Publications by authors named "Lauren Brady"

64 Publications

Differential CircRNA Expression Signatures May Serve as Potential Novel Biomarkers in Prostate Cancer.

Front Cell Dev Biol 2021 25;9:605686. Epub 2021 Feb 25.

Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.

Circular RNAs (circRNAs), a recently discovered non-coding RNA, have a number of functions including the regulation of miRNA expression. They have been detected in a number of malignancies including prostate cancer (PCa). The differential expression pattern of circRNAs associated with PCa and androgen receptor (AR) status was investigated in this study. circRNA profiling was performed using a high throughout microarray assay on a panel of prostate cell lines, which consisted of normal, benign, and malignant cells ( = 9). circRNAs were more commonly significantly up-regulated ( < 0.05) than downregulated in malignant cell lines ( = 3,409) vs. benign cell lines ( = 2,949). In a grouped analysis based on AR status, there were 2,127 down-regulated circRNAs in androgen independent cell lines compared to 2,236 in androgen dependent cell lines, thus identifying a potential circRNA signature reflective of androgen dependency. Through a bioinformatics approach, the parental genes associated with the top 10 differentially expressed circRNAs were identified such as hsa_circ_0064644, whose predicted parental gene target is , and hsa_circ_0060539, whose predicted gene target is . Furthermore, we identified three circRNAs associated with the parental gene (hsa_circ_0021652, hsa_circ_0000288, and hsa_circ_0021647). Other studies have shown the importance of in PCa cell survival and drug resistance. Given the modified circRNA expression signatures identified here, these hypothesis generating results suggest that circRNAs may serve as potential putative diagnostic and predictive markers in PCa. However, further validation studies are required to assess the true potential of these markers in the clinical setting.
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http://dx.doi.org/10.3389/fcell.2021.605686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946979PMC
February 2021

Inter- and intra-tumor heterogeneity of metastatic prostate cancer determined by digital spatial gene expression profiling.

Nat Commun 2021 03 3;12(1):1426. Epub 2021 Mar 3.

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Metastatic prostate cancer (mPC) comprises a spectrum of diverse phenotypes. However, the extent of inter- and intra-tumor heterogeneity is not established. Here we use digital spatial profiling (DSP) technology to quantitate transcript and protein abundance in spatially-distinct regions of mPCs. By assessing multiple discrete areas across multiple metastases, we find a high level of intra-patient homogeneity with respect to tumor phenotype. However, there are notable exceptions including tumors comprised of regions with high and low androgen receptor (AR) and neuroendocrine activity. While the vast majority of metastases examined are devoid of significant inflammatory infiltrates and lack PD1, PD-L1 and CTLA4, the B7-H3/CD276 immune checkpoint protein is highly expressed, particularly in mPCs with high AR activity. Our results demonstrate the utility of DSP for accurately classifying tumor phenotype, assessing tumor heterogeneity, and identifying aspects of tumor biology involving the immunological composition of metastases.
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http://dx.doi.org/10.1038/s41467-021-21615-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930198PMC
March 2021

POLRMT mutations impair mitochondrial transcription causing neurological disease.

Nat Commun 2021 02 18;12(1):1135. Epub 2021 Feb 18.

Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.

While >300 disease-causing variants have been identified in the mitochondrial DNA (mtDNA) polymerase γ, no mitochondrial phenotypes have been associated with POLRMT, the RNA polymerase responsible for transcription of the mitochondrial genome. Here, we characterise the clinical and molecular nature of POLRMT variants in eight individuals from seven unrelated families. Patients present with global developmental delay, hypotonia, short stature, and speech/intellectual disability in childhood; one subject displayed an indolent progressive external ophthalmoplegia phenotype. Massive parallel sequencing of all subjects identifies recessive and dominant variants in the POLRMT gene. Patient fibroblasts have a defect in mitochondrial mRNA synthesis, but no mtDNA deletions or copy number abnormalities. The in vitro characterisation of the recombinant POLRMT mutants reveals variable, but deleterious effects on mitochondrial transcription. Together, our in vivo and in vitro functional studies of POLRMT variants establish defective mitochondrial transcription as an important disease mechanism.
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http://dx.doi.org/10.1038/s41467-021-21279-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893070PMC
February 2021

Variants in GNAI1 cause a syndrome associated with variable features including developmental delay, seizures, and hypotonia.

Genet Med 2021 Jan 20. Epub 2021 Jan 20.

Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.

Purpose: Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene.

Methods: Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual.

Results: We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy.

Conclusion: This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.
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http://dx.doi.org/10.1038/s41436-020-01076-8DOI Listing
January 2021

Dual molecular diagnoses in a neurometabolic specialty clinic.

Am J Med Genet A 2021 03 24;185(3):766-773. Epub 2020 Dec 24.

Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada.

