1
|
In Silico Identification and Characterization of circRNAs as Potential Virulence-Related miRNA/siRNA Sponges from Entamoeba histolytica and Encystment-Related circRNAs from Entamoeba invadens. Noncoding RNA 2022; 8:ncrna8050065. [PMID: 36287117 PMCID: PMC9607107 DOI: 10.3390/ncrna8050065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Ubiquitous eukaryotic non-coding circular RNAs regulate transcription and translation. We have reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica with esterified 3′ss and 5′ss. Their 5′ss GU-rich elements are essential for their biogenesis and their suggested role in transcription regulation. Here, we explored whether exonic, exonic-intronic, and intergenic circular RNAs are also part of the E. histolytica and E. invadens ncRNA RNAome and investigated their possible functions. Available RNA-Seq libraries were analyzed with the CIRI-full software in search of circular exonic RNAs (circRNAs). The robustness of the analyses was validated using synthetic decoy sequences with bona fide back splice junctions. Differentially expressed (DE) circRNAs, between the virulent HM1:IMSS and the nonvirulent Rahman E. histolytica strains, were identified, and their miRNA sponging potential was analyzed using the intaRNA software. Respectively, 188 and 605 reverse overlapped circRNAs from E. invadens and E. histolytica were identified. The sequence composition of the circRNAs was mostly exonic although different to human circRNAs in other attributes. 416 circRNAs from E. histolytica were virulent-specific and 267 were nonvirulent-specific. Out of the common circRNAs, 32 were DE between strains. Finally, we predicted that 8 of the DE circRNAs could function as sponges of the bioinformatically reported miRNAs in E. histolytica, whose functions are still unknown. Our results extend the E. histolytica RNAome and allow us to devise a hypothesis to test circRNAs/miRNAs/siRNAs interactions in determining the virulent/nonvirulent phenotypes and to explore other regulatory mechanisms during amoebic encystment.
Collapse
|
2
|
RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species. Microorganisms 2022; 10:microorganisms10020396. [PMID: 35208849 PMCID: PMC8874941 DOI: 10.3390/microorganisms10020396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/26/2022] [Accepted: 02/05/2022] [Indexed: 11/17/2022] Open
Abstract
Entamoeba is a genus of Amoebozoa that includes the intestine-colonizing pathogenic species Entamoeba histolytica. To understand the basis of gene regulation in E. histolytica from an evolutionary perspective, we have profiled the transcriptomes of its closely related species E. dispar, E. moshkovskii and E. invadens. Genome-wide identification of transcription start sites (TSS) and polyadenylation sites (PAS) revealed the similarities and differences of their gene regulatory sequences. In particular, we found the widespread initiation of antisense transcription from within the gene coding sequences is a common feature among all Entamoeba species. Interestingly, we observed the enrichment of antisense transcription in genes involved in several processes that are common to species infecting the human intestine, e.g., the metabolism of phospholipids. These results suggest a potentially conserved and compact gene regulatory system in Entamoeba.
Collapse
|
3
|
Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
Collapse
Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| |
Collapse
|
4
|
Kang Y, Wan L, Wang Q, Yin Y, Liu J, Liu L, Wu H, Zhang L, Zhang X, Xu S, Pang D. Long noncoding RNA SNHG1 promotes TERT expression by sponging miR-18b-5p in breast cancer. Cell Biosci 2021; 11:169. [PMID: 34465388 PMCID: PMC8407068 DOI: 10.1186/s13578-021-00675-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) plays a positive role in the progression of human malignant tumors. However, the molecular mechanism of SNHG1 remains elusive in breast cancer. RESULTS LncRNA SNHG1 was upregulated and had a positive relationship with poor prognosis according to bioinformatics analysis in pan-cancer including breast cancer. Silencing SNHG1 inhibited tumorigenesis in breast cancer both in vitro and in vivo. Mechanistically, SNHG1 functioned as a competing endogenous RNA (ceRNA) to promote TERT expression by sponging miR-18b-5p in breast cancer. miR-18b-5p acted as a tumor repressor in breast cancer. Moreover, the combination of SNHG1 knockdown and TERT inhibitor administration showed a synergistic inhibitory effect on breast cancer growth in vivo. Finally, E2F1 as a transcription factor, binding to SNHG1 promoter and enhanced SNHG1 transcription in breast cancer. CONCLUSIONS Our results provide a comprehensive understanding of the oncogenic mechanism of lncRNA SNHG1 in breast cancer. Importantly, we identified a novel E2F1-SNHG1-miR-18b-5p-TERT axis, which may be a potential therapeutic target for breast cancer. Our results also provided a potential treatment for breast cancer when knockdown SNHG1 and TERT inhibitor administration simultaneously.
