Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer
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, a...
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| Published in | Cancers Vol. 13; no. 19; p. 4902 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Basel
MDPI AG
29.09.2021
MDPI |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2072-6694 2072-6694 |
| DOI | 10.3390/cancers13194902 |
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| Abstract | 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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| AbstractList | Simple SummaryThe roles of “like-Smith” (LSM) proteins in breast cancer development and their clinical relevance remain unclear. In this study, multiple analyses based on 3593 patients with breast cancer and their mRNA expression values were utilized to investigate the clinical relevance of LSM family genes, including cancer aggressiveness, immune cell infiltration, prognostic outcomes, and related signaling pathways. We revealed that LSM4 had higher expression levels in breast tumor and breast cancer sub-types than in normal samples, and was associated with poor survival outcomes. Interestingly, infiltration levels of most immune cell types, including cluster of differentiation for positive CD4+ T cells, CD8+ T cells, T-cell follicular helpers, and myeloid-derived suppressor cells were positively correlated with LSM4 expression in several subclasses of breast cancer (basal, human epidermal growth factor receptor 2 (HER2), luminal A, and luminal B).AbstractIn 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. 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.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. 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. |
| Author | Anuraga, Gangga Phan, Nam Nhut Wu, Yung-Fu Wang, Chih-Yang Ku, Su-Chi Lee, Kuen-Haur Ta, Hoang Dang Khoa Wang, Wei-Jan An Ton, Nu Thuy |
| AuthorAffiliation | 3 Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan; cvcsky@cmu.edu.tw 8 Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan 6 Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia 5 NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; tntan@ntt.edu.vn 4 Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; pnnam@ntt.edu.vn 7 National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan; qrince@yahoo.com.tw 2 Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; b101104152@tmu.edu.tw 1 PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Scie |
| AuthorAffiliation_xml | – name: 5 NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; tntan@ntt.edu.vn – name: 8 Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan – name: 6 Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia – name: 3 Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan; cvcsky@cmu.edu.tw – name: 1 PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; d621109004@tmu.edu.tw (H.D.K.T.); g.anuraga@unipasby.ac.id (G.A.) – name: 4 Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; pnnam@ntt.edu.vn – name: 2 Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; b101104152@tmu.edu.tw – name: 7 National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan; qrince@yahoo.com.tw |
| Author_xml | – sequence: 1 givenname: Hoang Dang Khoa orcidid: 0000-0001-8809-239X surname: Ta fullname: Ta, Hoang Dang Khoa – sequence: 2 givenname: Wei-Jan surname: Wang fullname: Wang, Wei-Jan – sequence: 3 givenname: Nam Nhut surname: Phan fullname: Phan, Nam Nhut – sequence: 4 givenname: Nu Thuy surname: An Ton fullname: An Ton, Nu Thuy – sequence: 5 givenname: Gangga orcidid: 0000-0002-0902-3968 surname: Anuraga fullname: Anuraga, Gangga – sequence: 6 givenname: Su-Chi orcidid: 0000-0001-6832-9994 surname: Ku fullname: Ku, Su-Chi – sequence: 7 givenname: Yung-Fu surname: Wu fullname: Wu, Yung-Fu – sequence: 8 givenname: Chih-Yang surname: Wang fullname: Wang, Chih-Yang – sequence: 9 givenname: Kuen-Haur orcidid: 0000-0002-6354-3315 surname: Lee fullname: Lee, Kuen-Haur |
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| Snippet | In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain... Simple SummaryThe roles of “like-Smith” (LSM) proteins in breast cancer development and their clinical relevance remain unclear. In this study, multiple... |
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| SubjectTerms | 1-Phosphatidylinositol 3-kinase Adenomatous polyposis coli Algorithms Alzheimer's disease Anaphase-promoting complex Antigen-presenting cells Biomarkers Breast cancer CD4 antigen CD8 antigen Cell cycle Cell differentiation Datasets DNA methylation Epidermal growth factor ErbB-2 protein Gene expression Genomes Genomics Infiltration Interleukin 15 Lymphocytes T MAP kinase Medical prognosis Metastases Patients Protein expression Proteins Signal transduction Suppressor cells Survival analysis Transcription Tumorigenesis Tumors |
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| Title | Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer |
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