Abou-Shady M, Baer HU, Friess H et al (1999) Transforming growth factor betas and their signaling receptors in human hepatocellular carcinoma. Am J Surg 177:209–215. https://doi.org/10.1016/s0002-9610(99)00012-4

Article  PubMed  CAS  Google Scholar 

Argemi J, Ponz-Sarvise M, Sangro B (2022) Immunotherapies for hepatocellular carcinoma and intrahepatic cholangiocarcinoma: current and developing strategies. Adv Cancer Res 156:367–413. https://doi.org/10.1016/bs.acr.2022.03.002

Article  PubMed  Google Scholar 

Bang Y-J, Ueno M, Malka D et al (2019) Pembrolizumab (pembro) for advanced biliary adenocarcinoma: results from the KEYNOTE-028 (KN028) and KEYNOTE-158 (KN158) basket studies. J Clin Oncol 37:4079–4079. https://doi.org/10.1200/JCO.2019.37.15_suppl.4079

Article  Google Scholar 

Cai X, Zhang H, Li T (2022) The role of SPP1 as a prognostic biomarker and therapeutic target in head and neck squamous cell carcinoma. Int J Oral Maxillofac Surg 51:732–741. https://doi.org/10.1016/j.ijom.2021.07.022

Article  PubMed  CAS  Google Scholar 

Darvin P, Toor SM, Sasidharan Nair V et al (2018) Immune checkpoint inhibitors: recent progress and potential biomarkers. Exp Mol Med 50:1–11. https://doi.org/10.1038/s12276-018-0191-1

Article  CAS  Google Scholar 

Degrendele HC, Kosfiszer M, Estess P et al (1997) CD44 activation and associated primary adhesion is inducible via T cell receptor stimulation. J Immunol 159:2549–2553

PubMed  CAS  Google Scholar 

English NM, Lesley JF, Hyman R (1998) Site-specific de-N-glycosylation of CD44 can activate hyaluronan binding, and CD44 activation states show distinct threshold densities for hyaluronan binding. Cancer Res 58:3736–3742

PubMed  CAS  Google Scholar 

Guo X, Zhang Y, Zheng L et al (2018) Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat Med 24:978–985. https://doi.org/10.1038/s41591-018-0045-3

Article  PubMed  CAS  Google Scholar 

Hao Y, Hao S, Andersen-Nissen E et al (2021) Integrated analysis of multimodal single-cell data. Cell 184:3573-3587.e3529. https://doi.org/10.1016/j.cell.2021.04.048

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hornburg M, Desbois M, Lu S et al (2021) Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer. Cancer Cell 39:928-944.e926. https://doi.org/10.1016/j.ccell.2021.04.004

Article  PubMed  CAS  Google Scholar 

Jiang P, Zhang Y, Ru B et al (2021) Systematic investigation of cytokine signaling activity at the tissue and single-cell levels. Nat Methods 18:1181–1191. https://doi.org/10.1038/s41592-021-01274-5

Article  PubMed  PubMed Central  CAS  Google Scholar 

Jin S, Guerrero-Juarez CF, Zhang L et al (2021) Inference and analysis of cell-cell communication using cell chat. Nat Commun 12:1088. https://doi.org/10.1038/s41467-021-21246-9

Article  PubMed  PubMed Central  CAS  Google Scholar 

Katagiri YU, Sleeman J, Fujii H et al (1999) CD44 Variants but not CD44s cooperate with β1-containing Integrins to permit cells to bind to osteopontin independently of arginine-glycine-aspartic acid, thereby stimulating cell motility and chemotaxis1. Cancer Res 59:219–226

PubMed  CAS  Google Scholar 

Kelley RK, Bridgewater J, Gores GJ et al (2020) Systemic therapies for intrahepatic cholangiocarcinoma. J Hepatol 72:353–363. https://doi.org/10.1016/j.jhep.2019.10.009

Article  PubMed  CAS  Google Scholar 

Kim RD, Kim DW, Alese OB et al (2019) A phase II study of nivolumab in patients with advanced refractory biliary tract cancers (BTC). J Clin Oncol 37:4097–4097. https://doi.org/10.1200/JCO.2019.37.15_suppl.4097

Article  Google Scholar 

Klement JD, Paschall AV, Redd PS et al (2018) An osteopontin/CD44 immune checkpoint controls CD8+ T cell activation and tumor immune evasion. J Clin Invest 128:5549–5560. https://doi.org/10.1172/jci123360

Article  PubMed  PubMed Central  Google Scholar 

Korsunsky I, Millard N, Fan J et al (2019) Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16:1289–1296. https://doi.org/10.1038/s41592-019-0619-0

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lauer S, Gresham D (2019) An evolving view of copy number variants. Curr Genet 65:1287–1295. https://doi.org/10.1007/s00294-019-00980-0

