Bioimpacts最新文献

{"title":"Assessment of the biocompatibility and biodistribution of fluorescent oleic acid capped ZnSe/CdS/ core shell quantum dots after intravenous injection in Balb/c mice.","authors":"Aakriti Tyagi, Disha Mittal, S Bhanoth, Ankita Leekha, Anita K Verma","doi":"10.34172/bi.30467","DOIUrl":"https://doi.org/10.34172/bi.30467","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>Quantum dots (QDs) are semiconductor nanocrystals with inherent fluorescence having several advantages over traditional fluorescent probes including their small size (5-10 nm), tunable excitation and emission spectra, ease of surface functionalization, and robust photostability that makes them ideal candidates for <i>in vivo</i> imaging. The behavior of QDs is highly dependent on the surface functionality. <i>In vivo</i> toxicity of QDs in biological systems is the major limitation hindering their translation to clinics.</p><p><strong>Methods: </strong>In the present study, cytotoxicity of water soluble ZnSe/CdS core shell QDs capped with oleic acid was evaluated against human hepatocellular carcinoma cell line-Hep3B, Human Embryonic Kidney cell line-HEK 293 and Ehlrich Ascitic cells-EAC. To assess its <i>in vivo</i> therapeutic efficacy, the initial animal toxicity studies of OA capped ZnSe/ CdS QDs were done in Balb/c mice. Serum stability, pharmacokinetics, biodistribution and γ-scintigraphic imaging were observed in mice after intravenous (<i>i.v</i>) injection of QDs at a dose of 10 nM/kg/200 µL/mice up to 28 days.</p><p><strong>Results: </strong>IC₅₀ of OA capped QDs against Hep3B was 29.85 µg/mL at 24 hours. QDs toxicity was primarily due to the generation of reactive oxygen species as observed by LDH release in Hep3B cells. Negligible haemolysis indicated that OA capped QDs were biocompatible. OA capped QDs mainly accumulated in the liver and spleen with no retention in kidneys.</p><p><strong>Conclusion: </strong>OA capped ZnSe/ CdS QDs exhibited enhanced anti-cancer efficacy against Hep3B and EAC cell line. Further, minimum accumulation and retention were observed in vital organs in Balb/c mice protecting them from potential adverse side effects, underlining their potential for biomedical applications.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30467"},"PeriodicalIF":2.2,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overview of dendritic cells subsets and their involvement in immune-related pathological disease.","authors":"Mohsen Abbaszadeh, Bahar Naseri, Mohammad Taghizadeh-Teymorloei, Amirhossein Mardi, Mohammad Reza Javan, Javad Masoumi, Farid Ghorbaninezhad, Amirhossein Hatami-Sadr, Şengül Tural, Behzad Baradaran, Mohammad Reza Sadeghi","doi":"10.34172/bi.30671","DOIUrl":"https://doi.org/10.34172/bi.30671","url":null,"abstract":"<p><p>Dendritic cells (DCs) are specialized antigen-presenting cells (APCs) in linking innate and adaptive immune responses. In addition to presenting antigens to T cells, DCs must also provide co-stimulatory signals along with cytokines for T cells to induce an appropriate cellular immune response. Tolerance is also established and maintained by DCs under homeostatic circumstances. There is remarkable phenotypic heterogeneity in DCs, each with different functional flexibility and specific expression of various markers. The three primary categories of DCs comprise conventional DCs (cDCs), plasmacytoid DCs (pDCs), and monocyte-derived DCs (moDCs). Langerhans cells (LCs) are another type of DCs, which are found in the skin's epidermal layer. DCs may be positioned or triggered inappropriately as a result of dysregulation of DC. This phenomenon can cause an imbalance in immune responses and even immune-related pathological disorders, i.e., autoimmune diseases and malignancies. Herein, by reviewing the ontogeny, biology, characteristics, and function of DCs subsets in immune system, we discuss the contribution of these cells in the mentioned immune-related disorders.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30671"},"PeriodicalIF":2.2,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of specific lncRNAs, miRNAs, and mRNAs in different groups of prostate cancer.","authors":"Gelareh Vahabzadeh, Amirreza Pashapour-Yeganeh, Maryam Eini, Morad Roudbaraki, Ebrahim Esmati, Amirhoushang Poorkhani, Solmaz Khalighfard, Ali Mohammad Alizadeh","doi":"10.34172/bi.30510","DOIUrl":"https://doi.org/10.34172/bi.30510","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>LncRNAs interact with miRNAs and mRNAs that can have a special expression pattern in a specific cell type. We investigated the specific lncRNAs, miRNAs, and mRNAs in different groups of prostate cancer (PC).