Pub Date : 2023-12-01DOI: 10.1089/genbio.2023.29122.fli
Fay Lin
{"title":"Revelry and Reminiscence: 50 Years of Recombinant DNA at Cold Spring Harbor Laboratory","authors":"Fay Lin","doi":"10.1089/genbio.2023.29122.fli","DOIUrl":"https://doi.org/10.1089/genbio.2023.29122.fli","url":null,"abstract":"","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"65 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139013095","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 : 2023-12-01DOI: 10.1089/genbio.2023.29123.gli
G. Livshits
{"title":"Landmark CRISPR Approvals and the Rise of Epigenome Editing","authors":"G. Livshits","doi":"10.1089/genbio.2023.29123.gli","DOIUrl":"https://doi.org/10.1089/genbio.2023.29123.gli","url":null,"abstract":"","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"58 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138985998","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 : 2023-12-01DOI: 10.1089/genbio.2023.29119.cbe
Carolyn Bertozzi, Alex Philippidis, Kevin Davies
{"title":"Sweet Dreams are Made of This: An Interview with Carolyn Bertozzi","authors":"Carolyn Bertozzi, Alex Philippidis, Kevin Davies","doi":"10.1089/genbio.2023.29119.cbe","DOIUrl":"https://doi.org/10.1089/genbio.2023.29119.cbe","url":null,"abstract":"","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"399 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139022948","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 : 2023-12-01DOI: 10.1089/genbio.2023.0049
Alice Ghidini, Aleksandra Singh
{"title":"The RNA-Recognition Pathway: An Overlooked Transportation Mechanism for Extracellular and Therapeutic RNAs","authors":"Alice Ghidini, Aleksandra Singh","doi":"10.1089/genbio.2023.0049","DOIUrl":"https://doi.org/10.1089/genbio.2023.0049","url":null,"abstract":"","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"111 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139015491","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 : 2023-11-17DOI: 10.1089/genbio.2023.29118.cfp
Brian Aguado, Karmella Haynes, Ana Maria Porras
{"title":"Call for Special Issue Papers: Diversity, Equity, and Inclusion in Biotechnology","authors":"Brian Aguado, Karmella Haynes, Ana Maria Porras","doi":"10.1089/genbio.2023.29118.cfp","DOIUrl":"https://doi.org/10.1089/genbio.2023.29118.cfp","url":null,"abstract":"","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"32 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139262809","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 : 2023-10-27DOI: 10.1089/genbio.2023.0014
Alireza Daneshvar, Stefan N. Lukianov
Over 5% of newborns suffer from a genetic disease. These include single gene, polygenic, and chromosomal disorders. Many other noncongenital diseases with genetic components are activated by environmental triggers (autoimmune, cancer, and tissue injury). Sophisticated viral gene therapies could treat, and possibly cure, these diseases and significantly ease patient burden and improve quality of life. Current viral therapies are mostly limited to plasmid-based and adeno-associated virus variants with inefficient response rates and limited use, with some herpes, lenti, and retroviral modalities. Development is slow and expensive. Virtual prototyping of viral gene therapies through computational design, like in other engineering fields, may represent a useful process to accelerate and expand viral pipeline development by opening the human virome to therapeutic development and constructing specificity, potency, efficacy, and safety in silico. Contemporary computational tools (artificial intelligence, machine and deep learning, computer-aided design, high performance computing, cloud and edge computing, and physics-based modeling) now render this possibility feasible and, therefore, constitute powerful options for biopharma researchers to expand and accelerate precision medicine research and development for complex indications.
