Computational Biology and Chemistry最新文献

{"title":"Screening and computational characterization of novel antimicrobial cathelicidins from amphibian transcriptomic data","authors":"H. Varela-Rodríguez,&nbsp;A. Guzman-Pando,&nbsp;J. Camarillo-Cisneros","doi":"10.1016/j.compbiolchem.2024.108276","DOIUrl":"10.1016/j.compbiolchem.2024.108276","url":null,"abstract":"<div><div>As cold-blooded organisms living in damp and dark environments, amphibians have evolved robust defense mechanisms to protect themselves from predators and infections. Among the wide repertoire of bioactive compounds they produce are antimicrobial peptides (AMPs), which are required as part of innate immunity. One important class of AMPs is cathelicidins, known for their broad-spectrum activity against pathogens and their immunoregulatory roles. However, despite their promising biomedical potential and the increasing availability of omics data, few cathelicidins have been studied in amphibians, mostly through conventional experimental techniques. Here, we present 210 novel cathelicidin sequences from amphibian transcriptomes, identified through a comprehensive computational pipeline, which employed HMMER and BLAST tools to screen cathelicidin domains. These sequences reveal a typical tripartite domain architecture that was confirmed by SignalP and InterProScan analysis. Phylogenetic inference with IQ-TREE classified the sequences into six categories based on evolutionary relationships. Compared to cathelicidins from other vertebrates, amphibian mature peptides exhibit longer average lengths (around 50 amino acids), fewer aromatic and hydrophobic residues, and reduced thermal stability. Furthermore, these amphibian cathelicidins were characterized for their physicochemical and biological properties, revealing significant antimicrobial potential with lower hemolytic capability, especially in anurans, which suggests a balance between their antimicrobial and hemolytic activities predicted through AMPlify, ampir, AmpGram, and HemoPI. Secondary structure estimations, including three-dimensional modeling using AlphaFold2, indicate that amphibian cathelicidins predominantly feature <span><math><mi>α</mi></math></span>-helices and coils. Some representative models also display a high <span><math><mi>α</mi></math></span>-helix composition with amphipathic topology, facilitating interactions with simulated bacterial membranes as assessed by the PPM approach. Thus, these findings highlight the functional role of cathelicidins in amphibian immunity and their promising biomedical applicability, emphasizing the importance of applying computational methods to expand the scope and reveal the diverse landscape of cathelicidins across vertebrates.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108276"},"PeriodicalIF":2.6,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pharmacophore-guided in-silico discovery of SIRT1 inhibitors for targeted cancer therapy","authors":"Deepak Sharma,&nbsp;Rajiniraja Muniyan","doi":"10.1016/j.compbiolchem.2024.108275","DOIUrl":"10.1016/j.compbiolchem.2024.108275","url":null,"abstract":"<div><div>Epigenetic modifier, Sirtuin (SIRTs) is a family of seven isoforms (SIRT1‐7) and nicotinamide adenine dinucleotide (NAD+) dependent class III histone deacetylase (HDACs) protein. SIRT1 in association with the p53 protein can regulate crucial cell processes such as glucose metabolism, lipid metabolism, mitochondrial biogenesis, DNA repair, oxidative stress, apoptosis, and inflammation through the process of deacetylation. When SIRT1 deacetylates p53, it loses its tumor suppression property. To promote apoptosis and decrease cell proliferation by inhibiting SIRT1 protein and ultimately raising the acetylation of p53 to regain its tumor suppressor function. Though we have many SIRT1 protein inhibitors, they exhibited off-target effects and inefficiency at the clinical trial stage. This study has been executed to identify more potentially effective and reliable SIRT1 inhibitors that can perform better than the existing options. To do so, pharmacophore-based screening of compound libraries followed by virtual screening, pharmacokinetic, drug-likeness, and toxicity studies were conducted which gave 42 compounds to evaluate further. Subsequently, exhaustive molecular docking and molecular dynamics simulation predicted four potential hits to inhibit the SIRT1 protein better than the reference compound. Further studies such as principal components analysis, free energy landscape, and estimation of binding free energy were done which concluded Hit4 (PubChem ID: 55753455) to be a novel and potent SIRT1 small molecule inhibitor among the others. The total binding free energy for Hit4 was found to be −44.68 kcal/mol much better than the reference complex i.e., −29.38 kcal/mol.