Spatial immune scoring system predicts hepatocellular carcinoma recurrence – Nature
Zhai, W. et al. The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma. Nat. Commun. 8, 4565 (2017).
Google Scholar
Rumgay, H. et al. Global burden of primary liver cancer in 2020 and predictions to 2040. J. Hepatol. 77, 1598–1606 (2022).
Google Scholar
Wu, J. et al. A noninvasive approach to evaluate tumor immune microenvironment and predict outcomes in hepatocellular carcinoma. Phenomics 3, 549–564 (2023).
Google Scholar
Brown, Z. J. et al. Management of hepatocellular carcinoma: a review. JAMA Surgery 158, 410–420 (2023).
Google Scholar
Singal, A. G., Kudo, M. & Bruix, J. Breakthroughs in hepatocellular carcinoma therapies. Clin. Gastroenterol. Hepatol. 21, 2135–2149 (2023).
Google Scholar
Elderkin, J. et al. Hepatocellular carcinoma: surveillance, diagnosis, evaluation and management. Cancers 15, 5118 (2023).
Google Scholar
Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182, 1341–1359.e19 (2020).
Google Scholar
Casasent, A. K. et al. Multiclonal invasion in breast tumors identified by topographic single cell sequencing. Cell 172, 205–217.e12 (2018).
Google Scholar
Sun, C., Sun, H.-y, Xiao, W.-h, Zhang, C. & Tian, Z.-g Natural killer cell dysfunction in hepatocellular carcinoma and NK cell-based immunotherapy. Acta Pharmacol. Sin. 36, 1191–1199 (2015).
Google Scholar
Nersesian, S. et al. NK cell infiltration is associated with improved overall survival in solid cancers: a systematic review and meta-analysis. Transl. Oncol. 14, 100930 (2021).
Google Scholar
Lee, H. A. et al. Natural killer cell activity is a risk factor for the recurrence risk after curative treatment of hepatocellular carcinoma. BMC Gastroenterol. 21, 258 (2021).
Google Scholar
Juengpanich, S. et al. The role of natural killer cells in hepatocellular carcinoma development and treatment: a narrative review. Transl. Oncol. 12, 1092–1107 (2019).
Google Scholar
Xue, J. S. et al. The prognostic value of natural killer cells and their receptors/ligands in hepatocellular carcinoma: a systematic review and meta-analysis. Front. Immunol. 13, 872353 (2022).
Google Scholar
Zhao, J.-J. et al. Interleukin-37 mediates the antitumor activity in hepatocellular carcinoma: role for CD57+ NK cells. Sci. Rep. 4, 5177 (2014).
Google Scholar
Chew, V. et al. Toll-like receptor 3 expressing tumor parenchyma and infiltrating natural killer cells in hepatocellular carcinoma patients. J. Natl Cancer Inst. 104, 1796–1807 (2012).
Google Scholar
Wu, Y. et al. Monocyte/macrophage-elicited natural killer cell dysfunction in hepatocellular carcinoma is mediated by CD48/2B4 interactions. Hepatology 57, 1107–1116 (2013).
Google Scholar
Sun, H. et al. Accumulation of tumor-infiltrating CD49a+ NK cells correlates with poor prognosis for human hepatocellular carcinoma. Cancer Immunol. Res. 7, 1535–1546 (2019).
Google Scholar
Sun, H. et al. Human CD96 correlates to natural killer cell exhaustion and predicts the prognosis of human hepatocellular carcinoma. Hepatology 70, 168–183 (2019).
Google Scholar
Wu, M., Mei, F., Liu, W. & Jiang, J. Comprehensive characterization of tumor infiltrating natural killer cells and clinical significance in hepatocellular carcinoma based on gene expression profiles. Biomed. Pharmacother. 121, 109637 (2020).
Google Scholar
Pinyol, R. et al. Molecular predictors of prevention of recurrence in HCC with sorafenib as adjuvant treatment and prognostic factors in the phase 3 STORM trial. Gut 68, 1065–1075 (2019).
Google Scholar
Li, J. H. & O’Sullivan, T. E. Back to the future: spatiotemporal determinants of NK cell antitumor function. Front. Immunol. 12, 816658 (2022).