Reports of patients with concomitant diagnoses of two inherited genetic disorders, sometimes referred to as "double trouble," have appeared intermittently in the medical literature. We report eight additional cases with dual diagnoses of two genetic conditions. All cases had a phenotype atypical for their primary diagnosis, leading to the search for a second genetic diagnosis. These cases highlight the importance of the history, physical examination and continued work-up if the phenotype of the patient falls drastically outside what has been reported with their primary diagnosis. Some of the diagnoses of the patients presented here (e.g., Myotonic Dystrophy Type 1, fascioscapulohumeral muscular dystrophy) would not have been identified by genetic testing done on a next generation sequencing backbone (e.g., panel or exome sequencing). When the clinical picture is atypical or more severe than expected the possibility of a dual diagnosis (double trouble) should be considered. Identification of a second genetic condition can impact management and genetic counseling.
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http://dx.doi.org/10.1002/ajmg.a.62034DOI Listing
March 2021

Platelet cloaking of circulating tumour cells in patients with metastatic prostate cancer: Results from ExPeCT, a randomised controlled trial.

PLoS One 2020 18;15(12):e0243928. Epub 2020 Dec 18.

Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland.

Background: Circulating tumour cells (CTCs) represent a morphologically distinct subset of cancer cells, which aid the metastatic spread. The ExPeCT trial aimed to examine the effectiveness of a structured exercise programme in modulating levels of CTCs and platelet cloaking in patients with metastatic prostate cancer.

Methods: Participants (n = 61) were randomised into either standard care (control) or exercise arms. Whole blood was collected for all participants at baseline (T0), three months (T3) and six months (T6), and analysed for the presence of CTCs, CTC clusters and platelet cloaking. CTC data was correlated with clinico-pathological information.

Results: Changes in CTC number were observed within group over time, however no significant difference in CTC number was observed between groups over time. Platelet cloaking was identified in 29.5% of participants. A positive correlation between CTC number and white cell count (WCC) was observed (p = 0.0001), in addition to a positive relationship between CTC clusters and PSA levels (p = 0.0393).

Conclusion: The presence of platelet cloaking has been observed in this patient population for the first time, in addition to a significant correlation between CTC number and WCC.

Trial Registration: ClincalTrials.gov identifier NCT02453139.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0243928PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748139PMC
February 2021

Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population.

Am J Med Genet A 2021 02 10;185(2):486-499. Epub 2020 Dec 10.

Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.

Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.
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http://dx.doi.org/10.1002/ajmg.a.61998DOI Listing
February 2021

Missense variants in the N-terminal domain of the A isoform of FHF2/FGF13 cause an X-linked developmental and epileptic encephalopathy.

Am J Hum Genet 2021 01 26;108(1):176-185. Epub 2020 Nov 26.

Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Kids Neuroscience Centre, Kids Research, Children Hospital at Westmead, Sydney, NSW 2145, Australia; Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, NSW 2050, Australia.

Fibroblast growth factor homologous factors (FHFs) are intracellular proteins which regulate voltage-gated sodium (Na) channels in the brain and other tissues. FHF dysfunction has been linked to neurological disorders including epilepsy. Here, we describe two sibling pairs and three unrelated males who presented in infancy with intractable focal seizures and severe developmental delay. Whole-exome sequencing identified hemi- and heterozygous variants in the N-terminal domain of the A isoform of FHF2 (FHF2A). The X-linked FHF2 gene (also known as FGF13) has alternative first exons which produce multiple protein isoforms that differ in their N-terminal sequence. The variants were located at highly conserved residues in the FHF2A inactivation particle that competes with the intrinsic fast inactivation mechanism of Na channels. Functional characterization of mutant FHF2A co-expressed with wild-type Na1.6 (SCN8A) revealed that mutant FHF2A proteins lost the ability to induce rapid-onset, long-term blockade of the channel while retaining pro-excitatory properties. These gain-of-function effects are likely to increase neuronal excitability consistent with the epileptic potential of FHF2 variants. Our findings demonstrate that FHF2 variants are a cause of infantile-onset developmental and epileptic encephalopathy and underline the critical role of the FHF2A isoform in regulating Na channel function.
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http://dx.doi.org/10.1016/j.ajhg.2020.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820623PMC
January 2021

An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids.

Genet Med 2021 Apr 26;23(4):740-750. Epub 2020 Nov 26.

Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.

Purpose: In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu).

Methods: Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics.

Results: All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production.

Conclusion: Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.
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http://dx.doi.org/10.1038/s41436-020-01027-3DOI Listing
April 2021

Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia.

Proc Natl Acad Sci U S A 2020 06 8;117(25):14331-14341. Epub 2020 Jun 8.

Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239;

Acute myeloid leukemia (AML) is the most common acute leukemia in adults, with approximately four new cases per 100,000 persons per year. Standard treatment for AML consists of induction chemotherapy with remission achieved in 50 to 75% of cases. Unfortunately, most patients will relapse and die from their disease, as 5-y survival is roughly 29%. Therefore, other treatment options are urgently needed. In recent years, immune-based therapies have led to unprecedented rates of survival among patients with some advanced cancers. Suppression of T cell function in the tumor microenvironment is commonly observed and may play a role in AML. We found that there is a significant association between T cell infiltration in the bone marrow microenvironment of newly diagnosed patients with AML and increased overall survival. Functional studies aimed at establishing the degree of T cell suppression in patients with AML revealed impaired T cell function in many patients. In most cases, T cell proliferation could be restored by blocking the immune checkpoint molecules PD-1, CTLA-4, or TIM3. Our data demonstrate that AML establishes an immune suppressive environment in the bone marrow, in part through T cell checkpoint function.
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http://dx.doi.org/10.1073/pnas.1916206117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321988PMC
June 2020

A mitochondrial disorder with ptosis and exercise intolerance without ophthalmoparesis secondary to m.5865 T > C variant.

