Amphibian-derived peptides are promising therapeutics for metabolic dysfunction, oxidative stress, and immune imbalance. We investigated arenin, a Kunitz-type peptide from Dryophytes arenicolor, produced heterologously in E. coli, for anti-metabolic, antioxidant, and immunomodulatory activities. In insulin-resistant hepatocytes, arenin increased glucose uptake from 23.97 ± 2.79% (IR control) to 51.38 ± 2.95% at 250 µg/mL. Arenin also reduced intracellular reactive oxygen species (ROS) in a time-dependent manner. The most significant early effect (20 min) occurred at higher doses (500–1000 µg/mL), whereas at 24 h the effect shifted to lower–intermediate concentrations (15.62–250 µg/mL), with 15.62 µg/mL yielding the lowest ROS levels (15.78 ± 1.66%). In macrophages, nitric oxide (NO) production showed a concentration-dependent, multi-layered response, indicating immunomodulation. These data position arenin as a multifunctional bioactive capable of improving metabolic homeostasis, strengthening antioxidant defenses, and tuning innate immune responses, laying groundwork for peptide-based interventions against metabolic disturbances.
{"title":"Insulin Resistance, Anti-inflammatory, and Antioxidant In vitro Activity of Heterologously Expressed Arenin from Dryophytes arenicolor","authors":"Enrique Hidalgo-Vázquez , Marilena Antunes-Ricardo , Jesús Hernández-Pérez , Jorge Benavides","doi":"10.1016/j.btre.2026.e00947","DOIUrl":"10.1016/j.btre.2026.e00947","url":null,"abstract":"<div><div>Amphibian-derived peptides are promising therapeutics for metabolic dysfunction, oxidative stress, and immune imbalance. We investigated arenin, a Kunitz-type peptide from <em>Dryophytes arenicolor</em>, produced heterologously in <em>E. coli</em>, for anti-metabolic, antioxidant, and immunomodulatory activities. In insulin-resistant hepatocytes, arenin increased glucose uptake from 23.97 ± 2.79% (IR control) to 51.38 ± 2.95% at 250 µg/mL. Arenin also reduced intracellular reactive oxygen species (ROS) in a time-dependent manner. The most significant early effect (20 min) occurred at higher doses (500–1000 µg/mL), whereas at 24 h the effect shifted to lower–intermediate concentrations (15.62–250 µg/mL), with 15.62 µg/mL yielding the lowest ROS levels (15.78 ± 1.66%). In macrophages, nitric oxide (NO) production showed a concentration-dependent, multi-layered response, indicating immunomodulation. These data position arenin as a multifunctional bioactive capable of improving metabolic homeostasis, strengthening antioxidant defenses, and tuning innate immune responses, laying groundwork for peptide-based interventions against metabolic disturbances.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00947"},"PeriodicalIF":0.0,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1016/j.btre.2026.e00945
Ana Falcón-Piñeiro , Alberto Baños , Eva M. Molin , Elías González-Gragera , Annalisa Giampetruzzi , Raied Abou Kubaa , Livio Antonielli , Adrian Wallner , Günter Brader , Satish K. Verma , Antonio M. Martin-Platero , Manuel Martínez-Bueno , Stéphane Compant , Pasquale Saldarelli
Bacillus altitudinis GG-22, isolated from the phyllosphere of agricultural crops, has been identified as a promising biocontrol agent and plant growth-promoting bacterium with substantial potential in sustainable agriculture. In this study, whole-genome sequencing using Illumina technology, combined with ANI analysis, confirmed the strain's classification as B. altitudinis. The genome revealed a rich set of genes involved in biocontrol mechanisms, including the capacity of synthesis of siderophores (schizokinen and bacillibactin-like compounds), the lipopeptide pumilacidin, the bacteriocin pumilarin, alkylpyrones and Bacillus volatiles. In vitro antagonism assays demonstrated significant inhibitory effects against phytopathogenic fungi and oomycetes, such as Verticillium dahliae and Pythium sp., and B. altitudinis GG-22 also showed limited efficacy against bacterial phytopathogens, including Xylella fastidiosa. Transcriptomic profiling of olive trees treated with GG-22 indicated early activation of auxin transport and systemic acquired resistance (SAR) pathways, alongside substantial downregulation of cell wall remodelling genes. These findings suggest that B. altitudinis GG-22 primes plant defence responses and modulates hormonal pathways critical for growth and stress resilience. Future research should prioritize optimizing application strategies and exploring synergies with other microbial agents to fully harness the biocontrol and growth-promoting potential of B. altitudinis GG-22. This strain holds promise for sustainable agricultural practices, particularly in controlling fungal diseases and improving plant performance under stress conditions.
{"title":"Bacillus altitudinis GG-22: A novel plant growth-promoting bacterium with beneficial agronomic properties","authors":"Ana Falcón-Piñeiro , Alberto Baños , Eva M. Molin , Elías González-Gragera , Annalisa Giampetruzzi , Raied Abou Kubaa , Livio Antonielli , Adrian Wallner , Günter Brader , Satish K. Verma , Antonio M. Martin-Platero , Manuel Martínez-Bueno , Stéphane Compant , Pasquale Saldarelli","doi":"10.1016/j.btre.2026.e00945","DOIUrl":"10.1016/j.btre.2026.e00945","url":null,"abstract":"<div><div><em>Bacillus altitudinis</em> GG-22, isolated from the phyllosphere of agricultural crops, has been identified as a promising biocontrol agent and plant growth-promoting bacterium with substantial potential in sustainable agriculture. In this study, whole-genome sequencing using Illumina technology, combined with ANI analysis, confirmed the strain's classification as <em>B. altitudinis</em>. The genome revealed a rich set of genes involved in biocontrol mechanisms, including the capacity of synthesis of siderophores (schizokinen and bacillibactin-like compounds), the lipopeptide pumilacidin, the bacteriocin pumilarin, alkylpyrones and <em>Bacillus</em> volatiles. <em>In vitro</em> antagonism assays demonstrated significant inhibitory effects against phytopathogenic fungi and oomycetes, such as <em>Verticillium dahliae</em> and <em>Pythium</em> sp., and <em>B. altitudinis</em> GG-22 also showed limited efficacy against bacterial phytopathogens, including <em>Xylella fastidiosa</em>. Transcriptomic profiling of olive trees treated with GG-22 indicated early activation of auxin transport and systemic acquired resistance (SAR) pathways, alongside substantial downregulation of cell wall remodelling genes. These findings suggest that <em>B. altitudinis</em> GG-22 primes plant defence responses and modulates hormonal pathways critical for growth and stress resilience. Future research should prioritize optimizing application strategies and exploring synergies with other microbial agents to fully harness the biocontrol and growth-promoting potential of <em>B. altitudinis</em> GG-22. This strain holds promise for sustainable agricultural practices, particularly in controlling fungal diseases and improving plant performance under stress conditions.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00945"},"PeriodicalIF":0.0,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-12DOI: 10.1016/j.btre.2026.e00946
Valentina Varela , Monique Costa , Cecilia Maciel , Joaquín Barbeito , Exequiel E. Barrera , Erica Gutierre , Agustín Correa , Melania Elgue , Sebastián Carrasco , Magdalena Domínguez Larrosa , María Pereira , Josefina Correa , Nadia Crosignani , Joseph S. Beckman , Luis Barbeito , Emiliano Trias
Anti-NGF monoclonal antibodies have recently been approved for treating degenerative joint disease, including osteoarthritis pain, in dogs and cats. However, their widespread use is limited by high cost and the requirement for repeated injections. Nerve Growth Factor and Substance P play central roles in the initiation and maintenance of inflammation and chronic pain in OA. There is a pressing need for new, safe, cost-effective therapies that target the underlying mechanisms of OA chronic pain. Here, we designed and produced a novel recombinant fusion protein, termed rNGFSP, which functions as an immunogen due to its unique molecular structure combining amino acid sequences from NGF and SP in a non-native conformation. When formulated and administered as a vaccine, rNGFSP elicits dual anti-NGF and anti-SP therapeutic antibodies in the host. rNGFSP was produced in E. coli and purified from inclusion bodies using metal affinity chromatography under denaturing conditions. Mass spectrometry confirmed the expected molecular weight (17.5 kDa) and preserved amino acid sequence. Structural prediction using Alphafold2 revealed rNGFSP presented a non-natural folding, but a preserved NGF core and a flexible SP tail, supporting antigenic presentation. Vaccination of mice, rabbits, horses, and dogs, showed that rNGFSP elicited cross-reactive IgG antibodies against the native conformations of NGF and SP. Furthermore, immunoglobulins elicited in vaccinated dogs neutralized the biological activity of NGF and SP in cell cultures, suggesting a therapeutic potential. These findings support rNGFSP as a promising vaccine candidate simultaneously targeting endogenous NGF and SP species, providing a cost-effective alternative to monoclonal antibodies.
