bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the EMT-related signature to stratify prognosis and evaluate the tumor microenvironment in lung adenocarcinoma
Authors: Li Feng , Song Qing-Zhen , Zhang Yi-Fan , Wang Xing-Ru , Cao Li-Min , Li Nan , Zhao Ling-Xia , Zhang Sheng-Xiao , Zhuang Xiao-Fei 
Published: September 2022

Background: Epithelial-mesenchymal transition (EMT) is a critical process in tumor invasion and metastasis. EMT has been shown to significantly influence the invasion, metastasis, and poor prognosis in lung adenocarcinoma (LUAD). This study aimed to develop a novel EMT-related prognostic model capable of predicting overall survival (OS) in patients with LUAD.Methods: A total of 283 LUAD patients from TCGA RNA-seq dataset were assigned to a training cohort for model building, and 310 LUAD patients from GEO RNA-seq dataset were assigned to a validation cohort. EMT genes were acquired from MsigDB database and then prognosis-related EMT genes were identified by univariate Cox regression. Lasso regression was then performed to determine the genes and the corresponding variables to construct a prognosis risk model from the training cohort. Furthermore, characteristics of the tumor microenvironment (TME), mutation status and chemotherapy responses were analyzed to assess the differences between the two risk groups based on the prognostic model. In addition, RT-qPCR was employed to validate the expression patterns of the 6 genes derived from the risk model.Results: A six-gene EMT signature (PMEPA1, LOXL2, PLOD2, MMP14, SPOCK1 and DCN) was successfully constructed and validated. The signature assigned the LUAD patients into high-risk and low-risk groups. In comparison with the low-risk group, patients in the high-risk group had a significantly lower survival rate. ROC curves and calibration curves for the risk model demonstrated reliable stratification and predictive ability. The risk model was robustly correlated with multiple TME characteristics. Besides, the data showed that patients in the low-risk group had more immune activities, higher stemness scores and cytolytic activity scores and higher TMB. In addition, RT-qPCR results revealed that PMEPA1, LOXL2, PLOD2, MMP14, and SPOCK1 were notably upregulated in LUAD tissues, while DCN was downregulated.Conclusion: Our study successfully developed a novel EMT-related signature to predict prognosis of LUAD patients and guide treatment strategies. The six genes derived from the prediction signature might play a potential role in antitumor immunity and serve as promising therapeutic targets in LUAD.
Aberrant expression of SPAG6 and NM23 predicts poor prognosis of human osteosarcoma
Authors: Bao Zhengqi , Zhu Ruizhi , Fan Huagang , Ye Yuchen , Li Tian , Chai Damin 
Published: September 2022

Objective: To investigate the expression and clinical significance of sperm-associated antigen 6 and NM23 proteins in human osteosarcoma.Methods: The specimens of conventional osteosarcoma with follow-up from 42 Chinese patients were analyzed in this study, and 12 cases of osteochondroma were considered controls. The expression of SPAG6 and NM23 was inspected using immunohistochemical staining, qRT-PCR, and Western blotting methods.Results: The positive expression rate of SPAG6 protein (71.43%) in 42 cases of osteosarcoma tissue was significantly higher than that (33.33%) in 12 cases of osteochondroma tissues (p &lt; 0.05), while the positive rate of NM23 protein (35.71%) in osteosarcoma tissue was lower than that (58.33%) in osteochondroma tissue (p &lt; 0.05). The mRNA and protein levels of SPAG6 were significantly higher than those of the adjacent normal tissues, while the expression of NM23 was lower in osteosarcoma tissues than that in the controls (p &lt; 0.05 for all). There was a positive relationship between the expression of SPAG6 and pathological grade, metastasis, and Enneking stage (p &lt; 0.05 for all). The overall survival rate of osteosarcoma patients with SPAG6 positive expression was significantly lower than that with SPAG6 negative expression. The relationship between the expression of NM23 and pathological grade, metastasis, and Enneking stage was negative (p &lt; 0.05 for all). The overall survival rate of the osteosarcoma patients with NM23 positive expression was higher than that of the patients with NM23 negative expression (p &lt; 0.05).Conclusion: Overexpression of SPAG6 and low expression of NM23 are negatively related to pathological grade, metastasis, and Enneking stage and prognosis of osteosarcoma patients. This suggested that SPAG6 and NM23 should be considered candidate prognostic biomarkers for patients with osteosarcoma.
Integrated bioinformatics analysis for novel miRNAs markers and ceRNA network in diabetic retinopathy
Authors: Li Jingru , Li Chaozhong , Zhao Yulan , Wu Xinyu , Yu Shuai , Sun Guihu , Ding Peng , Lu Si , Zhang Lijiao , Yang Ping , Peng Yunzhu , Fu Jingyun , Wang Luqiao 
Published: September 2022

