Identification of gene signatures related to hypoxia and angiogenesis in pancreatic cancer to aid immunotherapy and prognosis

BackgroundOne of the most diverse tumors is pancreatic cancer (PC), which makes predicting the prognosis challenging. PC development is directly related to hypoxia, angiogenesis, and immunotherapy. It is still unclear how the three features are related.MethodsThe Genotype-Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) database were employed to obtain sequencing data for healthy pancreatic tissues and PC tissues, respectively. According to the constructed hypoxic prognostic model (HPM) and angiogenic prognostic model (APM), 4 subtypes of PC were identified. Hypoxia and angiogenesis prognostic model (HAPM) was established based on differentially expressed genes (DEGs) between high-angiogenesis/high-hypoxia (HH) and low-angiogenesis/low-hypoxia (LL) subgroups. Base on the median risk score, PC patients were separated into high-risk and low-risk groups, and clinical traits, prognosis, percentage of immune cell infiltration, PD-1 expression, and the fraction of T-cell depletion were compared between the groups. Finally, the predictive accuracy of the tumor immune dysfunction and rejection (TIDE) and tumor inflammatory signature (TIS) models, as well as HAPM, was compared.ResultWe analyzed the mRNA sequencing data from 178 PC tissues and 171 normal pancreatic tissues to obtain 9527 DEGs. We discovered 200 genes linked with hypoxia and 36 genes involved with angiogenesis through the literature. We found the core genes related with hypoxia and angiogenesis in PC by intersecting the DEGs of the HH and LL subgroups with those of PC via WGCNA. IL-17 signaling pathway, ECM-receptor interactions, cytokine receptor interactions, etc. were all enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) results of core genes. HAPM has good predictive efficiency, according to an evaluation of KM survival curves and ROC curves. The external dataset also validated the model’s ability to anticipate outcomes. Patients in the high- and low-risk groups were compared for PD1 expression and T-cell exclusion scores, which suggested that the model might be used to forecast which PC patients might benefit from immunotherapy.ConclusionsThe probable molecular processes connecting hypoxia and angiogenesis are described in this work, and a model is developed that may be utilized to forecast the prognosis for PC patients and the benefits of immunotherapy

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis

<p>Abstract</p> <p>Background</p> <p><it>SOX2 </it>is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. <it>SOX2 </it>appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of <it>SOX2 </it>in GBM has not yet been defined.</p> <p>Results</p> <p>We show that knockdown of the <it>SOX2 </it>gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the <it>SOX2 </it>response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 <it>SOX2 </it>binding regions in the GBM cancer genome. <it>SOX2 </it>binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 <it>SOX2 </it>binding regions. Microarray analysis identified 489 genes whose expression altered in response to <it>SOX2 </it>knockdown. Interesting findings include that <it>SOX2 </it>regulates the expression of SOX family proteins <it>SOX1 </it>and <it>SOX18</it>, and that <it>SOX2 </it>down regulates <it>BEX1 </it>(brain expressed X-linked 1) and <it>BEX2 </it>(brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by <it>SOX2</it>, including down regulation of miR-143, -145, -253-5p and miR-452. We also show that miR-145 and <it>SOX2 </it>form a double negative feedback loop in GBM cells, potentially creating a bistable system in GBM cells.</p> <p>Conclusions</p> <p>We present an integrated dataset of ChIP-seq, expression microarrays and microRNA sequencing representing the <it>SOX2 </it>response program in LN229 GBM cells. The insights gained from our integrated analysis further our understanding of the potential actions of <it>SOX2 </it>in carcinogenesis and serves as a useful resource for the research community.</p

RNA-Seq Analyses Generate Comprehensive Transcriptomic Landscape and Reveal Complex Transcript Patterns in Hepatocellular Carcinoma

RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome at both gene and exon levels and with a unique ability of identifying novel splicing variants. To date, RNA-seq analysis of HBV-related hepatocellular carcinoma (HCC) has not been reported. In this study, we performed transcriptome analyses for 10 matched pairs of cancer and non-cancerous tissues from HCC patients on Solexa/Illumina GAII platform. On average, about 21.6 million sequencing reads and 10.6 million aligned reads were obtained for samples sequenced on each lane, which was able to identify >50% of all the annotated genes for each sample. Furthermore, we identified 1,378 significantly differently expressed genes (DEGs) and 24, 338 differentially expressed exons (DEEs). Comprehensive function analyses indicated that cell growth-related, metabolism-related and immune-related pathways were most significantly enriched by DEGs, pointing to a complex mechanism for HCC carcinogenesis. Positional gene enrichment analysis showed that DEGs were most significantly enriched at chromosome 8q21.3–24.3. The most interesting findings were from the analysis at exon levels where we characterized three major patterns of expression changes between gene and exon levels, implying a much complex landscape of transcript-specific differential expressions in HCC. Finally, we identified a novel highly up-regulated exon-exon junction in ATAD2 gene in HCC tissues. Overall, to our best knowledge, our study represents the most comprehensive characterization of HBV-related HCC transcriptome including exon level expression changes and novel splicing variants, which illustrated the power of RNA-seq and provided important clues for understanding the molecular mechanisms of HCC pathogenesis at system-wide levels

