1
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Wang H, Gao Y, Vafaei S, Yu Q, Zhang J, Wang L. A chemoresistance lncRNA signature for recurrence risk stratification of colon cancer patients with chemotherapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:427-438. [PMID: 35036055 PMCID: PMC8733234 DOI: 10.1016/j.omtn.2021.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/09/2021] [Indexed: 02/07/2023]
Abstract
Chemotherapy is considered the nonsurgical treatment of choice for colon cancer patients. However, no precise molecular markers are available to determine which patients can actually benefit from it. In this study, we identified 55 chemotherapy-specific long non-coding RNAs (lncRNAs) of colon cancer patients through a systematic assessment of lncRNA expression profiles from a public database. These were taken from multiple cohorts of colon cancer patients who had received chemotherapy, or not. Based on these data, a chemoresistance lncRNA signature, named CRLSig, was constructed and successfully applied to divide chemotherapy patients into two groups with different recurrence-free survival (RFS) rates. Gene set enrichment analysis revealed that patients with low CRLSig had more infiltrating CD8+ T cells and macrophages, while those with high CRLSig had more infiltrating natural killer T cells. KEGG pathway analysis revealed that the low CRLSig group had more activated metabolic pathways compared with those in the high CRLSig group, indicating better response to chemotherapy. Single-cell sequencing analysis revealed that stromal cells and epithelial cells had higher CRLSig. Thus, we have constructed an auxiliary prognostic tool, CRLSig, able to discriminate patients at high risk of RFS, despite having received standard adjuvant chemotherapy treatment. A CRLSig was constructed for the first time CRLSig revealed chemotherapy patients with different RFS rates Low CRLSig group had more activated metabolic pathways ScRNA-seq analysis revealed stromal cells and epithelial cells had higher CRLSig
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Affiliation(s)
- Hao Wang
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuzhen Gao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Biomedical Research Center, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310013, China
| | - Somayeh Vafaei
- Department of Molecular Medicine, Faculty of advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Qiaoyan Yu
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Biomedical Research Center, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310013, China
| | - Liangjing Wang
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
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2
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Xie G, Peng Z, Liang J, Larabee SM, Drachenberg CB, Yfantis H, Raufman JP. Zinc finger protein 277 is an intestinal transit-amplifying cell marker and colon cancer oncogene. JCI Insight 2022; 7:150894. [PMID: 35015732 PMCID: PMC8876557 DOI: 10.1172/jci.insight.150894] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/05/2022] [Indexed: 01/10/2023] Open
Abstract
Sustained proliferative signaling and resisting cell death are hallmarks of cancer. Zinc finger protein 277 (ZNF277; murine Zfp277), a transcription factor regulating cellular senescence, is overexpressed in colon cancer, but its actions in intestinal homeostasis and neoplasia are unclear. Using human and murine intestine, human colon cancer cells, and ApcMin/+ mice with dysregulated β-catenin signaling and exuberant intestinal neoplasia, we explored the actions of ZNF277/Zfp277 and defined the underlying mechanisms. In normal human and murine intestine, ZNF277/Zfp277 was expressed uniquely in early stem cell progenitors, undifferentiated transit-amplifying cells (TACs). Zfp277 was overexpressed in the ApcMin/+ mouse colon, implicating ZNF277/Zfp277 as a transcriptional target of β-catenin signaling. We confirmed this by showing β-catenin knockdown reduced ZNF277 expression and, using chromatin IP, identified 2 β-catenin binding sites in the ZNF277 promoter. Zfp277 deficiency attenuated intestinal epithelial cell proliferation and tumor formation, and it strikingly prolonged ApcMin/+ mouse survival. RNA-Seq and PCR analyses revealed that Zfp277 modulates expression of genes in key cancer pathways, including β-catenin signaling, the HOXD family that regulates development, and p21WAF1, a cell cycle inhibitor and tumor suppressor. In both human colon cancer cells and the murine colon, ZNF277/Zfp277 deficiency induced p21WAF1 expression and promoted senescence. Our findings identify ZNF277/Zfp277 as both a TAC marker and colon cancer oncogene that regulates cellular proliferation and senescence, in part by repressing p21WAF1 expression.
