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Zong HF, Li X, Han L, Wang L, Liu JJ, Yue YL, Chen J, Ke Y, Jiang H, Xie YQ, Zhang BH, Zhu JW. A novel bispecific antibody drug conjugate targeting HER2 and HER3 with potent therapeutic efficacy against breast cancer. Acta Pharmacol Sin 2024:10.1038/s41401-024-01279-8. [PMID: 38605180 DOI: 10.1038/s41401-024-01279-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Antibody drug conjugate (ADC) therapy has become one of the most promising approaches in cancer immunotherapy. Bispecific targeting could enhance the efficacy and safety of ADC by improving its specificity, affinity and internalization. In this study we constructed a HER2/HER3-targeting bispecific ADC (BsADC) and characterized its physiochemical properties, target specificity and internalization in vitro, and assessed its anti-tumor activities in breast cancer cell lines and in animal models. The HER2/HER3-targeting BsADC had a drug to antibody ratio (DAR) of 2.89, displayed a high selectivity against the target JIMT-1 breast cancer cells in vitro, as well as a slightly higher level of internalization than HER2- or HER3-monospecific ADCs. More importantly, the bispecific ADC potently inhibited the viability of MCF7, JIMT-1, BT474, BxPC-3 and SKOV-3 cancer cells in vitro. In JIMT-1 breast cancer xenograft mice, a single injection of bispecific ADC (3 mg/kg, i.v.) significantly inhibited the tumor growth with an efficacy comparable to that caused by combined injection of HER2 and HER3-monospecific ADCs (3 mg/kg for each). Our study demonstrates that the bispecific ADC concept can be applied to development of more potent new cancer therapeutics than the monospecific ADCs.
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Affiliation(s)
- Hui-Fang Zong
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
- Jecho Institute Co., Ltd., Shanghai, 200240, China
| | - Xi Li
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Han
- Jecho Institute Co., Ltd., Shanghai, 200240, China
| | - Lei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun-Jun Liu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ya-Li Yue
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Chen
- Jecho Institute Co., Ltd., Shanghai, 200240, China
| | - Yong Ke
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Jiang
- Jecho Laboratories, Inc., Frederick, MD, 21704, USA
| | - Yue-Qing Xie
- Jecho Institute Co., Ltd., Shanghai, 200240, China
- Jecho Laboratories, Inc., Frederick, MD, 21704, USA
| | - Bao-Hong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jian-Wei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Jecho Institute Co., Ltd., Shanghai, 200240, China.
- Jecho Laboratories, Inc., Frederick, MD, 21704, USA.
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Sarkar A, Hildebrandt ER, Patel KV, Mai ET, Shah SS, Kim JH, Schmidt WK. Comprehensive analysis of CXXX sequence space reveals that S. cerevisiae GGTase-I mainly relies on a 2X substrate determinants. bioRxiv 2024:2024.03.04.583369. [PMID: 38496651 PMCID: PMC10942308 DOI: 10.1101/2024.03.04.583369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a three-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C - cysteine, a - aliphatic, L - often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving two distinct reporters were employed in this study to assess S. cerevisiae GGTase-I specificity, for which limited data exists, towards all 8000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of non-canonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a non-polar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity.
