Germline Factors Research Articles

PLK-1 regulates MEX-1 polarization in the C. elegans zygote.

The one-cell C. elegans embryo undergoes an asymmetric cell division during which germline factors such as the RNA-binding proteins POS-1 and MEX-1 segregate to the posterior cytoplasm, leading to their asymmetric inheritance to the posterior germline daughter cell. Previous studies found that the RNA-binding protein MEX-5 recruits polo-like kinase PLK-1 to the anterior cytoplasm where PLK-1 inhibits the retention of its substrate POS-1, leading to POS-1 segregation to the posterior. In this study, we tested whether PLK-1 similarly regulates MEX-1 polarization. We find that both the retention of MEX-1 in the anterior and the segregation of MEX-1 to the posterior depend on PLK kinase activity and on the interaction between MEX-5 and PLK-1. Human PLK1 directly phosphorylates recombinant MEX-1 on 9 predicted PLK-1 sites in vitro, four of which were identified in previous phosphoproteomic analysis of C. elegans embryos. The introduction of alanine substitutions at these four PLK-1 phosphorylation sites (MEX-1(4A)) significantly weakened the inhibition of MEX-1 retention in the anterior, thereby weakening MEX-1 segregation to the posterior. In contrast, mutation of a predicted CDK1 phosphorylation site had no effect on MEX-1 retention or on MEX-1 segregation. MEX-1(4A) mutants are viable and fertile but display significant sterility and fecundity defects at elevated temperatures. Taken together with our previous findings, these findings suggest PLK-1 phosphorylation drives both MEX-1 and POS-1 polarization during the asymmetric division of the zygote.

Identifying Novel Germline Mutations and Copy Number Variations in Patients With SCLC

IntroductionSCLC has traditionally been considered to arise from toxic exposure factors, such as smoking. Recent evidence has revealed that germline mutations may also affect the development of SCLC; however, these alterations remain understudied. We sought to identify novel germline mutations in SCLC including germline copy number variations (CNVs) in our cohort of patients. MethodsWe designed a custom hybrid-capture gene panel to evaluate germline alterations in 192 cancer-predisposition and frequently mutated genes in SCLC. We applied this panel to germline analysis of a treatment-naive cohort of 67 patients with SCLC at our institution. Subsequently, we annotated the variants using the American College of Medical Genetics criteria and further classified variants of uncertain significance using a set of in silico tools, including DeepMind AlphaMissense, MutationTaster, SIFT, and Polyphen2. ResultsWe identified American College of Medical Genetics pathogenic/likely pathogenic alterations in seven of 67 patients. Five (71%) were novel alterations (BCORL1, FANCC, ATR, and BBC3) and a novel CNV (SLFN11) with two (29%) previously described mutations (CHEK1 and BRIP1). We also identified 191 variants of uncertain significance in 60 of 67 patients, of which, depending on the in silico tool, 5% to 14% were predicted to be pathogenic. Patients with SCLC with the seven pathogenic alterations were observed to have a numerically longer overall survival (hazard ratio = 0.50) and progression-free survival (hazard ratio = 0.45) though not statistically significant compared with the remaining cohort. ConclusionsOur study identifies novel germline alterations, including a CNV, and provides additional evidence that germline factors could be important contributing factors to the development of SCLC.

The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells

Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DEAD-box helicase 4 (DDX4), a germline factor and RNA helicase conserved in all multicellular organisms, contributes to increased cell motility and cisplatin-mediated drug resistance in small cell lung cancer (SCLC) cells. Proteomic analysis suggests that DDX4 expression upregulates proteins related to DNA repair and immune/inflammatory response. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Further, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of immune/inflammatory response markers. Taken together, we propose that DDX4 increases SCLC cell survival, by increasing the DNA damage and immune response pathways, especially under challenging conditions such as cisplatin treatment.

Clonal hematopoiesis, multi-omics and coronary artery disease.

Studies of the genetic architecture of cardiovascular disease once focused on heritable germline factors. Newer work has shed light on the role of somatic mutations in blood cells. These mechanistic and multi-omics studies, along with phenotypic analyses, offer the prospect of new precision cardiovascular medicine paradigms.

Mapping the genomic diaspora of gastric cancer.

