1
|
Yuan X, Hao X, Chan HL, Zhao N, Pedroza DA, Liu F, Le K, Smith AJ, Calderon SJ, Lieu N, Soth MJ, Jones P, Zhang XHF, Rosen JM. CBP/P300 BRD Inhibition Reduces Neutrophil Accumulation and Activates Antitumor Immunity in TNBC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590983. [PMID: 38712292 PMCID: PMC11071628 DOI: 10.1101/2024.04.25.590983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tumor-associated neutrophils (TANs) have been shown to promote immunosuppression and tumor progression, and a high TAN frequency predicts poor prognosis in triple-negative breast cancer (TNBC). Dysregulation of CREB binding protein (CBP)/P300 function has been observed with multiple cancer types. The bromodomain (BRD) of CBP/P300 has been shown to regulate its activity. In this study, we found that IACS-70654, a novel and selective CBP/P300 BRD inhibitor, reduced TANs and inhibited the growth of neutrophil-enriched TNBC models. In the bone marrow, CBP/P300 BRD inhibition reduced the tumor-driven abnormal differentiation and proliferation of neutrophil progenitors. Inhibition of CBP/P300 BRD also stimulated the immune response by inducing an IFN response and MHCI expression in tumor cells and increasing tumor-infiltrated CTLs. Moreover, IACS-70654 improved the response of a neutrophil-enriched TNBC model to docetaxel and immune checkpoint blockade. This provides a rationale for combining a CBP/P300 BRD inhibitor with standard-of-care therapies in future clinical trials for neutrophil-enriched TNBC. Summary In neutrophil-enriched triple-negative breast cancer (TNBC) models, CREB binding protein (CBP)/P300 bromodomain (BRD) inhibition reduces tumor growth and systemic neutrophil accumulation while stimulating an antitumor immune response. This improves standard-of-care therapies, suggesting a potential therapeutic benefit of CBP/P300 BRD inhibitors for neutrophil-enriched TNBC.
Collapse
|
2
|
Piórkowska K, Zygmunt K, Hunter W, Wróblewska K. MALAT1: A Long Non-Coding RNA with Multiple Functions and Its Role in Processes Associated with Fat Deposition. Genes (Basel) 2024; 15:479. [PMID: 38674413 PMCID: PMC11049917 DOI: 10.3390/genes15040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) belongs to the lncRNA molecules, which are involved in transcriptional and epigenetic regulation and the control of gene expression, including the mechanism of chromatin remodeling. MALAT1 was first discovered during carcinogenesis in lung adenocarcinoma, hence its name. In humans, 66 of its isoforms have been identified, and in pigs, only 2 are predicted, for which information is available in Ensembl databases (Ensembl Release 111). MALAT1 is expressed in numerous tissues, including adipose, adrenal gland, heart, kidney, liver, ovary, pancreas, sigmoid colon, small intestine, spleen, and testis. MALAT1, as an lncRNA, shows a wide range of functions. It is involved in the regulation of the cell cycle, where it has pro-proliferative effects and high cellular levels during the G1/S and mitotic (M) phases. Moreover, it is involved in invasion, metastasis, and angiogenesis, and it has a crucial function in alternative splicing during carcinogenesis. In addition, MALAT1 plays a significant role in the processes of fat deposition and adipogenesis. The human adipose tissue stem cells, during differentiation into adipocytes, secrete MALAT1 as one the most abundant lncRNAs in the exosomes. MALAT1 expression in fat tissue is positively correlated with adipogenic FABP4 and LPL. This lncRNA is involved in the regulation of PPARγ at the transcription stage, fatty acid metabolism, and insulin signaling. The wide range of MALAT1 functions makes it an interesting target in studies searching for drugs to prevent obesity development in humans. In turn, in farm animals, it can be a source of selection markers to control the fat tissue content.
Collapse
Affiliation(s)
- Katarzyna Piórkowska
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
| | - Karolina Zygmunt
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
| | - Walter Hunter
- Faculty of Biotechnology and Horticulture, University of Agriculture in Cracow, 31-120 Cracow, Poland;
| | - Ksenia Wróblewska
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
| |
Collapse
|
3
|
Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
Collapse
Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
| |
Collapse
|
4
|
Tomic Vujovic K, Ugrin M, Tosic N, Vukovic V, Marjanovic I, Kostic T, Stankovic S, Otasevic V, Sarac S, Antic D, Pavlovic S, Karan-Djurasevic T. Expression Pattern and Prognostic Significance of the Long Non-Coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 in Chronic Lymphocytic Leukemia. Int J Mol Sci 2024; 25:922. [PMID: 38255996 PMCID: PMC10815316 DOI: 10.3390/ijms25020922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Dysregulated expression of the long non-coding RNA MALAT1 has been implicated in the pathogenesis and progression of a variety of cancers, including hematological malignancies, but it has been poorly investigated in chronic lymphocytic leukemia (CLL). In this study, the expression of MALAT1 was measured using a quantitative reverse-transcriptase polymerase chain reaction in the peripheral blood mononuclear cells of 114 unselected, newly diagnosed CLL patients in order to analyze its association with clinical, laboratory, and molecular patients' characteristics at diagnosis, as well as its prognostic relevance. MALAT1 was found to be upregulated in CLL patients in comparison to healthy controls, and expression levels were not related to age, leukocyte, lymphocyte and platelet count, serum β2-microglobulin, and IGHV somatic hypermutational status. On the other hand, high MALAT1 expression was associated with several favorable prognostic markers (high hemoglobin, low serum lactate dehydrogenase, earlier clinical stages, CD38-negative status), but also with unfavorable cytogenetics. Furthermore, an association between high MALAT1 levels and longer time to first treatment and overall survival in IGHV-unmutated CLL subtype was observed. In summary, our results imply that high MALAT1 expression at diagnosis may be a predictor of better prognosis and point to MALAT1 expression profiling as a candidate biomarker potentially useful in clinical practice.
Collapse
Affiliation(s)
- Kristina Tomic Vujovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Vojin Vukovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Irena Marjanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Tatjana Kostic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Sanja Stankovic
- Center for Medical Biochemistry, University Clinical Center of Serbia, 11000 Belgrade, Serbia;
- Department of Biochemistry, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Vladimir Otasevic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Sofija Sarac
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Darko Antic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Teodora Karan-Djurasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| |
Collapse
|
5
|
Bhat AA, Afzal O, Afzal M, Gupta G, Thapa R, Ali H, Hassan Almalki W, Kazmi I, Alzarea SI, Saleem S, Samuel VP, Gubbiyappa SK, Subramaniyan V. MALAT1: A key regulator in lung cancer pathogenesis and therapeutic targeting. Pathol Res Pract 2024; 253:154991. [PMID: 38070223 DOI: 10.1016/j.prp.2023.154991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Lung cancer remains a formidable global health burden, necessitating a comprehensive understanding of the underlying molecular mechanisms driving its progression. Recently, lncRNAs have become necessary controllers of various biological functions, including cancer development. MALAT1 has garnered significant attention due to its multifaceted role in lung cancer progression. Lung cancer, among other malignancies, upregulates MALAT1. Its overexpression has been associated with aggressive tumor behavior and poor patient prognosis. MALAT1 promotes cellular proliferation, epithelial-mesenchymal transition (EMT), and angiogenesis in lung cancer, collectively facilitating tumor growth and metastasis. Additionally, MALAT1 enhances cancer cell invasion by interacting with numerous signaling pathways. Furthermore, MALAT1 has been implicated in mediating drug resistance in lung cancer, contributing to the limited efficacy of conventional therapies. Recent advancements in molecular biology and high-throughput sequencing technologies have offered fresh perspectives into the regulatory networks of MALAT1 in lung cancer. It exerts its oncogenic effects by acting as a ceRNA to sponge microRNAs, thereby relieving their inhibitory effects on target genes. Moreover, MALAT1 also influences chromatin remodeling and post-translational modifications to modulate gene expression, further expanding its regulatory capabilities. This review sheds light on the multifaceted roles of MALAT1 in lung cancer progression, underscoring its potential as an innovative therapeutic target and diagnostic biomarker. Targeting MALAT1 alone or combined with existing therapies holds promise to mitigate lung cancer progression and improve patient outcomes.
Collapse
Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
| | | | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| |
Collapse
|
6
|
Liu Y, Schmiderer L, Hjort M, Lang S, Bremborg T, Rydström A, Schambach A, Larsson J, Karlsson S. Engineered human Diamond-Blackfan anemia disease model confirms therapeutic effects of clinically applicable lentiviral vector at single-cell resolution. Haematologica 2023; 108:3095-3109. [PMID: 37199130 PMCID: PMC10620578 DOI: 10.3324/haematol.2022.282068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/11/2023] [Indexed: 05/19/2023] Open
Abstract
Diamond-Blackfan anemia is a rare genetic bone marrow failure disorder which is usually caused by mutations in ribosomal protein genes. In the present study, we generated a traceable RPS19-deficient cell model using CRISPR-Cas9 and homology-directed repair to investigate the therapeutic effects of a clinically applicable lentiviral vector at single-cell resolution. We developed a gentle nanostraw delivery platform to edit the RPS19 gene in primary human cord bloodderived CD34+ hematopoietic stem and progenitor cells. The edited cells showed expected impaired erythroid differentiation phenotype, and a specific erythroid progenitor with abnormal cell cycle status accompanied by enrichment of TNFα/NF-κB and p53 signaling pathways was identified by single-cell RNA sequencing analysis. The therapeutic vector could rescue the abnormal erythropoiesis by activating cell cycle-related signaling pathways and promoted red blood cell production. Overall, these results establish nanostraws as a gentle option for CRISPR-Cas9- based gene editing in sensitive primary hematopoietic stem and progenitor cells, and provide support for future clinical investigations of the lentiviral gene therapy strategy.
