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TMEM161B-AS1 suppresses proliferation, invasion and glycolysis by targeting miR-23a-3p/HIF1AN signal axis in oesophageal squamous cell carcinoma

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JOUrnaL OF CELLULAR AND MOLECULAR MEDICINE 2021年第14期25卷 6535-6549页

作者： Shi, Zuxuan Li, Guanghui Li, Zhen Liu, Junhao Tang, Yu Zhengzhou Univ Henan Prov Peoples Hosp Dept Med Oncol Peoples Hosp Zhengzhou Peoples R China Henan Prov Peoples Hosp Dept Endocrinol Zhengzhou Peoples R China Zhengzhou Univ Dept Endocrinol Cent China Fuwai Hosp 1 Fuwai Ave Zhengzhou 451464 Peoples R China

Mounting data have shown that long non-coding rnas (lncrnas) widely participate in tumour initiation, development, progression and glycolysis in a variety of tumours. However, the clinical prognosis and molecular mechanisms of TMEM161B-AS1 in oesophageal squamous cell carcinoma (ESCC) remain still unknown. Here, TMEM161B-AS1 and HIF1AN were significantly lower in ESCC tissues than in normal samples, and their low expressions were both related to TNM stage, lymph node metastasis and poor prognosis of ESCC patients. Functionally, TMEM161B-AS1 overexpression or miR-23a-3p depletion suppressed the proliferation, invasion and glycolysis as well as reduced glucose consumption and lactate production in ESCC cells. Mechanistically, TMEM161B-AS1 manipulated HIF1AN expression by competitively sponging miR-23a-3p in ESCC cells. MiR-23a-3p mimic and HIF1AN sirna partly reversed cell phenotypes mediated by TMEM161B-AS1 in ESCC cells. Collectively, TMEM161B-AS1, miR-23a-3p and HIF1AN may be tightly involved in ESCC development and progression as well as patients' prognosis, and TMEM161B-AS1/miR-23a-3p/HIF1AN signal axis may be a promising target for the treatment of ESCC patients.

关键词： competitive endogenous rna long non‐ coding rna oesophageal squamous cell carcinoma prognosis TMEM161B‐ AS1

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Analysis of the characteristics and expression profiles of coding and noncoding rnas of human dental pulp stem cells in hypoxic conditions

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STEM CELL RESEARCH & THERAPY 2019年第1期10卷 89-89页

作者： Shi, Ruitang Yang, Haoqing Lin, Xiao Cao, Yangyang Zhang, Chen Fan, Zhipeng Hou, Benxiang Capital Med Univ Beijing Stomatol Hosp Sch Stomatol Dept Endodont Beijing Peoples R China Capital Med Univ Lab Mol Signaling & Stem Cells Therapy Beijing Key Lab Tooth Regenerat & Funct Reconstru Beijing Stomatol HospSch Stomatol Beijing Peoples R China Capital Med Univ Sch Stomatol Beijing Stomatol Hosp Dept Implant Dent Beijing Peoples R China

