Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target

L Llaó-Cid; Jkl Wong; I Fernandez Botana; Y Paul; M Wierz; L-M Pilger; A Floerchinger; C L Tan; S Gonder; G Pagano; M Chazotte; K Bestak; C Schifflers; M Iskar; T Roider; F Czernilofsky; P-M Bruch; J P Mallm; A Cosma; D E Campton; E Gerhard-Hartmann; A Rosenwald; D Colomer; E Campo; D Schapiro; E W Green; S Dietrich; P Lichter; E Moussay; J Paggetti; M Zapatka; M Seiffert

doi:10.1038/s41467-025-61822-x

Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target

L Llaó-Cid
, Jkl Wong
, I Fernandez Botana
, Y Paul
, M Wierz
, L-M Pilger
, A Floerchinger
, C L Tan
, S Gonder
, G Pagano
, M Chazotte
, K Bestak
, C Schifflers
, M Iskar
, T Roider
, F Czernilofsky
, P-M Bruch
, J P Mallm
, A Cosma
, D E Campton

E Gerhard-Hartmann, A Rosenwald, D Colomer, E Campo, D Schapiro, E W Green, S Dietrich, P Lichter, E Moussay, J Paggetti, M Zapatka, M Seiffert^*

^*Corresponding author for this work

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

7 Citations (Scopus)

Abstract

T-cell exhaustion contributes to immunotherapy failure in chronic lymphocytic leukemia (CLL). Here, we analyze T cells from CLL patients' blood, bone marrow, and lymph nodes, as well as from a CLL mouse model, using single-cell RNA sequencing, mass cytometry, and tissue imaging. T cells in CLL lymph nodes show the most distinct profiles, with accumulation of regulatory T cells and CD8 + T cells in various exhaustion states, including precursor (T PEX) and terminally exhausted (T EX) cells. Integration of T-cell receptor sequencing data and use of the predicTCR classifier suggest an enrichment of CLL-reactive T cells in lymph nodes. Interactome studies reveal potential immunotherapy targets, notably galectin-9, a TIM3 ligand. Inhibiting galectin-9 in mice reduces disease progression and TIM3 + T cells. Galectin-9 expression also correlates with worse survival in CLL and other cancers, suggesting its role in immune evasion and potential as a therapeutic target.

Original language	English
Article number	7271
Number of pages	22
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-61822-x
Publication status	Published - 7 Aug 2025

Keywords

Galectins/metabolism
Leukemia, Lymphocytic, Chronic, B-Cell/immunology
Humans
Animals
Mice
Hepatitis A Virus Cellular Receptor 2/metabolism
Immunotherapy/methods
T-Lymphocytes, Regulatory/immunology
Lymph Nodes/immunology
CD8-Positive T-Lymphocytes/immunology
Female
Male
Disease Models, Animal
Multiomics

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Llaó-Cid, L., Wong, J., Fernandez Botana, I., Paul, Y., Wierz, M., Pilger, L.-M., Floerchinger, A., Tan, C. L., Gonder, S., Pagano, G., Chazotte, M., Bestak, K., Schifflers, C., Iskar, M., Roider, T., Czernilofsky, F., Bruch, P.-M., Mallm, J. P., Cosma, A., ... Seiffert, M. (2025). Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target. Nature Communications, 16(1), Article 7271. https://doi.org/10.1038/s41467-025-61822-x

@article{f964eea16e694de3b5077b92b9247df2,

title = "Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target",

abstract = "T-cell exhaustion contributes to immunotherapy failure in chronic lymphocytic leukemia (CLL). Here, we analyze T cells from CLL patients' blood, bone marrow, and lymph nodes, as well as from a CLL mouse model, using single-cell RNA sequencing, mass cytometry, and tissue imaging. T cells in CLL lymph nodes show the most distinct profiles, with accumulation of regulatory T cells and CD8 + T cells in various exhaustion states, including precursor (T PEX) and terminally exhausted (T EX) cells. Integration of T-cell receptor sequencing data and use of the predicTCR classifier suggest an enrichment of CLL-reactive T cells in lymph nodes. Interactome studies reveal potential immunotherapy targets, notably galectin-9, a TIM3 ligand. Inhibiting galectin-9 in mice reduces disease progression and TIM3 + T cells. Galectin-9 expression also correlates with worse survival in CLL and other cancers, suggesting its role in immune evasion and potential as a therapeutic target. ",

keywords = "Galectins/metabolism, Leukemia, Lymphocytic, Chronic, B-Cell/immunology, Humans, Animals, Mice, Hepatitis A Virus Cellular Receptor 2/metabolism, Immunotherapy/methods, T-Lymphocytes, Regulatory/immunology, Lymph Nodes/immunology, CD8-Positive T-Lymphocytes/immunology, Female, Male, Disease Models, Animal, Multiomics",

