7 research outputs found
From risk modification to precision therapy : integrated strategies for enhancing cancer prevention and treatment
No full textEl càncer de mama és el càncer diagnosticat amb més freqüència i la principal causa de mort relacionada amb el càncer entre les dones a nivell mundial. Les alteracions genètiques hereditàries (germinals) i adquirides (somàtiques) contribueixen al desenvolupament de la malaltia. Les variants patogèniques en els gens de susceptibilitat al càncer de mama BRCA1 i BRCA2 s'associen a un alt risc de càncer i defineixen tumors amb característiques moleculars i vulnerabilitats específiques. Tanmateix, els determinants genètics germinals de l'inici del càncer no es comprenen completament, i els factors biològics somàtics que influeixen en la progressió del càncer i en la resposta als tractaments encara no han estan del tot definits. Abordar aquestes llacunes en el coneixement podria millorar els esforços de prevenció primària i optimitzar les estratègies de tractament personalitzat. Aquesta tesi té com a objectiu explorar com els modificadors genètics i els trets immunitaris contribueixen al risc de càncer de mama, amb la finalitat d'identificar possibles biomarcadors precoços de la malaltia i determinants d'una característica somàtica clau dels tumors corresponents-impulsada per una activitat diferencial en els processos de reparació del dany a l'ADN-que estan vinculats a vulnerabilitats terapèutiques. En primer lloc, vam analitzar estadístiques de GWAS i perfils transcriptòmics de tumors, i vam validar HMMR com a modificador de risc del càncer de mama associat a BRCA1 en demostrar el seu paper en l'augment de la inestabilitat genòmica. Separadament, vam identificar 4.093 variants genètiques de pleiotropia que associen trets hematològics amb el risc de càncer, i vam trobar un enriquiment significatiu a prop de loci de Y-RNA. A partir d'aquesta observació, vam establir el Y-RNA com un possible biomarcador en plasma, indicat per un augment del risc de càncer de mama. A continuació, vam proposar una nova estratègia terapèutica dirigida tant a hipòxia com a la via d'unió d'extrems alternativa (alternative end-joining), essencials per a la supervivència de les cèl·lules canceroses amb mutacions a BRCA1/BRCA2. En concret, el bloqueig de HIF1α-un regulador clau de la hipòxia-fa que les cèl·lules siguin més vulnerables a la inhibició de PARP o POLQ, independentment de l'estat de recombinació homòloga. Finalment, per fer possible la translació clínica, vam entrenar models d'aprenentatge profund que avaluaven l'activitat de les vies d'unió d'extrems alternativa i de la hipòxia mitjançant imatges patològiques tumorals, oferint un mètode de precisió assistit per IA per a l'estratificació de pacients. En conjunt, aquests resultats amplien el coneixement sobre la biologia del càncer de mama, proporcionen nous objectius terapèutics i permeten enfocaments clínics més precisos.El cáncer de mama es el cáncer más diagnosticado y la principal causa de muerte relacionada con el cáncer en mujeres a nivel mundial. Las alteraciones genéticas heredadas (germinales) y adquiridas (somáticas) contribuyen al desarrollo de la enfermedad. Las variantes patogénicas en los genes de susceptibilidad al cáncer de mama BRCA1 y BRCA2 están asociadas con un alto riesgo de cáncer y definen tumores con características moleculares y vulnerabilidades específicas. Sin embargo, los determinantes genéticos germinales del inicio del cáncer no se comprenden completamente, y las características biológicas somáticas que influyen en la progresión del cáncer y los resultados terapéuticos aún no están completamente caracterizados. Abordar estas brechas de conocimiento podría mejorar los esfuerzos de prevención primaria y optimizar las estrategias de tratamiento personalizado. Esta tesis tuvo como objetivo explorar cómo los modificadores genéticos y los rasgos del sistema inmunitario contribuyen al riesgo de cáncer de mama, con el fin de identificar posibles biomarcadores tempranos de la enfermedad y determinantes de una característica somática clave en los tumores correspondientes-impulsada por una actividad diferencial en los procesos de reparación del daño en el ADN-que están vinculados a vulnerabilidades terapéuticas. En primer lugar, analizamos datos de GWAS y perfiles