Collapse
Affiliation(s)
- Yang Liu
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184, Sweden; Department of Medicine, Huddinge, Karolinska Institutet, 14157 Stockholm.
| | - Ludwig Schmiderer
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184
| | - Martin Hjort
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, 22100 Lund, Sweden; Navan Technologies, MBC Biolabs, San Carlos, CA 94070; NanoLund, Lund University, Box 118, 22100 Lund
| | - Stefan Lang
- Division of Molecular Hematology and Stem Cell Center, Lund University, Lund
| | - Tyra Bremborg
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184
| | - Anna Rydström
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184
| | - Stefan Karlsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund 22184.
| |
Collapse
|
7
|
Athanasopoulou K, Chondrou V, Xiropotamos P, Psarias G, Vasilopoulos Y, Georgakilas GK, Sgourou A. Transcriptional repression of lncRNA and miRNA subsets mediated by LRF during erythropoiesis. J Mol Med (Berl) 2023; 101:1097-1112. [PMID: 37486375 PMCID: PMC10482784 DOI: 10.1007/s00109-023-02352-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
Non-coding RNA (ncRNA) species, mainly long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been currently imputed for lesser or greater involvement in human erythropoiesis. These RNA subsets operate within a complex circuit with other epigenetic components and transcription factors (TF) affecting chromatin remodeling during cell differentiation. Lymphoma/leukemia-related (LRF) TF exerts higher occupancy on DNA CpG rich sites and is implicated in several differentiation cell pathways and erythropoiesis among them and also directs the epigenetic regulation of hemoglobin transversion from fetal (HbF) to adult (HbA) form by intervening in the γ-globin gene repression. We intended to investigate LRF activity in the evolving landscape of cells' commitment to the erythroid lineage and specifically during HbF to HbA transversion, to qualify this TF as potential repressor of lncRNAs and miRNAs. Transgenic human erythroleukemia cells, overexpressing LRF and further induced to erythropoiesis, were subjected to expression analysis in high LRF occupancy genetic loci-producing lncRNAs. LRF abundance in genetic loci transcribing for studied lncRNAs was determined by ChIP-Seq data analysis. qPCRs were performed to examine lncRNA expression status. Differentially expressed miRNA pre- and post-erythropoiesis induction were assessed by next-generation sequencing (NGS), and their promoter regions were charted. Expression levels of lncRNAs were correlated with DNA methylation status of flanked CpG islands, and contingent co-regulation of hosted miRNAs was considered. LRF-binding sites were overrepresented in LRF overexpressing cell clones during erythropoiesis induction and exerted a significant suppressive effect towards lncRNAs and miRNA collections. Based on present data interpretation, LRF's multiplied binding capacity across genome is suggested to be transient and associated with higher levels of DNA methylation. KEY MESSAGES: During erythropoiesis, LRF displays extensive occupancy across genetic loci. LRF significantly represses subsets of lncRNAs and miRNAs during erythropoiesis. Promoter region CpG islands' methylation levels affect lncRNA expression. MiRNAs embedded within lncRNA loci show differential regulation of expression.
Collapse
Affiliation(s)
- Katerina Athanasopoulou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Panagiotis Xiropotamos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Georgios Psarias
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Georgios K. Georgakilas
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| |
Collapse
|
8
|
Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
Collapse
Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| |
Collapse
|
9
|
Rocca R, Polerà N, Juli G, Grillone K, Maruca A, Di Martino MT, Artese A, Amato J, Pagano B, Randazzo A, Tagliaferri P, Tassone P, Alcaro S. Hit identification of novel small molecules interfering with MALAT1 triplex by a structure-based virtual screening. Arch Pharm (Weinheim) 2023; 356:e2300134. [PMID: 37309243 DOI: 10.1002/ardp.202300134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
Nowadays, RNA is an attractive target for the design of new small molecules with different pharmacological activities. Among several RNA molecules, long noncoding RNAs (lncRNAs) are extensively reported to be involved in cancer pathogenesis. In particular, the overexpression of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays an important role in the development of multiple myeloma (MM). Starting from the crystallographic structure of the triple-helical stability element at the 3'-end of MALAT1, we performed a structure-based virtual screening of a large commercial database, previously filtered according to the drug-like properties. After a thermodynamic analysis, we selected five compounds for the in vitro assays. Compound M5, characterized by a diazaindene scaffold, emerged as the most promising molecule enabling the destabilization of the MALAT1 triplex structure and antiproliferative activity on in vitro models of MM. M5 is proposed as a lead compound to be further optimized for improving its affinity toward MALAT1.
Collapse
Affiliation(s)
- Roberta Rocca
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Nicoletta Polerà
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Annalisa Maruca
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Anna Artese
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Pietrosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| |
Collapse
|
10
|
Gencel-Augusto J, Wu W, Bivona TG. Long Non-Coding RNAs as Emerging Targets in Lung Cancer. Cancers (Basel) 2023; 15:3135. [PMID: 37370745 DOI: 10.3390/cancers15123135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) are mRNA-like molecules that do not encode for proteins and that are longer than 200 nucleotides. LncRNAs play important biological roles in normal cell physiology and organism development. Therefore, deregulation of their activities is involved in disease processes such as cancer. Lung cancer is the leading cause of cancer-related deaths due to late stage at diagnosis, distant metastasis, and high rates of therapeutic failure. LncRNAs are emerging as important molecules in lung cancer for their oncogenic or tumor-suppressive functions. LncRNAs are highly stable in circulation, presenting an opportunity for use as non-invasive and early-stage cancer diagnostic tools. Here, we summarize the latest works providing in vivo evidence available for lncRNAs role in cancer development, therapy-induced resistance, and their potential as biomarkers for diagnosis and prognosis, with a focus on lung cancer. Additionally, we discuss current therapeutic approaches to target lncRNAs. The evidence discussed here strongly suggests that investigation of lncRNAs in lung cancer in addition to protein-coding genes will provide a holistic view of molecular mechanisms of cancer initiation, development, and progression, and could open up a new avenue for cancer treatment.
Collapse
Affiliation(s)
- Jovanka Gencel-Augusto
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
- UCSF Hellen Diller Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Wei Wu
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
- UCSF Hellen Diller Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Trever G Bivona
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
- UCSF Hellen Diller Comprehensive Cancer Center, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
11
|
Sadaf H, Ambroziak M, Binkowski R, Kluebsoongnoen J, Paszkiewicz-Kozik E, Steciuk J, Markowicz S, Walewski J, Sarnowska E, Sarnowski TJ, Konopinski R. New molecular targets in Hodgkin and Reed-Sternberg cells. Front Immunol 2023; 14:1155468. [PMID: 37266436 PMCID: PMC10230546 DOI: 10.3389/fimmu.2023.1155468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Recent discoveries shed light on molecular mechanisms responsible for classical Hodgkin lymphoma (HL) development and progression, along with features of Hodgkin - Reed and Sternberg cells (HRS). Here, we summarize current knowledge on characteristic molecular alterations in HL, as well as existing targeted therapies and potential novel treatments for this disease. We discuss the importance of cluster of differentiation molecule 30 (CD30) and the programmed cell death-1 protein (PD-1) and ligands (PD-L1/2), and other molecules involved in immune modulation in HL. We highlight emerging evidence indicating that the altered function of SWI/SNF-type chromatin remodeling complexes, PRC2, and other epigenetic modifiers, contribute to variations in chromatin status, which are typical for HL. We postulate that despite of the existence of plentiful molecular data, the understanding of HL development remains incomplete. We therefore propose research directions involving analysis of reverse signaling in the PD-1/PD-L1 mechanism, chromatin remodeling, and epigenetics-related alterations, in order to identify HL features at the molecular level. Such attempts may lead to the identification of new molecular targets, and thus will likely substantially contribute to the future development of more effective targeted therapies.
Collapse
Affiliation(s)
- Hummaira Sadaf
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Biotechnology, Sardar Bahadur Khan Womens’ University, Balochistan, Pakistan
| | - Maciej Ambroziak
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Robert Binkowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | | | - Ewa Paszkiewicz-Kozik
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jaroslaw Steciuk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Sergiusz Markowicz
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Elzbieta Sarnowska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | | | - Ryszard Konopinski
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| |
Collapse
|
12
|
Liu J, Ali MK, Mao Y. Emerging role of long non-coding RNA MALAT1 related signaling pathways in the pathogenesis of lung disease. Front Cell Dev Biol 2023; 11:1149499. [PMID: 37250901 PMCID: PMC10213921 DOI: 10.3389/fcell.2023.1149499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are endogenously expressed RNAs longer than 200 nt that are not translated into proteins. In general, lncRNAs bind to mRNA, miRNA, DNA, and proteins and regulate gene expression at various cellular and molecular levels, including epigenetics, transcription, post-transcription, translation, and post-translation. LncRNAs play important roles in many biological processes, such as cell proliferation, apoptosis, cell metabolism, angiogenesis, migration, endothelial dysfunction, endothelial-mesenchymal transition, regulation of cell cycle, and cellular differentiation, and have become an important topic of study in genetic research in health and disease due to their close link with the development of various diseases. The exceptional stability, conservation, and abundance of lncRNAs in body fluids, have made them potential biomarkers for a wide range of diseases. LncRNA MALAT1 is one of the best-studied lncRNAs in the pathogenesis of various diseases, including cancers and cardiovascular diseases. A growing body of evidence suggests that aberrant expression of MALAT1 plays a key role in the pathogenesis of lung diseases, including asthma, chronic obstructive pulmonary diseases (COPD), Coronavirus Disease 2019 (COVID-19), acute respiratory distress syndrome (ARDS), lung cancers, and pulmonary hypertension through different mechanisms. Here we discuss the roles and molecular mechanisms of MALAT1 in the pathogenesis of these lung diseases.
Collapse
Affiliation(s)
- Jun Liu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Md Khadem Ali
- Devission of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Yuqiang Mao
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
- Clinical Skills Practice Teaching Center, Shengjing Hospital of China Medical University, Shenyang, China
| |
Collapse
|
13
|
Abstract
CONTEXT The prevalence of diabetic neuropathy is drastically increasing in the world. To halt the progression of diabetic neuropathy, there is an unmet need to have potential biomarkers for the diagnosis and new drug discovery. OBJECTIVE To study various biomarkers involved in the pathogenesis of diabetic neuropathy. METHODS The literature was searched with the help of various scientific databases and resources like PubMed, ProQuest, Scopus, and Google scholar from the year 1976 to 2020. RESULTS Biomarkers of diabetic neuropathy are categorised as inflammatory biomarkers such as MCP-1, VEGF, TRPV1, NF-κB; oxidative biomarkers such as adiponectin, NFE2L2; enzyme biomarkers like NADPH, ceruloplasmin, HO-1, DPP-4, PARP α; miscellaneous biomarkers such as SIRT1, caveolin 1, MALAT1, and microRNA. All biomarkers have a significant role in the pathogenesis of diabetic neuropathy. CONCLUSION These biomarkers have a potential role in the progression of diabetic neuropathy and can be considered as potential targets for new drug discovery.
