Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment

Stemness regulation in prostate cancer: prostate cancer stem cells and targeted therapy

BACKGROUND

Increasing evidence indicates that cancer stem cells (CSCs) and cancer stem-like cells form a special subpopulation of cells that are ubiquitous in tumors. These cells exhibit similar characteristics to those of normal stem cells in tissues; moreover, they are capable of self-renewal and differentiation, as well as high tumorigenicity and drug resistance. In prostate cancer (PCa), it is difficult to kill these cells using androgen signaling inhibitors and chemotherapy drugs. Consequently, the residual prostate cancer stem cells (PCSCs) mediate tumor recurrence and progression.

OBJECTIVE

This review aims to provide a comprehensive and up-to-date overview of PCSCs, with a particular emphasis on potential therapeutic strategies targeting these cells.

METHODS

After searching in PubMed and Embase databases using 'prostate cancer' and 'cancer stem cells' as keywords, studies related were compiled and examined.

RESULTS

In this review, we detail the origin and characteristics of PCSCs, introduce the regulatory pathways closely related to CSC survival and stemness maintenance, and discuss the link between epithelial-mesenchymal transition, tumor microenvironment and tumor stemness. Furthermore, we introduce the currently available therapeutic strategies targeting CSCs, including signaling pathway inhibitors, anti-apoptotic protein inhibitors, microRNAs, nanomedicine, and immunotherapy. Lastly, we summarize the limitations of current CSC research and mention future research directions.

CONCLUSION

A deeper understanding of the regulatory network and molecular markers of PCSCs could facilitate the development of novel therapeutic strategies targeting these cells. Previous preclinical studies have demonstrated the potential of this treatment approach. In the future, this may offer alternative treatment options for PCa patients.

CCL20-CCR6 signaling in tumor microenvironment: Functional roles, mechanisms, and immunotherapy targeting

Chemokine CC motif ligand 20 (CCL20) is a molecule with immunomodulatory properties that is involved in the regulation of diseases such as chronic inflammation, autoimmune diseases, and cancer. It operates by binding to its specific receptor, CC chemokine receptor type 6 (CCR6), and activating a complex intracellular signaling network. Building on its established role in inflammatory diseases, recent research has expanded our understanding of CCL20 to encompass its critical contributions to the tumor microenvironment (TME), highlighting its significance in cancer progression. Numerous studies have emphasized its prominent role in regulating immune responses. Consequently, Monoclonal antibodies against CCL20 and inhibitors of CCR6 have been successfully developed to block downstream signaling, making the CCL20-CCR6 axis a promising and critical target in the TME. This offers potential immunotherapeutic strategies for cancers. In this review, we summarize the biological consequences of CCL20-CCR6 mediated signaling, its role and mechanisms in the TME, and its potential applications. We suggest that the CCL20-CCR6 axis may be a novel biomarker for tumor diagnosis and prognosis, as well as a therapeutic target in various cancers.

Artificial intelligence approaches for tumor phenotype stratification from single-cell transcriptomic data

Single-cell RNA-sequencing (scRNA-seq) coupled with robust computational analysis facilitates the characterization of phenotypic heterogeneity within tumors. Current scRNA-seq analysis pipelines are capable of identifying a myriad of malignant and non-malignant cell subtypes from single-cell profiling of tumors. However, given the extent of intra-tumoral heterogeneity, it is challenging to assess the risk associated with individual cell subpopulations, primarily due to the complexity of the cancer phenotype space and the lack of clinical annotations associated with tumor scRNA-seq studies. To this end, we introduce SCellBOW, a scRNA-seq analysis framework inspired by document embedding techniques from the domain of Natural Language Processing (NLP). SCellBOW is a novel computational approach that facilitates effective identification and high-quality visualization of single-cell subpopulations. We compared SCellBOW with existing best practice methods for its ability to precisely represent phenotypically divergent cell types across multiple scRNA-seq datasets, including our in-house generated human splenocyte and matched peripheral blood mononuclear cell (PBMC) dataset. For tumor cells, SCellBOW estimates the relative risk associated with each cluster and stratifies them based on their aggressiveness. This is achieved by simulating how the presence or absence of a specific cell subpopulation influences disease prognosis. Using SCellBOW, we identified a hitherto unknown and pervasive AR-/NElow (androgen-receptor-negative, neuroendocrine-low) malignant subpopulation in metastatic prostate cancer with conspicuously high aggressiveness. Overall, the risk-stratification capabilities of SCellBOW hold promise for formulating tailored therapeutic interventions by identifying clinically relevant tumor subpopulations and their impact on prognosis.

Targeting the tumor microenvironment, a new therapeutic approach for prostate cancer

BACKGROUND

A growing number of studies have shown that in addition to adaptive immune cells such as CD8 + T cells and CD4 + T cells, various other cellular components within prostate cancer (PCa) tumor microenvironment (TME), mainly tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs) and myeloid-derived suppressor cells (MDSCs), have been increasingly recognized as important modulators of tumor progression and promising therapeutic targets.

OBJECTIVE

In this review, we aim to delineate the mechanisms by which TAMs, CAFs and MDSCs interact with PCa cells in the TME, summarize the therapeutic advancements targeting these cells and discuss potential new therapeutic avenues.

METHODS

We searched PubMed for relevant studies published through December 10 2023 on TAMs, CAFs and MDSCs in PCa.

RESULTS

TAMs, CAFs and MDSCs play a critical role in the tumorigenesis, progression, and metastasis of PCa. Moreover, they substantially mediate therapeutic resistance against conventional treatments including anti-androgen therapy, chemotherapy, and immunotherapy. Therapeutic interventions targeting these cellular components have demonstrated promising effects in preclinical models and several clinical trials for PCa, when administrated alone, or combined with other anti-cancer therapies. However, the lack of reliable biomarkers for patient selection and incomplete understanding of the mechanisms underlying the interactions between these cellular components and PCa cells hinder their clinical translation and utility.

CONCLUSION

New therapeutic strategies targeting TAMs, CAFs, and MDSCs in PCa hold promising prospects. Future research endeavors should focus on a more comprehensive exploration of the specific mechanisms by which these cells contribute to PCa, aiming to identify additional drug targets and conduct more clinical trials to validate the safety and efficacy of these treatment strategies.

A novel bone metastasis-related gene signature for predicting prognosis, anti-androgen resistance, and drug choice in prostate cancer

Objective

Prostate cancer (PCa) often metastasizes to the bone, posing a significant clinical challenge. This study aims to develop a bone metastasis-related risk model for PCa.

Methods

Bone metastasis-related genes (BMRGs) were identified through a combination of differential gene expression analysis and WGCNA using GSE32269 and GSE77930 datasets. Consensus clustering analysis was employed to determine the significance of these genes in molecular subtyping of PCa. LASSO-Cox regression analysis was utilized to construct the bone metastasis-related prognostic gene signature (BMRPS). The predictive performance of BMRPS was assessed using ROC curves, Kaplan-Meier survival curves, and a predictive nomogram. The immune landscape heterogeneity of subgroups was analyzed using CIBERSORT, ESTIMATE, and xCell algorithms. Drug sensitivity and molecular docking analysis were performed to identify drugs associated with BMRPS.

Results

Forty-four BMRGs associated with the prognosis of PCa were identified. Consensus clustering revealed the pivotal role of these genes in stratifying PCa into three distinct prognostic clusters. The BMRPS, consisting of 14 BMRGs, demonstrated excellent predictive accuracy for prognosis and served as an independent prognostic factor in PCa. BMRPS effectively predicted the overall survival of bone metastatic PCa and differentiated bone metastasis from other metastatic types. BMRPS showed a close correlation with the immune landscape and immunotherapeutic response biomarkers. Additionally, BMRPS was associated with anti-androgen resistance, and AZD8186 was identified as a potential BMRPS-related drug that holds promise for personalized treatment in PCa.

