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Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov FA, Kondrashov AS, Bazykin GA, Valle L. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. Eur J Hum Genet 2024:10.1038/s41431-024-01598-8. [PMID: 38658779 DOI: 10.1038/s41431-024-01598-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.
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Affiliation(s)
- Maria A Andrianova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Vladimir B Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Beatriz Sánchez-Heras
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Medical Oncology Department, Cancer Genetic Counseling Unit. Elche University Hospital, Elche, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain
| | - José Luis Soto
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Molecular Genetics Unit, Elche University Hospital, Elche, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Emma Borràs
- Molecular Genetics Unit, Consorci Sanitari de Terrassa, Terrassa, Spain
| | - Fyodor A Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Georgii A Bazykin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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2
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Punsoda-Puche P, Barajas A, Mamano-Grande M, Jiménez-Lafuente A, Ochoa S. Relationship between social cognition and premorbid adjustment in psychosis: a systematic review. Schizophrenia (Heidelb) 2024; 10:36. [PMID: 38491028 PMCID: PMC10942991 DOI: 10.1038/s41537-023-00428-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 12/20/2023] [Indexed: 03/18/2024]
Abstract
This systematic review provides a comprehensive overview of the association between premorbid adjustment and social cognition in people with psychotic spectrum disorder. Obtaining evidence of this association will facilitate early detection and intervention before the onset of psychosis. Literature searches were conducted in Scopus, PubMed and PsycINFO. Studies were eligible if they included patients with a psychotic disorder or at a high-risk state; social cognition and premorbid adjustment were measured; and the relationship between premorbid adjustment and social cognition was analysed. The authors independently extracted data from all included articles, and discrepancies were resolved through discussion. Literature searches were conducted in Scopus, PubMed and PsycINFO. Studies were eligible if they included patients with a psychotic disorder or at a high-risk state; social cognition and premorbid adjustment were measured; and the relationship between premorbid adjustment and social cognition was analysed. The authors independently extracted data from all included articles, and discrepancies were resolved through discussion. Of 229 studies identified, 23 met the inclusion criteria. Different methods of assessment were used to measure premorbid adjustment, such as the Premorbid Adjustment Scale or premorbid IQ, among others. Social cognition was assessed as a global measure or by domains using different instruments. A total of 16 articles found a relationship between social cognition (or its domains) and premorbid adjustment: general social cognition (n = 3); Theory of Mind (n = 12); Emotional Recognition and Social Knowledge (n = 1). This review shows evidence of a significant relationship between social cognition and premorbid adjustment, specifically between Theory of Mind and premorbid adjustment. Social cognition deficits may already appear in phases prior to the onset of psychosis, so an early individualized intervention with stimulating experiences in people with poor premorbid adjustment can be relevant for prevention. We recommend some future directions, such as carrying out longitudinal studies with people at high-risk of psychosis, a meta-analysis study, broadening the concept of premorbid adjustment, and a consensual assessment of social cognition and premorbid adjustment variables. PROSPERO registration number: CRD42022333886.
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Affiliation(s)
- P Punsoda-Puche
- Parc Sanitari Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
- Etiopatogènia i tractament dels trastorns mentals greus (MERITT), Institut de Recerca Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
| | - A Barajas
- Department of Clinical and Health Psychology-Serra Húnter Programme, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
- Department of Research, Centre d'Higiene Mental Les Corts, C/ de Numància, 107, 08029, Barcelona, Spain.
| | - M Mamano-Grande
- Parc Sanitari Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
| | - A Jiménez-Lafuente
- Parc Sanitari Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
| | - S Ochoa
- Parc Sanitari Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
- Etiopatogènia i tractament dels trastorns mentals greus (MERITT), Institut de Recerca Sant Joan de Déu, C/ del Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Barcelona, Spain
- Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Spain
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3
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Thambyrajah R, Maqueda M, Neo WH, Imbach K, Guillén Y, Grases D, Fadlullah Z, Gambera S, Matteini F, Wang X, Calero-Nieto FJ, Esteller M, Florian MC, Porta E, Benedito R, Göttgens B, Lacaud G, Espinosa L, Bigas A. Cis inhibition of NOTCH1 through JAGGED1 sustains embryonic hematopoietic stem cell fate. Nat Commun 2024; 15:1604. [PMID: 38383534 PMCID: PMC10882055 DOI: 10.1038/s41467-024-45716-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Hematopoietic stem cells (HSCs) develop from the hemogenic endothelium (HE) in the aorta- gonads-and mesonephros (AGM) region and reside within Intra-aortic hematopoietic clusters (IAHC) along with hematopoietic progenitors (HPC). The signalling mechanisms that distinguish HSCs from HPCs are unknown. Notch signaling is essential for arterial specification, IAHC formation and HSC activity, but current studies on how Notch segregates these different fates are inconsistent. We now demonstrate that Notch activity is highest in a subset of, GFI1 + , HSC-primed HE cells, and is gradually lost with HSC maturation. We uncover that the HSC phenotype is maintained due to increasing levels of NOTCH1 and JAG1 interactions on the surface of the same cell (cis) that renders the NOTCH1 receptor from being activated. Forced activation of the NOTCH1 receptor in IAHC activates a hematopoietic differentiation program. Our results indicate that NOTCH1-JAG1 cis-inhibition preserves the HSC phenotype in the hematopoietic clusters of the embryonic aorta.