{"title":"Production and characterization of rNGFSP: a recombinant fusion immunogen eliciting dual anti-NGF and anti-Substance P therapeutic antibodies for Degenerative Joint Disease","authors":"Valentina Varela , Monique Costa , Cecilia Maciel , Joaquín Barbeito , Exequiel E. Barrera , Erica Gutierre , Agustín Correa , Melania Elgue , Sebastián Carrasco , Magdalena Domínguez Larrosa , María Pereira , Josefina Correa , Nadia Crosignani , Joseph S. Beckman , Luis Barbeito , Emiliano Trias","doi":"10.1016/j.btre.2026.e00946","DOIUrl":"10.1016/j.btre.2026.e00946","url":null,"abstract":"<div><div>Anti-NGF monoclonal antibodies have recently been approved for treating degenerative joint disease, including osteoarthritis pain, in dogs and cats. However, their widespread use is limited by high cost and the requirement for repeated injections. Nerve Growth Factor and Substance P play central roles in the initiation and maintenance of inflammation and chronic pain in OA. There is a pressing need for new, safe, cost-effective therapies that target the underlying mechanisms of OA chronic pain. Here, we designed and produced a novel recombinant fusion protein, termed rNGFSP, which functions as an immunogen due to its unique molecular structure combining amino acid sequences from NGF and SP in a non-native conformation. When formulated and administered as a vaccine, rNGFSP elicits dual anti-NGF and anti-SP therapeutic antibodies in the host. rNGFSP was produced in <em>E. coli</em> and purified from inclusion bodies using metal affinity chromatography under denaturing conditions. Mass spectrometry confirmed the expected molecular weight (17.5 kDa) and preserved amino acid sequence. Structural prediction using Alphafold2 revealed rNGFSP presented a non-natural folding, but a preserved NGF core and a flexible SP tail, supporting antigenic presentation. Vaccination of mice, rabbits, horses, and dogs, showed that rNGFSP elicited cross-reactive IgG antibodies against the native conformations of NGF and SP. Furthermore, immunoglobulins elicited in vaccinated dogs neutralized the biological activity of NGF and SP in cell cultures, suggesting a therapeutic potential. These findings support rNGFSP as a promising vaccine candidate simultaneously targeting endogenous NGF and SP species, providing a cost-effective alternative to monoclonal antibodies.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00946"},"PeriodicalIF":0.0,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145976932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-31DOI: 10.1016/j.btre.2025.e00942
Danilo Menegatti , Giulia Fiscon , Alessandro Giuseppi , Paola Paci , Antonio Pietrabissa
Gene selection from expression data represents a challenging task, primarily due to the high data dimensionality and the vast number of genes that would be identified, many of which may be unrelated to cancer-relevant biological processes. To tackle this issue, filtering methods constitute an effective solution to identify the most informative genes, which can serve as potential biomarkers to tailor cancer therapies. This work proposes a novel neural-based filtering approach which aims to identify genes by means of their latent representation extracted from RNA Sequencing expression data. This approach has been applied to study breast invasive carcinoma dataset, aiming to identify the most relevant genes of two breast cancer subtypes, Luminal-A and Basal-like, to better investigate their molecular landscape.
