CRISPR-enhanced human adipocyte browning as cell therapy for metabolic disease.
Adipocytes, Brown
/ metabolism
Adipocytes, White
/ metabolism
Adult Stem Cells
/ physiology
Animals
CRISPR-Cas Systems
/ genetics
Cell Culture Techniques
/ methods
Cell Differentiation
Diet, High-Fat
/ adverse effects
Disease Models, Animal
Fatty Liver
/ etiology
Gene Editing
/ methods
Glucose Intolerance
/ etiology
Humans
Lipid Metabolism
/ genetics
Male
Mice
Nuclear Receptor Interacting Protein 1
/ genetics
Obesity
/ complications
RNA, Guide, Kinetoplastida
/ genetics
Subcutaneous Fat
/ cytology
Thermogenesis
/ genetics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
26 11 2021
26 11 2021
Historique:
received:
28
10
2020
accepted:
08
11
2021
entrez:
27
11
2021
pubmed:
28
11
2021
medline:
8
1
2022
Statut:
epublish
Résumé
Obesity and type 2 diabetes are associated with disturbances in insulin-regulated glucose and lipid fluxes and severe comorbidities including cardiovascular disease and steatohepatitis. Whole body metabolism is regulated by lipid-storing white adipocytes as well as "brown" and "brite/beige" adipocytes that express thermogenic uncoupling protein 1 (UCP1) and secrete factors favorable to metabolic health. Implantation of brown fat into obese mice improves glucose tolerance, but translation to humans has been stymied by low abundance of primary human beige adipocytes. Here we apply methods to greatly expand human adipocyte progenitors from small samples of human subcutaneous adipose tissue and then disrupt the thermogenic suppressor gene NRIP1 by CRISPR. Ribonucleoprotein consisting of Cas9 and sgRNA delivered ex vivo are fully degraded by the human cells following high efficiency NRIP1 depletion without detectable off-target editing. Implantation of such CRISPR-enhanced human or mouse brown-like adipocytes into high fat diet fed mice decreases adiposity and liver triglycerides while enhancing glucose tolerance compared to implantation with unmodified adipocytes. These findings advance a therapeutic strategy to improve metabolic homeostasis through CRISPR-based genetic enhancement of human adipocytes without exposing the recipient to immunogenic Cas9 or delivery vectors.
Identifiants
pubmed: 34836963
doi: 10.1038/s41467-021-27190-y
pii: 10.1038/s41467-021-27190-y
pmc: PMC8626495
doi:
Substances chimiques
NRIP1 protein, human
0
Nuclear Receptor Interacting Protein 1
0
RNA, Guide
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
6931Subventions
Organisme : NCATS NIH HHS
ID : UH3 TR002668
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK089101
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM115911
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK123028
Pays : United States
Organisme : NHLBI NIH HHS
ID : F31 HL147482
Pays : United States
Organisme : NIDDK NIH HHS
ID : R37 DK030898
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK030898
Pays : United States
Organisme : NCATS NIH HHS
ID : UG3 TR002668
Pays : United States
Organisme : NIDDK NIH HHS
ID : U2C DK093000
Pays : United States
Informations de copyright
© 2021. The Author(s).
Références
Pittenger, M. F. et al. Mesenchymal stem cell perspective: cell biology to clinical progress. NPJ Regen. Med. 2, 22 (2019).
doi: 10.1038/s41536-019-0083-6
Kean, L. S. Defining success with cellular therapeutics: the current landscape for clinical end point and toxicity analysis. Blood 131, 2630–2639 (2018).
pubmed: 29728399
pmcid: 6032897
doi: 10.1182/blood-2018-02-785881
Rosenberg, S. A. & Restifo, N. P. Adoptive cell transfer as personalized immunotherapy for human cancer. Science 348, 62–68 (2015).
pubmed: 25838374
pmcid: 6295668
doi: 10.1126/science.aaa4967
Finck, A., Gill, S. I. & June, C. H. Cancer immunotherapy comes of age and looks for maturity. Nat. Commun. 11, 3325 (2020).
pubmed: 32620755
pmcid: 7335079
doi: 10.1038/s41467-020-17140-5
Czech, M. P. Insulin action and resistance in obesity and type 2 diabetes. Nat. Med. 23, 804–814 (2017).