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Affiliation(s)
- Guofeng Xie
- University of Maryland School of Medicine, Baltimore, United States of America
| | - Zhongsheng Peng
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
| | - Jinqing Liang
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
| | - Shannon M Larabee
- Department of Surgery, University of Maryland School of Medicine, Baltimore, United States of America
| | - Cinthia B Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, United States of America
| | - Harris Yfantis
- Department of Pathology and Laboratory Medicine, Baltimore Veterans Affairs Medical Center, Baltimore, United States of America
| | - Jean-Pierre Raufman
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
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3
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Poliacikova G, Maurel-Zaffran C, Graba Y, Saurin AJ. Hox Proteins in the Regulation of Muscle Development. Front Cell Dev Biol 2021; 9:731996. [PMID: 34733846 PMCID: PMC8558437 DOI: 10.3389/fcell.2021.731996] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes encode evolutionary conserved transcription factors that specify the anterior-posterior axis in all bilaterians. Being well known for their role in patterning ectoderm-derivatives, such as CNS and spinal cord, Hox protein function is also crucial in mesodermal patterning. While well described in the case of the vertebrate skeleton, much less is known about Hox functions in the development of different muscle types. In contrast to vertebrates however, studies in the fruit fly, Drosophila melanogaster, have provided precious insights into the requirement of Hox at multiple stages of the myogenic process. Here, we provide a comprehensive overview of Hox protein function in Drosophila and vertebrate muscle development, with a focus on the molecular mechanisms underlying target gene regulation in this process. Emphasizing a tight ectoderm/mesoderm cross talk for proper locomotion, we discuss shared principles between CNS and muscle lineage specification and the emerging role of Hox in neuromuscular circuit establishment.
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Affiliation(s)
| | | | - Yacine Graba
- Aix-Marseille University, CNRS, IBDM, UMR 7288, Marseille, France
| | - Andrew J Saurin
- Aix-Marseille University, CNRS, IBDM, UMR 7288, Marseille, France
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4
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Wei B, Xiao GR, Wu CL, Xu YQ. HAGLR promotes neuron differentiation through the miR-130a-3p-MeCP2 axis. Open Med (Wars) 2021; 16:1121-1131. [PMID: 34430707 PMCID: PMC8345017 DOI: 10.1515/med-2021-0301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disease. Currently, the molecular mechanisms underlying the progressions of PD are not fully understood. The human neuroblastoma cell line SH-SY5Y has been widely used as an in vitro model for PD. This study aims to investigate the molecular mechanisms of the non-coding RNA-mediated SH-SY5Y differentiation induced by retinoic acid (RA). By microArray analysis, lncRNA HAGLR was observed to be significantly upregulated during the RA-induced SH-SY5Y differentiation. Silencing HAGLR blocked the RA-induced SH-SY5Y differentiation. Moreover, bioinformatical analysis illustrated that miR-130a-3p contains binding sites for HAGLR. The RNA-pull down assay and luciferase assay demonstrated that HAGLR functioned as a ceRNA of miR-130a-3p in SH-SY5Y cells. Overexpression of miR-130a-3p effectively inhibited SH-SY5Y differentiation. We identified MeCP2, a vital molecule in neuronal diseases, to be a direct target of miR-130a-3p in SH-SY5Y cells by western blot and luciferase assays. The rescue experiments verified that recovery of miR-130a-3p in HAGLR-overexpressing SH-SY5Y cells could successfully overcome the RA-induced SH-SY5Y differentiation by targeting MeCP2. In summary, this study reveals a potential molecular mechanism for the lncRNA-HAGLR-promoted in vitro neuron differentiation by targeting the miR-130a-3p-MeCP2 axis, contributing to the understanding of the pathogenesis and progression of PD.