author = "L Lla{\'o}-Cid and Jkl Wong and \{Fernandez Botana\}, I and Y Paul and M Wierz and L-M Pilger and A Floerchinger and Tan, \{C L\} and S Gonder and G Pagano and M Chazotte and K Bestak and C Schifflers and M Iskar and T Roider and F Czernilofsky and P-M Bruch and Mallm, \{J P\} and A Cosma and Campton, \{D E\} and E Gerhard-Hartmann and A Rosenwald and D Colomer and E Campo and D Schapiro and Green, \{E W\} and S Dietrich and P Lichter and E Moussay and J Paggetti and M Zapatka and M Seiffert",

note = "Funding: The NCP is supported by funding from Luxembourg{\textquoteright}s Ministry of Higher Education and Research (MESR). Tissue microarrays and lymph node sections were provided by the Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany in accordance with the regulations of the tissue bank and the approval of the ethics committee of Heidelberg University. This study was supported by a research grant of the German Cancer Aid (Deutsche Krebshilfe, grant 70114114) and the Euranet Transcan-3 project ImmuMet to M.S., by grants from FNRS-T{\'e}l{\'e}vie to I.F.B. (7.4529.19, 7.6603.21), M.W. (7.6504.18), G.P. (7.4501.18, 7.6518.20), S.G. (7.4502.19, 7.6604.21), and from the Luxembourg National Research Fund (FNR), Fondation Cancer and Plooschter Projet to E.M. and J.P. (C20/BM/14582635, C20/BM/14592342, and C23/BM/17987391). E.C. was supported by the “la Caixa” Foundation Health Research 2022 Program (CLLSYSTEMS LCF/PR/HR22/52420015 (HR22-00172). C.L.T. was supported by a DKFZ Hector Seed Funding Kick-start EarlyCareer fellowship (C-3PO). The authors gratefully acknowledge the data sto- rage service SDS@hd supported by the Ministry of Science, Research and the Arts Baden-W{\"u}rttemberg (MWK) and the German Research Foundation (DFG) through grant INST 35/1503-1 FUGG. The authors acknowledge support by the state of Baden-W{\"u}rttemberg through bwHPC and the German Research Foundation (DFG) through grant INST 35/1597-1 FUGG. M.C., K.B., and D.S. were supported by the German Federal Ministry of Education and Research (BMBF 01ZZ2004). D.S. was additionally supported by the Ministry for Science, Research and Science Baden-W{\"u}rttemberg “AI Health Innovation Cluster“ and “MULTI-SPACE”; research funding from Cellzome, a GSK company, the Bruno and Helene J{\"o}ster Stiftung, and the Carl-Zeiss- Stiftung through the Multi-dimensionAI project (CZS-Project number: P2022-08-101). {\textcopyright} 2025. The Author(s).",

year = "2025",

month = aug,

day = "7",

doi = "10.1038/s41467-025-61822-x",

language = "English",

volume = "16",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

Llaó-Cid, L, Wong, J, Fernandez Botana, I, Paul, Y, Wierz, M, Pilger, L-M, Floerchinger, A, Tan, CL, Gonder, S, Pagano, G, Chazotte, M, Bestak, K, Schifflers, C, Iskar, M, Roider, T, Czernilofsky, F, Bruch, P-M, Mallm, JP, Cosma, A, Campton, DE, Gerhard-Hartmann, E, Rosenwald, A, Colomer, D, Campo, E, Schapiro, D, Green, EW, Dietrich, S, Lichter, P, Moussay, E , Paggetti, J, Zapatka, M & Seiffert, M 2025, 'Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target', Nature Communications, vol. 16, no. 1, 7271. https://doi.org/10.1038/s41467-025-61822-x

