SLC25A21 was found to be significantly downregulated in AML, and was associated with high white blood cell (WBC) counts, high pretrial blood (PB) and bone marrow (BM) blast abundance, FLT3 mutation, NPM1 mutation, and death events . We validated the expression of SLC25A21 in our clinical cohort, and found that SLC25A21 was downregulated in AML. Moreover, we identified low expression of SLC25A21 as an independent prognostic factor by univariate Cox regression  and multivariate Cox regression analysis . A survival prediction nomogram was established with a C-index of 0.735, which indicated reliable prognostic prediction. Subsequently, based on the median SLC25A21 expression level, patients in the TCGA-LAML cohort were divided into low- and high-expression groups. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs highlighted growth factor binding, extracellular structure organization, cytokine‒cytokine receptor interaction, etc. The results of gene set enrichment analysis (GSEA) indicated that the epithelial-mesenchymal transition, KRAS signalling, oxidative phosphorylation, and reactive oxygen species pathways were enriched. Through gene coexpression and protein‒protein interaction (PPI) network analysis, we identified two hub genes, EGFR and COL1A2, which were linked to worse clinical outcomes. Furthermore, we found that lower SLC25A21 expression was closely associated with a significant reduction in the levels of infiltrating immune cells, which might be associated with immune escape of AML cells. A similar trend was observed for the expression of checkpoint genes . Finally, drug sensitivity testing suggested that the low-expression SLC25A21 group is sensitive to doxorubicin, mitomycin C, linifanib but resistant to JQ1, belinostat, and dasatinib. Hence, our study demonstrated that a low expression level of SLC25A21 predicts an unfavourable prognosis in patients with AML.Acute myeloid leukaemia (AML) is a heterogeneous disease associated with poor outcomes. To identify AML-specific genes with prognostic value, we analysed transcriptome and clinical information from The Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) datasets, and Genotype-Tissue Expression (GTEx) project. The metabolism-related gene,  Acute myeloid leukaemia (AML) is a genetically and clinically heterogeneous disease characterized by clonal expansion, differentiation arrest, and evasion of apoptosis. Despite recent advances in chemotherapy, immunotherapy, and bone marrow transplantation, large numbers of AML patients still have a dismal prognosis, with a 5-years survival rate of only approximately 20% . The devSLC25A21) as an AML-specific prognostic marker. SLC25A21, also called ODC, is a metabolism-related gene located on chromosome 14q13.3, and it encodes a protein known as mitochondrial 2-oxodicarboxylate carrier  analysis, Kaplan-Meier analysis and Cox regression analysis helped us screen out Solute Carrier Family 25 Member 21  (n = 573) (n = 163) (n = 70) was extracted from the GTEx project (https://xenabrowser.net/datapages/) (https://www.ncbi.nlm.nih.gov/geo/). To maintain the comparability of data from different databases, TPM values from RNA-Seq were determined for intrasample comparison after log2 transformation. In our study, specimens with no survival data were excluded.We included 804 samples from three independent cohorts in this study: the TCGA LAML cohort  , the GSEn = 573)  and the n = 163) . The mat project . The RNAapages/) . The micp value <0.05 and |log2FC| ≥ 0.15 (https://bioinfogp.cnb.csic.es/tools/venny/).To analyse the gene expression profiles of AML, 705 bone samples from the GSE13159 and LAML datasets were used. The GSE13159 dataset was collected from the Microarray Innovations in Leukaemia Study. The DEGs were predicted using the limma package in R, with an adjusted | ≥ 0.15 . A list p value <0.05 were selected using univariate Cox hazard regression analysis for further research. The external cohort GSE12417 (n = 163) was used to validate our results  from MsigDB . ResultsSLC25A21 and the expression of other genes were assessed using the LinkedOmics database (http://www.linkedomics.org/login.php). We derived the PPI network from the STRING database (https://string-db.org/) to estimate the interactional correlations of the DEGs  in the R package gsva, Spearman correlation coefficients were computed between the expression level of n levels . The invThe half-maximal inhibitory concentration (IC50), calculated using the pRRophetic package in R , was usehttps://www.r-project.org/). The Wilcoxon rank-sum test and Kruskal–Wallis test were used to detect differences among continuous variables. The correlation of clinical features with low and high SLC25A21 expression were analysed with Pearson’s correlation χ2 test. For survival analysis, Cox proportional hazards analysis was conducted by using “survival” and “survminer” in R. Variables significant in Cox univariate analysis were selected for multivariate analysis. The Kaplan-Meier method was used for univariate analyses of OS. Receiver operating characteristic (ROC) curves and AUC values were generated by pROC in R to assess the diagnostic efficacy of SLC25A21 for AML. All tests were two-sided, and a p value < 0.05 was considered to indicate statistical significance. A flow chart of the analyses is presented in All statistical analyses were performed with R, version 4.1.3  by using the limma package in R. The volcano plots are shown in p value < 0.05) with DESeq2, a total of 683 differentially expressed genes were obtained, which are shown in IL1R2, MMP8, FGF13, SLC25A21, etc. In pan-cancer analysis, we determined the expression profiles of these genes in normal and malignant samples. Remarkably, SLC25A21 was downregulated in multiple malignancies, especially in AML  and healthy donors (n = 10) by qPCR. SLC25A21 was significantly downregulated in AML samples, with a p value of 0.0007 . We identified 61 upregulated and 365 downregulated DEGs in the AML group . Meanwhile, increasing age and unfavourable cytogenetics were also risk factors associated with poor outcomes. Then, all variables significant in univariate Cox regression analysis  were included in multivariate Cox regression analysis. Subsequently, age, unfavourable cytogenetics and low levels of SLC25A21 expression  were identified as independent prognostic factors for OS. The forest plots present the Cox regression results in In addition, univariate and multivariate logistic regression analyses were performed to determine whether low expression of Moreover, a nomogram including the prediction model was established based on multivariable logistic regression analysis. The established nomogram was well calibrated and had good discriminative power, with a concordance index (C-index) of 0.735 for OS prediction . FurtherSLC25A21 in AML. We identified DEGs between the low- and high- SLC25A21 expression groups. The final list of DEGs included 1,270 genes, with 128 genes upregulated and 1,142 genes downregulated . The heatmap and the volcano map are shown in Next, we aimed to further investigate the underlying mechanisms and functional pathways of SLC25A21 in AML, we performed enrichment analyses. The top 15 GO enrichment items  between the above two gene lists. In addition, we detected the associations between SLC25A21 and hub genes. The results showed that SLC25A21 had significant correlations with EGFR , CDH1 , CXCL12 , CD8A , MMP9 , SOX9 , BMP4 , and COL1A2   . Finallywith AML .SLC25A21 expression and immune infiltration in AML. The results showed that the expression level of SLC25A21 had an obvious positive correlation with the numbers of infiltrating B cells, T-cells, Th1 cells, Th2 cells, T helper cells, Tfh cells, CD8 T-cells, cytotoxic cells and Tcm cells  expression. In our study, SLC25A21 was significantly correlated with CTLA4, LAG3, TIGIT, CD274, and TIGIT. Details of the correlation analysis are shown in Furthermore, we clarified the relationship between SLC25A21 groups showed that the SLC25A21 low expression group may be more sensitive to cell cycle inhibitors (doxorubicin and mitomycin C), vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitors (linifanib and 7-oxozeaenol), p53 activators (JNJ-26854165 and Nutlin-3a), and heat shock protein 90 (HsP90) inhibitors (CCT018159 and 17-AAG) but resistant to histone deacetylase (HDAC) inhibitors  and tyrosine kinase inhibitors (dasatinib). These results indicated that SLC25A21 has a significant correlation with chemotherapy and targeted therapy regimens for AML  pathway.SCL25A21 resulted in efflux of α-KG from mitochondria, leading to upregulation of ROS accumulation, which in turn induced mitochondrial apoptosis  that could accurately predict the prognosis of AML were found. It has been reported that dysregulation of EGFR can lead to the development of malignancy , leading to the regeneration of normal haematopoietic cells. Experimental studies have shown that deletion of EGFR in progenitor cells results in reduced DNA-PKcs activity, thus reducing the ability of the cells to regenerate normal HSCs , which serve as activation markers of T-cells and affect antitumor immunity. We speculate that this may be because the number of infiltrating immune cells is significantly reduced, resulting in decreased expression of molecular markers of T-cell activation. These results suggest that SLC25A21 may lead to immune escape in AML. This observation may provide a framework to guide further investigation of SLC25A21 in clinical and basic science research.Additionally, metabolic molecular abnormalities may facilitate AML cell escape and immune detection and severely reduce the efficacy of immunotherapy . SeveralSLC25A21 and drug resistance in AML. Patients with low SLC25A21 expression levels were sensitive to doxorubicin, mitomycin, lapatinib, midostaurin, sorafenib, linifanib, Nutlin-3a, 17-AAG, 5-fluorouracil, 7-oxozeaenol, JNJ-26854165, CCT018159, bleomycin, and FH535 but resistant to JQ1, CUDC-101, dasatinib, and GNF-2. These results indicate that downregulation of SLC25A21 may promote sensitivity to doxorubicin, the