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Affiliation(s)
- Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Khushi V. Patel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Emily T. Mai
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Sumil S. Shah
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
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Nautiyal G, Sharma SK, Kaushik D, Pandey P. Nano - Based Therapeutic Strategies in Management of Rheumatoid Arthritis. Recent Pat Nanotechnol 2023; 17:NANOTEC-EPUB-133918. [PMID: 37904559 DOI: 10.2174/1872210517666230822100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic autoimmune disease, progressively distinctive via cartilage destruction, auto-antibody production, severe joint pain, and synovial inflammation. Nanotechnology represents as one of the utmost promising scientific technologies of the 21st century. It exhibits remarkable potential in the field of medicine, including imaging techniques and diagnostic tools, drug delivery systems and providing advances in treatment of several diseases with nanosized structures (less than 100nm). OBJECTIVE Conventional drugs as a cornerstone of RA management including disease-modifying antirheumatic drugs (DMARDS), Glucocorticosteroids, etc are under clinical practice. Nevertheless, their low solubility profile, poor pharmacokinetics behaviour, and non-targeted distribution not only hamper their effectiveness, but also give rise to severe adverse effects which leads to the need for the emergence of nanoscale drug delivery systems. METHODS Several types of nano-diagnostic agents and nanocarriers have been identified; including polymeric nanoparticles (NPs), liposomes, nanogels, metallic NPs, nanofibres, carbon nanotubes, nano fullerene etc. Various patents and clinical trial data have been reported in relevance to RA treatment. RESULTS Nanocarriers, unlike standard medications, encapsulate molecules with high drug loading efficacy and avoid drug leakage and burst release before reaching the inflamed sites. Because of its enhanced targeting specificity with the ability to solubilise hydrophobic drugs, it acts as an enhanced drug delivery system. CONCLUSION This study explores nanoparticles potential role in RA as a carrier for site-specific delivery and its promising strategies to overcome the drawbacks. Hence, it concludes that nanomedicine is advantageous compared with conventional therapy to enhanced futuristic approach.
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Affiliation(s)
- Gunjan Nautiyal
- Department of Pharmaceutical Sciences, Gurugram University, Gurugram - 122018, India
| | - Shiv Kant Sharma
- Department of Pharmaceutical Sciences, Gurugram University, Gurugram - 122018, India
| | - Dhirender Kaushik
- Department of Pharmaceutical Sciences, Gurugram University, Gurugram - 122018, India
| | - Parijat Pandey
- Department of Pharmaceutical Sciences, Gurugram University, Gurugram - 122018, India
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). Plant J 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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Abstract
Alzheimer's disease is undoubtedly the most well-studied neurodegenerative disease. Consequently, the amyloid-β (Aβ) protein ranks at the top in terms of getting attention from the scientific community for structural property-based characterization. Even after decades of extensive research, there is existing volatility in terms of understanding and hence the effective tackling procedures against the disease that arises due to the lack of knowledge of both specific target- and site-specific drugs. Here, we develop a multidimensional approach based on the characterization of the common static-dynamic-thermodynamic trait of the monomeric protein, which efficiently identifies a small target sequence that contains an inherent tendency to misfold and consequently aggregate. The robustness of the identification of the target sequence comes with an abundance of a priori knowledge about the length and sequence of the target and hence guides toward effective designing of the target-specific drug with a very low probability of bottleneck and failure. Based on the target sequence information, we further identified a specific mutant that showed the maximum potential to act as a destabilizer of the monomeric protein as well as enormous success as an aggregation suppressor. We eventually tested the drug efficacy by estimating the extent of modulation of binding affinity existing within the fibrillar form of the Aβ protein due to a single-point mutation and hence provided a proof of concept of the entire protocol.
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Affiliation(s)
- Hasathi Bhagavatula
- Department of Biotechnology, Progressive Education Society's Modern College of Arts Science and Commerce, Shivajinagar, Pune 411005, India
| | - Archishman Sarkar
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra Mallick Road, Kolkata, West Bengal 700032, India
| | - Binit Santra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kalyanpur, Kanpur, Uttar Pradesh 208016, India
| | - Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Ferdausi N, Islam S, Rimti FH, Quayum ST, Arshad EM, Ibnat A, Islam T, Arefin A, Ema TI, Biswas P, Dey D, Azad SA. Point-specific interactions of isovitexin with the neighboring amino acid residues of the hACE2 receptor as a targeted therapeutic agent in suppressing the SARS-CoV-2 influx mechanism. J Adv Vet Anim Res 2022; 9:230-240. [PMID: 35891654 PMCID: PMC9298103 DOI: 10.5455/javar.2022.i588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/02/2022] Open
Abstract
