Advanced Genomic Technology, Llc

LOUISVILLE, KY, United States

Advanced Genomic Technology, Llc

LOUISVILLE, KY, United States
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Kolbert C.P.,Advanced Genomic Technology, Llc | Kahl J.C.,Mayo Medical School | Asmann Y.W.,Mayo Medical School
AIDS | Year: 2010

OBJECTIVE: HIV infection of CD4 T cells can lead to HIV protease-mediated cleavage of procaspase 8 generating a novel, HIV-specific peptide called Casp8p41. Casp8p41 has at least two biologic functions: induction of cell death via mitochondrial depolarization and release of cytochrome C, as well as activation of nuclear factor kappa B (NFκB). We have previously shown that Casp8p41-induced NFκB activation enhances HIV LTR transcription and consequently increases HIV replication. Herein, we questioned whether Casp8p41-induced NFκB activation impacts the cytokine profile of cells expressing Casp8p41. DESIGN: Analysis of cells expressing Casp8p41 and HIV-infected T cells. METHODS: We assessed whether host genes are transcriptionally activated following Casp8p41 production, using microarray analysis, cytokine quantification, followed by western blot and flow cytometry. RESULTS: Microarray analysis identified 259 genes significantly upregulated following expression of Casp8p41. Furthermore, Casp8p41 expression in primary CD4 T cells results in increased production of interleukin (IL)-2, IL-15 and tumor necrosis factor (TNF), as well as IL-1RA; whereas levels of granulocyte macrophage colony-stimulating factor and interferon (IFN)-γ were reduced in the Casp8p41 expressing cells. Intracellular flow cytometry confirmed the co-association of Casp8p41 with elevated TNF in HIV-infected cells. CONCLUSION: These data indicate that the expression of Casp8p41 in HIV-infected CD4 T cells in addition to promoting apoptosis and enhancing HIV replication also promotes a proinflammatory cytokine milieu, which is characteristic of untreated HIV infection. © 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Kosari F.,Laboratory Medicine and Pathology Mayo Clinic | Ida C.M.,Mayo Medical School | Aubry M.-C.,Mayo Medical School | Yang L.,Mayo Medical School | And 11 more authors.
Oncogene | Year: 2014

ASCL1 is an important regulatory transcription factor in pulmonary neuroendocrine (NE) cell development, but its value as a biomarker of NE differentiation in lung adenocarcinoma (AD) and as a potential prognostic biomarker remains unclear. We examined ASCL1 expression in lung cancer samples of varied histologic subtype, clinical outcome and smoking status and compared with expression of traditional NE markers. ASCL1 mRNA expression was found almost exclusively in smokers with AD, in contrast to non-smokers and other lung cancer subtypes. ASCL1 protein expression by immunohistochemical (IHC) analysis correlated best with synaptophysin compared with chromogranin and CD56/NCAM. Analysis of a compendium of 367 microarray-based gene expression profiles in stage I lung adenocarcinomas identified significantly higher expression levels of the RET oncogene in ASCL1-positive tumors (ASCL1 +) compared with ASCL1-tumors (q-value <10-9). High levels of RET expression in ASCL1 + but not in ASCL1-tumors was associated with significantly shorter overall survival (OS) in stage 1 (P=0.007) and in all AD (P=0.037). RET protein expression by IHC had an association with OS in the context of ASCL1 expression. In silico gene set analysis and in vitro experiments by ASCL1 shRNA in AD cells with high endogenous expression of ASCL1 and RET implicated ASCL1 as a potential upstream regulator of the RET oncogene. Also, silencing ASCL1 in AD cells markedly reduced cell growth and motility. These results suggest that ASCL1 and RET expression defines a clinically relevant subgroup of ∼10% of AD characterized by NE differentiation. © 2014 Macmillan Publishers Limited All rights reserved.


PubMed | Advanced Genomic Technology, Llc, Mayo Medical School and Molecular Therapeutics
Type: Journal Article | Journal: Oncogene | Year: 2014

ASCL1 is an important regulatory transcription factor in pulmonary neuroendocrine (NE) cell development, but its value as a biomarker of NE differentiation in lung adenocarcinoma (AD) and as a potential prognostic biomarker remains unclear. We examined ASCL1 expression in lung cancer samples of varied histologic subtype, clinical outcome and smoking status and compared with expression of traditional NE markers. ASCL1 mRNA expression was found almost exclusively in smokers with AD, in contrast to non-smokers and other lung cancer subtypes. ASCL1 protein expression by immunohistochemical (IHC) analysis correlated best with synaptophysin compared with chromogranin and CD56/NCAM. Analysis of a compendium of 367 microarray-based gene expression profiles in stage I lung adenocarcinomas identified significantly higher expression levels of the RET oncogene in ASCL1-positive tumors (ASCL1(+)) compared with ASCL1(-) tumors (q-value <10(-9)). High levels of RET expression in ASCL1(+) but not in ASCL1(-) tumors was associated with significantly shorter overall survival (OS) in stage 1 (P=0.007) and in all AD (P=0.037). RET protein expression by IHC had an association with OS in the context of ASCL1 expression. In silico gene set analysis and in vitro experiments by ASCL1 shRNA in AD cells with high endogenous expression of ASCL1 and RET implicated ASCL1 as a potential upstream regulator of the RET oncogene. Also, silencing ASCL1 in AD cells markedly reduced cell growth and motility. These results suggest that ASCL1 and RET expression defines a clinically relevant subgroup of 10% of AD characterized by NE differentiation.