cornerstone regimen for AML. These results suggest that while SLC25A21 affects prognosis in AML, patients with low expression of SLC25A21 may still benefit from traditional chemotherapy regimens.Last, the ultimate objective of our research is to provide clinicians with guidelines to choose the appropriate therapeutic regimens for each AML patient. With the development of next-generation sequencing technology, several genetic aberrations have been found to contribute to drug resistance in AML . In thisSLC25A21 in 6 independent AML studies  and found a frequency of approximately 0.1%–0.2% (SLC25A21 remains to be uncovered. Second, we evaluated the diagnostic value and drug sensitivity of SLC25A21 by using public resources. However, we have not yet tested some new clinically emerging targeted drugs, such as venetoclax, due to the limitations of the training database. Last, all associations between SCL25A21 and AML-associated immune molecules lack functional validation and detection of the potential cellular and molecular mechanisms. Future studies will build on these points with a view toward providing new options for precision medicine approaches and improving the treatment of AML patients.However, our study has several limitations. First, we explored the mutational frequency of .1%–0.2% . In addiSLC25A21 had an unfavourable effect on the overall survival of AML patients and may be correlated with immune escape. A low level of SLC25A21 could be an independent predictor of poor prognostic for AML patients. This discovery could promote the development of novel targeted drugs and provide therapeutic options for personalized therapy.Taken together, our preliminary findings showed that low expression levels of the metabolism-related gene


As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation. Plants always suffer from various kinds of abiotic stresses, such as drought, salinity, heat and cold stress. The stresses impair the growth of plants and cause serious yield loss in global major crops ,2,3,4. ATo evade and ameliorate drought-induced damage, plants have developed a variety of strategies through diverse morphological and physiological changes, including stomatal adjustment, osmotic adjustments, antioxidant metabolism and ion regulation ,5,6. SomMpGR-RBP1 from Malus prunifolia was up-regulated by salinity, oxidation, or abscisic acid [MpGR-RBP1 in Arabidopsis thaliana enhanced salt and oxidative stress tolerance. The expression of OsRBGD3 was induced by cold, drought and salt stress in a drought tolerant rice cultivar [OsRBGD3 in Arabidopsis thaliana conferred cold stress tolerance and ABA sensitivity. Expressing NtGR-RBP1 in E. coli enhanced salinity, drought, cold and heat shock tolerance [Glycine-rich RNA binding proteins (GRPs) have been reported to participate in various RNA processes, including mRNA stability, RNA splicing and RNA transport to regulate plant growth and development processes . Magdalesic acid . The ectcultivar . The conolerance . AtGRP7,olerance , osmoticolerance ,24, oxidolerance , plant iolerance  and circolerance ,28,29,30PAL) in Nicotiana tabacum [CAD2 and CAD3 in Cucumis melo [Manihot esculenta [IbLEA14 in Ipomoea batatas [PuC3H35 in Populus ussuriensis [OsTF1L and OsERF71 in rice [Phenylpropanoid metabolism contributes to plant development and plant-environment interactions ,32,33. T tabacum , CAD2 anmis melo , or promsculenta , leads t batatas , PuC3H35 in rice ,46, alsoOs03g0670700), which interacted with OsDi19-4 through two-hybrid bacteria screening [Previously, we identified a glycine-rich RNA-binding protein, OsGRP3  domain, which was composed of approximately 80 amino acids A. The phhttp://rice.uga.edu/, accessed on 19 August 2020). The heatmap of the expression data indicated that the expression pattern of OsGRP3 was similar to that of OsGR-RBP4. They were both highly expressed in various stages and organizations . The results indicated that the expression of OsGRP3 was periodic, and it was significantly affected by all the treatments except SA , methyl jasmonate (MeJA), salicylic acid (SA), gibberellic acid (GA), PEG6000, NaCl, Hxcept SA A–H. Bothe points A,B. The e points I. All ofOsGRP3 was significantly induced by PEG6000, we generated transgenic plants to investigate how OsGRP3 responds to drought stress. Three overexpression (OE) lines, OE-91, OE-109 and OE-127, were obtained, as well as three knockout (KO) lines, Osgrp3-27, Osgrp3-52 and Osgrp3-59. The mutant sites are shown in As the expression of Then, the 21-day-old seedlings of transgenic plants and wild-type ZH11 (WT) grown in soil were drought-treated for two weeks and then re-watered for 9 days. When compared with the WT, the OE lines developed better and had greater survival rates under stress conditions, whereas the KO lines showed lower survival rates A,B. ThesN. benthamiana leaf and rice protoplasts  PEG6000 treatments. The heat map of differentially expressed genes (DEGs) showed that the results of sequencing were repeatable, and the expression levels of numerous genes were changed between WT and Osgrp3-27 under both conditions , metabolic pathways (ko01100) and phenylpropanoid biosynthesis (ko00940) under normal conditions C. Under The phenylpropanoid biosynthesis pathway has been reported to participate in various life processes during plant growth . AdditioOsgrp3-27 compared with WT, as shown in the transcriptome profiling, while most of them were up-regulated in OE-127 compared with WT  variety Zhonghua 11 (ZH11) was grown in Yoshida solution in a greenhouse at 28 °C under a 12 h light/12 h dark photoperiod with relative humidity of around 70%. The leaf tissue of the two-week-old seedlings were harvested at 0, 1, 3, 6, 9, 12, 24, 27, 30 and 36 h after treatment with 20% (w/v) PEG6000 solution, 150 mM NaCl, 100 μM abscisic acid (ABA), 100 μM methyl jasmonate (MeJA), 100 μM salicylic acid (SA), 100 μM gibberellic acid (GA) and 1 mM H2O2. Then, the expressions of OsGRP3 were detected using qRT-PCR. The seedlings of transgenic lines and WT were grown in soil for 3 weeks, then not watered for 2 weeks and rewatered for 9 days. The survival rates were counted.The rice . Then, these sequences were aligned using ClustalW in MEGA v.7.0.26 [https://www.evolgenius.info/evolview/#login, accessed on 24 May 2019).Homology sequences of OsGRP3 were retrieved from a database of plant gene phylogeny, Gcorn Plant  and JW772 (CLUC). Then, the constructs were transformed into the Agrobacterium tumefacien GV3101 (pSoup-p19) competent cell. The 4-week-old Nicotiana benthamiana leaves were injected with different combinations of the constructs for BiLC analyses and grew for 48 h under a 12 h light/12 h dark period. Then, the leaves were injected with 1 mM luciferin, and the luciferase signals were detected and captured using the Tanon-5200 image system . The experiments were repeated at least three times, and yielded similar results.The coding sequence of OsGRP3 was cloned into vectors pSPYNE and pSPYCE. Additionally, the constructs were co-transferred into rice protoplasts. The fluorescence of the yellow fluorescent protein was observed and imaged under a confocal laser scanning microscope  using 510 nm laser excitation (5% power), a ×63 oil immersion lens and a wavelength detection window of 520–580 nm.The coding sequence of OsGRP3 was cloned into the pHBT vector. Additionally, the constructs were transferred into rice protoplasts, which were isolated and transfected according to the protocol in [The coding sequence of tocol in . The fluTotal RNA was extracted using the Trizol reagent  according to the instruction manual. Complementary DNA was synthesized using HiScript II reverse transcriptase  according to the manufacturer’s instructions. qRT-PCR was performed in triplicate on the CFX96 Touch™ Real-Time PCR Detection System  with the Hieff qPCR SYBR Green Master Mix  according to the manufacturer’s instructions. Expression analysis was performed with three biological replicates. All primers used for gene expression analysis are listed in OsGRP3 was cloned and inserted into the vector pCAMBIA1301 under the control of the UBI promoter using a one-step clone kit  for the overexpression of OsGRP3. The vector for knockout lines was constructed referring to the CRISPR/Cas9 System [The coding sequence of 9 System . The plaOsgrp3-27 lines were planted in Yoshida solution for two weeks, as described above, and then half of them were treated with 20% PEG6000 for six hours. The total RNA was extracted as described above from simples, which were fully ground in liquid nitrogen, and thoroughly mixed with 6 complete individuals growing under normal condition and PEG6000 treatment. Three biological replicates were performed. The mRNA libraries were constructed and sequenced using Seqhealth  with the Hiseq-PE150  high-throughput sequencing platform. The clean reads were mapped to the Nipponbare reference genome . The DEGs between samples were defined using a cut-off change of at least a 2-fold change (|FC| ≥ 2.0) and p value < 0.05. KEGG analysis wasperformed using the OmicShare tool, a free online platform for data analysis .The WT and The lignin content of the second stem above ground of mature rice was determined using the Lignin Content Assay Kit  according to the instructions. The experiments were repeated at least three times.Osgrp3-27 and OE-127 were taken from the first stem below the panicle at 10 cm above the stem node, and then stained with phloroglucinol-HCl solution ; 36% HCl) for 5 min to distinguish the lignified cell walls and imaged using a Leica DMi8 equipped with a DMC6200 camera Vibratome cross-sections (150 μm) of WT, t-test at p < 0.05.All experiments in this study were carried out with at least three biological replicates. Significant differences were determined using the Student’s In this study, we demonstrated that various stresses and hormone treatments could induce the expression of OsGRP3, which could form homodimers or homomultimers with itself like some other GRPs. OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid pathway and further promoting lignin accumulation.


