Publications by authors named "Zhaolei Zhang"

122 Publications

Deep Learning Classification of Unipolar Electrograms in Human Atrial Fibrillation: Application in Focal Source Mapping.

Front Physiol 2021 30;12:704122. Epub 2021 Jul 30.

Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University Health Network, Toronto, ON, Canada.

Focal sources are potential targets for atrial fibrillation (AF) catheter ablation, but they can be time-consuming and challenging to identify when unipolar electrograms (EGM) are numerous and complex. Our aim was to apply deep learning (DL) to raw unipolar EGMs in order to automate putative focal sources detection. We included 78 patients from the Focal Source and Trigger (FaST) randomized controlled trial that evaluated the efficacy of adjunctive FaST ablation compared to pulmonary vein isolation alone in reducing AF recurrence. FaST sites were identified based on manual classification of sustained periodic unipolar QS EGMs over 5-s. All periodic unipolar EGMs were divided into training ( = 10,004) and testing cohorts ( = 3,180). DL was developed using residual convolutional neural network to discriminate between FaST and non-FaST. A gradient-based method was applied to interpret the DL model. DL classified FaST with a receiver operator characteristic area under curve of 0.904 ± 0.010 (cross-validation) and 0.923 ± 0.003 (testing). At a prespecified sensitivity of 90%, the specificity and accuracy were 81.9 and 82.5%, respectively, in detecting FaST. DL had similar performance (sensitivity 78%, specificity 89%) to that of FaST re-classification by cardiologists (sensitivity 78%, specificity 79%). The gradient-based interpretation demonstrated accurate tracking of unipolar QS complexes by select DL convolutional layers. In conclusion, our novel DL model trained on raw unipolar EGMs allowed automated and accurate classification of FaST sites. Performance was similar to FaST re-classification by cardiologists. Future application of DL to classify FaST may improve the efficiency of real-time focal source detection for targeted AF ablation therapy.
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http://dx.doi.org/10.3389/fphys.2021.704122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360838PMC
July 2021

Improving domain adaptation in de-identification of electronic health records through self-training.

J Am Med Inform Assoc 2021 Sep;28(10):2093-2100

Google, Toronto, Ontario, Canada.

Objective: De-identification is a fundamental task in electronic health records to remove protected health information entities. Deep learning models have proven to be promising tools to automate de-identification processes. However, when the target domain (where the model is applied) is different from the source domain (where the model is trained), the model often suffers a significant performance drop, commonly referred to as domain adaptation issue. In de-identification, domain adaptation issues can make the model vulnerable for deployment. In this work, we aim to close the domain gap by leveraging unlabeled data from the target domain.

Materials And Methods: We introduce a self-training framework to address the domain adaptation issue by leveraging unlabeled data from the target domain. We validate the effectiveness on 4 standard de-identification datasets. In each experiment, we use a pair of datasets: labeled data from the source domain and unlabeled data from the target domain. We compare the proposed self-training framework with supervised learning that directly deploys the model trained on the source domain.

Results: In summary, our proposed framework improves the F1-score by 5.38 (on average) when compared with direct deployment. For example, using i2b2-2014 as the training dataset and i2b2-2006 as the test, the proposed framework increases the F1-score from 76.61 to 85.41 (+8.8). The method also increases the F1-score by 10.86 for mimic-radiology and mimic-discharge.

Conclusion: Our work demonstrates an effective self-training framework to boost the domain adaptation performance for the de-identification task for electronic health records.
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http://dx.doi.org/10.1093/jamia/ocab128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8449604PMC
September 2021

Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila.

Nucleic Acids Res 2021 06;49(11):6196-6212

Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada.

Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links for Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion inhibited cellular growth and reduced the expression levels of Anqa1 and Lin9. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.
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http://dx.doi.org/10.1093/nar/gkab413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216455PMC
June 2021

ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes.

Brief Bioinform 2021 May 8. Epub 2021 May 8.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.

Different subtypes of the same cancer often show distinct genomic signatures and require targeted treatments. The differences at the cellular and molecular levels of tumor microenvironment in different cancer subtypes have significant effects on tumor pathogenesis and prognostic outcomes. Although there have been significant researches on the prognostic association of tumor infiltrating lymphocytes in selected histological subtypes, few investigations have systemically reported the prognostic impacts of immune cells in molecular subtypes, as quantified by machine learning approaches on multi-omics datasets. This paper describes a new computational framework, ProTICS, to quantify the differences in the proportion of immune cells in tumor microenvironment and estimate their prognostic effects in different subtypes. First, we stratified patients into molecular subtypes based on gene expression and methylation profiles by applying nonnegative tensor factorization technique. Then we quantified the proportion of cell types in each specimen using an mRNA-based deconvolution method. For tumors in each subtype, we estimated the prognostic effects of immune cell types by applying Cox proportional hazard regression. At the molecular level, we also predicted the prognosis of signature genes for each subtype. Finally, we benchmarked the performance of ProTICS on three TCGA datasets and another independent METABRIC dataset. ProTICS successfully stratified tumors into different molecular subtypes manifested by distinct overall survival. Furthermore, the different immune cell types showed distinct prognostic patterns with respect to molecular subtypes. This study provides new insights into the prognostic association between immune cells and molecular subtypes, showing the utility of immune cells as potential prognostic markers. Availability: R code is available at https://github.com/liu-shuhui/ProTICS.
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http://dx.doi.org/10.1093/bib/bbab164DOI Listing
May 2021

Prognostic impact of the adverse molecular-genetic profile on long-term outcomes following allogeneic hematopoietic stem cell transplantation in acute myeloid leukemia.

