Background
Tumor mutational burden (TMB) measured via next‐generation sequencing (NGS)‐based gene panel is a promising biomarker for response to immune checkpoint inhibitors (ICIs) in solid tumors. ...However, little is known about the preanalytical factors that can affect the TMB score.
Materials and Methods
Data of 199 patients with solid tumors who underwent multiplex NGS gene panel (OncoPrime), which was commercially provided by a Clinical Laboratory Improvement Amendments‐licensed laboratory and covered 0.78 megabase (Mb) of capture size relevant to the TMB calculation, were reviewed. Associations between the TMB score and preanalytical factors, including sample DNA quality, sample type, sampling site, and storage period, were analyzed. Clinical outcomes of patients with a high TMB score (≥10 mutations per megabase) who received anti‐programmed cell death protein 1 antibodies (n = 22) were also analyzed.
Results
Low DNA library concentration (<5 nM), formalin‐fixed paraffin‐embedded tissue (FFPE), and the prolonged sample storage period (range, 0.9–58.1 months) correlated with a higher TMB score. After excluding low DNA library samples from the analysis, FFPE samples, but not the sample storage period, exhibited a marked correlation with a high TMB score. Of 22 patients with a high TMB score, we observed the partial response in 2 patients (9.1%).
Conclusion
Our results indicate that the TMB score estimated via NGS‐based gene panel could be affected by the DNA library concentration and sample type. These factors could potentially increase the false‐positive and/or artifactual variant calls. As each gene panel has its own pipeline for variant calling, it is unknown whether these factors have a significant effect in other platforms.
Implications for Practice
A high tumor mutational burden score, as estimated via next‐generation sequencing‐based gene panel testing, should be carefully interpreted as it could be affected by the DNA library concentration and sample type.
Little is known about the preanalytical factors that could affect the tumor mutational burden score from next‐generation sequencing‐based multiplex gene panels, a promising biomarker to predict response to immune checkpoint inhibitors. This article investigates the association.
Fibrates have renal toxicity limiting their use in subjects with chronic kidney disease (CKD). However, pemafibrate has fewer toxic effects on renal function. In the present analysis, we evaluated ...the effects of pemafibrate on the renal function of diabetic subjects with or without CKD in a real-world clinical setting.
We performed a sub-analysis of data collected during a multi-center, prospective, observational study of the effects of pemafibrate on lipid metabolism in subjects with type 2 diabetes mellitus complicated by hypertriglyceridemia (the PARM-T2D study). The participants were allocated to add pemafibrate to their existing regimen (ADD-ON), switch from their existing fibrate to pemafibrate (SWITCH), or continue conventional therapy (CTRL). The changes in estimated glomerular filtration rate (eGFR) over 52 weeks were compared among these groups as well as among subgroups created according to CKD status.
Data for 520 participants (ADD-ON, n=166; SWITCH, n=96; CTRL, n=258) were analyzed. Of them, 56.7% had CKD. The eGFR increased only in the SWITCH group, and this trend was also present in the CKD subgroup (P<0.001). On the other hand, eGFR was not affected by switching in participants with severe renal dysfunction (G3b or G4) and/or macroalbuminuria. Multivariate analysis showed that being older and a switch from fenofibrate were associated with elevation in eGFR (both P<0.05).
A switch to pemafibrate may be associated with an elevation in eGFR, but to a lesser extent in patients with poor renal function.
•We generated CDA patient-derived iPSCs carrying the KLF1 E325K mutation (CDA-iPSCs).•We developed an inducible expression system of KLF1 E325K using CDA-iPSCs.•We found that KLF1 E325K induced G1 ...cell cycle arrest at the CD71+/CD235a+ stage.
Krüppel-like factor 1 (KLF1), a transcription factor controlling definitive erythropoiesis, is involved in sequential control of terminal cell division and enucleation via fine regulation of key cell cycle regulator gene expression in erythroid lineage cells. Type IV congenital dyserythropoietic anemia (CDA) is caused by a monoallelic mutation at the second zinc finger of KLF1 (c.973G>A, p.E325K). We recently diagnosed a female patient with type IV CDA with the identical missense mutation. To understand the mechanism underlying the dyserythropoiesis caused by the mutation, we generated induced pluripotent stem cells (iPSCs) from the CDA patient (CDA-iPSCs). The erythroid cells that differentiated from CDA-iPSCs (CDA-erythroid cells) displayed multinucleated morphology, absence of CD44, and dysregulation of the KLF1 target gene expression. In addition, uptake of bromodeoxyuridine by CDA-erythroid cells was significantly decreased at the CD235a+/CD71+ stage, and microarray analysis revealed that cell cycle regulator genes were dysregulated, with increased expression of negative regulators such as CDKN2C and CDKN2A. Furthermore, inducible expression of the KLF1 E325K, but not the wild-type KLF1, caused a cell cycle arrest at the G1 phase in CDA-erythroid cells. Microarray analysis of CDA-erythroid cells and real-time polymerase chain reaction analysis of the KLF1 E325K inducible expression system also revealed altered expression of several KLF1 target genes including erythrocyte membrane protein band 4.1 (EPB41), EPB42, glutathione disulfide reductase (GSR), glucose phosphate isomerase (GPI), and ATPase phospholipid transporting 8A1 (ATP8A1). Our data indicate that the E325K mutation in KLF1 is associated with disruption of transcriptional control of cell cycle regulators in association with erythroid membrane or enzyme abnormalities, leading to dyserythropoiesis.
