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1. A genome-wide association study of adults with community-acquired pneumonia

Author

Eva Suarez-Pajes, Itahisa Marcelino-Rodriguez, Elisa Hernández Brito, Silvia Gonzalez-Barbuzano, Melody Ramirez-Falcon, Eva Tosco-Herrera, Luis A. Rubio-Rodríguez, María Luisa Briones, Olga Rajas, Luis Borderías, Jose Ferreres, Antoni Payeras, Leonardo Lorente, Javier Aspa, Jose M. Lorenzo Salazar, José Manuel Valencia-Gallardo, Nieves Carbonell, Jorge L. Freixinet, Felipe Rodríguez de Castro, Jordi Solé Violán, Carlos Flores, and Carlos Rodríguez-Gallego

Subjects
GWAS, Pneumonia, Host genetics, Inborn errors of immunity, Diseases of the respiratory system, RC705-779
Abstract

Abstract Background Community-acquired pneumonia (CAP) is associated with high morbidity and hospitalization rate. In infectious diseases, host genetics plays a critical role in susceptibility and immune response, and the immune pathways involved are highly dependent on the microorganism and its route of infection. Here we aimed to identify genetic risk loci for CAP using a case-control genome-wide association study (GWAS). Methods We performed a GWAS on 3,765 Spanish individuals, including 257 adult patients hospitalized with CAP and 3,508 population controls. Pneumococcal CAP was documented in 30% of patients; the remaining 70% were selected among patients with unidentified microbiological etiology. We tested 7,6 million imputed genotypes using logistic regressions. UK Biobank GWAS of bacterial pneumonia were used for results validation. Subsequently, we prioritized genes and likely causal variants based on Bayesian fine mapping and functional evidence. Imputation and association of classical HLA alleles and amino acids were also conducted. Results Six independent sentinel variants reached the genome-wide significance (p

Published
2024
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2. Primary immunodeficiency diseases in lung disease: warning signs, diagnosis and management

Author

Pere Soler-Palacín, Javier de Gracia, Luis Ignacio González-Granado, Carlos Martín, Carlos Rodríguez-Gallego, Silvia Sánchez-Ramón, and Lung ID-Signal Group

Subjects
“Immunoglobulins/deficiency”[mesh], “Antibodies/deficiency”[mesh], “Immunoglobulins/administration and dosage”[mesh], “Respiratory Tract Infections”[mesh], “Immunologic Deficiency Syndromes”[mesh], Diseases of the respiratory system, RC705-779
Abstract

Abstract Background Pulmonary complications are common in primary immunodeficiency diseases (PID) and contribute to morbidity and mortality in these patients. However, their varied presentation and a general lack of awareness of PID in this setting make early diagnosis and treatment difficult. The aim of this study was to define the warning signs of PID in patients with respiratory manifestations, the necessary diagnostic tests, and the therapeutic management of both children and adults. Methods A review of the literature was performed, and 43 PID interdisciplinary specialists were consulted. Results This document identifies the pulmonary and extrapulmonary manifestations that should prompt a suspicion of PID, the immunological and respiratory tests that should be included in the diagnostic process according to the level of care, recommendations regarding the use of immunoglobulin replacement therapy according to the specific immunodeficiency, and the minimum recommended immunological and pulmonary monitoring in these patients. Conclusions This document is the first to combine scientific evidence with the opinion of a broad panel of experts specializing in the treatment of patients with immunodeficiencies. It aims to provide a useful tool for all practitioners who are regularly involved in the management of these patients.

Published
2018
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3. Correction: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Author

