The Simple Chordate <i>Ciona intestinalis</i> Has a Reduced Complement of Genes Associated with Fanconi Anemia

Stanley, Edward C.; Azzinaro, Paul A.; Vierra, David A.; Howlett, Niall G.; Irvine, Steven Q.

doi:10.4137/ebo.s37920

Cited by 7 publications

(10 citation statements)

References 111 publications

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“…31 FANCE recruits FANCD2 to the FA core complex for ubiquitination and subsequent DNA repair. 32 It is interesting to note that FANCD2, FANCL, and FANCE homologs form a subset of the FA genes present in Ciona intestinalis, which is believed to be the closest invertebrate relative of vertebrates 33,34 ; thus, these homologs appear to be an evolutionarily conserved part of the FA pathway. It is likely that mutations affecting FANCD2, FANCE, or FANCL modify cancer susceptibility through altered DNA repair and genomic instability.…”

Section: Discussionmentioning

confidence: 99%

Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50

Chandrasekharappa

Chinn

Donovan

et al. 2017

Cancer

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Patients with Fanconi anemia (FA) have increased risk for head and neck squamous cell carcinoma (HNSCC). We sought to determine the prevalence of undiagnosed FA and FA carriers in patients with HNSCC and an age cutoff for FA genetic screening. Screening germline DNA from 417 HNSCC patients under age 50 revealed 194 FA gene variants in 185 patients (44%). The variant spectrum was comprised of 183 nonsynonymous point mutations, nine indels, one large deletion, and one synonymous variant predicted to effect splicing. 108 patients (26%) had at least one rare variant predicted to be damaging, and 57 (14%) had at least one rare variant predicted to be damaging and previously reported. Fifteen patients carried two rare variants, or an X-linked variant, in an FA gene. Overall, we did not identify an age cutoff for FA screening among young HNSCC patients, as there were no significant differences in mutation rates when patients were stratified by age, tumor site, ethnicity, smoking status, or human papillomavirus status. However, we observed an increased burden, or mutation load, of FA gene variants in FANCD2, FANCE, and FANCL in our HNSCC patient cohort relative to the 1000 Genomes population. FANCE and FANCL, components of the core complex, are known to be responsible for the recruitment and ubiquitination, respectively, of FANCD2, a critical step in the FA DNA repair pathway. FA germline functional variants offer a novel area of study in HNSCC tumorigenesis, and the increased mutation burden of critical genes indicates the importance of the FA pathway in HNSCC.

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Section: Discussionmentioning

confidence: 99%

Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50

Chandrasekharappa

Chinn

Donovan

et al. 2017

Cancer

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“…Only a fraction of FA gene homologs are present in any invertebrate model organism [24, 25], limiting the utility of these models. All are present in zebrafish with the exception of FANCS/BRCA1 [26, 27].…”

