bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA-sequencing analysis reveals the long noncoding RNA profile in the mouse myopic retina
Authors: Li Yuanjun , Lu Ying , Du Kaixuan , Yin Yewei , Hu Tu , Fu Qiuman , Zhang Yanni , Wen Dan , Wu Xiaoying , Xia Xiaobo
Published: October 2022

Aim: Myopia is a prevalent public health problem. The long noncoding RNA (lncRNA) mechanisms for dysregulated retinal signaling in the myopic eye have remained elusive. The aim of this study was to analyze the expression profiles and possible pathogenic roles of lncRNAs in mouse form-deprived myopia (FDM) retinas.

Methods: A mouse FDM model was induced and retinas from the FDM right eyes and the contralateral eyes were collected for RNA sequencing. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and lncRNA-mRNA coexpression network analyses were conducted to explore the biological functions of the differentially expressed lncRNAs. In addition, the levels of differentially expressed lncRNAs in the myopic retinas were validated by quantitative real-time PCR (qRT–PCR). Fluorescence in situ hybridization (FISH) was used to detect the localization of lncRNAs in mouse retinas.

Results: FDM eyes exhibited reduced refraction and increased ocular axial length compared to control fellow eyes. RNA sequencing revealed that there were 655 differentially expressed lncRNAs between the FDM and control retinas. Functional enrichment analysis indicated that the differentially expressed RNAs were mostly enriched in cellular processes, cytokine-cytokine receptor interactions, retinol metabolism, and rhythmic processes. Differentially expressed lncRNAs were validated by qRT–PCR. Additionally, RNA FISH showed that XR_384718.4 (Gm35369) localized in the ganglion cell (GCL) and inner nuclear layers (INL).

Conclusion: This study identified the differential expression profiles of lncRNAs in myopic mouse retinas. Our results provide scientific evidence for investigations of myopia and the development of putative interventions in the future.
A novel prognostic signature based on N7-methylguanosine-related long non-coding RNAs in breast cancer
Authors: Huang Zhidong , Lou Kaixin , Liu Hong
Published: October 2022

Long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on N7-methylguanosine (m7G)-related lncRNA in breast cancer is lacking. Therefore, the present study explored the prognostic value, gene expression characteristics, and effects of m7G-related lncRNA on tumor immune cell infiltration and tumor mutational burden (TMB) in breast cancer. lncRNA expression matrices and clinical follow-up data of patients with breast cancer were obtained from The Cancer Genome Atlas, revealing eight significantly differentially expressed and prognostically relevant m7G-related lncRNAs in breast cancer tissues: BAIAP2-DT, COL4A2-AS1, FARP1-AS1, RERE-AS1, NDUFA6-DT, TFAP2A-AS1, LINC00115, and MIR302CHG. A breast cancer prognostic signature was created based on these m7G-related lncRNAs according to least absolute shrinkage and selection operator Cox regression. The prognostic signature combined with potential prognostic factors showed independent prognostic value, reliability, and specificity. Meanwhile, we constructed a risk score-based nomogram to assist clinical decision-making. Gene set enrichment analysis revealed that low- and high-risk group were associated with metabolism-related pathways. Our study demonstrated the association between tumor immune cell infiltration based on analyses with the CIBERSORT algorithm and prognostic signature. We also assessed the correlation between prognostic signature and TMB. Lastly, quantitative real-time polymerase chain reaction analysis was performed to validate differentially expressed lncRNAs. The effective prognostic signature based on m7G-related lncRNAs has the potential to predict the survival prognosis of patients with breast cancer. The eight m7G-related lncRNAs identified in this study might represent potential biomarkers and therapeutic targets of breast cancer.
Depletion of PARP10 inhibits the growth and metastatic potential of oral squamous cell carcinoma
Authors: Zhou Zihui , Wei Bing , Liu Yu , Liu Tian , Zeng Sien , Gan Jinfeng , Qi Guangying
Published: October 2022

Background: Although poly (ADP-ribose) polymerase family member 10 (PARP10) has been implicated in the progression of multiple cancer types, its role in oral squamous cell carcinoma (OSCC) remains unknown. This study aimed to examine the function of PARP10 in OSCC and investigate the underlying mechanisms.

Methods: The expression of PARP10 in OSCC was investigated in OSCC patient cohorts. Kaplan-Meier curve analysis was performed to assess the association between PARP10 and prognosis in OSCC. Correlation between PARP10 expression and the related variables was analyzed by χ2 test. CKK-8, transwell assay, western blot, immunohistochemistry, immunofluorescence, and bioinformatic analysis, were applied to clarify the role of PARP10 in OSCC.

Results: PARP10 was found to be markedly elevated in OSCC tissues. The upregulation of PARP10 predicted shorter overall survival and disease-specific survival and was significantly correlated with several malignant features. Moreover, depletion of PARP10 markedly inhibited the proliferation, migration, and invasion of OSCC cells, and promoted OSCC cell apoptosis, and resulted in alterations of relevant proteins. Furthermore, a positive correlation was observed between the expression of PARP10 and Ki67, PARP1, MMP2, and VEGF. In addition, depletion of PARP10 impaired the PI3K-AKT and MAPK signaling pathways.

