BRCA1-associated protein 1 deficiency in lung adenocarcinoma predicts poor outcome and increased tumor invasion

BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway

Due to their stem-like characteristics and immunosuppressive properties, Mesenchymal stem cells (MSCs) offer remarkable potential in regenerative medicine. Much effort has been devoted to enhancing the efficacy of MSC therapy by enhancing MSC migration. In this study, we identified deubiquitinase BRCA1- associated protein 1 (BAP1) as an inhibitor of MSC migration. Using deubiquitinase siRNA library screening based on an in vitro wound healing assay, we found that silencing BAP1 significantly augmented MSC migration. Conversely, BAP1 overexpression reduced the migration and invasion capabilities of MSCs. BAP1 depletion in MSCs upregulates ERK phosphorylation, thereby increasing the expression of the migration factor, osteopontin. Further examination revealed that BAP1 interacts with phosphorylated ERK1/2, deubiquitinating their ubiquitins, and thus attenuating the ERK signaling pathway. Overall, our study highlights the critical role of BAP1 in regulating MSC migration through its deubiquitinase activity, and suggests a novel approach to improve the therapeutic potential of MSCs in regenerative medicine. [BMB Reports 2024; 57(5): 250-255].

Bioinformatics analysis and in vivo validation study of Ophiocordyceps sinensis (Berk.)G.H.Sungetal against lung adenocarcinoma

ETHNOPHARMACOLOGICAL RELEVANCE

Lung adenocarcinoma (LUAD) is one of the main types of lung cancer. Ophiocordyceps sinensis has many potentially useful pharmacologic features, such as lung protection, and both anti-inflammatory and antioxidant activities.

AIM OF THE STUDY

This study was conducted to investigate-using bioinformatics and in vivo experimental validation-the possible role of O. sinensis against LUAD.

MATERIALS AND METHODS

We obtained important targets of O. sinensis for the treatment of LUAD using network pharmacology techniques and deep mining of the TCGA database, and validated them by molecular docking techniques and in vivo experiments.

RESULTS

Through bioinformatics analysis and research, we screened BRCA1 and CCNE1 as important biomarkers for LUAD and as core targets of O. sinensis against LUAD. The non-small cell lung cancer signaling pathway, PI3K-Akt signaling pathway, and HIF-1 signaling pathway are potentially important pathways of O. sinensis against LUAD. The molecular docking results showed good binding between the active components in O. sinensis and the two core targets, and the in vivo experimental validation results indicated that O. sinensis had good inhibitory effects in the Lewis lung cancer (LLC) model.

CONCLUSIONS

BRCA1 and CCNE1 are crucial biomarkers for LUAD and are important targets for O. sinensis to exert anti-LUAD effects.

Deubiquitinase BAP1 regulates stability of BRCA1 protein and inactivates the NF-κB signaling to protect mice from sepsis-induced acute kidney injury

Sepsis and its associated organ dysfunction syndrome is a leading cause of death in critically ill patients. Breast cancer susceptibility protein 1 (BRCA1)-associated protein 1 (BAP1) is a potential regulator in immune regulation and inflammatory responses. This study aims to investigate the function of BAP1 in sepsis-induced acute kidney injury (AKI). A mouse model with sepsis-induced AKI was induced by cecal ligation and puncture, and renal tubular epithelial cells (RTECs) were treated with lipopolysaccharide (LPS) to mimic an AKI condition in vitro. BAP1 was significantly poorly expressed in the kidney tissues of model mice and the LPS-treated RTECs. Artificial upregulation of BAP1 ameliorated the pathological changes, tissue injury and inflammatory responses in kidney tissues of the mice, and it reduced the LPS-induced injury and apoptosis of the RTECs. BAP1 was found to interact with BRCA1 and enhance stability of BRCA1 protein through deubiquitination modification. Further downregulation of BRCA1 activated the nuclear factor-kappa B (NF-κB) signaling pathway and blocked the protective roles of BAP1 in sepsis-induced AKI. In conclusion, this study demonstrates that BAP1 protects mice from sepsis-induced AKI through enhancing stability of BRCA1 protein and inactivating the NF-κB signaling.

