# Proteotranscriptomic Dissection of Breast Cancer T Cell States Identifies CD103+ Tfh-derived Cytotoxic Cells Linked to Immunotherapy Response

**Authors:** Ghamdan Al-Eryani, Sophie Van Der Leij, Etienne Masle-Farquhar, Chia-Ling Chan, Kate Harvey, Sunny Z. Wu, Dan Roden, Taopeng Wang, John Reeves, Bertrand Z. Yeung, Christopher C. Goodnow, Cindy S. Ma, Charles M. Perou, Nir Hacohen, Aziz M. Al’Khafaji, Mats Nilsson, Joakim Lundeberg, Marcel Batten, Simon Junankar, Alexander Swarbrick

PMC · DOI: 10.21203/rs.3.rs-8394722/v1 · Research Square · 2026-01-07

## TL;DR

This study identifies a specific type of CD4 T cell in breast cancer linked to better immunotherapy response, offering new insights into cancer immunity.

## Contribution

The study discovers a CD103+ cytotoxic CD4 Tfh cell state in breast cancer associated with improved immunotherapy outcomes.

## Key findings

- CD103+ Tfh-like cells exhibit tissue residency, exhaustion, and cytotoxicity and co-localize with tumor foci.
- A higher ratio of CD103+ to IGFL2high Tfh cells correlates with improved tumor immunity and better checkpoint blockade response.
- CD103+ Tfh cells interact with CXCL10+ macrophages via CCL chemokines and CSF1.

## Abstract

While cancer immunotherapies have primarily focused on activation of cytotoxic CD8 cells, CD4 T cell activity is also associated with survival and immunotherapeutic response in numerous cancers. We applied integrated single-cell RNA sequencing and multiplexed protein epitope profiling to breast cancer samples to resolve the complexity of immune cell states within the tumor microenvironment. This approach enhanced phenotypic resolution, identifying three distinct states within the CD4 T follicular helper-like (Tfh) cell cluster. A CXCR4high progenitor state gave rise to two differentiated states: an IGFL2high subset resembling conventional Tfh cells and localised to B cell-rich lymphoid aggregates, and a CD103+ subset, exhibiting features of tissue residency, exhaustion, and cytotoxicity, which co-localised with tumor foci. CD103+ Tfh-like cells were found to interact with CXCL10+ macrophages through production of CCL chemokines and CSF1. A higher CD103+ Tfh to IGFL2high Tfh ratio, together with the selective clonal expansion of the CD103+ subset, was strongly associated with improved tumour immunity and superior responses to anti-PD-1 checkpoint blockade, surpassing the predictive value of exhausted CD8 T cells. These findings integrate Tfh and CD4 with cytotoxic potential in breast cancer, offering new insight into anti-tumor immunity and response to checkpoint blockade.

## Linked entities

- **Genes:** CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852], IGFL2 (IGF like family member 2) [NCBI Gene 147920], CRYGC (crystallin gamma C) [NCBI Gene 1420], CSF1 (colony stimulating factor 1) [NCBI Gene 1435], CXCL10 (C-X-C motif chemokine ligand 10) [NCBI Gene 3627]
- **Diseases:** breast cancer (MONDO:0004989)

