{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T22:14:23Z","timestamp":1790028863356,"version":"4.0.1"},"reference-count":82,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T00:00:00Z","timestamp":1756166400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Malignant genitourinary tumors have demonstrated a rising incidence and are characterized by significant morbidity and mortality. Advances in sequencing technologies have greatly enhanced our understanding of the genetic and molecular mechanisms that drive tumor biology. In recent years, spatial transcriptomics technologies have rapidly evolved, enabling precise quantification and visualization of gene expression within the spatial context of tissues. Unlike conventional transcriptomics, which focuses on gene expression levels, spatial transcriptomics provides additional insights into the spatial distribution of genes within tissues, cellular composition, and cell-to-cell interactions within biological samples. In this narrative review, we outline the emerging role and future potential of spatial transcriptomics technology in genitourinary cancers.<\/jats:p>","DOI":"10.3390\/cancers17172774","type":"journal-article","created":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T10:35:17Z","timestamp":1756204517000},"page":"2774","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Current Role and Future Frontiers of Spatial Transcriptomics in Genitourinary Cancers"],"prefix":"10.3390","volume":"17","author":[{"given":"Firas","family":"Hatoum","sequence":"first","affiliation":[{"name":"Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adnan","family":"Fazili","sequence":"additional","affiliation":[{"name":"Department of Genitourinary Oncology, H. 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Biology, 12.","DOI":"10.3390\/biology12091183"},{"key":"ref_2","first-page":"229","article-title":"Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s12964-020-0530-4","article-title":"Tumor Microenvironment Complexity and Therapeutic Implications at a Glance","volume":"18","author":"Baghban","year":"2020","journal-title":"Cell Commun. Signal."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","article-title":"Museum of Spatial Transcriptomics","volume":"19","author":"Moses","year":"2022","journal-title":"Nat. Methods"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Molla Desta, G., and Birhanu, A.G. (2025). Advancements in Single-Cell RNA Sequencing and Spatial Transcriptomics: Transforming Biomedical Research. Acta Biochim. Pol., 72.","DOI":"10.3389\/abp.2025.13922"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/s41586-024-08087-4","article-title":"Tumour Evolution and Microenvironment Interactions in 2D and 3D Space","volume":"634","author":"Mo","year":"2024","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"302","DOI":"10.20517\/2394-4722.2017.34","article-title":"Tumor Heterogeneity and Therapy Resistance\u2014Implications for Future Treatments of Prostate Cancer","volume":"3","author":"Frame","year":"2017","journal-title":"J. Cancer Metastasis Treat."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"152389","DOI":"10.1016\/j.seminoncol.2025.152389","article-title":"From Tissue Architecture to Clinical Insights: Spatial Transcriptomics in Solid Tumor Studies","volume":"52","author":"Sharma","year":"2025","journal-title":"Semin. Oncol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1158\/1078-0432.CCR-14-1213","article-title":"Intratumoral Heterogeneity: From Diversity Comes Resistance","volume":"21","author":"Pribluda","year":"2015","journal-title":"Clin. Cancer Res."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R.P., Banday, S., Mishra, A.K., and Das, G. (2023). Next-Generation Sequencing Technology: Current Trends and Advancements. Biology, 12.","DOI":"10.3390\/biology12070997"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2206939","DOI":"10.1002\/advs.202206939","article-title":"Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research","volume":"10","author":"Park","year":"2023","journal-title":"Adv. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.eururo.2024.08.025","article-title":"Clinical Implications of Basic Research: Exploring the Transformative Potential of Spatial \u2019Omics in Uro-Oncology","volume":"87","author":"Figiel","year":"2025","journal-title":"Eur. Urol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1186\/s12967-025-06358-w","article-title":"Spatial Relationships and Interactions of Immune Cell Niches Are Linked to the Pathologic Response of Muscle-Invasive Bladder Cancer to Neoadjuvant Therapy","volume":"23","author":"Wahafu","year":"2025","journal-title":"J. Transl. Med."