Gastric cancer (GC) is a leading contributor to global cancer incidence and mortality. Pioneering genomic studies, focusing largely on primary GCs, revealed driver alterations in genes such as ERBB2, FGFR2, TP53 and ARID1A as well as multiple molecular subtypes. However, clinical efforts targeting these alterations have produced variable results, hampered by complex co-alteration patterns in molecular profiles and intra-patient genomic heterogeneity. In this Review, we highlight foundational and translational advances in dissecting the genomic cartography of GC, including non-coding variants, epigenomic aberrations and transcriptomic alterations, and describe how these alterations interplay with environmental influences, germline factors and the tumour microenvironment. Mapping of these alterations over the GC life cycle in normal gastric tissues, metaplasia, primary carcinoma and distant metastasis will improve our understanding of biological mechanisms driving GC development and promoting cancer hallmarks. On the translational front, integrative genomic approaches are identifying diverse mechanisms of GC therapy resistance and emerging preclinical targets, enabled by technologies such as single-cell sequencing and liquid biopsies. Validating these insights will require specifically designed GC cohorts, converging multi-modal genomic data with longitudinal data on therapeutic challenges and patient outcomes. Genomic findings from these studies will facilitate 'next-generation' clinical initiatives in GC precision oncology and prevention.

O1-3 Defined lifestyle and germline factors predispose Asian populations to gastric cancer

O1-3 Defined lifestyle and germline factors predispose Asian populations to gastric cancer

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.

Maternal germline factors associated with aneuploid pregnancy loss: a systematic review.

Miscarriage describes the spontaneous loss of pregnancy before the threshold of viability; the vast majority occur before 12 weeks of gestation. Miscarriage affects one in four couples and is the most common complication of pregnancy. Chromosomal abnormalities of the embryo are identified in ∼50% of first trimester miscarriages; aneuploidy accounts for 86% of these cases. The majority of trisomic miscarriages are of maternal origin with errors occurring during meiotic division of the oocytes. Chromosome segregation errors in oocytes may be sporadic events secondary to advancing maternal age; however, there is increasing evidence to suggest possible maternal germline contributions to this. The objective of this review was to appraise critically the existing evidence relating to maternal germline factors associated with pregnancy loss secondary to embryo aneuploidy, identify limitations in the current evidence base and establish areas requiring further research. The initial literature search was performed in September 2019 and updated in January 2021 using the electronic databases OVID MEDLINE, EMBASE and the Cochrane Library. No time or language restrictions were applied to the searches and only primary research was included. Participants were women who had suffered pregnancy loss secondary to numerical chromosomal abnormalities of the embryo. Study identification and subsequent data extraction were performed by two authors independently. The Newcastle-Ottawa Scale was used to judge the quality of the included studies. The results were synthesized narratively. The literature search identified 2198 titles once duplicates were removed, of which 21 were eligible for inclusion in this systematic review. They reported on maternal germline factors having variable degrees of association with pregnancy loss of aneuploid origin. The Online Mendelian Inheritance in Man (OMIM) gene ontology database was used as a reference to establish the functional role currently attributed to the genes reported. The majority of the cases reported and included were secondary to the inheritance of maternal structural factors such as Robertsonian translocations, deletions and insertions. Germline factors with a plausible role in aneuploid pregnancy loss of maternal origin included skewed X-inactivation and CGG repeats in the fragile X mental retardation (FMR1) gene. Studies that reported the association of single gene mutations with aneuploid pregnancy loss were conflicting. Single gene mutations with an uncertain or no role in aneuploid pregnancy loss included mutations in synaptonemal complex protein 3 (SYCP3), mitotic polo-like kinase 4 (PLK4) and meiotic stromal antigen 3 (STAG3) spindle integrity variants and 5,10-methylenetetrahydrofolate reductase (MTHFR). Identifying maternal genetic factors associated with an increased risk of aneuploidy will expand our understanding of cell division, non-disjunction and miscarriage secondary to embryo aneuploidy. The candidate germline factors identified may be incorporated in a screening panel for women suffering miscarriage of aneuploidy aetiology to facilitate counselling for subsequent pregnancies.

Molecular and morphological sex differentiation in sablefish (Anoplopoma fimbria), a marine teleost with XX/XY sex determination.