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Affiliation(s)
- Bo Wei
- Department of Neurology, Shaoxing People's Hospital, Shaoxing, Zhejiang, 312000, China
| | - Gui-Rong Xiao
- Department of Neurology, Shaoxing People's Hospital, Shaoxing, Zhejiang, 312000, China
| | - Cheng-Long Wu
- Department of Neurology, Shaoxing People's Hospital, Shaoxing, Zhejiang, 312000, China
| | - Yi-Qin Xu
- Department of Neurology, Shaoxing People's Hospital, Shaoxing, Zhejiang, 312000, China
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5
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Abstract
We have known for decades that long noncoding RNAs (lncRNAs) can play essential functions across most forms of life. The maintenance of chromosome length requires an lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis. Thus, lncRNAs can represent powerful RNA machines. More recently, it has become clear that mammalian genomes encode thousands more lncRNAs. Thus, we raise the question: Which, if any, of these lncRNAs could also represent RNA-based machines? Here we synthesize studies that are beginning to address this question by investigating fundamental properties of lncRNA genes, revealing new insights into the RNA structure-function relationship, determining cis- and trans-acting lncRNAs in vivo, and generating new developments in high-throughput screening used to identify functional lncRNAs. Overall, these findings provide a context toward understanding the molecular grammar underlying lncRNA biology.
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Affiliation(s)
- John L Rinn
- BioFrontiers Institute, Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA;
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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6
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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep 2020; 10:20457. [PMID: 33235280 PMCID: PMC7686352 DOI: 10.1038/s41598-020-77586-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.
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7
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Li J, Jiang X, Li Z, Huang L, Ji D, Yu L, Zhou Y, Cui Y. SP1-induced HOXD-AS1 promotes malignant progression of cholangiocarcinoma by regulating miR-520c-3p/MYCN. Aging (Albany NY) 2020; 12:16304-16325. [PMID: 32857725 PMCID: PMC7485728 DOI: 10.18632/aging.103660] [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: 04/21/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
The purpose of this article is to explore the function and mechanism of HOXD-AS1 in cholangiocarcinoma. TCGA, StarBase and JASPAR were applied to predict the differential expression and molecular mechanism. The qRT-PCR was conducted to detect molecular expression. The effect of HOXD-AS1 on tumor proliferation, metastasis and stemness was measured through corresponding experiments. ChIP, luciferase reporter and RIP assays were implemented to explore the regulatory mechanism of HOXD-AS1 in CCA. In this study, HOXD-AS1 expression was significantly upregulated in CCA tissues and cells compared with control groups, respectively. Increased HOXD-AS1 was markedly correlated with lymph node invasion, advanced TNM stage and poor survival of CCA patients. Moreover, HOXD-AS1 was confirmed to be an unfavorable independent prognostic factor for CCA patients. Functionally, gain- and loss-of-function experiments demonstrated that HOXD-AS1 facilitated tumor proliferation, migration, invasion, EMT, stemness and drug resistance in vitro and in vivo. For the mechanism, transcription factor SP1-induced HOXD-AS1 upregulated oncogene MYCN through competitively binding to miR-520c-3p. Furthermore, HOXD-AS1-induced malignant phenotypes were rescued by interfering miR-520c-3p and MYCN, respectively. SP1/HOXD-AS1/miR-520c-3p/MYCN plays a vital role in initiation and progression of CCA, and HOXD-AS1 is expected to be an efficient biomarker and therapeutic target.
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Affiliation(s)
- Jinglin Li
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Xingming Jiang
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Zhenglong Li
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Lining Huang
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Daolin Ji
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Liang Yu
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Yongxu Zhou
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Yunfu Cui
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
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8
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Sun W, Nie W, Wang Z, Zhang H, Li Y, Fang X. Lnc HAGLR Promotes Colon Cancer Progression Through Sponging miR-185-5p and Activating CDK4 and CDK6 in vitro and in vivo. Onco Targets Ther 2020; 13:5913-5925. [PMID: 32606801 PMCID: PMC7319508 DOI: 10.2147/ott.s246092] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIM LncRNA plays a key role in tumor progression. HAGLR functions as an oncogene in many cancers. However, the molecular mechanism of HAGLR in colon cancer is still unclear. METHODS qRT-PCR was used to measure the expression of HAGLR, miR-185-5p in colon cancer. The expression of CDK4 and CDK6 was detected by Western blot. CCK-8 assay, EdU staining, transwell and Annexin V-FITC/PI assay were used to analyze the effect of HAGLR and miR-185-5p on cell proliferation, invasion, migration and apoptosis. Bioinformatic analysis and luciferase were used to analyze the target genes of HAGLR and miR-185-5p. Nude mice were used to detect mouse tumor changes. RESULTS Compared with normal colon cancer tissues and cells, the expression of HAGLR was increased in colon cancer tissues and cells. In addition, the expression of HAGLR down-regulation inhibited the growth, migration, and invasion of colon cancer cells. MiR-185-5p was reduced in colon cancer, and CDK4 and CDK6 acted as target genes of miR-185-5p to regulate the progress of colon cancer. And CDK4 and CDK6 were predicted as downstream targets of miR-185-5p. Finally, it was demonstrated that HAGLR regulated tumor progression in vivo. CONCLUSION Lnc HAGLR promoted the development of colon cancer by miR-185-5p/CDK4/CDK6 axis, and lnc HAGLR might be potential target for colon cancer.
