1
|
Srinath S, Jishnu PV, Varghese VK, Shukla V, Adiga D, Mallya S, Chakrabarty S, Sharan K, Pandey D, Chatterjee A, Kabekkodu SP. Regulation and tumor-suppressive function of the miR-379/miR-656 (C14MC) cluster in cervical cancer. Mol Oncol 2024; 18:1608-1630. [PMID: 38400534 PMCID: PMC11161731 DOI: 10.1002/1878-0261.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/05/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Cervical cancer (CC) is a key contributor to cancer-related mortality in several countries. The identification of molecular markers and the underlying mechanism may help improve CC management. We studied the regulation and biological function of the chromosome 14 microRNA cluster (C14MC; miR-379/miR-656) in CC. Most C14MC members exhibited considerably lower expression in CC tissues and cell lines in The Cancer Genome Atlas (TCGA) cervical squamous cell carcinoma and endocervical adenocarcinoma patient cohorts. Bisulfite Sanger sequencing revealed hypermethylation of the C14MC promoter in CC tissues and cell lines. 5-aza-2 deoxy cytidine treatment reactivated expression of the C14MC members. We demonstrated that C14MC is a methylation-regulated miRNA cluster via artificial methylation and luciferase reporter assays. C14MC downregulation correlated with poor overall survival and may promote metastasis. C14MC activation via the lentiviral-based CRISPRa approach inhibited growth, proliferation, migration, and invasion; enhanced G2/M arrest; and induced senescence. Post-transcriptional regulatory network analysis of C14MC transcriptomic data revealed enrichment of key cancer-related pathways, such as metabolism, the cell cycle, and phosphatidylinositol 3-kinase (PI3K)-AKT signaling. Reduced cell proliferation, growth, migration, invasion, and senescence correlated with the downregulation of active AKT, MYC, and cyclin E1 (CCNE1) and the overexpression of p16, p21, and p27. We showed that C14MC miRNA activation increases reactive oxygen species (ROS) levels, intracellular Ca2+ levels, and lipid peroxidation rates, and inhibits epithelial-mesenchymal transition (EMT). C14MC targets pyruvate dehydrogenase kinase-3 (PDK3) according to the luciferase reporter assay. PDK3 is overexpressed in CC and is inversely correlated with C14MC. Both miR-494-mimic transfection and C14MC activation inhibited PDK3 expression. Reduced glucose uptake and lactate production, and upregulation of PDK3 upon C14MC activation suggest the potential role of these proteins in metabolic reprogramming. Finally, we showed that C14MC activation may inhibit EMT signaling. Thus, C14MC is a tumor-suppressive and methylation-regulated miRNA cluster in CC. Reactivation of C14MC can be useful in the management of CC.
Collapse
Grants
- Fund for Improvement of S&T Infrastructure (FIST), Department of Science and Technology, Government of India
- Karnataka Fund for Infrastructure Strengthening in Science and Technology (K-FIST), the Government of Karnataka
- MTR/2021/000182 Department of Science and Technology, Ministry of Science and Technology, India
- EMR/2016/002314 Science and Engineering Research Board (SERB)
- Manipal Academy of Higher Education, Manipal
- IA/I/22/1/506240 DBT-Wellcome Trust India Alliance
- SPARC/2019-2020/P2297/SL SPARC
- IA/I/22/1/506240 Wellcome Trust DBT India Alliance, Government of India
- Builder Grant, Department of Biotechnology, Government of India
- Technology Information Forecasting and Assessment Council (TIFAC) Core in Pharmacogenomics at MAHE, the Manipal
- Wellcome Trust
- Science and Engineering Research Board (SERB)
- Department of Science and Technology, Ministry of Science and Technology, India
- SPARC
- Technology Information Forecasting and Assessment Council (TIFAC) Core in Pharmacogenomics at MAHE, the Manipal
Collapse
Affiliation(s)
- Sriharikrishnaa Srinath
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
- Center for DNA Repair and Genome Stability (CDRGS)Manipal Academy of Higher EducationIndia
| | - Krishna Sharan
- Department of Radiotherapy OncologyKasturba Medical CollegeManipalIndia
| | - Deeksha Pandey
- Department of Obstetrics & GynecologyKasturba Medical CollegeManipalIndia
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of MedicineUniversity of OtagoDunedinNew Zealand
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
- Center for DNA Repair and Genome Stability (CDRGS)Manipal Academy of Higher EducationIndia
| |
Collapse
|
2
|
Dastsooz H, Anselmi F, Lauria A, Cicconetti C, Proserpio V, Mohammadisoleimani E, Firoozi Z, Mansoori Y, Haghi-Aminjan H, Caizzi L, Oliviero S. Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development. Front Cell Dev Biol 2024; 12:1295403. [PMID: 38859961 PMCID: PMC11163233 DOI: 10.3389/fcell.2024.1295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Patients with breast cancer show altered expression of genes within the pectoralis major skeletal muscle cells of the breast. Through analyses of The Cancer Genome Atlas (TCGA)-breast cancer (BRCA), we identified three previously uncharacterized putative novel tumor suppressor genes expressed in normal muscle cells, whose expression was downregulated in breast tumors. We found that NEDD4 binding protein 2-like 1 (N4BP2L1), pleckstrin homology domain-containing family A member 4 (PLEKHA4), and brain-enriched guanylate kinase-associated protein (BEGAIN) that are normally highly expressed in breast myoepithelial cells and smooth muscle cells were significantly downregulated in breast tumor tissues of a cohort of 50 patients with this cancer. Our data revealed that the low expression of PLEKHA4 in patients with menopause below 50 years correlated with a higher risk of breast cancer. Moreover, we identified N4BP2L1 and BEGAIN as potential biomarkers of HER2-positive breast cancer. Furthermore, low BEGAIN expression in breast cancer patients with blood fat, heart problems, and diabetes correlated with a higher risk of this cancer. In addition, protein and RNA expression analysis of TCGA-BRCA revealed N4BP2L1 as a promising diagnostic protein biomarker in breast cancer. In addition, the in silico data of scRNA-seq showed high expression of these genes in several cell types of normal breast tissue, including breast myoepithelial cells and smooth muscle cells. Thus, our results suggest their possible tumor-suppressive function in breast cancer and muscle development.
