Therapeutic validation of MMR-associated genetic modifiers in a human ex vivo model of Huntington disease DOI Creative Commons
Ross Ferguson,

Robert Goold,

Lucy A. Coupland

et al.

The American Journal of Human Genetics, Journal Year: 2024, Volume and Issue: 111(6), P. 1165 - 1183

Published: May 14, 2024

The pathological huntingtin (HTT) trinucleotide repeat underlying Huntington disease (HD) continues to expand throughout life. Repeat length correlates both with earlier age at onset (AaO) and faster progression, making slowing its expansion an attractive therapeutic approach. Genome-wide association studies have identified candidate variants associated altered AaO many found in DNA mismatch repair (MMR)-associated genes. We examine whether lowering expression of these genes affects the rate human ex vivo models using HD iPSCs iPSC-derived striatal medium spiny neuron-enriched cultures. generated a stable CRISPR interference iPSC line which we can specifically efficiently lower gene from donor carrying over 125 CAG repeats. Lowering each member MMR complexes MutS (MSH2, MSH3, MSH6), MutL (MLH1, PMS1, PMS2, MLH3), LIG1 resulted characteristic deficiencies. Reduced MSH2, MLH1 slowed largest degree, while either or MLH3 it lesser degree. These effects were recapitulated cultures where factor was lowered. CRISPRi-mediated key levels feasibly achievable by current approaches able effectively slow HTT tract. highlight members family as potential targets pathogenic aim delay progression potentially other disorders exhibiting somatic instability.

Language: Английский

High-content CRISPR screening DOI Open Access
Christoph Bock, Paul Datlinger, Florence M. Chardon

et al.

Nature Reviews Methods Primers, Journal Year: 2022, Volume and Issue: 2(1)

Published: Feb. 10, 2022

Language: Английский

Citations

375
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq DOI Creative Commons
Joseph M. Replogle, Reuben A. Saunders, Angela N. Pogson

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(14), P. 2559 - 2575.e28

Published: June 9, 2022

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, date, have been used at limited scales. Here, we perform genome-scale targeting all expressed genes CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes predict function poorly characterized genes, uncovering new regulators ribosome biogenesis (including CCDC86, ZNF236, SPATA5L1), transcription (C7orf26), mitochondrial respiration (TMEM242). In addition assigning gene function, allow for in-depth dissection complex cellular phenomena—from RNA processing differentiation. leverage this ability systematically identify genetic drivers consequences aneuploidy discover an unanticipated layer stress-specific regulation genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait function.

Language: Английский

Citations

363
CRISPR in cancer biology and therapy DOI Open Access
Alyna Katti, Bianca J. Diaz, Christina M. Caragine

et al.

Nature reviews. Cancer, Journal Year: 2022, Volume and Issue: 22(5), P. 259 - 279

Published: Feb. 22, 2022

Language: Английский

Citations

296
High-content CRISPR screening DOI
Christoph Bock, Paul Datlinger, Florence M. Chardon

et al.

Nature Reviews Methods Primers, Journal Year: 2022, Volume and Issue: 2(1)

Published: Feb. 10, 2022

Language: Английский

Citations

207
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression DOI Creative Commons
Parker C. Wilson, Yoshiharu Muto, Hao Wu

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Sept. 6, 2022

Abstract The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic disease leads to injury changes in chromatin accessibility that modify the activity transcription factors involved metabolism inflammation. Here we use single nucleus RNA ATAC sequencing show diabetic reduced glucocorticoid receptor binding sites an injury-associated expression signature tubule. We hypothesize regulated by genetic background closely-intertwined with metabolic memory, which pre-programs respond differently external stimuli. Glucocorticoid excess has long been known increase risk for type 2 diabetes, raises possibility inhibition may mitigate adverse effects disease.

Language: Английский

Citations

107
Identification and functional characterization of transcriptional activators in human cells DOI Creative Commons
Nader Alerasool,

He Leng,

Zhen‐Yuan Lin

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(3), P. 677 - 695.e7

Published: Jan. 10, 2022

Language: Английский

Citations

103
Optophysiology: Illuminating cell physiology with optogenetics DOI Creative Commons
Peng Tan, Lian He, Yun Huang

et al.

Physiological Reviews, Journal Year: 2022, Volume and Issue: 102(3), P. 1263 - 1325

Published: Jan. 24, 2022

Optogenetics combines light and genetics to enable precise control of living cells, tissues, organisms with tailored functions. has the advantages noninvasiveness, rapid responsiveness, tunable reversibility, superior spatiotemporal resolution. Following initial discovery microbial opsins as light-actuated ion channels, a plethora naturally occurring or engineered photoreceptors photosensitive domains that respond at varying wavelengths ushered in next chapter optogenetics. Through protein engineering synthetic biology approaches, genetically encoded photoswitches can be modularly into scaffolds host cells myriad biological processes, well behavioral disease intervention vivo. Here, we summarize these optogenetic tools on basis their fundamental photochemical properties better inform chemical design principles. We also highlight exemplary applications opsin-free optogenetics dissecting cellular physiology (designated "optophysiology") describe current progress, future trends, wireless optogenetics, which enables remote interrogation physiological processes minimal invasiveness. This review is anticipated spark novel thoughts next-generation devices promise accelerate both basic translational studies.

Language: Английский

Citations

82
CRISPR technologies for genome, epigenome and transcriptome editing DOI
Lukas Villiger,

Julia Joung,

Luke W. Koblan

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2024, Volume and Issue: 25(6), P. 464 - 487

Published: Feb. 2, 2024

Language: Английский

Citations

73
CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi DOI Creative Commons

Louise Bendixen,

Trine I. Jensen, Rasmus O. Bak

et al.

Molecular Therapy, Journal Year: 2023, Volume and Issue: 31(7), P. 1920 - 1937

Published: March 24, 2023

The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred variety different types genetic engineering platforms such as transcriptional modulation CRISPR activation (CRISPRa) interference (CRISPRi) systems. This review introduces creation these modulators, various methods delivery utilized systems, technological developments. CRISPRa CRISPRi also been implemented screens interrogating function discovering genes involved biological pathways. We describe compelling examples how tools become powerful means unravel networks uncovering important information about devastating diseases. Finally, we provide an overview preclinical studies used therapeutically, discuss potential future directions novel modalities.

Language: Английский

Citations

56
A universal deep-learning model for zinc finger design enables transcription factor reprogramming DOI Creative Commons
David M. Ichikawa, Osama Abdin, Nader Alerasool

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(8), P. 1117 - 1129

Published: Jan. 26, 2023

Cys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, structurally intricate engagement ZF DNA has made their design challenging. Here we describe screening 49 billion protein-DNA interactions and development a deep-learning model, ZFDesign, that solves any genomic target. ZFDesign is modern machine learning method models global target-specific differences induced by range library environments specifically takes into account compatibility neighboring fingers using novel hierarchical transformer architecture. We demonstrate versatility designed ZFs as nucleases well activators repressors seamless reprogramming human transcription factors. These factors could be used upregulate allele haploinsufficiency, downregulate gain-of-function mutation or test consequence single opposed genes factor would normally influence.

Language: Английский

Citations

52