Daniela Matuozzo, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, Alexandre Bolze, Matthieu Chaldebas, Baptiste Milisavljevic, Adrian Gervais, Paul Bastard, Takaki Asano, Lucy Bizien, Federica Barzaghi, Hassan Abolhassani, Ahmad Abou Tayoun, Alessandro Aiuti, Ilad Alavi Darazam, Luis M. Allende, Rebeca Alonso-Arias, Andrés Augusto Arias, Gokhan Aytekin, Peter Bergman, Simone Bondesan, Yenan T. Bryceson, Ingrid G. Bustos, Oscar Cabrera-Marante, Sheila Carcel, Paola Carrera, Giorgio Casari, Khalil Chaïbi, Roger Colobran, Antonio Condino-Neto, Laura E. Covill, Ottavia M. Delmonte, Loubna El Zein, Carlos Flores, Peter K. Gregersen, Marta Gut, Filomeen Haerynck, Rabih Halwani, Selda Hancerli, Lennart Hammarström, Nevin Hatipoğlu, Adem Karbuz, Sevgi Keles, Christèle Kyheng, Rafael Leon-Lopez, Jose Luis Franco, Davood Mansouri, Javier Martinez-Picado, Ozge Metin Akcan, Isabelle Migeotte, Pierre-Emmanuel Morange, Guillaume Morelle, Andrea Martin-Nalda, Giuseppe Novelli, Antonio Novelli, Tayfun Ozcelik, Figen Palabiyik, Qiang Pan-Hammarström, Rebeca Pérez de Diego, Laura Planas-Serra, Daniel E. Pleguezuelo, Carolina Prando, Aurora Pujol, Luis Felipe Reyes, Jacques G. Rivière, Carlos Rodriguez-Gallego, Julian Rojas, Patrizia Rovere-Querini, Agatha Schlüter, Mohammad Shahrooei, Ali Sobh, Pere Soler-Palacin, Yacine Tandjaoui-Lambiotte, Imran Tipu, Cristina Tresoldi, Jesus Troya, Diederik van de Beek, Mayana Zatz, Pawel Zawadzki, Saleh Zaid Al-Muhsen, Mohammed Faraj Alosaimi, Fahad M. Alsohime, Hagit Baris-Feldman, Manish J. Butte, Stefan N. Constantinescu, Megan A. Cooper, Clifton L. Dalgard, Jacques Fellay, James R. Heath, Yu-Lung Lau, Richard P. Lifton, Tom Maniatis, Trine H. Mogensen, Horst von Bernuth, Alban Lermine, Michel Vidaud, Anne Boland, Jean-François Deleuze, Robert Nussbaum, Amanda Kahn-Kirby, France Mentre, Sarah Tubiana, Guy Gorochov, Florence Tubach, Pierre Hausfater, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Isabelle Meyts, Shen-Ying Zhang, Anne Puel, Luigi D. Notarangelo, Stephanie Boisson-Dupuis, Helen C. Su, Bertrand Boisson, Emmanuelle Jouanguy, Jean-Laurent Casanova, Qian Zhang, Laurent Abel, and Aurélie Cobat

Subjects
Medicine, Genetics, QH426-470
Published
2024
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4. Primary immunodeficiency diseases in lung disease: warning signs, diagnosis and management

Author

Luis Ignacio Gonzalez-Granado, Silvia SÁNCHEZ-RAMÓN, Alexandru Vlagea, Javier De Gracia, MENDEZ ECHEVARRIA ANA, Jaime Pons de Ves, Mónica Martínez Gallo, and Carlos Rodríguez-Gallego

Subjects
0301 basic medicine, Lung Diseases, medicine.medical_specialty, síndromes de inmunodeficiencia, “Immunoglobulins/deficiency”[mesh], Respiratory Tract Infections[mesh], humanos, Immunoglobulins, Immunologic Deficiency Syndromes[mesh], Antibodies, 03 medical and health sciences, testimonio experto, Medicine, Humans, In patient, deficiency[mesh], Intensive care medicine, Expert Testimony, Immunodeficiency, lcsh:RC705-779, business.industry, Research, Immunologic Deficiency Syndromes, Disease Management, Diagnostic test, “Immunologic Deficiency Syndromes”[mesh], administration and dosage[mesh], “Respiratory Tract Infections”[mesh], lcsh:Diseases of the respiratory system, enfermedades pulmonares, medicine.disease, “Immunoglobulins/administration and dosage”[mesh], 030104 developmental biology, Warning signs, Lung disease, “Antibodies/deficiency”[mesh], Primary immunodeficiency, Level of care, business
Abstract

BackgroundPulmonary complications are common in primary immunodeficiency diseases (PID) and contribute to morbidity and mortality in these patients. However, their varied presentation and a general lack of awareness of PID in this setting make early diagnosis and treatment difficult. The aim of this study was to define the warning signs of PID in patients with respiratory manifestations, the necessary diagnostic tests, and the therapeutic management of both children and adults.MethodsA review of the literature was performed, and 43 PID interdisciplinary specialists were consulted.ResultsThis document identifies the pulmonary and extrapulmonary manifestations that should prompt a suspicion of PID, the immunological and respiratory tests that should be included in the diagnostic process according to the level of care, recommendations regarding the use of immunoglobulin replacement therapy according to the specific immunodeficiency, and the minimum recommended immunological and pulmonary monitoring in these patients.ConclusionsThis document is the first to combine scientific evidence with the opinion of a broad panel of experts specializing in the treatment of patients with immunodeficiencies. It aims to provide a useful tool for all practitioners who are regularly involved in the management of these patients., This study was funded by CSL Behring.

