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The Molecular Microscope Diagnostic System: Assessment of Rejection and Injury in Heart Transplant Biopsies. Transplantation 2023; 107:27-44. [PMID: 36508644 DOI: 10.1097/tp.0000000000004323] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review describes the development of the Molecular Microscope Diagnostic System (MMDx) for heart transplant endomyocardial biopsies (EMBs). MMDx-Heart uses microarrays to measure biopsy-based gene expression and ensembles of machine learning algorithms to interpret the results and compare each new biopsy to a large reference set of earlier biopsies. MMDx assesses T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), recent parenchymal injury, and atrophy-fibrosis, continually "learning" from new biopsies. Rejection-associated transcripts mapped in kidney transplants and experimental systems were used to identify TCMR, AMR, and recent injury-induced inflammation. Rejection and injury emerged as gradients of intensity, rather than binary classes. AMR was one-third donor-specific antibody (DSA)-negative, and many EMBs first considered to have no rejection displayed minor AMR-like changes, with increased probability of DSA positivity and subtle inflammation. Rejection-associated transcript-based algorithms now classify EMBs as "Normal," "Minor AMR changes," "AMR," "possible AMR," "TCMR," "possible TCMR," and "recent injury." Additionally, MMDx uses injury-associated transcript sets to assess the degree of parenchymal injury and atrophy-fibrosis in every biopsy and study the effect of rejection on the parenchyma. TCMR directly injures the parenchyma whereas AMR usually induces microcirculation stress but relatively little initial parenchymal damage, although slowly inducing parenchymal atrophy-fibrosis. Function (left ventricular ejection fraction) and short-term risk of failure are strongly determined by parenchymal injury. These discoveries can guide molecular diagnostic applications, either as a central MMDx system or adapted to other platforms. MMDx can also help calibrate noninvasive blood-based biomarkers to avoid unnecessary biopsies and monitor response to therapy.
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Kuscu C, Kiran M, Mohammed A, Kuscu C, Satpathy S, Wolen A, Bardhi E, Bajwa A, Eason JD, Maluf D, Mas V, Akalin E. Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. Int J Mol Sci 2021; 22:ijms22126218. [PMID: 34207555 PMCID: PMC8226568 DOI: 10.3390/ijms22126218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transplant glomerulopathy develops through multiple mechanisms, including donor-specific antibodies, T cells and innate immunity. This study investigates circulating small RNA profiles in serum samples of kidney transplant recipients with biopsy-proven transplant glomerulopathy. Among total small RNA population, miRNAs were the most abundant species in the serum of kidney transplant patients. In addition, fragments arising from mature tRNA and rRNA were detected. Most of the tRNA fragments were generated from 5′ ends of mature tRNA and mainly from two parental tRNAs: tRNA-Gly and tRNA-Glu. Moreover, transplant patients with transplant glomerulopathy displayed a novel tRNA fragments signature. Gene expression analysis from allograft tissues demonstrated changes in canonical pathways related to immune activation such as iCos-iCosL signaling pathway in T helper cells, Th1 and Th2 activation pathway, and dendritic cell maturation. mRNA targets of down-regulated miRNAs such as miR-1224-5p, miR-4508, miR-320, miR-378a from serum were globally upregulated in tissue. Integration of serum miRNA profiles with tissue gene expression showed that changes in serum miRNAs support the role of T-cell mediated mechanisms in ongoing allograft injury.
