Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments

Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)—a toxicant that impairs mitochondrial function—across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide spring P. mexicana, but not ancestral lineages from nonsulfidic habitats, due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. At a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes of genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and—in some instances—codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.Significance StatementSome organisms can tolerate environments lethal for most others, but we often do not know what adaptations allow them to persist and whether the same mechanisms underly adaptation in different lineages exposed to the same stressors. Investigating fish inhabiting springs rich in toxic hydrogen sulfide (H2S), we show that tolerance is mediated by the modification of pathways that are inhibited by H2S and those that can detoxify it. Sulfide spring fishes across multiple genera have evolved similar modifications of toxicity targets and detoxification pathways, despite abundant lineage-specific variation. Our study highlights how constraints associated with the physiological consequences of a stressor limit the number of adaptive solutions and lead to repeatable evolutionary outcomes across organizational and evolutionary scales.

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Epigenetic Inheritance is Gated by Naive Pluripotency and Dppa2

10.1101/2021.05.11.443595 ◽

2021 ◽

Author(s):

Valentina Carlini ◽

Cristina Policarpi ◽

Jamie A Hackett

Keyword(s):

De Novo ◽

Epigenetic Inheritance ◽

Developmental Model ◽

Lineage Specification ◽

Chromatin States ◽

Genome Wide ◽

Mechanistic Basis ◽

Endogenous Loci ◽

Epigenetic Editing

Environmental factors can trigger cellular responses that propagate across mitosis or even generations. Perturbations to the epigenome could underpin such acquired changes, however, the extent and contexts in which modified chromatin states confer heritable memory in mammals is unclear. Here we exploit a modular epigenetic editing strategy to establish de novo heterochromatin domains (epialleles) at endogenous loci and track their inheritance in a developmental model. We find that naive pluripotent phases systematically erase ectopic domains of heterochromatin via active mechanisms, which acts as an intergenerational safeguard against transmission of epialleles. Upon lineage specification however, acquired chromatin states can be probabilistically inherited under selectively favourable conditions, including propagation of p53 silencing through in vivo development. Using genome-wide CRISPR screening, we identify the mechanisms that block heritable silencing memory in pluripotent cells, and demonstrate removal of Dppa2 unlocks the potential for epigenetic inheritance uncoupled from DNA sequence. Our study outlines a mechanistic basis for how epigenetic inheritance is restricted in mammals, and reveals genomic- and developmental- contexts in which heritable memory is feasible.

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Paternally inherited noncoding structural variants contribute to autism

10.1101/102327 ◽

2017 ◽

Cited By ~ 5

Author(s):

William M. Brandler ◽

Danny Antaki ◽

Madhusudan Gujral ◽

Morgan L. Kleiber ◽

Michelle S. Maile ◽

...

Keyword(s):

De Novo ◽

Fetal Brain ◽

Wide Distribution ◽

Autism Spectrum ◽

Structural Variants ◽

De Novo Mutations ◽

Whole Genome Analysis ◽

Protein Coding ◽

Genome Wide ◽

Exome Aggregation Consortium

AbstractThe genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the genome-wide distribution and functional impact of structural variants (SVs) through whole genome analysis (≥30X coverage) of 3,169 subjects from 829 families affected by ASD. Genes that are intolerant to inactivating variants in the exome aggregation consortium (ExAC) were depleted for SVs in parents, specifically within fetal-brain promoters, UTRs and exons. Rare paternally-inherited SVs that disrupt promoters or UTRs were over-transmitted to probands (P = 0.0013) and not to their typically-developing siblings. Recurrent functional noncoding deletions implicate the gene LEO1 in ASD. Protein-coding SVs were also associated with ASD (P = 0.0025). Our results establish that rare inherited SVs predispose children to ASD, with differing contributions from each parent.

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HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

10.1101/220830 ◽

2017 ◽

Cited By ~ 1

Author(s):

Xin Zhou ◽

Serafim Batzoglou ◽

Arend Sidow ◽

Lu Zhang

Keyword(s):

False Positive ◽

De Novo ◽

False Positives ◽

Sequencing Data ◽

De Novo Mutations ◽

Congenital Diseases ◽

Genome Wide ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Haplotype Information

AbstractBackgroundDe novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls.ResultsTo address this challenge, we develop HAPDeNovo, a program that leverages phasing information from linked read sequencing, to remove false positive DNMs from candidate lists generated by DNM-detection tools. Short reads from each phasing block are allocated to each of the two haplotypes followed by generating a haploid genotype for each putative DNM.HAPDeNovo removes variants that are called as heterozygous in one of the haplotypes because they are almost certainly false positives. Our experiments on 10X Chromium linked read sequencing trio data reveal that HAPDeNovo eliminates 80% to 99% of false positives regardless of how large the candidate DNM set is.ConclusionsHAPDeNovo leverages the haplotype information from linked read sequencing to remove spurious false positive DNMs effectively, and it increases accuracy of DNM detection dramatically without sacrificing sensitivity.

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STEM-05. FUNCTIONAL MAPPING REVEALS WIDESPREAD REMODELLING AND UNRECOGNIZED PATHWAY DEPENDENCIES IN RECURRENT GLIOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noab196.081 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi22-vi22

Author(s):

Chirayu R Chokshi ◽

David Tieu ◽

Kevin R Brown ◽

Chitra Venugopal ◽

Lina Liu ◽

...