Objectives This study sought to determine whether whole-heart coronary magnetic resonance angiography (CMRA) can predict cardiac events in patients with suspected coronary artery disease. Background ...Recent studies demonstrated that the presence of stenosis on coronary computed tomography angiography has a significant prognostic impact on the prediction of cardiac events. However, the prognostic value of whole-heart CMRA is unknown. Methods We studied 207 patients with suspected coronary artery disease who underwent non-contrast-enhanced free-breathing whole-heart CMRA acquired with a 1.5-T MR system and 32-channel cardiac coils. The presence of significant coronary stenosis (≥50% diameter reduction) was visually determined on sliding thin- maximum intensity projection images. Follow-up information was obtained for occurrence of severe cardiac events (cardiac death, myocardial infarction, and unstable angina) and all cardiac events (additionally including revascularization>90 days after CMRA). Results During a median follow-up of 25 months, 10 cardiac events, of which 5 were severe, were observed in 84 patients with significant stenosis. Whereas, in 123 patients without significant stenosis, only 1 cardiac event with no severe event was observed. Kaplan-Meier curves demonstrated a significant difference in event-free survival between the 2 groups for severe events (annual event rate, 3.9% and 0%, respectively; log-rank test, p = 0.003), as well as for all cardiac events (6.3% and 0.3%; p < 0.001). Cox regression analysis showed that presence of significant stenosis on CMRA was associated with a >20-fold hazard increase for all cardiac events (hazard ratio: 20.78; 95% confidence interval: 2.65 to 162.70; p = 0.001). Conclusions Whole-heart CMRA is useful for predicting the future risk for cardiac events in patients with suspected coronary artery disease.
IntroductionIncretin-based therapies exert antihyperglycaemic effects in patients with type 2 diabetes (T2D) in a blood glucose concentration-dependent fashion. The first-in-class oral glucagon-like ...peptide-1 receptor agonist semaglutide has potent effects on glycaemic and weight control, but little evidence has been published for the superiority of semaglutide for glycaemic control in patients after switching from a dipeptidyl peptidase-4 (DPP-4) inhibitor. Therefore, we aim to verify the efficacy of oral semaglutide in patients with T2D being treated with a DPP-4 inhibitor.Methods and analysisThis study is a multicentre, prospective, randomised, open-label, parallel-group trial. In total, 172 participants with T2D who have been treated with a DPP-4 inhibitor for more than 12 weeks and who have a glycated haemoglobin (HbA1c) level of 7.0%–9.9% will be randomised to continue using their existing DPP-4 inhibitor or switch to oral semaglutide for 24 weeks. Biochemical analyses and physical assessment will be performed, and adverse events will be recorded at baseline and at the end of the study. The primary endpoint will be the effect of oral semaglutide on the change in HbA1c. The secondary endpoints will be the mean changes in body weight, abdominal circumference, systolic and diastolic blood pressure (BP), pulse rate, the relationship between improvement of metabolic parameters including HbA1c and patient background characteristics, side effects and other laboratory parameters.Ethics and disseminationThis will be the first study to compare the effects of switching from a DPP-4 inhibitor to oral semaglutide on glycaemic control in patients with T2D. The results will be disseminated in peer-reviewed journals and at scientific conferences. Hokkaido University Certified Review Board (CRB no.1180001) has approved the protocol (no. 020–013).Trial registration numberUMIN000045270 in the University Hospital Medical Information Network; jRCT1011210032 in the Japan Registry of Clinical Trials.
Recently developed transcription activator-like effector nuclease (TALEN) technology has enabled the creation of knockout mice, even for genes on the Y chromosome. In this study, we generated a ...knockout mouse for Sry, a sex-determining gene on the Y chromosome, using microinjection of TALEN RNA into pronuclear stage oocytes. As expected, the knockout mouse had female external and internal genitalia, a female level of blood testosterone and a female sexually dimorphic nucleus in the brain. The knockout mouse exhibited an estrous cycle and performed copulatory behavior as females, although it was infertile or had reduced fertility. A histological analysis showed that the ovary of the knockout mouse displayed a reduced number of oocytes and luteinized unruptured follicles, implying that a reduced number of ovulated oocytes is a possible reason for infertility and/or reduced fertility in the KO mouse.
