Tissue-specific modifier alleles determine Mertk loss-of-function traits

  1. Yemsratch T Akalu
  2. Maria E Mercau
  3. Marleen Ansems
  4. Lindsey D Hughes
  5. James Nevin
  6. Emily J Alberto
  7. Xinran N Liu
  8. Li-Zhen He
  9. Diego Alvarado
  10. Tibor Keler
  11. Yong Kong
  12. William M Philbrick
  13. Marcus Bosenberg
  14. Silvia C Finnemann
  15. Antonio Iavarone
  16. Anna Lasorella
  17. Carla V Rothlin  Is a corresponding author
  18. Sourav Ghosh  Is a corresponding author
  1. Yale University, United States
  2. Celldex Therapeutics, United States
  3. Fordham University, United States
  4. Columbia University, United States

Abstract

Knockout (KO) mouse models play critical roles in elucidating biological processes behind disease-associated or disease-resistant traits. As a presumed consequence of gene KO, mice display certain phenotypes. Based on insight into the molecular role of said gene in a biological process, it is inferred that the particular biological process causally underlies the trait. This approach has been crucial towards understanding the basis of pathological and/or advantageous traits associated with Mertk KO mice. Mertk KO mice suffer from severe, early-onset retinal degeneration. MERTK, expressed in retinal pigment epithelia, is a receptor tyrosine kinase with a critical role in phagocytosis of apoptotic cells or cellular debris. Therefore, early-onset, severe retinal degeneration was described to be a direct consequence of failed MERTK-mediated phagocytosis of photoreceptor outer segments by retinal pigment epithelia. Here we report that the loss of Mertk alone is not sufficient for retinal degeneration. The widely used Mertk KO mouse carries multiple coincidental changes in its genome that affect the expression of a number of genes, including the Mertk paralog Tyro3. Retinal degeneration manifests only when the function of Tyro3 is concomitantly lost. Furthermore, Mertk KO mice display improved anti-tumor immunity. MERTK is expressed in macrophages. Therefore, enhanced anti-tumor immunity was inferred to result from the failure of macrophages to dispose of cancer cell corpses, resulting in a pro-inflammatory tumor microenvironment. The resistance against two syngeneic mouse tumor models observed in Mertk KO mice is not, however, phenocopied by the loss of Mertk alone. Neither Tyro3, nor macrophage phagocytosis by alternate genetic redundancy, account for the absence of anti-tumor immunity. Collectively, our results indicate that context-dependent epistasis of independent modifier alleles determines Mertk KO traits.

Data availability

RNA-sequencing data sets and the processed data that support the findings of this study have been deposited to the Gene Expression Omnibus (GEO) under accession ID: GSE205070. All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for all figures included.

The following data sets were generated

Article and author information

Author details

  1. Yemsratch T Akalu

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0829-7972
  2. Maria E Mercau

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6971-8676
  3. Marleen Ansems

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  4. Lindsey D Hughes

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1764-4553
  5. James Nevin

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  6. Emily J Alberto

    Department of Immunobiology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  7. Xinran N Liu

    Department of Cell Biology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  8. Li-Zhen He

    Celldex Therapeutics, New Haven, United States
    Competing interests
    Li-Zhen He, is affiliated with Celldex Therapeutics. The author has no financial interests to declare.
  9. Diego Alvarado

    Celldex Therapeutics, New Haven, United States
    Competing interests
    Diego Alvarado, is affiliated with Celldex Therapeutics. The author has no financial interests to declare..
  10. Tibor Keler

    Celldex Therapeutics, New Haven, United States
    Competing interests
    Tibor Keler, is affiliated with Celldex Therapeutics. The author has no financial interests to declare..
  11. Yong Kong

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2881-5274
  12. William M Philbrick

    Center on Endocrinology and Metabolism, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  13. Marcus Bosenberg

    Department of Dermatology, Yale University, New Haven, United States
    Competing interests
    No competing interests declared.
  14. Silvia C Finnemann

    Department of Biological Sciences, Fordham University, Bronx, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9298-0736
  15. Antonio Iavarone

    Department of Neurology, Columbia University, New York, United States
    Competing interests
    No competing interests declared.
  16. Anna Lasorella

    Department of Neurology, Columbia University, New York, United States
    Competing interests
    No competing interests declared.
  17. Carla V Rothlin

    Department of Immunobiology, Yale University, New Haven, United States
    For correspondence
    carla.rothlin@yale.edu
    Competing interests
    Carla V Rothlin, Senior editor, eLife.Is a scientific founder and member of the Scientific Advisory Board (SAB) of Surface Oncology, a member of Janessen Immuology SAB, and a consultant for the Roche Immunology Incubator. Has received grant support from Mirati Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5693-5572
  18. Sourav Ghosh

    Department of Neurology, Yale University, New Haven, United States
    For correspondence
    sourav.ghosh@yale.edu
    Competing interests
    Sourav Ghosh, has received grant support from Mirati Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5990-8708

Funding

National Institutes of Health (R01CA212376)

  • Carla V Rothlin
  • Sourav Ghosh

Howard Hughes Medical Institute

  • Carla V Rothlin

Yale Cancer Center (YSPORE Career Development Award DRP27)

  • Carla V Rothlin

Fordham University (Kim B. and Stephen E. Bepler Professorship in Biology)

  • Silvia C Finnemann

Dutch Cancer Society (BUIT 2012-5347)

  • Marleen Ansems

National Science Foundation (DGE-1122492)

  • Lindsey D Hughes

Yale University (Richard K. Gershon Fellowship)

  • Lindsey D Hughes

National Cancer Institute (2T32CA193200-06)

  • James Nevin

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All experiments involving animals were performed in accordance with regulatory guidelines and standards set by the Institutional Animal Care and Use Committee (IACUC) protocol (#2021-11312) of Yale University.

