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Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome

Nature Geneticsvolume 50pages16501657 (2018) | Download Citation


Subcutaneous panniculitis-like T cell lymphoma (SPTCL), a non-Hodgkin lymphoma, can be associated with hemophagocytic lymphohistiocytosis (HLH), a life-threatening immune activation that adversely affects survival1,2. T cell immunoglobulin mucin 3 (TIM-3) is a modulator of immune responses expressed on subgroups of T and innate immune cells. We identify in ~60% of SPTCL cases germline, loss-of-function, missense variants altering highly conserved residues of TIM-3, c.245A>G (p.Tyr82Cys) and c.291A>G (p.Ile97Met), each with specific geographic distribution. The variant encoding p.Tyr82Cys TIM-3 occurs on a potential founder chromosome in patients with East Asian and Polynesian ancestry, while p.Ile97Met TIM-3 occurs in patients with European ancestry. Both variants induce protein misfolding and abrogate TIM-3’s plasma membrane expression, leading to persistent immune activation and increased production of inflammatory cytokines, including tumor necrosis factor-α and interleukin-1β, promoting HLH and SPTCL. Our findings highlight HLH–SPTCL as a new genetic entity and identify mutations causing TIM-3 alterations as a causative genetic defect in SPTCL. While HLH–SPTCL patients with mutant TIM-3 benefit from immunomodulation, therapeutic repression of the TIM-3 checkpoint may have adverse consequences.

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Data availability

Raw exome sequence data have been deposited at the European Genome-phenome Archive (EGA), which is hosted by the European Bioinformatics Institute (EMBL-EBI) and the Centre for Genomic Regulation (CRG), under accession number EGAS00001002765.

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Change history

  • 14 November 2018

    In the version of this article originally published, the main-text sentence “In three patients of European ancestry, we identified the germline variant encoding p.Ile97Met in TIM-3, which was homozygous in two (P12 and P13) and heterozygous in one (P15) in the germline but with no TIM-3 plasma membrane expression in the tumor” misstated the identifiers of the two homozygous individuals, which should have been P13 and P14. The error has been corrected in the HTML, PDF and print versions of the paper.


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This work was funded in part by the Foundation of Stars. N.J. is a member of the Penny Cole Laboratory and the recipient of a Chercheur Boursier, Chaire de Recherche Award from the Fonds de la Recherche du Québec en Santé. D.-A.K.-Q. is a Herman Clinical Fellow. We thank N. Brousse and the Groupe Français d’Etude des Lymphomes Cutanés for their valuable contributions. We also thank S. Lade from the Peter MacCallum Cancer Centre and the Victorian Comprehensive Cancer Centre, Melbourne; P. McKelvie from the Department of Pathology at St. Vincent’s Hospital Melbourne; D. MacGregor from the Department of Pathology at the Royal Children’s Hospital (RCH) Melbourne; L. Dalla-Pozza from the Cancer Center for Children at The Children’s Hospital at Westmead, Sydney; C. Picard from the Study Center of Immunodeficiencies (CEDI) at Hôpital-Necker Enfants Malades, Paris; and G. Ménasché from INSERM U1163 at Institut Imagine, Paris. The Children’s Cancer Centre Tissue Bank at RCH Melbourne runs thanks to the generous support of Cancer in Kids @ RCH, Leukaemia Auxiliary at RCH, the Murdoch Children’s Research Institute, and the RCH Foundation. The Tumour Bank at the Children’s Hospital at Westmead is generously supported by the Kids Cancer Project. W.D.F. is funded by the Canadian Institute for Health Research (FDN-148390). The G.d.S.B. lab (INSERM 1163 at Institut Imagine) is Equipe labélisée Fondation pour la Recherche Médicale (FRM: DEQ20150734354) and is supported by l’Agence Nationale de la Recherche (ANR-12-BSV1-0020-01 and the Investissements d’Avenir program) and by the Fondation Imagine. A.F. is supported by Collège de France. T.G. and J.P. are recipients of Canadian Institutes of Health Research and Fonds de Recherche du Québec postdoctoral fellowships, respectively. A.B. is a recipient of a Fonds de Recherche du Québec doctoral studentship. E.T.V. was granted funding by Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP, grant no. 2015/20142-0/Brazil), as part of a research fellowship abroad program to participate in this project. We thank M. Fu and S.-B. Feng of the Molecular Imaging facility at the Research Institute of the McGill University Health Centre for their assistance with the confocal microscope.

Author information

Author notes

  1. These authors contributed equally: Tenzin Gayden, Fernando E. Sepulveda, Dong-Anh Khuong-Quang, Jonathan Pratt.

  2. These authors jointly supervised this work: Bénédicte Neven, David Michonneau, Geneviève de Saint Basile, Nada Jabado.


