scholarly journals Proteome of larval metamorphosis induced by epinephrine in the Fujian oyster Crassostrea angulata

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guilan Di ◽  
Xiaohuo Xiao ◽  
Ming Him Tong ◽  
Xinhua Chen ◽  
Li Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Larval Settlement ◽  
Cytoskeletal Proteins ◽  
Differentially Expressed ◽  
Label Free ◽  
Larval Metamorphosis ◽  
Important Species ◽  
Expression Levels ◽  
Crassostrea Angulata ◽  
Settlement And Metamorphosis

Abstract Background The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological changes, the molecular mechanisms of which are as yet unclear. Results In this study, changes in proteins were investigated during larval settlement and metamorphosis of Crassostrea angulata using epinephrine induction. Protein abundance and identity were characterized using label-free quantitative proteomics, tandem mass spectrometry (MS/ MS), and Mascot methods. The results showed that more than 50% (764 out of 1471) of the quantified proteins were characterized as differentially expressed. Notably, more than two-thirds of the differentially expressed proteins were down-regulated in epinephrine-induced larvae. The results showed that “metabolic process” was closely related to the development of settlement and metamorphosis; 5 × 10− 4 M epinephrine induced direct metamorphosis of larvae and was non-toxic. Calmodulin and MAPK pathways were involved in the regulation of settlement of the oyster. Expression levels of immune-related proteins increased during metamorphosis. Hepatic lectin-like proteins, cadherins, calmodulin, calreticulin, and cytoskeletal proteins were involved in metamorphosis. The nervous system may be remodeled in larval metamorphosis induced by epinephrine. Expression levels of proteins that were enriched in the epinephrine signaling pathway may reflect the developmental stage of the larvae, that may reflect whether or not larvae were directly involved in metamorphosis when the larvae were treated with epinephrine. Conclusion The study provides insight into proteins that function in energy metabolism, immune responses, settlement and metamorphosis, and shell formation in C. angulata. The results contribute valuable information for further research on larval settlement and metamorphosis. Graphical abstract

scholarly journals Identification of Key Genes and MicroRNAs in Gastric Cancer via miRNA-mRNA Regulatory Network

2020 ◽  
Author(s):  
Chao Huang ◽  
Xiaojian Zhu ◽  
Jiefeng Zhao ◽  
Fanqin Bu ◽  
Jun Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Molecular Markers ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Receptor Interactions

Abstract Background Gastric cancer (GC) is a malignant tumor with high mortality. MicroRNAs (miRNAs) participate in various biological processes and disease pathogenesis by targeting messenger RNA (mRNA). The purpose of this study was to identify potential prognostic molecular markers of GC and to characterize the molecular mechanisms of GC. Methods A gene expression profiling dataset (GSE54129) and miRNA expression profiling dataset (GSE113486) were downloaded from the Gene Expression Omnibus (GEO) database. A miRNA-mRNA interaction network was established. Functional and pathway enrichment analyses were performed for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) using FunRich, the clusterProfiler package, and DIANA-mirPath. Survival analysis of key molecular markers was performed using the online tool Kaplan-Meier Plotter and the database OncomiR. Finally, experiments were carried out to verify the expression levels and biological functions of a key gene. Results A total of 390 DEMs and 341 DEGs were identified. Ultimately, 45 genes and 31 miRNAs were selected to establish a miRNA-mRNA regulatory network. Four hub genes (ZFPM2, FUT9, NEUROD1 and LIPH) and six miRNAs (hsa-let-7d-5p, hsa-miR-23b-3p, hsa-miR-23a-3p, hsa-miR-133b, hsa-miR-130a-3p and hsa-miR-124-3p) were identified in the network. DEGs and DEMs were associated with ECM-receptor interactions and metabolic pathways. Two genes (ZFPM2 and LIPH) and two miRNAs (hsa-miR-23a-3p and hsa-miR-130a-3p) were observed to be related to the prognosis of GC. ZFPM2 was highly expressed in GC tissues and various GC cell lines and could promote the proliferation, invasion and migration of GC cells. Conclusion The expression levels of ZFPM2, LIPH, hsa-miR-23a-3p and hsa-miR-130a-3p were closely related to the prognosis of GC. ZFPM2 may serve as a potential molecular marker and therapeutic target for GC. ECM receptor interactions and metabolic abnormalities play a critical role in the GC progression.

