node-metastasis (TNM) staging. The rs2305948 and rs699947 SNPs in VEGFR2 and VEGFA, respectively, were markers of poor prognosis correlating with locoregional relapse, a higher N stage, and metastatic shedding. In conclusion, VEGF and VEGFR SNPs, miRNAs, and Notch 1 levels are potential useful biomarkers for the management of advanced CRC under regorafenib treatment.

Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients.

Gene expression profiling can be used for predicting survival in multiple myeloma (MM) and identifying patients who will benefit from particular types of therapy. Some germline single nucleotide polymorphisms (SNPs) act as expression quantitative trait loci (eQTLs) showing strong associations with gene expression levels. We performed an association study to test whether eQTLs of genes reported to be associated with prognosis of MM patients are directly associated with measures of adverse outcome. Using the genotype-tissue expression portal, we identified a total of 16 candidate genes with at least one eQTL SNP associated with their expression with P < 10-7 either in EBV-transformed B-lymphocytes or whole blood. We genotyped the resulting 22 SNPs in 1327 MM cases from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and examined their association with overall survival (OS) and progression-free survival (PFS), adjusting for age, sex, country of origin and disease stage. Three polymorphisms in two genes (TBRG4-rs1992292, TBRG4-rs2287535 and ENTPD1-rs2153913) showed associations with OS at P < .05, with the former two also associated with PFS. The associations of two polymorphisms in TBRG4 with OS were replicated in 1277 MM cases from the International Lymphoma Epidemiology (InterLymph) Consortium. A meta-analysis of the data from IMMEnSE and InterLymph (2579 cases) showed that TBRG4-rs1992292 is associated with OS (hazard ratio=1.14, 95% confidence interval 1.04-1.26, P=.007). In conclusion, we found biologically a plausible association between a SNP in TBRG4 and OS of MM patients.

PTBP1 Genetic Variants Affect the Clinical Response to Androgen-deprivation Therapy in Patients With Prostate Cancer.

Heterogeneous nuclear ribonucleoproteins (hnRNPs) contribute to multiple cellular functions including RNA splicing, stabilization, transcriptional and translational regulation, and signal transduction. However, the prognostic importance of genetic variants of hnRNP genes in clinical outcomes of prostate cancer remains to be elucidated. We studied the association of 78 germline single-nucleotide polymorphisms (SNPs) in 23 hnRNP genes with the overall survival (OS), cancer-specific survival (CSS), and progression-free survival (PFS) in 630 patients with prostate cancer receiving androgen-deprivation therapy (ADT). PTBP1 rs10420407 was the most significant SNP (false discovery rate q=0.003) and carriers of the A allele exhibited poor OS, CSS, and PFS. Multivariate Cox analysis confirmed PTBP1 rs10420407 A allele was an independent negative prognostic factor for OS and PFS. Expression quantitative trait loci analysis showed that the rs10420407 A allele had a trend towards increased PTBP1 mRNA expression, and higher expression was correlated with prostate cancer aggressiveness and poor patient prognosis. Meta-analysis of 16 independent studies further indicated a tumorigenic effect of PTBP1, with a higher expression in prostate cancers than in adjacent normal tissues (p<0.001). Our data suggest that PTBP1 rs10420407 may influence patient response to ADT, and PTBP1 may be involved in the pathogenesis of prostate cancer progression.

Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

BackgroundThere were scarcely germline variants of familial lung cancer (LC) identified. We conducted an study with whole-exome sequencing of pedigrees with familial lung cancer to analyze the potential genetic susceptibility.MethodsProbands with the highest hereditary background were identified by our large-scale epidemiological study and five ones were enrolled as a learning set. The germline SNPs (single-nucleotide polymorphisms) of other five similar probands, four healthy individuals in the formerly pedigrees and three patients with sporadic LC were used as a validation set, controlled by three healthy individuals without family history of any cancer. The network of mutated genes was generated using STRING-DB and visualized using Cytoscape.ResultsSpecific and shared somatic mutations and germline SNPs were not the shared cause of familial lung cancer. However, individual germline SNPs showed distinct protein-protein interaction network patterns in probands versus healthy individuals and patients with sporadic lung cancer. SNP-containing genes were enriched in the PI3K/AKT pathway. These results were validated in the validation set. Furthermore, patients with familial lung cancer were distinguished by many germline variations in the PI3K/AKT pathway by a simple SVM classification method. It is worth emphasizing that one person with many germline variations in the PI3K/AKT pathway developed lung cancer during follow-up.ConclusionsThe phenomenon that the enrichments of germline SNPs in the PI3K/AKT pathway might be a major predictor of familial susceptibility to lung cancer.