TY - JOUR

T1 - Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target

AU - Llaó-Cid, L

AU - Wong, Jkl

AU - Fernandez Botana, I

AU - Paul, Y

AU - Wierz, M

AU - Pilger, L-M

AU - Floerchinger, A

AU - Tan, C L

AU - Gonder, S

AU - Pagano, G

AU - Chazotte, M

AU - Bestak, K

AU - Schifflers, C

AU - Iskar, M

AU - Roider, T

AU - Czernilofsky, F

AU - Bruch, P-M

AU - Mallm, J P

AU - Cosma, A

AU - Campton, D E

AU - Gerhard-Hartmann, E

AU - Rosenwald, A

AU - Colomer, D

AU - Campo, E

AU - Schapiro, D

AU - Green, E W

AU - Dietrich, S

AU - Lichter, P

AU - Moussay, E

AU - Paggetti, J

AU - Zapatka, M

AU - Seiffert, M

N1 - Funding: The NCP is supported by funding from Luxembourg’s Ministry of Higher Education and Research (MESR). Tissue microarrays and lymph node sections were provided by the Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany in accordance with the regulations of the tissue bank and the approval of the ethics committee of Heidelberg University. This study was supported by a research grant of the German Cancer Aid (Deutsche Krebshilfe, grant 70114114) and the Euranet Transcan-3 project ImmuMet to M.S., by grants from FNRS-Télévie to I.F.B. (7.4529.19, 7.6603.21), M.W. (7.6504.18), G.P. (7.4501.18, 7.6518.20), S.G. (7.4502.19, 7.6604.21), and from the Luxembourg National Research Fund (FNR), Fondation Cancer and Plooschter Projet to E.M. and J.P. (C20/BM/14582635, C20/BM/14592342, and C23/BM/17987391). E.C. was supported by the “la Caixa” Foundation Health Research 2022 Program (CLLSYSTEMS LCF/PR/HR22/52420015 (HR22-00172). C.L.T. was supported by a DKFZ Hector Seed Funding Kick-start EarlyCareer fellowship (C-3PO). The authors gratefully acknowledge the data sto- rage service SDS@hd supported by the Ministry of Science, Research and the Arts Baden-Württemberg (MWK) and the German Research Foundation (DFG) through grant INST 35/1503-1 FUGG. The authors acknowledge support by the state of Baden-Württemberg through bwHPC and the German Research Foundation (DFG) through grant INST 35/1597-1 FUGG. M.C., K.B., and D.S. were supported by the German Federal Ministry of Education and Research (BMBF 01ZZ2004). D.S. was additionally supported by the Ministry for Science, Research and Science Baden-Württemberg “AI Health Innovation Cluster“ and “MULTI-SPACE”; research funding from Cellzome, a GSK company, the Bruno and Helene Jöster Stiftung, and the Carl-Zeiss- Stiftung through the Multi-dimensionAI project (CZS-Project number: P2022-08-101). © 2025. The Author(s).

PY - 2025/8/7

Y1 - 2025/8/7

N2 - T-cell exhaustion contributes to immunotherapy failure in chronic lymphocytic leukemia (CLL). Here, we analyze T cells from CLL patients' blood, bone marrow, and lymph nodes, as well as from a CLL mouse model, using single-cell RNA sequencing, mass cytometry, and tissue imaging. T cells in CLL lymph nodes show the most distinct profiles, with accumulation of regulatory T cells and CD8 + T cells in various exhaustion states, including precursor (T PEX) and terminally exhausted (T EX) cells. Integration of T-cell receptor sequencing data and use of the predicTCR classifier suggest an enrichment of CLL-reactive T cells in lymph nodes. Interactome studies reveal potential immunotherapy targets, notably galectin-9, a TIM3 ligand. Inhibiting galectin-9 in mice reduces disease progression and TIM3 + T cells. Galectin-9 expression also correlates with worse survival in CLL and other cancers, suggesting its role in immune evasion and potential as a therapeutic target.

AB - T-cell exhaustion contributes to immunotherapy failure in chronic lymphocytic leukemia (CLL). Here, we analyze T cells from CLL patients' blood, bone marrow, and lymph nodes, as well as from a CLL mouse model, using single-cell RNA sequencing, mass cytometry, and tissue imaging. T cells in CLL lymph nodes show the most distinct profiles, with accumulation of regulatory T cells and CD8 + T cells in various exhaustion states, including precursor (T PEX) and terminally exhausted (T EX) cells. Integration of T-cell receptor sequencing data and use of the predicTCR classifier suggest an enrichment of CLL-reactive T cells in lymph nodes. Interactome studies reveal potential immunotherapy targets, notably galectin-9, a TIM3 ligand. Inhibiting galectin-9 in mice reduces disease progression and TIM3 + T cells. Galectin-9 expression also correlates with worse survival in CLL and other cancers, suggesting its role in immune evasion and potential as a therapeutic target.

KW - Galectins/metabolism

KW - Leukemia, Lymphocytic, Chronic, B-Cell/immunology

KW - Humans

KW - Animals

KW - Mice

KW - Hepatitis A Virus Cellular Receptor 2/metabolism

KW - Immunotherapy/methods

KW - T-Lymphocytes, Regulatory/immunology

KW - Lymph Nodes/immunology

KW - CD8-Positive T-Lymphocytes/immunology

KW - Female

KW - Male

KW - Disease Models, Animal

KW - Multiomics

UR - https://pubmed.ncbi.nlm.nih.gov/40775219/

U2 - 10.1038/s41467-025-61822-x

DO - 10.1038/s41467-025-61822-x

M3 - Article

C2 - 40775219

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 7271

ER -

Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target

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Keywords

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