Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease

Single-cell transcriptomic reveals network topology changes of cancer at the individual level

Network biology facilitates a better understanding of complex diseases. Single-sample networks retain individual information and have the potential to distinguish disease status. Previous studies mainly used bulk RNA sequencing data to construct single-sample networks, but different cell types in the tissue microenvironment perform significantly different functions. In this study, we investigated whether network topology features of cell-type-specific networks varied in different pathological states at the individual level. Protein-protein interaction network (PPI) and co-expression network of cancer and ulcerative colitis were established using four publicly single-cell RNA sequencing (scRNA-seq) datasets. We analyzed cell-cell interactions of epithelial cells and immune cells using CellChat R package. Network topology changes between normal tissues and pathological tissues were analyzed using Cytoscape software and QUACN R package. Results showed cell-cell interactions of epithelial cells were enhanced in carcinoma and adenoma. The average number of neighbors and graphindex of co-expression network increased in epithelial cells of adenoma, carcinoma and paracancer compared with normal tissues. The co-expression network density of T cells in tumors was significantly higher than that in normal tissues. The co-expression network complexity of epithelial cells in the benign tissues was associated with the grade group of paired tumors. This study suggests topological properties of cell-type-specific individual network vary in different pathological states, providing an insight into understanding complex diseases.

Association of High Tumor-Stroma Ratio with Prostate Cancer Progression: Insights from Clinical and Genomic Data

Background

Tumor stroma ratio (TSR) is a prognostic factor in various cancers, but its role in prostate adenocarcinoma (PRAD) remains unclear. This study investigates TSR's prognostic value in PRAD using clinicopathological data, bulk/single-cell RNA sequencing to explore tumor-stroma interactions and identify therapeutic targets.

Methods

Two PRAD cohorts (The Cancer Genome Atlas cohort, TCGA; Lanzhou University Second Hospital, LUSH) were analyzed for TSR associations with clinicopathological features and biochemical recurrence (BCR). TSR was assessed via digital image analysis and expert pathologist review. Publicly available bulk/single-cell RNA sequencing data were analyzed to identify TSR-associated genes and predict drug targets, pathways, and immunotherapy responses. Quantitative real-time PCR validated mRNA expression. In vitro assays assessed cell proliferation, growth, and migration, while in vivo xenograft assays validated BGN's role in promoting tumorigenesis.

Results

TSR significantly correlated with clinicopathological features (age, Gleason score, stage, seminal vesicle invasion, BCR) in both TCGA (n = 453) and LUSH (n = 320) cohorts. High TSR independently predicted BCR in multivariable Cox regression. High TSR was associated with copy number variations, differentially expressed miRNAs/transcription factors, and metabolic pathways. Predicted anti-cancer drug targets, like Ki8751, showed potential benefit in high-TSR patients. High TSR may correlate with poor immunotherapy response. Notably, downregulation of BGN in cancer-associated fibroblasts (CAFs) significantly suppressed cell proliferation, migration, and invasion in vitro, and in vivo xenograft assays confirmed that BGN downregulation inhibited tumor growth.

Conclusion

This study highlights TSR's prognostic significance in prostate cancer and its association with adverse clinical outcomes and complex tumor-stroma interactions, identifying BGN, a stromal cell-related gene, as a potential therapeutic target for CAFs. However, these findings are limited by the retrospective design, necessitating prospective validation.

Bolstering CD8+ T Cells' Antitumor Immunity: A Promising Strategy to Improve the Response to Advanced Prostate Cancer Treatment

Prostate cancer is among the most frequently diagnosed and deadly cancers among men in the Western world. It is typically classified as an immune "cold" tumor due to its sparse immune cell presence and limited immunogenic response. Recent research has revealed the significant role of immune cells, especially CD8+ T cells, in both prostate cancer progression and treatment efficacy. This review integrates recent findings to provide a comprehensive overview of the current understanding of CD8+ T cell dynamics in prostate cancer and discusses emerging strategies to improve treatment outcomes. The ongoing exploration of new molecular targets and the development of innovative immunotherapeutic approaches hold promise for more effective management of prostate cancer, particularly in the context of advanced and resistant forms of the disease.

Development of a machine learning-based predictive risk model combining fatty acid metabolism and ferroptosis for immunotherapy response and prognosis in prostate cancer

Prostate cancer (PCa) remains a leading cause of cancer-related mortality, necessitating robust prognostic models and personalized therapeutic strategies. This study integrated bulk RNA sequencing, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics to construct a prognostic model based on genes shared between ferroptosis and fatty acid metabolism (FAM). Using the TCGA-PRAD dataset, we identified 73 differentially expressed genes (DEGs) at the intersection of ferroptosis and FAM, of which 19 were significantly associated with progression-free survival (PFS). A machine learning-based prognostic model, optimized using the Lasso + Random Survival Forest (RSF) algorithm, achieved a high C-index of 0.876 and demonstrated strong predictive accuracy (1-, 2-, and 3-year AUCs: 0.77, 0.75, and 0.78, respectively). The model, validated in the DFKZ cohort, stratified patients into high- and low-risk groups, with the high-risk group exhibiting worse PFS and higher tumor mutation burden (TMB). Functional enrichment analysis revealed distinct pathway activities, with high-risk patients showing enrichment in immune-related and proliferative pathways, while low-risk patients were enriched in metabolic pathways. Immune microenvironment analysis revealed heightened immune activity in high-risk patients, characterized by increased infiltration of CD8 + T cells, regulatory T cells, and M2 macrophages, alongside elevated TIDE scores, suggesting immune evasion and resistance to immunotherapy. In contrast, low-risk patients exhibited higher infiltration of plasma cells and neutrophils and demonstrated better responses to immune checkpoint inhibitors (ICIs). Spatial transcriptomics and scRNA-seq further elucidated the spatial distribution of model genes, highlighting the central role of macrophages in mediating risk stratification. Additionally, chemotherapy sensitivity analysis identified potential therapeutic agents, such as Erlotinib and Picolinic acid, for low-risk patients. In vitro experiments showed that overexpression of CD38 in the PC-3 cell line led to elevated lipid peroxidation (C11-BODIPY) and reactive oxygen species (ROS), suggesting increased cell ferroptosis. These findings provide a comprehensive framework for risk stratification and personalized treatment in PCa, bridging molecular mechanisms with clinical outcomes.

Immunomodulation and Immunotherapy for Patients with Prostate Cancer: An Up-to-Date Review

Immunotherapy alone or in combination with chemotherapy or radiotherapy is the frontline treatment for melanoma and lung cancer. However, its role in prostate cancer is usually as a fourth-line treatment. It is usually employed in patients with metastasis, after androgen blockade and chemotherapy. This article reviews the immunosuppressive effects of prostate cancer and possible uses of various types of immunotherapies. It also considers when would be the optimal time to employ this type of therapy.

CTHRC1 expresses in cancer-associated fibroblasts and is associated with resistance to anti-androgen therapy in prostate cancer

BACKGROUND

CTHRC1 overexpresses in prostate cancer and is associated with the proliferation, invasion and migration of prostate cancer cells. However, the roles and mechanisms of CTHRC1 expression in prostate cancer prognosis and treatment outcomes remain unknown.

OBJECTIVE

This study aimed to explore the expression and gene function of CTHRC1 in prostate cancer, investigate the prognostic value and potential effect in the treatment of prostate cancer.

METHODS

Bulk and single-cell RNA sequencing analyses were used to evaluate the expression of CTHRC1 in prostate cancer. All data used in the study were obtained from publicly available sources to ensure transparency. Study enrolled 1999 cases of prostate cancer and 531 normal controls. Single-cell RNA sequencing profile included 62,995 cells from seven prostate primary tumors. CTHRC1 expression and prognosis analyses were conducted with these samples and verified by immunohistochemical staining. CIBERSORT algorithm was used to assess the tumor immune infiltrating cells based on bulk mRNA sequencing profiles. Genomics of drug sensitivity in cancer (GDSC) database was used to predict IC50 to anti-androgen therapy (ADT) drugs of the samples.

