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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 26, 2022 |
| Title |
Tissue-specific modifier alleles determine Mertk loss-of-function traits |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Knockout (KO) mouse models play critical roles in elucidating biological processes behind disease-associated or disease-resistant traits. As a 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. MERTK 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 phagocytosis of photoreceptor outer segments by retinal pigment epithelia. Similarly, enhanced anti-tumor immunity was inferred to result from the failure of macrophages to dispose cancer cell corpses, resulting in a pro-inflammatory tumor microenvironment. Here we report that the loss of Mertk alone is not sufficient for retinal degeneration. This trait only manifests when the function of the paralog Tyro3 is concomitantly lost. Additionally, the dramatic resistance against two syngeneic mouse tumor models observed in Mertk KO cannot, at least entirely, be ascribed to the loss of Mertk. The widely used Mertk KO carries multiple coincidental changes in its genome that affect the expression of a number of genes, including Tyro3. Nonetheless, neither Tyro3, nor macrophage phagocytosis by alternate genetic redundancy, accounts for the absence of anti-tumor immunity in two independent Mertk KOs. Collectively, our results indicate that context-dependent epistasis of independent modifier alleles determine Mertk KO traits.
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| Overall design |
We performed gene expression profiling analysis using data obtained from RNA-sequencing of bone-marrow-derived macrophages (BMDMs) and retinal pigment epithelial (RPE) cells from C57BL/6, Mertk-/-V1, Mertk-/-V2 and Mertk-/-V3 mice.
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| Contributor(s) |
Akalu YT, Mercau ME, Ansems M, Wagage S, Hughes LD, Nevin J, Alberto E, Liu X, He L, Alvarado D, Keler T, Kong Y, Philbrick WM, Finnemann SC, Iavarone A, Lasorella A, Rothlin CV, Ghosh S |
| Citation(s) |
35969037, 36662852 |
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| Submission date |
May 30, 2022 |
| Last update date |
Feb 10, 2023 |
| Contact name |
Yemsratch Tadesse Akalu |
| E-mail(s) |
yemsratch.akalu@yale.edu
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| Organization name |
Yale University
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| Department |
Immunobiology
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| Street address |
300 Cedar Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (30)
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| GSM6204774 |
BMDM, MertkOV1, Biol rep 1 |
| GSM6204775 |
BMDM, MertkOV1, Biol rep 2 |
| GSM6204776 |
BMDM, MertkOV1, Biol rep 3 |
| GSM6204777 |
BMDM, MertkOV2, Biol rep 1 |
| GSM6204778 |
BMDM, MertkOV2, Biol rep 2 |
| GSM6204779 |
BMDM, MertkOV2, Biol rep 3 |
| GSM6204780 |
BMDM, MertkOV3, Biol rep 1 |
| GSM6204781 |
BMDM, MertkOV3, Biol rep 2 |
| GSM6204782 |
BMDM, MertkOV3, Biol rep 3 |
| GSM6204783 |
RPE, C57BL/6, P25, Biol rep 1 |
| GSM6204784 |
RPE, C57BL/6, P25, Biol rep 2 |
| GSM6204785 |
RPE, C57BL/6, P25, Biol rep 3 |
| GSM6204786 |
RPE, C57BL/6, P25, Biol rep 4 |
| GSM6204787 |
RPE, C57BL/6, P25, Biol rep 5 |
| GSM6204788 |
RPE, C57BL/6, P25, Biol rep 6 |
| GSM6204789 |
RPE, MertkOV1, P25, Biol rep 1 |
| GSM6204790 |
RPE, MertkOV1, P25, Biol rep 2 |
| GSM6204791 |
RPE, MertkOV1, P25, Biol rep 3 |
| GSM6204792 |
RPE, MertkOV1, P25, Biol rep 4 |
| GSM6204793 |
RPE, MertkOV1, P25, Biol rep 5 |
| GSM6204794 |
RPE, MertkOV1, P25, Biol rep 6 |
| GSM6204795 |
RPE, MertkOV2, P25, Biol rep 1 |
| GSM6204796 |
RPE, MertkOV2, P25, Biol rep 2 |
| GSM6204797 |
RPE, MertkOV2, P25, Biol rep 3 |
| GSM6204798 |
RPE, MertkOV3, P25, Biol rep 1 |
| GSM6204799 |
RPE, MertkOV3, P25, Biol rep 2 |
| GSM6204800 |
RPE, MertkOV3, P25, Biol rep 3 |
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| Relations |
| BioProject |
PRJNA843677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE205070_BMDMs_normalizedcount_all_samples.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE205070_P25_RPE_normalizedcount_all_samples.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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