In order to seek a more outstanding diagnosis and treatment of diabetic retinopathy (DR), we predicted the miRNA biomarkers of DR and explored the pathological mechanism of DR through bioinformatics analysis.Method: Based on public omics data and databases, we investigated ncRNA (non-coding RNA) functions based on the ceRNA hypothesis.Result: Among differentially expressed miRNAs (DE-miRNAs), hsa-miR-1179, -4797-3p and -665 may be diagnosis biomarkers of DR. Functional enrichment analysis revealed differentially expressed mRNAs (DE-mRNAs) enriched in mitochondrial transport, cellular respiration and energy derivation. 18 tissue/organ-specific expressed genes, 10 hub genes and gene cluster modules were identified. The ceRNA networks lncRNA FBXL19-AS1/miR-378f/MRPL39 and lncRNA UBL7-AS1/miR-378f/MRPL39 might be potential RNA regulatory pathways in DR.Conclusion: Differentially expressed hsa-miR-1179, -4797-3p and -665 can be used as powerful markers for DR diagnosis, and the ceRNA network: lncRNA FBXL19-AS1/UBL7-AS1-miR-378f-MRPL39 may represent an important regulatory role in DR progression.
Comprehensive analysis of SLC43A2 on the tumor immune microenvironment and prognosis of liver hepatocellular carcinoma
Authors: Liao Yan , Weng Junmei , Chen Lian , Hu Nan , Yuan Xun , Wang Jianhua , He Feng , Cai Yixin , Huang Qin , Wang Jianing , Huang Liu 
Published: September 2022

Background: Tumor cells outcompete T cells for methionine via overexpressing SLC43A2, causing T cells exhaustion. We explored the influence of SLC43A2 on tumor immune microenvironment (TIME), immune-related genes (IRGs) and the prognosis of liver hepatocellular carcinoma (LIHC) patients.Methods: The TCGA-LIHC dataset (n = 374) and the ICGC-LIRI-JP-LIHC (n = 231) datasets were used as training and validation cohort, respectively. IRGs were obtained from ImmPort. Statistical analyses were performed using R (V 4.0.5). Online databases such as GEPIA, GSCALite, the Kaplan–Meier plotter, KEGG, TIMER2, and CMap were used for differential expression, immune infiltration, functional enrichment, survival, and drug-induced gene perturbation analysis.Results: SLC43A2 expression was higher in LIHC, correlated with worse survival, but could not predict prognosis of LIHC separately (AUC = 0.467). SLC43A2 positively correlated with immune exhaustion markers (all p &lt; 0.001) and with increased infiltration of Tregs, macrophages and myeloid-derived suppressor cells (MDSC) (all p &lt; 0.05). SLC43A2 may regulate 120 IRGs. A prognostic risk score model was developed using the TCGA-LIHC cohort and validated by the ICGC-LIRI-JP cohort. Arachidonic acid, SB-202190 and guanethidine were identified as possible immunomodulators pharmacologically targeting SLC43A2 in LIHC.Conclusion: SLC43A2 may create suppressive tumor microenvironment and regulate related IRGs, thus affecting the prognosis of LIHC. Arachidonic acid, SB-202190, and guanethidine may be worthy of further study as immunomodulators on SLC43A2.
Identification of the circRNA–miRNA–mRNA regulatory network in osteoarthritis using bioinformatics analysis
Authors: Xu Wen-Bin , Kotheeranurak Vit , Zhang Huang-Lin , Feng Jin-Yi , Liu Jing-Wei , Chen Chien-Min , Lin Guang-Xun , Rui Gang 
Published: September 2022