Article  PubMed  CAS  Google Scholar 

Lee KE, Spata M, Bayne LJ et al (2016) Hif1a deletion reveals pro-neoplastic function of B cells in pancreatic neoplasia. Cancer Discov 6:256–269. https://doi.org/10.1158/2159-8290.Cd-15-0822

Article  PubMed  CAS  Google Scholar 

Li C, Jiang P, Wei S et al (2020) Regulatory T cells in tumor microenvironment: new mechanisms, potential therapeutic strategies and future prospects. Mol Cancer 19:116. https://doi.org/10.1186/s12943-020-01234-1

Article  PubMed  PubMed Central  Google Scholar 

Liu S, Galat V, Galat Y et al (2021) NK cell-based cancer immunotherapy: from basic biology to clinical development. J Hematol Oncol 14:7. https://doi.org/10.1186/s13045-020-01014-w

Article  PubMed  PubMed Central  CAS  Google Scholar 

Llovet JM, Castet F, Heikenwalder M et al (2022) Immunotherapies for hepatocellular carcinoma. Nat Rev Clin Oncol 19:151–172. https://doi.org/10.1038/s41571-021-00573-2

Article  PubMed  CAS  Google Scholar 

Ma L, Hernandez MO, Zhao Y et al (2019) Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer. Cancer Cell 36:418-430.e416. https://doi.org/10.1016/j.ccell.2019.08.007

Article  PubMed  PubMed Central  CAS  Google Scholar 

Martin-Serrano MA, Kepecs B, Torres-Martin M et al (2022) Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications. Gut. https://doi.org/10.1136/gutjnl-2021-326514

Article  PubMed  Google Scholar 

Mayakonda A, Lin DC, Assenov Y et al (2018) Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res 28:1747–1756. https://doi.org/10.1101/gr.239244.118

Article  PubMed  PubMed Central  CAS  Google Scholar 

Mcginnis CS, Murrow LM and Gartner ZJ (2019) DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors. Cell Syst 8:329–337.e324. https://doi.org/10.1016/j.cels.2019.03.003

Nallasamy P, Nimmakayala RK, Karmakar S et al (2021) Pancreatic tumor microenvironment factor promotes cancer stemness via SPP1–CD44 axis. Gastroenterology 161:1998-2013.e1997. https://doi.org/10.1053/j.gastro.2021.08.023

Article  PubMed  CAS  Google Scholar 

Nguyen CT, Caruso S, Maille P et al (2022) Immune profiling of combined hepatocellular- cholangiocarcinoma reveals distinct subtypes and activation of gene signatures predictive of response to immunotherapy. Clin Cancer Res 28:540–551. https://doi.org/10.1158/1078-0432.Ccr-21-1219

Article  PubMed  CAS  Google Scholar 

Peery AF, Crockett SD, Murphy CC et al (2019) Burden and cost of gastrointestinal, liver, and pancreatic diseases in the United States: update 2018. Gastroenterology 156:254-272.e211. https://doi.org/10.1053/j.gastro.2018.08.063

Article  PubMed  Google Scholar 

Peng J, Sun BF, Chen CY et al (2019) Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res 29:725–738. https://doi.org/10.1038/s41422-019-0195-y

Article  PubMed  PubMed Central  CAS  Google Scholar 

Puram SV, Tirosh I, Parikh AS et al (2017) Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 171:1611-1624.e1624. https://doi.org/10.1016/j.cell.2017.10.044

Article  PubMed  PubMed Central  CAS  Google Scholar 

Reinholt FP, Hultenby K, Oldberg A et al (1990) Osteopontin—a possible anchor of osteoclasts to bone. Proc Natl Acad Sci USA 87:4473–4475. https://doi.org/10.1073/pnas.87.12.4473

Article  PubMed  PubMed Central  CAS  Google Scholar 

Song G, Shi Y, Meng L et al (2022) Single-cell transcriptomic analysis suggests two molecularly distinct subtypes of intrahepatic cholangiocarcinoma. Nat Commun 13:1642. https://doi.org/10.1038/s41467-022-29164-0

Article  PubMed  PubMed Central  CAS  Google Scholar 

Syn NL, Teng MWL, Mok TSK et al (2017) De-novo and acquired resistance to immune checkpoint targeting. Lancet Oncol 18:e731–e741. https://doi.org/10.1016/S1470-2045(17)30607-1

Article  PubMed  Google Scholar 

Tanaka A, Sakaguchi S (2017) Regulatory T cells in cancer immunotherapy. Cell Res 27:109–118. https://doi.org/10.1038/cr.2016.151

Article  PubMed  CAS  Google Scholar 

Therneau TM, Grambsch PM (2000) Modeling survival data: extending the Cox model. Springer, New York

Book  Google Scholar 

Tirosh I, Izar B, Prakadan SM et al (2016) Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352:189–196. https://doi.org/10.1126/science.aad0501

Article  PubMed  PubMed Central  CAS  G