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Lee NK, Chang JW. Manufacturing Cell and Gene Therapies: Challenges in Clinical Translation. Ann Lab Med 2024; 44:314-323. [PMID: 38361427 PMCID: PMC10961620 DOI: 10.3343/alm.2023.0382] [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: 09/26/2023] [Revised: 11/24/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
The safety and efficacy of both cell and gene therapies have been demonstrated in numerous preclinical and clinical trials. Chimeric antigen receptor T (CAR-T) cell therapy, which leverages the technologies of both cell and gene therapies, has also shown great promise for treating various cancers. Advancements in pertinent fields have also highlighted challenges faced while manufacturing cell and gene therapy products. Potential problems and obstacles must be addressed to ease the clinical translation of individual therapies. Literature reviews of representative cell-based, gene-based, and cell-based gene therapies with regard to their general manufacturing processes, the challenges faced during manufacturing, and QC specifications are limited. We review the general manufacturing processes of cell and gene therapies, including those involving mesenchymal stem cells, viral vectors, and CAR-T cells. The complexities associated with the manufacturing processes and subsequent QC/validation processes may present challenges that could impede the clinical progression of the products. This article addresses these potential challenges. Further, we discuss the use of the manufacturing model and its impact on cell and gene therapy.
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Affiliation(s)
- Na Kyung Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Jong Wook Chang
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Cell and Gene Therapy Institute, ENCell Co. Ltd., Seoul, Korea
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2
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Fröhlich A, Hughes LS, Middlehurst B, Pfaff AL, Bubb VJ, Koks S, Quinn JP. CRISPR deletion of a SINE-VNTR- Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol 2023; 14:1273036. [PMID: 37840928 PMCID: PMC10570551 DOI: 10.3389/fneur.2023.1273036] [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: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Background SINE-VNTR-Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specific SVA element, termed SVA_67, was associated with differential expression of several genes at the MAPT locus, a locus associated with Parkinson's Disease (PD) and frontotemporal dementia. However, we were not able to demonstrate that causation of differential gene expression was directed by the SVA due to lack of functional validation. Methods We performed CRISPR to delete SVA_67 in the HEK293 cell line. Quantification of target gene expression was performed using qPCR to assess the effects on expression in response to the deletion of SVA_67. Differences between CRISPR edit and control cell lines were analysed using two-tailed t-test with a minimum 95% confidence interval to determine statistical significance. Results In this study, we provide data highlighting the SVA-specific effect on differential gene expression. We demonstrate that the hemizygous deletion of the endogenous SVA_67 in CRISPR edited cell lines was associated with differential expression of several genes at the MAPT locus associated with neurodegenerative diseases including KANSL1, MAPT and LRRC37A. Discussion This data is consistent with our previous bioinformatic work of differential gene expression analysis using transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) cohort. As SVAs have regulatory influences on gene expression, and insertion polymorphisms contribute to interpersonal differences in expression patterns, these results highlight the potential contribution of these elements to complex diseases with potentially many genetic components, such as PD.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Lauren S. Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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3
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Garcia-Cañadas M, Sanchez-Luque FJ, Sanchez L, Rojas J, Garcia Perez JL. LINE-1 Retrotransposition Assays in Embryonic Stem Cells. Methods Mol Biol 2023; 2607:257-309. [PMID: 36449167 DOI: 10.1007/978-1-0716-2883-6_13] [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] [Indexed: 06/17/2023]
Abstract
The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.
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Affiliation(s)
- Marta Garcia-Cañadas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Laura Sanchez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Johana Rojas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Jose L Garcia Perez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC)/University of Edinburgh, Western General Hospital Campus, Edinburgh, UK.
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4
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Van der Mude A. A proposed Information-Based modality for the treatment of cancer. Biosystems 2021; 211:104587. [PMID: 34915101 DOI: 10.1016/j.biosystems.2021.104587] [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: 06/13/2021] [Revised: 11/20/2021] [Accepted: 12/01/2021] [Indexed: 11/02/2022]
Abstract
Treatment modalities for cancer involve physical manipulations such as surgery, immunology, radiation, chemotherapy or gene editing. This is a proposal for an information-based modality. This modality does not change the internal state of the cancer cell directly - instead, the cancer cell is manipulated by giving it information to instruct the cell to perform an action. This modality is based on a theory of Structure Encoding in DNA, where information about body part structure controls the epigenetic state of cells in the process of development from pluripotent cells to fully differentiated cells. It has been noted that cancer is often due to errors in morphogenetic differentiation accompanied by associated epigenetic processes. This implies a model of cancer called the Epigenetic Differentiation Model. A major feature of the Structure Encoding Theory is that the characteristics of the differentiated cell are affected by inter-cellular information passed in the tissue microenvironment, which specifies the exact location of a cell in a body part structure. This is done by exosomes that carry fragments of long non-coding RNA and transposons, which convey structure information. In the normal process of epigenetic differentiation, the information passed may lead to apoptosis due to the constraints of a particular body part structure. The proposed treatment involves determining what structure information is being passed in a particular tumor, then adding artificial exosomes that overwhelm the current information with commands for the cells to go into apoptosis.