{"title":"Artificial Intelligence-Mediated Computer-Aided Design of Viral Gene Therapies","authors":"Alireza Daneshvar, Stefan N. Lukianov","doi":"10.1089/genbio.2023.0014","DOIUrl":"https://doi.org/10.1089/genbio.2023.0014","url":null,"abstract":"Over 5% of newborns suffer from a genetic disease. These include single gene, polygenic, and chromosomal disorders. Many other noncongenital diseases with genetic components are activated by environmental triggers (autoimmune, cancer, and tissue injury). Sophisticated viral gene therapies could treat, and possibly cure, these diseases and significantly ease patient burden and improve quality of life. Current viral therapies are mostly limited to plasmid-based and adeno-associated virus variants with inefficient response rates and limited use, with some herpes, lenti, and retroviral modalities. Development is slow and expensive. Virtual prototyping of viral gene therapies through computational design, like in other engineering fields, may represent a useful process to accelerate and expand viral pipeline development by opening the human virome to therapeutic development and constructing specificity, potency, efficacy, and safety in silico. Contemporary computational tools (artificial intelligence, machine and deep learning, computer-aided design, high performance computing, cloud and edge computing, and physics-based modeling) now render this possibility feasible and, therefore, constitute powerful options for biopharma researchers to expand and accelerate precision medicine research and development for complex indications.","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"28 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136311682","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 : 2023-10-01DOI: 10.1089/genbio.2023.0029
Niyati Jhaveri, Bassem Ben Cheikh, Nadezhda Nikulina, Ning Ma, Dmytro Klymyshyn, James DeRosa, Ritu Mihani, Aditya Pratapa, Yasmin Kassim, Sidharth Bommakanti, Olive Shang, Shannon Berry, Nicholas Ihley, Michael McLane, Yan He, Yi Zheng, James Monkman, Caroline Cooper, Ken O'Byrne, Bhaskar Anand, Michael Prater, Subham Basu, Brett G.M. Hughes, Arutha Kulasinghe, Oliver Braubach
Head and neck squamous cell carcinomas (HNSCCs) are the seventh most common cancer and represent a global health burden. Immune checkpoint inhibitors (ICIs) have shown promise in treating recurrent/metastatic disease with durable benefit in ∼30% of patients. Current biomarkers for HNSCC are limited in their dynamic ability to capture tumor microenvironment (TME) features with an increasing need for deeper tissue characterization. Therefore, new biomarkers are needed to accurately stratify patients and predict responses to therapy. Here, we have optimized and applied an ultra-high plex, single-cell spatial protein analysis in HNSCC. Tissues were analyzed with a panel of 101 antibodies that targeted biomarkers related to tumor immune, metabolic and stress microenvironments. Our data uncovered a high degree of intra-tumoral heterogeneity intrinsic to HNSCC and provided unique insights into the biology of the disease. In particular, a cellular neighborhood analysis revealed the presence of six unique spatial neighborhoods enriched in functionally specialized immune subsets. In addition, functional phenotyping based on key metabolic and stress markers identified four distinct tumor regions with differential protein signatures. One region was marked by infiltration of CD8+ cytotoxic T cells and overexpression of BAK, a proapoptotic regulator, suggesting strong immune activation and stress. Another adjacent region within the same tumor had high expression of G6PD and MMP9, known drivers of tumor resistance and invasion, respectively. This dichotomy of immune activation-induced death and tumor progression in the same sample demonstrates the heterogenous niches and competing microenvironments that may underpin variable clinical responses. Our data integrate single-cell ultra-high plex spatial information with the functional state of the TME to provide insights into HNSCC biology and differential responses to ICI therapy. We believe that the approach outlined in this study will pave the way toward a new understanding of TME features associated with response and sensitivity to ICI therapies.