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Affiliation(s)
- Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
- Correspondence: ; Tel.: +1-901-448-3162
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Akram Mohammed
- Center for Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Sarthak Satpathy
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Aaron Wolen
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Elissa Bardhi
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Daniel Maluf
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Valeria Mas
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Enver Akalin
- Montefiore Medical Center, Abdominal Transplant Program, Albert Einstein College of Medicine, Bronx, NY 10467, USA;
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Stinkens R, van der Kolk BW, Jordan J, Jax T, Engeli S, Heise T, Jocken JW, May M, Schindler C, Havekes B, Schaper N, Albrecht D, Kaiser S, Hartmann N, Letzkus M, Langenickel TH, Goossens GH, Blaak EE. The effects of angiotensin receptor neprilysin inhibition by sacubitril/valsartan on adipose tissue transcriptome and protein expression in obese hypertensive patients. Sci Rep 2018; 8:3933. [PMID: 29500454 PMCID: PMC5834447 DOI: 10.1038/s41598-018-22194-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/19/2018] [Indexed: 01/30/2023] Open
Abstract
Increased activation of the renin-angiotensin system is involved in the onset and progression of cardiometabolic diseases, while natriuretic peptides (NP) may exert protective effects. We have recently demonstrated that sacubitril/valsartan (LCZ696), a first-in-class angiotensin receptor neprilysin inhibitor, which blocks the angiotensin II type-1 receptor and augments natriuretic peptide levels, improved peripheral insulin sensitivity in obese hypertensive patients. Here, we investigated the effects of sacubitril/valsartan (400 mg QD) treatment for 8 weeks on the abdominal subcutaneous adipose tissue (AT) phenotype compared to the metabolically neutral comparator amlodipine (10 mg QD) in 70 obese hypertensive patients. Abdominal subcutaneous AT biopsies were collected before and after intervention to determine the AT transcriptome and expression of proteins involved in lipolysis, NP signaling and mitochondrial oxidative metabolism. Both sacubitril/valsartan and amlodipine treatment did not significantly induce AT transcriptional changes in pathways related to lipolysis, NP signaling and oxidative metabolism. Furthermore, protein expression of adipose triglyceride lipase (ATGL) (Ptime*group = 0.195), hormone-sensitive lipase (HSL) (Ptime*group = 0.458), HSL-ser660 phosphorylation (Ptime*group = 0.340), NP receptor-A (NPRA) (Ptime*group = 0.829) and OXPHOS complexes (Ptime*group = 0.964) remained unchanged. In conclusion, sacubitril/valsartan treatment for 8 weeks did not alter the abdominal subcutaneous AT transcriptome and expression of proteins involved in lipolysis, NP signaling and oxidative metabolism in obese hypertensive patients.
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Affiliation(s)
- R Stinkens
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - B W van der Kolk
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - J Jordan
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany.,Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - T Jax
- Profil GmbH, Neuss, Germany
| | - S Engeli
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany
| | | | - J W Jocken
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - M May
- Clinical Research Center Hannover, Hannover Medical School, Hannover, Germany
| | - C Schindler
- Clinical Research Center Hannover, Hannover Medical School, Hannover, Germany
| | - B Havekes
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Internal Medicine, Division of Endocrinology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - N Schaper
- Department of Internal Medicine, Division of Endocrinology, Maastricht University Medical Center+, Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, CAPHRI School for Public Health and Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - D Albrecht
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - S Kaiser
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - N Hartmann
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - M Letzkus
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - T H Langenickel
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - G H Goossens
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - E E Blaak
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.
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Wang TH, Chen CC, Liang KH, Chen CY, Chuang WY, Ueng SH, Chu PH, Huang CG, Chen TC, Hsueh C. A Multivariate Evaluation of Factors Affecting the Quality of Freshly Frozen Tissue Specimens. Biopreserv Biobank 2017; 15:344-349. [DOI: 10.1089/bio.2016.0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Tong-Hong Wang
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chin-Chuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan
| | - Kung-Hao Liang
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chi-Yuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Wen-Yu Chuang
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Shir-Hwa Ueng
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Pao-Hsien Chu
- Healthcare Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tse-Ching Chen
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chuen Hsueh
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
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Gandhi D, Tarale P, Naoghare PK, Bafana A, Krishnamurthi K, Arrigo P, Saravanadevi S. An integrated genomic and proteomic approach to identify signatures of endosulfan exposure in hepatocellular carcinoma cells. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 125:8-16. [PMID: 26615145 DOI: 10.1016/j.pestbp.2015.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/16/2015] [Accepted: 06/19/2015] [Indexed: 06/05/2023]
Abstract
Present study reports the identification of genomic and proteomic signatures of endosulfan exposure in hepatocellular carcinoma cells (HepG2). HepG2 cells were exposed to sublethal concentration (15μM) of endosulfan for 24h. DNA microarray and MALDI-TOF-MS analyses revealed that endosulfan induced significant alterations in the expression level of genes and proteins involved in multiple cellular pathways (apoptosis, transcription, immune/inflammatory response, carbohydrate metabolism, etc.). Furthermore, downregulation of PHLDA gene, upregulation of ACIN1 protein and caspase-3 activation in exposed cells indicated that endosulfan can trigger apoptotic cascade in hepatocellular carcinoma cells. In total 135 transcripts and 19 proteins were differentially expressed. This study presents an integrated approach to identify the alteration of biological/cellular pathways in HepG2 cells upon endosulfan exposure.
