Prognoses and genomic analyses of proteasome 26S subunit, ATPase (PSMC) family genes in clinical breast cancer

Kao, Tzu-Jen; Wu, Chung-Che; Phan, Nam Nhut; Liu, Yen-Hsi; Ta, Hoang Dang Khoa; Anuraga, Gangga; Wu, Yung-Fu; Lee, Kuen-Haur; Chuang, Jian Ying; Wang, Chih‐Yang

doi:10.18632/aging.203345

Cited by 82 publications

(69 citation statements)

References 57 publications

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“…Recently, BRCA overtook lung cancer to rank first among the commonly occurring malignancies in women worldwide [ 54 ]. Delays in diagnosis and treatment that worsen the patient’s outcomes, along with the enormous burdens resulting from long-term and high-cost therapies, have once again undisputedly driven BRCA to become a major public health concern for scientists [ 55 , 56 , 57 , 58 , 59 ]. Clinical practice reveals that the heterogeneity of this disease, observed in both staging systems and histopathologic classification based on molecular standpoints, may complicate the accurate stratification and challenge the selection of respective therapeutic strategies [ 60 , 61 , 62 , 63 ].…”

Section: Discussionmentioning

confidence: 99%

Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer

et al. 2021

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The complexity of breast cancer includes many interacting biological processes, and proteasome alpha (PSMA) subunits are reported to be involved in many cancerous diseases, although the transcriptomic expression of this gene family in breast cancer still needs to be more thoroughly investigated. Consequently, we used a holistic bioinformatics approach to study the PSMA genes involved in breast cancer by integrating several well-established high-throughput databases and tools, such as cBioPortal, Oncomine, and the Kaplan–Meier plotter. Additionally, correlations of breast cancer patient survival and PSMA messenger RNA expressions were also studied. The results demonstrated that breast cancer tissues had higher expression levels of PSMA genes compared to normal breast tissues. Furthermore, PSMA2, PSMA3, PSMA4, PSMA6, and PSMA7 showed high expression levels, which were correlated with poor survival of breast cancer patients. In contrast, PSMA5 and PSMA8 had high expression levels, which were associated with good prognoses. We also found that PSMA family genes were positively correlated with the cell cycle, ubiquinone metabolism, oxidative stress, and immune response signaling, including antigen presentation by major histocompatibility class, interferon-gamma, and the cluster of differentiation signaling. Collectively, these findings suggest that PSMA genes have the potential to serve as novel biomarkers and therapeutic targets for breast cancer. Nevertheless, the bioinformatic results from the present study would be strengthened with experimental validation in the future by prospective studies on the underlying biological mechanisms of PSMA genes and breast cancer.

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Section: Discussionmentioning

confidence: 99%

Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer

et al. 2021

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“…The Kaplan–Meier plotter contains information about the associations of gene expressions with the survival of patients with many kinds of cancers ( , accessed on 15 April 2021) [ 26 ]. We analyzed the prognostic merits of the target genes [ 27 ] with the KM plotter using median values, hazard ratios (HRs) >1, and a log rank of <0.05 [ 28 , 29 , 30 , 31 , 32 , 33 ].…”

Section: Methodsmentioning

confidence: 99%

Potential Prognostic Biomarkers of OSBPL Family Genes in Patients with Pancreatic Ductal Adenocarcinoma

Chou

Hsieh

et al. 2021

Biomedicines

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Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal malignancy with poor survival outcomes. In addition, oxysterol-binding protein-like (OSBPL) family members are reported to be involved in lipid binding and transport and play critical roles in tumorigenesis. However, relationships between PDAC and OSBPL family members have not comprehensively been elucidated. In this study, we used the Oncomine and GEPIA 2 databases to analyze OSBPL transcription expressions in PDAC. The Kaplan–Meier plotter and TIMER 2.0 were used to assess the relationships between overall survival (OS) and immune-infiltration with OSBPL family members. Co-expression data from cBioPortal were downloaded to assess the correlated pathways with OSBPL gene family members using DAVID. The expressions of OSBPL3, OSBPL8, OSBPL10, and OSBPL11 were found to be highly upregulated in PDAC. Low expressions of OSBPL3, OSBPL8, and OSBPL10 indicated longer OS. The functions of OSBPL family members were mainly associated with several potential signaling pathways in cancer cells, including ATP binding, integrin binding, receptor binding, and the renin-angiotensin system (RAS) signaling pathway. The transcription levels of OSBPL gene family members were connected with several immune infiltrates. Collectively, OSBPL family members are influential biomarkers for the early diagnosis of PDAC and have prognostic value, with the promise of precise treatment of PDAC in the future.

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“…A heatmap of expression levels of 1222 BRCA patients was also performed using the "DESeq2" package to illustrate differences between the two phenotypes: "normal" and "tumor". We selected the top 10% of genes, ranked by the log2[fold change (FC) expression values], with |logFC| > 1.5 set as the threshold [50][51][52][53][54].…”

Section: Differentially Expressed Genes (Degs) Analysismentioning

confidence: 99%

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Wang

Phan

et al. 2021

Cancers

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In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The “Like-Smith” (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan–Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21–1.51, p for trend = 3.4 × 10−7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as “Cell cycle role of APC in cell cycle regulation” and “Immune response IL-15 signaling via MAPK and PI3K cascade” in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.

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Prognoses and genomic analyses of proteasome 26S subunit, ATPase (PSMC) family genes in clinical breast cancer

Cited by 82 publications

References 57 publications

Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer

Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer

Potential Prognostic Biomarkers of OSBPL Family Genes in Patients with Pancreatic Ductal Adenocarcinoma

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

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