Phenotypic sex of an organism is determined by molecular changes in the gonads, so-called molecular sex differentiation, which should precede the rise of cellular or anatomical sex-distinguishing features. This study characterized molecular and morphological sex differentiation in sablefish (Anoplopoma fimbria), a marine teleost with established XX/XY genotypic sex determination. Next generation sequencing was conducted on sablefish ovarian and testicular mRNAs to obtain sequences for transcripts associated with vertebrate sex determination and differentiation and early reproductive development. Gene-specific PCRs were developed to determine the distribution and ontogenetic gonadal expression of transcription, growth, steroidogenic and germline factors, as well as gonadotropin and steroid receptors. Molecular changes associated with sex differentiation were first apparent in both XY- and XX-genotype sablefish at~60mm in body length and prior to histological signs of sex differentiation. The earliest and most robust markers of testicular differentiation were gsdf, amh, dmrt1, cyp11b, star, sox9a, and fshr. Markedly elevated mRNA levels of several steroidogenesis-related genes and ar2 in differentiating testes suggested that androgens play a role in sablefish testicular differentiation. The earliest markers of ovarian differentiation were cyp19a1a, lhcgr, foxl2, nr0b1, and igf3. Other transcripts such as figla, zp3, and pou5f3 were expressed predominantly in XX-genotype fish and significantly increased with the first appearance and subsequent development of primary oocytes. This study provides valuable insight to the developmental sequence of events associated with gonadal sex differentiation in marine teleosts with XX/XY sex determination. It also implicates particular genes in processes of male and female development and establishes robust molecular markers for phenotypic sex in sablefish, useful for ongoing work related to sex control and reproductive sterilization.

Defined lifestyle and germline factors predispose Asian populations to gastric cancer.

Germline and environmental effects on the development of gastric cancers (GC) and their ethnic differences have been poorly understood. Here, we performed genomic-scale trans-ethnic analysis of 531 GCs (319 Asian and 212 non-Asians). There was one distinct GC subclass with clear alcohol-associated mutation signature and strong Asian specificity, almost all of which were attributable to alcohol intake behavior, smoking habit, and Asian-specific defective ALDH2 allele. Alcohol-related GCs have low mutation burden and characteristic immunological profiles. In addition, we found frequent (7.4%) germline CDH1 variants among Japanese GCs, most of which were attributed to a few recurrent single-nucleotide variants shared by Japanese and Koreans, suggesting the existence of common ancestral events among East Asians. Specifically, approximately one-fifth of diffuse-type GCs were attributable to the combination of alcohol intake and defective ALDH2 allele or to CDH1 variants. These results revealed uncharacterized impacts of germline variants and lifestyles in the high incidence areas.

Molecular and Functional Characterization of the Somatic PIWIL1/piRNA Pathway in Colorectal Cancer Cells.

PIWI-like (PIWIL) proteins and small non-coding piRNAs, involved in genome regulation in germline cells, are found aberrantly expressed in human tumors. Gene expression data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, and the European Genome-Phenome Archive (EGA) indicate that the PIWIL1 gene is ectopically activated in a significant fraction of colorectal cancers (CRCs), where this is accompanied by promoter demethylation, together with germline factors required for piRNA production. Starting from this observation, the PIWIL/piRNA pathway was studied in detail in COLO 205 CRC cells, which express significant levels of this protein, to investigate role and significance of ectopic PIWIL1 expression in human tumors. RNA sequencing and cell and computational biology led to the demonstration that PIWIL1 localizes in a nuage-like structure located in the perinuclear region of the cell and that a significant fraction of the piRNAs expressed in these cells are methylated, and, therefore, present in an active form. This was further supported by RNA immunoprecipitation, which revealed how several piRNAs can be found loaded into PIWIL1 to form complexes also comprising their target mRNAs. The mature transcripts associated with the PIWIL–piRNA complex encode key regulatory proteins involved in the molecular mechanisms sustaining colorectal carcinogenesis, suggesting that the PIWI/piRNA pathway may actively contribute to the establishment and/or maintenance of clinico-pathological features of CRCs.

Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing.

