Identification of novel potential homologous repair deficiency-associated genes in pancreatic adenocarcinoma via WGCNA coexpression network analysis and machine learning.

Homologous repair deficiency (HRD) impedes double-strand break repair, which is a common driver of carcinogenesis. Positive HRD status can be used as theranostic markers of response to platinum- and PARP inhibitor-based chemotherapies. Here, we aimed to fully investigate the therapeutic and prognostic potential of HRD in pancreatic adenocarcinoma (PAAD) and identify effective biomarkers related to HRD using comprehensive bioinformatics analysis. The HRD score was defined as the unweighted sum of the LOH, TAI, and LST scores, and it was obtained based on the previous literature. To characterize PAAD immune infiltration subtypes, the "ConsensusClusterPlus" package in R was used to conduct unsupervised clustering. A WGCNA was conducted to elucidate the gene coexpression modules and hub genes in the HRD-related gene module of PAAD. The functional enrichment study was performed using Metascape. LASSO analysis was performed using the "glmnet" package in R, while the random forest algorithm was realized using the "randomForest" package in R. The prognostic variables were evaluated using univariate Cox analysis. The prognostic risk model was built using the LASSO approach. ROC curve and KM survival analyses were performed to assess the prognostic potential of the risk model. The half-maximal inhibitory concentration (IC50) of the PARP inhibitors was estimated using the "pRRophetic" package in R and the Genomics of Drug Sensitivity in Cancer database. The "rms" package in R was used to create the nomogram. A high HRD score indicated a poor prognosis and an advanced clinical process in PAAD patients. PAAD tumors with high HRD levels revealed significant T helper lymphocyte depletion, upregulated levels of cancer stem cells, and increased sensitivity to rucaparib, Olaparib, and veliparib. Using WGCNA, 11 coexpression modules were obtained. The red module and 122 hub genes were identified as the most correlated with HRD in PAAD. Functional enrichment analysis revealed that the 122 hub genes were mainly concentrated in cell cycle pathways. One novel HRD-related gene signature consisting of CKS1B, HJURP, and TPX2 were screened via LASSO analysis and a random forest algorithm, and they were validated using independent validation sets. No direct association between HRD and CKS1B, HJURP, or TPX2 has not been reported in the literature so far. Thus, these findings indicated that CKS1B, HJURP, and TPX2 have potential as diagnostic and prognostic biomarkers for PAAD. We constructed a novel HRD-related prognostic model that provides new insights into PAAD prognosis and immunotherapy. Based on bioinformatics analysis, we comprehensively explored the therapeutic and prognostic potential of HRD in PAAD. One novel HRD-related gene signature consisting of CKS1B, HJURP, and TPX2 were identified through the combination of WGCNA, LASSO analysis and a random forest algorithm. A novel HRD-related risk model that can predict clinical prognosis and immunotherapeutic response in PAAD patients was constructed.

miR-34a/DRP-1-mediated mitophagy participated in cisplatin-induced ototoxicity via increasing oxidative stress.

PURPOSE: Cisplatin is a widely used and effective chemotherapeutic agent for most solid malignant tumors. However, cisplatin-induced ototoxicity is a common adverse effect that limits the therapeutic efficacy of tumors in the clinic. To date, the specific mechanism of ototoxicity has not been fully elucidated, and the management of cisplatin-induced ototoxicity is also an urgent challenge. Recently, some authors believed that miR34a and mitophagy played a role in age-related and drug-induced hearing loss. Our study aimed to explore the involvement of miR-34a/DRP-1-mediated mitophagy in cisplatin-induced ototoxicity. METHODS: In this study, C57BL/6 mice and HEI-OC1 cells were treated with cisplatin. MiR-34a and DRP-1 levels were analyzed by qRT‒PCR and western blotting, and mitochondrial function was assessed via oxidative stress, JC-1 and ATP content. Subsequently, we detected DRP-1 levels and observed mitochondrial function by modulating miR-34a expression in HEI-OC1 cells to determine the effect of miR-34a on DRP-1-mediated mitophagy. RESULTS: MiR-34a expression increased and DRP-1 levels decreased in C57BL/6 mice and HEI-OC1 cells treated with cisplatin, and mitochondrial dysfunction was involved in this process. Furthermore, the miR-34a mimic decreased DRP-1 expression, enhanced cisplatin-induced ototoxicity and aggravated mitochondrial dysfunction. We further verified that the miR-34a inhibitor increased DRP-1 expression, partially protected against cisplatin-induced ototoxicity and improved mitochondrial function. CONCLUSION: MiR-34a/DRP-1-mediated mitophagy was related to cisplatin-induced ototoxicity and might be a novel target for investigating the treatment and protection of cisplatin-induced ototoxicity.