{"title":"Mapping the Spatial Proteome of Head and Neck Tumors: Key Immune Mediators and Metabolic Determinants in the Tumor Microenvironment","authors":"Niyati Jhaveri, Bassem Ben Cheikh, Nadezhda Nikulina, Ning Ma, Dmytro Klymyshyn, James DeRosa, Ritu Mihani, Aditya Pratapa, Yasmin Kassim, Sidharth Bommakanti, Olive Shang, Shannon Berry, Nicholas Ihley, Michael McLane, Yan He, Yi Zheng, James Monkman, Caroline Cooper, Ken O'Byrne, Bhaskar Anand, Michael Prater, Subham Basu, Brett G.M. Hughes, Arutha Kulasinghe, Oliver Braubach","doi":"10.1089/genbio.2023.0029","DOIUrl":"https://doi.org/10.1089/genbio.2023.0029","url":null,"abstract":"Head and neck squamous cell carcinomas (HNSCCs) are the seventh most common cancer and represent a global health burden. Immune checkpoint inhibitors (ICIs) have shown promise in treating recurrent/metastatic disease with durable benefit in ∼30% of patients. Current biomarkers for HNSCC are limited in their dynamic ability to capture tumor microenvironment (TME) features with an increasing need for deeper tissue characterization. Therefore, new biomarkers are needed to accurately stratify patients and predict responses to therapy. Here, we have optimized and applied an ultra-high plex, single-cell spatial protein analysis in HNSCC. Tissues were analyzed with a panel of 101 antibodies that targeted biomarkers related to tumor immune, metabolic and stress microenvironments. Our data uncovered a high degree of intra-tumoral heterogeneity intrinsic to HNSCC and provided unique insights into the biology of the disease. In particular, a cellular neighborhood analysis revealed the presence of six unique spatial neighborhoods enriched in functionally specialized immune subsets. In addition, functional phenotyping based on key metabolic and stress markers identified four distinct tumor regions with differential protein signatures. One region was marked by infiltration of CD8+ cytotoxic T cells and overexpression of BAK, a proapoptotic regulator, suggesting strong immune activation and stress. Another adjacent region within the same tumor had high expression of G6PD and MMP9, known drivers of tumor resistance and invasion, respectively. This dichotomy of immune activation-induced death and tumor progression in the same sample demonstrates the heterogenous niches and competing microenvironments that may underpin variable clinical responses. Our data integrate single-cell ultra-high plex spatial information with the functional state of the TME to provide insights into HNSCC biology and differential responses to ICI therapy. We believe that the approach outlined in this study will pave the way toward a new understanding of TME features associated with response and sensitivity to ICI therapies.","PeriodicalId":73134,"journal":{"name":"GEN biotechnology","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135809421","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 : 2023-10-01DOI: 10.1089/genbio.2023.29113.fdu
