scholarly journals Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities

2019 ◽  
Author(s):  
Caitlin A. Nichols ◽  
William J. Gibson ◽  
Meredith S. Brown ◽  
Jack A. Kosmicki ◽  
John P. Busanovich ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Loss Of Heterozygosity ◽  
Gene Editing ◽  
Therapeutic Targets ◽  
Essential Genes ◽  
Specific Gene ◽  
Driver Genes ◽  
Normal Cells ◽  
Allele Specific ◽  
Potential Cancer

AbstractAlterations in non-driver genes represent an emerging class of potential therapeutic targets in cancer. Hundreds to thousands of non-driver genes undergo loss of heterozygosity (LOH) events per tumor, generating discrete differences between tumor and normal cells. Here we interrogate LOH of polymorphisms in essential genes as a novel class of therapeutic targets. We hypothesized that monoallelic inactivation of the allele retained in tumors can selectively kill cancer cells but not somatic cells, which retain both alleles. We identified 5664 variants in 1278 essential genes that undergo LOH in cancer and evaluated the potential for each to be targeted using allele-specific gene-editing, RNAi, or small-molecule approaches. We further show that allele-specific inactivation of either of two essential genes (PRIM1 and EXOSC8) reduces growth of cells harboring that allele, while cells harboring the non-targeted allele remain intact. We conclude that LOH of essential genes represents a rich class of non-driver cancer vulnerabilities.

scholarly journals Allele-specific gene editing rescues pathology in a human model of Charcot-Marie-Tooth disease type 2E

2021 ◽  
Author(s):  
Carissa M. Feliciano ◽  
Kenneth Wu ◽  
Hannah L. Watry ◽  
Chiara B.E. Marley ◽  
Gokul N. Ramadoss ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Light Chain ◽  
Gene Editing ◽  
Human Model ◽  
Specific Gene ◽  
Neurofilament Light Chain ◽  
Neurofilament Light ◽  
Light Chain Gene ◽  
Charcot Marie Tooth ◽  
Allele Specific

Many neuromuscular disorders are caused by dominant missense mutations that lead to dominant-negative or gain-of-function pathology. This category of disease is challenging to address via drug treatment or gene augmentation therapy because these strategies may not eliminate the effects of the mutant protein or RNA. Thus, effective treatments are severely lacking for these dominant diseases, which often cause severe disability or death. The targeted inactivation of dominant disease alleles by gene editing is a promising approach with the potential to completely remove the cause of pathology with a single treatment. Here, we demonstrate that allele-specific CRISPR gene editing in a human model of axonal Charcot-Marie-Tooth (CMT) disease rescues pathology caused by a dominant missense mutation in the neurofilament light chain gene (NEFL, CMT type 2E). We utilized a rapid and efficient method for generating spinal motor neurons from human induced pluripotent stem cells (iPSCs) derived from a patient with CMT2E. Diseased motor neurons recapitulated known pathologic phenotypes at early time points of differentiation, including aberrant accumulation of neurofilament light chain protein in neuronal cell bodies. We selectively inactivated the disease NEFL allele in patient iPSCs using Cas9 enzymes to introduce a frameshift at the pathogenic N98S mutation. Motor neurons carrying this allele-specific frameshift demonstrated an amelioration of the disease phenotype comparable to that seen in an isogenic control with precise correction of the mutation. Our results validate allele-specific gene editing as a therapeutic approach for CMT2E and as a promising strategy to silence dominant mutations in any gene for which heterozygous loss-of-function is well tolerated. This highlights the potential for gene editing as a therapy for currently untreatable dominant neurologic diseases.

scholarly journals Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model

2021 ◽  
Author(s):  
Kathleen R. Chirco ◽  
Shereen Chew ◽  
Anthony T. Moore ◽  
Jacque L. Duncan ◽  
Deepak A. Lamba
Keyword(s):  
Gene Editing ◽  
Specific Gene ◽  
Allele Specific

scholarly journals Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Caitlin A. Nichols ◽  
William J. Gibson ◽  
Meredith S. Brown ◽  
Jack A. Kosmicki ◽  
John P. Busanovich ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Essential Genes ◽  
Potential Cancer

scholarly journals Gene interfered-ferroptosis therapy for cancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jinliang Gao ◽  
Tao Luo ◽  
Jinke Wang
Keyword(s):  
Drug Resistance ◽  
Cancer Therapy ◽  
Growth Inhibition ◽  
Cancer Cells ◽  
Iron Nanoparticles ◽  
Tumor Growth Inhibition ◽  
Specific Gene ◽  
Normal Cells ◽  
Adeno Associated Virus ◽  
Metabolic Genes

