Citations

Abstract Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methods allow us to carry out multiomics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, next‐generation sequencing and high‐resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs is employed. Analysis of 145 million paired‐end reads from next‐generation sequencing confirmed expression of 12 186 protein‐coding genes (FPKM ≥0.1), 439 novel long non‐coding RNAs, and revealed 6089 novel isoforms that were not annotated in GENCODE. Proteomics analysis identifies 6477 proteins including confirmation of N ‐termini for 1091 proteins, isoforms for 149 proteins, and 1034 phosphosites. A database search to specifically identify other post‐translational modifications provide evidence for a number of modification sites on 117 proteins which include ubiquitylation, lysine acetylation, and mono‐, di‐ and tri‐methylation events. Evidence for 11 “missing proteins,” which are proteins for which there was insufficient or no protein level evidence, is provided. Peptides supporting missing protein and novel events are validated by comparison of MS/MS fragmentation patterns with synthetic peptides. Finally, 245 variant peptides derived from 207 expressed proteins in addition to alternate translational start sites for seven proteins and evidence for novel proteoforms for five proteins resulting from alternative splicing are identified. Overall, it is believed that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.

OBJECTIVE To determine whether burden of multiple chronic conditions (MCCs) influences the risk of receiving inappropriate vs appropriate device therapies. DESIGN Retrospective cohort study. SETTING Seven US healthcare delivery systems. PARTICIPANTS Adults with left ventricular systolic dysfunction receiving an implantable cardioverter‐defibrillator (ICD) for primary prevention. MEASUREMENTS Data on 24 comorbid conditions were captured from electronic health records and categorized into quartiles of comorbidity burden (0‐3, 4‐5, 6‐7 and 8‐16). Incidence of ICD therapies (shock and antitachycardia pacing [ATP] therapies), including appropriateness, was collected for 3 years after implantation. Outcomes included time to first ICD therapy, total ICD therapy burden, and risk of inappropriate vs appropriate ICD therapy. RESULTS Among 2235 patients (mean age = 69 ± 11 years, 75% men), the median number of comorbidities was 6 (interquartile range = 4‐8), with 98% having at least two comorbidities. During a mean 2.2 years of follow‐up, 18.3% of patients experienced at least one appropriate therapy and 9.9% experienced at least one inappropriate therapy. Higher comorbidity burden was associated with an increased risk of first inappropriate therapy (adjusted hazard ratio [HR] = 1.94 [95% confidence interval {CI} = 1.14‐3.31] for 4‐5 comorbidities; HR = 2.25 [95% CI = 1.25‐4.05] for 6‐7 comorbidities; and HR = 2.91 [95% CI = 1.54‐5.50] for 8‐16 comorbidities). Participants with 8‐16 comorbidities had a higher total burden of ICD therapy (adjusted relative risk [RR] = 2.12 [95% CI = 1.43‐3.16]), a higher burden of inappropriate therapy (RR = 3.39 [95% CI = 1.67‐6.86]), and a higher risk of receiving inappropriate vs appropriate therapy (RR = 1.74 [95% CI = 1.07‐2.82]). Comorbidity burden was not significantly associated with receipt of appropriate ICD therapies. Patterns were similar when separately examining shock or ATP therapies. CONCLUSIONS In primary prevention ICD recipients, MCC burden was independently associated with an increased risk of inappropriate but not appropriate device therapies. Comorbidity burden should be considered when engaging patients in shared decision making about ICD implantation.

Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial‐to‐mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer‐compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.

The lymphocyte crossmatch is currently the only cell‐based compatibility assay performed by histocompatibility laboratories for transplant purposes. While in many transplant programs the complement‐dependent cytotoxicity crossmatch (CDCXM) remains in use, when available, the flow cytometry crossmatch (FCXM) is the method of choice because of its superior sensitivity and specificity. Unfortunately, the maintenance and cost of a flow cytometer is a considerable limitation for small histocompatibility laboratories. Therefore, in this study, we evaluated the use of the Cellometer Vision CBA image cytometer (Nexcelom Bioscience LLC, Lawrence, Massachusetts) as an alternative instrument to perform the crossmatch assay. The 3‐color FCXM protocol was modified into two separate 2‐color panel image cytometry crossmatches (IXMs), one for T cells and one for B cells. After initial serum and cell incubation, a cocktail consisting of PE/Cy5‐conjugated anti‐human CD3 or CD19 and PE‐conjugated anti‐human IgG F(ab′)2was added to the T cell and B cell panels, respectively. The final cell preparation was added to a separate counting chamber. Images were captured using the Cellometer Vision CBA, an image cytometer designed for cell counting, size analysis and fluorescence intensity measurement. Thirty‐nine IXMs were performed and compared with the FCXM. We obtained a concordance sensitivity of 94.1% and 100% and specificity of 100% and 88.9% for T cells and B cells, respectively. The linearity of the system was verified using dilutions of a sample containing known donor‐specific anti‐HLA antibodies (DSA) against the target cells. This feasibility study demonstrates that the FCXM test could be easily adapted to the Cellometer Vision CBA image cytometer without compromising specificity and sensitivity. The low instrumentation cost, minimal maintenance, and simple operation allow for efficient implementation or transition from the FCXM to the IXM method.

OBJECTIVEThe AANS launched the Quality Outcomes Database (QOD), a prospective longitudinal registry that includes demographic, clinical, and patient-reported outcome (PRO) data to measure the safety and quality of spine surgery. Registry data offer “real-world” insights into the utility of spinal fusion and decompression surgery for lumbar spondylolisthesis. Using the QOD, the authors compared the initial 12-month outcome data for patients undergoing fusion and those undergoing laminectomy alone for grade 1 degenerative lumbar spondylolisthesis.METHODSData from 12 top enrolling sites were analyzed and 426 patients undergoing elective single-level spine surgery for degenerative grade 1 lumbar spondylolisthesis were found. Baseline, 3-month, and 12-month follow-up data were collected and compared, including baseline clinical characteristics, readmission rates, reoperation rates, and PROs. The PROs included Oswestry Disability Index (ODI), back and leg pain numeric rating scale (NRS) scores, and EuroQol–5 Dimensions health survey (EQ-5D) results.RESULTSA total of 342 (80.3%) patients underwent fusion, with the remaining 84 (19.7%) undergoing decompression alone. The fusion cohort was younger (60.7 vs 69.9 years, p < 0.001), had a higher mean body mass index (31.0 vs 28.4, p < 0.001), and had a greater proportion of patients with back pain as a major component of their initial presentation (88.0% vs 60.7%, p < 0.001). There were no differences in 12-month reoperation rate (4.4% vs 6.0%, p = 0.93) and 3-month readmission rates (3.5% vs 1.2%, p = 0.45). At 12 months, both cohorts improved significantly with regard to ODI, NRS back and leg pain, and EQ-5D (p < 0.001, all comparisons). In adjusted analysis, fusion procedures were associated with superior 12-month ODI (β −4.79, 95% CI −9.28 to −0.31; p = 0.04).CONCLUSIONSSurgery for grade 1 lumbar spondylolisthesis—regardless of treatment strategy—was associated with significant improvements in disability, back and leg pain, and quality of life at 12 months. When adjusting for covariates, fusion surgery was associated with superior ODI at 12 months. Although fusion procedures were associated with a lower rate of reoperation, there was no statistically significant difference at 12 months. Further study must be undertaken to assess the durability of either surgical strategy in longer-term follow-up.