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Understanding Diabetes through P

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Understanding Diabetes through P Powered By Docstoc
					Understanding Diabetes through
      Pathway Analysis



          Maggie Cam
     Genomics Core Laboratory
          NIDDK, NIH
Pathophysiology of type 2 diabetes and „prediabetes‟




                          Patti: Curr Opin Clin Nutr Metab Care, 7(4): 383-390, 2004
Patti: Curr Opin Clin Nutr Metab Care, 7(4): 383-390, 2004
Key processes dysregulated in adipose cells in early Type
                      2 diabetes


• Insulin signaling defect
    –  IRS-1 protein
    –  IRS-1 tyrosine phosphorylation
    –  PI3K activity
    –  GLUT4 mRNA and protein

•  LPL activity  hypertriglyceridemia
•  adipocyte differentiation markers (aP2, adiponectin)
•  PPARG coactivator (PGC-1) mRNA and protein
                    Gene Expression Profiling

•   Human IR Subjects                      •   Zucker Fatty (fa/fa) Rat

    –   Normoglycemic                           –   Normoglycemic
    –   Family history                          –   Leptin-resistant, hyperphagic
    –   Non-obese                               –   Obese
    –   Normal insulin                          –   Hyperinsulinemic

    – Insulin resistant                         – Insulin resistant
                                                – Treated with roziglitazone (TZD,
                                                  PPAR Agonist)  insulin sensitive

    Adipose cells                               Adipose tissue
    HuGeneFL, Hu35KsubA-D                       RAE230A

    3 Biological replicates: Control and        4 Biological replicates: Control and 4, 8,
       Insulin-resistant                           12, 16 days of TZD treatment
                              PST: Parameters trained on real-time PCR data

      Selected Genes                      PST                         RMA                          MAS 5.0                  RT-PCR

                                  Fold                        Fold    Anova     Cyber T    Fold     Anova     CyberT     Fold
    Probe Set          Gene               P-value   Change                                                                       P-value
                                 Change                      Change   P-value   P-value   Change    P-value   P-value   Change

X03635_at        ESR1             -1.85    0.08       NC      -1.94    0.16      0.01      -1.36     0.05      0.00      -1.6    0.115

X99101_at        ESR2*            -1.25    0.04       D       -1.03    0.72      0.85      -1.06     0.48      0.55      -1.6    <0.001

J02874_at        FABP4            -1.35   0.006       D       -2.22   0.041      0.005     -1.34    0.021     0.005      -1.7    0.002

M94856_at        FABP5            -1.37    0.05       MD      -1.35    0.30      0.14      -1.35     0.31      0.02      -1.4    0.001

M94630_at        HNRPD            -1.36    0.02       D       -1.11    0.44      0.46      -1.19     0.01      0.06      1.0     0.617

X04602_s_at      IL6              3.63    <0.001       I      2.36    0.022      0.000     3.54     0.022     0.001      12.5    0.001

S62539_at        IRS1             -1.58    0.06       MD      -1.48    0.46      0.10      -1.47     0.44      0.02      -1.4    0.194

RC_AA101767_at   IRS2             -1.34   0.019       MD      -1.52    0.15      0.02      -1.18     0.18      0.11      -1.47   <0.001

L05624_s_at      MAP2K1           1.4      0.17       NC      1.24     0.38      0.20      1.26      0.25      0.04      1.6     0.519

X99728_at        NDUFV3           -1.12    0.24       NC      -1.24    0.05      0.17      -1.08     0.17      0.46      -1.8    0.299

Z29090_at        PIK3CA           -1.24    0.05       MD      -1.28    0.13      0.22      -1.20     0.26      0.08      -1.2    0.018

M61906_at        PIK3R1           1.29     0.31       NC      1.43     0.65      0.38      1.36      0.54      0.11      1.4     0.566

D88532_at        PIK3R3           1.36     0.03       NC      -1.08    0.96      0.95      -1.17     0.67      0.47      1.3     0.122