Conclusion

BMRPS facilitates the prediction of prognosis and resistance to anti-androgens in PCa. It also offers insights into the molecular mechanisms of bone metastasis and aids in drug selection for the treatment of PCa.

Single-Cell Analysis Reveals that Vitamin C Inhibits Bone Metastasis of Renal Cancer via Cell Cycle Arrest and Microenvironment Remodeling

Bone metastasis is the second most common site of distant metastatic spread in renal cell carcinoma (RCC) patients, significantly contributing to cancer-related mortality. The metastatic process is driven by both intrinsic tumor cell properties, such as cancer stem cell-like characteristics, and the bone microenvironment. Understanding the complex interactions between cancer cells and their niche is crucial for identifying therapeutic targets to eliminate metastasis-initiating cells and prevent overt metastasis. In this study, a murine bone metastasis model is developed using renal cancer cells derived from fibrin gel-induced 3D tumor spheres, which exhibit stem-like phenotypes. It is found that a stable form of vitamin C, L-ascorbic acid 2-phosphate sesquimagnesium (APM), significantly inhibits the growth of renal cancer stem-like cells in vitro and the progression of RCC bone metastasis in vivo. Single-cell RNA sequencing revealed that APM induces cell cycle arrest and reduces the metastatic potential of cancer cells. Furthermore, APM remodels the tumor microenvironment by suppressing osteoclast differentiation and neutrophil recruitment. Combining APM with a CXCR2 antagonist, SB225002, further inhibits bone metastasis progression. This study provides a high-resolution profile of vitamin C's antitumor effects in the bone metastatic microenvironment and supports the rationale for clinical trials of vitamin C in bone metastatic RCC.

Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization

Bone is a common site for metastasis of solid cancers. The diversity of histological and molecular characteristics of bone metastases (BMs) remains poorly studied. Here, we performed single-cell RNA sequencing on 42 BMs from eight cancer types, identifying three distinct ecosystem archetypes, each characterized by an enrichment of specific immune cells: macrophages/osteoclasts, regulatory/exhausted T cells, or monocytes. We validated these archetypes by immunostaining on tissue sections and bioinformatic analysis of bulk RNA sequencing/microarray data from 158 BMs across more than 10 cancer types. Interestingly, we found only a modest correlation between the BM archetypes and the tissues of origin; BMs from the same cancer type often fell into different archetypes, while BMs from different cancer types sometimes converged on the same archetype. Additional analyses revealed parallel immunosuppression and bone remodeling mechanisms, some of which were experimentally validated. Overall, we discovered unappreciated heterogeneity of BMs across different cancers.

Histone methyltransferase ASH1L primes metastases and metabolic reprogramming of macrophages in the bone niche

Bone metastasis is a major cause of cancer death; however, the epigenetic determinants driving this process remain elusive. Here, we report that histone methyltransferase ASH1L is genetically amplified and is required for bone metastasis in men with prostate cancer. ASH1L rewires histone methylations and cooperates with HIF-1α to induce pro-metastatic transcriptome in invading cancer cells, resulting in monocyte differentiation into lipid-associated macrophage (LA-TAM) and enhancing their pro-tumoral phenotype in the metastatic bone niche. We identified IGF-2 as a direct target of ASH1L/HIF-1α and mediates LA-TAMs' differentiation and phenotypic changes by reprogramming oxidative phosphorylation. Pharmacologic inhibition of the ASH1L-HIF-1α-macrophages axis elicits robust anti-metastasis responses in preclinical models. Our study demonstrates epigenetic alterations in cancer cells reprogram metabolism and features of myeloid components, facilitating metastatic outgrowth. It establishes ASH1L as an epigenetic driver priming metastasis and macrophage plasticity in the bone niche, providing a bona fide therapeutic target in metastatic malignancies.

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.

Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer

The clinical and pathological outcomes differ between early-onset (diagnosed in men ≤55 years of age) and late-onset prostate cancer, potentially attributed to the changes in hormone levels and immune activities associated with aging. Exploring the heterogeneity therein holds potential for developing age-specific precision interventions. Here, through single-cell and spatial transcriptomic analyses of prostate cancer tissues, we identified that an androgen response-related transcriptional meta-program (AR-MP) might underlie the age-related heterogeneity of tumor cells and microenvironment. APOE+ tumor-associated macrophages infiltrated AR-MP-activated tumor cells in early-onset prostate cancer, potentially facilitating tumor progression and immunosuppression. By contrast, inflammatory cancer-associated fibroblasts in late-onset prostate cancer correlated with downregulation of AR-MP of tumor cells and increased epithelial-to-mesenchymal transition and pre-existing castration resistance, which may also be linked to smoking. This study provides potential insights for tailoring precision treatments by age groups, emphasizing interventions that include targeting AR and tumor-associated macrophages in young patients but anchoring epithelial-to-mesenchymal transition and inflammatory cancer-associated fibroblasts in old counterparts.

Bone metastases diminish extraosseous response to checkpoint blockade immunotherapy through osteopontin-producing osteoclasts

Bone metastatic lesions typically associate with suboptimal responses to immune checkpoint blockade (ICB) therapies. In this study, we observed that across multiple clinical cohorts and a variety of mouse models, the presence of osseous metastases induces ICB resistance in extraosseous tumors. Mechanistically, this long-distance communication is mediated by osseous tumor-conditioned osteoclasts producing osteopontin (OPN). Through circulation, OPN reprograms the extraosseous tumor microenvironment and impairs T cell recruitment and differentiation of CD8+TCF1+ precursor cells, an essential population for ICB efficacy. In mice, ICB responsiveness is restored by αRANKL blockade of osteoclastogenesis, neutralization of OPN in circulation, or tissue-specific depletion of OPN in osteoclasts. Both the mode of action and therapeutic benefit were validated in clinical cohorts with the αRANKL-ICB combinatory regimen. These findings establish bone as a specific immunoregulatory organ exploited by tumor metastasis and suggest osteoclastogenesis as a promising target to improve ICB prognosis in patients with bone metastasis.

Multi-omics analysis constructs a novel neuroendocrine prostate cancer classifier and classification system

Neuroendocrine prostate cancer (NEPC), a subtype of prostate cancer (PCa) with poor prognosis and high heterogeneity, currently lacks accurate markers. This study aims to identify a robust NEPC classifier and provide new perspectives for resolving intra- tumoral heterogeneity. Multi-omics analysis included 19 bulk transcriptomics, 14 single-cell transcriptomics, 1 spatial transcriptomics, 16 published NE signatures and 10 cellular experiments combined with multiple machine learning algorithms to construct a novel NEPC classifier and classification. A comprehensive single-cell atlas of prostate cancer was created from 70 samples, comprising 196,309 cells, among which 9% were identified as NE cells. Within this framework and in combination with bulk transcriptomics, a total of 100 high-quality NE-specific feature genes were identified and differentiated into NEPup sig and NEPdown sig. The random forest (RF) algorithm proved to be the most effective classifier for NEPC, leading to the establishment of the NEP100 model, which demonstrated robust validation across various datasets. In clinical settings, the use of the NEP100 model can greatly improve the diagnostic and prognostic prediction of NEPC. Hierarchical clustering based on NEP100 revealed four distinct NEPC subtypes, designated VR_O, Prol_N, Prol_P, and EMT_Y, each of which presented unique biological characteristics. This allows us to select different targeted therapeutic strategies for different subtypes of phenotypic pathways. Notably, NEP100 expression correlated positively with neuroendocrine differentiation and disease progression, while the VR-NE phenotype dominated by VR_O cells indicated a propensity for treatment resistance. Furthermore, AMIGO2, a component of the NEP100 signature, was associated with chemotherapy resistance and a poor prognosis, indicating that it is a pivotal target for future therapeutic strategies. This study used multi-omics analysis combined with machine learning to construct a novel NEPC classifier and classification system. NEP100 provides a clinically actionable framework for NEPC diagnosis and subtyping.

