Biotechnology and Bioengineering最新文献

{"title":"Insights into yeast response to chemotherapeutic agent through time series genome-scale metabolic models","authors":"Muhammed E. Karabekmez","doi":"10.1002/bit.28833","DOIUrl":"10.1002/bit.28833","url":null,"abstract":"<p>Organism-specific genome-scale metabolic models (GSMMs) can unveil molecular mechanisms within cells and are commonly used in diverse applications, from synthetic biology, biotechnology, and systems biology to metabolic engineering. There are limited studies incorporating time-series transcriptomics in GSMM simulations. Yeast is an easy-to-manipulate model organism for tumor research. Here, a novel approach (TS-GSMM) was proposed to integrate time-series transcriptomics with GSMMs to narrow down the feasible solution space of all possible flux distributions and attain time-series flux samples. The flux samples were clustered using machine learning techniques, and the clusters' functional analysis was performed using reaction set enrichment analysis. A time series transcriptomics response of Yeast cells to a chemotherapeutic reagent—doxorubicin—was mapped onto a Yeast GSMM. Eleven flux clusters were obtained with our approach, and pathway dynamics were displayed. Induction of fluxes related to bicarbonate formation and transport, ergosterol and spermidine transport, and ATP production were captured. Integrating time-series transcriptomics data with GSMMs is a promising approach to reveal pathway dynamics without any kinetic modeling and detects pathways that cannot be identified through transcriptomics-only analysis. The codes are available at https://github.com/karabekmez/TS-GSMM.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 10","pages":"3351-3359"},"PeriodicalIF":3.5,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28833","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142090516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increase in polyunsaturated fatty acids and carotenoid accumulation in the microalga Golenkinia brevispicula (Chlorophyceae) by manipulating spectral irradiance and salinity","authors":"T. A. Rearte,&nbsp;P. S. M. Celis-Pla,&nbsp;R. Abdala-Díaz,&nbsp;P. Castro-Varela,&nbsp;S. N. Marsili,&nbsp;C. García,&nbsp;M. C. Cerón-García,&nbsp;F. L. Figueroa","doi":"10.1002/bit.28831","DOIUrl":"10.1002/bit.28831","url":null,"abstract":"<p>Microalgal biotechnology offers a promising platform for the sustainable production of diverse renewable bioactive compounds. The key distinction from other microbial bioprocesses lies in the critical role that light plays in cultures, as it serves as a source of environmental information to control metabolic processes. Therefore, we can use these criteria to design a bioprocess that aims to stimulate the accumulation of target molecules by controlling light exposure. We study the effect on biochemical and photobiological responses of <i>Golenkinia brevispicula</i> FAUBA-3 to the exposition of different spectral irradiances (specifically, high-fluence PAR of narrow yellow spectrum complemented with low intensity of monochromatic radiations of red, blue, and UV-A) under prestress and salinity stress conditions. High light (HL) intensity coupled to salinity stress affected the photosynthetic activity and photoprotection mechanisms as shown by maximal quantum yield (<i>F</i>_<i>v</i><i>/F</i>_<i>m</i>) and non-photochemical quenching (NPQ_max) reduction, respectively. HL treatments combined with the proper dose of UV-A radiation under salinity stress induced the highest carotenoid content (2.75 mg g dry weight [DW]⁻¹) composed mainly of lutein and β-carotene, and the highest lipid accumulation (35.3% DW) with the highest polyunsaturated fatty acid content (alpha-linolenic acid (C18:3) and linoleic acid (C18:2)). Our study can guide the strategies for commercial indoor production of <i>G. brevispicula</i> for high-value metabolites.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3715-3727"},"PeriodicalIF":3.5,"publicationDate":"2024-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multidose transient transfection of human embryonic kidney 293 cells modulates recombinant adeno-associated virus2/5 Rep protein expression and influences the enrichment fraction of filled capsids","authors":"Prasanna Srinivasan,&nbsp;Christopher T. Canova,&nbsp;Sha Sha,&nbsp;Tam N. T. Nguyen,&nbsp;John Joseph,&nbsp;Jose Sangerman,&nbsp;Andrew J. Maloney,&nbsp;Georgios Katsikis,&nbsp;Rui Wen Ou,&nbsp;Moo Sun Hong,&nbsp;Jaclyn Ng,&nbsp;Arella Yuan,&nbsp;Daniel Antov,&nbsp;Sally Song,&nbsp;Wenyu Chen,&nbsp;Caleb Neufeld,&nbsp;Jacqueline M. Wolfrum,&nbsp;Paul