L40904_at        PPARG            -1.26   0.008       D       -1.55    0.17      0.01      -1.23     0.12      0.06      -1.4    0.017

M31724_at        PTPN1            1.26     0.03       MI      1.11     0.11      0.66      1.05      0.48      0.51      1.1     0.753

J03764_at        SERPINE1         1.1      0.09       NC      1.24     0.05      0.35      1.07      0.02      0.53      1.9     0.491

M91463_rna1_at   SLC2A4           -1.63    0.03       MD      -1.42    0.24      0.06      -1.61     0.20      0.01      -1.4    0.075

U00968_at        SREBF1*          1.2      0.04       MI      -1.01    0.94      0.92      1.07      0.17      0.48      1.3     0.098

U94592_at        UCP2             1.06     0.21       NC      1.04     0.70      0.79      -1.02     0.92      0.94      -1.2    0.122

U75362_at        USP13*           -1.38   0.009       MD      -1.20    0.31      0.45      -1.06     0.27      0.50      -1.5    0.014

M36205_at        VAMP2            1.14     0.22       NC      -1.23    0.19      0.50      -1.97     0.22      0.01      -1.2    0.059

X03072_at        WNT1*            -1.28    0.03       MD      -1.37    0.47      0.21      -1.02     0.64      0.80      -5.1     0.04
               PST: Test datasets (entire Human and Rat GeneChips)
                        compared with alternate algorithms


Total number of probe sets (homologous genes) significantly changed (p<0.1) by each algorithm


                             Human                       Rat                         Human-Rat
                        42,843 probe sets         15,923 probe sets               Homolog Intersection
                        (5,607 homologs)          (5,607 homologs)
                                                                            Increased in        Decreased in
                      Increase     Decrease     Increase     Decrease        human and           human and
                                                                          decreased in rat     increased in rat
     MAS5-Anova      1814 (577)   1780 (512)   1637 (787)    1704 (765)         103                  78
     MAS5-CT         2308 (701)   2079 (566)   1640 (772)    1963 (858)         134                  65
     RMA-Anova       1672 (525)   1784 (481)   2081 (946)    2129 (885)         79                   81
     RMA-CT          1572 (482)   1833 (575)   2052 (927)    2401 (991)         106                  107
     PST             1541 (633)   1355 (503)   1304 (642)    1696 (815)         120                  86




                                                                                GO categories
             Overlap in genelists from multiple analysis algorithms


Homologs Increased in Human Insulin Resistance and Decreased in Rosiglitazone-treated Zucker Fatty Rats


                          PST         RMA-Anova        RMA-CT         MAS5-Anova       MAS5-CT

                                120
       PST                                 24              50              23              37
                     86
                                                79
       RMA-Anova           18                              27              18              49
                                      81
                                                                106
       RMA-CT              45              17                              27              48
                                                     107
                                                                                103
       MAS5-Anova          24              13              18                              49
                                                                      78
                                                                                                134
       MAS5-CT             25              7               26              14
                                                                                      65




Homologs Decreased in Human Insulin Resistance and Increased in Rosiglitazone-treated Zucker Fatty Rats
                                                                                                                                                                                                                                                                                                                                      -50


                                                                                                                                                                                                                                                                                                                                            -40


                                                                                                                                                                                                                                                                                                                                                  -30


                                                                                                                                                                                                                                                                                                                                                              -20


                                                                                                                                                                                                                                                                                                                                                                          -10
                                              -50

                                                          -40


                                                                 -30

                                                                             -20

                                                                                     -10




                                                                                                                                                                                                                                                                      -50


                                                                                                                                                                                                                                                                            -40


                                                                                                                                                                                                                                                                                  -30


                                                                                                                                                                                                                                                                                          -20


                                                                                                                                                                                                                                                                                                -10
                                                                                                                                                                                                           -50


                                                                                                                                                                                                                 -40


                                                                                                                                                                                                                       -30


                                                                                                                                                                                                                             -20


                                                                                                                                                                                                                                     -10




                                                                                                                                                                                                                                                                                                                                                                                                          10


                                                                                                                                                                                                                                                                                                                                                                                                                    20
                                                                                                                         -50