</p><p><strong>Methods: </strong>The mRNAs with significant expression differences were first analyzed using the GEO and TCGA databases. The lncRNAs and miRNAs were then identified in the miRWalk2, miRmap, OncomiR, miRGator 3.0, miRCancerDB, LncRNA2target, TANRIC, LncRNADisease, Lnc2Cancer v3.0, and LncBase. Seventy subjects, including sixty PC patients classified as local, locally advanced, biochemical relapse, metastatic, and benign groups, as well as ten normal individuals, were then included. Finally, real-time PCR determined the expression of the candidate biomarkers.</p><p><strong>Results: </strong>The bioinformatics analysis detected candidate 6 miRNAs, 6 lncRNAs, and 6 mRNAs in different groups of PC patients. Unlike the significant decrease in candidate tumor suppressors, the expression levels of specific onco-lncRNA, onco-miRNA, and oncogenes exhibited a substantial increase in different groups of the patients compared to the normal group. The expression of lncRNAs, including LINC01128 (<i>P</i>=0.0182), LINC02246 (<i>P</i><0.0001), and LINC02288 (<i>P</i><0.0001), LINC00857 (<i>P</i><0.0001), GNAS-AS1 (<i>P</i><0.0001), and LINC02371 (<i>P</i><0.0001), the expression of miRNAs, including miR-217 (<i>P</i><0.0001), miR-375 (<i>P</i><0.0001), miR-203a (<i>P</i><0.0001), miR-876 (<i>P</i>=0.0046), miR-27b (<i>P</i><0.0001), and miR-152 (<i>P</i><0.0001), and the expression of oncogenes, including ST14 (<i>P</i><0.0001), CD24 (<i>P</i><0.0001), CDH1 (<i>P</i><0.0001), DSC2 (<i>P</i><0.0001), TGFB3 (<i>P</i><0.0001), and MYL2 (<i>P</i>=0.0186) had significant changes at different groups of PC patients.</p><p><strong>Conclusion: </strong>Our results identified promising biomarkers that play a role in specific groups of prostate cancer patients. Detecting specific biomarkers may be an effective strategy for different groups of PC patients.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30510"},"PeriodicalIF":2.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mesenchymal stem cells as a therapeutic strategy to combat oxidative stress-mediated neuropathic pain.","authors":"Aidin Shahrezaei, Maryam Sohani, Farinaz Nasirinezhad","doi":"10.34172/bi.30648","DOIUrl":"https://doi.org/10.34172/bi.30648","url":null,"abstract":"<p><p>Neuropathic pain, a chronic condition resulting from somatosensory system damage, remains a significant clinical challenge due to its complex pathophysiology and inadequate response to traditional therapies. Oxidative stress, characterized by an imbalance between free radicals production and antioxidant defenses, plays a pivotal role in the development and maintenance of neuropathic pain. Mesenchymal stem cells (MSCs) are multipotent stromal cells with the ability to differentiate into various cell types and possess immunomodulatory, anti-inflammatory, and regenerative properties, making them promising candidates for novel pain management strategies. Preclinical studies demonstrate that MSCs can reduce inflammation, scavenge reactive oxygen species (ROS), promote nerve regeneration, and modulate pain signaling pathways. Various administration routes, including intravenous and intrathecal, have been investigated to optimize MSC delivery and efficacy. Additionally, MSC-derived extracellular vesicles (EVs) represent a cell-free alternative with substantial therapeutic potential. Despite encouraging preclinical findings, further research is needed to refine MSC-based therapies, including the exploration of combination treatments and rigorous clinical trials, to translate these promising results into effective clinical applications for neuropathic pain relief. This review explores the therapeutic potential of MSCs in alleviating oxidative stress-mediated neuropathic pain.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30648"},"PeriodicalIF":2.2,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting drug protein interactions based on improved support vector data description in unbalanced data.","authors":"Alireza Khorramfard, Jamshid Pirgazi, Ali Ghanbari Sorkhi","doi":"10.34172/bi.30468","DOIUrl":"https://doi.org/10.34172/bi.30468","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>Predicting drug-protein interactions is critical in drug discovery, but traditional laboratory methods are expensive and time-consuming. Computational approaches, especially those leveraging machine learning, are increasingly popular. This paper introduces VASVDD, a multi-step method to predict drug-protein interactions. First, it extracts features from amino acid sequences in proteins and drug structures. To address the challenge of unbalanced datasets, a Support Vector Data Description (SVDD) approach is employed, outperforming standard techniques like SMOTE and ENN in balancing data. Subsequently, dimensionality reduction using a Variational Autoencoder (VAE) reduces features from 1074 to 32, improving computational efficiency and predictive performance.