Quiescence unveils a novel mutational force in fission yeast

To maintain life across a fluctuating environment, cells alternate between phases of cell division and quiescence. During cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation (Luria and Delbrück, 1943; Lea and Coulson, 1949), whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. The novel mutational landscape of quiescence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide variants (SNVs), and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.

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Base editing generates substantial off-target single nucleotide variants

10.1101/480145 ◽

2018 ◽

Cited By ~ 5

Author(s):

Erwei Zuo ◽

Yidi Sun ◽

Wu Wei ◽

Tanglong Yuan ◽

Wenqin Ying ◽

...

Keyword(s):

Mammalian Cells ◽

Biomedical Application ◽

Spontaneous Mutation ◽

Great Promise ◽

Single Nucleotide Variants ◽

Spontaneous Mutation Rate ◽

Single Nucleotide ◽

Base Editing ◽

Genome Wide ◽

Target Effects

AbstractGenome editing tools including CRISPR/Cas9 and base editors hold great promise for correcting pathogenic mutations. Unbiased genome-wide off-target effects of the editing in mammalian cells is required before clinical applications, but determination of the extent of off-target effects has been difficult due to the existence of single nucleotide polymorphisms (SNPs) in individuals. Here, we developed a method named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) to detect off-target mutations without interference of SNPs. We applied GOTI to both the CRISPR-Cas9 and base editing (BE3) systems by editing one blastomere of the two-cell mouse embryo and then compared whole genome sequences of progeny-cell populations at E14.5 stage. Sequence analysis of edited and non-edited cell progenies showed that undesired off-target single nucleotide variants (SNVs) are rare (average 10.5) in CRISPR-edited mouse embryos, with a frequency close to the spontaneous mutation rate. By contrast, BE3 editing induced over 20-fold higher SNVs (average 283), raising the concern of using base-editing approaches for biomedical application.

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Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

Science ◽

10.1126/science.aav9973 ◽

2019 ◽

pp. eaav9973 ◽

Cited By ~ 84

Author(s):

Erwei Zuo ◽

Yidi Sun ◽

Wu Wei ◽

Tanglong Yuan ◽

Wenqin Ying ◽

...

Keyword(s):

Spontaneous Mutation ◽

Mouse Embryos ◽

Single Nucleotide Variants ◽

Spontaneous Mutation Rate ◽

Single Nucleotide ◽

Base Editing ◽

Genome Wide ◽

Cell Embryo ◽

Adenine Base ◽

Target Effects

Genome editing holds promise for correcting pathogenic mutations. However, it is difficult to determine off-target effects of editing due to single nucleotide polymorphism in individuals. Here, we developed a method named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) to detect off-target mutations by editing one blastomere of two-cell mouse embryos using either CRISPR-Cas9 or base editors. Comparison of the whole genome sequences of progeny cells of edited vs. non-edited blastomeres at E14.5 showed that off-target single nucleotide variants (SNVs) were rare in embryos edited by CRISPR-Cas9 or adenine base editor, with a frequency close to the spontaneous mutation rate. In contrast, cytosine base editing induced SNVs with over 20-fold higher frequencies, requiring a solution to address its fidelity.

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Post-lingual non-syndromic hearing loss phenotype: a novel homozygous missense mutation in MITF

10.21203/rs.2.13328/v2 ◽

2019 ◽

Author(s):

Athar Khalil ◽

Samer Bou Karroum ◽

Rana Barake ◽

Gabriel Dunya ◽

Samer Abou-Rizk ◽

...

Keyword(s):

Hearing Loss ◽

Exome Sequencing ◽

Missense Mutation ◽

The Novel ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Genetic Hearing Loss ◽

Syndromic Hearing Loss ◽

And Function

Abstract Background Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases. Methods In the current study, we report a multifactorial genetic mode of inheritance in a NSHL consanguineous family using exome sequencing technology. We evaluated the possible effects of the single nucleotide variants (SNVs) detected in our patients using in silico methods. Results Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes (MYO7A and MYH14). The novel p. Pro338Leu missense mutation on the MITF protein was predicted to change the protein structure and function. Conclusion The novel MITF variant is the first bi-allelic SNV in this gene to be associated with an autosomal recessive non-syndromic HL case with a post-lingual onset. Our findings highlight the importance of whole exome sequencing for a comprehensive assessment of the genetic heterogeneity of HL.

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Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab431 ◽

2021 ◽

Author(s):

Skylar R Wyant ◽

M Fernanda Rodriguez ◽

Corey K Carter ◽

Wayne A Parrott ◽

Scott A Jackson ◽

...