Fyodor D. Urnov, Jonathan D. Grinstein
GEN BiotechnologyVol. 2, No. 5 Asked & AnsweredFree AccessEngineering CRISPR Cures: An Interview with Fyodor UrnovFyodor D. Urnov and Jonathan D. GrinsteinFyodor D. Urnov*Address correspondence to: Fyodor D. Urnov, Director of the Center for Translational Genomics at the Innovative Genomics Institute. E-mail Address: [email protected]Director of the Center for Translational Genomics at the Innovative Genomics Institute.Search for more papers by this author and Jonathan D. GrinsteinSenior Editor, GEN Media Group.Search for more papers by this authorPublished Online:16 Oct 2023https://doi.org/10.1089/genbio.2023.29113.fduAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Fyodor Urnov, Director of the Center for Translational Genomics at the Innovative Genomics Institute (IGI)Fyodor Urnov is a pioneer in the field of genome editing and one of the scientists most invested in expanding the availability and utility of CRISPR-based therapies to the broadest possible population. He envisions a world in which genome editing can treat the nearly 400 million people who are suffering from one of the 7000 diseases brought on by gene mutations.After his PhD in 1996 from Brown University, Urnov worked as a postdoctoral fellow in the laboratory of Alan Wolffe at the National Institutes of Health (NIH). In 2000, Urnov joined Wolffe in moving to Sangamo Therapeutics in California. During his 16 years at Sangamo, Urnov and his colleagues performed the first demonstration using zinc-finger nucleases to modify DNA in human cells in 2005, coining the term “genome editing” in the process.1After that, Urnov led collaborative teams that created large-scale genome editing applications in crop genetics, model animal reverse genetics, and human somatic cell genetics. While at Sangamo, Urnov also led a cross-functional team from basic discovery to the initial design of the first-in-human clinical trials for sickle cell disease and beta-thalassemia, which are being conducted in collaboration with UCSF Benioff Children's Hospital and UCLA Broad Stem Cell Research Center.In 2019, Urnov became the Director of the Center for Translational Genomics at the Innovative Genomics Institute (IGI), working alongside Nobel laureate Jennifer Doudna, and a Professor in the Departments of Genetics, Genomics, and Development at the University of California, Berkeley. At the IGI, Urnov works in collaborative teams to develop first-in-human applications of experimental CRISPR-based therapeutics for sickle cell disease (with Mark Walters, UCSF), genetic disorders of the immune system (with Alexander Marson, UCSF/IGI), radiation injury (with Jonathan Weissman, MIT/Whitehead Institute), cystic fibrosis (with Ross Wilson, IGI), and neurological disorders (with Weill Neurohub and Roche/Genentech).In this exclusive interview, GEN Biotechnology talks to Urnov about his career in
