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Bonelli M, Di Giuseppe F, Tupone N, Di Virgilio V, Catena AM, Locatelli M, Ascani G, Giammaria G, Ciccarelli R, D’Ovidio C, Angelucci S. Proteomic Characterization of Changes in Mouse Brain Cortex Protein Expression at Different Post-Mortem Intervals: A Preliminary Study for Forensic Biomarker Identification. Int J Mol Sci 2024; 25:8736. [PMID: 39201424 PMCID: PMC11354345 DOI: 10.3390/ijms25168736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Accuracy in the evaluation of death-induced tissue degradation for thanato-chronological purposes is strictly dependent on the condition of the biological source as well as on the precision of post-mortem interval (PMI) estimation. Thus, the optimization of tissue handling and identification of sensitive post-mortem biomarkers could help establish a timeline for post-mortem events. To this aim, we investigated the proteome changes in cortex samples of 6-week-old female SAMR1 mice over a post-mortem time course. After death, brain tissue was removed immediately (T0), and after 4, 8, 12, 24, and 32 h, four mice were used for each time period, and animals were maintained at 4 °C until brain removal. Dissected tissues were frozen at -80 °C until processed. Proteomic analysis, performed on samples related to early and late PMIs (<24 h and >24 h post-mortem, respectively) showed protein level changes as compared to T0 samples, with a remarkable increase in Calpain11 in the early PMI, as well as in Caspases 7 and 8 together with Gasdermin 3 in late PMI. These findings were confirmed by LIFT mass spectrometry technology and western blot analysis and, although requiring further investigation in other biological samples, suggest that these proteins could be considered as putative biomarkers of different PMIs.
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Affiliation(s)
- Martina Bonelli
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.B.); (C.D.)
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
| | - Fabrizio Di Giuseppe
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Nicola Tupone
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Vimal Di Virgilio
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Antonio Maria Catena
- Forensic Medicine, Facoltà di Medicina e Chirurgia Via Montpellier, Tor Vergata University, 100133 Roma, Italy;
| | - Marcello Locatelli
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
| | - Giuliano Ascani
- UOSD Maxillofacial Surgery, Azienda Sanitaria Locale di Pescara, Via Renato Paolini 47, 65124 Pescara, Italy;
| | | | - Renata Ciccarelli
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
| | - Cristian D’Ovidio
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.B.); (C.D.)
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
| | - Stefania Angelucci
- Center for Advanced Studies and Technologies (CAST), University “G. d’Annunzio” of Chieti-Pescara, Via Luigi Polacchi 13, 66100 Chieti, Italy; (F.D.G.); (N.T.); (V.D.V.); (S.A.)
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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Marrone A, La Russa D, Barberio L, Murfuni MS, Gaspari M, Pellegrino D. Forensic Proteomics for the Discovery of New post mortem Interval Biomarkers: A Preliminary Study. Int J Mol Sci 2023; 24:14627. [PMID: 37834074 PMCID: PMC10572818 DOI: 10.3390/ijms241914627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Estimating the time since death (post mortem interval, PMI) represents one of the most important tasks in daily forensic casework. For decades, forensic scientists have investigated changes in post mortem body composition, focusing on different physical, chemical, or biological aspects, to discover a reliable method for estimating PMI; nevertheless, all of these attempts remain unsuccessful considering the currently available methodical spectrum characterized by great inaccuracies and limitations. However, recent promising approaches focus on the post mortem decomposition of biomolecules. In particular, significant advances have been made in research on the post mortem degradation of proteins. In the present study, we investigated early post mortem changes (during the first 24 h) in the proteome profile of the pig skeletal muscle looking for new PMI specific biomarkers. By mass spectrometry (MS)-based proteomics, we were able to identify a total of nine potential PMI biomarkers, whose quantity changed constantly and progressively over time, directly or inversely proportional to the advancement of post mortem hours. Our preliminary study underlines the importance of the proteomic approach in the search for a reliable method for PMI determination and highlights the need to characterize a large number of reliable marker proteins useful in forensic practice for PMI estimation.
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Affiliation(s)
- Alessandro Marrone
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (A.M.); (D.L.R.); (L.B.)
| | - Daniele La Russa
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (A.M.); (D.L.R.); (L.B.)
| | - Laura Barberio
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (A.M.); (D.L.R.); (L.B.)
| | - Maria Stella Murfuni
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (M.S.M.); (M.G.)
| | - Marco Gaspari
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (M.S.M.); (M.G.)
| | - Daniela Pellegrino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (A.M.); (D.L.R.); (L.B.)
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Naldurtiker A, Batchu P, Kouakou B, Terrill TH, Shaik A, Kannan G. RNA-Seq exploration of the influence of stress on meat quality in Spanish goats. Sci Rep 2022; 12:20573. [PMID: 36446782 PMCID: PMC9709060 DOI: 10.1038/s41598-022-23269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5194 up regulated; 5439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.
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Affiliation(s)
- Aditya Naldurtiker
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Phaneendra Batchu
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Brou Kouakou
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Thomas H Terrill
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Arshad Shaik
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Govind Kannan
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA.
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Martínez-Rivera V, Cárdenas-Monroy CA, Millan-Catalan O, González-Corona J, Huerta-Pacheco NS, Martínez-Gutiérrez A, Villavicencio-Queijeiro A, Pedraza-Lara C, Hidalgo-Miranda A, Bravo-Gómez ME, Pérez-Plasencia C, Guardado-Estrada M. Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. PeerJ 2021; 9:e11102. [PMID: 33986977 PMCID: PMC8086579 DOI: 10.7717/peerj.11102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023] Open
Abstract
Background The post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI. Methods We designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression. Results An upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h of PMI. Using a multivariate analysis, it was possible to predict the FC of miR-381-3p of all but 6 h-PMI analyzed PMIs. Discussion The present results suggest that miR-23b-3p and miR-381-3p participate at the early PMI, probably regulating the expression of some genes related to the autolysis process as EPC1 gene. Although the miR-381-3p gene expression is a potential estimator of PMI, further studies will be required to obtain better estimates.
