Claudia L. Kleinman
McGill University
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Featured researches published by Claudia L. Kleinman.
Science | 2012
Claudia L. Kleinman; Jacek Majewski
Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported large numbers of differences between DNA and messenger RNA in human cells, indicating unprecedented levels of RNA editing, and including sequence changes not produced by any of the known RNA editing mechanisms. However, common sources of systematic errors in high-throughput sequencing technology, which were not properly accounted for in this study, explain most of the claimed differences.
Nature Genetics | 2014
Claudia L. Kleinman; Noha Gerges; Simon Papillon-Cavanagh; Patrick Sin-Chan; Albena Pramatarova; Dong Anh Khuong Quang; Véronique Adoue; Stephan Busche; Maxime Caron; Haig Djambazian; Amandine Bemmo; Adam M. Fontebasso; Tara Spence; Jeremy Schwartzentruber; Steffen Albrecht; Péter Hauser; Miklós Garami; Almos Klekner; László Bognár; Jose Luis Montes; Alfredo Staffa; Alexandre Montpetit; Pierre Bérubé; Magdalena Zakrzewska; Krzysztof Zakrzewski; Pawel P. Liberski; Zhifeng Dong; Peter M. Siegel; Thomas F. Duchaine; Christian Perotti
Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.
Genome Research | 2011
Emilie Lalonde; Kevin C.H. Ha; Zibo Wang; Amandine Bemmo; Claudia L. Kleinman; Tony Kwan; Tomi Pastinen; Jacek Majewski
Expression levels of many human genes are under the genetic control of expression quantitative trait loci (eQTLs). Despite technological advances, the precise molecular mechanisms underlying most eQTLs remain elusive. Here, we use deep mRNA sequencing of two CEU individuals to investigate those mechanisms, with particular focus on the role of splicing control loci (sQTLs). We identify a large number of genes that are differentially spliced between the two samples and associate many of those differences with nearby single nucleotide polymorphisms (SNPs). Subsequently, we investigate the potential effect of splicing SNPs on eQTL control in general. We find a significant enrichment of alternative splicing (AS) events within a set of highly confident eQTL targets discovered in previous studies, suggesting a role of AS in regulating overall gene expression levels. Next, we demonstrate high correlation between the levels of mature (exonic) and unprocessed (intronic) RNA, implying that ∼75% of eQTL target variance can be explained by control at the level of transcription, but that the remaining 25% may be regulated co- or post-transcriptionally. We focus on eQTL targets with discordant mRNA and pre-mRNA expression patterns and use four examples: USMG5, MMAB, MRPL43, and OAS1, to dissect the exact downstream effects of the associated genetic variants.
PLOS Genetics | 2012
Yves B. Beaulieu; Claudia L. Kleinman; Anne-Marie Landry-Voyer; Jacek Majewski; François Bachand
The poly(A)-binding protein nuclear 1 (PABPN1) is a ubiquitously expressed protein that is thought to function during mRNA poly(A) tail synthesis in the nucleus. Despite the predicted role of PABPN1 in mRNA polyadenylation, little is known about the impact of PABPN1 deficiency on human gene expression. Specifically, it remains unclear whether PABPN1 is required for general mRNA expression or for the regulation of specific transcripts. Using RNA sequencing (RNA–seq), we show here that the large majority of protein-coding genes express normal levels of mRNA in PABPN1–deficient cells, arguing that PABPN1 may not be required for the bulk of mRNA expression. Unexpectedly, and contrary to the view that PABPN1 functions exclusively at protein-coding genes, we identified a class of PABPN1–sensitive long noncoding RNAs (lncRNAs), the majority of which accumulated in conditions of PABPN1 deficiency. Using the spliced transcript produced from a snoRNA host gene as a model lncRNA, we show that PABPN1 promotes lncRNA turnover via a polyadenylation-dependent mechanism. PABPN1–sensitive lncRNAs are targeted by the exosome and the RNA helicase MTR4/SKIV2L2; yet, the polyadenylation activity of TRF4-2, a putative human TRAMP subunit, appears to be dispensable for PABPN1–dependent regulation. In addition to identifying a novel function for PABPN1 in lncRNA turnover, our results provide new insights into the post-transcriptional regulation of human lncRNAs.
