Replication-Based Rearrangements Are a Common Mechanism for SNCA Duplication in Parkinson's Disease

Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine

The path to completion of the functional annotation of the haploid human genome reference build, exploration of the clan genomics hypothesis, understanding human gene and genome functional biology, and gene genome and organismal evolution, is in reach.

Robust Computational Approaches to Defining Insights on the Interface of DNA Repair with Replication and Transcription in Cancer

The massive amount of experimental DNA and RNA sequence information provides an encyclopedia for cell biology that requires computational tools for efficient interpretation. The ability to write and apply simple computing scripts propels the investigator beyond the boundaries of online analysis tools to more broadly interrogate laboratory experimental data and to integrate them with all available datasets to test and challenge hypotheses. Here we describe robust prototypic bash and C++ scripts with metrics and methods for validation that we have made publicly available to address the roles of non-B DNA-forming motifs in eliciting genetic instability and to query The Cancer Genome Atlas. Importantly, the methods presented provide practical data interpretation tools to examine fundamental relationships and to enable insights and correlations between alterations in gene expression patterns and patient outcome. The exemplary source codes described are simple and can be efficiently modified, elaborated, and applied to other relationships and areas of investigation.

Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA

The biologically critical, exquisite specificity and efficiency of nucleases, such as those acting in DNA repair and replication, often emerge in the context of multiple other macromolecules. The evolved complexity also makes biologically relevant nuclease assays challenging and low-throughput. Meiotic recombination 11 homolog 1 (MRE11) is an exemplary nuclease that initiates DNA double-strand break (DSB) repair and processes stalled DNA replication forks. Thus, DNA resection by MRE11 nuclease activity is critical for multiple DSB repair pathways as well as in replication. Traditionally, in vitro nuclease activity of purified enzymes is studied either through gel-based assays or fluorescence-based assays like fluorescence resonance energy transfer (FRET). However, adapting these methods for a high-throughput application such as inhibitor screening can be challenging. Gel-based approaches are slow, and FRET assays can suffer from interference and distance limitations. Here we describe an alternative methodology to monitor nuclease activity by measuring the small-angle X-ray scattering (SAXS) interference pattern from gold nanoparticles (Au NPs) conjugated to 5'-ends of dsDNA using X-ray scattering interferometry (XSI). In addition to reporting on the enzyme activity, XSI can provide insight into DNA-protein interactions, aiding in the development of inhibitors that trap enzymes on the DNA substrate. Enabled by efficient access to synchrotron beamlines, sample preparation, and the feasibility of high-throughput XSI data collection and processing pipelines, this method allows for far greater speeds with less sample consumption than conventional SAXS techniques. The reported metrics and methods can be generalized to monitor not only other nucleases but also most other DNA-protein interactions.

Distinct sequence features underlie microdeletions and gross deletions in the human genome

Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ², p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.

Clan genomics: From OMIM phenotypic traits to genes and biology

Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.

XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells

Homologous recombination/end joining (HR/HEJ)-deficient cancers with BRCA mutations utilize alternative DNA double-strand break repair pathways, particularly alternative non-homologous end joining or microhomology-mediated end joining (alt-EJ/MMEJ) during S and G2 cell cycle phases. Depletion of alt-EJ factors, including XRCC1, PARP1 and POLQ, is synthetically lethal with BRCA2 deficiency; yet, XRCC1 roles in HR-deficient cancers and replication stress are enigmatic. Here, we show that after replication stress, XRCC1 forms an active repair complex with POLQ and MRE11 that supports alt-EJ activity in vitro. BRCA2 limits XRCC1 recruitment and repair complex formation to suppress alt-EJ at stalled forks. Without BRCA2 fork protection, XRCC1 enables cells to complete DNA replication at the expense of increased genome instability by promoting MRE11-dependent fork resection and restart. High XRCC1 and MRE11 gene expression negatively impacts Kaplan–Meier survival curves and hazard ratios for HR-deficient breast cancer patients in The Cancer Genome Atlas. The additive effects of depleting both BRCA2 and XRCC1 indicate distinct pathways for replication restart. Our collective data show that XRCC1-mediated processing contributes to replication fork degradation, replication restart and chromosome aberrations in BRCA2-deficient cells, uncovering new roles of XRCC1 and microhomology-mediated repair mechanisms in HR-deficient cancers, with implications for chemotherapeutic strategies targeting POLQ and PARP activities.

Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease

Objective

To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms.

Methods

We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing.

Results

Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors.

Conclusions

Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.