  1. Department of Human Genetics, McGill University, Montreal, Quebec, Canada

    • Tenzin Gayden
    • , Jonathan Pratt
    • , Elvis T. Valera
    • , Leonie G. Mikael
    • , Andrea Bajic
    • , Hamid Nikbakht
    • , Jacek Majewski
    • , William D. Foulkes
    •  & Nada Jabado
  2. Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM U1163, Institut Imagine, and Université Paris Descartes-Sorbonne Paris Cité, Paris, France

    • Fernando E. Sepulveda
    • , Alexandrine Garrigue
    • , Frédéric Guerin
    •  & Geneviève de Saint Basile
  3. Children’s Cancer Center, The Royal Children’s Hospital and Murdoch Children’s Research Institute, Parkville, Victoria, Australia

    • Dong-Anh Khuong-Quang
    • , Rachel Conyers
    •  & Paul G. Ekert
  4. Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia

    • Dong-Anh Khuong-Quang
    • , Rachel Conyers
    •  & Paul G. Ekert
  5. Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil

    • Elvis T. Valera
  6. Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada

    • Susan Kelso
    • , Frank Sicheri
    • , Dzana Dervovic
    •  & Daniel Schramek
  7. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    • Susan Kelso
    • , Frank Sicheri
    • , Daniel Schramek
    •  & Mikko Taipale
  8. Cancer Research Program, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada

    • Nancy Hamel
    •  & William D. Foulkes
  9. Canadian Centre for Computational Genomics, Montreal, Quebec, Canada

    • Rola Dali
    •  & Hamid Nikbakht
  10. Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada

    • Shriya Deshmukh
  11. McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada

    • Jacek Majewski
    •  & Simon Gravel
  12. Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France

    • Despina Moshous
    • , Brigitte Bader-Meunier
    • , Jean-Sebastien Diana
    • , Stephane Blanche
    • , Alain Fischer
    •  & Bénédicte Neven
  13. Division of Hematology and Oncology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, Quebec, Canada

    • Janie Charlebois
    • , Sharon Abish
    •  & David Mitchell
  14. Plateforme de Génomique, Institut Imagine, Paris, France

    • Christine Bole-Feysot
  15. Plateforme de Bioinformatique, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France

    • Patrick Nitschke
  16. Hematology and Oncology Unit, Saint Louis Hospital, Paris, France

    • Catherine Thieblemont
  17. Paris Diderot University, Université Sorbonne Paris Cité, Paris, France

    • Catherine Thieblemont
    • , Maxime Battistella
    •  & David Michonneau
  18. Cytology and Pathology Laboratory, Saint Louis Hospital, Paris, France

    • Maxime Battistella
  19. Department of Pathology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, Quebec, Canada

    • Van-Hung Nguyen
  20. Department of Surgical Oncology, Peter MacCallum Cancer Institute, University of Melbourne, Melbourne, Victoria, Australia

    • Chris McCormack
  21. Department of Dermatology, St. Vincent’s Hospital, Fitzroy, Victoria, Australia

    • Chris McCormack
  22. Epworth Healthcare, Melbourne, Victoria, Australia

    • H. Miles Prince
  23. Department of Medical Oncology, Sir Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia

    • H. Miles Prince
  24. Department of Neonatology, Centre Hospitalier de Polynésie Française, Papeete, French Polynesia

    • Marianne Besnard
  25. Department of Anatomy and Cytology/Pathology, Centre Hospitalier Universitaire Paris, Hôpital Necker-Enfants Malades, Paris, France

    • Sylvie Fraitag
  26. Collège de France, Paris, France

    • Alain Fischer
  27. INSERM U1163, Institut Imagine and Université Paris Descartes -Sorbonne Paris Cité, Paris, France

    • Alain Fischer
    •  & Bénédicte Neven
  28. Hematology and Transplantation Unit, Saint Louis Hospital, Paris, France

    • David Michonneau
  29. Centre d’Etudes des Déficits Immunitaires, Centre Hospitalier Universitaire Paris, Hôpital Necker-Enfants Malades, Paris, France

    • Geneviève de Saint Basile
  30. Department of Pediatrics, McGill University, Montreal, Quebec, Canada

    • Nada Jabado
  31. Research Institute, McGill University Health Centre, Montreal, Quebec, Canada

    • Nada Jabado


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T.G., D.-A.K.-Q., J.P., E.T.V., A.G., S.K., F.S., L.G.M., N.H., M.T., A.B., S.D., D.D., D.S., and F.G. performed experiments and analyzed data. H.N., J.M., W.D.F., S.G., and R.D. analyzed data. D.Moshous, J.C., S.A., C.B.-F., P.N., B.B.-M., D.Mitchell, C.T., M.Battistella, V.-H.N., R.C., J.-S.D., C.M., H.M.P., M.Besnard, S.B., P.G.E., S.F., and A.F. contributed materials and analyzed data. F.E.S., B.N., D.Michonneau, G.d.S.B., and N.J. conceived and designed the experiments and analyzed data. All authors contributed to the written manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Geneviève de Saint Basile or Nada Jabado.

