1
|
Tycko J, Van MV, Aradhana, DelRosso N, Ye H, Yao D, Valbuena R, Vaughan-Jackson A, Xu X, Ludwig C, Spees K, Liu K, Gu M, Khare V, Mukund AX, Suzuki PH, Arana S, Zhang C, Du PP, Ornstein TS, Hess GT, Kamber RA, Qi LS, Khalil AS, Bintu L, Bassik MC. Development of compact transcriptional effectors using high-throughput measurements in diverse contexts. Nat Biotechnol 2024:10.1038/s41587-024-02442-6. [PMID: 39487265 DOI: 10.1038/s41587-024-02442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/20/2024] [Indexed: 11/04/2024]
Abstract
Transcriptional effectors are protein domains known to activate or repress gene expression; however, a systematic understanding of which effector domains regulate transcription across genomic, cell type and DNA-binding domain (DBD) contexts is lacking. Here we develop dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous target genes and test effector function for a library containing 5,092 nuclear protein Pfam domains across varied contexts. We also map context dependencies of effectors drawn from unannotated protein regions using a larger library tiling chromatin regulators and transcription factors. We find that many effectors depend on target and DBD contexts, such as HLH domains that can act as either activators or repressors. To enable efficient perturbations, we select context-robust domains, including ZNF705 KRAB, that improve CRISPRi tools to silence promoters and enhancers. We engineer a compact human activator called NFZ, by combining NCOA3, FOXO3 and ZNF473 domains, which enables efficient CRISPRa with better viral delivery and inducible control of chimeric antigen receptor T cells.
Collapse
Affiliation(s)
- Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Mike V Van
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Hanrong Ye
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Alun Vaughan-Jackson
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Connor Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Katherine Liu
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Mingxin Gu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Venya Khare
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | | | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sophia Arana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Catherine Zhang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Thea S Ornstein
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Gaelen T Hess
- Department of Biomolecular Chemistry and Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Roarke A Kamber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Kamizono J, Nishikawaji Y, Nagano S, Ikeda M, Horikawa Y, Kamisasanuki T, Mitsui K, Matsuda E, Kosai KI. Triple-regulated conditionally replicating adenovirus for effective and safer treatment of peritoneal carcinomatosis. Biochem Biophys Res Commun 2024; 737:150894. [PMID: 39481189 DOI: 10.1016/j.bbrc.2024.150894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/02/2024]
Abstract
There is no effective therapy for peritoneal carcinomatosis derived from gastric cancer. An ideal conditionally replicating adenovirus (CRA) that selectively replicates in and kills cancer cells has not been developed for gastric cancer-derived peritoneal carcinomatosis. Using our platform technology of CRA regulated and treating tumors with multiple factors (m-CRA), we generated two types of survivin-responsive m-CRAs, Surv.m-CRA-CMVp and Surv.m-CRA-CEAp, consisting of E1A downstream of the survivin promoter, and the mutated E1B gene downstream of the human cytomegalovirus immediate early gene enhancer/promoter and carcinoembryonic antigen promoter, respectively. Survivin mRNA was expressed at high and undetectable levels in two gastric cancer cells and eleven normal cells, respectively. Carcinoembryonic antigen was expressed at high and very low levels in MKN-45 gastric cancer and normal PrEC cells, respectively, and was not detected in other cell types. While both Surv.m-CRA-CEAp and Surv.m-CRA-CMVp exhibited potent cytotoxic effects on MKN-45 cells in vitro, Surv.m-CRA-CEAp significantly reduced cytotoxicity to normal cells compared to Surv.m-CRA-CMVp. Control mice that received an intraperitoneal injection of MKN-45 cells gradually lost body weight and died of peritoneal carcinomatosis within 98 days. In contrast, all mice receiving Surv.m-CRA-CEAp or Surv.m-CRA-CMVp-infected MKN-45 cells increased their body weight and survived 120 days. In conclusion, the triple-regulated Surv.m-CRA-CEAp enhances cancer specificity (i.e., safety) without reducing the potent therapeutic effect for carcinoembryonic antigen-positive gastric cancer-derived peritoneal carcinomatosis. The modified E1B promoter strategy of CRA facilitates the development of novel CRAs for the effective and safe treatment of a variety of refractory cancers.
