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Stalder D, Yakunin I, Pereira C, Eden J, Gershlick DC. Recruitment of PI4KIIIβ to the Golgi by ACBD3 is dependent on an upstream pathway of a SNARE complex and golgins. Mol Biol Cell 2024; 35:ar20. [PMID: 38134218 PMCID: PMC7615549 DOI: 10.1091/mbc.e23-09-0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
ACBD3 is a protein localised to the Golgi apparatus and recruits other proteins, such as PI4KIIIβ, to the Golgi. However, the mechanism through which ACBD3 itself is recruited to the Golgi is poorly understood. This study demonstrates there are two mechanisms for ACBD3 recruitment to the Golgi. First, we identified that an MWT374-376 motif in the unique region upstream of the GOLD domain in ACBD3 is essential for Golgi localization. Second, we use unbiased proteomics to demonstrate that ACBD3 interacts with SCFD1, a Sec1/Munc-18 (SM) protein, and a SNARE protein, SEC22B. CRISPR-KO of SCFD1 causes ACBD3 to become cytosolic. We also found that ACBD3 is redundantly recruited to the Golgi apparatus by two golgins: golgin-45 and giantin, which bind to ACBD3 through interaction with the MWT374-376 motif. Taken together, our results suggest that ACBD3 is recruited to the Golgi in a two-step sequential process, with the SCFD1-mediated interaction occurring upstream of the interaction with the golgins.
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Affiliation(s)
- Danièle Stalder
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Igor Yakunin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Jessica Eden
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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2
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Dcona MM, Chougoni KK, Dcona DT, West JL, Singh SJ, Ellis KC, Grossman SR. Combined Targeting of NAD Biosynthesis and the NAD-dependent Transcription Factor C-terminal Binding Protein as a Promising Novel Therapy for Pancreatic Cancer. CANCER RESEARCH COMMUNICATIONS 2023; 3:2003-2013. [PMID: 37707363 PMCID: PMC10549224 DOI: 10.1158/2767-9764.crc-22-0521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 08/07/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Cancer therapies targeting metabolic derangements unique to cancer cells are emerging as a key strategy to address refractory solid tumors such as pancreatic ductal adenocarcinomas (PDAC) that exhibit resistance to extreme nutrient deprivation in the tumor microenvironment. Nicotinamide adenine dinucleotide (NAD) participates in multiple metabolic pathways and nicotinamide phosphoribosyl transferase (NAMPT) is one of the key intracellular enzymes that facilitate the synthesis of NAD. C-terminal binding proteins 1 and 2 (CtBP) are paralogous NAD-dependent oncogenic transcription factors and dehydrogenases that nucleate an epigenetic complex regulating a cohort of genes responsible for cancer proliferation and metastasis. As adequate intracellular NAD is required for CtBP to oligomerize and execute its oncogenic transcriptional coregulatory activities, we hypothesized that NAD depletion would synergize with CtBP inhibition, improving cell inhibitory efficacy. Indeed, depletion of cellular NAD via the NAMPT inhibitor GMX1778 enhanced growth inhibition induced by either RNAi-mediated CtBP1/2 knockdown or the CtBP dehydrogenase inhibitor 4-chlorophenyl-2-hydroxyimino propanoic acid as much as 10-fold in PDAC cells, while untransformed pancreatic ductal cells were unaffected. The growth inhibitory effects of the NAMPT/CtBP inhibitor combination correlated pharmacodynamically with on-target disruption of CtBP1/2 dimerization, CtBP2 interaction with the CoREST epigenetic regulator, and transcriptional activation of the oncogenic target gene TIAM1. Moreover, this same therapeutic combination strongly attenuated growth of PDAC cell line xenografts in immunodeficient mice, with no observable toxicity. Collectively, our data demonstrate that targeting CtBP in combination with NAD depletion represents a promising therapeutic strategy for PDAC. SIGNIFICANCE Effective precision therapies are lacking in PDAC. We demonstrate that simultaneous inhibition of NAD metabolism and the oncoprotein CtBP is potently effective at blocking growth of both PDAC cells in culture and human PDAC-derived tumors in mice and should be explored further as a potential therapy for patients with PDAC.