Bone Marrow Transplant 2021 Aug 25;56(8):1908-1918. Epub 2021 Mar 25.

Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.

The impact of adverse risk genetic profiles on outcomes in acute myeloid leukemia (AML) patients following allogeneic hematopoietic stem cell transplantation (HCT) has not been fully elucidated. Accordingly, we have profiled somatic mutations at diagnosis using next-generation sequencing (NGS) in 178 AML patients who received allogeneic HCT. NGS revealed 598 somatic mutations in 165/178 patients (92.7%). Frequently mutated genes include DNMT3A, TET2, NPM1, RUNX1, IDH2, and FLT3. Commonly detected cytogenetic profiles include normal karyotype, trisomy 8, monosomal karyotype (MK), deletion 5, complex karyotype (CK), and monosomy 7. In univariate analyses, TP53 mutation, MK, CK, and monosomy 7 were associated with decreased overall survival (OS), relapse-free survival (RFS), and a higher relapse incidence (RI). We defined adverse molecular-genetic profile as harboring at least one of the molecular/genetic abnormalities of TP53 mutation, MK, CK, monosomy 7, and deletion 5. The patients harboring adverse molecular-genetic profile (n = 30) showed a lower 2-year OS (24.9% vs. 57.9%; p = 0.003), RFS (23.7% vs. 57.9%; p = 0.002), and higher RI (47.2% and 17.2%; p = 0.001) after HCT when compared to patients without those lesions. Multivariate analysis confirmed adverse molecular-genetic profile as an independent prognostic factor, associated with decreased OS (HR 2.19), RFS (HR 2.23), and higher RI (HR 2.94).
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http://dx.doi.org/10.1038/s41409-021-01255-4DOI Listing
August 2021

Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis.

BMC Genomics 2021 Jan 6;22(1):18. Epub 2021 Jan 6.

Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.

Background: The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome.

Results: In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved.

Conclusions: Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
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http://dx.doi.org/10.1186/s12864-020-07287-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7789530PMC
January 2021

Allogeneic transplant can abrogate the risk of relapse in the patients of first remission acute myeloid leukemia with detectable measurable residual disease by next-generation sequencing.

Bone Marrow Transplant 2021 05 5;56(5):1159-1170. Epub 2020 Dec 5.

Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.

In patients with acute myeloid leukemia (AML) consolidation treatment options are between allogeneic hematopoietic stem cell transplantation (HCT) and chemotherapy, based on disease risk at the time of initial presentation and age. Measurable residual disease (MRD) following induction chemotherapy could be incorporated as a useful parameter for treatment decisions. The present study evaluated treatment outcomes according to the next-generation sequencing (NGS)-based MRD status and the type of consolidation therapy in patients with normal karyotype (NK)-AML. By sequencing 278 paired samples collected at diagnosis and first remission (CR1), we identified 361 mutations in 124 patients at diagnosis and tracked these at CR1. After excluding mutations associated with age-related clonal hematopoiesis, 82 mutations in 50 of the 124 patients (40.3%) were detected at CR1. Survival benefit was observed in favor of allogeneic HCT over chemotherapy consolidation in the MRD subgroup with respect to overall survival (HR 0.294, p = 0.003), relapse-free survival (HR 0.376, p = 0.015) and cumulative incidence of relapse (HR 0.279, p = 0.004) in multivariate analysis, but not in the MRD subgroup. In summary, these data support allogeneic HCT in NK-AML patients with detectable MRD by NGS in CR1. Randomized clinical trials will be required to confirm this observation.
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http://dx.doi.org/10.1038/s41409-020-01165-xDOI Listing
May 2021

RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor acute myeloid leukemia.

Sci Rep 2020 11 18;10(1):20119. Epub 2020 Nov 18.

Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.

