RNA-seq Characterization of Sex-Differences in Adipose Tissue of Obesity Affected Patients: Computational Analysis of Differentially Expressed Coding and Non-Coding RNAs

Obesity is a multifactorial disease presenting sex-related differences including adipocyte functions, sex hormone effects, genetics, and metabolic inflammation. These can influence individuals’ risk for metabolic dysfunctions, with an urgent need to perform sex-based analysis to improve prevention, treatment, and rehabilitation programs. This research work is aimed at characterizing the transcriptional differences present in subcutaneous adipose tissue (SAT) of five obesity affected men versus five obesity affected women, with an additional focus on the role of long non-coding RNAs. Through RNA-sequencing, we highlighted the presence of both coding and non-coding differentially expressed RNAs, and with numerous computational analyses we identified the processes in which these genes are implicated, along with their role in co-morbidities development. We report 51 differentially expressed transcripts, 32 of which were coding genes and 19 were non-coding. Using the WGCNA R package (Weighted Correlation Network Analysis, version 1.70-3), we describe the interactions between coding and non-coding RNAs, and the non-coding RNAs association with the insurgence of specific diseases, such as cancer development, neurodegenerative diseases, and schizophrenia. In conclusion, our work highlights a specific gender sex-related transcriptional signature in the SAT of obesity affected patients.

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Identification of differentially expressed Long non-coding RNAs in follicular granulosa cells from polycystic ovary syndrome patients and controls

10.26226/morressier.573c1514d462b80296c98c63 ◽

2016 ◽

Author(s):

Zheng Yan

Keyword(s):

Polycystic Ovary Syndrome ◽

Granulosa Cells ◽

Polycystic Ovary ◽

Differentially Expressed ◽

Ovary Syndrome ◽

Non Coding Rnas

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Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Cancers ◽

10.3390/cancers13143530 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3530

Author(s):

Penn Muluhngwi ◽

Carolyn M. Klinge

Keyword(s):

Breast Cancer ◽

Cancer Survival ◽

Expression Patterns ◽

Endocrine Resistance ◽

Estrogen Receptor Α ◽

Resistant Cell ◽

Differentially Expressed ◽

Primary Tumors ◽

Non Coding Rnas ◽

Mcf 7

Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.

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Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽

10.1186/s12864-021-07692-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Huili Qiao ◽

Jingya Wang ◽

Yuanzhuo Wang ◽

Juanjuan Yang ◽

Bofan Wei ◽

...

Keyword(s):

Bombyx Mori ◽

Target Gene ◽

Fat Body ◽

Expression Profiles ◽

Functional Characterization ◽

Differentially Expressed ◽

Post Injection ◽

Biological Processes ◽

Potential Target ◽

Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

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Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Animals ◽

10.3390/ani11051268 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1268

Author(s):

Shengchao Zhang ◽

Sibtain Ahmad ◽

Yuxia Zhang ◽

Guohua Hua ◽

Jianming Yi

Keyword(s):

Mammary Gland ◽

Crude Protein ◽

Regulatory Mechanism ◽

Differentially Expressed ◽

Milk Replacer ◽

Rna Seq ◽

Fat Pad ◽

Mammary Fat Pad ◽

Non Coding Rnas ◽

Gland Development

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

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Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly

International Journal of Molecular Sciences ◽

10.3390/ijms22041539 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1539

Author(s):

Paola De Sanctis ◽

Giuseppe Filardo ◽

Provvidenza Maria Abruzzo ◽

Annalisa Astolfi ◽

Alessandra Bolotta ◽

...

Keyword(s):

Exercise Training ◽

High Intensity ◽

Vastus Lateralis ◽

Mammalian Target Of Rapamycin ◽

Differentially Expressed ◽

Transcriptional Networks ◽

Vastus Lateralis Muscle ◽

Age Related ◽

Wide Range ◽

Non Coding Rnas

In a previous study, the whole transcriptome of the vastus lateralis muscle from sedentary elderly and from age-matched athletes with an exceptional record of high-intensity, life-long exercise training was compared—the two groups representing the two extremes on a physical activity scale. Exercise training enabled the skeletal muscle to counteract age-related sarcopenia by inducing a wide range of adaptations, sustained by the expression of protein-coding genes involved in energy handling, proteostasis, cytoskeletal organization, inflammation control, and cellular senescence. Building on the previous study, we examined here the network of non-coding RNAs participating in the orchestration of gene expression and identified differentially expressed micro- and long-non-coding RNAs and some of their possible targets and roles. Unsupervised hierarchical clustering analyses of all non-coding RNAs were able to discriminate between sedentary and trained individuals, regardless of the exercise typology. Validated targets of differentially expressed miRNA were grouped by KEGG analysis, which pointed to functional areas involved in cell cycle, cytoskeletal control, longevity, and many signaling pathways, including AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR), which had been shown to be pivotal in the modulation of the effects of high-intensity, life-long exercise training. The analysis of differentially expressed long-non-coding RNAs identified transcriptional networks, involving lncRNAs, miRNAs and mRNAs, affecting processes in line with the beneficial role of exercise training.

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MicroRNA expression profile in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci

Veterinary Research ◽

10.1186/s13567-021-00912-2 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Emilia Bagnicka ◽

Ewelina Kawecka-Grochocka ◽

Klaudia Pawlina-Tyszko ◽

Magdalena Zalewska ◽

Aleksandra Kapusta ◽

...