RESULTS

CTHRC1 expressed in prostate cancer was higher than that in normal prostate tissue, and the expression increased with the progress of prostate cancer. CTHRC1 was the risk factor of progression-free interval (PFI). CTHRC1 was positively correlated with the infiltration of tumor-associated macrophages (TAMs). Myofibroblast-like cancer-associated fibroblasts (myCAFs) were the major CTHRC1 expressers in prostate cancer. TGF-β signaling activated in CTHRC1-positive myCAFs and was involved in TAMs polarization. Biological functions of myCAFs were enriched in hormone response and metabolism. CTHRC1 may regulate androgen receptor signaling through CCN2/CAV1/AR pathway. Moreover, ADT drug Bicalutamide and AZD3514 were less sensitive in the high CTHRC1 expression tumors.

CONCLUSIONS

As a potential molecular target of ADT resistance in prostate cancer, CTHRC1 provides a new promising molecular approach for the diagnosis and treatment of prostate cancer.

Reduction of alternative polarization of macrophages by short-term activated hepatic stellate cell-derived small extracellular vesicles

BACKGROUND

Activated hepatic stellate cells (HSCs) induce alternative (M2) polarization of macrophages and contribute to the progression of fibrosis and hepatocellular carcinoma (HCC). However, the effects of small extracellular vesicles released by HSCs (HSC-sEVs) during activation remain largely unknown.

METHODS

The aim of this study was to investigate the role of extracellular vesicles released by HSCs (HSC-sEVs) at different stages of activation in macrophage polarization. The effects of sEVs from short-term activated and long-term activated HSCs on liver macrophages was studied. Small RNA sequencing analyses were performed to obtain differential miRNAs transported by the short-term and long-term activated HSC- sEVs. The in vivo effects of short-term activated HSC-sEV-specific miRNA on liver macrophage and liver fibrosis were confirmed in a CCl4-induced liver injury mouse model. To study the tumor suppressive effects of the macrophages educated by short-term activated HSC-sEV-specific miRNA, human hepatoma cells were mixed and subcutaneously cotransplanted with miR-99a-5p mimic-pretreated macrophages.

RESULTS

We found that consistent with activated HSCs, long-term activated HSC-sEVs (14dHSC-sEVs) induce bone marrow-derived monocytes (MOs) toward an M2 phenotype, but short-term activated HSC-sEVs (3dHSC-sEVs) induce the resident macrophages (Kupffer cells, KCs) toward a classically activated (M1) phenotype. We identified five 3dHSC-sEV-specific miRNAs, including miR-99a-5p. In vitro and in vivo experiments support that miR-99a-5p negatively regulates alternative polarization of macrophages, decreases collagen deposition in chronic liver injury model, and suppresses the progression of hepatoma in a xenograft model partially by targeting CD93.

CONCLUSION

Collectively, our work reveals an unexpected proinflammatory role of 3dHSC-sEVs, preliminarily explores the underlying mechanism, and evaluates the therapeutic potential of 3dHSC-sEV-specific miR-99a-5p for liver fibrosis and tumorigenesis.

Applications of gene pair methods in clinical research: advancing precision medicine

The rapid evolution of high-throughput sequencing technologies has revolutionized biomedical research, producing vast amounts of gene expression data that hold immense potential for biological discovery and clinical applications. Effectively mining these large-scale, high-dimensional data is crucial for facilitating disease detection, subtype differentiation, and understanding the molecular mechanisms underlying disease progression. However, the conventional paradigm of single-gene profiling, measuring absolute expression levels of individual genes, faces critical limitations in clinical implementation. These include vulnerability to batch effects and platform-dependent normalization requirements. In contrast, emerging approaches analyzing relative expression relationships between gene pairs demonstrate unique advantages. By focusing on binary comparisons of two genes' expression magnitudes, these methods inherently normalize experimental variations while capturing biologically stable interaction patterns. In this review, we systematically evaluate gene pair-based analytical frameworks. We classify eleven computational approaches into two fundamental categories: expression value-based methods quantifying differential expression patterns, and rank-based methods exploiting transcriptional ordering relationships. To bridge methodological development with practical implementation, we establish a reproducible analytical pipeline incorporating feature selection, classifier construction, and model evaluation modules using real-world benchmark datasets from pulmonary tuberculosis studies. These findings position gene pair analysis as a transformative paradigm for mining high-dimensional omics data, with direct implications for precision biomarker discovery and mechanistic studies of disease progression.

TREM2+ macrophages: a key role in disease development

Triggering receptors expressed on myeloid cells 2 (TREM2), an immune receptor expressed on myeloid cells, has garnered considerable attention in recent years due to its role in unique signaling pathways and diverse biological functions, including phagocytosis, lipid metabolism, cell survival, and inflammatory responses. Although TREM2 is expressed in various cell types, such as macrophages, dendritic cells (DCs), osteoclasts, and others, where it exhibits context-dependent functional characteristics, it is mainly expressed in macrophages. Notably, TREM2 is implicated in the development and progression of multiple diseases, playing dual and often opposing roles in noncancerous diseases and cancers. This review aims to highlight the pivotal role of TREM2 in macrophages and immune-related diseases, elucidate its underlying mechanisms of action, explore its potential as a clinical diagnostic and prognostic marker, and propose therapeutic strategies targeting TREM2 based on current clinical trial data, providing comprehensive guidance and references for clinical practice.

Single-cell and transcriptome analyses revealed CTHRC1 a potential therapeutic target mediating invasion and tumor microenvironment in TNBC: experimental validation

Background

Investigating the pivotal role of CTHRC1 in the tumor microenvironment of triple-negative breast cancer (TNBC).

Method

The RNA transcriptomic data obtained from the Cancer Genome Atlas and single-cell sequencing data from TNBC in Gene Expression Omnibus (GEO) were acquired and subjected to analysis. A comprehensive investigation was conducted with a specific focus on characterizing CTHRC1 in TNBC and its correlation with invasive genes. Furthermore, additional analyses were performed to explore the relationship between CTHRC1, tumor immune cell infiltration, and immunotherapy in TNBC. The expression of CTHRC1 in the tumor microenvironment, cellular differentiation, and cellular communication was systematically analyzed using single-cell data from TNBC.

Result

The expression of CTHRC1 in patients with TNBC gradually increases concomitantly with the progression of tumor T-stage and N-stage. Simultaneously, there is a concurrent increase in the expression of most invasive gene sets. Furthermore, there is a significant augmentation in both infiltration abundance and activity of M2-type macrophages associated with elevated levels of CTHRC1 expression. Single-cell data reveal an upregulated expression of the invasive gene set in CTHRC1-positive cancer associated fibroblasts (CAFs), thereby modulating their interaction with M2-type macrophages. Multiple immunofluorescence analyses confirmed that CTHRC1 modulates immune cell infiltration and tumor cell invasion through the mediation of CAFs.

Conclusion

CTHRC1 was a molecule that exhibits characteristic expression in TNBC. CTHRC1 positive CAFs exert regulatory effects within the immunosuppressive microenvironment of TNBC by modulating M2-type macrophages.

Recent advances in basic research on prostate cancer: Where we are heading?

In the over 80 years since androgens were found to play a pivotal role in prostate cancer (PCa) progression, androgen deprivation therapy (ADT) has been a cornerstone in treating advanced PCa. Castration-resistant PCa persists, however, with some of these tumors evolving to androgen receptor (AR)-independent forms like neuroendocrine PCa. The development of novel diagnostic and therapeutic approaches to PCa is therefore crucial. This review provides an overview of recent basic research in PCa, focusing on two main areas: PCa cells and their tumor microenvironments. The first section describes current knowledge on the intricate mechanisms of AR signaling pathways, emphasizing the roles of coactivators and chromatin state alterations in gene regulation. Genomic analyses have revealed recurrent mutations and copy number alterations critical for precision medicine. Liquid biopsy has become a promising tool for real-time tumor monitoring, identifying genetic alterations in circulating-tumor DNA or extracellular vesicles. The second section describes the tumor microenvironment of PCa, highlighting its immunosuppressive landscape and the potential of combining ADT with immunotherapy. Advanced techniques, including single-cell RNA sequencing and spatial transcriptomics offer insights into cellular heterogeneity and interactions within the tumor microenvironment, paving the way for novel therapeutic strategies. Integration of these diverse research areas will provide a comprehensive understanding of the current state and future directions of PCa research, underscoring the importance of personalized medicine and the dynamic nature of cancer treatment strategies.