Objective: Despite the development of several vaccines against severe acute respiratory syndrome coronavirus-2, the need for an additional prophylactic agent is evident. In recent in silico studies, isovitexin exhibited a higher binding affinity against the human angiotensin converting-enzyme 2 (hACE2) receptor than existing antiviral drugs. The research aimed to find out the point specificity of isovitexin for the hACE2 receptor and to assess its therapeutic potential, depending on the stability of the isovitexin–hACE2 complex. Materials and Methods: The pharmacokinetic profile of isovitexin was analyzed. The crystal structure of the hACE2 receptor and the ligand isovitexin were docked to form a ligand–protein complex following molecular optimization. To determine the isovitexin–hACE2 complex stability, their binding affinity, hydrogen bonding, and hydrophobic interactions were studied. Lastly, the root mean square deviation (RMSD), root mean square fluctuation, solvent accessible surface area, molecular surface area, radius of gyration (Rg), polar surface area, and principal component analysis values were found by simulating the complex with molecular dynamic (MD). Results: The predicted Lethal dose50 for isovitexin was 2.56 mol/kg, with an acceptable maximum tolerated dose and no hepatotoxicity or AMES toxicity. Interactions with the amino acid residues Thr371, Asp367, Glu406, Pro346, His345, Phe274, Tyr515, Glu375, Thr347, Glu402, and His374 of the hACE2 protein were required for the high binding affinity and specificity of isovitexin. Based on what was learned from the MD simulation, the hACE2 receptor-blocking properties of isovitexin were looked at. Conclusions: Isovitexin is a phytochemical with a reasonable bioactivity and safety profile for use in humans, and it can potentially be used as a hACE2-specific therapeutic to inhibit COVID-19 infection.
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Affiliation(s)
- Nourin Ferdausi
- Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Samarth Islam
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Fahmida Hoque Rimti
- Bachelor of Medicine and Surgery, Chittagong Medical College, Chittagong, Bangladesh
| | - Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Efat Muhammad Arshad
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Aashian Ibnat
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Tamnia Islam
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, United Kingdom.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Adittya Arefin
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, United Kingdom.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
| | - Salauddin Al Azad
- Fermentation Engineering Major, School of Biotechnology, Jiangnan University, Wuxi, PR China.,Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, Bangladesh
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Zhang F, Huang Z. Mechanistic insights into the versatile class II CRISPR toolbox. Trends Biochem Sci 2021; 47:433-450. [PMID: 34920928 DOI: 10.1016/j.tibs.2021.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
The constantly expanding group of class II CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated) effectors and their engineered variants exhibit distinct editing modes and efficiency, fidelity, target range, and molecular size. Their enormous diversity of capabilities provides a formidable toolkit for a large array of technologies. We review the structural and biochemical mechanisms of versatile effector proteins from class II CRISPR-Cas systems to provide mechanistic insights into their target specificity, protospacer adjacent motif (PAM) restriction, and activity regulation, and discuss possible strategies to enhance genome-engineering tools in terms of accuracy, efficiency, applicability, and controllability.
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Affiliation(s)
- Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.
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López-Vidriero I, Godoy M, Grau J, Peñuelas M, Solano R, Franco-Zorrilla JM. DNA features beyond the transcription factor binding site specify target recognition by plant MYC2-related bHLH proteins. Plant Commun 2021; 2:100232. [PMID: 34778747 PMCID: PMC8577090 DOI: 10.1016/j.xplc.2021.100232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/09/2021] [Accepted: 08/10/2021] [Indexed: 05/22/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to cis-regulatory sequences in the promoters of target genes. Recent research is helping to decipher in part the cis-regulatory code in eukaryotes, including plants, but it is not yet fully understood how paralogous TFs select their targets. Here we addressed this question by studying several proteins of the basic helix-loop-helix (bHLH) family of plant TFs, all of which recognize the same DNA motif. We focused on the MYC-related group of bHLHs, that redundantly regulate the jasmonate (JA) signaling pathway, and we observed a high correspondence between DNA-binding profiles in vitro and MYC function in vivo. We demonstrated that A/T-rich modules flanking the MYC-binding motif, conserved from bryophytes to higher plants, are essential for TF recognition. We observed particular DNA-shape features associated with A/T modules, indicating that the DNA shape may contribute to MYC DNA binding. We extended this analysis to 20 additional bHLHs and observed correspondence between in vitro binding and protein function, but it could not be attributed to A/T modules as in MYCs. We conclude that different bHLHs may have their own codes for DNA binding and specific selection of targets that, at least in the case of MYCs, depend on the TF-DNA interplay.