Keyword(s):

Mammary Gland ◽

Immune System ◽

Differentially Expressed ◽

Bacterial Invasion ◽

Coagulase Negative Staphylococci ◽

Cellular Processes ◽

Differentially Expressed Mirnas ◽

Non Coding Rnas ◽

Coagulase Positive Staphylococci ◽

Generation Sequencing

AbstractMicroRNAs (miRNAs) are short, non-coding RNAs, 21–23 nucleotides in length which are known to regulate biological processes that greatly impact immune system activity. The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphylococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. The miRNA profile of the parenchyma was found to change during mastitis, with its profile depending on the type of pathogen. Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identified, including 32 that were differentially expressed (p ≤ 0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identified: 10 were upregulated (p ≤ 0.05), and 2 downregulated (p ≤ 0.05). In addition, comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identified; in both comparisons, differentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identified in each comparison, with 2 being common to both immune system processes and signal transduction. Our results indicate that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).

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Long Noncoding RNA THAP9-AS1 and TSPOAP1-AS1 Provide Potential Diagnostic Signatures for Pediatric Septic Shock

BioMed Research International ◽

10.1155/2020/7170464 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Yong Wu ◽

Qigai Yin ◽

Xiaobao Zhang ◽

Pin Zhu ◽

Hengfei Luan ◽

...

Keyword(s):

Septic Shock ◽

Logistic Regression ◽

Regression Model ◽

Logistic Regression Model ◽

Pediatric Patients ◽

R Package ◽

Differentially Expressed ◽

Blood Samples ◽

Health Control ◽

Control Samples

Background. Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We downloaded the mRNA profiles GSE13904 and GSE4607, of which GSE13904 includes 106 blood samples of pediatric patients with septic shock and 18 health control samples; GSE4607 includes 69 blood samples of pediatric patients with septic shock and 15 health control samples. The differentially expressed lncRNAs were identified through the limma R package; meanwhile, GO terms and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. The protein-protein interaction (PPI) network was constructed based on the STRING database using the targets of differently expressed lncRNAs. The MCODE plug-in of Cytoscape was used to screen significant clustering modules composed of key genes. Finally, stepwise regression analysis was performed to screen the optimal lncRNAs and construct the logistic regression model, and the ROC curve was applied to evaluate the accuracy of the model. Results. A total of 13 lncRNAs which simultaneously exhibited significant differences in the septic shock group compared with the control group from two sets were identified. According to the 18 targets of differentially expressed lncRNAs, we identified some inflammatory and immune response-related pathways. In addition, several target mRNAs were predicted to be potentially involved in the occurrence of septic shock. The logistic regression model constructed based on two optimal lncRNAs THAP9-AS1 and TSPOAP1-AS1 could efficiently separate samples with septic shock from normal controls. Conclusion. In summary, a predictive model based on the lncRNAs THAP9-AS1 and TSPOAP1-AS1 provided novel lightings on diagnostic research of septic shock.

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Transcriptomic and ChIP-seq Integrative Analysis Reveals Important Roles of Epigenetically Regulated lncRNAs in Placental Development in Meishan Pigs

Genes ◽

10.3390/genes11040397 ◽

2020 ◽

Vol 11 (4) ◽

pp. 397

Author(s):

Dadong Deng ◽

Xihong Tan ◽

Kun Han ◽

Ruimin Ren ◽

Jianhua Cao ◽

...

Keyword(s):

Differentially Expressed ◽

Rna Seq ◽

Sequencing Data ◽

Placental Development ◽

Cytoskeleton Organization ◽

New Class ◽

Chromatin Immunoprecipitation Sequencing ◽

Non Coding Rnas ◽

Two Stages ◽

Regulatory Functions

The development of the placental fold, which increases the maternal–fetal interacting surface area, is of primary importance for the growth of the fetus throughout the whole pregnancy. However, the mechanisms involved remain to be fully elucidated. Increasing evidence has revealed that long non-coding RNAs (lncRNAs) are a new class of RNAs with regulatory functions and could be epigenetically regulated by histone modifications. In this study, 141 lncRNAs (including 73 up-regulated and 68 down-regulated lncRNAs) were identified to be differentially expressed in the placentas of pigs during the establishment and expanding stages of placental fold development. The differentially expressed lncRNAs and genes (DElncRNA-DEgene) co-expression network analysis revealed that these differentially expressed lncRNAs (DElncRNAs) were mainly enriched in pathways of cell adhesion, cytoskeleton organization, epithelial cell differentiation and angiogenesis, indicating that the DElncRNAs are related to the major events that occur during placental fold development. In addition, we integrated the RNA-seq (RNA sequencing) data with the ChIP-seq (chromatin immunoprecipitation sequencing) data of H3K4me3/H3K27ac produced from the placental samples of pigs from the two stages (gestational days 50 and 95). The analysis revealed that the changes in H3K4me3 and/or H3K27ac levels were significantly associated with the changes in the expression levels of 37 DElncRNAs. Furthermore, several H3K4me3/H3K27ac-lncRNAs were characterized to be significantly correlated with genes functionally related to placental development. Thus, this study provides new insights into understanding the mechanisms for the placental development of pigs.

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