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Affiliation(s)
- Deepa Gandhi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Prashant Tarale
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Pravin K Naoghare
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Amit Bafana
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Kannan Krishnamurthi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | | | - Sivanesan Saravanadevi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.
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6
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Stem cell and hepatocyte proliferation in hepatitis C cirrhosis and hepatocellular carcinoma: transplant implications. Ann Hepatol 2014. [DOI: 10.1016/s1665-2681(19)30903-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Tang W, Hu Z, Muallem H, Gulley ML. Clinical implementation of RNA signatures for pharmacogenomic decision-making. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2011; 4:95-107. [PMID: 23226056 PMCID: PMC3513222 DOI: 10.2147/pgpm.s14888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Indexed: 12/14/2022]
Abstract
RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system.
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Affiliation(s)
- Weihua Tang
- Department of Pathology and Laboratory Medicine
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8
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Gruber HE, Watts JA, Hoelscher GL, Bethea SF, Ingram JA, Zinchenko NS, Hanley EN. Mitochondrial gene expression in the human annulus: in vivo data from annulus cells and selectively harvested senescent annulus cells. Spine J 2011; 11:782-91. [PMID: 21784712 DOI: 10.1016/j.spinee.2011.06.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 04/01/2011] [Accepted: 06/14/2011] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT Mitochondrial dysfunction is recognized during cell senescence and apoptosis, two important components of human disc aging/degeneration. We hypothesize that mitochondrial dysfunction is present in the degenerating and senescent annulus cells. The objective of the present study was to analyze gene expression profiles related to mitochondrial function in vivo. PURPOSE This study had two objectives in the analysis of gene expression patterns related to mitochondria in the human annulus: First, to assess human annulus cells in a genome-wide microarray analysis approach to evaluate mitochondrial gene expression in annulus tissue from degenerated compared with healthier discs. Second, to use laser capture microdissection (LCM) to selectively isolate senescent versus nonsenescent annulus cells to evaluate their mitochondrial gene expression patterns. STUDY DESIGN Following approval by our Human Subjects Institutional Review Board, annulus cells from 20 human lumbar discs were analyzed for gene groups related to mitochondrial function; a subset was also analyzed, which focused on senescent versus nonsenescent annulus cells in a study of annulus cells from 10 lumbar discs. PATIENT SAMPLE Human annulus tissue was used in molecular studies following institutional review board approval. OUTCOME MEASURES Gene expression levels identified with microarray analyses were statistically evaluated using GeneSifter Web-based software (VizX Labs, Seattle, WA, USA). METHODS Human annulus specimens were assessed for gene expression related to mitochondrial function. Approaches used whole annulus tissue and senescent or nonsenescent annulus cells selectively harvested using LCM. Microarray data were analyzed using gene ontology searches and GeneSifter Web-based software. RESULTS Analysis of annulus cells compared mitochondrial gene expression patterns in annulus cells from more degenerated discs with patterns in annulus cells derived from healthier discs. Important findings included significant upregulation of p53 and several proapoptotic genes (including apoptosis-inducing factor, mitochondrion-associated 1, BCL2-like 11 [an apoptosis facilitator]; caspase 7 apoptosis-related cysteine peptidase; proteasome 26S subunit nonadenosine triphosphatase 10, programmed cell death 6, and reticulon 3). Methionine sulfoxide reductase (Msr), a repair enzyme that reduces methionine sulfoxide residues in proteins damaged by oxidation, was also significantly upregulated (2.02-fold increase). The gene "membrane-associated ring finger (C3HC4) 5" was significantly upregulated and relevant because it is believed to play a role in preventing cell senescence acting to regulate mitochondrial quality control. Nitric oxide synthase 3 (endothelial nitric oxide synthase [eNOS]) showed a 5.9-fold downregulation in more degenerated versus healthier annulus cells. In LCM-harvested senescent cells, Msr was significantly downregulated in senescent versus nonsenescent cells, a finding previously recognized in other types of senescent cells. CONCLUSIONS Novel data showed that significant gene expression patterns are present in the human annulus related to mitochondrial dysfunction; changes were identified in important genes involving apoptosis, eNOS and Msr expressions, and solute carrier genes. Because current research efforts are focusing on bioactive compounds for mitochondria, we suggest that future biologic cell-based therapies for annulus degeneration should also consider mitochondrial-focused therapies.