OBJECTIVES:Serrated polyposis syndrome (SPS) is a complex disorder with a high risk of colorectal cancer for which the germline factors remain largely unknown. Here, we combined whole-exome sequencing (WES) and linkage studies in families with multiple members affected by SPS to identify candidate genes harboring rare variants with higher penetrance effects.METHODS:Thirty-nine affected subjects from 16 extended SPS families underwent WES. Genome-wide linkage analysis was performed under linear and exponential models. The contribution of rare coding variants selected to be highly pathogenic was assessed using the gene-based segregation test.RESULTS:A significant linkage peak was identified on chromosome 3p25.2-p22.3 (maxSNP = rs2293787; LODlinear = 2.311, LODexp = 2.11), which logarithm of the odds (LOD) score increased after fine mapping for the same marker (maxSNP = rs2293787; LODlinear = 2.4, LODexp = 2.25). This linkage signal was replicated in 10 independent sets of random markers from this locus. To assess the contribution of rare variants predicted to be pathogenic, we performed a family-based segregation test with 11 rare variants predicted to be deleterious from 10 genes under the linkage intervals. This analysis showed significant segregation of rare variants with SPS in CAPT7, TMEM43, NGLY1, and FBLN2 genes (weighted P value > 0.007).DISCUSSION:Protein network analysis suggested FBLN2 as the most plausible candidate genes for germline SPS predisposition. Etiologic rare variants implicated in disease predisposition may be identified by combining traditional linkage with WES data. This powerful approach was effective for the identification of a new candidate gene for hereditary SPS.

Abstract 4175: Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer

Abstract Mutations in twenty genes have been associated with heritable breast cancer (BCA), yet the prevalence and clinical implications of most of these genes have not been well described in African American women (AAW). AAW who harbor inherited mutations in BCA susceptibility (BCS) genes are less likely to be identified and thus less likely to receive standard of surgical and preventive care for heritable BCA. A better understanding of heritable mutations in AAW with BCA would ultimately help to define guidelines for clinical management of high risk AAW. We performed targeted sequencing for 288 AAW diagnosed with invasive BCA unselected for family history, age, or BCA subtype. Participants were enrolled in the Detroit Research on Cancer Survivors (ROCS) cohort study or the Karmanos Cancer Institute Biobank. A custom sequencing panel captured the coding sequence of 43 genes (Known: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53; Candidate: MLH1, MSH2, PMS1, SEC23B, BLM, ATR, BAP1, BBC3, CDKN1A, FAM175A, FANCA, FANCC, FANCI, FANCL, FANCM, GEN1, RAD51B, RBBP8, RECQL, RINT1, TP53BP1, XRCC1, XRCC3). Samples were sequenced using the Illumina MiSeq platform multiplexed for 100X mean depth of coverage. Intronic or synonymous exonic variants and those with &amp;lt;40 reads, or alternative allele frequency &amp;gt;3% in African populations in the 1000 Genomes, ExAC, or NHLBI ESP6500SI databases were filtered. Only variants in known BCS genes could be considered definitively pathogenic (DP), defined as missense variants categorized as pathogenic in ClinVar and all frameshift, nonsense, and splice site variants. All other variants were defined as variants of uncertain significance (VUS). We identified 54 women harboring DP mutations in 15 known BCS genes. Mutations in BRCA1/2 accounted for 32% of all DP mutations. Notably, nearly 17% of DP mutations were in MSH6, a gene only recently described as associated with increased risk of BCA in the general population. Among women with these DP mutations, nearly 25% had no high-risk characteristics. Ten VUS in known BCS genes were identified, where 4 were reported in ClinVar (BARD1, RAD5C, BRCA2, PMS2) and 6 were novel (PMS2, BRCA1, MUTYH, MSH6, NBN, MRE11). Among the candidate BCS genes, 63 VUS were identified: 51 frameshift variants, 5 nonsense variants, 3 splice site variants, and 4 missense mutations predicted to be pathogenic by ≥8/9 algorithms. Nearly 60% of participants had neither a DP mutation or VUS. These data suggest that AAW with BCA have a unique mutation spectrum and may benefit from BCS gene sequencing regardless of family history, age, or subtype. Additional sequencing in AAW will lay the foundation for identification of germline factors associated with BCA risk and prognosis specifically in AAW and offer opportunities for personalized risk assessment. Citation Format: Kristen Purrington, Gregory Dyson, Douglas Craig, Julie Boerner, Julie Madden, Jennifer Beebe-Dimmer, Ann G. Schwartz, Michael Simon. Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer [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 4175.

