A single-cell multi-omics integration analysis reveals prostate cancer (PCa) heterogeneity. Prostate cancer is a heterogeneous disease with a complex tumor microenvironment (TME). This study integrates single-cell RNA sequencing, spatial transcriptomics, and bulk ATAC-seq from PCa and healthy control patients. A stemness subset of club cells marked by SOX9high/ARlow expression is identified, which is enriched after neoadjuvant androgen-deprivation therapy (ADT). A subset of CD8+CXCR6+ T cells, functioning as effector T cells, is reduced in malignant PCa. Spatial transcriptome analysis uses machine learning and computational intelligence to identify prostate cancer cell diversity and cell-cell communication. Macrophage and neutrophil state transitions along cancer progression are examined. The immunosuppressive microenvironment in advanced PCa is associated with regulatory T cell (Treg) infiltration, potentially induced by FAP+ fibroblast subset. The study delineates cellular heterogeneity in stage-specific PCa microenvironment at single-cell resolution, uncovering reciprocal crosstalk with disease progression, which can aid in PCa diagnosis and therapy. Prostate cancer is a heterogeneous disease with different biological subtypes and prognostic impacts. Androgen-deprivation therapy (ADT) is the standard therapy for metastatic PCa. Although ADT is initially effective, luminal epithelial cells undergo redifferentiation or transdifferentiation and are resistant to this treatment. Previous studies show that late relapse often arises from Darwinian selection in genetically heterogeneous cancer cell populations. Prostate cancer stem cells (CSCs) are another source of biochemical recurrence after ADT. Guo et al. reported a prostate stem/progenitor cell subset marked with PSCA, CK4, and TACSTD2 expression, which exhibited a greater capacity for organoid formation in vitro and prostate epithelial duct regeneration in vivo, suggesting a potential cellular origin of prostate cancer. Another report identified a subpopulation of luminal progenitors with LY6D expression that were intrinsically resistant to castration with a bilineage gene expression pattern, indicating that there are pre-existing CSCs or progenitors that contribute to late relapses. Two rare subpopulations with unique transcriptional profiles have been reported in independent studies. One subset, named "club cell," is characterized by the expression of PIGR, MMP7, and CP. Interestingly, patient PIGR-enriched extracellular vesicles drive cancer stemness, tumorigenesis, and metastasis by activating PDK1/Akt/GSK3β/β-catenin signaling cascades in hepatocellular carcinoma. MMP7 is closely related to the EMT process, promoting invasion and migration of cancer cells. The other subset, termed "hillock cell," has a transcriptomic profile very close to club cell but uniquely expresses KRT5 and KRT13. Although previous studies haveA single-cell multi-omics integration analysis reveals prostate cancer (PCa) heterogeneity. Prostate cancer is a heterogeneous disease with a complex tumor microenvironment (TME). This study integrates single-cell RNA sequencing, spatial transcriptomics, and bulk ATAC-seq from PCa and healthy control patients. A stemness subset of club cells marked by SOX9high/ARlow expression is identified, which is enriched after neoadjuvant androgen-deprivation therapy (ADT). A subset of CD8+CXCR6+ T cells, functioning as effector T cells, is reduced in malignant PCa. Spatial transcriptome analysis uses machine learning and computational intelligence to identify prostate cancer cell diversity and cell-cell communication. Macrophage and neutrophil state transitions along cancer progression are examined. The immunosuppressive microenvironment in advanced PCa is associated with regulatory T cell (Treg) infiltration, potentially induced by FAP+ fibroblast subset. The study delineates cellular heterogeneity in stage-specific PCa microenvironment at single-cell resolution, uncovering reciprocal crosstalk with disease progression, which can aid in PCa diagnosis and therapy. Prostate cancer is a heterogeneous disease with different biological subtypes and prognostic impacts. Androgen-deprivation therapy (ADT) is the standard therapy for metastatic PCa. Although ADT is initially effective, luminal epithelial cells undergo redifferentiation or transdifferentiation and are resistant to this treatment. Previous studies show that late relapse often arises from Darwinian selection in genetically heterogeneous cancer cell populations. Prostate cancer stem cells (CSCs) are another source of biochemical recurrence after ADT. Guo et al. reported a prostate stem/progenitor cell subset marked with PSCA, CK4, and TACSTD2 expression, which exhibited a greater capacity for organoid formation in vitro and prostate epithelial duct regeneration in vivo, suggesting a potential cellular origin of prostate cancer. Another report identified a subpopulation of luminal progenitors with LY6D expression that were intrinsically resistant to castration with a bilineage gene expression pattern, indicating that there are pre-existing CSCs or progenitors that contribute to late relapses. Two rare subpopulations with unique transcriptional profiles have been reported in independent studies. One subset, named "club cell," is characterized by the expression of PIGR, MMP7, and CP. Interestingly, patient PIGR-enriched extracellular vesicles drive cancer stemness, tumorigenesis, and metastasis by activating PDK1/Akt/GSK3β/β-catenin signaling cascades in hepatocellular carcinoma. MMP7 is closely related to the EMT process, promoting invasion and migration of cancer cells. The other subset, termed "hillock cell," has a transcriptomic profile very close to club cell but uniquely expresses KRT5 and KRT13. Although previous studies have