Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

Jack Humphrey^{1

2

3

4

5}, Erica Brophy^{1

2

3

4

5}, Roman Kosoy^{1

2

4

6

7}, Biao Zeng^{1

2

4

6

7}, Elena Coccia^{1

2

3

4

5}, Daniele Mattei^{1

2

3

4

5}, Ashvin Ravi^{1

2

3

4

5}, Tatsuhiko Naito^{1

2

3

4

5}, Anastasia G Efthymiou^{1

2

3}, Elisa Navarro^{1

2

3

4

5

8

9

10}, Claudia De Sanctis^{2

3

11}, Victoria Flores-Almazan¹¹, Benjamin Z Muller^{1

2

3

4

5}, Gijsje J L J Snijders^{2

3

7}, Amanda Allan^{1

2

3

4

5}, Alexandra Münch^{1

2

3}, Reta Birhanu Kitata¹², Steven P Kleopoulos^{1

2

4

6

7}, Stathis Argyriou^{1

2

4

6

7}, Periklis Malakates^{1

2

4

6

7}, Konstantina Psychogyiou^{1

2

4

6

7}, Zhiping Shao^{1

2

4

6

7}, Nancy Francoeur^{1

4}, Chia-Feng Tsai¹², Marina A Gritsenko¹², Matthew E Monroe¹², Vanessa L Paurus¹², Karl K Weitz¹², Tujin Shi¹², Robert Sebra^{1

4

13

14}, Tao Liu¹², Lot D de Witte^{2

3

7}, Alison M Goate^{1

2

3

4

5}, David A Bennett¹⁵, Vahram Haroutunian^{2

16}, Gabriel E Hoffman^{1

2

4

6

7}, John F Fullard^{1

2

4

6

7}, Panos Roussos^#^{17

18

19

20

21

22}, Towfique Raj^#^{23

24

25

26

27}

Affiliations

¹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
² Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
³ Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁴ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁵ Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁶ Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁷ Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁸ Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain.
⁹ Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
¹⁰ Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain.
¹¹ Department of Pathology, Department of Artificial Intelligence & Human Health, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹² Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
¹³ Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁴ Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁵ Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
¹⁶ Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
¹⁷ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
¹⁸ Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
¹⁹ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²⁰ Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²¹ Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²² Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA. panagiotis.roussos@mssm.edu.
²³ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁴ Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁵ Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁶ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁷ Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.

^# Contributed equally.

PMID: 40033057
DOI: 10.1038/s41588-025-02099-0

Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

Jack Humphrey et al. Nat Genet. 2025 Mar.

. 2025 Mar;57(3):604-615.

doi: 10.1038/s41588-025-02099-0. Epub 2025 Mar 3.

Authors

Affiliations

¹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
² Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
³ Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁴ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁵ Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁶ Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁷ Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁸ Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain.
⁹ Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
¹⁰ Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain.
¹¹ Department of Pathology, Department of Artificial Intelligence & Human Health, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹² Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
¹³ Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁴ Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁵ Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
¹⁶ Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
¹⁷ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
¹⁸ Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
¹⁹ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²⁰ Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²¹ Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. panagiotis.roussos@mssm.edu.
²² Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA. panagiotis.roussos@mssm.edu.
²³ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁴ Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁵ Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁶ Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.
²⁷ Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. towfique.raj@mssm.edu.

^# Contributed equally.

PMID: 40033057
DOI: 10.1038/s41588-025-02099-0

Abstract

Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. Mapping the genetics of gene expression in human microglia has identified several loci associated with disease-associated genetic variants in microglia-specific regulatory elements. However, identifying genetic effects on splicing is challenging because of the use of short sequencing reads. Here, we present the isoform-centric microglia genomic atlas (isoMiGA), which leverages long-read RNA sequencing to identify 35,879 novel microglia isoforms. We show that these isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ancestry meta-analysis of 555 human microglia short-read RNA sequencing samples from 391 donors, and found associations with genetic risk loci in Alzheimer's and Parkinson's disease. We nominate several loci that may act through complex changes in isoform and splice-site usage.

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Conflict of interest statement

Competing interests: The following authors wish to disclose their industry relations: A.M.G. is a scientific advisory board member for Genentech and Muna Therapeutics; R.S. is currently a paid consultant and equity holder at GeneDx; N.F. is currently an employee of Pacific Biosciences; B.Z.M. is currently an employee of Abbvie; A.G.E. is an employee of BlueRock Therapeutics. All other authors declare no competing interests.

Update of

Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing.
Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Humphrey J, et al. medRxiv [Preprint]. 2023 Dec 1:2023.12.01.23299073. doi: 10.1101/2023.12.01.23299073. medRxiv. 2023. Update in: Nat Genet. 2025 Mar;57(3):604-615. doi: 10.1038/s41588-025-02099-0. PMID: 38076956 Free PMC article. Updated. Preprint.

References

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1. Lambert, J. C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat. Genet. 45, 1452–1458 (2013). - PubMed - PMC - DOI
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Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

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Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

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Abstract

Conflict of interest statement

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