Pub Date : 2025-02-15DOI: 10.1016/j.bbrep.2025.101949
Christophe Desterke , Raquel Francés , Claudia Monge , Yuanji Fu , Agnès Marchio , Pascal Pineau , Jorge Mata-Garrido
Intrahepatic cholangiocarcinoma (ICA) is a highly aggressive primary liver cancer, which originates from the epithelial cells of the bile ducts. The transcriptional profile of metabolic enzymes was investigated at both bulk and single-cell levels in tumor samples from distinct ICA cohorts. In a training cohort (TCGA consortium), 16 genes encoding for metabolic enzymes were found overexpressed in cases with poor survival. A computed metabolic gene expression score was significantly associated with worse ICA prognosis at the univariate level (overall survival [OS] log-rank p = 8.2e-4). After adjusting for Ishak fibrosis score and tumor staging, the metabolic expression remained an independent predictor of poor prognosis (multivariate OS log-rank p = 0.01). Seven genes encoding key enzymes (FH, MAT2B, PLOD2, PLOD1, PDE6D, ALDOC, and NT5DC3) were validated as markers of the proliferative subclass of ICA in the GSE32225 dataset, related to poor prognosis. The metabolic score was significantly different between the inflammatory and proliferative subclasses in the validation cohort (p < 2.2e-16). At the single-cell level, in the tumor microenvironment of 10 ICA patients, these seven enzymes were predominantly expressed by malignant cells. The single-cell metabolic score was thus higher in malignant cells. This study identifies a metabolic transcriptional program linked to poor prognosis in ICA, independent of fibrosis and tumor staging.
{"title":"Single-cell RNAseq reveals adverse metabolic transcriptional program in intrahepatic cholangiocarcinoma malignant cells","authors":"Christophe Desterke , Raquel Francés , Claudia Monge , Yuanji Fu , Agnès Marchio , Pascal Pineau , Jorge Mata-Garrido","doi":"10.1016/j.bbrep.2025.101949","DOIUrl":"10.1016/j.bbrep.2025.101949","url":null,"abstract":"<div><div>Intrahepatic cholangiocarcinoma (ICA) is a highly aggressive primary liver cancer, which originates from the epithelial cells of the bile ducts. The transcriptional profile of metabolic enzymes was investigated at both bulk and single-cell levels in tumor samples from distinct ICA cohorts. In a training cohort (TCGA consortium), 16 genes encoding for metabolic enzymes were found overexpressed in cases with poor survival. A computed metabolic gene expression score was significantly associated with worse ICA prognosis at the univariate level (overall survival [OS] log-rank p = 8.2e-4). After adjusting for Ishak fibrosis score and tumor staging, the metabolic expression remained an independent predictor of poor prognosis (multivariate OS log-rank p = 0.01). Seven genes encoding key enzymes (FH, MAT2B, PLOD2, PLOD1, PDE6D, ALDOC, and NT5DC3) were validated as markers of the proliferative subclass of ICA in the GSE32225 dataset, related to poor prognosis. The metabolic score was significantly different between the inflammatory and proliferative subclasses in the validation cohort (p < 2.2e-16). At the single-cell level, in the tumor microenvironment of 10 ICA patients, these seven enzymes were predominantly expressed by malignant cells. The single-cell metabolic score was thus higher in malignant cells. This study identifies a metabolic transcriptional program linked to poor prognosis in ICA, independent of fibrosis and tumor staging.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101949"},"PeriodicalIF":2.3,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-15DOI: 10.1016/j.bbrep.2025.101944
Chew W. Cheng, Lucia Pedicini, Cintli Morales Alcala, Fenia Deligianni, Jessica Smith, Ryan D. Murray, Harriet J. Todd, Niamh Forde, Lynn McKeown
EFCAB4B is an evolutionarily conserved protein that encodes for the Rab GTPase Rab46, and the CRAC channel modulator, CRACR2A. Previous genome wide association studies have demonstrated the association of EFCAB4B variants in the progression of non-alcoholic fatty liver disease (NAFLD). In this study we show that mice with global depletion of Efcab4b−/− have significantly larger livers than their wild-type (WT) counterparts. We performed RNA-sequencing (RNA-seq) analysis of liver tissues to investigate differential global gene expression among Efcab4b−/− and WT mice. Of the 69 differentially expressed genes (DEGs), analyses of biological processes found significant enrichment in liver and bile development, with 6 genes (Pck1, Aacs, Onecut1, E2f8, Xbp1, and Hes1) involved in both processes. Specific consideration of possible roles of DEGs or their products in NAFLD progression to (NASH) and hepatocarcinoma (HCC), demonstrated DEGs in the livers of Efcab4b−/− mice had roles in molecular pathways including lipid metabolism, inflammation, ER stress and fibrosis. The results in this study provide additional insights into molecular mechanisms responsible for increasing susceptibility of liver injuries associated with EFCAB4B.