W. Barone,&nbsp;Anthony J. Sinskey,&nbsp;Stacy L. Springs,&nbsp;Richard D. Braatz","doi":"10.1002/bit.28828","DOIUrl":"10.1002/bit.28828","url":null,"abstract":"<p>Recombinant adeno-associated virus (rAAV) is a commonly used in vivo gene therapy vector because of its nonpathogenicity, long-term transgene expression, broad tropism, and ability to transduce both dividing and nondividing cells. However, rAAV vector production via transient transfection of mammalian cells typically yields a low fraction of filled-to-total capsids (~1%–30% of total capsids produced). Analysis of our previously developed mechanistic model for rAAV2/5 production attributed these low fill fractions to a poorly coordinated timeline between capsid synthesis and viral DNA replication and the repression of later phase capsid formation by Rep proteins. Here, we extend the model by quantifying the expression dynamics of total Rep proteins and their influence on the key steps of rAAV2/5 production using a multiple dosing transfection of human embryonic kidney 293 (HEK293) cells. We report that the availability of preformed empty capsids and viral DNA copies per cell are not limiting to the capsid-filling reaction. However, optimal expression of Rep proteins (&lt;240 ± 13 ag per cell) enables enrichment of the filled capsid population (&gt;12% of total capsids/cell) upstream. Our analysis suggests increased enrichment of filled capsids via regulating the expression of Rep proteins is possible but at the expense of per cell capsid titer in a triple plasmid transfection. Our study reveals an intrinsic limitation of scaling rAAV2/5 vector genome (vg) production and underscores the need for approaches that allow for regulating the expression of Rep proteins to maximize vg titer per cell upstream.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3694-3714"},"PeriodicalIF":3.5,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic mutational analysis reveals an essential role of N275 in IgE stability","authors":"Shikha Kumari,&nbsp;Sanjay Ghosh,&nbsp;Saurabh Joshi,&nbsp;Ralf Guenther,&nbsp;Vanessa Siegmund,&nbsp;Achim Doerner","doi":"10.1002/bit.28826","DOIUrl":"10.1002/bit.28826","url":null,"abstract":"<p>Therapeutic antibodies have predominantly been IgG-based. However, the ongoing clinical trial of MOv18 IgE has highlighted the potential of using IgE antibodies in cancer therapy. While extensive studies targeting IgG glycosylation resulted in a rational basis for the development of enhanced biotherapeutics, IgE glycosylation remains an area with limited analyses. Previous studies on the role of IgE glycosylation present conflicting data with one study emphasizing the importance of N275 and T277 residues for FcεRI binding whereas another asserts the nonsignificance of IgE glycosylation in receptor interaction. While existing literature underscores the significance of glycans at the N275 position for binding to FcεR1 receptor and initiation of anaphylaxis, the role of other IgE glycosylation sites in folding or receptor binding remains elusive. This study systematically investigates the functional significance of N-linked glycosylation sites in the heavy chain of IgE which validates the pivotal role of N275 residue in IgE secretion and stability. Replacement of this asparagine to non-amine group moieties does not affect IgE function in vitro, yet substitution with aspartic acid compromises antibody yield. The deglycosylated IgE variant exhibits superior efficacy, challenging the conventional importance of glycosylation for effector function. In summary, our study unveils an intricate relationship between N-glycosylation sites and the structural–functional dynamics of IgE antibodies. Furthermore, it offers novel insights into the IgE scaffold, paving the way for the development of more effective and stable IgE-based therapeutics.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3782-3795"},"PeriodicalIF":3.5,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CILF: CRISPR/Cas9 based integration of large DNA fragments in Saccharomyces cerevisiae","authors":"Shijie Xu,&nbsp;Jie Meng,&nbsp;Qi Zhang,&nbsp;Baisong Tong,&nbsp;Zihe Liu,&nbsp;Jinyu Fu,&nbsp;Shuobo Shi","doi":"10.1002/bit.28830","DOIUrl":"10.1002/bit.28830","url":null,"abstract":"<p>Genome integration technology has markedly expedited the construction of cell factories. However, its application is currently limited by the inefficient integration of large DNA fragments. Here, we report a CRISPR/Cas9 based integration of large DNA fragments (CILF) method to efficiently integrate large DNA fragments in <i>Saccharomyces cerevisiae</i>. In this approach, a fusion protein, Cas9-Brex27-FadR, was employed for the targeted delivery of donor plasmid to double-strand breaks (DSBs), while simultaneously recruiting Rad51 to enhance the efficiency of homologous recombination (HR). Our findings demonstrate that this method can achieve an integration efficiency of 98% for 10 kb DNA fragments and nearly 80% for 40 kb DNA fragments at a single site, using donor plasmids with 1000 bp homology arms (HAs) and 12 FadR binding sites (BSs). The CILF technique significantly enriches the synthetic biology toolbox of <i>S. cerevisiae</i>, offering significant potential to propel advancements in both synthetic biology and metabolic engineering.