Clinical Decision Support System for All Stages of Gastric Carcinogenesis in Real-Time Endoscopy: Model Establishment and Validation Study.

BACKGROUND: Our research group previously established a deep-learning-based clinical decision support system (CDSS) for real-time endoscopy-based detection and classification of gastric neoplasms. However, preneoplastic conditions, such as atrophy and intestinal metaplasia (IM) were not taken into account, and there is no established model that classifies all stages of gastric carcinogenesis. OBJECTIVE: This study aims to build and validate a CDSS for real-time endoscopy for all stages of gastric carcinogenesis, including atrophy and IM. METHODS: A total of 11,868 endoscopic images were used for training and internal testing. The primary outcomes were lesion classification accuracy (6 classes: advanced gastric cancer, early gastric cancer, dysplasia, atrophy, IM, and normal) and atrophy and IM lesion segmentation rates for the segmentation model. The following tests were carried out to validate the performance of lesion classification accuracy: (1) external testing using 1282 images from another institution and (2) evaluation of the classification accuracy of atrophy and IM in real-world procedures in a prospective manner. To estimate the clinical utility, 2 experienced endoscopists were invited to perform a blind test with the same data set. A CDSS was constructed by combining the established 6-class lesion classification model and the preneoplastic lesion segmentation model with the previously established lesion detection model. RESULTS: The overall lesion classification accuracy (95% CI) was 90.3% (89%-91.6%) in the internal test. For the performance validation, the CDSS achieved 85.3% (83.4%-97.2%) overall accuracy. The per-class external test accuracies for atrophy and IM were 95.3% (92.6%-98%) and 89.3% (85.4%-93.2%), respectively. CDSS-assisted endoscopy showed an accuracy of 92.1% (88.8%-95.4%) for atrophy and 95.5% (92%-99%) for IM in the real-world application of 522 consecutive screening endoscopies. There was no significant difference in the overall accuracy between the invited endoscopists and established CDSS in the prospective real-clinic evaluation (P=.23). The CDSS demonstrated a segmentation rate of 93.4% (95% CI 92.4%-94.4%) for atrophy or IM lesion segmentation in the internal testing. CONCLUSIONS: The CDSS achieved high performance in terms of computer-aided diagnosis of all stages of gastric carcinogenesis and demonstrated real-world application potential.

Consistency of the estimated target weights and ECW/TBW using BIA after hemodialysis in patients between standing and lying-down positions.

BACKGROUND: As hemodialysis is administered with the patient lying down, the distribution of body fluid is stable in the lying position, which is why this position is recommended for bioimpedance analysis (BIA). Although the InBody S10 is widely used for hemodialysis patients in the lying position, clinicians must make the measurements in person. In contrast, patients can use the InBody 770 to obtain measurements by themselves in the standing position, which may be more convenient. Therefore, this study compared the measurements of hemodialysis patients' estimated target weight and ECW/TBW obtained lying down using the S10 to those obtained in the standing position using the 770. METHODS: This study was conducted among maintenance hemodialysis patients at Chuncheon Sacred Heart Hospital in October 2020. Measurements from 56 patients before and after hemodialysis were obtained using the 2 machines. Each (S10 or 770) estimated target weight, both pre- and post-hemodialysis, was considered ideal when the ECW/TBW ratio was 0.380. R2 was calculated and the Bland-Altman test was performed. RESULTS: The patients' median age was 64 years old, and 51% were men. The actual ultrafiltration was 2 kg, and the mean TBW change measured using the InBody devices was 1.5 L (R2 = 0.718) for the S10 and 1.7 L (R2 = 0.616) for the 770. The estimated target weight at pre- and post-hemodialysis showed a remarkably high correlation with the patients' actual pre- and post-hemodialysis weight (R2 > 0.095). The correlation between these measurements (lying vs. standing) before and after hemodialysis was also very close (R2 = 1.0000). In addition, ECW/TBW had a good correlation (R2 ≥ 0.970) The Bland-Altman test of dry weight and ECW/TBW yielded similar results. CONCLUSIONS: This study showed that patients' estimated target weights in the lying position using the InBody S10 device and in the standing position using the InBody 770 device were consistent in both pre- and post-hemodialysis states.