## Full-text entities

- **Genes:** Ifng (interferon gamma) [NCBI Gene 15978] {aka IFN-g, If2f, Ifg}, AIF1 (allograft inflammatory factor 1) [NCBI Gene 199] {aka AIF-1, IBA1, IRT-1, IRT1}, PRF1 (perforin 1) [NCBI Gene 5551] {aka HPLH2, P1, PFP}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, Cxcl10 (C-X-C motif chemokine ligand 10) [NCBI Gene 15945] {aka C7, CRG-2, INP10, IP-10, IP10, Ifi10}, KLRG1 (killer cell lectin like receptor G1) [NCBI Gene 10219] {aka 2F1, CLEC15A, MAFA, MAFA-2F1, MAFA-L, MAFA-LIKE}, ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, TPH2 (tryptophan hydroxylase 2) [NCBI Gene 121278] {aka ADHD7, NTPH}, KLRC1 (killer cell lectin like receptor C1) [NCBI Gene 3821] {aka CD159A, NKG2, NKG2A}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, BCL6 (BCL6 transcription repressor) [NCBI Gene 604] {aka BCL5, BCL6A, LAZ3, ZBTB27, ZNF51}, CD2 (CD2 molecule) [NCBI Gene 914] {aka LFA-2, SRBC, T11}, SPP1 (secreted phosphoprotein 1) [NCBI Gene 6696] {aka BNSP, BSPI, ETA-1, OPN}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, CSF1 (colony stimulating factor 1) [NCBI Gene 1435] {aka CSF-1, MCSF, PG-M-CSF}, LAG3 (lymphocyte activating 3) [NCBI Gene 3902] {aka CD223}, Cd274 (CD274 antigen) [NCBI Gene 60533] {aka A530045L16Rik, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1}, METRNL (meteorin like, glial cell differentiation regulator) [NCBI Gene 284207], FCGR3A (Fc gamma receptor IIIa) [NCBI Gene 2214] {aka CD16-II, CD16A, FCG3, FCGR3, FCRIIIA, FcGRIIIA}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, Cxcr4 (C-X-C motif chemokine receptor 4) [NCBI Gene 12767] {aka CD184, CXC-R4, CXCR-4, Cmkar4, LESTR, PB-CKR}, NMB (neuromedin B) [NCBI Gene 4828], Cxcr5 (C-X-C motif chemokine receptor 5) [NCBI Gene 12145] {aka Blr1, CXC-R5, CXCR-5, Gpcr6, MDR15}, CXCL13 (C-X-C motif chemokine ligand 13) [NCBI Gene 100524265], Tcf7 (transcription factor 7, T cell specific) [NCBI Gene 21414] {aka TCF-1, Tcf1}, CXCL10 (C-X-C motif chemokine ligand 10) [NCBI Gene 3627] {aka C7, IFI10, INP10, IP-10, SCYB10, crg-2}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, Cd4 (CD4 antigen) [NCBI Gene 12504] {aka L3T4, Ly-4}, CD4 (CD4 molecule) [NCBI Gene 404704], Fcr (Fc receptor) [NCBI Gene 109615], HAVCR2 (hepatitis A virus cellular receptor 2) [NCBI Gene 84868] {aka CD366, HAVcr-2, KIM-3, SPTCL, TIM3, TIMD-3}, CD69 (CD69 molecule) [NCBI Gene 969] {aka AIM, BL-AC/P26, CLEC2C, EA1, GP32/28, MLR-3}, FOXP3 (forkhead box P3) [NCBI Gene 50943] {aka AIID, DIETER, IPEX, JM2, PIDX, XPID}, TRBV20OR9-2 (T cell receptor beta variable 20/OR9-2 (non-functional)) [NCBI Gene 6962] {aka CDR3, TCRBV20S2, TCRBV2O, TCRBV2S2O}, NECTIN2 (nectin cell adhesion molecule 2) [NCBI Gene 5819] {aka CD112, HVEB, PRR2, PVRL2, PVRR2}, TXNIP (thioredoxin interacting protein) [NCBI Gene 10628] {aka ARRDC6, EST01027, HHCPA78, THIF, VDUP1}, ICOS (inducible T cell costimulator) [NCBI Gene 733597], CD48 (CD48 molecule) [NCBI Gene 962] {aka BCM1, BLAST, BLAST1, MEM-102, SLAMF2, hCD48}, Itgae (integrin alpha E, epithelial-associated) [NCBI Gene 16407] {aka