{"title":"Neural Latent Filtering for Gene Discovery in Breast Cancer Subtypes","authors":"Danilo Menegatti , Giulia Fiscon , Alessandro Giuseppi , Paola Paci , Antonio Pietrabissa","doi":"10.1016/j.btre.2025.e00942","DOIUrl":"10.1016/j.btre.2025.e00942","url":null,"abstract":"<div><div>Gene selection from expression data represents a challenging task, primarily due to the high data dimensionality and the vast number of genes that would be identified, many of which may be unrelated to cancer-relevant biological processes. To tackle this issue, filtering methods constitute an effective solution to identify the most informative genes, which can serve as potential biomarkers to tailor cancer therapies. This work proposes a novel neural-based filtering approach which aims to identify genes by means of their latent representation extracted from RNA Sequencing expression data. This approach has been applied to study breast invasive carcinoma dataset, aiming to identify the most relevant genes of two breast cancer subtypes, Luminal-A and Basal-like, to better investigate their molecular landscape.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00942"},"PeriodicalIF":0.0,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.btre.2025.e00944
Kanokporn Thiganta , Kaewta Rattanapisit , Pipob Suwanchaikasem , Wanlapa Roobsoong , Christine Joy I. Bulaon , Waranyoo Phoolcharoen
Malaria is primarily caused by Plasmodium parasites and remains a major global health threat due to drug resistance and limited vaccine efficacy. Monoclonal antibodies (mAbs) targeting the conserved NANP repeat region of the circumsporozoite protein (PfCSP), such as MS-1797, represent a promising prophylactic strategy. Here, we demonstrate the plant-based production of MS-1797 in glycoengineered Nicotiana benthamiana ΔXF. Two variants were generated: MS-01 (original MS-1797) and MS-02 (MS-1797-SEKDEL), which yielded up to 457.3 µg/g fresh weight and 415.7 µg/g FW at 6 days post-infiltration. The plant-derived mAbs were obtained in high purity (>90%) and displayed either human core glycans or high mannose structures. Notably, both MS-01 and MS-02 retained antigen specificity in vitro and bound native PfCSP on sporozoites by immunofluorescence assay. These results establish the feasibility of producing functional anti-malarial mAbs in plants and highlight their potential use as affordable reagents for malaria research, diagnostics, and future prophylactic interventions.
{"title":"Plant-produced monoclonal antibodies recognize the native circumsporozoite protein on Plasmodium falciparum sporozoites","authors":"Kanokporn Thiganta , Kaewta Rattanapisit , Pipob Suwanchaikasem , Wanlapa Roobsoong , Christine Joy I. Bulaon , Waranyoo Phoolcharoen","doi":"10.1016/j.btre.2025.e00944","DOIUrl":"10.1016/j.btre.2025.e00944","url":null,"abstract":"<div><div>Malaria is primarily caused by <em>Plasmodium</em> parasites and remains a major global health threat due to drug resistance and limited vaccine efficacy. Monoclonal antibodies (mAbs) targeting the conserved NANP repeat region of the circumsporozoite protein (PfCSP), such as MS-1797, represent a promising prophylactic strategy. Here, we demonstrate the plant-based production of MS-1797 in glycoengineered <em>Nicotiana benthamiana</em> ΔXF. Two variants were generated: MS-01 (original MS-1797) and MS-02 (MS-1797-SEKDEL), which yielded up to 457.3 µg/g fresh weight and 415.7 µg/g FW at 6 days post-infiltration. The plant-derived mAbs were obtained in high purity (>90%) and displayed either human core glycans or high mannose structures. Notably, both MS-01 and MS-02 retained antigen specificity <em>in vitro</em> and bound native PfCSP on sporozoites by immunofluorescence assay. These results establish the feasibility of producing functional anti-malarial mAbs in plants and highlight their potential use as affordable reagents for malaria research, diagnostics, and future prophylactic interventions.