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Lu B, Lim JM, Yu B, Song S, Neeli P, Sobhani N, K P, Bonam SR, Kurapati R, Zheng J, Chai D. The next-generation DNA vaccine platforms and delivery systems: advances, challenges and prospects. Front Immunol 2024; 15:1332939. [PMID: 38361919 PMCID: PMC10867258 DOI: 10.3389/fimmu.2024.1332939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Vaccines have proven effective in the treatment and prevention of numerous diseases. However, traditional attenuated and inactivated vaccines suffer from certain drawbacks such as complex preparation, limited efficacy, potential risks and others. These limitations restrict their widespread use, especially in the face of an increasingly diverse range of diseases. With the ongoing advancements in genetic engineering vaccines, DNA vaccines have emerged as a highly promising approach in the treatment of both genetic diseases and acquired diseases. While several DNA vaccines have demonstrated substantial success in animal models of diseases, certain challenges need to be addressed before application in human subjects. The primary obstacle lies in the absence of an optimal delivery system, which significantly hampers the immunogenicity of DNA vaccines. We conduct a comprehensive analysis of the current status and limitations of DNA vaccines by focusing on both viral and non-viral DNA delivery systems, as they play crucial roles in the exploration of novel DNA vaccines. We provide an evaluation of their strengths and weaknesses based on our critical assessment. Additionally, the review summarizes the most recent advancements and breakthroughs in pre-clinical and clinical studies, highlighting the need for further clinical trials in this rapidly evolving field.
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Affiliation(s)
- Bowen Lu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jing Ming Lim
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Boyue Yu
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, United States
| | - Siyuan Song
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Praveen Neeli
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Navid Sobhani
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Pavithra K
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Rajendra Kurapati
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Dafei Chai
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
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Petrone JR, Rios Glusberger P, George CD, Milletich PL, Ahrens AP, Roesch LFW, Triplett EW. RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing. Front Microbiol 2023; 14:1201064. [PMID: 37547696 PMCID: PMC10402275 DOI: 10.3389/fmicb.2023.1201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.
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Khan MAA, Ghosh P, Chowdhury R, Hossain F, Mahmud A, Faruque ASG, Ahmed T, Abd El Wahed A, Mondal D. Feasibility of MinION Nanopore Rapid Sequencing in the Detection of Common Diarrhea Pathogens in Fecal Specimen. Anal Chem 2022; 94:16658-16666. [DOI: 10.1021/acs.analchem.2c02771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, An den Tierkliniken 1, 04103Leipzig, Germany
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Araf Mahmud
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Abu S. G. Faruque
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Ahmed Abd El Wahed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
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Tanaka M, Yokoyama K, Hayashi H, Isaki S, Kitatani K, Wang T, Kawata H, Matsuzawa H, Gurumurthy CB, Miura H, Ohtsuka M. CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice. Genome Biol 2022; 23:228. [PMID: 36284311 PMCID: PMC9594901 DOI: 10.1186/s13059-022-02779-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesions or random insertions of donor DNAs. Simpler methods to identify off-target lesions and random insertions, using tail or earpiece DNA, are unavailable. We develop CRISPR-KRISPR (CRISPR-Knock-ins and Random Inserts Searching PRotocol), a method to identify both off-target lesions and random insertions. CRISPR-KRISPR uses as little as 3.4 μg of genomic DNA; thus, it can be easily incorporated as an additional step to genotype founder animals for further breeding.
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Affiliation(s)
- Masayuki Tanaka
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Keiko Yokoyama
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideki Hayashi
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Sanae Isaki
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Kanae Kitatani
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Ting Wang
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hisako Kawata
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideyuki Matsuzawa
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Channabasavaiah B. Gurumurthy
- grid.266813.80000 0001 0666 4105Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Genome Editing and Education Center Nebraska (GEEC-Nebraska), College of Medicine, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Hiromi Miura
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Masato Ohtsuka
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan ,grid.265061.60000 0001 1516 6626The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193 Japan
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