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Affiliation(s)
- Vanessa Martínez-Rivera
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Christian A Cárdenas-Monroy
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oliver Millan-Catalan
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jessica González-Corona
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - N Sofia Huerta-Pacheco
- Cátedras CONACYT-Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Antonio Martínez-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México
| | - Alexa Villavicencio-Queijeiro
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pedraza-Lara
- Laboratorio de Entomología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Nacional de Medicina Genomica, Ciudad de México, México
| | - María Elena Bravo-Gómez
- Laboratorio de Toxicología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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Zissler A, Stoiber W, Steinbacher P, Geissenberger J, Monticelli FC, Pittner S. Postmortem Protein Degradation as a Tool to Estimate the PMI: A Systematic Review. Diagnostics (Basel) 2020; 10:E1014. [PMID: 33256203 PMCID: PMC7760775 DOI: 10.3390/diagnostics10121014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives: We provide a systematic review of the literature to evaluate the current research status of protein degradation-based postmortem interval (PMI) estimation. Special attention is paid to the applicability of the proposed approaches/methods in forensic routine practice. Method: A systematic review of the literature on protein degradation in tissues and organs of animals and humans was conducted. Therefore, we searched the scientific databases Pubmed and Ovid for publications until December 2019. Additional searches were performed in Google Scholar and the reference lists of eligible articles. Results: A total of 36 studies were included. This enabled us to consider the degradation pattern of over 130 proteins from 11 different tissues, studied with different methods including well-established and modern approaches. Although comparison between studies is complicated by the heterogeneity of study designs, tissue types, methods, proteins and outcome measurement, there is clear evidence for a high explanatory power of protein degradation analysis in forensic PMI analysis. Conclusions: Although only few approaches have yet exceeded a basic research level, the current research status provides strong evidence in favor of the applicability of a protein degradation-based PMI estimation method in routine forensic practice. Further targeted research effort towards specific aims (also addressing influencing factors and exclusion criteria), especially in human tissue will be required to obtain a robust, reliable laboratory protocol, and collect sufficient data to develop accurate multifactorial mathematical decomposition models.
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Affiliation(s)
- Angela Zissler
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Walter Stoiber
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Peter Steinbacher
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Janine Geissenberger
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Fabio C. Monticelli
- Department of Forensic Medicine, University of Salzburg, 5020 Salzburg, Austria;
| | - Stefan Pittner
- Department of Forensic Medicine, University of Salzburg, 5020 Salzburg, Austria;
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Eržen I, Janáček J, Kreft M, Kubínová L, Cvetko E. Capillary Network Morphometry of Pig Soleus Muscle Significantly Changes in 24 Hours After Death. J Histochem Cytochem 2018; 66:23-31. [PMID: 29095670 PMCID: PMC5761944 DOI: 10.1369/0022155417737061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/20/2017] [Indexed: 11/22/2022] Open
Abstract
Capillary network characteristics are invaluable for diagnostics of muscle diseases. Biopsy material is limited in size and mostly not accessible for intensive research. Therefore, especially in human tissue, studies are performed on autopsy material. To approach the problem whether it is reliable to deduce hypotheses from autopsy material to explain physiological and pathological processes, we studied capillarity in pig soleus muscle 1 and 24 hr after death. Capillaries and muscle fibers were immunofluorescently marked, and images were acquired with a confocal microscope. Characteristics of the capillary network were estimated by image analysis methods using several plugins of the Ellipse program. Twenty-four hours after death, the measured characteristics of the capillary network differ by up to 50% when compared with samples excised 1 hr after death. Muscle fiber diameter, the measured capillary length, and tortuosity were reduced, and capillary network became more anisotropic. The main postmortem change that affects capillaries is evidently geometric deformation of muscle tissue. In conclusion, when comparing results from biopsy samples with those from autopsy samples, the effect of postmortem changes on the measured parameters must be carefully considered.
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Affiliation(s)
- Ida Eržen
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jiří Janáček
- Department of Biomathematics, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Marko Kreft
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Celica Biomedical, Ljubljana, Slovenia
| | - Lucie Kubínová
- Department of Biomathematics, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Erika Cvetko
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Lee DG, Yang KE, Hwang JW, Kang HS, Lee SY, Choi S, Shin J, Jang IS, An HJ, Chung H, Jung HI, Choi JS. Degradation of Kidney and Psoas Muscle Proteins as Indicators of Post-Mortem Interval in a Rat Model, with Use of Lateral Flow Technology. PLoS One 2016; 11:e0160557. [PMID: 27552165 PMCID: PMC4995019 DOI: 10.1371/journal.pone.0160557] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 07/21/2016] [Indexed: 11/29/2022] Open
Abstract
We investigated potential protein markers of post-mortem interval (PMI) using rat kidney and psoas muscle. Tissue samples were taken at 12 h intervals for up to 96 h after death by suffocation. Expression levels of eight soluble proteins were analyzed by Western blotting. Degradation patterns of selected proteins were clearly divided into three groups: short-term, mid-term, and long-term PMI markers based on the half maximum intensity of intact protein expression. In kidney, glycogen synthase (GS) and glycogen synthase kinase-3β were degraded completely within 48 h making them short-term PMI markers. AMP-activated protein kinase α, caspase 3 and GS were short-term PMI markers in psoas muscle. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was a mid-term PMI marker in both tissues. Expression levels of the typical long-term PMI markers, p53 and β-catenin, were constant for at least 96 h post-mortem in both tissues. The degradation patterns of GS and caspase-3 were verified by immunohistochemistry in both tissues. GAPDH was chosen as a test PMI protein to perform a lateral flow assay (LFA). The presence of recombinant GAPDH was clearly detected in LFA and quantified in a concentration-dependent manner. These results suggest that LFA might be used to estimate PMI at a crime scene.
