scholarly journals Identification of potential hub genes associated with the pathogenesis and prognosis of pancreatic duct adenocarcinoma using bioinformatics meta‑analysis of multi‑platform datasets

2019 ◽  
Author(s):  
Yufan Ma ◽  
Yinquan Pu ◽  
Li Peng ◽  
Xujuan Luo ◽  
Jin Xu ◽  
...  
Keyword(s):  
Pancreatic Duct ◽  
Meta Analysis ◽  
Hub Genes ◽  
Pancreatic Duct Adenocarcinoma

scholarly journals Laparoscopic Pancreaticoduodenectomy Versus Conventional Open Approach for Patients With Pancreatic Duct Adenocarcinoma: An Up-to-Date Systematic Review and Meta-Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Qingbo Feng ◽  
Wenwei Liao ◽  
Zechang Xin ◽  
Hongyu Jin ◽  
Jinpeng Du ◽  
...  
Keyword(s):  
Systematic Review ◽  
Overall Survival ◽  
Lymph Node ◽  
Blood Loss ◽  
Survival Time ◽  
Pancreatic Duct ◽  
Meta Analysis ◽  
R0 Resection ◽  
Node Dissection ◽  
Pancreatic Duct Adenocarcinoma

BackgroundTo compare perioperative and oncological outcomes of pancreatic duct adenocarcinoma (PDAC) after laparoscopic versus open pancreaticoduodenectomy (LPD vs. OPD), we performed a meta-analysis of currently available propensity score matching studies and large-scale retrospective cohorts to compare the safety and overall effect of LPD to OPD for patients with PDAC.MethodsA meta-analysis was registered at PROSPERO and the registration number is CRD42021250395. PubMed, Web of Science, EMBASE, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov databases were searched based on a defined search strategy to identify eligible studies before March 2021. Data on operative times, blood loss, 30-day mortality, reoperation, length of hospital stay (LOS), overall morbidity, Clavien–Dindo ≥3 complications, postoperative pancreatic fistula (POPF), blood transfusion, delayed gastric emptying (DGE), postpancreatectomy hemorrhage (PPH), and oncologic outcomes (R0 resection, lymph node dissection, overall survival, and long-term survival) were subjected to meta-analysis.ResultsOverall, we identified 10 retrospective studies enrolling a total of 11,535 patients (1,514 and 10,021 patients underwent LPD and OPD, respectively). The present meta-analysis showed that there were no significant differences in overall survival time, 1-year survival, 2-year survival, 30-day mortality, Clavien-Dindo ≥3 complications, POPF, DGE, PPH, and lymph node dissection between the LPD and OPD groups. Nevertheless, compared with the OPD group, LPD resulted in significantly higher rate of R0 resection (OR: 1.22; 95% CI 1.06–1.40; p = 0.005), longer operative time (WMD: 60.01 min; 95% CI 23.23–96.79; p = 0.001), lower Clavien–Dindo grade ≥III rate (p = 0.02), less blood loss (WMD: −96.49 ml; 95% CI −165.14 to −27.83; p = 0.006), lower overall morbidity rate (OR: 0.65; 95% CI 0.50 to 0.85; p = 0.002), shorter LOS (MD = −2.73; 95% CI −4.44 to −1.03; p = 0.002), higher 4-year survival time (p = 0.04), 5-year survival time (p = 0.001), and earlier time to starting adjuvant chemotherapy after surgery (OR: −10.86; 95% CI −19.42 to −2.30; p = 0.01).ConclusionsLPD is a safe and feasible alternative to OPD for patients with PDAC, and compared with OPD, LPD seemed to provide a similar OS.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/#recordDetails.

scholarly journals Endoscopic transmural drainage is associated with improved outcomes in disconnected pancreatic duct syndrome: a systematic review and meta-analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Eric Chong ◽  
Chathura Bathiya Ratnayake ◽  
Samantha Saikia ◽  
Manu Nayar ◽  
Kofi Oppong ◽  
...  
Keyword(s):  
Systematic Review ◽  
Pancreatic Duct ◽  
Meta Analysis ◽  
Fluid Collection ◽  
Significant Heterogeneity ◽  
Success Rates ◽  
Surgical Interventions ◽  
Transmural Drainage ◽  
Transpapillary Drainage ◽  
Duct Syndrome

Abstract Background Disconnected pancreatic duct syndrome (DPDS) is a complication of acute necrotizing pancreatitis in the neck and body of the pancreas often manifesting as persistent pancreatic fluid collection (PFC) or external pancreatic fistula (EPF). This systematic review and pairwise meta-analysis aimed to review the definitions, clinical presentation, intervention, and outcomes for DPDS. Methods The PubMed, EMBASE, MEDLINE, and SCOPUS databases were systematically searched until February 2020 using the PRISMA framework. A meta-analysis was performed to assess the success rates of endoscopic and surgical interventions for the treatment of DPDS. Success of DPDS treatment was defined as long-term resolution of symptoms without recurrence of PFC, EPF, or pancreatic ascites. Results Thirty studies were included in the quantitative analysis comprising 1355 patients. Acute pancreatitis was the most common etiology (95.3%, 936/982), followed by chronic pancreatitis (3.1%, 30/982). DPDS commonly presented with PFC (83.2%, 948/1140) and EPF (13.4%, 153/1140). There was significant heterogeneity in the definition of DPDS in the literature. Weighted success rate of endoscopic transmural drainage (90.6%, 95%-CI 81.0–95.6%) was significantly higher than transpapillary drainage (58.5%, 95%-CI 36.7–77.4). Pairwise meta-analysis showed comparable success rates between endoscopic and surgical intervention, which were 82% (weighted 95%-CI 68.6–90.5) and 87.4% (95%-CI 81.2–91.8), respectively (P = 0.389). Conclusions Endoscopic transmural drainage was superior to transpapillary drainage for the management of DPDS. Endoscopic and surgical interventions had comparable success rates. The significant variability in the definitions and treatment strategies for DPDS warrant standardisation for further research.