Background: Hepatocellular carcinoma (HCC), which has high rates of recurrence and metastasis and is the main reason and the most common tumor for cancer mortality worldwide, has an unfavorable prognosis. N7-methylguanosine (m7G) modification can affect the formation and development of tumors by affecting gene expression and other biological processes. In addition, many previous studies have confirmed the unique function of long noncoding RNAs (lncRNAs) in tumor progression; however, studies exploring the functions of m7G-related lncRNAs in HCC patients has been limited.Methods: Relevant RNA expression information was acquired from The Cancer Genome Atlas , and m7G-related lncRNAs were identified via gene coexpression analysis. Afterward, univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and multivariate regression analyses were implemented to construct an ideal risk model whose validity was verified using Kaplan–Meier survival, principal component, receiver operating characteristic (ROC) curve, and nomogram analyses. In addition, the potential functions of lncRNAs in the novel signature were explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses and gene set enrichment analysis (GSEA). At last, in both risk groups and subtypes classified based on the expression of the risk-related lncRNAs, we analyzed the immune characteristics and drug sensitivity of patients.Results: After rigorous screening processes, we built a model based on 11 m7G-related lncRNAs for predicting patient overall survival (OS). The results suggested that the survival status of patients with high-risk scores was lower than that of patients with low-risk scores, and a high-risk score was related to malignant clinical features. Cox regression analysis showed that the m7G risk score was an independent prognostic parameter. Moreover, immune cell infiltration and immunotherapy sensitivity differed between the risk groups.Conclusion: The m7G risk score model constructed based on 11 m7G-related lncRNAs can effectively assess the OS of HCC patients and may offer support for making individualized treatment and immunotherapy decisions for HCC patients. Primary hepatic carcinoma, the sixth most common malignant neoplasm and the third most common cause of cancer mortality worldwide, includes hepatocellular carcinoma (HCC) (which accounts for 75%–85% of cases) and other kinds of hepatic cancer .HCC is notoriously characterized by poor prognosis with locoregional treatments such as resection, percutaneous ablation, transarterial chemoembolization (TACE), and radioembolization . Owing tThe immune system has a considerable influence on tumor progression. The liver contains a variety of stromal cells and various immunoinhibitory substances that enable it to function as a tolerogenic immune organ to avoid adverse reactions to chronic pathogen exposure . Immune In recent years, gene signatures have been developed and found to have predictive value . Almost Furthermore, RNA modification greatly influences the regulation of gene expression , and manHowever, research on the posttranscriptional modification of lncRNAs is lacking. In eukaryotes, N7-methylguanosine (m7G), a frequent posttranscriptional alteration of mRNA and lncRNA, is needed for efficient gene expression and cell properties . AlthougGiven the potential of immunotherapy and the toned to rapidly identify novel and reliable screening methods that can enhance the diagnosis of and prediction of therapeutic benefit in HCC, here, a prospective prognostic model based on m7G-related lncRNAs was established. This model might help predict which patients will benefit from immunotherapy.http://www.gsea-msigdb.org) and previous literature  up to 1 February 2022. The clinical characteristics of patients with an overall survival time exceeding 30 days and sufficient clinical information were also retrieved, and the clinical information of samples is provided in terature , and thep < 0.001) were identified as m7G-associated lncRNAs -penalized Cox regression analysis, which aims to strengthen the predictive value and applicability of the prognostic model, as well as alternative methods and normalization were used. This approach has been widely used to minimize overfitting and identify the best features in high-dimensional data with low correlation and substantial predicted value. As a result, this strategy can efficiently identify the best predictive factors and provide prognostic indicators for predicting clinical outcomes.At last, we further utilized multivariate Cox regression analysis to build an m7G-associated lncRNA risk model for predicting OS. The following mathematical equation was utilized to compute the m-7G risk score:The results of univariate Cox analysis, LASSO penalized Cox regression analysis, and multivariate Cox analysis are shown in p-value of 0.05 was used to identify relevant independent predictive variables.Univariate Cox regression and multivariate Cox regression analyses were applied to validate the utility of the selected lncRNAs in the entire dataset, and relative clinical information was obtained from TCGA. A To improve the model’s accuracy, we used the R package “rms” to create a nomogram model based on the stage and risk score with independency and used this model to calculate risk scores.p-value < 0.05 were considered significant.Kaplan–Meier (K-M) analysis was performed using a log-rank test to investigate the predictive value of the m7G-lncRNA signature in HCC patients separated into distinct groups. Result with a Principal component analysis (PCA) was implemented to validate further the accuracy of the m7G-related lncRNA model in grouping samples based on differences in gene expression profiles.p-value < 0.05 and FDR < 0.25 were included in the enriched gene set.Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were adopted using the R package “cluster Profiler” to determine potential differentially enriched biological functions and pathways between the two risk groups. Gene set enrichment analysis (GSEA) investigated underlying functions associated with the obtained differentially expressed genes. Genes with normalized Unsupervised consensus clustering analysis using the R package “Consensus Cluster Plus” was used to identify molecular subgroups based on the risk-related lncRNA expression.+ T cells, neutrophils, memory B cells, cancer-associated fibroblasts, plasma B cells, M0 macrophages, M1 macrophages, activated natural killer (NK) cells, nonregulatory CD4+ T cells, activated memory CD4+ T cells, and so on.The XCELL , TIMER , QUANTISDifferentially expressed genes (DEGs) were identified using the R package “limma” (|log2FC| > 1 and FDR < 0.05).p-value < 0.01 was employed to predict potential treatments for patients in different risk groups.Using the R package “pRRophetic,” the drug response of HCC patients was predicted. A p-value < 0.05 were considered significant.The Chi-square test was conducted to identify differences between groups in various datasets, and the Wilcoxon test was used to compare two groups. In addition, the log-rank test was employed to perform the K-M survival analysis. Results with a A flowchart of the whole research, including the construction of the model and further studies, is depicted in In total, 276 prognosis-related m7G-related lncRNAs were recognized using univariate Cox regression analysis. These lncRNAs were further evaluated using LASSO penalized Cox regression analysis, resulting in 17 lncRNAs . MultivaAfterward, we attempted to verify this model in the complete dataset and carried out a bioinformatics analysis.The risk scores of the training set and testing set were calculated, and then the patients were divided into high- and low-risk groups according to the cutoff value of the risk score in the training set, and the median value of the risk score in the training set is identified as the cutoff value. The distributions of the signature risk score, survival status, and expression of relevant lncRNAs in the training set  and the The differences between the two risk groups in total gene expression profiles, the expression of the 29 m7G genes, and the expression of the m7G-related lncRNAs and 11 m7G-related risk lncRNAs in our study were each confirmed using PCA . FiguresThe accuracy of this model was assessed in both datasets using receiver operating characteristic (ROC) curve analysis. The acreage under the curve (AUC) values of the training set and validation set for 1-, 3-, and 5-year OS were 0.742, 0.806, and 0.810, respectively , and 0.7p < 0.001) and T stage  were independent predictors of HCC prognosis (p < 0.001) but also T stage  could independently predict patient OS in HCC  evaluates the predictive capability of independent factors based on the probability of the predicted outcome agreeing with the actual outcome. The CI of the risk score seemed to be higher than those of other clinical parameters, implying that the risk score may better predict the outcome of HCC patients . To inveTo determine whether the m7G-related prognostic lncRNAs are related to the immune response, Spearman’s correlation analysis was employed to determine the correlation between the risk score and diverse immune functions and infiltrating immune cell levels in the two groups.We investigated the levels of 22 infiltrating immune cells . The abuThe relationships between the risk score and various immune functions are depicted in + T cells Th2, M0 macrophages, common lymphoid progenitors, and regulatory T cells (Tregs) showed a surprising positive relationship with the risk score (p < 0.05). Immune cell subtype infiltration may have a significant impact on prognosis.The association of the risk score with immune cell infiltration was then evaluated using the XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT−ABS, and CIBERSORT algorithms . The immsk score   was analyzed, as depicted in TNFSF4, TNFSF18, NRP1, CD27, LGALS9, HAVCR2, LAIR1, IDO1, TIGIT, CD200R1, VTCN1, TNFRSF8, HHLA2, CD86, TNFRSF14, CTLA4, CD48, CD276, TNFRSF4, PDCD1, TNFRSF9, TNFRSF18, ICOS, LAG3, CD70, CD44, CD80, TNFSF15, and TNFSF9 was higher, while that of IDO2 was considerably lower in the low-risk group  was calculated with each risk score group to analyze further the correlation between the risk score and immunotherapy sensitivity. The TIDE score can be used to predict a patient’s response to immunotherapy (The tumor immune dysfunction and exclusion (TIDE) score   analysis confirmed that the two clusters could be distinguished . The K-M< 0.001) .TNFSF4, TNFSF18, NRP1, CD27, BTLA, LGALS9, HAVCR2, CD244, ICOSLG, LAIR1, IDO1, TIGIT, CD200R1, VTCN1, TNFRSF8, TNFRSF25, BTNL2, HHLA2, CD40LG, CD28, CD86, TNFRSF14, CTLA4, CD48, PDCD1LG2, CD276, TNFRSF4, PDCD1, TNFRSF9, TNFRSF18, CD200, ICOS, LAG3, CD70, CD44, CD80, CD160, TNFSF15, TNFSF9, CD274, and TNFSF9 was higher in Cluster 2, although IDO2 expression was significantly lower, somewhat consistent with the previous analyses. In addition, infiltration of various immune cells showed differences in the two clusters.We also detected the expression of multiple immune checkpoints in each subtype  and immuHCC is the sixth most common malignancy and has a poor prognosis worldwide; HCC prognosis can be distinctly improved by early detection and treatment . IdentifDetermining lncRNA-related modification mechanisms has become a common goal of current research , and bioIn addition, in previous studies, many studies have investigated the ability of posttranscriptional regulation-associated genes to predict patient prognosis in various diseases, especially in malignancies, including breast cancer , HCC Li, and gasHere, data from 343 patients with OS time of more than 30 days were retrieved from TCGA to identify m7G-related prognostic lncRNAs.AC026412.3, AC034229.4, AC091057.3, AC099066.2, AL049840.5, AL096678.1, AL158163.1, DUXAP8, GABPB1−AS1, LINC01224, and MKLN1−AS. Multivariate Cox regression analysis was utilized to construct an ideal risk model. The high expression of AC091057.3, AL158163.1, and MKLN1−AS was found to be beneficial to patient OS, with negative correlation coefficients, and the remaining lncRNAs in the signature may promote cancer progression, having positive correlation coefficients. Some of the lncRNAs have already been confirmed to be significantly related to patient prognosis. LINC01224 inhibited CRC cell proliferation, migration, and invasion while increasing apoptosis via the LINC01224/miR-485-5p axis. GABPB1-AS1 could inhibit GABPB1 transcription, resulting in the dysregulation of the gene encoding the peroxiredoxin-5 (PRDX5) peroxidase and the suppression of cellular antioxidant capacity, implying that increased GABPB1-AS1 levels may be linked to improved prognosis in HCC patients. In addition, DUXAP8 promotes the Akt/mTOR signaling pathway, increasing tumor formation. However, the role of lncRNAs related to m7G modifications has been scarcely explored.As a result, an 11-m7G-related-lncRNA signature was generated, and the risk score calculated based on this signature was strongly associated with patient OS; the following lncRNAs were included in the risk signature: The identified lncRNAs were used to group patients into two risk groups by calculating a risk score, which was proven to be a competent, credible, and independent factor for assessing patient OS.Given the importance of immunotherapy, the association between the risk score and immune cell infiltration was evaluated. Factors such as stromal cell abundance and enrichment of processes such as tumorigenesis and endothelial cell participation in the formation of new blood vessels and tumor microenvironment (TME) factor promotion of tumor aggressiveness have been shown to be relevant . The immPD-1, PD-L1, PD-L2, and CTLA4, are considered the primary therapy for many malignant tumors (CTLA4 and LAG3 expression in the high-risk group, and these markers are known to induce immunosuppression. Tregs have a constitutive expression of CTLA-4, which inhibits the immune response. CTLA-4 competes with CD28 for binding with CD80/CD86, thus decreasing activated T cells. At present, strategies to block immune checkpoints to prevent immune evasion, decrease Treg activity, and reactivate functions concerning antitumor immunotherapy are of interest (Co-inhibitory substances expressed by effector cells prevent the overactivation of immune checkpoints from delaying tumor development . Immune t tumors . In our interest . FurtherThe GO and KEGG results indicate that the DEGs were primarily enriched in organelle fission, nuclear division, chromosomal segregation, cell cycle, and cytokine–cytokine receptor contact. Organelle fission, a type of cell transformation associated with organelle biology, plays an essential role in tumorigenesis because it is needed for adaptability to cellular and environmental changes and cancer therapies . Repeat Furthermore, the GSEA results depicted high enrichment of pathways and hallmarks related to tumor progressions in the high-risk group, such as cell cycle, bladder cancer, DNA replication, ubiquitin-mediated proteolysis, MTOR signaling pathway, TGF BETA signaling, E2F targets, MTORC1 signaling, P53 pathway, MYC targets V1, NOTCH signaling, Pl3K/AKT/mTOR signaling and WNT/BETA CATENIN signaling. These findings suggest that m7G lncRNA methylation plays an underlying regulatory role in HCC development. For example, proteolysis mediated by relevant cyclin chaperones and kinase inhibitors promotes the sequential activation of cyclin-dependent kinases. In recent years, studies have shown that dysregulation of the cell cycle induced by inefficient proteolytic control leads to uncontrolled cell proliferation and, consequently, the occurrence of tumors . E2F tarWe also separated the HCC patients into Cluster 1 and Cluster 2 using NMF clustering analysis. Most of the results were in line with those for the previously defined risk groups, suggesting the effectiveness and reliability of the risk score model for aiding individual treatment decisions in HCC.in vivo and in vitro tests are needed to confirm the findings. Moreover, the clinical guidelines for using this prognostic model need to be identified.In summary, our predictive model based on 11 m7G-related lncRNAs showed high clinical applicability and would cost substantially less than sequencing. The model also performed well in predicting the survival of HCC patients. Regardless, the study has several limitations. First, the model was constructed using TCGA data, and a patient cohort was not used. In addition, In conclusion, we used various methods to investigate the expression levels and prognostic value of m7G-related lncRNAs. We created an 11-lncRNA model with stand-alone prognostic utility in HCC. This is the first study to develop an m7G-related lncRNA risk model for HCC.All the findings suggest that the developed m7G-related lncRNA signature can effectively assess patient OS and patient sensitivity to immunotherapy and other drugs, which may aid the discovery of novel immunotherapies and targeted therapies for HCC patients.