Overexpression of fibroblast activation protein (FAP) in the stroma of proliferative inflammatory atrophy (PIA) and primary adenocarcinoma of the prostate

Fibroblast activation protein (FAP) is a serine protease upregulated at sites of tissue remodelling and cancer that represents a promising therapeutic and molecular imaging target. In prostate cancer, studies of FAP expression using tissue microarrays are conflicting, such that its clinical potential is unclear. Furthermore, little is known regarding FAP expression in benign prostatic tissues. Here we demonstrated, using a novel iterative multiplex immunohistochemistry assay in standard tissue sections, that FAP was nearly absent in normal regions ​but was increased consistently in regions of proliferative inflammatory atrophy (PIA). In carcinoma, FAP was expressed in all cases ​but was highly heterogeneous. High FAP levels were associated with increased pathological stage and cribriform morphology. We verified that FAP levels in cancer correlated with CD163+ M2 macrophage density. In this first report to quantify FAP protein in benign prostate and primary tumours, using standard large tissue sections, we clarify that FAP is present in all primary prostatic carcinomas, supporting its potential clinical relevance. The finding of high levels of FAP within PIA supports the injury/regeneration model for its pathogenesis and suggests that it harbours a protumourigenic stroma, yet ​high levels of FAP in benign regions could lead to false-positive FAP-based molecular imaging results in clinically localised prostate cancer.

Molecular Landscape of Aggressive Histologic Subtypes of Localized Prostate Cancer

Despite incredible progress in describing the molecular underpinnings of prostate cancer over the last decades, pathologic examination remains indispensable for predicting aggressive behavior in the localized setting. Beyond pathologic grade, specific histologic findings have emerged as critical prognostic or predictive indicators. Here, the authors review molecular correlates of aggressive histologic subtypes of prostate cancer in the localized setting, demonstrating that many of the signature molecular alterations found in metastatic disease-such as tumor suppressor gene loss and DNA repair defects-are enriched in primary disease with adverse histologic features, presaging aggressive behavior, and presenting opportunities for earlier germline screening or targeted therapies.

Central nervous system and immune cells interactions in cancer: unveiling new therapeutic avenues

Cancer remains a leading cause of mortality worldwide. Despite significant advancements in cancer research, our understanding of its complex developmental pathways remains inadequate. Recent research has clarified the intricate relationship between the central nervous system (CNS) and cancer, particularly how the CNS influences tumor growth and metastasis via regulating immune cell activity. The interactions between the central nervous system and immune cells regulate the tumor microenvironment via various signaling pathways, cytokines, neuropeptides, and neurotransmitters, while also incorporating processes that alter the tumor immunological landscape. Furthermore, therapeutic strategies targeting neuro-immune cell interactions, such as immune checkpoint inhibitors, alongside advanced technologies like brain-computer interfaces and nanodelivery systems, exhibit promise in improving treatment efficacy. This complex bidirectional regulatory network significantly affects tumor development, metastasis, patient immune status, and therapy responses. Therefore, understanding the mechanisms regulating CNS-immune cell interactions is crucial for developing innovative therapeutic strategies. This work consolidates advancements in CNS-immune cell interactions, evaluates their potential in cancer treatment strategies, and provides innovative insights for future research and therapeutic approaches.

Urologic Imaging of the Prostate: Cancer and Mimics

This article provides a comprehensive overview of prostate cancer imaging, including detection of clinically significant cancer and initial staging. The role of multiparametric MRI in detection and local staging is discussed, along with the use of conventional imaging and advanced techniques such as Prostate-Specific Membrane Antigen-Positron Emission Tomography (PSMA-PET) for staging of nodal and distant metastases. The article also highlights the importance of differentiating benign prostatic conditions from prostate cancer on imaging to improve diagnostic accuracy and reduce false-positive interpretations.

Single-Cell RNA Profiling of Ocular Adnexal Sebaceous Carcinoma Reveals a Complex Tumor Microenvironment and Identifies New Biomarkers

PURPOSE

Ocular adnexal sebaceous carcinoma (OaSC) is an aggressive malignancy that often necessitates orbital exenteration. Its tumor composition and transcriptional profile remain largely unknown, which poses a significant barrier to medical advances. Here, we report the first in-depth transcriptomic analysis of OaSC at the single-cell resolution and discern mechanisms underlying cancer progression for the discovery of potential globe-sparing immunotherapies, targeted therapies, and biomarkers to guide clinical management.

DESIGN

Laboratory investigation with a retrospective observational case series.

METHODS

Single-cell RNA sequencing was performed on six patient specimens: three primary tumors, two tumors with pagetoid spread, and a normal tarsus sample. Cellular components were identified via gene signatures. Molecular pathways underlying tumorigenesis and pagetoid spread were discerned via gene ontology analysis of the differentially expressed genes between specimens. CALML5 immunohistochemistry was performed on an archival cohort of OaSC, squamous cell carcinoma, ocular surface squamous neoplasia (OSSN), and basal cell carcinoma cases.

RESULTS

Analysis of 29,219 cells from OaSC specimens revealed tumor, immune, and stromal cells. Tumor-infiltrating immune cells include a diversity of cell types, including exhausted T-cell populations. In primary OaSC tumors, mitotic nuclear division and oxidative phosphorylation pathways are upregulated, while lipid biosynthesis and metabolism pathways are downregulated. Epithelial tissue migration pathways are upregulated in tumor cells undergoing pagetoid spread. Single-cell RNA sequencing analyses also revealed that CALML5 is upregulated in OaSC tumor cells. Diffuse nuclear and cytoplasmic CALML5 staining was present in 28 of 28 (100%) OaSC cases. Diffuse nuclear and membranous CALML5 staining was present in 5 of 25 (20%) squamous cell carcinoma and OSSN cases, while diffuse nuclear staining was present in 1 of 12 (8%) basal cell carcinoma cases.

CONCLUSIONS

This study reveals a complex OaSC tumor microenvironment and confirms that the CALML5 immunohistochemical stain is a sensitive diagnostic marker.

Integrated analysis of single-cell and bulk transcriptomes uncovers clinically relevant molecular subtypes in human prostate cancer

Objective

Prostate cancer (PCa) is a complex disease characterized by diverse cellular ecosystems within the tumor microenvironment (TME) and high tumor heterogeneity, which challenges clinically stratified management and reinforces the need for novel strategies to fight against castration-resistant PCa (CRPC).

Methods

We performed single-cell RNA sequencing (scRNA-seq) on 10 untreated primary PCa tissues and integrated public scRNA-seq resources from three normal prostate tissues, two untreated primary PCa tissues, and six CRPC tumors to portray a comprehensive cellular and molecular interaction atlas of PCa. We further integrated the single-cell and bulk transcriptomes of PCa to establish a molecular classification system.

Results

scRNA-seq profiles revealed substantial inter- and intra-tumoral heterogeneity across different cell subpopulations in untreated PCa and CRPC tumors. In the malignant epithelial reservoir, cells evolved along decoupled paths in treatment-naive PCa and CRPC tumors, and distinct transcriptional reprogramming processes were activated, highlighting anti-androgen therapy-induced lineage plasticity. Based on the specifically expressed markers of the epithelial subpopulations, we conducted unsupervised clustering analysis in The Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) cohort and identified three molecularly and clinically distinct subtypes. The C1 subtype, characterized by high enrichment of CRPC-enriched epithelial cells, had a high risk of rapid development of anti-androgen resistance and might require active surveillance and additional promising intervention treatments, such as integrin A3 (ITGA3) + integrin B1 (ITGB1) inhibition. The C2 subtype resembled the immune-modulated subtype that was most likely to benefit from anti-LAG3 immunotherapy. The C3 subtype had a favorable prognosis.

Conclusions

Our study provides a comprehensive and high-resolution landscape of the intricate architecture of the PCa TME, and our trichotomic molecular taxonomy could help facilitate precision oncology.