Collapse
Affiliation(s)
- Kaveri M Adki
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, Mumbai, India
| | - Yogesh A Kulkarni
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, Mumbai, India
| |
Collapse
|
14
|
Ghanam AR, Ke S, Wang S, Elgendy R, Xie C, Wang S, Zhang R, Wei M, Liu W, Cao J, Zhang Y, Zhang Z, Xue T, Zheng Y, Song X. Alternative transcribed 3' isoform of long non-coding RNA Malat1 inhibits mouse retinal oxidative stress. iScience 2022; 26:105740. [PMID: 36594014 PMCID: PMC9804114 DOI: 10.1016/j.isci.2022.105740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/08/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The function of the cancer-associated lncRNA Malat1 during aging is as-of-yet uncharacterized. Here, we show that Malat1 interacts with Nucleophosmin (NPM) in young mouse brain, and with Lamin A/C, hnRNP C, and KAP1 with age. RNA-seq and RT-qPCR reveal a persistent expression of Malat1_2 (the 3'isoform of Malat1) in Malat1Δ1 (5'-1.5 kb deletion) mouse retinas and brains at 1/4th level of the full-length Malat1, while Malat1_1 (the 5'isoform) in Malat1Δ2 (deletion of 3'-conserved 5.7 kb) at a much lower level, suggesting an internal promoter driving the 3' isoform. The 1774 and 496 differentially expressed genes in Malat1Δ2 and Malat1Δ1 brains, respectively, suggest the 3' isoform regulates gene expression in trans and the 5' isoform in cis. Consistently, Malat1Δ2 mice show increased age-dependent retinal oxidative stress and corneal opacity, while Malat1Δ1 mice show no obvious phenotype. Collectively, this study reveals a physiological function of the lncRNA Malat1 3'-isoform during the aging process.
Collapse
Affiliation(s)
- Amr. R. Ghanam
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shengwei Ke
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China,Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Shujuan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ramy Elgendy
- Department of Pharmacology, College of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Chenyao Xie
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Siqi Wang
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ran Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Min Wei
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weiguang Liu
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jun Cao
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yan Zhang
- Stroke Center & Department of Neurology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhi Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Tian Xue
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China,Corresponding author
| | - Xiaoyuan Song
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China,Corresponding author
| |
Collapse
|
15
|
Guan X, Sun Y, Zhang C. LncRNAs in blood cells: Roles in cell development and potential pathogenesis in hematological malignancies. Crit Rev Oncol Hematol 2022; 180:103849. [DOI: 10.1016/j.critrevonc.2022.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 09/11/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
|
16
|
Sallé-Lefort S, Miard S, Henry C, Arias-Reyes C, Marcouiller F, Beaulieu MJ, Aubin S, Lechasseur A, Jubinville É, Marsolais D, Morissette MC, Joseph V, Soliz J, Bossé Y, Picard F. Malat1 deficiency prevents hypoxia-induced lung dysfunction by protecting the access to alveoli. Front Physiol 2022; 13:949378. [PMID: 36105289 PMCID: PMC9464821 DOI: 10.3389/fphys.2022.949378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Hypoxia is common in lung diseases and a potent stimulator of the long non-coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1). Herein, we investigated the impact of Malat1 on hypoxia-induced lung dysfunction in mice. Malat1-deficient mice and their wild-type littermates were tested after 8 days of normoxia or hypoxia (10% oxygen). Hypoxia decreased elastance of the lung by increasing lung volume and caused in vivo hyperresponsiveness to methacholine without altering the contraction of airway smooth muscle. Malat1 deficiency also modestly decreased lung elastance but only when tested at low lung volumes and without altering lung volume and airway smooth muscle contraction. The in vivo responsiveness to methacholine was also attenuated by Malat1 deficiency, at least when elastance, a readout sensitive to small airway closure, was used to assess the response. More impressively, in vivo hyperresponsiveness to methacholine caused by hypoxia was virtually absent in Malat1-deficient mice, especially when hysteresivity, a readout sensitive to small airway narrowing heterogeneity, was used to assess the response. Malat1 deficiency also increased the coefficient of oxygen extraction and decreased ventilation in conscious mice, suggesting improvements in gas exchange and in clinical signs of respiratory distress during natural breathing. Combined with a lower elastance at low lung volumes at baseline, as well as a decreased propensity for small airway closure and narrowing heterogeneity during a methacholine challenge, these findings represent compelling evidence suggesting that the lack of Malat1 protects the access to alveoli for air entering the lung.
Collapse
Affiliation(s)
- Sandrine Sallé-Lefort
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Pharmacy, Université Laval, Quebec, QC, Canada
| | - Stéphanie Miard
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Cyndi Henry
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Christian Arias-Reyes
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - François Marcouiller
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Marie-Josée Beaulieu
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Sophie Aubin
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Ariane Lechasseur
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Éric Jubinville
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - David Marsolais
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Mathieu C. Morissette
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Vincent Joseph
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Jorge Soliz
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Ynuk Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Medicine, Université Laval, Quebec, QC, Canada
- *Correspondence: Ynuk Bossé, ; Frédéric Picard,
| | - Frédéric Picard
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Pharmacy, Université Laval, Quebec, QC, Canada
- *Correspondence: Ynuk Bossé, ; Frédéric Picard,
| |
Collapse
|
17
|
Matuszyk J. MALAT1-miRNAs network regulate thymidylate synthase and affect 5FU-based chemotherapy. Mol Med 2022; 28:89. [PMID: 35922756 PMCID: PMC9351108 DOI: 10.1186/s10020-022-00516-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
Background The active metabolite of 5-Fluorouracil (5FU), used in the treatment of several types of cancer, acts by inhibiting the thymidylate synthase encoded by the TYMS gene, which catalyzes the rate-limiting step in DNA replication. The major failure of 5FU-based cancer therapy is the development of drug resistance. High levels of TYMS-encoded protein in cancerous tissues are predictive of poor response to 5FU treatment. Expression of TYMS is regulated by various mechanisms, including involving non-coding RNAs, both miRNAs and long non-coding RNAs (lncRNAs). Aim To delineate the miRNAs and lncRNAs network regulating the level of TYMS-encoded protein. Main body Several miRNAs targeting TYMS mRNA have been identified in colon cancers, the levels of which can be regulated to varying degrees by lncRNAs. Due to their regulation by the MALAT1 lncRNA, these miRNAs can be divided into three groups: (1) miR-197-3p, miR-203a-3p, miR-375-3p which are downregulated by MALAT1 as confirmed experimentally and the levels of these miRNAs are actually reduced in colon and gastric cancers; (2) miR-140-3p, miR-330-3p that could potentially interact with MALAT1, but not yet supported by experimental results; (3) miR-192-5p, miR-215-5p whose seed sequences do not recognize complementary response elements within MALAT1. Considering the putative MALAT1-miRNAs interaction network, attention is drawn to the potential positive feedback loop causing increased expression of MALAT1 in colon cancer and hepatocellular carcinoma, where YAP1 acts as a transcriptional co-factor which, by binding to the TCF4 transcription factor/ β-catenin complex, may increase the activation of the MALAT1 gene whereas the MALAT1 lncRNA can inhibit miR-375-3p which in turn targets YAP1 mRNA. Conclusion The network of non-coding RNAs may reduce the sensitivity of cancer cells to 5FU treatment by upregulating the level of thymidylate synthase.
Collapse
Affiliation(s)
- Janusz Matuszyk
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigla Street, 53-114, Wroclaw, Poland.
| |
Collapse
|
18
|
Gholami A, Farhadi K, Sayyadipour F, Soleimani M, Saba F. Long noncoding RNAs (lncRNAs) in human lymphomas. Genes Dis 2022; 9:900-914. [PMID: 35685474 PMCID: PMC9170579 DOI: 10.1016/j.gendis.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 01/17/2023] Open
Abstract
Lymphomas are a diverse group of haematologic malignancies, which occur in infection-fighting cells of the lymphatic system. Long non-coding RNAs (lncRNAs) are non-coding RNAs, which have recently received significant attention as the main mediators of gene expression. In this review, we summarize the current knowledge on lncRNAs involved in lymphomas, their molecular functions, as well as their potential clinical value. Relevant literature was identified by a PubMed search of English language papers using the following terms: Lymphoma, LncRNA, leukemia, proliferation, apoptosis, and prognosis. LncRNAs are imperative for lymphoma carcinogenesis through affecting apoptosis, cell proliferation, invasion, and response to chemotherapy. The expression level of lncRNAs can affect chemotherapy-induced apoptosis. Taken together, lncRNA dysregulation in lymphoma cells is not only an epiphenomenon but also lncRNA transcription is critically related to the initiation and progression of lymphomas. Aberrant expression of lncRNAs can lead to the transformation of normal lymphocytes into lymphoma cells.
Collapse
Affiliation(s)
- Ali Gholami
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Khosro Farhadi
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Fatemeh Sayyadipour
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Masoud Soleimani
- Department of Haematology, Tarbiat Modares University, Tehran 146899-5513, Iran
| | - Fakhredin Saba
- Department of Medical Laboratory Science, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| |
Collapse
|
19
|
Deciphering the acetylation code of p53 in transcription regulation and tumor suppression. Oncogene 2022; 41:3039-3050. [PMID: 35487975 PMCID: PMC9149126 DOI: 10.1038/s41388-022-02331-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022]
Abstract
Although it is well established that p53-mediated tumor suppression mainly acts through its ability in transcriptional regulation, the molecular mechanisms of this regulation are not completely understood. Among a number of regulatory modes, acetylation of p53 attracts great interests. p53 was one of the first non-histone proteins found to be functionally regulated by acetylation and deacetylation, and subsequent work has established that reversible acetylation is a general mechanism for regulation of non-histone proteins. Unlike other types of post-translational modifications occurred during stress responses, the role of p53 acetylation has been recently validated in vivo by using the knockin mice with both acetylation-defective and acetylation-mimicking p53 mutants. Here, we review the role of acetylation in p53-mediated activities, with a focus on which specific acetylation sites are critical for p53-dependent transcription regulation during tumor suppression and how acetylation of p53 recruits specific “readers” to execute its promoter-specific regulation of different targets. We also discuss the role of p53 acetylation in differentially regulating its classic activities in cell cycle arrest, senescence and apoptosis as well as newly identified unconventional functions such as cell metabolism and ferroptosis.
Collapse
|
20
|
Nukala SB, Jousma J, Cho Y, Lee WH, Ong SG. Long non-coding RNAs and microRNAs as crucial regulators in cardio-oncology. Cell Biosci 2022; 12:24. [PMID: 35246252 PMCID: PMC8895873 DOI: 10.1186/s13578-022-00757-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is one of the leading causes of morbidity and mortality worldwide. Significant improvements in the modern era of anticancer therapeutic strategies have increased the survival rate of cancer patients. Unfortunately, cancer survivors have an increased risk of cardiovascular diseases, which is believed to result from anticancer therapies. The emergence of cardiovascular diseases among cancer survivors has served as the basis for establishing a novel field termed cardio-oncology. Cardio-oncology primarily focuses on investigating the underlying molecular mechanisms by which anticancer treatments lead to cardiovascular dysfunction and the development of novel cardioprotective strategies to counteract cardiotoxic effects of cancer therapies. Advances in genome biology have revealed that most of the genome is transcribed into non-coding RNAs (ncRNAs), which are recognized as being instrumental in cancer, cardiovascular health, and disease. Emerging studies have demonstrated that alterations of these ncRNAs have pathophysiological roles in multiple diseases in humans. As it relates to cardio-oncology, though, there is limited knowledge of the role of ncRNAs. In the present review, we summarize the up-to-date knowledge regarding the roles of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in cancer therapy-induced cardiotoxicities. Moreover, we also discuss prospective therapeutic strategies and the translational relevance of these ncRNAs.