Serum levels of PSA and VEGF2 as the prognosis markers for bone metastasis of prostate cancer: A retrospective study

BACKGROUND AND OBJECTIVE

Prostate cancer (PCa) is the second most commonly diagnosed cancer in males, the mechanism of PCa with bone metastasis remains unclear. In this study, we aimed to utilize a retrospective clinical study to evaluate the diagnostic value of bone metastases from PCa and provide reference values for future applications.

METHODS

We retrospectively collected a total of 200 samples including 100 PCa patients with bone metastatic and 100 without from June 2019 to August 2021. Transrectal ultrasonography (TRUS) was applied for observing the microvascular blood flow in the lesion. The serum levels of prostate specific antigen (PSA), vascular endothelial growth factor 2 (VEGF2), interleukin-6 (IL-6) and Pro-gastrin-releasing peptide (ProGRP) was determined using Enzyme-linked immunosorbent assay Kit. Regression model was constructed to analyze the risk factors for PCa with bone metastasis, the prognosis value of which was evaluated using receiver operating characteristic (ROC) curves. Ultimately, dataset GSE32269 was employed for validation.

RESULTS

The focal blood perfusion was significantly improved in patients with bone metastasis than those without (P < 0.01). The examination results indicated that PCa patients with bone metastasis had higher levels of PSA, VEGF2, IL-6 and ProGRP than non-bone metastasis (P < 0.01). Moreover, the regression analysis indicated that the four cytokines were the risk factors for bone metastasis, and the ROC curves further confirmed that PSA and VEGF2 had high value of prediction value for bone metastasis with AUC of 0.901 and 0.8519.

CONCLUSION

The expression of PSA and VEGF2 in serum had high prognosis value for bone metastasis in PCa patients.

Live Cell Sorting of Differentiated Primary Human Osteoclasts Allows Generation of Transcriptomic Signature Matrix

Osteoclasts are specialized cells that degrade the bone matrix to create space for bone regeneration. During tumorigenesis, cancer cells metastasize to bone by disrupting bone's natural remodeling cycle. However, the mechanisms underlying critical bone-tumor interactions are poorly understood due to challenges in isolating osteoclasts from human bone. Thus, the conventional method to obtain osteoclasts for in vitro studies is via the differentiation of peripheral blood monocytes, which results in mixed cultures containing progenitor cells and osteoclasts of varying maturity and nuclearity. Presently, we hypothesized that the transcriptomic signatures of mature, multinucleated osteoclasts are distinct from osteoclasts with fewer nuclei. We established a live cell biomarker expression-based sorting protocol to allow purification of mature osteoclasts while maintaining viability and function. We observed that mature, multinucleated osteoclasts were transcriptomically distinct from those with fewer nuclei and that mature osteoclasts showed higher expression of genes that are associated with osteoclast fusion and function.

Exploring the impact of cuproptosis on prostate cancer prognosis via RNA methylation regulation based on single cell and bulk RNA sequencing data

Background

Cuproptosis, along with RNA methylation regulators, has recently come to the fore as innovative mechanisms governing cell death, exerting profound impact on the onset and progression of multiple cancers. Nonetheless, the prognostic implications and underlying regulatory mechanisms of them associated with prostate cancer (PCa) remain to be thoroughly investigated.

Methods

Genomic and clinical data for PCa from The Cancer Genome Atlas datasets were analyzed to identify a prognostic model through univariate and Least Absolute Shrinkage and Selection Operator Cox regression analyses that were validated utilizing external datasets. We used receiver operating characteristic curves and C-index to evaluate the accuracy of our prognostic model. In conjunction with this, we conducted single-cell RNA sequencing (scRNA-seq) analyses to investigate underlying mechanisms and evaluate the degree of immune infiltration, as well as to assess patients' responses to diverse chemotherapy agents. Especially, qPCR assay was utilized to unveil the expression of signature genes in PCa.

Results

We meticulously selected six Cuproptosis-Associated RNA Methylation Regulators (CARMRs) to establish a risk prognosis model, which was further verified to obtain enhanced predictive capacity in external validation cohorts. Insights from immune infiltration and scRNA-seq analyses have elucidated the immune characteristics of PCa, and highlighted the immunosuppressive role of regulatory T cells on immune response. Additionally, drug susceptibility analysis demonstrated that patients with PCa in the low-risk category derived better benefit from bicalutamide treatment, whereas those in the high-risk group exhibited a favor response to adriamycin and docetaxel treatments. The qPCR and immunohistochemistry (IHC) staining assays also reveal the a dramatically altered expression pattern of TRDMT1 and ALYREF in PCa tissues.

Conclusion

In general, we established a model involving CARMRs that can better predict the risk of recurrence of PCa and have identified the possible mechanisms affecting PCa progression, thereby promoting further research in this field.

Bone Metastasis Mediates Poor Prognosis in Early-Onset Gastric Cancer: Insights Into Immune Suppression, Coagulopathy, and Inflammation

BACKGROUND

The increasing incidence of gastric cancer (GC) in younger populations, coupled with population aging, has highlighted distinct age-related subtypes with unique clinical characteristics and outcomes. Although younger patients tend to have more aggressive tumors, the prognostic factors for early-onset gastric cancer (EOGC) remain underexplored. This study is dedicated to providing a comprehensive and in-depth analysis of prognostic factors in EOGC, aiming to refine personalized treatment strategies under the precision medicine paradigm.

METHODS

This retrospective study encompassed 413 local cohort EOGC patients and 8447 Surveillance, Epidemiology, and End Results database patients diagnosed with GC. Survival outcomes were assessed using Kaplan-Meier survival curves, and differences between groups were evaluated with the log-rank test. Prognostic factors were identified through logistic regression and Cox proportional hazards models. Mediation analysis was conducted to assess the indirect effects of clinical factors on EOGC and prognosis. Biomarker comparisons between bone metastasis early-onset gastric cancer and non-bone metastasis early-onset gastric cancer groups were evaluated using the Wilcoxon test for significant differences.

RESULTS

The overall survival and cancer-specific survival rates in the EOGC group were significantly lower than those in the non-early-onset gastric cancer group (p < 0.05). However, EOGC itself was not an independent risk factor for poor prognosis. Mediation analysis revealed that the adverse impact of EOGC on prognosis was predominantly mediated by metastasis, with bone metastasis identified as the most significant factor. Furthermore, bone metastasis emerged as an independent predictor of poor prognosis in EOGC patients, potentially linked to elevated coagulation markers, increased inflammation-related cytokines, and an imbalance in peripheral blood immune cell ratios.

CONCLUSIONS

Bone metastasis significantly contributes to the poor prognosis of EOGC. EOGC patients with bone metastasis demonstrate immune suppression, inflammation activation, and coagulopathy, highlighting the need for tailored management and prognostic strategies.

