Genetic determinants of ATR inhibitor sensitivity and resistance in Gastric Cancer

Synthetic lethal approaches in identifying genetic determinants of drug response is a powerful method in selecting patents for targeted cancer therapies. Ataxia-Telangiectasia Mutated (ATM) and Rad3-related protein kinase (ATR) is a valuable target to inhibit the DNA damage repair (DDR) pathway, that has been shown to be particularly effective in cancer cells harbouring other DDR defects, including truncating mutations in ARID1A, found in the 20% of gastric cancer (GC) patients. Although ATR inhibitors (ATRi) are emerging as promising cancer therapies, resistance mechanisms inevitably arise from these drugs as monotherapy, emphasising the importance of identifying genetic determinants of response and resistance to inform drug combinations that result in durable clinical responses. In this thesis, an integrated functional genomics approach was undertaken in order to identify genetic determinants to ATRi sensitivity and resistance in GC. First, I show that ARID1A defective GCs in vitro and in vivo models exhibit enhanced sensitivity to ATRi. Second, I have comprehensively identified and validated genetic determinants of ATRi-resistance by undertaking a genome-wide (GW) CRISPR/Cas9 screen and created ATRi resistant isogenic models, including CDC25B, HUWE1, CARD10, SMG8, SMG9, SMG1, HNRNPF, IRF9, and STAT2. Lastly, I have shown for the first time that mutations in the ATR FAT domain cause resistance to ATRi. These findings inform us about the biological mechanisms of ATRi sensitivity and resistance in GC. Furthermore, this data provides the preclinical rationale for assessing ATRi such as VX970, AZD6738 or M4344 in clinical trials, for patients with GC

Análisis de la asociación entre sexo y diferencias en pigmentación humana según el genotipo del gen MC1R

Introducción: La pigmentación cutánea basal y la respuesta al sol por bronceamiento son rasgos hereditarios influidos por varios genes, entre los que el gen mc1r es uno de los más importantes. Mutaciones en este gen afectan a los niveles y tipos de me-lanina dando lugar a patrones alterados de pigmentación. Recientemente, se ha iden-tificado una asociación entre el genotipo del gen oca2, el color de ojos y el sexo, su-giriendo que existe un factor relacionado con el sexo que contribuye a las variaciones en la pigmentación del iris humano. El actual estudio consistió en analizar una posible asociación entre el sexo y diferentes características fenotípicas de pigmentación, te-niendo en cuenta el genotipo del gen mc1r. metodología: Se recogieron datos feno-típicos de 446 individuos sanos (212 hombres y 234 mujeres) y 706 individuos con melanoma (325 hombres y 379 mujeres). Se secuenció el gen mc1r en todas las muestras, clasificando las muestras en wtmc1r (wild-type) o mutmc1r (mutante). Para el análisis estadístico se utilizó el software SPSS v20. resultados: Las mujeres pre-sentan una mayor asociación a fototipos i y ii, tanto al analizar el total de individuos como en individuos sanos y con melanoma por separado (p = 0,008, 0,014 y 0,024, respectivamente). Esta asociación se mantiene en muestras mutmc1r (p = 0,037), pero no en muestras wtmc1r (p = 0,061). Las mujeres también presentan menor nú-mero de nevus (p = 0,001), aunque esta asociación desaparece en individuos control y con genotipo mutmc1r. conclusión: Los resultados muestran una asociación entre el sexo y variaciones en la pigmentación, especialmente en lo que se refiere a la res-puesta y sensibilidad al sol. Además, esta asociación no parece ser independiente del genotipo de mc1rIntroduction: Basal skin pigmentation and sun-tanning capacity are hereditary traits influenced by several genes, including the mc1r gene. Mutations in this gene affect the levels and types of melanin produced, resulting in altered pigmentation patterns. Re-cently, we have identified an association between oca2 genotype, eye color and sex, suggesting that there is a sex-related factor contributing to changes in iris pigmentation. In this study, we analyzed a possible association between sex and different phenotypic pigmentation characteristics, taking into account the mc1r genotype. methodology: Phe-notypic data of 446 healthy individuals (212 men and 234 women) and 706 patients with melanoma (325 men and 379 women) were collected. The mc1r gene was sequenced in all samples, sorting the samples in wtmc1r (wild-type) or mutmc1r (mutant). For statistical analysis SPSS v20 software was used. results: Women have a greater as-sociation with skin phototypes i and ii, both when analyzing the total sample set as well as healthy and melanoma individuals separately (p = 0,008, 0,014 and 0,024, respec-tively). That association is observed in mutmc1r samples (p = 0,037) but not in wtmc1r samples (p = 0,061). Women also present fewer nevi (p = 0,001), although this asso-ciation disappears in controls and in mutmc1r samples. conclusion: The results show an association between sex and pigmentation variations, particularly with respect to the response and sensitivity to the sun. Moreover, this association does not appear to be independent of the mc1r genotype