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Affiliation(s)
- Irene López-Vidriero
- Genomics Unit, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Marta Godoy
- Genomics Unit, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Joaquín Grau
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - María Peñuelas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - José M. Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
- Corresponding author
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Arefin A, Ismail Ema T, Islam T, Hossen S, Islam T, Al Azad S, Uddin Badal N, Islam A, Biswas P, Alam NU, Islam E, Anjum M, Masud A, Kamran S, Rahman A, Kumar Paul P. Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach. J Biomed Res 2021; 35:459-473. [PMID: 34857680 PMCID: PMC8637655 DOI: 10.7555/jbr.35.20210111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lassa hemorrhagic fever, caused by Lassa mammarenavirus (LASV) infection, accumulates up to 5000 deaths every year. Currently, there is no vaccine available to combat this disease. In this study, a library of 200 bioactive compounds was virtually screened to study their drug-likeness with the capacity to block the α-dystroglycan (α-DG) receptor and prevent LASV influx. Following rigorous absorption, distribution, metabolism, and excretion (ADME) and quantitative structure-activity relationship (QSAR) profiling, molecular docking was conducted with the top ligands against the α-DG receptor. The compounds chrysin, reticuline, and 3-caffeoylshikimic acid emerged as the top three ligands in terms of binding affinity. Post-docking analysis revealed that interactions with Arg76, Asn224, Ser259, and Lys302 amino acid residues of the receptor protein were important for the optimum binding affinity of ligands. Molecular dynamics simulation was performed comprehensively to study the stability of the protein-ligand complexes. In-depth assessment of root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), polar surface area (PSA), B-Factor, radius of gyration (Rg), solvent accessible surface area (SASA), and molecular surface area (MolSA) values of the protein-ligand complexes affirmed that the candidates with the best binding affinity formed the most stable protein-ligand complexes. To authenticate the potentialities of the ligands as target-specific drugs, an in vivo study is underway in real time as the continuation of the research.
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Affiliation(s)
- Adittya Arefin
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Tamnia Islam
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Saddam Hossen
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Tariqul Islam
- Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang 25200, Malaysia
| | - Salauddin Al Azad
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Nasir Uddin Badal
- Department of Biomedical Technology, Tampere University, Tampere 33014, Finland
| | - Aminul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Nafee Ul Alam
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Enayetul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Maliha Anjum
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Afsana Masud
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Shaikh Kamran
- Applied Statistics and Data Science, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Ahsab Rahman
- Department of Mathematics and Natural Sciences, Brac University, Dhaka 1212, Bangladesh
| | - Parag Kumar Paul
- Department of Electrical and Electronic Engineering, United International University, Dhaka 1212, Bangladesh
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10
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Rasmussen M, Welinder C, Schwede F, Ekström P. The stereospecific interaction sites and target specificity of cGMP analogs in mouse cortex. Chem Biol Drug Des 2021; 99:206-221. [PMID: 34687134 DOI: 10.1111/cbdd.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
cGMP interactors play a role in several pathologies and may be targets for cGMP analog-based drugs, but the success of targeting depends on the biochemical stereospecificity between the cGMP-analog and the interactor. The stereospecificity between general cGMP analogs-or such that are selectivity-modified to obtain, for example, inhibitory actions on a specific target, like the cGMP-dependent protein kinase-have previously been investigated. However, the importance of stereospecificity for cGMP-analog binding to interactors is not known. We, therefore, applied affinity chromatography on mouse cortex proteins utilizing analogs with cyclic phosphate (8-AET-cGMP, 2-AH-cGMP, 2'-AHC-cGMP) and selectivity-modified analogs with sulfur-containing cyclic phosphorothioates (Rp/Sp-8-AET-cGMPS, Rp/Sp-2'-AHC-cGMPS) immobilized to agaroses. The results illustrate the cGMP analogs' stereospecific binding for PKG, PKA regulatory subunits and PKA catalytic subunits, PDEs, and EPAC2 and the involvement of these in various KEGG pathways. For the seven agaroses, PKG, PKA regulatory subunits, and PKA catalytic subunits were more prone to be enriched by 2-AH-, 8-AET-, Rp-8-AET-, and Sp-8-AET-cGMP, whereas PDEs and EPAC2 were more likely to be enriched by 2-AH-, Rp-2'-AHC-, and Rp-8-AET-cGMP. Our findings help elucidate the stereospecific-binding sites essential for the interaction between individual cGMP analogs and cGMP-binding proteins, as well as the cGMP analogs' target specificity, which are two crucial parameters in drug design.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
