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González-Sánchez GD, Granados-López AJ, López-Hernández Y, Robles MJG, López JA. miRNAs as Interconnectors between Obesity and Cancer. Noncoding RNA 2024; 10:24. [PMID: 38668382 PMCID: PMC11055034 DOI: 10.3390/ncrna10020024] [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: 12/18/2023] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
Obesity and cancer are a concern of global interest. It is proven that obesity may trigger the development or progression of some types of cancer; however, the connection by non-coding RNAs has not been totally explored. In the present review, we discuss miRNAs and lncRNAs dysregulation involved in obesity and some cancers, shedding light on how these conditions may exacerbate one another through the dysregulation of ncRNAs. lncRNAs have been reported as regulating microRNAs. An in silico investigation of lncRNA and miRNA interplay is presented. Our investigation revealed 44 upregulated and 49 downregulated lncRNAs in obesity and cancer, respectively. miR-375, miR-494-3p, miR-1908, and miR-196 were found interacting with 1, 4, 4 and 4 lncRNAs, respectively, which are involved in PPARγ cell signaling regulation. Additionally, miR-130 was found to be downregulated in obesity and reported as modulating 5 lncRNAs controlling PPARγ cell signaling. Similarly, miR-128-3p and miR-143 were found to be downregulated in obesity and cancer, interacting with 5 and 4 lncRNAs, respectively, associated with MAPK cell signaling modulation. The delicate balance between miRNA and lncRNA expression emerges as a critical determinant in the development of obesity-associated cancers, presenting these molecules as promising biomarkers. However, additional and deeper studies are needed to reach solid conclusions about obesity and cancer connection by ncRNAs.
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Affiliation(s)
- Grecia Denisse González-Sánchez
- Doctorate in Biosciences, University Center of Los Altos, University of Guadalajara, Tepatitlán de Morelos C.P. 47620, Mexico;
| | - Angelica Judith Granados-López
- Laboratory of microRNAs and Cancer, Academic Unit of Biological Sciences, Autonomous University of Zacatecas “Francisco García Salinas”, Zacatecas C.P. 98066, Mexico;
| | - Yamilé López-Hernández
- Laboratory of Proteomics and Metabolomics, Cátedras-CONACYT, Academic Unit of Biological Sciences, Autonomous University of Zacatecas “Francisco García Salinas”, Zacatecas C.P. 98066, Mexico;
| | - Mayra Judith García Robles
- Biotechnology Department of the Polytechnic, University of Zacatecas, Fresnillo, Zacatecas C.P. 99059, Mexico
| | - Jesús Adrián López
- Laboratory of microRNAs and Cancer, Academic Unit of Biological Sciences, Autonomous University of Zacatecas “Francisco García Salinas”, Zacatecas C.P. 98066, Mexico;
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Dashti P, Lewallen EA, Gordon JAR, Montecino MA, Davie JR, Stein GS, van Leeuwen JPTM, van der Eerden BCJ, van Wijnen AJ. Epigenetic regulators controlling osteogenic lineage commitment and bone formation. Bone 2024; 181:117043. [PMID: 38341164 DOI: 10.1016/j.bone.2024.117043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bone formation and homeostasis are controlled by environmental factors and endocrine regulatory cues that initiate intracellular signaling pathways capable of modulating gene expression in the nucleus. Bone-related gene expression is controlled by nucleosome-based chromatin architecture that limits the accessibility of lineage-specific gene regulatory DNA sequences and sequence-specific transcription factors. From a developmental perspective, bone-specific gene expression must be suppressed during the early stages of embryogenesis to prevent the premature mineralization of skeletal elements during fetal growth in utero. Hence, bone formation is initially inhibited by gene suppressive epigenetic regulators, while other epigenetic regulators actively support osteoblast differentiation. Prominent epigenetic regulators that stimulate or attenuate osteogenesis include lysine methyl transferases (e.g., EZH2, SMYD2, SUV420H2), lysine deacetylases (e.g., HDAC1, HDAC3, HDAC4, HDAC7, SIRT1, SIRT3), arginine methyl transferases (e.g., PRMT1, PRMT4/CARM1, PRMT5), dioxygenases (e.g., TET2), bromodomain proteins (e.g., BRD2, BRD4) and chromodomain proteins (e.g., CBX1, CBX2, CBX5). This narrative review provides a broad overview of the covalent modifications of DNA and histone proteins that involve hundreds of enzymes that add, read, or delete these epigenetic modifications that are relevant for self-renewal and differentiation of mesenchymal stem cells, skeletal stem cells and osteoblasts during osteogenesis.