Collapse
Affiliation(s)
- Hassan Dastsooz
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- IIGM-Italian Institute for Genomic Medicine, IRCCS, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo Cancer (IT), Torino, Italy
| | - Francesca Anselmi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Chiara Cicconetti
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Zahra Firoozi
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
| | - Yaser Mansoori
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Hamed Haghi-Aminjan
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Livia Caizzi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- IIGM-Italian Institute for Genomic Medicine, IRCCS, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo Cancer (IT), Torino, Italy
| |
Collapse
|
3
|
Olszewska AM, Nowak JI, Myszczynski K, Słominski A, Żmijewski MA. Dissection of an impact of VDR and RXRA on the genomic activity of 1,25(OH) 2D 3 in A431 squamous cell carcinoma. Mol Cell Endocrinol 2024; 582:112124. [PMID: 38123121 PMCID: PMC10872374 DOI: 10.1016/j.mce.2023.112124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/24/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Human skin is the natural source, place of metabolism, and target for vitamin D3. The classical active form of vitamin D3, 1,25(OH)2D3, expresses pluripotent properties and is intensively studied in cancer prevention and therapy. To define the specific role of vitamin D3 receptor (VDR) and its co-receptor retinoid X receptor alpha (RXRA) in genomic regulation, VDR or RXRA genes were silenced in the squamous cell carcinoma cell line A431 and treated with 1,25(OH)2D3 at long incubation time points 24 h/72 h. Extending the incubation time of A431 WT (wild-type) cells with 1,25(OH)2D3 resulted in a two-fold increase in DEGs (differentially expressed genes) and a change in the amount of downregulated from 37% to 53%. VDR knockout led to a complete loss of 1,25(OH)2D3-induced genome-wide gene regulation at 24 h time point, but after 72 h, 20 DEGs were found, of which 75% were downregulated, and most of them belonged to the gene ontology group "immune response". This may indicate the existence of an alternative, secondary response to 1,25(OH)2D3. In contrast, treatment of A431 ΔRXRA cells with 1,25(OH)2D3 for 24 h only partially affected DEGs, suggesting RXRA-independent regulation. Interestingly, overexpression of classic 1,25(OH)2D3 targets, like CYP24A1 (family 24 of subfamily A of cytochrome P450 member 1) or CAMP (cathelicidin antimicrobial peptide) was found to be RXRA-independent. Also, immunofluorescence staining of A431 WT cells revealed partial VDR/RXRA colocalization after 24 h and 72 h 1,25(OH)2D3 treatment. Comparison of transcriptome changes induced by 1,25(OH)2D3 in normal keratinocytes vs. cancer cells showed high cell type specific expression pattern with only a few genes commonly regulated by 1,25(OH)2D3. Activation of the genomic pathway at least partially reversed the expression of cancer-related genes, forming a basis for anti-cancer activates of 1,25(OH)2D3. In summary, VDR or RXRA independent genomic activities of 1,25(OH)2D3 suggest the involvement of alternative factors, opening new challenges in this field.