Conclusion: PARP10 is involved in the progression of OSCC via regulation of PI3K-AKT and MAPK signaling pathways.
Pan-cancer analysis of the prognostic and immunological roles of DEAD-box helicase 5 (DDX5) in human tumors
Authors: Liu Shixuan , Liu Yanbin , Zhang Xi , Song Xuanlin , Zhang Boxiang , Zhang Yong
Published: October 2022

Background: Recent studies have demonstrated the significance of the DEAD-box helicase 5 (DDX5) gene, which is involved in pathways concerning the modification of RNA structures. DDX5 functions as a coregulator of cellular transcription and splicing, and participates in the processing of small noncoding RNAs. The aberrant regulation of DDX5 expression possibly plays a significant role in the genesis of cancer. However, there are no comprehensive pan-cancer studies on DDX5. This study is the first to conduct a pan-cancer analysis of DDX5 for aiding the diagnosis and treatment of cancer.

Methods: The gene expression, genetic alterations, protein phosphorylation, promoter methylation, immune infiltration, and enrichment analyses of DDX5 were performed using data retrieved from The Cancer Genome Atlas (TCGA), Genotype-tissue Expression (GTEx), Human Protein Atlas (HPA), Tumor Immunological Estimation Resource 2.0 (TIMER2.0), Gene Expression Profiling Interactive Analysis (GEPIA), DNA methylation interactive visualization database (DNMIVD), and Search Tool for the Retrieval of Interaction Genes/Proteins (STRING). Data analyses were performed with the R software and other webtools.

Results: The expression of DDX5 mRNA decreased significantly in 17 cancer types, but increased significantly in eight cancer types. The enhanced expression of DDX5 mRNA in the tumor samples was related to decreased overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) in three cancers, but increased OS, PFI, and DSS in other cancers. The DNA promoter methylation level was significantly reduced in eight cancer types, and there were exceptions in the methylation levels of the DDX5 promoter in four cancer types. The expression of DDX5 mRNA was highly correlated with the infiltration of CD8+ T cells, cancer-associated fibroblasts, and B cells in a wide variety of malignancies. The findings revealed a strong association between DDX5 and its co-expressed genes in numerous cancer types. Enrichment analysis suggested that DDX5 was associated with multiple cellular pathways, including RNA splicing, Notch signaling pathway, and viral carcinogenesis, which was consistent with the results of previous studies.

Conclusion: The findings obtained herein provide further information on the oncogenic potential of DDX5 in diverse tumor types. We propose that DDX5 has important roles in tumor immunity and the diagnosis of cancer.
Prognostic model and immunotherapy prediction based on molecular chaperone-related lncRNAs in lung adenocarcinoma
Authors: Xu Yue , Tao Tao , Li Shi , Tan Shuzhen , Liu Haiyan , Zhu Xiao
Published: October 2022

Introduction: Molecular chaperones and long non-coding RNAs (lncRNAs) have been confirmed to be closely related to the occurrence and development of tumors, especially lung cancer. Our study aimed to construct a kind of molecular chaperone-related long non-coding RNAs (MCRLncs) marker to accurately predict the prognosis of lung adenocarcinoma (LUAD) patients and find new immunotherapy targets.

Methods: In this study, we acquired molecular chaperone genes from two databases, Genecards and molecular signatures database (MsigDB). And then, we downloaded transcriptome data, clinical data, and mutation information of LUAD patients through the Cancer Genome Atlas (TCGA). MCRLncs were determined by Spearman correlation analysis. We used univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to construct risk models. Kaplan-meier (KM) analysis was used to understand the difference in survival between high and low-risk groups. Nomogram, calibration curve, concordance index (C-index) curve, and receiver operating characteristic (ROC) curve were used to evaluate the accuracy of the risk model prediction. In addition, we used gene ontology (GO) enrichment analysis and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses to explore the potential biological functions of MCRLncs. Immune microenvironmental landscapes were constructed by using single-sample gene set enrichment analysis (ssGSEA), tumor immune dysfunction and exclusion (TIDE) algorithm, “pRRophetic” R package, and “IMvigor210” dataset. The stem cell index based on mRNAsi expression was used to further evaluate the patient’s prognosis.

Results: Sixteen MCRLncs were identified as independent prognostic indicators in patients with LUAD. Patients in the high-risk group had significantly worse overall survival (OS). ROC curve suggested that the prognostic features of MCRLncs had a good predictive ability for OS. Immune system activation was more pronounced in the high-risk group. Prognostic features of the high-risk group were strongly associated with exclusion and cancer-associated fibroblasts (CAF). According to this prognostic model, a total of 15 potential chemotherapeutic agents were screened for the treatment of LUAD. Immunotherapy analysis showed that the selected chemotherapeutic drugs had potential application value. Stem cell index mRNAsi correlates with prognosis in patients with LUAD.

Conclusion: Our study established a kind of novel MCRLncs marker that can effectively predict OS in LUAD patients and provided a new model for the application of immunotherapy in clinical practice.
Association between genetic variants (rs920778, rs4759314, and rs217727) in LncRNAs and cervical cancer susceptibility in Chinese population: A systematic review and meta-analysis
Authors: Liu Yi , Zhang Qian , Ni Rong
Published: October 2022

Objective: The relationship between gene polymorphisms in long non-coding RNAs (LncRNAs) and cervical cancer susceptibility has been thoroughly analyzed; however, the conclusions are inconsistent. Therefore, this systematic review and meta-analysis aimed to accurately assess the relationship between them.

Method: Eligible literatures were retrieved from PubMed, Medline, China National Knowledge Infrastructure (CNKI), and WanFang databases before 1 April 2022. The odds ratios with the corresponding 95% confidence intervals were used to evaluate the strength of these relationships. Sensitivity analysis for publication bias was conducted to assess the stability and reliability of included literatures.