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Affiliation(s)
- Roshana Thambyrajah
- Program in Cancer Research. Institut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Barcelona, Spain.
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.
- Centro de Investigacion Biomedica en Red (CIBER), Madrid, Spain.
| | - Maria Maqueda
- Program in Cancer Research. Institut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Wen Hao Neo
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Kathleen Imbach
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Yolanda Guillén
- Program in Cancer Research. Institut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Daniela Grases
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Zaki Fadlullah
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Stefano Gambera
- Molecular Genetics of Angiogenesis Group. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Francesca Matteini
- Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia (P-CMR[C]), Barcelona, Spain
| | - Xiaonan Wang
- Department of Haematology, Wellcome - MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Fernando J Calero-Nieto
- Department of Haematology, Wellcome - MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Maria Carolina Florian
- Centro de Investigacion Biomedica en Red (CIBER), Madrid, Spain
- Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia (P-CMR[C]), Barcelona, Spain
| | - Eduard Porta
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Berthold Göttgens
- Department of Haematology, Wellcome - MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Georges Lacaud
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Lluis Espinosa
- Program in Cancer Research. Institut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER), Madrid, Spain
| | - Anna Bigas
- Program in Cancer Research. Institut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Barcelona, Spain.
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.
- Centro de Investigacion Biomedica en Red (CIBER), Madrid, Spain.
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de Campos-Mata L, Trinité B, Modrego A, Tejedor Vaquero S, Pradenas E, Pons-Grífols A, Rodrigo Melero N, Carlero D, Marfil S, Santiago C, Raïch-Regué D, Bueno-Carrasco MT, Tarrés-Freixas F, Abancó F, Urrea V, Izquierdo-Useros N, Riveira-Muñoz E, Ballana E, Pérez M, Vergara-Alert J, Segalés J, Carolis C, Arranz R, Blanco J, Magri G. A monoclonal antibody targeting a large surface of the receptor binding motif shows pan-neutralizing SARS-CoV-2 activity. Nat Commun 2024; 15:1051. [PMID: 38316751 PMCID: PMC10844294 DOI: 10.1038/s41467-024-45171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Here we report the characterization of 17T2, a SARS-CoV-2 pan-neutralizing human monoclonal antibody isolated from a COVID-19 convalescent individual infected during the first pandemic wave. 17T2 is a class 1 VH1-58/κ3-20 antibody, derived from a receptor binding domain (RBD)-specific IgA+ memory B cell, with a broad neutralizing activity against former and new SARS-CoV-2 variants, including XBB.1.16 and BA.2.86 Omicron subvariants. Consistently, 17T2 demonstrates in vivo prophylactic and therapeutic activity against Omicron BA.1.1 infection in K18-hACE2 mice. Cryo-electron microscopy reconstruction shows that 17T2 binds the BA.1 spike with the RBD in "up" position and blocks the receptor binding motif, as other structurally similar antibodies do, including S2E12. Yet, unlike S2E12, 17T2 retains its neutralizing activity against all variants tested, probably due to a larger RBD contact area. These results highlight the impact of small structural antibody changes on neutralizing performance and identify 17T2 as a potential candidate for future clinical interventions.
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Affiliation(s)
- Leire de Campos-Mata
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Andrea Modrego
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Sonia Tejedor Vaquero
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Edwards Pradenas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Anna Pons-Grífols
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Natalia Rodrigo Melero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Carlero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - César Santiago
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Dàlia Raïch-Regué
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | | | - Ferran Tarrés-Freixas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ferran Abancó
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Mónica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Rocío Arranz
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain.