A530055J10, CD103, aM290, alpha-E1, alpha-M290}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, GZMK (granzyme K) [NCBI Gene 3003] {aka GrK, TRYP2}, CRYGC (crystallin gamma C) [NCBI Gene 1420] {aka CCL, CRYG3, CTRCT2}, PGR (progesterone receptor) [NCBI Gene 5241] {aka NR3C3, PR}, TPSB2 (tryptase beta 2) [NCBI Gene 64499] {aka TPS2, tryptaseB, tryptaseC}, CD82 (CD82 molecule) [NCBI Gene 3732] {aka 4F9, C33, GR15, IA4, KAI1, R2}, IL10 (interleukin 10) [NCBI Gene 3586] {aka CSIF, GVHDS, IL-10, IL10A, TGIF}, CD68 (CD68 molecule) [NCBI Gene 968] {aka GP110, LAMP4, SCARD1}, CCR5 (C-C motif chemokine receptor 5) [NCBI Gene 1234] {aka CC-CKR-5, CCCKR5, CCR-5, CD195, CKR-5, CKR5}, CD40LG (CD40 ligand) [NCBI Gene 959] {aka CD154, CD40L, HIGM1, IGM, IMD3, T-BAM}, IGFL2 (IGF like family member 2) [NCBI Gene 147920] {aka UNQ645, VPRI645}, CCL27 (C-C motif chemokine ligand 27) [NCBI Gene 10850] {aka ALP, CTACK, CTAK, ESKINE, ILC, PESKY}, TNFRSF4 (TNF receptor superfamily member 4) [NCBI Gene 7293] {aka ACT35, CD134, IMD16, OX40, TXGP1L}, IFI30 (IFI30 lysosomal thiol reductase) [NCBI Gene 10437] {aka GILT, IFI-30, IP-30, IP30}, CD163 (CD163 molecule) [NCBI Gene 9332] {aka M130, MM130, SCARI1}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, CSF1R (colony stimulating factor 1 receptor) [NCBI Gene 1436] {aka BANDDOS, C-FMS, CD115, CSF-1R, CSFR, FIM2}, Lag3 (lymphocyte-activation gene 3) [NCBI Gene 16768] {aka CD223, LAG-3, Ly66}, ZFP36L1 (ZFP36 like 1 zinc finger CCCH-type) [NCBI Gene 677] {aka BRF1, Berg36, ERF-1, ERF1, RNF162B, TIS11B}, ENTPD1 (ectonucleoside triphosphate diphosphohydrolase 1) [NCBI Gene 953] {aka ATP-DPH, ATPDase, CD39, NTPDase-1, SPG64}, SIGLEC1 (sialic acid binding Ig like lectin 1) [NCBI Gene 6614] {aka CD169, SIGLEC-1, SN}
- **Diseases:** Solid tumors (MESH:D009369), melanoma colorectal cancer (MESH:D015179), lung cancer (MESH:D008175), ADT (MESH:C566904), autoimmune (MESH:D001327), melanoma (MESH:D008545), inflammation (MESH:D007249), TNBC (MESH:D064726), Breast Cancer (MESH:D001943), cytotoxic (MESH:D064420)
- **Chemicals:** ADT (-), PBS (MESH:D007854), lipid (MESH:D008055), paraffin (MESH:D010232), Formalin (MESH:D005557), nitrogen (MESH:D009584), DMSO (MESH:D004121), chromium (MESH:D002857), H&amp;E (MESH:D006371)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** C06 — Homo sapiens (Human), Melanoma, Cancer cell line (CVCL_S857), 3T3 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0594), C30 — Homo sapiens (Human), Ovarian endometrioid adenocarcinoma, Cancer cell line (CVCL_F639), C06b — Homo sapiens (Human), Melanoma, Cancer cell line (CVCL_A705), C24 — Homo sapiens (Human), Finite cell line (CVCL_AK27), C15 — Homo sapiens (Human), Lung squamous cell carcinoma, Cancer cell line (CVCL_H624)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12803361/full.md

## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12803361/full.md

## References

95 references — full list in the complete paper: https://tomesphere.com/paper/PMC12803361/full.md

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Source: https://tomesphere.com/paper/PMC12803361