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00944"},"PeriodicalIF":0.0,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Photoautotrophic cyanobacteria convert CO₂ into bioproducts. However, efficient cell harvesting remains a major obstacle. Auto-bioflocculation offers a promising solution. In cultures of Synechocystis sp. PCC 6803, Synechocystis co-flocculated with natural fungal contaminant (identified as Penicillium sp.) into spherical clusters with internal hollow spaces—but only in the presence of erythromycin (EM), and not without EM. Optimized co-cultivation of Synechocystis and Penicillium for five days in BG11 medium (lacking organic compounds) supplemented with 5 µM EM resulted in complete biomass co-flocculation, yielding up to 2.0 g/L. This corresponds to atmospheric CO₂ capture rate of 0.50 g/L/day, representing a 7.9-fold increase in biomass and a 7.0-fold enhancement in CO₂ capture compared to axenic Synechocystis culture. Protein was the major component of the flocculated biomass, accounting for 39–61 % of dry weight. Increasing EM concentrations (from 0.3 to 10 µM) led to an increase in floc diameter from 0.5 to 1.9 mm. Scaling the culture volume from 100 to 200–1000 mL changed the surface texture of the co-flocculates from relatively smooth to rough with thorn-like structures. Transcriptomic analysis indicated that co-flocculation was associated with upregulation of genes involved in S-layer protein synthesis, molecular chaperones, exopolysaccharide polymerization, and pilin regulation. Genes related to minor pilin proteins, pili function, and capsular polysaccharide synthesis were downregulated. Differentially expressed genes between smooth-surfaced and rough-surfaced co-flocs were reported. This bio-flocculation demonstrates low-energy, organic-free strategy that boosts CO₂ capture, highlighting strong potential for carbon-negative bioprocesses. The protein-rich co-flocs offer opportunities for downstream use in animal feed or biorefinery.
{"title":"Cyanobacterium-Penicillium co-flocculation under erythromycin treatment: increased CO2 capture and biomass production in an organic compound-free co-cultivation","authors":"Jidapa Leksingto , Panutchaya Pichaiyotinkul , Kobkul Boorachokwiwat , Janine Kaewbai-ngam , Nichaphat Kanoksinwuttipong , Nannaphat Sukkasam , Tanakarn Monshupanee","doi":"10.1016/j.btre.2025.e00943","DOIUrl":"10.1016/j.btre.2025.e00943","url":null,"abstract":"<div><div>Photoautotrophic cyanobacteria convert CO₂ into bioproducts. However, efficient cell harvesting remains a major obstacle. Auto-bioflocculation offers a promising solution. In cultures of <em>Synechocystis</em> sp. PCC 6803, <em>Synechocystis</em> co-flocculated with natural fungal contaminant (identified as <em>Penicillium</em> sp.) into spherical clusters with internal hollow spaces—but only in the presence of erythromycin (EM), and not without EM. Optimized co-cultivation of <em>Synechocystis</em> and <em>Penicillium</em> for five days in BG11 medium (lacking organic compounds) supplemented with 5 µM EM resulted in complete biomass co-flocculation, yielding up to 2.0 g/L. This corresponds to atmospheric CO₂ capture rate of 0.50 g/L/day, representing a 7.9-fold increase in biomass and a 7.0-fold enhancement in CO₂ capture compared to axenic <em>Synechocystis</em> culture. Protein was the major component of the flocculated biomass, accounting for 39–61 % of dry weight. Increasing EM concentrations (from 0.3 to 10 µM) led to an increase in floc diameter from 0.5 to 1.9 mm. Scaling the culture volume from 100 to 200–1000 mL changed the surface texture of the co-flocculates from relatively smooth to rough with thorn-like structures. Transcriptomic analysis indicated that co-flocculation was associated with upregulation of genes involved in S-layer protein synthesis, molecular chaperones, exopolysaccharide polymerization, and pilin regulation. Genes related to minor pilin proteins, pili function, and capsular polysaccharide synthesis were downregulated. Differentially expressed genes between smooth-surfaced and rough-surfaced co-flocs were reported. This bio-flocculation demonstrates low-energy, organic-free strategy that boosts CO₂ capture, highlighting strong potential for carbon-negative bioprocesses. The protein-rich co-flocs offer opportunities for downstream use in animal feed or biorefinery.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00943"},"PeriodicalIF":0.0,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-02DOI: 10.1016/j.btre.2025.e00940