Ganglioside Monosialic Acid Alleviates Peripheral Neuropathy Induced by Utidelone Plus Capecitabine in Metastatic Breast Cancer From a Phase III Clinical Trial.

PurposeThis study aimed to assess the efficacy of utidelone, a novel genetically engineered epothilone analog, combined with capecitabine in our center and, furthermore, to identify whether ganglioside monosialic acid (GM1) improved chemotherapy-induced peripheral neurotoxicity (CIPN).MethodsFifty-five eligible female patients with metastatic breast cancer were enrolled in our single-center phase III BG01-1323L trial. Utidelone combined with capecitabine-induced peripheral neuropathy was analyzed, and susceptible genes were detected in a germline panel by next-generation sequencing (NGS).ResultsIn our single-center study, median progression-free survival and overall survival (OS) improved in the utidelone plus capecitabine group (mPFS: 238 vs. 189 days, P = 0.263; OS: 20.9 vs. 12.9 months, P = 0.326). The median time to severe CIPN reported was 29 days in grade 1, 49 days in grade 2, and 103 days in grade 3. Greatly longer improvement time was indicated in grade 1 (77 vs. 20 days in grade 2, 13 days in grade 3). In the combined group, 19 patients with G2 or G3 CIPN were assigned to the GM1 group and 9 patients to the control group. After intervention, the GM1 group was reported to demonstrate a statistically lower incidence of grade 3 CIPN [GM1 group: 1 of 19 (5.3%); control group: 4 of 9 (44.4%), P = 0.026]. However, there were no statistically significant differences in germline single nucleotide polymorphism (SNP) between grade 3 and grade 1 CIPN cohorts.ConclusionGanglioside monosialic acid potentially decreases severe utidelone plus capecitabine-induced peripheral neuropathy in metastatic breast cancer, and further investigation is needed to validate the manageable efficacy of GM1 in CIPN.Clinical Trial RegistrationClinicalTrials.gov, identifier NCT02253459.

Abstract 3513: Genome-wide scan for novel prostate cancer susceptibility loci with clinical consequence utilizing increased genetic drift of the Finnish population

Abstract Background: Prostate cancer (PC) is the second most common cancer in men worldwide with a rising prevalence. However, only limited number of clinically actionable variants are known. The objective of this study is to identify novel PC susceptibility loci with potential clinical relevance utilizing the increased genetic drift and reduced selective pressure of the recently bottlenecked powerful resource of the Finnish population. Methods: We meta-analysed &amp;gt;185.000 germline single nucleotide polymorphisms (SNPs) in 2738 PC cases and 2401 controls of Finnish origin in the Collaborative Oncological Gene-Environment Study (COGS) using Illumina iSelect custom SNP genotyping platform. Results: Altogether 160 variants remain significant on GWAS level (p&amp;lt;5 × 10−8) in 18 different gene regions. Out of the 160 identified PC susceptibility hits 78 (49%) are novel variants not reported earlier in association with PC. PC associated signals are in close proximity to one another forming genetic hot-spots on chromosomes 8, 7, 11, 17 and 19. The strength of association varies for 101 PC risk variants (OR 1.24-1.86) and 59 protective SNPs (OR 0.59-0.80). The strongest risk gene is CASC8 (OR=1.86; p=1.214 × 10−11). The most significant signals were found at the 8p21.2 chromosomal region (p&amp;lt;7.6 × 10−16). Functional annotation identified a missense coding SNP at KLK3 gene to be a candidate causal variant. We showed evidence for association both with early-onset PC (OR 1.73; P=0.02), high serum PSA level at diagnosis (OR 1.36; P=0.024) and with aggressive PC (Gleason score ≥8; OR 1.44; P=0.02) at 17q21. Conclusion: The results facilitate risk stratification for screening, clinical studies, treatment choices and functional research of PC Citation Format: Csilla Sipeky, Teuvo L. Tammela, Anssi Auvinen, Johanna Schleutker. Genome-wide scan for novel prostate cancer susceptibility loci with clinical consequence utilizing increased genetic drift of the Finnish population [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3513.