Quality of life in patients with diabetic nephropathy: findings from the KNOW-CKD (Korean Cohort Study for Outcomes in Patients with Chronic Kidney Disease) cohort.

BACKGROUND: Diabetic nephropathy (DN) can affect quality of life (QoL) because it requires arduous lifelong management. This study analyzed QoL differences between DN patients and patients with other chronic kidney diseases (CKDs). METHODS: The analysis included subjects (n = 1,766) from the KNOW-CKD (Korean Cohort Study for Outcomes in Patients with Chronic Kidney Disease) cohort who completed the Kidney Disease Quality of Life Short Form questionnaire. After implementing propensity score matching (PSM) using factors that affect the QoL of DN patients, QoL differences between DN and non-DN participants were examined. RESULTS: Among all DN patients (n = 390), higher QoL scores were found for taller subjects, and lower scores were found for those who were unemployed or unmarried, received Medical Aid, had lower economic status, had higher platelet counts or alkaline phosphatase levels, or used clopidogrel or insulin. After PSM, the 239 matched DN subjects reported significantly lower patient satisfaction (59.9 vs. 64.5, p = 0.02) and general health (35.3 vs. 39.1, p = 0.04) than the 239 non-DN subjects. Scores decreased in both groups during the 5-year follow-up, and the scores in the work status, sexual function, and role-physical domains were lower among DN patients than non-DN patients, though those differences were not statistically significant. CONCLUSION: Socioeconomic factors of DN were strong risk factors for impaired QoL, as were high platelet, alkaline phosphatase, and clopidogrel and insulin use. Clinicians should keep in mind that the QoL of DN patients might decrease in some domains compared with non-DN CKDs.

Macrosphelide A Exhibits a Specific Anti-Cancer Effect by Simultaneously Inactivating ENO1, ALDOA, and FH.

Aerobic glycolysis in cancer cells, also known as the Warburg effect, is an indispensable hallmark of cancer. This metabolic adaptation of cancer cells makes them remarkably different from normal cells; thus, inhibiting aerobic glycolysis is an attractive strategy to specifically target tumor cells while sparing normal cells. Macrosphelide A (MSPA), an organic small molecule, is a potential lead compound for the design of anti-cancer drugs. However, its role in modulating cancer metabolism remains poorly understood. MSPA target proteins were screened using mass spectrometry proteomics combined with affinity chromatography. Direct and specific interactions of MSPA with its candidate target proteins were confirmed by in vitro binding assays, competition assays, and simulation modeling. The siRNA-based knockdown of MSPA target proteins indirectly confirmed the cytotoxic effect of MSPA in HepG2 and MCF-7 cancer cells. In addition, we showed that MSPA treatment in the HEPG2 cell line significantly reduced glucose consumption and lactate release. MSPA also inhibited cancer cell proliferation and induced apoptosis by inhibiting critical enzymes involved in the Warburg effect: aldolase A (ALDOA), enolase 1 (ENO1), and fumarate hydratase (FH). Among these enzymes, the purified ENO1 inhibitory potency of MSPA was further confirmed to demonstrate the direct inhibition of enzyme activity to exclude indirect/secondary factors. In summary, MSPA exhibits anti-cancer effects by simultaneously targeting ENO1, ALDOA, and FH.

Low Muscle Mass in Patients Receiving Hemodialysis: Correlations with Vascular Calcification and Vascular Access Failure.