Collapse
Affiliation(s)
- Sarath Babu Nukala
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Jordan Jousma
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Yoonje Cho
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Won Hee Lee
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ, 85004, USA.
| | - Sang-Ging Ong
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA.
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA.
| |
Collapse
|
21
|
Choy M, Xue R, Wu Y, Fan W, Dong Y, Liu C. Role of N6-methyladenosine Modification in Cardiac Remodeling. Front Cardiovasc Med 2022; 9:774627. [PMID: 35224032 PMCID: PMC8866307 DOI: 10.3389/fcvm.2022.774627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Cardiac remodeling is the critical process in heart failure due to many cardiovascular diseases including myocardial infarction, hypertension, cardiovascular disease and cardiomyopathy. However, treatments for heart failure focusing on cardiac remodeling show relatively limited effectiveness. In recent decades, epitranscriptomic modifications were found abundantly present throughout the progression of cardiac remodeling, and numerous types of biochemical modifications were identified. m6A modification is the methylation of the adenosine base at the nitrogen-6 position, and dysregulation of m6A modification has been implicated in a wide range of diseases. However, function of m6A modifications still remain largely unknown in cardiac diseases, especially cardiac remodeling. LncRNAs are also shown to play a vital role in the pathophysiology of cardiac remodeling and heart failure. The crosstalk between lncRNAs and m6A modification provides a novel prospective for exploring possible regulatory mechanism and therapeutic targets of cardiac remodeling. This review summarizes the role of m6A modification in cardiac remodeling in the current researches.
Collapse
Affiliation(s)
- ManTing Choy
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Ruicong Xue
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Yuzhong Wu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Wendong Fan
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Yugang Dong
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Chen Liu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chen Liu
| |
Collapse
|
22
|
Ruan L, Mendhe B, Parker E, Kent A, Isales CM, Hill WD, McGee-Lawrence M, Fulzele S, Hamrick MW. Long Non-coding RNA MALAT1 Is Depleted With Age in Skeletal Muscle in vivo and MALAT1 Silencing Increases Expression of TGF-β1 in vitro. Front Physiol 2022; 12:742004. [PMID: 35126169 PMCID: PMC8814451 DOI: 10.3389/fphys.2021.742004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are thought to function as “sponges” for microRNAs, but a role for such competing endogenous RNAs (ceRNAs) in muscle aging is not well understood. We therefore examined in skeletal muscles of young (4–6 months) and aged (22–24) male and female mice the expression of lncRNA MALAT1, which is predicted in silico to bind the senescence-associated microRNA miR-34a-5p. Results indicate a significant decrease in lncRNA MALAT1 expression in mouse skeletal muscle with age that coincides with an age-related increase in miR-34a-5p expression. In vitro studies using mouse C2C12 myoblasts demonstrate that MALAT1 silencing using siRNA increases miR-34a expression, consistent with a role for MALAT1 as an inhibitor of miR-34a-5p activity. Levels of reactive oxygen species (ROS) are known to increase in muscle with age, and so we treated C2C12 cells with hydrogen peroxide (10 and 100 μM) to examine changes in MALAT1 expression. MALAT1 expression decreased significantly with H2O2 treatment, but this effect was attenuated with p53 siRNA. Finally, miR-34a-5p is implicated in tissue fibrosis, and so we assessed the expression of TGF-β1 after MALAT1 silencing. MALAT1 siRNA significantly increased the expression of TGF-β1 in C2C12 cells. These findings suggest that age-related fibrosis and muscle atrophy mediated by ROS may result at least in part from an increase in miR-34a bioavailability resulting from a decline in miR-34a “sponging” due to ceRNA MALAT1 depletion. Crosstalk between MALAT1 and miR-34a may therefore represent a therapeutic target for improving muscle function with aging.
Collapse
Affiliation(s)
- Ling Ruan
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Bharati Mendhe
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Emily Parker
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Andrew Kent
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Carlos M. Isales
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - William D. Hill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | | | - Sadanand Fulzele
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Mark W. Hamrick
- Medical College of Georgia, Augusta University, Augusta, GA, United States
- *Correspondence: Mark W. Hamrick,
| |
Collapse
|
23
|
Fernandes M, Marques H, Teixeira AL, Medeiros R. ceRNA Network of lncRNA/miRNA as Circulating Prognostic Biomarkers in Non-Hodgkin Lymphomas: Bioinformatic Analysis and Assessment of Their Prognostic Value in an NHL Cohort. Int J Mol Sci 2021; 23:ijms23010201. [PMID: 35008626 PMCID: PMC8745130 DOI: 10.3390/ijms23010201] [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: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Research has been focusing on identifying novel biomarkers to better stratify non-Hodgkin lymphoma patients based on prognosis. Studies have demonstrated that lncRNAs act as miRNA sponges, creating ceRNA networks to regulate mRNA expression, and its deregulation is associated with lymphoma development. This study aimed to identify novel circulating prognostic biomarkers based on miRNA/lncRNA-associated ceRNA network for NHL. Herein, bioinformatic analysis was performed to construct ceRNA networks for hsa-miR-150-5p and hsa-miR335-5p. Then, the prognostic value of the miRNA–lncRNA pairs’ plasma levels was assessed in a cohort of 113 NHL patients. Bioinformatic analysis identified MALAT1 and NEAT1 as hsa-miR-150-5p and has-miR-335-5p sponges, respectively. Plasma hsa-miR-150-5p/MALAT1 and hsa-miR335-5p/NEAT1 levels were significantly associated with more aggressive and advanced disease. The overall survival and progression-free survival analysis indicated that hsa-miR-150-5p/MALAT1 and hsa-miR335-5p/NEAT1 pairs’ plasma levels were remarkably associated with NHL patients’ prognosis, being independent prognostic factors in a multivariate Cox analysis. Low levels of hsa-miR-150-5p and hsa-miR-335-5p combined with high levels of the respective lncRNA pair were associated with poor prognosis of NHL patients. Overall, the analysis of ceRNA network expression levels may be a useful prognostic biomarker for NHL patients and could identify patients who could benefit from more intensive treatments.
Collapse
MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cohort Studies
- Computational Biology
- Disease-Free Survival
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Lymphoma, Non-Hodgkin/blood
- Lymphoma, Non-Hodgkin/genetics
- MicroRNAs/blood
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Prognosis
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Risk Factors
Collapse
Affiliation(s)
- Mara Fernandes
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s—PT Government Associate Laboratory, 4805-017 Braga/Guimarães, Portugal
- Department of Oncology, Hospital de Braga, 4710-243 Braga, Portugal
- CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University (UFP), 4249-004 Porto, Portugal
- Correspondence: ; Tel.: +351-225-084-000 (ext. 5414)
| |
Collapse
|
24
|
Fa B, Wei T, Zhou Y, Johnston L, Yuan X, Ma Y, Zhang Y, Yu Z. GapClust is a light-weight approach distinguishing rare cells from voluminous single cell expression profiles. Nat Commun 2021; 12:4197. [PMID: 34234139 PMCID: PMC8263561 DOI: 10.1038/s41467-021-24489-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/02/2021] [Indexed: 01/07/2023] Open
Abstract
Single cell RNA sequencing (scRNA-seq) is a powerful tool in detailing the cellular landscape within complex tissues. Large-scale single cell transcriptomics provide both opportunities and challenges for identifying rare cells playing crucial roles in development and disease. Here, we develop GapClust, a light-weight algorithm to detect rare cell types from ultra-large scRNA-seq datasets with state-of-the-art speed and memory efficiency. Benchmarking on diverse experimental datasets demonstrates the superior performance of GapClust compared to other recently proposed methods. When applying our algorithm to an intestine and 68 k PBMC datasets, GapClust identifies the tuft cells and a previously unrecognised subtype of monocyte, respectively.
Collapse
Affiliation(s)
- Botao Fa
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Zhou
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Luke Johnston
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yuan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Centre for Biostatistics, Shanghai Jiao Tong University, Shanghai, China.
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China.
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
25
|
Comparative genomics in the search for conserved long noncoding RNAs. Essays Biochem 2021; 65:741-749. [PMID: 33885137 PMCID: PMC8564735 DOI: 10.1042/ebc20200069] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as prominent regulators of gene expression in eukaryotes. The identification of lncRNA orthologs is essential in efforts to decipher their roles across model organisms, as homologous genes tend to have similar molecular and biological functions. The relatively high sequence plasticity of lncRNA genes compared with protein-coding genes, makes the identification of their orthologs a challenging task. This is why comparative genomics of lncRNAs requires the development of specific and, sometimes, complex approaches. Here, we briefly review current advancements and challenges associated with four levels of lncRNA conservation: genomic sequences, splicing signals, secondary structures and syntenic transcription.
Collapse
|
26
|
El-Desoky MM, Shemies RS, El-Bahnasawy AS, Mostafa N, Elhelaly M. Dysregulation in growth arrest-specific 5 and metastasis-associated lung adenocarcinoma transcript 1 gene expression predicts diagnosis and renal fibrosis in systemic lupus erythematosus patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-020-00112-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Background
Biomarkers that enhance overall diagnosis and prognosis of systemic lupus erythematosus (SLE) have a growing need to be recognized. The use of long non-coding ribonucleic acids (lncRNAs) as biomarkers in this regard is still largely unexplored. This study aimed to evaluate lncRNA [metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and growth arrest-specific 5 (GAS5)] expression in SLE patients with/without nephritis. Their relation to disease activity/chronicity changes has been identified. A total of 40 SLE patients and 40 healthy controls were tested using real-time quantitative polymerase chain reaction (PCR) for expression levels of MALAT1 and GAS5.
Results
MALAT1 expression was aberrantly upregulated, while GAS5 was downregulated in patients with SLE versus controls. GAS5 relative expression was significantly downregulated in lupus nephritis (LN) patients compared to non-lupus nephritis (NN) patients. GAS5 was also correlated with glomerulosclerosis, interstitial fibrosis, tubular atrophy, and hypertension.
Conclusion
The lncRNA (GAS5 and MALAT1) may serve as diagnostic biomarkers for SLE. Moreover, GAS5 may distinguish SLE LN patients from NN patients and may predict renal fibrosis in LN patients.