Collapse
Affiliation(s)
- Yujuan Kang
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Lin Wan
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Qin Wang
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Yanling Yin
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Jiena Liu
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Lei Liu
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Hao Wu
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Lei Zhang
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Xin Zhang
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040 China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150040, China. .,Heilongjiang Academy of Medical Sciences, Harbin, China.
| |
Collapse
|
5
|
Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N. Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica. Sci Rep 2020; 10:20190. [PMID: 33214622 PMCID: PMC7677554 DOI: 10.1038/s41598-020-77010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/02/2020] [Indexed: 01/27/2023] Open
Abstract
Natural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.
Collapse
Affiliation(s)
- Damien Mornico
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France.
| | - Chung-Chau Hon
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France.,Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho. Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikael Koutero
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Christian Weber
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France
| | - Jean-Yves Coppee
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Marie-Agnes Dillies
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Nancy Guillen
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France. .,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France. .,Centre National de La Recherche Scientifique, CNRS ERL9195, Paris, France.
| |
Collapse
|
6
|
Yu Y, Chen Q, Zhang X, Yang J, Lin K, Ji C, Xu A, Yang L, Miao L. Long noncoding RNA ANRIL promotes the malignant progression of cholangiocarcinoma by epigenetically repressing ERRFI1 expression. Cancer Sci 2020; 111:2297-2309. [PMID: 32378752 PMCID: PMC7385372 DOI: 10.1111/cas.14447] [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: 12/10/2019] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have recently been verified to have significant regulatory functions in many types of human cancers. The lncRNA ANRIL is transcribed from the INK4b-ARF-INK4a gene cluster in the opposite direction. Whether ANRIL can act as an oncogenic molecule in cholangiocarcinoma (CCA) remains unknown. Our data show that ANRIL knockdown greatly inhibited CCA cell proliferation and migration in vitro and in vivo. According to the results of RNA sequencing analysis, ANRIL knockdown dramatically altered target genes associated with the cell cycle, cell proliferation, and apoptosis. By binding to a component of the epigenetic modification complex enhancer of zeste homolog 2 (EZH2), ANRIL could maintain lysine residue 27 of histone 3 (H3K27me3) levels in the promoter of ERBB receptor feedback inhibitor 1 (ERRFI1), which is a tumor suppressor gene in CCA. In this way, ERRFI1 expression was suppressed in CCA cells. These data verified the key role of the epigenetic regulation of ANRIL in CCA oncogenesis and indicate its potential as a target for CCA intervention.