CPSF1 positively regulates NSDHL by alternative polyadenylation and promotes gastric cancer progression.

Gastric cancer (GC) is a common malignancies with unfavourable prognosis. As one of the most common RNA modifications in nature, alternative polyadenylation (APA) plays a critical role in the progression of carcinomas. CPSF1 is a critical APA-related factor and is involved in many cancers. Nevertheless, the roles and underlying mechanisms of CPSF1 remain unclear in GC. In this work, we identified that CPSF1 is significantly upregulated in GC and that high CPSF1 expression indicates an unfavourable prognosis in GC patients. Moreover, CPSF1 expression levels were closely associated with tumour size, TNM stage and lymph node metastasis. CPSF1 depletion dramatically weakened GC cell proliferation and metastasis. We then performed RNA sequencing and found numerous downstream genes involved the regulation of CPSF1 with remarkable changes in 3'UTR length, among which NSDHL was positively regulated by CPSF1 and promoted GC progression. In addition, rescue assays demonstrated that NSDHL mediated the carcinogenic effect of CPSF1, and this process potentially involved APA. Therefore, this study showed that CPSF1 promotes GC progression, at least in part, by enhancing NSDHL and offered new insights into therapeutic targets for GC.

Shortening of the KHDRBS1 3'UTR by alternative cleavage and polyadenylation alters miRNA-mediated regulation and promotes gastric cancer progression.

The shortening of the 3' untranslated regions (3'UTRs) due to alternative polyadenylation (APA) has become an important characteristic of cancer. However, the function of APA-induced 3'UTR shortening in gastric cancer (GC) remains unclear. KHDRBS1 (sam68), as an RNA-binding protein (RBP), is significantly upregulated in GC. In this study, we found that the 3'UTR of KHDRBS1 is generally shortened in GC tissues compared to paracancer tissues. Moreover, KHDRBS1 mRNA with a shortened 3'UTR can escape the inhibitory effect of miRNAs, resulting in its increased expression in GC. Overexpression of KHDRBS1, especially KHDRBS1 with a shortened 3'UTR, promotes the growth and metastasis of GC in vivo and in vitro. In conclusion, the experimental results show that shortening of the KHDRBS1 mRNA 3'UTR can mediate the overexpression of KHDRBS1 in GC cells and promote the progression of GC.

NOL12 as an Oncogenic Biomarker Promotes Hepatocellular Carcinoma Growth and Metastasis.

Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis worldwide. However, the pathogenesis of HCC remains poorly understood. In this study, we found that NOL12 was significantly overexpressed in independent HCC datasets from TCGA database. We confirmed that the expression level of NOL12 was upregulated in human HCC tissues and cell lines by RT-qPCR. High expression of NOL12 is associated with worse reduced overall survival (OS), high pathological grade, node metastasis, and advanced clinical stage in patients with HCC. Moreover, knockdown of NOL12 dramatically inhibits the proliferation and metastasis of HCC cells in vitro and in vivo. CIBERSORTx analysis revealed that twelve types of tumor-infiltrating immune cells (TICs) are correlated with NOL12 expression. The risk signature based on 8 NOL12-related genes is an independent prognostic factor for patients with HCC. The OS rate of patients in the low-risk score group was better than that in the high-risk score group. In addition, the total tumor mutation burden (TMB) in the high-risk score group increased significantly, and the risk scores could be used as an alternative indicator of immune checkpoint inhibitor (ICI) response. In conclusion, our findings indicated that NOL12 might be involved in the progression of HCC and can be used as a potential therapeutic target. Moreover, the NOL12-related risk signature may have predictive relevance with regard to ICI therapy.

circ-0007707/miR-429/PDGFD Pathway Regulates the Progression of Gastric Cancer by Modulating the Immune-Gene Signature.