</p><p><strong>Methods: </strong>The proposed method was evaluated on four datasets related to enzymes, G-protein-coupled receptors, ion channels, and nuclear receptors. Without preprocessing, the Gradient Boosting Classifier showed bias towards the majority class. However, balancing and dimensionality reduction significantly improved accuracy, sensitivity, specificity, and F1 scores. VASVDD demonstrated superior performance compared to other dimensionality reduction methods, such as kernel principal component analysis (kernel PCA) and Principal Component Analysis (PCA), and was validated across multiple classifiers, achieving higher AUROC values than existing techniques.</p><p><strong>Results: </strong>The results highlight VASVDD's effectiveness and generalizability in predicting drug-target interactions. The method outperforms state-of-the-art techniques in terms of accuracy, robustness, and efficiency, making it a promising tool in bioinformatics for drug discovery.</p><p><strong>Conclusion: </strong>The datasets analyzed during the current study are not publicly available but are available from the corresponding author upon reasonable request and source code are available on GitHub: https://github.com/alirezakhorramfard/vasvdd.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30468"},"PeriodicalIF":2.2,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thalidomide augments maturation and T helper 1-inducing capacity of monocyte-derived dendritic cells in vitro.","authors":"Mohsen Abbaszadeh, Bahar Naseri, Javad Masoumi, Elham Baghbani, Behzad Baradaran, Mohammad Reza Sadeghi","doi":"10.34172/bi.30588","DOIUrl":"https://doi.org/10.34172/bi.30588","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>Dendritic cells (DCs) possess specialized abilities to present antigens and stimulate T cells, making them essential in triggering adaptive immune responses. Thalidomide and its derivatives are classified as a group of medications that possess immunomodulatory properties. Numerous studies have demonstrated the contentious impact of these drugs on DCs. Therefore, the objective of the present study was to assess the influence of Thalidomide therapy on the maturation and stimulation of monocyte-derived DCs, and subsequently examine the consequences of these treated DCs on the immune responses of autologous T cells.</p><p><strong>Methods: </strong>The immature DCs derived from monocytes were subjected to exposure to Thalidomide and Lipopolysaccharides (LPS) on the fifth day of differentiation, followed by a 24-hour incubation period. On the sixth day, the phenotypic features of the DCs in both the control and treatment groups were assessed using flow cytometry. Subsequently, the gene expression in both the DCs and autologous T cells co-cultured with the DCs was evaluated using the real-time PCR method.</p><p><strong>Results: </strong>Thalidomide-treated DCs exhibited a significant augmentation in the expression of maturation and stimulatory surface markers CD11c, HLA-DR, and CD86 (<i>P</i> ≤ 0.01), as well as gene expression of TNF-α and IL-12 (<i>P</i> ≤ 0.01) when compared to the control group. Furthermore, co-culture of Thalidomide-treated DCs with T cells increased T-bet and IFN-γ (<i>P</i> ≤ 0.01) expression, while diminished FOXP3 and TGF-β (<i>P</i> ≤ 0.01) expression compared to T cells co-cultured with untreated DCs.</p><p><strong>Conclusion: </strong>Our findings indicate that in vitro Thalidomide treatment shifts DCs towards an immunogenic state and elevates their T helper 1 inducing capacity, which may be efficient in immunotherapy of various cancers.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30588"},"PeriodicalIF":2.2,"publicationDate":"2024-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anti-Alzheimer effects of the newly synthesized cationic compounds as multi-target dual hAChE/hBuChE inhibitor: An <i>in silico</i>, <i>in vitro</i>, and <i>in vivo</i> approach.","authors":"Hosna Karami, Somaieh Soltani, Gerhard Wolber, Saeed Sadigh-Eteghad, Roghaye Nikbakht, Hanieh Farrokhi, Farzaneh Narimani, Reza Teimuri-Mofrad, Mohammad-Reza Rashidi","doi":"10.34172/bi.24196","DOIUrl":"10.34172/bi.24196","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>Multi-target anti-Alzheimer's disease (AD) compounds are promising leads for the development of AD modifying agents. Ionic compounds containing quaternary ammonium moiety were synthesized, and their multi-targeted anti-AD effects were examined.