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Affiliation(s)
- Weixuan Sun
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Wenting Nie
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Zhaoyi Wang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Haolong Zhang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Yezhou Li
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
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9
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Seiler KM, Goo WH, Zhang Q, Courtney C, Bajinting A, Guo J, Warner BW. Adaptation of extracellular matrix to massive small bowel resection in mice. J Pediatr Surg 2020; 55:1107-1112. [PMID: 32164986 PMCID: PMC7299777 DOI: 10.1016/j.jpedsurg.2020.02.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/20/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Extracellular matrix (ECM) affects cell behavior, and vice versa. How ECM changes after small bowel resection (SBR) to support adaptive cellular processes has not been described. Here we characterize changes in ECM following SBR and integrate this with concomitant transcriptional perturbations. METHODS A 50% proximal SBR or sham surgery was performed on mice. On postoperative day 7, ileal tissue was sequentially depleted of protein components to generate an ECM-enriched fraction. ECM was analyzed for protein composition using mass spectrometry with subsequent Ingenuity Pathway Analysis (IPA) to identify predicted pathways and upstream regulators. qPCR and RNA-sequencing (RNA-Seq) were performed to corroborate these predicted pathways. RESULTS 3034 proteins were differentially regulated between sham and SBR, of which 95 were significant (P < 0.05). IPA analysis predicted PPARα agonism to be an upstream regulator of the observed proteomic changes (P < 0.001). qPCR and RNA-Seq with KEGG analysis confirmed significant engagement of the PPAR pathway (P < 0.05). CONCLUSION Transcriptional signatures of adapting bowel predict subsequent ECM changes after SBR. How ECM communicates with surrounding cells to drive adaptation and vice versa merits further investigation. Our findings thus far suggest ECM supports tissue hyperplasia and altered metabolic demand following SBR.
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Affiliation(s)
- Kristen M. Seiler
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | | | - Qiang Zhang
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, MO
| | - Cathleen Courtney
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | - Jun Guo
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO
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10
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Chen KW, Chen JA. Functional Roles of Long Non-coding RNAs in Motor Neuron Development and Disease. J Biomed Sci 2020; 27:38. [PMID: 32093746 PMCID: PMC7041250 DOI: 10.1186/s12929-020-00628-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have gained increasing attention as they exhibit highly tissue- and cell-type specific expression patterns. LncRNAs are highly expressed in the central nervous system and their roles in the brain have been studied intensively in recent years, but their roles in the spinal motor neurons (MNs) are largely unexplored. Spinal MN development is controlled by precise expression of a gene regulatory network mediated spatiotemporally by transcription factors, representing an elegant paradigm for deciphering the roles of lncRNAs during development. Moreover, many MN-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are associated with RNA metabolism, yet the link between MN-related diseases and lncRNAs remains obscure. In this review, we summarize lncRNAs known to be involved in MN development and disease, and discuss their potential future therapeutic applications.