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Affiliation(s)
- Dong-Gi Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Kyeong Eun Yang
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Jeong Won Hwang
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Hwan-Soo Kang
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Seung-Yeul Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Seoyeon Choi
- National Core Research Center for Nanomedical Technology, Yonsei University, Seoul, Republic of Korea
| | - Joonchul Shin
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
| | - Ik-Soon Jang
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Heesun Chung
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Hyo-Il Jung
- National Core Research Center for Nanomedical Technology, Yonsei University, Seoul, Republic of Korea
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
- * E-mail: (HIJ); (JSC)
| | - Jong-Soon Choi
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (HIJ); (JSC)
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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Jakovski Z, Ajanovska RJ, Stankov A, Pavlovski G, Poposka V, Marjanovic D. Comparative study of two dna extraction methods in different tissues and conditions of degradation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Malila Y, Srimarut Y, U-Chupaj J, Strasburg G, Visessanguan W. Monitoring of Chicken RNA Integrity as a Function of Prolonged Postmortem Duration. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1649-56. [PMID: 26580287 PMCID: PMC4647106 DOI: 10.5713/ajas.15.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/20/2015] [Accepted: 05/04/2015] [Indexed: 12/13/2022]
Abstract
Gene expression profiling has offered new insights into postmortem molecular changes associated with meat quality. To acquire reliable transcript quantification, high quality RNA is required. The objective of this study was to analyze integrity of RNA isolated from chicken skeletal muscle (pectoralis major) and its capability of serving as the template in quantitative real-time polymerase chain reaction (qPCR) as a function of postmortem intervals representing the end-points of evisceration, carcass chilling and aging stages in chicken abattoirs. Chicken breast muscle was dissected from the carcasses (n = 6) immediately after evisceration, and one-third of each sample was instantly snap-frozen and labeled as 20 min postmortem. The remaining muscle was stored on ice until the next rounds of sample collection (1.5 h and 6 h postmortem). The delayed postmortem duration did not significantly affect A260/A280 and A260/A230 (p≥0.05), suggesting no altered purity of total RNA. Apart from a slight decrease in the 28s:18s ribosomal RNA ratio in 1.5 h samples (p<0.05), the value was not statistically different between 20 min and 6 h samples (p≥0.05), indicating intact total RNA up to 6 h. Abundance of reference genes encoding beta-actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), hypoxanthine-guanine phosphoribosyltransferase (HPRT), peptidylprolylisomerase A (PPIA) and TATA box-binding protein (TBP) as well as meat-quality associated genes (insulin-like growth factor 1 (IGF1), pyruvate dehydrogenase kinase isozyme 4 (PDK4), and peroxisome proliferator-activated receptor delta (PPARD) were investigated using qPCR. Transcript abundances of ACTB, GAPDH, HPRT, and PPIA were significantly different among all postmortem time points (p<0.05). Transcript levels of PDK4 and PPARD were significantly reduced in the 6 h samples (p<0.05). The findings suggest an adverse effect of a prolonged postmortem duration on reliability of transcript quantification in chicken skeletal muscle. For the best RNA quality, chicken skeletal muscle should be immediately collected after evisceration or within 20 min postmortem, and rapidly preserved by deep freezing.
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Affiliation(s)
- Yuwares Malila
- Department of Food Technology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Yanee Srimarut
- Department of Food Technology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Juthawut U-Chupaj
- Department of Food Technology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Gale Strasburg
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Wonnop Visessanguan
- Department of Food Technology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
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11
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Pittner S, Monticelli FC, Pfisterer A, Zissler A, Sänger AM, Stoiber W, Steinbacher P. Postmortem degradation of skeletal muscle proteins: a novel approach to determine the time since death. Int J Legal Med 2015; 130:421-31. [PMID: 26041514 DOI: 10.1007/s00414-015-1210-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/26/2015] [Indexed: 11/30/2022]
Abstract
Estimating the time since death is a very important aspect in forensic sciences which is pursued by a variety of methods. The most precise method to determine the postmortem interval (PMI) is the temperature method which is based on the decrease of the body core temperature from 37 °C. However, this method is only useful in the early postmortem phase (~0-36 h). The aim of the present work is to develop an accurate method for PMI determination beyond this present limit. For this purpose, we used sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting, and casein zymography to analyze the time course of degradation of selected proteins and calpain activity in porcine biceps femoris muscle until 240 h postmortem (hpm). Our results demonstrate that titin, nebulin, desmin, cardiac troponin T, and SERCA1 degraded in a regular and predictable fashion in all samples investigated. Similarly, both the native calpain 1 and calpain 2 bands disintegrate into two bands subsequently. This degradation behavior identifies muscular proteins and enzymes as promising substrates for future molecular-based PMI determination technologies.
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Affiliation(s)
- Stefan Pittner
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Fabio C Monticelli
- Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Ignaz-Harrer-Straße 79, 5020, Salzburg, Austria
| | - Alexander Pfisterer
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Angela Zissler
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Alexandra M Sänger
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Walter Stoiber
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Peter Steinbacher
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria.
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12
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Skeletal muscle microRNA and messenger RNA profiling in cofilin-2 deficient mice reveals cell cycle dysregulation hindering muscle regeneration. PLoS One 2015; 10:e0123829. [PMID: 25874796 PMCID: PMC4395318 DOI: 10.1371/journal.pone.0123829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/07/2015] [Indexed: 12/19/2022] Open
Abstract
Congenital myopathies are rare skeletal muscle diseases presenting in early age with hypotonia and weakness often linked to a genetic defect. Mutations in the gene for cofilin-2 (CFL2) have been identified in several families as a cause of congenital myopathy with nemaline bodies and cores. Here we explore the global messenger and microRNA expression patterns in quadriceps muscle samples from cofillin-2-null mice and compare them with sibling-matched wild-type mice to determine the molecular pathways and mechanisms involved. Cell cycle processes are markedly dysregulated, with altered expression of genes involved in mitotic spindle formation, and evidence of loss of cell cycle checkpoint regulation. Importantly, alterations in cell cycle, apoptosis and proliferation pathways are present in both mRNA and miRNA expression patterns. Specifically, p21 transcript levels were increased, and the expression of p21 targets, such as cyclin D and cyclin E, was decreased. We therefore hypothesize that deficiency of cofilin-2 is associated with interruption of the cell cycle at several checkpoints, hindering muscle regeneration. Identification of these pathways is an important step towards developing appropriate therapies against various congenital myopathies.
