Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival

Rho GTPases control cell division, motility, adhesion, vesicular trafficking and phagocytosis, which may affect progression and/or prognosis of cancers. Here, we investigated associations between genetic variants of Rho GTPases-related genes and cutaneous melanoma-specific survival (CMSS) by re-analyzing a published melanoma genome-wide association study (GWAS) and validating the results in another melanoma GWAS. In the single-locus analysis of 36,018 SNPs in 129 Rho-related genes, 427 SNPs were significantly associated with CMSS (p  C, ARHGAP22 rs3851552 T > C, ARHGAP44 rs72635537 C > T and ARHGEF10 rs7826362 A > T) were independently predictive of CMSS (a meta-analysis derived p = 9.04 × 10-4 , 9.58 × 10-4 , 1.21 × 10-4 and 8.47 × 10-4 , respectively). Additionally, patients with an increasing number of unfavorable genotypes (NUGs) of these loci had markedly reduced CMSS in both discovery dataset and validation dataset (ptrend =1.47 × 10-7 and 3.12 × 10-5 ). The model including the NUGs and clinical variables demonstrated a significant improvement in predicting the five-year CMSS. Moreover, rs10916352C and rs3851552C alleles were significantly associated with an increased mRNA expression levels of RHOU (p = 1.8 × 10-6 ) and ARHGAP22 (p = 5.0 × 10-6 ), respectively. These results may provide promising prognostic biomarkers for CM personalized management and treatment

Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival

Remodeling or deregulation of the calcium signaling pathway is a relevant hallmark of cancer including cutaneous melanoma (CM). In this study, using data from a published genome-wide association study (GWAS) from The University of Texas M.D. Anderson Cancer Center, we assessed the role of 41,377 common single-nucleotide polymorphisms (SNPs) of 167 calcium signaling pathway genes in CM survival. We used another GWAS from Harvard University as the validation dataset. In the single-locus analysis, 1830 SNPs were found to be significantly associated with CM-specific survival (CMSS; P ≤ 0.050 and false-positive report probability ≤ 0.2), of which 9 SNPs were validated in the Harvard study (P ≤ 0.050). Among these, three independent SNPs (i.e. PDE1A rs6750552 T>C, ITPR1 rs6785564 A>G and RYR3 rs2596191 C>A) had a predictive role in CMSS, with a meta-analysis-derived hazards ratio of 1.52 (95% confidence interval = 1.19–1.94, P = 7.21 × 10−4), 0.49 (0.33–0.73, 3.94 × 10−4) and 0.67 (0.53–0.86, 0.0017), respectively. Patients with an increasing number of protective genotypes had remarkably improved CMSS. Additional expression quantitative trait loci analysis showed that these genotypes were also significantly associated with mRNA expression levels of the genes. Taken together, these results may help us to identify prospective biomarkers in the calcium signaling pathway for CM prognosis

Novel genetic variants of PIP5K1C and MVB12B of the endosome-related pathway predict cutaneous melanoma-specific survival

Endosomes regulate cell polarity, adhesion, signaling, immunity, and tumor progression, which may influence cancer outcomes. Here we evaluated associations between 36,068 genetic variants of 228 endosome-related pathway genes and cutaneous melanoma disease-specific survival (CMSS) using genotyping data from two previously published genome-wide association studies. The discovery dataset included 858 CM patients with 95 deaths from The University of Texas MD Anderson Cancer Center, and the replication dataset included 409 CM patients with 48 deaths from the Nurses’ Health Study (NHS) and the Health Professionals Follow-up Study (HPFS). In multivariate Cox proportional hazards regression analysis, we found that two novel SNPs (PIP5K1C rs11666894 A>C and MVB12B rs12376285 C>T) predicted CMSS, with adjusted hazards ratios of 1.47 (95% confidence interval = 1.15-1.89 and P = 0.002) and 1.73 (1.30-2.31 and 0.0002), respectively. Combined analysis of risk genotypes of these two SNPs revealed a dose-dependent decrease in CMSS associated with an increased number of risk genotypes (P trend = 0.0002). Subsequent expression quantitative trait loci (eQTL) analysis revealed that PIP5K1C rs11666894 was associated with mRNA expression levels in lymphoblastoid cell lines from 373 European descendants (P<0.0001) and that MVB12B rs12376285 was associated with mRNA expression levels in cultured fibroblasts from 605 European-Americans (P<0.0001). Our findings suggest that novel genetic variants of PIP5K1C and MVB12B in the endosome-related pathway genes may be promising prognostic biomarkers for CMSS, but these results need to be validated in future larger studies