DNA sequencing-based measurable residual disease (MRD) detection has shown to be clinically relevant in AML. However, the same methodology cannot be applied to fusion gene-driven subtypes of AML such as core-binding factor AML (CBF-AML). Here in this study, we evaluated the effectiveness of using DNA and RNA sequencing in MRD detection and in tracking clonal dynamics in CBF-AML. Using RNA-seq, we were able to quantify expression levels of RUNX1-RUNX1T1 and CBFB-MYH11 at diagnosis and their levels of reduction during remission (P < 6.3e-05 and P < 2.2e-13). The level of reduction of RUNX1-RUNX1T1 as measured by RNA-seq and qPCR were highly correlated (R = 0.74, P < 5.4e-05). A decision tree analysis, based on 3-log reduction of RUNX1-RUNX1T1 and cKIT-D816 at diagnosis, stratified RUNX1-RUNX1T1 AML patients into three subgroups. These three subgroups had 2-year overall survival rates at 87%, 74%, and 33% (P < 0.08) and 2-year relapse incidence rates at 13%, 42%, and 67% (P < 0.05). On the other hand, although low residual allelic burden was common, it was not associated with long-term outcome, indicating that mutation clearance alone cannot be interpreted as MRD-negative. Overall, our study demonstrates that the clinical utility of RNA sequencing as a potential tool for MRD monitoring in fusion gene-driven AML such as RUNX1-RUNX1T1 AML.
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http://dx.doi.org/10.1038/s41598-020-76933-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674449PMC
November 2020

A Survey of Regulatory Interactions Among RNA Binding Proteins and MicroRNAs in Cancer.

Front Genet 2020 8;11:515094. Epub 2020 Sep 8.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.

Recent advances in genomics and proteomics generated a large amount of regulatory data such as those mediated by RNA binding proteins (RBPs) and microRNAs. Since many regulators target 3' UTR of mRNA transcripts, it is likely that there would be interactions, i.e., competitive or cooperative effect, among these factors. We compiled the available RBP and microRNA binding sites, mapped them to the mRNA transcripts, and correlated the binding data with mRNA expression data generated by The Cancer Genome Atlas (TCGA). We separated pairs of RBPs and microRNAs into three scenarios: those that have overlapping target sites on the same mRNA transcript (), those that have target sites on the same mRNA transcript but non-overlapping (), and those that do not target the same mRNA transcript (). Through a regression analysis on expression profiles, we indeed observed interaction effect between RBPs and microRNAs in the majority of the cancer expression data sets. We further discussed implication of such widespread interactions in the context of cancer and diseases.
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http://dx.doi.org/10.3389/fgene.2020.515094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7506142PMC
September 2020

Long Noncoding RNA and Predictive Model To Improve Diagnosis of Clinically Diagnosed Pulmonary Tuberculosis.

J Clin Microbiol 2020 06 24;58(7). Epub 2020 Jun 24.

Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China

Clinically diagnosed pulmonary tuberculosis (PTB) patients lack microbiological evidence of , and misdiagnosis or delayed diagnosis often occurs as a consequence. We investigated the potential of long noncoding RNAs (lncRNAs) and corresponding predictive models to diagnose these patients. We enrolled 1,764 subjects, including clinically diagnosed PTB patients, microbiologically confirmed PTB cases, non-TB disease controls, and healthy controls, in three cohorts (screening, selection, and validation). Candidate lncRNAs differentially expressed in blood samples of the PTB and healthy control groups were identified by microarray and reverse transcription-quantitative PCR (qRT-PCR) in the screening cohort. Logistic regression models were developed using lncRNAs and/or electronic health records (EHRs) from clinically diagnosed PTB patients and non-TB disease controls in the selection cohort. These models were evaluated by area under the concentration-time curve (AUC) and decision curve analyses, and the optimal model was presented as a Web-based nomogram, which was evaluated in the validation cohort. Three differentially expressed lncRNAs (, , and ) were identified. The optimal model (i.e., nomogram) incorporated these three lncRNAs and six EHRs (age, hemoglobin, weight loss, low-grade fever, calcification detected by computed tomography [CT calcification], and interferon gamma release assay for tuberculosis [TB-IGRA]). The nomogram showed an AUC of 0.89, a sensitivity of 0.86, and a specificity of 0.82 in differentiating clinically diagnosed PTB cases from non-TB disease controls of the validation cohort, which demonstrated better discrimination and clinical net benefit than the EHR model. The nomogram also had a discriminative power (AUC, 0.90; sensitivity, 0.85; specificity, 0.81) in identifying microbiologically confirmed PTB patients. lncRNAs and the user-friendly nomogram could facilitate the early identification of PTB cases among suspected patients with negative microbiological evidence.
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http://dx.doi.org/10.1128/JCM.01973-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315016PMC
June 2020

Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?

Trends Genet 2019 12 29;35(12):892-902. Epub 2019 Oct 29.

Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada. Electronic address:

Our recent ability to sequence entire genomes, along with all of their transcribed RNAs, has led to the surprising finding that only ∼1% of the human genome is used to encode proteins. This finding has led to vigorous debate over the functional importance of the transcribed but untranslated portions of the genome. Currently, scientists tend to assume coding genes are functional until proven not to be, while the opposite is true for noncoding genes. This review takes a new look at the evidence for and against widespread noncoding gene functionality. We focus in particular on long noncoding RNA (noncoding RNAs longer than 200 nucleotides) genes and their 'junk' associates, transposable elements, and satellite repeats. Taken together, the suggestion put forward is that more of this junk DNA may be functional than nonfunctional and that noncoding RNAs and transposable elements act symbiotically to drive evolution.
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http://dx.doi.org/10.1016/j.tig.2019.09.006DOI Listing
December 2019

Remission clone in acute myeloid leukemia shows growth advantage after chemotherapy but is distinct from leukemic clone.

Exp Hematol 2019 07 12;75:26-30. Epub 2019 Jun 12.

Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.

In a previously published case study of acute myeloid leukemia, we tracked the dynamics of somatic mutations over 9 years. Interestingly, we observed a group of mutations that expanded during remission, which we named the "remission clone." To determine the nature of the remission clones, we performed flow cytometry-based cell sorting followed by ultradeep sequencing. The remission clone repeatedly expanded after chemotherapeutic cycles and was suppressed during relapse in the myeloid lineage (multipotent hematopoietic stem, progenitor, and myeloid cells). On the other hand, the remission clone was consistently observed in lymphoid lineages (B and T cells) regardless of the disease state. When transfected into the HEK-293 cell line, the NR2C2(A93V) mutant exhibited a growth advantage (all p values < 0.05). The results indicate that the remission clone seems to be another form of clonal hematopoiesis, but without a clear association with leukemia. As the remission clone is present in both myeloid and lymphoid lineages, it likely originates from ancestral hematopoietic cell lineages. More importantly, the remission clone is distinct from the leukemic clone; therefore, mutations expanded during remission require special interpretation when performing next-generation sequencing-based measurable residual disease assessment.
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http://dx.doi.org/10.1016/j.exphem.2019.06.001DOI Listing
July 2019

Integrating exosomal microRNAs and electronic health data improved tuberculosis diagnosis.

EBioMedicine 2019 Feb 8;40:564-573. Epub 2019 Feb 8.

Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China. Electronic address:

Background Tuberculosis (TB) is difficult to diagnose under complex clinical conditions as electronic health records (EHRs) are often inadequate in making an affirmative diagnosis. As exosomal miRNAs emerged as promising biomarkers, we investigated the potential of using exosomal miRNAs and EHRs in TB diagnosis.

Methods: A total of 370 individuals, including pulmonary tuberculosis (PTB), tuberculous meningitis (TBM), non-TB disease controls and healthy state controls, were enrolled. Exosomal miRNAs were profiled in the exploratory cohort using microarray and miRNA candidates were selected in the selection cohort using qRT-PCR. EHRs and follow-up information of the patients were collected accordingly. miRNAs and EHRs were used to develop diagnostic models for PTB and TBM in the selection cohort with the Support Vector Machine (SVM) algorithm. These models were further evaluated in an independent testing cohort.

Findings: Six exosomal miRNAs (miR-20a, miR-20b, miR-26a, miR-106a, miR-191, miR-486) were differentially expressed in the TB patients. Three SVM models, "EHR+miRNA", "miRNA only" and "EHR only" were compared, and "EHR + miRNA" model achieved the highest diagnostic efficacy, with an AUC up to 0.97 (95% CI 0.80-0.99) in TBM and 0.97 (0.87-0.99) in PTB, respectively. However, "EHR only" model only showed an AUC of 0.67 (0.46-0.83) in TBM. After 2-month anti-tuberculosis therapy, overexpressed miRNAs presented a decreased expression trend (p= 4.80 × 10).

Interpretation: Our results showed that the combination of exosomal miRNAs and EHRs could potentially improve clinical diagnosis of TBM and PTB. FUND: Funds for the Central Universities, the National Natural Science Foundation of China.
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http://dx.doi.org/10.1016/j.ebiom.2019.01.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413343PMC
February 2019

Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates.

Mol Cell 2019 03 4;73(5):900-914.e9. Epub 2019 Feb 4.

Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada. Electronic address:

Post-replication repair (PRR) allows tolerance of chemical- and UV-induced DNA base lesions in both an error-free and an error-prone manner. In classical PRR, PCNA monoubiquitination recruits translesion synthesis (TLS) DNA polymerases that can replicate through lesions. We find that PRR responds to DNA replication stress that does not cause base lesions. Rad5 forms nuclear foci during normal S phase and after exposure to types of replication stress where DNA base lesions are likely absent. Rad5 binds to the sites of stressed DNA replication forks, where it recruits TLS polymerases to repair single-stranded DNA (ssDNA) gaps, preventing mitotic defects and chromosome breaks. In contrast to the prevailing view of PRR, our data indicate that Rad5 promotes both mutagenic and error-free repair of undamaged ssDNA that arises during physiological and exogenous replication stress.
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http://dx.doi.org/10.1016/j.molcel.2019.01.001DOI Listing
March 2019

Next-generation sequencing-based posttransplant monitoring of acute myeloid leukemia identifies patients at high risk of relapse.

Blood 2018 10 14;132(15):1604-1613. Epub 2018 Aug 14.

Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.

Next-generation sequencing (NGS) has been applied to define clinically relevant somatic mutations and classify subtypes in acute myeloid leukemia (AML). Persistent allelic burden after chemotherapy is associated with higher relapse incidence, but presence of allelic burden in AML patients after receiving allogeneic hematopoietic cell transplantation (HCT) has not been examined longitudinally. As such, we aimed to assess the feasibility of NGS in monitoring AML patients receiving HCT. Using a targeted gene panel, we performed NGS in 104 AML patients receiving HCT using samples collected at diagnosis, pre-HCT, and post-HCT at day 21 (post-HCT). NGS detected 256 mutations in 90 of 104 patients at diagnosis, which showed stepwise clearances after chemotherapy and HCT. In a subset of patients, mutations were still detectable pre-HCT and post-HCT. Most post-HCT mutations originate from mutations initially detected at diagnosis. Post-HCT allelic burdens in relapsed patients were higher than in nonrelapsed patients. Post-HCT mutations in relapsed patients all expanded at relapse. Assessment of variant allele frequency (VAF) revealed that overall VAF post-HCT (VAF-post-HCT) is associated with an increased risk of relapse (56.2% vs 16.0% at 3 years; < .001) and worse overall survival (OS; 36.5% vs 67.0% at 3 years; = .006). Multivariate analyses confirmed that VAF-post-HCT is an adverse prognostic factor for OS (hazard ratio [HR], 3.07; = .003) and relapse incidence (HR, 4.75; < .001), independent of the revised European LeukemiaNet risk groups. Overall, current study demonstrates that NGS-based posttransplant monitoring in AML patients is feasible and can distinguish high-risk patients for relapse.
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http://dx.doi.org/10.1182/blood-2018-04-848028DOI Listing
October 2018

Publisher Correction: N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 Aug;21(8):1139

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

In the version of this article initially published online, there were errors in URLs for www.southernbiotech.com, appearing in Methods sections "m6A dot-blot" and "Western blot analysis." The first two URLs should be https://www.southernbiotech.com/?catno=4030-05&type=Polyclonal#&panel1-1 and the third should be https://www.southernbiotech.com/?catno=6170-05&type=Polyclonal. In addition, some Methods URLs for bioz.com, www.abcam.com and www.sysy.com were printed correctly but not properly linked. The errors have been corrected in the PDF and HTML versions of this article.
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http://dx.doi.org/10.1038/s41593-018-0169-2DOI Listing
August 2018

Assessment of a new genomic classification system in acute myeloid leukemia with a normal karyotype.

Oncotarget 2018 Jan 22;9(4):4961-4968. Epub 2017 Dec 22.

Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.

This study was performed to assess if a recently recommended genomic classification is predictive in patients with normal-karyotype (NK) acute myeloid leukemia (AML). A total of 393 patients were included. Analysis of genetic mutations was performed using targeted resequencing with an Illumina Hiseq 2000. We identified driver mutations across 40 genes, with one or more driver mutations identified in 95.7% of patients. The molecular subclassification was as follows: 34.6% patients (n = 136) with AML with the mutation, 10.7% (n = 42) with AML with mutated chromatin or RNA-splicing genes or both, 1.5% (n = 6) with AML with mutations, 13.5% (n = 53) with AML with biallelic mutations, 2.0% (n = 8) with AML with 72 mutations and no other class-defining lesion, 29.5% (n = 116) with AML with driver mutations but no detected class-defining lesion, 4.3% (n = 17) with AML with no detected driver mutation, and 3.8% (n = 15) patients with AML who met the criteria for ≥2 genomic subgroups. The 5-year overall survival and relapse rate of subgroup in AML with mutated chromatin, RNA-splicing genes, or both was 11.6% (95% CI = 1.4-21.8%) and 71.4% (95% CI = 45.7-86.5%), respectively. This study suggests that the recently recommended genomic classification is an appropriate and replicable categorization system in the NK AML population. The subgroup of AML with mutated chromatin, RNA-splicing genes, or both showed extremely poor survival in NK-AML; thus, a novel approach is needed to improve their prognosis.
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http://dx.doi.org/10.18632/oncotarget.23575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797026PMC
January 2018

Downregulation of exosomal miR-204-5p and miR-632 as a biomarker for FTD: a GENFI study.

J Neurol Neurosurg Psychiatry 2018 08 6;89(8):851-858. Epub 2018 Feb 6.

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.

Objective: To determine whether exosomal microRNAs (miRNAs) in cerebrospinal fluid (CSF) of patients with frontotemporal dementia (FTD) can serve as diagnostic biomarkers, we assessed miRNA expression in the Genetic Frontotemporal Dementia Initiative (GENFI) cohort and in sporadic FTD.

Methods: GENFI participants were either carriers of a pathogenic mutation in progranulin, chromosome 9 open reading frame 72 or microtubule-associated protein tau or were at risk of carrying a mutation because a first-degree relative was a known symptomatic mutation carrier. Exosomes were isolated from CSF of 23 presymptomatic and 15 symptomatic mutation carriers and 11 healthy non-mutation carriers. Expression of 752 miRNAs was measured using quantitative PCR (qPCR) arrays and validated by qPCR using individual primers. MiRNAs found differentially expressed in symptomatic compared with presymptomatic mutation carriers were further evaluated in a cohort of 17 patients with sporadic FTD, 13 patients with sporadic Alzheimer's disease (AD) and 10 healthy controls (HCs) of similar age.

Results: In the GENFI cohort, miR-204-5p and miR-632 were significantly decreased in symptomatic compared with presymptomatic mutation carriers. Decrease of miR-204-5p and miR-632 revealed receiver operator characteristics with an area of 0.89 (90% CI 0.79 to 0.98) and 0.81 (90% CI 0.68 to 0.93), respectively, and when combined an area of 0.93 (90% CI 0.87 to 0.99). In sporadic FTD, only miR-632 was significantly decreased compared with AD and HCs. Decrease of miR-632 revealed an area of 0.90 (90% CI 0.81 to 0.98).

Conclusions: Exosomal miR-204-5p and miR-632 have potential as diagnostic biomarkers for genetic FTD and miR-632 also for sporadic FTD.
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http://dx.doi.org/10.1136/jnnp-2017-317492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045452PMC
August 2018

N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Nat Neurosci 2018 02 15;21(2):195-206. Epub 2018 Jan 15.

Tumor Initiation and Maintenance Program, NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

Internal N-methyladenosine (mA) modification is widespread in messenger RNAs (mRNAs) and is catalyzed by heterodimers of methyltransferase-like protein 3 (Mettl3) and Mettl14. To understand the role of mA in development, we deleted Mettl14 in embryonic neural stem cells (NSCs) in a mouse model. Phenotypically, NSCs lacking Mettl14 displayed markedly decreased proliferation and premature differentiation, suggesting that mA modification enhances NSC self-renewal. Decreases in the NSC pool led to a decreased number of late-born neurons during cortical neurogenesis. Mechanistically, we discovered a genome-wide increase in specific histone modifications in Mettl14 knockout versus control NSCs. These changes correlated with altered gene expression and observed cellular phenotypes, suggesting functional significance of altered histone modifications in knockout cells. Finally, we found that mA regulates histone modification in part by destabilizing transcripts that encode histone-modifying enzymes. Our results suggest an essential role for mA in development and reveal mA-regulated histone modifications as a previously unknown mechanism of gene regulation in mammalian cells.
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http://dx.doi.org/10.1038/s41593-017-0057-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317335PMC
February 2018

Exome sequencing reveals DNMT3A and ASXL1 variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy.

Leuk Res 2017 08 16;59:142-148. Epub 2017 Jun 16.

Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.

Objective: The development of tyrosine kinase inhibitors (TKIs) has significantly improved the treatment of chronic myeloid leukemia (CML). However, approximately one third of patients are resistant to TKI and/or progress to advanced disease stages. TKI therapy failure has a well-known association with ABL1 kinase domain (KD) mutations, but only around half of TKI non-responders have detectable ABL1 KD mutations.

Method: We attempt to identify genetic markers associated with TKI therapy failure in 13 patients (5 resistant, 8 progressed) without ABL1 KD mutations using whole-exome sequencing.

Results: In 6 patients, we detected mutations in 6 genes commonly mutated in other myeloid neoplasms: ABL1, ASXL1, DNMT3A, IDH1, SETBP1, and TP63. We then used targeted deep sequencing to validate our finding in an independent cohort consisting of 100 CML patients with varying drug responses (74 responsive, 18 resistant, and 8 progressed patients). Mutations in genes associated with epigenetic regulations such as DNMT3A and ASXL1 seem to play an important role in the pathogenesis of CML progression and TKI-resistance independent of ABL1 KD mutations.

Conclusion: This study suggests the involvement of other somatic mutations in the development of TKI resistant progression to advanced disease stages in CML, particularly in patients lacking ABL1 KD mutations.
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http://dx.doi.org/10.1016/j.leukres.2017.06.009DOI Listing
August 2017

Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease.

Neurobiol Aging 2017 09 25;57:104-119. Epub 2017 May 25.

Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. Electronic address:

Cholinergic neurotransmission is impaired in Alzheimer's disease (AD), and loss of basal forebrain cholinergic neurons is a key component of disease pathogenicity and symptomatology. To explore the molecular basis of this cholinergic dysfunction, we paired translating ribosome affinity purification (TRAP) with RNA sequencing (TRAP-Seq) to identify the actively translating mRNAs in anterior forebrain cholinergic neurons in the TgCRND8 mouse model of AD. Bioinformatic analyses revealed the downregulation of 67 of 71 known cholinergic-related transcripts, consistent with cholinergic neuron dysfunction in TgCRND8 mice, as well as transcripts related to oxidative phosphorylation, neurotrophins, and ribosomal processing. Upregulated transcripts included those related to axon guidance, glutamatergic synapses and kinase activity and included AD-risk genes Sorl1 and Ptk2b. In contrast, the total transcriptome of the anterior forebrain showed upregulation in cytokine signaling, microglia, and immune system pathways, including Trem2, Tyrobp, and Inpp5d. Hence, TRAP-Seq clearly distinguished the differential gene expression alterations occurring in cholinergic neurons of TgCRND8 mice compared with wild-type littermates, providing novel candidate pathways to explore for therapeutic development in AD.
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http://dx.doi.org/10.1016/j.neurobiolaging.2017.05.014DOI Listing
September 2017

Mitochondria-targeting Au nanoclusters enhance radiosensitivity of cancer cells.

J Mater Chem B 2017 Jun 17;5(22):4190-4197. Epub 2017 May 17.

Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China.

Radiotherapy is an important technology for the clinical treatment of cancer, but the patients suffer from the severe side effects after exposure to radiation. There is an urgent need to develop theranostic agents with excellent imaging capability and effective radiosensitization in order to minimize X-ray irradiation. Herein, we report an approach to synthesize peptide-templated Au nanoclusters (AuNCs) for theranostic radiosensitization. A new peptide (CCYKFR) is designed for the preparation of AuNCs with uniform size distribution and fluorescence (656 nm) of high photostability. CCYKFR-AuNCs feature highly efficient targeting/accumulation on mitochondria after endocytosis. With a series of experiments, we demonstrate that CCYKFR-AuNCs irradiated by 4 Gy X-rays can introduce a burst of mitoROS and severe DNA damage leading to cancer cell death. This study presents an important strategy to design theranostic nanomaterials with improved radiosensitization for the development of new anti-cancer therapies.
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http://dx.doi.org/10.1039/c7tb00422bDOI Listing
June 2017

Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity.

G3 (Bethesda) 2017 01 5;7(1):95-108. Epub 2017 Jan 5.

Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada

Disruption of protein quality control can be detrimental, having toxic effects on single cell organisms and contributing to neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's in humans. Here, we examined the effects of polyglutamine (polyQ) aggregation in a major fungal pathogen of humans, Candida albicans, with the goal of identifying new approaches to disable this fungus. However, we discovered that expression of polyQ stretches up to 230Q had no effect on C. albicans ability to grow and withstand proteotoxic stress. Bioinformatics analysis demonstrates that C. albicans has a similarly glutamine-rich proteome to the unicellular fungus Saccharomyces cerevisiae, which exhibits polyQ toxicity with as few as 72Q. Surprisingly, global transcriptional profiles indicated no significant change upon induction of up to 230Q. Proteomic analysis highlighted two key interactors of 230Q, Sis1 and Sgt2; however, loss of either protein had no additional effect on C. albicans toxicity. Our data suggest that C. albicans has evolved powerful mechanisms to overcome the toxicity associated with aggregation-prone proteins, providing a unique model for studying polyQ-associated diseases.
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http://dx.doi.org/10.1534/g3.116.035675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217127PMC
January 2017

Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes.

Genome Biol Evol 2016 12 31;8(11):3433-3445. Epub 2016 Dec 31.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China

Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
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http://dx.doi.org/10.1093/gbe/evw239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203780PMC
December 2016

Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy.

Blood 2017 01 12;129(1):38-47. Epub 2016 Oct 12.

Department of Medical Oncology, Princess Margaret Cancer Center, University Health Network, Faculty of Medicine and.

Somatic mutations commonly detected in a variety of myeloid neoplasms have not been systematically investigated in chronic myeloid leukemia (CML). We performed targeted deep sequencing on a total of 300 serial samples from 100 CML patients; 37 patients carried mutations. Sixteen of these had evidence of mutations originating from preleukemic clones. Using unsupervised hierarchical clustering, we identified 5 distinct patterns of mutation dynamics arising following tyrosine kinase inhibitor (TKI) therapy. This study demonstrates that patterns of mutation acquisition, persistence, and clearance vary but have a number of interesting correlations with clinical outcomes. Mutation burden often persisted despite successful TKI response (pattern 1), providing indirect evidence that these mutations also originated from preleukemic mutations, whereas patients exhibiting mutation clearance (pattern 3) showed mixed clinical outcomes. Unsurprisingly, patients acquiring new mutations during treatment failed TKI therapy (pattern 2). These patterns show that CML mutation dynamics following TKI therapy are markedly distinct from other myeloid neoplasms. In summary, clinical implications of mutation profiles and dynamics in CML should be interpreted with caution.
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http://dx.doi.org/10.1182/blood-2016-04-708560DOI Listing
January 2017

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.

Cell Syst 2016 09 8;3(3):264-277.e10. Epub 2016 Sep 8.

The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address:

A significant challenge of functional genomics is to develop methods for genome-scale acquisition and analysis of cell biological data. Here, we present an integrated method that combines genome-wide genetic perturbation of Saccharomyces cerevisiae with high-content screening to facilitate the genetic description of sub-cellular structures and compartment morphology. As proof of principle, we used a Rad52-GFP marker to examine DNA damage foci in ∼20 million single cells from ∼5,000 different mutant backgrounds in the context of selected genetic or chemical perturbations. Phenotypes were classified using a machine learning-based automated image analysis pipeline. 345 mutants were identified that had elevated numbers of DNA damage foci, almost half of which were identified only in sensitized backgrounds. Subsequent analysis of Vid22, a protein implicated in the DNA damage response, revealed that it acts together with the Sgs1 helicase at sites of DNA damage and preferentially binds G-quadruplex regions of the genome. This approach is extensible to numerous other cell biological markers and experimental systems.
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http://dx.doi.org/10.1016/j.cels.2016.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689480PMC
September 2016

G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis.

Stem Cell Reports 2016 09 18;7(3):454-470. Epub 2016 Aug 18.

Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada. Electronic address:

Proliferating progenitor cells undergo changes in competence to give rise to post-mitotic progeny of specialized function. These cell-fate transitions typically involve dynamic regulation of gene expression by histone methyltransferase (HMT) complexes. However, the composition, roles, and regulation of these assemblies in regulating cell-fate decisions in vivo are poorly understood. Using unbiased affinity purification and mass spectrometry, we identified the uncharacterized C2H2-like zinc finger protein ZNF644 as a G9a/GLP-interacting protein and co-regulator of histone methylation. In zebrafish, functional characterization of ZNF644 orthologs, znf644a and znf644b, revealed complementary roles in regulating G9a/H3K9me2-mediated gene silencing during neurogenesis. The non-overlapping requirements for znf644a and znf644b during retinal differentiation demarcate critical aspects of retinal differentiation programs regulated by differential G9a-ZNF644 associations, such as transitioning proliferating progenitor cells toward differentiation. Collectively, our data point to ZNF644 as a critical co-regulator of G9a/H3K9me2-mediated gene silencing during neuronal differentiation.
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http://dx.doi.org/10.1016/j.stemcr.2016.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031922PMC
September 2016

Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment.

Oncotarget 2016 Aug;7(31):50027-50042

Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada.

Application of tumor genome sequencing has identified numerous loss-of-function alterations in cancer cells. While these alterations are difficult to target using direct interventions, they may be attacked with the help of the synthetic lethality (SL) approach. In this approach, inhibition of one gene causes lethality only when another gene is also completely or partially inactivated. The EPHB6 receptor tyrosine kinase has been shown to have anti-malignant properties and to be downregulated in multiple cancers, which makes it a very attractive target for SL applications. In our work, we used a genome-wide SL screen combined with expression and interaction network analyses, and identified the SRC kinase as a SL partner of EPHB6 in triple-negative breast cancer (TNBC) cells. Our experiments also reveal that this SL interaction can be targeted by small molecule SRC inhibitors, SU6656 and KX2-391, and can be used to improve elimination of human TNBC tumors in a xenograft model. Our observations are of potential practical importance, since TNBC is an aggressive heterogeneous malignancy with a very high rate of patient mortality due to the lack of targeted therapies, and our work indicates that FDA-approved SRC inhibitors may potentially be used in a personalized manner for treating patients with EPHB6-deficient TNBC. Our findings are also of a general interest, as EPHB6 is downregulated in multiple malignancies and our data serve as a proof of principle that EPHB6 deficiency may be targeted by small molecule inhibitors in the SL approach.
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http://dx.doi.org/10.18632/oncotarget.10569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226566PMC
August 2016

Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders.

Cell Syst 2015 Nov;1(5):361-374

Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA.

The prevalence of autism spectrum disorders (ASDs) is rapidly growing, yet its molecular basis is poorly understood. We used a systems approach in which ASD candidate genes were mapped onto the ubiquitous human protein complexes and the resulting complexes were characterized. The studies revealed the role of histone deacetylases (HDAC1/2) in regulating the expression of ASD orthologs in the embryonic mouse brain. Proteome-wide screens for the co-complexed subunits with HDAC1 and six other key ASD proteins in neuronal cells revealed a protein interaction network, which displayed preferential expression in fetal brain development, exhibited increased deleterious mutations in ASD cases, and were strongly regulated by FMRP and MECP2 causal for Fragile X and Rett syndromes, respectively. Overall, our study reveals molecular components in ASD, suggests a shared mechanism between the syndromic and idiopathic forms of ASDs, and provides a systems framework for analyzing complex human diseases.
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http://dx.doi.org/10.1016/j.cels.2015.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776331PMC
November 2015

MTE1 Functions with MPH1 in Double-Strand Break Repair.

Genetics 2016 05 26;203(1):147-57. Epub 2016 Feb 26.

Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada

Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.
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http://dx.doi.org/10.1534/genetics.115.185454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858770PMC
May 2016
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