Background: Osteoarthritis (OA) is a degenerative joint disease that seriously affects the quality of people. Unfortunately, the pathogenesis of OA has not been fully known. Therefore, this study aimed to construct a ceRNA regulatory network related to OA to explore the pathogenesis of OA.Methods: Differentially expressed circRNAs (DEcircRNAs), microRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were obtained from the Gene Expression Omnibus microarray data (GSE175959, GSE105027, and GSE169077). The miRNA response elements and target mRNAs were identified using bioinformatics approaches. Additionally, a circRNA–miRNA–mRNA network was established using Cytoscape version 3.8.0. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of mRNAs in the network were conducted to explore the possible mechanisms underlying OA development. Protein–protein interaction (PPI) analysis was performed to determine the hub genes. Based on the hub genes, a sub network was constructed using Cytoscape 3.8.0 version. Finally, connectivity map (CMap) and drug–gene interaction database (DGIdb) analyses were performed to identify the potential therapeutic targets for OA.Results: Altogether, five DEcircRNAs, 89 DEmiRNAs, and 345 DEmRNAs were identified. Moreover, a circRNA–miRNA–mRNA network was established using three circRNAs, seven miRNAs, and 37 mRNAs. GO and KEGG analyses demonstrated that the mRNAs in the network could be related to the occurrence and development of OA. PPI analysis was performed and six key genes, namely serpin family H member 1 [SERPINH1], collagen type VIII alpha 2 chain [COL8A2], collagen type XV alpha 1 chain [COL15A1], collagen type VI alpha 3 chain [COL6A3], collagen type V alpha 1 chain [COL5A1], and collagen type XI alpha 1 chain [COL11A1], were identified. Furthermore, a circRNA–miRNA–hub gene subnetwork was established in accordance with two circRNAs (hsa_circ_0075320 and hsa_circ_0051428), two miRNAs (hsa-miR-6124 and hsa-miR-1207-5p), and six hub genes (COL11A1, SERPINH1, COL6A3, COL5A1, COL8A2, and COL15A1). Finally, three chemicals (noscapine, diazepam, and TG100-115) based on CMap analysis and two drugs (collagenase Clostridium histolyticum and ocriplasmin) based on DGIdb were discovered as potential treatment options for OA.Conclusion: This study presents novel perspectives on the pathogenesis and treatment of OA based on circRNA-related competitive endogenous RNA regulatory networks.
Regulation of CIRP by genetic factors of SP1 related to cold sensitivity
Authors: Kim Soo Yeon , Ban Hyo-Jeong , Lee Siwoo , Jin Hee-Jeong 
Published: September 2022

Cold-inducible RNA-binding-protein (CIRP) is a cold shock protein that plays a protective role in genotoxic stress response. CIRP modulates inflammation in human diseases, inhibits cell proliferation, and protects cells from genotoxic damage during cellular stress. The mild cold responsive element and specificity protein 1 (SP1) play a role in Cirp expression at low temperatures. Although previous studies have provided insights into the immune functions of SP1 or CIRP, the mechanisms by which CIRP and SP1 me	diate inflammatory responses remain largely unknown. Therefore, in the current study, we examined whether Cirp expression is affected by genetic factors related to temperature sensitivity as well as under low temperature. We performed a genome-wide association study on cold sensitivity in 2,000 participants. Fifty-six genome-wide significant trait-locus pairs were identified (p&lt;1×10-5, false discovery rate &lt; 0.05). Among these variants, rs1117050 and rs11170510 had a strong linkage disequilibrium (r2 &gt; 0.8) relationship and expression quantitative trait locus-associated signals with the nearest Sp1 gene. We confirmed that the minor alleles of rs11170510 and rs58123204 were associated with increased Sp1 expression. Additionally, Sp1 overexpression led to CIRP translocation from the nucleus to the cytoplasm. CIRP protein levels increased in serum samples that had minor alleles of rs11170510 and rs58123204. Levels of various pro-inflammatory cytokines were also significantly increased in human peripheral blood mononuclear cells with minor alleles of rs11170510 and rs58123204. These results suggest that genetic factors related to cold sensitivity regulate CIRP expression and function and provide valuable insights into prediction of potential diseases through analysis of inherent genetic factors in humans.
Comparison of high-intensity focused ultrasound ablation and uterine artery embolization in the management of cervical pregnancy
Authors: Li Waixing , Gan Xiaoli , Kashyap Nidhi , Zou Lingxiao , Zhang Aiqian , Xu Dabao 
Published: September 2022

