Genomic and functional approaches to genetic adaptation

The genetic basis of phenotypes that have contributed to the adaptation of species and organisms to new environments is a central question in evolutionary genetics. The recent accumulation of genetic variability data has allowed a genome-wide search for different signatures of positive selection which has led to the discovery of hundreds of putative candidate genes that may have played a role in adaptation. However, such hypothesis-free approaches do not reveal either causal variants or the actual biological mechanisms that have made each adaptation possible. Furthermore, the detection of molecular signatures is limited both by the complex architecture of the genome and by the possible polygenic nature of the selected trait. In this thesis, through different evolutionary and functional approaches, we have disentangled the adaptive role of two non-synonymous variants in two different candidate genes encoding for a lymphocyte receptor and a zinc transporter, respectively. In past human adaptation, they were most likely selected as more effective means to fight pathogens. We have also revealed differences in the action of natural selection between different pathways and different coding and non-coding genomic elements in the chimpanzee lineage by analyzing polymorphisms and divergence data together. Thus, the results of this PhD thesis have contributed to detect new instances of genetic adaptation and provide biological explanation to them.La base genética de los carácteres que han contribuido a la adaptación de los organismos y las especies ha sido siempre una pregunta central en biología evolutiva. Gracias a la acumulación masiva de datos de variabilidad genética, en los últimos años se ha podido detectar en el genoma diferentes señales de selección positiva y también localizar cientos de genes candidatos que han podido tener un papel en la adaptación de las poblaciones a diferentes ambientes. Sin embargo en estos estudios, donde no hay una hipótesis a priori, se desconoce qué variantes dentro de estos genes fueron realmente las que proporcionaron una ventaja selectiva y por qué. Además, la compleja arquitectura del genoma y la naturaleza poligénica de muchos carácteres hace que sea difícil detectar casos más complejos de adaptación. En esta tesis se intenta resolver algunos de estos problemas. En primer lugar, mediante un enfoque evolutivo y funcional, hemos descifrado el rol adaptativo de dos variantes genéticas, una en un receptor linfocitario y la otra en un transportador de zinc, que probablemente fueron seleccionadas por conferir resistencia a patógenos. En segundo lugar, mediante el análisis de datos de polimorfismo y divergencia conjuntamente, también hemos detectado distintos mecanismos de acción de la selección natural en distintos pathways y entre elementos codificantes y elementos no codificantes reguladores en chimpancé

Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection

SARS-CoV-2 infection can cause an inflammatory syndrome (COVID-19) leading, in many cases, to bilateral pneumonia, severe dyspnea, and in ~5% of these, death. DNAmethylation is known to play an important role in the regulation of the immune processes behind COVID-19 progression, however it has not been studied in depth. In this study, we aim to evaluate the implication of DNA methylation in COVID-19 progression by means of a genome-wide DNA methylation analysis combined with DNA genotyping. The results reveal the existence of epigenomic regulation of functional pathways associated with COVID-19 progression andmediated by genetic loci.We find an environmental trait-related signature that discriminatesmild from severe cases and regulates, among other cytokines, IL-6 expression via the transcription factor CEBP. The analyses suggest that an interaction between environmental contribution, genetics, and epigenetics might be playing a role in triggering the cytokine storm described in the most severe cases.Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades of the regional government of AndaluciaEuropean Union through European Regional Development Fund CV20-10150Consejo Superior de Investigaciones cientificas CSIC-COV19-016/202020E155Junta de Castilla y Leon COVID 07.04.467B04.74011.0Consejeria de Salud y Familias of the regional government of Andalucia PECOVID-0072-2020Instituto de Salud Carlos III (ISCIII, Spanish Health Ministry) through the Sara Borrell subprogram CD18/00153Programa Estrategico Instituto de Biologia y Genetica Molecular, IBGM excellence programme CLU-2029-02 CCVC848

Impact of the functional CD5 polymorphism A471V on the response of chronic lymphocytic leukaemia to conventional chemotherapy regimens.

Chronic lymphocytic leukaemia (CLL) represents an abnormal clonal expansion of mature antigen-experienced CD5+ B1a cells (Chiorazzi et al, 2005), which present with a highly heterogeneous clinical course depending on associated chromosomal aberrations, somatic mutations within the immunoglobulin variable heavy chain genes (IGHV), and surface CD38 or intracytoplasmic ZAP-70 expression. Given that key signalling components of the B-cell receptor (BCR) are relevant contributors to the variable clinical behaviour of CLL (Stevenson et al, 2011) we explored the influence of functionally relevant germline CD5 variants on CLL prognosis

Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases

Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjogren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression

Objectives Systemic Lupus Erythematosus is a complex autoimmune disease that leads to significant worsening of quality of life and mortality. Flares appear unpredictably during the disease course and therapies used are often only partially effective. These challenges are mainly due to the molecular heterogeneity of the disease, and in this context, personalized medicine-based approaches offer major promise. With this work we intended to advance in that direction by developing MyPROSLE, an omic-based analytical workflow for measuring the molecular portrait of individual patients to support clinicians in their therapeutic decisions. Methods Immunological gene-modules were used to represent the transcriptome of the patients. A dysregulation score for each gene-module was calculated at the patient level based on averaged z-scores. Almost 6100 Lupus and 750 healthy samples were used to analyze the association among dysregulation scores, clinical manifestations, prognosis, flare and remission events and response to Tabalumab. Machine learning-based classification models were built to predict around 100 different clinical parameters based on personalized dysregulation scores. Results MyPROSLE allows to molecularly summarize patients in 206 gene-modules, clustered into nine main lupus signatures. The combination of these modules revealed highly differentiated pathological mechanisms. We found that the dysregulation of certain gene-modules is strongly associated with specific clinical manifestations, the occurrence of relapses or the presence of long-term remission and drug response. Therefore, MyPROSLE may be used to accurately predict these clinical outcomes. Conclusions MyPROSLE (https://myprosle.genyo.es) allows molecular characterization of individual Lupus patients and it extracts key molecular information to support more precise therapeutic decisions.PID2020-119032RB-I00 supported by MCIN/AEI/10.13039/501100011033FEDER and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR)European Union’s Horizon 2020EFPIAFEDER/Junta de Andalucía-Consejer’a de Transformación Económica, Industria, Conocimiento y Universidades (grants P20_00335 and B-CTS-40-UGR20)‘Consejería de Transformación Económica, Industria, Conocimiento y Universidades’ (CTEICU)European Union through the European Social Fund (ESF) named ‘Andalucía se mueve con Europa”Andalusian ESF Operational Program 2014–2020ISCIII CD18/00149Ministerio de Universidades (Spain’s Government) and the European Union – NextGenerationE

Investigating the epigenetic discrimination of identical twins using buccal swabs, saliva, and cigarette butts in the forensic setting

Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal swabs as typical forensic reference material, and saliva and cigarette butts as commonly encountered forensic trace materials. As an analog to a forensic case, we analyzed one MZ twin pair. Epigenome-wide microarray analysis in reference-type buccal DNA revealed 25 candidate tDMSs with >0.5 twin-to-twin differences. MethyLight quantitative PCR (qPCR) of 22 selected tDMSs in trace-type DNA revealed in saliva DNA that six tDMSs (27.3%) had >0.1 twin-to-twin differences, seven (31.8%) had smaller (<0.1) but robustly detected differences, whereas for nine (40.9%) the differences were in the opposite direction relative to the microarray data; for cigarette butt DNA, results were 50%, 22.7%, and 27.3%, respectively. The discrepancies between reference-type and trace-type DNA outcomes can be explained by cell composition differences, method-to-method variation, and other technical reasons including bisulfite conversion inefficiency. Our study highlights the importance of the DNA source and that careful characterization of biological and technical effects is needed before epigenetic MZ twin differentiation is applicable in forensic casework

Expression Quantitative Trait Locus Analysis in Systemic Sclerosis Identifies New Candidate Genes Associated With Multiple Aspects of Disease Pathology

Objective: To identify the genetic variants that affect gene expression (expression quantitative trait loci [eQTLs]) in systemic sclerosis (SSc) and to investigate their role in the pathogenesis of the disease. Methods: We performed an eQTL analysis using whole-blood sequencing data from 333 SSc patients and 524 controls and integrated them with SSc genome-wide association study (GWAS) data. We integrated our findings from expression modeling, differential expression analysis, and transcription factor binding site enrichment with key clinical features of SSc. Results: We detected 49,123 validated cis-eQTLs from 4,539 SSc-associated single-nucleotide polymorphisms (SNPs) (PGWAS 0.05). As a result, 233 candidates were identified, 134 (58%) of them associated with hallmarks of SSc and 105 (45%) of them differentially expressed in the blood cells, skin, or lung tissue of SSc patients. Transcription factor binding site analysis revealed enriched motifs of 24 transcription factors (5%) among SSc eQTLs, 5 of which were found to be differentially regulated in the blood cells (ELF1 and MGA), skin (KLF4 and ID4), and lungs (TBX4) of SSc patients. Ten candidate genes (4%) can be targeted by approved medications for immune-mediated diseases, of which only 3 have been tested in clinical trials in patients with SSc. Conclusion: The findings of the present study indicate a new layer to the molecular complexity of SSc, contributing to a better understanding of the pathogenesis of the disease