Inborn errors of immunity reveal molecular requirements for generation and maintenance of human CD4⁺ IL-9-expressing cells

Geetha Rao¹, Corinne D Mack¹, Tina Nguyen², Natalie Wong¹, Kathryn Payne¹, Lisa Worley², Paul E Gray³, Melanie Wong⁴, Peter Hsu⁴, Michael O Stormon⁵, Kahn Preece⁶, Daniel Suan¹, Michael O'Sullivan⁷, Annaliesse K Blincoe⁸, Jan Sinclair⁸, Satoshi Okada⁹, Sophie Hambleton¹⁰, Peter D Arkwright¹¹, Kaan Boztug¹², Polina Stepensky¹³, Megan A Cooper¹⁴, Liliana Bezrodnik¹⁵, Kari C Nadeau¹⁶, Hassan Abolhassani¹⁷, Roshini S Abraham¹⁸, Mikko R J Seppänen¹⁹, Vivien Béziat²⁰, Jacinta Bustamante²¹, Lisa R Forbes Satter²², Jennifer W Leiding²³, Isabelle Meyts²⁴, Emmanuelle Jouanguy²⁵, Stéphanie Boisson-Dupuis²⁰, Gulbu Uzel²⁶, Anne Puel²⁰, Jean-Laurent Casanova²⁷, Stuart G Tangye², Cindy S Ma²⁸

Affiliations

¹ Garvan Institute of Medical Research, Darlinghurst, Australia.
² Garvan Institute of Medical Research, Darlinghurst, Australia; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
³ Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, UNSW Sydney, Sydney, Australia.
⁴ Children's Hospital at Westmead, Westmead, Australia; Faculty of Medicine, University of Sydney, Sydney, Australia.
⁵ Children's Hospital at Westmead, Westmead, Australia.
⁶ John Hunter Children's Hospital, Newcastle, Australia.
⁷ Immunology Department, Fiona Stanley Hospital, Murdoch, Australia.
⁸ Starship Children's Hospital, Auckland, New Zealand.
⁹ Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
¹⁰ Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
¹¹ Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, United Kingdom.
¹² St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Medical University of Vienna, Department of Paediatrics and Adolescent Medicine, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
¹³ Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Hebrew University Medical Centre, Jerusalem, Israel.
¹⁴ Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, St Louis, Mo.
¹⁵ Grupo de Inmunología-Instituto Multidisciplinario de Investigaciones en Patologias Pediatricas (IMIPP-CONICET), Hospital de Niños "Dr. Ricardo Gutierrez," Buenos Aires, Argentina; Center for Clinical Immunology, Buenos Aires, Argentina.
¹⁶ Sean N. Parker Center for Allergy and Asthma Research, Stanford, Calif; Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, Calif.
¹⁷ Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
¹⁸ Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.
¹⁹ Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Rare Diseases Center and Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; ERN-RITA Core Center, RITAFIN, Helsinki, Finland.
²⁰ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.
²¹ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France.
²² Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, William T. Shearer Center for Human Immunobiology, Department of Allergy, Immunology, and Retrovirology, Houston, Tex.
²³ Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Baltimore, Md; Institute for Clinical and Translational Research and the Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St Petersburg, Fla.
²⁴ Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Inborn Errors of Immunity, University Hospitals Leuven, Leuven, Belgium; FWO Vlaanderen, Brussels, Belgium.
²⁵ Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France.
²⁶ Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
²⁷ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Howard Hughes Medical Institute, New York, NY; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France.
²⁸ Garvan Institute of Medical Research, Darlinghurst, Australia; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia. Electronic address: c.ma@garvan.org.au.

PMID: 39622295
PMCID: PMC11972900 (available on 2026-04-01)
DOI: 10.1016/j.jaci.2024.11.031

Inborn errors of immunity reveal molecular requirements for generation and maintenance of human CD4⁺ IL-9-expressing cells

Geetha Rao et al. J Allergy Clin Immunol. 2025 Apr.

. 2025 Apr;155(4):1161-1178.

doi: 10.1016/j.jaci.2024.11.031. Epub 2024 Nov 30.