Intraductal Carcinoma and Cribriform Pattern in Prostate Cancer: Challenges and Emerging Perspectives

The detection of intraductal carcinoma and cribriform pattern in prostate cancer biopsies and imaging remains challenging, affecting risk stratification and treatment. Further research is essential.

p53-loss induced prostatic epithelial cell plasticity and invasion is driven by a crosstalk with the tumor microenvironment

Prostate cancer is a heterogeneous disease with a slow progression and a highly variable clinical outcome. The tumor suppressor genes PTEN and TP53 are frequently mutated in prostate cancer and are predictive of early metastatic dissemination and unfavorable patient outcomes. The progression of solid tumors to metastasis is often associated with increased cell plasticity, but the complex events underlying TP53-loss-induced disease aggressiveness remain incompletely understood. Using genetically engineered mice, we show that Trp53 deficiency in Pten-null prostatic epithelial cells (PECs) does not impact early cell proliferation and neoplasia formation, nor growth arrest and senescence entry at a later time. However, Trp53-deficiency enhances invasive adenocarcinoma development and promotes metastatic cell dissemination. Importantly, our single-cell transcriptomic and chromatin accessibility analyses combined with histological examinations uncovered an epithelial cell population characterized by an induction of Jak/Stat3 signaling and displaying mesenchymal features. Moreover, we show that the transcriptomic signature of this cell population is prominent in tumors of patients with high-risk prostate cancer or metastatic disease. In addition, our in vivo and organoid-based experiments provide evidence that PEC plasticity occurs through bi-directional communication with cancer-associated fibroblasts (CAFs). Thus, our study demonstrates that p53 loss induces a protumorigenic crosstalk between PECs and CAFs, and identifies new vulnerabilities that might be targeted to limit cancer progression.

Brain gliomas new transcriptomic discoveries from differentially expressed genes to therapeutic targets

Gliomas are a prevalent form of primary malignant brain tumor, yet the intricate molecular mechanisms underlying its pathogenesis remain unclear. This study aimed to identify new genetic targets linked to glioma by analyzing microarray datasets to uncover genetic factors involved in its onset and progression. We obtained two independent glioma datasets from the Gene Expression Omnibus database, processed and normalized them using R software, and evaluated the relationship between differentially expressed genes and glioma by differential expression, expression quantitative trait loci, and Mendelian randomization (MR) analyses. Gene set enrichment analysis and immunocytometric analysis further explored the biological functions and pathways of identified genes, which were validated using The Cancer Genome Atlas and Genotype-Tissue Expression datasets. We identified eight co-expressed genes-C1QB, GPX3, LRRC8B, TRIOBP, SNAPC5, SPI1, TSPYL5, and FBXL16-that are crucial in various biological processes. CIBERSORT analysis revealed significant immune cell-type distributions within gliomas, underscoring the significance of immune cell infiltration. Validation in additional datasets confirmed the MR analysis results and upstream regulatory factors were identified using NetworkAnalyst. Our findings offer fresh perspectives on the molecular underpinnings of glioma and highlight potential targets for therapeutic interventions.

Intermediate risk prostate tumors contain lethal subtypes

In 2024, prostate cancer (PCa) remains the most common non-skin cancer in males within the United States, with an estimated 299,010 new cases, the highest increase incident trend rate (3.8%) of all cancers, and one of the eight deadliest. PCa cases are projected to double from 1.8 million to 2.9 million per year between 2020 and 2040. According to the National Comprehensive Cancer Network (NCCN) treatment guidelines, most cases (65%) are intermediate risk (Gleason sum score <7 [3 + 4, 4 + 3], prostate organ-confined, and PSA < 20) with treatment options limited to active surveillance, external beam radiation, and/or surgery to prevent metastasis in the long term (>10 years). It is increasingly recognized that the two most common subtypes of intermediate risk PCa are cribriform architecture (CA) and intraductal carcinoma of the prostate (IDC-P), which can occur together, and both are associated with increased metastatic risk, biochemical recurrence, and disease-specific mortality. Both subtypes display hypoxia, genomic instability, and are identified as Gleason 4 in pathology reports. However, since false negatives are common (up to 50%) in these subtypes on biopsy, more research is needed to reliably detect these subtypes that have an increased risk for invasive disease. We note that even with mpMRI-guided biopsies, the sensitivity is 54% for cribriform architecture and only 37% for IDC-P. The presence of these PCa subtypes in biopsy or radical prostatectomy (RP) tissue can exclude patients from active surveillance and from designation as intermediate risk disease, further underscoring the need for increased molecular understanding of these subtypes for diagnostic purposes. Understanding the heterogeneity of intermediate risk primary PCa phenotypes, using computational pathology approaches to evaluate the fixed biopsy specimen, or video microscopy of the surgical specimen with AI-driven analysis is now achievable. New research associating the resulting phenotypes with the different therapeutic choices and vulnerabilities will likely prevent extracapsular extension, the definition of high-risk disease, and upstaging of the final pathologic stage.

Cancer-associated fibroblasts as therapeutic targets for cancer: advances, challenges, and future prospects

Research into cancer treatment has been mainly focused on developing therapies to directly target cancer cells. Over the past decade, extensive studies have revealed critical roles of the tumour microenvironment (TME) in cancer initiation, progression, and drug resistance. Notably, cancer-associated fibroblasts (CAFs) have emerged as one of the primary contributors in shaping TME, creating a favourable environment for cancer development. Many preclinical studies have identified promising targets on CAFs, demonstrating remarkable efficacy of some CAF-targeted treatments in preclinical models. Encouraged by these compelling findings, therapeutic strategies have now advanced into clinical evaluation. We aim to provide a comprehensive review of relevant subjects on CAFs, including CAF-related markers and targets, their multifaceted roles, and current landscape of ongoing clinical trials. This knowledge can guide future research on CAFs and advocate for clinical investigations targeting CAFs.

Gold Nanoparticle Inhibits the Tumor-Associated Macrophage M2 Polarization by Inhibiting m6A Methylation-Dependent ATG5/Autophagy in Prostate Cancer

Background: This study aims to study how gold nanoparticles (AuNPs) function in the recruitment and polarization of tumor-associated macrophages (TAMs) in hormone-sensitive prostate cancer (HSPC) and castration-resistant prostate cancer (CRPC). Methods: Phorbol ester (PMA)-treated THP-1 cells were cocultured with LNCaP or PC3 cells to simulate TAMs. Macrophage M2 polarization levels were detected using flow cytometry and M2 marker determination. ATG5 expression was detected by western blotting. Luciferase reporter assay was used to analyze the N6-methyladenosine (m6A) site activity of ATG5 3' untranslated regions (3'-UTRs). Methylated RNA immune precipitation (MeRIP)-quantitative polymerase chain reaction (qPCR) was performed to determine the m6A levels at ATG5 3'-UTR. Xenograft mouse models were used to determine the function of AuNPs in vivo. Results: Macrophages exhibited reduced M2 polarization in both HSPC and CRPC cells after AuNP treatment which was prevented by induction of autophagy. AuNP treatment decreased the m6A levels in the 3'-UTR of ATG5. Mutational analysis of potential m6A sites within ATG5 3'-UTR revealed that these sites were required for AuNP regulation, indicating that AuNPs inhibited ATG5 levels in an m6A-dependent manner. The mouse model revealed that AuNPs significantly reduced the M2 polarization of TAMs in an autophagy-dependent manner in vivo. This suggests that AuNPs inhibit tumor growth in vivo partially through targeting M2 TAM. Conclusion: The ATG5/autophagy pathway is inhibited by AuNP treatment in an METTL3/m6A-dependent manner. AuNPs inhibit the TAM M2 polarization in HSPC and CRPC by inhibiting ATG5/autophagy.

Tumor-intrinsic regulators of the immune-cold microenvironment of prostate cancer

Prostate cancer (PC) is a notoriously immune-cold tumor in that it often lacks substantial infiltration by antitumor immune cells, and in advanced diseases such as neuroendocrine PC, it could be devoid of immune cells. A majority of PC patients thus have, unfortunately, been unable to benefit from recent advances in immunotherapies. What causes this immunosuppressive microenvironment around PC? In this review, we discuss various genetic and epigenetic regulators intrinsic to prostate tumor cells that could have profound effects on the tumor microenvironment, thus contributing to this immune-cold status. It will be essential to target the cancer cells themselves in order to change the tumor microenvironment to harness existing and developing immunotherapies that had great success in other tumors.