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5
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Babarinde IA, Ma G, Li Y, Deng B, Luo Z, Liu H, Abdul MM, Ward C, Chen M, Fu X, Shi L, Duttlinger M, He J, Sun L, Li W, Zhuang Q, Tong G, Frampton J, Cazier JB, Chen J, Jauch R, Esteban MA, Hutchins AP. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. Nucleic Acids Res 2021; 49:9132-9153. [PMID: 34390351 PMCID: PMC8450112 DOI: 10.1093/nar/gkab710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable of transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II can be copied as parts of primary transcripts; however, their full contribution to mature transcript sequences remains unresolved. Here, using long and short read (LR and SR) RNA sequencing data, we show that 26% of coding and 65% of noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families are incorporated into RNAs in unique patterns, with consequences to transcript structure and function. The presence of TE sequences within a transcript is correlated with TE-type specific changes in its subcellular distribution, alterations in steady-state levels and half-life, and differential association with RNA Binding Proteins (RBPs). We identify hPSC-specific incorporation of endogenous retroviruses (ERVs) and LINE:L1 into protein-coding mRNAs, which generate TE sequence-derived peptides. Finally, single cell RNA-seq reveals that hPSCs express ERV-containing transcripts, whilst differentiating subpopulations lack ERVs and express SINE and LINE-containing transcripts. Overall, our comprehensive analysis demonstrates that the incorporation of TE sequences into the RNAs of hPSCs is more widespread and has a greater impact than previously appreciated.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gang Ma
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhao Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Boping Deng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mazid Md Abdul
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Minchun Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiuling Fu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martha Duttlinger
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Li Sun
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qiang Zhuang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoqing Tong
- Center for Reproductive Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200120, China
| | - Jon Frampton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.,Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Jiekai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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6
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Gazquez-Gutierrez A, Witteveldt J, R Heras S, Macias S. Sensing of transposable elements by the antiviral innate immune system. RNA (NEW YORK, N.Y.) 2021; 27:rna.078721.121. [PMID: 33888553 PMCID: PMC8208052 DOI: 10.1261/rna.078721.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/17/2021] [Indexed: 05/15/2023]
Abstract
Around half of the genome in mammals is composed of transposable elements (TEs) such as DNA transposons and retrotransposons. Several mechanisms have evolved to prevent their activity and the detrimental impact of their insertional mutagenesis. Despite these potentially negative effects, TEs are essential drivers of evolution, and in certain settings, beneficial to their hosts. For instance, TEs have rewired the antiviral gene regulatory network and are required for early embryonic development. However, due to structural similarities between TE-derived and viral nucleic acids, cells can misidentify TEs as invading viruses and trigger the major antiviral innate immune pathway, the type I interferon (IFN) response. This review will focus on the different settings in which the role of TE-mediated IFN activation has been documented, including cancer and senescence. Importantly, TEs may also play a causative role in the development of complex autoimmune diseases characterised by constitutive type I IFN activation. All these observations suggest the presence of strong but opposing forces driving the coevolution of TEs and antiviral defence. A better biological understanding of the TE replicative cycle as well as of the antiviral nucleic acid sensing mechanisms will provide insights into how these two biological processes interact and will help to design better strategies to treat human diseases characterised by aberrant TE expression and/or type I IFN activation.