Background: Sarcopenia involves an age-related decline in skeletal muscle mass with functional disability or low muscle strength. Vascular calcification (VC) occurs commonly in patients with chronic kidney disease, in whom it is associated with cardiovascular disease. We aimed to investigate the correlations of low muscle mass with the quantified vascular calcification score (VCS) of the arm of vascular access, as well as whether low muscle mass is associated with the incidence of vascular access failure. Methods: The VCS was measured on non-contrast, arm computed tomography using the Agatston method. The lower muscle mass (LMM) group comprised subjects whose skeletal muscle mass of the lower extremities, as measured using bioelectrical impedance, was lower than the median. Higher VC was defined as a score of 500 or above, corresponding to the highest 40% of VCS. The relationship between LMM and VC was explored using univariate and multivariate logistic regression analyses. Results: Seventy-five patients were included, of whom forty-two (56.0%) were men. The median age was 64 years (interquartile range 58-72 years). Of the 75 patients, 73 satisfied the diagnostic criteria for sarcopenia. The median hemodialysis vintage was 49.4 months (range 32.1-99.2 months). No significant differences were found between the non-LMM and LMM groups in sex, end-stage renal disease etiology, and type of vascular access, although the LMM group showed significantly older age and hemodialysis vintage. LMM presented a significant association with VC (hazard ratio (HR) 3.562; 95% CI, 1.341-9.463; p = 0.011). Upon adjustment for hemodialysis vintage, diabetes, and systolic blood pressure, LMM demonstrated an independent association with VC (HR, 10.415; 95% CI, 2.357-46.024; p = 0.002). The risk of vascular access failure was higher in the LMM group (HR, 3.652; 95%, CI 1.135-11.749; p = 0.03). VC was a full mediator in the relationship of LMM with recurrent vascular access failure. Conclusions: We quantified LMM via bioimpedance analysis and found a heretofore-unreported association between LMM and vascular access failure. LMM increases the risk of VC and has the potential to predict vascular access failure.

Use of Endoscopic Images in the Prediction of Submucosal Invasion of Gastric Neoplasms: Automated Deep Learning Model Development and Usability Study.

BACKGROUND: In a previous study, we examined the use of deep learning models to classify the invasion depth (mucosa-confined versus submucosa-invaded) of gastric neoplasms using endoscopic images. The external test accuracy reached 77.3%. However, model establishment is labor intense, requiring high performance. Automated deep learning (AutoDL) models, which enable fast searching of optimal neural architectures and hyperparameters without complex coding, have been developed. OBJECTIVE: The objective of this study was to establish AutoDL models to classify the invasion depth of gastric neoplasms. Additionally, endoscopist-artificial intelligence interactions were explored. METHODS: The same 2899 endoscopic images that were employed to establish the previous model were used. A prospective multicenter validation using 206 and 1597 novel images was conducted. The primary outcome was external test accuracy. Neuro-T, Create ML Image Classifier, and AutoML Vision were used in establishing the models. Three doctors with different levels of endoscopy expertise were asked to classify the invasion depth of gastric neoplasms for each image without AutoDL support, with faulty AutoDL support, and with best performance AutoDL support in sequence. RESULTS: The Neuro-T-based model reached 89.3% (95% CI 85.1%-93.5%) external test accuracy. For the model establishment time, Create ML Image Classifier showed the fastest time of 13 minutes while reaching 82.0% (95% CI 76.8%-87.2%) external test accuracy. While the expert endoscopist's decisions were not influenced by AutoDL, the faulty AutoDL misled the endoscopy trainee and the general physician. However, this was corrected by the support of the best performance AutoDL model. The trainee gained the most benefit from the AutoDL support. CONCLUSIONS: AutoDL is deemed useful for the on-site establishment of customized deep learning models. An inexperienced endoscopist with at least a certain level of expertise can benefit from AutoDL support.

Automated Classification of Colorectal Neoplasms in White-Light Colonoscopy Images via Deep Learning.

Background: Classification of colorectal neoplasms during colonoscopic examination is important to avoid unnecessary endoscopic biopsy or resection. This study aimed to develop and validate deep learning models that automatically classify colorectal lesions histologically on white-light colonoscopy images. Methods: White-light colonoscopy images of colorectal lesions exhibiting pathological results were collected and classified into seven categories: stages T1-4 colorectal cancer (CRC), high-grade dysplasia (HGD), tubular adenoma (TA), and non-neoplasms. The images were then re-classified into four categories including advanced CRC, early CRC/HGD, TA, and non-neoplasms. Two convolutional neural network models were trained, and the performances were evaluated in an internal test dataset and an external validation dataset. Results: In total, 3828 images were collected from 1339 patients. The mean accuracies of ResNet-152 model for the seven-category and four-category classification were 60.2% and 67.3% in the internal test dataset, and 74.7% and 79.2% in the external validation dataset, respectively, including 240 images. In the external validation, ResNet-152 outperformed two endoscopists for four-category classification, and showed a higher mean area under the curve (AUC) for detecting TA+ lesions (0.818) compared to the worst-performing endoscopist. The mean AUC for detecting HGD+ lesions reached 0.876 by Inception-ResNet-v2. Conclusions: A deep learning model presented promising performance in classifying colorectal lesions on white-light colonoscopy images; this model could help endoscopists build optimal treatment strategies.