UQCRB and LBH are correlated with Gleason score progression in prostate cancer: Spatial transcriptomics and experimental validation

Prostate cancer (PCa) is a multifocal disease characterized by genomic and phenotypic heterogeneity within a single gland. In this study, Visium spatial transcriptomics (ST) analysis was applied to PCa tissues with different histological structures to infer the molecular events involved in Gleason score (GS) progression. The spots in tissue sections were classified into various groups using Principal Component Analysis (PCA) and Louvain clustering analysis based on transcriptome data. Anotation of the spots according to GS revealed notable similarities between transcriptomic profiles and histologically identifiable structures. The accuracy of macroscopic GS determination was bioinformatically verified through malignancy-related feature analysis, specifically inferred copy number variation (inferCNV), as well as developmental trajectory analyses, such as diffusion pseudotime (DPT) and partition-based graph abstraction (PAGA). Genes related to GS progression were identified from the differentially expressed genes (DEGs) through pairwise comparisons of groups along a GS gradient. The proteins encoded by the representative oncogenes UQCRB and LBH were found to be highly expressed in advanced-stage PCa tissues. Knockdown of their mRNAs significantly suppressed PCa cell proliferation and invasion. These findings were validated using The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) dataset, as well as through histological and cytological experiments. The results presented here establish a foundation for ST-based evaluation of GS progression and provide valuable insights into the GS progression-related genes UQCRB and LBH.

Molecular Hallmarks of Prostate-specific Membrane Antigen in Treatment-naïve Prostate Cancer

BACKGROUND AND OBJECTIVE

We characterized tumor prostate-specific membrane antigen (PSMA) levels as a reflection of cancer biology and treatment sensitivities for treatment-naïve prostate cancer.

METHODS

We first correlated PSMA positron emission tomography (PET) maximum standardized uptake values (SUVmax) in primary prostate cancer with tumor FOLH1 (PSMA RNA abundance) to establish RNA as a proxy (n = 55). We then discovered and validated molecular pathways associated with PSMA RNA levels in two large primary tumor cohorts. We validated those associations in independent cohorts (18 total; 5684 tumor samples) to characterize the pathways and treatment responses associated with PSMA.

KEY FINDINGS AND LIMITATIONS

PSMA RNA abundance correlates moderately with SUVmax (ρ = 0.41). In independent cohorts, androgen receptor signaling is more active in tumors with high PSMA. Accordingly, patients with high PSMA tumors experienced longer cancer-specific survival when managed with androgen deprivation therapy for biochemical recurrence (adjusted hazard ratio [AHR] 0.54 [0.34-0.87]; n = 174). PSMA low tumors possess molecular markers of resistance to radiotherapy. Consistent with this, patients with high PSMA tumors experience longer time to recurrence following primary radiotherapy (AHR 0.50 [0.28-0.90]; n = 248). In the SAKK09/10 trial (n = 224), patients with high PSMA tumors who were managed with salvage radiotherapy experienced longer time to progression in the 64-Gy arm (restricted mean survival time [RMST] +7.60 [0.05-15.16]), but this effect was mitigated in the 70-Gy arm (RMST 3.52 [-3.30 to 10.33]). Limitations include using PSMA RNA as a surrogate for PET SUVmax.

CONCLUSIONS AND CLINICAL IMPLICATIONS

PSMA levels in treatment-naïve prostate cancer differentiate tumor biology and treatment susceptibilities. These results warrant validation using PET metrics to substantiate management decisions based on imaging.

Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 120 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells are associated with myeloid inflammation previously linked to androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.

Metabolic adaptations in prostate cancer

Prostate cancer is one of the most commonly diagnosed cancers in men and is a major cause of cancer-related deaths worldwide. Among the molecular processes that contribute to this disease, the weight of metabolism has been placed under the limelight in recent years. Tumours exhibit metabolic adaptations to comply with their biosynthetic needs. However, metabolites also play an important role in supporting cell survival in challenging environments or remodelling the tumour microenvironment, thus being recognized as a hallmark in cancer. Prostate cancer is uniquely driven by androgen receptor signalling, and this knowledge has also influenced the paths of cancer metabolism research. This review provides a comprehensive perspective on the metabolic adaptations that support prostate cancer progression beyond androgen signalling, with a particular focus on tumour cell intrinsic and extrinsic pathways.

The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling

T cell activation is governed through T cell receptors (TCRs), heterodimers of two sequence-variable chains (often an α and β chain) that synergistically recognize antigen fragments presented on cell surfaces. Despite this, there only exist repositories dedicated to collecting single-chain, not paired-chain, TCR sequence data. We addressed this gap by creating the Observed TCR Space (OTS) database, a source of consistently processed and annotated, full-length, paired-chain TCR sequences. Currently, OTS contains 5.35 million redundant (1.63 million non-redundant), predominantly human sequences from across 50 studies and at least 75 individuals. Using OTS, we identify pairing biases, public TCRs, and distinct chain coherence patterns relative to antibodies. We also release a paired-chain TCR language model, providing paired embedding representations and a method for residue in-filling conditional on the partner chain. OTS will be updated as a central community resource and is freely downloadable and available as a web application.

The co-location of CD14+APOE+ cells and MMP7+ tumour cells contributed to worse immunotherapy response in non-small cell lung cancer

Intra-tumour immune infiltration is a crucial determinant affecting immunotherapy response in non-small cell lung cancer (NSCLC). However, its phenotype and related spatial structure have remained elusive. To overcome these restrictions, we undertook a comprehensive study comprising spatial transcriptomic (ST) data (28 712 spots from six samples). We identified two distinct intra-tumour infiltration patterns: immune exclusion (characterised by myeloid cells) and immune activation (characterised by plasma cells). The immune exclusion and immune activation signatures showed adverse and favourable roles in NSCLC patients' survival, respectively. Notably, CD14+APOE+ cells were recognised as the main cell type in immune exclusion samples, with increased epithelial‒mesenchymal transition and decreased immune activities. The co-location of CD14+APOE+ cells and MMP7+ tumour cells was observed in both ST and bulk transcriptomics data, validated by multiplex immunofluorescence performed on 20 NSCLC samples. The co-location area exhibited the upregulation of proliferation-related pathways and hypoxia activities. This co-localisation inhibited T-cell infiltration and the formation of tertiary lymphoid structures. Both CD14+APOE+ cells and MMP7+ tumour cells were associated with worse survival. In an immunotherapy cohort from the ORIENT-3 clinical trial, NSCLC patients who responded unfavourably exhibited higher infiltration of CD14+APOE+ cells and MMP7+ tumour cells. Within the co-location area, the MK, SEMA3 and Macrophage migration inhibitory factor (MIF) signalling pathway was most active in cell‒cell communication. This study identified immune exclusion and activation patterns in NSCLC and the co-location of CD14+APOE+ cells and MMP7+ tumour cells as contributors to immune resistance.

Identification of miRNA signature in cancer-associated fibroblast to predict recurrent prostate cancer

BACKGROUND

Cancer-associated fibroblasts (CAFs) are one of the major components of prostate stromal cells, which play a crucial part in tumor development and treatment resistance. This study aimed to establish a model of CAFs-related microRNAs (miRNAs) to assess prognostic differences, tumor microenvironments, and screening of anticancer drugs by integrating data from single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (buRNA-seq).

METHODS

scRNA-seq and buRNA-seq data of primary prostate cancer (PCa) were downloaded from Gene Expression Omnibus and The Cancer Genome Atlas databases. Statistical methods including Least absolute shrinkage and selection operator (Lasso), Lasso penalized, Random Forest, Random Forest Combination, and Support Vector Machine (SVM) were performed to select hub miRNAs. Pathway analyses and assessment of infiltrating immune cells were conducted using Gene Set Enrichment Analysis and the CIBERSORT algorithm. The expression of CAFs-related miRNAs in fibroblast cell lines were validated through quantitative real-time PCR. Cell Counting Kit 8 (CCK8), wound-healing, clone formation, and cell migration assays were used to explore cell proliferation, growth, and migration in vitro. A mouse xenograft model was established to investigate the effect of CAFs on tumor growth in vivo.

RESULTS

Through single-cell transcriptomics analysis in 34 PCa patients, 89 CAFs-related mRNAs were identified. A prognostic model based on 9 CAFs-related miRNAs (hsa-miR-1258, hsa-miR-133b, hsa-miR-222-3p, hsa-miR-145-3p, hsa-miR-493-5p, hsa-miR-96-5p, hsa-miR-15b-5p, hsa-miR-106b-5p, and hsa-miR-191-5p) was established to predict biochemical recurrence (BCR). We have determined through two prediction methods that NVP-TAE684 may be the optimal targeted therapy drug for treating CAFs. Downregulation of hsa-miR-106b-5p in CAFs significantly suppressed cell proliferation, migration, and colony formation in vitro. In vivo studies using a xenograft model further confirmed that hsa-miR-106b-5p downregulation significantly reduced tumor growth.