pubmed: 28697184
pmcid: 6048953
doi: 10.1038/nm.4350
Roden, M. & Shulman, G. I. The integrative biology of type 2 diabetes. Nature 576, 51–60 (2019).
pubmed: 31802013
doi: 10.1038/s41586-019-1797-8
Petersen, M. C., Vatner, D. F. & Shulman, G. I. Regulation of hepatic glucose metabolism in health and disease. Nat. Rev. Endocrinol. 13, 572–587 (2017).
pubmed: 28731034
pmcid: 5777172
doi: 10.1038/nrendo.2017.80
Kusminski, C. M., Bickel, P. E. & Scherer, P. E. Targeting adipose tissue in the treatment of obesity-associated diabetes. Nat. Rev. Drug Disco. 15, 639–660 (2016).
doi: 10.1038/nrd.2016.75
Guilherme, A., Virbasius, J. V., Puri, V. & Czech, M. P. Adipocyte dysfunctions linking obesity to insulin resistance and type 2 diabetes. Nat. Rev. Mol. Cell Biol. 9, 367–377 (2008).
pubmed: 18401346
pmcid: 2886982
doi: 10.1038/nrm2391
Lee, Y. S., Wollam, J. & Olefsky, J. M. An integrated view of immunometabolism. Cell 172, 22–40 (2018).
pubmed: 29328913
pmcid: 8451723
doi: 10.1016/j.cell.2017.12.025
Funcke, J. B. & Scherer, P. E. Beyond adiponectin and leptin: adipose tissue-derived mediators of inter-organ communication. J. Lipid Res. 60, 1648–1684 (2019).
pubmed: 31209153
pmcid: 6795086
doi: 10.1194/jlr.R094060
Kajimura, S., Spiegelman, B. M. & Seale, P. Brown and Beige Fat: physiological roles beyond heat generation. Cell Metab. 22, 546–559 (2015).
pubmed: 26445512
pmcid: 4613812
doi: 10.1016/j.cmet.2015.09.007
Villarroya, F., Cereijo, R., Villarroya, J. & Giralt, M. Brown adipose tissue as a secretory organ. Nat. Rev. Endocrinol. 13, 26–35 (2017).
pubmed: 27616452
doi: 10.1038/nrendo.2016.136
Klepac, K., Georgiadi, A., Tschöp, M. & Herzig, S. The role of brown and beige adipose tissue in glycaemic control. Mol. Asp. Med. 68, 90–100 (2019).
doi: 10.1016/j.mam.2019.07.001
Nedergaard, J. & Cannon, B. The changed metabolic world with human brown adipose tissue: therapeutic visions. Cell Metab. 11, 268–272 (2010).
pubmed: 20374959
doi: 10.1016/j.cmet.2010.03.007
Wu, J. et al. Beige adipocytes are a distinct type of thermogenic fat cell in mouse and human. Cell 150, 366–376 (2012).
pubmed: 22796012
pmcid: 3402601
doi: 10.1016/j.cell.2012.05.016
Rosenwald, M., Perdikari, A., Rülicke, T. & Wolfrum, C. Bi-directional interconversion of brite and white adipocytes. Nat. Cell Biol. 15, 659–667 (2013).
pubmed: 23624403
doi: 10.1038/ncb2740
Wang, G. X. et al. The brown fat-enriched secreted factor Nrg4 preserves metabolic homeostasis through attenuation of hepatic lipogenesis. Nat. Med. 2014, 1436–1443 (2014).
doi: 10.1038/nm.3713
Chen, Z. et al. Nrg4 promotes fuel oxidation and a healthy adipokine profile to ameliorate diet-induced metabolic disorders. Mol. Metab. 6, 863–872 (2017).
pubmed: 28752050
pmcid: 5518721
doi: 10.1016/j.molmet.2017.03.016
Stanford, K. I. et al. Brown adipose tissue regulates glucose homeostasis and insulin sensitivity. J. Clin. Investig. 123, 215–223 (2013).
pubmed: 23221344
doi: 10.1172/JCI62308
White, J. D., Dewal, R. S. & Stanford, K. I. The beneficial effects of brown adipose tissue transplantation. Mol. Asp. Med. 68, 74–81 (2019).