Amoxicillin or tetracycline in bismuth-containing quadruple therapy as first-line treatment for Helicobacter pylori infection.

AIM: To compare the efficacy and safety between modified quadruple- and bismuth-containing quadruple therapy as first-line eradication regimen for Helicobacter pylori infection. METHODS: This study was a multicenter, randomized-controlled, non-inferiority trial. Subjects endoscopically diagnosed with H. pylori infection were randomly allocated to receive modified quadruple- (rabeprazole 20 mg bid, amoxicillin 1 g bid, metronidazole 500 mg tid, bismuth subcitrate 300 mg qid [elemental bismuth 480 mg]; PAMB) or bismuth-containing quadruple therapy (rabeprazole 20 mg bid, bismuth subcitrate 300 mg qid, metronidazole 500 mg tid, tetracycline 500 mg qid; PBMT) for 14 days. Rates of eradication success and adverse events were investigated. Antibiotic resistance was determined using the agar dilution and DNA sequencing of the clarithromycin resistance point mutations in the 23 S rRNA gene of H. pylori. RESULTS: In total, 233 participants were randomized, 27 were lost to follow-up, and four violated the protocol. Both regimens showed an acceptable eradication rate in the intention-to-treat (PAMB: 87.2% vs. PBMT: 82.8%, P = .37), modified intention-to-treat (96.2% vs. 96%, P > .99), and per-protocol (96.2% vs. 96.9%, P > .99) analyses. Non-inferiority in the eradication success between PAMB and PBMT was confirmed. The amoxicillin-, metronidazole-, tetracycline-, clarithromycin-, and levofloxacin-resistance rates were 8.3, 40, 9.4, 23.5, and 42.2%, respectively. Antimicrobial resistance did not significantly affect the efficacy of either therapy. Overall compliance was 98.1%. Adverse events were not significantly different between the two therapies. CONCLUSION: Modified quadruple therapy comprising rabeprazole, amoxicillin, metronidazole, and bismuth is an effective first-line treatment for the H. pylori infection in regions with high clarithromycin and metronidazole resistance.

Delta Neutrophil Index for the Prediction of Prognosis in Acute Gastrointestinal Diseases; Diagnostic Test Accuracy Meta-Analysis.

Delta neutrophil index (DNI) is a novel diagnostic and prognostic biomarker of various infectious or inflammatory conditions. However, data on optimal measurement time are scarce, and no studies have evaluated the potential role of the DNI as a prognostic biomarker of gastrointestinal diseases with diagnostic test accuracy meta-analysis. Core databases were searched. The inclusion criteria were as follows: patients who have gastrointestinal diseases and DNI measurements presenting diagnostic indices for predicting the prognosis, including severity, surgical outcomes, and mortality from gastrointestinal diseases. We identified twelve studies for the systematic review and ten studies for the quantitative analysis. Pooled area under the curve, sensitivity, specificity, and diagnostic odds ratio of DNI at the initial admission date were 0.82 (95% confidence interval: 0.78-0.85), 0.75 (0.52-0.89), 0.76 (0.63-0.86), and 10 (3-35), respectively. Meta-regression showed no reasons for heterogeneity and publication bias was not detected. Fagan's nomogram indicated that the posterior probability of 'poor prognosis' was 76% if the test was positive, and 'no poor prognosis' was 25% if the test was negative. The DNI can be considered as a reliable initial measurement biomarker for predicting prognosis in patients with gastrointestinal diseases.