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3906-3911"},"PeriodicalIF":3.5,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glycosylation in Drosophila S2 cells","authors":"Tingting Xu,&nbsp;Lixiang Tong,&nbsp;Zhifu Zhang,&nbsp;Hairong Zhou,&nbsp;Peilin Zheng","doi":"10.1002/bit.28827","DOIUrl":"10.1002/bit.28827","url":null,"abstract":"<p>In recent years, there has been a remarkable surge in the approval of therapeutic protein drugs, particularly recombinant glycoproteins. <i>Drosophila melanogaster</i> S2 cells have become an appealing platform for the production of recombinant proteins due to their simplicity and low cost in cell culture. However, a significant limitation associated with using the S2 cell expression system is its propensity to introduce simple paucimannosidic glycosylation structures, which differs from that in the mammalian expression system. It is well established that the glycosylation patterns of glycoproteins have a profound impact on the physicochemical properties, bioactivity, and immunogenicity. Therefore, understanding the mechanisms behind these glycosylation modifications and implementing measures to address it has become a subject of considerable interest. This review aims to comprehensively summarize recent advancements in glycosylation modification in S2 cells, with a particular focus on comparing the glycosylation patterns among S2, other insect cells, and mammalian cells, as well as developing strategies for altering the glycosylation patterns of recombinant glycoproteins.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3672-3683"},"PeriodicalIF":3.5,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequential delivery of photosensitizers and checkpoint inhibitors by engineered bacteria for enhanced cancer photodynamic immunotherapy","authors":"Xinyu Liu,&nbsp;Yali Fan,&nbsp;Xinyu Zhang,&nbsp;Lianyue Li,&nbsp;Chao Yang,&nbsp;Xiaoyan Ma,&nbsp;Guijie Bai,&nbsp;Dawei Sun,&nbsp;Yaxin Wang,&nbsp;Junyi Wang,&nbsp;Yong Li,&nbsp;Yanyan Shi,&nbsp;Jing Liu,&nbsp;Yingying Zhang,&nbsp;Hanjie Wang","doi":"10.1002/bit.28829","DOIUrl":"10.1002/bit.28829","url":null,"abstract":"<p>Engineered bacteria-based cancer therapy has increasingly been considered to be a promising therapeutic strategy due to the development of synthetic biology. Wherein, engineering bacteria-mediated photodynamic therapy (PDT)-immunotherapy shows greater advantages and potential in treatment efficiency than monotherapy. However, the unsustainable regeneration of photosensitizers (PSs) and weak immune responses limit the therapeutic efficiency. Herein, we developed an engineered bacteria-based delivery system for sequential delivery of PSs and checkpoint inhibitors in cancer PDT-immunotherapy. The biosynthetic pathway of 5-aminolevulinic acid (5-ALA) was introduced into <i>Escherichia coli</i>, yielding a supernatant concentration of 172.19 mg/L after 10 h of growth. And another strain was endowed with the light-controllable releasement of anti-programmed cell death-ligand 1 nanobodies (anti-PD-L1). This system exhibited a collaborative effect, where PDT initiated tumor cell death and the released tumor cell fragments stimulated immunity, followed by the elimination of residual tumor cells. The tumor inhibition rate reached 74.97%, and the portion of activated T cells and inflammatory cytokines were reinforced. The results demonstrated that the engineered bacteria-based collaborative system could sequentially deliver therapeutic substance and checkpoint inhibitors, and achieve good therapeutic therapy. This paper will provide a new perspective for the cancer PDT-immunotherapy.