{"title":"RNA-seq analysis reveals transcriptome changes in livers from Efcab4b knockout mice","authors":"Chew W. Cheng, Lucia Pedicini, Cintli Morales Alcala, Fenia Deligianni, Jessica Smith, Ryan D. Murray, Harriet J. Todd, Niamh Forde, Lynn McKeown","doi":"10.1016/j.bbrep.2025.101944","DOIUrl":"10.1016/j.bbrep.2025.101944","url":null,"abstract":"<div><div><em>EFCAB4B</em> is an evolutionarily conserved protein that encodes for the Rab GTPase Rab46, and the CRAC channel modulator, CRACR2A. Previous genome wide association studies have demonstrated the association of <em>EFCAB4B</em> variants in the progression of non-alcoholic fatty liver disease (NAFLD). In this study we show that mice with global depletion of <em>Efcab4b</em><sup><em>−/−</em></sup> have significantly larger livers than their wild-type (WT) counterparts. We performed RNA-sequencing (RNA-seq) analysis of liver tissues to investigate differential global gene expression among <em>Efcab4b</em><sup><em>−/−</em></sup> and WT mice. Of the 69 differentially expressed genes (DEGs), analyses of biological processes found significant enrichment in liver and bile development, with 6 genes (<em>Pck1, Aacs, Onecut1, E2f8, Xbp1,</em> and <em>Hes1</em>) involved in both processes. Specific consideration of possible roles of DEGs or their products in NAFLD progression to (NASH) and hepatocarcinoma (HCC), demonstrated DEGs in the livers of <em>Efcab4b</em><sup><em>−/−</em></sup> mice had roles in molecular pathways including lipid metabolism, inflammation, ER stress and fibrosis. The results in this study provide additional insights into molecular mechanisms responsible for increasing susceptibility of liver injuries associated with <em>EFCAB4B</em>.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101944"},"PeriodicalIF":2.3,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-15DOI: 10.1016/j.bbrep.2025.101953
Mahya Anahid , Karim Mahnam , Behnaz Saffar
Future threats to humanity may stem from the rise of antimicrobial resistance, which has compromised the effectiveness of existing antibiotics. Antimicrobial peptides possess the ability to directly eliminate pathogens and cancer cells, generally without the development of resistance. Among these peptides is RP9 (RGSALTHLP), derived from the white blood cells of crocodiles. In this research, three mutations were initially designed: LR-mut (RGSALTHLR), KR-mut (RGSAKTHLR), and WP-mut (RGSAWTHLP). The physicochemical characteristics of these peptides were assessed, revealing that KR-mut exhibited the most favorable biophysical properties. Subsequently, twenty molecular dynamics simulations were conducted for all peptides in pure water and at four different octanol concentrations (30 %, 50 %, 70 %, and 100 %) to evaluate their biophysical attributes. The findings from the 4000 ns molecular dynamics simulations revealed that the KR-mut exhibited reduced values of RMSD, the radius of gyration, solvent accessible surface area, and RMSF, while simultaneously showing an increased number of hydrogen bonds and interactions with water molecules. This peptide also showed the lowest free energy of solvation and the highest solubility across various octanol concentrations compared to the other peptides. The results obtained from the biophysical assessments and molecular dynamics simulations were consistent, resulting in the conclusion that KR-mut is expected to exhibit superior antibacterial activity compared to both the other mutated peptides and the wild type peptides. These theoretical findings were validated through experimental minimum inhibitory concentration (MIC) tests on gram-negative Escherichia coli and gram-positive Staphylococcus aureus. The outcomes of this study suggest that molecular dynamics simulations can effectively predict changes in the bactericidal efficacy of peptides at varying octanol concentrations, potentially enhancing the speed and efficiency of antimicrobial peptide design while reducing associated costs.