BackgroundCervical pregnancy (CP) is an uncommon type of ectopic pregnancy with a rising risk to life. Currently, there is no universal protocol for the safe and effective management of CP. This study aimed to investigate the clinical efficacy of high-intensity focused ultrasound ablation (HIFU) vs. uterine artery embolization (UAE) in the management of CP to develop a standard for the treatment of CP.MethodsFrom January 2015 to October 2021, 36 patients with CP were diagnosed, treated, and followed up at the Department of Gynecology of Third Xiangya Hospital of Central South University. A total of 11 patients were treated with HIFU followed by suction curettage under hysteroscopic guidance, and 25 patients were treated with UAE followed by suction curettage under hysteroscopic guidance. Medical records and pregnancy outcomes were retrospectively analyzed.ResultsCompared to the UAE group, the HIFU group had a shorter interval time (1.5 ± 0.21 days vs. 2.6 ± 0.26 days), shorter duration of hospitalization (5.5 ± 0.31 days vs. 6.6 ± 0.21 days), shorter recovery time of menstruation (30.6 ± 7.09 days vs. 36.9 ± 5.54 days), fewer adverse reactions (0/11 vs. 9/25), and fewer postoperative complications (1/11 vs. 8/25). There were no significant differences in age, gravidity, parity, abortion, gestational age, cardiac pulsation, admission symptoms, hemoglobin level, largest diameter of the sac/mass, serum human chorionic gonadotropin (hCG) level at admission, hospitalization expenses, hospitalization days, blood loss during curettage, degree of hCG decline, residue after curettage, fertility requirement, and pregnancy outcomes.ConclusionBoth HIFU and UAE are safe and effective in the treatment of patients with CP. Compared to UAE, HIFU treatment for CP is a safer and more effective therapeutic schedule owing to the advantages of being more minimally invasive, shorter interval time, shorter hospitalization days and recovery time of menstruation, fewer adverse reactions, and fewer postoperative complications.
Hospital admissions and mortality for acute exacerbations of COPD during the COVID-19 pandemic: A nationwide study in France
Authors: Poucineau Jonas , Delory Tristan , Lapidus Nathanaël , Hejblum Gilles , Chouaïd Christos , Le Cœur Sophie , Khlat Myriam 
Published: September 2022

