Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

doi:10.1084/jem.20241993

. 2025 Aug 4;222(8):e20241993.

doi: 10.1084/jem.20241993. Epub 2025 May 2.

Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Riccardo Castagnoli^#¹, Francesca Pala^#¹, Poorani Subramanian^#², Cihan Oguz^#³, Benjamin Schwarz⁴, Ai Ing Lim⁵, Andrew S Burns⁶, Elena Fontana⁷, Marita Bosticardo¹, Cristina Corsino¹, Angelina Angelova², Ottavia M Delmonte¹, Heather Kenney¹, Deanna Riley⁸, Grace Smith⁸, Lisa Ott de Bruin⁹, Vasileios Oikonomou¹, Lucas Dos Santos Dias¹, Danielle Fink¹⁰, Eric Bohrnsen⁴, Cole D Kimzey⁴, Gian Luigi Marseglia^{11

12}, Guisela Alva-Lozada¹³, Jenna R E Bergerson¹, Ana Brett^{14

15}, Karlla W Brigatti¹⁶, Dimana Dimitrova¹⁷, Cullen M Dutmer¹⁸, Alexandra F Freeman¹, Hanadys Ale¹⁹, Steven M Holland¹, Francesco Licciardi²⁰, Srdjan Pasic²¹, Laura E Poskitt¹⁶, David E Potts²², Joseph F Dasso²², Svetlana O Sharapova²³, Kevin A Strauss¹⁶, Brant R Ward²⁴, Melis Yilmaz²², Douglas B Kuhns¹⁰, Michail S Lionakis¹, Stephen R Daley²⁵, Heidi H Kong²⁶, Julia A Segre²⁷, Anna Villa^{28

29}, Stefania Pittaluga⁸, Jolan E Walter²², Ivan Vujkovic-Cvijin³⁰, Yasmine Belkaid^{5

31}, Luigi D Notarangelo¹

Affiliations

¹ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
² Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA.
³ Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁴ Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Hamilton, MT, USA.
⁵ Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁶ NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA.
⁷ IRCCS Humanitas Research Hospital , Milan, Italy.
⁸ Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
⁹ Willem-Alexander Children's Hospital, Department of Pediatrics, Pediatric Stem Cell Transplantation Program, Leiden University Medical Center , Leiden, Netherlands.
¹⁰ Neutrophil Monitoring Lab, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
¹¹ Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy.
¹² Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy.
¹³ Allergy and Immunology Division Hospital Nacional Edgardo Rebagliati Martins , Lima, Peru.
¹⁴ Hospital Pediátrico, Unidade Local de Saúde de Coimbra , Coimbra, Portugal.
¹⁵ Clínica Universitária de Pediatria, Faculdade de Medicina, Universidade de Coimbra , Coimbra, Portugal.
¹⁶ Clinic for Special Children , Gordonville, PA, USA.
¹⁷ Experimental Transplantation and Immunotherapy Branch, National Cancer Institute of the National Institutes of Health , Bethesda, MD, USA.
¹⁸ Allergy and Immunology, Children's Healthcare of Atlanta, Emory University School of Medicine , Atlanta, GA, USA.
¹⁹ Division of Immunology, Allergy and Rheumatology, Joe DiMaggio Children's Hospital, Memorial Healthcare System, Hollywood, FL, USA.
²⁰ Immuno-reumatologia, Pediatria Specialistica Universitaria, Ospedale Infantile Regina Margherita , Torino, Italy.
²¹ Department of Pediatric Immunology, Mother and Child Health Institute, Medical Faculty, University of Belgrade, Belgrade, Serbia.
²² Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA.
²³ Belarusian Research Center for Pediatric Oncology, Hematology and Immunology , Minsk, Belarus.
²⁴ Division of Allergy and Immunology, Children's National Hospital, Washington, DC, USA.
²⁵ Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology , Brisbane, Australia.
²⁶ Cutaneous Microbiome and Inflammation Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
²⁷ Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
²⁸ San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute , Milan, Italy.
²⁹ Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy.
³⁰ Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
³¹ Department of Immunology, Institut Pasteur, Paris, France.

^# Contributed equally.

PMID: 40314722
PMCID: PMC12047384 (available on 2026-05-02)
DOI: 10.1084/jem.20241993

Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Riccardo Castagnoli et al. J Exp Med. 2025.

. 2025 Aug 4;222(8):e20241993.

doi: 10.1084/jem.20241993. Epub 2025 May 2.