Published
2018

5. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Author

Daniela Matuozzo, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, Alexandre Bolze, Matthieu Chaldebas, Baptiste Milisavljevic, Adrian Gervais, Paul Bastard, Takaki Asano, Lucy Bizien, Federica Barzaghi, Hassan Abolhassani, Ahmad Abou Tayoun, Alessandro Aiuti, Ilad Alavi Darazam, Luis M. Allende, Rebeca Alonso-Arias, Andrés Augusto Arias, Gokhan Aytekin, Peter Bergman, Simone Bondesan, Yenan T. Bryceson, Ingrid G. Bustos, Oscar Cabrera-Marante, Sheila Carcel, Paola Carrera, Giorgio Casari, Khalil Chaïbi, Roger Colobran, Antonio Condino-Neto, Laura E. Covill, Ottavia M. Delmonte, Loubna El Zein, Carlos Flores, Peter K. Gregersen, Marta Gut, Filomeen Haerynck, Rabih Halwani, Selda Hancerli, Lennart Hammarström, Nevin Hatipoğlu, Adem Karbuz, Sevgi Keles, Christèle Kyheng, Rafael Leon-Lopez, Jose Luis Franco, Davood Mansouri, Javier Martinez-Picado, Ozge Metin Akcan, Isabelle Migeotte, Pierre-Emmanuel Morange, Guillaume Morelle, Andrea Martin-Nalda, Giuseppe Novelli, Antonio Novelli, Tayfun Ozcelik, Figen Palabiyik, Qiang Pan-Hammarström, Rebeca Pérez de Diego, Laura Planas-Serra, Daniel E. Pleguezuelo, Carolina Prando, Aurora Pujol, Luis Felipe Reyes, Jacques G. Rivière, Carlos Rodriguez-Gallego, Julian Rojas, Patrizia Rovere-Querini, Agatha Schlüter, Mohammad Shahrooei, Ali Sobh, Pere Soler-Palacin, Yacine Tandjaoui-Lambiotte, Imran Tipu, Cristina Tresoldi, Jesus Troya, Diederik van de Beek, Mayana Zatz, Pawel Zawadzki, Saleh Zaid Al-Muhsen, Mohammed Faraj Alosaimi, Fahad M. Alsohime, Hagit Baris-Feldman, Manish J. Butte, Stefan N. Constantinescu, Megan A. Cooper, Clifton L. Dalgard, Jacques Fellay, James R. Heath, Yu-Lung Lau, Richard P. Lifton, Tom Maniatis, Trine H. Mogensen, Horst von Bernuth, Alban Lermine, Michel Vidaud, Anne Boland, Jean-François Deleuze, Robert Nussbaum, Amanda Kahn-Kirby, France Mentre, Sarah Tubiana, Guy Gorochov, Florence Tubach, Pierre Hausfater, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID-STORM Clinicians, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Isabelle Meyts, Shen-Ying Zhang, Anne Puel, Luigi D. Notarangelo, Stephanie Boisson-Dupuis, Helen C. Su, Bertrand Boisson, Emmanuelle Jouanguy, Jean-Laurent Casanova, Qian Zhang, Laurent Abel, and Aurélie Cobat

Subjects
Rare variants, COVID-19, Immunity, Type I interferon, Medicine, Genetics, QH426-470
Abstract

Abstract Background We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

Published
2023
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6. Radiation induced apoptosis and initial DNA damage are inversely related in locally advanced breast cancer patients

Author

Elisa Bordón, Marta Lloret, María Isabel Núñez, Pedro C. Lara, Carlos Rodríguez-Gallego, Beatriz Pinar, Mariano Ruiz de Almodóvar, Luis Alberto Henríquez-Hernández, [Pinar B, Lara PC, Lloret M] Radiation Oncology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Spain. [Pinar B, Henríquez-Hernández LA, Bordon E, Rodriguez-Gallego C, Lloret M] Instituto Canario de Investigación del Cáncer (ICIC), Spain. [Henríquez-Hernández LA] Clinical Sciences Department, Universidad de Las Palmas de Gran Canaria, Spain. [Rodriguez-Gallego C] Immunology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Spain. [Nuñes, MI, and Ruiz de Almodovar, M] Radiology Department, Hospital Universitario San Cecilio, Universidad de Granada, Spain.