Results: A total of 59 SNPs in 11 LncRNAs were summarized for a systematic review in this study, and then, a meta-analysis of rs920778 and rs4759314 polymorphisms in HOTAIR and rs217727 polymorphisms in H19 was conducted. The results demonstrated that rs920778 and rs4759314 polymorphisms were significantly correlated with cervical cancer susceptibility. Further subgroup analysis of rs920778 polymorphism showed that both small sample size and large sample size subgroups were associated with cervical cancer susceptibility. However, no association was found between rs217727 polymorphism and cervical cancer risk in all five genetic models.

Conclusion: In conclusion, the rs4759314, rs920778, and rs217717 polymorphisms of HOTAIR and H19 may be associated with cervical cancer. However, the results should be interpreted with caution due to the limited sample and heterogeneity in this study. Large-scale and well-designed studies need to be practiced to validate our results.
Gut microbiota in anxiety and depression: Pathogenesis and therapeutics
Authors: Bibbò Stefano , Fusco Salvatore , Ianiro Gianluca , Settanni Carlo Romano , Ferrarese Daniele , Grassi Claudio , Cammarota Giovanni , Gasbarrini Antonio
Published: October 2022

Depression and anxiety disorders represent a burdensome clinical issue. Considering the unsatisfactory clinical response of some patients to antidepressant therapy, new personalized approaches are being studied. In recent years, pre-clinical and clinical studies have investigated the role of intestinal microbiota demonstrating the importance of the gut-brain axis in these diseases. Indeed, gut microbes are able to interact with the brain interfering with behavior through some mechanisms such as amino acid metabolism, short–chain fatty acids, vagus nerve, endocrine signaling and immune responses. Experiments of gut microbiota transfer from subjects with major depression to animal models corroborated the causative role of intestinal microbes in mood disorders and anxiety. Furthermore, the incidence of dysbiosis in patients with anxiety and depression suggests a potential role for gut microbiota modulators in the treatment of these disorders. In particular, several probiotics and synbiotics have been shown to be effective in improving clinical symptoms, promising results have emerged also from fecal microbiota transplantation, but the evidence is still limited. These promising results switch on the use of gut microbiota modulators as an adjunctive tool to anti-depressant therapy. Developing pharmaceutical or nutraceutical strategies to modify the composition of gut microbiota may offer novel and personalized therapeutic tools against anxiety and depression.
Bibliometric and visualization analysis of mesenchymal stem cells and rheumatoid arthritis (from 2012 to 2021)
Authors: Liu Jiaxi , Gao Jinfang , Niu Qing , Wu Fengping , Wu Zewen , Zhang Liyun
Published: October 2022

Background

Rheumatoid arthritis (RA) is a chronic autoimmune disease that can lead to joint deformity and loss of function. Recent studies have shown great progress in the research of mesenchymal stem cells (MSCs) in RA. However, thus far, there have been no bibliometric or visualization analyses in this field. This bibliometric analysis provides a comprehensive overview of the general information and research hotspots of MSCs and RA.

Methods

Articles relevant to MSCs and RA, published between 2012 and 2021, were searched using the Web of Science Core Collection database. Irrelevant publications were excluded from the analysis. Bibliometric and visualization analyses were conducted using VOSviewer, CiteSpace, and Scimago Graphica.

Results

A total of 577 articles were analyzed. The annual number of publications increased from 2012 to 2017 and plateaued from 2017 to 2021. China and the USA had the largest number of publications. Collaboration among different organizations mainly occurs between institutes of the same country. Stem Cell Research and Therapy and Frontiers in Immunology were the most popular journals in this field. All the top 20 co-cited authors had a positive co-citation relationship. The top references indicate that MSCs can contribute to RA research and treatment mainly via immunomodulation. From 2012 to 2021, “collagen-induced arthritis,” “immunomodulation,” and “therapy” were some of the keywords associated with MSCs and RA, while “extracellular vesicles” showed a strong keyword burst from 2019 to 2021.

Conclusion

MSCs and RA have been widely studied in different countries and institutions and by different authors over the last ten years. China and the USA had the largest number of publications. Different types of journals provide admirable sources for researchers. Some keywords, including immunomodulation and extracellular vesicles, may be hot spots in the near future. There will be more basic research and clinical translation of MSCs and RA, and substantial new treatments for RA will soon be developed.
Human MHC class I molecule, HLA-A2.1, mediates activation of CD8+ T cell IFN-γ production and the T cell-dependent protection against reactivation of cerebral Toxoplasma infection
Authors: Mani Rajesh , Abdelaziz Mohamed H. , Michelon Alexandra , Suzuki Yasuhiro
Published: October 2022