Collapse
|
27
|
Exosomes in Immune Regulation. Noncoding RNA 2021; 7:ncrna7010004. [PMID: 33435564 PMCID: PMC7838779 DOI: 10.3390/ncrna7010004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/26/2020] [Accepted: 01/04/2021] [Indexed: 02/08/2023] Open
Abstract
Exosomes, small extracellular vesicles mediate intercellular communication by transferring their cargo including DNA, RNA, proteins and lipids from cell to cell. Notably, in the immune system, they have protective functions. However in cancer, exosomes acquire new, immunosuppressive properties that cause the dysregulation of immune cells and immune escape of tumor cells supporting cancer progression and metastasis. Therefore, current investigations focus on the regulation of exosome levels for immunotherapeutic interventions. In this review, we discuss the role of exosomes in immunomodulation of lymphoid and myeloid cells, and their use as immune stimulatory agents to elicit specific cytotoxic responses against the tumor.
Collapse
|
28
|
Paronetto MP, Dimauro I, Grazioli E, Palombo R, Guidotti F, Fantini C, Sgrò P, De Francesco D, Di Luigi L, Capranica L, Caporossi D. Exercise-mediated downregulation of MALAT1 expression and implications in primary and secondary cancer prevention. Free Radic Biol Med 2020; 160:28-39. [PMID: 32768573 DOI: 10.1016/j.freeradbiomed.2020.06.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 01/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in various biological functions and disease processes including cancer. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) was initially identified as a lncRNA with elevated expression in primary human non-small cell lung tumors with high propensity to metastasize, and subsequently shown to be highly expressed in numerous other human cancers including breast, ovarian, prostate, cervical, endometrial, gastric, pancreatic, sarcoma, colorectal, bladder, brain, multiple myeloma, and lymphoma. MALAT1 is deeply involved in several physiological processes, including alternative splicing, epigenetic modification of gene expression, cellular senescence, healthy aging, and redox homeostasis. The aim of this work was to investigate the modulation exerted by a single bout of endurance exercise on the level of MALAT1 expression in peripheral blood mononuclear cells (PBMCs) from healthy male donors displaying different training status and redox homeostasis features. Our findings show that MALAT1 is downregulated after acute endurance exercise in subjects whose fitness level guarantee a high expression of SOD1 and SOD2 antioxidant genes and low levels of endogenous oxidative damage. In vitro protocols in Jurkat lymphoblastoid cells exposed to pro-oxidant environment confirmed the link between MALAT1 expression and antioxidant gene modulation, documenting p53 phosphorylation and its recruitment to MALAT1 promoter. Remarkably, analyses of Microarray-Based Gene Expression Profiling revealed high MALAT1 expression in leukemia patients in comparison to healthy control and a significant negative correlation between MALAT1 and SOD1 expression. Collectively our results highlight the beneficial effect of a physically active lifestyle in counteracting aberrant cancer-related gene expression programs by improving the redox buffering capacity.
Collapse
Affiliation(s)
- Maria Paola Paronetto
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy; Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Elisa Grazioli
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Flavia Guidotti
- Sport Performance Laboratory, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Cristina Fantini
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Paolo Sgrò
- Endocrinology Unit, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Dario De Francesco
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Luigi Di Luigi
- Endocrinology Unit, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Laura Capranica
- Sport Performance Laboratory, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy.
| |
Collapse
|
29
|
Marzano F, Caratozzolo MF, Consiglio A, Licciulli F, Liuni S, Sbisà E, D'Elia D, Tullo A, Catalano D. Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. Front Genet 2020; 11:552490. [PMID: 33193626 PMCID: PMC7531330 DOI: 10.3389/fgene.2020.552490] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily conserved in plants and mammals. In recent years, although a growing number of papers debate the role of plant miRNAs on human gene expression, the molecular mechanisms through which this effect is achieved are still not completely elucidated. Some evidence suggest that this interaction might be sequence specific, and in this work, we investigated this possibility by transcriptomic and bioinformatics approaches. Plant and human miRNA sequences from primary databases were collected and compared for their similarities (global or local alignments). Out of 2,588 human miRNAs, 1,606 showed a perfect match of their seed sequence with the 5′ end of 3,172 plant miRNAs. Further selections were applied based on the role of the human target genes or of the miRNA in cell cycle regulation (as an oncogene, tumor suppressor, or a biomarker for prognosis, or diagnosis in cancer). Based on these criteria, 20 human miRNAs were selected as potential functional analogous of 7 plant miRNAs, which were in turn transfected in different cell lines to evaluate their effect on cell proliferation. A significant decrease was observed in colorectal carcinoma HCT116 cell line. RNA-Seq demonstrated that 446 genes were differentially expressed 72 h after transfection. Noteworthy, we demonstrated that the plant mtr-miR-5754 and gma-miR4995 directly target the tumor-associated long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and nuclear paraspeckle assembly transcript 1 (NEAT1) in a sequence-specific manner. In conclusion, according to other recent discoveries, our study strengthens and expands the hypothesis that plant miRNAs can have a regulatory effect in mammals by targeting both protein-coding and non-coding RNA, thus suggesting new biotechnological applications.
Collapse
Affiliation(s)
- Flaviana Marzano
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Mariano Francesco Caratozzolo
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Arianna Consiglio
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Flavio Licciulli
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Sabino Liuni
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Elisabetta Sbisà
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Domenica D'Elia
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Apollonia Tullo
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Domenico Catalano
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| |
Collapse
|
30
|
Babenko V, Babenko R, Orlov Y. Analyzing a putative enhancer of optic disc morphology. BMC Genet 2020; 21:73. [PMID: 33092545 PMCID: PMC7583307 DOI: 10.1186/s12863-020-00873-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023] Open
Abstract
Background Genome-wide association studies have identified the CDC7-TGFBR3 intergenic region on chromosome 1 to be strongly associated with optic disc area size. The mechanism of its function remained unclear until new data on eQTL markers emerged from the Genotype-Tissue Expression project. The target region was found to contain a strong silencer of the distal (800 kb) Transcription Factor (TF) gene GFI1 (Growth Factor Independent Transcription Repressor 1) specifically in neuroendocrine cells (pituitary gland). GFI1 has also been reported to be involved in the development of sensory neurons and hematopoiesis. Therefore, GFI1, being a developmental gene, is likely to affect optic disc area size by altering the expression of the associated genes via long-range interactions. Results Distribution of haplotypes in the putative enhancer region has been assessed using the data on four continental supergroups generated by the 1000 Genomes Project. The East Asian (EAS) populations were shown to manifest a highly homogenous unimodal haplotype distribution pattern within the region with the major haplotype occurring with the frequency of 0.9. Another European specific haplotype was observed with the frequency of 0.21. The major haplotype appears to be involved in silencing GFI1repressor gene expression, which might be the cause of increased optic disc area characteristic of the EAS populations. The enhancer/eQTL region overlaps AluJo element, which implies that this particular regulatory element is primate-specific and confined to few tissues. Conclusion Population specific distribution of GFI1 enhancer alleles may predispose certain ethnic groups to glaucoma.
Collapse
Affiliation(s)
- Vladimir Babenko
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia.
| | - Roman Babenko
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia
| | - Yuri Orlov
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia.,I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Trubetskaya 8-2, Moscow, 119991, Russia
| |
Collapse
|
31
|
Shirvani Farsani Z, Zahirodin A, Ghaderian SMH, Shams J, Naghavi Gargari B. The role of long non-coding RNA MALAT1 in patients with bipolar disorder. Metab Brain Dis 2020; 35:1077-1083. [PMID: 32458337 DOI: 10.1007/s11011-020-00580-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 01/08/2023]
Abstract
Bipolar disorders are known as chronic, recurrent, and heterogenic diseases. Regarding, diagnosis and treatment of them are very complex. The molecular mechanism and pathophysiology of bipolar disorder are slightly known. Accordingly, long noncoding RNAs are considered as one of the main factors that are dysfunctional in many diseases such as the nervous system diseases. Hence, we aim to investigate the expression of two long non coding RNAs, MALAT1 and UCA1, in patients in bipolar disorder. The levels of MALAT1 and UCA1 lncRNA were evaluated in peripheral blood mononuclear cells (PBMCs) of 50 bipolar patients and 50 healthy controls with real-time PCR. Also, ROC curve analysis and correlation analysis were performed between the gene expression and some clinical features of bipolar individuals. The significant decline of MALAT1 expression level was found in the patients compared to controls; but no significant difference was observed in the UCA1 expression level between the patients and controls. Furthermore, computational analysis of CpG Islands and miRNAs binding sites on LncRNAs, MALAT1, and UCA1 was conducted. Also, The ROC curve area (AUC) of MALAT1 was 0.80. The current results suggest that the expression level of MALAT1 could serve as a potential diagnostic biomarker for bipolar patients.
Collapse
Affiliation(s)
- Zeinab Shirvani Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, IR, Iran
| | - Alireza Zahirodin
- Behavioral Science Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IR, Iran
| | | | - Jamal Shams
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, IR, Iran
| | - Bahar Naghavi Gargari
- Department of Basic Sciences, Faculty of Nursing & Midwifery, Shahid Beheshti University of Medical Sciences, IR, Tehran, Iran.
| |
Collapse
|
32
|
Chen H, Fan Y, Jing H, Tang S, Zhou J. Emerging role of lncRNAs in renal fibrosis. Arch Biochem Biophys 2020; 692:108530. [PMID: 32768395 DOI: 10.1016/j.abb.2020.108530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
Fibrosis is the final common pathological feature of a wide variety of chronic kidney disease (CKD). However, an understanding of the mechanisms underlying the development of renal fibrosis remains challenging and controversial. As the current focus of molecular research, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular noncoding RNAs (circRNAs), have powerful and abundant biological functions, which essentially makes them mediators of the physiological and pathological processes of various system diseases. The role of ncRNAs in renal fibrosis has also received great attention in recent years, but most research has mainly focused on miRNAs. In fact, although a large number of studies of lncRNAs have emerged recently, the role these molecules play in renal fibrosis haven't been fully understood till now. Thus, this review discusses the discovery of lncRNAs and their biological functions in different types of renal fibrosis, as well as the imminent applications of these findings in clinical use. Undoubtedly, in the future, further understanding of the function of all types of lncRNAs will reveal large breakthroughs in the treatment of renal fibrosis.