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Jespersen, J., Lindgaard, C., Iisager, L., Ahrenfeldt, J., and Lyskj\u00e6r, I. (Nat. Rev. Urol., 2025). Lessons learned from spatial transcriptomic analyses in clear-cell renal cell carcinoma, Nat. Rev. Urol., Online ahead of print.","DOI":"10.1038\/s41585-024-00980-x"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1038\/225946a0","article-title":"Autoradiographic Detection of Molecular Hybrids between RNA and DNA in Tissue Sections","volume":"225","author":"Amaldi","year":"1970","journal-title":"Nature"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nmeth.2892","article-title":"Single-Cell in Situ RNA Profiling by Sequential Hybridization","volume":"11","author":"Lubeck","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s12943-024-02040-9","article-title":"Advances in Spatial Transcriptomics and Its Applications in Cancer Research","volume":"23","author":"Jin","year":"2024","journal-title":"Mol. Cancer"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"110671","DOI":"10.1016\/j.ygeno.2023.110671","article-title":"Spatial Transcriptomics: Technologies, Applications and Experimental Considerations","volume":"115","author":"Wang","year":"2023","journal-title":"Genomics"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Lim, H.J., Wang, Y., Buzdin, A., and Li, X. (2025). A Practical Guide for Choosing an Optimal Spatial Transcriptomics Technology from Seven Major Commercially Available Options. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11235-3"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Jacobsen, S.B., Tfelt-Hansen, J., Smerup, M.H., Andersen, J.D., and Morling, N. (2023). Comparison of Whole Transcriptome Sequencing of Fresh, Frozen, and Formalin-Fixed, Paraffin-Embedded Cardiac Tissue. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0283159"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1038\/s41467-018-04724-5","article-title":"Spatial Maps of Prostate Cancer Transcriptomes Reveal an Unexplored Landscape of Heterogeneity","volume":"9","author":"Berglund","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e1338","DOI":"10.1002\/ctm2.1338","article-title":"Integrated Single-Cell and Spatial Transcriptomic Profiling Reveals Higher Intratumour Heterogeneity and Epithelial-Fibroblast Interactions in Recurrent Bladder Cancer","volume":"13","author":"Shi","year":"2023","journal-title":"Clin. Transl. Med."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Chen, T.-Y., You, L., Hardillo, J.A.U., and Chien, M.-P. (2023). Spatial Transcriptomic Technologies. Cells, 12.","DOI":"10.3390\/cells12162042"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Du, M.R.M., Wang, C., Law, C.W., Amann-Zalcenstein, D., Anttila, C.J.A., Ling, L., Hickey, P.F., Sargeant, C.J., Chen, Y., and Ioannidis, L.J. (2025). Benchmarking Spatial Transcriptomics Technologies with the Multi-Sample SpatialBenchVisium Dataset. Genome Biol., 26.","DOI":"10.1186\/s13059-025-03543-4"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1186\/s12967-023-04150-2","article-title":"Advances in Spatial Transcriptomics and Related Data Analysis Strategies","volume":"21","author":"Du","year":"2023","journal-title":"J. Transl. Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e669","DOI":"10.1002\/ctm2.669","article-title":"Clinical Challenges of Tissue Preparation for Spatial Transcriptome","volume":"12","author":"Liu","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1016\/j.cels.2024.09.005","article-title":"SpotGF: Denoising Spatially Resolved Transcriptomics Data Using an Optimal Transport-Based Gene Filtering Algorithm","volume":"15","author":"Du","year":"2024","journal-title":"Cell Syst."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s44272-024-00018-8","article-title":"Spatial Transcriptomics: A New Frontier in Cancer Research","volume":"3","author":"Huang","year":"2024","journal-title":"CCB"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1016\/j.csbj.2023.01.016","article-title":"A Guidebook of Spatial Transcriptomic Technologies, Data Resources and Analysis Approaches","volume":"21","author":"Yue","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial Transcriptomics at Subspot Resolution with BayesSpace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chakrabarti, A., Ni, Y., and Mallick, B.K. (2024). Joint Bayesian Estimation of Cell Dependence and Gene Associations in Spatially Resolved Transcriptomic Data. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-60002-z"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1038\/s41467-023-37168-7","article-title":"A Comprehensive Benchmarking with Practical Guidelines for Cellular Deconvolution of Spatial Transcriptomics","volume":"14","author":"Li","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2055","DOI":"10.1002\/ijc.34708","article-title":"Spatial Whole Transcriptome Profiling of Primary Tumor from Patients with Metastatic Prostate Cancer","volume":"153","author":"Salachan","year":"2023","journal-title":"Int. J. Cancer"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Chen, Z., Cao, W., Luo, J., Abdelrahman, Z., Lu, Q., Wang, H., and Wang, X. (2023). Gene Set Enrichment Analysis Identifies Immune Subtypes of Kidney Renal Clear Cell Carcinoma with Significantly Different Molecular and Clinical Properties. Front. Immunol., 14.","DOI":"10.3389\/fimmu.2023.1191365"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Zvirblyte, J., Nainys, J., Juzenas, S., Goda, K., Kubiliute, R., Dasevicius, D., Kincius, M., Ulys, A., Jarmalaite, S., and Mazutis, L. (2024). Single-Cell Transcriptional Profiling of Clear Cell Renal Cell Carcinoma Reveals a Tumor-Associated Endothelial Tip Cell Phenotype. Commun. Biol., 7.","DOI":"10.1038\/s42003-024-06478-x"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/s41417-024-00755-x","article-title":"The Integrate Profiling of Single-Cell and Spatial Transcriptome RNA-Seq Reveals Tumor Heterogeneity, Therapeutic Targets, and Prognostic Subtypes in ccRCC","volume":"31","author":"Zhang","year":"2024","journal-title":"Cancer Gene Ther."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Wang, Y., Zheng, X.-D., Zhu, G.-Q., Li, N., Zhou, C.-W., Yang, C., and Zeng, M.-S. (2022). Crosstalk Between Metabolism and Immune Activity Reveals Four Subtypes with Therapeutic Implications in Clear Cell Renal Cell Carcinoma. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.861328"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/s41585-023-00847-7","article-title":"Molecular Profile of Bladder Cancer Progression to Clinically Aggressive Subtypes","volume":"21","author":"Guo","year":"2024","journal-title":"Nat. Rev. Urol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/s41585-020-0304-1","article-title":"Genomic Heterogeneity in Bladder Cancer: Challenges and Possible Solutions to Improve Outcomes","volume":"17","author":"Meeks","year":"2020","journal-title":"Nat. Rev. Urol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Chen, H., Yang, W., Xue, X., Li, Y., Jin, Z., and Ji, Z. (2022). Neoadjuvant Immunotherapy and Chemoimmunotherapy for Stage II-III Muscle Invasive Bladder Cancer. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.986359"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2098","DOI":"10.1016\/j.ccell.2024.10.016","article-title":"Molecular Heterogeneity in Urothelial Carcinoma and Determinants of Clinical Benefit to PD-L1 Blockade","volume":"42","author":"Hamidi","year":"2024","journal-title":"Cancer Cell"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3225","DOI":"10.1200\/JCO.22.02144","article-title":"Novel Genetic Subtypes of Urothelial Carcinoma with Differential Outcomes on Immune Checkpoint Blockade","volume":"41","author":"Sarfaty","year":"2023","journal-title":"J. Clin. Oncol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s40425-018-0314-1","article-title":"Biomarkers of Immunotherapy in Urothelial and Renal Cell Carcinoma: PD-L1, Tumor Mutational Burden, and Beyond","volume":"6","author":"Zhu","year":"2018","journal-title":"J. Immunother. Cancer"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1038\/s41467-021-22465-w","article-title":"An Integrated Multi-Omics Analysis Identifies Prognostic Molecular Subtypes of Non-Muscle-Invasive Bladder Cancer","volume":"12","author":"Lindskrog","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Mo, Q., Li, R., Adeegbe, D.O., Peng, G., and Chan, K.S. (2020). Integrative Multi-Omics Analysis of Muscle-Invasive Bladder Cancer Identifies Prognostic Biomarkers for Frontline Chemotherapy and Immunotherapy. Commun. Biol., 3.","DOI":"10.1038\/s42003-020-01491-2"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e008571","DOI":"10.1136\/jitc-2023-008571","article-title":"Spatial Comparison of Molecular Features Associated with Resistance to Pembrolizumab in BCG Unresponsive Bladder Cancer","volume":"12","author":"Meghani","year":"2024","journal-title":"J. Immunother. Cancer"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"9949","DOI":"10.1038\/s41467-024-54364-1","article-title":"Single Cell and Spatial Transcriptomics Highlight the Interaction of Club-like Cells with Immunosuppressive Myeloid Cells in Prostate Cancer","volume":"15","author":"Kiviaho","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/onc.2013.235","article-title":"Androgen Receptor Functions in Castration-Resistant Prostate Cancer and Mechanisms of Resistance to New Agents Targeting the Androgen Axis","volume":"33","author":"Yuan","year":"2014","journal-title":"Oncogene"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Kwon, W.