ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Dogan, Ayca ^a   Lasch, Peter ^b   Neuschl, Christina ^a   Millrose, Marion K ^a   Alberts, Rudi ^c   Schughart, Klaus ^c   Naumann, Dieter ^b   Brockmann, Gudrun A ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

^b ROBERT KOCH INSTITUTE   (Germany)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Apoptosis; Collagen; Collectin 11; Endoplasmic reticulum; Liver steatosis; Remodeling; Viperin

Indexed keywords

CELL PROTEIN; COLLAGEN; COLLECTIN; UNCLASSIFIED DRUG; VIPERIN;

ADIPOSE TISSUE; ANIMAL GENETICS; APOPTOSIS; ARTICLE; ATTENUATED TOTAL REFLECTANCE SPECTOSCOPY; CHROMOSOME 12; CHROMOSOME 17; COLEC11 GENE; COLLAGEN SYNTHESIS; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; FAT CONTENT; GENE; GENE ACTIVATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HOMOZYGOSITY; INBRED STRAIN; INFRARED SPECTROSCOPY; LINKAGE ANALYSIS; LIPID DIET; LIPOGENESIS; LIVER; MOUSE; MUSCLE TISSUE; NONHUMAN; OBESITY; PHENOTYPE; PROTEIN FUNCTION; QUANTITATIVE TRAIT LOCUS; REFLECTOMETRY; RSAD2 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE REACTION;

ANIMALS; DIET, HIGH-FAT; DNA, RECOMBINANT; GENOMICS; INBREEDING; MALE; MICE; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

MUS;

EID: 84878698899     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-386     Document Type: Article

References (67)

