1
|
Taşdelen E, Sezer A, An I. A founder deletion in ECM1 of 1163 bp causes lipoid proteinosis in the southeast region of Turkiye. Am J Med Genet A 2024:e63782. [PMID: 38842389 DOI: 10.1002/ajmg.a.63782] [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: 03/14/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024]
Abstract
Lipoid proteinosis (LP) is an inherited disorder characterized by the accumulation of hyaline-like material in the skin, oral cavity, and larynx. The primary symptoms include hoarseness, restricted tongue movements, and various skin lesions. LP is caused by biallelic pathogenic variants in the ECM1 gene. We studied 20 patients from nine different families with LP, 19 of whom are from Şanlıurfa in the southeastern region of Turkiye. Overall, the clinical features of the patient cohort were consistent with those mentioned in the literature, except for one exhibited an atrophoderma vermiculatum-like lesion, which is atypical for LP. The clinical exome sequencing analysis revealed three different homozygous variants in the ECM1 gene (NM_004425). While c.1246C>T p.(Arg416*) on Exon 8 and c.806G>A p.(Cys269Tyr) on Exon 7 were detected in 1 patient each, an intragenic deletion of 1163 base-pairs including Exons 9 and 10 (c.1304 + 33_*300del) was identified in 18 patients from 7 unrelated families. The haplotype analysis of the deletion variant indicated a founder effect in the families from the Şanlıurfa province of Turkiye. Based on all this information, copy number variation analysis is recommended for patients with LP. In addition to this rare observation, this study represents the largest examination of the molecular spectrum of LP patients in Turkiye, alongside the clinical spectrum.
Collapse
Affiliation(s)
- Elifcan Taşdelen
- Department of Medical Genetics, Ankara Etlik City Hospital, Ankara, Turkey
- Department of Medical Genetics, Sanliurfa Education and Research Hospital, Sanliurfa, Turkey
| | - Abdullah Sezer
- Department of Medical Genetics, Ankara Etlik City Hospital, Ankara, Turkey
| | - Isa An
- Department of Dermatology, Sanliurfa Education and Research Hospital, Sanliurfa, Turkey
| |
Collapse
|
2
|
Sun Y, Huang Y, Hao Z, Zhang S, Tian Q. MRLC controls apoptotic cell death and functions to regulate epidermal development during planarian regeneration and homeostasis. Cell Prolif 2024; 57:e13524. [PMID: 37357415 PMCID: PMC10771114 DOI: 10.1111/cpr.13524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/27/2023] Open
Abstract
Adult stem cells (ASCs) are pluripotent cells with the capacity to self-renew and constantly replace lost cells due to physiological turnover or injury. Understanding the molecular mechanisms of the precise coordination of stem cell proliferation and proper cell fate decision is important to regeneration and organismal homeostasis. The planarian epidermis provides a highly tractable model to study ASC complex dynamic due to the distinct spatiotemporal differentiation stages during lineage development. Here, we identified the myosin regulatory light chain (MRLC) homologue in the Dugesia japonica transcriptome. We found high expression levels of MRLC in wound region during regeneration and also expressed in late epidermal progenitors as an essential regulator of the lineage from neoblasts to mature epidermal cells. We investigated the function of MRLC using in situ hybridization, real-time polymerase chain reaction and double fluorescent and uncovered the potential mechanism. Knockdown of MRLC leads to a remarkable increase in cell death, causes severe abnormalities during regeneration and homeostasis and eventually leads to animal death. The global decrease in epidermal cell in MRLC RNAi animals induces accelerated epidermal proliferation and differentiation. Additionally, we find that MRLC is co-expressed with cdc42 and acts cooperatively to control the epidermal lineage development by affecting cell death. Our results uncover an important role of MRLC, as an inhibitor of apoptosis, involves in epidermal development.
Collapse
Affiliation(s)
- Yujia Sun
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yongding Huang
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Zhitai Hao
- Department of Biochemistry and Molecular PharmacologyNew York University, School of MedicineNew YorkUSA
| | - Shoutao Zhang
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
- Longhu Laboratory of Advanced ImmunologyZhengzhouHenanChina
| | - Qingnan Tian
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| |
Collapse
|
3
|
Roso-Mares A, Andújar I, Díaz Corpas T, Sun BK. Non-coding RNAs as skin disease biomarkers, molecular signatures, and therapeutic targets. Hum Genet 2023:10.1007/s00439-023-02588-4. [PMID: 37580609 DOI: 10.1007/s00439-023-02588-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/23/2023] [Indexed: 08/16/2023]
Abstract
Non-coding RNAs (ncRNAs) are emerging as biomarkers, molecular signatures, and therapeutic tools and targets for diseases. In this review, we focus specifically on skin diseases to highlight how two classes of ncRNAs-microRNAs and long noncoding RNAs-are being used to diagnose medical conditions of unclear etiology, improve our ability to guide treatment response, and predict disease prognosis. Furthermore, we explore how ncRNAs are being used as both as drug targets and associated therapies have unique benefits, risks, and challenges to development, but offer a distinctive promise for improving patient care and outcomes.
Collapse
Affiliation(s)
- Andrea Roso-Mares
- Department of Dermatology, University of California San Diego, San Diego, CA, USA
- Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Isabel Andújar
- Department of Pharmacology, University of Valencia, Valencia, Spain
| | - Tania Díaz Corpas
- Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Department of Dermatology, Hospital Dr Peset, Valencia, Spain
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego, San Diego, CA, USA.
| |
Collapse
|
4
|
Chen Z, Chu X, Xu J. Detection and analysis of long noncoding RNA expression profiles related to epithelial-mesenchymal transition in keloids. Biomed Eng Online 2022; 21:2. [PMID: 35012558 PMCID: PMC8751032 DOI: 10.1186/s12938-022-00976-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/03/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The role of epithelial-mesenchymal transition (EMT) in the pathogenesis of keloids is currently raising increasing attention. Long noncoding RNAs (lncRNAs) govern a variety of biological processes, such as EMT, and their dysregulation is involved in many diseases including keloid disease. The aim of this study was to identify differentially expressed EMT-related lncRNAs in keloid tissues versus normal tissues and to interpret their functions. RESULTS Eleven lncRNAs and 16 mRNAs associated with EMT were identified to have differential expression between keloid and normal skin tissues (fold change > 1.5, P < 0.05). Gene Ontology (GO) analysis showed that these differentially expressed mRNAs functioned in the extracellular matrix, protein binding, the positive regulation of cellular processes, the Set1C/COMPASS complex and histone acetyltransferase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these mRNAs are involved in pathways in cancer. The lncRNA, XLOC_000587 may promote cell proliferation and migration by enhancing the expression of ENAH, while AF268386 may facilitate the invasive growth of keloids by upregulating DDR2. CONCLUSIONS We characterized the differential expression profiles of EMT-related lncRNAs and mRNAs in keloids, which may contribute to preventing the occurrence and development of keloids by targeting the corresponding signaling pathways. These lncRNAs and mRNAs may provide biomarkers for keloid diagnosis and serve as potential targets for the treatment of this disease.
