Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target

• Published in: bioRxiv
• Main Authors: Alvisi, Giorgia, Termanini, Alberto, Soldani, Cristiana, Portale, Federica, Carriero, Roberta, Pilipow, Karolina, Polidoro, Michela, Franceschini, Barbara, Malenica, Ines, Puccio, Simone, Lise, Veronica, Zanon, Veronica, Colombo, Federico Simone, Tufano, Michele, Peano, Clelia, Aghemo, Alessio, Luca Di Tommaso, Cibella, Javier, Iannacone, Matteo, Roychoudhuri, Rahul, Donadon, Matteo, Torzilli, Guido, Kunderfranco, Paolo, Diletta Dimitri, Lugli, Enrico, Lleo, Ana
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 07.03.2022
• Subjects: Biliary tract; CD4 antigen; CD69 antigen; CD8 antigen; Cholangiocarcinoma; Dendritic cells; Effector cells; Epigenetics; Flow cytometry; Homeobox; Immunoregulation; Immunosuppression; Immunotherapy; Infiltration; Lymphocytes; Lymphocytes T; Mesenchyme; Metastases; Therapeutic targets; Transcription factors; Tumor-infiltrating lymphocytes
• DOI: 10.1101/2022.03.06.483155

The quality of the immune infiltrate of intrahepatic cholangiocarcinoma (iCCA), a rare, yet aggressive tumor of the biliary tract, remains poorly characterized, limiting development of successful immunotherapies. We used high-dimensional flow cytometry to characterise the T cell and myeloid compartments of iCCA comparing these with their tumor-free peritumoral and circulating counterparts. We found poor infiltration of putative tumor-specific CD39+ CD8+ T cells accompanied by abundant infiltration of hyperactivated CD4+ regulatory T cells (Tregs), whose frequency in relation to that of CD4+ CD69+ T cells and conventional type 2 dendritic cells was associated with poor prognosis. Single-cell RNA-sequencing identified an altered network of transcription factors in iCCA-infiltrating compared to peritumoral T cells, suggesting reduced effector functions by tumor-infiltrating CD8+ T cells and enhanced immunosuppression by CD4+ Tregs. Specifically, we found that expression of mesenchyme homeobox 1 (MEOX1) was highly enriched in tumor-infiltrating Tregs, and demonstrated that MEOX1 overexpression is sufficient to reprogram circulating precursors to acquire the transcriptional and epigenetic landscape of tumor-infiltrating Tregs. Interfering with hyperactivated Tregs should be thus explored to enhance anti-tumor immunity in iCCA. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://github.com/luglilab/Cytophenograph