Tran Chi Linh , Nguyen Khanh Dung
Type 1 diabetes (T1D) is an autoimmune disease marked by selective destruction of pancreatic β-cells, resulting in absolute insulin deficiency. Although insulin replacement remains the standard therapy, it does not address the underlying autoimmune process or prevent long-term complications. Advances in understanding the pathogenesis have highlighted the interaction of genetic susceptibility, environmental triggers, and immune dysregulation, paving the way for innovative immunotherapies. Current strategies include nonspecific immunosuppressants, monoclonal antibodies (e.g., teplizumab, rituximab), peptide vaccines, and cell-based therapies such as regulatory T cells and stem cells. Among these, teplizumab has gained FDA approval to delay disease onset in high-risk individuals, representing a milestone in preventive intervention. Nevertheless, limited durability, high costs, and safety concerns restrict broader clinical application. Looking forward, personalized treatment strategies, rational drug combinations, and early preclinical interventions are expected to optimize outcomes, offering new hope for improving prognosis and quality of life in T1D patients.
{"title":"Pathogenesis and advances in immunotherapy for type 1 diabetes treatment","authors":"Tran Chi Linh , Nguyen Khanh Dung","doi":"10.1016/j.btre.2025.e00940","DOIUrl":"10.1016/j.btre.2025.e00940","url":null,"abstract":"<div><div>Type 1 diabetes (T1D) is an autoimmune disease marked by selective destruction of pancreatic β-cells, resulting in absolute insulin deficiency. Although insulin replacement remains the standard therapy, it does not address the underlying autoimmune process or prevent long-term complications. Advances in understanding the pathogenesis have highlighted the interaction of genetic susceptibility, environmental triggers, and immune dysregulation, paving the way for innovative immunotherapies. Current strategies include nonspecific immunosuppressants, monoclonal antibodies (e.g., teplizumab, rituximab), peptide vaccines, and cell-based therapies such as regulatory T cells and stem cells. Among these, teplizumab has gained FDA approval to delay disease onset in high-risk individuals, representing a milestone in preventive intervention. Nevertheless, limited durability, high costs, and safety concerns restrict broader clinical application. Looking forward, personalized treatment strategies, rational drug combinations, and early preclinical interventions are expected to optimize outcomes, offering new hope for improving prognosis and quality of life in T1D patients.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00940"},"PeriodicalIF":0.0,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Many diseases have a genetic origin, and analyzing intracellular structures through genetic data yields specific features for the diagnosis and classification of viral disease samples. In this study, 30 types of viruses were analyzed using a graph-based approach on genetic data. Genetic data has been modeled in the form of genomic sequences at the nucleotide scale using the graph theory of complex networks concepts. Degree and eigenvector centrality metrics were employed to extract features. The decision tree was utilized as a machine learning classifier algorithm on the resulting feature space. The results, presented in the form of interpretable rules, enable the classification and identification of virus types from both a binary and multi-class perspective. The model achieved high accuracy and f1 score, which exceeded 99 % on >173,000 samples. Additionally, the feature extraction algorithm demonstrated robust performance across all datasets and classifiers.