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Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada; CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada.
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | | | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Andre J van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
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3
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Daneshian Y, Lewallen EA, Badreldin AA, Dietz AB, Stein GS, Cool SM, Ryoo HM, Cho YD, van Wijnen AJ. Fundamentals and Translational Applications of Stem Cells and Biomaterials in Dental, Oral and Craniofacial Regenerative Medicine. Crit Rev Eukaryot Gene Expr 2024; 34:37-60. [PMID: 38912962 DOI: 10.1615/critreveukaryotgeneexpr.2024053036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Regenerative dental medicine continuously expands to improve treatments for prevalent clinical problems in dental and oral medicine. Stem cell based translational opportunities include regenerative therapies for tooth restoration, root canal therapy, and inflammatory processes (e.g., periodontitis). The potential of regenerative approaches relies on the biological properties of dental stem cells. These and other multipotent somatic mesenchymal stem cell (MSC) types can in principle be applied as either autologous or allogeneic sources in dental procedures. Dental stem cells have distinct developmental origins and biological markers that determine their translational utility. Dental regenerative medicine is supported by mechanistic knowledge of the molecular pathways that regulate dental stem cell growth and differentiation. Cell fate determination and lineage progression of dental stem cells is regulated by multiple cell signaling pathways (e.g., WNTs, BMPs) and epigenetic mechanisms, including DNA modifications, histone modifications, and non-coding RNAs (e.g., miRNAs and lncRNAs). This review also considers a broad range of novel approaches in which stem cells are applied in combination with biopolymers, ceramics, and composite materials, as well as small molecules (agonistic or anti-agonistic ligands) and natural compounds. Materials that mimic the microenvironment of the stem cell niche are also presented. Promising concepts in bone and dental tissue engineering continue to drive innovation in dental and non-dental restorative procedures.
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Affiliation(s)
- Yasaman Daneshian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | - Amr A Badreldin
- Laboratory of Molecular Signaling, Division of Oral and Systemic Health Sciences, School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Allan B Dietz
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Simon M Cool
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Hyun-Mo Ryoo
- School of Dentistry, Seoul National University, 28 Yeonkun-dong, Chongro-gu Seoul, 110-749, Republic of Korea
| | - Young Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, 101 Daehak‑no, Jongno‑gu, Seoul 03080, Republic of Korea
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
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Gordon JAR, Tye CE, Banerjee B, Ghule PN, van Wijnen AJ, Kabala FS, Page NA, Falcone MM, Stein JL, Stein GS, Lian JB. LINC01638 sustains human mesenchymal stem cell self-renewal and competency for osteogenic cell fate. Sci Rep 2023; 13:20314. [PMID: 37985890 PMCID: PMC10662126 DOI: 10.1038/s41598-023-46202-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023] Open
Abstract
The skeleton forms from multipotent human mesenchymal stem cells (hMSCs) competent to commit to specific lineages. Long noncoding RNAs (lncRNAs) have been identified as key epigenetic regulators of tissue development. However, regulation of osteogenesis by lncRNAs as mediators of commitment to the bone phenotype is largely unexplored. We focused on LINC01638, which is highly expressed in hMSCs and has been studied in cancers, but not in regulating osteogenesis. We demonstrated that LINC01638 promotes initiation of the osteoblast phenotype. Our findings reveal that LINC01638 is present at low levels during the induction of osteoblast differentiation. CRISPRi knockdown of LINC01638 in MSCs prevents osteogenesis and alkaline phosphatase expression, inhibiting osteoblast differentiation. This resulted in decreased MSC growth rate, accompanied by double-strand breaks, DNA damage, and cell senescence. Transcriptome profiling of control and LINC01638-depleted hMSCs identified > 2000 differentially expressed mRNAs related to cell cycle, cell division, spindle formation, DNA repair, and osteogenesis. Using ChIRP-qPCR, molecular mechanisms of chromatin interactions revealed the LINC01638 locus (Chr 22) includes many lncRNAs and bone-related genes. These novel findings identify the obligatory role for LINC01638 to sustain MSC pluripotency regulating osteoblast commitment and growth, as well as for physiological remodeling of bone tissue.
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Affiliation(s)
- Jonathan A R Gordon
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Coralee E Tye
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | | | - Prachi N Ghule
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Fleur S Kabala
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Natalie A Page
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Michelle M Falcone
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Janet L Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Jane B Lian
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA.