Pan-cancer analysis of the prognostic and immunological role of BRCA1-associated protein 1 gene (BAP1): friend or foe?

BACKGROUND

BRCA1-associated protein 1 gene (BAP1) plays a key role in some cancers. However, it has not yet been elucidated whether BAP1 modulates the pathogenesis and progression of human cancers through some common cellular and molecular mechanisms, and a pan-cancer analysis for the roles of BAP1 has not yet been conducted.

METHODS

A systematic assessment of the BAP1 gene was presented using bioinformatics analysis and R software. Based on gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, differential expression of BAP1, survival prognosis and genetic alterations of BAP1, correlations between BAP1 expression and immune infiltrates, enrichment analysis and receiver operating curves (ROC) were performed across 33 TCGA cancers.

RESULTS

BAP1 was highly expressed in several cancers and high BAP1 expression resulted in different survival prognoses. BAP1 DNA methylation status was changed in uveal melanoma (UVM) cases and a high level of BAP1 phosphorylation was found at the S292 locus in several cancers (colon cancer, lung adenocarcinoma, breast cancer, ovarian cancer, and uterine cancer). The statistically significant correlations of BAP1 expression and immune infiltration may contribute to the prognostic survivals in several cancers including UVM, skin cutaneous melanoma (SKCM), and lung adenocarcinoma (LUAD). Additionally, the correlations between BAP1 expression and tumor mutation burden (TMB)/microsatellite instability (MSI) across TCGA cancers were also explored. Finally, the analysis revealed that BAP1 expression level had high sensitivity and specificity for liver hepatocellular carcinoma (LIHC), kidney renal clear cell carcinoma (KIRC), and pancreatic adenocarcinoma (PAAD) patients.

CONCLUSION

This study has revealed statistically significant correlations of BAP1 expression with survival analysis, DNA methylation, protein phosphorylation, genetic alteration, and immune infiltration across multiple TCGA cancers, suggesting that BAP1 may potentially serve as a potential therapeutic target and prognostic biomarker for several cancers.

Molecular Regulation of the Polycomb Repressive-Deubiquitinase

Post-translational modification of histone proteins plays a major role in histone–DNA packaging and ultimately gene expression. Attachment of ubiquitin to the C-terminal tail of histone H2A (H2AK119Ub in mammals) is particularly relevant to the repression of gene transcription, and is removed by the Polycomb Repressive-Deubiquitinase (PR-DUB) complex. Here, we outline recent advances in the understanding of PR-DUB regulation, which have come through structural studies of the Drosophila melanogaster PR-DUB, biochemical investigation of the human PR-DUB, and functional studies of proteins that associate with the PR-DUB. In humans, mutations in components of the PR-DUB frequently give rise to malignant mesothelioma, melanomas, and renal cell carcinoma, and increase disease risk from carcinogens. Diverse mechanisms may underlie disruption of the PR-DUB across this spectrum of disease. Comparing and contrasting the PR-DUB in mammals and Drosophila reiterates the importance of H2AK119Ub through evolution, provides clues as to how the PR-DUB is dysregulated in disease, and may enable new treatment approaches in cancers where the PR-DUB is disrupted.