Comparative diagnostic performance of 68Ga-PSMA-11 PET/CT and 68Ga-PSMA-11 PET/MRI in detecting biochemical recurrent bone metastasis in prostate cancer: a systematic review and meta-analysis

BackgroundThe comparative diagnostic performance of 68Gallium (Ga)-PSMA-11 PET/CT and 68Ga-PSMA-11 PET/MRI in detecting bone metastases in prostate cancer (PCa) remains unclear.PurposeTo systematically evaluate the early detection rate of biochemical recurrent (BCR) bone metastasis in PCa utilizing 68Ga-PSMA-11 PET/CT and 68Ga-PSMA-11 PET/MRI.Material and MethodsWe searched PubMed, Embase, and Web of Science for relevant articles up to April 2023 and extracted studies that examined the positivity rate of both 68Ga-PSMA-11 PET/CT and 68Ga-PSMA-11 PET/MRI in the context of the BCR bone metastasis of PCa patients. Random-effects model was used to compare positivity rates for two imaging modalities. Heterogeneity among studies was assessed using the I2 statistic. To evaluate the methodological quality of studies, we employed Quality Assessment of Diagnostic Performance Studies method. The study protocol was registered in PROSPERO (CRD42023454118).ResultsA total of 1670 publications were originally identified; 58 studies, encompassing a cohort of 8037 patients, met the inclusion criteria. Regarding the evaluation of BCR bone metastasis, results suggest no statistically significant difference in the utilization of 68Ga-PSMA-11 PET/CT versus 68Ga-PSMA-11 PET/MRI in 58 non-head-to-head studies (0.21, 95% CI=0.19-0.24 and 0.17, 95% CI=0.11-0.23; P = 0.19) and four head-to-head studies (0.16, 95% CI=0.08-0.27 and 0.16, 95% CI=0.08-0.27; P = 1.00). Meta-regression showed the study design of influenced the heterogeneity in the PET/MRI group (P < 0.01); but analysis of PET/CT did not identify the potential reason for heterogeneity.ConclusionThere was no statistically significant difference in identifying BCR bone metastasis in PCa patients between 68Ga-PSMA-11 PET/CT and 68Ga-PSMA-11 PET/MRI.

Fast, flexible analysis of differences in cellular composition with crumblr

Changes in cell type composition play an important role in human health and disease. Recent advances in single-cell technology have enabled the measurement of cell type composition at increasing cell lineage resolution across large cohorts of individuals. Yet this raises new challenges for statistical analysis of these compositional data to identify changes in cell type frequency. We introduce crumblr (DiseaseNeurogenomics.github.io/crumblr), a scalable statistical method for analyzing count ratio data using precision-weighted linear mixed models incorporating random effects for complex study designs. Uniquely, crumblr performs statistical testing at multiple levels of the cell lineage hierarchy using a multivariate approach to increase power over tests of one cell type. In simulations, crumblr increases power compared to existing methods while controlling the false positive rate. We demonstrate the application of crumblr to published single-cell RNA-seq datasets for aging, tuberculosis infection in T cells, bone metastases from prostate cancer, and SARS-CoV-2 infection.

CCL20 in the tumor microenvironment: implications for cancer progression and therapeutic approaches

Increasing knowledge of the immunosuppressive tumor microenvironment in cancer-related processes has led to the developing of novel immune-based therapies that have changed the cancer treatment paradigm. In the tumor microenvironment, the plethora of soluble factors secreted by tumor cells interacts with immune cells and non-immune components to deliver signals necessary for tumor progression. Accordingly, targeting tumor-derived factors inducing this immunosuppressive tumor microenvironment has become an appealing therapeutic potential in advancing cancer treatment. CCL20, a chemokine best known to induce leucocyte migration in response to pathological and inflammatory conditions, has been implicated in tumor proliferation, angiogenesis, metastasis, immunosuppression, and therapeutic resistance. Notably, CCL20 and its receptor CCR6 are important in tumor microenvironment interactions. This review discusses the interaction between the CCL20-CCR6 axis and the tumor microenvironment and how these interactions promote tumor progression. Also, an outline of studies utilizing CCL20 in combination with other standard cancer treatments has been shed.

N, Huang J, Li Y, Zhao G, Liu M. Exosome tropism and various pathways in lung cancer metastasis

Lung cancer, characterized by its high morbidity and mortality rates, has the capability to metastasize to various organs, thereby amplifying its detrimental impact and fatality. The metastasis of lung cancer is a complex biological phenomenon involving numerous physiological transformations. Exosomes, small membranous vesicles enriched with biologically active components, are pivotal in mediating intercellular communication and regulating physiological functions due to their specificity and stability. Extensive research has elucidated the production and functions of exosomes in cancer contexts. Multitude of evidence demonstrates a strong association between lung cancer metastasis and exosomes. Additionally, the concept of the pre-metastatic niche is crucial in the metastatic process facilitated by exosomes. This review emphasizes the role of exosomes in mediating lung cancer metastasis and their impact on the disease's development and the progression to other tissues. Furthermore, it explores the potential of exosomes as biomarkers for lung cancer metastasis, offering significant insights for future clinical advancements.

GATA3-Driven ceRNA Network in Lung Adenocarcinoma Bone Metastasis Progression and Therapeutic Implications

Background/Objectives: Bone metastasis is a common and severe complication of lung adenocarcinoma (LUAD), impacting prognosis and treatment outcomes. Understanding the molecular mechanisms behind LUAD bone metastasis (LUADBM) is essential for developing new therapeutic strategies. The interactions between long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in the competing endogenous RNA (ceRNA) network are crucial in cancer progression and metastasis, but the regulatory mechanisms in LUADBM remain unclear. Methods: Microarray analysis was performed on clinical samples, followed by weighted gene co-expression network analysis (WGCNA) and construction of a ceRNA network. Molecular mechanisms were validated using colony formation assays, transwell migration assays, wound healing assays to assess cell migration, and osteoclastogenesis assays to evaluate osteoclast differentiation. Potential therapeutic drugs and their binding affinities were predicted using the CMap database and Kdeep. The interaction between the small-molecule drug and its target protein was confirmed by surface plasmon resonance (SPR) and drug affinity responsive target stability (DARTS) assays. Mechanistic insights and therapeutic efficacy were further validated using patient-derived organoid (PDO) cultures, drug sensitivity assays, and in vivo drug treatments. Results: Our results identified the XLOC_006941/hsa-miR-543/NPRL3 axis as a key regulatory pathway in LUADBM. We also demonstrated that GATA3-driven Th2 cell infiltration creates an immunosuppressive microenvironment that promotes metastasis. Additionally, we confirmed that the inhibitor E7449 effectively targets NPRL3, and its combination with the IL4R-blocking antibody dupilumab resulted in improved therapeutic outcomes in LUADBM. Conclusions: These findings offer new insights into the molecular mechanisms of LUADBM and highlight potential therapeutic targets, including the XLOC_006941/miR-543/NPRL3 axis and GATA3-driven Th2 cell infiltration. The dual-target therapy combining E7449 with dupilumab shows promise for improving patient outcomes in LUADBM, warranting further clinical evaluation.

