LEAP: Using machine learning to support variant classification in a clinical setting.

Advances in genome sequencing have led to a tremendous increase in the discovery of novel missense variants, but evidence for determining clinical significance can be limited or conflicting. Here, we present Learning from Evidence to Assess Pathogenicity (LEAP), a machine learning model that utilizes a variety of feature categories to classify variants, and achieves high performance in multiple genes and different health conditions. Feature categories include functional predictions, splice predictions, population frequencies, conservation scores, protein domain data, and clinical observation data such as personal and family history and covariant information. L2-regularized logistic regression and random forest classification models were trained on missense variants detected and classified during the course of routine clinical testing at Color Genomics (14,226 variants from 24 cancer-related genes and 5,398 variants from 30 cardiovascular-related genes). Using 10-fold cross-validated predictions, the logistic regression model achieved an area under the receiver operating characteristic curve (AUROC) of 97.8% (cancer) and 98.8% (cardiovascular), while the random forest model achieved 98.3% (cancer) and 98.6% (cardiovascular). We demonstrate generalizability to different genes by validating predictions on genes withheld from training (96.8% AUROC). High accuracy and broad applicability make LEAP effective in the clinical setting as a high-throughput quality control layer.

Iron administration before stem cell harvest enables MR imaging tracking after transplantation.

PURPOSE: To determine whether intravenous ferumoxytol can be used to effectively label mesenchymal stem cells (MSCs) in vivo and can be used for tracking of stem cell transplants. MATERIALS AND METHODS: This study was approved by the institutional animal care and use committee. Sprague-Dawley rats (6-8 weeks old) were injected with ferumoxytol 48 hours prior to extraction of MSCs from bone marrow. Ferumoxytol uptake by these MSCs was evaluated with fluorescence, confocal, and electron microscopy and compared with results of traditional ex vivo-labeling procedures. The in vivo-labeled cells were subsequently transplanted in osteochondral defects of 14 knees of seven athymic rats and were evaluated with magnetic resonance (MR) imaging up to 4 weeks after transplantation. T2 relaxation times of in vivo-labeled MSC transplants and unlabeled control transplants were compared by using t tests. MR data were correlated with histopathologic results. RESULTS: In vivo-labeled MSCs demonstrated significantly higher ferumoxytol uptake compared with ex vivo-labeled cells. With electron microscopy, iron oxide nanoparticles were localized in secondary lysosomes. In vivo-labeled cells demonstrated significant T2 shortening effects in vitro and in vivo when they were compared with unlabeled control cells (T2 in vivo, 15.4 vs 24.4 msec; P < .05) and could be tracked in osteochondral defects for 4 weeks. Histologic examination confirmed the presence of iron in labeled transplants and defect remodeling. CONCLUSION: Intravenous ferumoxytol can be used to effectively label MSCs in vivo and can be used for tracking of stem cell transplants with MR imaging. This method eliminates risks of contamination and biologic alteration of MSCs associated with ex vivo-labeling procedures.

Effect of muscle fatigue of the thoracic erector spinae on neuromuscular control when performing the upper extremity functional tasks in people with adolescent idiopathic scoliosis.

Adolescent idiopathic scoliosis (AIS) disrupts spinal alignment and increases the intrinsic demand for active stabilization to maintain postural stability. Understanding the paraspinal muscle fatigability and its effects on spinal alignment and kinematics informs the importance of paraspinal muscle endurance for postural stability. This study aims to investigate the effects of fatigue of thoracic erector spinae on the spinal muscle activity and spinal kinematics in individuals with scoliosis. Spinal muscle activity, posture and mobility measured by electromyography and surface tomography were compared between 15 participants with scoliosis and 15 age- and gender-matched healthy controls during unilateral shoulder flexion and abduction with and without holding a 2-kg weight and performed before and after a fatigue task (prone isometric chest raise). No between-groups difference was found for the spinal extensor endurance. Erector spinae activity at the convex side of AIS group was significantly higher than that at their concave side and than that of healthy controls during shoulder elevations, regardless of the fatigue status. Significant decreases in translational and rotational mobility were found at convex side of AIS group during weighted abduction tasks after fatigue. In contrast, a significant increase in rotational mobility was demonstrated at convex side of AIS participants during weighted flexion tasks after fatigue. Our results revealed a comparable level of spinal extensor endurance between individuals with or without AIS. The increase in muscle activation post-fatigue provides no additional active postural stability but may increase the risk of back pain over the convex side in individuals with scoliosis. Findings highlight imbalances in muscles and the potential implications in optimising neuromuscular activation and endurance capacity in the rehabilitation for AIS patients. Future research is needed to investigate if endurance training of the convex-sided back extensors could optimize the impaired neuromuscular control in the AIS patients.