The sarcoplasmic reticulum contains several proteins, some of which support Ca2+ storage and release, while others regulate the formation and maintenance of this highly convoluted organelle and mediate the interaction with other components of the muscle fiber. In this review, some of the main issues concerning the biology of the sarcoplasmic reticulum will be described and discussed; particular attention will be addressed to the structure and function of the two domains of the sarcoplasmic reticulum supporting the excitation–contraction coupling and Ca2+-uptake mechanisms.The sarcoplasmic reticulum of skeletal muscle cells is a highly ordered structure consisting of an intricate network of tubules and cisternae specialized for regulating Ca Studies with electron microscopes (EMs) have revealed that, in striated muscle cells, the SR is organized into numerous interconnected tubules forming a network of longitudinal elements surrounding each myofibril [2+ from the cytosol, an activity operated by the sarcoplasmic/endoplasmic reticulum Ca2+ ATPases (SERCA) that actively pump Ca2+ from the cytoplasm to the lumen of the SR. In skeletal muscle fibers, the l-SR is localized around the A and I bands of each sarcomere. At regular intervals, which correspond to the borders between A and I bands of sarcomeres, the tubules of the l-SR merge into enlarged sac-shaped structures, known as terminal cisternae. Here, two terminal cisternae are positioned at the opposite sides of tubular infoldings in direct continuity with the plasma membrane, named transverse tubules (TT) . The region of the terminal cisternae that opposes the TT membrane is called junctional SR (j-SR), and, in this region, the Ryanodine Receptors type 1 (RyR1) Ca2+ release channels are localized.The sarcoplasmic reticulum (SR) is a specialized form of the endoplasmic reticulum of muscle cells, dedicated to calcium ion (Cayofibril . These eles (TT) . The strThe proper relationship between the elongated tubules of the l-SR and myofibrils is a pivotal structural prerequisite to organize the different domains of the SR and allow an efficient muscle contraction ,2. As of2+ channel located on the TT that, following sarcolemma depolarization induced by motor-neuron stimulation, undergoes a conformational change that allows the opening of RyR1, the Ca2+ channel located on the terminal cisternae of the j-SR, resulting in a massive Ca2+ efflux from the SR into the myoplasm and activation of muscle contraction [The triad is the membrane structure that supports ECC in skeletal muscle fibers by allowing the interaction between the dihydropyridine receptor (DHPR) and RyR1 . The DHPtraction .The events that characterize TT maturation and triads formation have been morphologically defined by electron and confocal microscopy studies. These revealed that the juxtaposition of j-SR and TT begins in the embryonic (E) period of development and evolves through sequential steps in the postnatal life ,15. In mTT development appears to start immediately after that of the SR. At day E15, small tubular invaginations can be observed at the periphery of developing muscle fibers. By day E19, these invaginations expand deeper into the fiber, although remaining almost longitudinally oriented. After birth, the TT system starts acquiring its final transverse position over the borders between the A and I bands, achieving its definitive localization at around three weeks of age in mice ,14. A reWhile several details of the morphological events that characterize TT and SR maturation have been defined, the molecular mechanisms that drive this process remain more elusive. RyR1 and DHPR, although essential for ECC, have been shown to be dispensable for the formation of triads; indeed, triad formation was observed in knockout mice for RyR1, also called “dyspedic” mice since RyRs were defined as “junctional feet”. Triad formation was also observed in mice carrying muscular dysgenesis in DHPR, a natural mutation that causes lethal paralysis in mice. Finally, mice lacking both RyR1 and DHPR also show triad formation, further supporting the idea that these two proteins are not directly involved in triad formation or maintenance ,20,21. SAmphiphysin 2, also known as Bridging integrator-1 (Bin1), is a member of a family of ubiquitous proteins able to shape lipid membranes; thanks to their BAR (Bin/Amphiphysin/Rvs) domain, they can interact with membrane lipids and detect and/or generate membrane curvatures . Bin1 caCaveolin-3 (Cav-3) is the muscle-specific isoform of caveolins, which mediates the formation of peripheral invaginations in cholesterol-rich regions of the plasma membrane ,34,35. C2+ [DYSF gene cause myopathies, including limb–girdle muscular dystrophy type 2B (LGMD2B), Miyoshi myopathy (MM), and distal anterior compartment myopathy [2+-dependent vesicle fusion with the plasma membrane [2+-activated chloride channel, which was also suggested to display phospholipid scramblase activity [2+ overload due to membrane damage [Dystrophy-associated fer-1-like protein (DYSF) is an integral protein belonging to the ferlin family, characterized by multiple C2 domains able to bind membrane phospholipids in the presence of Ca2+ . It is m2+ ,49. Mutamyopathy ,51,52. Dmembrane . Annexinactivity . Mutatioactivity ,56. Moree damage .Mitsugumin-53 (MG53), also known as tripartite motif 72 (TRIM72), is a skeletal and cardiac muscle-specific protein that contributes to vesicle trafficking involved in the membrane repair machinery ,58. MG532+ transients during skeletal muscle contraction [Mitsugumin-29 (MG29), which belongs to the synaptophysin family and is characterized by early expression during myogenesis, associates with newly formed SR vesicles ,62. Duritraction .MTM1 are associated with X-linked myotubular myopathy, a skeletal muscle disorder that results in severe muscle weakness with abnormal nuclei positioning [SPEG have been linked to centronuclear myopathies with disruptions of triadic structures and impairment of ECC [Myotubularin (MTM1) is a lipid phosphatase localized at triads. Mutations in human itioning . Mice knitioning . MTM1 deitioning . This suitioning . On the itioning , indicatitioning ,73. Finaitioning ; mutatiot of ECC .Junctophilins mediate the apposition between ER/SR and plasma membrane in different cell types. In mammals, Junctophilin 1 (JPH1) and Junctophilin 2 (JPH2) are expressed in striated muscles ,77,78. A2+ release complex [2+ homeostasis due to a partial loss in RyR1 and DHPR co-localization [2+ homeostasis [In skeletal muscle, both JPH1 and JPH2 are present at triads, where they are essential for the formation and maintenance of these contact sites. In addition to their structural role, JPHs can also bind and regulate various proteins at triads, acting as a scaffold for assembly of the Ca complex ,82,83. J complex ,89,90,91 complex . Downreglization ,85,86. Jlization ,94, whillization . In the lization ,99,100. lization . The seclization ; severaleostasis ,104,105.eostasis ,104. Neveostasis ,104,105.2+ binding proteins calsequestrin (CASQ) and histidine-rich calcium (HRC) binding protein [At triads, several proteins participate in the ECC process, including integral membrane proteins such as RyR1, DHPR, triadin, junctin, j-SR protein 1 (jp45), and mitsugumin-56, the STAC3 adaptor protein, or luminal proteins such as the Ca protein ,106,107 2+ release channels that represent the largest ion channels known to date. In skeletal muscle, two RyR isoforms, RyR1 and RyR3, are expressed, although only RyR1 is essential for ECC activation. In skeletal muscle, RyR1 is primarily activated by a conformational coupling with the DHPR, a mechanism defined as depolarization-induced Ca2+ release (DICR) [2+-induced Ca2+-release (CICR) mechanism, whereby an increase in cytosolic Ca2+ causes RyR3 opening and, thus, Ca2+ release from intracellular stores [2+ concentration, or, in the micromolar range, as a channel inhibitor [2+, Homer 1c, the scorpion venom imperatoxin, halothane, dantrolene, PCB95, ryanodine, ruthenium red, methylxanthines, and 4-chloro-m-cresol [RYR1 that result in RyR1 hyperactivation, leading to massive and uncontrolled Ca2+ efflux from the SR. Dantrolene was historically used as a skeletal muscle relaxant, and later, it was demonstrated to be able to block calcium release from the SR. Although the molecular mechanism responsible for dantrolene action on RYR1 is still not completely defined, its introduction for the clinical treatment of MH led to a significant decrease in mortality, from more than 90% to less than 5% [2+/CaM-dependent protein kinase II (CaMKII), and phosphatases  [RyRs are a family of Cae (DICR) . At varir stores ,108,109.r stores . RyRs har stores ,111. EM r stores ,111,112.nhibitor . One of nhibitor . RyR1 isnhibitor ,116. Addm-cresol ,118. Amo than 5% . Finally PDE4D3) .2+ channels located on the TT. The skeletal muscle DHPR is composed of a heteromultimeric complex that includes the α1s, α2, and δ, β1α, and γ1 subunits [α1s subunit  is an integral membrane protein containing four transmembrane domains, each composed of six alpha helices, acting as the pore-forming and the voltage-sensing unit. The voltage-sensing domain of α1s interacts with the γ1 subunit that regulates channel inactivation [β1a subunit is also located in proximity to the voltage-sensing domain of the α1s subunit and supports the assembly of DHPRs in tetrads, where one DHPR tetrad faces one of the four subunits of the tetrameric RyR1 channel [α1s or β1a subunits die perinatally, indicating that these subunits are essential for ECC [α1s subunit [2+ release from the SR by physically interacting with RyR1, according to “orthograde” signaling [2+ current mediated by DHPR is smaller than that measured in the presence of RyR1, suggesting that RyR1 can promote the Ca2+ channel activity of DHPR and accelerates DHPR activation. Interestingly, this activity is unique to RyR1 since RyR2 was found not to be able to restore either orthograde or retrograde signaling. Different regions in DHPR and RyR1 have been proposed to be important for their reciprocal association and regulation; the II-III loop of the α1s subunit is generally accepted to be involved in both orthograde and retrograde coupling, while the site of interaction on RyR1 has not yet been completely defined [DHPRs are L-type voltage-gated Casubunits . The α1stivation . The β1a channel ,123,124. for ECC ,126. The subunit . Despiteignaling . RyR1 isignaling ,128. In  defined ,127,129.