{"title":"Improving the antimicrobial activity of RP9 peptide through theoretical and experimental investigation","authors":"Mahya Anahid , Karim Mahnam , Behnaz Saffar","doi":"10.1016/j.bbrep.2025.101953","DOIUrl":"10.1016/j.bbrep.2025.101953","url":null,"abstract":"<div><div>Future threats to humanity may stem from the rise of antimicrobial resistance, which has compromised the effectiveness of existing antibiotics. Antimicrobial peptides possess the ability to directly eliminate pathogens and cancer cells, generally without the development of resistance. Among these peptides is RP9 (RGSALTHLP), derived from the white blood cells of crocodiles. In this research, three mutations were initially designed: LR-mut (RGSALTHLR), KR-mut (RGSAKTHLR), and WP-mut (RGSAWTHLP). The physicochemical characteristics of these peptides were assessed, revealing that KR-mut exhibited the most favorable biophysical properties. Subsequently, twenty molecular dynamics simulations were conducted for all peptides in pure water and at four different octanol concentrations (30 %, 50 %, 70 %, and 100 %) to evaluate their biophysical attributes. The findings from the 4000 ns molecular dynamics simulations revealed that the KR-mut exhibited reduced values of RMSD, the radius of gyration, solvent accessible surface area, and RMSF, while simultaneously showing an increased number of hydrogen bonds and interactions with water molecules. This peptide also showed the lowest free energy of solvation and the highest solubility across various octanol concentrations compared to the other peptides. The results obtained from the biophysical assessments and molecular dynamics simulations were consistent, resulting in the conclusion that KR-mut is expected to exhibit superior antibacterial activity compared to both the other mutated peptides and the wild type peptides. These theoretical findings were validated through experimental minimum inhibitory concentration (MIC) tests on gram-negative <em>Escherichia coli</em> and gram-positive <em>Staphylococcus aureus</em>. The outcomes of this study suggest that molecular dynamics simulations can effectively predict changes in the bactericidal efficacy of peptides at varying octanol concentrations, potentially enhancing the speed and efficiency of antimicrobial peptide design while reducing associated costs.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101953"},"PeriodicalIF":2.3,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13DOI: 10.1016/j.bbrep.2025.101938
Yanguo Li , Zixing Meng , Chengjiang Fan , Hao Rong , Yang Xi , Qi Liao
Essential genes are indispensable for the survival of cancer cell. CRISPR/Cas9-based pooled genetic screens have distinguished the essential genes and their functions in distinct cellular processes. Nevertheless, the landscape of essential genes at the single cell levels and the effect on the tumor microenvironment (TME) remains limited. Here, we identified 396 essential protein-coding genes (ESPs) by integration of 8 genome-wide CRISPR loss-of-function screen datasets of colorectal cancer (CRC) cell lines and single-cell RNA sequencing (scRNA-seq) data of CRC tissues. Then, 29 essential long non-coding genes (ESLs) were predicted using Hypergeometric Test (HT) and Personalized PageRank (PPR) algorithms based on ESPs and co-expressed network constructed from scRNA-seq. CRISPR/Cas9 knockout experiment verified the effect of several ESPs and ESLs on the survival of CRC cell line. Furthermore, multi-omics features of ESPs and ESLs were illustrated by examining their expression patterns and transcription factor (TF) regulatory network at the single cell level, as well as DNA mutation and DNA methylation events at bulk level. Finally, through integrating multiple intracellular regulatory networks with cell-cell communication network (CCN), we elucidated that CD47 and MIF are regulated by multiple CRC essential genes, and the anti-cancer drugs sunitinib can interfere the expression of them potentially. Our findings provide a comprehensive asset of CRC ESPs and ESLs, sheding light on the mining of potential therapy targets for CRC.
{"title":"Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer","authors":"Yanguo Li , Zixing Meng , Chengjiang Fan , Hao Rong , Yang Xi , Qi Liao","doi":"10.1016/j.bbrep.2025.101938","DOIUrl":"10.1016/j.bbrep.2025.101938","url":null,"abstract":"<div><div>Essential genes are indispensable for the survival of cancer cell. CRISPR/Cas9-based pooled genetic screens have distinguished the essential genes and their functions in distinct cellular processes. Nevertheless, the landscape of essential genes at the single cell levels and the effect on the tumor microenvironment (TME) remains limited. Here, we identified 396 essential protein-coding genes (ESPs) by integration of 8 genome-wide CRISPR loss-of-function screen datasets of colorectal cancer (CRC) cell lines and single-cell RNA sequencing (scRNA-seq) data of CRC tissues. Then, 29 essential long non-coding genes (ESLs) were predicted using Hypergeometric Test (HT) and Personalized PageRank (PPR) algorithms based on ESPs and co-expressed network constructed from scRNA-seq. CRISPR/Cas9 knockout experiment verified the effect of several ESPs and ESLs on the survival of CRC cell line. Furthermore, multi-omics features of ESPs and ESLs were illustrated by examining their expression patterns and transcription factor (TF) regulatory network at the single cell level, as well as DNA mutation and DNA methylation events at bulk level. Finally, through integrating multiple intracellular regulatory networks with cell-cell communication network (CCN), we elucidated that <em>CD47</em> and <em>MIF</em> are regulated by multiple CRC essential genes, and the anti-cancer drugs sunitinib can interfere the expression of them potentially. Our findings provide a comprehensive asset of CRC ESPs and ESLs, sheding light on the mining of potential therapy targets for CRC.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101938"},"PeriodicalIF":2.3,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143402956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-12DOI: 10.1016/j.bbrep.2025.101937
Amisha Gupta , Darakhshan Parveen , Faizul Azam , M. Shaquiquzzaman , Mymoona Akhter , Mariusz Jaremko , Abdul-Hamid Emwas , Mohammad Ahmed Khan , Suhel Parvez , Suruchi Khanna , Rituparna Palit , Umar Jahangir , M. Mumtaz Alam
Cancer presents a formidable and complex foe, standing as one of the foremost contributors to disease-related fatalities across the globe. According to data from the Global Cancer Observatory (GLOBOCAN), projections indicate a staggering 28.4 million cases of cancer, encompassing both new diagnoses and deaths, by 2040. Therefore, developing effective and comprehensive treatment approaches for cancer patients is essential and the conventional approved treatments for cancers are associated with various harmful side effects. Our study aims to address the critical and widespread need for alternative therapies that can effectively combat cancer with minimal side effects.