Collapse
Affiliation(s)
- Hongtao Chen
- Department of Anesthesiology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong Province, 510060, China
| | - Youling Fan
- Department of Anesthesiology, Panyu Central Hospital, Guangzhou, Guangdong Province, 511400, China
| | - Huan Jing
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China
| | - Simin Tang
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China
| | - Jun Zhou
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China.
| |
Collapse
|
33
|
Samimi H, Sajjadi-Jazi SM, Seifirad S, Atlasi R, Mahmoodzadeh H, Faghihi MA, Haghpanah V. Molecular mechanisms of long non-coding RNAs in anaplastic thyroid cancer: a systematic review. Cancer Cell Int 2020; 20:352. [PMID: 32760219 PMCID: PMC7392660 DOI: 10.1186/s12935-020-01439-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND anaplastic thyroid cancer (ATC) is one of the most lethal and aggressive cancers. Evidence has shown that the tumorigenesis of ATC is a multistep process involving the accumulation of genetic and epigenetic changes. Several studies have suggested that long non-coding RNAs (lncRNAs) may play an important role in the development and progression of ATC. In this article, we have collected the published reports about the role of lncRNAs in ATC. METHODS "Scopus", "Web of Science", "PubMed", "Embase", etc. were systematically searched for articles published since 1990 to 2020 in English language, using the predefined keywords. RESULTS 961 papers were reviewed and finally 33 papers which fulfilled the inclusion and exclusion criteria were selected. Based on this systematic review, among a lot of evidences on examining the function of lncRNAs in thyroid cancer, there are only a small number of studies about the role of lncRNAs and their molecular mechanisms in the pathogenesis of ATC. CONCLUSIONS lncRNAs play a crucial role in regulation of different processes involved in the development and progression of ATC. Currently, just a few lncRNAs have been identified in ATC that may serve as prognosis markers such as GAS5, MIR22HG, and CASC2. Also, because of the dysregulation of Klhl14-AS, HOTAIRM1, and PCA3 during ATC development and progression, they may act as therapeutic targets. However, for most lncRNAs, only a single experiment has evaluated the expression profile in ATC tissues/cells. Therefore, further functional studies and expression profiling is needed to resolve this limitation and identify novel and valid biomarkers.
Collapse
Affiliation(s)
- Hilda Samimi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sayed Mahmoud Sajjadi-Jazi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Soroush Seifirad
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, PERFUSE Study Group, Boston, MA USA
| | - Rasha Atlasi
- Evidence Based Practice Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Department of Surgery, Iranian National Cancer Institute, Imam Khomeini Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Dr. Faghihi’s Medical Genetic Center, Shiraz, Iran
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, USA
| | - Vahid Haghpanah
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center (EMRC), Dr. Shariati Hospital, North Kargar Ave., Tehran, 14114 Iran
| |
Collapse
|
34
|
Tu J, Chen Y, Li Z, Yang H, Chen H, Yu Z. Long non-coding RNAs in ovarian granulosa cells. J Ovarian Res 2020; 13:63. [PMID: 32503679 PMCID: PMC7275442 DOI: 10.1186/s13048-020-00663-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Granulosa cells (GCs) are somatic cells surrounding oocytes within follicles and are essential for folliculogenesis. Pathological changes in GCs are found in several ovarian disorders. Recent reports have indicated that long non-coding RNAs (lncRNAs), which modulate gene expression via multiple mechanisms, are key regulators of the normal development of GCs, follicles, and ovaries. In addition, accumulating evidence has suggested that lncRNAs can be utilized as biomarkers for the diagnosis and prognosis of GC-related diseases, such as polycystic ovary syndrome (PCOS) and premature ovarian insufficiency (POI). Therefore, lncRNAs not only play a role in GCs that are involved in normal folliculogenesis, but they may also be considered as potential candidate biomarkers and therapeutic targets in GCs under pathological conditions. In the future, a detailed investigation of the in vivo delivery or targeting of lncRNAs and large-cohort-validation of the clinical applicability of lncRNAs is required.
Collapse
Affiliation(s)
- Jiajie Tu
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China. .,Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui province, China.
| | - Yu Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China
| | - Zhe Li
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China
| | - Huan Yang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China
| | - He Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China
| | - Zhiying Yu
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518000, Guangdong province, China.
| |
Collapse
|
35
|
LncRNA MALAT1 induces the dysfunction of β cells via reducing the histone acetylation of the PDX-1 promoter in type 1 diabetes. Exp Mol Pathol 2020; 114:104432. [DOI: 10.1016/j.yexmp.2020.104432] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/27/2020] [Accepted: 03/28/2020] [Indexed: 12/14/2022]
|
36
|
Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls. Int J Mol Sci 2020; 21:E3292. [PMID: 32384694 PMCID: PMC7247587 DOI: 10.3390/ijms21093292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid β-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.
Collapse
Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Harald M. Hammon
- Institute of Nutritional Physiology “Oskar Kellner”, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia 4067 QLD, Australia;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
| |
Collapse
|
37
|
Li Y, Liu YD, Chen SL, Chen X, Ye DS, Zhou XY, Zhe J, Zhang J. Down-regulation of long non-coding RNA MALAT1 inhibits granulosa cell proliferation in endometriosis by up-regulating P21 via activation of the ERK/MAPK pathway. Mol Hum Reprod 2020; 25:17-29. [PMID: 30371869 DOI: 10.1093/molehr/gay045] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Is there a specific mechanism underlying the association between lung adenocarcinoma transcript 1 (MALAT1) and endometriosis-related infertility? SUMMARY ANSWER The down-regulation of MALAT1 in endometriosis granulosa cells (GCs) may have an adverse effect on the growth and development of oocytes by inhibiting GC proliferation, due to cell cycle-dependent mechanisms that enhance P21 expression through activation of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) pathway. WHAT IS KNOWN ALREADY The association between endometriosis and infertility is well supported throughout the literature, and endometriosis per se and its surgical treatment have an adverse effect on the ovarian reserve and on oocyte development. MALAT1, one of the most extensively expressed and evolutionarily conserved transcripts, has been implicated to play a role in human development and many diseases. However, little is known about the role of MALAT1 long non-coding RNA (lncRNA) in endometriosis and its associated infertility. STUDY DESIGN, SIZE, DURATION We measured MALAT1 lncRNA expression levels in GCs from 52 endometriosis patients and 52 controls. Also, MALAT1 was knocked down in a human GC tumor-derived cell line, KGN, to investigate the role of MALAT1 and its molecular mechanism in cell proliferation. PARTICIPANTS/MATERIALS, SETTING, METHODS GCs were collected from women with or without endometriosis undergoing IVF or ICSI treatment. All endometriosis patients were diagnosed by laparoscopy or laparotomy, and control patients were limited to male factor or tubal disease and had a normal ovarian reserve. Quantitative real-time PCR (qRT-PCR) was used to measure the differential expression levels of MALAT1 lncRNA between endometriosis patients and controls. The receiver operating characteristic (ROC) curve was drawn to evaluate the diagnostic values of MALAT1 in endometriosis. In the KGN cell line, MALAT1 was knocked down with locked nucleic acid GapmeRs. Cell counting kit-8 assays, ethynyl-2-deoxyuridine assays and flow cytometry were used to study the role of MALAT1 in cell proliferation and cell-cycle progression, and western blotting was performed to detect the potential underlying mechanism. MAIN RESULTS AND THE ROLE OF CHANCE We first found that MALAT1 lncRNA was significantly down-regulated in endometriosis GCs and was associated with the antral follicle count (R = 0.376, P < 0.001 versus control). In addition, MALAT1 lncRNA levels were significantly lower in the GCs of infertile women with advanced stages of endometriosis (P = 0.01 versus control). The ROC curves illustrated strong separation between all the endometriosis patients and the control group (AUC: 0.705; 95% CI: 0.606-0.804; P < 0.001), Stage I-II and control group (AUC: 0.651; 95% CI: 0.536-0.767; P = 0.016), and Stage III-IV and control group (AUC: 0.827; 95% CI: 0.718-0.936; P < 0.001). MALAT1 lncRNA was primarily localized in the nuclei of GCs. We found a negative correlation between MALAT1 lncRNA and P21 mRNA in the GCs from patients (R = -0.628; P < 0.001). MALAT1 knockdown in KGN cells inhibited cell proliferation and cell-cycle progression. In addition, MALAT1 knockdown induced an increase in both the mRNA and protein levels of P21, and of P53, phosphorylated ERK1/2 (p-ERK1/2) and phosphorylated c-Jun N-terminal protein kinase (p-JNK) protein levels, as well as causing a decrease in cyclin dependent kinase 2 (CDK2), cyclin D1 and p-P38 MAPK protein levels. Furthermore, inhibition of the ERK/MAPK pathway with U0126, the up-regulation of p-ERK1/2, P21 and P53, and the down-regulation of CDK2 and cyclin D1 by the knockdown of MALAT1 were all attenuated by MALAT1 knockdown. Therefore, MALAT1 may regulate GC proliferation through P21/P53-dependent control of the cell cycle, and the ERK/MAPK pathway participates in this process. LARGE SCALE DATA None. LIMITATIONS, REASONS FOR CAUTION The hormonal treatment used in IVF and surgical removal of endometriotic lesions may have altered MALAT1 expression in GCs. The ovarian granulosa-like tumor cell line, KGN, was used for further functional and mechanistic studies due to the difficulties in obtaining human GCs in sizable amounts and maintaining primary cultures. WIDER IMPLICATIONS OF THE FINDINGS Our finding represents the first example of an lncRNA-based mechanism in endometriosis GCs. Women with endometriosis show altered MALAT1 expression levels in GCs that may impair fertility by regulating the function of GCs. Therefore, analysis of MALAT1 and its molecular mechanisms of action provide new insights into the pathogenesis of endometriosis and its associated infertility. STUDY FUNDING/COMPETING INTEREST(s) This work was supported by the National Natural Science Foundation of China (grant number: 81671524) and the National key research and development program of China (grant number: 2017YFC1001100). The authors declare there is no conflict of interest.
Collapse
Affiliation(s)
- Ying Li
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yu-Dong Liu
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shi-Ling Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xin Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - De-Sheng Ye
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xing-Yu Zhou
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jing Zhe
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jun Zhang
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| |
Collapse
|
38
|
Fawzy MS, Abu AlSel BT, Al Ageeli E, Al-Qahtani SA, Abdel-Daim MM, Toraih EA. Long non-coding RNA MALAT1 and microRNA-499a expression profiles in diabetic ESRD patients undergoing dialysis: a preliminary cross-sectional analysis. Arch Physiol Biochem 2020; 126:172-182. [PMID: 30270667 DOI: 10.1080/13813455.2018.1499119] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background: Circulating non-coding RNAs (ncRNAs) have been implicated in health and disease. This study aimed to evaluate the serum expression profile of microRNA-499a (miR-499a) and its selected bioinformatically predicted partner long-ncRNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) in diabetes-related end-stage renal disease (ESRD) patients and to correlate the expressions with the patients' clinicolaboratory data.Subjects and methods: Real-time quantitative polymerase chain reaction was applied in diabetics with and without ESRD (n = 90 for each).Results: Serum MALAT1 expression levels were increased in the ESRD group relative to diabetics without ESRD with median (quartile) values of 10.5 (1.41-126.7) (p < .001). However, miR-499a levels were decreased in more than half of ESRD patients with a median of 0.96 (0.13-3.14). Both MALAT1 and miR-499a expression levels were inversely correlated in the ESRD patient-group.Conclusions: MALAT1 up-regulation and miR-499 down-regulation might be involved in diabetic nephropathy-related ESRD pathogenesis. Functional validation studies are warranted to confirm the MALAT1/miR-499a partnership.
