Integration of multi-omics and clinical treatment data reveals bladder cancer therapeutic vulnerability gene combinations and prognostic risks

Multi-Omics Profiling and Experimental Verification of Lysosomes-Related Genes in Hepatocellular Carcinoma

Lysosomes play a crucial role in regulating the growth, invasion and metastasis of different tumour types. However, the specific function of lysosomes in hepatocellular carcinoma (HCC) remains uncertain. We retrieved gene expression and clinical data from the TCGA and GEO databases for HCC samples and established a new lysosome-associated prognostic therapeutic index (LAPTI) based on lysosome-related genes through machine learning. We then systematically analysed clinical characteristics, functional enrichment, tumour immune microenvironment, molecular docking, chemotherapy response and immunotherapy response in HCC. LAPTI, composed of four lysosome-related genes (CTSV, LAPTM4B, DNAJC6, AP1M2), is a reliable prognostic indicator for hepatocellular carcinoma patients and is validated in external data sets. Compared with the low LAPTI group, the high LAPTI group showed poorer prognosis and higher immune cell infiltration levels. We also observed that knocking down CTSV in vitro inhibited the proliferation and migration of hepatocellular carcinoma. This study provides valuable insights into the future clinical treatment of hepatocellular carcinoma by accurately assessing the prognosis of patients with hepatocellular carcinoma.

P4HB maintains Wnt-dependent stemness in glioblastoma stem cells as a precision therapeutic target and serum marker

Glioblastoma stem cells (GSCs) are pivotal in the recurrence and drug resistance of glioblastoma multiforme (GBM). However, precision therapeutic and diagnostic markers for GSCs have not been fully established. Here, using bioinformatics and experimental analysis, we identified P4HB, a protein disulfide isomerase, as a serum marker that maintains stemness in GSCs through the Wnt/β-catenin signaling pathway. Transcriptional silencing of P4HB induces apoptosis and diminishes stem cell-like characteristics in GSCs. Treatments with the chemical CCF624 or the China National Medical Products Administration (NMPA)-approved securinine significantly prolonged survival in patient-derived xenograft mouse models, underscoring P4HB's potential as a therapeutic target and presenting an expedited path to clinical application through drug repurposing. Additionally, elevated P4HB levels in patient serum were found to correlate with disease progression, underscoring its utility as a biomarker and its promise for precision medicine.

Deciphering the molecular heterogeneity of intermediate- and (very-)high-risk non-muscle-invasive bladder cancer using multi-layered -omics studies

Bladder cancer (BC) is the most common malignancy of the urinary tract. About 75% of all BC patients present with non-muscle-invasive BC (NMIBC), of which up to 70% will recur, and 15% will progress in stage and grade. As the recurrence and progression rates of NMIBC are strongly associated with some clinical and pathological factors, several risk stratification models have been developed to individually predict the short- and long-term risks of disease recurrence and progression. The NMIBC patients are stratified into four risk groups as low-, intermediate-, high-risk, and very high-risk by the European Association of Urology (EAU). Significant heterogeneity in terms of oncological outcomes and prognosis has been observed among NMIBC patients within the same EAU risk group, which has been partly attributed to the intrinsic heterogeneity of BC at the molecular level. Currently, we have a poor understanding of how to distinguish intermediate- and (very-)high-risk NMIBC with poor outcomes from those with a more benign disease course and lack predictive/prognostic tools that can specifically stratify them according to their pathologic and molecular properties. There is an unmet need for developing a more accurate scoring system that considers the treatment they receive after TURBT to enable their better stratification for further follow-up regimens and treatment selection, based also on a better response prediction to the treatment. Based on these facts, by employing a multi-layered -omics (namely, genomics, epigenetics, transcriptomics, proteomics, lipidomics, metabolomics) and immunohistopathology approach, we hypothesize to decipher molecular heterogeneity of intermediate- and (very-)high-risk NMIBC and to better stratify the patients with this disease. A combination of different -omics will provide a more detailed and multi-dimensional characterization of the tumor and represent the broad spectrum of NMIBC phenotypes, which will help to decipher the molecular heterogeneity of intermediate- and (very-)high-risk NMIBC. We think that this combinatorial multi-omics approach has the potential to improve the prediction of recurrence and progression with higher precision and to develop a molecular feature-based algorithm for stratifying the patients properly and guiding their therapeutic interventions in a personalized manner.