Veterinary Parasitology | 2015
Catherine Bourguinat; Alice C.Y. Lee; Regina Lizundia; Byron L. Blagburn; Janice L. Liotta; Marc S. Kraus; Kathy Keller; Christian Epe; Louis Letourneau; Claudia L. Kleinman; Tara Paterson; Elena Carretón Gómez; José Alberto Montoya-Alonso; Hubert Smith; Aron Bhan; Andrew S. Peregrine; James Carmichael; Jason Drake; Rudolf Schenker; Ronald Kaminsky; Dwight D. Bowman; Timothy G. Geary; Roger K. Prichard
Macrocyclic lactone (ML) endectocides are used as chemoprophylaxis for heartworm infection (Dirofilaria immitis) in dogs and cats. Claims of loss of efficacy (LOE) of ML heartworm preventives have become common in some locations in the USA. We directly tested whether resistance to MLs exists in LOE isolates of D. immitis and identified genetic markers that are correlated with, and therefore can predict ML resistance. ML controlled studies showed that LOE strains of D. immitis established infections in dogs despite chemoprophylaxis with oral ivermectin or injectable moxidectin. A whole genome approach was used to search for loci associated with the resistance phenotype. Many loci showed highly significant differences between pools of susceptible and LOE D. immitis. Based on 186 potential marker loci, Sequenom(®) SNP frequency analyses were conducted on 663 individual parasites (adult worms and microfilariae) which were phenotypically characterized as susceptible (SUS), confirmed ML treatment survivors/resistant (RES), or suspected resistant/loss of efficacy (LOE) parasites. There was a subset of SNP loci which appears to be promising markers for predicting ML resistance, including SNPs in some genes that have been associated with ML resistance in other parasites. These data provide unequivocal proof of ML resistance in D. immitis and identify genetic markers that could be used to monitor for ML resistance in heartworms.
RNA | 2012
Claudia L. Kleinman; Véronique Adoue; Jacek Majewski
RNA editing, the post-transcriptional recoding of RNA molecules, has broad potential implications for gene expression. Several recent studies of human transcriptomes reported a high number of differences between DNA and RNA, including events not explained by any known mammalian RNA-editing mechanism. However, RNA-editing estimates differ by orders of magnitude, since technical limitations of high-throughput sequencing have been sometimes overlooked and sequencing errors have been confounded with editing sites. Here, we developed a series of computational approaches to analyze the extent of this process in the human transcriptome, identifying and addressing the major sources of error of a large-scale approach. We apply the detection pipeline to deep sequencing data from lymphoblastoid cell lines expressing ADAR1 at high levels, and show that noncanonical editing is unlikely to occur, with at least 85%-98% of candidate sites being the result of sequencing and mapping artifacts. By implementing a method to detect intronless gene duplications, we show that most noncanonical sites previously validated originate in read mismapping within these regions. Canonical A-to-G editing, on the other hand, is widespread in noncoding Alu sequences and rare in exonic and coding regions, where the validation rate also dropped. The genomic distribution of editing sites we find, together with the lack of consistency across studies or biological replicates, suggest a minor quantitative impact of this process in the overall recoding of protein sequences. We propose instead a primary role of ADAR1 protein as a defense system against elements potentially damaging to the genome.
EMBO Reports | 2017
Hana Antonicka; Karine Choquet; Zhen-Yuan Lin; Anne-Claude Gingras; Claudia L. Kleinman; Eric A. Shoubridge
Pseudouridylation is a common post‐transcriptional modification in RNA, but its functional consequences at the cellular level remain largely unknown. Using a proximity‐biotinylation assay, we identified a protein module in mitochondrial RNA granules, platforms for post‐transcriptional RNA modification and ribosome assembly, containing several proteins of unknown function including three uncharacterized pseudouridine synthases, TRUB2, RPUSD3, and RPUSD4. TRUB2 and RPUSD4 were previously identified as core essential genes in CRISPR/Cas9 screens. Depletion of the individual enzymes produced specific mitochondrial protein synthesis and oxidative phosphorylation assembly defects without affecting mitochondrial mRNA levels. Investigation of the molecular targets in mitochondrial RNA by pseudouridine‐Seq showed that RPUSD4 plays a role in the pseudouridylation of a single residue in the 16S rRNA, a modification that is essential for its stability and assembly into the mitochondrial ribosome, while TRUB2/RPUSD3 were similarly involved in pseudouridylating specific residues in mitochondrial mRNAs. These results establish essential roles for epitranscriptomic modification of mitochondrial RNA in mitochondrial protein synthesis, oxidative phosphorylation, and cell survival.
