Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics

OSI-027 as a Potential Drug Candidate Targeting Upregulated Hub Protein TAF1 in Potential Mechanism of Sinonasal Squamous Cell Carcinoma: Insights from Proteomics and Molecular Docking

Sinonasal squamous cell carcinoma (SNSCC) is a rare tumor with high mortality and recurrence rates. However, SNSCC carcinogenesis mechanisms and potential therapeutic drugs have not been fully elucidated. This study investigated the key molecular mechanisms and hub proteins involved in SNSCC carcinogenesis using proteomics and bioinformatic analysis. Dysregulated proteins were validated by RT-qPCR in SNSCC and nasal polyp (NP) tissues. Proteomic analysis revealed that differentially expressed proteins were clustered using MCODE scores ≥ 4 into three modules. The specific hub proteins in each module were analyzed in carcinogenesis pathways using STRING, highlighting potential mechanisms of histone modification and spliceosome dysregulation. Spliceosome components SNRNP200 and SF3A3 were significantly downregulated in SNSCC by RT-qPCR. Web-based applications L1000CDS2 and iLINCS were applied to identify 10 potential repurposable drugs that could reverse the gene expression pattern associated with SNSCC. Docking studies of TAF1, a protein in histone modification, with these 10 small molecule inhibitors indicated OSI-027 to be the most promising due to its strong binding interactions with key residues. These findings suggest that hub proteins involved in the underlying mechanism of SNSCC carcinogenesis may serve as valuable targets for drug development, with OSI-027 emerging as a novel candidate against TAF1 in SNSCC.

Integrative analysis of bulk RNA-seq and scRNA-seq data indicates the prognostic and immunologic values of SERPINH1 in glioma

BACKGROUND

SERPINH1 is abnormally expressed in multiple cancers and is associated with malignant progression. However, few reports detail its role in the etiopathogenesis of glioma. Hence, the aim of this article was to investigate the potential value of SERPINH1 in glioma using an integrative analysis.

METHODS

Data of RNA-seq and scRNA-seq was obtained and evaluated using online databases. The expression of SERPINH1 was confirmed by qRT-PCR and immunohistochemistry. The prognostic value of SERPINH1 was evaluated using univariate and multivariate Cox regression analyses. SERPINH1-related signaling pathways and the interaction of SERPINH1 with immunity were also investigated.

RESULTS

SERPINH1 exhibited a markedly elevated expression in glioma compared to normal brain tissues in the online databases. Similar results were confirmed by qRT-PCR and immunohistochemistry. SERPINH1 was found to be an independent prognosis factor, and high expression of SERPINH1 indicated poor survival. Moreover, a nomogram was constructed to predict prognosis more accurately and intuitively. GSEA analysis showed that SERPINH1 was involved in seven signaling pathways, including JAK-STAT pathway. Further analysis indicated SERPINH1 was significantly associated with immunity, especially in low-grade glioma. Additionally, an examination of scRNA-seq data revealed that SERPINH1 was primarily expressed in T cells of the CD4+ and CD8+ subsets.

CONCLUSIONS

SERPINH1 is a key biomarker of glioma prognosis and is immunologically relevant, which provides additional options for targeted therapy of glioma.

Causal association between telomere length and colorectal polyps: A bidirectional two-sample Mendelian randomization study

We performed a bidirectional 2-sample Mendelian randomization (MR) design to explore the causal relation between telomere length (TL) and colorectal polyps. Genome-wide association study summary data of TL and colorectal polyps were extracted from the IEU open genome-wide association study database. Single nucleotide polymorphisms were served as instrumental variables at the significance threshold of P < 5 × 10-8. The inverse variance weighted method, MR-Egger method, and weight median method were performed for causal estimation in MR. Cochran Q test, MR-Egger intercept test, and leave-one-out analyses were performed to evaluate the pleiotropy of the MR results. One hundred and twenty-four single nucleotide polymorphisms were selected as instrumental variables. We found significant casual association between TL and colorectal polyps. Long TL increased the risk of colorectal polyps using the inverse variance weighted method [ukb-a-521: odds ratio (OR): 1.004, 95% confidence interval (CI): 1.001-1.007, P = .004; ukb-d-D12: OR: 1.008, CI: 1.004-1.012, P < .001; finn-b-CD2_BENIGN_COLORECANI_EXALLC2: OR: 1.170, CI: 1.027-1.332, P = .018]. Sensitivity analyses validated that the causality between TL and colorectal polyps was robust. The study provided a causal association between TL and colorectal polyps which indicated that TL might be served as a potential biomarker of colorectal polyps for screening and prevention. Nonetheless, the conclusions need further validation.

