Isolation of TTF-1 Positive Circulating Tumor Cells for Single-Cell Sequencing by Using an Automatic Platform Based on Microfluidic Devices.

Single-cell sequencing provides promising information in tumor evolution and heterogeneity. Even with the recent advances in circulating tumor cell (CTC) technologies, it remains a big challenge to precisely and effectively isolate CTCs for downstream analysis. The Cell RevealTM system integrates an automatic CTC enrichment and staining machine, an AI-assisted automatic CTC scanning and identification system, and an automatic cell picking machine for CTC isolation. H1975 cell line was used for the spiking test. The identification of CTCs and the isolation of target CTCs for genetic sequencing were performed from the peripheral blood of three cancer patients, including two with lung cancer and one with both lung cancer and thyroid cancer. The spiking test revealed a mean recovery rate of 81.81% even with extremely low spiking cell counts with a linear relationship between the spiked cell counts and the recovered cell counts (Y = 0.7241 × X + 19.76, R2 = 0.9984). The three cancer patients had significantly higher TTF-1+ CTCs than healthy volunteers. All target CTCs were successfully isolated by the Cell Picker machine for a subsequent genetic analysis. Six tumor-associated mutations in four genes were detected. The present study reveals the Cell RevealTM platform can precisely identify and isolate target CTCs and then successfully perform single-cell sequencing by using commercially available genetic devices.

Blockade of the pentraxin 3/CD44 interaction attenuates lung injury-induced fibrosis.

BACKGROUND: Fibrosing interstitial lung diseases (fILD) are potentially fatal with limited therapeutic options and no effective strategies to reverse fibrogenesis. Myofibroblasts are chief effector cells in fibrosis that excessively deposit collagen in the pulmonary interstitium and lead to progressive impairment of gaseous exchange. METHODS: Plasma and lung specimens from patients with fILD were applied for detecting pentraxin 3 (PTX3) abundance by ELISA and Immunohistochemistry. Masson's trichrome and Sirius red stains and hydroxyproline assay were performed for assessing collagen accumulation in the lungs of bleomycin-exposed conditional Ptx3-deficient and PTX3-neutralizing antibody (αPTX3i)-treated mice. Downstream effectors including signaling pathways and fibrotic genes were examined for assessing CD44-involved PTX3-induced fibrosis in HFL1 and primary mouse fibroblasts. RESULTS: PTX3 was upregulated in the lungs and plasma of bleomycin-exposed mice and correlated with disease severity and adverse outcomes in fILD patients. Decreased collagen accumulation, attenuation of alveolar fibrosis and fibrotic markers, and improved lung function were observed in bleomycin-exposed conditional Ptx3-deficient mice. PTX3 activates lung fibroblasts to differentiate towards migrative and highly collagen-expressing myofibroblasts. Lung fibroblasts with CD44 inactivation attenuated the PI3K-AKT1, NF-κB, and JNK signaling pathways and fibrotic markers. αPTX3i mimic-based therapeutic studies demonstrated abrogation of the migrative fibroblast phenotype and myofibroblast activation in vitro. Notably, αPTX3i inhibited lung fibrosis, reduced collagen deposition, increased mouse survival, and improved lung function in bleomycin-induced pulmonary fibrosis. CONCLUSIONS: The present study reveals new insights into the involvement of the PTX3/CD44 axis in fibrosis and suggests PTX3 as a promising therapeutic target in fILD patients.

Zero-contrast percutaneous coronary intervention for chronic total occlusions guided by intravascular ultrasound with ChromaFlo mode: a case report.

BACKGROUND: Contrast agent allergy may result in severe adverse events that prevent the use of percutaneous coronary intervention (PCI) in some patients, especially for those with complex lesions. CASE SUMMARY: We describe a 59-year-old man who presented with the multi-vessel disease and suffered from contrast allergy. The patient refused to have coronary artery bypass grafting surgery, thus two-stage PCI procedures without iodinated contrast media were performed after a detailed discussion with the heart team, including a chronic total occlusion (CTO) lesion in the proximal left anterior descending artery. The intravascular ultrasound (IVUS) was used for finding the entry point of the proximal fibre cap, and assessing the lesion, thereby marking the positions of the proximal and distal edges of the stent. After PCI, stent expansion and subtle edge dissection or incomplete apposition were confirmed by IVUS and ChromaFlo imaging. Zero-contrast PCI was done successfully without any complication. DISCUSSION: This case report illustrates the feasibility and safety of performing CTO-PCI without contrast agent in carefully and well prepared selected patients.

DriverDBv3: a multi-omics database for cancer driver gene research.