A PSMA-Targeted Tri-Specific Killer Engager Enhances NK Cell Cytotoxicity against Prostate Cancer

NK cell tumor infiltration is associated with good prognosis in patients with metastatic castration-resistant prostate cancer (mCRPC). NK cells recognize and kill targets by a process called natural cytotoxicity. We hypothesized that promoting an antigen-specific synapse with coactivation may enhance NK cell function in mCRPC. We describe a tri-specific killer engager (TriKE) construct that engages with the activating receptor CD16 on NK cells and prostate-specific membrane antigen (PSMA) on mCRPC cells and has an IL15 moiety that is essential for NK cell survival, proliferation, and priming. We show that the PSMA TriKE specifically binds to PSMA-expressing cells and significantly enhances expansion, degranulation, and cytokine production of NK cells derived from healthy donors or patients with prostate cancer. Bystander killing of PSMA-negative tumor cells was also achieved with PSMA TriKE treatment when cocultured with PSMA-positive cells, suggesting potential PSMA TriKE benefit in controlling tumor antigen escape. When tested under physiologic conditions recapitulating the mCRPC tumor microenvironment, NK cells treated with PSMA TriKE and prolonged exposure to hypoxia or myeloid-derived suppressor cells maintained their potent function whereas IL15-treated NK cells showed greatly impaired cytotoxicity. Finally, in vivo testing of PSMA TriKE showed improved tumor control and survival of mice as compared with IL15-treated and untreated control groups. In conclusion, PSMA TriKE demonstrates potential as a new therapy for advanced prostate cancer by providing additional signals to NK cells to maximize their antitumor potential in prostate cancer, especially in the setting of a hostile tumor microenvironment.

The Recruitment and Immune Suppression Mechanisms of Myeloid-Derived Suppressor Cells and Their Impact on Bone Metastatic Cancer

BACKGROUND

MDSCs are immature neutrophils and monocytes with immunosuppressive potentials, involving mononuclear MDSCs (M-MDSCs) and polymorphonuclear MDSCs (PMN-MDSCs).

RECENT FINDINGS

They are significant components of the tumor microenvironment (TME). Besides, recent studies also verified that MDSCs also facilitated the progression of bone metastasis by regulating the network of cytokines and the function of immune cells.

CONCLUSION

It is necessary to summarize the mechanisms of MDSC recruitment and immunosuppression, and their impact on bone metastasis.

Identification of diagnostic biomarkers in prostate cancer-related fatigue by construction of predictive models and experimental validation

BACKGROUND

Cancer-related fatigue (CRF) is a prominent cancer-related complication occurring in Prostate cancer (PCa) patients, profoundly affecting prognosis. The lack of diagnostic criteria and biomarkers hampers the management of CRF.

METHODS

The CRF-related data and PCa single-cell data were retrieved from the GEO database and clinical data was downloaded from the TCGA database. The univariate logistic/Cox regression analysis were used to construct the prediction models. The predictive value of models was analyzed using the ROC curve and Kaplan-Meier survival. The hub genes were screened by an intersection analysis of DEGs. The mice model of PCa and PCa-related fatigue were established, and fatigue-like behaviors of mice were detected. The expression of selected hub genes was validated by RT-PCR and IHC analysis.

RESULTS

The diagnosis and risk models showed great predictive value both in the training and validation dataset. Five genes (Baiap2l2, Cacng4, Sytl2, Sec31b and Ms4a1) that enriched the CXCL signaling were identified as hub genes. Among all hub genes, the MS4A1 expression is the most significant in PCa-related fatigue mice.

CONCLUSIONS

We identified MS4A1 as a promising biomarker for the diagnosis of PCa-related fatigue. Our findings would lay a foundation for revealing the pathogenesis and developing therapies for PCa-related fatigue.

Prostate Cancer Bone Metastasis: Molecular Mechanisms of Tumor and Bone Microenvironment

Prostate cancer is prevalent among men aged 65 and older. Bone metastasis occurs in up to 90% of advanced prostate cancer patients, metastatic prostate cancer is generally considered a non-curative condition which can impact quality of life. The tumor microenvironment, comprising diverse cellular and non-cellular elements, interacts with prostate cancer cells to affect tumor growth and bone metastasis. Within the bone microenvironment, different cell types, including osteoblasts, osteoclasts, adipocytes, endothelial cells, hematopoietic stem cells, and immune cells, engage with tumor cells. Some cells alter tumor behavior, while others are impacted or overpowered by tumor cells, leading to different phases of tumor cell movement, dormancy, latency, resistance to treatment, and advancement to visible bone metastasis. This review summarizes recent research on the tumor microenvironment and bone microenvironment in prostate cancer bone metastasis, exploring underlying mechanisms and the potential value of targeting these environments for treatment.

Inhibiting HnRNP L-mediated alternative splicing of EIF4G1 counteracts immune checkpoint blockade resistance in Castration-resistant prostate Cancer

Immunotherapy with checkpoint inhibitors produced significant clinical responses in a subset of cancer patients who were resistant to prior therapies. However, Castration-resistant prostate cancer (CRPC) is seriously lack of T cell infiltration, which greatly limits the clinical application of immunotherapy, but the mechanism is unclear. In the present study, in silico analyses and experimental data show that HnRNP L was significantly negatively correlated with CD4+ and CD8+ T cells infiltration in patients; besides, we found deficiency of HnRNP L recruites CD4+ and CD8+ T cells infiltration and impairs tumorigenesis. Mechanically, HnRNP L enhanced the translation of c-Myc and then promoted CXCL8 secretion via alternative splicing of EIF4G1. In vivo, inhibition of EIF4G1 by the inhibitor, SBI-0640756, attenuated HnRNP l-induced tumor progression and immunosuppressive activity. And most of all, therapeutic synergy between HnRNP L knockdown and Anti-PD-1 could significantly suppress xenograft prostate cancer growth. In summary, this study revealled the molecular mechanism of HnRNP L regulating the immune infiltration, which provides a new theoretical basis for overcoming the limitation of immunotherapy for CRPC.

New players in the landscape of renal cell carcinoma bone metastasis and therapeutic opportunities

Approximately one-third of advanced renal cell carcinoma (RCC) patients develop osteolytic bone metastases, leading to skeletal complications. In this review, we first provide a comprehensive perspective of seminal studies on bone metastasis of RCC describing the main molecular modulators and growth factor signaling pathways most important for the RCC-stimulated osteoclast-mediated bone destruction. We next focus on newer developments revealing with in-depth details, the bidirectional interplay between renal cancer cells and the immune and stromal microenvironment that can through epigenetic reprogramming, profoundly affect the behaviors of transformed cells. Understanding their mechanistic interactions is of paramount importance for advancing both fundamental and translational research. These new investigations into the landscape of RCC-bone metastasis offer novel insights and identify potential avenues for future therapeutic interventions.

Fast, flexible analysis of differences in cellular composition with crumblr

Changes in cell type composition play an important role in human health and disease. Recent advances in single-cell technology have enabled the measurement of cell type composition at increasing cell lineage resolution across large cohorts of individuals. Yet this raises new challenges for statistical analysis of these compositional data to identify changes in cell type frequency. We introduce crumblr (DiseaseNeurogenomics.github.io/crumblr), a scalable statistical method for analyzing count ratio data using precision-weighted linear mixed models incorporating random effects for complex study designs. Uniquely, crumblr performs statistical testing at multiple levels of the cell lineage hierarchy using a multivariate approach to increase power over tests of one cell type. In simulations, crumblr increases power compared to existing methods while controlling the false positive rate. We demonstrate the application of crumblr to published single-cell RNA-seq datasets for aging, tuberculosis infection in T cells, bone metastases from prostate cancer, and SARS-CoV-2 infection.

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.

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.