Keyword(s):

Tumor Recurrence ◽

De Novo ◽

Tyrosine Phosphatase ◽

Treatment Resistance ◽

Recurrent Glioblastoma ◽

De Novo Mutations ◽

Genome Wide ◽

Molecule Inhibitor ◽

Signaling Axis ◽

Single Domain Antibodies

Abstract Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. Here, we explore the functional drivers of post-treatment recurrent GBM. By conducting genome-wide CRISPR-Cas9 screens in patient-derived GBM models, we uncover distinct genetic dependencies in recurrent tumor cells that were absent in their patient-matched primary predecessors, accompanied by increased mutational burden and differential transcript and protein expression. These analyses support parallel tumor-intrinsic mechanisms of treatment resistance which rely on acquisition of immunosuppressive capacity, including a defective mismatch repair pathway, ablation of PTEN activity, and a novel combination of de novo mutations in SWI/SNF components. We map a multilayered genetic and functional response to resist chemoradiotherapy and drive tumor recurrence, identifying protein tyrosine phosphatase 4A2 (PTP4A2) as a novel driver of self-renewal, proliferation and tumorigenicity at GBM recurrence. Mechanistically, genetic perturbation and a small molecule inhibitor of PTP4A2 repress axon guidance activity through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1) and exploit a genetic dependency on ROBO signaling. Importantly, engineered anti-ROBO1 single-domain antibodies also mimic the effects of PTP4A2 inhibition. We conclude that functional reprogramming drives tumorigenicity and present a dependence on a PTP4A2-ROBO1 signaling axis at GBM recurrence.

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Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation

10.1101/017277 ◽

2015 ◽

Cited By ~ 1

Author(s):

Jinmyung Choi ◽

Parisa Shooshtari ◽

Kaitlin E Samocha ◽

Mark J Daly ◽

Chris Cotsapas

Keyword(s):

De Novo ◽

Sequence Data ◽

Fetal Brain ◽

Selective Constraint ◽

Adverse Outcomes ◽

Integrated Analysis ◽

Disease Genes ◽

De Novo Mutations ◽

Strong Constraint ◽

Genome Wide

Using robust, integrated analysis of multiple genomic datasets, we show that genes depleted for non-synonymous de novo mutations form a subnetwork of 72 members under strong selective constraint. We further show this subnetwork is preferentially expressed in the early development of the human hippocampus and is enriched for genes mutated in neurological, but not other, Mendelian disorders. We thus conclude that carefully orchestrated developmental processes are under strong constraint in early brain development, and perturbations caused by mutation have adverse outcomes subject to strong purifying selection. Our findings demonstrate that selective forces can act on groups of genes involved in the same process, supporting the notion that adaptation can act coordinately on multiple genes. Our approach provides a statistically robust, interpretable way to identify the tissues and developmental times where groups of disease genes are active. Our findings highlight the importance of considering the interactions between genes when analyzing genome-wide sequence data.

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Identification of de novo mutations in the Chinese ASD cohort via whole-exome sequencing unveils brain regions implicated in autism

10.1101/2021.07.14.21260545 ◽

2021 ◽

Author(s):

Bo Yuan ◽

Mengdi Wang ◽

Xinran Wu ◽

Peipei Cheng ◽

Ran Zhang ◽

...

Keyword(s):

Human Brain ◽

De Novo ◽

Brain Regions ◽

Imaging Data ◽

De Novo Mutations ◽

Genetic Studies ◽

Single Cell Sequencing ◽

Genome Wide ◽

Whole Exome ◽

Brain Imaging Data

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder characterized by deficits in social interactions and repetitive behaviors. Although hundreds of ASD risk genes, implicated in synaptic formation and transcriptional regulation, have been identified through human genetic studies, the East Asian ASD cohorts is still under-represented in the genome-wide genetic studies. Here we performed whole-exome sequencing on 369 ASD trios including probands and unaffected parents of Chinese origin. Using a joint-calling analytical pipeline based on GATK toolkits, we identified numerous de novo mutations including 55 high-impact variants and 165 moderate-impact variants, as well as de novo copy number variations containing known ASD-related genes. Importantly, combining with single-cell sequencing data from the developing human brain, we found that expression of genes with de novo mutations were specifically enriched in pre-, post-central gyrus (PRC, PC) and banks of superior temporal (BST) regions in the human brain. By further analyzing the brain imaging data with ASD and health controls, we found that the gray volume of the right BST in ASD patients significantly decreased comparing to health controls, suggesting the potential structural deficits associated with ASD. Finally, we found that there was decrease in the seed-based functional connectivity (FC) between BST/PC/PRC and sensory areas, insula, as well as frontal lobes in ASD patients. This work indicated that the combinatorial analysis with genome-wide screening, single-cell sequencing and brain imaging data would reveal brain regions contributing to etiology of ASD.

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Genome-Wide Noninvasive Prenatal Diagnosis of De Novo Mutations

Methods in Molecular Biology - Deep Sequencing Data Analysis ◽

10.1007/978-1-0716-1103-6_12 ◽

2021 ◽

pp. 249-269

Author(s):

Ravit Peretz-Machluf ◽

Tom Rabinowitz ◽

Noam Shomron

Keyword(s):

Prenatal Diagnosis ◽

De Novo ◽

De Novo Mutations ◽

Noninvasive Prenatal Diagnosis ◽

Genome Wide

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Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

Science ◽

10.1126/science.aat6576 ◽

2018 ◽

Vol 362 (6420) ◽

pp. eaat6576 ◽

Cited By ~ 83

Author(s):

Joon-Yong An ◽

Kevin Lin ◽

Lingxue Zhu ◽

Donna M. Werling ◽

Shan Dong ◽

...

Keyword(s):

Autism Spectrum Disorder ◽

Risk Score ◽

De Novo ◽

Autism Spectrum ◽

Spectrum Disorder ◽

De Novo Mutations ◽

Promoter Regions ◽

Complex Disorders ◽

Genome Wide ◽

Evolutionarily Conserved

Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribute to ASD.

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