Prognostic role of RDW in hematological malignancies: a systematic review and meta-analysis

Abstract Background Red blood cell distribution width (RDW), a biomarker for discrimination of anemia, has been recently identified as a prognostic factor in various types of cancer. Here we performed a meta-analysis in order to assess the correlation between RDW and the survival outcomes in patients with hematologic malignances. Patients/methods We systematically searched PubMed, Embase, and ISI Web of Science for relevant studies, to investigate the prognostic significance of RDW in hematological malignancies. Odds ratios or hazards ratios (HRs) with corresponding 95% confidence intervals (CIs) are pooled to estimate the association between RDW and clinicopathological parameters of patients with hematologic malignances. Results Seven trials with 1031 patients suffering from hematological malignancies were included in the meta-analysis, and the results indicated that increased pretreatment RDW predicted poor overall survival (HR = 2.35, 95% CI 1.70–3.24), poor progress-free survival (HR = 2.44, 95% CI 1.70–3.49) and poor event-free survival (EFS) (HR = 3.15, 95% CI 1.59–6.25). Furthermore, the similar results were observed in subgroup analysis stratified by cancer type, such as multiple myeloma, and diffuse large B cell lymphoma, etc. Conclusions As for hematologic malignances, patients with higher RDW are more likely to have poorer prognosis than those with lower RDW

Prognostic and clinicopathological significance of long noncoding RNA HOXA11-AS expression in human solid tumors: a meta-analysis

Abstract Background Recent studies have emphasized the important prognostic role of long noncoding RNAs (lncRNAs) in various types of cancers. Here we conducted a meta-analysis to investigate whether lncRNA HOXA11-AS can be served as a prognostic biomarker in human cancers. Patients/methods We systematically searched PubMed, Embase, ISI Web of Science, and SCOPUS for relevant studies, to investigate the prognostic significance of HOXA11-AS expression in cancer patients. Odds ratios (ORs) or hazards ratios (HRs) with corresponding 95% confidence intervals (CIs) are pooled to estimate the association between HOXA11-AS expression and clinicopathological parameters or survival of cancer patients. Results A total of eight eligible studies with 1320 cancer patients were enrolled in our meta-analysis. The results revealed that increased expression level of HOXA11-AS was significantly associated with clinicopathological parameters including more lymph node metastasis (OR = 2.06, 95% CI 1.31–3.25), advanced tumor stage (OR = 4.22, 95% CI 2.60–6.85), as well as poor tumor differentiation (OR = 2.49, 95 CI 1.47–4.20), but not correlated with age (p = 0.101) or gender (p = 0.845). In addition, cancer patients with high HOXA11-AS are prognosed to have shorter OS (pooled HR = 1.86, 95% CI 1.39–2.48) and PFS (pooled HR = 2.47, 95% CI 1.29–4.75). Conclusions HOXA11-AS overexpression might be a convinced unfavorable prognostic factor that helps the clinical decision-making process

Tumor-infiltrating B cells as a favorable prognostic biomarker in breast cancer: a systematic review and meta-analysis

Abstract Background Tumor-infiltrating B lymphocytes (TIL-Bs) is a heterogeneous population of lymphocytes. The prognostic value of TIL-Bs in patients with breast cancer remains controversial. Here we conducted this meta-analysis to clarify the association of TIL-Bs with outcomes of patients with breast cancer. Methods We searched PubMed, Embase, and Web of Science to identify relevant studies assessing the prognostic significance of TIL-Bs in patients with breast cancer. Fixed- or random-effects models were used to evaluate the pooled hazard ratios (HRs) for overall survival (OS), breast cancer-specific survival (BCSS), disease-free survival (DFS), and relapse-free survival (RFS) in breast cancer. Results A total of 8 studies including 2628 patients were included in our study. Pooled analyses revealed that high level of TIL-Bs was associated with longer OS (pooled HR = 0.42, 95% CI 0.24–0.60), BCSS (pooled HR = 0.66, 95% CI 0.47–0.85), and DFS/RFS (pooled HR = 0.41, 95% CI 0.27–0.55). Conclusions This meta-analysis suggests that TIL-Bs could be a promising prognostic marker for breast cancer. Novel therapeutic strategies for breast cancer treatment could be developed by enhancement of B cell-mediated antitumor immunity

Polydopamine-Based Surface Modification of ZnO Nanoparticles on Sericin/Polyvinyl Alcohol Composite Film for Antibacterial Application