To examine whether the HLA-A2.1, one of the most common MHC class I molecules in humans, activates the protective immunity against reactivation of cerebral infection withToxoplasma gondii, HLA-A2.1-transgenic and wild-type (WT) mice were infected and treated with sulfadiazine to establish chronic infection in their brains. One month after discontinuation of sulfadiazine, which initiates reactivation of the infection, mRNA levels for tachyzoite (the acute stage form)-specific SAG1 and numbers of the foci associated tachyzoites were significantly less in the brains of the HLA-A2.1-transgenic than WT mice. Greater numbers of IFN-γ-producing CD8+T cells were detected in the spleens of infected transgenic than WT mice, and CD8+T cells from the former produced markedly greater amounts of IFN-γ than the T cells from the latter in response to tachyzoite antigensin vitro. When their CD8+T cells were systemically transferred to infected immunodeficient NSG mice expressing the HLA-A2.1, the CD8+T cells from HLA-A2.1-transgenic mice inhibited reactivation of the cerebral infection in the recipients more efficiently than did the WT T cells. Furthermore, the inhibition of reactivation of the infection by CD8+T cells from the transgenic mice was associated with increased cerebral expression of IFN-γ and effector molecules against tachyzoites in the recipients when compared to the WT CD8+T cell recipients. Thus, the human HLA-A2.1 is able to effectively activate IFN-γ production of CD8+T cells againstT. gondiitachyzoites and confer a potent protection against reactivation of cerebral infection with this parasite through the CD8+T cells activation.
The commonness in immune infiltration of rheumatoid arthritis and atherosclerosis: Screening for central targets via microarray data analysis
Authors: Wang Zuoxiang , Xia Qingyue , Su Wenxing , Zhang Mingyang , Gu Yiyu , Xu Jialiang , Chen Weixiang , Jiang Tingbo
Published: October 2022

Background

Although increasing evidence has reported an increased risk of atherosclerosis (AS) in rheumatoid arthritis (RA), the communal molecular mechanism of this phenomenon is still far from being fully elucidated. Hence, this article aimed to explore the pathogenesis of RA complicated with AS.

Methods

Based on the strict inclusion/exclusion criteria, four gene datasets were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the communal differentially expressed genes (DEGs) and hub genes, comprehensive bioinformatics analysis, including functional annotation, co-expression analysis, expression validation, drug-gene prediction, and TF-mRNA-miRNA regulatory network construction, was conducted. Moreover, the immune infiltration of RA and AS was analyzed and compared based on the CIBERSORT algorithm, and the correlation between hub genes and infiltrating immune cells was evaluated in RA and AS respectively.

Results

A total of 54 upregulated and 12 downregulated communal DEGs were screened between GSE100927 and GSE55457, and functional analysis of these genes indicated that the potential pathogenesis lies in immune terms. After the protein-protein interaction (PPI) network construction, a total of six hub genes (CCR5, CCR7, IL7R, PTPRC, CD2, and CD3D) were determined as hub genes, and the subsequent comprehensive bioinformatics analysis of the hub genes re-emphasized the importance of the immune system in RA and AS. Additionally, three overlapping infiltrating immune cells were found between RA and AS based on the CIBERSORT algorithm, including upregulated memory B cells, follicular helper T cells and γδT cells.

Conclusions

Our study uncover the communal central genes and commonness in immune infiltration between RA and AS, and the analysis of six hub genes and three immune cells profile might provide new insights into potential pathogenesis therapeutic direction of RA complicated with AS.
Non-invasive measurement of tumor immune microenvironment and prediction of survival and chemotherapeutic benefits from 18F fluorodeoxyglucose PET/CT images in gastric cancer
Authors: Li Junmeng , Zhang Chao , Guo Huihui , Li Shuang , You Yang , Zheng Peiming , Zhang Hongquan , Wang Huanan , Bai Junwei
Published: October 2022

Background

The tumor immune microenvironment could provide prognostic and predictive information. It is necessary to develop a noninvasive radiomics-based biomarker of a previously validated tumor immune microenvironment signature of gastric cancer (GC) with immunohistochemistry staining.

Methods

A total of 230 patients (training (n = 153) or validation (n = 77) cohort) with gastric cancer were subjected to (Positron Emission Tomography-Computed Tomography) radiomics feature extraction (80 features). A radiomics tumor immune microenvironment score (RTIMS) was developed to predict the tumor immune microenvironment signature with LASSO logistic regression. Furthermore, we evaluated its relation with prognosis and chemotherapy benefits.

Results

A 8-feature radiomics signature was established and validated (area under the curve=0.692 and 0.713). The RTIMS signature was significantly associated with disease-free survival and overall survival both in the training and validation cohort (all P<0.001). RTIMS was an independent prognostic factor in the Multivariate analysis. Further analysis revealed that high RTIMS patients benefitted from adjuvant chemotherapy (for DFS, stage II: HR 0.208(95% CI 0.061-0.711), p=0.012; stage III: HR 0.321(0.180-0.570), p<0.001, respectively); while there were no benefits from chemotherapy in a low RTIMS patients.

Conclusion

This PET/CT radiomics model provided a promising way to assess the tumor immune microenvironment and to predict clinical outcomes and chemotherapy response. The RTIMS signature could be useful in estimating tumor immune microenvironment and predicting survival and chemotherapy benefit for patients with gastric cancer, when validated by further prospective randomized trials.
Correlation between serologic parameters and disease activity of IgG4-related disease: Differences between patients with normal and elevated serum IgG4 concentrations
Authors: Kwon Oh Chan , Park Min-Chan , Kim Yong-Gil
Published: October 2022

Objective

We aimed to identify serologic parameters that correlate with the disease activity of IgG4-related disease (IgG4-RD) in patients with normal and elevated serum IgG4 concentrations, respectively.

Methods

This retrospective cohort study included 148 patients with IgG4-RD. Patients were categorized into normal (≤201 mg/dL) and elevated (>201 mg/dL) serum IgG4 concentration groups. Disease activity was assessed using the IgG4-RD responder index (RI). The correlations between IgG4-RD RI and serologic parameters (erythrocyte sedimentation rate [ESR], C-reactive protein, C3, C4, IgG4 concentration, IgG concentration, and IgG4/IgG ratio) were evaluated in each group, using Spearman’s correlation coefficient.