Abstract B15: Bladder cancer susceptibility polymorphisms and mortality from non-muscle and muscle-invasive bladder cancer

Abstract Introduction: Genome-wide association studies (GWAS) have identified several common germline single-nucleotide polymorphisms (SNPs) associated with increased risk of bladder cancer. Little is known about whether these variants are also associated with overall and bladder cancer-specific mortality. We examined the association between 13 GWAS-identified bladder cancer risk SNPs and overall and bladder cancer-specific survival in 316 bladder cancer cases recruited as part of a population-based case-control study. Methods: Residents of New Hampshire with primary bladder cancer diagnosed between 2002-2004 were identified from the New Hampshire State Cancer Registry. Medical history and lifestyle factors were collected via in-person interviews at time of enrollment. DNA was isolated from peripheral blood or buccal specimens and genotyping was performed using the Illumina Human610-Quad BeadChip. Date and cause of death were ascertained from the National Death Index with follow-up through December 31, 2013. Non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) were examined separately. We used Cox proportional hazards models to estimate adjusted hazard ratios (HR) and 95% confidence intervals (CI) for overall and bladder cancer-specific survival, assuming a log-additive genetic model. HR estimates for MIBC individuals were adjusted for age at diagnosis, sex, smoking status, American Joint Committee on Cancer stage, initial treatment (including extent of resection, cystectomy, and use of chemotherapy or radiation), and three principal components for genetic ancestry. HR estimates for NMIBC were additionally adjusted for 2004 World Health Organization/International Society of Urologic Pathologists classification. An alpha of 0.05 was used to determine statistical significance. Results: Among 43 participants with MIBC, 30 deaths occurred over a median follow-up of 6.4 years, including 19 from bladder cancer. Among 273 participants with NMIBC, 94 deaths occurred over a median follow-up of 10.3 years, including 23 from bladder cancer. The risk allele [A] of enhancer-associated intergenic SNP rs710521 near TP63 was associated with poorer overall survival after MIBC diagnosis (HR=3.21, 95% CI=1.26-8.16). The risk allele [C] of synonymous SNP rs10936599 of MYNN/TERC was associated with better overall survival after NMIBC diagnosis (HR=0.66, 95% CI=0.46-0.94). No associations with bladder cancer-specific survival were identified. Conclusions: Common bladder cancer susceptibility variants rs710521 and rs10936599 may be associated with overall survival after diagnosis of MIBC and NMIBC, respectively. Citation Format: Reno C. Leeming, Michael S. Zens, John D. Seigne, Brock C. Christensen, Diane Gilbert-Diamond, Margaret R. Karagas, Michael N. Passarelli. Bladder cancer susceptibility polymorphisms and mortality from non-muscle and muscle-invasive bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B15.