Collapse
Affiliation(s)
- Anna M Olszewska
- Department of Histology, Medical University of Gdansk, 1a Debinki, 80-211Gdansk, Poland
| | - Joanna I Nowak
- Department of Histology, Medical University of Gdansk, 1a Debinki, 80-211Gdansk, Poland
| | - Kamil Myszczynski
- Centre of Biostatistics and Bioinformatics Analysis Medical University of Gdansk, 1aDebinki, 80-211 Gdansk, Poland
| | - Andrzej Słominski
- Department of Dermatology, University of Alabama at Birmingham, AL 35292, USA; Birmingham Veteran Administration Medical Center, Birmingham, AL 35292, USA
| | - Michał A Żmijewski
- Department of Histology, Medical University of Gdansk, 1a Debinki, 80-211Gdansk, Poland.
| |
Collapse
|
4
|
Nowak JI, Olszewska AM, Piotrowska A, Myszczyński K, Domżalski P, Żmijewski MA. PDIA3 modulates genomic response to 1,25-dihydroxyvitamin D 3 in squamous cell carcinoma of the skin. Steroids 2023; 199:109288. [PMID: 37549780 DOI: 10.1016/j.steroids.2023.109288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
An active form of vitamin D3 (1,25-dihydroxyvitamin D3) acts through vitamin D receptor (VDR) initiating genomic response, but several studies described also non-genomic actions of 1,25-dihydroxyvitamin D3, implying the role of PDIA3 in the process. PDIA3 is a membrane-associated disulfide isomerase involved in disulfide bond formation, protein folding, and remodeling. Here, we used a transcriptome-based approach to identify changes in expression profiles in PDIA3-deficient squamous cell carcinoma line A431 after 1,25-dihydroxyvitamin D3 treatment. PDIA3 knockout led to changes in the expression of more than 2000 genes and modulated proliferation, cell cycle, and mobility of cells; suggesting an important regulatory role of PDIA3. PDIA3-deficient cells showed increased sensitivity to 1,25-dihydroxyvitamin D3, which led to decrease migration. 1,25-dihydroxyvitamin D3 treatment altered also genes expression profile of A431ΔPDIA3 in comparison to A431WT cells, indicating the existence of PDIA3-dependent genes. Interestingly, classic targets of VDR, including CAMP (Cathelicidin Antimicrobial Peptide), TRPV6 (Transient Receptor Potential Cation Channel Subfamily V Member 6), were regulated differently by 1,25-dihydroxyvitamin D3, in A431ΔPDIA3. Deletion of PDIA3 impaired 1,25-dihydroxyvitamin D3-response of genes, such as PTGS2, MMP12, and FOCAD, which were identified as PDIA3-dependent. Additionally, response to 1,25-dihydroxyvitamin D3 in cancerous A431 cells differed from immortalized HaCaT keratinocytes, used as non-cancerous control. Finally, silencing of PDIA3 and 1,25-dihydroxyvitamin D3, at least partially reverse the expression of cancer-related genes in A431 cells, thus targeting PDIA3 and use of 1,25-dihydroxyvitamin D3 could be considered in a prevention and therapy of the skin cancer. Taken together, PDIA3 has a strong impact on gene expression and physiology, including genomic response to 1,25-dihydroxyvitamin D3.
Collapse
Affiliation(s)
- Joanna I Nowak
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Anna M Olszewska
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Anna Piotrowska
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Kamil Myszczyński
- Centre of Biostatistics and Bioinformatics Analysis Medical University of Gdansk, 1a Debinki, 80-211 Gdansk, Poland.
| | - Paweł Domżalski
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Michał A Żmijewski
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| |
Collapse
|
5
|
Shukla V, Mallya S, Adiga D, Sriharikrishnaa S, Chakrabarty S, Kabekkodu SP. Bioinformatic Analysis of miR-200b/429 and Hub Gene Network in Cervical Cancer. Biochem Genet 2023; 61:1898-1916. [PMID: 36879084 PMCID: PMC10517900 DOI: 10.1007/s10528-023-10356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
The miR-200b/429 located at 1p36 is a highly conserved miRNA cluster emerging as a critical regulator of cervical cancer. Using publicly available miRNA expression data from TCGA and GEO followed by independent validation, we aimed to identify the association between miR-200b/429 expression and cervical cancer. miR-200b/429 cluster was significantly overexpressed in cancer samples compared to normal samples. miR-200b/429 expression did not correlate with patient survival; however, its overexpression correlated with histological type. Protein-protein interaction analysis of 90 target genes of miR-200b/429 identified EZH2, FLT1, IGF2, IRS1, JUN, KDR, SOX2, MYB, ZEB1, and TIMP2 as the top ten hub genes. PI3K-AKT and MAPK signaling pathways emerged as major target pathways of miR-200b/429 and their hub genes. Kaplan-Meier survival analysis showed the expression of seven miR-200b/429 target genes (EZH2, FLT1, IGF2, IRS1, JUN, SOX2, and TIMP2) to influence the overall survival of patients. The miR-200a-3p and miR-200b-5p could help predict cervical cancer with metastatic potential. The cancer hallmark enrichment analysis showed hub genes to promote growth, sustained proliferation, resistance to apoptosis, induction of angiogenesis, activation of invasion, and metastasis, enabling replicative immortality, evading immune destruction, and tumor-promoting inflammation. The drug-gene interaction analysis identified 182 potential drugs to interact with 27 target genes of miR-200b/429 with paclitaxel, doxorubicin, dabrafenib, bortezomib, docetaxel, ABT-199, eribulin, vorinostat, etoposide, and mitoxantrone emerging as the top ten best candidate drugs. Taken together, miR-200b/429 and associated hub genes can be helpful for prognostic application and clinical management of cervical cancer.