The present contribution outlines a targeted approach using Lysine Specific Demethylase 1 (LSD1) to evaluate novel cyano-pyrimidine pendant chalcone derivatives as potential antiproliferative agents. Two sets of novel cyano-pyrimidine pendant chalcone derivatives were produced, and molecular docking was performed on the LSD1 protein. The ligands A1 and B1 belonging to series A and B, respectively, were found to have the highest docking scores of −11.095 and −10.773 kcal/mol, in that order. The ADME and toxicity studies of the ligands showed promising responses with respect to various pharmacokinetic and physicochemical parameters. The Molecular dynamics (MD) simulation results indicated effective diffusion of both complexes inside the protein cavity, facilitated by prominent interactions with various amino acids. Additionally, the complexes displayed high relative binding free energy. The computational screening of ligands indicates that ligands A1 and B1 exhibit potential for further exploration using various in vitro and in vivo techniques. These ligands may then serve as promising leads in the discovery of cancer drugs. The in-silico screening of the novel library of cyano-pyrimidine pendant chalcone derivatives was performed with a combination of molecular docking, MM-GBSA, ADME, toxicity and MD simulation. Molecular docking and MM-GBSA were conducted using the Glide and Prime tools, respectively, of the Schrödinger suite 12.8. The ligands were analysed for ADME using the Swiss ADME, while toxicity risks were evaluated using Osiris Property Explorer. Additionally, a 400ns MD simulation of LIGA1 and LIGB1 against the protein LSD1 was performed using the Desmond tool of Schrödinger suite 12.8 to validate the docking results and analyse the behaviour and stability of the complexes.
{"title":"Mechanistic insights into novel cyano-pyrimidine pendant chalcone derivatives as LSD1 inhibitors by docking, ADMET, MM/GBSA, and molecular dynamics simulation","authors":"Amisha Gupta , Darakhshan Parveen , Faizul Azam , M. Shaquiquzzaman , Mymoona Akhter , Mariusz Jaremko , Abdul-Hamid Emwas , Mohammad Ahmed Khan , Suhel Parvez , Suruchi Khanna , Rituparna Palit , Umar Jahangir , M. Mumtaz Alam","doi":"10.1016/j.bbrep.2025.101937","DOIUrl":"10.1016/j.bbrep.2025.101937","url":null,"abstract":"<div><div>Cancer presents a formidable and complex foe, standing as one of the foremost contributors to disease-related fatalities across the globe. According to data from the Global Cancer Observatory (GLOBOCAN), projections indicate a staggering 28.4 million cases of cancer, encompassing both new diagnoses and deaths, by 2040. Therefore, developing effective and comprehensive treatment approaches for cancer patients is essential and the conventional approved treatments for cancers are associated with various harmful side effects. Our study aims to address the critical and widespread need for alternative therapies that can effectively combat cancer with minimal side effects.</div><div>The present contribution outlines a targeted approach using Lysine Specific Demethylase 1 (LSD1) to evaluate novel cyano-pyrimidine pendant chalcone derivatives as potential antiproliferative agents. Two sets of novel cyano-pyrimidine pendant chalcone derivatives were produced, and molecular docking was performed on the LSD1 protein. The ligands A1 and B1 belonging to series A and B, respectively, were found to have the highest docking scores of −11.095 and −10.773 kcal/mol, in that order. The ADME and toxicity studies of the ligands showed promising responses with respect to various pharmacokinetic and physicochemical parameters. The Molecular dynamics (MD) simulation results indicated effective diffusion of both complexes inside the protein cavity, facilitated by prominent interactions with various amino acids. Additionally, the complexes displayed high relative binding free energy. The computational screening of ligands indicates that ligands A1 and B1 exhibit potential for further exploration using various <em>in vitro</em> and <em>in vivo</em> techniques. These ligands may then serve as promising leads in the discovery of cancer drugs. The <em>in-silico</em> screening of the novel library of cyano-pyrimidine pendant chalcone derivatives was performed with a combination of molecular docking, MM-GBSA, ADME, toxicity and MD simulation. Molecular docking and MM-GBSA were conducted using the Glide and Prime tools, respectively, of the Schrödinger suite 12.8. The ligands were analysed for ADME using the Swiss ADME, while toxicity risks were evaluated using Osiris Property Explorer. Additionally, a 400ns MD simulation of LIGA1 and LIGB1 against the protein LSD1 was performed using the Desmond tool of Schrödinger suite 12.8 to validate the docking results and analyse the behaviour and stability of the complexes.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101937"},"PeriodicalIF":2.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143386380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C–C chemokine receptor type 7 (CCR7) is a member of the G protein-coupled receptor family and functions as a lymph node-homing receptor for immune cells. Upon ligand binding, CCR7 promotes the migration of immune cells to secondary lymphoid organs. In cancers, CCR7 has been revealed as a critical molecule in lymph node metastasis. Consequently, anti-CCR7 monoclonal antibodies (mAbs) have been developed as cancer therapeutic agents. In this study, we established an anti-mouse CCR7 (mCCR7) mAb, C7Mab-7 (rat IgG1, kappa) using the Cell-Based Immunization and Screening (CBIS) method. C7Mab-7 demonstrated high sensitivity in flow cytometry. The dissociation constant (KD) value of C7Mab-7 was determined to be 2.5 × 10⁻⁹ M for mCCR7-overexpressed Chinese hamster ovary-K1 (CHO/mCCR7) cells. Furthermore, C7Mab-7 detected mCCR7 with high sensitivity in western blot and immunohistochemistry. C7Mab-7, developed by the CBIS method, accelerates the development of CCR7-targeted antibody therapies and cancer diagnostics.