Background: Immunotherapy is an important treatment modality for gastric cancer, therefore, it is crucial to understand the regulators of the tumor microenvironment in gastric cancer. Numerous studies have shown that noncoding RNAs have a critical status in the tumor progression, and the influence of competing endogenous RNA (ceRNA) networks on gastric adenocarcinoma has been widely discussed over the years, but the connection between ceRNA networks and the immune microenvironment of cancer is unclear. This study was aimed at exploring how ceRNA networks influence the prognosis of patients with gastric cancer by modulating the tumor microenvironment. Methods: The Gene Expression Omnibus was analyzed to obtain differential expression matrixes of the noncoding RNAs (circular RNAs (circRNAs), microRNAs (miRNAs)), and mRNAs. The Circular RNA Interactome web tool and TargetScan were applied to determine the miRNA binding sites of the circRNAs and miRNA target genes. The Cancer Genome Atlas provided prognostic genes for gastric cancer, and Cytoscape created the ceRNA networks. Real-time quantitative reverse transcription polymerase chain reaction and western blot assay were adopted to find out how the ceRNA network regulates the expression of the hub gene. Additionally, the TISIDB and TIMER databases were used to assess the link between the hub gene and immunotherapy, with TISIDB providing the immune genes that are coexpressed with the hub gene. Furthermore, the immune-gene signature was constructed by using Cox regression analysis. Moreover, the nomogram, which could predict the prognostic role of gastric cancer patients was created on the basis of the immune-gene signature. Results: In gastric cancer, the circ-0007707/miR-429/PDGFD pathway had a differential expression. The results demonstrated that the pathway could regulate the progression and immune microenvironment of gastric cancer by modulating the immune-gene signature, which included two immune genes (TAB1 and CXCR4). Moreover, the low-risk group patients had better survival. Conclusion: The circ-0007707/miR-429/PDGFD pathway may play a regulatory role in the progression and prognosis of gastric cancer by interfering with the tumor microenvironment, and the PDGFD-related immune-gene signature could be considered a moderator of prognostic factor for gastric cancer and to guide immunotherapy programs.

A Deep Learning Approach to Predict Conductive Hearing Loss in Patients With Otitis Media With Effusion Using Otoscopic Images.

Importance: Otitis media with effusion (OME) is one of the most common causes of acquired conductive hearing loss (CHL). Persistent hearing loss is associated with poor childhood speech and language development and other adverse consequence. However, to obtain accurate and reliable hearing thresholds largely requires a high degree of cooperation from the patients. Objective: To predict CHL from otoscopic images using deep learning (DL) techniques and a logistic regression model based on tympanic membrane features. Design, Setting, and Participants: A retrospective diagnostic/prognostic study was conducted using 2790 otoscopic images obtained from multiple centers between January 2015 and November 2020. Participants were aged between 4 and 89 years. Of 1239 participants, there were 209 ears from children and adolescents (aged 4-18 years [16.87%]), 804 ears from adults (aged 18-60 years [64.89%]), and 226 ears from older people (aged >60 years, [18.24%]). Overall, 679 ears (54.8%) were from men. The 2790 otoscopic images were randomly assigned into a training set (2232 [80%]), and validation set (558 [20%]). The DL model was developed to predict an average air-bone gap greater than 10 dB. A logistic regression model was also developed based on otoscopic features. Main Outcomes and Measures: The performance of the DL model in predicting CHL was measured using the area under the receiver operating curve (AUC), accuracy, and F1 score (a measure of the quality of a classifier, which is the harmonic mean of precision and recall; a higher F1 score means better performance). In addition, these evaluation parameters were compared to results obtained from the logistic regression model and predictions made by three otologists. Results: The performance of the DL model in predicting CHL showed the AUC of 0.74, accuracy of 81%, and F1 score of 0.89. This was better than the results from the logistic regression model (ie, AUC of 0.60, accuracy of 76%, and F1 score of 0.82), and much improved on the performance of the 3 otologists; accuracy of 16%, 30%, 39%, and F1 scores of 0.09, 0.18, and 0.25, respectively. Furthermore, the DL model took 2.5 seconds to predict from 205 otoscopic images, whereas the 3 otologists spent 633 seconds, 645 seconds, and 692 seconds, respectively. Conclusions and Relevance: The model in this diagnostic/prognostic study provided greater accuracy in prediction of CHL in ears with OME than those obtained from the logistic regression model and otologists. This indicates great potential for the use of artificial intelligence tools to facilitate CHL evaluation when CHL is unable to be measured.