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Soltys DT, Pereira CPM, Ishibe GN, de Souza-Pinto NC. Effects of post mortem interval and gender in DNA base excision repair activities in rat brains. Mutat Res 2015; 776:48-53. [PMID: 26255940 DOI: 10.1016/j.mrfmmm.2015.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
Most human tissues used in research are of post mortem origin. This is the case for all brain samples, and due to the difficulty in obtaining a good number of samples, especially in the case of neurodegenerative diseases, male and female samples are often included in the same experimental group. However, the effects of post mortem interval (PMI) and gender differences in the endpoints being analyzed are not always fully understood, as is the case for DNA repair activities. To investigate these effects, in a controlled genetic background, base excision repair (BER) activities were measured in protein extracts obtained from Wistar rat brains from different genders and defined PMI up to 24 hours, using a novel fluorescent-based in vitro incision assay. Uracil and AP-site incision activity in nuclear and mitochondrial extracts were similar in all groups included in this study. Our results show that gender and PMI up to 24 hours have no influence in the activities of the BER proteins UDG and APE1 in rat brains. These findings demonstrate that these variables do not interfere on the BER activities included in these study, and provide a security window to work with UDG and APE1 proteins in samples of post mortem origin.
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Affiliation(s)
- Daniela Tathiana Soltys
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
| | | | - Gabriela Naomi Ishibe
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
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14
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Satterlee JS, Beckel-Mitchener A, Little R, Procaccini D, Rutter JL, Lossie AC. Neuroepigenomics: Resources, Obstacles, and Opportunities. NEUROEPIGENETICS 2015; 1:2-13. [PMID: 25722961 PMCID: PMC4337407 DOI: 10.1016/j.nepig.2014.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Long-lived post-mitotic cells, such as the majority of human neurons, must respond effectively to ongoing changes in neuronal stimulation or microenvironmental cues through transcriptional and epigenomic regulation of gene expression. The role of epigenomic regulation in neuronal function is of fundamental interest to the neuroscience community, as these types of studies have transformed our understanding of gene regulation in post-mitotic cells. This perspective article highlights many of the resources available to researchers interested in neuroepigenomic investigations and discusses some of the current obstacles and opportunities in neuroepigenomics.
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Affiliation(s)
- John S. Satterlee
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Andrea Beckel-Mitchener
- National Institute on Mental Health (NIMH), Division of Neuroscience and Basic Behavioral Science, 6001 Executive Boulevard Bethesda, MD 20892-9641, USA
| | - Roger Little
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Dena Procaccini
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Joni L. Rutter
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Amy C. Lossie
- Office of Behavioral and Social Sciences Research (OBSSR), Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director/National Institutes of Health (NIH), 31 Center Drive, Bethesda, MD 20892, USA
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15
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Ye XC, Pegado V, Patel MS, Wasserman WW. Strabismus genetics across a spectrum of eye misalignment disorders. Clin Genet 2014; 86:103-11. [PMID: 24579652 PMCID: PMC4233980 DOI: 10.1111/cge.12367] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 01/24/2023]
Abstract
Eye misalignment, called strabismus, is amongst the most common phenotypes observed, occurring in up to 5% of individuals in a studied population. While misalignment is frequently observed in rare complex syndromes, the majority of strabismus cases are non-syndromic. Over the past decade, genes and pathways associated with syndromic forms of strabismus have emerged, but the genes contributing to non-syndromic strabismus remain elusive. Genetic testing for strabismus risk may allow for earlier diagnosis and treatment, as well as decreased frequency of surgery. We review human and model organism literature describing non-syndromic strabismus, including family, twin, linkage, and gene expression studies. Recent advances in the genetics of Duane retraction syndrome are considered, as relatives of those impacted show elevated familial rates of non-syndromic strabismus. As whole genome sequencing efforts are advancing for the discovery of the elusive strabismus genes, this overview is intended to support the interpretation of the new findings.
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Affiliation(s)
- X C Ye
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, Vancouver, BC, Canada
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16
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Chung U, Seo JS, Kim YH, Son GH, Hwang JJ. Quantitative analyses of postmortem heat shock protein mRNA profiles in the occipital lobes of human cerebral cortices: implications in cause of death. Mol Cells 2012; 34:473-80. [PMID: 23135635 PMCID: PMC3887795 DOI: 10.1007/s10059-012-0214-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 09/24/2012] [Accepted: 10/03/2012] [Indexed: 01/11/2023] Open
Abstract
Quantitative RNA analyses of autopsy materials to diagnose the cause and mechanism of death are challenging tasks in the field of forensic molecular pathology. Alterations in mRNA profiles can be induced by cellular stress responses during supravital reactions as well as by lethal insults at the time of death. Here, we demonstrate that several gene transcripts encoding heat shock proteins (HSPs), a gene family primarily responsible for cellular stress responses, can be differentially expressed in the occipital region of postmortem human cerebral cortices with regard to the cause of death. HSPA2 mRNA levels were higher in subjects who died due to mechanical asphyxiation (ASP), compared with those who died by traumatic injury (TI). By contrast, HSPA7 and A13 gene transcripts were much higher in the TI group than in the ASP and sudden cardiac death (SCD) groups. More importantly, relative abundances between such HSP mRNA species exhibit a stronger correlation to, and thus provide more discriminative information on, the death process than does routine normalization to a housekeeping gene. Therefore, the present study proposes alterations in HSP mRNA composition in the occipital lobe as potential forensic biological markers, which may implicate the cause and process of death.