Collapse
Affiliation(s)
- Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
- Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
- Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka, India.
| |
Collapse
|
6
|
Wu HW, Wu JD, Yeh YP, Wu TH, Chao CH, Wang W, Chen TW. DoSurvive: A webtool for investigating the prognostic power of a single or combined cancer biomarker. iScience 2023; 26:107269. [PMID: 37609633 PMCID: PMC10440714 DOI: 10.1016/j.isci.2023.107269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/26/2023] [Accepted: 06/28/2023] [Indexed: 08/24/2023] Open
Abstract
We present DoSurvive, a user-friendly survival analysis web tool and a cancer prognostic biomarker centered database. DoSurvive is the first database that allows users to perform multivariant survival analysis for cancers with customized gene/patient list. DoSurvive offers three survival analysis methods, Log rank test, Cox regression and accelerated failure time model (AFT), for users to analyze five types of quantitative features (mRNA, miRNA, lncRNA, protein and methylation of CpG islands) with four survival types, i.e. overall survival, disease-specific survival, disease-free interval, and progression-free interval, in 33 cancer types. Notably, the implemented AFT model provides an alternative method for genes/features which failed the proportional hazard assumption in Cox regression. With the unprecedented number of survival models implemented and high flexibility in analysis, DoSurvive is a unique platform for the identification of clinically relevant targets for cancer researcher and practitioners. DoSurvive is freely available at http://dosurvive.lab.nycu.edu.tw/.
Collapse
Affiliation(s)
- Hao-Wei Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jian-De Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yen-Ping Yeh
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Timothy H. Wu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Hong Chao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Weijing Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| |
Collapse
|
7
|
Adiga D, Bhat S, Shukla V, Shah HV, Kuthethur R, Chakrabarty S, Kabekkodu SP. Double C-2 like domain beta (DOC2B) induces calcium dependent oxidative stress to promote lipotoxicity and mitochondrial dysfunction for its tumor suppressive function. Free Radic Biol Med 2023; 201:1-13. [PMID: 36913987 DOI: 10.1016/j.freeradbiomed.2023.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Mitochondria are biosynthetic and bioenergetic organelles that regulate many biological processes, including metabolism, oxidative stress, and cell death. Cervical cancer (CC) cells show impairments in mitochondrial structure and function and are linked with cancer progression. DOC2B is a tumor suppressor with anti-proliferative, anti-migratory, anti-invasive, and anti-metastatic function in CC. For the first time, we demonstrated the role of the DOC2B-mitochondrial axis with tumor growth regulatory functions in CC. We used DOC2B overexpression and knockdown model systems to show that DOC2B is localized to mitochondria and induces Ca2+-mediated lipotoxicity. DOC2B expression induced mitochondrial morphological changes with the subsequent reduction in mitochondrial DNA copy number, mitochondrial mass, and mitochondrial membrane potential. Intracellular and mitochondrial Ca2+, intracellular O.-2, and ATP levels were substantially elevated in the presence of DOC2B. DOC2B manipulation reduced glucose uptake, lactate production, and mitochondrial complex-IV activity. The presence of DOC2B significantly reduced the proteins associated with mitochondrial structure and biogenesis with the concomitant activation of AMPK signaling. Augmented lipid peroxidation (LPO) in the presence of DOC2B was a Ca2+-dependent process. Our findings demonstrated that DOC2B promotes lipid accumulation, oxidative stress, and LPO through intracellular Ca2+ overload, which may contribute to mitochondrial dysfunction and tumor-suppressive properties of DOC2B. We propose that the DOC2B-Ca2+-oxidative stress-LPO-mitochondrial axis could be targeted for confining CC. Further, the induction of lipotoxicity in tumor cells by activating DOC2B could serve as a novel therapeutic approach in CC.
