48 research outputs found

    "Time sweet time": circadian characterization of galectin-1 null mice

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    International audienceABSTRACT: BACKGROUND: Recent evidence suggests a two-way interaction between the immune and circadian systems. Circadian control of immune factors, as well as the effect of immunological variables on circadian rhythms, might be key elements in both physiological and pathological responses to the environment. Among these relevant factors, galectin-1 is a member of a family of evolutionarily-conserved glycan-binding proteins with both extracellular and intracellular effects, playing important roles in immune cell processes and inflammatory responses. Many of these actions have been studied through the use of mice with a null mutation in the galectin-1 (Lgals1) gene. To further analyze the role of endogenous galectin-1 in vivo, we aimed to characterize the circadian behavior of galectin-1 null (Lgals1-/-) mice. METHODS: We analyzed wheel-running activity in light-dark conditions, constant darkness, phase responses to light pulses (LP) at circadian time 15, and reentrainment to 6 hour shifts in light-dark schedule in wild-type (WT) and Lgals1-/- mice. RESULTS: We found significant differences in free-running period, which was longer in mutant than in WT mice (24.02 vs 23.57 h, p<0.005), phase delays in response to LP (2.92 vs 1.90 circadian h, p<0.05), and also in alpha (14.88 vs. 12.35 circadian h, p<0.05). CONCLUSIONS: Given the effect of a null mutation on circadian period and entrainment, we indicate that galectin-1 could be involved in the regulation of murine circadian rhythmicity. This is the first study implicating galectin-1 in the mammalian circadian system

    Apoptosis resistance in HIV-1 persistently-infected cells is independent of active viral replication and involves modulation of the apoptotic mitochondrial pathway

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    <p>Abstract</p> <p>Background</p> <p>HIV triggers the decline of CD4<sup>+ </sup>T cells and leads to progressive dysfunction of cell-mediated immunity. Although an increased susceptibility to cell death occurs during the acute phase of HIV infection, persistently-infected macrophages and quiescent T-cells seem to be resistant to cell death, representing a potential reservoir for virus production.</p> <p>Results</p> <p>Lymphoid (H9/HTLVIII<sub>B </sub>and J1.1) and pro-monocytic (U1) HIV-1 persistently-infected cell lines were treated with hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and staurosporine (STS) for 24 h, and susceptibility to apoptosis was evaluated and compared with uninfected counterparts (H9, Jurkat and U937 respectively). When exposed to different pro-apoptotic stimuli, all persistently-infected cell lines showed a dramatic reduction in the frequency of apoptotic cells in comparison with uninfected cells. This effect was independent of the magnitude of viral replication, since the induction of viral production in lymphoid or pro-monocytic cells by exposure to TNF-Îą or PMA did not significantly change their susceptibility to H<sub>2</sub>O<sub>2</sub>- or STS-induced cell death. A mechanistic analysis revealed significant diferences in mitochondrial membrane potential (MMP) and caspase-3 activation between uninfected and persistently-infected cells. In addition, Western blot assays showed a dramatic reduction of the levels of pro-apototic Bax in mitochondria of persistently-infected cells treated with H<sub>2</sub>O<sub>2 </sub>or STS, but not in uninfected cells.</p> <p>Conclusion</p> <p>This study represents the first evidence showing that resistance to apoptosis in persistently-infected lymphoid and monocytic cells is independent of active viral production and involves modulation of the mitochondrial pathway. Understanding this effect is critical to specifically target the persistence of viral reservoirs, and provide insights for future therapeutic strategies in order to promote complete viral eradication.</p

    Galectin-1 Deactivates Classically Activated Microglia and Protects from Inflammation-Induced Neurodegeneration

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    SummaryInflammation-mediated neurodegeneration occurs in the acute and the chronic phases of multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). Classically activated (M1) microglia are key players mediating this process. Here, we identified Galectin-1 (Gal1), an endogenous glycan-binding protein, as a pivotal regulator of M1 microglial activation that targets the activation of p38MAPK-, CREB-, and NF-κB-dependent signaling pathways and hierarchically suppresses downstream proinflammatory mediators, such as iNOS, TNF, and CCL2. Gal1 bound to core 2 O-glycans on CD45, favoring retention of this glycoprotein on the microglial cell surface and augmenting its phosphatase activity and inhibitory function. Gal1 was highly expressed in the acute phase of EAE, and its targeted deletion resulted in pronounced inflammation-induced neurodegeneration. Adoptive transfer of Gal1-secreting astrocytes or administration of recombinant Gal1 suppressed EAE through mechanisms involving microglial deactivation. Thus, Gal1-glycan interactions are essential in tempering microglial activation, brain inflammation, and neurodegeneration, with critical therapeutic implications for MS