AbstractAlthough some effective therapies have been available for cancer, it still poses a great threat to human health and life due to its drug resistance and low response in patients. Here, we develop a ferroptosis-based therapy by combining iron nanoparticles and cancer-specific gene interference. The expression of two iron metabolic genes (FPN and LCN2) was selectively knocked down in cancer cells by Cas13a or microRNA controlled by a NF-κB-specific promoter. Cells were simultaneously treated by iron nanoparticles. As a result, a significant ferroptosis was induced in a wide variety of cancer cells. However, the same treatment had little effect on normal cells. By transferring genes with adeno-associated virus and iron nanoparticles, the significant tumor growth inhibition and durable cure were obtained in mice with the therapy. In this work, we thus show a cancer therapy based on gene interference-enhanced ferroptosis.

scholarly journals Gene interfered-ferroptosis therapy of cancer

2020 ◽  
Author(s):  
Jinliang Gao ◽  
Tao Luo ◽  
Na Lin ◽  
Jinke Wang
Keyword(s):  
Gene Expression ◽  
Drug Resistance ◽  
Cancer Cells ◽  
Iron Metabolism ◽  
Iron Content ◽  
Iron Nanoparticles ◽  
Specific Gene ◽  
Novel Therapy ◽  
Normal Cells ◽  
Gene Vectors

AbstractAlthough some effective therapies have been available for cancer, it still poses a great threat to human health and life due to its drug resistance and low response in patients. Here, we developed a novel therapy named as gene interfered-ferroptosis therapy (GIFT) by combining iron nanoparticles and cancer-specific gene interference. Using a promoter consisted of a NF-κB decoy and a minimal promoter (DMP), we knocked down the expression of two iron metabolism-related genes (FPN and Lcn2) selectively in cancer cells. At the same time, we treated cells with Fe3O4 nanoparticles. As a result, a significant ferroptosis was induced in a wide variety of cancer cells representing various hematological and solid tumors. However, the same treatment had no effect on normal cells. By using AAV and PEI-coated Fe3O4 nanoparticles as gene vectors, we found that the tumor growth in mice could be also significantly inhibited by the intravenously injected GIFT reagents. By detecting ROS, iron content and gene expression, we confirmed that the mechanism underlying the therapy is gene inference-enhanced ferroptosis.

Allele-specific genome editing using CRISPR-Cas9 causes off-target mutations in diploid yeast

2018 ◽  
Author(s):  
Arthur R. Gorter de Vries ◽  
Lucas G. F. Couwenberg ◽  
Marcel van den Broek ◽  
Pilar de la Torre Cortés ◽  
Jolanda ter Horst ◽  
...  
Keyword(s):  
Genome Editing ◽  
Loss Of Heterozygosity ◽  
Genetic Modification ◽  
Large Scale ◽  
Gene Editing ◽  
Yeast Genome ◽  
Dna Double Strand Breaks ◽  
Homology Directed Repair ◽  
Eukaryotic Gene ◽  
Allele Specific

ABSTRACTTargeted DNA double-strand breaks (DSBs) with CRISPR-Cas9 have revolutionized genetic modification by enabling efficient genome editing in a broad range of eukaryotic systems. Accurate gene editing is possible with near-perfect efficiency in haploid or (predominantly) homozygous genomes. However, genomes exhibiting polyploidy and/or high degrees of heterozygosity are less amenable to genetic modification. Here, we report an up to 99-fold lower gene editing efficiency when editing individual heterozygous loci in the yeast genome. Moreover, Cas9-mediated introduction of a DSB resulted in large scale loss of heterozygosity affecting DNA regions up to 360 kb that resulted in introduction of nearly 1700 off-target mutations, due to replacement of sequences on the targeted chromosome by corresponding sequences from its non-targeted homolog. The observed patterns of loss of heterozygosity were consistent with homology directed repair. The extent and frequency of loss of heterozygosity represent a novel mutagenic side-effect of Cas9-mediated genome editing, which would have to be taken into account in eukaryotic gene editing. In addition to contributing to the limited genetic amenability of heterozygous yeasts, Cas9-mediated loss of heterozygosity could be particularly deleterious for human gene therapy, as loss of heterozygous functional copies of anti-proliferative and pro-apoptotic genes is a known path to cancer.