Comparative Study of Plan Robustness for Breast Radiotherapy: Volumetric Modulated Arc Therapy Plans with Robust Optimization versus Manual Flash Approach.

A previous study investigated robustness of manual flash (MF) and robust optimized (RO) volumetric modulated arc therapy plans for breast radiotherapy based on five patients in 2020 and indicated that the RO was more robust than the MF, although the MF is still current standard practice. The purpose of this study was to compare their plan robustness in terms of dose variation to clinical target volume (CTV) and organs at risk (OARs) based on a larger sample size. This was a retrospective study involving 34 female patients. Their plan robustness was evaluated based on measured volume/dose difference between nominal and worst scenarios (ΔV/ΔD) for each CTV and OARs parameter, with a smaller difference representing greater robustness. Paired sample t-test was used to compare their robustness values. All parameters (except CTV ΔD98%) of the RO approach had smaller ΔV/ΔD values than those of the MF. Also, the RO approach had statistically significantly smaller ΔV/ΔD values (p < 0.001-0.012) for all CTV parameters except the CTV ΔV95% and ΔD98% and heart ΔDmean. This study's results confirm that the RO approach was more robust than the MF in general. Although both techniques were able to generate clinically acceptable plans for breast radiotherapy, the RO could potentially improve workflow efficiency due to its simpler planning process.

Synthesis and SAR studies of novel 2-(6-aminomethylaryl-2-aryl-4-oxo-quinazolin-3(4H)-yl)acetamide vasopressin V1b receptor antagonists.

Synthesis and structure-activity relationships (SAR) of a novel series of vasopressin V(1b) antagonists are described. 2-(6-Aminomethylaryl-2-aryl-4-oxo-quinazolin-3(4H)-yl)acetamide have been identified with low nanomolar affinity for the V(1b) receptor and good selectivity with respect to related receptors V(1a), V(2) and OT. Optimised compound 16 shows a good pharmacokinetic profile and activity in a mechanistic model of HPA dysfunction.

The use of the Digit Span Test in screening for cognitive impairment in acute medical inpatients.

BACKGROUND: There is no valid instrument currently in use at acute-care hospitals in Hong Kong to aid the detection of cognitive impairment. The objectives of this study were to (1) validate the Digit Span Test (DST) in the identification and differentiation of dementia and delirium; and (2) determine the prevalence of major cognitive impairment in elderly people in an acute medical unit. METHODS: During the study period from January to February 2010, 144 patients aged 75 years or more who had had unplanned medical admissions were assessed by nurses, using the Digit Span Forwards (DSF) and the Digit Span Backwards (DSB) tests. The DST scores were compared with the psychiatrists' DSM-IV-based diagnoses. Receiver Operating Characteristics curve (ROC) was used in conjunction with sensitivity and specificity measures to assess the performance of DST. RESULTS: The prevalence rates of dementia alone, delirium alone and delirium superimposed on dementia were 21.5%, 9% and 9% respectively. The prior case-note documentation rate was 13.2% for dementia and 2.8% for delirium. Regarding the detection of major cognitive impairment, the ROC curve of DSB showed a sensitivity of 0.77 and specificity of 0.78 at the optimal cutoff of <3. A significant association between scores on the DST and the Cantonese version of the Mini-Mental State Examination (CMMSE) was found in this study (p < 0.05 for DSF, p = 0.00 for DSB). CONCLUSIONS: Dementia and delirium were prevalent, yet under-recognized, in acute medical geriatric inpatients. The DSB is an effective tool in identifying patients with major cognitive impairment.

A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.

Tumor vaccines in 2010: need for integration.

Induction of tumor-specific immunity is an attractive approach to cancer therapy, however to date every major pivotal trial has resulted in failure. While the phenomena of tumor-mediated immune suppression has been known for decades, only recently have specific molecular pathways been elucidated, and for the first time, rationale means of intervening and observing results of intervention have been developed. In this review we describe major advances in our understanding of tumor escape from immunological pressure and provide some possible therapeutic scenarios for enhancement of efficacy in future cancer vaccine trials.

Enhancement of DNA cancer vaccine efficacy by combination with anti-angiogenesis in regression of established subcutaneous B16 melanoma.