Mitochondrion 2020 07 30;53:150-153. Epub 2020 May 30.

Department of Paediatrics, McMaster University, 1200 Main St. W., Hamilton, Ontario L8N 3Z5, Canada. Electronic address:

We describe a novel mitochondrial variant (m.5865 T > C) in a patient with decreased exercise endurance and juvenile onset slowly progressive bilateral ptosis without ophthamloparesis. The m.5865 T > C variant was seen in 82.9% of mtDNA molecules in skeletal muscle tissue and ~8% of mtDNA molecules in urine epithelium, but was not detected in blood leukocytes. The proband does not demonstrate any additional features often seen in individuals with a mitochondrial disorder (i.e., sensorineural hearing loss, type 2 diabetes, stroke-like episodes, muscle weakness, ophthalmoparesis, cardiomyopathy or cardiac arrhythmias). This case suggests that ptosis and exercise intolerance, without ophthalmoparesis, are the primary clinical features of the m.5865 T > C mtDNA variant.
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http://dx.doi.org/10.1016/j.mito.2020.05.006DOI Listing
July 2020

Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients.

J Med Genet 2021 Apr 6;58(4):284-288. Epub 2020 May 6.

Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, Ontario, Canada

Charcot-Marie-Tooth disease (CMT) is one of the most common Mendelian disorders characterised by genetic heterogeneity, progressive distal muscle weakness and atrophy, foot deformities and distal sensory loss. In this report, we describe genetic testing data including comprehensive sequencing and copy number analysis of 34 CMT-related genes in a Canadian cohort of patients with suspected CMT. We have demonstrated a notable gender testing bias, with an overall diagnostic yield of 15% in males and 21% in females. We have identified a large number of novel pathogenic variants as well as variants of unknown clinical significance in CMT-related genes. In this largest to date analysis of gene CNVs in CMT, in addition to the common PMP22 deletion/duplication, we have described a significant contribution of pathogenic CNVs in several CMT-related genes. This study significantly expand the mutational spectrum of CMT genes, while demonstrating the clinical utility of a comprehensive sequence and copy number next-generation sequencing-based clinical genetic testing in patients with suspected diagnosis of CMT.
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http://dx.doi.org/10.1136/jmedgenet-2019-106641DOI Listing
April 2021

Congenital myasthenic syndrome-associated agrin variants affect clustering of acetylcholine receptors in a domain-specific manner.

JCI Insight 2020 04 9;5(7). Epub 2020 Apr 9.

Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA.

Congenital myasthenic syndromes (CMS) are caused by mutations in molecules expressed at the neuromuscular junction. We report clinical, structural, ultrastructural, and electrophysiologic features of 4 CMS patients with 6 heteroallelic variants in AGRN, encoding agrin. One was a 7.9-kb deletion involving the N-terminal laminin-binding domain. Another, c.4744G>A - at the last nucleotide of exon 26 - caused skipping of exon 26. Four missense mutations (p.S1180L, p.R1509W, p.G1675S, and p.Y1877D) expressed in conditioned media decreased AChR clusters in C2C12 myotubes. The agrin-enhanced phosphorylation of MuSK was markedly attenuated by p.Y1877D in the LG3 domain and moderately attenuated by p.R1509W in the LG1 domain but not by the other 2 mutations. The p.S1180L mutation in the SEA domain facilitated degradation of secreted agrin. The p.G1675S mutation in the LG2 domain attenuated anchoring of agrin to the sarcolemma by compromising its binding to heparin. Anchoring of agrin with p.R1509W in the LG1 domain was similarly attenuated. Mutations of agrin affect AChR clustering by enhancing agrin degradation or by suppressing MuSK phosphorylation and/or by compromising anchoring of agrin to the sarcolemma of the neuromuscular junction.
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http://dx.doi.org/10.1172/jci.insight.132023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7205260PMC
April 2020

Phenotypic convergence in Charcot-Marie-Tooth 2Y with novel VCP mutation.

Neuromuscul Disord 2020 03 7;30(3):232-235. Epub 2020 Feb 7.

McMaster University, Physical Medicine and Neurology, Neuromuscular Disease Clinic, Ontario L8S 4L8, Canada. Electronic address:

Charcot-Marie-Tooth (CMT) disease, a hereditary motor and sensory neuropathy, has subtypes with varied inheritance patterns and phenotypic presentation. Subtypes additionally vary by genetic variants in a number of genes. Pathogenic variants in the VCP gene have newly been associated with CMT type 2. We present a family with CMT type 2 with a novel heterozygous VCP variant and phenotypic variability between the proband, his brother, and father.
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http://dx.doi.org/10.1016/j.nmd.2020.02.002DOI Listing
March 2020

Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor.

Front Mol Neurosci 2020 11;13:12. Epub 2020 Feb 11.

Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia.