</p><p><strong>Methods: </strong>Imidazole derivatives containing a quaternary ammonium moiety were synthesized and evaluated for their potential anti-Alzheimer properties using computational (<i>in silico</i>), cellular (<i>in vitro</i>), and animal (<i>in vivo</i>) models. The inhibition kinetics of both human acetylcholinesterase (hAChE) and butyrylcholinesterase (hBuChE) were assessed. Neuroprotective effects in amyloid-beta (Aβ)-exposed PC12 cells were also examined. Furthermore, the compounds' impact on Aβ-induced memory impairment in Wistar rats was evaluated, with a detailed analysis of the underlying mechanisms.</p><p><strong>Results: </strong>Compound 5g demonstrated acceptable cytotoxicity against human cells. This compound exhibited non-competitive dual inhibition of both hAChE and hBuChE. Additionally, compound 5g mitigated the morphological changes induced by amyloid-beta (Aβ) in PC12 cells and decreased cell mortality. It exhibited anti-oxidative stress properties, evident by reduction in reactive oxygen species (ROS) production, and inhibition of lipid peroxidation. The compound also down regulated the expression of pro-inflammatory genes IL-1β and TNF-α. In vitro studies validated compound 5g's ability to inhibit lactate dehydrogenase (LDH), attenuate neuroinflammation, and prevent the autophagy-apoptosis cascade. When administered to rats with Aβ-induced memory dysfunction, compound 5g enhanced cognitive function and improved spatial memory. In the hippocampi of treated rats, there was a noted downregulation of TNF-α and NF-kB. Furthermore, compound 5g counteracted the elevated activity of AChE. Molecular modeling validated the binding of compound 5g to both steric and catalytic sites of cholinesterase enzymes.</p><p><strong>Conclusion: </strong>The novel quaternary ammonium derivative, compound 5g, demonstrated multi-target anti-AD properties, as evidenced by <i>in silico, in vitro</i> and <i>in vivo</i> studies. Behavioral assessments and molecular analyses further confirmed its therapeutic efficacy in amyloid-beta (Aβ)-challenged rats.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"24196"},"PeriodicalIF":2.2,"publicationDate":"2024-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of tumor microenvironment and self-organization in cancer progression: Key insights for therapeutic development.","authors":"Milad Asadi, Venus Zafari, Sanam Sadeghi-Mohammadi, Dariush Shanehbandi, Ufuk Mert, Zahra Soleimani, Ayşe Caner, Habib Zarredar","doi":"10.34172/bi.30713","DOIUrl":"https://doi.org/10.34172/bi.30713","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>The tumor microenvironment (TME) plays a pivotal role in cancer progression, influencing tumor initiation, growth, invasion, metastasis, and response to therapies. This study explores the dynamic interactions within the TME, particularly focusing on self-organization-a process by which tumor cells and their microenvironment reciprocally shape one another, leading to cancer progression and resistance. Understanding these interactions can reveal new prognostic markers and therapeutic targets within the TME, such as extracellular matrix (ECM) components, immune cells, and cytokine signaling pathways.</p><p><strong>Methods: </strong>A comprehensive search method was employed to investigate the current academic literature on TME, particularly focusing on self-organization in the context of cancer progression and resistance across the PubMed, Google Scholar, and Science Direct databases.</p><p><strong>Results: </strong>Recent studies suggest that therapies that disrupt TME self-organization could improve patient outcomes by defeating drug resistance and increasing the effectiveness of conventional therapy. Additionally, this research highlights the essential of understanding the biophysical properties of the TME, like cytoskeletal alterations, in the development of more effective malignancy therapy.</p><p><strong>Conclusion: </strong>This review indicated that targeting the ECM and immune cells within the TME can improve therapy effectiveness. Also, by focusing on TME self-organization, we can recognize new therapeutic plans to defeat drug resistance.