BNIP3 Upregulation Characterizes Cancer Cell Subpopulation With Increased Fitness and Proliferation

Pan-cancer analysis reveals TRA16 as a master regulator of human carcinogenesis

Introduction

The nuclear receptor TR4 binding protein, TRA16, has been implicated in lung carcinogenesis; however, its broader role across diverse human cancers remains poorly understood. Understanding TRA16's involvement in cancer biology could uncover novel regulatory mechanisms and potential therapeutic targets.

Methods

We conducted a comprehensive pan-cancer analysis of TRA16 expression and function across multiple human malignancies. Gene co-expression networks, pathway enrichment, transcription factor analysis, organoid modeling, and intercellular communication profiling were employed. Tumor mutation burden (TMB) and microenvironmental features were also assessed in relation to TRA16 expression, stratified by TP53 mutation status.

Results

Correlation analysis identified the cell cycle as the top enriched pathway among TRA16-associated genes, with key transcription factors, including RB-E2F, MYC, and TP53, regulating genes co-expressed with TRA16. In liver cancer organoid models, TRA16 and its co-expressed genes were significantly upregulated. Intercellular communication analysis showed that TRA16-positive cells exhibited increased autocrine signaling and overall signaling activity. Importantly, patients with high TRA16 expression demonstrated elevated TMB and decreased stromal and immune features.

Discussion

These findings highlight TRA16 as a potential master regulator of oncogenic processes, contributing to tumor progression through coordinated regulation of cell cycle genes, intercellular signaling, and genomic instability. Our results provide new insights into TRA16's role across cancers and support its potential as a novel oncogene.

PDP1 related ferroptosis risk signature indicates distinct immune microenvironment and prognosis of breast cancer patients

Objective

We aim to construct a RiskScore model to aid in the early prognosis of breast cancer (BC).

Methods

BC mRNA expression profiles were obtained from TCGA and GEO databases. Differential gene expression analysis identifies PDP1-ferroptosis-related genes. LASSO Cox regression was utilized to screen genes to build a RiskScore model, and survival analysis were performed to investigate the reliability in BC prognosis. Immune cell infiltration proportions were calculated using CIBERSORT and xCell algorithms. Single-cell data processing and analysis were conducted using "Seurat", "monocle", and "iTALK" packages. PDP1 was silenced to validate its influence on the target genes.

Results

Data from public databases revealed significant upregulation of PDP1 in BC samples compared to normal tissues. A RiskScore model based on PDP1-related differential ferroptosis-related genes (FRGs) ACSL1, BNIP3, and EMC2 was developed, which effectively predicted BC patient prognosis. High-risk BC samples exhibited poorer overall survival and were associated with immune microenvironment. The model remained significant in multivariate Cox regression analysis, indicating that it could independently predict the survival of BC patients. ACSL1, BNIP3, and EMC2 were downregulated after knockdown of PDP1.

Conclusion

RiskScore model constructed by PDP1-ferroptosis-related genes ACSL1, BNIP3, and EMC2 is able to help predict the prognosis of BC patients.

ONC201 (Dordaviprone) Induces Integrated Stress Response and Death in Cervical Cancer Cells

Cervical cancer is a leading cause of death in women globally. Systemic chemotherapy offers only limited therapeutic benefit for advanced-stage disease due to toxicity and drug resistance. ONC201 (also known as TIC10 or dordaviprone) is a TRAIL (TNF-Related Apoptosis-Inducing Ligand) and cIpP (caseinolytic protease) agonist currently in Phase II clinical trials for different types of cancer. In the present study, we investigated the anticancer potential of ONC201 in HPV-positive cervical cancer cell lines. ONC201 exerted significant cytotoxicity and inhibited the clonogenic potential of cervical cancer cells. It induced integrated stress response along with S/G2-M arrest and apoptosis in both cell lines. Yet, surprisingly, well-known targets of ONC201 viz. TRAIL, DR5 (death receptor 5) and cIpP were found to be upregulated only in HeLa but not in SiHa cells in response to ONC201 treatment. In addition, expression of BNIP3 and Beclin-1 (both involved in regulation of autophagy) increased in response to certain doses of ONC201. Furthermore, ONC201 exhibited synergism in combination with standard drugs against cervical cancer cells. This study provides a proof of concept for the anticancer activity of versatile drug ONC201 against cervical cancer cells and also delineates its mechanism of action.