Multiple TREX mRNA export complex subunits (e.g., THOC1, THOC2, THOC5, THOC6, THOC7) have now been implicated in neurodevelopmental disorders (NDDs), neurodegeneration and cancer. We previously implicated missense and splicing-defective variants in NDDs and a broad range of other clinical features. Here we report 10 individuals from nine families with rare missense variants including the first case of a recurrent variant (p.Arg77Cys), and an additional individual with an intragenic microdeletion (Del-Ex37-38). missense variant testing and patient-derived cell line data from current and published studies show 9 of the 14 missense THOC2 variants result in reduced protein stability. The splicing-defective and deletion variants result in a loss of small regions of the C-terminal THOC2 RNA binding domain (RBD). Interestingly, reduced stability of THOC2 variant proteins has a flow-on effect on the stability of the multi-protein TREX complex; specifically on the other NDD-associated THOC subunits. Our current, expanded cohort refines the core phenotype of THOC2 NDDs to language disorder and/or ID, with a variable severity, and disorders of growth. A subset of affected individuals' has severe-profound ID, persistent hypotonia and respiratory abnormalities. Further investigations to elucidate the pathophysiological basis for this severe phenotype are warranted.
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http://dx.doi.org/10.3389/fnmol.2020.00012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026477PMC
February 2020

A comparison of prostate cancer cell transcriptomes in 2D monoculture vs 3D xenografts identify consistent gene expression alterations associated with tumor microenvironments.

Prostate 2020 05 18;80(6):491-499. Epub 2020 Feb 18.

Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington.

Background: Prostate cancer (PC) research has relied heavily on patient-derived cell lines, which may be used for in vitro (two-dimensional [2D]) studies or cultivated as three-dimensional (3D) xenografts in mice. These approaches are likely to have differential impacts on cell phenotypes, with implications for experimental outcomes. Therefore, defining and comparing the transcriptional signatures associated with 2D and 3D approaches may be useful for designing experiments and interpreting research results.

Methods: In this study, LNCaP, VCaP, and 22Rv1 human PC cells were either cultivated in monolayers or as xenografts in NOD SCID mice, and their gene transcription profiles were quantitated and compared using microarray and real-time polymerase chain reaction techniques. Immunohistochemistry was used to evaluate protein expression in cancer cell xenografts.

Results: Comparisons of gene expression profiles of tumor cells grown in 2D vs 3D environments identified gene sets featuring similar expression patterns in all three cancer cell lines and unique transcriptional signatures associated with 3D vs 2D growth. Pathways related to cell-cell interactions, differentiation, and the extracellular matrix were enriched in 3D conditions. Immunohistochemical analyses confirmed that gene upregulation in xenografts occurred in implanted cancer cells and not in mouse stromal cells. Cultivating cells in vitro in the presence of mouse, rather than bovine serum failed to elicit the gene transcription profile observed in xenografts, further supporting the hypothesis that this profile reflects 3D growth and enhanced microenvironmental interactions, rather than exposure to species-specific serum factors.

Conclusions: Overall, these findings define the expression profiles observed in PC cells cultivated in 2D monolayers and in 3D xenografts, highlighting differentially regulated pathways in each setting and providing information for interpreting research results in model systems.
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http://dx.doi.org/10.1002/pros.23963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148119PMC
May 2020

EphA2 contributes to disruption of the blood-brain barrier in cerebral malaria.

PLoS Pathog 2020 01 30;16(1):e1008261. Epub 2020 Jan 30.

Department of Pathology, University of Utah, Salt Lake City, UT, United States of America.

Disruption of blood-brain barrier (BBB) function is a key feature of cerebral malaria. Increased barrier permeability occurs due to disassembly of tight and adherens junctions between endothelial cells, yet the mechanisms governing junction disassembly and vascular permeability during cerebral malaria remain poorly characterized. We found that EphA2 is a principal receptor tyrosine kinase mediating BBB breakdown during Plasmodium infection. Upregulated on brain microvascular endothelial cells in response to inflammatory cytokines, EphA2 is required for the loss of junction proteins on mouse and human brain microvascular endothelial cells. Furthermore, EphA2 is necessary for CD8+ T cell brain infiltration and subsequent BBB breakdown in a mouse model of cerebral malaria. Blocking EphA2 protects against BBB breakdown highlighting EphA2 as a potential therapeutic target for cerebral malaria.
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http://dx.doi.org/10.1371/journal.ppat.1008261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991964PMC
January 2020

Choline transporter-like 1 deficiency causes a new type of childhood-onset neurodegeneration.

Brain 2020 01;143(1):94-111

Department of Human Health and Nutritional Sciences, University of Guelph, Canada.

Cerebral choline metabolism is crucial for normal brain function, and its homoeostasis depends on carrier-mediated transport. Here, we report on four individuals from three families with neurodegenerative disease and homozygous frameshift mutations (Asp517Metfs*19, Ser126Metfs*8, and Lys90Metfs*18) in the SLC44A1 gene encoding choline transporter-like protein 1. Clinical features included progressive ataxia, tremor, cognitive decline, dysphagia, optic atrophy, dysarthria, as well as urinary and bowel incontinence. Brain MRI demonstrated cerebellar atrophy and leukoencephalopathy. Moreover, low signal intensity in globus pallidus with hyperintensive streaking and low signal intensity in substantia nigra were seen in two individuals. The Asp517Metfs*19 and Ser126Metfs*8 fibroblasts were structurally and functionally indistinguishable. The most prominent ultrastructural changes of the mutant fibroblasts were reduced presence of free ribosomes, the appearance of elongated endoplasmic reticulum and strikingly increased number of mitochondria and small vesicles. When chronically treated with choline, those characteristics disappeared and mutant ultrastructure resembled healthy control cells. Functional analysis revealed diminished choline transport yet the membrane phosphatidylcholine content remained unchanged. As part of the mechanism to preserve choline and phosphatidylcholine, choline transporter deficiency was implicated in impaired membrane homeostasis of other phospholipids. Choline treatments could restore the membrane lipids, repair cellular organelles and protect mutant cells from acute iron overload. In conclusion, we describe a novel childhood-onset neurometabolic disease caused by choline transporter deficiency with autosomal recessive inheritance.
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http://dx.doi.org/10.1093/brain/awz376DOI Listing
January 2020