BackgroundHuman dental pulp stem cell (DPSC)-mediated regenerative endodontics is a promising therapy for damaged teeth;however, the hypoxic environment in root canals can affect tissue regeneration. In this study, we investigate the characteristics and possible regulatory mechanisms of DPSC function under hypoxic *** DPSCs were cultured under normoxia (20% O-2) and hypoxia (3% O-2). DPSC proliferation and osteo/odontogenic differentiation potential were assessed by Cell Counting Kit-8 (CCK8) assay, carboxyfluorescein succinimidyl ester (CFSE) assay, alkaline phosphatase (ALP) activity, Alizarin red staining, real-time RT-PCR assays, and western blot analysis. Microarray and bioinformatic analyses were performed to investigate the differences in the mrna, lncrna, and mirna expression profiles of *** exhibited a more powerful proliferation ability and lower osteo/odontogenic differentiation potential in hypoxic conditions. A total of 60 mrnas (25 upregulated and 35 downregulated), 47 lncrnas (20 upregulated and 27 downregulated), and 14 mirnas (7 upregulated and 7 downregulated) in DPSCs were differentially expressed in the hypoxia group compared with the normoxia group. Bioinformatic analysis identified that 7 mrnas (GRPR, ERO1L, ANPEP, EPHX1, PGD, ANGPT1, and NQO1) and 5 lncrnas (AF085958, AX750575, uc002czn.2, RP3-413H6.2, and six-twelve leukemia (STL)) may be associated with DPSCs during hypoxia according to CNC network analysis, while 28 mrnas (including GYS1, PRKACB, and NQO1) and 13 mirnas (including hsa-miR-3916 and hsa-miR-192-5p) may be involved according to mirna target gene network analysis. The depletion of one candidate lncrna, STL, inhibited the osteo/odontogenic differentiation potentials of *** results revealed that hypoxia could enhance the proliferation ability and impair the osteo/odontogenic differentiation potential of DPSCs in vitro. Furthermore, our results identified candidate coding and non

关键词： Hypoxia Dental pulp stem cells (DPSCs) coding rna Long noncoding rna (lncrna) Microrna (mirna)

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Circulating exosomal small rnas are promising non-invasive diagnostic biomarkers for gastric cancer

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JOUrnaL OF CELLULAR AND MOLECULAR MEDICINE 2020年第24期24卷 14502-14513页

作者： Ge, Lichen Zhang, Nan Li, Dandan Wu, Yingmin Wang, Hongsheng Wang, Junjun Nanjing Univ Jinling Hosp Med Sch Dept Clin Lab 305 East Zhongshan Rd Nanjing 210002 Peoples R China Sun Yat Sen Univ Sch Pharmaceut Sci Key Lab Chiral Mol & Drug Discovery Guangzhou Peoples R China

Dysregulation of small non-coding rna (ncrna) is associated with various human diseases including cancer. This study aimed to evaluate the circulating exosomal small rnas including micrornas (mirnas) and P-element-induced wimpy testis (PIWI)-interacting rnas (pirnas) as sensitive and specific non-invasive biomarkers for gastric cancer (GC) diagnosis. Serum exosomal small rna transcriptome was examined using unique molecular identifiers (UMI) small rna sequencing. Dysregulated mirnas and pirnas were verified in 70 GC patients and 60 healthy controls (HC) by reverse transcription quantitative PCR. The expressions of miR-1307-3p, piR-019308, piR-004918 and piR-018569 in serum exosomes were significantly increased in GC group as compared to those in HC group. Moreover, GC patients with metastasis had significantly higher expression levels of piR-004918 and piR-019308 than GC patients without metastasis. The area under the curve (AUC) for miR-1307-3p, piR-019308, piR-004918 and piR-018569 in the GC group was 0.845, 0.820, 0.754 and 0.732, respectively. The combination of carcinoembryonic antigen (CEA) and carbohydrate antigen (CA) 199 can improve the AUC of miR-1307-3p to 0.902 and piR-019308 to 0.914 for GC diagnosis. In conclusion, our findings indicate that serum exosomal pirnas are promising non-invasive diagnostic biomarkers for GC patients and potential markers for monitoring metastasis.

关键词： diagnosis gastric cancer non‐ coding rna PIWI‐ interacting rnas serum exosomes

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Unveiling gibberellin-responsive coding and long noncoding rnas in maize

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PLANT MOLECULAR BIOLOGY 2018年第4-5期98卷 427-438页

作者： Wang, Yijun Wang, Yali Zhao, Jia Huang, Jiayu Shi, Yining Deng, Dexiang Yangzhou Univ Jiangsu Key Lab Crop Genet & Physiol Jiangsu Key Lab Crop Genom & Mol Breeding Key Lab Plant Funct GenomMinist EducAgr Coll Yangzhou 225009 Jiangsu Peoples R China Yangzhou Univ Jiangsu Coinnovat Ctr Modern Prod Technol Grain C Yangzhou 225009 Jiangsu Peoples R China