Identification of Marker Genes That Discriminate between Different Myeloproliferative Disorders and Normal Individuals Including RUNX3 (AML2).

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3522-3522
Author(s):  
Claudia I. Muller ◽  
Quang T. Luong ◽  
Letetia C. Jones ◽  
Julian C. Desmond ◽  
Norihiko Kawamata ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Myeloproliferative Disorders ◽  
Differentially Expressed ◽  
Tnf Alpha ◽  
Cytokine Signaling ◽  
Marker Genes ◽  
Mrna Levels ◽  
Tgf Beta ◽  
Myeloid Metaplasia ◽  
Expression Levels

Abstract Myeloproliferative disorders (MPD) are clonal stem cell diseases, which are defined by excessive production of cells in one or more hematopoietic lineages. The molecular mechanisms underlying the development of agnogenic myeloid metaplasia (AMM), polycythemia vera (PV), and essential thrombocythemia (ET) are currently poorly understood. We performed microarray analysis on 26 granulocyte samples from AMM (4), ET (5), PV (6) and normal (11) individuals in order to identify genes that: 1) distinguish MPD from normal samples and 2) distinguish between these diseases. Our data revealed a group of genes that were differentially expressed in MPD compared to normal or were differentially expressed between the three different diseases. Cytokine signaling has often been reported in development or progression of these diseases. Several of these aberrantly expressed genes included those involved in TGF-beta signaling. RUNX3 (AML2), a transcription factor that is involved in the signaling cascade mediated by TGF-beta, was markedly overexpressed in MPD (AMM 4.9-fold; PV 8.1-fold; ET 9.5-fold) compared to normal. TIEG1 (TGF-beta-inducible early growth response 1) was upregulated in AMM (6.4-fold), PV (9.5-fold), ET (16.7-fold) compared to normal. Moreover, TNFAIP3 (TNF alpha-induced protein 3) was overexpressed in MPD (AMM 13.8-fold; PV 11.6-fold; ET 9.3-fold) compared to normal, which might also suggest a potential role of TNF-alpha signaling in the pathogenesis of MPD. We also found several genes that could discriminate each disease from each other. For example, ZNF292 (zinc finger protein 292) was overexpressed in PV and ET (7.1-fold and 2.9-fold, respectively), but AMM had similar expression levels to normals. CCNL2 (cyclin L2) was overexpressed in ET (2.4-fold), unchanged in PV and downregulated by 5-fold in AMM compared to normal. Expression levels of all of these genes were confirmed by real-time PCR, and immunohistochemistry staining of normal and MPD samples for RUNX3 was comparable to our array data. We hypothesize that RUNX3 might play a role in myelopoiesis. RUNX3 mRNA levels in HL-60 cells cultured with ATRA (100 and 1000 nM) markedly (16 to 20-fold) and maximally increased by day 3. Levels subsided to control levels by day 7, suggesting that RUNX3 may be initially involved in HL-60 differentiation but returns to normal levels as these cells matured or underwent terminal differentiation. In MPD, the high levels of RUNX3 in the aberrant neutrophils might indicate that these cells are blocked at approximately the equivalent timepoint (day 3 for HL-60). Their differentiation program has been initiated, but they cannot undergo the final stages of terminal maturation as reflected by their high RUNX3 levels. In summary, this study identified genes, whose expression levels may serve as diagnostic markers in MPD.