Antibody-Based Targeting of Interferon-Beta-1a Mutein in HER2-Positive Cancer Enhances Antitumor Effects Through Immune Responses and Direct Cell Killing.

Type I interferon (IFN) has been approved as an anticancer agent to treat some malignancies. However, IFNs have a short in vivo half-life, systemic toxicity, and poor biophysical properties, which prevent it from being widely used for cancer therapy. This study aimed to construct recombinant IFN-ß-1a mutein immunocytokines that comprise a human epidermal growth factor receptor 2 (HER2)-targeting antibody and IFN-ß muteins with an additional glycosylation, which can overcome the limitation of the cytokine itself. Hence, the molecular design aims to 1) enhance productivity and biophysical properties by adding secondary glycosylation in IFN-ß, 2) increase the therapeutic index of IFN-ß therapy by preferential retention at the tumor by possessing high affinity for HER2-expressing cancer cells, and 3) improve the pharmacokinetics and, thus, the convenience of IFN-ß administration. The yield of trastuzumab-IFN-ß mutein was higher than that of trastuzumab-wild-type IFN-ß in the mammalian cell culture system. Trastuzumab-IFN-ß mutein showed similar IFN activity and HER2-targeting ability equivalent to that of IFN-ß mutein and trastuzumab, respectively. Trastuzumab-IFN-ß mutein directly inhibited the growth of HER2-positive gastric cancer cell lines and was more effective than trastuzumab or IFN-ß mutein alone. Trastuzumab-IFN-ß mutein and IFN-ß mutein displayed enhanced immune cell-mediated cytotoxicity. Collectively, trastuzumab-IFN-ß mutein may have indirect immune cell-mediated antitumor effects and direct cell growth inhibitory effects. Tumor-targeting effect of trastuzumab-IFN-ß mutein was analyzed using in vivo fluorescence imaging. The accumulation of trastuzumab-IFN-ß mutein was observed in HER2-positive tumors rather than other tissues except the liver. To evaluate the both direct tumor growth inhibition effect and indirect immune cell-mediated antitumor effect, we tested the effect of trastuzumab-IFN-ß mutein in HER2-positive cancer xenograft models using nude mice or humanized mice. Trastuzumab-IFN-ß mutein could significantly enhance tumor regression when compared with trastuzumab or IFN-ß mutein. In addition, an increase in tumor-infiltrating lymphocytes was observed in the trastuzumab-IFN-ß mutein-treated group, implying that the tumor-targeting IFN-ß may have an enhanced antitumor effect through increased immune response. Therefore, targeting IFN-ß with an anti-HER2 monoclonal antibody makes the immunocytokine more potent than either agent alone. These novel findings suggest that trastuzumab-IFN-ß mutein merits clinical evaluation as a new candidate of anticancer therapeutics.

Bone Diseases in Patients with Chronic Liver Disease.

Osteoporosis is a frequently observed complication in patients with chronic liver disease, particularly liver cirrhosis and cholestatic liver diseases. In addition, osteoporosis is critical in patients receiving a liver transplant. Nevertheless, few studies have evaluated bone diseases in patients with more frequently observed chronic liver disease, such as chronic viral hepatitis, nonalcoholic fatty liver disease and alcoholic liver disease. Osteoporosis is a disease caused by an imbalance in the activities of osteoblasts and osteoclasts. Over the last few decades, many advances have improved our knowledge of the pathogenesis of osteoporosis. Importantly, activated immune cells affect the progression of osteoporosis, and chronic inflammation may exert an additional effect on the existing pathophysiology of osteoporosis. The microbiota of the intestinal tract may also affect the progression of bone loss in patients with chronic liver disease. Recently, studies regarding the effects of chronic inflammation on dysbiosis in bone diseases have been conducted. However, mechanisms underlying osteoporosis in patients with chronic liver disease are complex and precise mechanisms remain unknown. The following special considerations in patients with chronic liver disease are reviewed: bone diseases in patients who underwent a liver transplant, the association between chronic hepatitis B virus infection treatment and bone diseases, the association between sarcopenia and bone diseases in patients with chronic liver disease, and the association between chronic liver disease and avascular necrosis of the hip. Few guidelines are currently available for the management of low bone mineral density or bone diseases in patients with chronic liver disease. Due to increased life expectancy and therapeutic advances in chronic liver disease, the importance of managing osteoporosis and other bone diseases in patients with chronic liver disease is expected to increase. Consequently, specific guidelines need to be established in the near future.