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Affiliation(s)
- Helen E Gruber
- Department of Orthopaedic Surgery, Orthopaedic Research Biology, Cannon Building, Carolinas Medical Center, P.O. Box 32861, Charlotte, NC 28232, USA.
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Gruber HE, Hoelscher GL, Ingram JA, Bethea S, Zinchenko N, Hanley EN. Variations in aggrecan localization and gene expression patterns characterize increasing stages of human intervertebral disk degeneration. Exp Mol Pathol 2011; 91:534-9. [PMID: 21689646 DOI: 10.1016/j.yexmp.2011.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 06/03/2011] [Indexed: 01/07/2023]
Abstract
During disk degeneration, annulus dehydration and matrix fraying culminate in the formation of tears through which nucleus and annulus disk material may rupture, causing radicular pain. Annular tears are present in more than half of the patients in early adulthood and are almost always present in the elderly. Aggrecan, which provides the disk with a shock absorber function under loading, is a key disk extracellular matrix (ECM) component. The objective of the present study was to assess the immunolocalization of aggrecan in the annulus, and to assess molecular gene expression patterns in the annulus ECM utilizing microarray analysis. Immunohistochemistry was performed on 45 specimens using an anti-human aggrecan antibody. Affymetrix microarray gene expression studies used the extracellular matrix ontology approach to evaluate an additional 6 grade I-II, 9 grade III, and 4 grade IV disks. Grade III/IV disks were compared to healthier grade I/II disks. Healthy and less degenerated disks showed a general uniform aggrecan immunolocalization; more degenerated disks contained regions with little or no identifiable aggrecan localization. In degenerated disks, molecular studies showed a significant downregulation of aggrecan, ADAMTS-like 3, and ADAMTS10. Collagen types III and VIII, fibronectin, decorin, connective tissue growth factor, TIMP-3, latent TGF-β binding protein 2 and TGF-β1 were significantly upregulated with fold changes ranging from 2.4 to 9.8. Findings here help us better understand changes in the immunohistochemical distribution of a key proteoglycan during disk aging. Such information may have application as we work towards biologic therapies to improve the aging/degenerating disk matrix.
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Affiliation(s)
- Helen E Gruber
- Department of Orthopaedic Surgery, Carolinas Medical Center, PO Box 32861, Charlotte, NC 28232, USA.
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Mueller TF, Solez K, Mas V. Assessment of kidney organ quality and prediction of outcome at time of transplantation. Semin Immunopathol 2011; 33:185-99. [PMID: 21274534 DOI: 10.1007/s00281-011-0248-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 01/13/2011] [Indexed: 12/13/2022]
Abstract
The critical importance of donor organ quality, i.e., number of surviving nephrons, ability to withstand injury, and capacity for repair in determining short- and long-term outcomes is becoming increasingly clear. This review provides an overview of studies to assess donor kidney quality and subsequent transplant outcomes based on clinical pathology and transcriptome-based variables available at time of transplantation. Prediction scores using clinical variables function when applied to large data sets but perform poorly for the individual patient. Histopathology findings in pre-implantation or post-reperfusion biopsies help to assess structural integrity of the donor kidney, provide information on pre-existing donor disease, and can serve as a baseline for tracking changes over time. However, more validated approaches of analysis and prospective studies are needed to reduce the number of discarded organs, improve allocation, and allow prediction of outcomes. Molecular profiling detects changes not seen by morphology or captured by clinical markers. In particular, molecular profiles provide a quantitative measurement of inflammatory burden or immune activation and reflect coordinated changes in pathways associated with injury and repair. However, description of transcriptome patterns is not an end in itself. The identification of predictive gene sets and the application to an individualized patient management needs the integration of clinical and pathology-based variables, as well as more objective reference markers of transplant function, post-transplant events, and long-term outcomes.