CONCLUSION

Our findings conducted an integrated bioinformatic analysis to develop a CAFs-related miRNAs model that provides prognostic insights into individualized and precise treatment for prostate adenocarcinoma patients. Downregulation of miR-106b-5p in CAFs significantly suppressed tumor growth, suggesting a potential therapeutic target for cancer treatment.

Convergent alterations in the tumor microenvironment of MYC-driven human and murine prostate cancer

How prostate cancer cells and their precursors mediate changes in the tumor microenvironment (TME) to drive prostate cancer progression is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we perform extensive single-cell RNA-sequencing (scRNA-seq) and molecular pathology of the comparative biology between human prostate cancer and key stages in the disease evolution of a genetically engineered mouse model (GEMM) of prostate cancer. Our studies of human tissues reveal that cancer cell-intrinsic activation of MYC signaling is a common denominator across the well-known molecular and pathological heterogeneity of human prostate cancer. Cell communication network and pathway analyses in GEMMs show that MYC oncogene-expressing neoplastic cells, directly and indirectly, reprogram the TME during carcinogenesis, leading to a convergence of cell state alterations in neighboring epithelial, immune, and fibroblast cell types that parallel key findings in human prostate cancer.

Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis

Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising publicly available cohorts and data generated by our research team, and established the Human Prostate Single cell Atlas (HuPSA) and Mouse Prostate Single cell Atlas (MoPSA) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution re-classified human PCa specimens, validating the presence of these novel subtypes. We then developed a user-friendly web application, "HuPSA-MoPSA" ( https://pcatools.shinyapps.io/HuPSA-MoPSA/ ), for visualizing gene expression across all newly established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.

Metabolic imaging across scales reveals distinct prostate cancer phenotypes

Hyperpolarised magnetic resonance imaging (HP-13C-MRI) has shown promise as a clinical tool for detecting and characterising prostate cancer. Here we use a range of spatially resolved histological techniques to identify the biological mechanisms underpinning differential [1-13C]lactate labelling between benign and malignant prostate, as well as in tumours containing cribriform and non-cribriform Gleason pattern 4 disease. Here we show that elevated hyperpolarised [1-13C]lactate signal in prostate cancer compared to the benign prostate is primarily driven by increased tumour epithelial cell density and vascularity, rather than differences in epithelial lactate concentration between tumour and normal. We also demonstrate that some tumours of the cribriform subtype may lack [1-13C]lactate labelling, which is explained by lower epithelial lactate dehydrogenase expression, higher mitochondrial pyruvate carrier density, and increased lipid abundance compared to lactate-rich non-cribriform lesions. These findings highlight the potential of combining spatial metabolic imaging tools across scales to identify clinically significant metabolic phenotypes in prostate cancer.

Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome

Tumor-associated myeloid-derived cells (MDCs) significantly impact cancer prognosis and treatment responses due to their remarkable plasticity and tumorigenic behaviors. Here, we integrate single-cell RNA-sequencing data from different cancer types, identifying 29 MDC subpopulations within the tumor microenvironment. Our analysis reveals abnormally expanded MDC subpopulations across various tumors and distinguishes cell states that have often been grouped together, such as TREM2+ and FOLR2+ subpopulations. Using deconvolution approaches, we identify five subpopulations as independent prognostic markers, including states co-expressing TREM2 and PD-1, and FOLR2 and PDL-2. Additionally, TREM2 alone does not reliably predict cancer prognosis, as other TREM2+ macrophages show varied associations with prognosis depending on local cues. Validation in independent cohorts confirms that FOLR2-expressing macrophages correlate with poor clinical outcomes in ovarian and triple-negative breast cancers. This comprehensive MDC atlas offers valuable insights and a foundation for futher analyses, advancing strategies for treating solid cancers.

Macrophage and fibroblast trajectory inference and crosstalk analysis during myocardial infarction using integrated single-cell transcriptomic datasets

BACKGROUND

Cardiac fibrosis after myocardial infarction (MI) has been considered an important part of cardiac pathological remodeling. Immune cells, especially macrophages, are thought to be involved in the process of fibrosis and constitute a niche with fibroblasts to promote fibrosis. However, the diversity and variability of fibroblasts and macrophages make it difficult to accurately depict interconnections.

METHODS

We collected and reanalyzed scRNA-seq and snRNA-seq datasets from 12 different studies. Differentiation trajectories of these subpopulations after MI injury were analyzed by using scVelo, PAGA and Slingshot. We used CellphoneDB and NicheNet to infer fibroblast-macrophage interactions. Tissue immunofluorescence staining and in vitro experiments were used to validate our findings.

RESULTS

We discovered two subsets of ECM-producing fibroblasts, reparative cardiac fibroblasts (RCFs) and matrifibrocytes, which appeared at different times after MI and exhibited different transcriptional profiles. We also observed that CTHRC1+ fibroblasts represent an activated fibroblast in chronic disease states. We identified a macrophage subset expressing the genes signature of SAMs conserved in both human and mouse hearts. Meanwhile, the SPP1hi macrophages were predominantly found in the early stages after MI, and cell communication analysis indicated that SPP1hi macrophage-RCFs interactions are mainly involved in collagen deposition and scar formation.

CONCLUSIONS

Overall, this study comprehensively analyzed the dynamics of fibroblast and macrophage subsets after MI and identified specific subsets of fibroblasts and macrophages involved in scar formation and collagen deposition.

Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis

Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into disease heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising both publicly available cohorts and data generated by our research team, and established the HuPSA (Human Prostate Single cell Atlas) and the MoPSA (Mouse Prostate Single cell Atlas) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression, and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution allowed for the re-classification of human PCa specimens, validating the presence of these novel subtypes. Leveraging these findings, we developed a user-friendly web application, "HuPSA-MoPSA" (https://pcatools.shinyapps.io/HuPSA-MoPSA/), for visualizing gene expression across all newly-established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.

The role of collagen triple helix repeat containing 1 (CTHRC1) in cancer development and progression

INTRODUCTION

Collagen triple helix repeat containing 1 (CTHRC1) is a protein that has been implicated in pro-migratory pathways, arterial tissue-repair processes, and inhibition of collagen deposition via the regulation of multiple signaling cascades. Studies have also demonstrated an upregulation of CTHRC1 in multiple cancers where it has been linked to enhanced proliferation, invasion, and metastasis. However, the understanding of the exact role and mechanisms of CTHRC1 in cancer is far from complete.

AREAS COVERED

This review focuses on analyzing the role of CTHRC1 in cancer as well as its associations with clinicopathologies and cancer-related processes and signaling. We have also summarized the available literature information regarding the role of CTHRC1 in tumor microenvironment and immune signaling. Finally, we have discussed the mechanisms associated with CTHRC1 regulations, and opportunities and challenges regarding the development of CTHRC1 as a potential target for cancer management.

EXPERT OPINION

CTHRC1 is a multifaceted protein with critical roles in cancer progression and other pathological conditions. Its association with lower overall survival in various cancers, and impact on the tumor immune microenvironment make it an intriguing target for further research and potential therapeutic interventions in cancer.

Unveiling the Genomic Landscape of Intraductal Carcinoma of the Prostate Using Spatial Gene Expression Analysis

Intraductal carcinoma of the prostate (IDCP) has recently attracted increasing interest owing to its unfavorable prognoses. To effectively identify the IDCP-specific gene expression profile, we took a novel approach of characterizing a typical IDCP case using spatial gene expression analysis. A formalin-fixed, paraffin-embedded sample was subjected to Visium CytAssist Spatial Gene Expression analysis. IDCP within invasive prostate cancer sites was recognized as a distinct cluster separate from other invasive cancer clusters. Highly expressed genes defining the IDCP cluster, such as MUC6, MYO16, NPY, and KLK12, reflected the aggressive nature of high-grade prostate cancer. IDCP sites also showed increased hypoxia markers HIF1A, BNIP3L, PDK1, and POGLUT1; decreased fibroblast markers COL1A2, DCN, and LUM; and decreased immune cell markers CCR5 and FCGR3A. Overall, these findings indicate that the hypoxic tumor microenvironment and reduced recruitment of fibroblasts and immune cells, which reflect morphological features of IDCP, may influence the aggressiveness of high-grade prostate cancer.