Genes co-amplified with ERBB2 or MET as novel potential cancer-promoting genes in gastric cancer.

Gastric cancer (GC), one of the most common cancers worldwide, has a high mortality rate due to limited treatment options. Identifying novel and promising molecular targets is a major challenge that must be overcome if treatment of advanced GC is to be successful. Here, we used comparative genomic hybridization and gene expression microarrays to examine genome-wide DNA copy number alterations (CNAs) and global gene expression in 38 GC samples from old and young patients. We identified frequent CNAs, which included copy number gains on chromosomes 3q, 7p, 8q, 20p, and 20q and copy number losses on chromosomes 19p and 21p. The most frequently gained region was 7p21.1 (55%), whereas the most frequently deleted region was 21p11.1 (50%). Recurrent highly amplified regions 17q12 and 7q31.1-7q31.31 harbored two well-known oncogenes: ERBB2 and MET. Correlation analysis of CNAs and gene expression levels identified CAPZA2 (co-amplified with MET) and genes GRB7, MIEN1, PGAP3, and STARD3 (co-amplified with ERBB2) as potential candidate cancer-promoting genes (CPGs). Public dataset analysis confirmed co-amplification of these genes with MET or ERBB2 in GC tissue samples, and revealed that high expression (except for PGAP3) was significantly associated with shorter overall survival. Knockdown of these genes using small interfering RNA led to significant suppression of GC cell proliferation and migration. Reduced GC cell proliferation mediated by CAPZA2 knockdown was attributable to attenuated cell cycle progression and increased apoptosis. This study identified novel candidate CPGs co-amplified with MET or ERBB2, and suggests that they play a functional role in GC.

Unforeseen clonal evolution of tumor cell population in recurrent and metastatic dermatofibrosarcoma protuberans.

Dermatofibrosarcoma protuberans (DFSP) is a very rare soft tissue sarcoma, generally of low-grade malignancy. DFSP is locally aggressive with a high recurrence rate, but metastasis occurs rarely. To investigate the mechanism of metastasis in DFSP, we analyzed the whole exome sequencing data of serial tumor samples obtained from a patient who had a 10-year history of recurrent and metastatic DFSP. Tracking various genomic alterations, namely somatic mutations, copy number variations, and chromosomal rearrangements, we observed a dramatic change in tumor cell population during the occurrence of metastasis in this DFSP case. The new subclone that emerged in metastatic DFSP harbored a completely different set of somatic mutations and new focal amplifications, which had not been observed in the primary clone before metastasis. The COL1A1-PDGFB fusion, characteristic of DFSP, was found in all of the serial samples. Moreover, the break position on the fusion gene was identical in all samples. Based on these observations, we suggest a clonal evolution model to explain the mechanism underlying metastasis in DFSP and identified several candidate target genes responsible for metastatic DFSP by utilizing The Cancer Genome Atlas database. This is the first study to observe clonal evolution in metastatic DFSP and provide insight for a possible therapeutic strategy for imatinib-resistant or metastatic DFSP.

Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients.

Triple-negative breast cancer is characterized by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2, and is associated with a poorer outcome than other subtypes of breast cancer. Moreover, there are no accurate prognostic genes or effective therapeutic targets, thereby necessitating continued intensive investigation. This study analyzed the genetic mutation landscape in 70 patients with triple-negative breast cancer by targeted exome sequencing of tumor and matched normal samples. Sequencing showed that more than 50% of these patients had deleterious mutations and homozygous deletions of DNA repair genes, such as ATM, BRCA1, BRCA2, WRN, and CHEK2. These findings suggested that a large number of patients with triple-negative breast cancer have impaired DNA repair function and that therefore a poly ADP-ribose polymerase inhibitor may be an effective drug in the treatment of this disease. Notably, homozygous deletion of three genes, EPHA5, MITF, and ACSL3, was significantly associated with an increased risk of recurrence or distant metastasis in adjuvant chemotherapy-treated patients.