SNHG9 was upregulated in NSCLC and associated with DDP-resistance and poor prognosis of NSCLC patients.

Lung cancer, a leading cause of cancer-related mortalities worldwide and non-small cell lung cancer (NSCLC) is the main subtype of lung cancer. As a first-line chemotherapeutic drug used for NSCLC, acquired resistance retarded the clinical application of cisplatin (DDP). We herein reported long non-coding RNA SNHG9 was over-expressed in NSCLC tissues and cell lines compared with normal lung tissues and cell line; Increased SNHG9 was also observed in DDP resistant NSCLC tissues and cell lines compared with their DDP sensitive counterparts. Elevated expression of SNHG9 was associated with lower overall survival (OS) rate in NSCLC patients. Besides, silence of SNHG9 suppressed DDP resistance of NSCLC cells. Furthermore, CAPRIN1 was positively regulated by SNHG9 and mediated the promoting role of SNHG9 in DDP resistance of NSCLC cells. SNHG9 could be used as a potential target for DDP resistant NSCLC therapy.

Diagnosis accuracy of Raman spectroscopy in colorectal cancer: A PRISMA-compliant systematic review and meta-analysis.

BACKGROUND: The clinical significance of Raman spectroscopy (RS) in colorectal cancer (CRC) patients still remains underestimated. We performed this meta-analysis to elucidate the diagnostic value in CRC patients. METHODS: We systematically searched electronic databases for published articles. Fixed effect model and random effect model were used to calculate the pooled sensitivity, specificity, diagnostic accuracy, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and positive posttest probability (PPP) of CRC. Meta-regression and subgroup analysis were conducted to assess potential source of heterogeneity. We also used Egger linear regression tests to assess risk of publication bias. RESULTS: Thirteen studies had been included (679 patients: 186 with premalignant lesions and 493 with malignant lesions). The pooled sensitivity, specificity, diagnostic accuracy, PLR, NLR, DOR and PPP for CRC screening using RS were 0.94 (0.92-0.96), 0.94 (0.88-0.97), 0.96 (0.94-0.98), 16.44 (7.80-34.63), 0.062 (0.043-0.090), 263.65 (99.03-701.96) and 86%, respectively. CONCLUSION: RS is a potentially useful tool for future CRC screening. It also offers potentially early detection for CRC patients.

Long non-coding RNA LINC00472 suppresses hepatocellular carcinoma cell proliferation, migration and invasion through miR-93-5p/PDCD4 pathway.