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Affiliation(s)
- Ukhee Chung
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
| | | | | | - Gi Hoon Son
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
| | - Juck-Joon Hwang
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
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17
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O'Brien JE, Kibiryeva N, Zhou XG, Marshall JA, Lofland GK, Artman M, Chen J, Bittel DC. Noncoding RNA expression in myocardium from infants with tetralogy of Fallot. ACTA ACUST UNITED AC 2012; 5:279-86. [PMID: 22528145 DOI: 10.1161/circgenetics.111.961474] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The importance of noncoding RNAs (ncRNA), especially microRNAs (miRNAs), for maintaining stability in the developing vertebrate heart has recently become apparent; however, there is little known about the expression pattern of ncRNA in the human heart with developmental anomalies. METHODS AND RESULTS We examined the expression of miRNAs and small nucleolar RNAs (snoRNAs) in right ventricular myocardium from 16 infants with nonsyndromic tetralogy of Fallot (TOF) without a 22q11.2 deletion, 3 fetal heart samples, and 8 normally developing infants. We found 61 miRNAs and 135 snoRNAs to be significantly changed in expression in myocardium from children with TOF compared with normally developing comparison subjects. The pattern of ncRNA expression in TOF myocardium had a surprising resemblance to expression patterns in fetal myocardium, especially for the snoRNAs. Potential targets of miRNAs with altered expression were enriched for gene networks of importance to cardiac development. We derived a list of 229 genes known to be critical to heart development and found 44 had significantly changed expression in TOF myocardium relative to normally developing myocardium. These 44 genes had significant negative correlation with 33 miRNAs, each of which also had significantly changed expression. The primary function of snoRNAs is targeting specific nucleotides of ribosomal RNAs and spliceosomal RNAs for biochemical modification. The targeted nucleotides of the differentially expressed snoRNAs were concentrated in the 28S and 18S ribosomal RNAs and 2 spliceosomal RNAs, U2 and U6. In addition, in myocardium from children with TOF, we observed splicing variants in 51% of genes that are critical for cardiac development. Taken together, these observations suggest a link between levels of snoRNA that target spliceosomal RNAs, spliceosomal function, and heart development. CONCLUSIONS This is the first report characterizing ncRNA expression in a congenital heart defect. The striking shift in expression of ncRNAs reflects a fundamental change in cell biology, likely impacting expression, transcript splicing, and translation of developmentally important genes and possibly contributing to the cardiac defect.
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Affiliation(s)
- James E O'Brien
- Section of Cardiovascular and Thoracic Surgery, Children's Mercy Hospitals and Clinics, Kansas City, MO 64108, USA
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18
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Fontanesi L, Galimberti G, Calò D, Colombo M, Astolfi A, Formica S, Russo V. Microarray gene expression analysis of porcine skeletal muscle sampled at several post mortem time points. Meat Sci 2011; 88:604-9. [DOI: 10.1016/j.meatsci.2011.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
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19
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Ricci M, Mohapatra B, Urbiztondo A, Birusingh RJ, Morgado M, Rodriguez MM, Lincoln J, Vatta M. Differential changes in TGF-β/BMP signaling pathway in the right ventricular myocardium of newborns with hypoplastic left heart syndrome. J Card Fail 2010; 16:628-34. [PMID: 20670841 DOI: 10.1016/j.cardfail.2010.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/17/2010] [Accepted: 03/10/2010] [Indexed: 01/28/2023]
Abstract
BACKGROUND Hypoplastic left heart syndrome (HLHS) is characterized by underdevelopment of the left ventricle (LV) and increased biomechanical stress on the right ventricle (RV) from single ventricle physiology. Despite the clinical significance, the signaling pathways active during RV remodeling and disease progression are not known. To address this, we examined differential changes in expression of genes associated with transforming growth factor-beta (TGF-beta)/bone morphogenetic protein (BMP) signaling in RV tissue isolated from HLHS patients relative to RV and LV tissue from control subjects. METHODS AND RESULTS Quantitative real-time polymerase chain reaction was used to detect changes in expression of 84 genes involved in TGF-beta/BMP-mediated cardiac development, cell growth, and differentiation in RV tissue collected from 6 neonates with HLHS undergoing stage 1 Norwood procedure (age, 1-7 days; mean, 4 days) and RV and LV tissue obtained from 5 infants with noncardiac pathology (age range, 1-135 days: mean, 85 days) that served as controls. Analysis of gene expression profiles between control-LV and control-RV revealed significant depression of TGF-beta/BMP signaling in RV compared with LV. Of the 84 genes analyzed, 38 were differentially expressed between HLHS-RV and control-RV, whereas only 22 compared with control-LV. Significant changes were observed in: tissue remodeling genes including Activin receptor type IIA (ACVR2A) (+2.13) and Activin receptor-like kinase 1 (ACVRL1) (+2.22); and cell survival, growth, and differentiation genes including CDC25A (+2.18), p21 (-3.64), p15 (+2.15), BMP5 (+4.58), BMP3 (+2.16), GDF3 (+8.59), NODAL (+2.32), and BMP binding endothelial regulator (BMPER) (+4.58). The most significant changes common to HLHS-RV versus control-RV and control-LV sample groups is observed for Anti müllerian hormone receptor 2 (AMHR2) (+18.79 control-RV, +3.38 control-LV), and the BMP antagonist Inhibin alpha (INHA) (+11.47 control-RV, +5.73 control-LV). CONCLUSIONS Although this descriptive study does not allow cause-effect inferences, our results suggest changes in cardiac development pathways and upregulation of genes associated with cell growth and differentiation in the neonatal RV of children with HLHS. These molecular profiles are more closely related to those observed in the normal LV rather than normal RV at similar maturational age. This work provides the basis for future mechanistic studies to elucidate the molecular mechanisms regulating RV remodeling in HLHS.
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Affiliation(s)
- Marco Ricci
- Division of Cardiothoracic Surgery, University of Miami Miller School of Medicine and Holtz Children's Hospital, Miami, FL, USA.
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20
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Role of Esrrg in the fibrate-mediated regulation of lipid metabolism genes in human ApoA-I transgenic mice. THE PHARMACOGENOMICS JOURNAL 2009; 10:165-79. [PMID: 19949424 PMCID: PMC2875298 DOI: 10.1038/tpj.2009.51] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have used a new ApoA-I transgenic mouse model to identify by global gene expression profiling, candidate genes that affect lipid and lipoprotein metabolism in response to fenofibrate treatment. Multilevel bioinformatical analysis and stringent selection criteria (2-fold change, 0% false discovery rate) identified 267 significantly changed genes involved in several molecular pathways. The fenofibrate-treated group did not have significantly altered levels of hepatic human APOA-I mRNA and plasma ApoA-I compared with the control group. However, the treatment increased cholesterol levels to 1.95-fold mainly due to the increase in high-density lipoprotein (HDL) cholesterol. The observed changes in HDL are associated with the upregulation of genes involved in phospholipid biosynthesis and lipid hydrolysis, as well as phospholipid transfer protein. Significant upregulation was observed in genes involved in fatty acid transport and β-oxidation, but not in those of fatty acid and cholesterol biosynthesis, Krebs cycle and gluconeogenesis. Fenofibrate changed significantly the expression of seven transcription factors. The estrogen receptor-related gamma gene was upregulated 2.36-fold and had a significant positive correlation with genes of lipid and lipoprotein metabolism and mitochondrial functions, indicating an important role of this orphan receptor in mediating the fenofibrate-induced activation of a specific subset of its target genes.