Immunotherapy of cancer offers great promise, however translation into human studies has yielded relatively poor results to date. The concept of combining cancer vaccination with angiogenesis inhibition is appealing, due to favorable safety profile of both approaches, as well as possible biological synergies. Here we studied the anti-tumor effects of combining plasmid DNA (pDNA) vaccination and anti-angiogenesis in B16F10 murine model. By using electroporation-mediated gene/pDNA delivery, the anti-tumor efficacy of vaccination with pDNAs encoding gp100, TRP2 and Ii-PADRE was facilitated by administration of soluble form of EphB4 fused with human serum albumin (sEphB4-HSA), or by co-delivery of pDNAs encoding Angiostatin and/or Endostatin. In an optimized administration protocol, melanoma vaccination together with intratumoral delivery of pDNAs encoding Angiostatin and Endostatin resulted in 57% tumor-free survival over 90 days after challenge. These data support the general concept that suppression of angiogenesis may allow for enhanced efficacy of anti-tumor immunity, suggesting the synergetic effects of therapeutic pDNA vaccination and angiogenesis inhibition in cancer therapy.

Endovascular repair of traumatic mesocaval fistula.

A patient presented with a posttraumatic fistula between the superior mesenteric artery and inferior vena cava with associated pseudoaneurysm after multiple thoracoabdominal gunshot wounds. Endovascular management with placement of two overlapping stent-grafts resulted in complete resolution of the lesions with documented patency at 15 months and no known complications. This minimally invasive therapy spared the patient the morbidity of conventional open surgical repair.

High sensitivity 8-color flow cytometry assay for paroxysmal nocturnal hemoglobinuria granulocyte and monocyte detections.

Flow cytometry is the gold standard in diagnosis of paroxysmal nocturnal hemoglobinuria (PNH) by detecting the absence of glycol-phosphatidyl inositol (GPI)-linked protein expression on granulocyte and monocyte surfaces. However, the current assays are not optimized and require improvement, particularly in reducing background fluorescence and optimizing sensitivity and specificity. With more fluorochromes available and with advances in instrument engineering, rare populations may be identified with high sensitivity. The present study assessed an 8-color combination of comprehensive GPI-linked markers, namely fluorescein-labeled proaerolysin (FLAER), cluster of differentiation 157 (CD157), CD24 and CD14, and the lineage markers for granulocyte (CD15) and monocyte (CD64) cells to detect PNH clones. Additionally, to optimize the PNH flow assay, a 'dump' channel was used, comprised of CD5 and CD19, to exclude non-specific binding in order to reduce background. This method aimed to improve sensitivity and reduce the background to create an optimized PNH flow cocktail. The results demonstrated that the current 4-color PNH combination identifies a CD55- and FLAER+ population that is not PNH clones. By contrast, the 8-color panel delineated PNH clones from both monocyte and granulocytes by using granulocyte antigen (CD15) and monocyte antigen (CD64) as a gating strategy. The sensitivity was 0.01% for granulocytes and 0.05% for monocytes with an acquisition of 100,000 monocyte and granulocyte events. The background on a normal whole blood sample was 0.00076% on monocytes and 0.00277% on granulocytes. Thus, overall, the 8-color PNH assay exhibited high levels of specificity and sensitivity. The 8-color combination facilitated the improvement and enhancement of sensitivity in PNH clone identification, and may provide a useful tool for pathologists in PNH diagnosis and for monitoring patients at risk of developing classical/hemolytic PNH, to enable treatment to be delivered promptly.

Induction of cytotoxic T cell response against HCA661 positive cancer cells through activation with novel HLA-A *0201 restricted epitopes.

HCA661 is a cancer-testis (CT) antigen frequently expressed in human hepatocellular carcinoma (HCC). To search for immunogenic peptides of HCA661, bioinformatics analysis and CD8(+) T cell IFN-gamma ELISPOT assay were employed, and two HLA-A *0201 restricted peptides, H110 and H246, were identified. These two HCA661 peptides are naturally processed in dendritic cells (DCs) and when used for DCs loading, they are sufficient to prime autologous CD8(+) T cells to elicit cytotoxic response against HCA661(+) human cancer cells. The HCA661 peptides, H110 and H246, are hence attractive candidates for human cancer immunotherapy.

Stabilization of pre-optimized multicolor antibody cocktails for flow cytometry applications.