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Affiliation(s)
- M. Michael Dcona
- USC Norris Comprehensive Cancer Center and Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kranthi Kumar Chougoni
- USC Norris Comprehensive Cancer Center and Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Diana T. Dcona
- USC Norris Comprehensive Cancer Center and Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jacqueline L. West
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
| | - Sahib J. Singh
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Keith C. Ellis
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Steven R. Grossman
- USC Norris Comprehensive Cancer Center and Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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3
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Skoufou-Papoutsaki N, Adler S, D'Santos P, Mannion L, Mehmed S, Kemp R, Smith A, Perrone F, Nayak K, Russell A, Zilbauer M, Winton DJ. Efficient genetic editing of human intestinal organoids using ribonucleoprotein-based CRISPR. Dis Model Mech 2023; 16:dmm050279. [PMID: 37772705 PMCID: PMC10565108 DOI: 10.1242/dmm.050279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Organoids, combined with genetic editing strategies, have the potential to offer rapid and efficient investigation of gene function in many models of human disease. However, to date, the editing efficiency of organoids with the use of non-viral electroporation methods has only been up to 30%, with implications for the subsequent need for selection, including turnaround time and exhaustion or adaptation of the organoid population. Here, we describe an efficient method for intestinal organoid editing using a ribonucleoprotein-based CRISPR approach. Editing efficiencies of up to 98% in target genes were robustly achieved across different gut anatomical locations and developmental timepoints from multiple patient samples with no observed off-target editing. The method allowed us to study the effect of loss of the tumour suppressor gene PTEN in normal human intestinal cells. Analysis of PTEN-deficient organoids defined phenotypes that likely relate to its tumour suppressive function in vivo, such as a proliferative advantage and increased organoid budding. Transcriptional profiling revealed differential expression of genes in pathways commonly known to be associated with PTEN loss, including mTORC1 activation.
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Affiliation(s)
- Nefeli Skoufou-Papoutsaki
- CRUK Cambridge Institute, Cambridge CB2 0RE, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0RE, UK
| | - Sam Adler
- CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | | | - Liz Mannion
- CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | | | | | - Amy Smith
- CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | | | - Komal Nayak
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0RE, UK
| | | | | | - Douglas J. Winton
- CRUK Cambridge Institute, Cambridge CB2 0RE, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0RE, UK
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4
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Pereira C, Stalder D, Anderson GS, Shun-Shion AS, Houghton J, Antrobus R, Chapman MA, Fazakerley DJ, Gershlick DC. The exocyst complex is an essential component of the mammalian constitutive secretory pathway. J Cell Biol 2023; 222:e202205137. [PMID: 36920342 PMCID: PMC10041652 DOI: 10.1083/jcb.202205137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Secreted proteins fulfill a vast array of functions, including immunity, signaling, and extracellular matrix remodeling. In the trans-Golgi network, proteins destined for constitutive secretion are sorted into post-Golgi carriers which fuse with the plasma membrane. The molecular machinery involved is poorly understood. Here, we have used kinetic trafficking assays and transient CRISPR-KO to study biosynthetic sorting from the Golgi to the plasma membrane. Depletion of all canonical exocyst subunits causes cargo accumulation in post-Golgi carriers. Exocyst subunits are recruited to and co-localize with carriers. Exocyst abrogation followed by kinetic trafficking assays of soluble cargoes results in intracellular cargo accumulation. Unbiased secretomics reveals impairment of soluble protein secretion after exocyst subunit knockout. Importantly, in specialized cell types, the loss of exocyst prevents constitutive secretion of antibodies in lymphocytes and of leptin in adipocytes. These data identify exocyst as the functional tether of secretory post-Golgi carriers at the plasma membrane and an essential component of the mammalian constitutive secretory pathway.
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Affiliation(s)
- Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Danièle Stalder
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Amber S. Shun-Shion
- Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Jack Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Daniel J. Fazakerley
- Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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5
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Jin D, Loh KL, Shamekhi T, Ting YT, Lim Kam Sian TCC, Roest J, Ooi JD, Vivian JP, Faridi P. Engineering Cell Lines for Specific Human Leukocyte Antigen Presentation. Methods Mol Biol 2023; 2691:351-369. [PMID: 37355557 DOI: 10.1007/978-1-0716-3331-1_25] [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: 06/26/2023]
Abstract
Epitope-specific immunotherapies have enabled the targeted treatment of a variety of diseases, ranging from cancer, infection, and autoimmune disorders. For CD8+ T cell-based therapies, the precise identification of immunogenic peptides presented by human leukocyte antigen (HLA) class I is essential which can be achieved by immunopeptidomics. Here, using lentivirus-mediated transduction and cell sorting approaches, we present a method to engineer a cell line that does not express its native HLA but instead expresses an HLA of interest (in this instance HLA-A*02:01). This technique can be used to elucidate the immunopeptidome of cell lines expressing different HLAs.
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Affiliation(s)
- Dongbin Jin
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
| | - Khai Lee Loh
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Tima Shamekhi
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
| | - Yi Tian Ting
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Terry C C Lim Kam Sian
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - James Roest
- St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Joshua D Ooi
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Julian P Vivian
- St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.
- Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia.