transcriptómicos de tumores, y validamos a HMMR como un modificador de riesgo en el cáncer de mama asociado a BRCA1, al demostrar su papel en el aumento de la inestabilidad genómica. Por separado, identificamos 4.093 variantes genéticas de pleiotropía que asocian rasgos hematológicos con el riesgo de cáncer, y encontramos un enriquecimiento significativo cerca de loci de Y-RNA. A partir de esta observación, establecimos al Y-RNA como un posible biomarcador plasmático, indicado por un mayor riesgo de cáncer de mama. A continuación, propusimos una nueva estrategia terapéutica dirigida tanto a la hipoxia como a las vías de unión alternativa de extremos (alternative end-joining), crítica para la supervivencia de células cancerosas con mutaciones en BRCA1/BRCA2. Específicamente, el bloqueo de HIF1α-regulador clave de la hipoxia-hace que las células sean más vulnerables a la inhibición de PARP o POLQ, independientemente del estado de recombinación homóloga. Finalmente, para habilitar la aplicación clínica, entrenamos modelos de aprendizaje profundo que evaluaron la actividad de las vías de unión alternativa de extremos y de hipoxia utilizando imágenes patológicas de tumores, ofreciendo un método de precisión asistido por IA para la estratificación de pacientes. En conjunto, estos hallazgos amplían el conocimiento sobre la biología del cáncer de mama, proporcionan nuevos objetivos terapéuticos y permiten enfoques clínicos más precisos.Breast cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death among women worldwide. Inherited (germline) and acquired (somatic) genetic alterations contribute to disease development. Pathogenic variants in the breast cancer susceptibility genes BRCA1 and BRCA2 are associated with a high risk of cancer and define tumors with specific molecular features and vulnerabilities. However, the germline genetic determinants of cancer initiation are not fully understood, and the somatic biological features that influence cancer progression and therapeutic outcomes remain incompletely characterized. Addressing these knowledge gaps could enhance primary preventive efforts and improve personalized treatment strategies. This thesis aimed to explore how genetic modifiers and immune traits contribute to breast cancer risk, with the goal of identifying potential early disease biomarkers determinants of a key somatic feature of the corresponding tumors-driven by differential activity in DNA damage repair processes-which are linked to therapeutic vulnerabilities. First, we analyzed GWAS summary statistics and transcriptomic profiles from tumors and we validated HMMR as a risk modifier of BRCA1-associated breast cancer by demonstrating its role in enhancing genomic instability. Separately, we identified 4,093 pleiotropy genetic variants associating blood traits with cancer risk, and found a significant enrichment near Y-RNA loci. Based on this observation, we then established Y-RNA as a possible biomarker in plasma, indicated by an increased risk of breast cancer. Next, we proposed a novel therapeutic strategy that targets both the hypoxia and alternative end-joining pathways, which is critical for the survival of BRCA1/BRCA2-mutant cancer cells. Specifically, blocking HIF1a-key regulator of hypoxia-rendering cells more vulnerable to PARP or POLQ inhibition, regardless of homologous recombination status. Finally, to enable clinical translation, we trained deep-learning models that assessed the activity of alternative end-joining and hypoxia pathways by using tumor pathology images, offering an AI-assisted precision method for patient stratification. Together, these findings advance breast cancer biology knowledge, providing novel therapeutic targets, and enable more precise, clinical approaches
Harnessing transcriptional regulation of alternative end-joining to predict cancer treatment