BACKGROUND: Flow cytometry has a multitude of applications in nearly all fields of biology. Newly described biological markers enable the creation of novel reagents which then aid in the elucidation of unique subsets of cells and their potential role in health and disease. In order to enable the simultaneous detection of an even greater number of parameters, the future progress of flow cytometry relies on advances in instrument engineering and the parallel development of new fluorophores. METHODS: In order to address the issues of reagent reliability, reproducibility, and work-flow optimization, we have used the freeze-dry technique to stabilize pre-mixed, pre-optimized, multicolor 'cocktails' of antibodies within 12 × 75 mm flow cytometry tubes (Lyotube). In this study we describe several lyophilized stabilized reagent combinations that are functional for extended periods of time (18 months and beyond), and can be stored at ambient temperature, eliminating cold-chain requirements during transportation and storage. This improves precision and reduces the redundant labor and error-potential associated with mixing antibodies to create "home-brew" cocktails. RESULTS: We have stained different types of samples including normal and leukemic whole blood, bone marrow, and PBMCs, as well as cell lines, directly with BD Lyotube reagents: The data show comparable and consistent performance of multiple batches of dehydrated, stabilized mixtures of antibodies and their liquid counterparts. CONCLUSIONS: The approach we describe here, the Lyotube, facilitates the improvement and implementation of standardization measures in clinical settings and in multi-site studies, a useful tool which can also be applied to determining the efficacy and safety of candidate therapeutics and vaccines. © 2016 International Clinical Cytometry Society.

Improved approach for chondrogenic differentiation of human induced pluripotent stem cells.

Human induced pluripotent stem cells (hiPSCs) have demonstrated great potential for hyaline cartilage regeneration. However, current approaches for chondrogenic differentiation of hiPSCs are complicated and inefficient primarily due to intermediate embryoid body formation, which is required to generate endodermal, ectodermal, and mesodermal cell lineages. We report a new, straightforward and highly efficient approach for chondrogenic differentiation of hiPSCs, which avoids embryoid body formation. We differentiated hiPSCs directly into mesenchymal stem /stromal cells (MSC) and chondrocytes. hiPSC-MSC-derived chondrocytes showed significantly increased Col2A1, GAG, and SOX9 gene expression compared to hiPSC-MSCs. Following transplantation of hiPSC-MSC and hiPSC-MSC-derived chondrocytes into osteochondral defects of arthritic joints of athymic rats, magnetic resonance imaging studies showed gradual engraftment, and histological correlations demonstrated hyaline cartilage matrix production. Results present an efficient and clinically translatable approach for cartilage tissue regeneration via patient-derived hiPSCs, which could improve cartilage regeneration outcomes in arthritic joints.

Dendritomas formed by fusion of mature dendritic cells with allogenic human hepatocellular carcinoma cells activate autologous cytotoxic T lymphocytes.

Mature dendritic cells (DCs) have highly expressed CD1a, MHC class I, MHC class II, B7-1, B7-2 and ICAM-I molecules, all of which are essential for activation of naïve T cells. In this study, dendritomas were formed by fusion of hepatocellular carcinoma (HCC) SMMC-7721 cells with autologous DCs in vitro. DCs were obtained from adherent monocytes cultured in the presence of GM-CSF and IL-4 and were matured in monocyte-conditioned media. Expression of MHC class II and HCC-specific antigen by these dendritomas were determined using a specific murine anti-HCC monoclonal antibody (mAb) specific for HCC cell line SMMC-7721, and a murine anti-human HLA-DR mAb, and was also confirmed using bi-dimensional flow cytometry and immuno-histostaining. Dendritomas were co-cultured with autologous T cells, resulting in activation of T cell proliferation and priming of naïve T cells to induce MHC class I restricted lysis of HCC SMMC-7721 cells. The results imply that these dendritomas may have potential for use in HCC immunotherapy.

Comparison of measurement of cross-sectional coronary atherosclerotic plaque and vessel areas by 16-slice multidetector computed tomography versus intravascular ultrasound.

In 26 patients, 16-slice multidetector computed tomography (MDCT) with 0.75-mm collimation and intravascular ultrasound (IVUS) of 1 coronary artery were performed. At 100 sites within the coronary arteries, the measurement of cross-sectional luminal area and, if detectable, the cross-sectional area of atherosclerotic plaque was performed independently with IVUS and MDCT. The mean luminal area (r = 0.92), measured at 100 sites, and plaque area (r = 0.55), measured at 65 sites, were significantly correlated (p <0.001) between MDCT and IVUS. The mean luminal area and mean plaque area were slightly but significantly overestimated with MDCT. MDCT permits the noninvasive measurement of coronary cross-sectional luminal and plaque areas with moderate accuracy.

