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Laboratory and epidemiological studies have shown that short sleep time is associated with obesity. In this study, we conducted a post-GWAS analysis to test genetic correlation between children’s sleep and obesity due to linkage disequilibrium (LD) SNPs, shared genes and pathways. Our analysis showed that genetic heritability was 0.14 (p-value = 0.0005) and 0.41 (p-value = 1.18E−24) for children’s sleep and obesity, respectively, but genetic correlation due to LD SNPs was insignificant. Gene associations at children’s GWAS were measured based on SNP associations and ranked by their uniform score (U-score). After adjusting for gene size, measured as the number of independent SNPs, children’s sleep and obesity GWAS had significant gene correlation (r = 0.23). Pathway enrichment analysis showed that “Suz12 target genes” was the significant pathway for both children’s sleep and obesity; pathways were significantly shared among top enriched pathways with an OR of 8.1–59.4; and significant correlation coefficient of pathway U-score was r = 0.36. Analysis of sleep time and obesity GWAS variants for all ages in the NHGRI-EBI GWAS Catalog also presented significant pathway correlation (r = 0.30). The “PAX3-FOXO1 target genes” was the significant pathway for all-age obesity phenotype and ranked as the second top associated pathway for all-age sleep time. Our study suggested that genetic correlation of children’s sleep time and obesity is attributed to genes with pleiotropy effects and common pathway regulations that may contain only weak SNP associations.

Objective. Triple-negative breast cancer (TNBC) is an aggressive disease with highly invasive nature and poor outcomes. Due to the absence of specific treatment strategies for this tumor subgroup, patients with TNBC are treated with conventional therapeutics, frequently leading to systemic relapse. In this study, we sought to investigate apatinib combined with conventional chemotherapy regimens in treating patients with advanced TNBC concerning the efficacy, safety, expressions of tumor markers, and patient survival. Methods. This is a prospective study including 150 cases of advanced TNBC who were randomly arranged into a conventional group and combined group, with 75 cases per group. The patients in the conventional group were treated with conventional chemotherapy, and those in the combined group were treated with apatinib combined with conventional chemotherapy. The peripheral blood was collected from each patient, and carcinoembryonic antigen (CEA), carbohydrate antigen 153 (CA153), and carbohydrate antigen 125 (CA125) were determined. The expressions of nuclear proliferation antigen marker (Ki67), β-catenin, and E-cadherin were determined in the biopsy collected from each patient. Results. The objective remission rate (ORR) and disease control rate (DCR) (41.33% and 81.33%) in the combined group were notably higher than those in the conventional group (29.33% and 68.00%) ( P < 0.05 ). After treatment, the serum levels of CEA, CA153, and CA125 and the expressions of Ki67 and β-catenin were declined, but the expression of E-cadherin was increased in both groups; the combined group exhibited lower serum levels of CEA, CA153, and CA125, and the expressions of Ki67 and β-catenin were concurrent with a higher expression of E-cadherin than the conventional group ( P < 0.05 ). No significant difference was noted between the two groups regarding the occurrence of adverse reactions ( P > 0.05 ). Improved progression-free survival (PFS) was observed in the combined group compared to the conventional group ( P < 0.05 . Conclusion. These findings suggest that apatinib combined with conventional chemotherapy regimens confers a prolonged PFS for treating patients with advanced TNBC.

Double Cortin-like Kinase 1 (DCLK1) is a cancer stem cell (CSC) marker that is over-expressed in CSCs and epithelial-mesenchymal transition (EMT) cells of many cancers. Due to its expression in the chemoresistant, tumorigenic subpopulation in cancer tissue, DCLK1 plays critical roles in indefinite cell proliferation, tumorigenesis, tumor metastasis, and recurrence of cancer. Further evidence has shown that the deregulation or inhibition of DCLK1 directly causes a decrease in cancer succession and reduces the possibility of relapse. DCLK1 has five isoforms and association of each isoform with human colorectal cancer (hCRC) is unclear. For the current project, we aim to reveal correlation of the DCLK1 isoform 2 (DCLK1-S) with invasion and migration capability of hCRC cells. In order to achieve our goal, we established the isogenic DCLK1-S over-expression cells using the HCT116 cell line, performed the scratching assay, and used ImageJ software to determine the wound healing speed of DCLK1-S over-expression cells and HCT116 cells. Our preliminary results demonstrated that DCLK1-S was not associated with increased migration and invasion capability of hCRC cells. Compared to the HCT116 cells, the wound healing speed of DCLK1-S over-expression cells significantly decreased (P Citation Format: Valeria Brown, Lianna Li. The effects of DCLK1 isoform 2 upon the migration and invasion capabilities of colorectal cancer cells [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-135.

