Integrated Proteotranscriptomics of Human Myometrium in Labor Landscape Reveals the Increased Molecular Associated With Inflammation Under Hypoxia Stress

During labor, a variety of coordinated physiological and biochemical events cause the myometrium to transition from a quiescent to contractile state; the molecular mechanisms responsible for this transition, however, remain unclear. To better understand this transition at a molecular level, the global transcriptome and proteome of human myometrial samples in labor and those not in labor were investigated through RNA sequencing (RNA-seq) and quantitative liquid chromatography–tandem mass spectrometry (LC-MS/MS) via data-independent acquisition (DIA) and parallel reaction monitoring (PRM) methods. Furthermore, an integrated proteotranscriptomic analysis was performed to explore biological processes and pathway alterations during labor; this analysis identified 1,626 differentially expressed mRNAs (1,101 upregulated, 525 downregulated) and 135 differentially expressed proteins (97 upregulated, 38 downregulated) in myometrium between nonlabor and in labor groups. The comprehensive results of these analyses showed that the upregulated mRNAs and proteins increased inflammation under hypoxia stress in the myometrium under labor, and related proteins and cytokines were validated by PRM and Luminex assays. Our study confirmed the biological process of inflammation and hypoxia in laboring myometrium at the transcriptome and proteome levels and provided recourse to discover new molecular and biological changes during labor.

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Quantitative LC-MS/MS Uncovers The Regulatory Role of Autophagy in Immune Thrombocytopenia

10.21203/rs.3.rs-105355/v1 ◽

2020 ◽

Author(s):

Rui-Jie Sun ◽

Dai Yuan ◽

Dong-mei Yin ◽

Shu-yan Liu ◽

Jing-jing Zhu ◽

...

Keyword(s):

Bone Marrow ◽

Immune Thrombocytopenia ◽

Differentially Expressed ◽

Bone Marrow Mononuclear Cell ◽

Protein Protein Interaction ◽

Parallel Reaction Monitoring ◽

Liquid Chromatography Tandem Mass ◽

Pathway Analyses ◽

Haemorrhagic Disease ◽

Related Proteins

Abstract Background: Immune thrombocytopenia (ITP) is an autoimmune haemorrhagic disease whose pathogenesis is associated with bone marrow megakaryocyte maturation disorder and microenvironment destruction of haematopoietic stem cells.Method: In this study, we report the qualitative and quantitative profile of the proteome in ITP. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was conducted to detect the protein profiles in clinical bone marrow mononuclear cell (BMMC) samples from ITP patients and healthy volunteers (controls). Gene Ontology (GO) and Kyoto Encyclopedia Genes and Genome (KEGG) pathway analyses were performed for the annotation of differentially expressed proteins. The protein-protein interaction (PPI) network was constructed with the BLAST online database. Target proteins associated with autophagy were quantitatively identified by parallel reaction monitoring (PRM) analysis.Results: Our approaches showed that of the differentially expressed autophagy-related proteins, namely, HSPA8, PARK7, YWHAH, ITGB3 and CSF1R, were the most changed. The expression of the CSF1R protein in ITP patients was higher than that in controls, while the expression of other autophagy-related proteins was lower in ITP patients than in controls.Conclusion: Bioinformatics analysis indicated that the abnormal autophagy pathway is a potential pathological mechanism of ITP. These results can provide a new direction for exploring the molecular mechanism of ITP.

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Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20102391 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2391 ◽

Cited By ~ 3

Author(s):

Jiayang Xu ◽

Qiansi Chen ◽

Pingping Liu ◽

Wei Jia ◽

Zheng Chen ◽

...

Keyword(s):

Salinity Stress ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Crop Yields ◽

Antioxidant Activities ◽

Expression Patterns ◽

Differentially Expressed ◽

Alkali Stress ◽

Rna Seq ◽

Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

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RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity

Blood ◽

10.1182/blood-2010-07-293332 ◽

2011 ◽

Vol 117 (2) ◽

pp. e27-e38 ◽

Cited By ~ 42

Author(s):

Brian T. Wilhelm ◽

Mathieu Briau ◽

Pamela Austin ◽

Amélie Faubert ◽

Geneviève Boucher ◽

...

Keyword(s):

Stem Cell ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Leukemic Cells ◽

Rna Seq ◽

Self Renewal ◽

Leukemia Stem Cell ◽

Cellular Behavior ◽

Transcriptome Variation ◽

G Protein Coupled

Abstract The molecular mechanisms regulating self-renewal of leukemia stem cells remain poorly understood. Here we report the generation of 2 closely related leukemias created through the retroviral overexpression of Meis1 and Hoxa9. Despite their apparent common origin, these clonal leukemias exhibit enormous differences in stem cell frequency (from 1 in 1.4, FLA2; to 1 in 347, FLB1), suggesting that one of these leukemias undergoes nearly unlimited self-renewal divisions. Using next-generation RNA-sequencing, we characterized the transcriptomes of these phenotypically similar, but biologically distinct, leukemias, identifying hundreds of differentially expressed genes and a large number of structural differences (eg, alternative splicing and promoter usage). Focusing on ligand-receptor pairs, we observed high expression levels of Sdf1-Cxcr4; Jagged2-Notch2/1; Osm-Gp130; Scf-cKit; and Bmp15-Tgfb1/2. Interestingly, the integrin beta 2-like gene (Itgb2l) is both highly expressed and differentially expressed between our 2 leukemias (∼ 14-fold higher in FLA2 than FLB1). In addition, gene ontology analysis indicated G-protein-coupled receptor had a much higher proportion of differential expression (22%) compared with other classes (∼ 5%), suggesting a potential role regulating subtle changes in cellular behavior. These results provide the first comprehensive transcriptome analysis of a leukemia stem cell and document an unexpected level of transcriptome variation between phenotypically similar leukemic cells.