MX 2 is a novel regulator of cell cycle in melanoma cells

MX2 protein is a dynamin‐like GTPase2 that has recently been identified as an interferon‐induced restriction factor of HIV‐1 and other primate lentiviruses. A single nucleotide polymorphism (SNP), rs45430, in an intron of the MX2 gene, was previously reported as a novel melanoma susceptibility locus in genome‐wide association studies. Functionally, however, it is still unclear whether and how MX2 contributes to melanoma susceptibility and tumorigenesis. Here, we show that MX2 is differentially expressed in melanoma tumors and cell lines, with most metastatic cell lines showing lower MX2 expression than primary melanoma cell lines and melanocytes. Furthermore, high expression of MX2 RNA in primary melanoma tumors is associated with better patient survival. Overexpression of MX2 reduces in vivo proliferation partially through inhibition of AKT activation, suggesting that it can act as a tumor suppressor in melanoma. However, we have also identified a subset of melanoma cell lines with high endogenous MX2 expression where downregulation of MX2 leads to reduced proliferation. In these cells, MX2 downregulation interfered with DNA replication and cell cycle processes. Collectively, our data for the first time show that MX2 is functionally involved in the regulation of melanoma proliferation but that its function is context‐dependent

Characterization of genetic factors associated with melanoma susceptibility and prognosis

[eng] Melanoma is the malignant tumor arising from melanocytes and is the most aggressive of the common skin cancers. Melanoma is the tumor with the highest heritability (58%) and around 10% of cases occur in a familial context. Genetic susceptibility can be explained due to the inheritance of low, medium or high-risk variants, or a combination of them. To date, germline mutations in high-risk genes have been detected in 20-30% of melanoma-prone families. Interestingly, there is an important relationship between genetic factors associated with the risk to develop melanoma and genetic factors modulating melanoma outcome. The thesis hypotheses were: a) The proper characterization of known melanoma risk genes in a specific population context will facilitate genetic counseling in melanoma b) The use of genome-wide linkage can allow the identification of new melanoma susceptibility loci in our population. c) Melanoma susceptibility and nevus-related genes can play a role in melanoma prognosis. d) Variants in immune checkpoints genes can play a role in melanoma prognosis. Based on those hypotheses, the aims of this thesis were: 1) To characterize known risk genes in patients at high-risk to develop melanoma in Spain to refine genetic counseling. 2) To identify new familial melanoma loci using genome-wide linkage analysis. 3) To study the role of candidate genes in melanoma prognosis. To answer those aims we designed six studies. In the first study, we evaluated the prevalence of CDKN2A germline mutations in patients at high risk to develop melanoma in our population and characterize families with mutation. We identified a higher prevalence of lung, breast and pancreatic cancer cases in families with mutation. Based on the study results, CDKN2A mutation carriers, besides sun protection advice and dermatologic surveillance, should receive recommendations on avoiding smoking and can be included in early detection programs for pancreatic, lung and breast cancers. In the second study, we evaluated the prevalence of MITF p.Glu318Lys carriers and assessed their characteristics detecting fast-growing melanoma among carriers. Thus, MITF p.Glu318Lys should be given fast-track visits to dermatology as they may be at risk to develop fast-growing melanomas and can be included in early detection programs for renal cancer. In the third study we identified that POT1 is mutated in a subset of melanoma families in Spain, thus genetic testing in melanoma should include the analysis of this gene. In the fourth study we identified a new melanoma locus at 11q associated with familial melanoma. Next-generation sequencing studies focused on the analysis of this region may allow the identification of new melanoma susceptibility genes or variants. Finally, in the last two studies, we focused on melanoma prognosis. We determined that IRF4 rs12203592 T functional variant, associated with a low melanogenesis (and low nevus count) and immune tolerance, correlates with a worse melanoma survival. Moreover, inherited functional variants of the lymphocyte receptor CD5, associated with more immune reactivity, correlated with better melanoma outcome. To conclude, we have established the genetic bases of melanoma susceptibility in our population and refined genetic counseling, knowing the mutation prevalence of each gene and adapting secondary prevention measures in melanoma and other tumors according to the genetic testing results. Genome-wide linkage analysis in melanoma-prone families from Spain has allowed the identification of a new locus at 11q involved in familial melanoma. We have identified new genes modulating melanoma outcome based on the study of candidate genes involved in melanoma susceptibility, nevi count, and immune regulation.[cat] El melanoma és el més agressiu dels càncers de pell comuns. És el tumor amb una major heretabilitat. La susceptibilitat genètica depèn de variants d’alt, mig o baix risc, o la seva combinació. Hi ha una gran correlació entre factors genètics associats al risc i al pronòstic del melanoma. Els objectius d’aquesta tesi han estat: 1. Caracteritzar gens coneguts en pacients amb alt risc a desenvolupar melanoma per millorar el consell genètic. 2. Identificar nous loci implicats en la susceptibilitat a melanoma mitjançant anàlisi de lligament massiu. 3. Estudiar el paper de gens candidats en el pronòstic del melanoma En els primers tres estudis, es va avaluar la prevalença de mutacions a CDKN2A, POT1, promotor de TERT i la variant p.Glu318Lys a MITF en pacients amb alt risc a desenvolupar melanoma. També es van estudiar les característiques de les famílies i portadors d’aquestes variants. Els resultats observats mostren que els portadors de mutació a CDKN2A, a banda de les mesures de fotoprotecció i seguiment dermatològic, haurien d’evitar el tabac i es poden incloure en programes de detecció precoç de càncer de pàncrees, pulmó o mama. Els portadors de la variant p.Glu318Lys a MITF haurien de tenir accés ràpid a la consulta dermatològica pel risc a desenvolupar melanoma de ràpid creixement. POT1 s’hauria d’incloure en el test genètic. En el quart, hem identificat un nou locus a 11q associat a la susceptibilitat del melanoma familiar. Finalment, en els dos últims treballs, hem observat que la variant funcional d’IRF4 rs12203592 T, associada a un recompte de nevus baix i immunotolerància, correlaciona amb un pitjor pronòstic. A més, variants funcionals de CD5 associades amb una major reactivitat immunològica correlacionen amb un millor pronòstic. En conclusió, hem establert les bases genètiques de la susceptibilitat del melanoma en la nostra població i millorat el consell genètic. Estudis de lligament massiu han permès la identificació d’un nou locus associat al melanoma familiar. Per acabar, hem identificat nous gens que modulen el pronòstic del melanoma basant-nos en l’estudi de candidats relacionats amb la susceptibilitat a melanoma, el recompte de nevus i la regulació del sistema immune