A prominent function of TGIF1 is suppression of transforming growth factor beta (TGF‐β) signaling, whose inactivation is deemed instrumental to the progression of pancreatic ductal adenocarcinoma (PDAC), as exemplified by the frequent loss of the tumor suppressor gene SMAD4 in this malignancy. Surprisingly, we found that genetic inactivation of Tgif1 in the context of oncogenic Kras, Kras(G12D), culminated in the development of highly aggressive and metastatic PDAC despite de‐repressing TGF‐β signaling. Mechanistic experiments show that TGIF1 associates with Twist1 and inhibits Twist1 expression and activity, and this function is suppressed in the vast majority of human PDACs by Kras(G12D)/MAPK‐mediated TGIF1 phosphorylation. Ablating Twist1 in Kras (G12D) ;Tgif1 (KO) mice completely blunted PDAC formation, providing the proof‐of‐principle that TGIF1 restrains Kras(G12D)‐driven PDAC through its ability to antagonize Twist1. Collectively, these findings pinpoint TGIF1 as a potential tumor suppressor in PDAC and further suggest that sustained activation of TGF‐β signaling might act to accelerate PDAC progression rather than to suppress its initiation.

Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/.

Seven gene sets were significantly enriched for SNP associations with diabetes, and considered as potential diabetes pathways in a previous meta-analysis of diabetes GWAS. This study aims to examine if these gene sets also have expression associations with diabetes. The analysis was conducted using pooled data from 23 diabetes gene expression studies. Gene associations were examined using linear modeling with an empirical Bayes approach, and pathway associations were investigated by testing enrichment for significant genes. Meta-analyses were performed to investigate gene and pathway associations in all studies and tissue types. The analysis showed that six gene sets and three member genes of ACADSB, RASSF2, and KLF12 had significant associations with diabetes traits. The findings suggest that these gene sets are related to diabetes regulation, and their functions tend to be tissue non-specific.

We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

Because healthcare workers played an important role in the battle against novel pandemic (H1N1) 2009 influenza, a clinical study was conducted to examine the immunogenicity and safety of a single dose of a China-made monovalent, split-virus, pandemic (H1N1) 2009 influenza vaccine in this special high-risk population. Healthcare workers in the First Affiliated Hospital of Guangzhou Medical College who received the pandemic (H1N1) 2009 influenza vaccine were prospectively enrolled. Antibody titers were measured at enrollment and 14 days later using hemagglutination-inhibition (HI) and microneutralization assays. Adverse events were recorded within 7 days and 6 months after vaccination. Double sera were provided by 51 of 65 enrolled subjects. Postvaccination titers of 1:40 or more on HI assay were observed in 96% of recipients. Seroconversion or a significant increase in titer on HI assay occurred in 59% of subjects. The factor increase in GMTs was 4.3. The majority of complaints were mild to moderate in intensity. Although more than half of healthcare workers seemed immune to the pandemic (H1N1) influenza A virus before vaccination, most of the subjects still showed a fast, robust immune response to a single 15-μg dose of a monovalent, split-virus unadjuvanted pandemic H1N1 2009 influenza vaccine.