Collapse
Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Samatha Bhat
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Henil Vinit Shah
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Raviprasad Kuthethur
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India.
| |
Collapse
|
8
|
Khan NG, Eswaran S, Adiga D, Sriharikrishnaa S, Chakrabarty S, Rai PS, Kabekkodu SP. Integrated bioinformatic analysis to understand the association between phthalate exposure and breast cancer progression. Toxicol Appl Pharmacol 2022; 457:116296. [PMID: 36328110 DOI: 10.1016/j.taap.2022.116296] [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: 05/14/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
Phthalates have been extensively used as plasticizers while manufacturing plastic-based consumer products. Estradiol mimicking properties and association studies suggest phthalates may contribute to breast cancer (BC). We performed an in-silico analysis and functional studies to understand the association between phthalate exposure and BC progression. Search for phthalate-responsive genes using the comparative toxicogenomics database identified 20 genes as commonly altered in response to multiple phthalates exposure. Of the 20 genes, 12 were significantly differentially expressed between normal and BC samples. In BC samples, 9 out of 20 genes showed a negative correlation between promoter methylation and its expression. AHR, BAX, BCL2, CAT, ESR2, IL6, and PTGS2 expression differed significantly between metastatic and non-metastatic BC samples. Gene set enrichment analysis identified metabolism, ATP-binding cassette transporters, insulin signaling, and type II diabetes as highly enriched pathways. The diagnostic assessment based on 20 genes expression suggested a sensitivity and a specificity >0.91. The aberrantly expressed phthalate interactive gene influenced the overall survival of BC patients. Drug-gene interaction analysis identified 14 genes and 523 candidate drugs, including 19 BC treatment-approved drugs. Di(2-ethylhexyl) phthlate (DEHP) exposure increased the growth, proliferation, and migration of MCF-7 and MDA-MB-231 cells in-vitro. DEHP exposure induced morphological changes, actin cytoskeletal remodeling, increased ROS content, reduced basal level lipid peroxidation, and induced epithelial to mesenchymal transition (EMT). The present approach can help to explore the potentially damaging effects of environmental agents on cancer risk and understand the underlined pathways and molecular mechanisms.
Collapse
Affiliation(s)
- Nadeem G Khan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| |
Collapse
|
9
|
CmirC: an integrated database of clustered miRNAs co-localized with copy number variations in cancer. Funct Integr Genomics 2022; 22:1229-1241. [DOI: 10.1007/s10142-022-00909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022]
Abstract
AbstractGenomic rearrangements and copy number variations (CNVs) are the major regulators of clustered microRNAs (miRNAs) expression. Several clustered miRNAs are harbored in and around chromosome fragile sites (CFSs) and cancer-associated genomic hotspots. Aberrant expression of such clusters can lead to oncogenic or tumor suppressor activities. Here, we developed CmirC (Clustered miRNAs co-localized with CNVs), a comprehensive database of clustered miRNAs co-localized with CNV regions. The database consists of 481 clustered miRNAs co-localized with CNVs and their expression patterns in 35 cancer types of the TCGA. The portal also provides information on CFSs, miRNA cluster candidates, genomic coordinates, target gene networks, and gene functionality. The web portal is integrated with advanced tools such as JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3 to help the researchers in data analysis, visualization, and browsing. This portal provides a promising avenue for integrated data analytics and offers additional evidence for the complex regulation of clustered miRNAs in cancer. The web portal is freely accessible at http://slsdb.manipal.edu/cmirclust to explore clinically significant miRNAs.
Collapse
|
10
|
Mo H, Breitling R, Francavilla C, Schwartz JM. Data integration and mechanistic modelling for breast cancer biology: Current state and future directions. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2022; 24:None. [PMID: 36034741 PMCID: PMC9402443 DOI: 10.1016/j.coemr.2022.100350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Breast cancer is one of the most common cancers threatening women worldwide. A limited number of available treatment options, frequent recurrence, and drug resistance exacerbate the prognosis of breast cancer patients. Thus, there is an urgent need for methods to investigate novel treatment options, while taking into account the vast molecular heterogeneity of breast cancer. Recent advances in molecular profiling technologies, including genomics, epigenomics, transcriptomics, proteomics and metabolomics data, enable approaching breast cancer biology at multiple levels of omics interaction networks. Systems biology approaches, including computational inference of ‘big data’ and mechanistic modelling of specific pathways, are emerging to identify potential novel combinations of breast cancer subtype signatures and more diverse targeted therapies.
Collapse
|
11
|
Wang PW, Su YH, Chou PH, Huang MY, Chen TW. Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways. BMC Genomics 2022; 22:918. [PMID: 35508961 PMCID: PMC9066720 DOI: 10.1186/s12864-022-08581-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Background Pan-cancer studies have disclosed many commonalities and differences in mutations, copy number variations, and gene expression alterations among cancers. Some of these features are significantly associated with clinical outcomes, and many prognosis-predictive biomarkers or biosignatures have been proposed for specific cancer types. Here, we systematically explored the biological functions and the distribution of survival-related genes (SRGs) across cancers. Results We carried out two different statistical survival models on the mRNA expression profiles in 33 cancer types from TCGA. We identified SRGs in each cancer type based on the Cox proportional hazards model and the log-rank test. We found a large difference in the number of SRGs among different cancer types, and most of the identified SRGs were specific to a particular cancer type. While these SRGs were unique to each cancer type, they were found mostly enriched in cancer hallmark pathways, e.g., cell proliferation, cell differentiation, DNA metabolism, and RNA metabolism. We also analyzed the association between cancer driver genes and SRGs and did not find significant over-representation amongst most cancers. Conclusions In summary, our work identified all the SRGs for 33 cancer types from TCGA. In addition, the pan-cancer analysis revealed the similarities and the differences in the biological functions of SRGs across cancers. Given the potential of SRGs in clinical utility, our results can serve as a resource for basic research and biotech applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08581-x.