Collapse
Affiliation(s)
- Zhixiong Chen
- Department of Plastic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, People's Republic of China
| | - Xi Chu
- Department of Plastic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, People's Republic of China
- Zhejiang University School of Medicine, Hangzhou, 310000, People's Republic of China
| | - Jinghong Xu
- Department of Plastic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, People's Republic of China.
| |
Collapse
|
5
|
Shefler A, Patrick MT, Wasikowski R, Chen J, Sarkar MK, Gudjonsson JE, Tsoi LC. Skin-Expressing lncRNAs in Inflammatory Responses. Front Genet 2022; 13:835740. [PMID: 35559048 PMCID: PMC9086234 DOI: 10.3389/fgene.2022.835740] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/08/2022] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have attracted attention for their potential roles in modulating keratinocyte differentiation and inflammatory response; however, for many identified skin-expressing lncRNAs, there is no comprehensive characterization regarding their biological roles. In addition, the reported expression profiles for lncRNAs can be ambiguous due to their low-expressing nature. The objective of this review is to utilize large scale genomic data to characterize the prominent skin-expressing lncRNAs, aiming to provide additional insights for their potential roles in the pathology of inflammatory skin of psoriasis and atopic dermatitis by integrating in vitro and in vivo data. We highlighted the different skin-expressing lncRNAs, including H19, which is significantly down-regulated in lesional skin of AD/psoriasis and upon cytokine stimulation in keratinocytes; it is also negatively correlated with CYP1A1 (r = -0.75, p = 8 × 10-73), a gene involved in drug metabolism and skin barrier homeostasis, in keratinocytes. In addition, SPRR2C, a potential regulator that modulates IL-22 stimulation, was upregulated in both atopic dermatitis and psoriasis lesional skin and was also downstream of the IL-17A and IL-17 + TNF signaling in keratinocytes. Using scRNAseq, we further revealed the cell type specificity of lncRNAs, including basal-expressing nature of H19 in the epidermis. Interestingly, instead of having cell type specific expression profile, we found few lncRNAs that are express across different cell types in skin, including MALAT1, NEAT1, and GAS5. While lncRNAs in general have lower expression, our results combining in vitro and in vivo experimental data demonstrate how some of these lncRNAs can play mediator roles in the cytokine-stimulated pathway.
Collapse
Affiliation(s)
- Alanna Shefler
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Rachael Wasikowski
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jiahan Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
| | - Mrinal K. Sarkar
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Lam C. Tsoi,
| |
Collapse
|
6
|
Klopot A, Baida G, Kel A, Tsoi LC, Perez White BE, Budunova I. Transcriptome analysis reveals intrinsic pro-inflammatory signaling in healthy African American skin. J Invest Dermatol 2021; 142:1360-1371.e15. [PMID: 34757068 PMCID: PMC9038646 DOI: 10.1016/j.jid.2021.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/23/2022]
Abstract
Differences in morphology and physiology of darkly pigmented compared to lightly pigmented skin are well recognized. There are also disparities in prevalence and clinical features for many inflammatory skin diseases including atopic dermatitis and psoriasis; however, the underlying mechanisms are largely unknown. We compared the baseline gene expression in full thickness skin biopsies from healthy individuals self-reporting as African American (AA) or White Non-Hispanic (WNH). Extensively validated RNA-Seq analysis identified 570 differentially expressed genes (DEG) in AA skin including immunoglobulins and their receptors such as FCER1G; pro-inflammatory genes such as TNFα, IL-32; EDC (epidermal differentiation cluster) and keratin genes. DEGs were functionally enriched for inflammatory responses, keratinization, cornified envelope formation. RNA-seq analysis of 3D human skin equivalents (HSE) made from AA and WNH primary keratinocytes revealed 360 DEGs (some shared with skin) which were enriched by similar functions. AA HSE appeared more responsive to TNFα pro-inflammatory effects. Finally, AA-specific DEGs in skin and HSE significantly overlapped with molecular signatures of skin in AD and psoriasis patients. Overall, these findings suggest the existence of intrinsic pro-inflammatory circuits in AA keratinocytes/skin that may account for disease disparities and will help to build a foundation for the development of targeted skin disease prevention.
Collapse
Affiliation(s)
- Anna Klopot
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Gleb Baida
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Alexander Kel
- geneXplain GmbH, Wolfenbüttel, Germany; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Bethany E Perez White
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Irina Budunova
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| |
Collapse
|
7
|
Rusek M, Krasowska D. Non-Coding RNA in Systemic Sclerosis: A Valuable Tool for Translational and Personalized Medicine. Genes (Basel) 2021; 12:1296. [PMID: 34573278 PMCID: PMC8471866 DOI: 10.3390/genes12091296] [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: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors are heritable and ultimately play a role in modulating gene expression and, thus, in regulating cell functions. Non-coding RNAs have growing recognition as novel biomarkers and crucial regulators of pathological conditions in humans. Their characteristic feature is being transcribed in a tissue-specific pattern. Now, there is emerging evidence that lncRNAs have been identified to be involved in the differentiation of human skin, wound healing, fibrosis, inflammation, and immunological response. Systemic sclerosis (SSc) is a heterogeneous autoimmune disease characterized by fibrosis, vascular abnormalities, and immune system activation. The pathogenesis remains elusive, but clinical manifestations reveal autoimmunity with the presence of specific autoantibodies, activation of innate and adaptive immunity, vascular changes, and active deposition of extracellular matrix components leading to fibrosis. The use of multi-omics studies, including NGS, RNA-seq, or GWAS, has proposed that the non-coding genome may be a significant player in its pathogenesis. Moreover, it may unravel new therapeutic targets in the future. The aim of this review is to show the pathogenic role of long non-coding RNAs in systemic sclerosis. Investigation of these transcripts' functions has the potential to elucidate the molecular pathology of SSc and provide new opportunities for drug-targeted therapy for this disorder.
Collapse
Affiliation(s)
- Marta Rusek
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
- Department of Pathophysiology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
| |
Collapse
|
8
|
Lee J, Wu Y, Harada BT, Li Y, Zhao J, He C, Ma Y, Wu X. N 6 -methyladenosine modification of lncRNA Pvt1 governs epidermal stemness. EMBO J 2021; 40:e106276. [PMID: 33729590 DOI: 10.15252/embj.2020106276] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 11/09/2022] Open
Abstract
Dynamic chemical modifications of RNA represent novel and fundamental mechanisms that regulate stemness and tissue homeostasis. Rejuvenation and wound repair of mammalian skin are sustained by epidermal progenitor cells, which are localized within the basal layer of the skin epidermis. N6 -methyladenosine (m6 A) is one of the most abundant modifications found in eukaryotic mRNA and lncRNA (long noncoding RNA). In this report, we survey changes of m6 A RNA methylomes upon epidermal differentiation and identify Pvt1, a lncRNA whose m6 A modification is critically involved in sustaining stemness of epidermal progenitor cells. With genome-editing and a mouse genetics approach, we show that ablation of m6 A methyltransferase or Pvt1 impairs the self-renewal and wound healing capability of skin. Mechanistically, methylation of Pvt1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells. Our study presents a global view of epitranscriptomic dynamics that occur during epidermal differentiation and identifies the m6 A modification of Pvt1 as a key signaling event involved in skin tissue homeostasis and wound repair.
