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Full-Text Articles in Molecular Biology

The Impact Of Lncrna Dysregulation On Clinicopathology And Survival Of Breast Cancer: A Systematic Review And Meta-Analysis, Tian Tian, Meng Wang, Shuai Lin, Zhiming Dan, Kang Liu, Wenge Zhu, +Several Additional Authors Sep 2018

The Impact Of Lncrna Dysregulation On Clinicopathology And Survival Of Breast Cancer: A Systematic Review And Meta-Analysis, Tian Tian, Meng Wang, Shuai Lin, Zhiming Dan, Kang Liu, Wenge Zhu, +Several Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

Dysregulation of multiple long non-coding RNAs (lncRNAs) was reported to play major roles in breast cancer (BC). Here we aimed to collect most of the relevant literature to assess the prognostic value of lncRNAs in BC. To this end, we systematically searched PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang to identify published articles on the associations of lncRNAs with clinicopathology and/or survival of BC. Via this searching, we identified 70 articles involving 9,307 BC patients and regarding 48 lncRNAs. The expression of 41 lncRNAs was related to one or more clinicopathological parameters of ...


Rgn-259 (Thymosin Β4) Improves Clinically Important Dry Eye Efficacies In Comparison With Prescription Drugs In A Dry Eye Model., Chae Eun Kim, Hynda K Kleinman, Gabriel Sosne, George W Ousler, Kyeongsoon Kim, Sinwook Kang, Jaewook Yang Jul 2018

Rgn-259 (Thymosin Β4) Improves Clinically Important Dry Eye Efficacies In Comparison With Prescription Drugs In A Dry Eye Model., Chae Eun Kim, Hynda K Kleinman, Gabriel Sosne, George W Ousler, Kyeongsoon Kim, Sinwook Kang, Jaewook Yang

Biochemistry and Molecular Medicine Faculty Publications

This study evaluated the clinical activity of RGN-259 (thymosin β4) in comparison with cyclosporine A (CsA), diquafosol (DQS), and lifitegrast (LFA) in a murine model of dry eye. The model was NOD.B10-H2b mice in a 30-40% humidified environment together with daily scopolamine hydrobromide injections for 10 days. After desiccation stress, all drugs were evaluated after 10 treatment days. RGN-259 increased tear production similar to that in the DQS- and LFA-treated mice while CsA was inactive. RGN-259 improved corneal smoothness and decreased fluorescein staining similar to that of LFA group while CsA and DQS were inactive. Corneal epithelial detachment was ...


Loss And Gain Of N-Linked Glycosylation Sequons Due To Single-Nucleotide Variation In Cancer., Yu Fan, Yu Hu, Cheng Yan, Radoslav Goldman, Yang Pan, Raja Mazumder, Hayley M Dingerdissen Mar 2018

Loss And Gain Of N-Linked Glycosylation Sequons Due To Single-Nucleotide Variation In Cancer., Yu Fan, Yu Hu, Cheng Yan, Radoslav Goldman, Yang Pan, Raja Mazumder, Hayley M Dingerdissen

Biochemistry and Molecular Medicine Faculty Publications

Despite availability of sequence site-specific information resulting from years of sequencing and sequence feature curation, there have been few efforts to integrate and annotate this information. In this study, we update the number of human N-linked glycosylation sequons (NLGs), and we investigate cancer-relatedness of glycosylation-impacting somatic nonsynonymous single-nucleotide variation (nsSNV) by mapping human NLGs to cancer variation data and reporting the expected loss or gain of glycosylation sequon. We find 75.8% of all human proteins have at least one NLG for a total of 59,341 unique NLGs (includes predicted and experimentally validated). Only 27.4% of all NLGs ...