Integrated supplementary information

  1. Supplementary Figure 1

    Sequencing chromatograms showing HAVCR2 mutations from homozygous affected individuals and heterozygous healthy relatives compared to wild-type HAVCR2 from a healthy control.

  2. Supplementary Figure 2 Frequencies of the Y82C and I97M variants in different populations according to their ethnic origin.

    (a), Distributions of the Y82C and I97M variants across all gnomAD populations. (b), Frequency of the Y82C variant in the Tahiti population from Polynesia. The chi-squared test was used to calculate Hardy–Weinberg equilibrium (HWE) P values.

  3. Supplementary Figure 3 Expression of TIM-3 mutants in SPTCL patients and stably transfected HEK-293 cells.

    (a), Flow cytometry of TIM-3 expression on monocytes (CD14+) from a Y82C TIM-3 heterozygous individual shows an intermediate level of expression as compared to TIM-3 expression on patient and control cells. One representative experiment of the four heterozygous individuals analyzed is provided. (b), Complete image of the western blot shown in Fig. 3c.

  4. Supplementary Figure 4 Y82C and I97M lead to TIM-3 protein misfolding and impaired surface expression.

    (a), Plot showing the impaired surface expression of the two TIM-3 mutants on the same HEK-293T cells as in Fig. 3d, using flow cytometry analysis, by APC-conjugated TIM-3 antibody or isotype control antibody. (b), Cell lysates from wild-type and Y82C or I97M TIM-3-transfected HEK-293 cells were put on a 7.5% native gel and immunoblotted against α-FLAG. Misfolded aggregates are highlighted with arrows. (c), The same lysates from (b) were submitted to an N-deglycosylation assay using the PNGase F enzyme and following the manufacturer’s denaturation protocol. These lysates as well as control lysates (without PNGase F) were immunoblotted with α-FLAG and α-β-actin. Experiments in (b) and (c) were repeated three times, and representative gels are shown. (d), Analysis of the wild-type and mutant (Y82C and I97M) bands before and after PNGase F treatment. MW, molecular weight.

  5. Supplementary Figure 5 Cytotoxic lymphocytes from P4 display similar degranulation activity to control lymphocytes.

    One representative experiment over four patients analyzed (P1–P4) is shown.

  6. Supplementary Figure 6 Increased secretion of inflammatory cytokines by TIM-3-deficient leukocytes.

    (a), Cytokine production by T lymphoblasts from Y82C TIM-3 patients as compared to controls. TNF-α, IL-2 and IFN-γ were quantified by CBA (*P < 0.05). Data are means +/− s.d. from three different patients (P3, P4, P11). Data represent the results of different independent experiments performed with different biological samples (cell cultures from cells obtained at different time points) obtained from different controls and three different TIM-3 Y82C patients. An unpaired t test was used to determine statistical significance between control (n = 15) and Y82C (n = 10) samples. b,c, Increased TNF-α production (b) and IL-1β production (c) by macrophages from patients (P3 and P11) with Y82C TIM-3, as compared to wild-type TIM-3 controls, in response to TLR4 (LPS) and NLRP3 (nigericin) activation (as done in Fig. 4). Graphs represent means +/− s.e.m. from two independent experiments in duplicate (*P < 0.05).

  7. Supplementary Figure 7 FOXP3+CD4+ Treg cells are significantly decreased in panniculitis from TIM-3-mutant (Y82C, I97M) SPTCL as compared to TIM-3-wild-type SPTCL.

    Immunofluorescence using anti-CD4 and anti-FOXP3 antibodies was performed on consecutive slides from a wild-type (WT) SPTCL sample for TIM-3 (left) or the same slide for Y82C (middle) and I97M (right) TIM-3-mutant SPTCL samples. Cells positive for FOXP3 and CD4 staining were counted using Fiji software, and graphs represent means +/− s.e.m. for CD4+ and FOXP3+CD4+ cells from five different fields (lower left). A significantly decreased number of CD4+ and FOXP3+CD4+ cells in TIM-3-mutant SPTCL was observed when comparing TIM-3-mutant to TIM-3-wild-type SPTCL (P < 0.001, one-way ANOVA). Representative images mounted using Photoshop are shown.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–7 and Supplementary Note

  2. Reporting Summary

  3. Supplementary Table 1

    Clinical information on the 27 SPTCL patients analyzed in this study

  4. Supplementary Table 2

    Summary of whole-exome sequencing metrics for 17 SPTCL patients

  5. Supplementary Table 3

    List of the variants identified in exome datasets of 17 SPTCL cases, including 7 tumor–normal pairs, 7 tumors only and 3 germline-only samples

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