Google Scholar
Fu, T. et al. Spatial architecture of the immune microenvironment orchestrates tumor immunity and therapeutic response. J. Hematol. Oncol. 14, 98 (2021).
Google Scholar
Wu, L. et al. Spatially-resolved transcriptomics analyses of invasive fronts in solid tumors. Preprint at bioRxiv https://doi.org/10.1101/2021.10.21.465135 (2021).
Sorin, M. et al. Single-cell spatial landscapes of the lung tumour immune microenvironment. Nature 614, 548–554 (2023).
Google Scholar
Elhanani, O., Ben-Uri, R. & Keren, L. Spatial profiling technologies illuminate the tumor microenvironment. Cancer Cell 41, 404–420 (2023).
Google Scholar
Zhao, N. et al. Spatial maps of hepatocellular carcinoma transcriptomes highlight an unexplored landscape of heterogeneity and a novel gene signature for survival. Cancer Cell Int. 22, 57 (2022).
Google Scholar
Wu, R. et al. Comprehensive analysis of spatial architecture in primary liver cancer. Sci. Adv. 7, eabg3750 (2021).
Google Scholar
Sun, Y. et al. Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma. Cell 184, 404–421.e16 (2021).
Google Scholar
Chang, J. et al. Genomic alterations driving precancerous to cancerous lesions in esophageal cancer development. Cancer Cell 41, 2038–2050.e5 (2023).
Google Scholar
Li, L. et al. Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes. Nat. Commun. 14, 1751 (2023).
Google Scholar
Mund, A. et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat. Biotechnol. 40, 1231–1240 (2022).
Google Scholar
Xiang, H. et al. Region-resolved multi-omics of the mouse eye. Cell Rep. 42, 112121 (2023).
Google Scholar
Qu, Y. et al. A proteogenomic analysis of clear cell renal cell carcinoma in a Chinese population. Nat. Commun. 13, 2052 (2022).
Google Scholar
Cheung, C. C. L. et al. Residual SARS-CoV-2 viral antigens detected in GI and hepatic tissues from five recovered patients with COVID-19. Gut 71, 226–229 (2022).
Google Scholar
Kaya, N. A. et al. Multimodal molecular landscape of response to Y90-resin microsphere radioembolization followed by nivolumab for advanced hepatocellular carcinoma. J. Immunother. Cancer 11, e007106 (2023).
Google Scholar
Xu, X. F. et al. Risk factors, patterns, and outcomes of late recurrence after liver resection for hepatocellular carcinoma: a multicenter study from China. JAMA Surg. 154, 209–217 (2019).
Google Scholar
Lee, S. K. et al. Immunological markers, prognostic factors and challenges following curative treatments for hepatocellular carcinoma. Int. J. Mol. Sci. 22, 10271 (2021).
Google Scholar
Jin, S. et al. Inference and analysis of cell–cell communication using CellChat. Nat. Commun. 12, 1088 (2021).
Google Scholar
Medaglia, C. et al. Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq. Science 358, 1622–1626 (2017).
Google Scholar
Predina, J. D. et al. Characterization of surgical models of postoperative tumor recurrence for preclinical adjuvant therapy assessment. Am. J. Transl. Res. 4, 206–218 (2012).
Google Scholar
Feng, Y. X. et al. Sorafenib suppresses postsurgical recurrence and metastasis of hepatocellular carcinoma in an orthotopic mouse model. Hepatology 53, 483–492 (2011).
Google Scholar
Lim, K. C. et al. Microvascular invasion is a better predictor of tumor recurrence and overall survival following surgical resection for hepatocellular carcinoma compared to the Milan criteria. Ann. Surg. 254, 108–113 (2011).
Google Scholar
Roayaie, S. et al. A system of classifying microvascular invasion to predict outcome after resection in patients with hepatocellular carcinoma. Gastroenterology 137, 850–855 (2009).
Google Scholar
Hack, S. P. et al. IMbrave 050: a phase III trial of atezolizumab plus bevacizumab in high-risk hepatocellular carcinoma after curative resection or ablation. Future Oncol. 16, 975–989 (2020).