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Determining time of death: temperature-dependent postmortem changes in calcineurin A, MARCKS, CaMKII, and protein phosphatase 2A in mouse. Int J Legal Med 2009; 123:305-14. [DOI: 10.1007/s00414-009-0343-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 03/16/2009] [Indexed: 11/26/2022]
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22
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Pryshchep O, Ma-Krupa W, Younge BR, Goronzy JJ, Weyand CM. Vessel-specific Toll-like receptor profiles in human medium and large arteries. Circulation 2008; 118:1276-84. [PMID: 18765390 DOI: 10.1161/circulationaha.108.789172] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Inflammatory vasculopathies, ranging from the vasculitides (Takayasu arteritis, giant cell arteritis, and polyarteritis nodosa) to atherosclerosis, display remarkable target tissue tropisms for selected vascular beds. Molecular mechanisms directing wall inflammation to restricted anatomic sites within the vascular tree are not understood. We have examined the ability of 6 different human macrovessels (aorta and subclavian, carotid, mesenteric, iliac, and temporal arteries) to initiate innate and adaptive immune responses by comparing pathogen-sensing and T-cell-stimulatory capacities. METHODS AND RESULTS Gene expression analysis for pathogen-sensing Toll-like receptors (TLRs) 1 to 9 showed vessel-specific profiles, with TLR2 and TLR4 ubiquitously present, TLR7 and TLR9 infrequent, and TLR1, TLR3, TLR5, TLR6, and TLR8 expressed in selective patterns. Experiments with vessel walls stripped of the intimal or adventitial layer identified dendritic cells at the media-adventitia junction as the dominant pathogen sensors. In human artery-severe combined immunodeficiency (SCID) mouse chimeras, adoptively transferred human T cells initiated vessel wall inflammation if wall-embedded dendritic cells were conditioned with TLR ligands. Wall-infiltrating T cells displayed vessel-specific activation profiles with differential production of CD40L, lymphotoxin-alpha, and interferon-gamma. Vascular bed-specific TLR fingerprints were functionally relevant, as exemplified by differential responsiveness of iliac and subclavian vessels to TLR5 but not TLR4 ligands. CONCLUSIONS Populated by indigenous dendritic cells, medium and large human arteries have immune-sensing and T-cell-stimulatory functions. Each vessel in the macrovascular tree exhibits a distinct TLR profile and supports selective T-cell responses, imposing vessel-specific risk for inflammatory vasculopathies.
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Affiliation(s)
- Olga Pryshchep
- Lowance Center for Human Immunology and Rheumatology, Emory University, School of Medicine, Atlanta, GA 30322, USA
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23
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Zidar N, Odar K, Glavac D, Jerse M, Zupanc T, Stajer D. Cyclooxygenase in normal human tissues--is COX-1 really a constitutive isoform, and COX-2 an inducible isoform? J Cell Mol Med 2008; 13:3753-63. [PMID: 18657230 PMCID: PMC4516524 DOI: 10.1111/j.1582-4934.2008.00430.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Cyclooxygenase (COX) is a key enzyme in prostanoid synthesis. It exists in two isoforms, COX-1 and COX-2. COX-1 is referred to as a ‘constitutive isoform’, and is considered to be expressed in most tissues under basal conditions. In contrast, COX-2 is referred to as an ‘inducible isoform’, which is believed to be undetectable in most normal tissues, but can be up-regulated during various conditions, many of them pathological. Even though the role of COX in homeostasis and disease in now well appreciated, controversial information is available concerning the distribution of COX isoforms in normal human tissues. There is mounting evidence that it is much more complex than generally believed. Our aim was therefore to analyse the expression and distribution of COX isoforms in normal human tissues, using immunohistochemistry, Western blotting and real-time RT-PCR. Autopsy samples from 20 healthy trauma victims and samples from 48 biopsy surgical specimens were included. COX-1 was found in blood vessels, interstitial cells, smooth muscle cells, platelets and mesothelial cells. In contrast, COX-2 was found predominantly in the parenchymal cells of many tissues, with few exceptions, for example the heart. Our results confirm the hypothesis that the distribution of COX isoforms in healthy tissues is much more complex than generally believed. This and previous studies indicate that both isoforms, not only COX-1, are present in many normal human tissues, and that both isoforms, not only COX-2, are up-regulated in various pathological conditions. We may have to revise the concept of ‘constitutive’ and ‘inducible’ COX isoforms.
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Affiliation(s)
- Nina Zidar
- Medical Faculty, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.
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24
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Fontanesi L, Colombo M, Beretti F, Russo V. Evaluation of post mortem stability of porcine skeletal muscle RNA. Meat Sci 2008; 80:1345-51. [PMID: 22063878 DOI: 10.1016/j.meatsci.2008.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 06/09/2008] [Accepted: 06/18/2008] [Indexed: 11/19/2022]
Abstract
The objective of this study was to evaluate the effect of postmortem times on the quality of porcine skeletal muscle total RNA in order to consider the possibility to use postmortem material for gene expression analysis. Samples of Musculus semimembranosus were collected at 20min, 2h, 6h, 24h and 48h postmortem from the left legs of four commercial heavy pigs. Total RNA was analysed by agarose gel electrophoresis stained with ethidium bromide and by microfluidic capillary electrophoresis on an Agilent 2100 Bioanalyzer instrument obtaining 28S:18S rRNA peak ratios and RIN values. The average RIN values of the analysed samples were 7.45±0.13, 7.43±0.15, 7.45±0.10, 7.33±0.15 and 3.95±0.58 for the same postmortem times, respectively, indicating that RNA degradation was present at 48h postmortem. In a similar experiment, carried out by other authors on beef cattle muscle total RNA extracted at different postmortem times, RNA was stable up to 8days after death as indicated by intact 28S and 18S rRNA bands. Thus, differences among species or other environmental factors might affect the level of RNA degradation. In the porcine postmortem samples, qualitative assessment of GAPDH transcripts by PCR amplification of different cDNA fragments indicated that postmortem stages did not affect the possibility of analysing this housekeeping gene. Thus, postmortem porcine skeletal muscle can be an useful tissue to obtain gene expression based information.
