Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer.

As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer-promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1 In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1 gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention.

KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition.

Lung squamous cell carcinoma (LUSC) represents a major subtype of lung cancer with limited treatment options. KMT2D is one of the most frequently mutated genes in LUSC (>20%), and yet its role in LUSC oncogenesis remains unknown. Here, we identify KMT2D as a key regulator of LUSC tumorigenesis wherein Kmt2d deletion transforms lung basal cell organoids to LUSC. Kmt2d loss increases activation of receptor tyrosine kinases (RTKs), EGFR and ERBB2, partly through reprogramming the chromatin landscape to repress the expression of protein tyrosine phosphatases. These events provoke a robust elevation in the oncogenic RTK-RAS signaling. Combining SHP2 inhibitor SHP099 and pan-ERBB inhibitor afatinib inhibits lung tumor growth in Kmt2d-deficient LUSC murine models and in patient-derived xenografts (PDXs) harboring KMT2D mutations. Our study identifies KMT2D as a pivotal epigenetic modulator for LUSC oncogenesis and suggests that KMT2D loss renders LUSC therapeutically vulnerable to RTK-RAS inhibition.

GlioMarker: An integrated database for knowledge exploration of diagnostic biomarkers in gliomas.

Gliomas are the most frequent malignant and aggressive tumors in the central nervous system. Early and effective diagnosis of glioma using diagnostic biomarkers can prolong patients' lives and aid in the development of new personalized treatments. Therefore, a thorough and comprehensive understanding of the diagnostic biomarkers in gliomas is of great significance. To this end, we developed the integrated and web-based database GlioMarker (http://gliomarker.prophetdb.org/), the first comprehensive database for knowledge exploration of glioma diagnostic biomarkers. In GlioMarker, accurate information on 406 glioma diagnostic biomarkers from 1559 publications was manually extracted, including biomarker descriptions, clinical information, associated literature, experimental records, associated diseases, statistical indicators, etc. Importantly, we integrated many external resources to provide clinicians and researchers with the capability to further explore knowledge on these diagnostic biomarkers based on three aspects. (1) Obtain more ontology annotations of the biomarker. (2) Identify the relationship between any two or more components of diseases, drugs, genes, and variants to explore the knowledge related to precision medicine. (3) Explore the clinical application value of a specific diagnostic biomarker through online analysis of genomic and expression data from glioma cohort studies. GlioMarker provides a powerful, practical, and user-friendly web-based tool that may serve as a specialized platform for clinicians and researchers by providing rapid and comprehensive knowledge of glioma diagnostic biomarkers to subsequently facilitates high-quality research and applications.

ceRNAshiny: An Interactive R/Shiny App for Identification and Analysis of ceRNA Regulation.

The competing endogenous RNA (ceRNA) network is a newly discovered post-transcriptional regulation that controls both physiological and pathological progresses. Increasing research studies have been pivoted on this theory to explore the function of novel non-coding RNAs, pseudogenes, circular RNAs, and messenger RNAs. Although there are several R packages or computational tools to analyze ceRNA networks, an urgent need for easy-to-use computational tools still remains to identify ceRNA regulation. Besides, the conventional tools were mainly devoted to investigating ceRNAs in malignancies instead of those in neurodegenerative diseases. To fill this gap, we developed ceRNAshiny, an interactive R/Shiny application, which integrates widely used computational methods and databases to provide and visualize the construction and analysis of the ceRNA network, including differential gene analysis and functional annotation. In addition, demo data in ceRNAshiny could provide ceRNA network analyses about neurodegenerative diseases such as Parkinson's disease. Overall, ceRNAshiny is a user-friendly application that benefits all researchers, especially those who lack an established bioinformatic pipeline and are interested in studying ceRNA networks.

Accurate prediction of epidermal growth factor receptor mutation status in early-stage lung adenocarcinoma, using radiomics and clinical features.

