1
|
Singh DK, Cong Z, Song YJ, Liu M, Chaudhary R, Liu D, Wang Y, Prasanth R, K C R, Lizarazo S, Akhnoukh M, Gholamalamdari O, Moitra A, Jenkins LM, Bhargava R, Nelson ER, Van Bortle K, Prasanth SG, Prasanth KV. MANCR lncRNA Modulates Cell-Cycle Progression and Metastasis by Cis-Regulation of Nuclear Rho-GEF. Mol Cell Biol 2024:1-19. [PMID: 39133105 DOI: 10.1080/10985549.2024.2383773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024] Open
Abstract
A significant number of the genetic alterations observed in cancer patients lie within nonprotein-coding segments of the genome, including regions coding for long noncoding RNAs (lncRNAs). LncRNAs display aberrant expression in breast cancer (BrCa), but the functional implications of this altered expression remain to be elucidated. By performing transcriptome screen in a triple negative BrCa (TNBC) isogenic 2D and 3D spheroid model, we observed aberrant expression of >1000 lncRNAs during BrCa progression. The chromatin-associated lncRNA MANCR shows elevated expression in metastatic TNBC. MANCR is upregulated in response to cellular stress and modulates DNA repair and cell proliferation. MANCR promotes metastasis as MANCR-depleted cells show reduced cell migration, invasion, and wound healing in vitro, and reduced metastatic lung colonization in xenograft experiments in vivo. Transcriptome analyses reveal that MANCR modulates expression and pre-mRNA splicing of genes, controlling DNA repair and checkpoint response. MANCR promotes the transcription of NET1A, a Rho-GEF that regulates DNA damage checkpoint and metastatic processes in cis, by differential promoter usage. Experiments suggest that MANCR regulates the expression of cancer-associated genes by modulating the association of various transcription factors and RNA-binding proteins. Our results identified the metastasis-promoting activities of MANCR in TNBC by cis-regulation of gene expression.
Collapse
Affiliation(s)
- Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Zhengmin Cong
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Minxue Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yu Wang
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Rajendra K C
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Miriam Akhnoukh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anurupa Moitra
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Rohit Bhargava
- Department of Bioengineering, Cancer Center at Illinois, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Erik R Nelson
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology-Anticancer Discovery from Pets to People, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
2
|
Zhang B, Zhao R, Wang Q, Zhang YJ, Yang L, Yuan ZJ, Yang J, Wang QJ, Yao L. An EMT-Related Gene Signature to Predict the Prognosis of Triple-Negative Breast Cancer. Adv Ther 2023; 40:4339-4357. [PMID: 37462865 PMCID: PMC10499992 DOI: 10.1007/s12325-023-02577-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION Epithelial-mesenchymal transition (EMT) is an important biological process in tumor invasion and metastasis, and thus a potential indicator of the progression and drug resistance of breast cancer. This study comprehensively analyzed EMT-related genes in triple-negative breast cancer (TNBC) to develop an EMT-related prognostic gene signature. METHODS With the application of The Cancer Genome Atlas (TCGA) database, Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), and the Genotype-Tissue Expression (GTEx) database, we identified EMT-related signature genes (EMGs) by Cox univariate regression and LASSO regression analysis. Risk scores were calculated and used to divide patients with TNBC into high-risk group and low-risk groups by the median value. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curve analyses were applied for model validation. Independent prognostic predictors were used to develop nomograms. Then, we assessed the risk model in terms of the immune microenvironment, genetic alteration and DNA methylation effects on prognosis, the probability of response to immunotherapy and chemotherapy, and small molecule drugs predicted by The Connectivity Map (Cmap) database. RESULTS Thirteen EMT-related genes with independent prognostic value were identified and used to stratify the patients with TNBC into high- and low-risk groups. The survival analysis revealed that patients in the high-risk group had significantly poorer overall survival than patients in the low-risk group. Populations of immune cells, including CD4 memory resting T cells, CD4 memory activated T cells, and activated dendritic cells, significantly differed between the high- and low-risk groups. Moreover, some therapeutic drugs to which the high-risk group might show sensitivity were identified. CONCLUSIONS Our research identified the significant impact of EMGs on prognosis in TNBC, providing new strategies for personalizing TNBC treatment and improving clinical outcomes.