α1s subunit of DHPR and regulates the coupling of DHPR with RyR1 [RYR1, DHPR, and STAC3 were identified in several human congenital myopathies, as summarized in STAC3 is a recently identified component of the ECC machinery. It is an adaptor protein that supports the trafficking of the ith RyR1 ,131,132.2+-binding protein (HRC) [Triadin is encoded by the TRDN gene that generates, via alternative splicing, four different isoforms named according to their molecular weight: the skeletal muscle isoforms are Trisk 95 and Trisk 51, both displaying a triadic localization; the main cardiac isoform Trisk 32  and Trisk 49, which does not localize at the j-SR in skeletal muscle fibers ,138. Triin (HRC) . Triadinin (HRC) . Triadinin (HRC) ,152. In 2+-cycling parameters in cardiac muscle [2+ release, suggesting that junctin may display a different role in cardiac and skeletal muscles [Junctin is structurally similar to triadin and, like triadin, can bind calsequestrin and the ryanodine receptor ,154,155.c muscle , but no c muscle . Similarc muscle , while i muscles .2+-binding properties. [2+ concentration [2+ concentration, front-to-front and back-to-back interactions take place. This finally results in the assembly of large ribbon-like structures, where negatively charged cavities may accommodate additional Ca2+ [2+ concentration and the presence of CASQ-binding proteins or post-translational modification [2+ depletion, it was shown that almost all CASQ is present in its depolymerized status. In this condition, progressive closure of the RyRs was reported, with a consequent reduction in Ca2+ release aimed to prevent dangerous levels of SR Ca2+ depletion. Accordingly, it has been proposed that CASQ1 depolymerization may represent the intracellular switch that induces RyR1 closing [In skeletal muscle, two isoforms of calsequestrin (CASQ) have been identified: CASQ1 and CASQ2. CASQ1 is expressed in fast- and slow-twitch skeletal muscle fibers, whereas CASQ2 is expressed in slow-twitch skeletal muscle fibers and in cardiac muscle . The twoperties. ,163. CASntration ,165. CASntration . Park annal Ca2+ . CASQ1 pfication ,170,171. closing .2+ release complex [2+ content and marked SR Ca2+ depletion during high-frequency stimulation [2+ entry that may compensate for the reduced total SR Ca2+ content [CASQ1 gene have been identified in patients affected by a rare vacuolar myopathy [In skeletal muscle, CASQs interact with RyR1, triadin, and junctin, forming a quaternary Ca complex ,173,174. complex ,180,181.mulation ,183. Recmulation ,185. Ind content ,187. Mutmyopathy  and in pmyopathy ,190.2+ and to interact with triadin [2+ levels, HRC has a pentameric structure, but when Ca2+-binding sites are saturated due to increased SR Ca2+ concentration, the protein shifts to a monomeric form [2+ homeostasis. Indeed, HRC may function as a negative regulator of RyRs and, in cardiac muscle, it was suggested to interact with SERCA pumps, acting as a negative regulator of Ca2+ re-uptake [HRC is far less abundant than CASQs, suggesting that it works as a secondary calcium-binding protein ,192. It  triadin ,194. Undric form . Althouge-uptake ,197.2+ re-uptake, although some ligand-gated Ca2+ channels, such as inositol 1,4,5-trisphosphate receptors (InsP3R), which release Ca2+ to regulate signaling pathways apart from myofibrils contraction, are also present here [2+ replenishing. SERCAs belong to the P-type ATPases family, a large superfamily of integral membrane proteins that pump ions and lipids across cellular membranes using the energy derived from ATP hydrolysis. The P-type ATPases family is composed of five subfamilies, defined as P1–P5. SERCAs belong to the P2A-ATPases subfamily and are specific for Ca2+ transport, while P4-ATPases act as phospholipid flippases to maintain lipid asymmetry in a variety of membranes [2+ ions for each hydrolyzed ATP. In vertebrates, SERCA pumps are encoded by three different genes, named ATP2A1-3. More than 10 protein variants are generated through alternative splicing occurring in the 3′-end of the main transcripts [The l-SR is mainly involved in Caent here . SERCA pembranes ,200. SERnscripts ,202.ATP2A1 encodes two major skeletal muscle proteins: SERCA1a and SERCA1b, highly expressed in fast-twitch skeletal muscle fibers. SERCA1b is expressed during neonatal stages and in regenerating muscles, while it is replaced by SERCA1a in adult skeletal muscles [ATP2A2 gene. SERCA 2a is expressed in cardiac muscle, slow-twitch skeletal muscle fibers, and smooth muscle cells. SERCA2b is reported to be ubiquitously expressed, and it represents the main SERCA isoform in the brain [ATP2A3 codes for six isoforms (SERCA3a–f), mostly identified in non-muscle cells, although SERCA3a, 3d, and 3f were also detected in cardiac muscle cells [2+ affinities have also been reported between SERCA2b and SERCA3 [2+ concentrations, the inhibitory effect of PLN is mitigated due to Ca2+/calmodulin kinase (CaMKII)- and/or Protein Kinase A (PKA)-dependent phosphorylation [2+, SLN uncouples ATP hydrolysis from Ca2+ transport [2+ binding protein, namely, Sarcalumenin (SAR) [2+ due to SERCA1 impairment directly contribute to muscle stiffness [ muscles ,204,205.he brain ,207,208.he brain  and cardhe brain . ATP2A3 le cells ,210. Thele cells ,212, andd SERCA3 ,214,215 d SERCA3 ,217,218.rylation ,220,221.ransport , thus prransport ,223. Thiin (SAR) , which cin (SAR) . Furtherin (SAR) ,227. Muttiffness ,229,230.2+ clearance following muscle contraction, a trans-sarcolemmal flux toward the extracellular environment also occurs in striated muscles. This is mediated by Plasma Membrane Calcium ATPases (PMCAs) and Na+/Ca2+ exchangers localized in the sarcolemma. Similar to SERCAs, PMCAs also belong to the P-type ATPase superfamily. They can transport one Ca2+ for each hydrolyzed ATP and are directly activated by interaction with Ca2+-calmodulin, which enhances PMCAs affinity for Ca2+ [+ ions and one Ca2+ ion across the sarcolemma in a high capacity and low Ca2+ affinity manner. Depending on the electrochemical gradient across the plasma membrane, NCX can either extrude intracellular Ca2+  or take up extracellular Ca2+ (a reverse mechanism) [2+ extrusion from the cytoplasm during diastole [Although SERCAs represent the key enzymes that contribute to sarcoplasmic Cafor Ca2+ . PMCAs afor Ca2+ . Among tfor Ca2+ ,234. NCXchanism) . In mammchanism) ,237, whidiastole ,239.2+ from the extracellular environment in response to a decrease in the endoplasmic reticulum Ca2+ content is a ubiquitous mechanism present in all cell types. The key elements of this pathway, named Store Operated Calcium Entry (SOCE), are STIM1 and Orai1 proteins [2+ content; when intracellular Ca2+ stores are full, it is in a Ca2+-bound monomeric conformation. Depletion of the intracellular Ca2+ store results in dissociation of Ca2+ from STIM1, which forms aggregates that relocate at ER–plasma membrane contact sites, where they interact with and activate the Orai1 channels on the plasma membrane, allowing Ca2+ entry from the extracellular environment and refill of intracellular stores. Ca2+ entry from the extracellular environment through the SOCE mechanism is also present in skeletal muscle [2+ to refill the SR Ca2+ stores, after intense, prolonged activity, has been shown to result in the assembly of additional intracellular junctions between the SR and the plasma membrane, providing additional space for STIM1 and Orai1 interaction. These newly identified sites, named Ca2+ Entry Units (CEU), support increased Ca2+ entry via Orai1, and their activity appears to contribute to improving fatigue resistance under continuous muscle activity [Entry of Caproteins . STIM1 il muscle . More reactivity ,243,244 activity ,248,249.activity ,190.2+ uniporter (MCU), a low-affinity Ca2+ transport protein , populated by several proteins and protein complexes that act as tethers between the SR and the outer mitochondrial membrane . In stri protein . It has ytoplasm . This hiniporter . From a nd FADH2 ,262, thund FADH2 . In cardmulation .2+ signaling [Alterations of SR/mitochondria interaction or of mitochondrial morphology and function in striated muscles are often observed in human muscle diseases or mouse models of muscle diseases characterized by alterations in Caignaling ,266,267.2+ handling. One may therefore ask what happened to the ER in striated muscle cells. In eukaryotic cells, the ER is dedicated to Ca2+ storage, protein synthesis and folding, and lipid and sterol synthesis. Although ER-related functions are clearly present in striated muscles, the distribution of the ER within the SR membranes is less evident. The recognized idea is that the SR and the ER represent a continuous membrane system made of different specialized subdomains [This review started with the statement that the SR is a specialized form of ER of muscle cells dedicated to Cabdomains . Compartbdomains ,269. Simbdomains . A less-bdomains .2+-signaling events. These junctions were identified based on the observation that nicotinic acid adenine dinucleotide phosphate (NAADP), a Ca2+-mobilizing second messenger, induced the release of Ca2+ from a lysosome-related Ca2+ store, and this was amplified by the generation of intracellular Ca2+ waves supported by RyR3 opening, following a CICR mechanism [2+ is released with a quantal pattern; upon reaching an activation threshold, RyR3 channels open, and calcium oscillations are generated. More recently, nanojunctions between lysosomes, SR, and mitochondria have been described at the ultrastructural level in rabbit ventricular myocytes. At difference with junctions observed in pulmonary arterial myocytes, in cardiac myocytes, lysosomes are distributed with a periodicity consistent with the length of a sarcomere, allowing the association with specific areas of the SR [2+ regulation, mainly following beta-adrenergic stimulation [In eukaryotic cells, the ER is engaged in a complex network of interactions with many intracellular components, such as the nuclear envelope (NE), the plasma membrane, mitochondria, the Golgi complex, peroxisomes, endosomes, lysosomes, and lipid droplets . All theechanism . Accordif the SR . The rolmulation .2+ signaling  with functions correlated with protein synthesis and the regulation of intra-nuclear Caignaling . The NE d the NE . EM analignaling . InsP3R, by RyRs ,279, while cells . In cardexpected .Drosophila melanogaster suggests that this interaction may be mediated by a three-partner connection where amphiphysin 2 on TT binds, at the same time, Ma2/d, a protein present on both TT and SR membranes, and, at the nuclear membrane, Msp30, a protein previously described to mediate connections between the NE and the Z disks [An additional issue is represented by the SR/nuclei juxtaposition within the overall skeletal muscle architecture. In skeletal muscle, nuclei are positioned at the fiber periphery between myofibrils and the sarcolemma, in proximity to T-tubules. The positioning of nuclei is regulated by different mechanisms, including the formation of a specific microtubule network, and is critical for muscle function; indeed, improper myonuclear localization is observed in muscle diseases, such as centronuclear myopathy and muscular dystrophies . The mol Z disks ,284,285.This review provides an updated view of the structural, molecular, and functional organization of the SR in skeletal muscle, highlighting