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Affiliation(s)
- Kuan-Wei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
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11
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Darbellay F, Necsulea A. Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs. Mol Biol Evol 2020; 37:240-259. [PMID: 31539080 PMCID: PMC6984365 DOI: 10.1093/molbev/msz212] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for individual lncRNAs. Most lncRNAs with proven functions were implicated in gene expression regulation, in pathways related to cellular pluripotency, differentiation, and organ morphogenesis, suggesting that functional lncRNAs may be more abundant in embryonic development, rather than in adult organs. To test this hypothesis, we perform a multidimensional comparative transcriptomics analysis, across five developmental time points (two embryonic stages, newborn, adult, and aged individuals), four organs (brain, kidney, liver, and testes), and three species (mouse, rat, and chicken). We find that, overwhelmingly, lncRNAs are preferentially expressed in adult and aged testes, consistent with the presence of permissive transcription during spermatogenesis. LncRNAs are often differentially expressed among developmental stages and are less abundant in embryos and newborns compared with adult individuals, in agreement with a requirement for tighter expression control and less tolerance for noisy transcription early in development. For differentially expressed lncRNAs, we find that the patterns of expression variation among developmental stages are generally conserved between mouse and rat. Moreover, lncRNAs expressed above noise levels in somatic organs and during development show higher evolutionary conservation, in particular, at their promoter regions. Thus, we show that functionally constrained lncRNA loci are enriched in developing organs, and we suggest that many of these loci may function in an RNA-independent manner.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anamaria Necsulea
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
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12
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Milan M, Balestrieri C, Alfarano G, Polletti S, Prosperini E, Spaggiari P, Zerbi A, Diaferia GR, Natoli G. FOXA2 controls the cis-regulatory networks of pancreatic cancer cells in a differentiation grade-specific manner. EMBO J 2019; 38:e102161. [PMID: 31531882 PMCID: PMC6792020 DOI: 10.15252/embj.2019102161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/04/2023] Open
Abstract
Differentiation of normal and tumor cells is controlled by regulatory networks enforced by lineage-determining transcription factors (TFs). Among them, TFs such as FOXA1/2 bind naïve chromatin and induce its accessibility, thus establishing new gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the coexistence of well- and poorly differentiated cells at all stages of disease. How the transcriptional networks determining such massive cellular heterogeneity are established remains to be determined. We found that FOXA2, a TF controlling pancreas specification, broadly contributed to the cis-regulatory networks of PDACs. Despite being expressed in both well- and poorly differentiated PDAC cells, FOXA2 displayed extensively different genomic distributions and controlled distinct gene expression programs. Grade-specific functions of FOXA2 depended on its partnership with TFs whose expression varied depending on the differentiation grade. These data suggest that FOXA2 contributes to the regulatory networks of heterogeneous PDAC cells via interactions with alternative partner TFs.
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Affiliation(s)
- Marta Milan
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanoItaly
| | - Chiara Balestrieri
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Gabriele Alfarano
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Sara Polletti
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Elena Prosperini
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | | | - Alessandro Zerbi
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Giuseppe R Diaferia
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanoItaly
| | - Gioacchino Natoli
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
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13
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Li L, Wang Y, Song G, Zhang X, Gao S, Liu H. HOX cluster-embedded antisense long non-coding RNAs in lung cancer. Cancer Lett 2019; 450:14-21. [PMID: 30807784 DOI: 10.1016/j.canlet.2019.02.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
Homeobox (HOX) genes play vital roles in embryonic development and oncogenesis. In humans, there are 39 HOX genes found in four clusters that are located on different chromosomes. The HOX clusters also contain numerous non-protein-coding RNAs, including some lncRNAs. The HOX cluster-embedded lncRNAs (HOX-lncRNAs), most notably, HOTTIP and HOTAIR play a major role in the regulation of their adjacent coding genes. Recently, most HOX-lncRNAs have been shown to impact tumorigenesis and cancer progression. Several HOX-lncRNAs, including HOTTIP, HOXA11-AS, HOTAIRM1, HOXA-AS3, HOXA10-AS, HOTAIR, and HAGLR, are dysregulated in lung cancer. Moreover, their expression levels are correlated with the clinical features of this disease. These HOX-lncRNAs regulate the proliferation, invasion, migration, and chemo-resistance of lung cancer cells through various molecular mechanisms. Although lncRNAs have received much attention lately, the functions of some HOX-lncRNAs in the development of cancer are unclear. Thus, HOX-embedded lncRNAs should be widely investigated in cancer. Here, we review the functions of HOX-lncRNAs in lung cancer.
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Affiliation(s)
- Lianlian Li
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan, 250102, China
| | | | - Xiaoyu Zhang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Shan Gao
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Hongyan Liu
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China.