Elevated IgM and abnormal free light chain ratio are increased in relatives from high-risk chronic lymphocytic leukemia pedigrees

Abnormal serum immunoglobulin (Ig) free light chains (FLC) are established biomarkers of early disease in multiple B-cell lymphoid malignancies, including chronic lymphocytic leukemia (CLL). Heavy chains have also been shown to be biomarkers in plasma cell disorders. An unanswered question is whether these Ig biomarkers are heritable, i.e., influenced by germline factors. CLL is heritable but highly heterogeneous. Heritable biomarkers could elucidate steps of disease pathogenesis that are affected by germline factors, and may help partition heterogeneity and identify genetic pleiotropies across malignancies. Relatives in CLL pedigrees present an opportunity to identify heritable biomarkers. We compared FLCs and heavy chains between relatives in 23 high-risk CLL pedigrees and population controls. Elevated IgM (eIgM) and abnormal FLC (aFLC) ratio was significantly increased in relatives, suggesting that these Ig biomarkers are heritable and could offer risk stratification in pedigree relatives. Within high-risk CLL pedigrees, B-cell lymphoid malignancies were five times more prevalent in close relatives of individuals with eIgM, prostate cancer was three times more prevalent in relatives of individuals with aFLC, and monoclonal B-cell lymphocytosis increased surrounding individuals with normal Ig levels. These different clustering patterns suggest Ig biomarkers have the potential to partition genetic heterogeneity in CLL and provide insight into distinct heritable pleiotropies associated with CLL.

Abstract 2968: Imputation of the prostate cancer transcriptome in over 230,000 men reveals novel germline-somatic interaction mechanism of cancer risk

Abstract Although genome-wide association studies of prostate cancer have revealed numerous genetic loci associated with disease risk, efforts to characterize the causal mechanisms of germline genetic variants have been unsystematic in their approach. While select studies have evaluated the effects of the most significantly associated variants on the expression of highly proximal genes, both the complex nature of gene expression regulation, as well as the majority fraction of prostate cancer risk unaccounted for by genome-wide association study loci, suggest that certain risk genes and variants remain undiscovered. In pursuit of such causal genetic factors, we analyzed germline genotype data paired with gene expression data from normal prostate tissue in 471 subjects to build regularized statistical models of how gene expression of the prostate is influenced by cis-genetic variation. By applying these models to genome-wide association study data, predictions of transcript expression levels were generated transcriptome-wide for over 230,000 male subjects (14,616 prostate cancer cases, 219,339 controls) from the UK Biobank, GERA Cohort, ProHealth Study, and California Men's Health Study. Finally, these transcript abundances were assessed in relation to prostate cancer case-control status to identify those genes with expression levels most predictive of prostate cancer diagnosis. Among the 12,014 genes for which models were successfully fit, 29 were transcriptome-wide significant via Bonferroni correction, while another 9 exhibited p-values that were suggestive. Moreover, 19 of the 38 significant or suggestive genes replicated in the validation cohort of Kaiser Permanente health plan members (GERA, ProHealth, CMHS). At previously implicated risk loci for prostate cancer, numerous genes were significantly associated with disease risk, including MSMB, NCOA4, and AGAP7 at 10q11.22, HNF1B at 17q12, as well as POU5F1B and PCAT1 at 8q24.21. Furthermore, several genes whose expression levels were not previously implicated were associated with prostate cancer risk. The most noteworthy of these was TMPRSS2, part of the TMPRSS2-ERG gene-fusion, which represents the most frequent somatic alteration discovered in prostate cancer tumors. When conditioned on a previously reported prostate cancer GWAS cis-variant at 21q22.3, TMPRSS2 retained transcriptome-wide significance. Further analysis of the genetic effects on TMPRSS2-ERG expression in prostate cancer tumors from The Cancer Genome Atlas (TCGA) suggested a novel mechanism by which germline and somatic factors cooperate to increase disease risk. By systematically characterizing gene expression of the prostate in this transcriptome-wide association study (TWAS) of prostate cancer, we identified prostate cancer risk genes and propose a novel germline-somatic interaction mechanism of cancer risk. Citation Format: Nima C. Emami, Joshua Hoffman, Elad Ziv, John S. Witte. Imputation of the prostate cancer transcriptome in over 230,000 men reveals novel germline-somatic interaction mechanism of cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2968.