Collapse
Affiliation(s)
- Bo Zhang
- Department of Breast Oncology, Shanxi Provincial Cancer Hospital, Taiyuan, China
| | - Rong Zhao
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Ya-Jing Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Liu Yang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Zhou-Jun Yuan
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Jun Yang
- Department of Breast Oncology, Shanxi Provincial Cancer Hospital, Taiyuan, China
| | - Qian-Jun Wang
- Department of Breast Oncology, Shanxi Provincial Cancer Hospital, Taiyuan, China
| | - Liang Yao
- Department of Breast Oncology, Shanxi Provincial Cancer Hospital, Taiyuan, China.
| |
Collapse
|
3
|
Li C, Yu S, Chen J, Hou Q, Wang S, Qian C, Yin S. Risk stratification based on DNA damage-repair-related signature reflects the microenvironmental feature, metabolic status and therapeutic response of breast cancer. Front Immunol 2023; 14:1127982. [PMID: 37033959 PMCID: PMC10080010 DOI: 10.3389/fimmu.2023.1127982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
DNA damage-repair machinery participates in maintaining genomic integrity and affects tumorigenesis. Molecular signatures based on DNA damage-repair-related genes (DRGs) capable of comprehensively indicating the prognosis, tumor immunometabolic profile and therapeutic responsiveness of breast cancer (BRCA) patients are still lacking. Integrating public datasets and bioinformatics algorithms, we developed a robust prognostic signature based on 27 DRGs. Multiple patient cohorts identified significant differences in various types of survival between high- and low-risk patients stratified by the signature. The signature correlated well with clinicopathological factors and could serve as an independent prognostic indicator for BRCA patients. Furthermore, low-risk tumors were characterized by more infiltrated CD8+ T cells, follicular helper T cells, M1 macrophages, activated NK cells and resting dendritic cells, and fewer M0 and M2 macrophages. The favorable immune infiltration patterns of low-risk tumors were also accompanied by specific metabolic profiles, decreased DNA replication, and enhanced antitumor immunity. Low-risk patients may respond better to immunotherapy, and experience improved outcomes with conventional chemotherapy or targeted medicine. Real-world immunotherapy and chemotherapy cohorts verified the predictive results. Additionally, four small molecule compounds promising to target high-risk tumors were predicted. In vitro experiments confirmed the high expression of GNPNAT1 and MORF4L2 in BRCA tissues and their association with immune cells, and the knockdown of these two DRGs suppressed the proliferation of human BRCA cells. In summary, this DNA damage-repair-related signature performed well in predicting patient prognosis, immunometabolic profiles and therapeutic sensitivity, hopefully contributing to precision medicine and new target discovery of BRCA.
Collapse
Affiliation(s)
| | | | | | | | | | - Cheng Qian
- *Correspondence: Cheng Qian, ; Shulei Yin,
| | - Shulei Yin
- *Correspondence: Cheng Qian, ; Shulei Yin,
| |
Collapse
|
4
|
Zhang Y, Tong GH, Wei XX, Chen HY, Liang T, Tang HP, Wu CA, Wen GM, Yang WK, Liang L, Shen H. Identification of Five Cytotoxicity-Related Genes Involved in the Progression of Triple-Negative Breast Cancer. Front Genet 2022; 12:723477. [PMID: 35046993 PMCID: PMC8762060 DOI: 10.3389/fgene.2021.723477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Breast cancer is one of the deadly tumors in women, and its incidence continues to increase. This study aimed to identify novel therapeutic molecules using RNA sequencing (RNA-seq) data of breast cancer from our hospital. Methods: 30 pairs of human breast cancer tissue and matched normal tissue were collected and RNA sequenced in our hospital. Differentially expressed genes (DEGs) were calculated with raw data by the R package "edgeR", and functionally annotated using R package "clusterProfiler". Tumor-infiltrating immune cells (TIICs) were estimated using a website tool TIMER 2.0. Effects of key genes on therapeutic efficacy were analyzed using RNA-seq data and drug sensitivity data from two databases: the Cancer Cell Line Encyclopedia (CCLE) and the Cancer Therapeutics Response Portal (CTRP). Results: There were 2,953 DEGs between cancerous and matched normal tissue, as well as 975 DEGs between primary breast cancer and metastatic breast cancer. These genes were primarily enriched in PI3K-Akt signaling pathway, calcium signaling pathway, cAMP signaling pathway, and cell cycle. Notably, CD8+ T cell, M0 macrophage, M1 macrophage, regulatory T cell and follicular helper T cell were significantly elevated in cancerous tissue as compared with matched normal tissue. Eventually, we found five genes (GALNTL5, MLIP, HMCN2, LRRN4CL, and DUOX2) were markedly corelated with CD8+ T cell infiltration and cytotoxicity, and associated with therapeutic response. Conclusion: We found five key genes associated with tumor progression, CD8+ T cell and therapeutic efficacy. The findings would provide potential molecular targets for the treatment of breast cancer.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China.,Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Gui-Hui Tong
- Department of Pathology,The first Affiliated Hospital,Guangzhou Medical University, Guangzhou, China
| | - Xu-Xuan Wei
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Hai-Yang Chen
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Tian Liang
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Hong-Ping Tang
- Department of Pathology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Chuan-An Wu
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Guo-Ming Wen
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Wei-Kang Yang
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Li Liang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Hong Shen
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|