{"title":"A novel anti-mouse CCR7 monoclonal antibody, C7Mab-7, demonstrates high sensitivity in flow cytometry, western blot, and immunohistochemistry","authors":"Hiroyuki Satofuka, Hiroyuki Suzuki, Tomohiro Tanaka, Rena Ubukata, Miu Hirose, Haruto Yamamoto, Yu Kaneko, Shiori Fujisawa, Guanjie Li, Mika K. Kaneko, Yukinari Kato","doi":"10.1016/j.bbrep.2025.101948","DOIUrl":"10.1016/j.bbrep.2025.101948","url":null,"abstract":"<div><div>C–C chemokine receptor type 7 (CCR7) is a member of the G protein-coupled receptor family and functions as a lymph node-homing receptor for immune cells. Upon ligand binding, CCR7 promotes the migration of immune cells to secondary lymphoid organs. In cancers, CCR7 has been revealed as a critical molecule in lymph node metastasis. Consequently, anti-CCR7 monoclonal antibodies (mAbs) have been developed as cancer therapeutic agents. In this study, we established an anti-mouse CCR7 (mCCR7) mAb, C<sub>7</sub>Mab-7 (rat IgG<sub>1</sub>, kappa) using the Cell-Based Immunization and Screening (CBIS) method. C<sub>7</sub>Mab-7 demonstrated high sensitivity in flow cytometry. The dissociation constant (<em>K</em><sub>D</sub>) value of C<sub>7</sub>Mab-7 was determined to be 2.5 × 10⁻⁹ M for mCCR7-overexpressed Chinese hamster ovary-K1 (CHO/mCCR7) cells. Furthermore, C<sub>7</sub>Mab-7 detected mCCR7 with high sensitivity in western blot and immunohistochemistry. C<sub>7</sub>Mab-7, developed by the CBIS method, accelerates the development of CCR7-targeted antibody therapies and cancer diagnostics.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101948"},"PeriodicalIF":2.3,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-10DOI: 10.1016/j.bbrep.2025.101945
Nickolette Kong , Natalia Penaloza , Gustavo Agreda , Angela B. Nguyen , Joseph Gutheinz , Alison Tran , Nhi Nguyen , Tuong Vi Ho , Ana Marin , Birgit Mellis , Richa Chandra
Cardiovascular disease (CVD) is the number one cause of mortality worldwide, with oxidative stress contributing significantly to its pathogenesis. Lipoproteins, key biomolecules in lipid transport, are particularly susceptible to oxidative modifications, which can contribute to atherogenesis. The need for advanced analytical tools to better understand the pathogenesis of cardiovascular disease (CVD) is critical due to its significant impact on public health. Clinicians often rely on indirect calculations of low-density lipoprotein (LDL) as a primary diagnostic indicator, which can oversimplify and overlook the complex changes in lipoprotein structure and function and therefore the complex etiology of CVD. Here it is demonstrated that dynamic light scattering (DLS) is sensitive and effective at measuring variation in lipoprotein size distributions following oxidative damage caused by peroxidation and nitration—two common physiological processes that play dual roles in both normal and pathogenic states. We establish the utility of DLS in detecting subtle variations in lipoprotein size, including potential aggregation and fission events resulting from chemical modifications. Our work highlights the value of DLS in advancing our understanding of the pathogenic mechanisms underlying CVD development, while also providing a foundational framework to study other biological processes and their effects on lipoproteins, ultimately guiding the development of therapies to address these harmful processes.