Infantile-Onset Syndromic Cerebellar Ataxia and CACNA1G Mutations.

Pediatr Neurol 2020 03 19;104:40-45. Epub 2019 Oct 19.

Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.

Background: Congenital ataxias associated with cerebellar atrophy are clinically heterogeneous conditions with a variable age of onset and a diverse molecular basis. The hypothesis-free approach of genomic sequencing has led to the discovery of new genes implicated in these disorders and the identification of unexpected genotype-phenotype correlations. Although a recurrent heterozygous mutation (p.Arg1715His) in CACNA1G is known to cause adult-onset spinocerebellar ataxia 42 (SCA42*616795), gain-of-function mutations in this gene have recently been identified by whole exome sequencing (WES) in four children with cerebellar atrophy and ataxia, psychomotor delay, and other variable features.

Methods: We describe four children from unrelated families with cerebellar anomalies on magnetic resonance imaging (atrophy or hypoplasia of the cerebellar vermis), hypertonia, psychomotor and speech delay, severe intellectual disability, ophthalmologic features and peculiar dysmorphic traits. All patients underwent a trio-based WES analysis. Clinical records were used to characterize the clinical profile of this newly recognized disorder.

Results: Two previously reported de novo disease-causing mutations in CACNA1G (c.2881G>A, p.Ala961Thr and c.4591A>G, p.Met1531Val) were identified in these patients, providing further evidence of the specific impact of these variants. All four patients exhibit distinctive dysmorphic and ectodermal features which overlap those of the previously reported patients, allowing us to define the major features characterizing this homogeneous neurodevelopmental syndromic disorder associated with upregulated CACNA1G function.

Conclusion: Our findings confirm the specific association between a narrow spectrum of missense mutations in CACNA1G and a novel syndrome with infantile-onset cerebellar ataxiaand provide a dysmorphologic delineation of this novel neurodevelopmental trait.
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http://dx.doi.org/10.1016/j.pediatrneurol.2019.09.005DOI Listing
March 2020

An evaluation of genetic causes and environmental risks for bilateral optic atrophy.

PLoS One 2019 25;14(11):e0225656. Epub 2019 Nov 25.

Department of Pediatrics, McMaster University, Hamilton, ON, Canada.

Purpose: To assess the clinical utility of next-generation sequencing (NGS) for the diagnosis of patients with optic atrophy (OA).

Design: Retrospective cohort study.

Methods: 97 patients were referred to the McMaster University Medical Center (Hamilton, Ontario) for evaluation of bilateral OA. All patients were sent for NGS including a 22 nuclear gene panel and/or complete mitochondrial DNA (mtDNA) sequencing. Positive genetic test results and abnormal vibration sensation were compared in patients +/- environmental exposures or a family history.

Results: 19/94 (20.2%) had a positive nuclear variant, of which 15/19 (78.9%) were in the OPA1 gene. No positive mtDNA variants were identified. The detection of a positive genetic variant was significantly different in patients who reported excessive ethanol use, but not in patients who smoke (0/19 (0%) vs. 19/78 (24.4%), P = 0.0164 and 4/22 (18.2%) vs. 15/74 (20.3%), P = 0.829, respectively). Patients with a positive family history were more likely to have a positive genetic variant compared to patients with a negative family history (P = 0.0112). There were significantly more excessive drinkers with an abnormal vibration sensation (P = 0.026), and with a similar trend in smokers (P = 0.074).

Conclusions: All positive genetic variants were identified in nuclear genes. We identified a potential independent pathophysiological link between a history of excessive ethanol consumption and bilateral OA. Further investigations should evaluate and identify potential environmental risk factors for OA.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225656PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876833PMC
March 2020

Expanding the Clinical Spectrum of -Related Mitochondrial Cytopathy.

Front Neurol 2019 4;10:981. Epub 2019 Oct 4.

Department of Pediatrics, McMaster University, Hamilton, ON, Canada.