Germline genetic variation and predicting immune checkpoint inhibitor induced toxicity

Immune checkpoint inhibitor (ICI) therapy has revolutionised the treatment of various cancer types. ICIs reinstate T-cell function to elicit an anti-cancer immune response. The resulting immune response can however have off-target effects which manifest as autoimmune type serious immune-related adverse events (irAE) in ~10–55% of patients treated. It is currently challenging to predict both who will experience irAEs and to what severity. Identification of patients at high risk of serious irAE would revolutionise patient care. While the pathogenesis driving irAE development is still unclear, host genetic factors are proposed to be key determinants of these events. This review presents current evidence supporting the role of the host genome in determining risk of irAE. We summarise the spectrum and timing of irAEs following treatment with ICIs and describe currently reported germline genetic variation associated with expression of immuno-modulatory factors within the cancer immunity cycle, development of autoimmune disease and irAE occurrence. We propose that germline genetic determinants of host immune function and autoimmune diseases could also explain risk of irAE development. We also endorse genome-wide association studies of patients being treated with ICIs to identify genetic variants that can be used in polygenic risk scores to predict risk of irAE

Genetic variants in the metzincin metallopeptidase family genes predict melanoma survival

Metzincins are key molecules in the degradation of the extracellular matrix and play an important role in cellular processes such as cell migration, adhesion, and cell fusion of malignant tumors, including cutaneous melanoma (CM). We hypothesized that genetic variants of the metzincin metallopeptidase family genes would be associated with CM-specific survival (CMSS). To test this hypothesis, we first performed Cox proportional hazards regression analysis to evaluate the associations between genetic variants of 75 metzincin metallopeptidase family genes and CMSS using the dataset from the genome-wide association study (GWAS) from The University of Texas MD Anderson Cancer Center (MDACC) which included 858 non-Hispanic white patients with CM, and then validated using the dataset from the Harvard GWAS study which had 409 non-Hispanic white patients with invasive CM. Four independent SNPs (MMP16 rs10090371 C>A, ADAMTS3 rs788935 T>C, TLL2 rs10882807 T>C and MMP9 rs3918251 A>G) were identified as predictors of CMSS, with a variant-allele attributed hazards ratio (HR) of 1.73 (1.32-2.29, 9.68E-05), 1.46 (1.15-1.85, 0.002), 1.68 (1.31-2.14, 3.32E-05) and 0.67 (0.51-0.87, 0.003), respectively, in the meta-analysis of these two GWAS studies. Combined analysis of risk genotypes of these four SNPs revealed a decreased CMSS in a dose-response manner as the number of risk genotypes increased (Ptrend < 0.001). An improvement was observed in the prediction model (area under the curve [AUC] = 81.4% vs. 78.6%), when these risk genotypes were added to the model containing non-genotyping variables. Our findings suggest that these genetic variants may be promising prognostic biomarkers for CMSS

Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma

Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility

Genetic variants in the vitamin D pathway genes VDBP and RXRA modulate cutaneous melanoma disease-specific survival

Single nucleotide polymorphisms (SNPs) in the vitamin D pathway genes have been implicated in cutaneous melanoma (CM) risk, but their role in CM disease-specific survival (DSS) remains obscure. We comprehensively analyzed the prognostic roles of 2669 common SNPs in the vitamin D pathway genes using data from a published genome-wide association study (GWAS) at The University of Texas M.D. Anderson Cancer Center (MDACC) and then validated the SNPs of interest in another GWAS from the Nurses' Health Study and Health Professionals Follow-up Study. Among the 2669 SNPs, 203 were significantly associated with DSS in MDACC dataset (P C was associated with a better DSS [combined hazards ratio (HR) = 0.66]; and the same for RXRA rs7850212 C > A (combined HR = 0.38), which were further confirmed by the Fine and Gray competing-risks regression model. Further bioinformatics analyses indicated that these loci may modulate corresponding gene methylation status