-A., and Joung, J.Y. (2025). Immunotherapy in Prostate Cancer: From a \u201cCold\u201d Tumor to a \u201cHot\u201d Prospect. Cancers, 17.","DOI":"10.3390\/cancers17071064"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.eururo.2018.03.028","article-title":"Update on Systemic Prostate Cancer Therapies: Management of Metastatic Castration-Resistant Prostate Cancer in the Era of Precision Oncology","volume":"75","author":"Nuhn","year":"2019","journal-title":"Eur. Urol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1080\/10408363.2023.2266482","article-title":"Therapeutic Biomarkers in Metastatic Castration-Resistant Prostate Cancer: Does the State Matter?","volume":"61","author":"Slootbeek","year":"2024","journal-title":"Crit. Rev. Clin. Lab. Sci."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.eururo.2024.03.038","article-title":"Single-Cell Atlas of Penile Cancer Reveals TP53 Mutations as a Driver of an Aggressive Phenotype, Irrespective of Human Papillomavirus Status, and Provides Clues for Treatment Personalization","volume":"86","author":"Elst","year":"2024","journal-title":"Eur. Urol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1097\/MOU.0000000000001183","article-title":"Recent Contributions of Single-Cell and Spatial Profiling to the Understanding of Bladder Cancer","volume":"34","author":"Grausenburger","year":"2024","journal-title":"Curr. Opin. Urol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Feng, C., Wang, Y., Song, W., Liu, T., Mo, H., Liu, H., Wu, S., Qin, Z., Wang, Z., and Tao, Y. (2024). Spatially-Resolved Analyses of Muscle Invasive Bladder Cancer Microenvironment Unveil a Distinct Fibroblast Cluster Associated with Prognosis. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1522582"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"18","DOI":"10.2174\/138920209787581307","article-title":"The Role of Androgen Receptor Mutations in Prostate Cancer Progression","volume":"10","author":"Brooke","year":"2009","journal-title":"Curr. Genom."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Miyagi, H., Yu, X., Peak, T., Dhillon, J., Le, C., Wang, X., Yoder, S., Marchion, D., Lu, X., and Pettaway, C. (2025). Progressive T Cell Exhaustion and Predominance of Aging Tissue Associated Macrophages with Advancing Disease Stage in Penile Squamous Cell Carcinoma. Sci. Rep., 15.","DOI":"10.1038\/s41598-025-89760-0"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1038\/s41467-023-37211-7","article-title":"Epigenetic and Transcriptomic Characterization Reveals Progression Markers and Essential Pathways in Clear Cell Renal Cell Carcinoma","volume":"14","author":"Wu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Wang, Y., Ma, S., and Ruzzo, W.L. (2020). Spatial Modeling of Prostate Cancer Metabolic Gene Expression Reveals Extensive Heterogeneity and Selective Vulnerabilities. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-60384-w"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"115206","DOI":"10.1016\/j.celrep.2024.115206","article-title":"Tumor-Induced Metabolic Immunosuppression: Mechanisms and Therapeutic Targets","volume":"44","author":"Ricci","year":"2025","journal-title":"Cell Rep."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1016\/j.cell.2024.02.041","article-title":"Cancer Biomarkers: Emerging Trends and Clinical Implications for Personalized Treatment","volume":"187","author":"Passaro","year":"2024","journal-title":"Cell"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1016\/j.ccell.2024.09.001","article-title":"Spatial Oncology: Translating Contextual Biology to the Clinic","volume":"42","author":"Gong","year":"2024","journal-title":"Cancer Cell"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Lee, Y., Lee, M., Shin, Y., Kim, K., and Kim, T. (2025). Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26093949"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"104190","DOI":"10.1016\/j.labinv.2025.104190","article-title":"Rigor and Reproducibility of Spatial Transcriptomics Performed on Clinically Sourced Human Tissues","volume":"105","author":"Smith","year":"2025","journal-title":"Lab. Investig."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"101918","DOI":"10.1016\/j.xcrm.2024.101918","article-title":"Single-Molecule Systems for the Detection and Monitoring of Plasma-Circulating Nucleosomes and Oncoproteins in Diffuse Midline Glioma","volume":"6","author":"Erez","year":"2025","journal-title":"Cell Rep. Med."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"7280","DOI":"10.1038\/s41467-024-50904-x","article-title":"Inferring Histology-Associated Gene Expression Gradients in Spatial Transcriptomic Studies","volume":"15","author":"Kueckelhaus","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"100723","DOI":"10.1016\/j.xgen.2024.100723","article-title":"scTrends: A Living Review of Commercial Single-Cell and Spatial \u2019omic Technologies","volume":"4","author":"Opzoomer","year":"2024","journal-title":"Cell Genom."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Vitorino, R. (2024). Transforming Clinical Research: The Power of High-Throughput Omics Integration. Proteomes, 12.","DOI":"10.3390\/proteomes12030025"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e71542","DOI":"10.7554\/eLife.71542","article-title":"Spatial Transcriptomics Reveals Metabolic Changes Underly Age-Dependent Declines in Digit Regeneration","volume":"11","author":"Tower","year":"2022","journal-title":"eLife"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Kreitmann, L., D\u2019Souza, G., Miglietta, L., Vito, O., Jackson, H.R., Habgood-Coote, D., Levin, M., Holmes, A., Kaforou, M., and Rodriguez-Manzano, J. (2024). A Computational Framework to Improve Cross-Platform Implementation of Transcriptomics Signatures. eBioMedicine, 105.","DOI":"10.1016\/j.ebiom.2024.105204"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1038\/s41467-023-40271-4","article-title":"Spatial Transcriptomics Reveals Distinct and Conserved Tumor Core and Edge Architectures That Predict Survival and Targeted Therapy Response","volume":"14","author":"Arora","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"8123","DOI":"10.1038\/s41467-023-43915-7","article-title":"STalign: Alignment of Spatial Transcriptomics Data Using Diffeomorphic Metric Mapping","volume":"14","author":"Clifton","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"100325","DOI":"10.1016\/j.crmeth.2022.100325","article-title":"Challenges and Considerations for Single-Cell and Spatially Resolved Transcriptomics Sample Collection during Spaceflight","volume":"2","author":"Overbey","year":"2022","journal-title":"Cell Rep. Methods"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"6692","DOI":"10.1038\/s41467-021-27017-w","article-title":"Machine Learning of Genomic Features in Organotropic Metastases Stratifies Progression Risk of Primary Tumors","volume":"12","author":"Jiang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.7150\/thno.95908","article-title":"Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery","volume":"14","author":"Cao","year":"2024","journal-title":"Theranostics"},{"key":"ref_75","first-page":"21","article-title":"The Implications of Single-Cell RNA-Seq Analysis in Prostate Cancer: Unraveling Tumor Heterogeneity, Therapeutic Implications and Pathways towards Personalized Therapy","volume":"11","author":"Feng","year":"2024","journal-title":"Mil. Med. Res."},{"key":"ref_76","unstructured":"(2025, April 16). Deep Learning in Integrating Spatial Transcriptomics with Other Modalities|Briefings in Bioinformatics|Oxford Academic. Available online: https:\/\/academic.oup.com\/bib\/article\/26\/1\/bbae719\/7952009."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/s43018-024-00904-z","article-title":"Spatially Resolved Transcriptomics and Graph-Based Deep Learning Improve Accuracy of Routine CNS Tumor Diagnostics","volume":"6","author":"Ritter","year":"2025","journal-title":"Nat. Cancer"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/s41585-022-00571-8","article-title":"Therapeutic Potential of CDK4\/6 Inhibitors in Renal Cell Carcinoma","volume":"19","author":"Sager","year":"2022","journal-title":"Nat. Rev. Urol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Monjo, T., Koido, M., Nagasawa, S., Suzuki, Y., and Kamatani, Y. (2022). Efficient Prediction of a Spatial Transcriptomics Profile Better Characterizes Breast Cancer Tissue Sections without Costly Experimentation. Sci. Rep., 12.","DOI":"10.1038\/s41598-022-07685-4"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"100374","DOI":"10.1016\/j.xgen.2023.100374","article-title":"A Standard for Sharing Spatial Transcriptomics Data","volume":"3","author":"Jackson","year":"2023","journal-title":"Cell Genom."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Moody, S.C., Fietz, D., Nathaniel, B., Frydenberg, M., Tran, B., Schuppe, H.C., and Loveland, K.L. (Andrology, 2025). Spatial transcriptomics mapping of immune cell and TGF\u03b2 signalling path-way heterogeneity in testicular germ cell tumours, Andrology, Online ahead of print.","DOI":"10.1111\/andr.70100"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"8462","DOI":"10.1038\/s41467-023-44305-9","article-title":"Single-Cell Multi-Omics Analysis of Human Testicular Germ Cell Tumor Reveals Its Molecular Features and Microenvironment","volume":"14","author":"Lu","year":"2023","journal-title":"Nat. Commun."}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/17\/2774\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:32:51Z","timestamp":1760034771000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/17\/2774"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,26]]},"references-count":82,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["cancers17172774"],"URL":"https:\/\/doi.org\/10.3390\/cancers17172774","relation":{},"ISSN":["2072-6694"],"issn-type":[{"value":"2072-6694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,26]]}}}