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Affiliation(s)
| | - Jeroen Witteveldt
- University of Edinburgh - Institute of Immunology and Infection Research
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research, Pfizer University of Granada
| | - Sara Macias
- Institute of Immunology and Infection Research
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7
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Savage AL, Lopez AI, Iacoangeli A, Bubb VJ, Smith B, Troakes C, Alahmady N, Koks S, Schumann GG, Al-Chalabi A, Quinn JP. Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis. Mol Brain 2020; 13:154. [PMID: 33187550 PMCID: PMC7666467 DOI: 10.1186/s13041-020-00694-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
Long interspersed element-1 (LINE-1/L1) is the only autonomous transposable element in the human genome that currently mobilises in both germline and somatic tissues. Recent studies have identified correlations between altered retrotransposon expression and the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) in a subset of patients. The risk of an individual developing ALS is dependent on an interaction of genetic variants and subsequent modifiers during life. These modifiers could include environmental factors, which can lead to epigenetic and genomic changes, such as somatic mutations, occurring in the neuronal cells that degenerate as the disease develops. There are more than 1 million L1 copies in the human genome today, but only 80-100 L1 loci in the reference genome are considered to be retrotransposition-competent (RC) and an even smaller number of these RC-L1s loci are highly active. We hypothesise that RC-L1s could affect normal cellular function through their mutagenic potential conferred by their ability to retrotranspose in neuronal cells and through DNA damage caused by the endonuclease activity of the L1-encoded ORF2 protein. To investigate whether either an increase in the genomic burden of RC-L1s or epigenetic changes to RC-L1s altering their expression, could play a role in disease development, we chose a set of seven well characterised genomic RC-L1 loci that were reported earlier to be highly active in a cellular L1 retrotransposition reporter assay or serve as major source elements for germline and/or somatic retrotransposition events. Analysis of the insertion allele frequency of five polymorphic RC-L1s, out of the set of seven, for their presence or absence, did not identify an increased number individually or when combined in individuals with the disease. However, we did identify reduced levels of methylation of RC-L1s in the motor cortex of those individuals with both familial and sporadic ALS compared to control brains. The changes to the regulation of the loci encompassing these RC-L1s demonstrated tissue specificity and could be related to the disease process.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ana Illera Lopez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Biostatistics and Health Informatics, King's College London, London, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Bradley Smith
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Nada Alahmady
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Biology, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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8
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Kumar D, Anand T, Talluri TR, Kues WA. Potential of transposon-mediated cellular reprogramming towards cell-based therapies. World J Stem Cells 2020; 12:527-544. [PMID: 32843912 PMCID: PMC7415244 DOI: 10.4252/wjsc.v12.i7.527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/09/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem (iPS) cells present a seminal discovery in cell biology and promise to support innovative treatments of so far incurable diseases. To translate iPS technology into clinical trials, the safety and stability of these reprogrammed cells needs to be shown. In recent years, different non-viral transposon systems have been developed for the induction of cellular pluripotency, and for the directed differentiation into desired cell types. In this review, we summarize the current state of the art of different transposon systems in iPS-based cell therapies.
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Affiliation(s)
- Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India
| | - Taruna Anand
- NCVTC, ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Thirumala R Talluri
- Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner 334001, India
| | - Wilfried A Kues
- Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics, Department of Biotechnology, Mariensee 31535, Germany
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9
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Emamalipour M, Seidi K, Zununi Vahed S, Jahanban-Esfahlan A, Jaymand M, Majdi H, Amoozgar Z, Chitkushev LT, Javaheri T, Jahanban-Esfahlan R, Zare P. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression. Front Cell Dev Biol 2020; 8:229. [PMID: 32509768 PMCID: PMC7248198 DOI: 10.3389/fcell.2020.00229] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.
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Affiliation(s)
- Melissa Emamalipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hasan Majdi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - L T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States.,Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland.,Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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10
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Hematopoietic regeneration under the spell of epigenetic-epitranscriptomic factors and transposable elements. Curr Opin Hematol 2020; 27:264-272. [DOI: 10.1097/moh.0000000000000585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Tristan-Ramos P, Morell S, Sanchez L, Toledo B, Garcia-Perez JL, Heras SR. sRNA/L1 retrotransposition: using siRNAs and miRNAs to expand the applications of the cell culture-based LINE-1 retrotransposition assay. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190346. [PMID: 32075559 DOI: 10.1098/rstb.2019.0346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cell culture-based retrotransposition reporter assay has been (and is) an essential tool for the study of vertebrate Long INterspersed Elements (LINEs). Developed more than 20 years ago, this assay has been instrumental in characterizing the role of LINE-encoded proteins in retrotransposition, understanding how ribonucleoprotein particles are formed, how host factors regulate LINE mobilization, etc. Moreover, variations of the conventional assay have been developed to investigate the biology of other currently active human retrotransposons, such as Alu and SVA. Here, we describe a protocol that allows combination of the conventional cell culture-based LINE-1 retrotransposition reporter assay with short interfering RNAs (siRNAs) and microRNA (miRNAs) mimics or inhibitors, which has allowed us to uncover specific miRNAs and host factors that regulate retrotransposition. The protocol described here is highly reproducible, quantitative, robust and flexible, and allows the study of several small RNA classes and various retrotransposons. To illustrate its utility, here we show that siRNAs to Fanconi anaemia proteins (FANC-A and FANC-C) and an inhibitor of miRNA-20 upregulate and downregulate human L1 retrotransposition, respectively. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Pablo Tristan-Ramos