The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy

In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.

Identification of recurrent BRAF non-V600 mutations in intraductal carcinoma of the prostate in Chinese populations

While BRAF alterations have been established as a driver in various solid malignancies, the characterization of BRAF alterations in prostate cancer (PCa) has not been thoroughly interrogated. By bioinformatics analysis, we first found that BRAF alterations were associated with advanced PCa and exhibited mutually exclusive pattern with ERG alteration across multiple cohorts. Of the most interest, recurrent non-V600 BRAF mutations were found in 3 of 21 (14.3 %) PCa patients demonstrating IDC-P morphology. Furthermore, experimental overexpression of BRAFK601E and BRAFL597R exhibited emergence of oncogenic phenotypes with intensified MAPK signaling in vitro, which could be targeted by MEK inhibitors. Comparison of the incidence of BRAF alterations in IDC-P between western and Chinese ancestry revealed an increased prevalence in the Chinese population. The BRAF mutation may represent important genetic alteration in a subset of IDC-P, highlighting the role of MAPK signaling pathway in this subtype of PCa. To the best of knowledge, this is the first description of non-V600 BRAF mutation in setting of IDC-P, which may in part explain the aggressive phenotype seen in IDC-P and could also bring more treatment options for PCa patients with IDC-P harboring such mutations.

Modulator of TMB-associated immune infiltration (MOTIF) predicts immunotherapy response and guides combination therapy

Patients with high tumor mutational burden (TMB) levels do not consistently respond to immune checkpoint inhibitors (ICIs), possibly because a high TMB level does not necessarily result in adequate infiltration of CD8+ T cells. Using bulk ribonucleic acid sequencing (RNA-seq) data from 9311 tumor samples across 30 cancer types, we developed a novel tool called the modulator of TMB-associated immune infiltration (MOTIF), which comprises genes that can determine the extent of CD8+ T cell infiltration prompted by a certain TMB level. We confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity cycle. By analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors, we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8+ T cell infiltration. Using pretreatment RNA-seq data from 13 ICI-treated cohorts, we validated the use of MOTIF in predicting CD8+ T cell infiltration and ICI efficacy. Among the components of MOTIF, we identified EMC3 as a negative regulator of CD8+ T cell infiltration, which was validated via in vivo studies. Additionally, MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8+ T cell infiltration and improve ICI efficacy.

Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties

Inhibiting androgen receptor (AR) signaling through androgen deprivation therapy (ADT) reduces prostate cancer (PCa) growth in virtually all patients, but response may be temporary, in which case resistance develops, ultimately leading to lethal castration-resistant prostate cancer (CRPC). The tumor microenvironment (TME) plays an important role in the development and progression of PCa. In addition to tumor cells, TME-resident macrophages and fibroblasts express AR and are therefore also affected by ADT. However, the interplay of different TME cell types in the development of CRPC remains largely unexplored. To understand the complex stochastic nature of cell-cell interactions, we created a PCa-specific agent-based model (PCABM) based on in vitro cell proliferation data. PCa cells, fibroblasts, "pro-inflammatory" M1-like and "pro-tumor" M2-like polarized macrophages are modeled as agents from a simple set of validated base assumptions. PCABM allows us to simulate the effect of ADT on the interplay between various prostate TME cell types. The resulting in vitro growth patterns mimic human PCa. Our PCABM can effectively model hormonal perturbations by ADT, in which PCABM suggests that CRPC arises in clusters of resistant cells, as is observed in multifocal PCa. In addition, fibroblasts compete for cellular space in the TME while simultaneously creating niches for tumor cells to proliferate in. Finally, PCABM predicts that ADT has immunomodulatory effects on macrophages that may enhance tumor survival. Taken together, these results suggest that AR plays a critical role in the cellular interplay and stochastic interactions in the TME that influence tumor cell behavior and CRPC development.

Identification macrophage signatures in prostate cancer by single-cell sequencing and machine learning

BACKGROUND

The tumor microenvironment (TME) encompasses a variety of cells that influence immune responses and tumor growth, with tumor-associated macrophages (TAM) being a crucial component of the TME. TAM can guide prostate cancer in different directions in response to various external stimuli.

METHODS

First, we downloaded prostate cancer single-cell sequencing data and second-generation sequencing data from multiple public databases. From these data, we identified characteristic genes associated with TAM clusters. We then employed machine learning techniques to select the most accurate TAM gene set and developed a TAM-related risk label for prostate cancer. We analyzed the tumor-relatedness of the TAM-related risk label and different risk groups within the population. Finally, we validated the accuracy of the prognostic label using single-cell sequencing data, qPCR, and WB assays, among other methods.

RESULTS

In this study, the TAM_2 cell cluster has been identified as promoting the progression of prostate cancer, possibly representing M2 macrophages. The 9 TAM feature genes selected through ten machine learning methods and demonstrated their effectiveness in predicting the progression of prostate cancer patients. Additionally, we have linked these TAM feature genes to clinical pathological characteristics, allowing us to construct a nomogram. This nomogram provides clinical practitioners with a quantitative tool for assessing the prognosis of prostate cancer patients.

CONCLUSION

This study has analyzed the potential relationship between TAM and PCa and established a TAM-related prognostic model. It holds promise as a valuable tool for the management and treatment of PCa patients.

CTHRC1 promotes colorectal cancer progression by recruiting tumor-associated macrophages via up-regulation of CCL15

Tumor-associated macrophages (TAMs) represent a key factor in the tumor immune microenvironment (TME), exerting significant influence over tumor migration, invasion, immunosuppressive features, and drug resistance. Collagen triple helix repeat containing 1 (CTHRC1), a 30 KDa protein which was secreted during the tissue-repair process, is highly expressed in several malignant tumors, including colorectal cancer (CRC). Previous studies demonstrated that CTHRC1 expression in TAMs was positively correlated to M2 macrophage polarization and liver metastasis, while our discovery suggesting a novel mechanism that CTHRC1 secreted from cancer cell could indirectly interplay with TAMs. In this study, the high expression level of CTHRC1 was evaluated in CRC based on GEO and TCGA databases. Further, CTHRC1 was detected high in all stages of CRC patients by ELISA and was correlated to poor prognosis. Multispectral imaging of IHC demonstrated that M2 macrophage infiltration was increased accompanied with CTHRC1 enrichment, suggesting that CTHRC1 may have chemotactic effect on macrophages. In vitro, CTHRC1 could have chemotactic ability of macrophage in the presence of HT-29 cell line. Cytokine microarray revealed that CTHRC1 could up-regulate the CCL15 level of HT-29, pathway analysis demonstrated that CTHRC1 could regulate CCL15 by controlling the TGFβ activation and Smad phosphorylation level. In vivo, knocking down of CTHRC1 from CT-26 also inhibits tumor formation. In conclusion, CTHRC1 could promote the chemotactic ability of macrophages by up-regulating CCL15 via TGFβ/Smad pathway; additionally, a high level of CTHRC1 could promote macrophage's M2 polarization. This discovery may be related to tumor immune tolerance and tumor immunotherapy resistance in CRC. KEY MESSAGES: CTHRC1 promotes CRC progression by up-regulating CCL15 via TGF-β/Smad pathways to further recruit tumor-associated macrophages. By the means of autocrine or paracrine, CTHRC1 can indeed promote macrophage chemotaxis and enhance the infiltration of macrophages in tumor tissues but in the presence of tumor cells. CAFs were another source of CTHRC1, indicating CTHRC1 can infiltrate tumor islet as well as the stomal and be secreted from both tumor cells and CAFs. This study validated CTHRC1 as a potential immune therapy target CRC.