Collapse
Affiliation(s)
- Yang Yu
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Qiaoyu Chen
- Department of Pathology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Xunlei Zhang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Jian Yang
- Department of Urology, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kaibo Lin
- Department of Assisted Reproduction, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Congfei Ji
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Aibing Xu
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Lei Yang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Lin Miao
- Medical Centre for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
7
|
Jiang T, Wang C, Zhu Y, Han H. LINC01410 promotes cell proliferation and migration of cholangiocarcinoma through modulating miR-124-3p/SMAD5 axis. J Gene Med 2020; 22:e3162. [PMID: 31951299 DOI: 10.1002/jgm.3162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 01/02/2020] [Accepted: 01/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is generally associated with high incidence and poor prognosis. Nowadays, increasing experimental data demonstrate that long non-coding RNA (lncRNA) plays an indispensable role in tumor occurrence. Nevertheless, the specific mechanism of lncRNA is not clear in CCA. METHODS The relative expressions of lncRNAs, miRNAs, and mRNAs were detected by real-time quantitative PCR (RT-qPCR). CCK8 and colony formation assays were applied to examine cell proliferation ability in CCA. Transwell assay was conducted to measure the migration and invasion capabilities of CCA cells. Nuclear and cytoplasmic separation assay was implemented to figure out the location of LINC01410. Luciferase reporter assay, RIP and RNA pull-down assays were applied to certify the molecular bindings. Western blot was applied to detect the protein level. RESULTS The high expression of LINC01410 was proved in CCA tissues and CCA cell lines. Also, CCA patients with high LINC01410 level presented poor prognosis. LINC01410 deficiency impeded cell proliferation, migration and invasion in HuCCT1 and RBE cell lines. What's more, LINC01410 interacted with miR-124-3p. Meanwhile, SMAD5 targeted and inhibited by miR-124-3p. SMAD5 expression was enhanced by LINC01410. CONCLUSION LINC01410 facilitates cell proliferation, migration and invasion through miR-124-3p/SMAD5 axis.
Collapse
Affiliation(s)
- Tao Jiang
- Department of Hepatobiliary surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Chunlin Wang
- Department of Hepatobiliary surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Yunxie Zhu
- Department of Hepatobiliary surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Huaxin Han
- Department of Hepatobiliary surgery, Guizhou Provincial Guandu Central Health Center, Chishui, Guizhou, China
| |
Collapse
|
8
|
Yu Y, Yang J, Yang S, Li Q, Zhang M, Wang L, Ji G, Miao L. Expression level and clinical significance of SNHG1 in human cancers: a meta-analysis. Onco Targets Ther 2019; 12:3119-3127. [PMID: 31114252 PMCID: PMC6497895 DOI: 10.2147/ott.s184803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/11/2019] [Indexed: 12/26/2022] Open
Abstract
Background: As reported by numerous research studies, the expression levels of SNHG1 (small nucleolar RNA host gene 1) are increased in different kinds of tumours, revealing that SNHG1 is likely to perform a crucial function in cancer prevalence and progression. Moreover, a mounting degree of evidence suggests that increased SNHG1 expression also has an association with poor medical outcomes among cancer patients. Materials and methods: Collection of qualifying research studies was performed through the retrieval of keywords in PubMed and Web of Science, up to March 20, 2018. This quantitative meta-analysis was carried out using Stata SE12.0 software and aimed at exploring the connection between the expression level of SNHG1 and clinicopathology. Results: Ten research studies, involving an aggregate of 715 patients, met the inclusion criteria. As suggested by the findings of the current meta-analysis, with regard to prognosis, the patients with high expression of SNHG1 had poorer overall survival (OS) (HR =3.36, 95% CI: 2.42, 4.67) and, with regard to their clinicopathology, increased SNHG1 was associated with advanced TNM stage (RR =1.88, 95% CI: 1.58, 2.24), poorly differentiated histological grade (RR =1.38, 95% CI:1.09, 1.76), and positive lymph node metastasis (RR =1.80, 95% CI: 1.42, 2.29). Conclusion: As revealed by this meta-analysis, elevated SNHG1 expression is typical in various types of cancer. In addition, elevated SNHG1 expression is likely to function as an advanced predictive element of poor prognosis and lymph node metastasis in various cancer types. Nonetheless, to date, it remains essential to carry out larger-size and better-designed research studies for the confirmation of our findings.