CD80 transfected human hepatocellular carcinoma cells activate cytotoxic T lymphocytes to target HCC cells with shared tumor antigens.

Human HCC cell lines (BEL-7402, SMMC-7721 and QGY-7703) do not express CD80 molecules, although they express MHC class I molecules and ICAM-1. HCC's poor immunogenicity may therefore be due to lack of CD80 molecules. This study first investigated whether CD80 molecules could provide minimal co-stimulatory signal for establishing an efficient anti-tumor immunity in HCC and second, whether the transfection of CD80 into the BEL-7402 cell line could induce T cell activation for targeting other HCC cell lines expressing shared common antigens. The transfection of cDNA encoding CD80 into ICAM-1+ HCC BEL-7402 cells was confirmed by flow cytometrical analysis. The CD80-transfected cells could enhance the immunogenicity of BEL-7402 cells as detected by T cell proliferation assay, and also activated the T cells at a higher proliferation rate comparing with the BEL-7402 cells transfected with vector only. The CD80-transfected cell line was also found able to activate T cells which subsequently induced cell lysis of SMMC-7721, QGY-7703 and parent BEL-7402 cell lines as detected by cytotoxicity assay. It can be concluded that the cytotoxicity was due to MHC class I restricted CD8+ cytotoxic T lymphocytes, but not natural killer (NK) cells, since this cytotoxic effect could be blocked by anti-MHC class I antibody and the cytotoxicity was shown very low in NK-cell-sensitive K562 cell line. Electroporation of CD80 cDNA into human HCC cells could increase the expression of the functional CD80 molecules and enhance the immunogenicity of the genetically-modified HCC cells to activate T cells for targeting 3 HCC cell lines in an HLA-restricted manner.

Prognostic and predictive markers in recurrent high grade glioma; results from the BR12 randomised trial.

We evaluated the prognostic and predictive value of a range of molecular changes in the setting of a randomised trial comparing standard PCV (procarbazine, CCNU (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea) and vincristine) chemotherapy with the standard temozolomide (TMZ) 5-day (200 mg/m2/day) schedule and a 21-day (100 mg/m2/day) schedule in chemo-naïve, high-grade glioma (non-oligodendroglial tumours; WHO (World Health Organisation) grades III and IV) patients at first progression following radiotherapy.354 samples (79.2%) from the first operation of the 447 randomised patients provided enough tumour DNA for some or all parts of the study. Genome-wide array comparative genomic hybridisation (aCGH), mutation analysis of IDH1/2 and TP53 and methylation analyses of the MGMT CpG-island was done.84% of grade III tumours and 17% of grade IV had IDH1 or IDH2 mutations that conferred a better prognosis in both; MGMT methylation (defined as average value across 16 CpGs ≥ 10%) occurred in 75% of tumours and was also associated with improved survival. Both were of independent prognostic value after accounting for clinical factors and tumour grade. None of the molecular changes investigated gave clear evidence of a predictive benefit of TMZ over PCV or 21-day TMZ over 5-day TMZ although power was limited and a role for MGMT methylation could not be ruled out. Loss of 1p and 19q was seen in only 4 patients although hemizygous loss of 1p36 occurred in 20%.The findings support reports that IDH1/2 mutations and MGMT methylation can be used in addition to tumour grade and clinical factors to predict survival in patients with recurrent high grade gliomas when treated with any of the therapy regimes used.

Toward development of a comprehensive external quality assurance program for polyfunctional intracellular cytokine staining assays.

The External Quality Assurance Program Oversight Laboratory (EQAPOL) Flow Cytometry Program assesses the proficiency of NIH/NIAID/DAIDS-supported and potentially other interested research laboratories in performing Intracellular Cytokine Staining (ICS) assays. The goal of the EQAPOL Flow Cytometry External Quality Assurance Program (EQAP) is to provide proficiency testing and remediation for participating sites. The program is not punitive; rather, EQAPOL aims to help sites identify areas for improvement. EQAPOL utilizes a highly standardized ICS assay to minimize variability and readily identify those sites experiencing technical difficulties with their assays. Here, we report the results of External Proficiency 3 (EP3) where participating sites performed a 7-color ICS assay. On average, sites perform well in the Flow Cytometry EQAP (median score is "Good"). The most common technical issues identified by the program involve protocol adherence and data analysis; these areas have been the focus of site remediation. The EQAPOL Flow Cytometry team is now in the process of expanding the program to 8-color ICS assays. Evaluating polyfunctional ICS responses would align the program with assays currently being performed in support of HIV immune monitoring assays.