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Datta B, Paul D, Pal U, Rakshit T. Intriguing Biomedical Applications of Synthetic and Natural Cell-Derived Vesicles: A Comparative Overview. ACS Appl Bio Mater 2021; 4:2863-2885. [PMID: 35014382 DOI: 10.1021/acsabm.0c01480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The significant role of a vesicle is well recognized; however, only lately has the advancement in biomedical applications started to uncover their usefulness. Although the concept of vesicles originates from cell biology, it later transferred to chemistry and material science to develop nanoscale artificial vesicles for biomedical applications. Herein, we examine different synthetic and biological vesicles and their applications in the biomedical field in general. As our understanding of biological vesicles increases, more suitable biomimicking synthetic vesicles will be developed. The comparative discussion between synthetic and natural vesicles for biomedical applications is a relevant topic, and we envision this could enable the development of a proper approach to realize the next-generation treatment goals.
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Affiliation(s)
- Brateen Datta
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Debashish Paul
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Tatini Rakshit
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake City, Kolkata 700106, India
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12
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Abstract
The Ser/Thr protein kinase MELK (maternal embryonic leucine zipper kinase) has been considered an attractive therapeutic target for managing cancer since 2005. Studies using expression analysis have indicated that MELK expression is higher in numerous cancer cells and tissues than in their normal, nonneoplastic counterparts. Further, RNAi-mediated MELK depletion impairs proliferation of multiple cancers, including triple-negative breast cancer (TNBC), and these growth defects can be rescued with exogenous WT MELK, but not kinase-dead MELK complementation. Pharmacological MELK inhibition with OTS167 (alternatively called OTSSP167) and NVS-MELK8a, among other small molecules, also impairs cancer cell growth. These collective results led to MELK being classified as essential for cancer proliferation. More recently, in 2017, the proliferation of TNBC and other cancer cell lines was reported to be unaffected by genetic CRISPR/Cas9-mediated MELK deletion, calling into question the essentiality of this kinase in cancer. To date, the requirement of MELK in cancer remains controversial, and mechanisms underlying the disparate growth effects observed with RNAi, pharmacological inhibition, and CRISPR remain unclear. Our objective with this review is to highlight the evidence on both sides of this controversy, to provide commentary on the purported requirement of MELK in cancer, and to emphasize the need for continued elucidation of the functions of MELK.
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Affiliation(s)
- Ian M McDonald
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.,UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, North Carolina, USA
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13
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Leypold T, Bonus M, Spiegelhalter F, Schwede F, Schwabe T, Gohlke H, Kusch J. N 6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels. J Biol Chem 2019; 294:17978-17987. [PMID: 31615893 DOI: 10.1074/jbc.ra119.010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/15/2019] [Indexed: 11/06/2022] Open
Abstract
cAMP acts as a second messenger in many cellular processes. Three protein types mainly mediate cAMP-induced effects: PKA, exchange protein directly activated by cAMP (Epac), and cyclic nucleotide-modulated channels (cyclic nucleotide-gated or hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels). Discrimination among these cAMP signaling pathways requires specific targeting of only one protein. Previously, cAMP modifications at position N 6 of the adenine ring (PKA) and position 2'-OH of the ribose (Epac) have been used to produce target-selective compounds. However, cyclic nucleotide-modulated ion channels were usually outside of the scope of these previous studies. These channels are widely distributed, so possible channel cross-activation by PKA- or Epac-selective agonists warrants serious consideration. Here we demonstrate the agonistic effects of three PKA-selective cAMP derivatives, N 6-phenyladenosine-3',5'-cyclic monophosphate (N 6-Phe-cAMP), N 6-benzyladenosine-3',5'-cyclic monophosphate (N 6-Bn-cAMP), and N 6-benzoyl-adenosine-3',5'-cyclic monophosphate (N 6-Bnz-cAMP), on murine HCN2 pacemaker channels. Electrophysiological characterization in Xenopus oocytes revealed that these derivatives differ in apparent affinities depending on the modification type but that their efficacy and effects on HCN2 activation kinetics are similar to those of cAMP. Docking experiments suggested a pivotal role of Arg-635 at the entrance of the binding pocket in HCN2, either causing stabilizing cation-π interactions with the aromatic ring in N 6-Phe-cAMP or N 6-Bn-cAMP or a steric clash with the aromatic ring in N 6-Bnz-cAMP. A reduced apparent affinity of N 6-Phe-cAMP toward the variants R635A and R635E strengthened that notion. We conclude that some PKA activators also effectively activate HCN2 channels. Hence, when studying PKA-mediated cAMP signaling with cAMP derivatives in a native environment, activation of HCN channels should be considered.