    Glycosylation-dependent circuits synchronize the pro-angiogenic and immunoregulatory functions of myeloid-derived suppressor cells in cancer

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    Myeloid-derived suppressor cells (MDSCs) favor tumorprogression and therapy resistance by reprogramming antitumor immunity and promoting angiogenesis. To elucidatethe mechanisms that synchronize these functions, we investigated the role of glycosylation-dependent, galectin-1(Gal1)-driven circuits in coupling immunoregulatory andpro-angiogenic activities of MDSCs. Flow cytometry andHPLC-HILIC/WAX revealed an activation-dependent glycanprofile in monocytic and polymorphonuclear MDSCs (p=0.03)that controlled Gal1 binding and was more prominent in tumor microenvironments. Exposure to Gal1 led to concomitant activation of immunosuppression and angiogenesisprograms in bone marrow derived MDSCs. Flow cytometryof Gal1-conditioned MDSCs showed higher expression ofimmune checkpoint molecules, including programmed deathligand-1 (PD-L1) (p=0.005) and indoleamine 2,3-dioxygenase (IDO) (p=0.037) and greater production of reactive oxygen species (ROS) and nitric oxide (NO) (p=0.02). In vitro,Gal1-conditioned MDSCs showed greater T-cell suppressive capacity (p=0.03) and higher IL-10 (p=0.04) and IL-27(p=0.003) secretion. These effects were accompanied by enhanced endothelial cell migration, tube formation, 3D-sprouting and vascularization (p<0.05). In vivo, Gal1-conditionedMDSCs accelerated tumor growth (p=0.001) and fosteredimmune evasion and vascularization programs in Gal1-deficient colorectal tumors. Mechanistically, mass spectrometry,immunoblot and blocking assays identified the CD18/CD11b/CD177 complex as a bona fide Gal1 receptor and STAT3 asa key signaling pathway coupling these functions. Accordingly, a combined algorithm that integrates Gal1 expressionand MDSC phenotype, showed critical prognostic value bydelineating the immune landscape and clinical outcome ofhuman cancers. Thus, glycosylation-dependent Gal1-drivencircuits favor tumor progression by coupling immunoregulatory and pro-angiogenic programs of MDSCs via CD18- andSTAT3-dependent pathways.Fil: Blidner, Ada Gabriela. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Bach, Camila Agustina. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: GarcĂ­a, Pablo Alfredo. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Centro CientĂ­fico TecnolĂłgico Conicet - Mendoza. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias MĂŠdicas. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Cagnoni, Alejandro. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Manselle Cocco, Montana Nicolle. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Pinto, NicolĂĄs Alejandro. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Torres, NicolĂĄs. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Gatto, Sabrina Gisela. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Sarrias, Luciana. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de QuĂ­mica y FĂ­sico-QuĂ­mica BiolĂłgicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y BioquĂ­mica. Instituto de QuĂ­mica y FĂ­sico-QuĂ­mica BiolĂłgicas; ArgentinaFil: Giribaldi, MarĂ­a Laura. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Merlo, JoaquĂ­n Pedro. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: PĂŠrez SĂĄez, Juan Manuel. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Salatino, Mariana. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Troncoso, MarĂ­a Fernanda. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Oficina de CoordinaciĂłn Administrativa Houssay. Instituto de QuĂ­mica y FĂ­sico-QuĂ­mica BiolĂłgicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y BioquĂ­mica. Instituto de QuĂ­mica y FĂ­sico-QuĂ­mica BiolĂłgicas; ArgentinaFil: MariĂąo, Karina Valeria. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Abba, MartĂ­n Carlos. Universidad Nacional de La Plata; Argentina. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas; ArgentinaFil: Croci, Diego O.. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Centro CientĂ­fico TecnolĂłgico Conicet - Mendoza. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias MĂŠdicas. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Rabinovich, Gabriel AdriĂĄn. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaLXVI Annual Meeting of Sociedad Argentina de InvestigaciĂłn ClĂ­nica; LXIX Annual Meeting of Sociedad Argentina de InmunologĂ­a; LIII Annual Meeting of AsociaciĂłn Argentina de FarmacologĂ­a Experimental and XI Annual Meeting of AsociaciĂłn Argentina de NanomedicinasArgentinaSociedad Argentina de InvestigaciĂłn ClĂ­nicaSociedad Argentina de InmunologĂ­aAsociaciĂłn Argentina de FarmacologĂ­a ExperimentalAsociaciĂłn Argentina de Nanomedicin

    Galectin-1 fosters an immunosuppressive microenvironment in colorectal cancer by reprogramming CD8⁺ regulatory T cells