Results

Of the 148 patients with IgG4-RD, 38 (25.7%) and 110 (74.3%) patients were categorized into the normal and elevated serum IgG4 concentration groups, respectively. In the normal serum IgG4 concentration group, IgG concentration was the only serologic parameter that showed a significant correlation with IgG4-RD RI (rho=0.411, p=0.013). However, in the elevated serum IgG4 concentration group, ESR (rho=0.196, p=0.041), C3 (rho=-0.432, p<0.001), C4 (rho=-0.363, p=0.001), IgG4 concentration (rho=0.423, p<0.001), IgG concentration (rho=0.224, p=0.020), and IgG4/IgG ratio (rho=0.328, p=0.001) correlated with IgG4-RD RI. The combination of C3 and IgG4 concentration (rho=0.509, p<0.001) had the strongest correlation with IgG4-RD RI in this group.

Conclusion

Among the serologic parameters tested, IgG concentration was the only parameter that correlated with IgG4-RD RI in patients with normal serum IgG4 concentrations, whereas multiple parameters correlated with IgG4-RD RI in those with elevated serum IgG4 concentrations. The combination of C3 and IgG4 concentration had the strongest correlation coefficient in the latter group.
Neuropsychological decrements in midlife type-2 diabetes are not associated with peripheral NLRP3 inflammasome responsiveness
Authors: Dyer Adam H. , Batten Isabella , Reddy Conor , Townsend Liam , Woods Conor P. , O’Neill Desmond , Gibney James , Kennelly Sean P. , Bourke Nollaig M.
Published: October 2022

Midlife Type 2 Diabetes Mellitus (T2DM) is associated with an increased risk of Alzheimer Disease (AD) in later life, with altered inflammatory responses postulated as key pathological drivers. Previous studies have demonstrated increased responsiveness to NLR family pyrin domain containing 3 (NLRP3) inflammasome agonists, both in individuals with untreated T2DM in addition to those with established AD. We hypothesised that peripheral NLRP3 inflammasome responses may be altered during the early stages of T2DM-related cognitive dysfunction. Here, we assessed the relationship between NLPR3 responses in peripheral blood mononuclear cells (including to Aβ-42, the putative pathogenic protein in AD) and neuropsychological performance in uncomplicated midlife T2DM to identify early signatures of immune dysregulation which may predispose to later cognitive decline. We recruited a cross-sectional cohort of middle-aged adults with uncomplicated T2DM and matched Healthy Controls (HCs) for comprehensive neuropsychological assessment and in vitro PBMC responses to a range of NLRP3 agonists were assessed. T2DM was associated with subtle decrements on neuropsychological tests of delayed memory and executive function (both p<0.05). Overall, there were no differences between T2DM and HCs in immune responses induced by NLRP3 agonists. Further, we observed no relationship between the subtle neuropsychological decrements observed in T2DM and PBMC responsiveness to NLRP3 agonists. Our data suggests that peripheral NLRP3 inflammasome response dysregulation may not play a role in the early stages of cognitive dysfunction in midlife T2DM. Further longitudinal studies are warranted to examine the contribution of peripheral NLRP3 responses towards disease pathology and as cognitive decline accelerates in T2DM.
Altered transcription factor targeting is associated with differential peripheral blood mononuclear cell proportions in sarcoidosis
Authors: Ascoli Christian , Schott Cody A. , Huang Yue , Turturice Benjamin A. , Wang Wangfei , Ecanow Naomi , Sweiss Nadera J. , Perkins David L. , Finn Patricia W.
Published: October 2022

Introduction

In sarcoidosis, peripheral lymphopenia and anergy have been associated with increased inflammation and maladaptive immune activity, likely promoting development of chronic and progressive disease. However, the molecular mechanisms that lead to reduced lymphocyte proportions, particularly CD4+ T-cells, have not been fully elucidated. We posit that paradoxical peripheral lymphopenia is characterized by a dysregulated transcriptomic network associated with cell function and fate that results from altered transcription factor targeting activity.

Methods

Messenger RNA-sequencing (mRNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from ACCESS study subjects with sarcoidosis and matched controls and findings validated on a sarcoidosis case-control cohort and a sarcoidosis case series. Preserved PBMC transcriptomic networks between case-control cohorts were assessed to establish cellular associations with gene modules and define regulatory targeting involved in sarcoidosis immune dysregulation utilizing weighted gene co-expression network analysis and differential transcription factor involvement analysis. Network centrality measures identified master transcriptional regulators of subnetworks related to cell proliferation and death. Predictive models of differential PBMC proportions constructed from ACCESS target gene expression corroborated the relationship between aberrant transcription factor regulatory activity and imputed and clinical PBMC populations in the validation cohorts.

Results

We identified two unique and preserved gene modules significantly associated with sarcoidosis immune dysregulation. Strikingly, increased expression of a monocyte-driven, and not a lymphocyte-driven, gene module related to innate immunity and cell death was the best predictor of peripheral CD4+ T-cell proportions. Within the gene network of this monocyte-driven module, TLE3 and CBX8 were determined to be master regulators of the cell death subnetwork. A core gene signature of differentially over-expressed target genes of TLE3 and CBX8 involved in cellular communication and immune response regulation accurately predicted imputed and clinical monocyte expansion and CD4+ T-cell depletion.