doi: 10.1016/j.mam.2019.06.004
Lynes, M. D. et al. The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue. Nat. Med. 23, 631–637 (2017).
pubmed: 28346411
pmcid: 5699924
doi: 10.1038/nm.4297
Min, S. Y. et al. Human ‘brite/beige’ adipocytes develop from capillary networks, and their implantation improves metabolic homeostasis in mice. Nat. Med. 22, 312–318 (2016).
pubmed: 26808348
pmcid: 4777633
doi: 10.1038/nm.4031
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).
pubmed: 32051598
pmcid: 8992613
doi: 10.1038/s41586-020-1978-5
Hille, F. et al. The Biology of CRISPR-Cas: backward and forward. Cell 172, 1239–1259 (2018).
pubmed: 29522745
doi: 10.1016/j.cell.2017.11.032
Leonardsson, G. et al. Nuclear receptor corepressor RIP140 regulates fat accumulation. Proc. Natl Acad. Sci. USA 101, 8437–8442 (2004).
pubmed: 15155905
pmcid: 420412
doi: 10.1073/pnas.0401013101
Powelka, A. M. et al. Suppression of oxidative metabolism and mitochondrial biogenesis by the transcriptional corepressor RIP140 in mouse adipocytes. J. Clin. Invest. 116, 125–136 (2006).
pubmed: 16374519
doi: 10.1172/JCI26040
Shen, Y. et al. CRISPR-delivery particles targeting nuclear receptor-interacting protein 1 (Nrip1) in adipose cells to enhance energy expenditure. J. Biol. Chem. 293, 17291–17305 (2018).
pubmed: 30190322
pmcid: 6222111
doi: 10.1074/jbc.RA118.004554
Nautiyal, J., Christian, M. & Parker, M. G. Distinct functions for RIP140 in development, inflammation, and metabolism. Trends Endocrinol. Metab. 24, 451–459 (2013).
pubmed: 23742741
doi: 10.1016/j.tem.2013.05.001
Chung, J. Y., Ain, Q. U., Song, Y., Yong, S. B. & Kim, Y. H. Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance. Genome Res. 29, 1442–1452 (2019).
pubmed: 31467027
pmcid: 6724665
doi: 10.1101/gr.246900.118
Wang, C. H. et al. CRISPR-engineered human brown-like adipocytes prevent diet-induced obesity and ameliorate metabolic syndrome in mice. Sci. Transl. Med. 12, eaaz8664 (2020).
pubmed: 32848096
pmcid: 7704293
doi: 10.1126/scitranslmed.aaz8664
Charlesworth, C. T. et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 25, 249–254 (2019).
pubmed: 30692695
pmcid: 7199589
doi: 10.1038/s41591-018-0326-x
Hinderer, C. et al. Severe toxicity in nonhuman primates and piglets following high-dose intravenous administration of an Adeno-Associated Virus Vector expressing human SMN. Hum. Gene Ther. Mar. 29, 285–298 (2018).
doi: 10.1089/hum.2018.015
Kim, S., Kim, D., Cho, S. W., Kim, J. & Kim, J. S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012–1019 (2014).
pubmed: 24696461
pmcid: 4032847
doi: 10.1101/gr.171322.113
Huang, R. S., Shih, H. A., Lai, M. C., Chang, Y. J. & Lin, S. Enhanced NK-92 cytotoxicity by CRISPR genome engineering using Cas9 Ribonucleoproteins. Front Immunol. 11, 1008 (2020).
pubmed: 32528479
pmcid: 7256201
doi: 10.3389/fimmu.2020.01008
Friedman, S. L., Neuschwander-Tetri, B. A., Rinella, M. & Sanyal, A. J. Mechanisms of NAFLD development and therapeutic strategies. Nat. Med. 24, 908–922 (2018).
pubmed: 29967350
pmcid: 6553468
doi: 10.1038/s41591-018-0104-9
Cheng, Y. et al. Prediction of adipose browning capacity by systematic integration of transcriptional profiles. Cell Rep. 23, 3112–3125 (2018).
pubmed: 29874595
doi: 10.1016/j.celrep.2018.05.021
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).