Larval settlement and metamorphosis of two gregarious sabellariid polychaetes:Sabellaria alveolatacompared withPhragmatopoma californica

1988 ◽  
Vol 68 (1) ◽  
pp. 101-124 ◽  
Author(s):  
Joseph R. Pawlik
Keyword(s):  
Larval Settlement ◽  
Larval Metamorphosis ◽  
Specific Mechanism ◽  
The West ◽  
Cemented Sand ◽  
Larval Behaviour ◽  
Naturally Occurring ◽  
Phragmatopoma Californica ◽  
Settlement And Metamorphosis ◽  
High Concentrations

Two sabellariid polychaetes,Sabellaria alveolatafrom European waters andPhragmatopoma californicafrom the west coast of North America, are known from previous work to have larvae that settle and metamorphose preferentially on the cemented sand tubes of conspecific adults. The naturally occurring inducers of larval metamorphosis were recently isolated and identified forP. californica.In the present study, larval behaviour ofS. alveolataandP. californicawas compared in reciprocal laboratory settlement assays. For both species, metamorphosis occurred to a greater extent on conspecific tube sand than on control sand or on heterospecific tube sand. Extraction of the tube sand ofS. alveolatawith organic solvents diminished its capacity to induce metamorphosis pi conspecific larvae, but this capacity was not transferred to the extracts, as was the case forP. californica. The substance responsible for the enhanced metamorphosis ofS. alveolataon conspecific tube sand remains unknown. The free fatty acid (FFA) inducers of larval metamorphosis ofP. californicaeither inhibited, or had no effect on, metamorphosis ofS. alveolata. Both species responded abnormally upon exposure to unnaturally high concentrations of certain (particularly polyenoic) FFAs. Abnormal larval responses ofS. alveolata, however, did not incorporate behavioural components of normal metamorphosis, as were observed forP. californica. FFAs were isolated from the natural tube sand ofS. alveolataat less than one-tenth the concentration found in the natural tube sand ofP. californica. The differences between the two species provide further evidence that a very specific mechanism is responsible for the perception of FFAs by the larvae ofP. californica.

scholarly journals Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Zhaoyan Li ◽  
Lei Zhong ◽  
Zhenwu Du ◽  
Gaoyang Chen ◽  
Jing Shang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Hub Genes ◽  
Expression Levels ◽  
Network Analyses ◽  
Synovial Membranes

Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).

scholarly journals Bioinformatics Analysis of Differentially Expressed Rhythm Genes in Liver Hepatocellular Carcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Huaifeng Liu ◽  
Yu Gao ◽  
Shangshang Hu ◽  
Zhengran Fan ◽  
Xianggang Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Survival Rate ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Aberrant Expression ◽  
Expression Levels ◽  
Incidence And Mortality ◽  
Liver Hepatocellular Carcinoma

Liver Hepatocellular Carcinoma (LIHC), a malignant tumor with high incidence and mortality, is one of the most common cancers in the world. Multiple studies have found that the aberrant expression of rhythm genes is closely related to the occurrence of LIHC. This study aimed to use bioinformatics analysis to identify differentially expressed rhythm genes (DERGs) in LIHC. A total of 563 DERGs were found in LIHC, including 265 downregulated genes and 298 upregulated genes. KEGG pathway enrichment and GO analyses showed that DERGs were significantly enriched in rhythmic and metabolic processes. Survival analysis revealed that high expression levels of CNK1D, CSNK1E, and NPAS2 were significantly associated with the low survival rate in LIHC patients. Through cell experiment verification, the mRNA expression levels of CSNK1D, CSNK1E, and NPAS2 were found to be strongly upregulated, which was consistent with the bioinformatics analysis of LIHC patient samples. A total of 23 nodes and 135 edges were involved in the protein–protein interaction network of CSNK1D, CSNK1E, and NPAS2 genes. Clinical correlation analyses revealed that CSNK1D, CSNK1E, and NPAS2 expression levels were high-risk factors and independently connected with the overall survival rate in LIHC patients. In conclusion, the identification of these DERGs contributes to the exploration of the molecular mechanisms of LIHC occurrence and development and may be used as diagnostic and prognostic biomarkers and molecular targets for chronotherapy in LIHC patients in the future.

scholarly journals 3D Cell Culture-Based Global miRNA Expression Analysis Reveals miR-142-5p as a Theranostic Biomarker of Rectal Cancer Following Neoadjuvant Long-Course Treatment

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 613 ◽  
Author(s):  
Linas Kunigenas ◽  
Vaidotas Stankevicius ◽  
Audrius Dulskas ◽  
Elzbieta Budginaite ◽  
Gediminas Alzbutas ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Cell Lines ◽  
Mirna Expression ◽  
Molecular Mechanisms ◽  
Tumor Tissue ◽  
Differentially Expressed ◽  
Altered Expression ◽  
Expression Levels ◽  
3D Microenvironment ◽  
Long Course