{"title":"Oxidative impact on lipoprotein structure: Insights from dynamic light scattering","authors":"Nickolette Kong , Natalia Penaloza , Gustavo Agreda , Angela B. Nguyen , Joseph Gutheinz , Alison Tran , Nhi Nguyen , Tuong Vi Ho , Ana Marin , Birgit Mellis , Richa Chandra","doi":"10.1016/j.bbrep.2025.101945","DOIUrl":"10.1016/j.bbrep.2025.101945","url":null,"abstract":"<div><div>Cardiovascular disease (CVD) is the number one cause of mortality worldwide, with oxidative stress contributing significantly to its pathogenesis. Lipoproteins, key biomolecules in lipid transport, are particularly susceptible to oxidative modifications, which can contribute to atherogenesis. The need for advanced analytical tools to better understand the pathogenesis of cardiovascular disease (CVD) is critical due to its significant impact on public health. Clinicians often rely on indirect calculations of low-density lipoprotein (LDL) as a primary diagnostic indicator, which can oversimplify and overlook the complex changes in lipoprotein structure and function and therefore the complex etiology of CVD. Here it is demonstrated that dynamic light scattering (DLS) is sensitive and effective at measuring variation in lipoprotein size distributions following oxidative damage caused by peroxidation and nitration—two common physiological processes that play dual roles in both normal and pathogenic states. We establish the utility of DLS in detecting subtle variations in lipoprotein size, including potential aggregation and fission events resulting from chemical modifications. Our work highlights the value of DLS in advancing our understanding of the pathogenic mechanisms underlying CVD development, while also providing a foundational framework to study other biological processes and their effects on lipoproteins, ultimately guiding the development of therapies to address these harmful processes.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101945"},"PeriodicalIF":2.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143376536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-10DOI: 10.1016/j.bbrep.2025.101950
Héverton Mendes Araújo , Gabriel Acácio de Moura , Yasmim Mendes Rocha , Cristian Vicson Pinheiro Gomes , Valentina Nascimento e Melo de Oliveira , Ronaldo Nascimento de Oliveira , Larissa Deadame de Figueiredo Nicolete , Emanuel Paula Magalhães , Ramon R.P.P.B. de Menezes , Roberto Nicolete
Melanoma is the most aggressive and lethal type of skin cancer, responsible for approximately 60,000 deaths annually. The main strategy for treating melanoma is surgery to completely remove the lesion and its margins. However, for more advanced cases with a high recurrence rate, the preferred approach is to combine chemotherapy with immunotherapy treatments. Tumor-associated macrophages (TAMs) are the most abundant leukocytes in solid tumors. Current immunotherapy approaches target TAMs by inhibiting pro-tumoral TAMs and activating anti-tumoral TAMs, repolarizing them to the M1 phenotype. The antitumor and immunomodulatory activities of molecules derived from 1,2,4-oxadiazole, as demonstrated in the literature, highlight the potential of this class as a source of promising candidates for therapeutic applications. Thus, the present study aims to evaluate the antitumor and immunomodulatory effects of the synthetic derivative 1,2,4-oxadiazole, N-cyclohexyl-3-(3-methylphenyl)-1,2,4-oxadiazole-5-amine (1,2,4-oxadiazole derivative 2), in melanoma cells and murine Bone Marrow-Derived Macrophages (BMDMs). Cytotoxicity in B16–F10 and BMDMs cells was assessed using the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) MTT method. 1,2,4-oxadiazole derivative 2 exhibited antiproliferative effects on both cell lines, being 2.6 times more selective for B16–F10. Necrosis was identified as the active induced death pathway. BMDMs isolated and exposed to 1,2,4-oxadiazole derivative 2 polarize to the M1 phenotype and induce TNF-α at a concentration of 64.34 μM. Exposure to melanoma murine supernatants also promotes M1 polarization. Supernatants containing traces of 1,2,4-oxadiazole derivative 2 (Supernatants B, C, and D) increased the percentage of M1 cells compared to Supernatant A, as well as elevated levels of nitrite, TNF-α, and IL-12. 1,2,4-oxadiazole derivative 2 combined with Supernatant A and 1,2,4-oxadiazole derivative 2 combined with LPS also resulted in higher M1 polarization, suggesting a synergistic effect on M1 polarization and TNF-α production. Our findings underscore the significance of the 1,2,4-oxadiazole compound class and highlight the potential of 1,2,4-oxadiazole derivative 2 as an antitumoral and immunotherapeutic agent.