Evolution Of Echovirus 11 In A Chronically Infected Immunodeficient Patient., Majid Laassri, Tatiana Zagorodnyaya, Sharon Hassin-Baer, Rachel Handsher, Danit Sofer, Merav Weil, Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Lester Shulman Mar 2018

Evolution Of Echovirus 11 In A Chronically Infected Immunodeficient Patient., Majid Laassri, Tatiana Zagorodnyaya, Sharon Hassin-Baer, Rachel Handsher, Danit Sofer, Merav Weil, Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Lester Shulman

Biochemistry and Molecular Medicine Faculty Publications

Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of ...


Evolution Of Echovirus 11 In A Chronically Infected Immunodeficient Patient., Majid Laassri, Tatiana Zagorodnyaya, Sharon Hassin-Baer, Rachel Handsher, Danit Sofer, Merav Weil, Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Lester Shulman Mar 2018

Evolution Of Echovirus 11 In A Chronically Infected Immunodeficient Patient., Majid Laassri, Tatiana Zagorodnyaya, Sharon Hassin-Baer, Rachel Handsher, Danit Sofer, Merav Weil, Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Lester Shulman

Biochemistry and Molecular Medicine Faculty Publications

Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of ...


Cbx7 Regulates Stem Cell-Like Properties Of Gastric Cancer Cells Via P16 And Akt-Nf-Κb-Mir-21 Pathways., Su-Jie Ni, Li-Qin Zhao, Xiao-Feng Wang, Zhen-Hua Wu, Rui-Xi Hua, Chun-Hua Wan, Jie-Yun Zhang, Xiao-Wei Zhang, Ming-Zhu Huang, Lu Gan, Hua-Lin Sun, Goberdhan P Dimri, Wei-Jian Guo Feb 2018

Cbx7 Regulates Stem Cell-Like Properties Of Gastric Cancer Cells Via P16 And Akt-Nf-Κb-Mir-21 Pathways., Su-Jie Ni, Li-Qin Zhao, Xiao-Feng Wang, Zhen-Hua Wu, Rui-Xi Hua, Chun-Hua Wan, Jie-Yun Zhang, Xiao-Wei Zhang, Ming-Zhu Huang, Lu Gan, Hua-Lin Sun, Goberdhan P Dimri, Wei-Jian Guo

Biochemistry and Molecular Medicine Faculty Publications

BACKGROUND: Chromobox protein homolog 7 (CBX7), a member of the polycomb group (PcG) family of proteins, is involved in the regulation of cell proliferation and cancer progression. PcG family members, such as BMI, Mel-18, and EZH2, are integral constituents of the polycomb repressive complexes (PRCs) and have been known to regulate cancer stem cell (CSC) phenotype. However, the role of other PRCs' constituents such as CBX7 in the regulation of CSC phenotype remains largely elusive. This study was to investigate the role of CBX7 in regulating stem cell-like properties of gastric cancer and the underlying mechanisms.

METHODS: Firstly, the role ...


Integrated Genome-Wide Alu Methylation And Transcriptome Profiling Analyses Reveal Novel Epigenetic Regulatory Networks Associated With Autism Spectrum Disorder., Thanit Saeliw, Chayanin Tangsuwansri, Surangrat Thongkorn, Weerasak Chonchaiya, Kanya Suphapeetiporn, Apiwat Mutirangura, Tewin Tencomnao, Valerie W Hu, Tewarit Sarachana Jan 2018

Integrated Genome-Wide Alu Methylation And Transcriptome Profiling Analyses Reveal Novel Epigenetic Regulatory Networks Associated With Autism Spectrum Disorder., Thanit Saeliw, Chayanin Tangsuwansri, Surangrat Thongkorn, Weerasak Chonchaiya, Kanya Suphapeetiporn, Apiwat Mutirangura, Tewin Tencomnao, Valerie W Hu, Tewarit Sarachana

Biochemistry and Molecular Medicine Faculty Publications

Background: Alu elements are a group of repetitive elements that can influence gene expression through CpG residues and transcription factor binding. Altered gene expression and methylation profiles have been reported in various tissues and cell lines from individuals with autism spectrum disorder (ASD). However, the role of Alu elements in ASD remains unclear. We thus investigated whether Alu elements are associated with altered gene expression profiles in ASD.

Methods: We obtained five blood-based gene expression profiles from the Gene Expression Omnibus database and human Alu-inserted gene lists from the TranspoGene database. Differentially expressed genes (DEGs) in ASD were identified from ...


Association Of Two Foxp3 Polymorphisms With Breast Cancer In Chinese Han Women, Wenge Zhu, +Several Additional Authors Jan 2018

Association Of Two Foxp3 Polymorphisms With Breast Cancer In Chinese Han Women, Wenge Zhu, +Several Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

Background

Forkhead box P3 (FOXP3) is a key gene in the immune system which also plays a role in tumor development. This study aims to explore the association of two FOXP3 polymorphisms (rs3761548 and rs3761549) with susceptibility to breast cancer (BC).

Method

A case–control study was conducted, involving 560 patients and 583 healthy individuals from the Chinese Han population. The genotypes of FOXP3 polymorphisms were detected using the Sequenom MassARRAY method. The association between FOXP3 polymorphisms and BC risk was evaluated using a χ2 test with an odds ratio (OR) and 95% confidence intervals (95% CIs) under six genetic ...


Dexter: Disease-Expression Relation Extraction From Text., Samir Gupta, Hayley Dingerdissen, Karen E Ross, Yu Hu, Cathy H Wu, Raja Mazumder, K Vijay-Shanker Jan 2018

Dexter: Disease-Expression Relation Extraction From Text., Samir Gupta, Hayley Dingerdissen, Karen E Ross, Yu Hu, Cathy H Wu, Raja Mazumder, K Vijay-Shanker

Biochemistry and Molecular Medicine Faculty Publications

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases ...


The Igf2/Igf1r/Nanog Signaling Pathway Regulates The Proliferation Of Acute Myeloid Leukemia Stem Cells., Dan-Dan Xu, Ying Wang, Peng-Jun Zhou, Shu-Rong Qin, Rong Zhang, Yi Zhang, +Several Additional Authors Jan 2018

The Igf2/Igf1r/Nanog Signaling Pathway Regulates The Proliferation Of Acute Myeloid Leukemia Stem Cells., Dan-Dan Xu, Ying Wang, Peng-Jun Zhou, Shu-Rong Qin, Rong Zhang, Yi Zhang, +Several Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

Acute myeloid leukemia is an aggressive disease characterized by clonal proliferation and differentiation into immature hematopoietic cells of dysfunctional myeloid precursors. Accumulating evidence shows that CD34+CD38- leukemia stem cells (LSCs) are responsible for drug resistance, metastasis, and relapse of leukemia. In this study, we found that Nanog, a transcription factor in stem cells, is significantly overexpressed in CD34+ populations from patients with acute myeloid leukemia and in LSCs from leukemia cell lines. Our data demonstrate that the knockdown of Nanog inhibited proliferation and induced cell cycle arrest and cell apoptosis. Moreover, Nanog silencing suppressed the leukemogenesis of LSCs in ...


Total Flavonoids From Radix Glycyrrhiza Exert Anti-Inflammatory And Antitumorigenic Effects By Inactivating Inos Signaling Pathways., Yi-Xin Jiang, Yang-Yi Dai, Yi-Feng Pan, Xi-Min Wu, Yue Yang, Ka Bian, Dan-Dan Zhang Jan 2018

Total Flavonoids From Radix Glycyrrhiza Exert Anti-Inflammatory And Antitumorigenic Effects By Inactivating Inos Signaling Pathways., Yi-Xin Jiang, Yang-Yi Dai, Yi-Feng Pan, Xi-Min Wu, Yue Yang, Ka Bian, Dan-Dan Zhang

Biochemistry and Molecular Medicine Faculty Publications

Inducible nitric oxide synthase (iNOS) plays an important role in inflammation, which has also been considered as a major driver of breast cancer disease progression. Radix Glycyrrhiza (RG) has been broadly used for its anti-inflammatory and antitumorigenic effects. However, the mechanisms of regulation of iNOS in inflammation and cancer have not been fully explored. Total flavonoids isolated from RG (TFRG) exhibited anti-inflammatory activity through the regulation of ERK/NF-


Robust Expression Of Tumor Suppressor Mirna's Let-7 And Mir-195 Detected In Plasma Of Saudi Female Breast Cancer Patients., Amal Qattan, Haya Intabli, Wafa Alkhayal, Chafica Eltabache, Taher Tweigieri, Suad Bin Amer Nov 2017

Robust Expression Of Tumor Suppressor Mirna's Let-7 And Mir-195 Detected In Plasma Of Saudi Female Breast Cancer Patients., Amal Qattan, Haya Intabli, Wafa Alkhayal, Chafica Eltabache, Taher Tweigieri, Suad Bin Amer

Biochemistry and Molecular Medicine Faculty Publications

Background

Female breast cancer is frequently diagnosed at a later stage and the leading cause of cancer deaths world-wide. Levels of cell-free circulating microRNAs (miRNAs) can potentially be used as biomarkers to measure disease progression in breast cancer patients in a non-invasive way and are therefore of high clinical value.

Methods

Using quantitative RT-PCR, circulating miRNAs were measured in blood samples collected from disease-free individuals (n = 34), triple-negative breast tumours (TNBC) (n = 36) and luminal tumours (n = 57). In addition to intergroup comparisons, plasma miRNA expression levels of all groups were analyzed against RNASeq data from cancerous breast tissue via ...


An Organismal Model For Gene Regulatory Networks In The Gut-Associated Immune Response, Katherine M. Buckley, J P. Rast Oct 2017

An Organismal Model For Gene Regulatory Networks In The Gut-Associated Immune Response, Katherine M. Buckley, J P. Rast

Biochemistry and Molecular Medicine Faculty Publications

The gut epithelium is an ancient site of complex communication between the animal immune system and the microbial world. While elements of self-non-self receptors and effector mechanisms differ greatly among animal phyla, some aspects of recognition, regulation, and response are broadly conserved. A gene regulatory network (GRN) approach provides a means to investigate the nature of this conservation and divergence even as more peripheral functional details remain incompletely understood. The sea urchin embryo is an unparalleled experimental model for detangling the GRNs that govern embryonic development. By applying this theoretical framework to the free swimming, feeding larval stage of the ...


Engaging Medical Students In Problem-Based Search And Study Of The Biomedical Literature., Zhiyong Han, Samantha L Margulies, Divya Kurian, Joshua M Jabaut, Akshita Mehta, Ramzi Dudum, Huberta Koudoro, Ria S Roberts, Jay Lee, Jonathan Li, Hieu T Nguyen, Mark Elliott Aug 2017

Engaging Medical Students In Problem-Based Search And Study Of The Biomedical Literature., Zhiyong Han, Samantha L Margulies, Divya Kurian, Joshua M Jabaut, Akshita Mehta, Ramzi Dudum, Huberta Koudoro, Ria S Roberts, Jay Lee, Jonathan Li, Hieu T Nguyen, Mark Elliott

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.


Metastasis-Associated Protein 1 Deficiency Results In Compromised Pulmonary Alveolar Capillary Angiogenesis In Mice., Jun-Hui Qin, Zhen-Yu Ke, Qiang Zhou, Li Wang, Yuan Liang, Ying-Mei Wang, Tong Yang, Xing Gao, Jing Ye, Rekesh Kumar, Rui-An Wang Aug 2017

Metastasis-Associated Protein 1 Deficiency Results In Compromised Pulmonary Alveolar Capillary Angiogenesis In Mice., Jun-Hui Qin, Zhen-Yu Ke, Qiang Zhou, Li Wang, Yuan Liang, Ying-Mei Wang, Tong Yang, Xing Gao, Jing Ye, Rekesh Kumar, Rui-An Wang

Biochemistry and Molecular Medicine Faculty Publications

Background

The aim of this study was to investigate the effects of metastasis-associated protein 1 (MTA1) deficiency during angiogenesis of pulmonary alveolar capillaries in mice and to determine the molecular mechanisms involved.

Material/Methods

The expressions of MTA1, CD34, vascular endothelial growth factor (VEGF), alpha smooth muscle actin (α-SMA), and HIF-1α were analyzed in the lungs of MTA1-knockout (KO) and wild-type mice at embryonic day 18.5 and 2 months by quantitative PCR, immunoblotting, and immunohistochemistry. The morphological changes were investigated during pulmonary alveolar capillary formation. The heart weight/body weight (HW/BW) ratio and the size of the ...


Il-18 Polymorphisms Contribute To Hepatitis B Virus-Related Cirrhosis And Hepatocellular Carcinoma Susceptibility In Chinese Population: A Case-Control Study., Zhi-Jun Dai, Xing-Han Liu, Meng Wang, Yan Guo, Wenge Zhu, Xiao Li, Shuai Lin, Tian Tian, Kang Liu, Yi Zheng, Peng Xu, Tianbo Jin, Xiaopeng Li Jun 2017

Il-18 Polymorphisms Contribute To Hepatitis B Virus-Related Cirrhosis And Hepatocellular Carcinoma Susceptibility In Chinese Population: A Case-Control Study., Zhi-Jun Dai, Xing-Han Liu, Meng Wang, Yan Guo, Wenge Zhu, Xiao Li, Shuai Lin, Tian Tian, Kang Liu, Yi Zheng, Peng Xu, Tianbo Jin, Xiaopeng Li

Biochemistry and Molecular Medicine Faculty Publications

IL-18 polymorphisms influence the transcriptional activity of the IL-18 gene and associated with various diseases. However, their relationships with hepatitis B virus-related liver diseases had not reached a consensus. So we conducted this case-control study with a view to clarifying the association. We included four groups: healthy controls, chronic hepatitis B virus (CHB) carriers, liver cirrhosis (LC) and hepatocellular carcinoma (HCC) groups with each group of 250 persons. Odd ratios (ORs) and 95% confidence intervals (95%CIs) with or without adjustment were calculated. Haplotype analysis was also performed. The results showed people carrying rs187238 CG genotype had a lower risk ...


Safety And Potential Efficacy Of Gemfibrozil As A Supportive Treatment For Children With Late Infantile Neuronal Ceroid Lipofuscinosis And Other Lipid Storage Disorders., Kyeongsoon Kim, Hynda K Kleinman, Hahn-Jun Lee, Kalipada Pahan Jun 2017

Safety And Potential Efficacy Of Gemfibrozil As A Supportive Treatment For Children With Late Infantile Neuronal Ceroid Lipofuscinosis And Other Lipid Storage Disorders., Kyeongsoon Kim, Hynda K Kleinman, Hahn-Jun Lee, Kalipada Pahan

Biochemistry and Molecular Medicine Faculty Publications

Neuronal Ceroid Lipofuscinosis (NCL), also known as Batten disease, is a group of genetically distinct lysosomal disorders that mainly affect the central nervous system, resulting in progressive motor and cognitive decline primarily in children. Multiple distinct genes involved in the metabolism of lipids have been identified to date with various mutations in this family of diseases. There is no cure for these diseases but some new therapeutic approaches have been tested that offer more hope than the standard palliative care. Many of the therapeutic advances require invasive procedures but some progress in slowing the disease has been found and more ...


Long Non-Coding Rna Profile In Mantle Cell Lymphoma Identifies A Functional Lncrna Ror1-As1 Associated With Ezh2/Prc2 Complex., Guangzhen Hu, Shiv K Gupta, Tammy P Troska, Asha Nair, Mamta Gupta May 2017

Long Non-Coding Rna Profile In Mantle Cell Lymphoma Identifies A Functional Lncrna Ror1-As1 Associated With Ezh2/Prc2 Complex., Guangzhen Hu, Shiv K Gupta, Tammy P Troska, Asha Nair, Mamta Gupta

Biochemistry and Molecular Medicine Faculty Publications

Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma characterized by rapid disease progression. The needs for new therapeutic strategies for MCL patients call for further understanding on the molecular mechanisms of pathogenesis of MCL. Recently, long noncoding RNAs (lncRNAs) have been recognized as key regulators of gene expression and disease development, however, the role of lncRNAs in non-Hodgkin lymphoma and specifically in MCL is still unknown. Next generation RNA-sequencing was carried out on MCL patient samples along with normal controls and data was analyzed. As a result, several novel lncRNAs were found significantly overexpressed in the MCL samples with ...


Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3Α And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer, S Deivendran Apr 2017

Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3Α And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer, S Deivendran

Biochemistry and Molecular Medicine Faculty Publications

Despite a recognized role of DNA methyltransferase 3a (DNMT3a) in human cancer, the nature of its upstream regulator(s) and relationship with the master chromatin remodeling factor MTA1, continues to be poorly understood. Here, we found an inverse relationship between the levels of MTA1 and DNMT3a in human cancer and that high levels of MTA1 in combination of low DNMT3a status correlates well with poor survival of breast cancer patients. We discovered that MTA1 represses DNMT3a expression via HDAC1/YY1 transcription factor complex. Because IGFBP3 is an established target of DNMT3a, we investigated the effect of MTA1 upon IGFBP3 expression ...


Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3a And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer., S Deivendran, Hezlin Marzook, T R Santhoshkumar, Rakesh Kumar, M Radhakrishna Pillai Apr 2017

Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3a And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer., S Deivendran, Hezlin Marzook, T R Santhoshkumar, Rakesh Kumar, M Radhakrishna Pillai

Biochemistry and Molecular Medicine Faculty Publications

Despite a recognized role of DNA methyltransferase 3a (DNMT3a) in human cancer, the nature of its upstream regulator(s) and relationship with the master chromatin remodeling factor MTA1, continues to be poorly understood. Here, we found an inverse relationship between the levels of MTA1 and DNMT3a in human cancer and that high levels of MTA1 in combination of low DNMT3a status correlates well with poor survival of breast cancer patients. We discovered that MTA1 represses DNMT3a expression via HDAC1/YY1 transcription factor complex. Because IGFBP3 is an established target of DNMT3a, we investigated the effect of MTA1 upon IGFBP3 expression ...


Oxidative Stress And Inflammation In Hepatic Diseases: Current And Future Therapy., Karina Reyes-Gordillo, Ruchi Shah, Pablo Muriel Jan 2017

Oxidative Stress And Inflammation In Hepatic Diseases: Current And Future Therapy., Karina Reyes-Gordillo, Ruchi Shah, Pablo Muriel

Biochemistry and Molecular Medicine Faculty Publications

Liver disease is a highly prevalent disease that is one of the leading causes of death worldwide. The continuous exposure of the liver to some factors such as viruses, alcohol, fat, and biotransformed metabolites can cause hepatic injury, which can lead to inflammation and liver degeneration. When the injury is sustained for long time, it can cause chronic liver diseases (CLDs), which include a spectrum of disease states ranging from simple steatosis and steatohepatitis (steatosis with inflammation and hepatocyte injury and death) to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Multiple evidences indicate that oxidative stress and inflammation are the most ...


Metabolic Reprogramming Of Triple-Negative Breast Cancer: The Role Of Mirnas, Amal Qattan Jan 2017

Metabolic Reprogramming Of Triple-Negative Breast Cancer: The Role Of Mirnas, Amal Qattan

Biochemistry and Molecular Medicine Faculty Publications

MicroRNAs (miRNAs) are well known to influence the expression of the genes that regulate critical cellular functions. Various reports have suggested that they play critical roles in breast cancer metabolism through the regulation of various metabolic pathways, including the metabolism of glucose, lipids, glycolysis and the mitochondrial tricarboxylic acid cycle (TCA). miRNAs regulate the metabolic process by targeting key molecules (enzymes, kinases transporters) or by modifying the expression of key transcription molecules. In addition, miRNAs can indirectly regulate mRNA translation by targeting chromatin-remodeling enzymes. Furthermore, miRNAs influence the expression of both oncogenes and tumor suppressors and have a major impact ...


Ptpro Represses Erbb2-Driven Breast Oncogenesis By Dephosphorylation And Endosomal Internalization Of Erbb2., H Dong, L Ma, J Gan, W Lin, Rakesh Kumar, +9 Additional Authors Jan 2017

Ptpro Represses Erbb2-Driven Breast Oncogenesis By Dephosphorylation And Endosomal Internalization Of Erbb2., H Dong, L Ma, J Gan, W Lin, Rakesh Kumar, +9 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

The plasma membrane-associated tyrosine phosphatase PTPRO is frequently transcriptionally repressed in cancers and signifies poor prognosis of breast cancer patients. In this study, deletion of Ptpro inMMTV-Erbb2 transgenic mice dramatically shortened the mammary tumor latency and accelerated tumor growth due to loss of Ptpro within the breast cancer cells but not in surrounding tissue as confirmed by hetero-transplantation studies. Both in vitro and in vivo data demonstrated that the phosphatase activity was required for the inactivation of ERBB2 and its downstream signaling. PTPRO regulated the phosphorylation status of ERBB2 at Y1248. Co-immunoprecipitation and proximity ligation assay (Duolink) indicated that ...


Distribution Bias Analysis Of Germline And Somatic Single-Nucleotide Variations That Impact Protein Functional Site And Neighboring Amino Acids, Y Pan, C Yan, Y Hu, Y Fan, Qing Pan, Q Wan, J Torcivia-Rodriguez, Raja Mazumder Jan 2017

Distribution Bias Analysis Of Germline And Somatic Single-Nucleotide Variations That Impact Protein Functional Site And Neighboring Amino Acids, Y Pan, C Yan, Y Hu, Y Fan, Qing Pan, Q Wan, J Torcivia-Rodriguez, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Single nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types. By leveraging patient information for somatic pfsSNVs, we identified 17 loss of ...


The Vasodilatory Effects Of Anti-Inflammatory Herb Medications: A Comparison Study Of Four Botanical Extracts., Hong Ping Zhang, Dan-Dan Zhang, Yan Ke, Ka Bian Jan 2017

The Vasodilatory Effects Of Anti-Inflammatory Herb Medications: A Comparison Study Of Four Botanical Extracts., Hong Ping Zhang, Dan-Dan Zhang, Yan Ke, Ka Bian

Biochemistry and Molecular Medicine Faculty Publications

Inflammation plays a pivotal role in the development and progression of cardiovascular diseases, in which, the endothelium dysfunction has been a key element. The current study was designed to explore the vasodilatory effect of anti-inflammatory herbs which have been traditionally used in different clinical applications. The total saponins from Actinidia arguta radix (SAA), total flavonoids from Glycyrrhizae radix et rhizoma (FGR), total coumarins from Peucedani radix (CPR), and total flavonoids from Spatholobi caulis (FSC) were extracted. The isometric measurement of vasoactivity was used to observe the effects of herbal elements on the isolated aortic rings with or without endothelium. To ...


Genetic Polymorphisms In Caveolin-1 Associate With Breast Cancer Risk In Chinese Han Population, M Wang, T Tian, X Ma, W Zhu, Y Guo, Z Duan, J Fan, S Lin, K Liu, Y Zheng, Q Sheng, Z J. Dai, H Peng Jan 2017

Genetic Polymorphisms In Caveolin-1 Associate With Breast Cancer Risk In Chinese Han Population, M Wang, T Tian, X Ma, W Zhu, Y Guo, Z Duan, J Fan, S Lin, K Liu, Y Zheng, Q Sheng, Z J. Dai, H Peng

Biochemistry and Molecular Medicine Faculty Publications

Caveolin-1(CAV-1) was demonstrated to be a tumor suppressor gene and be implicated in the development of breast cancer (BC). Numerous potentially functional polymorphisms in CAV-1 have been identified, but their effects on BC were not clear. This case-control study aims to evaluate the relationship between CAV-1 polymorphisms and BC risk. 560 BC patients and 583 healthy controls were enrolled in the present study, all from Chinese Han population. We detected 3 single nucleotide polymorphisms (rs3807987, rs1997623, and rs7804372) in CAV-1 using the Sequenom MassARRAY method. The association between CAV-1genotypes and BC risk was assessed in six genetic models ...


Biomuta And Bioxpress: Mutation And Expression Knowledgebases For Cancer Biomarker Discovery, Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Kashay Jan 2017

Biomuta And Bioxpress: Mutation And Expression Knowledgebases For Cancer Biomarker Discovery, Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Kashay

Biochemistry and Molecular Medicine Faculty Publications

Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated single-nucleotide variations, and BioXpress, a database of cancer-associated differentially expressed genes and microRNAs, differ from other disease-associated variation and expression databases primarily through the aggregation of data across many studies into a single source with a unified representation and annotation of functional attributes. Early versions of these resources were initiated by pilot funding for specific ...


Presence Of A Prophage Determines Temperature-Dependent Capsule Production In Streptococcus Pyogenes., Leslie Brown, Jeong-Ho Kim, Kyu Hong Cho Sep 2016

Presence Of A Prophage Determines Temperature-Dependent Capsule Production In Streptococcus Pyogenes., Leslie Brown, Jeong-Ho Kim, Kyu Hong Cho

Biochemistry and Molecular Medicine Faculty Publications

A hyaluronic acid capsule is a major virulence factor in the pathogenesis of Streptococcus pyogenes. It acts as an anti-phagocytic agent and adhesin to keratinocytes. The expression of the capsule is primarily regulated at the transcriptional level by the two-component regulatory system CovRS, in which CovR acts as a transcriptional repressor. The covRS genes are frequently mutated in many invasive strains, and a subset of the invasive CovRS mutants does not produce a detectable level of the capsule at 37 °C, but produces a significant amount of the capsule at sub-body temperatures. Here, we report that a prophage has a ...


Rna2dnalign: Nucleotide Resolution Allele Asymmetries Through Quantitative Assessment Of Rna And Dna Paired Sequencing Data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, Anelia Horvath Aug 2016

Rna2dnalign: Nucleotide Resolution Allele Asymmetries Through Quantitative Assessment Of Rna And Dna Paired Sequencing Data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, Anelia Horvath

Biochemistry and Molecular Medicine Faculty Publications

We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting). We applied RNA2DNAlign on 360 ...


Inhibition Of Nuclear Factor-Kappa B Enhances The Tumor Growth Of Ovarian Cancer Cell Line Derived From A Low-Grade Papillary Serous Carcinoma In P53-Independent Pathway, Xue Xiao, Gong Yang, Peng Bai, Shunping Gui, Tri M. Bui Nguyen, +8 Additional Authors Aug 2016

Inhibition Of Nuclear Factor-Kappa B Enhances The Tumor Growth Of Ovarian Cancer Cell Line Derived From A Low-Grade Papillary Serous Carcinoma In P53-Independent Pathway, Xue Xiao, Gong Yang, Peng Bai, Shunping Gui, Tri M. Bui Nguyen, +8 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

Background: NF-kB can function as an oncogene or tumor suppressor depending on cancer types. The role of NF-kB in low-grade serous ovarian cancer, however, has never been tested. We sought to elucidate the function of NF-kB in the low-grade serous ovarian cancer.

Methods: The ovarian cancer cell line, HOC-7, derived from a low-grade papillary serous carcinoma. Introduction of a dominant negative mutant, IkBαM, which resulted in decrease of NF-kB function in ovarian cancer cell lines. The transcription ability, tumorigenesis, cell proliferation and apoptosis were observed in derivative cell lines in comparison with parental cells.

Results: Western blot analysis indicated increased ...