- CIBERINFEC, ISCIII, Madrid, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain.
| | - Giuliana Magri
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
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Pieren DKJ, Kuguel SG, Rosado J, Robles AG, Rey-Cano J, Mancebo C, Esperalba J, Falcó V, Buzón MJ, Genescà M. Limited induction of polyfunctional lung-resident memory T cells against SARS-CoV-2 by mRNA vaccination compared to infection. Nat Commun 2023; 14:1887. [PMID: 37019909 PMCID: PMC10074357 DOI: 10.1038/s41467-023-37559-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Resident memory T cells (TRM) present at the respiratory tract may be essential to enhance early SARS-CoV-2 viral clearance, thus limiting viral infection and disease. While long-term antigen-specific TRM are detectable beyond 11 months in the lung of convalescent COVID-19 patients, it is unknown if mRNA vaccination encoding for the SARS-CoV-2 S-protein can induce this frontline protection. Here we show that the frequency of CD4+ T cells secreting IFNγ in response to S-peptides is variable but overall similar in the lung of mRNA-vaccinated patients compared to convalescent-infected patients. However, in vaccinated patients, lung responses present less frequently a TRM phenotype compared to convalescent infected individuals and polyfunctional CD107a+ IFNγ+ TRM are virtually absent in vaccinated patients. These data indicate that mRNA vaccination induces specific T cell responses to SARS-CoV-2 in the lung parenchyma, although to a limited extend. It remains to be determined whether these vaccine-induced responses contribute to overall COVID-19 control.
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Affiliation(s)
- Daan K J Pieren
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Sebastián G Kuguel
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Joel Rosado
- Thoracic Surgery and Lung Transplantation Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Alba G Robles
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Joan Rey-Cano
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Cristina Mancebo
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Vicenç Falcó
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - María J Buzón
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Meritxell Genescà
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.
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6
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Díez-Villanueva A, Sanz-Pamplona R, Solé X, Cordero D, Crous-Bou M, Guinó E, Lopez-Doriga A, Berenguer A, Aussó S, Paré-Brunet L, Obón-Santacana M, Moratalla-Navarro F, Salazar R, Sanjuan X, Santos C, Biondo S, Diez-Obrero V, Garcia-Serrano A, Alonso MH, Carreras-Torres R, Closa A, Moreno V. COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients. Sci Data 2022; 9:595. [PMID: 36182938 PMCID: PMC9526730 DOI: 10.1038/s41597-022-01697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.
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Affiliation(s)
- Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Solé
- Molecular Biology CORE, Center for Biomedical Diagnostics, Hospital Clínic de Barcelona, 08036, Barcelona, Spain
- Translational Genomic and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036, Barcelona, Spain
| | - David Cordero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marta Crous-Bou
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO) - Bellvitge Biomedical Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Elisabet Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adriana Lopez-Doriga
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antoni Berenguer
- Rheumatology Department - Parc Taulí Research and Innovation Institute (I3PT), Barcelona, Spain
| | - Susanna Aussó
- TIC Salut Social Foundation. Ministry of Health of Generalitat de Catalunya, Barcelona, Spain
| | | | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Ramon Salazar
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Xavier Sanjuan
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Pathology Service, Bellvitge University Hospital (HUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Digestive Surgery Service, Bellvitge University Hospital (HUB). Hospitalet de Llobregat, Barcelona, Spain
| | - Virginia Diez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Ainhoa Garcia-Serrano
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Maria Henar Alonso
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adria Closa
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
| | - Víctor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain.
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7
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Pujantell M, Badia R, Galván-Femenía I, Garcia-Vidal E, de Cid R, Alcalde C, Tarrats A, Piñol M, Garcia F, Chamorro AM, Revollo B, Videla S, Parés D, Corral J, Tural C, Sirera G, Esté JA, Ballana E, Riveira-Muñoz E. ADAR1 function affects HPV replication and is associated to recurrent human papillomavirus-induced dysplasia in HIV coinfected individuals. Sci Rep 2019; 9:19848. [PMID: 31882741 PMCID: PMC6934649 DOI: 10.1038/s41598-019-56422-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/11/2019] [Indexed: 12/18/2022] Open
Abstract
Infection by human papillomavirus (HPV) alters the microenvironment of keratinocytes as a mechanism to evade the immune system. A-to-I editing by ADAR1 has been reported to regulate innate immunity in response to viral infections. Here, we evaluated the role of ADAR1 in HPV infection in vitro and in vivo. Innate immune activation was characterized in human keratinocyte cell lines constitutively infected or not with HPV. ADAR1 knockdown induced an innate immune response through enhanced expression of RIG-I-like receptors (RLR) signaling cascade, over-production of type-I IFNs and pro-inflammatory cytokines. ADAR1 knockdown enhanced expression of HPV proteins, a process dependent on innate immune function as no A-to-I editing could be identified in HPV transcripts. A genetic association study was performed in a cohort of HPV/HIV infected individuals followed for a median of 6 years (range 0.1-24). We identified the low frequency haplotype AACCAT significantly associated with recurrent HPV dysplasia, suggesting a role of ADAR1 in the outcome of HPV infection in HIV+ individuals. In summary, our results suggest that ADAR1-mediated innate immune activation may influence HPV disease outcome, therefore indicating that modification of innate immune effectors regulated by ADAR1 could be a therapeutic strategy against HPV infection.
