To validate and demonstrate the clinical discovery utility of a novel patient-mediated, medical record collection and data extraction platform developed to improve access and utilization of ...real-world clinical data.
Clinical variables were extracted from the medical records of 1011 consented patients with breast cancer. To validate the extracted data, case report forms completed using the structured data output of the platform were compared to manual chart review for 50 randomly-selected patients with metastatic breast cancer. To demonstrate the platform's clinical discovery utility, we identified 194 patients with early-stage clinical data who went on to develop distant metastases and utilized the platform-extracted data to assess associations between time to distant metastasis (TDM) and early-stage tumor histology, molecular type, and germline
status.
The platform-extracted data for the validation cohort had 97.6% precision (91.98%-100% by variable type) and 81.48% recall (58.15%-95.00% by variable type) compared to manual chart review. In our discovery cohort, the shortest TDM was significantly associated with metaplastic (739.0 days) and inflammatory histologies (1005.8 days), HR-/HER2- molecular types (1187.4 days), and positive
status (1042.5 days) as compared to other histologies, molecular types, and negative
status, respectively. Multivariable analyses did not produce statistically significant results.
The precision and recall of platform-extracted clinical data are reported, although specificity could not be assessed. The data can generate clinically-relevant insights.
The structured real-world data produced by a novel patient-mediated, medical record-extraction platform are reliable and can power clinical discovery.
Williams-Beuren Syndrome (WBS) is caused by the microdeletion of approximately 25 genes on chromosome 7q11.23, and is characterized by a spectrum of cognitive and behavioural features.
We generated ...cortical neurons from a WBS individual and unaffected (WT) control by directed differentiation of induced pluripotent stem cells (iPSCs). Single cell mRNA analyses and immunostaining demonstrated very efficient production of differentiated cells expressing markers of mature neurons of mixed subtypes and from multiple cortical layers. We found that there was a profound alteration in action potentials, with significantly prolonged WBS repolarization times and a WBS deficit in voltage-activated K(+) currents. Miniature excitatory synaptic currents were normal, indicating that unitary excitatory synaptic transmission was not altered. Gene expression profiling identified 136 negatively enriched gene sets in WBS compared to WT neurons including gene sets involved in neurotransmitter receptor activity, synaptic assembly, and potassium channel complexes.
Our findings provide insight into gene dysregulation and electrophysiological defects in WBS patient neurons.
PurposeAs part of the Epilepsy Genetics Initiative, we re-evaluated clinically generated exome sequence data from 54 epilepsy patients and their unaffected parents to identify molecular diagnoses not ...provided in the initial diagnostic interpretation.MethodsWe compiled and analyzed exome sequence data from 54 genetically undiagnosed trios using a validated analysis pipeline. We evaluated the significance of the genetic findings by reanalyzing sequence data generated at Ambry Genetics, and from a number of additional case and control cohorts.ResultsIn 54 previously undiagnosed trios, we identified two de novo missense variants in SCN8A in the highly expressed alternative exon 5 A-an exon only recently added to the Consensus Coding Sequence database. One additional undiagnosed epilepsy patient harboring a de novo variant in exon 5 A was found in the Ambry Genetics cohort. Missense variants in SCN8A exon 5 A are extremely rare in the population, further supporting the pathogenicity of the de novo alterations identified.ConclusionThese results expand the range of SCN8A variants in epileptic encephalopathy patients and illustrate the necessity of ongoing reanalysis of negative exome sequences, as advances in the knowledge of disease genes and their annotations will permit new diagnoses to be made.
SYNGAP1 encodes a brain-specific Ras GTPase activating protein (GAP) that regulates synaptic strength in glutamatergic neurons. Pathogenic variants in this gene are associated with a ...neurodevelopmental disorder characterized by intellectual and developmental disabilities, generalized epilepsy, hypotonia, and autism spectrum disorders. We describe a young male with suspected SYNGAP1-related disorder given clinical overlap and identification of an intronic variant of uncertain significance; clinical transcriptome analysis demonstrated activation of a cryptic acceptor splice site resulting in frameshift and introduction of a stop codon. This report highlights the utility of functional studies newly available to clinical practice in confirming a suspected genetic diagnosis, which can directly impact medical management and preclude the need for additional diagnostic testing.