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 12","pages":"3881-3892"},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnology and Bioengineering: Volume 121, Number 9, September 2024","authors":"","doi":"10.1002/bit.28825","DOIUrl":"https://doi.org/10.1002/bit.28825","url":null,"abstract":"","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 9","pages":"2543-2547"},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28825","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141980404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 high-titer scalable Chinese hamster ovary transient expression platform for production of biotherapeutics","authors":"Juan C. Gonzalez-Rivera,&nbsp;Alberto Galvan,&nbsp;Todd Ryder,&nbsp;Monica Milman,&nbsp;Kitty Agarwal,&nbsp;Lakshmi Kandari,&nbsp;Anurag Khetan","doi":"10.1002/bit.28817","DOIUrl":"10.1002/bit.28817","url":null,"abstract":"<p>Transient gene expression (TGE) in Chinese hamster ovary (CHO) cells offers a route to accelerate biologics development by delivering material weeks to months earlier than what is possible with conventional cell line development. However, low productivity, inconsistent product quality profiles, and scalability challenges have prevented its broader adoption. In this study, we develop a scalable CHO-based TGE system achieving 1.9 g/L of monoclonal antibody in an unmodified host. We integrated continuous flow-electroporation and alternate tangential flow (ATF) perfusion to enable an end-to-end closed system from N-1 perfusion to fed-batch 50-L bioreactor production. Optimization of both the ATF operation for three-in-one application—cell growth, buffer exchange, and cell mass concentration—and the flow-electroporation process, led to a platform for producing biotherapeutics using transiently transfected cells. We demonstrate scalability up to 50-L bioreactor, maintaining a titer over 1 g/L. We also show comparable quality between both transiently and stably produced material, and consistency across batches. The results confirm that purity, charge variants and N-glycan profiles are similar. Our study demonstrates the potential of CHO-based TGE platforms to accelerate biologics process development timelines and contributes evidence supporting its feasibility for manufacturing early clinical material, aiming to strengthen endorsement for TGE's wider implementation.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3454-3470"},"PeriodicalIF":3.5,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemically defined production of engineered cardiac tissue microspheres from hydrogel-encapsulated pluripotent stem cells","authors":"Ferdous B. Finklea,&nbsp;Mohammadjafar Hashemi,&nbsp;Yuan Tian,&nbsp;Hanna Hammons,&nbsp;Caroline Halloin,&nbsp;Wiebke Triebert,&nbsp;Robert Zweigerdt,&nbsp;Elizabeth A. Lipke","doi":"10.1002/bit.28818","DOIUrl":"10.1002/bit.28818","url":null,"abstract":"<p>Chemically defined, suspension culture conditions are a key requirement in realizing clinical translation of engineered cardiac tissues (ECTs). Building on our previous work producing functional ECT microspheres through differentiation of biomaterial encapsulated human induced pluripotent stem cells (hiPSCs), here we establish the ability to use chemically defined culture conditions, including stem cell media (E8) and cardiac differentiation media (chemically defined differentiation media with three components, CDM3). A custom microfluidic cell encapsulation system was used to encapsulate hiPSCs at a range of initial cell concentrations and diameters in the hybrid biomaterial, poly(ethylene glycol)-fibrinogen (PF), for the formation of highly spherical and uniform ECT microspheres for subsequent cardiac differentiation. Initial microsphere diameter could be tightly controlled, and microspheres could be produced with an initial diameter between 400 and 800 µm. Three days after encapsulation, cardiac differentiation was initiated through small molecule modulation of Wnt signaling in CDM3. Cardiac differentiation occurred resulting in in situ ECT formation; results showed that this differentiation protocol could be used to achieve cardiomyocyte (CM) contents greater than 90%, although there was relatively high variability in CM content and yield between differentiation batches. Spontaneous contraction of ECT microspheres initiated between Days 7 and 10 of differentiation and ECT microspheres responded to electrical pacing up to 1.5 Hz. Resulting CMs had well-defined sarcomeres and the gap junction protein, connexin 43, and had appropriate temporal changes in gene expression. In summary, this study demonstrated the proof-of-concept to produce functional ECT microspheres with chemically defined media in suspension culture in combination with biomaterial support of microsphere encapsulated hiPSCs.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3614-3628"},"PeriodicalIF":3.5,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}