Pan-cancer analysis reveals potential immunological and prognostic roles of COA6 in human cancers and preliminary exploration of COA6 in bladder cancer

BACKGROUND

Cytochrome C oxidase assembly factor 6 (COA6) is significantly involved in the progression of cancer and is aberrantly expressed in disease. Nevertheless, the comprehensive analysis of COA6 using many omics techniques, and its impact on the prognosis and immunological microenvironment of cancer patients, remains unexplored.

METHODS

We gathered data from 33 cancer cases and conducted a thorough analysis of abnormalities in COA6 gene expression. This analysis included examining its relevance to disease, its diagnostic and prognostic value, pathway enrichment, the immune microenvironment, its association with immune checkpoints, and its ability to predict patient response to immunotherapy and natural small molecule drugs that target the COA6 protein. Ultimately, we examined the function of COA6 in bladder cancer by in vitro research.

RESULTS

Our study revealed significant variations in gene expression and identified COA6 as a potential diagnostic biomarker for cancer. COA6 was also discovered to have a crucial function in pan-cancer involving the tumor microenvironment. COA6 has a strong correlation with well-known immunological checkpoints, including TMB and MSI. Molecular docking identified natural small chemical inhibitors that specifically target the COA6 protein. Ultimately, scientific evidence has verified that suppressing the expression of the COA6 gene hinders the growth and infiltration of bladder cancer cells.

CONCLUSIONS

Our study emphasizes the significant potential of COA6 as a predictive and immunotherapeutic response biomarker. This finding may lead to future investigation into the mechanism of tumor infiltration and the therapeutic possibilities of COA6 in cancer.

The vasculogenic mimicry related signature predicts the prognosis and immunotherapy response in renal clear cell carcinoma

BACKGROUND

Clear cell carcinoma of the kidney is a common urological malignancy characterized by poor patient prognosis and treatment outcomes. Modulation of vasculogenic mimicry in tumor cells alters the tumor microenvironment and the influx of tumor-infiltrating lymphocytes, and the combination of its inducers and immune checkpoint inhibitors plays a synergistic role in enhancing antitumor effects.

METHODS

We downloaded the data from renal clear cell carcinoma samples and vasculogenic mimicry-related genes to establish a new vasculogenic mimicry-related index (VMRI) using a machine learning approach. Based on VMRI, patients with renal clear cell carcinoma were divided into high VMRI and low VMRI groups, and patients' prognosis, clinical features, tumor immune microenvironment, chemotherapeutic response, and immunotherapeutic response were systematically analyzed. Finally, the function of CDH5 was explored in renal clear cell carcinoma cells.

RESULTS

VMRI can be used for prognostic and immunotherapy efficacy prediction in a variety of cancers, which consists of four vasculogenic mimicry-related genes (CDH5, MMP9, MAPK1, and MMP13), is a reliable predictor of survival and grade in patients with clear cell carcinoma of the kidney and has been validated in multiple external datasets. We found that the high VMRI group presented higher levels of immune cell infiltration, which was validated by pathological sections. We performed molecular docking prediction of vasculogenic mimicry core target proteins and identified natural small molecule drugs with the highest affinity for the target protein. Knockdown of CDH5 inhibited the proliferation and migration of renal clear cell carcinoma.

CONCLUSIONS

The VMRI identified in this study allows for accurate prognosis assessment of patients with renal clear cell carcinoma and identification of patient populations that will benefit from immunotherapy, providing valuable insights for future precision treatment of patients with renal clear cell carcinoma.