some of the specialized domains whereby this organelle supports activation of muscle contraction. The historical knowledge that the terminal cisternae of the SR engage with the T-tubules in forming the triad, which represents the first identified membrane contact site, is now expanded by evidence that in skeletal muscle, the SR participates in the assembly of at least two more types of membrane-contact sites.2+ stores under conditions of prolonged activity. The second contact site, MAM, between the SR and mitochondria, has the functional role of synchronizing the mitochondrial energy production rate with the metabolic demand of muscle fibers. Altogether, these new findings are changing the traditional view of the SR as a static organelle by depicting an unexpected dynamic ability to extend its complex structure to support muscle function.In one case, the identification of CEUs, dynamic membrane contact sites consisting of stacks of SR cisternae and the extension of T tubules, structurally and functionally different from triads, provides evidence of how skeletal muscle fibers can sustain refilling of intracellular CaAt the same time, there are several points that remain to be clarified. A major open question relates to the precise positioning of triads at the boundary of the I and A bands of the sarcomere. This highly precise pattern, evident in EM micrographs for about a half-century, is waiting for the identification of the proteins that tether triads to the sarcomere with such a regularly repetitive precision. Concerning CEU, we need to identify the molecules that support the dynamic assembly and disassembly of CEU and how Orai1 and STIM1 are recruited at these sites. Mitochondria, like many other organelles, in skeletal muscle, are localized with a well-defined pattern with respect to triads and sarcolemma, a pattern that differs in slow- and fast-twitch fibers. Additionally, in this case, the molecules that anchor mitochondria to these domains of muscle fibers remain to be identified.2+ homeostasis, but more likely, additional functions necessary to keep skeletal muscle fibers healthy and fully functional.In conclusion, we can anticipate that the above list is, certainly, still missing additional SR domains that are yet to be identified; these might probably involve activities related to the regulation of Ca


TP53, KIT, KRAS, BRCA1, ATM, JAK2, NTRK3, FGFR3 and EGFR genes, referring to a CGP study conducted in Japan, and we considered the possibility of developing molecular-targeted therapies for AML with tumor-agnostic mutations. We summarized the frequency, the prognosis, the structure and the function of these mutations as well as the current treatment strategies in solid tumors, revealed the genetical relationships between solid tumors and AML and developed tumor-agnostic molecular-targeted therapies and lifetime management strategies in AML.Comprehensive genomic profiling examinations (CGPs) have recently been developed, and a variety of tumor-agnostic mutations have been detected, leading to the development of new molecular-targetable therapies across solid tumors. In addition, the elucidation of hereditary tumors, such as breast and ovarian cancer, has pioneered a new age marked by the development of new treatments and lifetime management strategies required for patients with potential or presented hereditary cancers. In acute myeloid leukemia (AML), however, few tumor-agnostic or hereditary mutations have been the focus of investigation, with associated molecular-targeted therapies remaining poorly developed. We focused on representative tumor-agnostic mutations such as the  NTRK (neurotrophic tyrosine receptor kinase 3 gene) fusions, which are rare but are detected in multiple tumor types including salivary gland, thyroid, colon, lung, gastrointestinal stroma, appendix, breast, pancreas, sarcoma, melanoma and cholangiocarcinoma with NTRK gene fusions, showing highly positive results with larotrectinib treatment [In the recent past, the available treatments for patients with acute myeloid leukemia (AML) produced a poor prognosis and consisted only of cytotoxic agents without indication for radical operations or radiotherapies. Recently, a variety of tumor-agnostic mutations have been found, and novel molecular-targeted therapies have been developed that have rapidly improving the prognosis of patients with solid tumors. For example, EGFR  inhibitors were developed about twenty years ago and approved in Japan as molecular-targeted therapies for non-small-cell lung cancer (NSCLC); since then, a variety of EGFR inhibitors have been developed worldwide . Moreovereatment ,9,10,11.reatment . Moreovereatment ,13. Howereatment . The curreatment . Comprehreatment . AML is reatment . Most ofTP53 (tumor suppressor protein p53 gene), KIT (tyrosine-protein kinase gene), KRAS , BRCA1 (breast cancer gene 1), ATM (ataxia telangiectasia gene), JAK2 (janus kinase 2 gene), NTRK3, FGFR3 (fibroblast growth factor receptor 3 gene) and EGFR ((HM)-SCREEN-Japan 01 is a multicenter genomic observational study ,19. Patiand EGFR . These rTP53 maintains the harmony between cell arrest and growth during genomic stress. Approved drugs for TP53 mutations actually do not exist even for solid tumors, although some important studies are ongoing.We also showed a schematic drawing of cell proliferation . JAK2, KTP53 is known as a guardian of genomes, and its mutations are associated with decreased survival in AML patients. TP53 mutations have been reported in 8% of all AML cases, 4.3% of de novo AML, 16.7% of secondary AML, 25–45% of post-myeloproliferative neoplasm AML (MPN-AML) and 70% of AML with complex karyotype AML [TP53 mutations have also been reported in 14% of patients with therapy-related myelodysplastic syndrome (MDS) and AML [TP53 mutations are more common in therapy-related MDS (t-MDS) and are associated with a high risk of progression to AML [TP53 gene mutations (25–36%), and biallelic mutations are a feature of a subset of AEL [type AML ,22,23,24n to AML . TP53-mun to AML ,28. Patit of AEL . TP53-mut of AEL ,31.TP53 gene is located on chromosome 17p13.1. The functional loss of p53 is common in aggressive advanced cancers. The TP53 gene is largely a stress response protein with functions ranging from apoptosis to cell cycle control. Therefore, a mutation in the TP53 gene amplifies the effects of oncogenes leading to the unregulated growth of tumor cells. These mutations are known to result in a gain of function (GOF), a loss of function (LOF) or a non-mutational dysfunction or inactivation of the p53 protein [TP53 gene mutation in one TP53 allele, which can eventually lead to the loss or partial inactivation of the other WT allele over time or during disease progression, owing to the loss of heterozygosity (LOH). LOH is considered a genetic mutation that further develops tumor progression in the context of somatic and germline mutations [TP53 mutations in leukemia occur in the context of somatic and germline mutations, the latter being associated with Li–Fraumeni syndrome, which leads to the development of certain solid tumors. However, sporadic TP53 mutations appear to occur upon exposure to carcinogens  or genotoxic insults. This observation further reveals the robust functionality of p53 in maintaining genomic stability and preventing tumorigenesis [Normal  p53 protein encoded by the  protein . p53 inautations . TP53 muigenesis ,34,35.TP53 mutations. In a prospective clinical trial of decitabine (10-day courses) to treat AML or transfusion-dependent MDS, patients with TP53 mutations achieved a significantly higher clinical response rate  than patients with wildtype TP53 . Furthermore, patients with TP53-mutated AML or MDS experienced similar overall survival (OS) to those with wildtype TP53  [TP53 mutation with poor outcomes [TP53 mutation in MDS may predict complete response (CR) to decitabine, but in this report, TP53 mutation was associated with a shorter OS, even among patients with CR  [TP53 mutation has been associated with lower CR and CR with incomplete marrow recovery (CRi) rates in AML patients treated with venetoclax monotherapy, venetoclax plus chemotherapy or venetoclax in combination with decitabine as compared to wildtype TP53 patients in these settings [TP53 mutations exhibited elevated PD-L1 expression relative to those with unmutated TP53 [There are no approved therapies to address  = 0.79) . In contoutcomes ,37,38. Asettings ,41. A nusettings . Of thessettings ,43. In tP53 41%, /78. FurtKIT mutations have been reported in more than 90% of cases of mast cytosis [KIT mutations in AML have been mixed [KIT mutations have a poorer prognosis than those without [ cytosis , 80–85%  cytosis , 10–20%  cytosis  and 4–17 cytosis , primari cytosis . Reportsen mixed ,50, but  without ,51,52.KIT mutations within the activation loop (A-loop), including the amino acids C809, D816, D820, N822, Y823 and A829, have been reported to confer preclinical and clinical resistance to imatinib and sunitinib in GIST [The KIT gene is located on human chromosome segment 4q11 and consists of 21 exons . The KIT in GIST ,58,59. K in GIST . In a ra in GIST . KIT exo in GIST .On the basis of clinical evidence, primarily in GIST, AML and systemic mastocytosis, KIT-activating alterations are associated with sensitivity to KIT tyrosine kinase inhibitors (TKIs) including imatinib, sunitinib, sorafenib, dasatinib, nilotinib, ponatinib, midostaurin and avapritinib ,64,65. IKRAS mutations have been reported in 4–25% of AML cases, in 2% of AML associated with MDS and at varied frequency (0–11%) in other subgroups of AML [KRAS mutations are associated with distinct cytogenetic sub-groups but are not independent prognostic indicators of AML patient outcome. Studies have reported that KRAS mutation had no influence on clinical outcome in pediatric patients with AML, in AML patients under 60 years old, in patients with secondary AML or in patients with AML harboring CBFB-MYH11 fusions [s of AML ,79,80. K fusions ,82.H-RAS, K-RAS and N-RAS. They cause the constitutive activation of RAS-proteins-transducing receptor signals for cellular processes such as proliferation, differentiation and apoptosis [GOF mutations in the KRAS pathway are the most common form of AML in adults, including activating mutations of the upstream receptor tyrosine kinases FLT3 and KIT [There are three functional RAS genes, poptosis ,83,84,85poptosis ,90,91,92 and KIT . Each of and KIT .KRAS mutation in certain tumor types [In a phase II trial, sotorasib led to a durable clinical benefit in patients with previously treated KRAS p.G12C-mutated NSCLC and was approved by the FDA . Sotorasor types ,84,98. Tor types  and is bor types ,101,102.BRCA1 mutations have been observed in <0.5% of acute myeloid leukemia (AML) cases  [BRCA1 mutations have also been implicated in the development of leukemia. A family history of breast or ovarian cancer is associated with an increased