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RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations

Frontiers in Genetics ◽

10.3389/fgene.2021.605015 ◽

2021 ◽

Vol 12 ◽

Author(s):

Si Ying Li ◽

Chen Yi Wang ◽

Yun Xia Xiao ◽

Xiao Bing Tang ◽

Zheng Wei Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Transforming Growth Factor ◽

Quantitative Polymerase Chain Reaction ◽

Anorectal Malformations ◽

Normal Group ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Circular Rnas ◽

Rna Seq ◽

Pregnant Rats

Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. In this study, we explored the mechanism underlying ethylenethiourea (ETU)-induced ARMs by profiling circRNA expression via RNA-seq and constructing a regulatory circRNA-miRNA-mRNA network. Nine pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (ARM group) on gestational day 10 (GD10), and another 9 pregnant rats received a similar dose of saline (normal group) as a control. Embryos were obtained by cesarean section on the key time-points of anorectal development (GD14, GD15, and GD16). Hindgut samples isolated from the fetuses were evaluated by high-throughput sequencing and differentially expressed circRNAs were validated by reverse transcription-quantitative polymerase chain reaction, agarose gel electrophoresis, and Sanger cloning and sequencing. A total of 18295 circRNAs were identified in the normal and ARM groups. Based on the 425 differentially expressed circRNAs (|Fc| > 2, p < 0.05), circRNA-miRNA and miRNA-mRNA pairs were predicted using miREAP, miRanda, and TargetScan. A total of 55 circRNAs (14 up- and 41 downregulated in the ARM group compared to the normal group) were predicted to bind to 195 miRNAs and 947 mRNAs. Competing endogenous RNA networks and a Kyoto Encyclopedia of Genes and Genomes analysis revealed that novel_circ_001042 had the greatest connectivity and was closely related to ARM-associated signaling pathways, such as the Wingless Type MMTV integration site family, mitogen-activated protein kinase, and transforming growth factor-β pathways. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.

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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

10.20944/preprints202010.0158.v1 ◽

2020 ◽

Author(s):

Thiago Mateus Rosa-Santos ◽

Renan Gonçalves da Silva ◽

Poornasree Kumar ◽

Pratibha Kottapalli ◽

Chiquito Crasto ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Aluminum Tolerance ◽

Differentially Expressed ◽

Rna Seq ◽

Aluminum Stress ◽

Physiological Processes ◽

Aluminum Ions ◽

Detoxification Mechanism ◽

Genomic Studies

Sugarcane is an important sugar-source crop. As any other plant, it can be exposed to several abiotic stress conditions. Though some metals contribute to critical physiological processes in plants, the presence of aluminum ions (Al3+) can be very toxic. In order to develop plants that flourish in acidic soils, it is critical to gain insights into the molecular mechanisms of sugarcane response to aluminum stress. To determine the genes involved in sugarcane response to aluminum stress we generated 372 million paired-end RNA sequencing reads, from roots of CTC-2 and RB855453 two contrasting cultivars. Data normalization resulted in 162,161 contigs and 97,335 trinity genes. After the read cutoff, the differentially expressed genes were 4,858 in CTC-2 and 1,307 in the RB855453, Treatment Vs Control, respectively. The differentially expressed genes were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and down regulated in RB855453 (sensitive cultivar). Here, we present the first root-transcriptome of sugarcane under aluminum stress. The results and conclusions of this study provide a valuable resource for future genetic and genomic studies in sugarcane. This transcriptome analysis points out that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with the lateral root formation and activation of redox enzymes. Following our results, we present here, a hypothetical model for the aluminum tolerance in CTC-2 cultivar.

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Protein Regulation Strategies of Mouse Spleen in Response to Babesia Microti Infection

10.21203/rs.3.rs-81340/v1 ◽

2020 ◽

Author(s):

Xiaomin Xue ◽

Shuguang Ren ◽

Abolfazl Masoudi ◽

Yuhong Hu ◽

Xiaoshuang Wang ◽

...