Nuclear up regulation of the BRCA1-associated ubiquitinase BAP1 is associated with tumor aggressiveness in prostate cancers lacking the TMPRSS2:ERG fusion

Loss of the putative tumor suppressor BAP1 is a candidate biomarker for adverse prognosis in many cancer types, but conversely for improved survival in others. Studies on the expression and prognostic role of BAP1 in prostate cancer are currently lacking. We used a tissue microarray of 17,747 individual prostate cancer samples linked with comprehensive pathological, clinical and molecular data and studied the immunohistochemical expression of BAP1. BAP1 expression was typically up regulated in cancers as compared to adjacent normal prostatic glands. In 15,857 cancers, BAP1 staining was weak in 3.3%, moderate in 41.6% and strong in 17.4%. Strong BAP1 staining was associated with advanced tumor stage (p<0.0001), high classical and quantitative Gleason grade (p<0.0001), lymph node metastasis (p<0.0001), a positive surgical margin (p=0.0019) and early biochemical recurrence (p<0.0001). BAP1 expression was linked to ERG-fusion type cancers, with strong BAP1 staining in 12% of ERG-negative, but 30% of ERG-positive cancers (p<0.0001). Subset analyses in 5,415 cancers with and 4,217 cancers without TMPRSS2:ERG fusion revealed that these associations with tumor phenotype and patient outcome were largely driven by the subset of ERG-negative tumors. Multivariate analysis revealed that the prognostic impact was independent of established prognostic features in ERG negative p<0.001) but not in ERG positive cancers. BAP1 expression was further linked to androgen receptor (AR) expression: Only 2% of AR-negative, but 33% of strongly AR expressing cancers had strong BAP1 expression (p<0.0001). In conclusion, this study shows that BAP1 up regulation is linked to prostate cancer progression and aggressiveness.

The role of DUBs in the post-translational control of cell migration

Cell migration is a multifactorial/multistep process that requires the concerted action of growth and transcriptional factors, motor proteins, extracellular matrix remodeling and proteases. In this review, we focus on the role of transcription factors modulating Epithelial-to-Mesenchymal Transition (EMT-TFs), a fundamental process supporting both physiological and pathological cell migration. These EMT-TFs (Snail1/2, Twist1/2 and Zeb1/2) are labile proteins which should be stabilized to initiate EMT and provide full migratory and invasive properties. We present here a family of enzymes, the deubiquitinases (DUBs) which have a crucial role in counteracting polyubiquitination and proteasomal degradation of EMT-TFs after their induction by TGFβ, inflammatory cytokines and hypoxia. We also describe the DUBs promoting the stabilization of Smads, TGFβ receptors and other key proteins involved in transduction pathways controlling EMT.

Immunohistochemical Assessment of BAP1 Protein in Mucoepidermoid Carcinomas

Mucoepidermoid carcinomas are common malignant salivary gland tumors. Despite recent advances in diagnosis and treatment, there has not been much improvement in outcome of these patients, necessitating identification of novel targeted therapeutic agents. Genomic profiling of mucoepidermoid carcinomas has recently revealed aberrations in BAP1 gene. Therefore, we conducted this study to identify BAP1 loss by immunohistochemistry in these tumors. Mucoepidermoid carcinoma cases were retrieved; hematoxylin-and-eosin stained sections were reviewed. Immunohistochemistry for BAP1 was performed. Forty cases were assessed, including 25 salivary gland and 15 pulmonary mucoepidermoid carcinomas. There were 19 cases in the parotid (76%), two in submandibular gland (8%), and remaining 16% from minor salivary gland locations. Ten (40%) were low grade, nine (36%) were intermediate grade, and six (24%) were high grade mucoepidermoid carcinomas. Thirteen (86.7%) pulmonary mucoepidermoid carcinomas were tracheobronchial, while two (13.3%) were intraparenchymal; all were low grade mucoepidermoid carcinomas. On immunohistochemistry, BAP1 nuclear staining was retained in all cases (100%), irrespective of tumor location or grade. Therapeutic connotations necessitate the identification of readily applicable techniques to detect BAP1 loss in mucoepidermoid carcinomas. Using immunohistochemistry, loss of BAP1 staining was not seen in any of our cases, suggesting insensitivity of BAP1 IHC to detect aberrations at genomic level in these tumors. Analysis of BAP1 alterations by targeted sequencing may therefore be performed prior to excluding the possibility of response to BAP1-targeted therapeutics based on immunohistochemistry alone.