pubmed: 25513782
doi: 10.1038/nbt.3117
Bae, S., Park, J. & Kim, J. S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).
pubmed: 24463181
pmcid: 4016707
doi: 10.1093/bioinformatics/btu048
Tran, T. T. & Kahn, C. R. Transplantation of adipose tissue and stem cells: role in metabolism and disease. Nat. Rev. Endocrinol. Apr. 6, 195–213 (2010).
doi: 10.1038/nrendo.2010.20
Blumenfeld, N. R. et al. A direct tissue-grafting approach to increasing endogenous brown fat. Sci. Rep. 8, 7957 (2018).
pubmed: 29785004
pmcid: 5962549
doi: 10.1038/s41598-018-25866-y
Xiong, Y. et al. A novel brown adipocyte-enriched long non-coding RNA that is required for brown adipocyte differentiation and sufficient to drive thermogenic gene program in white adipocytes. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1863, 409–419 (2018).
pubmed: 29341928
doi: 10.1016/j.bbalip.2018.01.008
Ceddia, R. P. & Collins, S. A compendium of G-protein-coupled receptors and cyclic nucleotide regulation of adipose tissue metabolism and energy expenditure. Clin. Sci. 134, 473–512 (2020).
doi: 10.1042/CS20190579
Vakulskas, C. A. et al. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nat. Med. 24, 1216–1224 (2018).
pubmed: 30082871
pmcid: 6107069
doi: 10.1038/s41591-018-0137-0
Kleinstiver, B. P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).
pubmed: 26735016
pmcid: 4851738
doi: 10.1038/nature16526
Tran, K. V. et al. Human thermogenic adipocyte regulation by the long noncoding RNA LINC00473. Nat. Metab. 2, 397–412 (2020).
pubmed: 32440655
pmcid: 7241442
doi: 10.1038/s42255-020-0205-x
Wu, Y. et al. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat. Med. 25, 776–783 (2019).
pubmed: 30911135
pmcid: 6512986
doi: 10.1038/s41591-019-0401-y
Kamble, P. G. et al. Proof-of-concept for CRISPR/Cas9 gene editing in human preadipocytes: Deletion of FKBP5 and PPARG and effects on adipocyte differentiation and metabolism. Sci. Rep. 10, 10565 (2020).
pubmed: 32601291
pmcid: 7324390
doi: 10.1038/s41598-020-67293-y
Hsiau, T. et al. Inference of CRISPR Edits from Sanger Trace Data., bioRxiv 251082 https://doi.org/10.1101/251082 (2019).
Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).
Yukselen, O., Turkyilmaz, O., Ozturk, A. R., Garber, M. & Kucukural, A. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020).
pubmed: 32306927
pmcid: 7168977
doi: 10.1186/s12864-020-6714-x
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina Sequence Data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 12, 323 (2011).
doi: 10.1186/1471-2105-12-323
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNAseq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Durinck, S., Spellman, P., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191 (2009).
pubmed: 19617889
pmcid: 3159387
doi: 10.1038/nprot.2009.97
Yu, G., Wang, L., Han, Y. & He, Q. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A J. Integr. Biol. 16, 284–287 (2012).
doi: 10.1089/omi.2011.0118
Durinck, S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439–3440 (2005).
pubmed: 16082012
doi: 10.1093/bioinformatics/bti525
Carlson, M. org.Mm.eg.db: Genome wide annotation for Mouse. R package version 3.8.2. (2019).
Kucukural, A. et al. DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics 20, 6 (2019).
pubmed: 30611200
pmcid: 6321710
doi: 10.1186/s12864-018-5362-x
Rodríguez, T. C. et al. Genome-wide detection and analysis of CRISPR-Cas off-targets. Reprogramming the Genome: CRISPR-Cas-based Human Disease Therapy, Volume 181 (2021).
Zhu, L. J. et al. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics 18, 1–0 (2017).
doi: 10.1186/s12864-017-3746-y
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
pubmed: 30809026
pmcid: 6533916
doi: 10.1038/s41587-019-0032-3
UMass Medical School. CRISPR-enhanced human adipocyte browning as cell therapy for metabolic disease. 2021/07. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA745932 . NCBI:BioProject: PRJNA745932.