Hepatocellular carcinoma (HCC) is the fifth most prevalent cancer and the second leading cause of cancer-related deaths. In the present study, we have demonstrated that long non-coding RNA (lncRNA) LINC00472 was low expressed in human HCC tissues and cell lines compared with adjacent non-tumor liver tissues and normal liver cell lines respectively. LINC00472 was also low expressed in HCC tissues from patients with metastasis compared with tissues from patients without metastasis. Expression level of LINC00472 was positively correlated with patient overall survival (OS) rate. Forced expression of LINC00472 suppressed cell proliferation, migration, invasion and promoted cell apoptosis in HCC cells Huh-7 and SMMC-7721. MiR-93-5p was a direct target of LINC00472, and miR-93-5p directly targeted PDCD4. The miR-93-5p/PDCD4 pathway mediated the suppressing role of LINC00472 in HCC cells. Therefore, LINC00472 was an important tumor suppressor in human HCC, which could be used as a bio-marker for HCC therapy.

Prognostic Value of Long Noncoding RNAs in Patients with Gastrointestinal Cancer: A Systematic Review and Meta-Analysis.

Gastrointestinal cancers (GICs) are a huge threat to human health, which mainly include esophageal, gastric, and colorectal cancers. The purpose of this study was to clarify the prognostic value of long noncoding RNAs (lncRNAs) in GICs. A total of 111 articles were included, and 13103 patients (3123 with esophageal cancer, 4972 with gastric cancer, and 5008 with colorectal cancer) were enrolled in this study. The pooled hazard ratio (HR) values and corresponding 95% confidence interval (95% CI) of overall survival (OS) related to different lncRNA expressions in esophageal, gastric, colorectal, and gastrointestinal cancer patients were 1.92 (1.70-2.16), 1.96 (1.77-2.16), 2.10 (1.87-2.36), and 2.00 (1.87-2.13), respectively. We have identified 74 lncRNAs which were associated closely with poor prognosis of GIC patients, including 58 significantly upregulated lncRNA expression and 16 significantly downregulated lncRNA expression. In addition, 47 of the included studies revealed relative mechanisms and 12 of them investigated the correlation between lncRNAs and microRNAs. Taken together, this meta-analysis supports that specific lncRNAs are significantly related to the prognosis of GIC patients and may serve as novel markers for predicting the prognosis of GIC patients. Furthermore, lncRNAs may have a promising contribution to lncRNA-based targeted therapy and clinical decision-making in the future.

Prognostic role of microRNAs in human gastrointestinal cancer: A systematic review and meta-analysis.

BACKGROUND: Gastrointestinal cancers (GICs) mainly including esophageal, gastric and colorectal cancer, are the most common cause of cancer-related death and lead into high mortality worldwide. We performed this systematic review and meta-analysis to elucidate relationship between multiple microRNAs (miRs) expression and survival of GIC patients. METHODS: We searched a wide range of database. Fixed-effects and random-effects models were used to calculate the pooled hazard ratio values of overall survival and disease free survival. In addition, funnel plots were used to qualitatively analyze the publication bias and verified by Begg's test while it seems asymmetry. RESULTS: 60 studies involving a total of 6225 patients (1271 with esophageal cancer, 3467 with gastric cancer and 1517 with colorectal cancer) were included in our meta-analysis. The pooled hazard ratio values of overall survival related to different miRs expression in esophageal, gastric, colorectal and gastrointestinal cancer were 2.10 (1.78-2.49), 2.02 (1.83-2.23), 2.54 (2.14-3.02) and 2.15 (1.99-2.31), respectively. We have identified a total of 59 miRs including 23 significantly up-regulated expression miRs (miR-214, miR-17, miR-20a, miR-200c, miR-107, miR-27a, etc.) and 36 significantly down-regulated expression miRs (miR-433, let-7g, miR-125a-5p, miR-760, miR-206, miR-26a, miR-200b, miR-185, etc.) correlated with poor prognosis in GIC patients. Moreover, 35 of them revealed mechanisms. CONCLUSION: Overall, specific miRs are significantly associated with the prognosis of GIC patients and potentially eligible for the prediction of patients survival. It also provides a potential value for clinical decision-making development and may serve as a promising miR-based target therapy waiting for further elucidation.

[Neurotrophins up-express in peripheral blood of allergic rhinitis patients and related to Th2 hypothesis].