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Affiliation(s)
- Thomas F Mueller
- Division of Nephrology and Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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11
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Damaj MB, Beremand PD, Buenrostro-Nava MT, Riedel B, Molina JJ, Kumpatla SP, Thomas TL, Mirkov TE. Reproducible RNA preparation from sugarcane and citrus for functional genomic applications. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2010; 2009:765367. [PMID: 20148085 PMCID: PMC2817868 DOI: 10.1155/2009/765367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 09/12/2009] [Accepted: 10/13/2009] [Indexed: 05/09/2023]
Abstract
High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying molecules can negatively impact the functionality of some plant RNA preparations employed in these procedures. We present a simplified, rapid, and scalable SDS/phenol-based method that provides the high-quantity and -quality RNA required by the newly emerging biotechnology applications. The method is applied to isolating RNA from tissues of two biotechnologically important crop plants, sugarcane and citrus, which provide a challenge due to the presence of fiber, polysaccharides, or secondary metabolites. The RNA isolated by this method is suitable for several downstream applications including northern blot hybridization, microarray analysis, and quantitative RT-PCR. This method has been used in a diverse range of projects ranging from screening plant lines overexpressing mammalian genes to analyzing plant responses to viral infection and defense signaling molecules.
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Affiliation(s)
- Mona B. Damaj
- Department of Plant Pathology and Microbiology, Texas AgriLife Research, Texas A&M System, Weslaco, TX 78596, USA
| | - Phillip D. Beremand
- Laboratory for Functional Genomics, Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Marco T. Buenrostro-Nava
- Department of Plant Pathology and Microbiology, Texas AgriLife Research, Texas A&M System, Weslaco, TX 78596, USA
| | - Beth Riedel
- Laboratory for Functional Genomics, Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Joe J. Molina
- Department of Plant Pathology and Microbiology, Texas AgriLife Research, Texas A&M System, Weslaco, TX 78596, USA
| | - Siva P. Kumpatla
- Department of Trait Genetics and Technologies, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Terry L. Thomas
- Laboratory for Functional Genomics, Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - T. Erik Mirkov
- Department of Plant Pathology and Microbiology, Texas AgriLife Research, Texas A&M System, Weslaco, TX 78596, USA
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Archer KJ, Reese SE. Detection call algorithms for high-throughput gene expression microarray data. Brief Bioinform 2009; 11:244-52. [PMID: 19939941 DOI: 10.1093/bib/bbp055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Extensive methodological research has been conducted to improve gene expression summary methods. However, in addition to quantitative gene expression summaries, most platforms, including all those examined in the MicroArray Quality Control project, provide a qualitative detection call result for each gene on the platform. These detection call algorithms are intended to render an assessment of whether or not each transcript is reliably measured. In this paper, we review uses of these qualitative detection call results in the analysis of microarray data. We also review the detection call algorithms for two widely used gene expression microarray platforms, Affymetrix GeneChips and Illumina BeadArrays, and more clearly formalize the mathematical notation for the Illumina BeadArray detection call algorithm. Both algorithms result in a P-value which is then used for determining the qualitative detection calls. We examined the performance of these detection call algorithms and default parameters by applying the methods to two spike-in datasets. We show that the default parameters for qualitative detection calls yield few absent calls for high spike-in concentrations. When genes of interest are expected to be present at very low concentrations, spike-in datasets can be useful for appropriately adjusting the tuning parameters for qualitative detection calls.
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Affiliation(s)
- Kellie J Archer
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298-0032, USA.
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