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Affiliation(s)
- Tim Leypold
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | - Michele Bonus
- Institute for Pharmaceutical and Medical Chemistry, Heinrich Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany
| | - Felix Spiegelhalter
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | | | - Tina Schwabe
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medical Chemistry, Heinrich Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing, Jülich Supercomputing Centre and Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jana Kusch
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
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14
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Abstract
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection for bacteria and archaea against intruding genomic materials. The programmable nature of CRISPR-targeting mechanisms has enabled their adaptation as powerful genome engineering tools. Cas9, a type II CRISPR effector protein, has been widely used for gene-editing applications owing to the fact that a single-guide RNA can direct Cas9 to cleave desired genomic targets. An understanding of the role of different domains of the protein and guide RNA-induced conformational changes of Cas9 in selecting target DNA has been and continues to enable development of Cas9 variants with reduced off-targeting effects. It has been previously established that an arginine-rich bridge helix (BH) present in Cas9 is critical for its activity. In the present study, we show that two proline substitutions within a loop region of the BH of Streptococcus pyogenes Cas9 impair the DNA cleavage activity by accumulating nicked products and reducing target DNA linearization. This in turn imparts a higher selectivity in DNA targeting. We discuss the probable mechanisms by which the BH-loop contributes to target DNA recognition.
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Affiliation(s)
- Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Sherman Center, AS5.2007, Worcester MA 01605, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - S.D. Yogesha
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: Krystal Biotech, Inc. 2100 Wharton Street, Suite 701 Pittsburgh, PA, 15203, USA
| | - Richard Nguyen
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: College of Medicine, University of Oklahoma, Stanton L Young Blvd, Oklahoma City, OK 73117
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
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15
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Wang L, Mo CY, Wasserman MR, Rostøl JT, Marraffini LA, Liu S. Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity. Mol Cell 2018; 73:278-290.e4. [PMID: 30503774 DOI: 10.1016/j.molcel.2018.11.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022]
Abstract
Adaptive immune systems must accurately distinguish between self and non-self in order to defend against invading pathogens while avoiding autoimmunity. Type III CRISPR-Cas systems employ guide RNA to recognize complementary RNA targets, which triggers the degradation of both the invader's transcripts and their template DNA. These systems can broadly eliminate foreign targets with multiple mutations but circumvent damage to the host genome. To explore the molecular basis for these features, we use single-molecule fluorescence microscopy to study the interaction between a type III-A ribonucleoprotein complex and various RNA substrates. We find that Cas10-the DNase effector of the complex-displays rapid conformational fluctuations on foreign RNA targets, but is locked in a static configuration on self RNA. Target mutations differentially modulate Cas10 dynamics and tune the CRISPR interference activity in vivo. These findings highlight the central role of the internal dynamics of CRISPR-Cas complexes in self versus non-self discrimination and target specificity.