No full textTranscriptional regulation; Cancer treatmentRegulación transcripcional; Tratamiento del cáncerRegulació transcripcional; Tractament del càncerAlternative end-joining (alt-EJ) is an error-prone DNA repair pathway that cancer cells deficient in homologous recombination rely on, making them vulnerable to synthetic lethality via inhibition of poly(ADP-ribose) polymerase (PARP). Targeting alt-EJ effector DNA polymerase theta (POLθ), which synergizes with PARP inhibitors and can overcome resistance, is of significant preclinical and clinical interest. However, the transcriptional regulation of alt-EJ and its interactions with processes driving cancer progression remain poorly understood. Here, we show that alt-EJ is suppressed by hypoxia while positively associated with MYC (myelocytomatosis oncogene) transcriptional activity. Hypoxia reduces PARP1 and POLQ expression, decreases MYC binding at their promoters, and lowers PARylation and alt-EJ-mediated DNA repair in cancer cells. Tumors with HIF1A mutations overexpress the alt-EJ gene signature. Inhibition of hypoxia-inducible factor 1α or HIF1A expression depletion, combined with PARP or POLθ inhibition, synergistically reduces the colony-forming capacity of cancer cells. Deep learning reveals the anticorrelation between alt-EJ and hypoxia across regions in tumor images, and the predictions for these and MYC activity achieve area under the curve values between 0.70 and 0.86. These findings further highlight the critical role of hypoxia in modulating DNA repair and present a strategy for predicting and improving outcomes centered on targeting alt-EJ.This study was funded by the “GINKGO Apac del Berguedà” patient association; the Instituto de Salud Carlos III [co-funded by the European Regional Development Fund (ERDF), “A way to build Europe”] grants PI21/0136 and PI24/01327 to M.A.P., and PI19/00342 and PI23/00513 to A.A.; the Asociación Española Contra el Cáncer (AECC) grant LABAE21170 to A.A.; the Department of Defense PC210340 PCRP-IDA grant to A.A.; the Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación [co-funded by the European Regional Development Fund (ERDF), “A way to build Europe”] grants PID2020-117815RB-I00 and PID2023-150836OB-100 to F.V., and CNS2023-145615 to A.A.; and the Generalitat de Catalunya, Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) grants SGR 2017-449 and 2021-00184 to F.V. and M.A.P., and 2021-00895 to A.A. R.E. and M.A.P.-C. were supported by contracts from the Departament de Salut, Generalitat de Catalunya, PERIS-PFI SLT017-20-000076 and PERIS-Suport SLT017/20/000072, respectively, and A.S. was supported by Generalitat de Catalunya AGAUR fellowship 2022-FI-B01068. We also acknowledge the support of the Centres de Recerca de Catalunya (CERCA) Program to IDIBELL and IDIBGI. The open-access publication of this article was funded by the Instituto de Salud Carlos III grants PI24/01327 to M.A.P., PI23/00513 to A.A., and PID2023-150836OB-100 to F.V
Evidence for shared genetic risk factors between lymphangioleiomyomatosis and pulmonary function
No full textLymphangioleiomyomatosis; Risk factors; Pulmonary functionLinfangioleiomiomatosis; Factores de riesgo; Función pulmonarLimfangioleiomiomatosi; Factors de risc; Funció pulmonarIntroduction Lymphangioleiomyomatosis (LAM) is a rare low-grade metastasising disease characterised by cystic lung destruction. The genetic basis of LAM remains incompletely determined, and the disease cell-of-origin is uncertain. We analysed the possibility of a shared genetic basis between LAM and cancer, and LAM and pulmonary function.
Methods The results of genome-wide association studies of LAM, 17 cancer types and spirometry measures (forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC ratio and peak expiratory flow (PEF)) were analysed for genetic correlations, shared genetic variants and causality. Genomic and transcriptomic data were examined, and immunodetection assays were performed to evaluate pleiotropic genes.
Results There were no significant overall genetic correlations between LAM and cancer, but LAM correlated negatively with FVC and PEF, and a trend in the same direction was observed for FEV1. 22 shared genetic variants were uncovered between LAM and pulmonary function, while seven shared variants were identified between LAM and cancer. The LAM-pulmonary function shared genetics identified four pleiotropic genes previously recognised in LAM single-cell transcriptomes: ADAM12, BNC2, NR2F2 and SP5. We had previously associated NR2F2 variants with LAM, and we identified its functional partner NR3C1 as another pleotropic factor. NR3C1 expression was confirmed in LAM lung lesions. Another candidate pleiotropic factor, CNTN2, was found more abundant in plasma of LAM patients than that of healthy women.