创BiotechnologyVol。free AccessEngineering CRISPR Cures: a Interview with Fyodor D. Urnov and Jonathan D. GrinsteinFyodor D. Urnov*通讯地址:Fyodor D. Urnov, Innovative Genomics Institute翻译基因组学中心主任。电子邮件地址:[email protected]创新基因组学研究所转化基因组学中心主任。搜索本作者和Jonathan D. grinstein (GEN Media Group高级编辑)的更多论文。搜索本文作者的更多论文发表在线:2023年10月16日https://doi.org/10.1089/genbio.2023.29113.fduAboutSectionsPDF/EPUB权限& CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites返回出版物共享共享onFacebookTwitterLinked InRedditEmail Fyodor Urnov，创新基因组学研究所(IGI)转化基因组学中心主任Fyodor Urnov是基因组编辑领域的先驱，也是将crispr疗法的可用性和实用性扩展到尽可能广泛的人群中投入最多的科学家之一。他设想了一个基因组编辑可以治疗近4亿人的世界，这些人患有由基因突变引起的7000种疾病中的一种。1996年从布朗大学获得博士学位后，乌尔诺夫在美国国立卫生研究院(NIH)的艾伦·沃尔夫实验室担任博士后研究员。2000年，乌尔诺夫和沃尔夫一起搬到了加州的Sangamo Therapeutics。在Sangamo工作的16年里，乌尔诺夫和他的同事们在2005年首次演示了使用锌指核酸酶修饰人类细胞中的DNA，并在此过程中创造了“基因组编辑”一词。之后，乌尔诺夫领导的合作团队在作物遗传学、模型动物反向遗传学和人类体细胞遗传学方面创造了大规模的基因组编辑应用。在Sangamo期间，Urnov还领导了一个跨职能团队，从基础发现到最初设计镰状细胞病和-地中海贫血的首次人体临床试验，该团队正在与UCSF Benioff儿童医院和UCLA Broad干细胞研究中心合作进行。2019年，乌尔诺夫成为创新基因组学研究所(IGI)转化基因组学中心主任，与诺贝尔奖获得者詹妮弗·杜德纳(Jennifer Doudna)合作，并担任加州大学伯克利分校遗传学、基因组学和发展系教授。在IGI, Urnov与合作团队合作开发基于crispr的实验性治疗方法的首次人体应用，用于镰状细胞病(与Mark Walters, UCSF)，免疫系统遗传疾病(与Alexander Marson, UCSF/IGI)，辐射损伤(与Jonathan Weissman, MIT/Whitehead研究所)，囊性纤维化(与Ross Wilson, IGI)和神经系统疾病(与Weill Neurohub和Roche/Genentech)。在这次独家采访中，GEN Biotechnology与乌尔诺夫谈论了他在基因组编辑方面的职业生涯，从他早期在Sangamo的工作，到他与查尔斯·格斯巴赫和松野彰(总裁兼首席财务官)共同创立的Tune Therapeutics公司。他详细阐述了他的“按需CRISPR治疗”计划，以及阻碍他实现目标的挑战。(考虑到篇幅和准确性，本文经过了轻微编辑。)我通读了你2021年在《分子疗法》(Molecular Therapy)上发表的文章(《想象一下CRISPR疗法》)，我猜这篇文章参考了约翰·列侬(John Lennon)的歌曲，以及你2022年在《纽约时报》(New York Times)上发表的专栏文章(《我们可以通过编辑人的DNA来治愈疾病》)。为什么我们不是?”)在这些文章中，您列出了使CRISPR治疗n = 1疾病和罕见疾病成为现实所需的改进。在实现你的crispr按需治疗愿景方面，我们今天进展如何?乌尔诺夫:摆在我们面前的临床数据表明，基因疗法可以治愈严重疾病。这不是给定的。基因工程治疗疾病是1972年由加州大学圣地亚哥分校的泰德·弗里德曼提出的。那是50年前的事了!第一次基因治疗试验于1989年在美国国立卫生研究院进行。基因疗法能够起作用的曙光出现在本世纪头十年;CRISPR于2012年上线;2019年，首例人类接受了CRISPR治疗。回顾当时，我们很难想象，从1989年到2010年初这段早期的孵化期，一切都很顺利，有时也会出现故障。但后来这个领域取得了长足的进步，我们现在有15-20种基因疗法，仅仅是针对血液疾病，我们有相当惊人的疗效。我说的治愈，并不是指病人稍微好转。我的意思是像腺苷脱氨酶缺乏症，严重的综合免疫缺陷。唐·科恩(加州大学洛杉矶分校)和克莱尔·布斯(伦敦大学学院)有50个孩子肯定会死，他们基本上通过基因疗法治愈了，有两个病例通过骨髓移植治愈了。 我们早在21世纪初就知道我们可以做到这一点，但当你想到设计新型蛋白质的能力时，无论是在与DNA结合方面还是在改变表观基因组方面，当我们想到快速分析它们效力的方法时，它们是否能满足我们的需求，它们的特异性有多强?他们会去别的地方转化其他基因组吗?当我们考虑如何将它们输送到身体的特定细胞或器官时，在过去的20年里，所有这些都经历了一个渐进的变化，它经历了一个渐进的变化，我们可以把一个大型动物，比如人类灵长类动物，注射一茶匙由脂质纳米颗粒(LNP)配制的表观基因组编辑器。把它注射到猴子的血液循环中。LNP内部是一个表观基因组编辑器，用于关闭导致心血管疾病的基因。你瞧，在使用这种肾上腺素编辑器的几周内，基因就消失了。这是一个惊人的成就，只要这个系统被观察到，这个基因就不会出现。我们一直希望能够调整基因的开关，不仅仅是开或关，而是把它想象成一个音板，多一点低音，少一点高音，多一点鼓，当然少一点牛铃!这就是表观基因组编辑让你做的。就像你可以打开一个基因，也可以关闭一个基因，但你也可以调整它。声音输出，你不需要改变DNA序列。你只需在那个基因上加入新的分子组成，而不改变DNA的表达方式，基因就会礼貌地顺从。这是Spark Notes版本。25年前，当你还是已故艾伦·沃尔夫(Alan Wolffe)的博士后时，Tune Therapeutics实现了你的梦想吗?莫斯科:绝对!图灵相信表观遗传学和染色质是了解人类基因运作的关键。在20世纪90年代的时候，我们知道染色质的存在，但是人们认为染色质的存在是为了让真正的行动开始。我们现在知道情况并非如此，但在当时，它并不是研究基因控制或开发治疗方法的人们的首要和中心思想。图灵在两个方面明显领先于他的时代。首先，他只是认为染色质非常深，尽管我们不知道兔子洞有多深。其次，他很年轻。他在2001年的一次事故中不幸去世(42岁)。在过去的20年里，他的专业产出是惊人的。他是NIH历史上被任命为实验室主任的最年轻的实验室主任。他写了关于染色质和表观遗传学的权威专著，这是在这个领域工作的每个人的桌子上。我永远不会忘记我职业生涯中最具影响力的一
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