Blood Transcriptomes of SARS-CoV-2–Infected Kidney Transplant Recipients Associated with Immune Insufficiency Proportionate to Severity

  1. Zeguo Sun
  2. Zhongyang Zhang
  3. Khadija Banu
  4. Yorg Al Azzi
  5. Anand Reghuvaran
  6. Samuel Fredericks
  7. Marina Planoutene
  8. Susan Hartzell
  9. Yesl Kim
  10. John Pell
  11. Gregory Tietjen
  12. William Asch
  13. Sanjay Kulkarni
  14. Richard Formica
  15. Meenakshi Rana
  16. Jonathan S. Maltzman
  17. Weijia Zhang
  18. Enver Akalin
  19. Peter S. Heeger
  20. Paolo Cravedi
  21. Madhav C. Menon

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Abstract

Kidney transplant recipients are reported to have worse outcomes with COVID-19, and most centers have empirically reduced maintenance immunosuppression. Surprisingly, however, despite reduced immunosuppressant use, reported rates of acute rejection have been low among such patients. The authors evaluated the peripheral blood transcriptome of 64 kidney transplant recipients either during or after acute COVID-19. They identified transcriptomic signatures consistent with suppression of adaptive T cell responses that were significantly associated with disease severity during acute disease. These transcriptomic signatures also showed evidence of recovery after acute disease, even after adjustment for lymphocyte number. These transcriptomic findings of immune insufficiency during acute COVID-19 provide an explanation for the low rates of acute rejection among kidney transplant recipients despite reduced use of immunosuppressants.

Background

Among patients with COVID-19, kidney transplant recipients (KTRs) have poor outcomes compared with non-KTRs. To provide insight into management of immunosuppression during acute illness, we studied immune signatures from the peripheral blood during and after COVID-19 infection from a multicenter KTR cohort.

Methods

We ascertained clinical data by chart review. A single sample of blood was collected for transcriptome analysis. Total RNA was poly-A selected and RNA was sequenced to evaluate transcriptome changes. We also measured cytokines and chemokines of serum samples collected during acute infection.

Results

A total of 64 patients with COVID-19 in KTRs were enrolled, including 31 with acute COVID-19 (<4 weeks from diagnosis) and 33 with post-acute COVID-19 (>4 weeks postdiagnosis). In the blood transcriptome of acute cases, we identified genes in positive or negative association with COVID-19 severity scores. Functional enrichment analyses showed upregulation of neutrophil and innate immune pathways but downregulation of T cell and adaptive immune activation pathways. This finding was independent of lymphocyte count, despite reduced immunosuppressant use in most KTRs. Compared with acute cases, post-acute cases showed “normalization” of these enriched pathways after 4 weeks, suggesting recovery of adaptive immune system activation despite reinstitution of immunosuppression. Analysis of the non-KTR cohort with COVID-19 showed significant overlap with KTRs in these functions. Serum inflammatory cytokines followed an opposite trend ( i.e. , increased with disease severity), indicating that blood lymphocytes are not the primary source.

Conclusions

The blood transcriptome of KTRs affected by COVID-19 shows decreases in T cell and adaptive immune activation pathways during acute disease that, despite reduced immunosuppressant use, associate with severity. These pathways show recovery after acute illness.

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  1. Version published to 10.1681/asn.2022010125
  2. ScreenIT

    SciScore for 10.1101/2022.01.31.22270203: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsConsent: Study cohort: COVID-19 infected kidney transplant recipients (KTRs): Inclusion criteria: Adult KTRs (>18 years), who provided informed consent for sample collection, at both hospital systems (Montefiore Medical Center and Icahn School of Medicine at Mount Sinai) were enrolled during the study period (May 2020 to May 2021).
    IRB: Study approval: Independent institutional review board (IRB) approvals from Icahn school of medicine at Mount Sinai (IRB 20-03454) and Montefiore Medical Center (IRB 2020-11662) were obtained for prospective sample and data collection before initiation of the study protocol.
    Sex as a biological variableExclusion criteria: pregnant women, inability to give consent, active malignancy, or prior COVID vaccination.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    IgG antibody testing was performed using the Abbott SARS-CoV-2 IgG antibody test on the Abbott Architect Immunoassay Analyzer.
    SARS-CoV-2 IgG
    suggested: None
    The assay is a chemiluminescent microparticle immunoassay intended for the qualitative detection of IgG antibodies to SARS-CoV-2.
    SARS-CoV-2
    suggested: None
    The following fluorochrome-conjugated anti-human antibodies were used from BD Biosciences: CD3-FITC, CD3-PerCP-Cy5.5, and CD4-APC.
    anti-human
    suggested: (SouthernBiotech Cat# 9522-11S, RRID:AB_2796852)
    CD3-PerCP-Cy5.5
    suggested: None
    CD4-APC
    suggested: None
    Software and Algorithms
    SentencesResources
    IgG antibody testing was performed using the Abbott SARS-CoV-2 IgG antibody test on the Abbott Architect Immunoassay Analyzer.
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    After trimming the adapter sequences using cutadapt v2.9 (45), cleaned reads were mapped to the human genome (GRCh38) using STAR 2.5.3a (46) with default parameters.
    STAR
    suggested: (STAR, RRID:SCR_004463)
    Reads mapped to each gene locus was counted by HTseq 0.11.2 with “-m union --nonunique none”(47).
    HTseq
    suggested: (HTSeq, RRID:SCR_005514)
    The gene expression in the form of raw read counts were preprocessed with the voom method in limma (v3.38.3) (48) for subsequent transcriptome analysis.
    limma
    suggested: (LIMMA, RRID:SCR_010943)
    Differentially expressed genes (DEGs) were identified at nominal p-value ≤ 0.01, followed by functional enrichment analysis of identified DEGs with EnrichR (v2.1) (25)
    EnrichR
    suggested: (Enrichr, RRID:SCR_001575)
    The following fluorochrome-conjugated anti-human antibodies were used from BD Biosciences: CD3-FITC, CD3-PerCP-Cy5.5, and CD4-APC.
    BD Biosciences
    suggested: (BD Biosciences, RRID:SCR_013311)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    We acknowledge the lack of serial transcriptomic data from the same patients as a limitation of our work. However, our patients were enrolled during the early peak of the pandemic where in-person visits were minimized, making follow-up sample collection challenging. While we did not enroll a simultaneous non-KTR cohort, we used two different public non-KTR datasets to test the generalizability of our findings. We acknowledge that robust causal inferences cannot be made in our cross-sectional dataset. While overall signals of reduced T cell immunity during acute disease with subsequent recovery later were observed in our data, the signatures among individuals showed some heterogeneity. Our ability to molecularly detect signals consistent with reduced adaptive immunity could be exploited (and applied in external datasets) to develop and test biomarkers to potentially identify individual patients who would best tolerate IS reduction, and possibly guide timing of IS reinstitution. In summary, we demonstrate that blood transcriptomes of acute COVID-19 in KTRs suggest immune-insufficiency that is proportional to disease severity despite IS reduction. These signatures showed recovery after acute illness. These findings have implications for the pathogenesis and management, including IS reduction or antiviral approaches in COVID-19 infected KTRs.

    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.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.01.31.22270203v1 on medRxiv