Fatty Acids Regulate Germline Sex Determination through ACS-4-Dependent Myristoylation

Fat metabolism has been linked to fertility and reproductive adaptation in animals and humans, and environmental sex determination potentially plays a role in the process. To investigate the impact of fatty acids (FA) on sex determination and reproductive development, we examined and observed an impact of FA synthesis and mobilization by lipolysis in somatic tissues on oocyte fate in Caenorhabditis elegans. The subsequent genetic analysis identified ACS-4, an acyl-CoA synthetase and its FA-CoA product, as key germline factors that mediate the role of FA in promoting oocyte fate through protein myristoylation. Further tests indicated that ACS-4-dependent protein myristoylation perceives and translates the FA level into regulatory cues that modulate theactivities of MPK-1/MAPK and key factors inthe germline sex-determination pathway. These findings, including a similar role of ACS-4 in a male/femalespecies, uncover a likely conserved mechanism by which FA, an environmental factor, regulates sex determination and reproductive development.

Treatment patterns and impact of race in patients receiving first-line therapy for advanced penile squamous cell carcinoma (PSCC).

413 Background: Treatment patterns and outcomes with first-line therapy for PSCC are unclear. We conducted a retrospective analysis of the NCDB to study this issue and evaluate prognostic factors in treated patients (pts). Methods: Data from the NCDB was obtained for pts diagnosed with clinical stage 4 PSCC from 1998-2011. The following variables were evaluated: age, Charlson Comorbidity Index (CCI), race, survival, socioeconomic status (SES) based on median income of area of residence and therapy. Treatment patterns were described. Multivariate analyses (MVA) were conducted to assess the impact of factors on survival of pts receiving therapy. Results: Of 14,395 pts with PSCC, 614 pts with stage 4 PSCC were evaluable with complete data. The mean age was 61.9 (range 22-90), 498 (81.1%) were white and 91 (14.8%) were black. 300 (48.7%) pts received no anti-cancer therapy, 245 (39.9%) received chemotherapy (+/- other therapy) and 69 (11.24%) received radiation (+/- non-chemotherapy agents). Pts in the chemotherapy group were significantly younger (mean age 58.8 years) than those in the radiation (63.5 years) or no therapy (64.1 years) group (p &lt; 0.001), but there were no significant differences in other variables between the 3 groups. The median survival from date of therapy of those in the chemotherapy and radiation groups were 9.75 and 8.65 months, respectively. MVA of pts who received therapy showed that non-white race (p = 0.006) and shorter time from diagnosis to therapy (p = 0.005) were significantly associated with poor survival, while chemotherapy, SES, age and CCI did not impact survival. Additionally, non-white race showed a trend for association with poor survival (p = 0.089) in those not receiving anti-cancer therapy. Conclusions: A minority of pts (39.9%) with stage 4 PSCC received chemotherapy in this large NCDB cohort, who were younger than those who received radiation or no therapy. The association of non-white race with poor survival suggests the impact of germline factors and disparities in therapy. The absence of significant impact of chemotherapy on survival in this real world PSCC cohort highlights unmet needs in this orphan disease and the need for discovery of effective agents.

Defining the Influence of Germline Variation on Metastasis Using Systems Genetics Approaches.

Cancer is estimated to be responsible for 8 million deaths worldwide and over half a million deaths every year in the United States. The majority of cancer-related deaths in solid tumors is directly associated with the effects of metastasis. While the influence of germline factors on cancer risk and development has long been recognized, the contribution of hereditary variation to tumor progression and metastasis has only gained acceptance more recently. A variety of approaches have been used to define how hereditary variation influences tumor progression and metastasis. One approach that garnered much early attention was epidemiological studies of cohorts of cancer patients, which demonstrated that specific loci within the human genome are associated with a differential propensity for aggressive tumor development. However, a powerful, and somewhat underutilized approach has been the use of systems genetics approaches in transgenic mouse models of human cancer. Such approaches are typically multifaceted, and involve integration of multiple lines of evidence derived, for example, from genetic and transcriptomic screens of genetically diverse mouse models of cancer, coupled with bioinformatics analysis of human cancer datasets, and functional analysis of candidate genes. These methodologies have allowed for the identification of multiple hereditary metastasis susceptibility genes, with wide-ranging cellular functions including regulation of gene transcription, cell proliferation, and cell-cell adhesion. In this chapter, we review how each of these approaches have facilitated the identification of these hereditary metastasis modifiers, the molecular functions of these metastasis-associated genes, and the implications of these findings upon patient survival.

