Stability and Diversity of T Cell Receptor Repertoire Usage during Lymphocytic Choriomeningitis Virus Infection of Mice

Numerous studies have examined T cell receptor (TCR) usage of selected virus-specific T cell clones, yet little information is available regarding the stability and diversity of TCR repertoire usage during viral infections. Here, we analyzed the Vβ8.1 TCR repertoire directly ex vivo by complementarity-determining region 3 (CDR3) length spectratyping throughout the acute lymphocytic choriomeningitis virus (LCMV) infection, into memory, and under conditions of T cell clonal exhaustion. The Vβ8 population represented 30–35% of the LCMV-induced CD8+ T cells and included T cells recognizing several LCMV-encoded peptides, allowing for a comprehensive study of a multiclonal T cell response against a complex antigen. Genetically identical mice generated remarkably different T cell responses, as reflected by different spectratypes and different TCR sequences in same sized spectratype bands; however, a conserved CDR3 motif was found within some same sized bands. This indicated that meaningful studies on the evolution of the T cell repertoire required longitudinal studies within individual mice. Such longitudinal studies with peripheral blood lymphocyte samples showed that (a) the virus-induced T cell repertoire changes little during the apoptosis period after clearance of the viral antigens; (b) the LCMV infection dramatically skews the host T cell repertoire in the memory state; and (c) continuous selection of the T cell repertoire occurs under conditions of persistent infections

The pathological effects of CCR2+ inflammatory monocytes are amplified by an IFNAR1-triggered chemokine feedback loop in highly pathogenic influenza infection

Background: Highly pathogenic influenza viruses cause high levels of morbidity, including excessive infiltration of leukocytes into the lungs, high viral loads and a cytokine storm. However, the details of how these pathological features unfold in severe influenza infections remain unclear. Accumulation of Gr1 + CD11b + myeloid cells has been observed in highly pathogenic influenza infections but it is not clear how and why they accumulate in the severely inflamed lung. In this study, we selected this cell population as a target to investigate the extreme inflammatory response during severe influenza infection. Results: We established H1N1 IAV-infected mouse models using three viruses of varying pathogenicity and noted the accumulation of a defined Gr1 + CD11b + myeloid population correlating with the pathogenicity. Herein, we reported that CCR2+ inflammatory monocytes are the major cell compartments in this population. Of note, impaired clearance of the high pathogenicity virus prolonged IFN expression, leading to CCR2+ inflammatory monocytes amplifying their own recruitment via an interferon-alpha/beta receptor 1 (IFNAR1)-triggered chemokine loop. Blockage of IFNAR1-triggered signaling or inhibition of viral replication by Oseltamivir significantly suppresses the expression of CCR2 ligands and reduced the influx of CCR2+ inflammatory monocytes. Furthermore, trafficking of CCR2+ inflammatory monocytes from the bone marrow to the lung was evidenced by a CCR2-dependent chemotaxis. Importantly, leukocyte infiltration, cytokine storm and expression of iNOS were significantly reduced in CCR2-/- mice lacking infiltrating CCR2+ inflammatory monocytes, enhancing the survival of the infected mice. Conclusions: Our results indicated that uncontrolled viral replication leads to excessive production of inflammatory innate immune responses by accumulating CCR2+ inflammatory monocytes, which contribute to the fatal outcomes of high pathogenicity virus infections

Embracing monogenic Parkinson's disease: the MJFF Global Genetic PD Cohort

© 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Background: As gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a small fraction of the estimated number of subjects with monogenic PD worldwide are currently represented in the literature and availability of clinical data and clinical trial-ready cohorts is limited. Objective: The objectives are to (1) establish an international cohort of affected and unaffected individuals with PD-linked variants; (2) provide harmonized and quality-controlled clinical characterization data for each included individual; and (3) further promote collaboration of researchers in the field of monogenic PD. Methods: We conducted a worldwide, systematic online survey to collect individual-level data on individuals with PD-linked variants in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1, as well as selected pathogenic and risk variants in GBA and corresponding demographic, clinical, and genetic data. All registered cases underwent thorough quality checks, and pathogenicity scoring of the variants and genotype-phenotype relationships were analyzed. Results: We collected 3888 variant carriers for our analyses, reported by 92 centers (42 countries) worldwide. Of the included individuals, 3185 had a diagnosis of PD (ie, 1306 LRRK2, 115 SNCA, 23 VPS35, 429 PRKN, 75 PINK1, 13 DJ-1, and 1224 GBA) and 703 were unaffected (ie, 328 LRRK2, 32 SNCA, 3 VPS35, 1 PRKN, 1 PINK1, and 338 GBA). In total, we identified 269 different pathogenic variants; 1322 individuals in our cohort (34%) were indicated as not previously published. Conclusions: Within the MJFF Global Genetic PD Study Group, we (1) established the largest international cohort of affected and unaffected individuals carrying PD-linked variants; (2) provide harmonized and quality-controlled clinical and genetic data for each included individual; (3) promote collaboration in the field of genetic PD with a view toward clinical and genetic stratification of patients for gene-targeted clinical trials. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.Michael J. Fox Foundation for Parkinson's Research. Grant Number: ID 15015.02. NIHR Cambridge Biomedical Research Centre. Grant Number: BRC-1215-20014info:eu-repo/semantics/publishedVersio

Embracing Monogenic Parkinson's Disease: The MJFF Global Genetic PD Cohort

© 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.[Background] As gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a small fraction of the estimated number of subjects with monogenic PD worldwide are currently represented in the literature and availability of clinical data and clinical trial-ready cohorts is limited.[Objective] The objectives are to (1) establish an international cohort of affected and unaffected individuals with PD-linked variants; (2) provide harmonized and quality-controlled clinical characterization data for each included individual; and (3) further promote collaboration of researchers in the field of monogenic PD.[Methods] We conducted a worldwide, systematic online survey to collect individual-level data on individuals with PD-linked variants in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1, as well as selected pathogenic and risk variants in GBA and corresponding demographic, clinical, and genetic data. All registered cases underwent thorough quality checks, and pathogenicity scoring of the variants and genotype–phenotype relationships were analyzed.[Results] We collected 3888 variant carriers for our analyses, reported by 92 centers (42 countries) worldwide. Of the included individuals, 3185 had a diagnosis of PD (ie, 1306 LRRK2, 115 SNCA, 23 VPS35, 429 PRKN, 75 PINK1, 13 DJ-1, and 1224 GBA) and 703 were unaffected (ie, 328 LRRK2, 32 SNCA, 3 VPS35, 1 PRKN, 1 PINK1, and 338 GBA). In total, we identified 269 different pathogenic variants; 1322 individuals in our cohort (34%) were indicated as not previously published.[Conclusions] Within the MJFF Global Genetic PD Study Group, we (1) established the largest international cohort of affected and unaffected individuals carrying PD-linked variants; (2) provide harmonized and quality-controlled clinical and genetic data for each included individual; (3) promote collaboration in the field of genetic PD with a view toward clinical and genetic stratification of patients for gene-targeted clinical trials. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.This project was funded by The Michael J. Fox Foundation (ID 15015.02)Peer reviewe

Defining the causes of sporadic Parkinson's disease in the global Parkinson's genetics program (GP2)

The Global Parkinson’s Genetics Program (GP2) will genotype over 150,000 participants from around the world, and integrate genetic and clinical data for use in large-scale analyses to dramatically expand our understanding of the genetic architecture of PD. This report details the workflow for cohort integration into the complex arm of GP2, and together with our outline of the monogenic hub in a companion paper, provides a generalizable blueprint for establishing large scale collaborative research consortia

Multi-ancestry genome-wide association meta-analysis of Parkinson?s disease

Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations

Evolution of the T Cell Receptor Repertoire during and after Viral Infection: a Dissertation

The overall goal of this thesis is to examine how the T cell receptor (TCR) repertoire evolves during and after viral infections. Previous studies had examined TCR usage of selected virus-specific T cell clones, but little was known about how a diverse T cell repertoire changes during the transition between an acute infection and a memory response. It was also unclear how the T cell repertoire evolves under conditions of persistent infections associated with clonal exhaustion. To address these issues I used as a model system the lymphocytic choriomeningitis virus (LCMV) infection of mice, for which the T cell response is well-characterized. LCMV, strain Armstrong (LCMV-ARM), infection induces a strong CD8+ T cell response, which clears the virus and converts to a memory response. In contrast, high doses of LCMV clone 13 leads to persistent infections associated with T cell clonal exhaustion. These two extremes of T cell responses enable one to compare the evolution of the TCR repertoire under conditions where an acute T cell response converts to a memory response with that of T cell clonal exhaustion. In this thesis I analyzed the TCR repertoire usage directly ex vivo by the technique of CDR3 length spectratyping throughout the acute LCMV infection, into memory, after modulation by subsequent heterologous and homologous viral infections, and under conditions of T cell clonal exhaustion. Kinetic studies on the frequencies of precursor cytotoxic T lymphocytes (PCTL) to the three LCMV immunodominant peptides had suggested that the virus-specific T cell repertoire becomes fixed by day 7 postinfection, when the virus is cleared. The pCTL data also showed that a high frequency of the LCMV-specific memory T cells remained stable throughout the lifetime of the mouse. To examine any changes of the TCR repertoire usage that may develop during the acute LCMV infection and into memory, the Vβ8 population was subjected to spectratype analyses, because Vβ8 represented a substantial amount of the LCMV-induced CD8+ T cells recognizing several LCMV-encoded peptides. Analyses of the Vβ8.1 spectratype showed that genetically identical mice generated remarkably different T cell responses, as reflected by different spectratypes and different TCR sequences in same-sized spectratype bands; a conserved CDR3 motif was, however, found within some same-sized bands. This indicated that meaningful studies on the evolution of the T cell repertoire required longitudinal studies within individual mice instead of comparisons between mice. Such longitudinal studies with peripheral blood (PB) samples showed that the virus-induced T cell repertoire changed little after viral clearance and during the silencing phase of the T cell response and that dominant spectratype peaks were preserved into long term memory. To determine the effect of secondary LCMV infection on the spectratype, the recalled LCMV-induced spectratypes were analyzed. Most of the dominant peaks detected in the primary infections remained present in the secondary infection. Some new peaks were also detected for the first time in the secondary infection, suggesting a further selection of the virus-induced T cell repertoire. The spectratype data support the concepts that the LCMV-induced T cell repertoire remains unchanged during the silencing phase after clearance of the virus and that the LCMV infection dramatically skews the host T cell repertoire in the memory state long after the virus is cleared. Studies had shown that high doses of LCMV clone 13 induce a transient anti-viral CTL response followed by clonal exhaustion of T cells. To determine how the TCR repertoire evolves under conditions of persistent infections associated with T cell clonal exhaustion, the Vβ8.1 spectratypes were analyzed at various time points after the infection. In contrast to the stable LCMV-induced spectratype after viral clearance, continuous selection of the T cell repertoire occurred under conditions of persistent infections, as the T cell clones appeared and disappeared at different rates. The T cell repertoire ultimately returned to a Gaussian distribution under conditions of clonal exhaustion, indicating that clonal deletion occurs in the great majority of the virus-induced T cells. To test the stability of the LCMV-induced TCR repertoire under conditions of subsequent heterologous viral infections, the recalled LCMV-induced spectratypes were examined in the presence or absence of intervening heterologous viruses. The results showed that the intervening heterologous viruses disrupted the recalled Vβ8.1-Jβ1.3 spectratype on secondary LCMV infection; this otherwise remained stable in the absence of intervening heterologous viruses. This result supports the hypothesis that subsequent heterologous viral infections disrupt the stable LCMV-induced T cell repertoire. To detennine whether a subset of the memory T cells was deleted by the IFN-induced apoptosis of memory T cells, the LCMV-immune spectratypes were analyzed before and after the injection of the IFN inducer, poly I:C. The LCMV-immune spectratypes remained relatively stable after poly I:C injection, suggesting that there is no selective protection or deletion of discrete memory T cell clones during the IFN-induced apoptosis. In summary, the data in this thesis show that (i) the virus-induced T cell repertoire changes little after viral clearance and during the silencing phase of the T cell response, (ii) the LCMV infection dramatically skews the host T cell repertoire in the memory state, (iii) the evolution of the T cell repertoire occurs during secondary infections and under conditions of clonal exhaustion associated with persistent infections, (iv) genetically identical hosts generate different T cell responses to the same virus, and (v) intervening heterologous viral infections disrupt the recalled LCMV-induced T cell repertoire, but the LCMV-immune repertoire remained relatively stable upon the treatment of the IFN inducer, poly I:C