Collapse
Affiliation(s)
- Jimmy Lee
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Yuchen Wu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bryan T Harada
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuanyuan Li
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Jing Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyang Wu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
9
|
Abstract
In situ hybridization (ISH) and fluorescence in situ hybridization (FISH) techniques enable us to detect the expression of a specific RNA in fixed cells or tissue sections. Here, we describe in detail two procedures adjusted to reveal specifically lncRNAs in normal human keratinocytes and in skin tissue samples. Examples of the results obtained by the two different approaches are also shown.
Collapse
|
10
|
Kashyap MP, Sinha R, Mukhtar MS, Athar M. Epigenetic regulation in the pathogenesis of non-melanoma skin cancer. Semin Cancer Biol 2020; 83:36-56. [PMID: 33242578 DOI: 10.1016/j.semcancer.2020.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Understanding of cancer with the help of ever-expanding cutting edge technological tools and bioinformatics is revolutionizing modern cancer research by broadening the space of discovery window of various genomic and epigenomic processes. Genomics data integrated with multi-omics layering have advanced cancer research. Uncovering such layers of genetic mutations/modifications, epigenetic regulation and their role in the complex pathophysiology of cancer progression could lead to novel therapeutic interventions. Although a plethora of literature is available in public domain defining the role of various tumor driver gene mutations, understanding of epigenetic regulation of cancer is still emerging. This review focuses on epigenetic regulation association with the pathogenesis of non-melanoma skin cancer (NMSC). NMSC has higher prevalence in Caucasian populations compared to other races. Due to lack of proper reporting to cancer registries, the incidence rates for NMSC worldwide cannot be accurately estimated. However, this is the most common neoplasm in humans, and millions of new cases per year are reported in the United States alone. In organ transplant recipients, the incidence of NMSC particularly of squamous cell carcinoma (SCC) is very high and these SCCs frequently become metastatic and lethal. Understanding of solar ultraviolet (UV) light-induced damage and impaired DNA repair process leading to DNA mutations and nuclear instability provide an insight into the pathogenesis of metastatic neoplasm. This review discusses the recent advances in the field of epigenetics of NMSCs. Particularly, the role of DNA methylation, histone hyperacetylation and non-coding RNA such as long-chain noncoding (lnc) RNAs, circular RNAs and miRNA in the disease progression are summarized.
Collapse
Affiliation(s)
- Mahendra Pratap Kashyap
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rajesh Sinha
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohammad Athar
- UAB Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
11
|
Lazăr AD, Dinescu S, Costache M. The Non-Coding Landscape of Cutaneous Malignant Melanoma: A Possible Route to Efficient Targeted Therapy. Cancers (Basel) 2020; 12:cancers12113378. [PMID: 33203119 PMCID: PMC7696690 DOI: 10.3390/cancers12113378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
Considered to be highly lethal if not diagnosed in early stages, cutaneous malignant melanoma is among the most aggressive and treatment-resistant human cancers, and its incidence continues to rise, largely due to ultraviolet radiation exposure, which is the main carcinogenic factor. Over the years, researchers have started to unveil the molecular mechanisms by which malignant melanoma can be triggered and sustained, in order to establish specific, reliable biomarkers that could aid the prognosis and diagnosis of this fatal disease, and serve as targets for development of novel efficient therapies. The high mutational burden and heterogeneous nature of melanoma shifted the main focus from the genetic landscape to epigenetic and epitranscriptomic modifications, aiming at elucidating the role of non-coding RNA molecules in the fine tuning of melanoma progression. Here we review the contribution of microRNAs and lncRNAs to melanoma invasion, metastasis and acquired drug resistance, highlighting their potential for clinical applications as biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Andreea D. Lazăr
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
- Correspondence:
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
| |
Collapse
|
12
|
Khan AQ, Ahmad F, Raza SS, Zarif L, Siveen KS, Sher G, Agha MV, Rashid K, Kulinski M, Buddenkotte J, Uddin S, Steinhoff M. Role of non-coding RNAs in the progression and resistance of cutaneous malignancies and autoimmune diseases. Semin Cancer Biol 2020; 83:208-226. [PMID: 32717336 DOI: 10.1016/j.semcancer.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
|
13
|
Wang W, Liu G, Liu M, Li X. Long non-coding RNA SNHG7 promotes malignant melanoma progression through negative modulation of miR-9. Histol Histopathol 2020; 35:973-981. [PMID: 32365219 DOI: 10.14670/hh-18-225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Long non-coding small nucleolar RNA host gene 7 (lncRNA SNHG7) was verified to act as an onco-gene in human cancers. Nevertheless, the role of SNHG7 in malignant melanoma remains elusive. The present study showed an increase of SNHG7 expression in malignant melanoma tissues and cell lines. Besides, SNHG7 knockdown inhibited proliferation and migration in malignant melanoma cells. Bioinformatics analysis demonstrated that SNHG7 functions as a molecular sponge for miR-9 in biological behavior of melanoma cells. And miR-9 could inhibit the expression of PI3KR3 by binding with the 3'-UTR. Furthermore, PI3KR3, pAKT, cyclin D1 and Girdin expression was down-regulated after SNHG7 knockdown by siRNA. In addition, SNHG7 knockdown decreased xenograft growth in vivo. Taken together, this research demonstrated that SNHG7 was an oncogene in malignant melanoma, providing a novel insight for the pathogenesis and new potential therapeutic target for malignant melanoma.
Collapse
Affiliation(s)
- Wendi Wang
- Department of Plastic and Burn Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Guangjing Liu
- Department of Plastic and Burn Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Man Liu
- Department of Plastic and Burn Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Xiaobing Li
- Department of Plastic and Burn Surgery, Tianjin First Center Hospital, Tianjin, China.
| |
Collapse
|
14
|
Duan Q, Wang G, Wang M, Chen C, Zhang M, Liu M, Shao Y, Zheng Y. LncRNA RP6-65G23.1 accelerates proliferation and inhibits apoptosis via p-ERK1/2/p-AKT signaling pathway on keratinocytes. J Cell Biochem 2020; 121:4580-4589. [PMID: 32065443 DOI: 10.1002/jcb.29685] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022]
Abstract
Long non-coding RNAs (LncRNAs) play essential roles in the development of various diseases including hepatic carcinoma, melanoma, and psoriasis. Meanwhile, lncRNA-RP6-65G23.1 was upregulated in psoriasis. However, it is still unclear whether lncRNA-RP6-65G23.1 expression is upregulated and contributes to keratinocytes proliferation and apoptosis, and which mechanisms are responsible for these processes. The aims of this study are to address these issues. RP6-65G23.1 was significantly upregulated in M5-stimulated keratinocytes and stimulated the proliferation and inhibited the apoptosis of HaCaT cells. Knockdown of RP6-65G23.1 resulted in defects of growth and increased rates of apoptosis in HaCaT cells, while overexpression of RP6-65G23.1 manifested the opposite effects. Consistently, the expression of antiapoptotic proteins Bcl-xl and Bcl2 were decreased in RP6-65G23.1-knockdown cells but elevated in RP6-65G23.1 overexpression cells. In addition, RP6-65G23.1 depletion blunted the activity of extracellular regulated kinase 1/2 (ERK1/2) and AKT signaling pathways and induced G1 /S-growth arrest. By contrast, overexpression of RP6-65G23.1 activates the ERK1/2 and AKT signaling pathways and inhibits the expression of p21 and p27 in an AKT-dependent manner leading to promote the G1/S progression. Our results suggested that lncRNA-RP6-65G23.1 would contribute to the pathogenesis of psoriasis by regulating the proliferation and apoptosis of keratinocytes via the p-ERK1/2 and p-AKT pathways.