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Santiago Morell
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain
| | - Laura Sanchez
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain
| | - Belen Toledo
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jose L Garcia-Perez
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain.,MRC-Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sara R Heras
- Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, GENYO, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
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Govarthanan K, Vidyasekar P, Gupta PK, Lenka N, Verma RS. Glycogen synthase kinase 3β inhibitor- CHIR 99021 augments the differentiation potential of mesenchymal stem cells. Cytotherapy 2020; 22:91-105. [PMID: 31980369 DOI: 10.1016/j.jcyt.2019.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/22/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022]
Abstract
AIM Mesenchymal stem cells (MSCs) are immunomodulatory, non-teratogenic and multipotent alternatives to embryonic or induced pluripotent stem cells (ESCs or iPSCs). However, the potency of MSCs is not equivalent to the pluripotency of ESCs or iPSCs. We used CHIR 99021 to improve current protocols and methods of differentiation for the enhanced transdifferentiation potency of MSCs. MAIN METHODS We used Flurescence activated cell sorter (FACS) for MSC immunophenotyping and biochemical assay for demonstrating the trilineage potential of MSCs. We used real-time polymerase chain reaction, immunocytochemistry and Western blotting assay for analyzing the expression of lineage-specific markers. KEY FINDINGS CHIR 99021 treatment of MSCs resulted in enhanced transdifferentiation into neurological, hepatogenic and cardiomyocyte lineages with standardized protocols of differentiation. CHIR 99021-treated MSCs showed increased nuclear localization of β-catenin. These MSCs showed a significantly increased deposition of active histone marks (H3K4Me3, H3K36Me3), whereas no change was observed in repressive marks (H3K9Me3, H3K27Me3). Differential methylation profiling showed demethylation of the transcription factor OCT4 promoter region with subsequent analysis revealing increased gene expression and protein content. The HLA-DR antigen was absent in CHIR 99021-treated MSCs and their differentiated cell types, indicating their immune-privileged status. Karyotyping analysis showed that CHIR 99021-treated MSCs were genomically stable. Teratoma analysis of nude mice injected with CHIR 99021-treated MSCs showed the increased presence of cell types of mesodermal origin at the site of injection. SIGNIFICANCE MSCs pretreated with CHIR 99021 can be potent, abundant alternative sources of stem cells with enhanced differentiation capabilities that are well suited to cell-based regenerative therapy.
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Affiliation(s)
- Kavitha Govarthanan
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Prasanna Vidyasekar
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Piyush Kumar Gupta
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Nibedita Lenka
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Rama Shanker Verma
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India.
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Bhargava A, Shukla A, Bunkar N, Shandilya R, Lodhi L, Kumari R, Gupta PK, Rahman A, Chaudhury K, Tiwari R, Goryacheva IY, Mishra PK. Exposure to ultrafine particulate matter induces NF-κβ mediated epigenetic modifications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:39-50. [PMID: 31146237 DOI: 10.1016/j.envpol.2019.05.065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Exposure to ultrafine particulate matter (PM0.1) is positively associated with the etiology of different acute and chronic disorders; however, the in-depth biological imprints that link these submicron particles with the disturbances in the epigenomic machinery are not well defined. Earlier, we showed that exposure to these particles causes significant disturbances in the mitochondrial machinery and triggers PI-3-kinase mediated DNA damage responses. In the present study, we aimed to further understand the epigenomic insights of the ultrafine PM exposure. The higher levels of intracellular reactive oxygen species and depleted Nrf-2 in ultrafine PM exposed cells reconfirmed its potential to induce oxidative stress. Importantly, the observed increase in the levels of NF-κβ and associated cytokines among exposed cells suggested the activation of NF-κβ mediated inflammatory loop which potentially serves as a platform for initiating epigenetic insinuations. This fact was strongly supported by the altered miRNA expression profile of the ultrafine PM exposed cells. These NF-κβ induced miRNA alterations were also found to be associated with other epigenetic targets as the exposed cells showed higher expression levels of DNA methyltransferases which positively corresponded with the global changes in DNA methylation levels. Upon further analysis, significant alterations in histone code were also reported in ultrafine PM exposed cells. Conclusively our results suggested that NF-κβ acts as an inflammatory switch that possesses the potential to induce genome-wide epigenetic modification upon ultrafine PM exposure.
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Affiliation(s)
- Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Anushi Shukla
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Lalit Lodhi
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pushpendra Kumar Gupta
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Akhlaqur Rahman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Koel Chaudhury
- School of Medical Science & Technology, Indian Institute of Technology, Kharagpur, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Irina Yu Goryacheva
- Department of General and Inorganic Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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