Collapse
Affiliation(s)
- Yang Yu
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Jian Yang
- Department of Urology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Shengquan Yang
- Department of Orthopaedics, The No. 1 People's Hospital of Yancheng, Yancheng, Jiangsu Province, People's Republic of China
| | - Quanpeng Li
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Mingjiong Zhang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lijuan Wang
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Guozhong Ji
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lin Miao
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| |
Collapse
|
9
|
Naiyer S, Kaur D, Ahamad J, Singh SS, Singh YP, Thakur V, Bhattacharya A, Bhattacharya S. Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica. BMC Genomics 2019; 20:206. [PMID: 30866809 PMCID: PMC6416950 DOI: 10.1186/s12864-019-5570-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
Background Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the nature of highly transcribed genes, and downstream promoter motifs important for gene expression. To address these issues we generated RNA-Seq data and identified the high and low expressing genes, especially with respect to virulence potential. We analysed sequences both upstream and downstream of start site for important motifs. Results We used RNA-Seq data to classify genes according to expression levels, which ranged six orders of magnitude. Data were validated by reporter gene expression. Virulence-related genes (except AIG1) were amongst the highly expressed, while some kinases and BspA family genes were poorly expressed. We looked for conserved motifs in sequences upstream and downstream of the initiation codon. Following enrichment by AME we found seven motifs significantly enriched in high expression- and three in low expression-classes. Two of these motifs (M4 and M6) were located downstream of AUG, were exclusively enriched in high expression class, and were mostly found in ribosomal protein, and translation-related genes. Motif deletion resulted in drastic down regulation of reporter gene expression, showing functional relevance. Distribution of core promoter motifs (TATA, GAAC, and Inr) in all genes revealed that genes with downstream motifs were not preferentially associated with TATA-less promoters. We looked at gene expression changes in cells subjected to growth stress by serum starvation, and experimentally validated the data. Genes showing maximum up regulation belonged to the low or medium expression class, and included genes in signalling pathways, lipid metabolism, DNA repair, Myb transcription factors, BspA, and heat shock. Genes showing maximum down regulation belonged to the high or medium expression class. They included genes for signalling factors, actin, Ariel family, and ribosome biogenesis factors. Conclusion Our analysis has added important new information about the E. histolytica transcriptome. We report for the first time two downstream motifs required for gene expression, which could be used for over expression of E. histolytica genes. Most of the virulence-related genes in this parasite are highly expressed in culture. Electronic supplementary material The online version of this article (10.1186/s12864-019-5570-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Vivek Thakur
- Centre for Systems Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
10
|
Yu Y, Zhang M, Liu J, Xu B, Yang J, Wang N, Yan S, Wang F, He X, Ji G, Li Q, Miao L. Long Non-coding RNA PVT1 Promotes Cell Proliferation and Migration by Silencing ANGPTL4 Expression in Cholangiocarcinoma. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:503-513. [PMID: 30388624 PMCID: PMC6205330 DOI: 10.1016/j.omtn.2018.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022]
Abstract
Cholangiocarcinoma (CCA) is the most common biliary tract malignancy, with a low survival rate and limited treatment options. Long non-coding RNAs (lncRNAs) have recently been verified to have significant regulatory functions in many kinds of human cancers. It was discovered in this study that the lncRNA PVT1, whose expression is significantly elevated in CCA, could be a molecular marker of CCA. Experiments indicated that PVT1 knockdown greatly inhibited cell migration and proliferation in vitro and in vivo. According to RNA sequencing (RNA-seq) analysis, PVT1 knockdown dramatically influenced target genes associated with cell angiogenesis, cell proliferation, and the apoptotic process. RNA immunoprecipitation (RIP) analysis demonstrated that, by binding to epigenetic modification complexes (PRC2), PVT1 could adjust the histone methylation of the promoter of ANGPTL4 (angiopoietin-like 4) and, thus, promote cell growth, migration, and apoptosis progression. The data verified the significant functions of PVT1 in CCA oncogenesis, and they suggested that PVT1 could be a target for CCA intervention.