Collapse
Affiliation(s)
- Po-Wen Wang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Yi-Hsun Su
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Industrial Development PhD Program of the College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Po-Hao Chou
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Ming-Yueh Huang
- Institute of Statistical Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan. .,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan. .,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.
| |
Collapse
|
12
|
Firoozi Z, Mohammadisoleimani E, Shahi A, Mansoori H, Naghizadeh MM, Bastami M, Nariman‐Saleh‐Fam Z, Daraei A, Raoofat A, Mansoori Y. Potential roles of hsa_circ_000839 and hsa_circ_0005986 in breast cancer. J Clin Lab Anal 2022; 36:e24263. [PMID: 35098570 PMCID: PMC8906031 DOI: 10.1002/jcla.24263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/27/2021] [Accepted: 01/15/2022] [Indexed: 11/26/2022] Open
Abstract
Background Breast cancer (BC) is one of the leading causes of death among women around the world. Circular RNAs (circRNAs) are a newly discovered group of non‐coding RNAs that their roles are being investigated in BC and other cancer types. In this study, we evaluated the association of hsa_circ_0005986 and hsa_circ_000839 in tumor and adjacent normal tissues of BC patients with their clinicopathological characteristics. Materials and methods Total RNA was extracted from tumors and adjacent non‐tumor tissues by the Trizol isolation reagent, and cDNA was synthesized using First Strand cDNA Synthesis Kit (Thermo Scientific). The expression level of hsa_circ_0005986 and hsa_circ_000839 was quantified using RT‐qPCR. Online in silico tools were used for identifying potentially important competing endogenous RNA (ceRNA) networks of these two circRNAs. Results The expression level of hsa_circ_0005986 and hsa_circ_000839 was lower in the tumor as compared to adjacent tissues. The expression level of hsa_circ_0005986 in the patients who had used hair dye in the last 5 years was significantly lower. Moreover, a statistically significant negative correlation between body mass index (BMI) and hsa_circ_000839 expression was observed. In silico analysis of the ceRNA network of these circRNAs revealed mRNAs and miRNAs with crucial roles in BC. Conclusion Downregulation of hsa_circ_000839 and hsa_circ_0005986 in BC tumors suggests a tumor‐suppressive role for these circRNAs in BC, meriting the need for more experimentations to delineate the exact mechanism of their involvement in BC pathogenesis.
Collapse
Affiliation(s)
- Zahra Firoozi
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
| | | | - Abbas Shahi
- Department of Immunology School of Medicine Tehran University of Medical Science Tehran Iran
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
| | - Hosein Mansoori
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
| | | | - Milad Bastami
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
| | - Ziba Nariman‐Saleh‐Fam
- Women's Reproductive Health Research CenterTabriz University of Medical Sciences Tabriz Iran
| | - Abdolreza Daraei
- Department of Medical Genetics School of Medicine Babol University of Medical Sciences Babol Iran
| | - Atefeh Raoofat
- Department of Medical Genetics School of Medicine Shiraz University of Medical Sciences Shiraz Iran
| | - Yaser Mansoori
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
| |
Collapse
|
13
|
Eswaran S, Adiga D, Khan G N, S S, Kabekkodu SP. Comprehensive Analysis of the Exocytosis Pathway Genes in Cervical Cancer. Am J Med Sci 2022; 363:526-537. [PMID: 34995576 DOI: 10.1016/j.amjms.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/09/2021] [Accepted: 12/29/2021] [Indexed: 02/06/2023]
|
14
|
Bermúdez-Guzmán L. Pan-cancer analysis of non-oncogene addiction to DNA repair. Sci Rep 2021; 11:23264. [PMID: 34853396 PMCID: PMC8636604 DOI: 10.1038/s41598-021-02773-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer cells usually depend on the aberrant function of one or few driver genes to initiate and promote their malignancy, an attribute known as oncogene addiction. However, cancer cells might become dependent on the normal cellular functions of certain genes that are not oncogenes but ensure cell survival (non-oncogene addiction). The downregulation or silencing of DNA repair genes and the consequent genetic and epigenetic instability is key to promote malignancy, but the activation of the DNA-damage response (DDR) has been shown to become a type of non-oncogene addiction that critically supports tumour survival. In the present study, a systematic evaluation of DNA repair addiction at the pan-cancer level was performed using data derived from The Cancer Dependency Map and The Cancer Genome Atlas (TCGA). From 241 DDR genes, 59 were identified as commonly essential in cancer cell lines. However, large differences were observed in terms of dependency scores in 423 cell lines and transcriptomic alterations across 18 cancer types. Among these 59 commonly essential genes, 14 genes were exclusively associated with better overall patient survival and 19 with worse overall survival. Notably, a specific molecular signature among the latter, characterized by DDR genes like UBE2T, RFC4, POLQ, BRIP1, and H2AFX showing the weakest dependency scores, but significant upregulation was strongly associated with worse survival. The present study supports the existence and importance of non-oncogenic addiction to DNA repair in cancer and may facilitate the identification of prognostic biomarkers and therapeutic opportunities.