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    Colorectal cancer (CRC) represents the third most common malignancy and the second leading cause of cancer-related deaths worldwide. Although immunotherapy has taken center stage in mainstream oncology, it has shown limited clinical efficacy in CRC, generating an urgent need for discovery of new biomarkers and potential therapeutic targets. Galectin-1 (Gal-1), an endogenous glycan-binding protein, induces tolerogenic programs and contributes to tumor cell evasion of immune responses. Here, we investigated the relevance of Gal-1 in CRC and explored its modulatory activity within the CD8⁺ regulatory T cell (Treg) compartment. Mice lacking Gal-1 (Lgals1 -/- ) developed a lower number of tumors and showed a decreased frequency of a particular population of CD8⁺CD122⁺PD-1⁺ Tregs in the azoxymethane-dextran sodium sulfate model of colitis-associated CRC. Moreover, silencing of tumor-derived Gal-1 in the syngeneic CT26 CRC model resulted in reduced number and attenuated immunosuppressive capacity of CD8⁺CD122⁺PD-1⁺ Tregs, leading to slower tumor growth. Moreover, stromal Gal-1 also influenced the fitness of CD8⁺ Tregs, highlighting the contribution of both tumor and stromal-derived Gal-1 to this immunoregulatory effect. Finally, bioinformatic analysis of a colorectal adenocarcinoma from The Cancer Genome Atlas dataset revealed a particular signature characterized by high CD8⁺ Treg score and elevated Gal-1 expression, which delineates poor prognosis in human CRC. Our findings identify CD8⁺CD122⁺PD-1⁺ Tregs as a target of the immunoregulatory activity of Gal-1, suggesting a potential immunotherapeutic strategy for the treatment of CRC.Centro de Investigaciones Inmunológicas Båsicas y Aplicada

    Glioblastomas exploit truncated O-linked glycans for local and distant immune modulation via the macrophage galactose-type lectin

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    Glioblastoma is the most aggressive brain malignancy, for which immunotherapy has failed to prolong survival. Glioblastoma-associated immune infiltrates are dominated by tumor-associated macrophages and microglia (TAMs), which are key mediators of immune suppression and resistance to immunotherapy. We and others demonstrated aberrant expression of glycans in different cancer types. These tumor-associated glycans trigger inhibitory signaling in TAMs through glycan-binding receptors. We investigated the glioblastoma glycocalyx as a tumor-intrinsic immune suppressor. We detected increased expression of both tumor-associated truncated O-linked glycans and their receptor, macrophage galactose-type lectin (MGL), on CD163+ TAMs in glioblastoma patient-derived tumor tissues. In an immunocompetent orthotopic glioma mouse model overexpressing truncated O-linked glycans (MGL ligands), high-dimensional mass cytometry revealed a wide heterogeneity of infiltrating myeloid cells with increased infiltration of PD-L1+ TAMs as well as distant alterations in the bone marrow (BM). Our results demonstrate that glioblastomas exploit cell surface O-linked glycans for local and distant immune modulation.Fil: Dusoswa, Sophie A.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Verhoeff, Jan. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Abels, Erik. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Mendez Huergo, Santiago Patricio. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: Croci Russo, Diego Omar. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Centro CientĂ­fico TecnolĂłgico Conicet - Mendoza. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias MĂŠdicas. Instituto de HistologĂ­a y EmbriologĂ­a de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Kuijper, Lisan H.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: de Miguel, Elena. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Wouters, Valerie M. C. J.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Best, Myron G.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Rodriguez, Ernesto. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Cornelissen, Lenneke A.M.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: van Vliet, Sandra J.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Wesseling, Pieter. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Breakefield, Xandra O.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Noske, David P.. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: WĂźrdinger, Thomas. Harvard Medical School; Estados UnidosFil: Broekman, Marike L.D.. Harvard Medical School; Estados UnidosFil: Rabinovich, Gabriel AdriĂĄn. Consejo Nacional de Investigaciones CientĂ­ficas y TĂŠcnicas. Instituto de BiologĂ­a y Medicina Experimental. FundaciĂłn de Instituto de BiologĂ­a y Medicina Experimental. Instituto de BiologĂ­a y Medicina Experimental; ArgentinaFil: van Kooyk, Yvette. Vrije Universiteit Amsterdam; PaĂ­ses BajosFil: Garcia Vallejo, Juan J.. Vrije Universiteit Amsterdam; PaĂ­ses Bajo

    Circulating galectin-1 delineates response to bevacizumab in melanoma patients and reprograms endothelial cell biology