PTBP2 promotes cell survival and autophagy in chronic myeloid leukemia by stabilizing BNIP3

Polypyrimidine tract binding protein 2 (PTBP2) regulates alternative splicing in neuronal, muscle, and Sertoli cells. PTBP2 and its paralog, PTBP1, which plays a role in B-cell development, was found to be expressed aberrantly in myeloid leukemia. Genetic ablation of Ptbp2 in the cells resulted in decreased cellular proliferation and repopulating ability, decreased reactive oxygen species (ROS), and altered mitochondrial morphology. RNA immunoprecipitation followed by sequencing (RIP-seq) and functional assays confirmed that PTBP2 binds to Bcl-2 Interacting Protein 3 (Bnip3)-3'UTR and stabilizes its expression. Our study also suggests that PTBP2 promotes autophagy, as evidenced by the low levels of LC3-II expression in Ptbp2-knockout cells treated with Bafilomycin A1. This effect was restored upon overexpression of Bnip3 in the knockout cells. Notably, when KCL22-NTC cells were subcutaneously injected into the flanks of mice, they gave rise to malignant tumors, unlike Ptbp2-KO-KCL22 cells. Also, transplantation of KCL22 cells through the tail vein in NOD/SCID mice resulted in higher cell engraftment and increased infiltration of malignant cells in the extramedullary organs. Our study underscores the role of PTBP2 in promoting cell proliferation and tumor formation while enhancing autophagy through Bnip3, thereby supporting the role of PTBP2 as an oncogene in CML.

The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover

Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. This screen revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system and the ubiquitin-proteosome system regulated BNIP3 independently. Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. More broadly, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that tightly regulate endogenous tail-anchored protein localization.

A novel stratification framework based on anoikis-related genes for predicting the prognosis in patients with osteosarcoma

Background

Anoikis resistance is a prerequisite for the successful development of osteosarcoma (OS) metastases, whether the expression of anoikis-related genes (ARGs) correlates with OS prognosis remains unclear. This study aimed to investigate the feasibility of using ARGs as prognostic tools for the risk stratification of OS.

Methods

The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases provided transcriptome information relevant to OS. The GeneCards database was used to identify ARGs. Differentially expressed ARGs (DEARGs) were identified by overlapping ARGs with common differentially expressed genes (DEGs) between OS and normal samples from the GSE16088, GSE19276, and GSE99671 datasets. Anoikis-related clusters of patients were obtained by consistent clustering, and gene set variation analysis (GSVA) of the different clusters was completed. Next, a risk model was created using Cox regression analyses. Risk scores and clinical features were assessed for independent prognostic values, and a nomogram model was constructed. Subsequently, a functional enrichment analysis of the high- and low-risk groups was performed. In addition, the immunological characteristics of OS samples were compared between the high- and low-risk groups, and their sensitivity to therapeutic agents was explored.

Results

Seven DEARGs between OS and normal samples were obtained by intersecting 501 ARGs with 68 common DEGs. BNIP3 and CXCL12 were significantly differentially expressed between both clusters (P<0.05) and were identified as prognosis-related genes. The risk model showed that the risk score and tumor metastasis were independent prognostic factors of patients with OS. A nomogram combining risk score and tumor metastasis effectively predicted the prognosis. In addition, patients in the high-risk group had low immune scores and high tumor purity. The levels of immune cell infiltration, expression of human leukocyte antigen (HLA) genes, immune response gene sets, and immune checkpoints were lower in the high-risk group than those in the low-risk group. The low-risk group was sensitive to the immune checkpoint PD-1 inhibitor, and the high-risk group exhibited lower inhibitory concentration values by 50% for 24 drugs, including AG.014699, AMG.706, and AZD6482.

Conclusion

The prognostic stratification framework of patients with OS based on ARGs, such as BNIP3 and CXCL12, may lead to more efficient clinical management.

Programmed Cell Death Pathways in Cholangiocarcinoma: Opportunities for Targeted Therapy

Cholangiocarcinoma is a highly aggressive cancer arising from the bile ducts. The limited effectiveness of conventional therapies has prompted the search for new approaches to target this disease. Recent evidence suggests that distinct programmed cell death mechanisms, namely, apoptosis, ferroptosis, pyroptosis and necroptosis, play a critical role in the development and progression of cholangiocarcinoma. This review aims to summarize the current knowledge on the role of programmed cell death in cholangiocarcinoma and its potential implications for the development of novel therapies. Several studies have shown that the dysregulation of apoptotic signaling pathways contributes to cholangiocarcinoma tumorigenesis and resistance to treatment. Similarly, ferroptosis, pyroptosis and necroptosis, which are pro-inflammatory forms of cell death, have been implicated in promoting immune cell recruitment and activation, thus enhancing the antitumor immune response. Moreover, recent studies have suggested that targeting cell death pathways could sensitize cholangiocarcinoma cells to chemotherapy and immunotherapy. In conclusion, programmed cell death represents a relevant molecular mechanism of pathogenesis in cholangiocarcinoma, and further research is needed to fully elucidate the underlying details and possibly identify therapeutic strategies.

The ER membrane protein complex governs lysosomal turnover of a mitochondrial tail-anchored protein, BNIP3, to restrict mitophagy

Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, violate this assumption. Rather, BNIP3 and NIX are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all of its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. By this approach, we revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system regulates BNIP3 alongside, but independent of, the ubiquitin-proteosome system (UPS). Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. In short, while BNIP3 can be cleared by parallel and partially compensatory quality control pathways, non-autophagic lysosomal degradation of BNIP3 is a strong post-translational modifier of BNIP3 function. More broadly, these data reveal an unanticipated connection between mitophagy and TA protein quality control, wherein the endolysosomal system provides a critical axis for regulating cellular metabolism. Moreover, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that ensure tight regulation of endogenous TA protein localization.