Collapse
Affiliation(s)
- Luis Bermúdez-Guzmán
- Robotic Radiosurgery Center, International Cancer Center, San José, Costa Rica. .,Section of Genetics and Biotechnology, School of Biology, University of Costa Rica, San Pedro, San José, Costa Rica.
| |
Collapse
|
15
|
Meneur C, Eswaran S, Adiga D, S S, G NK, Mallya S, Chakrabarty S, Kabekkodu SP. Analysis of Nuclear Encoded Mitochondrial Gene Networks in Cervical Cancer. Asian Pac J Cancer Prev 2021; 22:1799-1811. [PMID: 34181336 PMCID: PMC8418845 DOI: 10.31557/apjcp.2021.22.6.1799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Cervical cancer (CC) is one of the most common female cancers in many developing and underdeveloped countries. High incidence, late presentation, and mortality suggested the need for molecular markers. Mitochondrial defects due to abnormal expression of nuclear-encoded mitochondrial genes (NEMG) have been reported during cancer progression. Nevertheless, the application of NEMG for the prognosis of CC is still elusive. Herein, we aimed to investigate the associations between NEMG and CC prognosis. MATERIALS AND METHODS The differentially expressed genes (DEG) in the TCGA-CESC dataset and NEMGs were retrieved from TACCO and Mitocarta2.0 databases, respectively. The impact of methylation on NEMG expression were predicted using DNMIVD and UALCAN tools. HCMDB tool was used to predict genes having metastatic potential. The prognostic models were constructed using DNMIVD, TACCO, GEPIA2, and SurvExpress. The functional enrichment analysis (FEA) was performed using clusterProfiler. The protein-protein interaction network (PPIN) was constructed to identify the hub genes (HG) using String and CytoHubba tools. Independent validation of the HG was performed using Oncomine and Human Protein Atlas databases. The druggable genes were predicted using DGIdb. RESULTS Among the 52 differentially expressed NEMG, 15 were regulated by DNA methylation. The expression level of 16, 10, and 7 has the potential for CC staging, prediction of metastasis, and prognosis. Moreover, 1 driver gene and 16 druggable genes were also identified. The FEA identified the enrichment of cancer-related pathways, including AMPK and carbon metabolism in cancer. The combined expression of 10 HG has been shown to affect patient survival. CONCLUSION Our findings suggest that the abnormal expression of NEMGs may play a critical role in CC development and progression. The genes identified in our study may serve as a prognostic indicator and therapeutic target in CC. .
Collapse
Affiliation(s)
- Cecile Meneur
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
- La Rochelle University, Avenue Albert Einstein, 17031, La Rochelle, France.
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Sriharikrishnaa S
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Nadeem Khan G
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India.
| |
Collapse
|
16
|
Martín J, Castellano JJ, Marrades RM, Canals J, Viñolas N, Díaz T, Molins L, Martinez D, Han B, Moisés J, He Y, Monzó M, Navarro A. Role of the epithelial-mesenchymal transition-related circular RNA, circ-10720, in non-small-cell lung cancer. Transl Lung Cancer Res 2021; 10:1804-1818. [PMID: 34012794 PMCID: PMC8107756 DOI: 10.21037/tlcr-20-920] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Circular RNAs (circRNAs) are non-coding RNAs with a circular structure that have recently emerged as important regulators of tumorogenesis. Recently, several circRNAS, including circ-10720 have been related to epithelial-mesenchymal transition (EMT) process. In the present study, we have analyzed the role of circ-10720 in non-small-cell lung cancer (NSCLC) and studied its prognostic relevance in resected stage I-IIIa NSCLC patients. Methods Circ-10720 expression was analyzed using a custom TaqMan assay in four NSCLC cell lines (HCC44, A549, H23 and H1299) and in the normal immortalized lung cell line BEAS2B. Silencing of circ-10720 was performed using two custom siRNAs which were transfected using lipofectamine 2000. Protein levels were evaluated by Western blot and immunofluorescence. Wound healing and invasion assays were performed to evaluate the impact the circRNA on cell motility. Apoptosis was analyzed by evaluation of Caspase 3-7 activity and proliferation by MTS assay. Moreover, the expression levels of the circRNA were studied in 119 resected NSCLC patients. The expression in tumor tissue was correlated with the main clinicopathological characteristics and with time to relapse (TTR). Results Circ-10720 was overexpressed in HCC44 and A549 and underexpressed in H23 and H1299 NSCLC cell lines in comparison to BEAS2B normal immortalized lung cell line. CircRNA knockdown in the two circ-10720 overexpressing cell lines was associated with a decrease of Vimentin (VIM) and an increase of E-cadherin (CDH1) protein levels, loss of mesenchymal phenotype, and a significant reduction of migration and invasion capacity. After silencing circ-10720, the apoptosis rate increased and the proliferation was significantly reduced. Furthermore, circ-10720 was upregulated in tumor vs. normal tissue from 119 resected NSCLC patients. In the group of patients not receiving adjuvant treatment, those with high levels of circ-10720 had a shorter TTR than those with low levels and emerged as an independent prognostic value in the multivariate analysis. In tumor tissue, circ-10720 levels positively correlated with the EMT gene Twist1 levels. Conclusions Circ-10720 regulates EMT, apoptosis and proliferation and acts as a biomarker of relapse in NSCLC.