Collapse
Affiliation(s)
- Junichi Kamizono
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Department of Orthopaedic Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Division of Gene Therapy and Regenerative Medicine, Cognitive and Molecular Research Institute of Brain Diseases, Kurume University, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Yuya Nishikawaji
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Satoshi Nagano
- Department of Orthopaedic Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Center for Innovative Therapy Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; South Kyushu Center for Innovative Medical Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Department of Clinical Physical Therapy, School of Health Sciences, Faculty of Medicine, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Division of Gene Therapy and Regenerative Medicine, Cognitive and Molecular Research Institute of Brain Diseases, Kurume University, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Minako Ikeda
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Yoshiharu Horikawa
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Department of Orthopaedic Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Taro Kamisasanuki
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kaoru Mitsui
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Center for Innovative Therapy Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; South Kyushu Center for Innovative Medical Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Eriko Matsuda
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Ken-Ichiro Kosai
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Center for Innovative Therapy Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; South Kyushu Center for Innovative Medical Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Center for Clinical and Translational Research, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Division of Gene Therapy and Regenerative Medicine, Cognitive and Molecular Research Institute of Brain Diseases, Kurume University, 67 Asahi-machi, Kurume, 830-0011, Japan.
| |
Collapse
|
3
|
Lawand PV, Desai S. Nanobiotechnology-Modified Cellular and Molecular Therapy as a Novel Approach for Autoimmune Diabetes Management. Pharm Nanotechnol 2022; 10:279-288. [PMID: 35927916 DOI: 10.2174/2211738510666220802111315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Several cellular and molecular therapies such as stem cell therapy, cell replacement therapy, gene modification therapy, and tolerance induction therapy have been researched to procure a permanent cure for Type 1 Diabetes. However, due to the induction of undesirable side effects, their clinical utility is questionable. These anti-diabetic therapies can be modified with nanotechnological tools for reducing adverse effects by selectively targeting genes and/or receptors involved directly or indirectly in diabetes pathogenesis, such as the glucagon-like peptide 1 receptor, epidermal growth factor receptor, human leukocyte antigen (HLA) gene, miRNA gene and hepatocyte growth factor (HGF) gene. This paper will review the utilities of nanotechnology in stem cell therapy, cell replacement therapy, beta-cell proliferation strategies, immune tolerance induction strategies, and gene therapy for type 1 diabetes management.
Collapse
Affiliation(s)
- Priyanka Vasant Lawand
- Department of Pharmacology, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, India
| | - Shivani Desai
- Department of Pharmacy Practice, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, India
| |
Collapse
|
4
|
Watanabe M, Nishikawaji Y, Kawakami H, Kosai KI. Adenovirus Biology, Recombinant Adenovirus, and Adenovirus Usage in Gene Therapy. Viruses 2021; 13:v13122502. [PMID: 34960772 PMCID: PMC8706629 DOI: 10.3390/v13122502] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is currently in the public spotlight. Several gene therapy products, including oncolytic virus (OV), which predominantly replicates in and kills cancer cells, and COVID-19 vaccines have recently been commercialized. Recombinant adenoviruses, including replication-defective adenoviral vector and conditionally replicating adenovirus (CRA; oncolytic adenovirus), have been extensively studied and used in clinical trials for cancer and vaccines. Here, we review the biology of wild-type adenoviruses, the methodological principle for constructing recombinant adenoviruses, therapeutic applications of recombinant adenoviruses, and new technologies in pluripotent stem cell (PSC)-based regenerative medicine. Moreover, this article describes the technology platform for efficient construction of diverse "CRAs that can specifically target tumors with multiple factors" (m-CRAs). This technology allows for modification of four parts in the adenoviral E1 region and the subsequent insertion of a therapeutic gene and promoter to enhance cancer-specific viral replication (i.e., safety) as well as therapeutic effects. The screening study using the m-CRA technology successfully identified survivin-responsive m-CRA (Surv.m-CRA) as among the best m-CRAs, and clinical trials of Surv.m-CRA are underway for patients with cancer. This article also describes new recombinant adenovirus-based technologies for solving issues in PSC-based regenerative medicine.
Collapse
Affiliation(s)
- Maki Watanabe
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Yuya Nishikawaji
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Hirotaka Kawakami
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Ken-Ichiro Kosai
- Department of Gene Therapy and Regenerative Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
- South Kyushu Center for Innovative Medical Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
- Center for Innovative Therapy Research and Application, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
- Center for Clinical and Translational Research, Kagoshima University Hospital, Kagoshima 890-8544, Japan
| |
Collapse
|