Keyword(s):

Fast Neutron ◽

De Novo ◽

Spontaneous Mutation ◽

Local Context ◽

Induced Mutations ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Frameshift Mutations ◽

Small Indels ◽

Standing Variation

Abstract The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single nucleotide variants. The accumulation of new single nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In FN treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes in generations following mutagenesis rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1–6 base pairs, are less abundant than in standing variation. Short deletions are more abundant and prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels, increasing the abundance of loss of function mutations that impact single genes.

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Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes

Molecular Biology and Evolution ◽

10.1093/molbev/msz177 ◽

2019 ◽

Vol 36 (12) ◽

pp. 2861-2877 ◽

Cited By ~ 7

Author(s):

Lorenzo Tattini ◽

Nicolò Tellini ◽

Simone Mozzachiodi ◽

Melania D’Angiolo ◽

Sophie Loeillet ◽

...

Keyword(s):

Loss Of Heterozygosity ◽

Copy Number Variants ◽

Sequence Divergence ◽

Diploid Hybrid ◽

Single Nucleotide Variants ◽

Evolutionary Processes ◽

Single Nucleotide ◽

Mutational Landscape ◽

Interspecies Hybrids ◽

Nucleotide Mutation

Abstract Mutations, recombinations, and genome duplications may promote genetic diversity and trigger evolutionary processes. However, quantifying these events in diploid hybrid genomes is challenging. Here, we present an integrated experimental and computational workflow to accurately track the mutational landscape of yeast diploid hybrids (MuLoYDH) in terms of single-nucleotide variants, small insertions/deletions, copy-number variants, aneuploidies, and loss-of-heterozygosity. Pairs of haploid Saccharomyces parents were combined to generate ancestor hybrids with phased genomes and varying levels of heterozygosity. These diploids were evolved under different laboratory protocols, in particular mutation accumulation experiments. Variant simulations enabled the efficient integration of competitive and standard mapping of short reads, depending on local levels of heterozygosity. Experimental validations proved the high accuracy and resolution of our computational approach. Finally, applying MuLoYDH to four different diploids revealed striking genetic background effects. Homozygous Saccharomyces cerevisiae showed a ∼4-fold higher mutation rate compared with its closely related species S. paradoxus. Intraspecies hybrids unveiled that a substantial fraction of the genome (∼250 bp per generation) was shaped by loss-of-heterozygosity, a process strongly inhibited in interspecies hybrids by high levels of sequence divergence between homologous chromosomes. In contrast, interspecies hybrids exhibited higher single-nucleotide mutation rates compared with intraspecies hybrids. MuLoYDH provided an unprecedented quantitative insight into the evolutionary processes that mold diploid yeast genomes and can be generalized to other genetic systems.

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Post-lingual non-syndromic hearing loss phenotype: a polygenic case with 2 biallelic mutations in MYO15A and MITF

10.21203/rs.2.13328/v5 ◽

2019 ◽

Author(s):

Athar Khalil ◽

Samer Bou Karroum ◽

Rana Barake ◽

Gabriel Dunya ◽

Samer Abou-Rizk ◽

...

Keyword(s):

Hearing Loss ◽

Exome Sequencing ◽

The Novel ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Genetic Hearing Loss ◽

Syndromic Hearing Loss ◽

Biallelic Mutations ◽

And Function

Abstract Background: Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases. Methods: In the current study , we reported a polygenic mode of inheritance in an NSHL consanguineous family using exome sequencing technology and we evaluated the possible effect of the detected single nucleotide variants (SNVs) using in silico methods. Results: Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes ( MYO7A and MYH14). The novel MITF p. Pro338Leu missense mutation was predicted to change the protein structure and function. Conclusion: A novel MITF mutation along with a previously described MYO15A mutation segregate with an autosomal recessive non-syndromic HL case with a post-lingual onset. The findings highlight the importance of carrying whole exome sequencing for a comprehensive assessment of HL genetic heterogeneity.

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Post-lingual non-syndromic hearing loss phenotype: a polygenic case with 2 biallelic mutations in MYO5A and MITF

10.21203/rs.2.13328/v3 ◽

2019 ◽

Author(s):

Athar Khalil ◽

Samer Bou Karroum ◽

Rana Barake ◽

Gabriel Dunya ◽

Samer Abou-Rizk ◽

...

Keyword(s):

Hearing Loss ◽

Exome Sequencing ◽

The Novel ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Genetic Hearing Loss ◽

Syndromic Hearing Loss ◽

Biallelic Mutations ◽

And Function

Abstract Background: Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases. Methods: In the current study , we reported a polygenic mode of inheritance in an NSHL consanguineous family using exome sequencing technology and we evaluated the possible effect of the detected single nucleotide variants (SNVs) using in silico methods. Results: Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes ( MYO7A and MYH14). The novel MITF p. Pro338Leu missense mutation was predicted to change the protein structure and function. Conclusion: A novel MITF mutation along with a previously described MYO15A mutation segregate with an autosomal recessive non-syndromic HL case with a post-lingual onset. The findings highlight the importance of carrying whole exome sequencing for a comprehensive assessment of HL genetic heterogeneity.