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Affiliation(s)
- Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charlie Y Mo
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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16
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Abstract
Recently, a novel technique named the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas)9 system has been rapidly developed. This genome editing tool has improved our ability tremendously with respect to exploring the pathogenesis of diseases and correcting disease mutations, as well as phenotypes. With a short guide RNA, Cas9 can be precisely directed to target sites, and functions as an endonuclease to efficiently produce breaks in DNA double strands. Over the past 30 years, CRISPR has evolved from the 'curious sequences of unknown biological function' into a promising genome editing tool. As a result of the incessant development in the CRISPR/Cas9 system, Cas9 co-expressed with custom guide RNAs has been successfully used in a variety of cells and organisms. This genome editing technology can also be applied to synthetic biology, functional genomic screening, transcriptional modulation and gene therapy. However, although CRISPR/Cas9 has a broad range of action in science, there are several aspects that affect its efficiency and specificity, including Cas9 activity, target site selection and short guide RNA design, delivery methods, off-target effects and the incidence of homology-directed repair. In the present review, we highlight the factors that affect the utilization of CRISPR/Cas9, as well as possible strategies for handling any problems. Addressing these issues will allow us to take better advantage of this technique. In addition, we also review the history and rapid development of the CRISPR/Cas system from the time of its initial discovery in 2012.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
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17
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Abstract
The CRISPR-Cas9 system, naturally a defense mechanism in prokaryotes, has been repurposed as an RNA-guided DNA targeting platform. It has been widely used for genome editing and transcriptome modulation, and has shown great promise in correcting mutations in human genetic diseases. Off-target effects are a critical issue for all of these applications. Here we review the current status on the target specificity of the CRISPR-Cas9 system.
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Affiliation(s)
- Xuebing Wu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea J Kriz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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Sorensen SA, Bernard A, Menon V, Royall JJ, Glattfelder KJ, Desta T, Hirokawa K, Mortrud M, Miller JA, Zeng H, Hohmann JG, Jones AR, Lein ES. Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity. ACTA ACUST UNITED AC 2013; 25:433-49. [PMID: 24014670 DOI: 10.1093/cercor/bht243] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The neocortex contains diverse populations of excitatory neurons segregated by layer and further definable by their specific cortical and subcortical projection targets. The current study describes a systematic approach to identify molecular correlates of specific projection neuron classes in mouse primary somatosensory cortex (S1), using a combination of in situ hybridization (ISH) data mining, marker gene colocalization, and combined retrograde labeling with ISH for layer-specific marker genes. First, we identified a large set of genes with specificity for each cortical layer, and that display heterogeneous patterns within those layers. Using these genes as markers, we find extensive evidence for the covariation of gene expression and projection target specificity in layer 2/3, 5, and 6, with individual genes labeling neurons projecting to specific subsets of target structures. The combination of gene expression and target specificity imply a great diversity of projection neuron classes that is similar to or greater than that of GABAergic interneurons. The covariance of these 2 phenotypic modalities suggests that these classes are both discrete and genetically specified.
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Affiliation(s)
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - Karla Hirokawa
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - Marty Mortrud
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, WA 98040, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98040, USA
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19
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Mallick B, Ghosh Z. Probing Evolutionary Biography of MicroRNAs and Associated Factors. Curr Genomics 2012; 13:144-52. [PMID: 23024606 PMCID: PMC3308325 DOI: 10.2174/138920212799860634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/15/2011] [Accepted: 09/28/2011] [Indexed: 12/21/2022] Open
Abstract
Intergenic DNA, often described as “playground of evolution”, harbors a plethora of cis and trans regulatory elements in the form of non-coding RNAs (ncRNAs). The evolution of the silencing mechanism mediated by microRNAs (miRNAs), an important class of ncRNA, involves the proliferation of miRNA biogenesis and effector proteins, continuing innovation of novel families by the diversification of established families and spawning additional paralogous family members. Such evolving miRNA pathways for spatiotemporal regulation of the transcriptome have shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms. Here, we focus on the emergence of new target specificity of the miRNAs along with the proliferation of core biogenesis and effector modules and show how this has contributed to generate diverse miRNA regulatory pathways.