Collapse
Affiliation(s)
- Qiqi Duan
- Department of Dermatology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Guorong Wang
- Department of General Surgery, ShaanXi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Dermatology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Caifeng Chen
- Department of Dermatology, Fujian Provincial Hospital, Fuzhou, China
| | - Mengdi Zhang
- Department of Dermatology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Meng Liu
- Department of Dermatology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Yongping Shao
- Frontier Institute of Science and Technology and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yan Zheng
- Department of Dermatology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| |
Collapse
|
15
|
Long noncoding RNA X-inactive specific transcript promotes malignant melanoma progression and oxaliplatin resistance. Melanoma Res 2019; 29:254-262. [PMID: 30640294 DOI: 10.1097/cmr.0000000000000560] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Long noncoding RNA X-inactive specific transcript (XIST) was confirmed to participate in the development of many cancers. However, the function of XIST in malignant melanoma (MM) remained largely unknown. In the current study, we found that the XIST expression level was upregulated in MM tissues and cell lines. In addition, the growth rate of MM cells transfected with silencing XIST was significantly decreased compared with that with silencing normal control. XIST knockdown inhibited proliferation and migration in MM cells and increased the oxaliplatin sensitivity of oxaliplatin-resistant MM cells. Bioinformatics analysis showed that XIST acts as a molecular sponge for miR-21 and miR-21 directly targets with 3'-UTR of PI3KR1. Furthermore, XIST knockdown inhibited PI3KRI and AKT expression, and promoted Bcl-2 and Bax expression. In short, the current study showed that XIST was a crucial regulator in progression and oxaliplatin resistance of MM, providing a novel insight into the pathogenesis and underlying therapeutic target for MM.
Collapse
|
16
|
Transcriptomic Network Interactions in Human Skin Treated with Topical Glucocorticoid Clobetasol Propionate. J Invest Dermatol 2019; 139:2281-2291. [PMID: 31247200 PMCID: PMC6814545 DOI: 10.1016/j.jid.2019.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 12/19/2022]
Abstract
Glucocorticoids are the most frequently used anti-inflammatory drugs in dermatology. However, the molecular signature of glucocorticoids and their receptor in human skin is largely unknown. Our validated bioinformatics analysis of human skin transcriptome induced by topical glucocorticoid clobetasol propionate (CBP) in healthy volunteers identified numerous unreported glucocorticoid-responsive genes, including over a thousand noncoding RNAs. We observed sexual and racial dimorphism in the CBP response including a shift toward IFN-α/IFN-γ and IL-6/Jak/Signal transducer and activator of transcription (STAT) 3 signaling in female skin; and a larger response to CBP in African-American skin. Weighted gene coexpression network analysis unveiled a dense skin network of 41 transcription factors including circadian Kruppel-like factor 9 (KLF9), and ∼260 of their target genes enriched for functional pathways representative of the entire CBP transcriptome. Using keratinocytes with Kruppel-like factor 9 knockdown, we revealed a feedforward loop in glucocorticoid receptor signaling, previously unreported. Interestingly, many of the CBP-regulated transcription factors were involved in the control of development, metabolism, circadian clock; and 80% of them were associated with skin aging showing similarities between glucocorticoid-treated and aged skin. Overall, these findings indicate that glucocorticoid receptor acts as an important regulator of gene expression in skin-both at the transcriptional and posttranscriptional level-via multiple mechanisms including regulation of noncoding RNAs and multiple core transcription factors.
Collapse
|
17
|
Fu C, Chen J, Lu J, Pei S, Hu S, Jiang L, Ding Y, Huang L, Xiang H, Huang J, Zeng Q. Downregulation of
TUG
1 promotes melanogenesis and
UVB
‐induced melanogenesis. Exp Dermatol 2019; 28:730-733. [PMID: 30924963 DOI: 10.1111/exd.13929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 03/18/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Chuhan Fu
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Jing Chen
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Jianyun Lu
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Shiyao Pei
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Shuanghai Hu
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Ling Jiang
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Yufang Ding
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Lihua Huang
- Central Laboratory Third Xiangya Hospital of Central South University Changsha China
| | - Hong Xiang
- Central Laboratory Third Xiangya Hospital of Central South University Changsha China
| | - Jinhua Huang
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| | - Qinghai Zeng
- Department of Dermatology Third Xiangya Hospital of Central South University Changsha China
| |
Collapse
|
18
|
Panda S, Setia M, Kaur N, Shepal V, Arora V, Singh DK, Mondal A, Teli A, Tathode M, Gajula R, Padhy LC, Shiras A. Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins. PLoS Biol 2018; 16:e2004204. [PMID: 30296263 PMCID: PMC6193740 DOI: 10.1371/journal.pbio.2004204] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/18/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs constitute a major fraction of the eukaryotic transcriptome, and together with proteins, they intricately fine-tune various growth regulatory signals to control cellular homeostasis. Here, we describe the functional characterisation of a novel pair of long intergenic noncoding RNAs (lincRNAs) comprised of complementary, fully overlapping sense and antisense transcripts Genomic Instability Inducing RNA (Ginir) and antisense RNA of Ginir (Giniras), respectively, from mouse cells. This transcript pair is expressed in a spatiotemporal manner during embryonic development. The individual levels of the sense and antisense transcripts are finely balanced during embryonic growth and in adult tissues. Functional studies of the individual transcripts performed using overexpression and knock-down strategies in mouse cells has led to the discovery that Ginir RNA is a regulator of cellular proliferation and can act as an oncogene having a preeminent role in malignant transformation. Mechanistically, we demonstrate that the oncogenic function of Ginir is mediated by its interaction with centrosomal protein 112 (Cep112). Additionally, we establish here a specific interaction between Cep112 with breast cancer type 1 susceptibility protein (Brca1), another centrosome-associated protein. Next, we prove that the mutual interaction between Cep112 with Brca1 is significant for mitotic regulation and maintenance of genomic stability. Furthermore, we demonstrate that the Cep112 protein interaction with Brca1 protein is impaired when an elevated level of Ginir RNA is present in the cells, resulting in severe deregulation and abnormality in mitosis, leading to malignant transformation. Inhibiting the Ginir RNA function in transformed cells attenuates transformation and restores genomic stability. Together, these findings unravel, to our knowledge, a hitherto-unknown mechanism of oncogenesis mediated by a long noncoding RNA and establishes a unique role of Cep112–Brca1 interaction being modulated by Ginir RNA in maintaining mitotic fidelity. The growth of multicellular organisms is tightly regulated by cellular homeostasis mediated by cell division. This is achieved with the help of various proteins acting in a highly coordinated manner via intricately woven intercellular signalling pathways, which regulate cell division. Here, we identify a long noncoding RNA pair, which we named Genomic Instability Inducing RNA (Ginir)/antisense RNA of Ginir (Giniras), and explore its function in cellular homeostasis. We show that this RNA pair is expressed in a spatiotemporally regulated manner during development and is enriched in the brain. We find that Ginir acts as a dominant oncogene when Ginir transcript levels are overexpressed in mouse fibroblasts and that centrosomal protein 112 (Cep112) is its interacting protein partner. We also report that Cep112 interacts with breast cancer type 1 susceptibility protein (Brca1), a protein well known for its role in genome surveillance. Our data reveal that interactions between these two proteins are perturbed in the presence of excessive levels of Ginir RNA, which results in aberrant mitosis and drives the cells towards neoplastic transformation.