Characterization of HOXB13 expression patterns in localized and metastatic castration-resistant prostate cancer

HOXB13 is a key lineage homeobox transcription factor that plays a critical role in the differentiation of the prostate gland. Several studies have suggested that HOXB13 alterations may be involved in prostate cancer development and progression. Despite its potential biological relevance, little is known about the expression of HOXB13 across the disease spectrum of prostate cancer. To this end, we validated a HOXB13 antibody using genetic controls and investigated HOXB13 protein expression in murine and human developing prostates, localized prostate cancers, and metastatic castration-resistant prostate cancers. We observed that HOXB13 expression increases during later stages of murine prostate development. All localized prostate cancers showed HOXB13 protein expression. Interestingly, lower HOXB13 expression levels were observed in higher-grade tumors, although no significant association between HOXB13 expression and recurrence or disease-specific survival was found. In advanced metastatic prostate cancers, HOXB13 expression was retained in the majority of tumors. While we observed lower levels of HOXB13 protein and mRNA levels in tumors with evidence of lineage plasticity, 84% of androgen receptor-negative castration-resistant prostate cancers and neuroendocrine prostate cancers (NEPCs) retained detectable levels of HOXB13. Notably, the reduced expression observed in NEPCs was associated with a gain of HOXB13 gene body CpG methylation. In comparison to the commonly used prostate lineage marker NKX3.1, HOXB13 showed greater sensitivity in detecting advanced metastatic prostate cancers. Additionally, in a cohort of 837 patients, 383 with prostatic and 454 with non-prostatic tumors, we found that HOXB13 immunohistochemistry had a 97% sensitivity and 99% specificity for prostatic origin. Taken together, our studies provide valuable insight into the expression pattern of HOXB13 during prostate development and cancer progression. Furthermore, our findings support the utility of HOXB13 as a diagnostic biomarker for prostate cancer, particularly to confirm the prostatic origin of advanced metastatic castration-resistant tumors. © 2023 The Pathological Society of Great Britain and Ireland.

ASPORIN: A root of the matter in tumors and their host environment

Asporin (ASPN) has been identified as one of the members of the class I small leucine-rich proteoglycans (SLRPs) family in the extracellular matrix (ECM). It is involved in classic ensigns of cancers such as self-dependent growth, resistance to growth inhibitors, restricting apoptosis, cancer metastasis, and bone-related disorders. ASPN is different from other members of SLRPs, such as decorin (DCN) and biglycan (BGN), in a way that it contains a distinctive length of aspartate (D) residues in the amino (N) -terminal region. These D-repeats residues possess germline polymorphisms and are identified to be linked with cancer progression and osteoarthritis (OA). The polyaspartate stretch in the N-terminal region of the protein and its resemblance to DCN are the reasons it is called asporin. In this review, we comprehensively summarized and updated the dual role of ASPN in various malignancies, its structure in mice and humans, variants, mutations, cancer-associated signalings and functions, the relationship between ASPN and cancer-epithelial, stromal fibroblast crosstalk, immune cells and immunosuppression in cancer and other diseases. In cancer and other bone-related diseases, ASPN is identified to be regulating various signaling pathways such as TGFβ, Wnt/β-catenin, notch, hedgehog, EGFR, HER2, and CD44-mediated Rac1. These pathways promote cancer cell invasion, proliferation, and migration by mediating the epithelial-to-mesenchymal transition (EMT) process. Finally, we discussed mouse models mimicking ASPN in vivo function in cancers and the probability of therapeutic targeting of ASPN in cancer cells, fibrosis, and other bone-related diseases.

Molecular Alterations in Intraductal Carcinoma of the Prostate

Intraductal carcinoma of the prostate is most commonly associated with high-grade invasive prostate cancer. However, isolated IDC-P without adjacent cancer or high-grade cancer is also well known. Common genetic alterations present in IDC-P with adjacent high-grade prostate cancer are those described in high-grade tumors, such as PTEN loss (69-84%). In addition, the rate of LOH involving TP53 and RB1 is significantly higher. IDC-P is common in the TCGA molecular subset of SPOP mutant cancers, and the presence of SPOP mutations are more likely in IDC-P bearing tumors. IDC-P without adjacent high-grade cancers are by far less common. They are less likely to have PTEN loss (47%) and rarely harbor an ERG fusion (7%). Molecular alterations that may predispose a person to the development of IDC-P include the loss of BRCA2 and PTEN as well as mutations in SPOP. However, the causative nature of these genetic alterations is yet to be validated.

Integrative multi-omics analysis unveils stemness-associated molecular subtypes in prostate cancer and pan-cancer: prognostic and therapeutic significance

BACKGROUND

Prostate cancer (PCA) is the fifth leading cause of cancer-related deaths worldwide, with limited treatment options in the advanced stages. The immunosuppressive tumor microenvironment (TME) of PCA results in lower sensitivity to immunotherapy. Although molecular subtyping is expected to offer important clues for precision treatment of PCA, there is currently a shortage of dependable and effective molecular typing methods available for clinical practice. Therefore, we aim to propose a novel stemness-based classification approach to guide personalized clinical treatments, including immunotherapy.

METHODS

An integrative multi-omics analysis of PCA was performed to evaluate stemness-level heterogeneities. Unsupervised hierarchical clustering was used to classify PCAs based on stemness signature genes. To make stemness-based patient classification more clinically applicable, a stemness subtype predictor was jointly developed by using four PCA datasets and 76 machine learning algorithms.

RESULTS

We identified stemness signatures of PCA comprising 18 signaling pathways, by which we classified PCA samples into three stemness subtypes via unsupervised hierarchical clustering: low stemness (LS), medium stemness (MS), and high stemness (HS) subtypes. HS patients are sensitive to androgen deprivation therapy, taxanes, and immunotherapy and have the highest stemness, malignancy, tumor mutation load (TMB) levels, worst prognosis, and immunosuppression. LS patients are sensitive to platinum-based chemotherapy but resistant to immunotherapy and have the lowest stemness, malignancy, and TMB levels, best prognosis, and the highest immune infiltration. MS patients represent an intermediate status of stemness, malignancy, and TMB levels with a moderate prognosis. We further demonstrated that these three stemness subtypes are conserved across pan-tumor. Additionally, the 9-gene stemness subtype predictor we developed has a comparable capability to 18 signaling pathways to make tumor diagnosis and to predict tumor recurrence, metastasis, progression, prognosis, and efficacy of different treatments.

CONCLUSIONS

The three stemness subtypes we identified have the potential to be a powerful tool for clinical tumor molecular classification in PCA and pan-cancer, and to guide the selection of immunotherapy or other sensitive treatments for tumor patients.

Lymphotropic Pattern of Prostate-specific Membrane Antigen-detected Metastases Among Biochemically Recurrent Radical Prostatectomy Patients with Cribriform Disease

BACKGROUND

Cribriform morphology portends worse oncologic outcomes, and has unique cellular intrinsic pathway alterations and tumor microenvironments that may impact metastatic spread patterns.

OBJECTIVE

To determine whether the presence of cribriform morphology in prostatectomy specimens of patients with biochemical recurrence after radical prostatectomy (RP) is associated with the presence of metastasis on prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) and a distinct pattern of spread.

DESIGN, SETTING, AND PARTICIPANTS

A cross-sectional analysis was conducted of all prostate cancer patients with biochemical recurrence after RP undergoing 18F-DCFPyL-PET/CT between December 2018 and February 2021 at the Princess Margaret Cancer Centre.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Outcomes were presence of any metastasis in the overall cohort and lymphatic versus bone/visceral metastases among patients with metastatic disease. The associations between the presence of intraductal (IDC) and/or invasive cribriform (ICC) carcinoma on the RP specimen and study outcomes were evaluated using logistic regression analyses.

RESULTS AND LIMITATIONS

The cohort included 176 patients. IDC and ICC were observed in 77 (43.8%) and 80 (45.5%) RP specimens, respectively. The median time from RP to PSMA-PET/CT was 5.0 yr. The median serum prostate-specific antigen level at PSMA-PET/CT was 1.12 ng/ml. Overall, metastasis was observed in 77 patients, of whom 58 were had lymphatic-only metastasis. On a multivariable analysis, presence of IDC on RP was associated with increased odds of overall metastasis (odds ratio [OR]: 2.17; 95% confidence interval [CI]: 1.07-4.45; p = 0.033). Presence of ICC on RP was associated with significantly increased odds of lymphatic versus bone/visceral metastases (OR: 3.13; 95% CI: 1.09-21.7; p = 0.004).

CONCLUSIONS

Presence of cribriform morphology on RP specimens of patients with biochemical failure after RP is associated with increased odds of PSMA-PET/CT-detected metastases with a lymphatic predominant pattern of spread. These findings have implications for the design and evaluation of post-RP salvage therapies.

PATIENT SUMMARY

We found that microscopic cribriform appearance correlates with disease spread on imaging in prostate cancer patients with recurrence and has a predilection for spread to lymph nodes, as opposed to bone or visceral organs.