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14
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Li L, Wang Y, Zhang X, Huang Q, Diao Y, Yin H, Liu H. Long non-coding RNA HOXD-AS1 in cancer. Clin Chim Acta 2018; 487:197-201. [DOI: 10.1016/j.cca.2018.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 01/26/2023]
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15
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Wang F, Liang R, Soibam B, Yang J, Liu Y. Coregulatory long non-coding RNA and protein-coding genes in serum starved cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:84-95. [PMID: 30503397 DOI: 10.1016/j.bbagrm.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 11/29/2022]
Abstract
Serum starvation is widely used in cell biology to trigger cell cycle arrest, apoptosis, autophagy, and metabolic adaptations. Serum starvation-related molecular events have been well characterized at protein level but not at transcript level: how long non-coding RNAs contribute to the regulation of protein-coding genes is largely unknown. Here, we captured the lncRNA transcriptome in serum starved mouse embryonic fibroblasts and identified three main modes of action: cis-acting/coregulatory, trans-acting, and "miRNA-carrier". Whole-genome and individual gene level analyses support that our annotation provides an important platform for understanding lncRNA/protein-coding gene coregulatory mechanisms in serum starvation.
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Affiliation(s)
- Fan Wang
- Department of Oncology, the First Affiliated Hospital of Xian Jiaotong University, Xi'an, Shaanxi Province 710061, China; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, United States of America
| | - Rui Liang
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, United States of America
| | - Benjamin Soibam
- Computer Science and Engineering Technology, University of Houston-Downtown, Houston, TX 77002, United States of America.
| | - Jin Yang
- Department of Oncology, the First Affiliated Hospital of Xian Jiaotong University, Xi'an, Shaanxi Province 710061, China.
| | - Yu Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, United States of America.
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16
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Kindgren P, Ard R, Ivanov M, Marquardt S. Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Nat Commun 2018; 9:4561. [PMID: 30385760 PMCID: PMC6212407 DOI: 10.1038/s41467-018-07010-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023] Open
Abstract
Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions. The function of most lncRNA is unknown. Here, the authors show that transcriptional read-through at the Arabidopsis SVALKA locus produces a cryptic lncRNA that overlaps with the neighboring cold-responsive CBF1 gene and limits CBF1 expression via an RNA polymerase II collision-based mechanism.
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Affiliation(s)
- Peter Kindgren
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Bulowsvej 34, Frederiksberg, 1871, Denmark
| | - Ryan Ard
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Bulowsvej 34, Frederiksberg, 1871, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Bulowsvej 34, Frederiksberg, 1871, Denmark
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Bulowsvej 34, Frederiksberg, 1871, Denmark.
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17
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Zakany J, Duboule D. Rescue of an aggressive female sexual courtship in mice by CRISPR/Cas9 secondary mutation in vivo. BMC Res Notes 2018; 11:193. [PMID: 29580290 PMCID: PMC5870235 DOI: 10.1186/s13104-018-3307-8] [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: 12/08/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE We had previously reported a mouse line carrying the Atypical female courtship (HoxD Afc ) allele, where an ectopic accumulation of Hoxd10 transcripts was observed in a sparse population of cells in the adult isocortex, as a result of a partial deletion of the HoxD gene cluster. Female mice carrying this allele displayed an exacerbated paracopulatory behavior, culminating in a severe mutilation of the studs' external genitals. To unequivocally demonstrate that this intriguing phenotype was indeed caused by an illegitimate function of the HOXD10 protein, we use CRISPR/Cas9 technology to induce a microdeletion into the homeobox of the Hoxd10 gene in cis with the HoxD Afc allele. RESULTS Females carrying this novel HoxDDel(1-9)d10hd allele no longer mutilate males. We conclude that a brain malfunction leading to a severe pathological behavior can be caused by the mere binding to DNA of a transcription factor expressed ectopically. We also show that in HoxD Afc mice, Hoxd10 was expressed in cells containing glutamate decarboxylase (Gad1) and Cholecystokinin (Cck) transcripts, corroborating our proposal that a small fraction of GABAergic neurons in adult hippocampus may participate to some aspects of female courtship.
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Affiliation(s)
- Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland. .,School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland.
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