Silk sericin (SS) is a type of natural macromolecular protein with excellent hydrophilicity, biocompatibility and biodegradability, but also has very poor mechanical properties. To develop sericin-based wound dressings, we utilized polyvinyl alcohol (PVA) to reinforce the mechanical property of sericin by blending PVA and sericin, then modified zinc oxide nanoparticles (ZnO NPs) on SS/PVA film with the assistance of polydopamine (PDA) to endow SS/PVA film with antibacterial activity. Scanning electron microscopy, energy dispersive spectroscopy and X-ray powder diffraction demonstrated ZnO NPs were well grafted on PDA-SS/PVA film. Fourier transform infrared spectra suggested PDA coating and ZnONPs modification did not alter the structure of sericin and PVA. Water contact angle and swelling tests indicated the excellent hydrophilicity and swellability of ZnO NPs-PDA-SS/PVA composite film. Mass loss analysis showed ZnO NPs-PDA-SS/PVA film had excellent stability. The mechanical performance test suggested the improved tensile strength and elongation at break could meet the requirement of ZnO NPs-PDA-SS/PVA film in biomaterial applications. The antibacterial assay suggested the prepared ZnO NPs-PDA-SS/PVA composite film had a degree of antimicrobial activity against Escherichia coli and Staphylococcus aureus. The excellent hydrophilicity, swellability, stability, mechanical property and antibacterial activity greatly promote the possibility of ZnO NPs-PDA-SS/PVA composite film in antibacterial biomaterials application

Prognostic role of myeloid-derived suppressor cells in cancers: a systematic review and meta-analysis

Abstract Background Myeloid-derived suppressor cells (MDSCs) is a heterogeneous population of immature myeloid cells, inhibiting both the innate and adaptive immunity. Recent studies validated that MDSCs caused immune suppression and promoted cancer progression through various mechanisms. However, the prognostic value of MDSCs in cancer remains controversial. Methods Here, we performed this meta-analysis to evaluate the prognostic value of MDSCs in various types of cancer. The electric databases, such as Pubmed, Embase and Web of Science, were searched for relevant publications. Hazards ratios (HRs) with the corresponding 95% confidence intervals (95%CIs) were calculated to evaluate the prognostic role of MDSCs in cancer. Results A total of 16 studies with 1864 patients were enrolled in our meta-analysis. Elevated MDSCs frequency was shown to be associated with shorter overall survival (OS) (HR = 2.46, 95%CI: 1.87–3.23), and poor disease-free survival / recurrence-free survival (DFS / RFS) (HR = 3.26, 95%CI: 2.10–5.04) after treatment. Furthermore, similar results were also observed in the stratified subgroup analysis, which included the analysis by region, sample size, cancer type, NOS scores, subtype and cut-off value of MDSCs. Conclusion High MDSCs might be related to poor clinical outcomes of patients with cancer, that is, MDSCs might be a potential prognostic biomarker in cancer

The Research and Application of Microbial Degradation Technology on Heavy Oil Reservoir in Huabei Oilfield

Mengulin sandstone reservoir in Huabei oilfield is low- temperature heavy oil reservoir. Recently, it is at later stage of waterflooding development. The producing degree of water flooding is poor, and it is difficult to keep yield stable. To improve oilfield development effect, according to the characteristics of reservoir geology, microbial enhanced oil recovery to improve oil displacement efficiency is researched. 2 microbial strains suitable for the reservoir conditions were screened indoor. The growth characteristics of strains, compatibility and function mechanism with crude oil were studied. Results show that the screened strains have very strong ability to utilize petroleum hydrocarbon to grow and metabolize, can achieve the purpose of reducing oil viscosity, and can also produce biological molecules with high surface activity to reduce the oil-water interfacial tension. 9 oil wells had been chosen to carry on the pilot test of microbial stimulation, of which 7 wells became effective with better experiment results. The measures effective rate is 77.8%, the increased oil is 1,093.5 tons and the valid is up to 190 days

The Research and Application of Microbial Degradation Technology on Heavy Oil Reservoir in Huabei Oilfield

Mengulin sandstone reservoir in Huabei oilfield is low- temperature heavy oil reservoir. Recently, it is at later stage of waterflooding development. The producing degree of water flooding is poor, and it is difficult to keep yield stable. To improve oilfield development effect, according to the characteristics of reservoir geology, microbial enhanced oil recovery to improve oil displacement efficiency is researched. 2 microbial strains suitable for the reservoir conditions were screened indoor. The growth characteristics of strains, compatibility and function mechanism with crude oil were studied. Results show that the screened strains have very strong ability to utilize petroleum hydrocarbon to grow and metabolize, can achieve the purpose of reducing oil viscosity, and can also produce biological molecules with high surface activity to reduce the oil-water interfacial tension. 9 oil wells had been chosen to carry on the pilot test of microbial stimulation, of which 7 wells became effective with better experiment results. The measures effective rate is 77.8%, the increased oil is 1,093.5 tons and the valid is up to 190 days