Evolution of myeloid-mediated immunotherapy resistance in prostate cancer

Patients with advanced metastatic castration-resistant prostate cancer (mCRPC) are refractory to immune checkpoint inhibitors (ICIs)1,2, partly because there are immunosuppressive myeloid cells in tumours3,4. However, the heterogeneity of myeloid cells has made them difficult to target, making blockade of the colony stimulating factor-1 receptor (CSF1R) clinically ineffective. Here we use single-cell profiling on patient biopsies across the disease continuum and find that a distinct population of tumour-associated macrophages with elevated levels of SPP1 transcripts (SPP1hi-TAMs) becomes enriched with the progression of prostate cancer to mCRPC. In syngeneic mouse modelling, an analogous macrophage population suppresses CD8+ T cell activity in vitro and promotes ICI resistance in vivo. Furthermore, Spp1hi-TAMs are not responsive to anti-CSF1R antibody treatment. Pathway analysis identifies adenosine signalling as a potential mechanism for SPP1hi-TAM-mediated immunotherapeutic resistance. Indeed, pharmacological inhibition of adenosine A2A receptors (A2ARs) significantly reverses Spp1hi-TAM-mediated immunosuppression in CD8+ T cells in vitro and enhances CRPC responsiveness to programmed cell death protein 1 (PD-1) blockade in vivo. Consistent with preclinical results, inhibition of A2ARs using ciforadenant in combination with programmed death 1 ligand 1 (PD-L1) blockade using atezolizumab induces clinical responses in patients with mCRPC. Moreover, inhibiting A2ARs results in a significant decrease in SPP1hi-TAM abundance in CRPC, indicating that this pathway is involved in both induction and downstream immunosuppression. Collectively, these findings establish SPP1hi-TAMs as key mediators of ICI resistance in mCRPC through adenosine signalling, emphasizing their importance as both a therapeutic target and a potential biomarker for predicting treatment efficacy.

Osteoblast-Derived ECM1 Promotes Anti-Androgen Resistance in Bone Metastatic Prostate Cancer

Acquired resistance to hormonal therapy, particularly enzalutamide (ENZ), remains a significant obstacle in the treatment of advanced bone metastatic prostate cancer. Here, it is demonstrated that under ENZ treatment, osteoblasts in the bone microenvironment secrete increased levels of extracellular matrix protein 1 (ECM1), which affects surrounding prostate cancer cells, promoting tumor cell proliferation and anti-androgen resistance. Mechanistically, ECM1 interacts with the enolase 1 (ENO1) receptor on the prostate cancer cell membrane, leading to its phosphorylation at the Y189 site. This event further recruits adapter proteins including growth factor receptor-bound protein 2 (GRB2) and son of sevenless homolog 1 (SOS1), which activates the downstream mitogen-activated protein kinase (MAPK) signaling pathway to induce anti-androgen resistance. Furthermore, inhibiting ECM1 or utilizing the ENO1-targeting inhibitor phosphonoacetohydroxamate (PhAH) significantly restores tumor cell sensitivity to ENZ. Taken together, a potential mechanism is identified through which osteoblast-derived ECM1 drives resistance in bone metastatic prostate cancer under ENZ treatment. Additionally, the findings indicate that ECM1 and ENO1 may serve as potential targets for developing therapies for bone metastatic castration-resistant prostate cancer.

Analysis and functional validations of multiple cell death patterns for prognosis in prostate cancer

Prostate cancer (PCa) has garnered significant attention due to its rising incidence, variable therapeutic outcomes, and the absence of reliable prognostic markers. The significance of different cell death patterns in tumor development underscores their potential as predictors of PCa prognosis. This study utilized The Cancer Genome Atlas (TCGA) datasets to evaluate the prognostic capabilities of 15 cell death patterns and established a Cell Death Index (CDI) signature based on necrosis and cuproptosis-related genes. The predictive efficacy of the CDI signature was validated in our PCa cohort and in two public datasets: Deutsches Krebsforschungszentrum (DKFZ) and Memorial Sloan-Kettering Cancer Center (MSKCC) PCa cohorts. Our comprehensive analysis examined the relationship between CDI signature and clinical characteristics, published prognostic signatures, gene mutations, immune cell infiltration, enrichment pathways, and drug sensitivity in PCa. In vitro and in vivo studies assessed the impact of EDA2R and LOXL2 on PCa progression. The CDI signature exhibited robust predictive performance across three independent validation sets, with 1-, 2-, 3-, 4-, and 5-year area under the curve (AUC) values in the TCGA cohort of 0.866, 0.77, 0.836, 0.776, and 0.787, respectively. Higher CDI scores were correlated with advanced T and N stages, elevated Gleason scores, increased immune cell infiltration, gene mutations, and drug sensitivity. EDA2R inhibited PCa cell proliferation and migration, related to tumor necrosis, while LOXL2 promoted these processes and was associated with cuproptosis. In summary, our study identified a novel CDI signature as an effective indicator for diagnosis, personalized treatment, and prognostic assessment in PCa.

Acetyltransferase NAT10 promotes an immunosuppressive microenvironment by modulating CD8+ T cell activity in prostate cancer

N-acetyltransferase 10 (NAT10), an enzyme responsible for ac4C acetylation, is implicated in cancer progression, though its specific biological function in prostate cancer remains insufficiently understood. This study clarifies NAT10's role in prostate cancer and its effects on the tumor immune microenvironment. NAT10 expression and clinical relevance were assessed through bioinformatics, RT-qPCR, and IHC analyses, comparing prostate cancer tissues with normal controls. The impact of NAT10 on tumor cell proliferation, migration, and invasion was investigated via in vitro assays-including CCK-8, EdU, wound healing, and 3D-Transwell-as well as in vivo mouse xenograft models and organoid studies. Further, NAT10's influence on immune cell infiltration was examined using flow cytometry, IHC, cell co-culture assays, and ELISA to elucidate downstream chemokine effects, specifically targeting CD8+ T cells. Findings indicated significant upregulation of NAT10 in prostate cancer cells, enhancing their proliferative and invasive capacities. Notably, NAT10 suppresses CD8+ T cell recruitment and cytotoxicity through the CCL25/CCR9 axis, fostering an immunosuppressive microenvironment that exacerbates tumor progression. An ac4C modification score was also devised based on NAT10's downstream targets, providing a novel predictive tool for evaluating immune infiltration and forecasting immunotherapy responses in patients with prostate cancer. This study underscores NAT10's pivotal role in modulating the prostate cancer immune microenvironment, offering insights into the immune desert phenomenon and identifying NAT10 as a promising therapeutic target for improving immunotherapy efficacy.

WWP1 targeting PTEN for polyubiquitination to promote bone metastasis of luminal breast cancer

Luminal breast cancer exhibits a high incidence of bone recurrence when metastasizing to distant organs. The mechanisms underlying the organotropism of luminal breast cancer cells remain unclear. In this study, we aimed to determine the role of WWP1 (WW domain-containing E3 ubiquitin protein ligase 1)-PTEN (phosphatase and tensin homolog deleted on chromosome ten) interaction in bone tropism in luminal breast cancer. We observed that WWP1 was overexpressed in luminal breast cancer tissues and associated with poor prognosis in breast cancer patients. In luminal breast cancer cells, WWP1 was found to mediate PTEN ubiquitination, resulting in the functional loss of PTEN. As a result, we demonstrate that WWP1 contributes to bone tropism in luminal breast cancer cells via the polyubiquitination of PTEN. Consequently, WWP1-mediated PTEN polyubiquitination contributed to the early metastasis of luminal breast cancer cells to the bone. Thus, our study provides a mechanistic insight into the bone tropism of luminal breast cancer cells and proposes a potential therapeutic strategy for mitigating cancer metastasis to the bone.

How the bone microenvironment shapes the pre-metastatic niche and metastasis

The bone is a frequent metastatic site, with changes in the mineralized bone and the bone marrow milieu that can also prime other sites for metastasis by educating progenitor cells to support metastatic spread. Stromal and immune populations cooperatively maintain the organizationally complex bone niches and are dysregulated in the presence of a distant primary tumor and metastatic disease. Interrogating the bone niches that facilitate metastatic spread using innovative technologies holds the potential to aid in preventing metastasis in and mediated by the bone. Here, we review recent advances in bone niche biology and its adaptations in the context of cancer.