Authors

Affiliations

¹ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
² Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA.
³ Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁴ Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Hamilton, MT, USA.
⁵ Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁶ NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA.
⁷ IRCCS Humanitas Research Hospital , Milan, Italy.
⁸ Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
⁹ Willem-Alexander Children's Hospital, Department of Pediatrics, Pediatric Stem Cell Transplantation Program, Leiden University Medical Center , Leiden, Netherlands.
¹⁰ Neutrophil Monitoring Lab, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
¹¹ Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy.
¹² Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy.
¹³ Allergy and Immunology Division Hospital Nacional Edgardo Rebagliati Martins , Lima, Peru.
¹⁴ Hospital Pediátrico, Unidade Local de Saúde de Coimbra , Coimbra, Portugal.
¹⁵ Clínica Universitária de Pediatria, Faculdade de Medicina, Universidade de Coimbra , Coimbra, Portugal.
¹⁶ Clinic for Special Children , Gordonville, PA, USA.
¹⁷ Experimental Transplantation and Immunotherapy Branch, National Cancer Institute of the National Institutes of Health , Bethesda, MD, USA.
¹⁸ Allergy and Immunology, Children's Healthcare of Atlanta, Emory University School of Medicine , Atlanta, GA, USA.
¹⁹ Division of Immunology, Allergy and Rheumatology, Joe DiMaggio Children's Hospital, Memorial Healthcare System, Hollywood, FL, USA.
²⁰ Immuno-reumatologia, Pediatria Specialistica Universitaria, Ospedale Infantile Regina Margherita , Torino, Italy.
²¹ Department of Pediatric Immunology, Mother and Child Health Institute, Medical Faculty, University of Belgrade, Belgrade, Serbia.
²² Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA.
²³ Belarusian Research Center for Pediatric Oncology, Hematology and Immunology , Minsk, Belarus.
²⁴ Division of Allergy and Immunology, Children's National Hospital, Washington, DC, USA.
²⁵ Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology , Brisbane, Australia.
²⁶ Cutaneous Microbiome and Inflammation Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
²⁷ Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
²⁸ San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute , Milan, Italy.
²⁹ Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy.
³⁰ Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
³¹ Department of Immunology, Institut Pasteur, Paris, France.

^# Contributed equally.

PMID: 40314722
PMCID: PMC12047384 (available on 2026-05-02)
DOI: 10.1084/jem.20241993

Abstract

Partial RAG deficiency (pRD) can manifest with systemic and tissue-specific immune dysregulation, with inflammatory bowel disease (IBD) in 15% of the patients. We aimed at identifying the immunopathological and microbial signatures associated with IBD in patients with pRD and in a mouse model of pRD (Rag1w/w) with spontaneous development of colitis. pRD patients with IBD and Rag1w/w mice showed a systemic and colonic Th1/Th17 inflammatory signature. Restriction of fecal microbial diversity, abundance of pathogenic bacteria, and depletion of microbial species producing short-chain fatty acid were observed, which were associated with impaired induction of lamina propria peripheral Treg cells in Rag1w/w mice. The use of vedolizumab in Rag1w/w mice and of ustekinumab in a pRD patient were ineffective. Antibiotics ameliorated gut inflammation in Rag1w/w mice, but only bone marrow transplantation (BMT) rescued the immunopathological and microbial signatures. Our findings shed new light in the pathophysiology of gut inflammation in pRD and establish a curative role for BMT to resolve the disease phenotype.

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Conflict of interest statement

Disclosures: B.R. Ward reported grants from Swedish Orphan Biovitrum, Astra Zeneca, and Blueprint Medicines, and personal fees from Carilion Services outside the submitted work. S.R. Daley reported grants from Resseptor Therapeutics Ltd. and personal fees from Resseptor Therapeutics Ltd. outside the submitted work. No other disclosures were reported.