Fatty pancreas or pancreatic steatosis has been associated with a variety of debilitating diseases, such as obesity, diabetes, pancreatitis, and pancreatic ductal adenocarcinoma (PDAC). Currently, neither the mechanisms underlying the pathogenesis of fatty pancreas nor the physiopathologic impacts of this disorder are well established. Serendipitously, we found that conditional overexpression of Twist1 in pancreatic progenitor cells in mice resulted in fatty pancreas development, leading to pancreatic insufficiency, severe hyperglycemia, and growth retardation. Molecular and genetic studies demonstrated that Twist1 drives fatty pancreas formation by selectively reprogramming acinar cells towards the adipocyte lineage albeit without affecting islet or ductal cell fate. Moreover, loss-of-function genetic experiments demonstrated that Twist1 plays a causative role in glucose tolerance, pancreatitis genesis, and PDAC progression. Finally, high levels of Twist1 expression correlate with fatty pancreas formation in patients with pancreatitis or PDAC, implicating Twist1 as a prognostic marker and possible target for attenuating several lethal diseases associated with fatty pancreas development. Citation Format: Thien Ly Nguyen, Purba Singh, Parash Parajuli, Lianna Li, Celine Prunier, Santosh Kumar, Sailaja Eragmerdi, Seval Ozkan, Hao Me, Jussara do Carmo, John Hall, Azeddine Atfi. Twist1-driven fatty pancreas formation facilitates pancreatitis and pancreatic ductal adenocarcinoma progression [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr A38.

The interferon-beta (IFN-beta) response is critical for protection against viral myocarditis in several mouse models, and IFN-alpha or -beta treatment is beneficial against human viral myocarditis. The IFN-beta response in cardiac myocytes and cardiac fibroblasts forms an integrated network for organ protection; however, the different IFN-alpha subtypes have not been studied in cardiac cells. We developed a quantitative RT-PCR assay that distinguishes between 13 highly conserved IFN-alpha subtypes and found that reovirus T3D induces five IFN-alpha subtypes in primary cardiac myocyte and fibroblast cultures: IFN-alpha1, -alpha2, -alpha4, -alpha5, and -alpha8/6. Murine IFN-alpha1, -alpha2, -alpha4, or -alpha5 treatment induced IRF7 and ISG56 and inhibited reovirus T3D replication in both cell types. This first investigation of IFN-alpha subtypes in cardiac cells for any virus demonstrates that IFN-alpha is induced in cardiac cells, that it is both subtype and cell type specific, and that it is likely important in the antiviral cardiac response.

Background Genetic heritability and expression study have shown that different diabetes traits have common genetic components and pathways. A computationally efficient pathway analysis of GWAS results will benefit post-GWAS study of SNP associations and identification of common genetic pathways from diabetes GWAS can help to improve understanding of the disease pathogenesis. Results We proposed a uniform-score gene-set analysis (USGSA) with implemented package to unify different gene measures by a uniform score for identifying pathways from GWAS data, and use a pre-generated permutation distribution table to quickly obtain multiple-testing adjusted p-value. Simulation studies of uniform score for four gene measures (minP, 2ndP, simP and fishP) have shown that USGSA has strictly controlled family-wise error rate. The power depends on types of gene measure. USGSA with a two-stage study strategy was applied to identify common pathways associated with diabetes traits based on public dbGaP GWAS results. The study identified 7 gene sets that contain binding motifs at promoter region of component genes for 5 transcription factors (TFs) of FOXO4, TCF3, NFAT, VSX1 and POU2F1, and 1 microRNA of mir-218. These gene sets include 25 common genes that are among top 5% of the gene associations over genome for all GWAS. Previous evidences showed that nearly all of these genes are mainly expressed in the brain. Conclusions USGSA is a computationally efficient approach for pathway analysis of GWAS data with promoted interpretability and comparability. The pathway analysis suggested that different diabetes traits share common pathways and component genes are potentially regulated by common TFs and microRNA. The result also indicated that the central nervous system has a critical role in diabetes pathogenesis. The findings will be important in formulating novel hypotheses for guiding follow-up studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1515-3) contains supplementary material, which is available to authorized users.

