Lessons learned from spatial transcriptomic analyses in clear-cell renal cell carcinoma

Hsieh, J. J. et al. Renal cell carcinoma. Nat. Rev. Dis. Primers 3, 17009 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Su, S., Akbarinejad, S. & Shahriyari, L. Immune classification of clear cell renal cell carcinoma. Sci. Rep. 11, 1–10 (2021).

CAS  Google Scholar 

Lyskjær, I. et al. Management of renal cell carcinoma: promising biomarkers and the challenges to reach the clinic. Clin. Cancer Res. 30, 663–672 (2024).

Article  PubMed  Google Scholar 

Raimondi, A. et al. Predictive biomarkers of response to immunotherapy in metastatic renal cell cancer. Front. Oncol. 10, 1644 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Motzer, R. J. et al. Nivolumab plus ipilimumab versus sunitinib in advanced renal-cell carcinoma. N. Engl. J. Med. 378, 1277–1290 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shapiro, D. D. et al. Understanding the tumor immune microenvironment in renal cell carcinoma. Cancers 15, 2500 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alchahin, A. M., Tsea, I. & Baryawno, N. Recent advances in single-cell RNA-sequencing of primary and metastatic clear cell renal cell carcinoma. Cancers 15, 4734 (2023).

Borcherding, N. et al. Mapping the immune environment in clear cell renal carcinoma basingle-cell genomics. Commun. Biol. 4, 122 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, G. et al. Metabolic heterogeneity in clear cell renal cell carcinoma revealed by single-cell RNA sequencing and spatial transcriptomics. J. Transl Med. 22, 210 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, R. et al. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 40, 1583–1599 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin, Y. et al. Advances in spatial transcriptomics and its applications in cancer research. Mol. Cancer 23, 1–24 (2024).

Article  Google Scholar 

Merritt, C. R. et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat. Biotechnol. 38, 586–599 (2020).

Article  CAS  PubMed  Google Scholar 

Hu, B., Sajid, M., Lv, R., Liu, L. & Sun, C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front. Immunol. 13, 996721 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

He, S. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat. Biotechnol. 40, 1794–1806 (2022).

Article  CAS  PubMed  Google Scholar 

Wang, Y. et al. Spatial transcriptomics: technologies, applications and experimental considerations. Genomics 115, 110671 (2023).

Article  CAS  PubMed  Google Scholar 

Meylan, M. et al. Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer. Immunity 55, 527–541 (2022).

Article  CAS  PubMed  Google Scholar 

Wu, Y. et al. Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma. Nat. Commun. 14, 1681 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gui, C.-P. et al. Single-cell and spatial transcriptomics reveal 5-methylcytosine RNA methylation regulators immunologically reprograms tumor microenvironment characterizations, immunotherapy response and precision treatment of clear cell renal cell carcinoma. Transl Oncol. 35, 101726 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davidson, G. et al. Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear cell renal cell carcinoma. Cancer Res. 83, 2952–2969 (2023).

Article  CAS  PubMed  Google Scholar 

Raghubar, A. M. et al. High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints. NPJ Precis. Oncol. 7, 88 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schoenfeld, D. A. et al. Location matters: LAG3 levels are lower in renal cell carcinoma metastatic sites compared to primary tumors, and expression at metastatic sites only may have prognostic importance. Front. Oncol. 12, 990367 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Soupir, A. C. et al. Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment. Genome Biol. 25, 308 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

López, J. I. et al. Distinct spatial landscapes in clear-cell renal cell carcinoma as revealed by whole transcriptome analysis. Immunooncol. Technol. 21, 100690 (2024).

Article  PubMed  Google Scholar 

Hu, J. et al. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat. Genet. 56, 442–457 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, T.-Y., You, L., Hardillo, J. A. U. & Chien, M.-P. Spatial transcriptomic technologies. Cells 12, 2042 (2023).

Rao, A., Barkley, D., França, G. S. & Yanai, I. Exploring tissue architecture using spatial transcriptomics. Nature 596, 211–220 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, H. et al. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues. Preprint at bioRxiv https://doi.org/10.1101/2023.12.07.570603 (2023).

Rademacher, A. et al. Comparison of spatial transcriptomics technologies using tumor cryosections. Preprint at bioRxiv https://doi.org/10.1101/2024.04.03.586404 (2024).

Cook, D. P. et al. A comparative analysis of imaging-based spatial transcriptomics platforms. Preprint at bioRxiv https://doi.org/10.1101/2023.12.13.571385 (2023).

Kinget, L. et al. A spatial architecture-embedding HLA signature to predict clinical response to immunotherapy in renal cell carcinoma. Nat. Med. 30, 1667–1679 (2024).

Vickovic, S. et al. High-definition spatial transcriptomics for in situ tissue profiling. Nat. Methods 16, 987–990 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cervilla, S. et al. Comparison of spatial transcriptomics technologies across six cancer types. Preprint at bioRxiv https://doi.org/10.1101/2024.05.21.593407 (2024).

Oliveira, M. F. et al. Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling. Preprint at bioRxiv https://doi.org/10.1101/2024.06.04.597233 (2024).

Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moffitt, J. R. & Zhuang, X. RNA imaging with multiplexed error-robust fluorescence in situ hybridization (MERFISH). Methods Enzymol. 572, 1–49 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, X. et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361, eaat5691 (2018).

Ingimarsson, J. P. et al. The impact of tumour size on the probability of synchronous metastasis and survival in renal cell carcinoma patients: a population-based study. BMC Urol. 14, 72 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Roussel, E. et al. Molecular heterogeneity between paired primary and metastatic lesions from clear ce

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