Key messageWe report coding and long noncoding rnas in maize upon phytohormone gibberellin *** hormone gibberellin (GA) orchestrates various facets of biological processes. Dissection the transcriptomic dynamics upon GA stimulation has biological significance. Feature of maize transcriptome in response to GA application remains largely elusive. Herein, two types of plants, one was with normal height, the other was GA-sensitive dwarfism, were selected from advanced backcross population for GA(3) treatment with different concentrations. In control and GA(3)-treated plants, we identified a large number of coding and long noncoding rnas (lncrnas) through sequencing eight ribosomal-depleted rna libraries. Transcripts encoding GA biosynthetic and metabolic enzymes KS, GA20ox, GA3ox, and GA2ox were significantly differentially expressed in GA(3)-treated samples. A total of 78 protein-coding transcripts were shared between GA(3)-treated normal height and dwarf plants. Shared transcripts encoding terpene synthase, MYB transcription factor, and receptor-like protein kinase were co-regulated with their corresponding partners. Out of identified lncrnas, 22 and 34 significantly differentially expressed lncrnas were responsive to GA application in normal height and dwarf plants, respectively. Shared GA-responsive lncrnas were found in GA(3)-treated normal height and dwarf plants. Some lncrnas corresponded to precursors of known mirna, such as zma-miR528a and zma-miR528b. Multiple promising targets of significantly differentially expressed lncrnas were discovered, including Lazy plant1 for auxin- and GA-mediated shoot gravitropism, bZIP transcription factor member for GA-controlled cell elongation. This study will improve our knowledge of GA-triggered transcriptome change and facilitate a comprehensive understanding of regulatory cascade centering on GA.

关键词： Gibberellin coding rna Long noncoding rna Advanced backcross population Maize (Zea mays L )

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Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs

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JOUrnaL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021年 210卷 105875页

作者： Tan, Shuwen Zhou, Yi Zhao, Haiquan Wu, Jinhua Yu, Hui Yang, Yin Yang, Yalan Zhao, Huabin Li, Hua Wuhan Univ Coll Life Sci Tibetan Ctr Ecol & Conservat WHU TU Hubei Key Lab Cell HomeostasisDept Ecol Wuhan 430072 Hubei Peoples R China Foshan Univ Sch Life Sci & Engn Guangdong Prov Key Lab Anim Mol Design & Precise Foshan 528225 Peoples R China Zunyi Med Univ Coll Basic Med Zunyi 563006 Guizhou Peoples R China Tibet Univ Coll Sci Lhasa 850000 Peoples R China

XX sex reversal, also called XX disorders of sex development (XX-DSD), is a condition affecting the development of the gonads or genitalia, and is relatively common in pigs. However, its genetic etiology and transcriptional regulation mechanism in the hypothalamic-pituitary-gonadal axis (HPGA) remain mostly unknown. XX-DSD (SRY-negative) pigs and normal sows were selected by external genitalia observation. The hypothalamus, which is the integrated center of the HPGA was sampled for whole-transcriptome rna-seq. The role of DEmirna was validated by its overexpression and knockdown in vitro. A total of 1,258 lncrnas, 1,086 mrnas, and 61 micrornas differentially expressed in XX-DSD pigs compared with normal female pigs. Genes in the hormone biosynthesis and secretion pathway significantly up-regulated, and the up-regulation of GNRH1, KISS1 and AVP may associate with the abnormal secretion of GnRH. We also predicted the lncrna-mirna-mrna co-expression triplets and constructed three competing endogenous rna (cerna) potentially associated with XX-DSD. Functional enrichment studies suggested that TCONS_00340886, TCONS_00000204 and miR-181a related to GnRH secretion. Further, miR-181a inhibitor up-regulated GNRH1, PAK6, and CAMK4 in the GT1-7 cells. Conversely, transfection of miR-181a mimics obtained the opposite trends. The expression levels of FSHR, LHR, ESR1 and ESR2 were significantly higher in XX-DSD gondas than those in normal sows. Taken together, we proposed that the balance of endocrine had broken in XX-DSD pigs. The current study is the first to examine the transcriptomic profile in the hypothalamus of XX-DSD pigs. It provides new insight into coding and non-coding rnas that may be associated with DSD in pigs.