Conclusions

Altered transcriptional regulation associated with aberrant gene expression of a monocyte-driven transcriptional network likely influences lymphocyte function and survival. Although further investigation is warranted, this indicates that crosstalk between hyperactive monocytes and lymphocytes may instigate peripheral lymphopenia and underlie sarcoidosis immune dysregulation and pathogenesis. Future therapies selectively targeting master regulators, or their targets, may mitigate dysregulated immune processes in sarcoidosis and disease progression.
Long-duration head-down tilt bed rest confirms the relevance of the neutrophil to lymphocyte ratio and suggests coupling it with the platelet to lymphocyte ratio to monitor the immune health of astronauts
Authors: Jacob Pauline , Bonnefoy Julie , Ghislin Stéphanie , Frippiat Jean-Pol
Published: October 2022

The identification of safe and easily-determined-inflight biomarkers to monitor the immune system of astronauts is mandatory to ensure their well-being and the success of the missions. In this report, we evaluated the relevance of two biomarkers whose determination could be easily implemented in a spacecraft in the near future by using bedridden volunteers as a ground-based model of the microgravity of spaceflight. Our data confirm the relevance of the neutrophil to lymphocyte ratio (NLR) and suggest platelet to lymphocyte ratio (PLR) monitoring to assess long-lasting immune diseases. We recommend coupling these ratios to other biomarkers, such as the quantification of cytokines and viral load measurements, to efficiently detect immune dysfunction, determine when countermeasures should be applied to promote immune recovery, prevent the development of disease, and track responses to treatment.
IL-6 deletion decreased REV-ERBα protein and influenced autophagy and mitochondrial markers in the skeletal muscle after acute exercise
Authors: Pinto Ana P. , Muñoz Vitor R. , da Rocha Alisson L. , Rovina Rafael L. , Ferrari Gustavo D. , Alberici Luciane C. , Simabuco Fernando M. , Teixeira Giovana R. , Pauli José R. , de Moura Leandro P. , Cintra Dennys E. , Ropelle Eduardo R. , Freitas Ellen C. , Rivas Donato A. , da Silva Adelino S. R.
Published: October 2022

Interleukin 6 (IL-6) acts as a pro and anti-inflammatory cytokine, has an intense correlation with exercise intensity, and activates various pathways such as autophagy and mitochondrial unfolded protein response. Also, IL-6 is interconnected to circadian clock-related inflammation and can be suppressed by the nuclear receptor subfamily 1, group D, member 1 (Nr1d1, protein product REV-ERBα). Since IL-6 is linked to physical exercise-modulated metabolic pathways such as autophagy and mitochondrial metabolism, we investigated the relationship of IL-6 with REV-ERBα in the adaptations of these molecular pathways in response to acute intense physical exercise in skeletal muscle. The present study was divided into three experiments. In the first one, wild-type (WT) and IL-6 knockout (IL-6 KO) mice were divided into three groups: Basal time (Basal; sacrificed before the acute exercise), 1 hour (1hr post-Ex; sacrificed 1 hour after the acute exercise), and 3 hours (3hr post-Ex; sacrificed 3 hours after the acute exercise). In the second experiment, C2C12 cells received IL-6 physiological concentrations or REV-ERBα agonist, SR9009. In the last experiment, WT mice received SR9009 injections. After the protocols, the gastrocnemius muscle or the cells were collected for reverse transcription-quantitative polymerase chain reaction (RTq-PCR) and immunoblotting techniques. In summary, the downregulation of REV-ERBα, autophagic flux, and most mitochondrial genes was verified in the IL-6 KO mice independent of exercise. The WT and IL-6 KO treated with SR9009 showed an upregulation of autophagic genes. C2C12 cells receiving IL-6 did not modulate the Nr1d1 mRNA levels but upregulated the expression of some mitochondrial genes. However, when treated with SR9009, IL-6 and mitochondrial gene expression were upregulated in C2C12 cells. The autophagic flux in C2C12 suggest the participation of REV-ERBα protein in the IL-6-induced autophagy. In conclusion, the present study verified that the adaptations required through physical exercise (increases in mitochondrial content and improvement of autophagy machinery) might be intermediated by an interaction between IL-6 and REVERBα.
Branched-chain ketoacids derived from cancer cells modulate macrophage polarization and metabolic reprogramming
Authors: Cai Zhengnan , Li Wan , Brenner Martin , Bahiraii Sheyda , Heiss Elke H. , Weckwerth Wolfram
Published: October 2022

Macrophages are prominent immune cells in the tumor microenvironment that can be educated into pro-tumoral phenotype by tumor cells to favor tumor growth and metastasis. The mechanisms that mediate a mutualistic relationship between tumor cells and macrophages remain poorly characterized. Here, we have shown in vitro that different human and murine cancer cell lines release branched-chain α-ketoacids (BCKAs) into the extracellular milieu, which influence macrophage polarization in an monocarboxylate transporter 1 (MCT1)-dependent manner. We found that α-ketoisocaproate (KIC) and α-keto-β-methylvalerate (KMV) induced a pro-tumoral macrophage state, whereas α-ketoisovalerate (KIV) exerted a pro-inflammatory effect on macrophages. This process was further investigated by a combined metabolomics/proteomics platform. Uptake of KMV and KIC fueled macrophage tricarboxylic acid (TCA) cycle intermediates and increased polyamine metabolism. Proteomic and pathway analyses revealed that the three BCKAs, especially KMV, exhibited divergent effects on the inflammatory signal pathways, phagocytosis, apoptosis and redox balance. These findings uncover cancer-derived BCKAs as novel determinants for macrophage polarization with potential to be selectively exploited for optimizing antitumor immune responses.
Distinct CD4+ T cell signature in ANA-positive young adult patients
Authors: Dei Zotti Flavia , Moriconi Chiara , Qiu Annie , Miller Anabel , Hudson Krystalyn E.
Published: October 2022