Collapse
Affiliation(s)
- Jara Martín
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Joan Josep Castellano
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Ramón María Marrades
- Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain.,Department of Pneumology, Institut Clínic Respiratori (ICR), Hospital Clínic de Barcelona, University of Barcelona, IDIBAPS, CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Jordi Canals
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Nuria Viñolas
- Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain.,Department of Medical Oncology, Institut Clínic de Malalties Hemato-Oncològiques (ICMHO), Hospital Clínic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Tania Díaz
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Laureano Molins
- Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain.,Department of Thoracic Surgery, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Daniel Martinez
- Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain.,Department of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Bing Han
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Jorge Moisés
- Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Yangyi He
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| |
Collapse
|
17
|
Parsons J, Francavilla C. 'Omics Approaches to Explore the Breast Cancer Landscape. Front Cell Dev Biol 2020; 7:395. [PMID: 32039208 PMCID: PMC6987401 DOI: 10.3389/fcell.2019.00395] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer incidence is increasing worldwide with more than 600,000 deaths reported in 2018 alone. In current practice treatment options for breast cancer patients consists of surgery, chemotherapy, radiotherapy or targeting of classical markers of breast cancer subtype: estrogen receptor (ER) and HER2. However, these treatments fail to prevent recurrence and metastasis. Improved understanding of breast cancer and metastasis biology will help uncover novel biomarkers and therapeutic opportunities to improve patient stratification and treatment. We will first provide an overview of current methods and models used to study breast cancer biology, focusing on 2D and 3D cell culture, including organoids, and on in vivo models such as the MMTV mouse model and patient-derived xenografts (PDX). Next, genomic, transcriptomic, and proteomic approaches and their integration will be considered in the context of breast cancer susceptibility, breast cancer drivers, and therapeutic response and resistance to treatment. Finally, we will discuss how 'Omics datasets in combination with traditional breast cancer models are useful for generating insights into breast cancer biology, for suggesting individual treatments in precision oncology, and for creating data repositories to undergo further meta-analysis. System biology has the potential to catalyze the next great leap forward in treatment options for breast cancer patients.
Collapse
Affiliation(s)
- Joseph Parsons
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| |
Collapse
|
18
|
Li B, Meng YQ, Li Z, Yin C, Lin JP, Zhu DJ, Zhang SB. MiR-629-3p-induced downregulation of SFTPC promotes cell proliferation and predicts poor survival in lung adenocarcinoma. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:3286-3296. [PMID: 31379200 DOI: 10.1080/21691401.2019.1648283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The long-term prognosis of patients with lung cancer remains poor and thus it is imminent to further elucidate the molecular mechanism for the oncogenesis of lung cancer. In this study, we observed that surfactant protein C (SFTPC) expression was downregulated in human lung adenocarcinoma tissues and cell lines, and low SFTPC expression correlated with poor overall survival of lung adenocarcinoma patients. Moreover, we found that overexpression of SFTPC could inhibit lung cancer cell proliferation in vitro and in vivo, but downregulation of SFTPC showed the opposite results. Besides, it was observed that miR-629-3p expression was upregulated in human lung adenocarcinoma tissues and cell lines. More importantly, we found that miR-629-3p could downregulate SFTPC expression by directly binding to the SFTPC 3'-UTR and inhibit the regulatory effect of SFTPC on lung adenocarcinoma cell proliferation. In conclusion, these data suggested that miR-629-3p-meditated downregulation of SFTPC may promote lung adenocarcinoma progression.
Collapse
Affiliation(s)
- Bin Li
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Yu-Qi Meng
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Zheng Li
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Ci Yin
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Jun-Ping Lin
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Duo-Jie Zhu
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| | - Shao-Bo Zhang
- a Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College , Lanzhou , Gansu , China
| |
Collapse
|