Subjects
Pathology, medicine.medical_treatment, Apoptosis, Cell Separation, Radiation Tolerance, Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], chemistry.chemical_compound, DNA Breaks, Double-Stranded, Citometría de Flujo, medicine.diagnostic_test, Neoplasias de la Mama, Femenino, Roturas del ADN de Doble Cadena, Flow Cytometry, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Humanos, 320101 Oncología, Oncology, Radiology Nuclear Medicine and imaging, Toxicity, Female, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Neoplasm Staging [Medical Subject Headings], Phenomena and Processes::Physical Phenomena::Electromagnetic Phenomena::Radiation::Radiation Tolerance [Medical Subject Headings], lcsh:Medical physics. Medical radiology. Nuclear medicine, medicine.medical_specialty, DNA damage, lcsh:R895-920, Locally advanced, Breast Neoplasms, lcsh:RC254-282, Flow cytometry, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Clinical Laboratory Techniques::Cytological Techniques::Cell Separation [Medical Subject Headings], Breast cancer, Phenomena and Processes::Genetic Phenomena::Genetic Processes::DNA Damage::DNA Breaks::DNA Breaks, Double-Stranded [Medical Subject Headings], medicine, Humans, Radiology, Nuclear Medicine and imaging, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Chemistry Techniques, Analytical::Photometry::Luminescent Measurements::Fluorometry::Cytophotometry::Flow Cytometry [Medical Subject Headings], Separación Celular, Diseases::Neoplasms::Neoplasms by Site::Breast Neoplasms [Medical Subject Headings], Neoplasm Staging, Tolerancia a Radiación, Anatomy::Urogenital System::Genitalia::Genitalia, Female [Medical Subject Headings], business.industry, Research, medicine.disease, Estadificación de Neoplasias, Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Death::Apoptosis [Medical Subject Headings], Radiation therapy, chemistry, Cancer research, business, DNA
Abstract

Background. DNA-damage assays, quantifying the initial number of DNA double-strand breaks induced by radiation, have been proposed as a predictive test for radiation-induced toxicity. Determination of radiation-induced apoptosis in peripheral blood lymphocytes by flow cytometry analysis has also been proposed as an approach for predicting normal tissue responses following radiotherapy. The aim of the present study was to explore the association between initial DNA damage, estimated by the number of double-strand breaks induced by a given radiation dose, and the radio-induced apoptosis rates observed. Methods. Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp). Radio-induced apoptosis at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide. Results. Radiation-induced apoptosis increased in order to radiation dose and data fitted to a semi logarithmic mathematical model. A positive correlation was found among radio-induced apoptosis values at different radiation doses: 1, 2 and 8 Gy (p < 0.0001 in all cases). Mean DSB/Gy/DNA unit obtained was 1.70 ± 0.83 (range 0.63-4.08; median, 1.46). A statistically significant inverse correlation was found between initial damage to DNA and radio-induced apoptosis at 1 Gy (p = 0.034). A trend toward 2 Gy (p = 0.057) and 8 Gy (p = 0.067) was observed after 24 hours of incubation. Conclusions. An inverse association was observed for the first time between these variables, both considered as predictive factors to radiation toxicity. Yes Daños en el ADN-ensayos, cuantificando el número inicial de ADN de doble cadena se rompe inducida por la radiación, se han propuesto como una prueba predictiva para la radiación inducida por la toxicidad. Determinación de la apoptosis inducida por radiación en linfocitos de sangre periférica mediante el análisis de citometría de flujo también ha sido propuesta como un método para predecir las respuestas normales del tejido después de la radioterapia. El objetivo del presente estudio fue explorar la asociación entre el daño del ADN inicial, estimada por el número de doble filamento se rompe inducida por una dosis de radiación que se administra, y se observaron las tasas de la apoptosis inducida por la radio. MÉTODOS: Linfocitos de sangre periférica fueron tomadas de 26 pacientes consecutivos con carcinoma de mama localmente avanzado. Radiosensibilidad de los linfocitos se cuantificó como el número inicial de ADN de doble cadena se rompe inducida por Gy y la unidad de ADN por (200 Mbps). Radio inducida por la apoptosis en Gy 1, 2 y 8 se midió por citometría de flujo utilizando anexina V / ioduro de propidio. RESULTADOS: La radiación inducida por aumento de la apoptosis con el fin de dosis de radiación y de datos instalados en un modelo matemático semi logarítmica. Una correlación positiva se encontró entre los valores de la apoptosis inducida por la radio a diferentes dosis de radiación: 1, 2 y 8 Gy (p

Published
2010

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