Altered expression of miRNAs in tumor tissue encourages the translation of this specific molecular pattern into clinical practice. However, the establishment of a selective biomarker signature for many tumor types remains an inextricable challenge. For this purpose, a preclinical experimental design, which could maintain a fast and sensitive discovery of potential biomarkers, is in demand. The present study suggests that the approach of 3D cell cultures as a preclinical cancer model that is characterized to mimic a natural tumor environment maintained in solid tumors could successfully be employed for the biomarker discovery and validation. Subsequently, in this study, we investigated an environment-dependent miRNA expression changes in colorectal adenocarcinoma DLD1 and HT29 cell lines using next-generation sequencing (NGS) technology. We detected a subset of 16 miRNAs differentially expressed in both cell lines cultivated in multicellular spheroids compared to expression levels in cells grown in 2D. Furthermore, results of in silico miRNA target analysis showed that miRNAs, which were differentially expressed in both cell lines grown in MCS, are involved in the regulation of molecular mechanisms implicated in cell adhesion, cell-ECM interaction, and gap junction pathways. In addition, integrins and platelet-derived growth factor receptors were determined to be the most significant target genes of deregulated miRNAs, which was concordant with the environment-dependent gene expression changes validated by RT-qPCR. Our results revealed that 3D microenvironment-dependent deregulation of miRNA expression in CRC cells potentially triggers essential molecular mechanisms predominantly including the regulation of cell adhesion, cell–cell, and cell–ECM interactions important in CRC initiation and development. Finally, we demonstrated increased levels of selected miR-142-5p in rectum tumor tissue samples after neoadjuvant long course treatment compared to miR-142-5p expression levels in tumor biopsy samples collected before the therapy. Remarkably, the elevation of miR-142-5p expression remained in tumor samples compared to adjacent normal rectum tissue as well. Therefore, the current study provides valuable insights into the molecular miRNA machinery of CRC and proposes a potential miRNA signature for the assessment of CRC in further clinical research.

scholarly journals Gene Expression and miRNA Regulation Changes in Leaves of Rice Backcross Introgression Lines

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1381
Author(s):  
Aqin Cao ◽  
Ruihua Wang ◽  
Jianbo Wang
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Introgression Line ◽  
Differentially Expressed ◽  
Mirna Regulation ◽  
Expression Levels ◽  
Expression Of Genes

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.

scholarly journals Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3024
Author(s):  
Xibi Fang ◽  
Lihong Qin ◽  
Haibin Yu ◽  
Ping Jiang ◽  
Lixin Xia ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Gonad Development ◽  
Male Reproduction ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Adult Cattle ◽  
Expression Levels ◽  
Regulated Gene Expression

This study aims to screen potential regulators and regulate fecundity networks between microRNAs (miRNAs) and target genes. The bovine testes of immature and mature Chinese Red Steppes were performed by genome-wide analysis of mRNAs and miRNAs. Compared with testicular tissues of newborns, 6051 upregulated genes and 7104 downregulated genes in adult cattle were identified as differentially expressed genes (DEGs). The DEGs were significantly enriched in 808 GO terms (p < 0.05) including male gonad development, male genitalia development, spermatogenesis, and sperm motility. Moreover, DEGs were also significantly enriched in 105 KEGG pathways (p < 0.05), including cGMP-PKG signaling pathway and calcium signaling pathway. To explore the expression of miRNA-regulated gene expression, 896 differentially expressed target genes negatively regulated with the expression levels of 31 differentially expressed miRNAs (DERs) were predicted and analyzed, and a network-integrated analysis was constructed. Furthermore, real-time PCR was performed to verify the expression levels of DEGs and DERs. Our results identified novel candidate DEGs and DERs correlated with male reproduction and intricate regulating networks between miRNAs and genes, which will be valuable for future genetic and epigenetic studies of sperm development and maturity, as well as providing valuable insights into the molecular mechanisms of male fertility and spermatogenesis in cattle.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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