Dexun Wang, Qianqian Li, Xiaopeng Diao, Qizun Wang
{"title":"Mitochondrial Oxidative Stress Related Diagnostic Model Accurately Assesses Rheumatoid Arthritis Risk Stratification and Immune Infiltration Characterization","authors":"Dexun Wang, Qianqian Li, Xiaopeng Diao, Qizun Wang","doi":"10.1002/biot.202400615","DOIUrl":"https://doi.org/10.1002/biot.202400615","url":null,"abstract":"<div>\u0000 \u0000 <p>Rheumatoid arthritis (RA) is a chronic autoimmune disease that affects synovial joints, leading to joint destruction, impaired physical function, and reduced quality of life. However, no accurate method for assessing RA risk currently exists. Given the critical role of early detection and intervention in RA management, further comprehensive risk assessments are essential. Mitochondrial oxidative stress (MOS) is a key factor in the initiation and progression of RA. The bidirectional interaction between RA and MOS supports the feasibility of MOS-based risk stratification for RA. Using public databases, we first applied the weighted gene co-expression network analysis (WGCNA) model to identify key genes involved in RA among MOS-related genes. Differential expression patterns of MOS-related genes were then analyzed using various machine learning algorithms to identify potential biomarkers. A nomogram model was established using CDKN1A, GADD45B, and MAFF genes to predict RA risk, followed by an evaluation of its reliability and stability. Additionally, we analyzed MOS-associated molecular subtypes and immune infiltration characteristics. Our findings highlight the significant role of MOS in RA development and underscore the clinical value of personalized treatment strategies.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Federico Di Bisceglie, Javier García Navarro, Eric Lombard, Regina Kratzer, Robert Kourist, Stéphane E. Guillouet
{"title":"Conceptual Approach for Aerobic Autotrophic Gas Cultivation in Shake Flasks: Overcoming the Inhibitory Effects of Oxygen in Cupriavidus necator","authors":"Federico Di Bisceglie, Javier García Navarro, Eric Lombard, Regina Kratzer, Robert Kourist, Stéphane E. Guillouet","doi":"10.1002/biot.202400641","DOIUrl":"https://doi.org/10.1002/biot.202400641","url":null,"abstract":"<div>\u0000 \u0000 <p>This study conceptualizes the design of a small-scale system (250 mL–1 L) for the autotrophic cultivation of hydrogen-oxidizing bacteria, such as the representative strain <i>Cupriavidus necator</i>. The research aimed to systematically investigate the impact of bottle volume and gas composition, particularly oxygen concentration, on the growth and performance of <i>C. necator</i> during autotrophic cultivations. To this end, customized, pressure-tight, baffled glass bottles of various sizes (250, 500, and 1000 mL) and gas mixtures with varying oxygen concentrations (4%, 8%, and 12% v/v) were tested. Growth was monitored by measuring optical density. The maximum specific growth rate (<i>µ</i><sub>max</sub>), the biomass production rate (BPR), the volumetric gas–liquid mass transfer coefficient (<i>k<sub>L</sub>a</i>), and the oxygen transfer rate were calculated. Among the various combinations, the 1000-mL bottles demonstrated the highest <i>µ</i><sub>max</sub> (0.13 h<sup>−1</sup>) and the second-highest BPR (0.074 g L<sup>−1 </sup>h<sup>−1</sup>) at an oxygen concentration of 8%, without the need to refill the headspace. The proposed small-scale system offers a swift and replicable method for concurrently investigating multiple autotrophic cultivations. In this regard, increasing the size of the bottle flask proved to be an efficient strategy to minimize the periodicity for gas refilling. Due to the inhibitory effect of oxygen, changing the liquid–gas volume ratio in hydrogen-driven shake flask cultivation had so far strongly influenced the growth rate. Our results provide a solid foundation for the scaling and optimization of small-scale cultivation of chemolithotrophic bacteria and will facilitate future parallelization and, hence, optimization of metabolic aspects.