Failure of immune tolerance can lead to autoantibody production resulting in autoimmune diseases, a broad spectrum of organ-specific or systemic disorders. Immune tolerance mechanisms regulate autoreactive T and B cells, yet some lymphocytes escape and promote autoantibody production. CD4+ T cell dysregulation, characterized by decreased or impaired regulatory cells (Tregs) and/or accumulation of memory and effector T cells such as TH17, plays a crucial role in the pathogenesis of these diseases. Antinuclear antibody (ANAs) testing is used as a first step for the diagnosis of autoimmune disorders, although most ANA-positive individuals do not have nor will develop an autoimmune disease. Studying the differences of T cell compartment among healthy blood donors, ANA-negative patients and ANA-positive patients, in which loss of tolerance have not led to autoimmunity, may improve our understanding on how tolerance mechanisms fail. Herein, we report that ANA-positive patients exhibit a distinct distribution of T cell subsets: significantly reduced frequencies of recent thymic emigrants (RTE) and naïve T cells, and significantly increased frequencies of central memory T cells, TH2 and TH17 cells; modulations within the T cell compartment are most profound within the 18-40 year age range. Moreover, CD4+ T cells in ANA-positive patients are metabolically active, as determined by a significant increase in mTORC1 and mTORC2 signals, compared to ANA-negative patients and healthy blood donors. No significant impairment of Treg numbers or pro-inflammatory cytokine production was observed. These results identify a unique T cell signature associated with autoantibody production in the absence of autoimmune disease.
Complement-targeted therapies in kidney transplantation—insights from preclinical studies
Authors: Anwar Imran J. , DeLaura Isabel , Ladowski Joseph , Gao Qimeng , Knechtle Stuart J. , Kwun Jean
Published: October 2022

Aberrant activation of the complement system contributes to solid-organ graft dysfunction and failure. In kidney transplantation, the complement system is implicated in the pathogenesis of antibody- and cell-mediated rejection, ischemia-reperfusion injury, and vascular injury. This has led to the evaluation of select complement inhibitors (e.g., C1 and C5 inhibitors) in clinical trials with mixed results. However, the complement system is highly complex: it is composed of more than 50 fluid-phase and surface-bound elements, including several complement-activated receptors—all potential therapeutic targets in kidney transplantation. Generation of targeted pharmaceuticals and use of gene editing tools have led to an improved understanding of the intricacies of the complement system in allo- and xeno-transplantation. This review summarizes our current knowledge of the role of the complement system as it relates to rejection in kidney transplantation, specifically reviewing evidence gained from pre-clinical models (rodent and nonhuman primate) that may potentially be translated to clinical trials.
Immune regulation and emerging roles of noncoding RNAs in Mycobacterium tuberculosis infection
Authors: Liang Shufan , Ma Jiechao , Gong Hanlin , Shao Jun , Li Jingwei , Zhan Yuejuan , Wang Zhoufeng , Wang Chengdi , Li Weimin
Published: October 2022

Tuberculosis, caused by Mycobacterium tuberculosis, engenders an onerous burden on public hygiene. Congenital and adaptive immunity in the human body act as robust defenses against the pathogens. However, in coevolution with humans, this microbe has gained multiple lines of mechanisms to circumvent the immune response to sustain its intracellular persistence and long-term survival inside a host. Moreover, emerging evidence has revealed that this stealthy bacterium can alter the expression of demic noncoding RNAs (ncRNAs), leading to dysregulated biological processes subsequently, which may be the rationale behind the pathogenesis of tuberculosis. Meanwhile, the differential accumulation in clinical samples endows them with the capacity to be indicators in the time of tuberculosis suffering. In this article, we reviewed the nearest insights into the impact of ncRNAs during Mycobacterium tuberculosis infection as realized via immune response modulation and their potential as biomarkers for the diagnosis, drug resistance identification, treatment evaluation, and adverse drug reaction prediction of tuberculosis, aiming to inspire novel and precise therapy development to combat this pathogen in the future.
H-TEX-mediated signaling between hepatocellular carcinoma cells and macrophages and exosome-targeted therapy for hepatocellular carcinoma
Authors: Yu Sihang , Zhou Lei , Fu Jiaying , Xu Long , Liu Buhan , Zhao Yuanxin , Wang Jian , Yan Xiaoyu , Su Jing
Published: October 2022

There is increasing evidence for the key role of the immune microenvironment in the occurrence and development of hepatocellular carcinoma. As an important component of the immune microenvironment, the polarization state and function of macrophages determine the maintenance of the immunosuppressive tumor microenvironment. Hepatocellular carcinoma tumor-derived exosomes, as information carriers, regulate the physiological state of cells in the microenvironment and control cancer progression. In this review, we focus on the role of the exosome content in disease outcomes at different stages in the progression of hepatitis B virus/hepatitis C virus-induced hepatocellular carcinoma. We also explore the mechanism by which macrophages contribute to the formation of hepatocellular carcinoma and summarize the regulation of macrophage functions by the heterogeneity of exosome loading in liver cancer. Finally, with the rise of exosome modification in immunotherapy research on hepatocellular carcinoma, we summarize the application prospects of exosome-based targeted drug delivery.
Novel imaging techniques for hydroxychloroquine retinopathy
Authors: Yusuf Imran H. , Charbel Issa Peter , Ahn Seong Joon
Published: October 2022

