Altered RECQ Helicase Expression in Sporadic Primary Colorectal Cancers

AbstractDeregulation of DNA repair enzymes occurs in cancers and may create a susceptibility to chemotherapy. Expression levels of DNA repair enzymes have been shown to predict the responsiveness of cancers to certain chemotherapeutic agents. The RECQ helicases repair damaged DNA including damage caused by topoisomerase I inhibitors, such as irinotecan. Altered expression levels of these enzymes in colorectal cancer (CRC) may influence the response of the cancers to irinotecan. Thus, we assessed RECQ helicase (WRN, BLM, RECQL, RECQL4, and RECQL5) expression in primary CRCs, matched normal colon, and CRC cell lines. We found that BLM and RECQL4 mRNA levels are significantly increased in CRC (P = .0011 and P < .0001, respectively), whereas RECQL and RECQL5 are significantly decreased (P = .0103 and P = .0029, respectively). RECQ helicase expression patterns varied between specific molecular subtypes of CRCs. The mRNA and protein expression of the majority of the RECQ helicases was closely correlated, suggesting that altered mRNA expression is the predominant mechanism for deregulated RECQ helicase expression. Immunohistochemistry localized the RECQ helicases to the nucleus. RECQ helicase expression is altered in CRC, suggesting that RECQ helicase expression has potential to identify CRCs that are susceptible to specific chemotherapeutic agents

CoreView: Fresh Tissue Biopsy Assessment at the Bedside Using a Millifluidic Imaging Chip

Minimally invasive core needle biopsies for medical diagnoses have become increasingly common for many diseases. Although tissue cores can yield more diagnostic information than fine needle biopsies and cytologic evaluation, there is no rapid evaluation at the point-of-care for intact tissue cores that is low-cost and non-destructive to the biopsy. We have developed a proof-of-concept 3D printed millifluidic histopathology lab-on-a-chip device to automatically handle, process, and image fresh core needle biopsies. This device, named CoreView, includes modules for biopsy removal from the acquisition tool, transport, staining and rinsing, imaging, segmentation, and multiplexed storage. Reliable removal from side-cutting needles and bidirectional fluid transport of core needle biopsies from five tissue types has been demonstrated with 0.5-mm positioning accuracy. Automation is aided by a MATLAB-based biopsy tracking algorithm that can detect the location of tissue and air bubbles in the channels of the millifluidic chip. With current and emerging optical imaging technologies, CoreView can be used for a rapid adequacy test at the point-of-care for tissue identification and glomeruli counting from renal core needle biopsies, and has the potential to be used for breast cancer diagnosis, phenotyping, and mapping of enriched tumorous regions for downstream analyses in global health applications.<br /

NDER: A novel web application using annotated whole slide images for rapid improvements in human pattern recognition

Context: Whole-slide images (WSIs) present a rich source of information for education, training, and quality assurance. However, they are often used in a fashion similar to glass slides rather than in novel ways that leverage the advantages of WSI. We have created a pipeline to transform annotated WSI into pattern recognition training, and quality assurance web application called novel diagnostic electronic resource (NDER). Aims: Create an efficient workflow for extracting annotated WSI for use by NDER, an attractive web application that provides high-throughput training. Materials and Methods: WSI were annotated by a resident and classified into five categories. Two methods of extracting images and creating image databases were compared. Extraction Method 1: Manual extraction of still images and validation of each image by four breast pathologists. Extraction Method 2: Validation of annotated regions on the WSI by a single experienced breast pathologist and automated extraction of still images tagged by diagnosis. The extracted still images were used by NDER. NDER briefly displays an image, requires users to classify the image after time has expired, then gives users immediate feedback. Results: The NDER workflow is efficient: annotation of a WSI requires 5 min and validation by an expert pathologist requires An additional one to 2 min. The pipeline is highly automated, with only annotation and validation requiring human input. NDER effectively displays hundreds of high-quality, high-resolution images and provides immediate feedback to users during a 30 min session. Conclusions: NDER efficiently uses annotated WSI to rapidly increase pattern recognition and evaluate for diagnostic proficiency