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Distinct mutational landscape between HR+ and HR- HER2+ early-stage breast cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.543 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 543-543

Author(s):

Bo Chen ◽

Ning Liao ◽

Guo-Chun Zhang ◽

Yulei Wang ◽

Xiaoqing Chen ◽

...

Keyword(s):

Breast Cancer ◽

Ductal Carcinoma ◽

Early Stage ◽

Treatment Strategies ◽

Genetic Alterations ◽

Breast Cancer Patients ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Mutational Landscape ◽

Her2 Breast Cancer

543 Background: HER2 targeted therapy has revolutionized the survival outcomes of early and advanced HER2+ breast cancer (BC). However, among HER2+ patients, the therapeutic response to HER2 inhibitors vary. To understand the molecular mechanism of the variability in therapeutic efficacies, the mutational landscape of HER2+ tumors need to be elucidated. Methods: 107 HER2+ Chinese stage I-III BC patients were included in the study, including 64 HR+ and 43 HR- patients. A majority of the patients were diagnosed with infiltrating ductal carcinoma (99/107). Capture-based targeted sequencing was performed using a panel consisting of 520 cancer-related genes spanning 1.64 MB of the human genome. Results: 1,119 alterations were detected, including 478 single nucleotide variants (SNVs), 14 insertions or deletions, 29 fusions, 593 copy number amplifications (CNA), 2 large genomic rearrangements and 3 CN deletions in 267 genes. Alterations in 99 genes were shared between HR+/HER2+ and HR-/HER2+ tumors; while 123 and 45 genes were only detected in either HR+/HER2+ or HR-/HER2+ tumors, respectively. CNA, splice site and frameshift mutations were significantly more in HR+/HER2+ patients ( p= 0.017). Specifically, CNA in SPOP, CCND1, FGF19, FGF3, FGF4, RNF43, RAD51C, ADGRA4 and MDM4 and various alterations in GATA3 were significantly more among HR+/HER2+ tumors ( p< 0.05). In addition to HER2 amplifications, concurrent fusions in ERBB2 (67%, 4/6), SNVs in ERBB3 (100%, 3/3) and ERBB4 (100%, 1/1) were more likely to be detected in HR+/HER2+ tumors, while concurrent EGFR amplifications were exclusively detected in HR-/HER2+ tumors. The trend of concurrent mutations was consistent with mutation types detected in HER2- tumors based on HR status, wherein EGFR amplifications were more frequent in HR-/HER2- tumors, while SNVs in EGFR, ERBB2, ERBB3 and ERBB4 were more predominant in HR+/HER2- tumors. Based on KEGG pathway analysis, HR+/HER2+ tumors had more frequent alterations in TGFb ( p= 0.007), WNT ( p= 0.002) and homologous recombination ( p= 0.004) pathways than HR-/HER2+ tumors. Furthermore, our data revealed that HR+/HER2+ and HR-/HER2+ patients had comparable TMB ( p= 0.24), with a median TMB of 4.0 mutations/Mb for both. Conclusions: Our study revealed genetic heterogeneity between HR+ and HR- HER2+ tumors. The distinct genetic alterations are potentially relevant in the development of optimal treatment strategies for such patients.

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Post-lingual non-syndromic hearing loss phenotype: a novel homozygous missense mutation in MITF

10.21203/rs.2.13328/v1 ◽

2019 ◽

Author(s):

Athar Khalil ◽

Samer Bou Karroum ◽

Rana Barake ◽

Gabriel Dunya ◽

Samer Abou-Rizk ◽

...

Keyword(s):

Hearing Loss ◽

Exome Sequencing ◽

Missense Mutation ◽

The Novel ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Genetic Hearing Loss ◽

Syndromic Hearing Loss ◽

And Function

Abstract Background Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases. Methods In the current study, we report a multifactorial genetic mode of inheritance in a NSHL consanguineous family using exome sequencing technology. We evaluated the possible effects of the single nucleotide variants (SNVs) detected in our patients using in silico methods. Results Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes (MYO7A and MYH14). The novel p. Pro338Leu missense mutation on the MITF protein was predicted to change the protein structure and function. Conclusion The novel MITF variant is the first bi-allelic SNV in this gene to be associated with an autosomal recessive non-syndromic HL case with a post-lingual onset. Our findings highlight the importance of whole exome sequencing for a comprehensive assessment of the genetic heterogeneity of HL.

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