Authors

Affiliations

¹ Garvan Institute of Medical Research, Darlinghurst, Australia.
² Garvan Institute of Medical Research, Darlinghurst, Australia; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
³ Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, UNSW Sydney, Sydney, Australia.
⁴ Children's Hospital at Westmead, Westmead, Australia; Faculty of Medicine, University of Sydney, Sydney, Australia.
⁵ Children's Hospital at Westmead, Westmead, Australia.
⁶ John Hunter Children's Hospital, Newcastle, Australia.
⁷ Immunology Department, Fiona Stanley Hospital, Murdoch, Australia.
⁸ Starship Children's Hospital, Auckland, New Zealand.
⁹ Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
¹⁰ Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
¹¹ Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, United Kingdom.
¹² St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Medical University of Vienna, Department of Paediatrics and Adolescent Medicine, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
¹³ Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Hebrew University Medical Centre, Jerusalem, Israel.
¹⁴ Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, St Louis, Mo.
¹⁵ Grupo de Inmunología-Instituto Multidisciplinario de Investigaciones en Patologias Pediatricas (IMIPP-CONICET), Hospital de Niños "Dr. Ricardo Gutierrez," Buenos Aires, Argentina; Center for Clinical Immunology, Buenos Aires, Argentina.
¹⁶ Sean N. Parker Center for Allergy and Asthma Research, Stanford, Calif; Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, Calif.
¹⁷ Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
¹⁸ Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.
¹⁹ Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Rare Diseases Center and Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; ERN-RITA Core Center, RITAFIN, Helsinki, Finland.
²⁰ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.
²¹ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France.
²² Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, William T. Shearer Center for Human Immunobiology, Department of Allergy, Immunology, and Retrovirology, Houston, Tex.
²³ Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Baltimore, Md; Institute for Clinical and Translational Research and the Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St Petersburg, Fla.
²⁴ Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Inborn Errors of Immunity, University Hospitals Leuven, Leuven, Belgium; FWO Vlaanderen, Brussels, Belgium.
²⁵ Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France.
²⁶ Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
²⁷ Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Howard Hughes Medical Institute, New York, NY; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France.
²⁸ Garvan Institute of Medical Research, Darlinghurst, Australia; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia. Electronic address: c.ma@garvan.org.au.

PMID: 39622295
PMCID: PMC11972900 (available on 2026-04-01)
DOI: 10.1016/j.jaci.2024.11.031

Abstract

Background: CD4⁺ T cells play essential roles in adaptive immunity. Distinct CD4⁺ T-cell subsets-T_H1, T_H2, T_H17, T_H22, T follicular helper, and regulatory T cells-have been identified, and their contributions to host defense and immune regulation are increasingly well defined. IL-9-producing T_H9 cells were first described in 2008 and appear to play both protective and pathogenic roles in human immunity. However, key requirements for generating human T_H9 cells remain incompletely defined.

Objective: We sought to define signaling pathways that regulate IL-9 production by human CD4⁺ T cells.

Methods: Human naive and memory CD4⁺ T cells were cultured under different conditions, and the molecular mechanisms regulating IL-9 induction were determined by assessing the ability of CD4⁺ T cells from a broad range of patients (n = 92) with pathogenic variants in key immune genes (n = 21) to differentiate into IL-9⁺ cells.

Results: We identified 2 culture conditions that yielded IL-9-expressing cells from naive CD4⁺ T cells and amplified IL-9 production by in vivo-generated memory CD4⁺ T cells: TGF-β plus IL-4 (ie, T_H9 polarizing condition), and the combination of IL-21, IL-23, IL-6, IL-1β, and TGF-β (ie, T_H17 polarizing condition). Combining these conditions had a synergistic effect in generating IL-9⁺CD4⁺ T cells. IL-9 induction required STAT3-activating cytokines as well as intact signaling via the T-cell receptor and STAT5. Importantly, IL-9 induction was restrained by IFN-γ/STAT1 and IL-10.

Conclusions: Our findings revealed critical molecules involved in inducing/restraining IL-9 production by human CD4⁺ T cells, thereby identifying pathways that could be targeted to modulate IL-9 in health and disease.

Keywords: IL-9 expression; T(H)9 cells; cytokines; human CD4(+) T-cell differentiation; inborn errors of immunity.

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Conflict of interest statement

Disclosure statement C.S.M. and S.G.T. are supported by the National Health and Medical Research Council of Australia (grants 2017463 and 1176665), the Allergy and Immunology Foundation of Australasia, and the Job Research Foundation. S.O. is supported by the Japan Agency for Medical Research and Development (AMED; grant number: JP23ek0109623 and JP24ek019754) and JSPS Program for Forming Japan's Peak Research Universities (JSPS J-PEAKS). I.M. is a senior clinical investigator at FWO Flanders. A.P. is supported by NIH grant (R01AI127564) and M.A.C. is supported by a NIH grant (P01AI155393). G.U. and her contribution are supported by NIAID intramural funds. J.L.C. is supported by grants from Institut National de la Santé et de la Recherche Médicale (INSERM), the Imagine Institute, Paris Cité University, St Giles Foundation, National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1TR001866), National Institute of Allergy and Infectious Diseases, NIH (R01AI095983), French National Research Agency (ANR) under “Investments for the future” program (ANR-10-IAHU-01), MAFMACRO (ANR-22-CE92-0008), Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), French Foundation for Medical Research (FRM) (EQU201903007798), Square Foundation, Grandir - Fonds de solidarité pour l’enfance, and W. E. Ford, General Atlantic’s Chairman and Chief Executive Officer, G. Caillaux, General Atlantic’s Co-President, Managing Director and Head of business in EMEA, and the General Atlantic Foundation. Disclosure of potential conflict of interest: The authors declare that they have no relevant conflicts of interest.

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Inborn errors of immunity reveal molecular requirements for generation and maintenance of human CD4⁺ IL-9-expressing cells

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Inborn errors of immunity reveal molecular requirements for generation and maintenance of human CD4⁺ IL-9-expressing cells

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Abstract

Conflict of interest statement

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