1. Berg AH, Scherer PE. Adipose tissue, inflammation, and cardiovascular disease. Circ Res 2005, 96(9):939-949. 10.1161/01.RES.0000163635.62927.34, 15890981.
2. Wellen KE, Hotamisligil GS. Inflammation, stress, and diabetes. J Clin Invest 2005, 115(5):1111-1119. 1087185, 15864338.
3. Hageman RS, Wagener A, Hantschel C, Svenson KL, Churchill GA, Brockmann GA. High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice. Physiol Genomics 2010, 42(1):55-66. 10.1152/physiolgenomics.00072.2009, 2888560, 20215417.
4. Matsuzaka T, Shimano H, Yahagi N, Kato T, Atsumi A, Yamamoto T, Inoue N, Ishikawa M, Okada S, Ishigaki N, et al. Crucial role of a long-chain fatty acid elongase, Elovl6, in obesity-induced insulin resistance. Nat Med 2007, 13(10):1193-1202. 10.1038/nm1662, 17906635.
5. Matsuzawa Y. Therapy Insight: adipocytokines in metabolic syndrome and related cardiovascular disease. Nat Clin Pract Cardiovasc Med 2006, 3(1):35-42. 10.1038/ncpcardio0380, 16391616.
6. Rance KA, Hambly C, Dalgleish G, Fustin JM, Bunger L, Speakman JR. Quantitative trait Loci for regional adiposity in mouse lines divergently selected for food intake. Obesity (Silver Spring) 2007, 15(12):2994-3004.
7. West DB, Waguespack J, York B, Goudey-Lefevre J, Price RA. Genetics of dietary obesity in AKR/J x SWR/J mice: segregation of the trait and identification of a linked locus on chromosome 4. Mamm Genome 1994, 5(9):546-552. 10.1007/BF00354928, 8000138.
8. Millward CA, Burrage LC, Shao H, Sinasac DS, Kawasoe JH, Hill-Baskin AE, Ernest SR, Gornicka A, Hsieh CW, Pisano S, et al. Genetic factors for resistance to diet-induced obesity and associated metabolic traits on mouse chromosome 17. Mamm Genome 2009, 20(2):71-82. 10.1007/s00335-008-9165-2, 19137372.
9. Neuschl C, Hantschel C, Wagener A, Schmitt AO, Illig T, Brockmann GA. A unique genetic defect on chromosome 3 is responsible for juvenile obesity in the Berlin Fat Mouse. Int J Obes (Lond) 2010, 34(12):1706-1714.
10. Pravenec M, Kazdova L, Landa V, Zidek V, Mlejnek P, Simakova M, Jansa P, Forejt J, Kren V, Krenova D, et al. Identification of mutated Srebf1 as a QTL influencing risk for hepatic steatosis in the spontaneously hypertensive rat. Hypertension 2008, 51(1):148-153.
11. Vogel H, Nestler M, Ruschendorf F, Block MD, Tischer S, Kluge R, Schurmann A, Joost HG, Scherneck S. Characterization of Nob3, a major quantitative trait locus for obesity and hyperglycemia on mouse chromosome 1. Physiol Genomics 2009, 38(2):226-232. 10.1152/physiolgenomics.00011.2009, 2712221, 19470805.
12. Kumazawa M, Kobayashi M, Io F, Kawai T, Nishimura M, Ohno T, Horio F. Searching for genetic factors of fatty liver in SMXA-5 mice by quantitative trait loci analysis under a high-fat diet. J Lipid Res 2007, 48(9):2039-2046. 10.1194/jlr.M700222-JLR200, 17595448.
13. Bell CG, Walley AJ, Froguel P. The genetics of human obesity. Nat Rev Genet 2005, 6(3):221-234.
14. Shao H, Reed DR, Tordoff MG. Genetic loci affecting body weight and fatness in a C57BL/6J x PWK/PhJ mouse intercross. Mamm Genome 2007, 18(12):839-851. 10.1007/s00335-007-9069-6, 2131744, 18008102.
15. Wang TD, Triadafilopoulos G, Crawford JM, Dixon LR, Bhandari T, Sahbaie P, Friedland S, Soetikno R, Contag CH. Detection of endogenous biomolecules in Barrett's esophagus by Fourier transform infrared spectroscopy. Proc Natl Acad Sci USA 2007, 104(40):15864-15869. 10.1073/pnas.0707567104, 2000401, 17901200.
16. Lasch P, Beekes M, Fabian H, Naumann D. Ante mortem Identification of Transmissible Spongiform Encephalopathies Encephalopathy (TSE) from Serum by Mid-IR Spectroscopy. Vibrational Spectroscopy in Medical Diagnosis 2008, John Wiley & Sons.
17. Jackson M, Mantsch HH. Infrared Spectroscopy of Biomolecules 1996, 311. Wiley-Liss, Inc: Wiley-Liss, Inc, Mantsch HH, Chapman D.
18. Beekes M, Lasch P, Naumann D. Analytical applications of Fourier transform-infrared (FT-IR) spectroscopy in microbiology and prion research. Vet Microbiol 2007, 123(4):305-319. 10.1016/j.vetmic.2007.04.010, 17540519.
19. Kazarian SG, Chan KL. Applications of ATR-FTIR spectroscopic imaging to biomedical samples. Biochim Biophys Acta 2006, 1758(7):858-867. 10.1016/j.bbamem.2006.02.011, 16566893.
20. Ozek NS, Tuna S, Erson-Bensan AE, Severcan F. Characterization of microRNA-125b expression in MCF7 breast cancer cells by ATR-FTIR spectroscopy. Analyst 2010, 135(12):3094-3102. 10.1039/c0an00543f, 20978686.