scholarly journals The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Hrant Hovhannisyan ◽  
Ester Saus ◽  
Ewa Ksiezopolska ◽  
Toni Gabaldón
Keyword(s):  
Gene Expression ◽  
Loss Of Heterozygosity ◽  
Opportunistic Pathogen ◽  
Specific Gene ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Content Type ◽  
Additional Layer ◽  
Allele Specific ◽  
Candida Orthopsilosis

ABSTRACT Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.

scholarly journals Regulation Network of Colorectal Cancer Specific Enhancers in Progression of Colorectal Cancer

2021 ◽  
Author(s):  
Bohan Chen ◽  
Yiping Ma ◽  
Jinfang Bi ◽  
Wenbin Wang ◽  
Anshun He ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Cells ◽  
Cancer Progression ◽  
Chromatin Structure ◽  
Therapeutic Targets ◽  
Higher Order ◽  
Epigenetic Changes ◽  
Rna Seq ◽  
Normal Cells ◽  
Regulation Network

Enhancers regulate multiple genes through higher-order chromatin structure and further affect cancer progression. Epigenetic changes in cancer cells activate several cancer specific enhancers that are silenced in normal cells. These cancer specific enhancers are potential therapeutic targets of cancer. However, functions and regulation network of colorectal cancer specific enhancers are still unknown. Here in this study, we profile colorectal cancer specific enhancers and reveal the regulation network of these enhancers by analysis of HiChIP, Hi-C and RNA-seq data. We propose the regulation network of colorectal cancer specific enhancers plays important role in progression of colorectal cancer.

scholarly journals Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E

2021 ◽  
Vol 9 ◽  
Author(s):  
Carissa M. Feliciano ◽  
Kenneth Wu ◽  
Hannah L. Watry ◽  
Chiara B. E. Marley ◽  
Gokul N. Ramadoss ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Light Chain ◽  
Gene Editing ◽  
Human Model ◽  
Specific Gene ◽  
Neurofilament Light Chain ◽  
Neurofilament Light ◽  
Light Chain Gene ◽  
Charcot Marie Tooth ◽  
Allele Specific

Many neuromuscular disorders are caused by dominant missense mutations that lead to dominant-negative or gain-of-function pathology. This category of disease is challenging to address via drug treatment or gene augmentation therapy because these strategies may not eliminate the effects of the mutant protein or RNA. Thus, effective treatments are severely lacking for these dominant diseases, which often cause severe disability or death. The targeted inactivation of dominant disease alleles by gene editing is a promising approach with the potential to completely remove the cause of pathology with a single treatment. Here, we demonstrate that allele-specific CRISPR gene editing in a human model of axonal Charcot-Marie-Tooth (CMT) disease rescues pathology caused by a dominant missense mutation in the neurofilament light chain gene (NEFL, CMT type 2E). We utilized a rapid and efficient method for generating spinal motor neurons from human induced pluripotent stem cells (iPSCs) derived from a patient with CMT2E. Diseased motor neurons recapitulated known pathologic phenotypes at early time points of differentiation, including aberrant accumulation of neurofilament light chain protein in neuronal cell bodies. We selectively inactivated the disease NEFL allele in patient iPSCs using Cas9 enzymes to introduce a frameshift at the pathogenic N98S mutation. Motor neurons carrying this allele-specific frameshift demonstrated an amelioration of the disease phenotype comparable to that seen in an isogenic control with precise correction of the mutation. Our results validate allele-specific gene editing as a therapeutic approach for CMT2E and as a promising strategy to silence dominant mutations in any gene for which heterozygous loss-of-function is well tolerated. This highlights the potential for gene editing as a therapy for currently untreatable dominant neurologic diseases.

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