References

1. Abdel-Gadir, A., Stephen-Victor E., Gerber G.K., Noval Rivas M., Wang S., Harb H., Wang L., Li N., Crestani E., Spielman S., et al. 2019. Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy. Nat. Med. 25:1164–1174. 10.1038/s41591-019-0461-z - DOI - PMC - PubMed
1. Al Nabhani, Z., Dulauroy S., Marques R., Cousu C., Al Bounny S., Déjardin F., Sparwasser T., Bérard M., Cerf-Bensussan N., and Eberl G.. 2019. A weaning reaction to microbiota is required for resistance to immunopathologies in the adult. Immunity. 50:1276–1288.e5. 10.1016/j.immuni.2019.02.014 - DOI - PubMed
1. Al-Hebshi, N.N., Nasher A.T., Idris A.M., and Chen T.. 2015. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: Application to oral carcinoma samples. J. Oral Microbiol. 7:28934. 10.3402/jom.v7.28934 - DOI - PMC - PubMed
1. Annunziato, F., Cosmi L., Santarlasci V., Maggi L., Liotta F., Mazzinghi B., Parente E., Filì L., Ferri S., Frosali F., et al. 2007. Phenotypic and functional features of human Th17 cells. J. Exp. Med. 204:1849–1861. 10.1084/jem.20070663 - DOI - PMC - PubMed
1. Ansaldo, E., Farley T.K., and Belkaid Y.. 2021. Control of immunity by the microbiota. Annu. Rev. Immunol. 39:449–479. 10.1146/annurev-immunol-093019-112348 - DOI - PubMed

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[1] Abdel-Gadir, A., Stephen-Victor E., Gerber G.K., Noval Rivas M., Wang S., Harb H., Wang L., Li N., Crestani E., Spielman S., et al. 2019. Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy. Nat. Med. 25:1164–1174. 10.1038/s41591-019-0461-z - DOI - PMC - PubMed

[2] Abdel-Gadir, A., Stephen-Victor E., Gerber G.K., Noval Rivas M., Wang S., Harb H., Wang L., Li N., Crestani E., Spielman S., et al. 2019. Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy. Nat. Med. 25:1164–1174. 10.1038/s41591-019-0461-z - DOI - PMC - PubMed

[3] Al Nabhani, Z., Dulauroy S., Marques R., Cousu C., Al Bounny S., Déjardin F., Sparwasser T., Bérard M., Cerf-Bensussan N., and Eberl G.. 2019. A weaning reaction to microbiota is required for resistance to immunopathologies in the adult. Immunity. 50:1276–1288.e5. 10.1016/j.immuni.2019.02.014 - DOI - PubMed

[4] Al Nabhani, Z., Dulauroy S., Marques R., Cousu C., Al Bounny S., Déjardin F., Sparwasser T., Bérard M., Cerf-Bensussan N., and Eberl G.. 2019. A weaning reaction to microbiota is required for resistance to immunopathologies in the adult. Immunity. 50:1276–1288.e5. 10.1016/j.immuni.2019.02.014 - DOI - PubMed

[5] Al-Hebshi, N.N., Nasher A.T., Idris A.M., and Chen T.. 2015. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: Application to oral carcinoma samples. J. Oral Microbiol. 7:28934. 10.3402/jom.v7.28934 - DOI - PMC - PubMed

[6] Al-Hebshi, N.N., Nasher A.T., Idris A.M., and Chen T.. 2015. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: Application to oral carcinoma samples. J. Oral Microbiol. 7:28934. 10.3402/jom.v7.28934 - DOI - PMC - PubMed

[7] Annunziato, F., Cosmi L., Santarlasci V., Maggi L., Liotta F., Mazzinghi B., Parente E., Filì L., Ferri S., Frosali F., et al. 2007. Phenotypic and functional features of human Th17 cells. J. Exp. Med. 204:1849–1861. 10.1084/jem.20070663 - DOI - PMC - PubMed

[8] Annunziato, F., Cosmi L., Santarlasci V., Maggi L., Liotta F., Mazzinghi B., Parente E., Filì L., Ferri S., Frosali F., et al. 2007. Phenotypic and functional features of human Th17 cells. J. Exp. Med. 204:1849–1861. 10.1084/jem.20070663 - DOI - PMC - PubMed

[9] Ansaldo, E., Farley T.K., and Belkaid Y.. 2021. Control of immunity by the microbiota. Annu. Rev. Immunol. 39:449–479. 10.1146/annurev-immunol-093019-112348 - DOI - PubMed

[10] Ansaldo, E., Farley T.K., and Belkaid Y.. 2021. Control of immunity by the microbiota. Annu. Rev. Immunol. 39:449–479. 10.1146/annurev-immunol-093019-112348 - DOI - PubMed

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Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Affiliations

Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Authors

Affiliations

Abstract

Conflict of interest statement

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References

MeSH terms

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Grants and funding

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Full Text Sources

Molecular Biology Databases

Miscellaneous

Abstract

Conflict of interest statement

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References

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