{"title":"In vitro antitumor and immunomodulatory activities of 1,2,4-oxadiazole derivatives","authors":"Héverton Mendes Araújo , Gabriel Acácio de Moura , Yasmim Mendes Rocha , Cristian Vicson Pinheiro Gomes , Valentina Nascimento e Melo de Oliveira , Ronaldo Nascimento de Oliveira , Larissa Deadame de Figueiredo Nicolete , Emanuel Paula Magalhães , Ramon R.P.P.B. de Menezes , Roberto Nicolete","doi":"10.1016/j.bbrep.2025.101950","DOIUrl":"10.1016/j.bbrep.2025.101950","url":null,"abstract":"<div><div>Melanoma is the most aggressive and lethal type of skin cancer, responsible for approximately 60,000 deaths annually. The main strategy for treating melanoma is surgery to completely remove the lesion and its margins. However, for more advanced cases with a high recurrence rate, the preferred approach is to combine chemotherapy with immunotherapy treatments. Tumor-associated macrophages (TAMs) are the most abundant leukocytes in solid tumors. Current immunotherapy approaches target TAMs by inhibiting pro-tumoral TAMs and activating anti-tumoral TAMs, repolarizing them to the M1 phenotype. The antitumor and immunomodulatory activities of molecules derived from 1,2,4-oxadiazole, as demonstrated in the literature, highlight the potential of this class as a source of promising candidates for therapeutic applications. Thus, the present study aims to evaluate the antitumor and immunomodulatory effects of the synthetic derivative 1,2,4-oxadiazole, N-cyclohexyl-3-(3-methylphenyl)-1,2,4-oxadiazole-5-amine (1,2,4-oxadiazole derivative 2), in melanoma cells and murine Bone Marrow-Derived Macrophages (BMDMs). Cytotoxicity in B16–F10 and BMDMs cells was assessed using the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) MTT method. 1,2,4-oxadiazole derivative 2 exhibited antiproliferative effects on both cell lines, being 2.6 times more selective for B16–F10. Necrosis was identified as the active induced death pathway. BMDMs isolated and exposed to 1,2,4-oxadiazole derivative 2 polarize to the M1 phenotype and induce TNF-α at a concentration of 64.34 μM. Exposure to melanoma murine supernatants also promotes M1 polarization. Supernatants containing traces of 1,2,4-oxadiazole derivative 2 (Supernatants B, C, and D) increased the percentage of M1 cells compared to Supernatant A, as well as elevated levels of nitrite, TNF-α, and IL-12. 1,2,4-oxadiazole derivative 2 combined with Supernatant A and 1,2,4-oxadiazole derivative 2 combined with LPS also resulted in higher M1 polarization, suggesting a synergistic effect on M1 polarization and TNF-α production. Our findings underscore the significance of the 1,2,4-oxadiazole compound class and highlight the potential of 1,2,4-oxadiazole derivative 2 as an antitumoral and immunotherapeutic agent.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101950"},"PeriodicalIF":2.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-08DOI: 10.1016/j.bbrep.2025.101936
Spoorthy Pathikonda , Li Tian , Clement Manohar Arava , Shuk Han Cheng , Yun Wah Lam
The susceptibility of cancer cells to DNA damages is influenced by their microenvironment. For example, unirradiated neighbors of irradiated cells can produce signals that reduce DNA damages. This phenomenon, known as Radiation-Induced Rescue Effect (RIRE), has profound implications on the efficacy of radiotherapy. Using bystander cells co-cultured with mock-irradiated cells as a control, we demonstrated, for the first time, two types of RIRE. Conditioned medium from naïve by stander cells, i.e., cells not exposed to irradiated cells, could mitigate UV-induced DNA damages in human breast carcinoma MCF7 cells, as judged by phospho-H2AX and 53BP1 immunostaining. This protective effect could be further enhanced by the prior treatment of bystander cells with factors from UV-irradiated cells. We named the former effect “basal RIRE” and the latter “active RIRE” which were cell type-dependent. As bystanders, MCF7 showed a significant active RIRE, whereas THP1-derived macrophages showed a strong basal RIRE but no active RIRE. Interestingly, RIRE of macrophages could further be modulated by polarisation. The basal RIRE of macrophages was abolished by M1 polarisation, while M2 and Tumour Associated Macrophages (TAM) demonstrated pronounced basal and active RIRE. When mixtures of MCF7 cells and polarised macrophages were used as bystanders, the overall RIRE was dictated by macrophage phenotypes: RIRE was suppressed by M1 macrophages but significantly enhanced by M2 and TAM. This study shows a previously unappreciated role of the innate immune system in RIRE. Depending on polarised phenotypes, macrophages in the tumour microenvironment can interfere with the effectiveness of radiotherapy by adjusting the RIRE magnitudes.