Conclusions This study suggests the existence of a common genetic aetiology between LAM and pulmonary function
Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants
No full textGermline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre-mRNA splicing, leading to three major in-frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull-down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene
Fatty acid synthase (FASN) is a tumor-cell-intrinsic metabolic checkpoint restricting T-cell immunity
No full textFatty acid synthase (FASN)-catalyzed endogenous lipogenesis is a hallmark of cancer metabolism. However, whether FASN is an intrinsic mechanism of tumor cell defense against T cell immunity remains unexplored. To test this hypothesis, here we combined bioinformatic analysis of the FASN-related immune cell landscape, real-time assessment of cell-based immunotherapy efficacy in CRISPR/Cas9-based FASN gene knockout (FASN KO) cell models, and mathematical and mechanistic evaluation of FASN-driven immunoresistance. FASN expression negatively correlates with infiltrating immune cells associated with cancer suppression, cytolytic activity signatures, and HLA-I expression. Cancer cells engineered to carry a loss-of-function mutation in FASN exhibit an enhanced cytolytic response and an accelerated extinction kinetics upon interaction with cytokine-activated T cells. Depletion of FASN results in reduced carrying capacity, accompanied by the suppression of mitochondrial OXPHOS and strong downregulation of electron transport chain complexes. Targeted FASN depletion primes cancer cells for mitochondrial apoptosis as it synergizes with BCL-2/BCL-XL-targeting BH3 mimetics to render cancer cells more susceptible to T-cell-mediated killing. FASN depletion prevents adaptive induction of PD-L1 in response to interferon-gamma and reduces constitutive overexpression of PD-L1 by abolishing PD-L1 post-translational palmitoylation. FASN is a novel tumor cell-intrinsic metabolic checkpoint that restricts T cell immunity and may be exploited to improve the efficacy of T cell-based immunotherapy
Tumour DDR1 promotes collagen fibre alignment to instigate immune exclusion
No full textImmune exclusion predicts poor patient outcomes in multiple malignancies, including triple-negative breast cancer (TNBC)1. The extracellular matrix (ECM) contributes to immune exclusion2. However, strategies to reduce ECM abundance are largely ineffective or generate undesired outcomes3,4. Here we show that discoidin domain receptor 1 (DDR1), a collagen receptor with tyrosine kinase activity5, instigates immune exclusion by promoting collagen fibre alignment. Ablation of Ddr1 in tumours promotes the intratumoral penetration of T cells and obliterates tumour growth in mouse models of TNBC. Supporting this finding, in human TNBC the expression of DDR1 negatively correlates with the intratumoral abundance of anti-tumour T cells. The DDR1 extracellular domain (DDR1-ECD), but not its intracellular kinase domain, is required for immune exclusion. Membrane-untethered DDR1-ECD is sufficient to rescue the growth of Ddr1-knockout tumours in immunocompetent hosts. Mechanistically, the binding of DDR1-ECD to collagen enforces aligned collagen fibres and obstructs immune infiltration. ECD-neutralizing antibodies disrupt collagen fibre alignment, mitigate immune exclusion and inhibit tumour growth in immunocompetent hosts. Together, our findings identify a mechanism for immune exclusion and suggest an immunotherapeutic target for increasing immune accessibility through reconfiguration of the tumour ECM
Understanding the functionality of transcript diversity
No full textRecent years have seen a huge increase in the amount of genomic DNA
being sequenced from a wide variety of organisms, giving us an unprecedented
insight into the molecular diversity seen in nature. As a
result a host of methods have been developed, both experimental and
computational, to understand the functional significance of such diversity
and how it relates to organismal and environmental complexity.
In this thesis I use comparative approaches to explore two areas of
molecular biology where there is evidence for large amounts of transcript
diversity. Firstly, I explore the unprecedented view of microbial
sequence diversity offered by metagenomic sequencing projects, using
sequence similarity and adapted genomic context methods to quantify
the amount of functional novelty in these samples. Secondly, I look
at the transcript diversity generated by alternative splicing. I develop
methods to detect and visualise alternative splicing events and apply
these to the detection of conserved alternative splicing events