Impact of severe aortic stenosis on quality of life

Stenosis; Quality of life; QuestionnairesEstenosis; Calidad de vida; CuestionariosEstenosi; Qualitat de vida; QüestionarisIntroduction Among individuals ≥ 65 years old, aortic stenosis is highly prevalent and the number of cases is expected to increase in the coming decades, due to the increased life expectancy. Nevertheless, the actual aortic stenosis burden is not well known in population settings and the impact of aortic stenosis on quality of life has not been studied. The aim of this study was to evaluate aortic stenosis impact on health-related quality of life in patients > 65 years old. Methods An epidemiological case-control study was carried out to compare quality of life in patients ≥65 years old with severe symptomatic aortic stenosis. Demographical and clinical information was prospectively obtained and quality of life information was collected with the Short Form Health Survey_v2 (SF-12) questionnaire. The association between quality of life and aortic stenosis was determined using multiple logistic regression models. Results Patients with severe aortic stenosis self-perceived worse quality of life on all dimensions and summary components of the SF-12 questionnaire. In the final multiple logistic regression model a significant inverse association was observed between the dimensions ‘physical role’ and ‘social role’ (p = 0.002 and p = 0.005) and an association close to significance with ‘physical role’ (p = 0.052) of the SF-12 questionnaire. Conclusion The use of quality of life scales allows the assessment of the impact of aortic stenosis on quality of life and may improve the therapeutic approach to severe aortic stenosis, providing evidence for patient‐centered care

Sex-specific genetic effects associated with pigmentation, sensitivity to sunlight, and melanoma in a population of Spanish origin

Background Human pigmentation is a polygenic quantitative trait with high heritability. In addition to genetic factors, it has been shown that pigmentation can be modulated by oestrogens and androgens via up- or down-regulation of melanin synthesis. Our aim was to identify possible sex differences in pigmentation phenotype as well as in melanoma association in a melanoma case-control population of Spanish origin. Methods Five hundred and ninety-nine females (316 melanoma cases and 283 controls) and 458 males (234 melanoma cases and 224 controls) were analysed. We genotyped 363 polymorphisms (single nucleotide polymorphisms (SNPs)) from 65 pigmentation gene regions. Results When samples were stratified by sex, we observed more SNPs associated with dark pigmentation and good sun tolerance in females than in males (107 versus 75; P = 2.32 × 10−6), who were instead associated with light pigmentation and poor sun tolerance. Furthermore, six SNPs in TYR, SILV/CDK2, GPR143, and F2RL1 showed strong differences in melanoma risk by sex (P < 0.01). Conclusions We demonstrate that these genetic variants are important for pigmentation as well as for melanoma risk, and also provide suggestive evidence for potential differences in genetic effects by sex.We thank the Madrid College of Lawyers and all patients from the different contributing Hospitals. We would like to thank Tais Moreno, M. Rosario Alonso, and Guillermo Pita for their expert technical assistance with Illumina genotyping, performed at the Spanish National Genotyping Centre (CeGen, Madrid). MI-V is funded by the “Ministry of Health Carlos III” under a Sara Borrell contract (CD15/00153). ML-C is funded by a Prometeo contract (2015/005). SSO is funded by the “ Ministry of Education, Culture and Sport” under a FPU fellowship (FPU13/04976). GR is funded by the “Ministry of Health Carlos III” under a Miquel Servet II contract (CPII14-00013). This work has also been partly funded by a research project from the Spanish Ministry of Economy and Competitiveness (CGL2014-58526-P), whose principal investigator is S

The landscape of expression and alternative splicing variation across human traits

Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.This study was funded by the HumTranscriptom project with reference PID2019-107937GA-I00. R.G.-P. was supported by a Juan de la Cierva fellowship (FJC2020-044119-I) funded by MCIN/AEI/10.13039/501100011033 and ‘‘European Union NextGenerationEU/PRTR.’’ J.M.R. was supported by a predoctoral fellowship from ‘‘la Caixa’’ Foundation (ID 100010434) with code LCF/BQ/DR22/11950022. A.R.-C. was supported by a Formación Personal Investigador (FPI) fellowship (PRE2019-090193) funded by MCIN/AEI. R.C.-G. was supported by an FPI fellowship (PRE2020-092510) funded by MCIN/AEI. M.M. was supported by a Ramon y Cajal fellowship (RYC-2017-22249).Peer ReviewedPostprint (published version

