CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations

Comprehensive pan-cancer analysis of ACSS3 as a biomarker for prognosis and immunotherapy response

Background

ACSS3 (acyl-CoA synthetase short-chain family member 3) is found in numerous tissues and is linked to tumor cell type development and metastasis.

Methods

We conducted a comprehensive pan-cancer analysis of ACSS3. The TCGA (Cancer Genome Atlas), CPTAC (Clinical Proteomic Tumor Analysis Consortium), and HPA databases were used to ascertain the connection between ACSS3 and various types of tumors. Genes in the TCGA database would be identified using cBioPortal queries, and their transcriptome expression would then be verified using GEO data. ACSS3 expression and cellular localization in various tumor tissues of most cancer types were analyzed using single-cell sequencing data from the TISCH database. According to HPA and CPTAC databases, we analyzed and evaluated protein expression levels. Predictive analysis based on precise survival data of ACSS3 expression levels for 26 cancer types predicted using the TCGA database. Furthermore, we investigated the relationship between ACSS3 and immune microenvironments in different tumor tissues using the TIMER and TISCH databases. CellMiner, GDSC, and CTRP data would clarify the relationship between ACSS3 and drug resistance and explore the chemicals that affect ACSS3 expression. The final part of our study explored and validated the role ACSS3 played in glioma proliferation, migration, and invasion.

Results

ACSS3 is differentially expressed in various tumors and exhibits early diagnostic value. ACSS3 expression is associated with clinical features, and high ACSS expression anticipates a worse prognosis in multiple tumors and may impact drug sensitivity. The changes in the immunosuppressive microenvironment of gliomas are closely related to the upregulation of ACSS3.

Conclusions

ACSS3 is a novel biomarker for forecasting different human cancer prognoses, as it can influence the biological process by modulating the immune microenvironment. ACSS3 is a critical prognostic factor for glioma and is related to its proliferation, migration, and invasion.

Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines

Sarcomas are a diverse group of rare malignancies composed of multiple different clinical and molecular subtypes. Due to their rarity and heterogeneity, basic, translational, and clinical research in sarcoma has trailed behind that of other cancers. Outcomes for patients remain generally poor due to an incomplete understanding of disease biology and a lack of novel therapies. To address some of the limitations impeding preclinical sarcoma research, we have developed Sarcoma_CellMinerCDB, a publicly available interactive tool that merges publicly available sarcoma cell line data and newly generated omics data to create a comprehensive database of genomic, transcriptomic, methylomic, proteomic, metabolic, and pharmacologic data on 133 annotated sarcoma cell lines. The reproducibility, functionality, biological relevance, and therapeutic applications of Sarcoma_CellMinerCDB described herein are powerful tools to address and generate biological questions and test hypotheses for translational research. Sarcoma_CellMinerCDB (https://discover.nci.nih.gov/SarcomaCellMinerCDB) aims to contribute to advancing the preclinical study of sarcoma.

TUBB, a robust biomarker with satisfying abilities in diagnosis, prognosis, and immune regulation via a comprehensive pan-cancer analysis

Purpose

TUBB can encode a beta-tubulin protein. At present, the role of TUBB has not been ascertained in cancers. Hence, the importance of further systematic pan-cancer analyses is stressed to explore its value in the diagnosis, prognosis, and immune function of cancers.

Methods

By collecting and handling integrative data from the TCGA, Firehose, UCSC Xena, cBioPortal, GEO, CPTAC, TIMER2.0, TISCH, CellMiner, GDSC, and CTRP databases, we explored the potential diagnostic and prognostic roles of TUBB in pan-cancers from multiple angles. Moreover, the GSEA analysis was conducted to excavate the biological functions of TUBB in pan-cancers. In addition, survival profiles were described, and the differential expressions of TUBB in different molecular subtypes were discussed. Also, we utilized the cMAP function to search drugs or micro-molecules that have an impact on TUBB expressions.

Results

Based on the TCGA data, we found that TUBB was differentially expressed in a variety of tumors and showed an early-diagnostic value. Mutations, somatic copy number alterations, and DNA methylation would lead to its abnormal expression. TUBB expressions had relations with many clinical features. What's more, TUBB expressions were validated to be related to many metabolism-related, metastasis-related, and immune-related pathways. High TUBB expressions were proved to have a great impact on the prognosis of various types of cancers and would affect the sensitivity of some drugs. We also demonstrated that the expression of TUBB was significantly correlated to immunoregulator molecules and biomarkers of lymphocyte subpopulation infiltration.

Conclusion

TUBB and its regulatory genes were systemically analyzed in this study, showing that TUBB had satisfying performances in disease diagnosing and prognosis predicting of multiple cancers. It could remodel the tumor microenvironment and play an integral role in guiding cancer therapies and forecasting responses to chemotherapy.

EXO1/P53/SREBP1 axis-regulated lipid metabolism promotes prostate cancer progression

Prostate cancer (PCa) is one of the most common malignant tumors affecting the male genitourinary system. However, there is currently a lack of effective treatments for patients with advanced prostate cancer, which significantly impacts men's overall health. Exonuclease 1 (EXO1), a protein with mismatch repair and recombination functions, has been found to play a vital role in various diseases. In our study, we discovered that EXO1 acts as a novel biomarker of PCa, which promotes prostate cancer progression by regulating lipid metabolism reprogramming in prostate cancer cells. Mechanistically, EXO1 promotes the expression of SREBP1 by inhibiting the P53 signaling pathway. In summary, our findings suggest that EXO1 regulated intracellular lipid reprogramming through the P53/SREBP1 axis, thus promoting PCa progression. The result could potentially lead to new insights and therapeutic targets for diagnosing and treating PCa.