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Affiliation(s)
- Maria Pujantell
- AIDS Research Institute-IrsiCaixa, Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Roger Badia
- AIDS Research Institute-IrsiCaixa, Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Iván Galván-Femenía
- Genomes for Life-GCAT Lab Group - Program of Predictive and Personalized Medicine of Cancer (PMPPC), Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Edurne Garcia-Vidal
- AIDS Research Institute-IrsiCaixa, Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT Lab Group - Program of Predictive and Personalized Medicine of Cancer (PMPPC), Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Carmen Alcalde
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Antonio Tarrats
- Department of Gynecology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Marta Piñol
- Department of Surgery, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Francesc Garcia
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Ana M Chamorro
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Boris Revollo
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Sebastian Videla
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - David Parés
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Javier Corral
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Cristina Tural
- Department of Internal Medicine, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Guillem Sirera
- Fundació Lluita contra la Sida, Hospital Germans Trias i Pujol, Badalona, Spain
| | - José A Esté
- AIDS Research Institute-IrsiCaixa, Badalona, Spain.
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.
| | - Ester Ballana
- AIDS Research Institute-IrsiCaixa, Badalona, Spain.
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.
| | - Eva Riveira-Muñoz
- AIDS Research Institute-IrsiCaixa, Badalona, Spain
- Health Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
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8
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Ceausu A, Rodríguez-Gallego E, Peraire J, López-Dupla M, Domingo P, Viladés C, Vidal-Gonzalez J, Peraire M, Perpiñán C, Pacheco YM, Veloso S, Alba V, Vargas M, Castellano AJ, Ruiz-Mateos E, Mallolas J, Vidal F, Rull A. IL-7/IL-7R gene variants impact circulating IL-7/IL-7R homeostasis and ART-associated immune recovery status. Sci Rep 2019; 9:15722. [PMID: 31673011 PMCID: PMC6823538 DOI: 10.1038/s41598-019-52025-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
A relationship between polymorphisms in genes encoding interleukin 7 (IL-7) and its cellular receptor (IL-7R) and antiretroviral therapy (ART)-associated immune recovery in HIV subjects has been previously reported. However, details of this relationship remain unclear, and the association of these polymorphisms with circulating IL-7/IL-7R levels is scarce. Here, we explored whether IL-7/IL-7R axis was associated with quantitative CD4+ T-cell recovery in HIV-infected subjects. IL-7/IL-7R polymorphisms were assessed by genotyping, and multiple inheritance models were used to estimate both, their association with low pre-ART CD4+ T-cell counts and incomplete immune recovery status after 48 weeks of suppressive ART. Integrated data from genetic variants association and soluble plasma IL-7/IL-7R quantification suggest that IL-7/IL-7R genotype expression could alter the homeostatic balance between soluble and membrane-bound receptors. The haplotype analyses indicates that allele combinations impacts pre-ART circulating CD4+ T-cell counts, immune recovery status and the absolute increment of CD4+ T-cell counts. The knowledge about how IL-7/IL-7R axis is related to quantitative CD4+ T-cell recovery and immune recovery status after initiating ART could be useful regarding T-cell reservoirs investigations in HIV subjects.
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Affiliation(s)
- Andra Ceausu
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Esther Rodríguez-Gallego
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Joaquim Peraire
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Miguel López-Dupla
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Pere Domingo
- Infectious Diseases Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Consuelo Viladés
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Judit Vidal-Gonzalez
- Universitat de Barcelona, Barcelona, Spain
- Servei de Medicina Interna-Hepatologia, Hospital Universitari de la Vall d'Hebron, VHIR, Barcelona, Spain
| | - Maria Peraire
- Universitat Rovira i Virgili, Tarragona, Spain
- Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Carles Perpiñán
- Universitat Rovira i Virgili, Tarragona, Spain
- Current address: Atenció Primària ICS, Cap Sant Pere, Reus, Spain
| | - Yolanda María Pacheco
- Laboratory of Immunology, Institute of Biomedicine of Seville, IBiS, UGC Clinical Laboratories, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Sergi Veloso
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Verónica Alba
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Montserrat Vargas
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Alfonso J Castellano
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Ezequiel Ruiz-Mateos
- Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Josep Mallolas
- HIV Unit. Infectious Diseases Service, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Vidal
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain.
| | - Anna Rull
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
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