Clinically Conserved Genomic Subtypes of Gastric Adenocarcinoma

Gastric adenocarcinoma (GAC) is a lethal disease characterized by genomic and clinical heterogeneity. By integrating 8 previously established genomic signatures for GAC subtypes, we identified 6 clinically and molecularly distinct genomic consensus subtypes (CGSs). CGS1 have the poorest prognosis, very high stem cell characteristics, and high IGF1 expression, but low genomic alterations. CGS2 is enriched with canonical epithelial gene expression. CGS3 and CGS4 have high copy number alterations and low immune reactivity. However, CGS3 and CGS4 differ in that CGS3 has high HER2 activation, while CGS4 has high SALL4 and KRAS activation. CGS5 has the high mutation burden and moderately high immune reactivity that are characteristic of microsatellite instable tumors. Most CGS6 tumors are positive for Epstein Barr virus and show extremely high levels of methylation and high immune reactivity. In a systematic analysis of genomic and proteomic data, we estimated the potential response rate of each consensus subtype to standard and experimental treatments such as radiation therapy, targeted therapy, and immunotherapy. Interestingly, CGS3 was significantly associated with a benefit from chemoradiation therapy owing to its high basal level of ferroptosis. In addition, we also identified potential therapeutic targets for each consensus subtype. Thus, the consensus subtypes produced a robust classification and provide for additional characterizations for subtype-based customized interventions

Fragile X Syndrome in Korea: A Case Series and a Review of the Literature

The purposes of this study were to present DNA analysis findings of our case series of fragile X syndrome (FXS) based on methylation-specific polymerase chain reaction (MS-PCR), PCR, and Southern blotting alongside developmental characteristics including psychological profiles and to review the literature on FXS in Korea. The reports of 65 children (male:female, 52:13; age, 6.12±4.00 yrs) referred for the diagnosis of FXS over a 26-months period were retrospectively reviewed for the identification of full mutation or premutation of fragile X mental retardation 1 (FMR1). Among the 65 children, there were 4 boys with full mutation, and one boy showed premutation of FMR1, yielding a 6.15% positive rate of FXS. All 4 children with full mutation showed significant developmental delay, cognitive dysfunction, and varying degrees of autistic behaviors. The boys with premutation showed also moderate mental retardation, severe drooling, and behavioral problems as severe as the boys with full mutation. Thirteen articles on FXS in Korea have been published since 1993, and they were reviewed. The positive rate of FXS was in the range of 0.77-8.51%, depending on the study groups and the method of diagnosis. Finally, the population-based prevalence study on FXS in Korea is required in the near future

Treatment Response and Long Term Follow-up Results of Nonspecific Interstitial Pneumonia

The purpose of this study was to investigate the long-term clinical course of non-specific interstitial pneumonia (NSIP) and to determine which factors are associated with a response to steroid therapy and relapse. Thirty-five patients with pathologically proven NSIP were included. Clinical, radiological, and laboratory data were reviewed retrospectively. The male-to-female ratio was 7:28 (median age, 52 yr). Thirty (86%) patients responded to steroid therapy, and the median follow-up was 55.2 months (range, 15.9-102.0 months). Five patients (14%) showed sustained disease progression and three died despite treatment. In the five with sustained disease progression, NSIP was associated with various systemic conditions, and the seropositivity of fluorescent antinuclear antibody was significantly associated with a poor response to steroids (P = 0.028). The rate of relapse was 25%, but all relapsed patients improved after re-treatment. The initial dose of steroids was significantly low in the relapse group (P = 0.020). In conclusion, progression is associated with various systemic conditions in patients who show progression. A low dose of initial steroids is significantly associated with relapse

Consensus Subtypes of Hepatocellular Carcinoma Associated With Clinical Outcomes and Genomic Phenotypes

BACKGROUND AND AIMS: Although many studies revealed transcriptomic subtypes of HCC, concordance of the subtypes are not fully examined. We aim to examine a consensus of transcriptomic subtypes and correlate them with clinical outcomes. APPROACH AND RESULTS: By integrating 16 previously established genomic signatures for HCC subtypes, we identified five clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features, but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent β-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high hepatocyte nuclear factor 4A activity. We also developed and validated a robust predictor of consensus subtype with 100 genes and demonstrated that five subtypes were well conserved in patient-derived xenograft models and cell lines. By analyzing serum proteomic data from the same patients, we further identified potential serum biomarkers that can stratify patients into subtypes. CONCLUSIONS: Five HCC subtypes are correlated with genomic phenotypes and clinical outcomes and highly conserved in preclinical models, providing a framework for selecting the most appropriate models for preclinical studies

Consensus Subtypes of Hepatocellular Carcinoma Associated With Clinical Outcomes and Genomic Phenotypes