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Affiliation(s)
- L Fontanesi
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Via F.lli Rosselli 107, 42100 Reggio Emilia, Italy
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25
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Sluimer JC, Kisters N, Cleutjens KB, Volger OL, Horrevoets AJ, van den Akker LH, Bijnens APJ, Daemen MJ. Dead or alive: gene expression profiles of advanced atherosclerotic plaques from autopsy and surgery. Physiol Genomics 2007; 30:335-41. [PMID: 17519360 DOI: 10.1152/physiolgenomics.00076.2007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Since inclusion of atherosclerotic tissues from different sources is often indispensable to study the full atherogenic spectrum, we investigated to what extent the expression profiles of advanced, stable atherosclerotic lesions obtained during autopsy and surgery are comparable. The gene expression profiles of human carotids with advanced atherosclerosis obtained at autopsy and at vascular surgery were studied by microarray analysis. Expression analysis was performed both at the single gene (Rosetta, Gene Ontology) and at the pathway level using Ingenuity and Gene Set Enrichment Analysis. In addition, mRNA and protein expression levels were validated using quantitative (q) RT-PCR and immunohistochemistry on unrelated advanced carotid lesions from autopsy and surgery. Microarray analysis indicated that the 97.2% of genes showed similar expression levels in advanced atherosclerotic lesions from autopsy and surgery. While the expression data revealed no differences in common atherosclerotic related pathways such as lipid metabolism and inflammation, the differentially expressed genes were mainly involved in basal cell metabolism and hypoxia driven pathways. qRT-PCR confirmed the differential expression of hypoxia-driven genes VEGF-A (2.3-fold upward arrow), glucose transporter (GLUT)-1 (2.5-fold upward arrow), GLUT3 (8.3-fold upward arrow), and hexokinase 1 (2.4-fold upward arrow) in autopsy vs. surgical specimens. Immunohistochemistry revealed that the transcriptional differences in these hypoxia-related genes were not reflected at the protein level. The gene expression profiles of advanced atherosclerotic lesions from autopsy and surgery are largely similar. However, >500 genes, mostly involved in basal cell metabolism and hypoxia were differentially expressed at mRNA, but not at the protein level.
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Affiliation(s)
- Judith C Sluimer
- University of Maastricht, Department of Pathology, Cardiovascular Research Institute Maastricht, Maastricht, The Netherlands
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26
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Curcio C, Asheld JJ, Chabla JM, Ayubcha D, Hallas BH, Horowitz JM, Torres G. Expression profile of Bag 1 in the postmortem brain. J Chem Neuroanat 2006; 32:191-5. [PMID: 17046197 PMCID: PMC1769523 DOI: 10.1016/j.jchemneu.2006.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 09/08/2006] [Accepted: 09/08/2006] [Indexed: 12/15/2022]
Abstract
Bag 1 is a protein intimately involved in signaling pathways that regulate cell survival. Here we examined the expression profile of Bag 1 in the brain to consider issues associated with the sampling of anti-apoptotic proteins in a rat model of the human postmortem process. Following a 4h postmortem interval, we analyzed the hippocampus of rats maintained at 24 or 4 degrees C storage temperatures using immunocytochemical and Western blotting techniques. Remarkably, postmortem tissue (up to 4h) showed a significant and prominent up-regulation of Bag 1 in CA1 and CA3 subfields of the hippocampal formation. Over-expression of Bag 1, however, could only be traced down to a storage temperature of 24 degrees C. These data suggest that storage temperatures, but not postmortem intervals, significantly affect the expression profile and cellular stability of Bag 1 proteins.
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Affiliation(s)
- Christine Curcio
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
| | - John J. Asheld
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
| | - Janet M. Chabla
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
| | - Diana Ayubcha
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
| | - Brian H. Hallas
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
| | - Judith M. Horowitz
- Clinical Neuroscience Laboratory, Medaille College, Buffalo, New York 14214 USA
| | - German Torres
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury New York, 11568 USA
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27
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Shah VO, Dominic EA, Moseley P, Pickett G, Fleet M, Ness S, Raj DSC. Hemodialysis modulates gene expression profile in skeletal muscle. Am J Kidney Dis 2006; 48:616-28. [PMID: 16997058 DOI: 10.1053/j.ajkd.2006.05.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 05/15/2006] [Indexed: 12/27/2022]
Abstract
BACKGROUND Uremia alters diverse metabolic pathways involving multiple organ systems, including skeletal muscle. Skeletal muscle has an important role in nutrition, metabolism, oxidative stress, and inflammation. We hypothesized that hemodialysis (HD) will change the genomic fingerprinting associated with uremia and facilitate expression of a distinct set of genes. METHODS Five patients with end-stage renal disease (ESRD) were studied. Skeletal muscle biopsy specimens from the vastus lateralis were obtained before (pre-HD) and during the last 10 minutes of HD (post-HD). Oligonucleotide microarray (version 2, GeneChip arrays; Affymetrix U95A, Santa Clara, CA) was used to analyze global transcriptional modification in skeletal muscle by HD. Pre-HD data were compared with data from 3 subjects without renal failure. RESULTS In skeletal muscle of patients with ESRD, 83 genes were upregulated and 8 genes were downregulated pre-HD compared with controls. Pathway analysis linked 55 genes to 5 gene networks involved in the regulation of cell cycle, cell proliferation, cellular organization, apoptosis, and inflammation. During HD, expression of 22 genes increased and 1 (TOB1) decreased. Pathway analysis mapped 20 genes to 2 genetic networks involved in: (1) inflammation, cell proliferation, and cell signaling; and (2) apoptosis, cell function, protein synthesis, and tissue morphology. Reverse-transcription polymerase chain reaction confirmed increased expression of GADD45A, BTG2, PDE4B, and CEBPD and downregulation of TOB1 in skeletal muscle intradialysis. CONCLUSION In response to the uremic milieu, skeletal muscle goes through very active transcriptional and translational changes. HD activates a diverse, yet biologically linked, network of genes related to inflammation and apoptosis in skeletal muscle.