关键词： Pig Hypothalamus coding rna Non-coding rna XX-DSD

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Microrna-223 in gastrointestinal cancers: A systematic review and diagnostic meta-analysis

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EUROPEAN JOUrnaL OF CLINICAL INVESTIGATION 2021年第2期51卷 e13448页

作者： Aalami, Amir Hossein Abdeahad, Hossein Mesgari, Mohammad Sahebkar, Amirhossein Islamic Azad Univ Mashhad Branch Dept Biol Mashhad Razavi Khorasan Iran Univ Utah Collogue Hlth Dept Nutr & Integrat Physiol Salt Lake City UT USA Ferdowsi Univ Mashhad Dept Biol Fac Sci Mashhad Razavi Khorasan Iran Mashhad Univ Med Sci Pharmaceut Technol Inst Biotechnol Res Ctr Mashhad Razavi Khorasan Iran Mashhad Univ Med Sci Neurogen Inflammat Res Ctr Mashhad Razavi Khorasan Iran Polish Mothers Mem Hosp Res Inst PMMHRI Lodz Poland FDA Halal Res Ctr IRI Tehran Iran

Background Several studies have been conducted on the diagnostic role of miR-223 in cancers related to the digestive system. However, the diagnostic role of this microrna in gastrointestinal (GI) cancers has not been fully elucidated. This meta-analysis aimed to accurately assess the diagnostic role of circulating miR-223 in GI cancers. Methods A literature search was performed in PubMed/Medline, Science Direct, Web of Science, Google Scholar, Embase and Scopus, up to 1st May 2020 databases. Twelve studies were eligible and included in the analysis. Meta-Disc software was used to calculate the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, area under the curve (AUC) and the summary receiver operating characteristic (SROC) based on true positive, true negative, false negative and false positive for each gastrointestinal cancer separately and in total. Results Twelve case-control studies were included with 1859 participants (1080 cases and 779 controls). Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio were 0.77 (95% CI: 0.74-0.79), 0.75 (95% CI: 0.72-0.78), 3.04 (95% CI: 2.20-4.18), 0.31 (95% CI: 0.22-0.42) and 10.77 (95% CI: 5.96-19.47), respectively. AUC was 0.83, suggesting a high-grade diagnostic precision of miR-223 in gastrointestinal cancers. Besides, subgroup analyses were performed to assess the diagnostic power of miR-223 based on the type of gastrointestinal cancer, sample type and country via calculating pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio. Conclusion Our meta-analysis showed the value of circulating miR-223 levels in the early diagnosis of diverse digestive system carcinomas.

关键词： carcinoma gastrointestinal tract meta‐ analysis microrna‐ 223 non‐ coding rna

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Identification of multiple rnas using feature fusion (vol , bbab178, 2021)

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BRIEFINGS IN BIOINFORMATICS 2021年第6期22卷 bbab178页

作者： Singh, Dalwinder Madhawan, Akansha Roy, Joy Natl Agri Food Biotechnol Inst Sect 81SAS Nagar Chandigarh 140306 Punjab India

Detection of novel transcripts with deep sequencing has increased the demand for computational algorithms as their identification and validation usingin vivotechniques is time-consuming, costly and unreliable. Most of these discovered transcripts belong to non-coding rnas, a large group known for their diverse functional roles but lacks the common taxonomy. Thus, upon the identification of the absence of coding potential in them, it is crucial to recognize their prime functional category. To address this heterogeneity issue, we divide the ncrnas into three classes and present rna classifier (rnaC) that categorizes the rnas into coding, housekeeping, small non-coding and long non-coding classes. rnaC utilizes the alignment-based genomic descriptors to extract statistical, local binary patterns and histogram features and fuse them to construct the classification models with extreme gradient boosting. The experiments are performed on four species, and the performance is assessed on multiclass and conventional binary classification (coding versus no-coding) problems. The proposed approach achieved >93% accuracy on both classification problems and also outperformed other well-known existing methods in coding potential prediction. This validates the usefulness of feature fusion for improved performance on both types of classification problems. Hence, rnaC is a valuable tool for the accurate identification of multiple rnas .