Osteoimmunology in bone malignancies: a symphony with evil

Bone marrow is pivotal for normal hematopoiesis and immune responses, yet it is often compromised by malignancies. The bone microenvironment (BME), composed of bone and immune cells, maintains skeletal integrity and blood production. The emergence of primary or metastatic tumors in the skeletal system results in severe complications and contributes significantly to cancer-related mortality. These tumors set off a series of interactions among cancer, bone, and immune cells, and disrupt the BME locally or distantly. However, the drivers, participants, and underlying molecules of these interactions are not fully understood. This review explores the crosstalk between bone metabolism and immune responses, synthesizing current knowledge on the intersection of cancer and osteoimmune biology. It outlines how bone marrow immune cells can either facilitate or hinder tumor progression by interacting with bone cells and pinpoints the molecules responsible for immunosuppression within bone tumors. Moreover, it discusses how primary tumors remotely alter the BME, leading to systemic immune suppression in cancer patients. This knowledge provides critical rationales for emerging immunotherapies in the treatment of bone-related tumors. Taken together, by summarizing the intricate relationship between tumor cells and the BME, this review aims to deepen the understanding of the diversity, complexity, and dynamics at play during bone tumor progression. Ultimately, it highlights the potential of targeting bone-tumor interactions to correct aberrant immune functions, thereby inhibiting tumor growth and metastasis.

Integrated analysis of single-cell RNA-seq and bulk RNA-seq revealed key genes for bone metastasis and chemoresistance in prostate cancer

BACKGROUND

Prostate cancer (PCa) is a serious malignancy. The main causes of PCa aggravation and death are unexplained resistance to chemotherapy and bone metastases.

OBJECTIVE

This study aimed to investigate the molecular mechanisms associated with the dynamic processes of progression, bone metastasis, and chemoresistance in PCa.

METHODS

Through comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data, Gene Expression Omnibus (GEO) tumor progression and metastasis-related genes were identified. These genes were subjected to lasso regression modeling using the Cancer Genome Atlas (TCGA) database. Tartrate-resistant acid phosphatase (TRAP) staining and real-time quantitative PCR (RT-qPCR) were used to evaluate osteoclast differentiation. CellMiner was used to confirm the effect of LDHA on chemoresistance. Finally, the relationship between LDHA and chemoresistance was verified using doxorubicin-resistant PCa cell lines.

RESULTS

7928 genes were identified as genes related to tumor progression and metastasis. Of these, 7 genes were found to be associated with PCa prognosis. The scRNA-seq and TCGA data showed that the expression of LDHA was higher in tumors and associated with poor prognosis of PCa. In addition, upregulation of LDHA in PCa cells induces osteoclast differentiation. Additionally, high LDHA expression was associated with resistance to Epirubicin, Elliptinium acetate, and doxorubicin. Cellular experiments demonstrated that LDHA knockdown inhibited doxorubicin resistance in PCa cells.

CONCLUSIONS

LDHA may play a potential contributory role in PCa initiation and development, bone metastasis, and chemoresistance. LDHA is a key target for the treatment of PCa.

FastTENET: an accelerated TENET algorithm based on manycore computing in Python

SUMMARY

TENET reconstructs gene regulatory networks from single-cell RNA sequencing (scRNAseq) data using the transfer entropy (TE), and works successfully on a variety of scRNAseq data. However, TENET is limited by its long computation time for large datasets. To address this limitation, we propose FastTENET, an array-computing version of TENET algorithm optimized for acceleration on manycore processors such as GPUs. FastTENET counts the unique patterns of joint events to compute the TE based on array computing. Compared to TENET, FastTENET achieves up to 973× performance improvement.

AVAILABILITY AND IMPLEMENTATION

FastTENET is available on GitHub at https://github.com/cxinsys/fasttenet.

Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet

Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer's disease cases and 149 controls.

Immunome profiling in prostate cancer: a guide for clinicians

Tumor immune microenvironment (TIME) plays a key role to understand how tumors respond to prostate cancer (PC) therapies and potential mechanisms of resistance. Previous research has suggested that specific genomic aberrations, such as microsatellite instability (MSI) or CDK12 bi-allelic loss can allow PC patients more likely to respond to immune checkpoint inhibitors (ICI) or other immune therapies. However, responses to these treatments remain highly variable even in selected patients. Thus, it is essential to obtain more information about tumor immune cells that infiltrate these tumors, and on their plasticity and interactions, in order to better understand the underlying biology to allow development of new therapeutic strategies. This review analyzes: 1) How interactions among immune cell populations and other cells infiltrating the tumor stroma can modulate the progression of PC, 2) How the standard therapies to treat PC (such as androgen deprivation therapy, new androgen-directed hormone therapy or chemotherapy) may influence the dynamic changes of the immunome and 3) What are the limitations in characterizing the immune landscape of the host´s response to tumors.

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.

Macrophage crosstalk and therapies: Between tumor cells and immune cells

In the tumor microenvironment, macrophages exhibit different phenotypes and functions in response to various signals, playing a crucial role in the initiation and progression of tumors. Several studies have indicated that intervention in the functions of different phenotypes of tumor-associated macrophages causes significant changes in the crosstalk between tumor cells and immune-related cells, such as T, NK, and B cells, markedly altering the course of tumor development. However, only a few specific therapeutic strategies targeting macrophages are yet available. This article comprehensively reviews the molecular biology mechanisms through which tumor-associated macrophages mediate the crosstalk between tumor cells and immune-related cells. Also, various treatment methods currently used in clinical practice and those in the clinical trial phase have been summarized, and the novel strategies for targeting tumor-associated macrophages have been categorized accordingly.

Bioinformatics-based screening of hub genes for prostate cancer bone metastasis and analysis of immune infiltration

Bioinformatics analysis of genes and immune cells that influence prostate cancer (PCa) bone metastases. Using the gene expression omnibus database, we analyzed a PCa bone metastasis dataset. Differentially expressed genes were identified through the utilization of GEO2R and weighted gene co-expression network analysis. Gene set enrichment analysis software was used to identify important pathways. In addition to creating a network of protein-protein interactions, functional enrichment analyses were conducted using Kyoto encyclopedia of genes databases. To screen hub genes, Cytoscape software was used with the CytoHubba plug-in and performed mRNA and survival curve validation analysis of key genes using the cBioPortal website and GEPIA2 database. Immune infiltration analysis was performed using the CIBERSORTx website, and finally, immune cell correlation analysis was performed for key genes according to the TIMER database. A total of 197 PCa bone metastasis risk genes were screened, "G2M_CHECKPOINT" was significantly enriched in PCa bone metastasis samples according to genomic enrichment analysis. Based on the protein interactions network, we have identified 10 alternative hub genes, and 3 hub genes, CCNA2, NUSAP1, and PBK, were validated by the cBioPortal website and the GEPIA2 database. T cells regulatory and macrophages M0 may influence PCa to metastasize to bones, according to CIBERSORTx immune cell infiltration analysis. TIMER database analysis found different degrees of correlation between 3 key genes and major immune cells. PCa bone metastasis has been associated with CCNA2, NUSAP1, and PBK. T cells regulatory and macrophages (M0) may also be involved.

Macrophage diversity in cancer dissemination and metastasis

Invasion and metastasis are hallmarks of cancer. In addition to the well-recognized hematogenous and lymphatic pathways of metastasis, cancer cell dissemination can occur via the transcoelomic and perineural routes, which are typical of ovarian and pancreatic cancer, respectively. Macrophages are a universal major component of the tumor microenvironment and, in established tumors, promote growth and dissemination to secondary sites. Here, we review the role of tumor-associated macrophages (TAMs) in cancer cell dissemination and metastasis, emphasizing the diversity of myeloid cells in different tissue contexts (lungs, liver, brain, bone, peritoneal cavity, nerves). The generally used models of lung metastasis fail to capture the diversity of pathways and tissue microenvironments. A better understanding of TAM diversity in different tissue contexts may pave the way for tailored diagnostic and therapeutic approaches.