Collapse
Affiliation(s)
- Yang Yu
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Mingjiong Zhang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Jie Liu
- Reproduction Centre of Xuzhou Maternity and Child Health Care Hospital, Xuzhou, Jiangsu Province, People's Republic of China
| | - Boming Xu
- Department of Gastroenterology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China
| | - Jian Yang
- Department of Urology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Ni Wang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Shuai Yan
- Department of Oncology, Affiliated Jiangyin Hospital of Southeast University Medical College, Jiangyin, Jiangsu Province, People's Republic of China
| | - Fei Wang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xuezhi He
- Research Centre for Bone and Stem Cells, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Guozhong Ji
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Quanpeng Li
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China.
| | - Lin Miao
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China.
| |
Collapse
|
11
|
Epigenetic silencing of tumor suppressor gene CDKN1A by oncogenic long non-coding RNA SNHG1 in cholangiocarcinoma. Cell Death Dis 2018; 9:746. [PMID: 29970899 PMCID: PMC6030364 DOI: 10.1038/s41419-018-0768-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/02/2018] [Accepted: 06/08/2018] [Indexed: 12/17/2022]
Abstract
Cholangiocarcinoma (CCA) is the as the most frequently observed biliary tract malignancy, which has low survival rate in addition to constrained treatment options; nevertheless, the fundamental molecular phenomenon underlying malignant progression of CCA is quite ambiguous. Recently long non-coding RNAs (lncRNAs) have been found to have significant regulatory functions in several human cancers. Herein, we have figured out that lncRNA SNHG1, with substantially enhanced expression in CCA, is capable of acting as the oncogenic molecule of CCA. As revealed by our data, SNHG1 knockdown extensively inhibited CCA cell migration as well as proliferation in vitro and in vivo. In addition, in accordance with the findings of the RNA-Seq analysis, SNHG1 knockdown exhibited a significant impact on the target genes that were linked to cell migration and regulation of cell proliferation, in addition to the apoptotic phenomenon. In a mechanistic manner, we also showed that SNHG1 bound to the histone methyltransferase enhancer of the zeste homolog 2 (EZH2, which is regarded as the catalytic subunit of the polycomb repressive complex 2 (PRC2), which is an extremely conserved protein complex regulating gene expression with the help of methylating lysine 27 on histone H3), specifying the histone alteration pattern on the target genes, including CDKN1A, and, as a result, altered the CCA cell biology. These data verified a major function of the epigenetic regulation of SNHG1 in CCA oncogenesis, in addition to its likely function as a target for CCA interruption.
Collapse
|
12
|
Narayanasamy RK, Castañón-Sanchez CA, Luna-Arias JP, García-Rivera G, Avendaño-Borromeo B, Labra-Barrios ML, Valdés J, Herrera-Aguirre ME, Orozco E. The Entamoeba histolytica TBP and TRF1 transcription factors are GAAC-box binding proteins, which display differential gene expression under different stress stimuli and during the interaction with mammalian cells. Parasit Vectors 2018. [PMID: 29514716 PMCID: PMC5842622 DOI: 10.1186/s13071-018-2698-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Entamoeba histolytica is the protozoan parasite responsible for human amebiasis. It causes up to 100,000 deaths worldwide each year. This parasite has two closely related basal transcription factors, the TATA-box binding protein (EhTBP) and the TBP-related factor 1 (EhTRF1). TBP binds to the canonical TATTTAAA-box, as well as to different TATA variants. TRF1 also binds to the TATTTAAA-box. However, their binding capacity to diverse core promoter elements, including the GAAC-element, and their role in gene regulation in this parasite remains unknown. METHODS EMSA experiments were performed to determine the binding capacity of recombinant TBP and TRF1 to TATA variants, GAAC and GAAC-like boxes. For the functional analysis under different stress stimuli (e.g. growth curve, serum depletion, heat-shock, and UV-irradiation) and during the interaction with mammalian cells (erythrocytes, MDCK cell monolayers, and hepatocytes of hamsters), RT-qPCR, and gene knockdown were performed. RESULTS Both transcription factors bound to the different TATA variants tested, as well as to the GAAC-boxes, suggesting that they are GAAC-box-binding proteins. The K D values determined for TBP and TRF1 for the different TATA variants and GAAC-box were in the range of 10-12 M to 10-11 M. During the death phase of growth or in serum depletion, Ehtbp mRNA levels significantly increased, whereas the mRNA level of Ehtrf1 did not change under these conditions. Ehtrf1 gene expression was negatively regulated by UV-irradiation and heat-shock stress, with no changes in Ehtbp gene expression. Moreover, Ehtrf1 gene also showed a negative regulation during erythrophagocytosis, liver abscess formation, and a transient expression level increase at the initial phase of MDCK cell destruction. Finally, the Ehtbp gene knockdown displayed a drastic decrease in the efficiency of erythrophagocytosis in G3 trophozoites. CONCLUSIONS To our knowledge, this study reveals that these basal transcription factors are able to bind multiple core promoter elements. However, their immediate change in gene expression level in response to different stimuli, as well as during the interaction with mammalian cells, and the diminishing of erythrophagocytosis by silencing the Ehtbp gene indicate the different physiological roles of these transcription factors in E. histolytica.