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108275"},"PeriodicalIF":2.6,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-layer neural network approach for the stability analysis of the Hepatitis B model","authors":"Muhammad Farhan ,&nbsp;Zhi Ling ,&nbsp;Zahir Shah ,&nbsp;Saeed Islam ,&nbsp;Mansoor H. Alshehri ,&nbsp;Elisabeta Antonescu","doi":"10.1016/j.compbiolchem.2024.108256","DOIUrl":"10.1016/j.compbiolchem.2024.108256","url":null,"abstract":"<div><div>In the present study, we explore the dynamics of Hepatitis B virus infection, a significant global health issue, through a newly developed dynamics system. This model is distinguished by its inclusion of asymptomatic carriers and the impact of vaccination and treatment strategies. Compared to Hepatitis A, Hepatitis B poses a more serious health risk, with some cases progressing from acute to chronic. To diagnose and predict disease recurrence, the basic reproduction number (<span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>) is calculated. We investigate the stability of the disease’s dynamics under different conditions, using the Lyapunov function to confirm our model’s global stability. Our findings highlight the relevance of vaccination and early treatment in reducing Hepatitis B virus spread, making them a useful tool for public health efforts aiming at eradicating Hepatitis B virus. In our research, we investigate the dynamics of a specific model that is characterized by a system of differential equations. This work uses deep neural networks (DNNs) technique to improve model accuracy, proving the use of DNNs in epidemiological modeling. Additionally, we want to find the curves that suit the target solutions with the minimum residual errors. The simulations we conducted demonstrate our methodology’s capability to accurately predict the behavior of systems across various conditions. We rigorously test the solutions obtained via the DNNs by comparing them to benchmark solutions and undergoing stages of testing, validation, and training. To determine the accuracy and reliability of our approach, we perform a series of analyses, including convergence studies, error distribution evaluations, regression analyses, and detailed curve fitting for each equation.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108256"},"PeriodicalIF":2.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the distinctive variations in multi-omics triggered by TP53 mutation in lung cancer subtypes: An insight from interaction among intratumoral microbiota, tumor microenvironment, and pathology","authors":"Shanhe Tong ,&nbsp;Kenan Huang ,&nbsp;Weipeng Xing ,&nbsp;Yuwen Chu ,&nbsp;Chuanqi Nie ,&nbsp;Lei Ji ,&nbsp;Wenyan Wang ,&nbsp;Geng Tian ,&nbsp;Bing Wang ,&nbsp;Jialiang Yang","doi":"10.1016/j.compbiolchem.2024.108274","DOIUrl":"10.1016/j.compbiolchem.2024.108274","url":null,"abstract":"<div><div>The TP53 mutation is one of the most common gene mutations in non-small cell lung cancer (NSCLC) and plays a significant role in the occurrence, development, and prognosis of both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Recent studies have also suggested the predictive value of TP53 mutations in the response to immunotherapy for NSCLC. It is known that intratumoral microbiota, tumor immune microenvironment (TIME) and histology are associated with the roles of TP53 mutation in NSCLC. However, the intrinsic associations among these three factors and their underlying interaction with TP53 mutation are not well understood. Additionally, the potential of predicting TP53 mutations using deep learning methods has not yet been fully evaluated. In this paper, we comprehensively evaluated the tissue microbiome, host gene expression characteristics, and histopathological slides of 992 NSCLC patients obtained from