BackgroundA global reduction in hospital admissions for acute exacerbations of chronic obstructive pulmonary disease (AECOPD) was observed during the first months of the COVID-19 pandemic. Large-scale studies covering the entire pandemic period are lacking. We investigated hospitalizations for AECOPD and the associated in-hospital mortality at the national level in France during the first 2 years of the pandemic.MethodsWe used the French National Hospital Database to analyse the time trends in (1) monthly incidences of hospitalizations for AECOPD, considering intensive care unit (ICU) admission and COVID-19 diagnoses, and (2) the related in-hospital mortality, from January 2016 to November 2021. Pandemic years were compared with the pre-pandemic years using Poisson regressions.ResultsThe database included 565,890 hospitalizations for AECOPD during the study period. The median age at admission was 74 years (interquartile range 65–83), and 37% of the stays concerned women. We found: (1) a dramatic and sustainable decline in hospitalizations for AECOPD over the pandemic period (from 8,899 to 6,032 monthly admissions, relative risk (RR) 0.65, 95% confidence interval (CI) 0.65–0.66), and (2) a concomitant increase in in-hospital mortality for AECOPD stays (from 6.2 to 7.6% per month, RR 1.24, 95% CI 1.21–1.27). The proportion of stays yielding ICU admission was similar in the pre-pandemic and pandemic years, 21.5 and 21.3%, respectively. In-hospital mortality increased to a greater extent for stays without ICU admission (RR 1.39, 95% CI 1.35–1.43) than for those with ICU admission (RR 1.09, 95% CI 1.05–1.13). Since January 2020, only 1.5% of stays were associated with a diagnosis of COVID-19, and their mortality rate was nearly three-times higher than those without COVID-19 (RR 2.66, 95% CI 2.41–2.93).ConclusionThe decline in admissions for AECOPD during the pandemic could be attributed to a decrease in the incidence of exacerbations for COPD patients and/or to a possible shift from hospital to community care. The rise in in-hospital mortality is partially explained by COVID-19, and could be related to restricted access to ICUs for some patients and/or to greater proportions of severe cases among the patients hospitalized during the pandemic.
Bacterial biomarkers capable of identifying recurrence or metastasis carry disease severity information for lung cancer
Authors: Yuan Xuelian , Wang Zhina , Li Changjun , Lv Kebo , Tian Geng , Tang Min , Ji Lei , Yang Jialiang 
Published: September 2022

BackgroundLocal recurrence and distant metastasis are the main causes of death in patients with lung cancer. Multiple studies have described the recurrence or metastasis of lung cancer at the genetic level. However, association between the microbiome of lung cancer tissue and recurrence or metastasis remains to be discovered. Here, we aimed to identify the bacterial biomarkers capable of distinguishing patients with lung cancer from recurrence or metastasis, and how it related to the severity of patients with lung cancer.MethodsWe applied microbiome pipeline to bacterial communities of 134 non-recurrence and non-metastasis (non-RM) and 174 recurrence or metastasis (RM) samples downloaded from The Cancer Genome Atlas (TCGA). Co-occurrence network was built to explore the bacterial interactions in lung cancer tissue of RM and non-RM. Finally, the Kaplan–Meier survival analysis was used to evaluate the association between bacterial biomarkers and patient survival.ResultsCompared with non-RM, the bacterial community of RM had lower richness and higher Bray–Curtis dissimilarity index. Interestingly, the co-occurrence network of non-RM was more complex than RM. The top 500 genera in relative abundance obtained an area under the curve (AUC) of 0.72 when discriminating between RM and non-RM. There were significant differences in the relative abundances of Acidovorax, Clostridioides, Succinimonas, and Shewanella, and so on between RM and non-RM. These biomarkers played a role in predicting the survival of lung cancer patients and were significantly associated with lung cancer stage.ConclusionThis study provides the first evidence for the prediction of lung cancer recurrence or metastasis by bacteria in lung cancer tissue. Our results highlights that bacterial biomarkers that distinguish RM and non-RM are also associated with patient survival and disease severity.
Reduced plasma levels of RGM-A predict stroke-associated pneumonia in patients with acute ischemic stroke: A prospective clinical study
Authors: Zhong Jiaju , Liao Juan , Zhang Rongrong , Zhou Chanjuan , Wang Zhenyu , Huang Siyuan , Huang Dan , Yang Mengliu , Zhang Lei , Ma Yue , Qin Xinyue 
Published: September 2022