Modelling MC1R rare variants: A structural evaluation of variants detected in a Mediterranean case-control study

4 páginas, 1 figura.This study was supported by a Grant from the Ministerio de Salud Carlos III (ISCIII) (FI10-00405) and Ministerio de Economia y Competitividad (SAF2012-31405). MP-C is funded by the VALi+d from the Generalitat Valenciana (ACIF/2011/207). MJLC is funded by the Generalitat Valenciana under a Geronimo Forteza contrat (FPA/2013/A/037). GR is funded by the Ministerio de Salud Carlos III under a ‘Miquel Servet’ contract (CP08-00069). We thank the Madrid College of Lawyers and all the participants from all contributing Hospitals.Peer reviewe

Gender and eye colour prediction discrepancies: A reply to criticisms (letter)

Letter to the editor: In a letter published in this same issue, Liu et al. reply to a recently published article by us contesting the main conclusion of our original paper, namely, that gender is a factor that contributes to the explanation of the discrepancies in eye colour prediction based on the HERC2/OCA2 genotype and the IrisPlex model..

A three-dimensional structural model to evaluate MC1R variants. The importance of rare variants

Póster presentado al 18th Meeting of the European Society for Pigment Cell Research Lisbon, Portugal | 9–12 September 2013. Abstract publicado en: Pigment Cell & Melanoma Research 26(5): E1-E31MC1R, the main genetic contributor to sporadic melanoma predisposition, is highly polymorphic in white populations. In this study, 41 MC1R variants detected in the Spanish population were mapped in a three-dimensional structure prediction model of the MC1R protein. Among these variants, 31 were rarely found, being Y298H described for the first time in our population. A total of 25 variants appeared to have structural implications including the functional traditionally-associated red and non red hair colour variants (RHC/NRHC) and a novel group of potentiallyfunctional rare variants. Evaluation of all changes according to the MC1R structure model, variant location and nature of the amino acid change, suggests three different putatively-functional MC1R regions: the GTPase signalling region, an alleged a-MSH-binding extracellular region, and a novel central core protein region. Firstly, the 3D model shows the GTPase signalling region which includes most of the well known functional RHC/NRHC variants, though with no apparent structural consequences. The second region shows an extracellular cluster of rare variants predicted to have no structural implications, although they may be potentially important for protein function due to their location in the putative a-MSH-binding site. Finally, an internal core with predicted lossof-function changes harvesting both some RHC/NHRC and rare variants is described for the first time. Furthermore, the ensuing outcomes of this MC1R variant modelling were highly consistent with data from previously published functional MC1R studies. Overall, we believe that this approach is more informative and could further evaluate the implication of different changesPeer reviewe

Impact of severe aortic stenosis on quality of life

Introduction Among individuals ≥ 65 years old, aortic stenosis is highly prevalent and the number of cases is expected to increase in the coming decades, due to the increased life expectancy. Nevertheless, the actual aortic stenosis burden is not well known in population settings and the impact of aortic stenosis on quality of life has not been studied. The aim of this study was to evaluate aortic stenosis impact on health-related quality of life in patients > 65 years old. Methods An epidemiological case-control study was carried out to compare quality of life in patients ≥65 years old with severe symptomatic aortic stenosis. Demographical and clinical information was prospectively obtained and quality of life information was collected with the Short Form Health Survey_v2 (SF-12) questionnaire. The association between quality of life and aortic stenosis was determined using multiple logistic regression models. Results Patients with severe aortic stenosis self-perceived worse quality of life on all dimensions and summary components of the SF-12 questionnaire. In the final multiple logistic regression model a significant inverse association was observed between the dimensions ‘physical role’ and ‘social role’ (p = 0.002 and p = 0.005) and an association close to significance with ‘physical role’ (p = 0.052) of the SF-12 questionnaire. Conclusion The use of quality of life scales allows the assessment of the impact of aortic stenosis on quality of life and may improve the therapeutic approach to severe aortic stenosis, providing evidence for patient‐centered care

Quality of life score of all dimensions and summary components of the SF-12 questionnaire in symptomatic patients with AS ≥ 65 years old.

MCS: Mental Component Summary, PCS: Physical Component Summary. Each bar indicates the score (0–100) for cases and controls of each specific dimension. The bounds are indicating the mean ± standard deviation.</p