Pathogenic variants in the gene have been associated with CODAS syndrome (Cerebral, Ocular, Dental, uricular, and keletal Anomalies Syndrome). A recent report identified the first newborn case with -related mitochondrial cytopathy due to a compound heterozygous pathogenic variant in without features of CODAS. The proband had manifested with severe congenital lactic acidosis and profound multiple respiratory chain complex activity deficiencies associated with the quantitative loss of mtDNA copy number in muscle. A subsequent report identified two siblings with regression during infancy, profound hypotonia and muscle weakness, severe intellectual disability, progressive cerebellar atrophy, where muscle biopsy showed an electron dense mitochondrial inclusions without ragged-red fibers and normal electron transport chain enzyme activities. Here, we report an additional case of autosomal recessive mitochondrial cytopathy due to a homozygous missense variant in that was identified on whole exome sequencing (c.810G > A; p.D463N). The proband, a 20-year-old male born to consanguineous parents, presented with global developmental delay, emotional outbursts, speech and swallowing difficulties, hypotonia, and ataxia since childhood. Muscle biopsy showed massive granular bodies, increased oxidative stress, and autophagic block and reduced mitochondrial state 3 respiration. We have identified another case of -related mitochondrial cytopathy further confirming a neurological phenotype without CODAS features.
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http://dx.doi.org/10.3389/fneur.2019.00981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787162PMC
October 2019

Genotypes of chronic progressive external ophthalmoplegia in a large adult-onset cohort.

Mitochondrion 2019 11 12;49:227-231. Epub 2019 Sep 12.

Department of Pediatrics, McMaster University, Hamilton, ON, Canada. Electronic address:

Chronic progressive external ophthalmoplegia (CPEO) is a common presentation of mitochondrial disease. We performed a retrospective evaluation of the molecular genetic testing and genotype-phenotype correlations in a large cohort of adult-onset CPEO patients (N = 111). One hundred percent of patients tested had at least one mitochondrial DNA (mtDNA) deletion. Genetic testing of nuclear genes encoding mitochondrial proteins identified pathogenic/likely pathogenic variants likely to be associated with CPEO in 7.6% of patients. As expected, the nuclear gene most associated with DNA variation was POLG. A single likely pathogenic mitochondrial DNA variant (m.12278T>C) was identified in two unrelated patients. No significant differences were noted in the clinical phenotypes of patients with pathogenic or likely pathogenic nuclear variants in comparison to those with negative nuclear gene testing. Analysis of deletion size and heteroplasmy in muscle-derived mtDNA showed significant correlations with age of symptom onset but not disease severity (number of canonical CPEO features). Results suggest that smaller mtDNA deletions (p = 0.0127, r = 0.1201) and higher heteroplasmy of single mtDNA deletions (p = 0.0112, r = 0.2483) are associated with an earlier age of onset in CPEO patients.
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http://dx.doi.org/10.1016/j.mito.2019.09.002DOI Listing
November 2019

Circular RNAs are differentially expressed in prostate cancer and are potentially associated with resistance to enzalutamide.

Sci Rep 2019 07 24;9(1):10739. Epub 2019 Jul 24.

Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland.

Most forms of castration-resistant prostate cancer (CRPC) are dependent on the androgen receptor (AR) for survival. While, enzalutamide provides a substantial survival benefit, it is not curative and many patients develop resistance to therapy. Although not yet fully understood, resistance can develop through a number of mechanisms, such as AR copy number gain, the generation of splice variants such as AR-V7 and mutations within the ligand binding domain (LBD) of the AR. circular RNAs (circRNAs) are a novel type of non-coding RNA, which can regulate the function of miRNA, and may play a key role in the development of drug resistance. circRNAs are highly resistant to degradation, are detectable in plasma and, therefore may serve a role as clinical biomarkers. In this study, AR-V7 expression was assessed in an isogenic model of enzalutamide resistance. The model consisted of age matched control cells and two sub-line clones displaying varied resistance to enzalutamide. circRNA profiling was performed on the panel using a high throughout microarray assay. Bioinformatic analysis identified a number of differentially expressed circRNAs and predicted five miRNA binding sites for each circRNA. miRNAs were stratified based on known associations with prostate cancer, and targets were validated using qPCR. Overall, circRNAs were more often down regulated in resistant cell lines compared with control (588 vs. 278). Of particular interest was hsa_circ_0004870, which was down-regulated in enzalutamide resistant cells (p ≤ 0.05, vs. sensitive cells), decreased in cells that highly express AR (p ≤ 0.01, vs. AR negative), and decreased in malignant cells (p ≤ 0.01, vs. benign). The associated parental gene was identified as RBM39, a member of the U2AF65 family of proteins. Both genes were down-regulated in resistant cells (p < 0.05, vs. sensitive cells). This is one of the first studies to profile and demonstrate discrete circRNA expression patterns in an enzalutamide resistant cell line model of prostate cancer. Our data suggests that hsa_circ_0004870, through RBM39, may play a critical role in the development of enzalutamide resistance in CRPC.
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http://dx.doi.org/10.1038/s41598-019-47189-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656767PMC
July 2019

Myasthenia graves-like symptoms associated with rare mitochondrial mutation (m.5728T>C).

Mitochondrion 2019 07 23;47:139-140. Epub 2019 Apr 23.

Depertment of Pediatric Laboratory Medicine, Divison of Clinical Biochemistry, The Hospital for Sick Children, Toronto, Ontario, M5G2L3, Canada.