BACKGROUND AND AIMS: Although many studies revealed transcriptomic subtypes of HCC, concordance of the subtypes are not fully examined. We aim to examine a consensus of transcriptomic subtypes and correlate them with clinical outcomes. APPROACH AND RESULTS: By integrating 16 previously established genomic signatures for HCC subtypes, we identified five clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features, but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent β-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high hepatocyte nuclear factor 4A activity. We also developed and validated a robust predictor of consensus subtype with 100 genes and demonstrated that five subtypes were well conserved in patient-derived xenograft models and cell lines. By analyzing serum proteomic data from the same patients, we further identified potential serum biomarkers that can stratify patients into subtypes. CONCLUSIONS: Five HCC subtypes are correlated with genomic phenotypes and clinical outcomes and highly conserved in preclinical models, providing a framework for selecting the most appropriate models for preclinical studies

Roles of Arrest-Defective Protein 1225 and Hypoxia-Inducible Factor 1α in Tumor Growth and Metastasis

Background Vascular endothelial growth factor A (VEGFA), a critical mediator of tumor angiogenesis, is a well-characterized target of hypoxia-inducible factor 1 (HIF-1). Murine arrest-defective protein 1A (mARD1A225) acetylates HIF-1??, triggering its degradation, and thus may play a role in decreased expression of VEGFA.Methods We generated ApcMin/+/mARD1A225 transgenic mice and quantified growth of intestinal polyps. Human gastric MKN74 and murine melanoma B16F10 cells overexpressing mARD1A225 were injected into mice, and tumor growth and metastasis were measured. VEGFA expression and microvessel density in tumors were assessed using immunohistochemistry. To evaluate the role of mARD1A 225 acetylation of Lys532 in HIF-1??, we injected B16F10-mARD1A225 cell lines stably expressing mutant HIF-1??/K532R into mice and measured metastasis. All statistical tests were two-sided, and P values less than. 05 were considered statistically significant.Results ApcMin/+/mARD1A225 transgenic mice (n = 25) had statistically significantly fewer intestinal polyps than Apc Min/+ mice (n = 21) (number of intestinal polyps per mouse: Apc Min/+ mice vs ApcMin/+/mARD1A225 transgenic mice, mean = 83.4 vs 38.0 polyps, difference = 45.4 polyps, 95% confidence interval [CI] = 41.8 to 48.6; P <. 001). The growth and metastases of transplanted tumors were also statistically significantly reduced in mice injected with mARD1A225-overexpressing cells than in mice injected with control cells (P <. 01). Moreover, overexpression of mARD1A 225 decreased VEGFA expression and microvessel density in tumor xenografts (P <. 04) and ApcMin/+ intestinal polyps (P =. 001). Mutation of lysine 532 of HIF-1?? in B16F10-mARD1A225 cells prevented HIF-1?? degradation and inhibited the antimetastatic effect of mARD1A225 (P <. 001).Conclusion mARD1A225 may be a novel upstream target that blocks VEGFA expression and tumor-related angiogenesis

ENSO Atmospheric Teleconnections and Their Response to Greenhouse Gas Forcing

This is the final version of the article. Available from AGU via the DOI in this record.El Niño and Southern Oscillation (ENSO) is the most prominent year-to-year climate fluctuation on Earth, alternating between anomalously warm (El Niño) and cold (La Niña) sea surface temperature (SST) conditions in the tropical Pacific. ENSO exerts its impacts on remote regions of the globe through atmospheric teleconnections, affecting extreme weather events worldwide. However, these teleconnections are inherently nonlinear and sensitive to ENSO SST anomaly patterns and amplitudes. In addition, teleconnections are modulated by variability in the oceanic and atmopsheric mean state outside the tropics and by land and sea ice extent. The character of ENSO as well as the ocean mean state have changed since the 1990s, which might be due to either natural variability or anthropogenic forcing, or their combined influences. This has resulted in changes in ENSO atmospheric teleconnections in terms of precipitation and temperature in various parts of the globe. In addition, changes in ENSO teleconnection patterns have affected their predictability and the statistics of extreme events. However, the short observational record does not allow us to clearly distinguish which changes are robust and which are not. Climate models suggest that ENSO teleconnections will change because the mean atmospheric circulation will change due to anthropogenic forcing in the 21st century, which is independent of whether ENSO properties change or not. However, future ENSO teleconnection changes do not currently show strong intermodel agreement from region to region, highlighting the importance of identifying factors that affect uncertainty in future model projections.S. W. Y. is supported by the KoreaMeteorological Administration Researchand Development Program under grant KMIPA2015-2112. Wenju Cai is supported by Earth System and Climate Change Hub of the Australia National Environmental Science Programme, and Centre for Southern Hemisphere Oceans Research, an international collaboration between CSIRO and Qingdao National Laboratory for Marine Sciences and Technology. B. Dewitte acknowledges supports from FONDECYT(1151185) and from LEFE-GMMC. Dietmar Dommenget is supported by ARC Centre of Excellence for Climate System Science (CE110001028)