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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6
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New Therapeutics for Extracellular Vesicles: Delivering CRISPR for Cancer Treatment. Int J Mol Sci 2022; 23:ijms232415758. [PMID: 36555398 PMCID: PMC9779094 DOI: 10.3390/ijms232415758] [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: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cancers are defined by genetic defects, which underlines the prospect of using gene therapy in patient care. During the past decade, CRISPR technology has rapidly evolved into a powerful gene editing tool with high fidelity and precision. However, one of the impediments slowing down the clinical translation of CRISPR-based gene therapy concerns the lack of ideal delivery vectors. Extracellular vesicles (EVs) are nano-sized membrane sacs naturally released from nearly all types of cells. Although EVs are secreted for bio-information conveyance among cells or tissues, they have been recognized as superior vectors for drug or gene delivery. Recently, emerging evidence has spotlighted EVs in CRISPR delivery towards cancer treatment. In this review, we briefly introduce the biology and function of the CRISPR system and follow this with a summary of current delivery methods for CRISPR applications. We emphasize the recent progress in EV-mediated CRISPR editing for various cancer types and target genes. The reported strategies for constructing EV-CRISPR vectors, as well as their limitations, are discussed in detail. The review aims to throw light on the clinical potential of engineered EVs and encourage the expansion of our available toolkit to defeat cancer.
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7
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Quach ABV, Little SR, Shih SCC. Viral Generation, Packaging, and Transduction on a Digital Microfluidic Platform. Anal Chem 2022; 94:4039-4047. [PMID: 35192339 DOI: 10.1021/acs.analchem.1c05227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viral-based systems are a popular delivery method for introducing exogenous genetic material into mammalian cells. Unfortunately, the preparation of lentiviruses containing the machinery to edit the cells is labor-intensive, with steps requiring optimization and sensitive handling. To mitigate these challenges, we introduce the first microfluidic method that integrates lentiviral generation, packaging, and transduction. The new method allows the production of viral titers between 106 and 107 (similar to macroscale production) and high transduction efficiency for hard-to-transfect cell lines. We extend the technique for gene editing applications and show how this technique can be used to knock out and knock down estrogen receptor gene─a gene prominently responsible for 70% of breast cancer cases. This new technique is automated with multiplexing capabilities, which have the potential to standardize the methods for viral-based genome engineering.
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Affiliation(s)
- Angela B V Quach
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Samuel R Little
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec H3G 1M8, Canada
| | - Steve C C Shih
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec H3G 1M8, Canada
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8
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Pallaseni A, Peets E, Koeppel J, Weller J, Vanderstichele T, Ho U, Crepaldi L, van Leeuwen J, Allen F, Parts L. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3551-3564. [PMID: 35286377 PMCID: PMC8989541 DOI: 10.1093/nar/gkac161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas base editors promise nucleotide-level control over DNA sequences, but the determinants of their activity remain incompletely understood. We measured base editing frequencies in two human cell lines for two cytosine and two adenine base editors at ∼14 000 target sequences and find that base editing activity is sequence-biased, with largest effects from nucleotides flanking the target base. Whether a base is edited depends strongly on the combination of its position in the target and the preceding base, acting to widen or narrow the effective editing window. The impact of features on editing rate depends on the position, with sequence bias efficacy mainly influencing bases away from the center of the window. We use these observations to train a machine learning model to predict editing activity per position, with accuracy ranging from 0.49 to 0.72 between editors, and with better generalization across datasets than existing tools. We demonstrate the usefulness of our model by predicting the efficacy of disease mutation correcting guides, and find that most of them suffer from more unwanted editing than pure outcomes. This work unravels the position-specificity of base editing biases and allows more efficient planning of editing campaigns in experimental and therapeutic contexts.
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Affiliation(s)
| | | | | | | | | | - Uyen Linh Ho
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Jolanda van Leeuwen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Leopold Parts
- To whom correspondence should be addressed. Tel: +44 1223 834 244;
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9
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Rajabzadeh A, Hamidieh AA, Rahbarizadeh F. Spinoculation and retronectin highly enhance the gene transduction efficiency of Mucin-1-specific chimeric antigen receptor (CAR) in human primary T cells. BMC Mol Cell Biol 2021; 22:57. [PMID: 34814824 PMCID: PMC8609792 DOI: 10.1186/s12860-021-00397-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Background Producing an appropriate number of engineered cells is considered as one of the influential factors in the successful treatments with chimeric antigen receptor (CAR) T cells. To this aim, the transduction rate of the viral vectors can play a significant role. In addition, improving transduction rates can affect the success rate of this treatment due to hard-transduced T lymphocytes. Results In this study, activated T cells were transduced using different transduction methods such as spinoculation, retronectin, polybrene, spinoculation + retronectin, and spinoculation + polybrene after selecting the most efficient transfection method to produce recombinant viral particles containing MUC1 CAR. PEI and lipofectamine with the amount of 73.72 and 72.53%, respectively, showed the highest transfection rates with respect to calcium phosphate (14.13%) for producing lentiviral particles. However, the cytotoxicity of transfection methods was not significantly different. Based on the results, spinoculation + retronectin leads to the highest transduction rates of T cells (63.19 ± 4.45%) relative to spinoculation + polybrene (34.6 ± 4.44%), polybrene (10.23 ± 0.79%), retronectin (10.37 ± 1.85%), and spinoculation (21.11 ± 1.55%). Further, the polybrene (40.02%) and spinoculation + polybrene (48.83% ± 4.83) increased cytotoxicity significantly compared to other groups. Conclusion Improving transduction conditions such as using spinoculation with retronectin can ameliorate the production of CAR-T cells by increasing the rate of transduction, as well as the success rate of treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00397-z.