Google Scholar
Bajorin, D. F. et al. Adjuvant nivolumab versus placebo in muscle-invasive urothelial carcinoma. N. Engl. J. Med. 384, 2102–2114 (2021).
Google Scholar
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
Google Scholar
Zhang, X. et al. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res. 47, D721–D728 (2019).
Google Scholar
Hu, C. et al. CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. Nucleic Acids Res. 51, D870–D876 (2023).
Google Scholar
Mootha, V. K. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).
Google Scholar
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
Google Scholar
Lim, J. C. T. et al. An automated staining protocol for seven-colour immunofluorescence of human tissue sections for diagnostic and prognostic use. Pathology 50, 333–341 (2018).
Google Scholar
Ng, H. H. M. et al. Immunohistochemical scoring of CD38 in the tumor microenvironment predicts responsiveness to anti-PD-1/PD-L1 immunotherapy in hepatocellular carcinoma. J. Immunother. Cancer 8, e000987 (2020).
Google Scholar
Yeong, J. et al. Prognostic value of CD8+PD-1+ immune infiltrates and PDCD1 gene expression in triple negative breast cancer. J. Immunother. Cancer 7, 34 (2019).
Google Scholar
Yeong, J. et al. High densities of tumor-associated plasma cells predict improved prognosis in triple negative breast cancer. Front. Immunol. 9, 1209 (2018).
Google Scholar
Bankhead, P. et al. QuPath: open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).
Google Scholar
Van Acker, H. H., Capsomidis, A., Smits, E. L. & Van Tendeloo, V. F. CD56 in the immune system: more than a marker for cytotoxicity? Front. Immunol. 8, 892 (2017).
Google Scholar
Sung, J. J. et al. Immunohistochemical expression and clinical significance of suggested stem cell markers in hepatocellular carcinoma. J. Pathol. Transl. Med. 50, 52–57 (2016).
Google Scholar
Tsuchiya, A. et al. Hepatocellular carcinoma with progenitor cell features distinguishable by the hepatic stem/progenitor cell marker NCAM. Cancer Lett. 309, 95–103 (2011).
Google Scholar
Phillips, D. et al. Highly multiplexed phenotyping of immunoregulatory proteins in the tumor microenvironment by CODEX tissue imaging. Front. Immunol. 12, 687673 (2021).
Google Scholar
Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021).
Google Scholar
Wu, H. et al. Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation. Nat. Commun. 13, 269 (2022).
Google Scholar
Li, R. et al. A body map of somatic mutagenesis in morphologically normal human tissues. Nature 597, 398–403 (2021).
Google Scholar
Emmert-Buck, M. R. et al. Laser capture microdissection. Science 274, 998–1001 (1996).
Google Scholar
Deng, M. et al. Proteogenomic characterization of cholangiocarcinoma. Hepatology 77, 411–429 (2023).
Google Scholar
Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).
Google Scholar
Li, T. et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 48, W509–W514 (2020).
Google Scholar
Andersen, P. K. & Gill, R. D. Cox’s regression model for counting processes: a large sample study. Ann. Stat. 10, 1100–1120 (1982).
Google Scholar
Therneau, T. M. & Grambsch, P. M. Modeling survival data: extending the Cox model. Stat. Biol. Health https://doi.org/10.1007/978-1-4757-3294-8 (2000).
Google Scholar
Li, J. et al. Biodegradable electrospun nanofibrous platform integrating antiplatelet therapy–chemotherapy for preventing postoperative tumor recurrence and metastasis. Theranostics 12, 3503–3517 (2022).
Google Scholar
Tang, M. et al. Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions. Cell Res. 30, 833–853 (2020).
Google Scholar
Wu, Y. et al. Blockade of T-cell receptor with Ig and ITIM domains elicits potent antitumor immunity in naturally occurring HBV-related HCC in mice. Hepatology 77, 965–981 (2023).
Google Scholar
Xu, X. et al. Group-2 innate lymphoid cells promote HCC progression through CXCL2-neutrophil-induced immunosuppression. Hepatology 74, 2526–2543 (2021).
Google Scholar