{"title":"Radiation-induced rescue effect on human breast carcinoma cells is regulated by macrophages","authors":"Spoorthy Pathikonda , Li Tian , Clement Manohar Arava , Shuk Han Cheng , Yun Wah Lam","doi":"10.1016/j.bbrep.2025.101936","DOIUrl":"10.1016/j.bbrep.2025.101936","url":null,"abstract":"<div><div>The susceptibility of cancer cells to DNA damages is influenced by their microenvironment. For example, unirradiated neighbors of irradiated cells can produce signals that reduce DNA damages. This phenomenon, known as Radiation-Induced Rescue Effect (RIRE), has profound implications on the efficacy of radiotherapy. Using bystander cells co-cultured with mock-irradiated cells as a control, we demonstrated, for the first time, two types of RIRE. Conditioned medium from naïve by stander cells, i.e., cells not exposed to irradiated cells, could mitigate UV-induced DNA damages in human breast carcinoma MCF7 cells, as judged by phospho-H2AX and 53BP1 immunostaining. This protective effect could be further enhanced by the prior treatment of bystander cells with factors from UV-irradiated cells. We named the former effect “basal RIRE” and the latter “active RIRE” which were cell type-dependent. As bystanders, MCF7 showed a significant active RIRE, whereas THP1-derived macrophages showed a strong basal RIRE but no active RIRE. Interestingly, RIRE of macrophages could further be modulated by polarisation. The basal RIRE of macrophages was abolished by M1 polarisation, while M2 and Tumour Associated Macrophages (TAM) demonstrated pronounced basal and active RIRE. When mixtures of MCF7 cells and polarised macrophages were used as bystanders, the overall RIRE was dictated by macrophage phenotypes: RIRE was suppressed by M1 macrophages but significantly enhanced by M2 and TAM. This study shows a previously unappreciated role of the innate immune system in RIRE. Depending on polarised phenotypes, macrophages in the tumour microenvironment can interfere with the effectiveness of radiotherapy by adjusting the RIRE magnitudes.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101936"},"PeriodicalIF":2.3,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143349611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-08DOI: 10.1016/j.bbrep.2025.101935
Gang Li , Jing Zhang , Bentuo Zhang , Dan Wang , Zequn Wang , Yan Pan , Lijie Ma
The diagnosis of primary pancreatic neuroendocrine tumors (pNETs) presents significant challenges, and metastatic pancreatic neuroendocrine tumors are associated with high mortality. Understanding the characteristics of these tumors, particularly the key molecules involved in metastasis, is essential. To address this, we utilized mRNA expression data from human pNET and metastatic pancreatic tumor tissues available in the GEO database and integrated this data with bioinformatics analyses. And then we collected clinical primary tumor and liver metastasis samples from patients with pNETs, we conducted a comprehensive analysis of circular RNAs (circRNAs) to identify key circRNAs associated with the onset and metastasis of pNETs. We found that in pNET development and metastasis, 11 genes and 14 circRNAs were notably upregulated, while 25 genes and 35 circRNAs were significantly downregulated, compared to nearby non-cancerous tissue. Our analysis of differentially expressed RNA and circRNA genes revealed that tumor cell adhesion and integrin activation, regulated by genes like PIEZO1, IFT74, SKAP1, GPX1, F7, VTN, and OMG, are strongly linked to pNET metastasis. We found that SKAP1 levels are positively associated with tumor progression in pNET patients. Overall, our research indicates that the SKAP1-mediated pathway is crucial in pNET development and metastasis.
{"title":"Comprehensive analysis of differential mRNA and circRNA profiles in primary and metastatic pancreatic neuroendocrine tumors","authors":"Gang Li , Jing Zhang , Bentuo Zhang , Dan Wang , Zequn Wang , Yan Pan , Lijie Ma","doi":"10.1016/j.bbrep.2025.101935","DOIUrl":"10.1016/j.bbrep.2025.101935","url":null,"abstract":"<div><div>The diagnosis of primary pancreatic neuroendocrine tumors (pNETs) presents significant challenges, and metastatic pancreatic neuroendocrine tumors are associated with high mortality. Understanding the characteristics of these tumors, particularly the key molecules involved in metastasis, is essential. To address this, we utilized mRNA expression data from human pNET and metastatic pancreatic tumor tissues available in the GEO database and integrated this data with bioinformatics analyses. And then we collected clinical primary tumor and liver metastasis samples from patients with pNETs, we conducted a comprehensive analysis of circular RNAs (circRNAs) to identify key circRNAs associated with the onset and metastasis of pNETs. We found that in pNET development and metastasis, 11 genes and 14 circRNAs were notably upregulated, while 25 genes and 35 circRNAs were significantly downregulated, compared to nearby non-cancerous tissue. Our analysis of differentially expressed RNA and circRNA genes revealed that tumor cell adhesion and integrin activation, regulated by genes like PIEZO1, IFT74, SKAP1, GPX1, F7, VTN, and OMG, are strongly linked to pNET metastasis. We found that SKAP1 levels are positively associated with tumor progression in pNET patients. Overall, our research indicates that the SKAP1-mediated pathway is crucial in pNET development and metastasis.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101935"},"PeriodicalIF":2.3,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143349612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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