the cancer genome atlas (TCGA) and validated the findings using multi-omics data of 332 NSCLC patients from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Compared to LUSC, LUAD exhibited more substantial differences between patients with and without TP53 mutation in all three aspects. In LUAD, our results imply underlying links between the tissue microbiome and immune cell components in the TIME, and show that the abundance of immune cells is reflected in histology slides. Furthermore, we propose a novel multimodal deep learning model that focuses on histopathology images, which achieves an area under the curve (AUC) of 0.84 in LUAD. In summary, TP53 mutation of LUAD resulted more significant changes in intratumoral microbiota, TIME and histology than that of LUSC. And histopathology images can be used to predict TP53 mutation in LUAD with reasonable accuracy.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108274"},"PeriodicalIF":2.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autoencoder-based drug synergy framework for malignant diseases","authors":"Pooja Rani ,&nbsp;Kamlesh Dutta ,&nbsp;Vijay Kumar","doi":"10.1016/j.compbiolchem.2024.108273","DOIUrl":"10.1016/j.compbiolchem.2024.108273","url":null,"abstract":"<div><div>Drug combination emerges as a viable option for the treatment of malignant diseases. Drug combination outperforms monotherapy by improving therapeutic efficacy, reducing toxicity, and overcoming drug resistance. To find viable drug combinations it is difficult to traverse empirically because of enormous combinational space. Machine learning and deep learning approaches are used to uncover novel synergistic drug combinations in enormous combinational space. Here, AESyn, a novel autoencoder-based drug synergy framework for malignant diseases using a bag of words encoding is proposed. The bag of word encoding technique is used to extract drug-targeted genes. The framework utilized screening data from NCI-ALMANAC, and O’Neil datasets. Autoencoders take drug embeddings with drug-targeted genes as input for processing. The autoencoder in the proposed framework is used to extract drug features. The proposed framework is evaluated on classification and regression metrics. The performance of the proposed framework is compared with existing methods of drug synergy. According to the findings, the proposed framework achieved high performance with an accuracy of 95%, AUROC of 94.2%, and MAPE of 7.2. The autoencoder-based framework for malignant diseases using an encoding technique provides a stable, order-independent drug synergy prediction.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108273"},"PeriodicalIF":2.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HiMolformer: Integrating graph and sequence representations for predicting liver microsome stability with SMILES","authors":"Seokwoo Yun ,&nbsp;Gibeom Nam ,&nbsp;Jahwan Koo","doi":"10.1016/j.compbiolchem.2024.108263","DOIUrl":"10.1016/j.compbiolchem.2024.108263","url":null,"abstract":"<div><div>In the initial stages of drug discovery or pre-clinical studies, understanding the metabolic stability of new molecules is crucial. Recently, research on pre-trained deep learning for molecular property prediction has been actively progressing, with various models being made open-source. However, most of these models rely on either 2D graph or 1D sequence for training, and the representation varies depending on the data format used. Consequently, combining multiple representations can broaden the scope of learning and may potentially be a manageable and most effective method to enhance performance.</div><div>Therefore, we propose a novel hybrid model for predicting metabolic stability, which integrates representations from both graph-based and sequence-based models pre-trained for molecular features. This approach utilizes the combined strengths of 2D topological and 1D sequential information of molecules. HiMol, a graph-based graph neural network (GNN) model, and Molformer, a sequence-based Transformer model, were selected for integration, thus we named it HiMolformer. HiMolformer demonstrated superior performance compared to other models. We also focus on regression task for prediction with a empirical dataset from Korea Chemical Bank (KCB), comprising 3,498 molecules with