Collapse
MESH Headings
- Adult
- Aged
- Base Pairing
- Base Sequence
- Cross-Sectional Studies
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/diagnosis
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/therapy
- Diabetic Nephropathies/diagnosis
- Diabetic Nephropathies/etiology
- Diabetic Nephropathies/genetics
- Diabetic Nephropathies/therapy
- Disease Progression
- Female
- Gene Expression Regulation
- Humans
- Kidney Failure, Chronic/diagnosis
- Kidney Failure, Chronic/etiology
- Kidney Failure, Chronic/genetics
- Kidney Failure, Chronic/therapy
- Male
- MicroRNAs/blood
- MicroRNAs/genetics
- Middle Aged
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- Renal Dialysis
Collapse
Affiliation(s)
- Manal S Fawzy
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Baraah T Abu AlSel
- Department of Microbiology, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, Jazan University, Jazan, Saudi Arabia
| | - Saeed Awad Al-Qahtani
- Department of Physiology, Faculty of Medicine, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman A Toraih
- Department of Histology and Cell Biology (Genetics Unit), Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence of Molecular and Cellular Medicine, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
39
|
Scherer M, Levin M, Butter F, Scheibe M. Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. Int J Mol Sci 2020; 21:ijms21031166. [PMID: 32050583 PMCID: PMC7037011 DOI: 10.3390/ijms21031166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/02/2023] Open
Abstract
The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.
Collapse
|
40
|
Gulati GS, Zukowska M, Noh JJ, Zhang A, Wesche DJ, Sinha R, George BM, Weissman IL, Szade K. Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5+ mouse long-term hematopoietic stem cells. Proc Natl Acad Sci U S A 2019; 116:25115-25125. [PMID: 31754028 PMCID: PMC6911217 DOI: 10.1073/pnas.1911024116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) self-renew and generate all blood cells. Recent studies with single cell transplants and lineage tracing suggest that adult HSCs are diverse in their reconstitution and lineage potentials. However, prospective isolation of these subpopulations has remained challenging. Here, we identify Neogenin-1 (NEO1) as a unique surface marker on a fraction of mouse HSCs labeled with Hoxb5, a specific reporter of long-term HSCs (LT-HSCs). We show that NEO1+Hoxb5+ LT-HSCs expand with age and respond to myeloablative stress in young mice while NEO1-Hoxb5+ LT-HSCs exhibit no significant change in number. Furthermore, NEO1+Hoxb5+ LT-HSCs are more often in the G2/S cell cycle phase compared to NEO1-Hoxb5+ LT-HSCs in both young and old bone marrow. Upon serial transplantation, NEO1+Hoxb5+ LT-HSCs exhibit myeloid-biased differentiation and reduced reconstitution while NEO1-Hoxb5+ LT-HSCs are lineage-balanced and stably reconstitute recipients. Gene expression analysis reveals erythroid and myeloid priming in the NEO1+ fraction and association of quiescence and self-renewal-related transcription factors with NEO1- LT-HSCs. Finally, transplanted NEO1+Hoxb5+ LT-HSCs rarely generate NEO1-Hoxb5+ LT-HSCs while NEO1-Hoxb5+ LT-HSCs repopulate both LT-HSC fractions. This supports a model in which dormant, balanced NEO1-Hoxb5+ LT-HSCs can hierarchically precede active, myeloid-biased NEO1+Hoxb5+ LT-HSCs.
Collapse
Affiliation(s)
- Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305;
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Krzysztof Szade
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305;
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| |
Collapse
|
41
|
Overexpression of MALAT1 Relates to Lung Injury through Sponging miR-425 and Promoting Cell Apoptosis during ARDS. Can Respir J 2019; 2019:1871394. [PMID: 31871512 PMCID: PMC6913333 DOI: 10.1155/2019/1871394] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/21/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Background Acute respiratory distress syndrome (ARDS) is a severe form of acute lung injury during which severe inflammatory responses induce cell apoptosis, necrosis, and fibrosis. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a multiple function long noncoding RNA that was found overexpressed during acute lung injury. However, the roles of MALAT1 in ARDS patients are still unknown. Methods Total RNA was extracted from the plasma, plasma exosome, and peripheral blood mononuclear cells (PBMCs) from 65 ARDS patients and 36 healthy controls. The MALAT1 and six candidate miRNAs levels were detected by qRT-PCR. The interaction between MALAT1 and miR-425 was predicted using a bioinformatics tool and verified by dual luciferase assay. Exosomes from ARDS patients were cultured with A549 and HFL-1 cells to confirm the delivery of miR-425 by exosomes. Cell apoptosis and viability were determined by flow cytometry and MTT assay. Results We found MALAT1 was significantly increased in the ARDS patients' plasma and PBMCs. The MALAT1 level in PBMCs was negatively correlated with exosomal miR-425 level. MALAT1 interacted with miR-425 and protected phosphatase and tensin homolog (PTEN) expression in A549 and HFL-1 cells. Exosomes from ARDS patients delivered less miR-425 into A549 and HFL-1 cells and induced cell apoptosis via upregulating PTEN. Conclusion This study identified increased MALAT1 and decreased miR-425 in ARDS patients and unveiled their roles during the pathogenesis of ARDS.
Collapse
|
42
|
Schwarzenbach H, Gahan PB. Circulating non-coding RNAs in recurrent and metastatic ovarian cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:399-418. [PMID: 35582568 PMCID: PMC8992516 DOI: 10.20517/cdr.2019.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022]
Abstract
Ovarian cancer has a poor outcome because it is usually detected at advanced tumor stages, and the majority of the patients develop disease relapse as a result of chemotherapy resistance. This most lethal gynecological malignancy metastasizes within the peritoneal fluid or ascites to pelvic and distal organs. In ovarian cancer progression and metastasis, small non-coding RNAs (ncRNAs), including long noncoding RNAs and microRNAs have been recognized as important regulators. Their dysregulation modulates gene expression and cellular signal pathways and can be detected in liquid biopsies. In this review, we provide an overview on circulating plasma and serum ncRNAs participating in tumor cell migration and invasion, and contributing to recurrence and metastasis of ovarian cancer. We will also discuss the development of potential, novel therapies using ncRNAs as target molecules or tumor markers for ovarian cancer.
Collapse
Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Peter B Gahan
- Fondazione "Enrico Puccinelli" Onlus, Perugia 06123, Italy
| |
Collapse
|
43
|
Wang ML, Liu JX. MALAT1 rs619586 polymorphism functions as a prognostic biomarker in the management of differentiated thyroid carcinoma. J Cell Physiol 2019; 235:1700-1710. [PMID: 31456244 DOI: 10.1002/jcp.29089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 06/04/2019] [Indexed: 12/15/2022]
Abstract
This study aimed to explore the roles of miR-214 and MALAT1 rs619586 polymorphism in the control and survival of differentiated thyroid carcinoma (DTC) via Cox regression analyses. The levels of MALAT1, miR-214, and CTNNB1 in different experimental groups were compared to study the interaction among MALAT1, miR-214, and CTNNB1. MTT and colony assays were used to investigate the role of rs619586 polymorphism in cell growth. The G allele of rs619586 polymorphism obviously decreased the 5-year survival of patients with DTC. Additionally, compared with AA-genotyped patients, patients carrying the AG/GG genotypes of MALAT1 rs619586 polymorphism showed much higher levels of DTC grade and CTNNB1 expression, along with lower levels of MALAT1 and miR-214 expression. Furthermore, the transcription activity of MALAT1 was significantly lowered by the rs619586G allele or miR-214 mimic, while the miR-214 inhibitor upregulated the luciferase activity of MALAT1. Additionally, miR-214 inhibited CTNNB1 expression by targeting CTNNB1 3'-untranslated region. Finally, the G allele of MALAT1 rs619586 polymorphism apparently promoted cell proliferation. Our study indicated that miR-214 inhibited MALAT1 expression by directly binding to the G allele of MALAT1 rs619586 polymorphism, thus inhibiting CTNNB1 expression and promoting cell proliferation in the pathogenesis of DTC. Therefore, MALAT1 rs619586 polymorphism could be used to predict the prognosis of DTC.
Collapse
Affiliation(s)
- Meng-Li Wang
- Department of Clinical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Jun-Xiao Liu
- Department of Clinical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| |
Collapse
|
44
|
Ma Z, Zhang J, Xu X, Qu Y, Dong H, Dang J, Huo Z, Xu G. LncRNA expression profile during autophagy and Malat1 function in macrophages. PLoS One 2019; 14:e0221104. [PMID: 31425535 PMCID: PMC6699732 DOI: 10.1371/journal.pone.0221104] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of functional non-coding transcripts that are longer than 200 nt and regulate gene expression via diverse mechanisms in eukaryotes. In fact, they have emerged as critical epigenetic and transcriptional regulators of autophagy in mammals in response to various stressors. Autophagy not only plays a crucial role in maintaining cellular homeostasis, but it is also essential to immunity, targets intracellular pathogens for degradation, modulates inflammation, and participates in adaptive immune responses. However, the expression profile of lncRNA and its role in regulating autophagy in macrophages have been poorly defined. Here, we used transcriptomic and bioinformatics to analysis LncRNA expression profile during autophagy and functional studies to evaluate the function of the metastasis-associated lung adenocarcinoma transcript-1 (Malat1) lncRNA in macrophages. A total of 1112 putative lncRNAs (240 novel lncRNAs) were identified, including 831 large intergenic, 129 intronic, and 152 anti-sense lncRNA, of which 59 differentially expressed transcripts exhibited a greater than 1.5-fold change under different conditions. The interaction of Malat1 lncRNA with microRNA (mir)-23-3p and lysosomal-associated membrane protein 1 (Lamp1) was found, Malat1 releases inhibition of Lamp1 expression in macrophages through competitive adsorption of mir-23-3p. The results of this study provide a better understanding of lncRNA function in macrophages and a basis for further investigation into the roles and mechanisms of ncRNA in immunology, particularly the functions of Malat1 and mir-23-3p in the pathogenesis of macrophages.