Increased expression of HDJ-2 (hsp40) in carotid artery atherosclerosis: A novel heat shock protein associated with luminal stenosis and plaque ulceration

AbstractPurpose: Evidence suggests that both humoral and cellular autoimmune processes directed toward heat shock proteins (hsp) contribute to the pathogenesis of atherosclerosis. We characterized a human hsp distinct from those previously characterized in atherosclerotic lesions, termed HDJ-2. Methods: To determine the role of HDJ-2 in atherosclerosis, we compared the level of HDJ-2 mRNA expression with the level of hsp60 and hsp70 mRNA expression in 26 carotid endarterectomy specimens and 17 normal arteries. The level of expression of HDJ-2 mRNA was also correlated to the presence of plaque ulceration and the degree of luminal stenosis associated with the lesion. Results: The expression of HDJ-2 and hsp70 was significantly higher in carotid artery plaques as compared with normal arteries: HDJ-2, 6.7 ± 1.6 vs 0.1 ± 0.04, (P =.001); hsp70, 9.5 ± 0.9 vs 3.7 ± 0.8, (P =.002). There was no significant difference in hsp60 expression between carotid artery plaques and normal arteries (21.0 ± 0.9 vs 20.6 ± 0.8, P =.65). Increased HDJ-2 expression in carotid artery plaques was independent of hsp70 (Pearson correlation, r = 0.11; Bartlett χ2 analysis, P =.71). Within the ulcerated plaque group, there was a correlation between degree of stenosis and high HDJ-2 mRNA expression (r = 0.896, P =.016). However, there was no correlation between degree of stenosis and high HDJ-2 mRNA expression within the nonulcerated plaque group (r = 0.530, P =.076) or within the entire group of patients (r = 0.0085, P =.97). Conclusion: These results demonstrate that expression of HDJ-2 is significantly increased in atherosclerotic carotid artery plaques as compared with hsp60 and hsp70 and correlates with luminal stenosis in ulcerated atherosclerotic carotid artery plaques. (J Vasc Surg 2001;33:1065-71.

Effects of Practicing With and Obtaining Crowdsourced Feedback From the Video-Based Communication Assessment App on Resident Physicians’ Adverse Event Communication Skills: Pre-post Trial

BackgroundUS residents require practice and feedback to meet Accreditation Council for Graduate Medical Education mandates and patient expectations for effective communication after harmful errors. Current instructional approaches rely heavily on lectures, rarely provide individualized feedback to residents about communication skills, and may not assure that residents acquire the skills desired by patients. The Video-based Communication Assessment (VCA) app is a novel tool for simulating communication scenarios for practice and obtaining crowdsourced assessments and feedback on physicians’ communication skills. We previously established that crowdsourced laypeople can reliably assess residents’ error disclosure skills with the VCA app. However, its efficacy for error disclosure training has not been tested. ObjectiveWe aimed to evaluate the efficacy of using VCA practice and feedback as a stand-alone intervention for the development of residents’ error disclosure skills. MethodsWe conducted a pre-post study in 2020 with pathology, obstetrics and gynecology, and internal medicine residents at an academic medical center in the United States. At baseline, residents each completed 2 specialty-specific VCA cases depicting medical errors. Audio responses were rated by at least 8 crowdsourced laypeople using 6 items on a 5-point scale. At 4 weeks, residents received numerical and written feedback derived from layperson ratings and then completed 2 additional cases. Residents were randomly assigned cases at baseline and after feedback assessments to avoid ordinal effects. Ratings were aggregated to create overall assessment scores for each resident at baseline and after feedback. Residents completed a survey of demographic characteristics. We used a 2×3 split-plot ANOVA to test the effects of time (pre-post) and specialty on communication ratings. ResultsIn total, 48 residents completed 2 cases at time 1, received a feedback report at 4 weeks, and completed 2 more cases. The mean ratings of residents’ communication were higher at time 2 versus time 1 (3.75 vs 3.53; P<.001). Residents with prior error disclosure experience performed better at time 1 compared to those without such experience (ratings: mean 3.63 vs mean 3.46; P=.02). No differences in communication ratings based on specialty or years in training were detected. Residents’ communication was rated higher for angry cases versus sad cases (mean 3.69 vs mean 3.58; P=.01). Less than half of all residents (27/62, 44%) reported prior experience with disclosing medical harm to patients; experience differed significantly among specialties (P<.001) and was lowest for pathology (1/17, 6%). ConclusionsResidents at all training levels can potentially improve error disclosure skills with VCA practice and feedback. Error disclosure curricula should prepare residents for responding to various patient affects. Simulated error disclosure may particularly benefit trainees in diagnostic specialties, such as pathology, with infrequent real-life error disclosure practice opportunities. Future research should examine the effectiveness, feasibility, and acceptability of VCA within a longitudinal error disclosure curriculum