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Affiliation(s)
- Vallabh O Shah
- Division of Nephrology and Department of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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28
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Kafel J, Baldinger L, Chabla JM, Hallas BH, Horowitz JM, Torres G. Blood content modulates the induction of heat shock proteins in the neurovascular network. Brain Res Bull 2006; 70:304-11. [PMID: 17027766 DOI: 10.1016/j.brainresbull.2006.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 04/24/2006] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
Heat shock proteins are ubiquitous members of a family of molecular chaperones that protect various cell populations from injury. Up-regulation of heat shock proteins, particularly the 70 kDa species, bind selectively to denatured or partially damaged polypeptides that would otherwise perturb cell function and initiate cell death programs. In this regard, induction of heat shock proteins provides protection from cerebral ischemia in animal models of stroke. Endothelial cells, in particular, are intimately involved in the above protective event as these cells mount a stress response with induction of the 70 kDa heat shock protein. However, the coupling of heat shock proteins and the neurovascular response are not yet known. Here we show that blood content is an important factor in this stress response as rats devoid of blood content do not display a heat shock response in the microvasculature of the hippocampal formation. This lack of stress response, however, is reversed when rats are reperfused with exogenous rat or human blood content. We propose a new ischemic-sensing role for blood that serves to integrate information about protein-damaging conditions and heat shock protein levels in the neurovascular network. Further characterization of this sensing role could represent an attractive new approach to treatment of global ischemia and other microvascular pathologies.
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Affiliation(s)
- John Kafel
- Department of Neuroscience, New York College of Osteopathic Medicine of New York Institute of Technology, Old Westbury, NY 11568, USA
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29
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Gruber MP, Coldren CD, Woolum MD, Cosgrove GP, Zeng C, Barón AE, Moore MD, Cool CD, Worthen GS, Brown KK, Geraci MW. Human lung project: evaluating variance of gene expression in the human lung. Am J Respir Cell Mol Biol 2006; 35:65-71. [PMID: 16498083 PMCID: PMC2658699 DOI: 10.1165/rcmb.2004-0261oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Nondiseased tissue is an important reference for microarray studies of pulmonary disease. We obtained 23 single lungs from multiorgan donors at time of procurement. Donors varied in age, sex, smoking history, and ethnicity. Lungs were dissected into upper and lower lobe peripheral sections for RNA extraction. Microarray analysis was performed using Affymetrix Hu-133 Plus 2.0 arrays. We observed that the relative variability of gene expression increased rapidly from technical (lowest), to regional, to population (highest). In addition, age and sex have measurable effects on gene expression. Gene expression variability is heterogeneously distributed among biologic categories. We conclude that gene expression variability is greater between individuals than within individuals and that population variability is the most important factor in the study design of microarray experiments of the human lung. Classes of genes with high population variability are biologically important and provide a novel perspective into lung physiology and pathobiology. Our study represents the first comprehensive analysis of nondiseased lung tissue. The generation of this robust dataset has important implications for the design and implementation of future comparative expression analysis with pulmonary disease states.
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Affiliation(s)
- Michael P Gruber
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Health Sciences Center, 4200 East Ninth Ave, Denver, CO 80262, USA
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30
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Kang PB, Kho AT, Sanoudou D, Haslett JN, Dow CP, Han M, Blasko JM, Lidov HGW, Beggs AH, Kunkel LM. Variations in gene expression among different types of human skeletal muscle. Muscle Nerve 2005; 32:483-91. [PMID: 15962335 DOI: 10.1002/mus.20356] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
There is a consistent variation in the response of different skeletal muscle groups to mutations in genes known to cause muscular dystrophy, yet these muscles appear histologically similar. To better understand these phenotypic differences, we analyzed gene expression patterns in control muscle specimens obtained from four sites at autopsy: deltoid, quadriceps, gastrocnemius, and tibialis anterior (TA). A total of 35 muscle samples from nine individuals (four pediatric and five geriatric) were studied. Factors potentially influencing gene expression in the different samples included individuality, age, muscle type, gender, cause of death, postmortem interval, and ethnicity. The first three factors, in decreasing order, were found to have a significant impact on the stratification of muscle specimens. A novel analytic method, using a second round of normalization, was used to elicit differences between muscle types. This approach may be extended to a broader survey, potentially elucidating a molecular classification of the skeletal muscles.
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Affiliation(s)
- Peter B Kang
- Genomics Program, Enders 561, Howard Hughes Medical Institute and Children's Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
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31
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Lee J, Hever A, Willhite D, Zlotnik A, Hevezi P. Effects of RNA degradation on gene expression analysis of human postmortem tissues. FASEB J 2005; 19:1356-8. [PMID: 15955843 DOI: 10.1096/fj.04-3552fje] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Affymetrix GeneChip platform was used to build a gene expression database of the normal human body. Postmortem human tissues represent a valuable source of biological materials for this type of study, but their use entails some delays before harvesting such tissues. We first evaluated the RNA quality obtained from tissues obtained 3-5 h postmortem and found variations that were both tissue and donor-dependent. RNAs extracted from brain regions were of higher quality than those obtained from the gut, while the cause of death was a significant factor in donor-dependent differences. To avoid these variables, we used rat duodenum to determine the effects of RNA degradation on the analysis of gene expression. Surprisingly, even samples exhibiting significant RNA degradation yielded robust gene expression results, comparable to those obtained using intact samples at a certain signal intensity cutoff. We extended these findings to our human expression database and obtained similar results, indicating that the Affymetrix platform, which is biased to the 3' end of transcripts for detection, can tolerate significant RNA degradation, while still yielding high quality expression data. Our resulting body index expression database is a valuable research tool. As examples of potential uses, we report novel expression sites for four potential therapeutic targets--CCL27, GPR22, GPR113 and GPR128--and as well as a set of thymus-specific genes, including three not previously associated with the thymus.
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Affiliation(s)
- Jerry Lee
- Department of Molecular Medicine, Neurocrine Biosciences Inc., San Diego, California, USA
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32
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Katsel PL, Davis KL, Haroutunian V. Large-Scale Microarray Studies of Gene Expression in Multiple Regions of the Brain in Schizophrenia and Alzheimer's Disease. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2005; 63:41-82. [PMID: 15797465 DOI: 10.1016/s0074-7742(05)63003-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pavel L Katsel
- Department of Psychiatry, The Mount Sinai School of Medicine New York, New York 10029 USA
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33
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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