We report here on a patient who presented with myasthenia gravis type symptoms (fatigable ptosis, increased jitter on single fiber EMG, and a thymic mass) who was subsequently diagnosed with a mitochondrial myopathy. Sequencing of the mitochondrial genome (mtDNA) identified a transition variant in the tRNA asparagine gene (MT-TN) (m.5728T>C) at in 41% of mtDNA molecules in muscle tissue. The variant was not detectable in blood. The m.5728T>C variant has been reported previously in a ten year old male with global developmental delays, failure to thrive, ataxia, weakness, cognitive regression, seizures, and glomerulosclerosis. The variant was seen in 97% of mtDNA molecules in muscle and 50% in blood. This case report supports the pathogenicity of the m.5728T>C and helps to establish the phenotypic spectrum of this condition at a lower heteroplasmy.
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http://dx.doi.org/10.1016/j.mito.2019.04.003DOI Listing
July 2019

Anti-NT5c1A Autoantibodies as Biomarkers in Inclusion Body Myositis.

Front Immunol 2019 9;10:745. Epub 2019 Apr 9.

Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.

Sporadic Inclusion Body Myositis (sIBM) is an inflammatory myopathy (IIM) without a specific diagnostic biomarker until autoantibodies to the cytosolic 5'-nucleotidase 1A (/Mup44) were reported. The objectives of our study were to determine the sensitivity and specificity of anti-NT5c1A for sIBM, demonstrate demographic, clinical and serological predictors for anti-NT5c1A positivity and determine if anti-nuclear antibody (ANA) indirect immunofluorescence (IIF) staining on HEp-2 cells is a reliable screening method for anti-NT5c1A. Sera from sIBM patients and controls were stored at -80°C until required for analysis. IgG antibodies to NT5c1A were detected by an addressable laser bead immunoassay (ALBIA) using a full-length human recombinant protein. Autoantibodies to other autoimmune myopathy antigens (Jo-1, OJ, TIF1y, PL-12, SAE, EJ, MDA5, PL7, SRP, NXP2, MI-2) were detected by line immunoassay (LIA), chemiluminescence immunoassay (CIA) or enzyme linked immunosorbent assay (ELISA) and ANA detected by IIF on HEp-2 substrate. Demographic, clinical and serological data were obtained by chart review. Forty-three patients with sIBM, 537 disease control patients with other autoimmune, degenerative and neuromuscular diseases, and 78 healthy controls were included. 48.8% (21/43) of sIBM patients were positive for anti-NT5c1A. The overall sensitivity, specificity, positive predictive value, and negative predictive value of anti-NT5c1A for sIBM were 0.49, 0.92, 0.29, and 0.96, respectively. Compared to sIBM, the frequency of anti-NT5c1A was lower in both the disease control group (8.8%, OR 0.10 [95%CI: 0.05-0.20], < 0.0001) and in the apparently healthy control group (5.1%, OR 0.06 [95%CI: 0.02-0.18], < 0.0001). In the univariable analysis, sIBM patients with more severe muscle weakness were more likely to be anti-NT5c1A positive (OR 4.10 [95% CI: 1.17, 14.33], = 0.027), although this was not statistically significant (adjusted OR 4.30 [95% CI: 0.89, 20.76], = 0.069) in the multivariable analysis. The ANA of sIBM sera did not demonstrate a consistent IIF pattern associated with anti-NT5c1A. Anti-NT5c1A has moderate sensitivity and high specificity for sIBM using ALBIA. The presence of anti-NT5c1A antibodies may be associated with muscle weakness. Anti-NT5c1A antibodies were not associated with a specific IIF staining pattern, hence screening using HEp-2 substrate is unlikely to be a useful predictor for presence of these autoantibodies.
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http://dx.doi.org/10.3389/fimmu.2019.00745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465553PMC
August 2020

Diagnostic Utility of Genome-wide DNA Methylation Testing in Genetically Unsolved Individuals with Suspected Hereditary Conditions.

Am J Hum Genet 2019 04 28;104(4):685-700. Epub 2019 Mar 28.

Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada. Electronic address:

Conventional genetic testing of individuals with neurodevelopmental presentations and congenital anomalies (ND/CAs), i.e., the analysis of sequence and copy number variants, leaves a substantial proportion of them unexplained. Some of these cases have been shown to result from DNA methylation defects at a single locus (epi-variants), while others can exhibit syndrome-specific DNA methylation changes across multiple loci (epi-signatures). Here, we investigate the clinical diagnostic utility of genome-wide DNA methylation analysis of peripheral blood in unresolved ND/CAs. We generate a computational model enabling concurrent detection of 14 syndromes using DNA methylation data with full accuracy. We demonstrate the ability of this model in resolving 67 individuals with uncertain clinical diagnoses, some of whom had variants of unknown clinical significance (VUS) in the related genes. We show that the provisional diagnoses can be ruled out in many of the case subjects, some of whom are shown by our model to have other diseases initially not considered. By applying this model to a cohort of 965 ND/CA-affected subjects without a previous diagnostic assumption and a separate assessment of rare epi-variants in this cohort, we identify 15 case subjects with syndromic Mendelian disorders, 12 case subjects with imprinting and trinucleotide repeat expansion disorders, as well as 106 case subjects with rare epi-variants, a portion of which involved genes clinically or functionally linked to the subjects' phenotypes. This study demonstrates that genomic DNA methylation analysis can facilitate the molecular diagnosis of unresolved clinical cases and highlights the potential value of epigenomic testing in the routine clinical assessment of ND/CAs.
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http://dx.doi.org/10.1016/j.ajhg.2019.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451739PMC
April 2019

Loss of the sphingolipid desaturase DEGS1 causes hypomyelinating leukodystrophy.