An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies published bioinformatics algorithms to identify driver genes/mutations. The updated DriverDBv3 database (http://ngs.ym.edu.tw/driverdb) is designed to interpret cancer omics' sophisticated information with concise data visualization. To offer diverse insights into molecular dysregulation/dysfunction events, we incorporated computational tools to define CNV and methylation drivers. Further, four new features, CNV, Methylation, Survival, and miRNA, allow users to explore the relations from two perspectives in the 'Cancer' and 'Gene' sections. The 'Survival' panel offers not only significant survival genes, but gene pairs synergistic effects determine. A fresh function, 'Survival Analysis' in 'Customized-analysis,' allows users to investigate the co-occurring events in user-defined gene(s) by mutation status or by expression in a specific patient group. Moreover, we redesigned the web interface and provided interactive figures to interpret cancer omics' sophisticated information, and also constructed a Summary panel in the 'Cancer' and 'Gene' sections to visualize the features on multi-omics levels concisely. DriverDBv3 seeks to improve the study of integrative cancer omics data by identifying driver genes and contributes to cancer biology.

Intrahepatic cholangiocarcinoma in the setting of HBV-related cirrhosis: Differentiation with hepatocellular carcinoma by using Intravoxel incoherent motion diffusion-weighted MR imaging.

Accurate preoperative differentiation of intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC) in the setting of cirrhotic liver is of great clinical significance because the treatment and prognosis of these entities differ markedly. Through a retrospectively research, we sought to determine the diagnostic performances of intravoxel incoherent motion (IVIM) and diffusion weighted imaging (DWI) parameters in the differentiating of ICC and HCC. According to the results, we found that apparent diffusion coefficient (ADC) derived from mono-exponential model and true ADC (ADCslow) derived from bi-exponential model can be used to distinguish the ICC and HCC, and ADCslowentailed the higher diagnostic performance than ADC. However, pseudo-ADC (ADCfast) and perfusion fraction (f) can not be used to differentiate ICC and HCC. These results suggested that IVIM and DWI parameters can be useful in differentiating ICC and HCC and might be helpful in selecting the treatment plan and predicting prognosis.

Quantitative free-breathing dynamic contrast-enhanced MRI in hepatocellular carcinoma using gadoxetic acid: correlations with Ki67 proliferation status, histological grades, and microvascular density.

PURPOSE: To validate a free-breathing dynamic contrast-enhanced-MRI (DCE-MRI) in hepatocellular carcinoma (HCC) patients using gadoxetic acid, and to determine the relationship between DCE-MRI parameters and histological results. METHODS: Thirty-four HCC patients were included in this prospective study. Free-breathing DCE-MRI data was acquired preoperatively on a 3.0 Tesla scanner. Perfusion parameters (K trans, K ep, V e and the semi-quantitative parameter of initial area under the gadolinium concentration-time curve, iAUC) were calculated and compared with tumor enhancement at contrast-enhanced CT. The relationship between DCE-MRI parameters and Ki67 indices, histological grades and microvascular density (MVD) was determined by correlation analysis. Differences of perfusion parameters between different histopathological groups were compared. Receiver operation characteristic (ROC) analysis of discriminating high-grades (grade III and IV) from low-grades (grade I and II) HCC was performed for perfusion parameters. RESULTS: Significant relationship was found between DCE-MRI and CT results. The DCE-MRI derived K trans were significantly negatively correlated with Ki-67 indices (rho = - 0.408, P = 0.017) and the histological grades (rho = - 0.444, P = 0.009) of HCC, and K ep and V e were significantly related with tumor MVD (rho = - 0.405, P = 0.017 for K ep; and rho = 0.385, P = 0.024 for V e). K trans, K ep, and iAUC demonstrated moderate diagnostic performance (iAUC = 0.78, 0.77 and 0.80, respectively) for discriminating high-grades from low-grades HCC without significant differences. CONCLUSIONS: The DCE-MRI derived parameters demonstrated weak but significant correlations with tumor proliferation status, histological grades or microvascular density, respectively. This free-breathing DCE-MRI is technically feasible and offers a potential avenue toward non-invasive evaluation of HCC malignancy.

Effectiveness of Implantation of Cardioverter-Defibrillators Therapy in Patients with Non-Ischemic Heart Failure: an Updated Systematic Review and Meta-Analysis.

OBJECTIVE: Implantable cardioverter-defibrillator has become the first-line therapy for prevention of sudden cardiac death. Controversial results still exist regarding the effectiveness of implantable cardioverter-defibrillator (ICD) in non-ischemic heart failure. METHODS: The PubMed, Embase, and Cochrane Central databases were searched for randomized trials comparing implantable cardioverter-defibrillator in combination with medical treatment versus medical treatment for non-ischemic heart failure. The primary endpoint was incidence of all-cause death. We derived pooled risk ratios with fixed-effects models. RESULTS: Five studies enrolling 2573 patients were included. Compared with medical treatment, implantable cardioverter-defibrillator with medical treatment was associated with a significantly lower risk for all-cause mortality (Risk ratio: 0.83; 95% confidence interval 0.71 to 0.97). CONCLUSION: Compared with medical treatment only, implantable cardioverter-defibrillator in combination with medical treatment reduces all-cause mortality.