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Methods for Eluting Intact Extracellular Vesicles From Aptamer-Based Affinity Chromatography: A Critical Evaluation Based on Downstream Applications","authors":"Lian Miller, Manjusri Misra, Huiyan Li","doi":"10.1002/biot.202400648","DOIUrl":"https://doi.org/10.1002/biot.202400648","url":null,"abstract":"<div>\u0000 \u0000 <p>Extracellular vesicles (EVs) are nanosized vesicles released by cells, containing molecular cargo such as proteins and nucleic acids. EVs offer promising avenues for the detection of biomarkers of disease and are excellent candidates for drug delivery and therapeutics. Although EVs can be obtained from biological fluids, it is challenging to obtain intact EVs from complex fluids and there is no universally accepted standard method of isolating EVs. When affinity chromatography-based isolation is used to isolate EVs from complex biofluids, there exist multiple ways to elute intact EVs from capture. This review aims to identify effective EV elution methods for preserving EV integrity and bioactivity after capture on aptamer-functionalized substrates, addressing the requirements of various downstream applications. We hypothesize that when used for elution, different materials and techniques influence the characteristics of EVs, such as their molecular content and bioactivity. The elution reagent and technique must be selected for the intended application for isolated EVs. However, currently, there is no agreement on the optimal elution method for EVs. This literature review aims to evaluate the different methods used to elute intact EVs from capture with regards to the downstream applications of isolated EVs. Based on the results of our analysis of recent literatures, the two elution reagents that are optimal for general purposes of the eluted intact EVs are deoxyribonuclease I and complementary oligonucleotides, as they both preserve EV characteristics that are required for molecular analysis and bioactivity, such as maintained morphology and protein profiles.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rita Ribeiro, Jorge M. B. Vítor, Anastasiya Voronovska, João N. Moreira, João Goncalves
{"title":"Novel Strategy of Antibody Affinity Maturation and Enhancement of Nucleolin-Mediated Antibody-Dependent Cellular Cytotoxicity Against Triple-Negative Breast Cancer","authors":"Rita Ribeiro, Jorge M. B. Vítor, Anastasiya Voronovska, João N. Moreira, João Goncalves","doi":"10.1002/biot.202400380","DOIUrl":"10.1002/biot.202400380","url":null,"abstract":"<div>\u0000 \u0000 <p>Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer that remains an unmet medical need. Because TNBC cells do not express the most common markers of breast cancers, there is an active search for novel molecular targets in triple-negative tumors. Additionally, this subtype of breast cancer presents strong immunogenic characteristics which have been encouraging the development of immunotherapeutic approaches against the disease. In this context, nucleolin arises as a promising target for immunotherapy against TNBC. Our group has previously developed an anti-nucleolin VHH-Fc antibody capable of eliciting antibody-dependent cellular cytotoxicity (ADCC). Moreover, we constructed and characterized an antibody library, that was screened against nucleolin-overexpressing cells, originating an enriched anti-nucleolin antibody pool. In this work, a strategy to select individual clones from the pool was designed, combining NGS data with 3D modeling. Two antibodies demonstrated a significant 4.4- and 6.1-fold increase in binding to nucleolin-overexpressing and TNBC cells, and an improvement in affinity to the sub-micromolar range (0.19 µM and 83.69 nM). Additionally, an increment in 4.6- and 3.1-fold in ADCC activity against respective cell lines was observed for the M2 antibody clone. Herein, the affinity maturation strategy developed was validated and corroborated a positive, but not proportional, correlation between antibody binding, affinity, and ADCC.