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
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5
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Gordon J, Tye CE, Banerjee B, Ghule PN, Wijnen AJ, Kabala FS, Page NA, Falcone MM, Stein JL, Stein GS, Lian JB. LINC01638 Sustains Human Mesenchymal Stem Cell Self-Renewal and Competency for Osteogenic Cell Fate. RESEARCH SQUARE 2023:rs.3.rs-3210911. [PMID: 37693373 PMCID: PMC10491330 DOI: 10.21203/rs.3.rs-3210911/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The skeleton forms from multipotent human mesenchymal stem cells (hMSCs) competent to commit to specific lineages. Long noncoding RNAs (lncRNAs) have been identified as key epigenetic regulators of tissue development. However, regulation of osteogenesis by lncRNAs as mediators of commitment to the bone phenotype is largely unexplored. We focused on LINC01638, which is highly expressed in hMSCs and has been studied in cancers, but not in regulating osteogenesis. We demonstrated that LINC01638 promotes initiation of the osteoblast phenotype. Our findings reveal that LINC01638 is present at low levels during the induction of osteoblast differentiation. CRISPRi knockdown of LINC01638 in MSCs prevents osteogenesis and alkaline phosphatase expression, inhibiting osteoblast differentiation. This resulted in decreased MSC cell growth rate, accompanied by double-strand breaks, DNA damage, and cell senescence. Transcriptome profiling of control and LINC01638-depleted hMSCs identified > 2,000 differentially expressed mRNAs related to cell cycle, cell division, spindle formation, DNA repair, and osteogenesis. Using ChIRP-qPCR, molecular mechanisms of chromatin interactions revealed the LINC01638 locus (Chr 22) includes many lncRNAs and bone-related genes. These novel findings identify the obligatory role for LINC01638 to sustain MSC pluripotency regulating osteoblast commitment and growth, as well as for physiological remodeling of bone tissue.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gary S Stein
- University of Vermont, Larner College of Medicine
| | - Jane B Lian
- University of Vermont, Larner College of Medicine
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Xu G, Wang H, Zhuang Y, Lin Q, Li Y, Cai Z, Lin G, Liu W. Identification of a ceRNA Network Driven by Copy Number Variations in Esophageal Cancer. J NIPPON MED SCH 2023; 90:426-438. [PMID: 38246614 DOI: 10.1272/jnms.jnms.2023_90-611] [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] [Indexed: 01/23/2024]
Abstract
BACKGROUND Copy number variation (CNV) is associated with progression of esophageal cancer (EC), a common gastrointestinal neoplasm. METHODS Using sequencing data, CNV data, and clinical data of EC transcriptome samples obtained from public databases, we performed differential expression analysis on sequencing data. Differentially expressed CNV-driven lncRNAs were screened using the chi-square test, and CNV-driven lncRNA-associated miRNAs and mRNAs were predicted. Cytoscape software was then used to construct ceRNA networks. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to investigate biological functions of mRNAs in the ceRNA network. Survival curves were plotted to explore correlations between lncRNAs in the ceRNA network and overall survival of CNV patients. Multiple databases were used to predict lncRNAs-related drugs. RESULTS A dysregulated lncRNA-associated ceRNA network driven by CNV in EC, including 11 lncRNAs, 11 miRNAs and 159 mRNAs, was constructed. Downstream enrichment of mRNAs was related to biological processes such as extracellular matrix organization, indicating that these mRNAs mainly participate in intercellular exchange between tumor cells. Additionally, expression of all lncRNAs in the ceRNA network, except LINC00950, LINC01270 and MIR181A1HG, was correlated with patients' CNV. In addition, none of the 11 lncRNAs was significantly correlated with overall survival of CNV patients. CH5424802 and PD-033299CNV mainly affected the RTK signaling pathway and the cell cycle of tumor cells via RP11-180N14.1 and RP11-273 G15.2 in the ceRNA network. CONCLUSIONS This study identified 11 CNV-driven lncRNAs that might affect EC development, 2 of which have promising effects if applied to drug treatment. These findings might assist in identifying novel treatments for EC.
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Affiliation(s)
- Guoxi Xu
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Huaishuai Wang
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Yixiang Zhuang
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Qiyi Lin
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Yinlin Li
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Zhicong Cai
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Gaofeng Lin
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Weibo Liu
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
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