BackgroundStroke-induced immunodepression syndrome is considered the major etiology of stroke-associated pneumonia (SAP). Repulsive guidance molecule A (RGM-A) is an immunomodulatory protein that is closely related to inflammation and immune responses. To explore the relationship between RGM-A and SAP and facilitate the early identification of patients at high risk of developing SAP, we investigated the predictive value of RGM-A in SAP.MethodsWe enrolled 178 patients with acute ischemic stroke (AIS) and finally analyzed 150 patients, among whom 69 had SAP and 81 had non-SAP. During the same period, 40 patients with community-acquired pneumonia and 40 healthy participants were included as controls. SAP was defined according to the modified US Centers for Disease Control and Prevention criteria. Blood samples were collected at 24 h, 48 h, 3 days, 4 to 7 days, and 8 to 14 days after stroke onset. An enzyme-linked immunosorbent assay was used to detect the plasma levels of RGM-A and interleukin-6.ResultsThe plasma RGM-A levels were significantly decreased in both patients with community-acquired pneumonia and those with AIS, and the decline was most pronounced in patients with SAP (P &lt; 0.001). RGM-A started to decline within 24 h after stroke in the SAP group, and the lowest levels were detected on day 3 and days 4 to 7 (P &lt; 0.001). The RGM-A levels in the SAP group were lower than those in the non-SAP group at all blood collection time points (P &lt; 0.05). In the logistic regression analyses, RGM-A was a protective factor for SAP after adjusting for confounders (adjusted odds ratio = 0.22, 95% confidence interval = 0.091–0.538, P = 0.001). Receiver operating characteristic curve analysis showed that the area under the curve for RGM-A was 0.766 (0.091–0.538; P = 0.001), the cutoff value was 4.881 ng/mL, and the sensitivity and specificity were 80.00 and 76.36%, respectively.ConclusionsWe demonstrated that reduced plasma levels of RGM-A might help in the early identification of high-risk patients with SAP and predict the occurrence of SAP in patients with AIS. RGM-A might provide new clues to a potential alternative therapy for SAP.
Optical coherence tomography assessment of axonal and neuronal damage of the retina in patients with familial and sporadic multiple sclerosis
Authors: Grudziecka Pyrek Monika , Selmaj Krzysztof 
Published: September 2022

ObjectiveTo assess axonal and neuronal damage of the retina in patients with familial (fMS) and sporadic multiple sclerosis (sMS).Methods87 relapsing-remitting MS patients (45 patients with sMS, 42 patients with fMS) and 30 healthy controls were included in the study. Optical coherence tomography (OCT) was performed with the spectral domain optical coherence tomography (SD-OCT, Heidelberg Engineering, Germany). The peripapillary retinal nerve fiber layer (pRNFL) thickness, ganglion cell-inner plexiform layer (GCIPL) thickness, total macular volume (TMV) and the inner nuclear layer (INL) thickness were measured.ResultsA significant reduction of the pRNFL thickness was detected in sMS and fMS compared to the control group (86.29 (+/- 16.13) μm in sMS, 84.78 (+/- 12.92) μm in fMS, 98.93 (+/- 6.71) μm in control group; p &lt; 0.001). There was no significant difference in the pRNFL thickness between sMS and fMS (p = 0.5239). The GCIPL thickness was significantly decreased in sMS and fMS compared to the control group [66.0581 (+/- 11.2674) μm in sMS, 63.8386 (+/-10.004) μm in fMS, 76.5074 (+/- 5.0004) μm in control group; p &lt; 0.001]. A significant reduction of the TMV was shown in sMS and fMS compared to the control group [8.4541(+/- 0.4727) mm3 in sMS, 8.3612 (+/- 0.4448) mm3 in fMS, 8.8387 (+/- 0.314) mm3 in control group; p &lt; 0.0011]. No difference in the GCIPL thickness and TMV between sMS and fMS was found (p = 0.3689 and p = 0.3758, respectively). The INL thickness in sMS and fMS did not differ compared to the control group [34.2323 (+/- 2.7006) μm in sMS, 34.5159 (+/- 2.9780) μm in fMS, 33.6148 (+/- 2.0811) μm in control group; p = 0.5971 and p = 0.1870, respectively] and between the two forms (p = 0.4894).ConclusionWe confirmed the presence of axonal and neuronal damage of the retina in sMS and fMS. Both forms of MS did not differ significantly from each other with respect to RFNL, GCIPL, MV and INL. ON induced significant reduction of the pRNFL, GCIPL and MV in both groups of pwMS.