OBJECTIVE: To detect the expression of NGF, BDNF, NT-3 mRNA in the peripheral blood of patients with allergic rhinitis (AR). And to analyze the correlation between NGF, BDNF, NT-3 mRNA expression and the epidsode of rhinitis through Th-2 Hypothesis. METHOD: This study was a group controlled trial. The expression of NGF, BDNF and NT-3 mRNA were tested by real-time quantitative RT-PCR and the concentrations of IL-4, IL-6, IL-10 and INF-alpha were tested by ELISA. RESULT: The expression of NGF, BDNF and NT-3 mRNA in AR patients were 2.44, 4.46 and 1.78 times the amount of those in the healthy adults, respectively. The increased expression of NT-3 correlated positively with the scores of visual analog scale of AR. The concentrations of IL-4, IL-6 and IL-10, which were 2198 +/- 472 pg/mL, 9407 +/- 703 pg/mL and 3917 +/- 323 pg/mL respectively, were higher than those in the healthy adults. The concentration of INF-alpha was 2198 +/- 472 pg/mL and less than the healthy adults. The increased expressions of NGF, NT-3 were positively related to the increase of IL-4, IL-6 and IL-10. CONCLUSION: The expressions of NGF, BDNF and NT-3 mRNA in AR patients are higher than those in the healthy adults. NGF, BDNF and NT-3 may contribute to the pathogenesis of AR. Moreover, NGF and NT-3 may induce the episode of rhinitis through Th-2 Hypothesis.

[Increase expression of neurotrophins mRNA in peripheral blood of patients with allergic rhinitis].

OBJECTIVE: To assess the expression of NGF, BDNF, NT-3 mRNA in the peripheral blood of patients with allergic rhinitis (AR). Meanwhile, to analysis whether the expression of NGF, BDNF, NT-3 mRNA correlate with the severity of rhinitis. METHOD: This study is a group controlled trial, which takes the healthy adults as control group. The total RNA have been extracted from the peripheral blood of AR patients. The expression of NGF, BDNF and NT-3 mRNA have been tested by real-time quantitative RT-PCR. RESULT: Comparing with the healthy adults, the expression of NGF, BDNF and NT-3 mRNA as 2(-deltadeltaCt) are 2.436 8, 4.4588 and 1.781 8 respectively. The increasing expression of NT-3 correlated positively with the scores of visual analog scale. CONCLUSION: The expression of NGF, BDNF and NT-3 mRNA are as high as 2.4368, 4.4588 and 1.7818 times to healthy adults. We propose NGF, BDNF and NT-3 may contribute to the pathogenesis of AR. NT-3 could reflect the severity of rhinitis as a molecular biological index.

Cilostazol prevents the degradation of collagen type II in human chondrocytes.

The alteration of extracellular matrix (ECM) in cartilage during the pathological development of Osteoarthritis (OA) changes the biomechanical environment of chondrocytes, which further drives the progression of the disease in the presence of inflammation. Healthy cartilage matrix mainly contains collagen type II, which is degraded by matrix metalloproteinase13 (MMP13), an important molecules responsible for joint damage in OA. Cilostazol (6-[4-(1-cyclohexyl-1H-tetrazol-5-yl)butoxy]-3,4-dihydro-2-(1H)-quinolinone) is a medication approved by the US Food and Drug Administration and used in the alleviation of the symptom of intermittent claudication in individuals with peripheral vascular disease. In this study, we reported that cilostazol is able to suppress the degradation of type II collagen in human chondrocytes induced by IL-1ß. Mechanistically, cilostazol treatment leads to inhibiting the expression of IRF-1, thereby prevents the induction of MMP-13. Signal transducers and activator of transcription 1 (STAT1) has been reported to play an essential role in regulating the activation of IRF-1. Our results indicated that cilostazol suppresses the activation of STAT1 by mitigating the phosphorylation of STAT1 at Ser727 and tyrosine phosphorylation of STAT1 at position 701 (Tyr701).