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Osteochondral Tissue Engineering: Scaffold Materials, Fabrication Techniques and Applications","authors":"Zhenyu Wang, Jie Xu, Jingjing Zhu, Huan Fang, Wanyu Lei, Xinrui Qu, Yuen Yee Cheng, Xiangqin Li, Yanchun Guan, Hongfei Wang, Kedong Song","doi":"10.1002/biot.202400699","DOIUrl":"10.1002/biot.202400699","url":null,"abstract":"<div>\u0000 \u0000 <p>Osteochondral damage, caused by trauma, tumors, or degenerative diseases, presents a major challenge due to the limited self-repair capacity of the tissue. Traditional treatments often result in significant trauma and unpredictable outcomes. Recent advances in bone/cartilage tissue engineering, particularly in scaffold materials and fabrication technologies, offer promising solutions for osteochondral regeneration. This review highlights the selection and design of scaffolds using natural and synthetic materials such as collagen, chitosan (Cs), and polylactic acid (PLA), alongside inorganic components like bioactive glass and nano-hydroxyapatite (nHAp). Key fabrication techniques—freeze-drying, electrospinning, and 3D printing—have improved scaffold porosity and mechanical properties. Special focus is placed on the design of multiphasic scaffolds that mimic natural tissue structures, promoting cell adhesion and differentiation and supporting the regeneration of cartilage and subchondral bone. In addition, the current obstacles and future directions for regenerating damaged osteochondral tissues will be discussed.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meshari Alkandari, Paritosh Barai, Gamal Abdel Nasser Atia, Sara Z. Mohamed, Mohamed Mohamady Ghobashy, Hany K. Shalaby, Tarek Foda, Muhammad Fazle Rabbee, Samir Mallick, Hasi Rani Barai, Mohammad Nazir Hossain
{"title":"Bioactive Functionalized Chitosan Thermo-Responsive Hydrogels as Promising Platforms for Therapeutic, Regenerative Oral, and Maxillofacial Applications","authors":"Meshari Alkandari, Paritosh Barai, Gamal Abdel Nasser Atia, Sara Z. Mohamed, Mohamed Mohamady Ghobashy, Hany K. Shalaby, Tarek Foda, Muhammad Fazle Rabbee, Samir Mallick, Hasi Rani Barai, Mohammad Nazir Hossain","doi":"10.1002/biot.202400653","DOIUrl":"10.1002/biot.202400653","url":null,"abstract":"<div>\u0000 \u0000 <p>Due to their superior physicochemical features, chitosan thermosensitive hydrogels are multipurpose platforms that are frequently used in the biomedical industry. Many investigations have been conducted recently to modify their pore dimensions, expansion, biodegradability, stimulus-reaction characteristics, and other characteristics in order to better tailor them to the complex craniofacial tissues. They have been the focus of various studies that have attempted to load biological cargos for therapeutic and regenerative uses in the oro-facial tissues. This article assesses the utility and advancements of chitosan thermosensitive hydrogel-based pharmaceutical delivery devices for the management of craniofacial disorders such as dental caries, endodontic diseases, periodontitis, temporomandibular disorders, mucosal diseases, cancer, and so forth.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sungje Park, Seunghyeon Shin, Gyucheol Han, Gyun Min Lee
{"title":"Knockout of Pro-Apoptotic BAX and BAK1 Genes in HEK293T Cells Enhances Adeno-Associated Virus (AAV) Production: AAV2 and AAV9","authors":"Sungje Park, Seunghyeon Shin, Gyucheol Han, Gyun Min Lee","doi":"10.1002/biot.202400529","DOIUrl":"10.1002/biot.202400529","url":null,"abstract":"<div>\u0000 \u0000 <p>Increasing demand for adeno-associated virus (AAV) used in gene therapy highlights the need to enhance AAV production. When intracellular AAV2 and extracellular AAV9 were produced in HEK293T cells using the triple transfection method, apoptosis occurred during the AAV production. To mitigate apoptosis induced by AAV production, the pro-apoptotic <i>BAX</i>/<i>BAK1</i> genes were knocked out in HEK293T cells. <i>BAX</i>/<i>BAK1</i> knockout (BBKO) in HEK293T cells significantly increased the production of both AAV2 and AAV9. For AAV2, BBKO increased the genome titer of AAV2 by 55% without negatively affecting the proportion of unwanted empty capsids generated during AAV production. Empty capsid ratios were determined based on viral genome and capsid titers and confirmed via transmission electron microscopy (TEM). Likewise, for AAV9, BBKO increased the genome titer of AAV9 by 66% without negatively affecting the proportion of empty capsids. Additionally, as assessed using a transduction assay, BBKO increased the functional titers of AAV2 and AAV9 by 30% and 46%, respectively. Therefore, BBKO increased AAV production, while maintaining full capsid ratio and infectivity. Taken together, BBKO proved to be an efficient method for enhancing AAV production in HEK293T cells for both AAV2 and AAV9.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ansuman Sahoo, Taku Tsukiadate, Bor-Ruei Lin, Erin Kotzbauer, Jason Houser, Misaal Patel, Xuanwen Li, Sri Ranganayaki Madabhushi