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20
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Lyckman AW, Jhaveri S, Feldheim DA, Vanderhaeghen P, Flanagan JG, Sur M. Enhanced plasticity of retinothalamic projections in an ephrin-A2/A5 double mutant. J Neurosci 2001; 21:7684-90. [PMID: 11567058 PMCID: PMC6762904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
Ascending sensory information reaches primary sensory cortical areas via thalamic relay neurons that are organized into modality-specific compartments or nuclei. Although the sensory relay nuclei of the thalamus show consistent modality-specific segregation of afferents, we now show in a wild-type mouse strain that the visual pathway can be surgically "rewired" so as to induce permanent retinal innervation of auditory thalamic cell groups. Applying the same rewiring paradigm to a transgenic mouse lacking the EphA receptor family ligands ephrin-A2 and ephrin-A5 results in more extensive rewiring than in the wild-type strain. We also show for the first time that ephrin-A2 and ephrin-A5 define a distinct border between visual and auditory thalamus. In the absence of this ephrin-A2/A5 border and after rewiring surgery, retinal afferents are better able to invade and innervate the deafferented auditory thalamus. These data suggest that signals that induce retinal axons to innervate the denervated auditory thalamus may compete with barriers, such as the ephrins, that serve to contain them within the normal target. The present findings thus show that the targeting of retinothalamic projections can be surgically manipulated in the mouse and that such plasticity can be controlled by proteins known to regulate topographic mapping.
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Affiliation(s)
- A W Lyckman
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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21
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Zhu Y, Zou S, Wright DA, Voytas DF. Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p. Genes Dev 1999; 13:2738-49. [PMID: 10541559 PMCID: PMC317113 DOI: 10.1101/gad.13.20.2738] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Retrotransposon and retroviral insertions are not randomly distributed on chromosomes, suggesting that retroelements actively select integration sites. This is the case for the yeast Ty5 retrotransposons, which preferentially integrate into domains of silent chromatin at the HM loci and telomeres. Here we demonstrate that loss of Sir3p or Sir4p-components of silent chromatin-causes a greater than ninefold decrease in Ty5 targeting to the HM loci and largely randomizes chromosomal integration patterns. Strains with a deletion of SIR4 also display an approximately 10-fold increase in cDNA recombination, which is due both to the expression a- and alpha-mating-type information and the loss of Sir4p. It is known that in old yeast cells or in strains carrying the sir4-42 allele, the Sir complex relocalizes to the rDNA. About 26% of Ty5 insertions occur within the rDNA in sir4-42 strains compared with 3% in wild type. Ty5, therefore, is sensitive to changes in chromatin, indicating that retrotransposons may be useful for dissecting chromatin dynamics that occur during developmental programs such as aging.
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Affiliation(s)
- Y Zhu
- Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA
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22
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Bi GQ, Poo MM. Synaptic modifications in cultured hippocampal neurons: dependence on spike timing, synaptic strength, and postsynaptic cell type. J Neurosci 1998; 18:10464-72. [PMID: 9852584 PMCID: PMC6793365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
In cultures of dissociated rat hippocampal neurons, persistent potentiation and depression of glutamatergic synapses were induced by correlated spiking of presynaptic and postsynaptic neurons. The relative timing between the presynaptic and postsynaptic spiking determined the direction and the extent of synaptic changes. Repetitive postsynaptic spiking within a time window of 20 msec after presynaptic activation resulted in long-term potentiation (LTP), whereas postsynaptic spiking within a window of 20 msec before the repetitive presynaptic activation led to long-term depression (LTD). Significant LTP occurred only at synapses with relatively low initial strength, whereas the extent of LTD did not show obvious dependence on the initial synaptic strength. Both LTP and LTD depended on the activation of NMDA receptors and were absent in cases in which the postsynaptic neurons were GABAergic in nature. Blockade of L-type calcium channels with nimodipine abolished the induction of LTD and reduced the extent of LTP. These results underscore the importance of precise spike timing, synaptic strength, and postsynaptic cell type in the activity-induced modification of central synapses and suggest that Hebb's rule may need to incorporate a quantitative consideration of spike timing that reflects the narrow and asymmetric window for the induction of synaptic modification.
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Affiliation(s)
- G Q Bi
- Department of Biology, University of California at San Diego, La Jolla, California 92093, USA
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