RRP12 suppresses cell migration and invasion in colorectal cancer cell via regulation of epithelial-mesenchymal transition

Background

The survival of patients with advanced colorectal cancer (CRC) is variable. The high rates of recurrence, metastasis, and drug resistance make clinical treatment difficult, which needs to further develop therapeutic and prognostic targets. Ribosomal RNA processing 12 homolog (RRP12), as a nucleolar protein involved in ribosome subunit maturation and export, plays important roles in cell cycle-related processes and the response to DNA damage, and regulates the occurrence and development of various cancers. The primary aim of this study was to identify the function of RRP12 in the process of epithelial-mesenchymal transition (EMT) in CRC.

Methods

In this study, the expression of RRP12 in tissue samples and the association with clinicopathological features in CRC was evaluated, and the correlation between RRP12 expression and aggressiveness of CRC was detected. After knockdown of RRP12 gene, the relationship between RRP12 and EMT-related indicators was verified in vivo and in vitro of CRC cells. Identification of RRP12-related genes and pathways through bioinformatic-based analyses was performed to find its potential mechanism.

Results

RRP12 is highly expressed in CRC cell lines and clinical samples and is associated with poor survival in CRC patients. RRP12 expression was positively associated with lymph node metastasis, tumor-node-metastasis (TNM) stage, and poor differentiation. Knockdown of RRP12 was found to suppress migration and invasion of CRC cells. RRP12 contributed to the EMT process of CRC cell lines in a ZEB1-mediated manner. RRP12 knockdown was found to reverse metastasis of CRC cells in vivo. Bioinformatic-based analyses indicated that RRP12 could serve as a potential biomarker for prognostic assessment of CRC patients.

Conclusions

RRP12 is involved in the tumorigenesis and metastasis of CRC by regulating the EMT process through ZEB1. Thus, RRP12 could be a potential therapeutic target for CRC therapy.

DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.

Prognostic and immunological role of SERPINH1 in pan-cancer

Background: The SERPINH1 gene plays a vital part in tumorigenesis and development, whereas its potential as an immunotherapy target is still unknown. Hence, this research aimed to probe the roles of SERPINH1 in human tumors. Method: Using The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) database, Oncomine, and SangerBox software, the pan-cancer expression of SERPINH1 and its correlation were systematically analyzed. SERPINH1 protein information was detected by the Human Protein Atlas (HPA) database and STRING database. The genomic alterations of SERPINH1 were studied using the c-BioPortal database. The influence of SERPINH1 on prognosis was analyzed using Kaplan-Meier plotter. The R package "clusterProfiler" was used for enrichment analysis to detect the role of SERPINH1. The TIMER2 database was used to further analyze the correlation between the immune cell infiltration score of TCGA samples and the expression of SERPINH1. Results: SERPINH1 overexpression was related to worse survival status in pan-cancer. In addition, high expression of SERPINH1 was positively associated with tumor stage and poor prognosis. Moreover, SERPINH1 played an important role in tumor microenvironment and immune regulation. Our study revealed that SERPINH1 expression has a strong correlation with immune cell filtration, immune regulation, chemokines, and immune checkpoints. Conclusion: Our research found that SERPINH1 was a risk factor and predictor of poor prognosis in various tumors. High expression of SERPINH1 may contribute to tumor immune-suppressive status. Also, SERPINH1 may become a potential immunotherapy target in pan-cancer.