scholarly journals MicroRNA-140 regulates cell growth and invasion in pancreatic duct adenocarcinoma by targeting iASPP

2016 ◽  
Vol 48 (2) ◽  
pp. 174-181 ◽  
Author(s):  
Shuai Liang ◽  
Xuejun Gong ◽  
Gewen Zhang ◽  
Gengwen Huang ◽  
Yebin Lu ◽  
...  
Keyword(s):  
Cell Growth ◽  
Pancreatic Duct ◽  
Pancreatic Duct Adenocarcinoma

scholarly journals WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 719 ◽  
Author(s):  
Mingdong Zhu ◽  
Hongjun Xie ◽  
Xiangjin Wei ◽  
Komivi Dossa ◽  
Yaying Yu ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Biological Processes ◽  
Salt Tolerant ◽  
Hub Genes ◽  
Pathway Gene ◽  
Salt Response ◽  
Genes Encoding ◽  
Bioinformatic Approaches ◽  
Salt Tolerant Cultivars ◽  
And Control

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.

scholarly journals Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

2019 ◽  
Vol 20 (16) ◽  
pp. 3930 ◽  
Author(s):  
Komivi Dossa ◽  
Marie A. Mmadi ◽  
Rong Zhou ◽  
Tianyuan Zhang ◽  
Ruqi Su ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Meta Analysis ◽  
Plant Responses ◽  
Proof Of Concept ◽  
Rna Seq ◽  
Wild Type ◽  
Salt Treatment ◽  
Hub Genes ◽  
Hub Gene ◽  
The Core

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

scholarly journals Weighted Gene Correlation Network Meta-Analysis Reveals Functional Candidate Genes Associated with High- and Sub-Fertile Reproductive Performance in Beef Cattle

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 543 ◽  
Author(s):  
Pablo A. S. Fonseca ◽  
Aroa Suárez-Vega ◽  
Angela Cánovas
Keyword(s):  
Candidate Genes ◽  
Meta Analysis ◽  
Economic Benefits ◽  
Correlation Network ◽  
Economic Losses ◽  
Hormone Regulation ◽  
Sequencing Data ◽  
Hub Genes ◽  
Gene Correlation ◽  
Upstream Regulators

Improved reproductive efficiency could lead to economic benefits for the beef industry, once the intensive selection pressure has led to a decreased fertility. However, several factors limit our understanding of fertility traits, including genetic differences between populations and statistical limitations. In the present study, the RNA-sequencing data from uterine samples of high-fertile (HF) and sub-fertile (SF) animals was integrated using co-expression network meta-analysis, weighted gene correlation network analysis, identification of upstream regulators, variant calling, and network topology approaches. Using this pipeline, top hub-genes harboring fixed variants (HF × SF) were identified in differentially co-expressed gene modules (DcoExp). The functional prioritization analysis identified the genes with highest potential to be key-regulators of the DcoExp modules between HF and SF animals. Consequently, 32 functional candidate genes (10 upstream regulators and 22 top hub-genes of DcoExp modules) were identified. These genes were associated with the regulation of relevant biological processes for fertility, such as embryonic development, germ cell proliferation, and ovarian hormone regulation. Additionally, 100 candidate variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)) were identified within those genes. In the long-term, the results obtained here may help to reduce the frequency of subfertility in beef herds, reducing the associated economic losses caused by this condition.

scholarly journals Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Daichi Shigemizu ◽  
Shintaro Akiyama ◽  
Sayuri Higaki ◽  
Taiki Sugimoto ◽  
Takashi Sakurai ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
High Risk ◽  
Prediction Model ◽  
Target Genes ◽  
Meta Analysis ◽  
Hub Genes ◽  
Blood Samples ◽  
Prognosis Prediction ◽  
Prognosis Prediction Model

Abstract Background Mild cognitive impairment (MCI) is a precursor to Alzheimer’s disease (AD), but not all MCI patients develop AD. Biomarkers for early detection of individuals at high risk for MCI-to-AD conversion are urgently required. Methods We used blood-based microRNA expression profiles and genomic data of 197 Japanese MCI patients to construct a prognosis prediction model based on a Cox proportional hazard model. We examined the biological significance of our findings with single nucleotide polymorphism-microRNA pairs (miR-eQTLs) by focusing on the target genes of the miRNAs. We investigated functional modules from the target genes with the occurrence of hub genes though a large-scale protein-protein interaction network analysis. We further examined the expression of the genes in 610 blood samples (271 ADs, 248 MCIs, and 91 cognitively normal elderly subjects [CNs]). Results The final prediction model, composed of 24 miR-eQTLs and three clinical factors (age, sex, and APOE4 alleles), successfully classified MCI patients into low and high risk of MCI-to-AD conversion (log-rank test P = 3.44 × 10−4 and achieved a concordance index of 0.702 on an independent test set. Four important hub genes associated with AD pathogenesis (SHC1, FOXO1, GSK3B, and PTEN) were identified in a network-based meta-analysis of miR-eQTL target genes. RNA-seq data from 610 blood samples showed statistically significant differences in PTEN expression between MCI and AD and in SHC1 expression between CN and AD (PTEN, P = 0.023; SHC1, P = 0.049). Conclusions Our proposed model was demonstrated to be effective in MCI-to-AD conversion prediction. A network-based meta-analysis of miR-eQTL target genes identified important hub genes associated with AD pathogenesis. Accurate prediction of MCI-to-AD conversion would enable earlier intervention for MCI patients at high risk, potentially reducing conversion to AD.

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