OBJECTIVES: To develop a nomogram based on CT radiomics and clinical features to predict the epidermal growth factor receptor (EGFR) mutations in early-stage lung adenocarcinomas. METHODS: A retrospective analysis of postoperative patients with pathologically confirmed lung adenocarcinoma, which had been tested for EGFR mutations was performed from January 2015 to December 2015. Patients were randomly assigned to training and validation cohorts. A total of 1,078 radiomics features were extracted. least absolute shrinkage and selection operator (LASSO) regression analysis was applied to select clinical and radiomics features, and to establish predictive models. The radiomics score (rad-score) of each patient was calculated. The discrimination of the model was evaluated with area under the curve. RESULTS: 1092 patients (444 men and 648 women; mean age: 59.59±9.6) were enrolled. The radiomics signature consisted of 28 radiomics features and emphysema. The mean validation cohort result of the rad-score for patients with EGFR mutations (0.814±0.988) was significantly higher than those with EGFR wild-type (0.315±1.237; p = 0.001). When combined with clinical features, LASSO regression analysis revealed four radiomics features, emphysema, and three clinical features including sex, age, and histologic subtype as associated with to EGFR mutation status. The nomogram that combined radiomics and clinical features significantly improved the predictive discrimination (AUC: 0.723), which is better than that of the radiomics signature alone (AUC: 0.646). CONCLUSION: A relationship between selected radiomics features and EGFR mutant lung adenocarcinomas is demonstrated. A nomogram, combining radiomics features and clinical features for EGFR prediction in early-stage lung adenocarcinomas, has shown a moderate discriminatory efficiency and high sensitivity, providing additional information for clinicians.

Genome-Wide Analysis of Lung Adenocarcinoma Identifies Novel Prognostic Factors and a Prognostic Score.

BACKGROUND AND OBJECTIVE: Lung adenocarcinoma (LUAD) is the most common histological type of all lung cancers and is associated with genetic and epigenetic aberrations. The tumor, node, and metastasis (TNM) stage is the most authoritative indicator of the clinical outcome in LUAD patients in current clinical practice. In this study, we attempted to identify novel genetic and epigenetic modifications and integrate them as a predictor of the prognosis for LUAD, to supplement the TNM stage with additional information. METHODS: A dataset of 445 patients with LUAD was obtained from The Cancer Genome Atlas database. Both genetic and epigenetic aberrations were screened for their prognostic impact on overall survival (OS). A prognostic score (PS) integrating all the candidate prognostic factors was then developed and its prognostic value validated. RESULTS: A total of two micro-RNAs, two mRNAs and two DNA methylation sites were identified as prognostic factors associated with OS. The low- and high-risk patient groups, divided by their PS level, showed significantly different OS (p < 0.001) and recurrence-free survival (RFS; p = 0.005). Patients in the early stages (stages I/II) and advanced stages (stages III/IV) of LUAD could be further subdivided by PS into four subgroups. PS remained efficient in stratifying patients into different OS (p < 0.001) and RFS (p = 0.005) when the low- and high-risk subgroups were in the early stages of the disease. However, there was only a significant difference in OS (p = 0.04) but not RFS (p = 0.2), between the low-risk and high-risk subgroups when both were in advanced stages. CONCLUSION: PS, in combination with the TNM stage, provides additional precision in stratifying patients with significantly different OS and RFS prognoses. Further studies are warranted to assess the efficiency of PS and to explain the effects of the genetic and epigenetic aberrations observed in LUAD.