Collapse
Affiliation(s)
- Suchismita Panda
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Meenakshi Setia
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Navjot Kaur
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Varsha Shepal
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Vivek Arora
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Divya Kumari Singh
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Abir Mondal
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - Abhishek Teli
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | | | - Rajendra Gajula
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
| | - L. C. Padhy
- Kalinga Institute of Industrial Technology, (KIIT), Bhubaneswar, India
- * E-mail: (LCP); (AS)
| | - Anjali Shiras
- National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India
- * E-mail: (LCP); (AS)
| |
Collapse
|
19
|
LINC00657 played oncogenic roles in esophageal squamous cell carcinoma by targeting miR-615-3p and JunB. Biomed Pharmacother 2018; 108:316-324. [PMID: 30227324 DOI: 10.1016/j.biopha.2018.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The prognosis of esophageal squamous cell carcinoma (ESCC) is relatively poor due to the absence of efficient treatment. In this manuscript, we have investigated the specific roles and molecular mechanisms of LINC00657 to order to identify novel therapeutic targets for ESCC. METHOD The LINC00657 expression in ESCC tissues and cell lines were evaluated by quantitative real-time PCR. The expression of LINC00657 in ESCC cells was regulated by lentivirus transfection. Online bioinformatics analysis tools were used to predict the potential targets of LINC00657 and miR-615-3p. TCGA database was used to analyze the prognosis of ESCC patients. Transwell, wound healing assay and MTT were performed to investigate the ESCC cells' biological functions. JunB expression was evaluated by Western blot. RESULT LINC00657 was moderately increased in ESCC both in vivo and in vitro and up regulated by irradiation. LINC00657 knockdown could inhibit the migration and proliferation of ESCC cells. And downregulation of LINC00657 significantly enhanced the radio-sensitivity. Moreover, LINC00657 could act as a ceRNA to increase the expression of JunB by binding to miR-615-3p. Meanwhile, overexpression of miR-615-3p resulted in anti-tumor effects and led to the down-regulation of JunB. Survival analysis from TCGA indicated that ESCC patients with higher JunB expression had significant poorer prognosis. CONCLUSION LINC00657 might be involved in regulating ESCC's response to radiation; and it functioned as an oncogene in ESCC by targeting miR-615-3p and JunB, providing novel potential therapeutic targets.
Collapse
|
20
|
Ji K, Fan R, Zhang J, Yang S, Dong C. Long non-coding RNA expression profile in Cdk5-knockdown mouse skin. Gene 2018; 672:195-201. [DOI: 10.1016/j.gene.2018.05.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 01/16/2023]
|
21
|
Lei L, Chen J, Huang J, Lu J, Pei S, Ding S, Kang L, Xiao R, Zeng Q. Functions and regulatory mechanisms of metastasis‐associated lung adenocarcinoma transcript 1. J Cell Physiol 2018; 234:134-151. [PMID: 30132842 DOI: 10.1002/jcp.26759] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/26/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Li Lei
- Department of Dermatology, Xiangya Hospital Central South University Changsha Hunan China
- Department of Hunan Key Laboratory of Skin Cancer and Psoriasis Xiangya Hospital, Central South University Changsha Hunan China
| | - Jing Chen
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Jinhua Huang
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Jianyun Lu
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Shiyao Pei
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Shu Ding
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Liyang Kang
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| | - Rong Xiao
- Department of Dermatology Second Xiangya Hospital, Central South University Changsha Hunan China
| | - Qinghai Zeng
- Department of Dermatology Third Xiangya Hospital, Central South University Changsha Hunan China
| |
Collapse
|
22
|
Hu G, Niu F, Humburg BA, Liao K, Bendi S, Callen S, Fox HS, Buch S. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget 2018; 9:18648-18663. [PMID: 29719633 PMCID: PMC5915100 DOI: 10.18632/oncotarget.24307] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.
Collapse
Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Niu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bree A. Humburg
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sunil Bendi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon Callen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S. Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
23
|
Luan W, Zhou Z, Ni X, Xia Y, Wang J, Yan Y, Xu B. Long non-coding RNA H19 promotes glucose metabolism and cell growth in malignant melanoma via miR-106a-5p/E2F3 axis. J Cancer Res Clin Oncol 2018; 144:531-542. [DOI: 10.1007/s00432-018-2582-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 01/11/2018] [Indexed: 12/15/2022]
|
24
|
Yang L, Lyu L, Wu W, Lei D, Tu Y, Xu D, Feng J, He L. Genome-wide identification of long non-coding RNA and mRNA profiling using RNA sequencing in subjects with sensitive skin. Oncotarget 2017; 8:114894-114910. [PMID: 29383128 PMCID: PMC5777740 DOI: 10.18632/oncotarget.23147] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Sensitive skin (SS) is a condition of subjective cutaneous hyper-reactivity. The role of long non-coding RNAs (lncRNAs) in subjects with SS is unclear. Therefore, the aim of the present study was to provide a comprehensive profile of the mRNAs and lncRNAs in subjects with SS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis presented the characteristics of associated protein-coding genes. In addition, a co-expression network of lncRNA and mRNA was constructed to identify potential underlying regulation targets; the results were verified by quantitative real-time PCR (qRT-PCR) and RNA-seq analyses in patients with SS and normal samples. Compared with the normal skin group, 266 novel lncRNAs and 6750 annotated lncRNAs were identified in the SS group. A total of 71 lncRNA transcripts and 2615 mRNA transcripts were differentially expressed (P < 0.05). The heat signature of the SS samples could be distinguished from the normal skin samples, whereas the majority of the genes that were present in enriched pathways were those that participated in focal adhesion, PI3K-Akt signaling, and cancer-related pathways. Five transcripts were selected for qRT-PCR analysis and the results were consistent with RNA-seq. The results suggested that LNC_000265 may play a role in the epidermal barrier structure of patient with SS. The data suggest novel genes and pathways that may be involved in the pathogenesis of SS and highlight potential targets that could be used for individualized treatment applications.