Collapse
Affiliation(s)
- Zhanbing Ma
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Jing Zhang
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Xiangrong Xu
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yuliang Qu
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Hui Dong
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Jie Dang
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Zhenghao Huo
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Guangxian Xu
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| |
Collapse
|
45
|
Gomes CP, Nóbrega-Pereira S, Domingues-Silva B, Rebelo K, Alves-Vale C, Marinho SP, Carvalho T, Dias S, Bernardes de Jesus B. An antisense transcript mediates MALAT1 response in human breast cancer. BMC Cancer 2019; 19:771. [PMID: 31382922 PMCID: PMC6683341 DOI: 10.1186/s12885-019-5962-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a substantial portion of the human transcriptome. LncRNAs present a very stringent cell-type/tissue specificity being potential candidates for therapeutical applications during aging and disease. As example, targeting of MALAT1, a highly conserved lncRNA originally identified in metastatic non-small cell lung cancer, has shown promising results in cancer regression. Nevertheless, the regulation and specificity of MALAT1 have not been directly addressed. Interestingly, MALAT1 locus is spanned by an antisense transcript named TALAM1. METHODS Here using a collection of breast cancer cells and in vitro and in vivo migration assays we characterized the dynamics of expression and demonstrated that TALAM1 regulates and synergizes with MALAT1 during tumorigenesis. RESULTS Down-regulation of TALAM1 was shown to greatly impact on the capacity of breast cancer cells to migrate in vitro or to populate the lungs of immunocompromised mice. Additionally, we demonstrated that TALAM1 cooperates with MALAT1 in the regulation of the properties guiding breast cancer aggressiveness and malignancy. CONCLUSIONS By characterizing this sense/anti-sense pair we uncovered the complexity of MALAT1 locus regulation, describing new potential candidates for cancer targeting.
Collapse
Affiliation(s)
- Carla Pereira Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Sandrina Nóbrega-Pereira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal.,Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Beatriz Domingues-Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Kenny Rebelo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Catarina Alves-Vale
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Sérgio Pires Marinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Tânia Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Sérgio Dias
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Bruno Bernardes de Jesus
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal. .,Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
| |
Collapse
|
46
|
Kim SS, Harford JB, Moghe M, Rait A, Pirollo KF, Chang EH. Targeted nanocomplex carrying siRNA against MALAT1 sensitizes glioblastoma to temozolomide. Nucleic Acids Res 2019; 46:1424-1440. [PMID: 29202181 PMCID: PMC5815062 DOI: 10.1093/nar/gkx1221] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Intrinsic therapeutic resistance especially in cancer stem cells (CSCs) together with extensive tumor cell infiltration and restricted permeation of the blood-brain barrier (BBB) by drugs may all contribute to the treatment failure in patients with glioblastoma multiforme (GBM). Accumulating evidence suggests that long non-coding RNA (lncRNA), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a role in tumor cell infiltration and therapeutic resistance of GBM. Using our tumor-targeted nanocomplex, we have modulated the expression of MALAT1 and investigated its impact on GBM cells. Importantly, our nanocomplex is able to target CSCs that are considered to be the prime culprits in therapeutic resistance and recurrence of GBM. Attenuation of MALAT1 by RNA interference significantly lowered the growth, motility and stemness of GBM cells. In addition, silencing of MALAT1 clearly improved the sensitivity of GBM cells to chemotherapeutic agents including the current first-line therapy of GBM [temozolomide (TMZ)]. In animal models of GBM, tumor involution with a modest but statistically significant survival benefit was achieved with concurrent treatment of TMZ and nanocomplex-mediated silencing of MALAT1. These results suggest that combining standard TMZ treatment with lncRNA-targeting therapies using our nanocomplex could substantially enhance the very poor prognosis for GBM patients.
Collapse
Affiliation(s)
- Sang-Soo Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.,SynerGene Therapeutics, Inc., Potomac, MD 20854, USA
| | - Joe B Harford
- SynerGene Therapeutics, Inc., Potomac, MD 20854, USA
| | - Manish Moghe
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Antonina Rait
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Kathleen F Pirollo
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Esther H Chang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| |
Collapse
|
47
|
Kong Y, Lu Z, Liu P, Liu Y, Wang F, Liang EY, Hou FF, Liang M. Long Noncoding RNA: Genomics and Relevance to Physiology. Compr Physiol 2019; 9:933-946. [PMID: 31187897 DOI: 10.1002/cphy.c180032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mammalian cell expresses thousands of long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides but do not encode any protein. lncRNAs can change the expression of protein-coding genes through both cis and trans mechanisms, including imprinting and other types of transcriptional regulation, and posttranscriptional regulation including serving as molecular sponges. Deep sequencing, coupled with analysis of sequence characteristics, is the primary method used to identify lncRNAs. Physiological roles of specific lncRNAs can be examined using genetic targeting or knockdown with modified oligonucleotides. Identification of nucleic acids or proteins with which an lncRNA interacts is essential for understanding the molecular mechanism underlying its physiological role. lncRNAs have been reported to contribute to the regulation of physiological functions and disease development in several organ systems, including the cardiovascular, renal, muscular, endocrine, digestive, nervous, respiratory, and reproductive systems. The physiological role of the majority of lncRNAs, many of which are species and tissue specific, remains to be determined. © 2019 American Physiological Society. Compr Physiol 9:933-946, 2019.
Collapse
Affiliation(s)
- Yiwei Kong
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zeyuan Lu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Sir Run Run Shaw Hospital, Institute of Translational Medicine, Zhejiang University, Zhejiang, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Feng Wang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Eugene Y Liang
- Center for Advancing Population Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Fan Fan Hou
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangzhou Regenerative Medicine and Health - Guangdong Laboratory, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| |
Collapse
|
48
|
Seiler KM, Waye SE, Kong W, Kamimoto K, Bajinting A, Goo WH, Onufer EJ, Courtney C, Guo J, Warner BW, Morris SA. Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice. Cell Mol Gastroenterol Hepatol 2019; 8:407-426. [PMID: 31195149 PMCID: PMC6718927 DOI: 10.1016/j.jcmgh.2019.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or "adapt"; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses to characterize molecular changes underpinning adaptation to SGS. METHODS Single-cell RNA sequencing was performed on epithelial cells isolated from distal SI of mice following 50% proximal small bowel resection (SBR) vs sham surgery. Single-cell profiles were clustered based on transcriptional similarity, reconstructing differentiation events from intestinal stem cells (ISCs) through to mature enterocytes. An unsupervised computational approach to score cell identity was used to quantify changes in regional (proximal vs distal) SI identity, validated using immunofluorescence, immunohistochemistry, qPCR, western blotting, and RNA-FISH. RESULTS Uniform Manifold Approximation and Projection-based clustering and visualization revealed differentiation trajectories from ISCs to mature enterocytes in sham and SBR. Cell identity scoring demonstrated segregation of enterocytes by regional SI identity: SBR enterocytes assumed more mature proximal identities. This was associated with significant upregulation of lipid metabolism and oxidative stress gene expression, which was validated via orthogonal analyses. Observed upstream transcriptional changes suggest retinoid metabolism and proximal transcription factor Creb3l3 drive proximalization of cell identity in response to SBR. CONCLUSIONS Adaptation to proximal SBR involves regional reprogramming of ileal enterocytes toward a proximal identity. Interventions bolstering the endogenous reprogramming capacity of SI enterocytes-conceivably by engaging the retinoid metabolism pathway-merit further investigation, as they may increase enteral feeding tolerance, and obviate intestinal failure, in SGS.
Collapse
Affiliation(s)
- Kristen M Seiler
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Sarah E Waye
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - William H Goo
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Cathleen Courtney
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Jun Guo
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Brad W Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
| |
Collapse
|
49
|
Stone JK, Kim JH, Vukadin L, Richard A, Giannini HK, Lim STS, Tan M, Ahn EYE. Hypoxia induces cancer cell-specific chromatin interactions and increases MALAT1 expression in breast cancer cells. J Biol Chem 2019; 294:11213-11224. [PMID: 31167784 DOI: 10.1074/jbc.ra118.006889] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/29/2019] [Indexed: 12/18/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA overexpressed in various cancers that promotes cell growth and metastasis. Although hypoxia has been shown to up-regulate MALAT1, only hypoxia-inducible factors (HIFs) have been implicated in activation of the MALAT1 promoter in specific cell types and other molecular mechanisms associated with hypoxia-mediated MALAT1 up-regulation remain largely unknown. Here, we demonstrate that hypoxia induces cancer cell-specific chromatin-chromatin interactions between newly identified enhancer-like cis-regulatory elements present at the MALAT1 locus. We show that hypoxia-mediated up-regulation of MALAT1 as well as its antisense strand TALAM1 occurs in breast cancer cells, but not in nontumorigenic mammary epithelial cells. Our analyses on the MALAT1 genomic locus discovered three novel putative enhancers that are located upstream and downstream of the MALAT1 gene body. We found that parts of these putative enhancers are epigenetically modified to a more open chromatin state under hypoxia in breast cancer cells. Furthermore, our chromosome conformation capture experiment demonstrated that noncancerous cells and breast cancer cells exhibit different interaction profiles under both normoxia and hypoxia, and only breast cancer cells gain specific chromatin interactions under hypoxia. Although the HIF-2α protein can enhance the interaction between the promoter and the putative 3' enhancer, the gain of chromatin interactions associated with other upstream elements, such as putative -7 and -20 kb enhancers, were HIF-independent events. Collectively, our study demonstrates that cancer cell-specific chromatin-chromatin interactions are formed at the MALAT1 locus under hypoxia, implicating a novel mechanism of MALAT1 regulation in cancer.
Collapse
Affiliation(s)
- Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Lana Vukadin
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Hannah K Giannini
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Ssang-Taek Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama 36688
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604.,Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama 36688
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604 .,Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama 36688
| |
Collapse
|
50
|
Yang J, Wang X. Role of long non-coding RNAs in lymphoma: A systematic review and clinical perspectives. Crit Rev Oncol Hematol 2019; 141:13-22. [PMID: 31202125 DOI: 10.1016/j.critrevonc.2019.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/04/2019] [Accepted: 05/10/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), are over 200 nucleotides in length, and they rarely act as templates for protein synthesis. Mounting studies have shown that lncRNAs play a crucial regulatory role in various processes that sustain life, such as epigenetic regulation, cell cycle control, splicing, and post-transcriptional regulation. LncRNAs were aberrantly expressed in most hematological malignancies including lymphoma, participating in tumor suppression or promoting oncogenesis and modulating key genes in different pathways. The specific expression patterns of lncRNAs in lymphoma make them good candidates to be used as diagnostic biomarkers or as therapeutic targets. LncRNAs can be targeted by multiple approaches including nucleic acid therapeutics, CRISPR/Cas genome editing techniques, small molecule inhibitors, and gene therapy. Efforts are made to develop therapeutic strategies aimed at targeting lncRNAs, but there are still some avenues to be covered before they can be applied to the clinical treatment of lymphoma.
Collapse
Affiliation(s)
- Juan Yang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, 250021, China; School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, 250021, China; School of Medicine, Shandong University, Jinan, Shandong, 250012, China; Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China; Key Laboratory for Kidney Regeneration of Shandong Province, Jinan, Shandong, 250021, China.
| |
Collapse
|