Section: Introductionmentioning

confidence: 99%

Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility

et al. 2018

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Fanconi Anemia (FA) is a genomic instability syndrome resulting in aplastic anemia, developmental abnormalities, and predisposition to hematological and other solid organ malignancies. Mutations in genes that encode proteins of the FA pathway fail to orchestrate the repair of DNA damage caused by DNA interstrand crosslinks. Zebrafish harbor homologs for nearly all known FA genes. We used multiplexed CRISPR/Cas9-mediated mutagenesis to generate loss-of-function mutants for 17 FA genes: fanca, fancb, fancc, fancd1/brca2, fancd2, fance, fancf, fancg, fanci, fancj/brip1, fancl, fancm, fancn/palb2, fanco/rad51c, fancp/slx4, fancq/ercc4, fanct/ube2t, and two genes encoding FA-associated proteins: faap100 and faap24. We selected two indel mutations predicted to cause premature truncations for all but two of the genes, and a total of 36 mutant lines were generated for 19 genes. Generating two independent mutant lines for each gene was important to validate their phenotypic consequences. RT-PCR from homozygous mutant fish confirmed the presence of transcripts with indels in all genes. Interestingly, 4 of the indel mutations led to aberrant splicing, which may produce a different protein than predicted from the genomic sequence. Analysis of RNA is thus critical in proper evaluation of the consequences of the mutations introduced in zebrafish genome. We used fluorescent reporter assay, and western blots to confirm loss-of-function for several mutants. Additionally, we developed a DEB treatment assay by evaluating morphological changes in embryos and confirmed that homozygous mutants from all the FA genes that could be tested (11/17), displayed hypersensitivity and thus were indeed null alleles. Our multiplexing strategy helped us to evaluate 11 multiple gene knockout combinations without additional breeding. Homozygous zebrafish for all 19 single and 11 multi-gene knockouts were adult viable, indicating FA genes in zebrafish are generally not essential for early development. None of the mutant fish displayed gross developmental abnormalities except for fancp-/- fish, which were significantly smaller in length than their wildtype clutch mates. Complete female-to-male sex reversal was observed in knockouts for 12/17 FA genes, while partial sex reversal was seen for the other five gene knockouts. All adult females were fertile, and among the adult males, all were fertile except for the fancd1 mutants and one of the fancj mutants. We report here generation and characterization of zebrafish knockout mutants for 17 FA disease-causing genes, providing an integral resource for understanding the pathophysiology associated with the disrupted FA pathway.

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“…Pre-and post-assembly statistics for each transcriptome can be found in Table 1; total number of assembled contiguous sequences (contigs) ranged from 30,871-61,516 with a mean length of 636 and average GC content of 40%. A. stephencolberti had the fewest contigs (30,871), while A. stanfordianus North had the most (61,516). On average, there were~35,700 unique genes with isoform group size ranging from 2 to 38.…”

Section: Sequencing and Data Processingmentioning

confidence: 99%

“…FANCD1, a core protein in the pathway, is an alternate name for the breast cancer associated gene BRCA2 [27]. The role and extent of this pathway outside of mammals is not well studied; however, a handful of Fanconi pathway orthologs have been detected in model invertebrates [28] and a reduction in the number of components has been uncovered in the simple chordate Ciona intestinalis [29,30]. The dearth of pathway components in Aptostichus may be an indication that Mygalomorph spiders have a modified Fanconi pathway relative to the araneomorph spider used as a reference.…”

Section: Sequencing and Data Processingmentioning

confidence: 99%

“…There were 4799 orthogroups with all species present and 1338 of these consisted entirely of single-copy genes. Uncorrected pairwise distances were calculated for alignments of single copy orthogroups recovered in the OrthoFinder analysis including outgroups (n = 1338) using the EM-BOSS utility distmat [30][31][32] and visualized using R (Fig. 4a).…”

Section: Ortholog Detectionmentioning

confidence: 99%

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Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex

2020

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Background: Mygalomorph spiders represent a diverse, yet understudied lineage for which genomic level data has only recently become accessible through high-throughput genomic and transcriptomic sequencing methods. The Aptostichus atomarius species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister speciesaffording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species. Results: An average of~44,000 contigs were assembled for eight spiders representing dune (n = 2), inland (n = 4), and atomarius species complex outgroup taxa (n = 2). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the atomarius complex members, > 5000 were detected in all species, and~4700 were shared between species complex members and outgroup Aptostichus species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the atomarius ingroup; four of the five top clusters include sequences strongly resembling other arthropod venom peptides. The COATS pipeline identified six gene clusters under positive selection on branches leading to dune species, three of which reflected the preferred species tree. Genes under selection were identified as Cytochrome P450 2c15 (also recovered in the FUSTr analysis), Niemann 2 Pick C1-like, and Kainate 2 isoform X1. Conclusions: We have generated eight draft transcriptomes for a closely related and ecologically diverse group of trapdoor spiders, identifying venom gene families potentially under selection across the Aptostichus atomarius complex and chemosensory-associated gene families under selection in dune endemic lineages.

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The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia

Cited by 7 publications

References 111 publications

Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50

Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50

Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility

Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex

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