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    Blockade of vascular endothelial growth factor (VEGF) signaling with bevacizumab, a humanized anti-VEGF monoclonal antibody (mAb), or with receptor tyrosine kinase inhibitors, has improved progression-free survival and, in some indications, overall survival across several types of cancers by interrupting tumor angiogenesis. However, the clinical benefit conferred by these therapies is variable, and tumors from treated patients eventually reinitiate growth. Previously we demonstrated, in mouse tumor models, that galectin-1 (Gal1), an endogenous glycan-binding protein, preserves angiogenesis in anti-VEGF–resistant tumors by co-opting the VEGF receptor (VEGFR)2 signaling pathway in the absence of VEGF. However, the relevance of these findings in clinical settings is uncertain. Here, we explored, in a cohort of melanoma patients from AVAST-M, a multicenter, open-label, randomized controlled phase 3 trial of adjuvant bevacizumab versus standard surveillance, the role of circulating plasma Gal1 as part of a compensatory mechanism that orchestrates endothelial cell programs in bevacizumab-treated melanoma patients. We found that increasing Gal1 levels over time in patients in the bevacizumab arm, but not in the observation arm, significantly increased their risks of recurrence and death. Remarkably, plasma Gal1 was functionally active as it was able to reprogram endothelial cell biology, promoting migration, tubulogenesis, and VEGFR2 phosphorylation. These effects were prevented by blockade of Gal1 using a newly developed fully human anti-Gal1 neutralizing mAb. Thus, using samples from a large-scale clinical trial from stage II and III melanoma patients, we validated the clinical relevance of Gal1 as a potential mechanism of resistance to bevacizumab treatment

    Fucans, but Not Fucomannoglucuronans, Determine the Biological Activities of Sulfated Polysaccharides from Laminaria saccharina Brown Seaweed

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    Sulfated polysaccharides from Laminaria saccharina (new name: Saccharina latissima) brown seaweed show promising activity for the treatment of inflammation, thrombosis, and cancer; yet the molecular mechanisms underlying these properties remain poorly understood. The aim of this work was to characterize, using in vitro and in vivo strategies, the anti-inflammatory, anti-coagulant, anti-angiogenic, and anti-tumor activities of two main sulfated polysaccharide fractions obtained from L. saccharina: a) L.s.-1.0 fraction mainly consisting of O-sulfated mannoglucuronofucans and b) L.s.-1.25 fraction mainly composed of sulfated fucans. Both fractions inhibited leukocyte recruitment in a model of inflammation in rats, although L.s.-1.25 appeared to be more active than L.s.-1.0. Also, these fractions inhibited neutrophil adhesion to platelets under flow. Only fraction L.s.-1.25, but not L.s.-1.0, displayed anticoagulant activity as measured by the activated partial thromboplastin time. Investigation of these fractions in angiogenesis settings revealed that only L.s.-1.25 strongly inhibited fetal bovine serum (FBS) induced in vitro tubulogenesis. This effect correlated with a reduction in plasminogen activator inhibitor-1 (PAI-1) levels in L.s.-1.25-treated endothelial cells. Furthermore, only parent sulfated polysaccharides from L. saccharina (L.s.-P) and its fraction L.s.-1.25 were powerful inhibitors of basic fibroblast growth factor (bFGF) induced pathways. Consistently, the L.s.-1.25 fraction as well as L.s.-P successfully interfered with fibroblast binding to human bFGF. The incorporation of L.s.-P or L.s.-1.25, but not L.s.-1.0 into Matrigel plugs containing melanoma cells induced a significant reduction in hemoglobin content as well in the frequency of tumor-associated blood vessels. Moreover, i.p. administrations of L.s.-1.25, as well as L.s.-P, but not L.s.-1.0, resulted in a significant reduction of tumor growth when inoculated into syngeneic mice. Finally, L.s.-1.25 markedly inhibited breast cancer cell adhesion to human platelet-coated surfaces. Thus, sulfated fucans are mainly responsible for the anti-inflammatory, anticoagulant, antiangiogenic, and antitumor activities of sulfated polysaccharides from L. saccharina brown seaweed

    The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males

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    The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired macroautophagy/autophagy and reduced TNF/TNFι production was demonstrated in HEK293 cells transfected with TLR3L412F-encoding plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (p = 0.038). An increased frequency of autoimmune disorders such as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways. Abbreviations: AP: autophagosome; AUC: area under the curve; BafA1: bafilomycin A1; COVID-19: coronavirus disease-2019; HCQ: hydroxychloroquine; RAP: rapamycin; ROC: receiver operating characteristic; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TLR: toll like receptor; TNF/TNF-ι: tumor necrosis factor

    Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

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    The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. Š 2021, The Author(s)
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