J Clin Invest 2019 03 11;129(3):1240-1256. Epub 2019 Feb 11.

Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.

Sphingolipid imbalance is the culprit in a variety of neurological diseases, some affecting the myelin sheath. We have used whole-exome sequencing in patients with undetermined leukoencephalopathies to uncover the endoplasmic reticulum lipid desaturase DEGS1 as the causative gene in 19 patients from 13 unrelated families. Shared features among the cases include severe motor arrest, early nystagmus, dystonia, spasticity, and profound failure to thrive. MRI showed hypomyelination, thinning of the corpus callosum, and progressive thalamic and cerebellar atrophy, suggesting a critical role of DEGS1 in myelin development and maintenance. This enzyme converts dihydroceramide (DhCer) into ceramide (Cer) in the final step of the de novo biosynthesis pathway. We detected a marked increase of the substrate DhCer and DhCer/Cer ratios in patients' fibroblasts and muscle. Further, we used a knockdown approach for disease modeling in Danio rerio, followed by a preclinical test with the first-line treatment for multiple sclerosis, fingolimod (FTY720, Gilenya). The enzymatic inhibition of Cer synthase by fingolimod, 1 step prior to DEGS1 in the pathway, reduced the critical DhCer/Cer imbalance and the severe locomotor disability, increasing the number of myelinating oligodendrocytes in a zebrafish model. These proof-of-concept results pave the way to clinical translation.
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http://dx.doi.org/10.1172/JCI123959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391109PMC
March 2019

BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin-Siris and Nicolaides-Baraitser syndromes.

Nat Commun 2018 11 20;9(1):4885. Epub 2018 Nov 20.

Department of Pathology and Laboratory Medicine, Western University, London, N6A 5W9, ON, Canada.

Coffin-Siris and Nicolaides-Baraitser syndromes (CSS and NCBRS) are Mendelian disorders caused by mutations in subunits of the BAF chromatin remodeling complex. We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2). We demonstrate that the degree of similarity in the epi-signatures of some CSS subtypes and NCBRS can be greater than that within CSS, indicating a link in the functional basis of the two syndromes. We show that chromosome 6q25 microdeletion syndrome, harboring ARID1B deletions, exhibits a similar CSS/NCBRS methylation profile. Specificity of this epi-signature was confirmed across a wide range of neurodevelopmental conditions including other chromatin remodeling and epigenetic machinery disorders. We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening.
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http://dx.doi.org/10.1038/s41467-018-07193-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6244416PMC
November 2018

Aberrant Drp1-mediated mitochondrial division presents in humans with variable outcomes.

Hum Mol Genet 2018 11;27(21):3710-3719

University of Washington School of Medicine, Department of Biochemistry, Seattle, WA, USA.

Mitochondrial dynamics, including mitochondrial division, fusion and transport, are integral parts of mitochondrial and cellular function. DNM1L encodes dynamin-related protein 1 (Drp1), a member of the dynamin-related protein family that is required for mitochondrial division. Several de novo mutations in DNM1L are associated with a range of disease states. Here we report the identification of five patients with pathogenic or likely pathogenic variants of DNM1L, including two novel variants. Interestingly, all of the positions identified in these Drp1 variants are fully conserved among all members of the dynamin-related protein family that are involved in membrane division and organelle division events. This work builds upon and expands the clinical spectrum associated with Drp1 variants in patients and their impact on mitochondrial division in model cells.
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http://dx.doi.org/10.1093/hmg/ddy287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196655PMC
November 2018

Implementation to Optimization: A Tailored, Data-Driven Approach to Improve Provider Efficiency and Confidence in Use of the Electronic Medical Record.

J Oncol Pract 2018 07 25;14(7):e421-e428. Epub 2018 Jun 25.

Dana-Farber Cancer Institute, and Partners Healthcare, Boston, MA.

Purpose: Nine months after the implementation of a new electronic medical record (EMR) system at a single institution, physicians (MDs), nurse practitioners (NPs), and physician assistants (PAs) expressed frustration with its use. We aimed to test if an individually tailored training approach reduced time spent with the EMR and increased confidence.

Materials And Methods: Two hours of training were conducted in a one-on-one manner with a trainer. Content was individualized according to the following: provider survey, EMR utilization profile, and shadowing in clinic. Surveys assessed confidence before training and immediately after training. Changes in time spent in various EMR activities before training and after training were compared.

Results: Three trainers delivered one-on-one training to 133 MDs, 42 NPs, and 10 PAs who specialized in medical oncology. Participants reported an increase in confidence across all activities, and almost all providers (98%) who responded to our survey agreed that the training enhanced their efficiency. A non-statistically significant trend toward reduction in the overall time in the system was observed. Time in system was reduced primarily in activities such as documentation and ordering of laboratory tests, imaging, medications, and chemotherapy.

Conclusion: A personalized and data-driven training approach was highly regarded by providers. EMR usage reports provided extensive data to identify and prioritize training content and were valuable to measure the impact of training on provider time in system. With the growth of EMR implementation and the reported relationship of EMR use to burnout, continuous and personalized training after EMR implementation is effective to reduce the time in system and increase confidence.
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http://dx.doi.org/10.1200/JOP.18.00093DOI Listing
July 2018