risk of leukemia in breast cancer patients, and BRCA1 mutations have been implicated in leukemogenesis [BRCA1 mutation carriers has been estimated to be as high as 87% [BRCA1 mutations in the general population is between 1:400 and 1:800, with an approximately 10-fold higher prevalence in the Ashkenazi Jewish population [ec 2018) . Reducedec 2018) . Rare caogenesis . Germlinogenesis ,106. Theh as 87% , and eleh as 87% . The estpulation ,110. In BRCA1 has an important role in maintaining genomic integrity, especially in rapidly dividing cells. In BRCA-deficient cells, the alternate, error prone, double strand DNA break–repair mechanisms predominate, leading to genomic instability . BRCA1 aBRCA1 mutations [BRCA1 mutations that appeared to be detected incidentally. They concluded that the BRCA1 variants found in this study did not play a major role in AML development. However, the accumulation of findings is needed to evaluate the relationships between BRCA1 mutation and AML development.BRCA1-deficient tumor cells are sensitive to inhibitors of poly (ADP-ribose) polymerase (PARP1) through the mechanism of synthetic lethality. Several PARP inhibitors have now received FDA approval for breast, ovarian and pancreatic cancers and mCRPC. Alterations that inactivate BRCA1 confer sensitivity to PARP inhibitors, such as olaparib, rucaparib or niraparib, and to DNA-damaging drugs, such as cisplatin or carboplatin ,117,118.utations ,117. A putations . HoweverPGVs) including BRCA1/2 [Fanconi anemia (FA), an inherited chromosomal instability disorder, is caused by at least 22 germline pathogenic gene mutations  cases, 1% of B-cell ALL (B-ALL) cases and <1% (1/416) of T-cell ALL (T-ALL) cases analyzed in the COSMIC database (Feb 2019). One study reported that a single nucleotide polymorphism in ATM (rs3092856) was associated with worse outcomes in AML [ATM mutations have been reported in 60% of children with T-ALL but were also found in 52% of controls; however, studies have isolated biologically significant alterations in the coding sequences of ATM that are suggested to lead to the development of T-ALL and predict unfavorable outcomes in pediatric patients [In the TCGA dataset, ML cases . In the s in AML . ATM mutpatients ,129.ATM encodes the protein ataxia telangiectasia mutated, which is a serine/threonine protein kinase that plays a key role in DNA damage response . Loss ofBRCA1, BRCA2 and ATM, have been reported in prostate cancer. The PARP enzyme complex is involved in the repair of DNA damage, and its inhibition causes the accumulation of DNA mutations in HRR-deficient cells. Several PARP inhibitors are under development, including talazoparib, niraparib, rucaparib and veliparib [Loss of functional ATM results in a defective DNA damage response, and homologous recombination-mediated DNA repair (HRR) predicts sensitivity to PARP inhibitors . Mutatioeliparib . For mCReliparib . In a pheliparib .JAK2) mutation was observed in fewer than 1% of samples, and amplification has not been reported [JAK2 mutation, specifically V617F, is prevalent in classic (BCR-ABL negative) myeloproliferative neoplasms (MPNs) and is reported in up to 95% of polycythemia vera, 50–60% of essential thrombocythemia and 40–50% of primary myelofibrosis cases [JAK2 V617F mutation did not impact overall survival in AML in a study [ASXL1, CBL, DNMT3A, MYD88, JAK2, TET2, SF3B1 and U2AF1, have been associated with clonal hematopoiesis of indeterminate potential (CHIP), which is age-related and associated with an increased risk of hematologic cancers [In the AML TCGA dataset, Janus kinase 2 , interfering with the basal inhibitory effect of the pseudokinase on the kinase domain, leading to constitutive JAK2 activation. JAK2 also activates the MAPK pathway, which is implicated in many cancers [JAK2 and the additional Janus kinase family members JAK1, JAK3 and TYK2 share a similar structure with seven Janus homology domains ,146, whi cancers  and cont cancers , which f cancers .JAK2 V617F mutation [On the basis of extensive clinical data on myelofibrosis, a disease type that frequently harbors the mutation ,152,153,mutation ,155. Pacmutation ,157,158;mutation . Other amutation ,164,165 mutation , may alsETS variant gene 6-neurotrophic tyrosine kinase receptor type 3 (ETV6-NTRK3) gene fusion was discovered by a breakpoint analysis of the t translocation associated with congenital fibrosarcoma, a pediatric soft tissue malignancy. ETV6-NTRK3 (EN) encodes the sterile alpha motif oligomerization domain of the ETV6 transcription factor linked to the protein tyrosine kinase domain of the neurotrophin-3 receptor NTRK3. The EN chimeric oncoprotein links to multiple signaling cascades, including RAS/MAPK and PI3K/AKT, through the IRS-1 adapter protein. Recent evidence indicates that a functional insulin-like growth factor 1 receptor axis and higher order polymer formation are essential for EN oncogenesis. EN rearrangements have been reported in case studies of patients with AML ,168. TheNTRK3, also known as TRKC, encodes the neurotrophin-3 (NT-3) growth factor receptor, a member of the neurotrophic tyrosine receptor kinase family, including TRKA, TRKB and TRKC; TRKs, which are activated by neurotrophins, play an important role in neuronal survival and differentiation and have also been shown to be involved in oncogenesis in both neurogenic and non-neurogenic cancers . TRK sigClinical and preclinical data indicate that NTRK fusions predict sensitivity to TRK inhibitors such as larotrectinib and entrectinib. Larotrectinib is a small-molecule kinase inhibitor that targets NTRK fusions that occur in multiple types of solid tumors. Its FDA approval represents the first instance of a treatment indication being designated as “tumor-agnostic” from the outset, based on actionable genomic insights. An analysis of combined data from several larotrectinib studies reported an ORR of 81% (88/109) in adult and pediatric patients with various solid tumors harboring NTRK fusions treated with larotrectinib; the responses were durable and CRs were observed in 17% of patients . A pooleFGFR3 mutation has been detected in fewer than 0.5% of AML samples analyzed in COSMIC (Oct 2019). However, published data investigating the prognostic implications of FGFR3 alterations in acute leukemia are limited.The fibroblast growth factor receptor (FGFR) family has emerged as being frequently altered in wide range of tumors, which is likely a result of the involvement of the FGFR pathway in signal transduction pathways regulating cell proliferation, differentiation, and migration, all of which are critical for tumorigenesis . FGFR2 aThe fibroblast growth factor (FGF) family comprises 23 highly regulated monomeric proteins that regulate a plethora of developmental and pathophysiological processes, including tissue repair, wound healing, angiogenesis and embryonic development . FGFR isFGFR3 mutation or amplification [Alterations that activate FGFR3 may predict sensitivity to FGFR inhibitors, including pan-FGFR inhibitors such as erdafitinib ,185 and fication ,192. Thefication .Epidermal growth factor receptor (EGFR) mutation was detected in <1% of AML samples analyzed in COSMIC (Aug 2020) . The pubEGFR/ERBB gene has been detected in a variety of human solid tumor cells, such as epithelial, mesenchymal, neuroectodermal and AML cells [EGFR belongs to a class of proteins called receptor tyrosine kinases. In response to signals from the environment, EGFR passes biochemical messages to the cell that stimulate it to grow and divide . The expML cells .EGFR-activating mutations may predict sensitivity to EGFR TKIs, including erlotinib , gefitinVarious factors and mechanisms have been revealed to influence cancer development, including gene signaling, genome instability, cancer immunity, growth suppression systems and angiogenesis. Moreover, a variety of drugs have been developed for solid tumors, for example, TKIs, PARP inhibitors, ICIs, cyclin-dependent kinase (CDK) inhibitors and vascular endothelial growth factor (VEGF) inhibitors. We listed the combinations of detectable genes and FDA-approved drugs in


Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a global pandemic since early 2020. Understanding the relationship between various systemic disease and COVID-19 through disease ontology (DO) analysis, an approach based on disease similarity studies, has found that COVID-19 is most strongly associated with atherosclerosis. The study provides new insights for the common pathogenesis of COVID-19 and atherosclerosis by looking for common transcriptional features. Two datasets (GSE152418 and GSE100927) were downloaded from GEO database to search for common differentially expressed genes (DEGs) and shared pathways. A total of 34 DEGs were identified. Among them, ten hub genes with high degrees of connectivity were picked out, namely C1QA, C1QB, C1QC, CD163, SIGLEC1, APOE, MS4A4A, VSIG4, CCR1 and STAB1. This study suggests the critical role played by Complement and coagulation cascades in COVID-19 and atherosclerosis. Our findings underscore the importance of C1q in the pathogenesis of COVID-19 and atherosclerosis. Activation of the complement system can lead to endothelial dysfunction. The DEGs identified in this study provide new biomarkers and potential therapeutic targets for the prevention of atherosclerosis. Coronavirus disease COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a global pandemic since early 2020. According to the WHO, until March 9, 2022, the number of confirmed cases worldwide was 448,313,293, including 6,011,482 deaths 9, caused. SARS-CoThe purpose of this study was to explore the pathophysiological association between SARS-CoV-2 and atherosclerosis, and to better understand the underlying mechanisms, so as to facilitate early detection and prevention of atherosclerosis. Two gene expression datasets (GSE152418 and GSE100927) were downloaded from Gene Expression Omnibus (GEO) database. We used bioinformatics and enrichment analysis to determine the common DEGs and their functions for COVID-19 and atherosclerosis. In addition, protein protein interaction (PPI) networks were established to reveal hub genes. These data can better understand the potential link between the two diseases and provide evidence for therapeutic targets.https://www.ncbi.nlm.nih.gov/geo) [Illumina NovaSeq 6000 (Homo sapiens)] platform was used for the GSE152418 dataset where samples were got from seventeen COVID-19 patients, and seventeen healthy people. On the contrary, for the GSE100927 dataset, GPL17077 [Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)] platform was adopted where samples were collected from sixty-nine atherosclerotic patients and thirty-five control subjects | more than or equal to 1 was set as a cut-off point for selecting DEGs. The “DOSE”  from the GSE152418 dataset and a adjusted e “DOSE” . packageP < 0.05 and |log2FC| more than or equal to 1.0, were considered as DEGs. Then the