Integrating genetic mutations and expression profiles for survival prediction of lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) is a set of heterogeneous diseases with distinct genetic and transcriptomic characteristics. Since the introduction of the 2011 International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society histologic classification, increasing evidence has provided insights into genomic mutations and rearrangements among individual histologic subtypes of LUAD. However, how genotypic and phenotypic features of LUAD are interconnected is not well understood. METHODS: We obtained the genomic, transcriptomic, and clinical data sets of 488 LUAD patients from The Cancer Genome Atlas database. Advanced statistical models were used to disentangle the interactions between genetic mutations and expression profiles, and to assess the alterations and changes in expression of each histologic subtype. The prognostic impacts of genetic mutations, expression profiles, and clinicopathological features were integrated to predict the outcomes of LUAD patients. RESULTS: From our data, one or more genetic mutations correlate with expression levels of 6054/18175 (33.3%) genes and explain 8-40% of observed variability in LUAD. The genetic mutations and expression profiles varied remarkably among the histologic subtypes of LUAD, which helped to explain the different prognostic impact based on subtype classification. Genomic, transcriptomic, and clinical data were all shown to have utility for predicting overall and recurrence-free survival, with the largest contribution from the transcriptome. CONCLUSION: Our prediction model integrating genetic mutations, expression profiles, and clinicopathological features exhibited superior accuracy over the current tumor node metastasis staging system to prognosticate outcomes of patients with LUAD (overall survival 67% vs. 55%, recurrence-free survival 57% vs. 49%; P < 0.01).

A Case of Bilateral Testicular Tumors Subsequently Diagnosed as Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency.

21-hydroxylase deficiency (21-OHD) caused congenital adrenal hyperplasia (CAH) is a group of autosomal recessive genetic disorders resulting from mutations in genes involved with cortisol (CO) synthesis in the adrenal glands. Testicular adrenal rest tumors (TARTs) are rarely the presenting symptoms of CAH. Here, we describe a case of simple virilizing CAH with TARTs, in a 15-year-old boy. The patient showed physical signs of precocious puberty. The levels of blood adrenocorticotropic hormone (ACTH), urinary 17-ketone steroids (17-KS), dehydroepiandrosterone sulfate (DHEA-S), and serum progesterone (PRGE) were elevated, whereas those of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and CO were reduced. Computed tomography (CT) of the adrenal glands and magnetic resonance imaging (MRI) of the testes showed a soft tissue density (more pronounced on the right side) and an irregularly swollen mass (more pronounced on the left side), respectively. Pathological examination of a specimen of the mass indicated polygonal/circular eosinophilic cytoplasm, cord-like arrangement of interstitial cells, and lipid pigment in the cytoplasm. Immunohistochemistry results precluded a diagnosis of Leydig cell tumors. DNA sequencing revealed a hackneyed homozygous mutation, I2g, on intron 2 of the CYP21A2 gene. The patient's symptoms improved after a three-month of dexamethasone therapy. Recent radiographic data showed reduced hyperplastic adrenal nodules and testicular tumors. A diagnosis of TART should be considered and prioritized in CAH patients with testicular tumors. Replacement therapy using a sufficient amount of dexamethasone in this case helps combat TART.

Non-chimerism and chimerism pseudo dicentric Y chromosome: two case reports about azoospermia and cytogenetic/molecular genetic analysis in the Chinese population.

OBJECTIVE: To report the cytogenetic and molecular genetic analysis of the first two cases of non-chimerism and chimerism karyotype in Chinese male patients who suffer from azoospermia, which may be caused by pseudo dicentric Y chromosomes. DESIGN: Case study. SETTING: Academic reproductive medicine center. PATIENTS: Two male patients with azoospermia, carrying pseudo dicentric Y chromosome. INTERVENTIONS: Review the records of inquiry, testicular biopsy, pathological examination, semen routine examination, endocrine evaluation, cytogenetic chromosomal analysis, and FISH detection of peripheral blood to evaluate Y chromosome deletion. MAIN OUTCOME MEASURES: To investigate the possible association among pseudo dicentric Y, chimeric status and azoospermia. RESULTS: Two patients were both diagnosed with azoospermia by a variety of andrology inspections. Further chromosomal analysis and FISH indicated their pseudo dicentric Y chromosome and different chimerism status. PCR confirmed simultaneous deletions of AZFb and AZFc regions in the Y chromosome of both patients. CONCLUSIONS: Pseudodicentric Y chromosome affecting the long arm may lead to a male phenotype by duplicating the sex-determining region of Y chromosome (SRY) fragment and chimeric status may further impact patient's hormone levels, which obstruct spermatogenesis. However, the deletion of the azoospermia factor (AZF) is likely the key factor that causes azoospermia.