{"title":"Proteomics Reveals Distinctive Host Cell Protein Expression Patterns in Fed-Batch and Perfusion Cell Culture Processes","authors":"Ansuman Sahoo, Taku Tsukiadate, Bor-Ruei Lin, Erin Kotzbauer, Jason Houser, Misaal Patel, Xuanwen Li, Sri Ranganayaki Madabhushi","doi":"10.1002/biot.202400567","DOIUrl":"10.1002/biot.202400567","url":null,"abstract":"<p>Chinese hamster ovary (CHO) cells are widely used to produce recombinant proteins, including monoclonal antibodies (mAbs), through various process modes. While fed-batch (FB) processes have been the standard, a shift toward high-density perfusion processes is being driven by increased productivity, flexible facility footprints, and lower costs. Ensuring the clearance of process-related impurities, such as host cell proteins (HCPs), is crucial in biologics manufacturing. Although purification processes remove most impurities, integrated strategies are being developed to enhance clearance of some high-risk HCPs. Current understanding of HCP expression dynamics in cell culture is limited. This study utilized data-independent acquisition (DIA) proteomics to compare the proteomic profiles of cell culture supernatants from 14 FB clones and three perfusion clones, all expressing the same mAb from the same host cell line. Results showed that perfusion processes enhance cell growth and productivity, exhibiting distinct proteomic profiles compared to FB processes. Perfusion processes also maintain a more comparable HCP abundance profile across clones, especially for 46 problematic HCPs monitored. Cluster analysis of FB proteomics revealed distinct abundance patterns and correlations with process parameters. Differential abundance analysis identified significant protein differences between the two processes. This is the first extensive study characterizing HCPs expressed by clones under different process modes. Further research could lead to strategies for preventing or managing problematic HCPs in biologics manufacturing.</p>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Flexible Hybrid Site-Specific Integration-Based Expression System in CHO Cells for Higher-Throughput Evaluation of Monoclonal Antibody Expression Cassettes","authors":"Alana C. Szkodny, Kelvin H. Lee","doi":"10.1002/biot.202400520","DOIUrl":"10.1002/biot.202400520","url":null,"abstract":"<p>The implementation of site-specific integration (SSI) systems in Chinese hamster ovary (CHO) cells for the production of monoclonal antibodies (mAbs) can alleviate concerns associated with production instability and reduce cell line development timelines. SSI cell line performance is driven by the interaction between genomic integration location, clonal background, and the transgene expression cassette, requiring optimization of all three parameters to maximize productivity. Systematic comparison of these parameters has been hindered by SSI platforms involving low-throughput enrichment strategies, such as cell sorting. This study presents a recombinase-mediated cassette exchange (RMCE)-capable SSI system that uses only chemical selection to enrich for transgene-expressing RMCE pools in less than one month. The system was used to compare eight mAb expression cassettes containing two novel genetic regulatory elements, the <i>Azin1</i> CpG island and the Piggybac transposase 5’ terminal repeat, in various orientations to improve the expression of two therapeutic mAbs from two genomic loci. Similar patterns of productivity and mRNA expression were observed across sites and mAbs, and the best performing cassette universally increased mAb productivity by 7- to 11-fold. This flexible system allows for higher-throughput comparison of expression cassettes from a consistent clonal and transcriptional background to optimize RMCE-derived cell lines for industrial production of mAbs.</p>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}