Abstract 488: Investigation of the Impact of Germ Line Variation in the K Channel Kcnj5 on the Renin-angiotensin Axis and Aldosterone Release in Human Subjects (linked)

Introduction: Somatic mutations in the KCNJ5 potassium channel are found in significant number of patients with primary aldosteronism (PA). In a previous study, a rare non-synonymous E&gt;Q (E282Q) single nucleotide polymorphism (SNP) rs7102584 in the KCNJ5 channel was identified and an in vitro study confirmed its functionality. This study tested the hypothesis that this germline SNP would affect release of aldosterone and raise blood pressure (BP) under salt-loaded conditions. Methods: Healthy volunteers (30 Group A = SNP heterozygous carriers and 30 Group B = homozygous wild type, mean age: 59±11) were recruited through the UK BioResource, with equal gender distribution in the two groups (40% males, 60% females). Investigators were blinded to the genotype of each recruit. Volunteers were on a low salt diet (≤6 g/d) for a week, and then exposed to high oral salt intake (&gt;9 g/d) for a week. Clinic BP, 24hour ambulatory blood pressure measurements (ABPM), 24hour urine electrolytes, renal biochemistry, renin, aldosterone and renin aldosterone ratio (ARR), were measured before and after high salt exposure. Data were analysed using repeated measures ANOVA and adjusted for age. Results: Following salt loading, the mean day average systolic blood pressure (SBP) and diastolic blood pressure (DBP) rise on ABPM was 2.5 ± 1 mm Hg and 0.7± 0.7 mm Hg. Similarly, night-time average SBP and DBP rise was 2.2 ±1.2 mm Hg and 1.6 ± 0.9 mm Hg respectively. The ARR fell by a mean of 5.0 ±1.7 pmol/mU. There were no significant differences between carriers of the E/Q KCNJ5 variant and wild-type subjects in BP values and biochemical parameters at baseline or under salt-loading. Conclusions: This is the first study we are aware of, that has attempted in vivo translation of this KCNJ5 germline variant. The germline variation does not seem to drive hyperaldosteronism in vivo, although we cannot exclude this in the rare subjects who are homozygous for the variation (mean allele frequency approximately &lt;1 in 1000).

Next-generation sequencing identifies novel single nucleotide polymorphisms in high-risk cutaneous squamous cell carcinoma: A pilot study.

Cutaneous squamous cell carcinoma (SCC) causes 1 million cases in the United States annually. There are germline single nucleotide polymorphisms (SNPs) that result in an increased risk of SCC and altered response to therapy. There may be biologically relevant SNPs not detected using traditional GWAS studies. There are clinically and biologically relevant SNPs in high-risk SCC that may only be appreciated with next-generation sequencing. We performed next-generation sequencing (NGS) on primary SCCs using a targeted mutation panel with 76 cancer-associated genes. We analysed the presence of SNPs in a cohort of 20 high-risk SCCs compared to the American population (AP) (dbSNP). Missense rs3822214 was present in significantly more SCC cases versus the AP. While the remainder is synonymous SNPs, there is growing evidence suggesting clinical relevance of these variants. A larger cohort to validate these findings would be useful.

High-Throughput Molecular Cancer Cell Line Characterization Using Digital Multiplex Ligation-Dependent Probe Amplification for Improved Standardization of in Vitro Research

Tumor cell lines are widely used for cancer research, but challenges regarding quality control of cell line identity, cross contamination, and tumor somatic molecular stability remain, demanding novel approaches beyond conventional short tandem repeat profiling. A total of 21 commonly used multiple myeloma cell lines obtained from public repositories were analyzed by digital multiplex ligation-dependent probe amplification (digitalMLPA) to characterize germline single-nucleotide polymorphisms, insertions/deletions, and somatic copy number aberrations (CNAs). Using generated profiles and an in-house developed analytical pipeline, blinded experiments were performed to determine capability of digitalMLPA to predict cell line identity and potential spike-in DNA contamination in 41 anonymized cell line samples. The dominant cell line was correctly identified in all cases, and cross contamination was correctly detected in 33 of 37 samples with spike-in DNA; there were no false-positive predictions. The four samples in which spike in was not detected all carried low levels of contamination (1%), whereas levels of contamination ≥5% were correctly identified in all cases. Unsupervised clustering of CNA profiles identified shared commonalities that correlated with initiating Ig heavy locus translocation events. Longitudinal CNA assessment of nine cell lines revealed changes under standard culturing conditions not detected by insertion/deletion profiling alone. Results suggest that digitalMLPA can be utilized as a high-throughput tool for advanced quality assurance for invitro cancer research.