mouse liver microsome (MLM) and human liver microsome (HLM) data obtained from actual metabolic reaction experiments. To the best of our knowledge, it is the first attempt to develop MLM and HLM prediction models using regression with a single SMILES input. The source code of this model is available at <span><span>https://github.com/YUNSEOKWOO/HiMolformer</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108263"},"PeriodicalIF":2.6,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of alternative splicing related with transcription factors and splicing regulators in breast cancer stem cells responding to fasting-mimicking diet","authors":"Hongshuang Qin,&nbsp;Qian Zhang,&nbsp;Yanxiang Guo","doi":"10.1016/j.compbiolchem.2024.108272","DOIUrl":"10.1016/j.compbiolchem.2024.108272","url":null,"abstract":"<div><div>Fasting-mimicking diet (FMD) can effectively inhibit the viability of breast cancer stem cells (CSCs). However, the molecular mechanisms underlying the inhibitory function of FMD on breast CSCs remain largely unknown. Elucidating the mechanisms by which FMD suppresses breast CSCs is beneficial to targeting breast CSCs. Herein, we systematically analyze alternative splicing and RNA binding protein (RBP) expression in breast CSCs during FMD. The analysis results show that a large number of regulated alternative splicing (RAS) and differentially expressed genes (DEGs) appear responding to FMD. Further studies show that there are potential regulatory relationships between transcription factors (TFs) with RAS (RAS-TFs) and their differentially expressed target genes (RAS-TF-DEGs). Moreover, differentially expressed RNA binding proteins (DERBPs) exhibit potential regulatory functions on RAS-TFs. In short, DERBPs potentially control the alternative splicing of TFs (RAS-TFs), regulating their target gene (RAS-TF-DEG) expression, which leads to the regulation of biological processes in breast CSCs during FMD. In addition, the alternative splicing and DEGs are compared between breast CSCs and differentiated cancer cells during FMD, providing new interpretations for the different responses of the two types of cells. Our studies will shed light on the understanding of the molecular mechanisms underlying breast CSC inhibition induced by FMD.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108272"},"PeriodicalIF":2.6,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and characterization of defined alpha-helix mini-proteins with intrinsic cell permeability","authors":"Xin-Chun Chen ,&nbsp;Xiang-Wei Kong ,&nbsp;Pin Chen ,&nbsp;Zi-Qian Li ,&nbsp;Nan Huang ,&nbsp;Zheng Zhao ,&nbsp;Jie Yang ,&nbsp;Ge-Xin Zhao ,&nbsp;Qing Mo ,&nbsp;Yu-Tong Lu ,&nbsp;Xiao-Ming Huang ,&nbsp;Guo-Kai Feng ,&nbsp;Mu-Sheng Zeng","doi":"10.1016/j.compbiolchem.2024.108271","DOIUrl":"10.1016/j.compbiolchem.2024.108271","url":null,"abstract":"<div><div>Proteins with intrinsic cell permeability that can access intracellular targets represent a promising strategy for novel drug development; however, a general design principle is still lacking. Here, we established a library of 46,678 <em>de novo</em>-designed mini-proteins and performed cell permeability screening via phage display. Analyses revealed a characteristic neighboring distribution of positive charges across helices among enriched mini-proteins of CPP7, CPP11, CPP55, CPP109 and CPP112. Compared with the state-of-the-art cell-penetrating mini-protein ZF5.3, the optimized mini-protein CPP11D36R exhibited a sevenfold increase in cell permeability. Endocytosis uptake and early endosome release are the key penetrating mechanisms. A machine learning model with high-throughput data achieved an F1 score of 0.41, significantly outperforming the previously reported CPP prediction models, including MLACP, CPPpred and CellPPD, by 41 %. Overall, our findings validate the effectiveness of a helical structure with a cationic distribution as a design principle on a large scale and present a robust approach for the development of cell-permeable mini-protein drugs.