MET Exon 14 Skipping Mutations in Lung Adenocarcinoma: Clinicopathologic Implications and Prognostic Values.

INTRODUCTION: Response to mesenchymal-epithelial transition (MET) inhibitors in NSCLC with mesenchymal-epithelial transition gene (MET) exon 14 skipping (METex14) has fueled molecular screening efforts and the search for optimal therapies. However, further work is needed to refine the clinicopathologic and prognostic implications of METex14 skipping. METHODS: Among 795 East Asian patients who underwent a surgical procedure for NSCLC, we screened 45 patients with quintuple-negative (EGFR-negative/KRAS-negative/anaplastic lymphoma kinase gene [ALK]-negative/ROS1-negative/ret proto-oncogene [RET]-negative) lung adenocarcinomas by using reverse-transcriptase polymerase chain reaction and found 17 patients (37.8%) with METex14 skipping. We also investigated the effect of small interfering RNA (siRNA) targeting skipping junction in cells with METex14 skipping. RESULTS: The median age of the 17 patients was 73 years. The acinar subtype was predominant (52.9%), followed by the solid subtype (35.3%). MET immunohistochemistry demonstrated 100% sensitivity and 70.4% specificity. Multivariate analyses showed that patients with METex14 skipping had a higher recurrence rate than those with ALK fusion (versus METex14 skipping) (hazard ratio = 0.283, 95% confidence interval: 0.119-0.670) in stage I to IIIA disease; however, the differences in overall survival were not significant after adjustment for pathologic stage (p = 0.669). Meanwhile, siRNA decreased MET-driven signaling pathways in Hs746T cells, and combined treatment with siRNA and crizotinib inhibited cell proliferation in crizotinib-resistant H596 cells. CONCLUSIONS: The prevalence of METex14 skipping was quite high in East Asian patients without other driver mutations in lung adenocarcinomas. METex14 skipping was associated with old age, the acinar or solid histologic subtype, and high MET immunohistochemical expression. The prognosis of patients with METex14 skipping was similar to that of patients with major driver mutations. siRNA targeting the junction of METex14 skipping could inhibit MET-driven signaling pathways in cells with METex14 skipping.

Essential Role of DNA Methyltransferase 1-mediated Transcription of Insulin-like Growth Factor 2 in Resistance to Histone Deacetylase Inhibitors.

Purpose: Histone deacetylase inhibitors (HDI) are promising anticancer therapies; however, drug resistance limits their efficacy. Here, we investigated the molecular mechanisms underlying HDI resistance, focusing on the mechanism of HDI-mediated induction of insulin-like growth factor 2 (IGF2) based on our previous study.Experimental Design: The methylation status of CCCTC-binding factor (CTCF)-binding sites in the IGF2/H19 imprinting control region (ICR) were determined by methylation-specific PCR and bisulfite sequencing. The effectiveness of single or combinatorial blockade of DNA methyltransferase 1 (DNMT1) and histone deacetylase (HDAC) was evaluated using cell viability assay and patient-derived tumor xenograft (PDX) model.Results: HDAC inhibition by vorinostat increased acetylated STAT3 (K685), resulting in transcriptional upregulation of DNMT1 DNMT1-mediated hypermethylation of CTCF-binding sites in the IGF2/H19 ICR decreased CTCF insulator activity, leading to a transcriptional upregulation of IGF2 and activation of the insulin-like growth factor 1 receptor (IGF-1R) pathway in cells with acquired or de novo vorinostat resistance. Strategies targeting DNMT1 diminished the IGF2 expression and potentiated vorinostat sensitivity in preclinical models of lung cancer with hypermethylation in the H19/IGF2 ICR. The degree of ICR hypermethylation correlated with vorinostat resistance in patient-derived lung tumors and in patients with hematologic malignancies.Conclusions: DNMT1-mediated transcriptional upregulation of IGF2 is a novel mechanism of resistance to HDIs, highlighting the role of epigenetic deregulation of IGF2 in HDI resistance and the potential value of the H19/IGF2 ICR hypermethylation and DNMT1 expression as predictive biomarkers in HDI-based anticancer therapies. Clin Cancer Res; 23(5); 1299-311. ©2016 AACR.

Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis.

AIMS: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. RESULTS: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. CONCLUSION: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

CD24 Overexpression Is Associated with Poor Prognosis in Luminal A and Triple-Negative Breast Cancer.

CD24 is associated with unfavourable prognoses in various cancers, but the prevalence of CD24 expression and its influence on clinical outcome in subtypes of breast cancers remain unclear. CD24 expression was analyzed by immunohistochemistry in 747 breast cancer tissues, and DNA methylation and histone modification status in the promoter region of CD24 were assessed using bisulfite sequencing and chromatin immunoprecipitation assay. 213 (28.5%) samples exhibited high CD24 expression in the membrane and/or cytoplasm of breast cancer cells, and CD24 overexpression was significantly correlated with the presence of lymph node metastasis and more advanced pathological stage. Patients with CD24-high tumours had significantly shorter patient survival than those with CD24-low tumours. Importantly, multivariate analysis that included tumour size, lymph node metastasis and chemotherapy demonstrated that high CD24 expression is independently associated with poorer survival in luminal A and triple-negative breast cancer (TNBC) subtypes. Furthermore, CD24 gene expression was associated with histone acetylation independent of DNA methylation, suggesting its epigenetic regulation in breast cancer. Our results suggest that CD24 overexpression is an independent unfavourable prognostic factor in breast cancer, especially for luminal A and TNBC subtypes, and CD24 may be a promising therapeutic target for specific subtypes of breast cancer.

Structural Origin of the Band Gap Anomaly of Quaternary Alloy Cd(x)Zn(1-x)S(y)Se(1-y) Nanowires, Nanobelts, and Nanosheets in the Visible Spectrum.

Single-crystalline alloy II-VI semiconductor nanostructures have been used as functional materials to propel photonic and optoelectronic device performance in a broad range of the visible spectrum. Their functionality depends on the stable modulation of the direct band gap (Eg), which can be finely tuned by controlling the properties of alloy composition, crystallinity, and morphology. We report on the structural correlation of the optical band gap anomaly of quaternary alloy CdxZn1-xSySe1-y single-crystalline nanostructures that exhibit different morphologies, such as nanowires (NWs), nanobelts (NBs), and nanosheets (NSs), and cover a wide range of the visible spectrum (Eg = 1.96-2.88 eV). Using pulsed laser deposition, the nanostructures evolve from NWs via NBs to NSs with decreasing growth temperature. The effects of the growth temperature are also reflected in the systematic variation of the composition. The alloy nanostructures firmly maintain single crystallinity of the hexagonal wurtzite and the nanoscale morphology, with no distortion of lattice parameters, satisfying the virtual crystal model. For the optical properties, however, we observed distinct structure-dependent band gap anomalies: the disappearance of bowing for NWs and maximum and slightly reduced bowing for NBs and NSs, respectively. We tried to uncover the underlying mechanism that bridges the structural properties and the optical anomaly using an empirical pseudopotential model calculation of electronic band structures. From the calculations, we found that the optical bowings in NBs and NSs were due to residual strain, by which they are also distinguishable from each other: large for NBs and small for NSs. To explain the origin of the residual strain, we suggest a semiempirical model that considers intrinsic atomic disorder, resulting from the bond length mismatch, combined with the strain relaxation factor as a function of the width-to-thickness ratio of the NBs or NSs. The model agreed well with the observed optical bowing of the alloy nanostructures in which a mechanism for the maximum bowing for NBs is explained. The present systematic study on the structural-optical properties correlation opens a new perspective to understand the morphology- and composition-dependent unique optical properties of II-VI alloy nanostructures as well as a comprehensive strategy to design a facile band gap modulation method of preparing photoconverting and photodetecting materials.