Collapse
Affiliation(s)
- Ravi Kumar Narayanasamy
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sanchez
- Programa de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del Instituto Politécnico Nacional (ENMH-IPN), Guillermo Massieu Helguera 239, Col. La Escalera, C.P, 07320, Ciudad de México, Mexico.,Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, C.P, 71256, Oaxaca, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico.
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Esther Herrera-Aguirre
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| |
Collapse
|
13
|
Bharadwaj R, Arya R, Shahid mansuri M, Bhattacharya S, Bhattacharya A. EhRho1 regulates plasma membrane blebbing through PI3 kinase inEntamoeba histolytica. Cell Microbiol 2017; 19. [DOI: 10.1111/cmi.12751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/03/2017] [Accepted: 04/16/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ravi Bharadwaj
- School of Biotechnology; Jawaharlal Nehru University; New Delhi India
| | - Ranjana Arya
- School of Biotechnology; Jawaharlal Nehru University; New Delhi India
| | | | - Sudha Bhattacharya
- School of environmental Sciences; Jawaharlal Nehru University; New Delhi India
| | - Alok Bhattacharya
- School of Life Sciences; Jawaharlal Nehru University; New Delhi India
| |
Collapse
|
14
|
Yu Y, Yang J, Li Q, Xu B, Lian Y, Miao L. LINC00152: A pivotal oncogenic long non-coding RNA in human cancers. Cell Prolif 2017; 50. [PMID: 28464433 PMCID: PMC6529135 DOI: 10.1111/cpr.12349] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/01/2017] [Indexed: 12/19/2022] Open
Abstract
In recent years, increasing evidence has shown the potential role of long non‐coding RNAs (lncRNAs) in multiple cancers. Deregulation of lncRNAs was detected being closely associated with many kinds of tumours where they can act as a tumour suppressor or accelerator. LINC00152 was identified as an oncogene involved in many kinds of cancers, such as gastric cancer, hepatocellular carcinoma, colon cancer, gallbladder cancer and renal cell carcinoma. Moreover, inhibition of LINC00152 can suppress proliferation, migration and invasion of the cancer cells. Increasing evidence has showed that LINC00152 may act as a diagnostic and prognostic biomarker for the above‐mentioned cancers. In our review, we summarize the recent research progress of the expression and role of LINC00152 in various kinds of cancers.