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30713"},"PeriodicalIF":2.2,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008505/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cancer diagnosis transformer model based on medical IoT data for clinical measurements in predictive care systems.","authors":"Panpan Li, Yan Lv, Haiyan Shang","doi":"10.34172/bi.30640","DOIUrl":"https://doi.org/10.34172/bi.30640","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>In recent years, advancements in information and communication technology (ICT) and the internet of things (IoT) have revolutionized the healthcare industry, enabling the collection, analysis, and utilization of medical data to improved patient care. One critical area of focus is the development of predictive care systems for early diagnosis and treatment of cancer and disease.</p><p><strong>Methods: </strong>Leveraging medical IoT data, this study proposes a novel approach based on transformer model for disease diagnosis. In this paper, features are first extracted from IoT images using a transformer network. The network utilizes a convolutional neural network (CNN) in the encoder part to extract suitable features and employs decoder layers along with attention mechanisms in the decoder part. In the next step, considering that the extracted features have high dimensions and many of these features are irrelevant and redundant, relevant features are selected using the Harris hawk optimization algorithm.</p><p><strong>Results: </strong>Various classifiers are used to label the input data. The proposed method is evaluated using a dataset consisting of 5 classes for testing and evaluation, and all results are provided into tables and plots.</p><p><strong>Conclusion: </strong>The experimental results demonstrate that the proposed method acceptable performance compared to other methods.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30640"},"PeriodicalIF":2.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The diagnostic and prognostic value of <i>C1orf174</i> in colorectal cancer.","authors":"Elham Nazari, Ghazaleh Khalili-Tanha, Ghazaleh Pourali, Fatemeh Khojasteh-Leylakoohi, Hanieh Azari, Mohammad Dashtiahangar, Hamid Fiuji, Zahra Yousefli, Alireza Asadnia, Mina Maftooh, Hamed Akbarzade, Mohammadreza Nassiri, Seyed Mahdi Hassanian, Gordon A Ferns, Godefridus J Peters, Elisa Giovannetti, Jyotsna Batra, Majid Khazaei, Amir Avan","doi":"10.34172/bi.30566","DOIUrl":"https://doi.org/10.34172/bi.30566","url":null,"abstract":"<p><p></p><p><strong>Introduction: </strong>Colorectal cancer (CRC) is among the lethal cancers, indicating the need for the identification of novel biomarkers for the detection of patients in earlier stages. RNA and microRNA sequencing were analyzed using bioinformatics and machine learning algorithms to identify differentially expressed genes (DEGs), followed by validation in CRC patients.</p><p><strong>Methods: </strong>The genome-wide RNA sequencing of 631 samples, comprising 398 patients and 233 normal cases was extracted from the Cancer Genome Atlas (TCGA). The DEGs were identified using DESeq package in R. Survival analysis was evaluated using Kaplan-Meier analysis to identify prognostic biomarkers. Predictive biomarkers were determined by machine learning algorithms such as Deep learning, Decision Tree, and Support Vector Machine. The biological pathways, protein-protein interaction (PPI), the co-expression of DEGs, and the correlation between DEGs and clinical data were evaluated. Additionally, the diagnostic markers were assessed with a combioROC package. Finally, the candidate tope score gene was validated by Real-time PCR in CRC patients.</p><p><strong>Results: </strong>The survival analysis revealed five novel prognostic genes, including <i>KCNK13</i>, <i>C1orf174</i>, <i>CLEC18A</i>, <i>SRRM5</i>, and <i>GPR89A</i>. Thirty-nine upregulated, 40 downregulated genes, and 20 miRNAs were detected by SVM with high accuracy and AUC. The upregulation of <i>KRT20</i> and <i>FAM118A</i> genes and the downregulation of <i>LRAT</i> and <i>PROZ</i> genes had the highest coefficient in the advanced stage. Furthermore, our findings showed that three miRNAs (<i>mir-19b-1, mir-326</i>, and <i>mir-330</i>) upregulated in the advanced stage. <i>C1orf174</i>, as a novel gene, was validated using RT-PCR in CRC patients. The combineROC curve analysis indicated that the combination of <i>C1orf174-AKAP4-DIRC1-SKIL-Scan29A4</i> can be considered as diagnostic markers with sensitivity, specificity, and AUC values of 0.90, 0.94, and 0.92, respectively.</p><p><strong>Conclusion: </strong>Machine learning algorithms can be used to Identify key dysregulated genes/miRNAs involved in the pathogenesis of diseases, leading to the detection of patients in earlier stages. Our data also demonstrated the prognostic value of <i>C1orf174</i> in colorectal cancer.</p>","PeriodicalId":48614,"journal":{"name":"Bioimpacts","volume":"15 ","pages":"30566"},"PeriodicalIF":2.2,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}