Colon cancer stem cells (CSCs) are implicated in colorectal cancer carcinogenesis, metastasis, and therapeutic resistance. The identification of these cells could help to develop novel therapeutic strategies. Doublecortin-like kinase 1 (DCLK1) has been viewed as a marker for gastrointestinal stem cells that fuel the self-renewal process, however others view them as a marker of Tuft cells or as an enteroendocrine subtype. The purpose of this study was to use a colon cancer cell line to identify and characterize the stem-like characteristics of the DCLK1+ cell population.To enrich stem-like cells, HCT116 cells (derived from colon adenocarcinomas) were cultured using serum-free media to form spheres under both normal oxygen and hypoxia condition. DCLK1 transcript expression in the adherent parental cells and spheroids was quantified using quantitative real time reverse transcription- polymerase chain reaction [(q)RT-PCR]. DCLK1 protein expression was determined using flow cytometry. Self-renewal capability from adherent parental cells and spheroids was determined using extreme limiting dilution analysis (ELDA).Under both normal oxygen and hypoxia condition, the adherent parental cells were composed of cells that express low levels of DCLK1. However, spheroids exhibited an increased frequency of cells expressing DCLK1 on both mRNA and protein levels. Cells derived from spheroids also possess stronger self-renewal capability.The higher fraction of DCLK1+ cells exhibited by spheroids and hypoxia reflects the stem-like characteristics of these cells. DCLK1 may represent an ideal marker to study and develop effective strategies to overcome chemo-resistance and relapse of colon cancer.

Apoptosis is a pathological hallmark of encephalitis and myocarditis caused by reovirus in newborn mice. In cell culture models, the antiviral transcription factor interferon regulatory factor 3 (IRF-3) enhances reovirus-induced apoptosis following activation via retinoic acid inducible gene I and interferon promoter-stimulating factor 1. To determine the role of IRF-3 in reovirus disease, we infected newborn IRF-3+/+and IRF-3−/−mice perorally with mildly virulent strain type 1 Lang (T1L) and fully virulent strain type 3 SA+ (T3SA+) and monitored infected animals for survival. Both wild-type and IRF-3−/−mice succumbed with equivalent frequencies to infection with T3SA+. However, the absence of IRF-3 was associated with significantly decreased survival rates following infection with T1L. The two virus strains achieved similar peak titers in IRF-3+/+and IRF-3−/−mice in the intestine, brain, heart, liver, and spleen. However, by day 12 postinoculation, titers in all organs examined were 10- to 100-fold higher in IRF-3−/−mice than those in wild-type mice. Increased titers were associated with marked pathological changes in all organs examined, especially in the heart, where absence of IRF-3 resulted in severe myocarditis. Cellular and humoral immune responses were equivalent in wild-type and IRF-3−/−animals, suggesting that IRF-3 functions independently of the adaptive immune response to enhance reovirus clearance. Thus, IRF-3 serves to facilitate virus clearance and prevent tissue injury in response to reovirus infection.

Viruses frequently infect the heart but clinical myocarditis is rare, suggesting that the cardiac antiviral response is uniquely effective. Indeed, the Type I interferon (IFN) response is cardiac cell type-specific and provides one integrated network of protection for the heart. Here, a proteomic approach was used to identify additional proteins that may be involved in the cardiac antiviral response. Reovirus-induced murine myocarditis reflects direct viral damage to cardiac cells, and offers an excellent system for study. Primary cultures of murine cardiac myocytes were infected with myocarditic or non-myocarditic reovirus strains, and whole cell lysates were compared by two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption / ionization – time-of-flight (MALDI-TOF/TOF) tandem mass spectrometry. Results were quantitative and reproducible, and demonstrated that whole proteome changes clustered according to viral pathogenic phenotype. Moreover, the data suggest that the heat shock protein Hsp25 is modulated differentially by myocarditic and non-myocarditic reoviruses and may play a role in the cardiac antiviral response. Members of seven virus families modulate Hsp25 or Hsp27 expression in a variety of cell types, suggesting that Hsp25 participation in the antiviral response may be widespread. However, results here provide the first evidence for a virus-induced decrease in Hsp25/27, and suggest that viruses may have evolved a mechanism to subvert this protective response, as they have for IFN.