Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

Kyle D. Gromer; Shang Yang Chen; Gaurav Gadhvi; Liang Feng; Colin Shearn; Swati Antala; Joshua B. Wechsler; Carla M. Cuda; Cara L. Mack; Ronald J. Sokol; William J. Janssen; Richard M. Green; Harris Perlman; Deborah R. Winter; Sarah Ann Taylor

doi:10.3389/fimmu.2025.1506195

Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

Kyle D. Gromer, Shang Yang Chen, Gaurav Gadhvi, Liang Feng, Colin Shearn, Swati Antala, Joshua B. Wechsler, Carla M. Cuda, Cara L. Mack, Ronald J. Sokol, William J. Janssen, Richard M. Green, Harris Perlman, Deborah R. Winter, Sarah Ann Taylor^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Introduction: Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA. Methods: We used multiparameter flow cytometry and RNA-sequencing analysis to profile recruited CD11b^hiCD64+ hepatic macrophages by cell surface expression of MHCII and Ly6c in the Rhesus rotavirus (RRV)-induced murine model of BA versus saline controls. Modulation of macrophage numbers via intra-peritoneal injections of clodronate-loaded liposomes was performed to determine the association between macrophage numbers and histologic injury (Ishak score). Results: Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Conclusions: Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.

Original language	English (US)
Article number	1506195
Journal	Frontiers in immunology
Volume	16
DOIs	https://doi.org/10.3389/fimmu.2025.1506195
State	Published - 2025

Funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Supported by the NIH National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK) K08 grant DK121937, National Institute of Allergy and Infectious Disease (NIAID) R21AI153747, the George Ferry Young Investigator Award from North American Society for Pediatric Gastroenterology Hepatology and Nutrition, the Pediatric Liver Research Fund from Lurie Children\u2019s Hospital Foundation in Chicago IL (ST); R01AI163742, R01AR080513, and American Heart Association (DW); Lupus Research Alliance Novel Research Grant, a Rheumatology Research Foundation Innovative Research Award, and a NIH NIAID R01AI170938 (CC). Acknowledgments Support for genomic sequencing and analysis was provided by the Metabolomics Core Facility at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University, and the Genomics Compute Cluster, which is jointly supported by the Feinberg School of Medicine, the Office of the Provost, the Office for Research, and Northwestern Information Technology.

Keywords

cholestasis
hepatic macrophages
innate immunity
obstructive cholangiopathy
pediatric liver disease

ASJC Scopus subject areas

Immunology and Allergy
Immunology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3389/fimmu.2025.1506195

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Gromer, K. D., Chen, S. Y., Gadhvi, G., Feng, L., Shearn, C., Antala, S., Wechsler, J. B., Cuda, C. M., Mack, C. L., Sokol, R. J., Janssen, W. J., Green, R. M., Perlman, H., Winter, D. R., & Taylor, S. A. (2025). Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions. Frontiers in immunology, 16, Article 1506195. https://doi.org/10.3389/fimmu.2025.1506195

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title = "Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions",

abstract = "Introduction: Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA. Methods: We used multiparameter flow cytometry and RNA-sequencing analysis to profile recruited CD11bhiCD64+ hepatic macrophages by cell surface expression of MHCII and Ly6c in the Rhesus rotavirus (RRV)-induced murine model of BA versus saline controls. Modulation of macrophage numbers via intra-peritoneal injections of clodronate-loaded liposomes was performed to determine the association between macrophage numbers and histologic injury (Ishak score). Results: Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Conclusions: Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.",

keywords = "cholestasis, hepatic macrophages, innate immunity, obstructive cholangiopathy, pediatric liver disease",

author = "Gromer, {Kyle D.} and Chen, {Shang Yang} and Gaurav Gadhvi and Liang Feng and Colin Shearn and Swati Antala and Wechsler, {Joshua B.} and Cuda, {Carla M.} and Mack, {Cara L.} and Sokol, {Ronald J.} and Janssen, {William J.} and Green, {Richard M.} and Harris Perlman and Winter, {Deborah R.} and Taylor, {Sarah Ann}",

note = "Publisher Copyright: Copyright {\textcopyright} 2025 Gromer, Chen, Gadhvi, Feng, Shearn, Antala, Wechsler, Cuda, Mack, Sokol, Janssen, Green, Perlman, Winter and Taylor.",

year = "2025",

doi = "10.3389/fimmu.2025.1506195",

language = "English (US)",

volume = "16",

journal = "Frontiers in immunology",

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Gromer, KD, Chen, SY, Gadhvi, G, Feng, L, Shearn, C, Antala, S, Wechsler, JB , Cuda, CM, Mack, CL, Sokol, RJ, Janssen, WJ, Green, RM , Perlman, H , Winter, DR & Taylor, SA 2025, 'Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions', Frontiers in immunology, vol. 16, 1506195. https://doi.org/10.3389/fimmu.2025.1506195

TY - JOUR

T1 - Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

AU - Gromer, Kyle D.

AU - Chen, Shang Yang

AU - Gadhvi, Gaurav

AU - Feng, Liang

AU - Shearn, Colin

AU - Antala, Swati

AU - Wechsler, Joshua B.

AU - Cuda, Carla M.

AU - Mack, Cara L.

AU - Sokol, Ronald J.

AU - Janssen, William J.

AU - Green, Richard M.

AU - Perlman, Harris

AU - Winter, Deborah R.

AU - Taylor, Sarah Ann

PY - 2025

Y1 - 2025

N2 - Introduction: Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA. Methods: We used multiparameter flow cytometry and RNA-sequencing analysis to profile recruited CD11bhiCD64+ hepatic macrophages by cell surface expression of MHCII and Ly6c in the Rhesus rotavirus (RRV)-induced murine model of BA versus saline controls. Modulation of macrophage numbers via intra-peritoneal injections of clodronate-loaded liposomes was performed to determine the association between macrophage numbers and histologic injury (Ishak score). Results: Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Conclusions: Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.

AB - Introduction: Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA. Methods: We used multiparameter flow cytometry and RNA-sequencing analysis to profile recruited CD11bhiCD64+ hepatic macrophages by cell surface expression of MHCII and Ly6c in the Rhesus rotavirus (RRV)-induced murine model of BA versus saline controls. Modulation of macrophage numbers via intra-peritoneal injections of clodronate-loaded liposomes was performed to determine the association between macrophage numbers and histologic injury (Ishak score). Results: Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Conclusions: Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.

KW - cholestasis

KW - hepatic macrophages

KW - innate immunity

KW - obstructive cholangiopathy

KW - pediatric liver disease

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DO - 10.3389/fimmu.2025.1506195

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SN - 1664-3224

VL - 16

JO - Frontiers in immunology

JF - Frontiers in immunology

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Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

Abstract

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Keywords

ASJC Scopus subject areas

UN SDGs

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