Effectiveness of implantation of cardioverter-defibrillators therapy in patients with non-ischemic heart failure: an updated systematic review and meta-analysis

Abstract Objective: Implantable cardioverter-defibrillator has become the first-line therapy for prevention of sudden cardiac death. Controversial results still exist regarding the effectiveness of implantable cardioverter-defibrillator (ICD) in non-ischemic heart failure. Methods: The PubMed, Embase, and Cochrane Central databases were searched for randomized trials comparing implantable cardioverter-defibrillator in combination with medical treatment versus medical treatment for non-ischemic heart failure. The primary endpoint was incidence of all-cause death. We derived pooled risk ratios with fixed-effects models. Results: Five studies enrolling 2573 patients were included. Compared with medical treatment, implantable cardioverter-defibrillator with medical treatment was associated with a significantly lower risk for all-cause mortality (Risk ratio: 0.83; 95% confidence interval 0.71 to 0.97). Conclusion: Compared with medical treatment only, implantable cardioverter-defibrillator in combination with medical treatment reduces all-cause mortality.

Evaluation of extrapancreatic inflammation on abdominal computed tomography as an early predictor of organ failure in acute pancreatitis as defined by the revised Atlanta classification.

The aim of the study was to determine whether extrapancreatic inflammation on computed tomography (EPIC) is helpful in predicting organ failure in the early phase of acute pancreatitis (AP) as defined by the 2012 revised Atlanta classification.Patients (n = 208) who underwent abdominal computed tomography (CT) within 24 hours after AP onset and admission were retrospectively identified. Each patient's EPIC score, Balthazar score, bedside index of severity in acute pancreatitis (BISAP), and systemic inflammatory response syndrome (SIRS) score were obtained. Primary endpoints were organ failure occurrence and death. Scores were evaluated by receiver operator characteristic (ROC) curve and area under the curve (AUC) analysis.Median age was 45 years (range: 18-83 years). Forty-seven patients (22.6%) developed organ failure, and 5 patients (2.4%) developed infection and underwent surgery. Two patients died. The median EPIC score was 2 (range: 0-7). EPIC score accuracy (AUC = 0.724) in predicting organ failure was similar to that of BISAP (0.773) and SIRS (0.801) scores, whereas Balthazar scoring was not significant (P = .293). An EPIC score of 3 or greater had a sensitivity and specificity of 80.65% and 63.16%, respectively. EPIC scores correlated moderately with organ failure severity (Spearman r = 0.321) and number of failed organs (r = 0.343).The EPIC scoring system can be useful in predicting the occurrence of organ failure, but it does not differentiate severity and number of failed organs in early phase AP.

YM500v3: a database for small RNA sequencing in human cancer research.

We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, 'Survival' and 'Cancer', in this updated version. The 'Survival' section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The 'Cancer' section provides the results of differential expression analyses, miRNA-gene interactions and cancer miRNA-related pathways. In the 'Expression' section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.

DriverDBv2: a database for human cancer driver gene research.

We previously presented DriverDB, a database that incorporates ∼ 6000 cases of exome-seq data, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. The database provides two points of view, 'Cancer' and 'Gene', to help researchers visualize the relationships between cancers and driver genes/mutations. In the updated DriverDBv2 database (http://ngs.ym.edu.tw/driverdb) presented herein, we incorporated >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and published papers. Seven additional computational algorithms (meaning that the updated database contains 15 in total), which were developed for driver gene identification, are incorporated into our analysis pipeline, and the results are provided in the 'Cancer' section. Furthermore, there are two main new features, 'Expression' and 'Hotspot', in the 'Gene' section. 'Expression' displays two expression profiles of a gene in terms of sample types and mutation types, respectively. 'Hotspot' indicates the hotspot mutation regions of a gene according to the results provided by four bioinformatics tools. A new function, 'Gene Set', allows users to investigate the relationships among mutations, expression levels and clinical data for a set of genes, a specific dataset and clinical features.

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.

We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.

DriverDB: an exome sequencing database for cancer driver gene identification.

Exome sequencing (exome-seq) has aided in the discovery of a huge amount of mutations in cancers, yet challenges remain in converting oncogenomics data into information that is interpretable and accessible for clinical care. We constructed DriverDB (http://ngs.ym.edu.tw/driverdb/), a database which incorporates 6079 cases of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic) and published bioinformatics algorithms dedicated to driver gene/mutation identification. We provide two points of view, 'Cancer' and 'Gene', to help researchers to visualize the relationships between cancers and driver genes/mutations. The 'Cancer' section summarizes the calculated results of driver genes by eight computational methods for a specific cancer type/dataset and provides three levels of biological interpretation for realization of the relationships between driver genes. The 'Gene' section is designed to visualize the mutation information of a driver gene in five different aspects. Moreover, a 'Meta-Analysis' function is provided so researchers may identify driver genes in customer-defined samples. The novel driver genes/mutations identified hold potential for both basic research and biotech applications.