Background and Objectives: Extracellular water is increased in patients with edema, such as those with chronic heart failure, and it is difficult to assess skeletal muscle mass with the skeletal ...muscle mass index when extracellular water is high. We investigated the relationship between phase angle and physical function, nutritional indices, and sarcopenia in patients with cardiovascular diseases, including chronic heart failure. Methods and Study Design: In 590 patients with cardiovascular diseases (372 men), handgrip strength, gait speed, and anterior midthigh muscle thickness by ultrasound were measured, and the skeletal muscle mass index, phase angle, and the extracellular water: total body water ratio were measured with a bioelectrical impedance analyzer, and presence of sarcopenia was evaluated. Results: Phase angle, but not the skeletal muscle mass index, was correlated with serum albumin (r = 0.377, p < 0.001) and hemoglobin values in women. Multivariate regression analysis showed that at the extracellular water: total body water ratio below 0.4, both phase angle and skeletal muscle mass index were independent determinants of handgrip strength and log mid-thigh muscle thickness in men, after adjustment for age and presence of chronic heart failure. In contrast, for the ratio of 0.4 or greater, after adjustment for age and presence of chronic heart failure, phase angle was a stronger independent determinant of handgrip strength and log mid-thigh muscle thickness than the skeletal muscle mass index in men. Conclusions: Phase angle is a good marker of muscle wasting and malnutrition in patients with cardiovascular disease, including chronic heart failure.
GDF1 (growth/differentiation factor 1), a Vg1-related member of the transforming growth factor-beta superfamily, is required for left-right patterning in the mouse, but the precise function of GDF1 ...has remained largely unknown. In contrast to previous observations, we now show that GDF1 itself is not an effective ligand but rather functions as a coligand for Nodal. GDF1 directly interacts with Nodal and thereby greatly increases its specific activity. Gdf1 expression in the node was found necessary and sufficient for initiation of asymmetric Nodal expression in the lateral plate of mouse embryos. Coexpression of GDF1 with Nodal in frog embryos increased the range of the Nodal signal. Introduction of Nodal alone into the lateral plate of Gdf1 knockout mouse embryos did not induce Lefty1 expression at the midline, whereas introduction of both Nodal and GDF1 did, showing that GDF1 is required for long-range Nodal signaling from the lateral plate to the midline. These results suggest that GDF1 regulates the activity and signaling range of Nodal through direct interaction.
Tachyarrhythmias, such as ventricular fibrillation and atrial fibrillation, are caused by abnormal and complex electrical excitation waves in the heart. Ventricular fibrillation is a fatal condition ...that can lead to sudden cardiac death, and atrial fibrillation increases the risk of stroke due to thrombosis. Today, ablation therapy is widely used to treat fibrillation by ablating the abnormally excited area. However, although various ablation strategies have been proposed, the optimal ablation strategy has not been established. To establish an objective and effective fibrillation ablation strategy, we attempted to construct a machine learning model that selects the optimal ablation target based on the excitation pattern during fibrillation. We report the results of training a deep neural network model that selects the best ablation target based on the time series of the membrane potential distribution, which represents the excitation state of each cell, using a two-dimensional electrophysiological simulation model.
Ventricular fibrillation (VF) causes failure of synchronous contraction of the heart ventricles, resulting in cardiac collapse. Currently, VF is still the major cause of sudden cardiac death, and ...strategies such as prevention, prediction, and immediate termination are not yet established. This article reviews the progress of research on VF mechanism and proposes a future direction to elucidate it. Historical hypotheses proposed for VF mechanism were wandering wavelets, mother rotors, and multiple foci. Current concept is a combination of these hypotheses, but remains to be explicated. Rotor, a spiral shape of the excitation wavefront, plays a major role in VF. The mother rotor eventually breaks up and creates multiple unstable rotors by pathological and electrophysiological abnormalities, terminating as irreversible VF. The dynamics of rotors are influenced by many factors such as ion channel modification, alternance of intracellular calcium, and restitution characteristics of the repolarization duration. The break-up of a rotor is created by head–tail interaction of the rotor, or the area of the ischemic tissue zone. The advance of computer approach has realized simulation of the complex heart model, which provides deep insight into electrophysiological background of VF in three dimensional settings. Also, many mapping techniques including not only activation and repolarization mapping, but also phase variance analysis help understanding the rotor/filament mechanism during VF. Topological analysis and chaotic approach have been developed to evaluate the mechanism of VF, but it is still impossible to control the chaotic behavior of VF. Many cardiac and non-cardiac factors induce or reduce the VF characteristics. Cardiac factors include Purkinje fiber, intracellular calcium dynamics, ion channels, and gap junction. Interventions of these parameters have the potential to prevent or induce VF. Optimal control of cardiac factor(s) may be used as VF control therapy, but a clinically useful method is yet to be developed. Non-cardiac factors influencing VF include hypokalemia, hypothermia, heart failure, cardiac ischemia, and autonomic nerve. The detailed mechanisms of VF modification for each factor have been clarified; however, no universal mechanism related to VF is established. The mechanism of VF remains to be determined in order to accomplish VF therapy.
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