Cancer Cell | 2017
Manav Pathania; Nicolas De Jay; Nicola Maestro; Ashot S. Harutyunyan; Justyna Nitarska; Pirasteh Pahlavan; Stephen Henderson; Leonie G. Mikael; Angela Richard-Londt; Ying Zhang; Joana R. Costa; Steven Hébert; Sima Khazaei; Nisreen Samir Ibrahim; Javier Herrero; Antonella Riccio; Steffen Albrecht; Robin Ketteler; Sebastian Brandner; Claudia L. Kleinman; Nada Jabado; Paolo Salomoni
Gain-of-function mutations in histone 3 (H3) variants are found in a substantial proportion of pediatric high-grade gliomas (pHGG), often in association with TP53 loss and platelet-derived growth factor receptor alpha (PDGFRA) amplification. Here, we describe a somatic mouse model wherein H3.3K27M and Trp53 loss alone are sufficient for neoplastic transformation if introduced in utero. H3.3K27M-driven lesions are clonal, H3K27me3 depleted, Olig2 positive, highly proliferative, and diffusely spreading, thus recapitulating hallmark molecular and histopathological features of pHGG. Addition of wild-type PDGFRA decreases latency and increases tumor invasion, while ATRX knockdown is associated with more circumscribed tumors. H3.3K27M-tumor cells serially engraft in recipient mice, and preliminary drug screening reveals mutation-specific vulnerabilities. Overall, we provide a faithful H3.3K27M-pHGG model which enables insights into oncohistone pathogenesis and investigation of future therapies.
Nature Communications | 2017
Ryuhjin Ahn; Valerie Sabourin; Alicia M. Bolt; Steven Hébert; Stephanie Totten; Nicolas De Jay; Maria Carolina Festa; Yoon Kow Young; Young Kyuen Im; Tony Pawson; Antonis E. Koromilas; William J. Muller; Koren K. Mann; Claudia L. Kleinman; Josie Ursini-Siegel
Tyrosine kinase signalling within cancer cells is central to the establishment of an immunosuppressive microenvironment. Although tyrosine kinase inhibitors act, in part, to augment adaptive immunity, the increased heterogeneity and functional redundancy of the tyrosine kinome is a hurdle to achieving durable responses to immunotherapies. We previously identified the Shc1 (ShcA) scaffold, a central regulator of tyrosine kinase signalling, as essential for promoting breast cancer immune suppression. Herein we show that the ShcA pathway simultaneously activates STAT3 immunosuppressive signals and impairs STAT1-driven immune surveillance in breast cancer cells. Impaired Y239/Y240-ShcA phosphorylation selectively reduces STAT3 activation in breast tumours, profoundly sensitizing them to immune checkpoint inhibitors and tumour vaccines. Finally, the ability of diminished tyrosine kinase signalling to initiate STAT1-driven immune surveillance can be overcome by compensatory STAT3 hyperactivation in breast tumours. Our data indicate that inhibition of pY239/240-ShcA-dependent STAT3 signalling may represent an attractive therapeutic strategy to sensitize breast tumours to multiple immunotherapies.
Cell Reports | 2017
Paul Savage; Alexis Blanchet-Cohen; Timothée Revil; Dunarel Badescu; Sadiq M. Saleh; Yu-Chang Wang; Dongmei Zuo; Leah Liu; Nicholas Bertos; Valentina Muñoz-Ramos; Mark Basik; Kevin Petrecca; Jamil Asselah; Sarkis Meterissian; Marie-Christine Guiot; Atilla Omeroglu; Claudia L. Kleinman; Morag Park; Jiannis Ragoussis
Therapies targeting epidermal growth factor receptor (EGFR) have variable and unpredictable responses in breast cancer. Screening triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), we identify a subset responsive to EGFR inhibition by gefitinib, which displays heterogeneous expression of wild-type EGFR. Deep single-cell RNA sequencing of 3,500 cells from an exceptional responder identified subpopulations displaying distinct biological features, where elevated EGFR expression was significantly enriched in a mesenchymal/stem-like cellular cluster. Sorted EGFRhi subpopulations exhibited enhanced stem-like features, including ALDH activity, sphere-forming efficiency, and tumorigenic and metastatic potential. EGFRhi cells gave rise to EGFRhi and EGFRlo cells in primary and metastatic tumors, demonstrating an EGFR-dependent expansion and hierarchical state transition. Similar tumorigenic EGFRhi subpopulations were identified in independent PDXs, where heterogeneous EGFR expression correlated with gefitinib sensitivity. This provides new understanding for an EGFR-dependent hierarchy in TNBC and for patient stratification for therapeutic intervention.