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It has been demonstrated that many nephrotoxic drugs, such as tunicamycin, induce endoplasmic reticulum (ER) stress as part of the mechanism by which they cause acute kidney injury ...(AKI). There are three main mechanisms by which the low molecular weight chemical chaperone 4‐phenylbutyrate (4‐PBA) can modify AKI: (1) as a histone deacetylase inhibitor, (2) as an ER stress inhibitor, and (3) as a mediator of waste nitrogen excretion. We hypothesized that 4‐PBA would inhibit tunicamycin‐induced acute kidney injury using one of these three mechanisms. C57BL/6J mice were either untreated or pre‐treated with 4‐PBA for one week, at a dose of 1 g/kg, delivered in the drinking water. Proximal tubular cell injury was then induced by intraperitoneal injection of tunicamycin (0.5 mg/kg) for 3 days. In the whole animal, tunicamycin was found to induce proximal tubule injury in the juxtamedullary region, demonstrated by the presence of tubular epithelial cell vacuolization, in PAS‐stained sections. 4‐PBA pretreatment reduced the injury score associated with tunicamycin‐induced AKI. The mechanism by which 4‐PBA prevents tunicamycin‐induced kidney injury is currently under investigation. Supported by CIHR OSO‐115895.
We have shown that thapsigargin (Tg), an endoplasmic reticulum (ER) stress inducer and activator of the unfolded protein response (UPR), causes epithelial‐to‐mesenchymal transition (EMT), the process ...by which epithelial cells transform to myofibroblasts. Myofibroblasts contribute to renal fibrosis and the progression of chronic kidney disease through their accumulative production of extracellular matrix. We hypothesize that EMT can be repressed through the use of low molecular weight chemical chaperones, such as 4‐Phenylbutyrate (4‐PBA) and tauroursodeoxycholic acid (TUDCA), in human renal proximal tubular epithelial cells (hRPTECs). 4‐PBA and TUDCA were found to inhibit hRPTEC death from Tg and TGFβ1 treatments as determined by LDH and TUNEL assays. Immunofluorescent labeling of myofibroblast markers showed that both 4‐PBA and TUDCA inhibited F‐actin cytoskeletal rearrangements and repressed β‐Catenin nuclear translocation in TGFβ1‐induced EMT. 4‐PBA inhibited the expression of ER stress marker GRP94 and myofibroblast marker α‐smooth muscle actin. TUDCA inhibited the expression of ER stress marker GRP78 and the focal adhesion complex component vinculin. Both 4‐PBA and TUDCA demonstrated partial inhibitory activity against Tg‐ and TGFβ1‐induced EMT in HK‐2 cells. 4‐PBA was found to inhibit TGFβ1‐induced EMT in primary hRPTECs. Funding was provided by St. Joseph's Healthcare Hamilton
Epithelial to mesenchymal transition (EMT) is a process through which endoplasmic reticulum (ER) stress may mediate the progression of chronic kidney disease. Thapsigargin (Tg) induced ER stress ...produced an EMT response in two human renal proximal tubular epithelial cell (hRPTEC) lines, HK‐2 and primary hRPTEC. We hypothesized that changes in cell shape induced by Tg were mediated by TDAG51 upregulation, resulting in an EMT response through β‐catenin signaling. Tg caused shape change as shown by F‐actin cytoskeletal rearrangement. This was accompanied by ER stress induction, TDAG51 upregulation and β‐catenin cytoplasmic and nuclear translocation. Transfection of TDAG51‐GFP plasmid into HK‐2 cells caused shape change and cytoskeletal rearrangement compared to eGFP controls. Scratch assays showed β‐catenin signaling augmented EMT induced by TGFβ1. Cells on the scratch edge showed greater β‐catenin signaling with vehicle and TGFβ1 treatment and also displayed greater EMT marker α‐smooth muscle actin (SMA) expression. However, Tg disrupted the monolayer and caused β‐catenin signaling accompanied by α‐SMA expression both at the scratch edge and in the monolayer. In conclusion, it appears that Tg induces hRPTEC EMT via β‐catenin signaling. TDAG51 induction via Tg treatment may mediate this effect. Supported by CIHR MOP‐67116 and St. Joseph's Healthcare Hamilton.
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