common genes of the GSE152418 and GSE100927 sets were identified by using the Venn diagram webtool (bioinformatics.psb.ugent.be/webtools/Venn/).The LIMMA package was used to detect the DEGs between atherosclerotic patients and healthy control from the GSE100927 dataset, and the adjusted P-value and |log2FC| were calculated. Genes that met the cutoff criteria, adjusted https://david.ncifcrf.gov/]. P-Value < 0.05 was used as the enrichment screening condition.To further analyze biological processes of common DEGs, GO annotation analysis and KEGG pathway enrichment analysis were carried out through the Database for Annotation, Visualization and Integrated Discovery [DAVID (2021 Update), http://string-db.org/) online database. The PPI pairs were extracted with a interaction score more than or equal to 0.15, and then the PPI network was visualized by Cytoscape software (www.cytoscape.org/). Here, we used Degree to evaluate and select hub genes.The PPI network was predicted using Search Tool for the Retrieval of Interacting Genes  is composed of six subunits, which form a molecule containing 18 polypeptide chains, while C1qA, C1qB, and C1qC genes encode three types of polypeptide chains, A, B, and C of the subunit of C1q, respectively . C1q is KEGG enrichment analysis is the best way to reflect the changes of pathways in organisms. Those results indicate that complement and coagulation cascades change most significantly in atherosclerosis and COVID-19. Macor et al. found positive lung C1q staining which suggests that the classical pathway is important for complement activation which may be triggered by IgG, antibodies widely distributed in patients' lungs . EndotheThe 10 hub genes selected by PPI were C1QA, C1QB, C1QC, CD163, SIGLEC1, APOE, MS4A4A, VSIG4, CCR1, and STAB1. The C1QA, C1QB, and C1QC genes had the highest degree in the PPI networks. Then v-set and immunoglobulin domain containing 4 (VSIG4) is the receptor of complement component 3 fragments C3b and iC3b, which activates macrophage immunity through C3b/iC3b binding . VSIG4 mStatins possess antiviral, immunomodulatory, antithrombotic, and anti-inflammatory properties, which may improve short- and long-term outcomes in COVID-19 patients.STAB1 encodes an unusual type of multifunctional scavenger receptor that causes increased lipid uptake and transient lipid depletion in virus-infected areas and is associated with poor prognosis for COVID-19 . STAB1 eThrough DO analysis, we also found several neurological disorders associated with COVID-19, such as focal epilepsy, temporal lobe epilepsy, migraine, epilepsy syndrome, neuroblastoma, and lateral sclerosis. There have been a large number of reported cases of these conditions, with a seizure prevalence ranging from 0 to 26% in COVID-19 patients , 40. MorIn conclusion, the study provides new insights for the common pathogenesis of COVID-19 and atherosclerosis by looking for common transcriptional features. The DEGs identified by bioinformatics data analysis, including C1QA, C1QB, C1QC, CD163, SIGLEC1, APOE, MS4A4A, VSIG4, CCR1, and STAB1, may be therapeutic targets for the atherosclerosis caused by COVID-19. However, more wet lab-based studies are required to validate the impact of COVID-19 severity on atherosclerosis. Studies on the long-term effects of SARS-CoV-2 infection, the effect of persistent endothelial dysfunction on atherosclerosis, and the role of preventive therapy are also needed.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.JZ performed the data analyses and wrote the manuscript. LZ helped perform the analysis with constructive discussions. Both authors approved the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Osteoporosis (OP) is commonly encountered, which is a kind of systemic injury of bone mass and microstructure, leading to brittle fractures. With the aging of the population, this disease will pose a more serious impact on medical, social, and economic aspects, especially postmenopausal osteoporosis (PMOP). This study is aimed at figuring out potential therapeutic targets and new biomarkers in OP via bioinformatics tools. After differentially expressed gene (DEG) analysis, we successfully identified 97 upregulated and 172 downregulated DEGs. They are mainly concentrated in actin binding, regulation of cytokine production, muscle cell promotion, chemokine signaling pathway, and cytokine-cytokine receiver interaction. According to the diagram of protein-protein interaction (PPI), we obtained 10 hub genes: CCL5, CXCL10, EGFR, HMOX1, IL12B, CCL7, TBX21, XCL1, PGR, and ITGA1. Expression analysis showed that Egfr, Hmox1, and Pgr were significantly upregulated in estrogen-treated osteoporotic patients, while Ccl5, Cxcl10, Il12b, Ccl7, Tbx21, Xcl1, and Itga1 were significantly downregulated. In addition, the analysis results of Pearson's correlation revealed that CCL7 has a strong positive association with IL12b, TBX21, and CCL5 and so was CCL5 with IL12b. Conversely, EGFR has a strong negative association with XCL1 and CXCL10. In conclusion, this study screened 10 hub genes related to OP based on the GEO database, laying a biological foundation for further research on new biomarkers and potential therapeutic targets in OP. Osteoporosis (OP) is a common systemic disease infiltrating bones, and it is age-related with bone microstructure destruction, bone mass reduction, and worsening bone fragility, as a result of the substantial increase in fracture occurrence risk . OP wereThe past decade sees a big increase in OP prevalence in China, and more than 1/3 of people over 50 years have been affected . OP inciOP is a highly insidious disease. Due to the lack of overt symptoms and sensitive biomarkers, many patients are only diagnosed after a fracture has occurred. Studies have now shown the presence of biomarkers in the OP, such as some potential biomarkers of OP that have been found in metabolomics studies. These metabolites are mainly concentrated in fats and amino acids . StudiesIn addition, the first-line drugs for the treatment of OP link to multiple complications produce an unsatisfactory effect on the overall management of this disease. With the development of several pharmaceutical technologies, novel medications, calcitonin, bisphosphonates, denosumab, and teriparatide, have been widely introduced for the prevention and treatment of OP by targeting osteoblast bone formation and resorption activity , 12. Unfhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163849). It is used to screen DEGs in OP. Eight specimens  were included.Gene expression profile data GSE163849 was screened and downloaded from the GEO database using the following link  was employed to determine the threshold of the P values. Q value represented the corrected P values. Subsequently, we calculated differential expression multiple according to FPKM values, that is, fold change. The screening index of this analysis is P value <0.05, log2FC > 1, or < -1.Gene differential expression analysis uses P value <0.05 is considered the critical standard.DEGs with statistical significance was analyzed subsequently via the R3.6.1 software with “biological conductor” and “goplot” software packages, Gene Ontology (GO) functions, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways which were enriched as well , 15. Thehttp://string.embl.de/) was used to construct the (protein-protein interaction) PPI network of the identified DEG and to present this network using Cytoscape visualization software version 3.6.1. The protein-protein interaction (PPI) network utilized to construct identified DEGs was presented using Cytoscape visualization software version 3.6.1. Then, modules with the most significance in the PPI diagram are determined by the molecular recombination detection tool (MCODE). The standard was set as score >2, cut-off degree = 2, and cut-off degree of node score = 0.2.The search tool for retrieving interacting genes (STRING) . Of the 11 methods, MCC had better performance in terms of accuracy in predicting essential proteins from PPI networks.R software 3.6.1 was used for DEG analysis. There were 269 DEGs identified with 97 genes upregulated and 172 downregulated . GSE163849 was selected, and the “limma” package in I band, and Z disc. The first three significantly enriched are actin-binding, serine-type endopeptidase activity, and growth factor binding during MF analysis. In biological process (BP), DEGs significantly enriched regulation of smooth muscle cell promotion, response to a toxic substance, and negative regulation of cytokine production , biological process (BP), and molecular function (MF) Figures  and 3. Coduction . The chooduction . In addioduction .There were 49 nodes (DEGs) in the PPI diagram. Ten key genes CCL5, CXCL10, EGFR, HMOX1, IL12B, CCL7, TBX21, XCL1, PGR, and ITGA1 were identified . Two impThe 10 hubs are presented using a plug-in “CytoHubba” of Cytoscape version 3.7.1 according to the degree . CompareBones with OP are fragile and tend to break easily. It is common in the elderly, especially in postmenopausal women . PrimaryAt present, bisphosphonates are introduced as the first-line drugs against OP, targeting OP management due to elevated levels of bone resorption . Howeverα can trigger the differentiation of osteoclast precursors into mature osteoclasts secreted by LPS/TLR4 signaling [α signal transduction in B cells is essential for controlling osteoclast production [Cytokine (CK) acts as molecular polypeptides or glycoproteins, mediating intercellular interactions. It is known to have participated in cell growth, maturation, differentiation, tumor growth, and decline . Among mignaling . CX3CL1 ignaling , 27. HIFoduction .It was found that p53 may play a central role in the development of OP . RBBP4 aκB and locates on mouse chromosome 11 [CCL5 is recognized as a downstream gene of NF-osome 11 . This chosome 11 . CXCL10 osome 11 . PRMT5 iosome 11 . As a meosome 11 . Transgeosome 11 . The EGFosome 11 .γ, and participate in cell-mediated immune responses [Withdrawal estrogen increased CCR2, CCL7, and CCL2 expression but reduced PMOP in mice after inhibition of CCL7 and CCL2 synthesis by administration of band . Hmox1 (esponses . Studiesesponses . The stuThis study has some limitations. Firstly, the microarray dataset sample size was not large enough. Secondly, despite several enriched pathways and key DEGs being identified, they have not been verified in vivo and in vitro experiments. Therefore, potential OP-related biomarkers remain to be further determined using a larger sample size.In conclusion, this study identified 10 genes significantly associated with OP, providing an essential foundation for investigating the molecular mechanism of OP biomarkers and therapeutic target selection. However, biological studies with larger sample sizes and validation are lacking; so, further experiments are needed to verify the diagnostic ability of these genes for OP before clinical application.