Collapse
Affiliation(s)
- Yang Yu
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jian Yang
- Department of Urology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Quanpeng Li
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Boming Xu
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yifan Lian
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Lin Miao
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| |
Collapse
|
15
|
Hendrick HM, Welter BH, Hapstack MA, Sykes SE, Sullivan WJ, Temesvari LA. Phosphorylation of Eukaryotic Initiation Factor-2α during Stress and Encystation in Entamoeba Species. PLoS Pathog 2016; 12:e1006085. [PMID: 27930733 PMCID: PMC5179133 DOI: 10.1371/journal.ppat.1006085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/22/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Entamoeba histolytica is an enteric pathogen responsible for amoebic dysentery and liver abscess. It alternates between the host-restricted trophozoite form and the infective environmentally-stable cyst stage. Throughout its lifecycle E. histolytica experiences stress, in part, from host immune pressure. Conversion to cysts is presumed to be a stress-response. In other systems, stress induces phosphorylation of a serine residue on eukaryotic translation initiation factor-2α (eIF2α). This inhibits eIF2α activity resulting in a general decline in protein synthesis. Genomic data reveal that E. histolytica possesses eIF2α (EheIF2α) with a conserved phosphorylatable serine at position 59 (Ser59). Thus, this pathogen may have the machinery for stress-induced translational control. To test this, we exposed cells to different stress conditions and measured the level of total and phospho-EheIF2α. Long-term serum starvation, long-term heat shock, and oxidative stress induced an increase in the level of phospho-EheIF2α, while short-term serum starvation, short-term heat shock, or glucose deprivation did not. Long-term serum starvation also caused a decrease in polyribosome abundance, which is in accordance with the observation that this condition induces phosphorylation of EheIF2α. We generated transgenic cells that overexpress wildtype EheIF2α, a non-phosphorylatable variant of eIF2α in which Ser59 was mutated to alanine (EheIF2α-S59A), or a phosphomimetic variant of eIF2α in which Ser59 was mutated to aspartic acid (EheIF2α-S59D). Consistent with the known functions of eIF2α, cells expressing wildtype or EheIF2α-S59D exhibited increased or decreased translation, respectively. Surprisingly, cells expressing EheIF2α-S59A also exhibited reduced translation. Cells expressing EheIF2α-S59D were more resistant to long-term serum starvation underscoring the significance of EheIF2α phosphorylation in managing stress. Finally, phospho-eIF2α accumulated during encystation in E. invadens, a model encystation system. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba species. Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess and is prevalent in underdeveloped countries that lack proper sanitation. Infection is acquired by ingestion of the cyst form in contaminated food or water. During infection, the parasite experiences stress including demanding growth conditions and host immune pressure. Conversion to the infective cyst may be induced by such stress. In other organisms, stress causes a decrease in protein biosynthesis by inducing phosphorylation of eIF2α, which participates in translation initiation. We exposed E. histolytica to six different stress conditions and observed that some of these conditions (long-term serum starvation, long-term heat shock, and oxidative stress) induced an increase in the level of phospho-eIF2α. Long-term serum starvation was also accompanied by a decrease in mRNA translation. A cell line expressing a mutant version of eIF2α that behaves as a phosphomimetic exhibited decreased translation and increased survival during long-term serum starvation. Finally, phospho-eIF2α accumulated in cysts of E. invadens, a reptilian pathogen that readily encysts in vitro. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba and may regulate encystation.
Collapse
Affiliation(s)
- Holland M. Hendrick
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Brenda H. Welter
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Matthew A. Hapstack
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Steven E. Sykes
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - William J. Sullivan
- Department of Pharmacology and Toxicology Indiana University School of Medicine Indianaplois, IN United States of America
- Department of Microbiology and Immunology Indiana University School of Medicine Indianapolis, IN United States of America
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
- * E-mail:
| |
Collapse
|
16
|
Morgado P, Manna D, Singh U. Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome. F1000Res 2016; 5:2578. [PMID: 27853522 PMCID: PMC5089142 DOI: 10.12688/f1000research.9241.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 01/04/2023] Open
Abstract
In recent years, substantial progress has been made in understanding the molecular and cell biology of the human parasite
Entamoeba histolytica, an important pathogen with significant global impact. This review outlines some recent advances in the
Entamoeba field in the last five years, focusing on areas that have not recently been discussed in detail: (i) molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis.
Collapse
Affiliation(s)
- Pedro Morgado
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Dipak Manna
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|