Deciphering the Tumor Microenvironment in Prostate Cancer: A Focus on the Stromal Component

Prostate cancer progression is significantly affected by its tumor microenvironment, in which mesenchymal cells play a crucial role. Stromal cells are modified by cancer mutations, response to androgens, and lineage plasticity, and in turn, engage with epithelial tumor cells via a complex array of signaling pathways and ligand-receptor interactions, ultimately affecting tumor growth, immune interaction, and response to therapy. The metabolic rewiring and interplay in the microenvironment play an additional role in affecting the growth and progression of prostate cancer. Finally, therapeutic strategies and novel clinical trials with agents that target the stromal microenvironment or disrupt the interaction between cellular compartments are described. This review underscores cancer-associated fibroblasts as essential contributors to prostate cancer biology, emphasizing their potential as prognostic indicators and therapeutic targets.

A tumour-associated macrophage-based signature for deciphering prognosis and immunotherapy response in prostate cancer

For the multistage progression of prostate cancer (PCa) and resistance to immunotherapy, tumour-associated macrophage is an essential contributor. Although immunotherapy is an important and promising treatment modality for cancer, most patients with PCa are not responsive towards it. In addition to exploring new therapeutic targets, it is imperative to identify highly immunotherapy-sensitive individuals. This research aimed to establish a signature risk model, which derived from the macrophage, to assess immunotherapeutic responses and predict prognosis. Data from the UCSC-XENA, GEO and TISCH databases were extracted for analysis. Based on both single-cell datasets and bulk transcriptome profiles, a macrophage-related score (MRS) consisting of the 10-gene panel was constructed using the gene set variation analysis. MRS was highly correlated with hypoxia, angiogenesis, and epithelial-mesenchymal transition, suggesting its potential as a risk indicator. Moreover, poor immunotherapy responses and worse prognostic performance were observed in the high-MRS group of various immunotherapy cohorts. Additionally, APOE, one of the constituent genes of the MRS, affected the polarisation of macrophages. In particular, the reduced level of M2 macrophage and tumour progression suppression were observed in PCa xenografts which implanted in Apolipoprotein E-knockout mice. The constructed MRS has the potential as a robust prognostic prediction tool, and can aid in the treatment selection of PCa, especially immunotherapy options.

Advances in and prospects of immunotherapy for prostate cancer

Immunotherapy has shown promising therapeutic effects in hematological malignancies and certain solid tumors and has emerged as a critical and highly potential treatment modality for cancer. However, prostate cancer falls under the category of immune-resistant cold tumors, for which immunotherapy exhibits limited efficacy in patients with solid tumors. Thus, it is important to gain a deeper understanding of the tumor microenvironment in prostate cancer to facilitate immune system activation and overcome immune suppression to advance immunotherapy for prostate cancer. In this review, we discuss the immunosuppressive microenvironment of prostate cancer, which is characterized by the presence of few tumor-infiltrating lymphocytes, abundant immunosuppressive cells, low immunogenicity, and a noninflammatory phenotype, which significantly influences the efficacy of immunotherapy for prostate cancer. Immunotherapy is mainly achieved by activating the host immune system and overcoming immunosuppression. In this regard, we summarize the therapeutic advances in immune checkpoint blockade, immunogenic cell death, reversal of the immunosuppressive tumor microenvironment, tumor vaccines, immune adjuvants, chimeric antigen receptor T-cell therapy, and overcoming penetration barriers in prostate cancer, with the aim of providing novel research insights and approaches to enhance the effectiveness of immunotherapy for prostate cancer.

Single-cell transcriptome analysis reveals evolving tumour microenvironment induced by immunochemotherapy in nasopharyngeal carcinoma

BACKGROUND

Combinatory therapeutic strategy containing immunochemotherapy as part of induction therapy components is one of the current trends in the treatment of high-risk metastatic locally advanced nasopharyngeal carcinoma (NPC). However, the mechanism underlying the heterogeneity of response at the single-cell level has not been underexplored.

METHODS

18 bulks and 11 single-cell RNA sequencing from paired before-treatment and on-treatment samples in patients with treatment-naive high-risk metastatic locally advanced NPCs were obtained. Following quality control, a total of 87 191 cells were included in the subsequence bioinformatics analysis.

RESULTS

Immunochemotherapy was associated with on-treatment tumour microenvironment (TME) remodelling, including upregulation of anti-TMEs signatures, downregulation of pro-TMEs signatures, reversing CD8+ T exhaustion, and repolarizing proinflammatory TAMs. For the patients achieving a complete response, the cytotoxic activity of CD8+ T cells was stimulated and more interferon-gamma was provided, which would be the key for TAMs proinflammatory repolarization and eventually promote the CD8+ T cells maturation in turn. Among patients who did not reach complete response, differentiation and hypoxia signatures for endothelial cells were elevated after therapy. These patients exhibited higher levels of immune checkpoint genes in malignant cells at the baseline (before treatment), and decreased tumour antigen presentation activity, which may underlie the resistance mechanism to therapy.

CONCLUSIONS

This study pictures a map of TME modulation following immunochemotherapy-based combination induction therapy and provides potential future approaches.

HIGHLIGHTS

Immunochemotherapy remodeled T cell phenotypes. For the patients achieving complete response, more interferon gamma was provided by CD8+ T cells after therapy, which would be the key for TAMs pro-inflammatory repolarization and eventually promote the CD8+ T cells maturation in turns. Among patients who did not reach complete response, malignant cells exhibited higher level of immune checkpoint genes before therapy, and decreased tumor antigen presentation activity, which may underlie the resistance mechanism to therapy.

Transcriptomic analysis of mouse TRAMP cell lines and tumors provide insights into shared pathways and therapeutic targets

The present study focused on comparing the gene expression profiles of different mouse models of prostate cancer, focusing on the TRAMP transgenic model and its derived cell lines and extending the comparisons to relevant genetically engineered mouse models and human prostate cancer datasets. Employing RNA sequencing, we examined different levels of prostate cancer aggressiveness from the original TRAMP cells to the TRAMP-C2 (TC2) derived cell line and extending to the aggressive TC2-Ras (TC2R) cells and tumors. TC2R acquire the ability to grow in bone tissue upon implantation, unlike the parental TC2 cells. Analysis identified upregulated genes in cell cycle regulation, immune response, and mitotic processes in TRAMP compared to wild-type tissues. TC2 cells exhibited unique gene profiles enriched in ECM organization and tissue development pathways, while TC2R cells showed increased cytokine signaling and motility genes, with decreased ECM and immune response pathways. In vivo TC2R models demonstrated enhanced ECM organization and receptor tyrosine kinase signaling in tumors, notably enriching immune processes and collagen degradation pathways in intratibial tumors. Comparative analysis among mouse and human datasets showed overlaps, particularly in pathways relating to mitotic cycle regulation, ECM organization, and immune interactions. A gene signature identified in TC2R tumors correlated with aggressive tumor behavior and poor survival in human datasets. Further immune cell landscape analysis of TC2R tumors revealed altered T cell subsets and macrophages, confirmed in single-cell RNA-seq from human samples. TC2R models thus hold significant promise in helping advance preclinical therapeutics, potentially contributing to improved prostate cancer patient outcomes.