Hydroxychloroquine retinopathy is an increasingly recognized cause of iatrogenic, irreversible visual impairment due to the expanding use of hydroxychloroquine in combination with improvements in disease detection following advances in retinal imaging techniques. The prevalence of disease is estimated to be greater than 5% amongst individuals who have used the drug for 5 years or more. In addition to conventional imaging modalities, such as spectral-domain optical coherence tomography (OCT) and fundus autofluorescence (FAF), novel retinal imaging techniques such as en face OCT, OCT angiography, fluorescence lifetime imaging ophthalmoscopy, quantitative autofluorescence, and retromode imaging are capable of detecting structural changes in the retina. These novel retinal imaging techniques have shown promise in detecting earlier disease than is possible with current mainstream imaging modalities. Moreover, these techniques may identify disease progression as well as enabling functional correlation. In the future, these novel imaging techniques may further reduce the risk of visual loss from hydroxychloroquine retinopathy through the earlier detection of pre-clinical disease.
Circular RNA hsa-circ-0005238 enhances trophoblast migration, invasion and suppresses apoptosis via the miR-370-3p/CDC25B axis
Authors: Huang Zhuomin , Zhu Litong , Zhang Quanfu , Zhao Depeng , Yao Jilong
Published: October 2022

Background

Fetal growth restriction (FGR) is attributed to various maternal, fetal, and placental factors. Trophoblasts participate in the establishment and maintenance of pregnancy from implantation and placentation to providing nutrition to fetus. Studies have reported that impaired trophoblast invasion and proliferation are among factors driving development of FGR. Circular RNAs (circRNAs) can regulate trophoblast function. We assessed the significance of circRNAs underlying FGR development.

Materials and methods

Next generation sequencing (NGS) was carried out to quantify levels of circRNAs in placenta tissues with and without FGR. In vitro experiments including transfection, (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2Htetrazolium) (MTS) assays, flow cytometry analyses, Transwell assays, wound healing assays, western blotting, qRT-PCR, dual-luciferase assays, immunofluorescence staining, and RIP assay were performed.

Results

There were 18 differentially expressed circRNAs between FGR placentas and uncomplicated pregnancies, while levels of hsa-circ-0005238 were markedly low in FGR placentas. Our in vitro experiments further revealed that hsa-circ-0005238 suppressed apoptosis and enhanced proliferation, migration, invasion of trophoblast cell lines. The hsa-miR-370-3p was identified as a direct target of hsa-circ-0005238. Mechanistically, hsa-miR-370-3p prevents invasion as well as migration of trophoblast cells by downregulating CDC25B.

Conclusion

The hsa-circ-0005238 modulates FGR pathogenesis by inhibiting trophoblast cell invasion and migration through sponging hsa-miR-370-3p. Hence, targeting this circRNA may be an attractive strategy for FGR treatment.
Radiomics analysis of contrast-enhanced CT scans can distinguish between clear cell and non-clear cell renal cell carcinoma in different imaging protocols
Authors: Budai Bettina Katalin , Stollmayer Róbert , Rónaszéki Aladár Dávid , Körmendy Borbála , Zsombor Zita , Palotás Lõrinc , Fejér Bence , Szendrõi Attila , Székely Eszter , Maurovich-Horvat Pál , Kaposi Pál Novák
Published: October 2022

Introduction

This study aimed to construct a radiomics-based machine learning (ML) model for differentiation between non-clear cell and clear cell renal cell carcinomas (ccRCC) that is robust against institutional imaging protocols and scanners.

Materials and methods

Preoperative unenhanced (UN), corticomedullary (CM), and excretory (EX) phase CT scans from 209 patients diagnosed with RCCs were retrospectively collected. After the three-dimensional segmentation, 107 radiomics features (RFs) were extracted from the tumor volumes in each contrast phase. For the ML analysis, the cases were randomly split into training and test sets with a 3:1 ratio. Highly correlated RFs were filtered out based on Pearson’s correlation coefficient (r > 0.95). Intraclass correlation coefficient analysis was used to select RFs with excellent reproducibility (ICC ≥ 0.90). The most predictive RFs were selected by the least absolute shrinkage and selection operator (LASSO). A support vector machine algorithm-based binary classifier (SVC) was constructed to predict tumor types and its performance was evaluated based-on receiver operating characteristic curve (ROC) analysis. The “Kidney Tumor Segmentation 2019” (KiTS19) publicly available dataset was used during external validation of the model. The performance of the SVC was also compared with an expert radiologist’s.

Results

The training set consisted of 121 ccRCCs and 38 non-ccRCCs, while the independent internal test set contained 40 ccRCCs and 13 non-ccRCCs. For external validation, 50 ccRCCs and 23 non-ccRCCs were identified from the KiTS19 dataset with the available UN, CM, and EX phase CTs. After filtering out the highly correlated and poorly reproducible features, the LASSO algorithm selected 10 CM phase RFs that were then used for model construction. During external validation, the SVC achieved an area under the ROC curve (AUC) value, accuracy, sensitivity, and specificity of 0.83, 0.78, 0.80, and 0.74, respectively. UN and/or EX phase RFs did not further increase the model’s performance. Meanwhile, in the same comparison, the expert radiologist achieved similar performance with an AUC of 0.77, an accuracy of 0.79, a sensitivity of 0.84, and a specificity of 0.69.

Conclusion

Radiomics analysis of CM phase CT scans combined with ML can achieve comparable performance with an expert radiologist in differentiating ccRCCs from non-ccRCCs.