Collapse
Affiliation(s)
- Li Yang
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lechun Lyu
- Technology Transfer Center, Kunming Medical University, Department of Physiology, Kunming Medical University, Kunming, China
| | - Wenjuan Wu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dongyun Lei
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ying Tu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Xu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiaqi Feng
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li He
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| |
Collapse
|
25
|
Kim KH, Kim HJ, Lee TR. Epidermal long non-coding RNAs are regulated by ultraviolet irradiation. Gene 2017; 637:196-202. [DOI: 10.1016/j.gene.2017.09.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/20/2022]
|
26
|
Luan W, Li R, Liu L, Ni X, Shi Y, Xia Y, Wang J, Lu F, Xu B. Long non-coding RNA HOTAIR acts as a competing endogenous RNA to promote malignant melanoma progression by sponging miR-152-3p. Oncotarget 2017; 8:85401-85414. [PMID: 29156728 PMCID: PMC5689618 DOI: 10.18632/oncotarget.19910] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022] Open
Abstract
HOX transcript antisense RNA (HOTAIR) is associated with the growth and metastasis of many human tumors, but its biological roles in malignant melanoma remain unclear. In this study, we show that HOTAIR is overexpressed in melanoma tissues and cells, especially in metastatic melanoma. High HOTAIR levels correlate with poor prognosis in melanoma patients. We also determined that HOTAIR functions as a competing endogenous RNA (ceRNA) for miR-152-3p. miR-152-3p was decreased and acted as a tumor suppressor in melanoma, and c-MET was the functional target of miR-152-3p. Furthermore, HOTAIR promotes the growth and metastasis of melanoma cells by competitively binding miR-152-3p, which functionally liberates c-MET mRNA and results in the activation of the downstream PI3k/Akt/mTOR signaling pathway. We determined that HOTAIR acts as a ceRNA to promote malignant melanoma progression by sponging miR-152-3p. This finding elucidates a new mechanism for HOTAIR in melanoma development and provides a potential therapeutic target for melanoma patients.
Collapse
Affiliation(s)
- Wenkang Luan
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Rubo Li
- Department of Neurosurgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Liang Liu
- Department of Neurosurgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Ni
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yan Shi
- Department of Neurosurgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yun Xia
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jinlong Wang
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Feng Lu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Bin Xu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| |
Collapse
|
27
|
The Molecular Revolution in Cutaneous Biology: Noncoding RNAs: New Molecular Players in Dermatology and Cutaneous Biology. J Invest Dermatol 2017; 137:e105-e111. [PMID: 28411840 DOI: 10.1016/j.jid.2017.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/10/2015] [Accepted: 02/01/2016] [Indexed: 02/06/2023]
Abstract
Progress in genome sequencing achieved during the last two decades revealed that only about 2% of the genome codes for proteins, while the largest genome fraction is encoding thousands of non-coding RNAs. Non-coding RNAs play indispensable roles in regulating the activity and stability of the genome. Recent research in the area of the non-coding transcriptome signified the crucial roles for RNA regulatory networks in the normal development and their implications in a variety of pathological conditions. Here, recent advances in our understanding of non-coding RNA-mediated regulation of skin development and homeostasis are highlighted, focusing mainly on the regulatory roles of miRNAs and lncRNAs.
Collapse
|
28
|
Yang ZY, Yang F, Zhang YL, Liu B, Wang M, Hong X, Yu Y, Zhou YH, Zeng H. LncRNA-ANCR down-regulation suppresses invasion and migration of colorectal cancer cells by regulating EZH2 expression. Cancer Biomark 2017; 18:95-104. [PMID: 27983539 DOI: 10.3233/cbm-161715] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our study aimed to explore the effects of long noncoding RNA (lncRNA)-ANCR on the invasion and migration of colorectal cancer (CRC) cells by regulating enhancer of zeste homolog 2 (EZH2) expression. CRC tissues and adjacent normal tissues were collected and CRC SW620 cells line and normal human intestinal epithelial cells (HIECs) were incubated. CRC SW620 cells line was transfected with ANCR-siRNA. The expressions of ANCR and EZH2 mRNA were measured by real-time quantitative polymerase chain reaction (RT-qPCR). EZH2 and trimethylation of H3K27 (H3K27me3) protein expressions were detected using Western blotting. The relationship between ANCR and EZH2 was determined through RNA pull-down and co-immunoprecipitation (co-IP) assays. Cell invasion and migration were determined by Trans-well and cell scratch assays. ANCR, EZH2 and H3K27me3 expressions were up-regulated in CRC tissues and SW620 cells (all P < 0.05). After transfected with ANCR-siRNA, SW620 cells showed decreased ANCR expression and EZH2 mRNA and protein expressions (all P < 0.05). According to the results of RNA pull-down and co-IP assays, ANCR could specifically bind to EZH2. The results of Trans-well and cell scratch tests showed that when ANCR expression was decreased, the invasion and migration abilities of SW620 cells significantly declined (both P < 0.05). In conclusion, these results suggest that lncRNA-ANCR could influence the invasion and migration of CRC cells by specifically binding to EZH2.
Collapse
Affiliation(s)
- Zhao-Yang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Fang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ying-Li Zhang
- Department of Internal Medicine, Harbin Red Cross Central Hospital, Harbin, Heilongjiang, China
| | - Bao Liu
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Meng Wang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xuan Hong
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yan Yu
- Department of Sixth Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yao-Hui Zhou
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hai Zeng
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
| |
Collapse
|
29
|
Ziegler C, Kretz M. The More the Merrier-Complexity in Long Non-Coding RNA Loci. Front Endocrinol (Lausanne) 2017; 8:90. [PMID: 28487673 PMCID: PMC5403818 DOI: 10.3389/fendo.2017.00090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/06/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Christian Ziegler
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
- *Correspondence: Markus Kretz,
| |
Collapse
|
30
|
Luan W, Li L, Shi Y, Bu X, Xia Y, Wang J, Djangmah HS, Liu X, You Y, Xu B. Long non-coding RNA MALAT1 acts as a competing endogenous RNA to promote malignant melanoma growth and metastasis by sponging miR-22. Oncotarget 2016; 7:63901-63912. [PMID: 27564100 PMCID: PMC5325412 DOI: 10.18632/oncotarget.11564] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/13/2016] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in tumorigenesis. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), an lncRNAs, is associated with the growth and metastasis of many human tumors, but its biological roles in malignant melanoma remain unclear. In this study, the aberrant up-regulation of MALAT1 was detected in melanoma. We determined that MALAT1 promotes melanoma cells proliferation, invasion and migration by sponging miR-22. MiR-22 was decreased and acted as a tumor suppressor in melanoma, and MMP14 and Snail were the functional targets of miR-22. Furthermore, MALAT1 could modulate MMP14 and Snail by operating as a competing endogenous RNA (ceRNA) for miR-22. The effects of MALAT1 in malignant melanoma is verified using a xenograft model. This finding elucidates a new mechanism for MALAT1 in melanoma development and provides a potential target for melanoma therapeutic intervention.
Collapse
Affiliation(s)
- Wenkang Luan
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lubo Li
- Department of Neurosurgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Shi
- Department of Neurosurgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xuefeng Bu
- Department of General Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yun Xia
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jinlong Wang
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Henry Siaw Djangmah
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaohui Liu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Xu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| |
Collapse
|
31
|
Labott AT, Lopez-Pajares V. Epidermal differentiation gene regulatory networks controlled by MAF and MAFB. Cell Cycle 2016; 15:1405-9. [PMID: 27097296 DOI: 10.1080/15384101.2016.1172148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Numerous regulatory factors in epidermal differentiation and their role in regulating different cell states have been identified in recent years. However, the genetic interactions between these regulators over the dynamic course of differentiation have not been studied. In this Extra-View article, we review recent work by Lopez-Pajares et al. that explores a new regulatory network in epidermal differentiation. They analyze the changing transcriptome throughout epidermal regeneration to identify 3 separate gene sets enriched in the progenitor, early and late differentiation states. Using expression module mapping, MAF along with MAFB, are identified as transcription factors essential for epidermal differentiation. Through double knock-down of MAF:MAFB using siRNA and CRISPR/Cas9-mediated knockout, epidermal differentiation was shown to be impaired both in-vitro and in-vivo, confirming MAF:MAFB's role to activate genes that drive differentiation. Lopez-Pajares and collaborators integrated 42 published regulator gene sets and the MAF:MAFB gene set into the dynamic differentiation gene expression landscape and found that lncRNAs TINCR and ANCR act as upstream regulators of MAF:MAFB. Furthermore, ChIP-seq analysis of MAF:MAFB identified key transcription factor genes linked to epidermal differentiation as downstream effectors. Combined, these findings illustrate a dynamically regulated network with MAF:MAFB as a crucial link for progenitor gene repression and differentiation gene activation.