21. Lasch P, Beekes M, Schmitt J, Naumann D. Detection of preclinical scrapie from serum by infrared spectroscopy and chemometrics. Anal Bioanal Chem 2007, 387(5):1791-1800. 10.1007/s00216-006-0764-z, 17036215.
22. Liu KZ, Shi MH, Mantsch HH. Molecular and chemical characterization of blood cells by infrared spectroscopy: a new optical tool in hematology. Blood Cells Mol Dis 2005, 35(3):404-412. 10.1016/j.bcmd.2005.06.009, 16126419.
23. Maziak DE, Do MT, Shamji FM, Sundaresan SR, Perkins DG, Wong PT. Fourier-transform infrared spectroscopic study of characteristic molecular structure in cancer cells of esophagus: an exploratory study. Cancer Detect Prev 2007, 31(3):244-253. 10.1016/j.cdp.2007.03.003, 17646059.
24. Palombo F, Cremers SG, Weinberg PD, Kazarian SG. Application of Fourier transform infrared spectroscopic imaging to the study of effects of age and dietary L-arginine on aortic lesion composition in cholesterol-fed rabbits. J R Soc Interface 2009, 6(37):669-680. 10.1098/rsif.2008.0325, 2839937, 18986964.
25. Toyran N, Lasch P, Naumann D, Turan B, Severcan F. Early alterations in myocardia and vessels of the diabetic rat heart: an FTIR microspectroscopic study. Biochem J 2006, 397(3):427-436. 10.1042/BJ20060171, 1533317, 16719841.
26. Liu KZ, Man A, Shaw RA, Liang B, Xu Z, Gong Y. Molecular determination of liver fibrosis by synchrotron infrared microspectroscopy. Biochim Biophys Acta 2006, 1758(7):960-967. 10.1016/j.bbamem.2006.05.006, 16806057.
27. Severcan F, Bozkurt O, Gurbanov R, Gorgulu G. FT-IR spectroscopy in diagnosis of diabetes in rat animal model. J Biophotonics 2010, 3(8-9):621-631.
28. Gaigneaux A, Decaestecker C, Camby I, Mijatovic T, Kiss R, Ruysschaert JM, Goormaghtigh E. The infrared spectrum of human glioma cells is related to their in vitro and in vivo behavior. Exp Cell Res 2004, 297(1):294-301. 10.1016/j.yexcr.2004.03.031, 15194444.
29. Khan T, Muise ES, Iyengar P, Wang ZV, Chandalia M, Abate N, Zhang BB, Bonaldo P, Chua S, Scherer PE. Metabolic dysregulation and adipose tissue fibrosis: role of collagen VI. Mol Cell Biol 2009, 29(6):1575-1591. 10.1128/MCB.01300-08, 2648231, 19114551.
30. West PA, Bostrom MP, Torzilli PA, Camacho NP. Fourier transform infrared spectral analysis of degenerative cartilage: an infrared fiber optic probe and imaging study. Appl Spectrosc 2004, 58(4):376-381. 10.1366/000370204773580194, 15104805.
31. Jackson M, Choo LP, Watson PH, Halliday WC, Mantsch HH. Beware of connective tissue proteins: assignment and implications of collagen absorptions in infrared spectra of human tissues. Biochim Biophys Acta 1995, 1270(1):1-6. 10.1016/0925-4439(94)00056-V, 7827129.
32. Peirce JL, Lu L, Gu J, Silver LM, Williams RW. A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. 420238, 15117419.
33. Colinayo VV, Qiao JH, Wang X, Krass KL, Schadt E, Lusis AJ, Drake TA. Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice. Mamm Genome 2003, 14(7):464-471. 10.1007/s00335-002-2187-2, 12925895.
34. Koutnikova H, Laakso M, Lu L, Combe R, Paananen J, Kuulasmaa T, Kuusisto J, Haring HU, Hansen T, Pedersen O, et al. Identification of the UBP1 locus as a critical blood pressure determinant using a combination of mouse and human genetics. PLoS Genet 2009, 5(8):e1000591. 10.1371/journal.pgen.1000591, 2715105, 19662162.
35. Mcclive PJ, Morahan G. Assignment of the Mouse Homologs of 6-Loci from Hsa1p to Chromosome-3 and Chromosome-4. Genomics 1994, 23(1):243-246. 10.1006/geno.1994.1485, 7829080.
36. Ghazalpour A, Doss S, Sheth SS, Ingram-Drake LA, Schadt EE, Lusis AJ, Drake TA. Genomic analysis of metabolic pathway gene expression in mice. Genome Biol 2005, 6(7):R59. 10.1186/gb-2005-6-7-r59, 1175990, 15998448.
37. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005, 37(7):710-717. 10.1038/ng1589, 2841396, 15965475.
38. Svenson KL, Von Smith R, Magnani PA, Suetin HR, Paigen B, Naggert JK, Li R, Churchill GA, Peters LL. Multiple trait measurements in 43 inbred mouse strains capture the phenotypic diversity characteristic of human populations. J Appl Physiol 2007, 102(6):2369-2378. 10.1152/japplphysiol.01077.2006, 17317875.
39. Funkat A, Massa CM, Jovanovska V, Proietto J, Andrikopoulos S. Metabolic adaptations of three inbred strains of mice (C57BL/6, DBA/2, and 129T2) in response to a high-fat diet. J Nutr 2004, 134(12):3264-3269.