Abstract POSTER-TECH-1118: Meta-analysis of cancer microarray data sets reveals a germ line expression profile in ovarian cancers: new biomarkers and potential drug targets

Abstract Overview: One of the main challenges facing oncology is the identification of highly restricted, cancer-specific biomarkers for use in early diagnostics, prognostics, patient stratification and as potential therapeutic targets, including immunotherapeutic and small drug targets. Germ line genes are normally only expressed in the reproductive organs and meiosis-specific genes are normally only activated within the foetal oocytes and/or the spermatocytes in adult males. Our work has been based on the hypothesis that these germ line genes become activated in cancers, driving the oncogenic process and serving as clinically relevant biomarkers / targets. Our approach and relevance to ovarian cancer: We have taken an in silico approach to identify human meiotic and germ line genes. We have used novel computational tools to determine whether these genes are restricted to immunologically privileged / germ line tissues in healthy adults and whether they are activated in human tumours. We have also experimentally validated these expression profiles. Our meta-analysis of human cancer gene expression microarray data reveals high incidences of germ line gene activation in human ovarian cancers1,2, suggesting that these cancers more readily take on a germ line state than other human tumour types. Subsequent laboratory-based work indicates that some of these genes are required for ovarian cancer cell proliferation. Conclusions / perspectives: Evidence is starting to emerge that human cancers adopt a more germ line state as part of the oncogenic process. In a Drosophila melanogaster brain tumour model it has been demonstrated that these germ line genes are required for oncogenesis; moreover, aberrantly expressed human germ line genes are required for the proliferation of human cancer cells in vitro. Indeed, it has been postulated that cancer cells become ‘addicted’ to these germ line factors, making them a very poorly explored pool of potential drug targets. Additionally, recent work has demonstrated that a sub-group of germ line genes can be used as powerful markers for the stratification of lung cancer patients. Our finding that ovarian cancers take on a highly active germ line transcriptional profile suggests that this might provide an important source of biomarkers and therapeutic targets for ovarian cancers. 1 Feichtinger et al. (2012) Meta-analysis of clinical data using human meiotic genes identifies a novel cohort of highly restricted cancer-specific marker genes. Oncotarget 3: 843-853. 2 Feichtionger et al. (2014) Meta-analysis of expression of l(3)mbt tumour-associated germline genes supports the model that a soma-to-germline transition is a hallmark of human cancers. Int. J. Cancer 134: 2359-2365. Citation Format: Ramsay McFarlane. Meta-analysis of cancer microarray data sets reveals a germ line expression profile in ovarian cancers: new biomarkers and potential drug targets [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-TECH-1118.

Cytoplasmic localization and asymmetric division in the early embryo of Caenorhabditis elegans.

During the initial cleavages of the Caenorhabditis elegans embryo, a series of rapid and invariant asymmetric cell divisions pattern the fate, size, and position of four somatic blastomeres and a single germline blastomere. These asymmetric divisions are orchestrated by a collection of maternally deposited factors that are initially symmetrically distributed in the newly fertilized embryo. Maturation of the sperm-derived centrosome in the posterior cytoplasm breaks this symmetry by triggering a dramatic and highly stereotyped partitioning of these maternal factors. A network of conserved cell polarity regulators, the PAR proteins, form distinct anterior and posterior domains at the cell cortex. From these domains, the PAR proteins direct the segregation of somatic and germline factors into opposing regions of the cytoplasm such that, upon cell division, they are preferentially inherited by the somatic blastomere or the germline blastomere, respectively. The segregation of these factors is controlled, at least in part, by a series of reaction-diffusion mechanisms that are asymmetrically deployed along the anterior/posterior axis. The characterization of these mechanisms has important implications for our understanding of how cells are polarized and how spatial organization is generated in the cytoplasm. For further resources related to this article, please visit the WIREs website.