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Affiliation(s)
- Alireza Rajabzadeh
- Department of Applied Cell Sciences, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Amir Ali Hamidieh
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell and Tissue Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran. .,Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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10
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Wu Y, Kröller L, Miao B, Boekhoff H, Bauer AS, Büchler MW, Hackert T, Giese NA, Taipale J, Hoheisel JD. Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer. Cancers (Basel) 2021; 13:4569. [PMID: 34572796 PMCID: PMC8471171 DOI: 10.3390/cancers13184569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/14/2021] [Accepted: 09/08/2021] [Indexed: 01/01/2023] Open
Abstract
Studies have indicated that some genes involved in carcinogenesis are highly methylated in their promoter regions but nevertheless strongly transcribed. It has been proposed that transcription factors could bind specifically to methylated promoters and trigger transcription. We looked at this rather comprehensively for pancreatic ductal adenocarcinoma (PDAC) and studied some cases in more detail. Some 2% of regulated genes in PDAC exhibited higher transcription coupled to promoter hypermethylation in comparison to healthy tissue. Screening 661 transcription factors, several were found to bind specifically to methylated promoters, in particular molecules of the NFAT family. One of them-NFATc1-was substantially more strongly expressed in PDAC than control tissue and exhibited a strong oncogenic role. Functional studies combined with computational analyses allowed determining affected genes. A prominent one was gene ALDH1A3, which accelerates PDAC metastasis and correlates with a bad prognosis. Further studies confirmed the direct up-regulation of ALDH1A3 transcription by NFATc1 promoter binding in a methylation-dependent process, providing insights into the oncogenic role of transcription activation in PDAC that is promoted by DNA methylation.
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Affiliation(s)
- Yenan Wu
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Lea Kröller
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Beiping Miao
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Henning Boekhoff
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Andrea S. Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
| | - Markus W. Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Nathalia A. Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Jussi Taipale
- Division of Functional Genomics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Solna, Sweden;
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
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11
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Ophinni Y, Miki S, Hayashi Y, Kameoka M. Multiplexed tat-Targeting CRISPR-Cas9 Protects T Cells from Acute HIV-1 Infection with Inhibition of Viral Escape. Viruses 2020; 12:E1223. [PMID: 33126728 PMCID: PMC7693572 DOI: 10.3390/v12111223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/23/2022] Open
Abstract
HIV-1 cure strategy by means of proviral knock-out using CRISPR-Cas9 has been hampered by the emergence of viral resistance against the targeting guide RNA (gRNA). Here, we proposed multiple, concentrated gRNA attacks against HIV-1 regulatory genes to block viral escape. The T cell line were transduced with single and multiple gRNAs targeting HIV-1 tat and rev using lentiviral-based CRISPR-Cas9, followed by replicative HIV-1NL4-3 challenge in vitro. Viral p24 rebound was observed for almost all gRNAs, but multiplexing three tat-targeting gRNAs maintained p24 suppression and cell viability, indicating the inhibition of viral escape. Multiplexed tat gRNAs inhibited acute viral replication in the 2nd round of infection, abolished cell-associated transmission to unprotected T cells, and maintained protection through 45 days, post-infection (dpi) after a higher dose of HIV-1 infection. Finally, we describe here for the first time the assembly of all-in-one lentiviral vectors containing three and six gRNAs targeting tat and rev. A single-vector tat-targeting construct shows non-inferiority to the tat-targeting multi-vector in low-dose HIV-1 infection. We conclude that Cas9-induced, DNA repair-mediated mutations in tat are sufficiently deleterious and deplete HIV-1 fitness, and multiplexed disruption of tat further limits the possibility of an escape mutant arising, thus elevating the potential of CRISPR-Cas9 to achieve a long-term HIV-1 cure.
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Affiliation(s)
- Youdiil Ophinni
- Division of Molecular Medicine and Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan;
| | - Sayaka Miki
- Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe 654-0142, Hyogo, Japan; (S.M.); (M.K.)
| | - Yoshitake Hayashi
- Division of Molecular Medicine and Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan;
| | - Masanori Kameoka
- Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe 654-0142, Hyogo, Japan; (S.M.); (M.K.)
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