Reviewing Editor

  1. Florent Ginhoux, Agency for Science Technology and Research, Singapore

Publication history

  1. Preprint posted: May 23, 2022 (view preprint)
  2. Received: May 24, 2022
  3. Accepted: August 13, 2022
  4. Accepted Manuscript published: August 15, 2022 (version 1)
  5. Version of Record published: August 31, 2022 (version 2)

Copyright

© 2022, Akalu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 978
    Page views
  • 254
    Downloads
  • 3
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Yemsratch T Akalu
  2. Maria E Mercau
  3. Marleen Ansems
  4. Lindsey D Hughes
  5. James Nevin
  6. Emily J Alberto
  7. Xinran N Liu
  8. Li-Zhen He
  9. Diego Alvarado
  10. Tibor Keler
  11. Yong Kong
  12. William M Philbrick
  13. Marcus Bosenberg
  14. Silvia C Finnemann
  15. Antonio Iavarone
  16. Anna Lasorella
  17. Carla V Rothlin
  18. Sourav Ghosh
(2022)
Tissue-specific modifier alleles determine Mertk loss-of-function traits
eLife 11:e80530.
https://doi.org/10.7554/eLife.80530

Further reading

    1. Immunology and Inflammation
    Warren Anderson, Fariba Barahmand-pour-Whitman ... David J Rawlings
    Research Article

    A genetic variant in the gene PTPN22 (R620W, rs2476601) is strongly associated with increased risk for multiple autoimmune diseases and linked to altered TCR regulation and T cell activation. Here, we utilize Crispr/Cas9 gene editing with donor DNA repair templates in human cord blood-derived, naive T cells to generate PTPN22 risk edited (620W), non-risk edited (620R) or knock out T cells from the same donor. PTPN22 risk edited cells exhibited increased activation marker expression following non-specific TCR engagement, findings that mimicked PTPN22 KO cells. Next, using lentiviral delivery of T1D patient-derived TCRs against the pancreatic autoantigen, islet-specific glucose-6 phosphatase catalytic subunit-related protein (IGRP), we demonstrate that loss of PTPN22 function led to enhanced signaling in T cells expressing a lower avidity self-reactive TCR, but not a high avidity TCR. In this setting, loss of PTPN22 mediated enhanced proliferation and Th1 skewing. Importantly, expression of the risk variant in association with a lower avidity TCR also increased proliferation relative to PTPN22 non-risk T cells. Together, these findings suggest that, in primary human T cells, PTPN22 rs2476601 contributes to autoimmunity risk by permitting increased TCR signaling and activation in mildly self-reactive T cells, thereby potentially expanding the self-reactive T cell pool and skewing this population toward an inflammatory phenotype.

    1. Epidemiology and Global Health
    2. Immunology and Inflammation
    Zaki A Sherif, Christian R Gomez ... RECOVER Mechanistic Pathway Task Force
    Review Article

    COVID-19, with persistent and new onset of symptoms such as fatigue, post-exertional malaise, and cognitive dysfunction that last for months and impact everyday functioning, is referred to as Long COVID under the general category of post-acute sequelae of SARS-CoV-2 infection (PASC). PASC is highly heterogenous and may be associated with multisystem tissue damage/dysfunction including acute encephalitis, cardiopulmonary syndromes, fibrosis, hepatobiliary damages, gastrointestinal dysregulation, myocardial infarction, neuromuscular syndromes, neuropsychiatric disorders, pulmonary damage, renal failure, stroke, and vascular endothelial dysregulation. A better understanding of the pathophysiologic mechanisms underlying PASC is essential to guide prevention and treatment. This review addresses potential mechanisms and hypotheses that connect SARS-CoV-2 infection to long-term health consequences. Comparisons between PASC and other virus-initiated chronic syndromes such as myalgic encephalomyelitis/chronic fatigue syndrome and postural orthostatic tachycardia syndrome will be addressed. Aligning symptoms with other chronic syndromes and identifying potentially regulated common underlining pathways may be necessary for understanding the true nature of PASC. The discussed contributors to PASC symptoms include sequelae from acute SARS-CoV-2 injury to one or more organs, persistent reservoirs of the replicating virus or its remnants in several tissues, re-activation of latent pathogens such as Epstein–Barr and herpes viruses in COVID-19 immune-dysregulated tissue environment, SARS-CoV-2 interactions with host microbiome/virome communities, clotting/coagulation dysregulation, dysfunctional brainstem/vagus nerve signaling, dysautonomia or autonomic dysfunction, ongoing activity of primed immune cells, and autoimmunity due to molecular mimicry between pathogen and host proteins. The individualized nature of PASC symptoms suggests that different therapeutic approaches may be required to best manage specific patients.