[Congenital adrenal hyperplasia complicated by testicular adrenal rest tumors: one-case clinical analysis].

OBJECTIVE: To investigate the early diagnosis and treatment of congenital adrenal hyperplasia (CAH) complicated by testicular adrenal rest tumors (TART). METHODS: We retrospectively analyzed the clinical data of 1 case of late-onset CAH complicated by TART diagnosed and treated in Xiamen Women and Children Health Care Hospital. RESULTS: The patient was a 15 years old boy, short statured and dark skinned, with skin pigmentation in the gum and external genital, secondary sex characteristics of the adult and irregular tubercles palpable in the bilateral testes. Laboratory examinations showed obviously increased levels of ACTH, 17-KS, DHEA-S and progesterone and evidently decreased levels of FSH, LH and CO. The low-dose dexamethasone suppression test reduced ACTH and DHEA-S to normal. Imaging examinations revealed soft tissue density in the bilateral adrenal glands, especially on the right, and irregularly increased volume of the bilateral testes, particularly on the left, with heterogeneous signals and septas and surrounded by the fluid signals. Histopathological examinations showed the eosinophilic cytoplasm to be polygon- or round-shaped, interstitium-like cells arranged in line, and lipopigment in the endochylema. Immunohistochemical results were negative for testicular interstitial cell tumor. The clinical signs of the patient were improved after 3 months of dexamethasone treatment, the hyperplastic nodules in the left testis decreased obviously and those in the right testis disappeared after 6 months, and the hyperplastic nodules in the adrenal glands vanished after 9 months. CONCLUSION: Based on the clinical manifestations and the results of auxiliary examinations, this case was diagnosed as late-onset CAH complicated by TART, which was attributed to the continued surge of ACTH induced by corticoadrenal insufficiency. Sufficient dexamethasone treatment could make the TART decrease or disappear and the CAH vanish; it could also improve the clinical symptoms and bring the laboratory results to normal.

Exogenous leptin promotes the recovery of regressed ovary in fasted ducks.

The present study was undertaken to examine the effect of administered recombinant mouse leptin on the recovery of regressed ovary in fasted ducks. Twenty-eight ducks were divided into five groups: fed ad libitum (control; n=5), fasted control (FC; n=5), fasted+low dose of leptin (F+L; n=5), fasted+medium dose of leptin (F+M; n=5) and fasted+high dose of leptin (F+H; n=3). All four fasted groups were fasted for 2 days and then ad libitum and the ducks were treated with leptin at doses of 0 (control and FC), 50 (F+L), 250 (F+M) and 1000 (F+H) microg/kg body weight/day on day 3-5. Results showed that a moderate dose of leptin (250 microg/kg body weight/day) injected during the re-feeding period: (i) promoted the recovery of the regressed ovary as evidenced by an increase in ovary weight and recovery of yellow hierarchical follicles; (ii) elevated the plasma 17beta-estradiol (E(2)) level; (iii) increased the mRNA levels of ovary follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR) and estrogen receptor-beta (ER-beta). Furthermore, the results also showed that a high dose of leptin (1000 microg/kg body weight/day) may have a negative effect on the recovery of the regressed ovary. In conclusion, this study indicates that, in ducks, leptin may be involved in the recovery of the regressed ovary caused by 2 days of fasting. This effect may be related to increased plasma E(2) levels and stimulation of the mRNA levels of ovarian FSHR, LHR and especially ER-beta.