Keyword(s):

Iron Metabolism ◽

Quantitative Proteomics ◽

Growth And Development ◽

Molecular Mechanisms ◽

Protozoan Parasite ◽

Babesia Microti ◽

Spleen Tissue ◽

Data Independent Acquisition ◽

Regulation Strategies ◽

Related Proteins

Abstract BackgroundBabesia is a protozoan parasite in red blood cells of some vertebrates. Some species of Babesia can cause zoonoses and cause great harm. As the largest immune organ in mammals, the spleen plays an important role in defending against Babesia infection. When infected with Babesia, the spleen is seriously injured, but it still actively initiates immunomodulatory responses.MethodsIn order to explore the molecular mechanisms underlying the immune regulation and self-repair of the spleen in response to infection, this study used data-independent acquisition (DIA) quantitative proteomics to analyse changes in expression levels of global proteins and changes in phosphorylation modification in spleen tissue after Babesia microti infection in mice.ResultsAfter the mice were infected with B. microti, their spleen were seriously damaged.Using bioinfor-matics methods to analyze the dynamic changes of a large number of proteins, we found that spleen still initiated immune response to deal with the infection, in which immune-related proteins played an important role, including CTSD, IFI44, ILF2, ILF, and STAT5A. In addition, some proteins related to iron metabolism were also involved in the repair of spleen against B. microti infection, including serotransferrin, lactoferrin, TfR1, and GCL. At the same time, the expression and phosphorylation of proteins related to the growth and development of the spleen also changed, including PKC-δ and MAPK3/1, Grb2, and PAK2. ConclusionsImmune-related proteins, iron metabolism-related proteins and growth and development-related proteins play an important important role in the regulation of spleen injury and maintenance of homeostasis. This study will provide important bases for the diagnosis and treatment of babesiosis.

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Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

10.21203/rs.2.15328/v1 ◽

2019 ◽

Author(s):

Huiyan Hu ◽

Qing Jia ◽

Jianzhong Xi ◽

Bo Zhou ◽

Zhiqiang Li

Keyword(s):

Molecular Mechanisms ◽

Ovarian Tissue ◽

Length Distribution ◽

Differentially Expressed ◽

Integrated Analysis ◽

Rna Seq ◽

Large White ◽

Reproductive Process ◽

Mrna Targets ◽

Micro Rnas

Abstract Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular phases (F) of the estrous cycle in Large White pigs with high (H) and low fecundity (L), and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs and can contribute to further experimental investigation of the functions of these genes.

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Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

PeerJ ◽

10.7717/peerj.12025 ◽

2021 ◽

Vol 9 ◽

pp. e12025

Author(s):

Wuping Yan ◽

Zhouchen Ye ◽

Shijia Cao ◽

Guanglong Yao ◽

Jing Yu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Differentially Expressed ◽

Perennial Herb ◽

Pcr Analysis ◽

Biosynthetic Pathways ◽

Rna Seq ◽

Patchouli Alcohol ◽

Pogostemon Cablin ◽

Polymerase Chain ◽

Distribution Frequency

Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

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Comparative Transcriptome Analysis of a Fan-shaped Inflorescence in Pineapple Using RNA-seq

10.21203/rs.3.rs-52110/v1 ◽

2020 ◽

Author(s):

Tao Xie ◽

Zhiquan Cai ◽

Aiping Luan ◽

Wei Zhang ◽

Jing Wu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Expression Patterns ◽

Soluble Sugar ◽

Differentially Expressed ◽

Soluble Solids ◽

Pcr Analysis ◽

Rna Seq ◽

Stem Apex ◽

Inflorescence Axis ◽

Flower Stem

Abstract Background: Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was evolved in an exceptional material, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between a fan-shaped inflorescence (FI) and a capitulum inflorescence (CI) pineapples were analyzed in the three tissues, i.e., the flower stem apex (FIs and CIs), the base of the inflorescence (FIb and CIb), and the inflorescence axis (FIa and CIa).Results: Except for a clear differentiation of inflorescence morphology, no significant differences in the structure of inflorescence organs and the main nutritional components (soluble solids, soluble sugar, titratable acid, and VC) in fruits were found between the two pineapples. Between the fan- and capitulum-shaped inflorescences, a total of 5370 differentially expressed genes (DEGs) were identified across the three tissues; and 3142, 2526 and 2255 DEGs were found in the flower stem apex, the base of the inflorescence, and the inflorescence axis, respectively. Of these genes, there were 489 overlapping DEGs in all three tissue comparisons. In addition, 5769 DEGs were identified between different tissues within each pineapple. Functional analysis indicated between the two pineapples that 444 transcription factors (TFs) and 206 inflorescence development related genes (IDGs) were differentially expressed in at least one tissue comparison, while 45 TFs and 21 IDGs were overlapped across the 3 tissues. Among the 489 overlapping DEGs in the 3 tissue comparisons between the two pineapples, excluding the IDGs and TFs, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the same gene expression patterns in the three tissues. Conclusions: Our result provided novel cues for understanding the molecular mechanisms of the formation of fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of the pineapples.

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Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

Marine Drugs ◽

10.3390/md18040186 ◽

2020 ◽

Vol 18 (4) ◽

pp. 186

Author(s):

Guoyong Yan ◽

Jin Sun ◽

Zishuai Wang ◽

Pei-Yuan Qian ◽

Lisheng He

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Lysyl Oxidase ◽

Enrichment Analysis ◽

Salivary Secretion ◽

Cement Gland ◽

Differentially Expressed ◽

Model Organisms ◽

Rna Seq ◽

Secretion Pathway

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

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