Collapse
Affiliation(s)
- Andrew T Labott
- a Program in Epithelial Biology, Stanford University , Stanford , CA , USA
| | | |
Collapse
|
32
|
Sand M, Bechara FG, Sand D, Gambichler T, Hahn SA, Bromba M, Stockfleth E, Hessam S. Expression profiles of long noncoding RNAs in cutaneous squamous cell carcinoma. Epigenomics 2016; 8:501-18. [PMID: 27067026 DOI: 10.2217/epi-2015-0012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite there being over 35,000 different long noncoding RNA (lncRNA) sequences described little is known regarding their molecular-pathological role in cutaneous squamous cell carcinoma (cSCC). MATERIALS & METHODS In this pilot study, lncRNA and mRNA expression profiles were determined in cSCC and control (n = 6) by an Arraystar human lncRNA Microarray. Kyoto Encyclopedia of Genes and Genomes pathway enrichment and gene ontology analysis of mRNAs was performed. RESULTS Analysis of differential expression revealed 1516 upregulated lncRNAs and 2586 downregulated lncRNAs in cSCC compared with controls. Data analysis identified known oncogenic lncRNAs, such as the HOX transcript antisense RNA HOTAIR, among the differentially expressed lncRNA sequences. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that focal adhesion, extracellular matrix and the oncogenic phosphatidylinositol 3'-kinase-Akt signaling pathway had the highest enrichment scores. CONCLUSION This study provides the first evidence for differential expression of lncRNA in cSCC and serves as a template for further, larger functional in-depth analyses regarding cSCC molecular lncRNAs.
Collapse
Affiliation(s)
- Michael Sand
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany.,Department of Plastic Surgery, St Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany
| | - Falk G Bechara
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Daniel Sand
- University of Michigan Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Thilo Gambichler
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Stephan A Hahn
- Department of Internal Medicine, Knappschaftskrankenhaus University of Bochum, Zentrum für Klinische Forschung, Labor für Molekulare Gastroenterologische Onkologie, 44780 Bochum, Germany
| | - Michael Bromba
- Department of Plastic Surgery, St Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany
| | - Eggert Stockfleth
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Schapoor Hessam
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| |
Collapse
|
33
|
Széll M, Danis J, Bata-Csörgő Z, Kemény L. PRINS, a primate-specific long non-coding RNA, plays a role in the keratinocyte stress response and psoriasis pathogenesis. Pflugers Arch 2016; 468:935-43. [PMID: 26935426 PMCID: PMC4893059 DOI: 10.1007/s00424-016-1803-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
In the last few years with the recent emergence of high-throughput technologies, thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome. However, assigning functional annotation and determining cellular contexts for these RNAs are still in its infancy. As information gained about lncRNA structure, interacting partners, and roles in human diseases may be helpful in the characterization of novel lncRNAs, we review our knowledge on a selected group of lncRNAs that were identified serendipitously years ago by large-scale gene expression methods used to study human diseases. In particular, we focus on the Psoriasis-susceptibility-Related RNA Gene Induced by Stress (PRINS) lncRNA, first identified by our research group as a transcript highest expressed in psoriatic non-lesional epidermis. Results gathered for PRINS in the last 10 years indicate that it is conserved in primates and plays a role in keratinocyte stress response. Elevated levels of PRINS expression in psoriatic non-lesional keratinocytes alter the stress response of non-lesional epidermis and contribute to disease pathogenesis. Finally, we propose a categorization for the PRINS lncRNA based on a recently elaborated system for lncRNA classification.
Collapse
Affiliation(s)
- Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Somogyi B. u. 4, 6720, Hungary. .,MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.
| | - Judit Danis
- Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Zsuzsanna Bata-Csörgő
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Lajos Kemény
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| |
Collapse
|
34
|
Long-noncoding RNAs in basal cell carcinoma. Tumour Biol 2016; 37:10595-608. [PMID: 26861560 DOI: 10.1007/s13277-016-4927-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 01/28/2016] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are fundamental regulators of pre- and post-transcriptional gene regulation. Over 35,000 different lncRNAs have been described with some of them being involved in cancer formation. The present study was initiated to describe differentially expressed lncRNAs in basal cell carcinoma (BCC). Patients with BCC (n = 6) were included in this study. Punch biopsies were harvested from the tumor center and nonlesional epidermal skin (NLES, control, n = 6). Microarray-based lncRNA and mRNA expression profiles were identified through screening for 30,586 lncRNAs and 26,109 protein-coding transcripts (mRNAs). The microarray data were validated by RT-PCR in a second set of BCC versus control samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of mRNAs were performed to assess biologically relevant pathways. A total of 1851 lncRNAs were identified as being significantly up-regulated, whereas 2165 lncRNAs were identified as being significantly down-regulated compared to nonlesional skin (p < 0.05). Oncogenic and/or epidermis-specific lncRNAs, such as CASC15 or ANRIL, were among the differentially expressed sequences. GO analysis showed that the highest enriched GO targeted by up-regulated transcripts was "extracellular matrix." KEGG pathway analysis showed the highest enrichment scores in "Focal adhesion." BCC showed a significantly altered lncRNA and mRNA expression profile. Dysregulation of previously described lncRNAs may play a role in the molecular pathogenesis of BCC and should be subject of further analysis.
Collapse
|
35
|
Analysis of lncRNAs expression in UVB-induced stress responses of melanocytes. J Dermatol Sci 2016; 81:53-60. [DOI: 10.1016/j.jdermsci.2015.10.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/30/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
|
36
|
Hombach S, Kretz M. Non-coding RNAs: Classification, Biology and Functioning. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 937:3-17. [PMID: 27573892 DOI: 10.1007/978-3-319-42059-2_1] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action.
Collapse
Affiliation(s)
- Sonja Hombach
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| |
Collapse
|
37
|
Abstract
Melanoma, one of the most virulent forms of human malignancy, is the primary cause of mortality from cancers arising from the skin. The prognosis of metastatic melanoma remains dismal despite targeted therapeutic regimens that exploit our growing understanding of cancer immunology and genetic mutations that drive oncogenic cell signaling pathways in cancer. Epigenetic mechanisms, including DNA methylation/demethylation, histone modifications and noncoding RNAs recently have been shown to play critical roles in melanoma pathogenesis. Current evidence indicates that imbalance of DNA methylation and demethylation, dysregulation of histone modification and chromatin remodeling, and altered translational control by noncoding RNAs contribute to melanoma tumorigenesis. Here, we summarize the most recent insights relating to epigenetic markers, focusing on diagnostic potential as well as novel therapeutic approaches for more effective treatment of advanced melanoma.