Bhatnagar S.,Advanced Genomic Technology, Llc | Chertkow H.,McGill University | Chertkow H.,Jewish General Hospital | Chertkow H.,Lady Davis Institute for Medical Research | And 8 more authors.
Frontiers in Molecular Neuroscience | Year: 2014

Circulating microRNAs, present either in the cellular component, peripheral blood mononuclear cells (PBMC), or in cell-free plasma, have emerged as biomarkers for age-dependent systemic, disease-associated changes in many organs. Previously, we have shown that microRNA (miR)-34a is increased in circulating PBMC of Alzheimer's disease (AD) patients. In the present study, we show that this microRNA's sister, miR-34c, exhibits even greater increase in both cellular and plasma components of AD circulating blood samples, compared to normal age-matched controls. Statistical analysis shows the accuracy of levels of miR-34c assayed by receiver operating characteristic (ROC) analysis: the area under the curve is 0.99 (p < 0.0001) and the 95% confidence level extends from 0.97 to 1. Pearson correlation between miR-34c levels and mild and moderate AD, as defined by the mini-mental state examination (MMSE), shows an r-value of -0.7, suggesting a relatively strong inverse relationship between the two parameters. These data show that plasma levels of microRNA 34c are much more prominent in AD than those of its sister, miR-34a, or than its own level in PBMC. Transfection studies show that miR-34c, as does its sister miR-34a, represses the expression of several selected genes involved in cell survival and oxidative defense pathways, such as Bcl2, SIRT1, and others, in cultured cells. Taken together, our results indicate that increased levels of miR-34c in both PBMC and plasma may reflect changes in circulating blood samples in AD patients, compared to age-matched normal controls. © 2014 Bhatnagar, Chertkow, Schipper, Yuan, Shetty, Jenkins, Jones and Wang.


PubMed | Advanced Genomic Technology, Llc and McGill University
Type: | Journal: Frontiers in molecular neuroscience | Year: 2014

Circulating microRNAs, present either in the cellular component, peripheral blood mononuclear cells (PBMC), or in cell-free plasma, have emerged as biomarkers for age-dependent systemic, disease-associated changes in many organs. Previously, we have shown that microRNA (miR)-34a is increased in circulating PBMC of Alzheimers disease (AD) patients. In the present study, we show that this microRNAs sister, miR-34c, exhibits even greater increase in both cellular and plasma components of AD circulating blood samples, compared to normal age-matched controls. Statistical analysis shows the accuracy of levels of miR-34c assayed by receiver operating characteristic (ROC) analysis: the area under the curve is 0.99 (p < 0.0001) and the 95% confidence level extends from 0.97 to 1. Pearson correlation between miR-34c levels and mild and moderate AD, as defined by the mini-mental state examination (MMSE), shows an r-value of -0.7, suggesting a relatively strong inverse relationship between the two parameters. These data show that plasma levels of microRNA 34c are much more prominent in AD than those of its sister, miR-34a, or than its own level in PBMC. Transfection studies show that miR-34c, as does its sister miR-34a, represses the expression of several selected genes involved in cell survival and oxidative defense pathways, such as Bcl2, SIRT1, and others, in cultured cells. Taken together, our results indicate that increased levels of miR-34c in both PBMC and plasma may reflect changes in circulating blood samples in AD patients, compared to age-matched normal controls.


Baxter R.M.,Synedgen | Dai T.,Massachusetts General Hospital | Dai T.,Harvard University | Kimball J.,HemCon Inc | And 7 more authors.
Journal of Biomedical Materials Research - Part A | Year: 2013

Burns are a significant health challenge and healing can result in scar formation. Chitosan, a derivative of chitin, has been used to promote wound healing. In this study we used gene expression profiling in a mouse model of full thickness cutaneous burn to assess the benefits of treating with a chitosan lactate dressing. Three days after wounding mice treated with chitosan showed increased expression of genes associated with formation of granulation tissue. At a later time point, seven days after wounding, genes that initially showed increased expression were now down-regulated, and there was increased expression of genes involved in remodeling suggesting that the chitosan treatment results in accelerated healing. Quantitative RT-PCR showed modulated mRNA levels for TGFb1 by the chitosan dressing. TGFb1 initially promotes healing but extended activity can result in scarring. Importantly we found that expression was elevated at day three, but decreased at day seven suggesting that chitosan treatment will not result in scar formation, and may even be beneficial in preventing scar formation. Additionally, the biphasic regulation of expression of TGFb1 could be a powerful biomarker for future studies of the wound-healing potential of chitosan based and other treatments for burn wounds. © 2012 WILEY PERIODICALS, INC.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 107.00K | Year: 2010

DESCRIPTION (provided by applicant): The present lack of blood-based diagnosis requires AD patients to be subjected to either invasive spinal fluid (CSF) tapping, expensive MRI or PET imaging, or arduous psychological testing, all unsuitable and costly for our elderly. Strategically, we shall address this unmet need by generating systemic biomarkers detectable in peripheral mononuclear cells (PBMC) and serum/plasma, focusing on two classes of molecules, micro- RNAs and their target genes, which generally exhibit an inverse relationship because the former noncoding RNA functions by partially repressing the latter s expression as a dimmer switch , via binding either at the co- ding region of the message, thus degrading it, or at the 3 -untranslated region, to inhibit translation. Thus, key microRNAs and their targets can serve as disease biomarkers, in see-saw balance, applicable for new diagnostics and/or therapy. Our pilot study with a small cohort of 16 AD and 16 age-matched normal elderly controls (NEC) revealed: 1. Predominant down-regulation of gene expression at the message level in AD PBMC; and 2. Correlated up-regulation of microRNA (miR) expression in PBMC of the same individuals. In this proposal, we focus on a specific up-regulated microRNA, miR-34a, whose known targets are SIRT1, cdk4, cdk6, cyclin E2, bcl2, etc. SIRT1 is a member of the 7-member Silent Information Regulator protein family. Caloric restriction extends longevity through triggering expression of SIRT1, which can also be mimicked by resveratrol, a red wine polyphenol. SIRT1 reduction is linked to accumulation of Tau and A242 production, two hallmarks of AD etiopathogenesis. Thus, we suggest that in AD there is a systemic effect detectable in PBMC and serum/plasma; up-regulated miR-34a may induce down-regulation of SIRT1, with attendant pathophysiologic results. In this proposal, we plan to generate for this see-saw of changes miR-34a/SIRT1 Target Pair Ratio (TPR) indices, to quantify both disease presence as well as progress; the indices should also provide an unprecedented evaluation of drug efficacy. This Fast-track proposal of two phases is planned with our existing small cohort study as the roadmap for the larger cohort investigation: Phase I of six months with our existing small 16 AD and 16 NEC sample cohorts to: Aim 1. study possible down-regulation of miR-34a s known targets; and Aim 2. develop a feasibility study of pilot miR-34a/SIRT1 TPR-indices; and Phase II of two years with larger cohorts of 200 AD and 200 NEC participants: Aim 1.Establish a Bio-Repository of PBMC-DNA, -RNA and -protein specimens, and serum/plasma samples for assays in Aims 2 and 3; Aim 2. Generate PBMC-based miR34a/SIRT1 (and other targets) TPR indices; and Aim 3. Perform feasibility study to develop serum/plasma-based miR- 34a/SIRT1-TPR indices. Success of this project will allow us to generate PBMC- and serum-based miR-TPR indices as personalized diagnostics for AD victims, meeting an urgent need in health care, a huge gain for disease victims, their caregivers, and our society at large. PUBLIC HEALTH RELEVANCE: At present, the absence of any blood-based diagnosis for Alzheimer s disease (AD) requires patients to enduring arduous neuropsychological testing, invasive cerebrospinal fluid tapping, and/or expensive MRI or PET imaging, with definitive diagnosis deferred until brain autopsy. Our preliminary findings, based on new science concerning a novel molecular species, microRNAs (miR) and their see-saw partial repression of the expression of their target gene(s), suggest that potential disease biomarkers for AD are detectable systemical- ly in peripheral blood mononuclear cells and/or serum/plasma, and may be quantified as miR-Target Pair Ra- tios (TPR). Our plan is to define AD-specific TPR indices, initially focusing on miR-34a and its target, SIRT1, whose reduction is known to be associated with increased Tau and A242, two hallmarks of AD etiopathogene- sis; our ultimate goal is a Tool-Box of TPR indices, miR-34a/SIRT1-TPR being the first such AD diagnostic, indicating not only disease presence, but also its progress (and even drug efficacy monitoring), a huge strate- gic gain for the victims of this costly disease, and our society at large


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 1.65M | Year: 2011

DESCRIPTION (provided by applicant): The present lack of blood-based diagnosis requires AD patients to be subjected to either invasive spinal fluid (CSF) tapping, expensive MRI or PET imaging, or arduous psychological testing, all unsuitable and costly forour elderly. Strategically, we shall address this unmet need by generating systemic biomarkers detectable in peripheral mononuclear cells (PBMC) and serum/plasma, focusing on two classes of molecules, micro- RNAs and their target genes, which generally exhibit an inverse relationship because the former noncoding RNA functions by partially repressing the latter s expression as a dimmer switch , via binding either at the co- ding region of the message, thus degrading it, or at the 3 -untranslated region, toinhibit translation. Thus, key microRNAs and their targets can serve as disease biomarkers, in see-saw balance, applicable for new diagnostics and/or therapy. Our pilot study with a small cohort of 16 AD and 16 age-matched normal elderly controls (NEC)revealed: 1. Predominant down-regulation of gene expression at the message level in AD PBMC; and 2. Correlated up-regulation of microRNA (miR) expression in PBMC of the same individuals. In this proposal, we focus on a specific up-regulated microRNA, miR-34a, whose known targets are SIRT1, cdk4, cdk6, cyclin E2, bcl2, etc. SIRT1 is a member of the 7-member Silent Information Regulator protein family. Caloric restriction extends longevity through triggering expression of SIRT1, which can also be mimicked byresveratrol, a red wine polyphenol. SIRT1 reduction is linked to accumulation of Tau and A242 production, two hallmarks of AD etiopathogenesis. Thus, we suggest that in AD there is a systemic effect detectable in PBMC and serum/plasma; up-regulated miR-34amay induce down-regulation of SIRT1, with attendant pathophysiologic results. In this proposal, we plan to generate for this see-saw of changes miR-34a/SIRT1 Target Pair Ratio (TPR) indices, to quantify both disease presence as well as progress; the indices should also provide an unprecedented evaluation of drug efficacy. This Fast-track proposal of two phases is planned with our existing small cohort study as the roadmap for the larger cohort investigation: Phase I of six months with our existing small16 AD and 16 NEC sample cohorts to: Aim 1. study possible down-regulation of miR-34a s known targets; and Aim 2. develop a feasibility study of pilot miR-34a/SIRT1 TPR-indices; and Phase II of two years with larger cohorts of 200 AD and 200 NEC participants: Aim 1.Establish a Bio-Repository of PBMC-DNA, -RNA and -protein specimens, and serum/plasma samples for assays in Aims 2 and 3; Aim 2. Generate PBMC-based miR34a/SIRT1 (and other targets) TPR indices; and Aim 3. Perform feasibility study to develop serum/plasma-based miR- 34a/SIRT1-TPR indices. Success of this project will allow us to generate PBMC- and serum-based miR-TPR indices as personalized diagnostics for AD victims, meeting an urgent need in health care, a huge gain for disease victims, their caregivers, and our society at large. PUBLIC HEALTH RELEVANCE: At present, the absence of any blood-based diagnosis for Alzheimer s disease (AD) requires patients to enduring arduous neuropsychological testing, invasive cerebrospinal fluid tapping, and/or expensive MRI or PET imaging, with definitive diagnosis deferred until brain autopsy. Our preliminary findings, based on new science concerning a novel molecular species, microRNAs (miR) and their see-saw partial repression of the expression of their target gene(s), suggest that potential disease biomarkers for AD are detectable systemical- ly in peripheral blood mononuclear cells and/or serum/plasma, and may be quantified as miR-Target Pair Ra- tios (TPR). Our plan is to define AD-specific TPR indices, initially focusing on miR-34a and its target, SIRT1, whose reduction is known to be associated with increased Tau and A242, two hallmarks of AD etiopathogene- sis; our ultimate goal is a Tool-Box of TPR indices, miR-34a/SIRT1-TPR being the first suchAD diagnostic, indicating not only disease presence, but also its progress (and even drug efficacy monitoring), a huge strate- gic gain for the victims of this costly disease, and our society at large


Patent
Advanced Genomic Technology, Llc | Date: 2015-09-28

Biomarker associated with Alzheimers Disease (AD) and/or Mild Cognitive Impairment (MCI), where the biomarker is an intracellular or circulating microRNA and/or target protein thereof, and use thereof in methods for determining, diagnosing, monitoring AD, mild AD, moderate Ad, severe AD, MCI, early MCI, late MCI, and the like, as well as in methods for selecting candidate therapeutic compounds for treating same.


A transgenic, non-human animal model for accelerated aging and/or age-related symptom, recombinant nucleic acid molecules, cells and methods that can be used to make such animal model and cells, methods of using the animal model and cells, to descendants of the transgenic non-human animal, obtained by breeding with the same or with another phenotype, and to a cell line or primary cell culture or to an organotypic brain slice culture, derived from the transgenic non-human animal or its descendants are disclosed.

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