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108271"},"PeriodicalIF":2.6,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identify the key genes and pathways of melatonin in age-dependent mice hippocampus regulation by transcriptome analysis","authors":"Yujia Gu ,&nbsp;Jiayu Zhou ,&nbsp;Qingchun Zhao ,&nbsp;Xiaowen Jiang ,&nbsp;Huiyuan Gao","doi":"10.1016/j.compbiolchem.2024.108267","DOIUrl":"10.1016/j.compbiolchem.2024.108267","url":null,"abstract":"<div><h3>Context</h3><div>Dysregulation of energy metabolism is a fundamental contributor to all the hallmarks of brain aging. Melatonin, primarily secreted by the pineal gland, is closely associated with molecules and signaling pathways that sense and affect energy metabolism. However, the impact of melatonin on age-related mRNA expression in the hippocampus of mice at different ages remains poorly understood.</div></div><div><h3>Objective</h3><div>The present study conducted transcriptome analysis of the hippocampus in melatonin-exposed mice at 9, 13, and 25 months of age. Differential gene analysis, GO and KEGG pathway enrichment analysis, GSEA analysis, as well as weighted gene co-expression network analysis (WGCNA), were performed on the transcriptome data.</div></div><div><h3>Results</h3><div>Our study demonstrated that melatonin exerts a more pronounced regulatory effect on the transcriptome of 25-month old mice, and significantly enhances the expression level of TTR in the hippocampus of 13-month old mice. WGCNA analysis revealed that melatonin primarily modulates the energy metabolism of mouse hippocampus through the mTOR signaling pathway and AMPK signaling pathway.</div></div><div><h3>Conclusions</h3><div>In conclusion, our study provides new insights into the comprehensive understanding of the mechanism of melatonin's age-dependent regulation of the mice hippocampus.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108267"},"PeriodicalIF":2.6,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deconvolution of cell-type-associated markers predictive of response to neoadjuvant radiotherapy","authors":"Min Zhu ,&nbsp;Xiao Sun ,&nbsp;Jinman Fang ,&nbsp;Xueling Li","doi":"10.1016/j.compbiolchem.2024.108269","DOIUrl":"10.1016/j.compbiolchem.2024.108269","url":null,"abstract":"<div><div>Tumor microenvironent contains prognostic molecular markers and therapeutic targets from different cellular sources, which are still not fully revealed in the resistance and recurrence after radiotherapy for rectal cancer. By integrating the scRNA-seq data, we deconvoluted the bulk transcriptomics of rectal cancer collected before preoperative neoadjuvant radiotherapy (nRT) into fractions and gene expression of the six cell types. The inferred cell-type-associated DEGs, abbreviated as caDEGs, of myeloid and stromal cells were enriched for overlapping yet unique biological processes including immunity, angiogenesis, and metabolism, respectively. Ecotyper analysis indicates that the caDEGs reflects cell states and ecotypes in association with nRT response. By mapping the caDEGs onto the context-free and newly built ligand-receptor and collagen-integrin lists from scRNA-Seq data, respectively, we inferred 297 cell-type-specific trans- and/or cis-collagen-integrin and 219 heterotypic ligand-receptor interactions potentially associated with nRT response, including interactions between stromal-associated COL1A2/COL6A1/COL6A2 and stromal or CMS1-associated ITGA1/B1, between epithelial-associated JAG1 and stromal-associated NOTCHs, between CMS2 epithelial-associated CCL15 and proliferating myeloid-associated CCR1, between myeloid-associated CCL4/CD86 and lymphatic endothelial-associated ACKR2, and between myeloid-associated TNFS13B and B cell-associated TNFRSF13B/C, etc. Intriguingly, results suggest a greater number of down-regulated cell-type-related markers in resistant cancers to nRT. Favorable myeloid-associated CD14, epithelial-associated DYM, stromal-associated COL1A2 and COL3A1, and unfavorable epithelial-associated CELSR3 and KCNH8 markers were inferred at least from two independent nCRT datasets of GSE119409, GSE35452, and GSE45404. The results provide insights into roles of the stromal and immune cells beside epithelial cells in resistance to radiotherapy for rectal cancers. The proposed approach can be applicable to other diseases as well. Codes and additional data are available at <span><span>https://github.com/Xueling21/rectalNRT_deconv</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108269"},"PeriodicalIF":2.6,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}