40. Brockmann GA, Kratzsch J, Haley CS, Renne U, Schwerin M, Karle S. Single QTL effects, epistasis, and pleiotropy account for two-thirds of the phenotypic F(2) variance of growth and obesity in DU6i x DBA/2 mice. Genome Res 2000, 10(12):1941-1957. 10.1101/gr.GR1499R, 313074, 11116089.
41. BioGps gene annotation portal svstem http://biogps.gnf.org.
42. Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, et al. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet 2008, 4(5):e1000070. 10.1371/journal.pgen.1000070, 2346558, 18464898.
43. Fawcett GL, Roseman CC, Jarvis JP, Wang B, Wolf JB, Cheverud JM. Genetic architecture of adiposity and organ weight using combined generation QTL analysis. Obesity (Silver Spring) 2008, 16(8):1861-1868.
44. Chin KC, Cresswell P. Viperin (cig5), an IFN-inducible antiviral protein directly induced by human cytomegalovirus. Proc Natl Acad Sci USA 2001, 98(26):15125-15130. 10.1073/pnas.011593298, 64994, 11752458.
45. Hinson ER, Cresswell P. The N-terminal amphipathic alpha-helix of viperin mediates localization to the cytosolic face of the endoplasmic reticulum and inhibits protein secretion. J Biol Chem 2009, 284(7):4705-4712. 2640954, 19074433.
46. Wang X, Hinson ER, Cresswell P. The interferon-inducible protein viperin inhibits influenza virus release by perturbing lipid rafts. Cell Host Microbe 2007, 2(2):96-105. 10.1016/j.chom.2007.06.009, 18005724.
47. Hinson ER, Cresswell P. The antiviral protein, viperin, localizes to lipid droplets via its N-terminal amphipathic alpha-helix. Proc Natl Acad Sci USA 2009, 106(48):20452-20457. 10.1073/pnas.0911679106, 2778571, 19920176.
48. Nextbio Research http://www.nextbio.com/b/search/da/Rsad2.
49. Boden G, Duan X, Homko C, Molina EJ, Song W, Perez O, Cheung P, Merali S. Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals. Diabetes 2008, 57(9):2438-2444. 10.2337/db08-0604, 2518495, 18567819.
50. Keshi H, Sakamoto T, Kawai T, Ohtani K, Katoh T, Jang SJ, Motomura W, Yoshizaki T, Fukuda M, Koyama S, et al. Identification and characterization of a novel human collectin CL-K1. Microbiol Immunol 2006, 50(12):1001-1013.
51. van de Wetering JK, van Golde LM, Batenburg JJ. Collectins: players of the innate immune system. Eur J Biochem 2004, 271(7):1229-1249. 10.1111/j.1432-1033.2004.04040.x, 15030473.
52. Ensembl genome browser http://www.ensembl.org.
53. Taylor BA, Wnek C, Kotlus BS, Roemer N, MacTaggart T, Phillips SJ. Genotyping new BXD recombinant inbred mouse strains and comparison of BXD and consensus maps. Mamm Genome 1999, 10(4):335-348. 10.1007/s003359900998, 10087289.
54. Lasch P, Haensch W, Naumann D, Diem M. Imaging of colorectal adenocarcinoma using FT-IR microspectroscopy and cluster analysis. Biochim Biophys Acta 2004, 1688(2):176-186. 10.1016/j.bbadis.2003.12.006, 14990348.
55. Naumann D. Infrared and Raman Spectroscopy of Biological Materials 2001, New York: Marcel Dekker.
56. Dixon WJ, Tukey JW. Approximate Behavior of Distribution of Winsorized T (Trimming/Winsorization 2). Technometrics 1968, 10(1):83.
57. GeneNetwork database http://www.genenetwork.org.
58. Wright S. Evolution and the Genetics of Populations Vol. 1 1968, Chicago: University of Chicago Press.
59. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005, 37(3):233-242. 10.1038/ng1518, 15711545.
60. Churchill GA, Doerge RW. Empirical Threshold Values for Quantitative Trait Mapping. Genetics 1994, 138(3):963-971. 1206241, 7851788.
61. Lu L, Wei L, Peirce JL, Wang X, Zhou J, Homayouni R, Williams RW, Airey DC. Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight. BMC Genomics 2008, 9:444. 10.1186/1471-2164-9-444, 2570693, 18817551.
62. Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, et al. Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 2007, 46(2):548-557. 10.1002/hep.21682, 3518845, 17542012.
63. Schmitt AO, Assmus J, Bortfeldt RH, Brockmann GA. CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics 26(7):969-970.
64. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 2002, 30(17):3894-3900. 10.1093/nar/gkf493, 137415, 12202775.
65. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4(7):1073-1081.
66. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162(1):156-159.
67. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25(4):402-408. 10.1006/meth.2001.1262, 11846609.