关键词： coding rna feature fusion local binary patterns machine learning non-coding rna XGBoost

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Role of micrornas in the pathophysiology of addiction

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WILEY INTERDISCIPLINARY REVIEWS-rna 2021年第3期12卷 e1637页

作者： Gowen, Austin M. Odegaard, Katherine E. Hernandez, Jordan Chand, Subhash Koul, Sneh Pendyala, Gurudutt Yelamanchili, Sowmya, V Univ Nebraska Med Ctr Dept Anesthesiol Omaha NE USA

Addiction is a chronic and relapsing brain disorder characterized by compulsive seeking despite adverse consequences. There are both heritable and epigenetic mechanisms underlying drug addiction. Emerging evidence suggests that non-coding rnas (ncrnas) such as micrornas (mirnas), long non-coding rnas, and circular rnas regulate synaptic plasticity and related behaviors caused by substances of abuse. These ncrnas modify gene expression and may contribute to the behavioral phenotypes of addiction. Among the ncrnas, the most widely researched and impactful are mirnas. The goal in this systematic review is to provide a detailed account of recent research involving the role of mirnas in addiction. This article is categorized under: rna Interactions with Proteins and Other Molecules > Small Molecule-rna Interactions rna in Disease and Development > rna in Disease

关键词： addiction epigenetic microrna non‐ coding rna

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Identification of non-coding and coding rnas in porcine endometrium

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GENOMICS 2017年第1期109卷 43-50页

作者： Wang, Yueying Hu, Tao Wu, Lihang Liu, Xiaoran Xue, Songyi Lei, Minggang Huazhong Agr Univ Coll Anim Sci & Technol Key Lab Agr Anim Genet Breeding & Reprod Key Lab Swine Genet & BreedinMinist AgrMinist E Wuhan Hubei Peoples R China

One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using rna sequencing (rna-seq). 237 mrnas, 34 lncrnas and 1 mirna were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes. In addition, our results showed that the differentially expressed genes (IL1R, FGF9, DUPS10, DUPS4, CD14 and MAP4K4) in MAPK pathway, and lncrnas of XLOC_2604764 and XLOC_2604756 may play a vital role in regulating embryo implantation. Besides, we investigated the lncrna-ssc-miR-132-mrna interactions, aiming to explain the regulatory networks of coding and non-coding genes that contributes to the establishment of the maternal pregnancy. (C) 2016 Elsevier Inc. All rights reserved.

关键词： Embryo implantation Non-coding rna coding rna Pig Endometrium

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Normalized long read rna sequencing in chicken reveals transcriptome complexity similar to human

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BMC GENOMICS 2017年第1期18卷 1-19页

作者： Kuo, Richard I. Tseng, Elizabeth Eory, Lel Paton, Ian R. Archibald, Alan L. Burt, David W. Univ Edinburgh Roslin Inst Easter Bush EH25 9RG Midlothian Scotland Univ Edinburgh Royal Dick Sch Vet Studies Easter Bush EH25 9RG Midlothian Scotland Pacific Biosci Menlo Pk CA USA Univ Queensland Canberra Qld 4072 Australia

Background: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read rnaseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform rna normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences. Results: We sequenced normalised chicken brain and embryo rna libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncrna transcripts with similar to 3 k classified as sense exonic overlapping lncrna, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences. Conclusions: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics.

关键词： Iso-Seq PacBio Single molecule long read sequencing Transcriptome sequencing rnaseq Chicken Avian Gallus gallus Genome annotation coding rna Non-coding rna

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