{"title":"EIOFX-DT: Leveraging graph centrality metrics for feature extraction and classification of viral genetic sequences","authors":"Amin Khodaei , Zahra Pourabbas , Fatemeh Hashem-zadehdizajyekan , Erfan Esmaeili","doi":"10.1016/j.btre.2025.e00939","DOIUrl":"10.1016/j.btre.2025.e00939","url":null,"abstract":"<div><div>Many diseases have a genetic origin, and analyzing intracellular structures through genetic data yields specific features for the diagnosis and classification of viral disease samples. In this study, 30 types of viruses were analyzed using a graph-based approach on genetic data. Genetic data has been modeled in the form of genomic sequences at the nucleotide scale using the graph theory of complex networks concepts. Degree and eigenvector centrality metrics were employed to extract features. The decision tree was utilized as a machine learning classifier algorithm on the resulting feature space. The results, presented in the form of interpretable rules, enable the classification and identification of virus types from both a binary and multi-class perspective. The model achieved high accuracy and f1 score, which exceeded 99 % on >173,000 samples. Additionally, the feature extraction algorithm demonstrated robust performance across all datasets and classifiers.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"49 ","pages":"Article e00939"},"PeriodicalIF":0.0,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Over the past few decades, technological advancements and declining costs of high-throughput data generation have revolutionized biomedical research, enabling the collection of large-scale datasets across multiple omics layers—including genomics, transcriptomics, proteomics, metabolomics, and epigenomics. The analysis and integration of these datasets provides global insights into biological processes and holds great promise in elucidating the myriad molecular interactions associated with human diseases, particularly multifactorial ones such as cancer, cardiovascular, and neurodegenerative disorders. However, integrating multi-omics data presents significant challenges due to high dimensionality and heterogeneity. This review explores computational methods for integrating multi-omics data, with a particular focus on network-based approaches that offer a holistic view of relationships among biological components in health and disease. Furthermore, this review showcases a selection of recent, successful applications of multi-omics data integration, moving beyond theoretical methods to demonstrate their transformative potential in biomarker discovery, patient stratification, and guiding therapeutic interventions in specific human diseases.
{"title":"Integrating multi-omics data: Methods and applications in human complex diseases","authors":"Pasquale Sibilio , Enrico De Smaele , Paola Paci , Federica Conte","doi":"10.1016/j.btre.2025.e00938","DOIUrl":"10.1016/j.btre.2025.e00938","url":null,"abstract":"<div><div>Over the past few decades, technological advancements and declining costs of high-throughput data generation have revolutionized biomedical research, enabling the collection of large-scale datasets across multiple omics layers—including genomics, transcriptomics, proteomics, metabolomics, and epigenomics. The analysis and integration of these datasets provides global insights into biological processes and holds great promise in elucidating the myriad molecular interactions associated with human diseases, particularly multifactorial ones such as cancer, cardiovascular, and neurodegenerative disorders. However, integrating multi-omics data presents significant challenges due to high dimensionality and heterogeneity. This review explores computational methods for integrating multi-omics data, with a particular focus on network-based approaches that offer a holistic view of relationships among biological components in health and disease. Furthermore, this review showcases a selection of recent, successful applications of multi-omics data integration, moving beyond theoretical methods to demonstrate their transformative potential in biomarker discovery, patient stratification, and guiding therapeutic interventions in specific human diseases.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00938"},"PeriodicalIF":0.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145578651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-15DOI: 10.1016/j.btre.2025.e00937
Chirantan Majumder , Anirban Manna , Satyajit Halder , Somesh Roy , Subhash C Mandal , Kuladip Jana , Mahadeb Pal
Current anti-breast cancer therapies often cause severe toxicity to normal cells and promote chemoresistance, while their exorbitant costs limit their accessibility to many patients. This underscores the need for safer, effective, and affordable alternative treatment strategies. In this study, we evaluated the anti-breast cancer potential of an alkaloid-rich dichloromethane fraction of Ervatamia coronaria (DFE) leaf extract, identified by LC-MS to contain eight indole-alkaloids as its major constituents. Using 4T1 cell-induced tumour allografts in BALB/c mice, alongside cell-based assays including cell viability, scratch assay, immunoblotting, immunohistochemistry, and scanning electron microscopy, we investigated its mechanisms of action. DFE treatment induced cell cycle arrest in the sub-G1 phase, triggering apoptosis, with little effect on normal cells. Mechanistically, elevated mitochondrial ROS were identified as the primary driver of toxicity, as pre-treatment with NAC reversed DFE’s effects. Additionally, DFE downregulated AKT signalling in breast cancer cells. Importantly, DFE significantly reduced 4T1 tumour growth in vivo, both alone and in combination with doxorubicin, without exerting significant toxicity on healthy mice. These findings support further evaluation of DFE in clinical models.
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