Collapse
Affiliation(s)
- Weimin Guo
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Ting Xu
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Jonathan J Lee
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - George F Murphy
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Christine G Lian
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| |
Collapse
|
38
|
Sarkar D, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Epigenetic regulation in human melanoma: past and future. Epigenetics 2015; 10:103-21. [PMID: 25587943 PMCID: PMC4622872 DOI: 10.1080/15592294.2014.1003746] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
Collapse
Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
Collapse
Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
| | | | | | | | | |
Collapse
|
39
|
Liang X, Ma L, Long X, Wang X. LncRNA expression profiles and validation in keloid and normal skin tissue. Int J Oncol 2015; 47:1829-38. [PMID: 26397149 DOI: 10.3892/ijo.2015.3177] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/04/2015] [Indexed: 11/06/2022] Open
Abstract
Keloid is a type of pathological skin scar. Pathogenesis of keloid is complex and is not fully understood. lncRNA can regulate gene expression on different levels. It also participates in cell cycle regulation and cell proliferation. The present study investigated the potential biological function of lncRNA in keloid. We identified differential expression of lncRNAs and mRNAs between 3 pairs of keloid and normal skin tissue by microarray. Differentially expressed lncRNAs were validated by quantitative reverse transcriptase-PCR (qRT-PCR). Gene ontology (GO) and pathway analysis presented the characteristics of associated protein-coding genes. Additionally, a co-expression network of lncRNA and mRNA was constructed to find potential underlying regulation targets. There were 1,731 lncRNAs constantly upregulated and 782 downregulated, 1,079 mRNAs upregulated and 3,282 downregulated in keloid respectively (fold change ≥ 2.0, p<0.05). We chose, respectively, 3 upregulated and 1 downregulated lncRNA for qRT-PCR and results were consistent with microarray. Moreover, 11 pathways were related with upregulated transcripts and 44 with downregulated in keloid. The co-expression network revealed that one lncRNA was connected with numerous mRNAs, and vice versa. Furthermore, bioinformation analysis suggested that lncRNA CACNA1G-AS1 may be crucial to keloid formation. In conclusion, groups of lncRNAs were aberrantly expressed in keloid compared with normal skin tissue, which indicated that differentially expressed lncRNAs may play a key role in keloid formation. The present study provides new insights into keloid pathology and potential targets for treatment of keloid.
Collapse
Affiliation(s)
- Xuebing Liang
- Division of Plastic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Lin Ma
- Division of Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Xiao Long
- Division of Plastic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Xiaojun Wang
- Division of Plastic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| |
Collapse
|
40
|
Luk ACS, Gao H, Xiao S, Liao J, Wang D, Tu J, Rennert OM, Chan WY, Lee TL. GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav044. [PMID: 25982314 PMCID: PMC4433719 DOI: 10.1093/database/bav044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/15/2015] [Indexed: 12/16/2022]
Abstract
Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs. GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis. Database URL: http://germlncrna.cbiit.cuhk.edu.hk/
Collapse
Affiliation(s)
- Alfred Chun-Shui Luk
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Huayan Gao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sizhe Xiao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jinyue Liao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Daxi Wang
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jiajie Tu
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Owen M Rennert
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Wai-Yee Chan
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and T
| | - Tin-Lap Lee
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and T
| |
Collapse
|
41
|
Isin M, Dalay N. LncRNAs and neoplasia. Clin Chim Acta 2015; 444:280-8. [PMID: 25748036 DOI: 10.1016/j.cca.2015.02.046] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/11/2022]
Abstract
Long noncoding RNAs are emerging as new mediators of tumorigenesis by virtue of their various functions and their capacity to induce different mechanisms as a result of their wide spectrum of interactions. They play critical roles in a broad range of cellular processes including regulation of gene expression, imprinting, chromatin modification, transcription and posttranslational processing. Expression and activity of lncRNAs are deregulated in several types of human cancer. Impairment of lncRNA activity may affect key components of the cellular gene regulatory networks and is associated with deregulation of a large number of cellular oncogenic pathways. LncRNAs are also being evaluated as diagnostic and prognostic biomarkers and may provide targets for potential therapeutic applications. An improved understanding of the roles played by lncRNAs in cancer will lead to more effective therapeutic strategies. In this review we summarize the current knowledge on lncRNAs and their function as mediators of tumor development.
Collapse
Affiliation(s)
- Mustafa Isin
- Oncology Institute, Istanbul University, Istanbul, Turkey
| | - Nejat Dalay
- Oncology Institute, Istanbul University, Istanbul, Turkey.
| |
Collapse
|
42
|
Li R, Zhang L, Jia L, Duan Y, Li Y, Bao L, Sha N. Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation. PLoS One 2014; 9:e100893. [PMID: 24967732 PMCID: PMC4072697 DOI: 10.1371/journal.pone.0100893] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/02/2014] [Indexed: 01/11/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to be implicated in the complex network of cancer including malignant melanoma and play important roles in tumorigenesis and progression. However, their functions and downstream mechanisms are largely unknown. This study aimed to investigate whether BRAF-activated non-coding RNA (BANCR), a novel and potential regulator of melanoma cell, participates in the proliferation of malignant melanoma and elucidate the underlying mechanism in this process. We found that BANCR was abnormally overexpressed in human malignant melanoma cell lines and tissues, and increased with tumor stages by quantitative PCR. BANCR knockdown induced by shRNA transfection significantly inhibited proliferation of tumor cells and inactivated MAPK pathway, especially by silencing the ERK1/2 and JNK component. Moreover, combination treatment of BANCR knockdown and suppression ERK1/2 or JNK (induced by specific inhibitors U0126 or SP600125 respectively) produced synergistic inhibitory effects in vitro. And the inhibitory effects induced by ERK1/2 or JNK could be rescued by BANCR overexpression. By tumorigenicity assay in BALB/c nude mice, we further found that BANCR knockdown inhibited tumor growth in vivo. In addition, patients with high expression of BANCR had a lower survival rate. Taken together, we confirmed the abnormal upregulation of a novel lncRNA, BANCR, in human malignant melanoma. BANCR was involved in melanoma cell proliferation both in vitro and in vivo. The linkage between BANCR and MAPK pathway may provide a novel interpretation for the mechanism of proliferation regulation in malignant melanoma.
Collapse
Affiliation(s)
- Ruiya Li
- Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Lingli Zhang
- Department of Pathology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Lizhou Jia
- Department of Pathology, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yan Duan
- Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yan Li
- Department of Dermatology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Lidao Bao
- Department of Pharmacy, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Na Sha
- Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| |
Collapse
|
43
|
Hannus M, Beitzinger M, Engelmann JC, Weickert MT, Spang R, Hannus S, Meister G. siPools: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Res 2014; 42:8049-61. [PMID: 24875475 PMCID: PMC4081087 DOI: 10.1093/nar/gku480] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Short interfering RNAs (siRNAs) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels. Here we demonstrate that novel, enzymatically generated siRNA pools—referred to as siPools—containing up to 60 accurately defined siRNAs eliminate off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically produced complex but accurately defined siRNA pools with potent on-target silencing but without detectable off-target effects.
Collapse
Affiliation(s)
- Michael Hannus
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Michaela Beitzinger
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Julia C Engelmann
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany
| | - Marie-Theresa Weickert
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany
| | - Stefan Hannus
- Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| |
Collapse
|