Video-Based Communication Assessment of Physician Error Disclosure Skills by Crowdsourced Laypeople and Patient Advocates Who Experienced Medical Harm: Reliability Assessment With Generalizability Theory

BackgroundResidents may benefit from simulated practice with personalized feedback to prepare for high-stakes disclosure conversations with patients after harmful errors and to meet American Council on Graduate Medical Education mandates. Ideally, feedback would come from patients who have experienced communication after medical harm, but medical researchers and leaders have found it difficult to reach this community, which has made this approach impractical at scale. The Video-Based Communication Assessment app is designed to engage crowdsourced laypeople to rate physician communication skills but has not been evaluated for use with medical harm scenarios. ObjectiveWe aimed to compare the reliability of 2 assessment groups (crowdsourced laypeople and patient advocates) in rating physician error disclosure communication skills using the Video-Based Communication Assessment app. MethodsInternal medicine residents used the Video-Based Communication Assessment app; the case, which consisted of 3 sequential vignettes, depicted a delayed diagnosis of breast cancer. Panels of patient advocates who have experienced harmful medical error, either personally or through a family member, and crowdsourced laypeople used a 5-point scale to rate the residents’ error disclosure communication skills (6 items) based on audiorecorded responses. Ratings were aggregated across items and vignettes to create a numerical communication score for each physician. We used analysis of variance, to compare stringency, and Pearson correlation between patient advocates and laypeople, to identify whether rank order would be preserved between groups. We used generalizability theory to examine the difference in assessment reliability between patient advocates and laypeople. ResultsInternal medicine residents (n=20) used the Video-Based Communication Assessment app. All patient advocates (n=8) and 42 of 59 crowdsourced laypeople who had been recruited provided complete, high-quality ratings. Patient advocates rated communication more stringently than crowdsourced laypeople (patient advocates: mean 3.19, SD 0.55; laypeople: mean 3.55, SD 0.40; P<.001), but patient advocates’ and crowdsourced laypeople’s ratings of physicians were highly correlated (r=0.82, P<.001). Reliability for 8 raters and 6 vignettes was acceptable (patient advocates: G coefficient 0.82; crowdsourced laypeople: G coefficient 0.65). Decision studies estimated that 12 crowdsourced layperson raters and 9 vignettes would yield an acceptable G coefficient of 0.75. ConclusionsCrowdsourced laypeople may represent a sustainable source of reliable assessments of physician error disclosure skills. For a simulated case involving delayed diagnosis of breast cancer, laypeople correctly identified high and low performers. However, at least 12 raters and 9 vignettes are required to ensure adequate reliability and future studies are warranted. Crowdsourced laypeople rate less stringently than raters who have experienced harm. Future research should examine the value of the Video-Based Communication Assessment app for formative assessment, summative assessment, and just-in-time coaching of error disclosure communication skills

Biome representational in silico karyotyping

Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping—biome representational in silico karyotyping (BRISK)—as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery