Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children
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- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and pathology of multiple organs in individuals under 21 years of age in the weeks following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although an autoimmune pathogenesis has been proposed, the genes, pathways and cell types causal to this new disease remain unknown. Here we perform RNA sequencing of blood from patients with MIS-C and controls to find disease-associated genes clustered in a co-expression module annotated to CD56 dim CD57 + natural killer (NK) cells and exhausted CD8 + T cells. A similar transcriptome signature is replicated in an independent cohort of Kawasaki disease (KD), the related condition after which MIS-C was initially named. Probing a probabilistic causal network previously constructed from over 1,000 blood transcriptomes both validates the structure of this module and reveals nine key regulators, including TBX21, a central coordinator of exhausted CD8 + T cell differentiation. Together, this unbiased, transcriptome-wide survey implicates downregulation of NK cells and cytotoxic T cell exhaustion in the pathogenesis of MIS-C.
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SciScore for 10.1101/2020.08.29.20182899: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Bayesian Network analysis: In the context of a large independent IBD study, whole blood RNA-seq data was obtained via a protocol approved by the Icahn School of Medicine at Mount Sinai Institutional Review Board.
Consent: Informed consent was obtained from all participants recruited into this independent study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources The quality-filtered raw data was then converted into FASTQ files using bcl2fastq Conversion tool (Illumina). bcl2fastqsuggested: (bcl2fastq , RRID:SCR_015058)RNA-seq reads were … SciScore for 10.1101/2020.08.29.20182899: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Bayesian Network analysis: In the context of a large independent IBD study, whole blood RNA-seq data was obtained via a protocol approved by the Icahn School of Medicine at Mount Sinai Institutional Review Board.
Consent: Informed consent was obtained from all participants recruited into this independent study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources The quality-filtered raw data was then converted into FASTQ files using bcl2fastq Conversion tool (Illumina). bcl2fastqsuggested: (bcl2fastq , RRID:SCR_015058)RNA-seq reads were aligned to the GRCh38 primary assembly with Gencode release annotation by STAR (v2.7.3a)(Dobin et al., 2013) using per-sample 2-pass mapping (--twopassMode Basic) and chimeric alignment options (--chimOutType Junctions SeparateSAMold -chimSegmentMin 15 - chimJunctionOverhangMin 15). Gencodesuggested: (GENCODE, RRID:SCR_014966)A customized version of MultiQC(Ewels et al., 2016) was used the compile and summarize the per-sample statistics from STAR, Picard Tools and featureCounts (i.e. gene-level counts, mtRNA counts, globinRNA counts, etc) into an interactive HTML report. STARsuggested: (STAR, RRID:SCR_015899)featureCountssuggested: (featureCounts, RRID:SCR_012919)After removing lowly expressed genes (keeping genes with counts per million > 1 in 10% of the samples), we normalized the raw count data of the 22,302 remaining genes using voom from the limma R package(Ritchie et al., 2015). limmasuggested: (LIMMA, RRID:SCR_010943)The normalized expression data was adjusted for the following covariates using the fitVarPartModel and the get_predictions function of the variancePartition R package version 1.19.6(Hoffman and Roussos, 2020; Hoffman and Schadt, 2016) (Batch, median insert size, RNA Integrity Number, percent chimeras, PF HQ error rate and median CV coverage and sex). variancePartitionsuggested: (variancePartition, RRID:SCR_019204)The median CV coverage is defined by Picard Tools(Broad Institute) as “the median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts” and the PF HQ error rate is defined as “the fraction of bases that mismatch the reference in PF HQ aligned reads. Picardsuggested: (Picard, RRID:SCR_006525)GO analyses were done using the R packages goseq, topGO and org. topGOsuggested: (topGO, RRID:SCR_014798)Conflicts of interest statement: S.G. reports consultancy and/or advisory roles for Merck, Neon Therapeutics and OncoMed and research funding from Bristol-Myers Squibb, Genentech, Immune Design, Agenus, Janssen R&D, Pfizer, Takeda, and Regeneron. Genentechsuggested: (Genentech, RRID:SCR_003997)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has several limitations. Due to the rarity of MIS-C and the urgency of the situation, we were only able to capture transcriptomic information for eight MIS-C cases. With fewer than 600 cases reported nationally at the time of writing(Godfred-Cato, 2020), the current cohort represents a non-trivial proportion (1.4%) of the total population afflicted to date in the United States. We did not detect genome-wide significant DEGs between MIS-C and HCs at this sample size, however, using L1 statistics, we estimated that ~15% of genes in the analysis are true DEGs. These observations suggest we were sufficiently powered to detect a transcriptome-wide MIS-C signature despite being underpowered to detect individual DEGs, which was further corroborated by the molecular overlap observed between MIS-C and KD. Another limitation is MIS-C cases and HCs were not matched for age or ethnicity. HCs were individuals working on-site who were asymptomatic for COVID-19. This was the most optimal study design that could be achieved given the study occurred in New York City at the local height of the COVID-19 pandemic. We mitigated the age mismatch using gene expression changes known to be associated with age, developing an approach that allowed us to account for the age contribution to gene expression without removing the disease signal. It was not possible to perform a similar correction for the ethnicity mismatch due to the lack of published ethnicity-specific blood expression signature...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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Strength of evidence
Reviewers: Moshe Arditi, Magali Noval Rivas, Rebecca A. Porritt (Cedars-Sinai Medical Center) | 📒📒📒◻️◻️
Ashraf Harahsheh, Vanessa Bundy (Children's National Hospital) | 📙📙 ◻️◻️◻️
Paolo Palma (Bambino Gesù Children's Hospital) | 📕 ◻️◻️◻️◻️ -
Paolo Palma
Review 3: "Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children"
This study compares transcriptomes from patients afflicted with MIS-C, a condition resulting from COVID-19, with other pediatric disorders and finds MIS-C shares a similar molecular etiology to Kawasaki Disease. Reviewers found the claims unsubstantiated and greatly misleading.
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Ashraf Harahsheh, Vanessa Bundy
Review 2: "Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children"
This study compares transcriptomes from patients afflicted with MIS-C, a condition resulting from COVID-19, with other pediatric disorders and finds MIS-C shares a similar molecular etiology to Kawasaki Disease. Reviewers found the claims unsubstantiated and greatly misleading.
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Moshe Arditi, Magali Noval Rivas, Rebecca A. Porritt
Review 1: "Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children"
This study compares transcriptomes from patients afflicted with MIS-C, a condition resulting from COVID-19, with other pediatric disorders and finds MIS-C shares a similar molecular etiology to Kawasaki Disease. Reviewers found the claims unsubstantiated and greatly misleading.
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