                                                                                                                                     -40


                                                                                                                                            -30


                                                                                                                                                        -20

                                                                                                                                                                    -10
                                                                                                         10

                                                                                                                20




                                                                                                                                                                                                                                                                                                                          10


                                                                                                                                                                                                                                                                                                                               20
                                                                                                                                                                                                                                                              10


                                                                                                                                                                                                                                                                      20
                                                                                                                                                                                          10


                                                                                                                                                                                                  20




                                                                                                                                                                                                                                                                                                                                                                                          0
                                                                                                 0




                                                                                                                                                                                                                                                                                                                0
                                                                                                                                                                                                                                                     0
                                                                                                                                                                                0
                                                                                                                                                                                            defense                                                  defense                                                             defense
                       defense response                                                                   13
                                                                                                 defense response                                                          -1            7                                                                3                                                            7                                                                              6
                                                                                                                                                                                           response                                                 response                                                           response
                                                                                                                                                                                         extracellular                                            extracellular                                                      extracellular
                       extracellular space                                                  -1 extracellular space
                                                                                                           15                                                             -2                    16                                         -4        7                                                    -2                 16                                                      -1                        11
                                                                                                                                                                                            space                                                    space                                                               space
                                                                                                                                                                                            immune                                                   immune                                                             immune
                       im m une response                                                                   17
                                                                                                 immune response                                                          -2                  14                                              -1   5                                                      -2              11                                                         -1                   8
                                                                                                                                                                                           response                                                 response                                                           response
                                                                                                                                                                                         extracellular                                            extracellular                                                      extracellular
                      extracellular m atrix                                                                11
                                                                                                 extracellular matrix                                                      -1              11                                                 -1   5                                                                      11                                                         -1           4
                                                                                                                                                                                            matrix                                                   matrix                                                             matrix
                                                                                                                                                                                        extracellular                                            extracellular                                                      extracellular
    extracellular m atrix (sensu Metazoa)                                                        10
                                                                       extracellular matrix (sensu Metazoa)                                                                -1              11                                                 -1   5                                                                      11                                                         -1           4
                                                                                                                                                                                        matrix (sensu                                            matrix (sensu                                                      matrix (sensu
                              extracellular                                                                   15
                                                                                                         extracellular                                                     -1               11
                                                                                                                                                                                          extracellular                                    -4             extracellular
                                                                                                                                                                                                                                                              9                                            -1        extracellular
                                                                                                                                                                                                                                                                                                                        9                                                            -1               5

                                                                                                                                                                                     non-motor actin                                               non-motor actin                                            non-motor actin
        non-m otor actin binding protein*                                                       7
                                                                             non-motor actin binding protein*                                                                           6                                                       -1                                                                 5                                                                                  5
                                                                                                                                                                                     binding protein*                                              binding protein*                                           binding protein*
                                                                                                                                                                                         insulin-like                                                  insulin-like                                               insulin-like
       insulin-like grow th factor binding                                insulin-like grow th4factor binding                                                                          5                                                               3                                                          4                                                                           2
                                                                                                                                                                                        growth factor                                                growth factor                                              growth factor
                                                                                                                                                                                        cell adhesion                                                 cell adhesion                                              cell adhesion
                 cell adhesion m olecule*                                                         3
                                                                                         cell adhesion molecule*                                                                         7                                                            2                                                           4molecule*                                                                  1
                                                                                                                                                                                          molecule*                                                     molecule*
   extracellular m atrix protein-m ediated                         extracellular matrix protein-mediated                                                                                extracellular                                                extracellular                                              extracellular
                                                                                          4                                                                                             6                                                              3                                                         3                                                                            1
                  signaling*                                                     signaling*                                                                                           matrix protein-                                               matrix protein-                                            matrix protein-
                                                                                                                                                                                         complement                                                    complement                                                 complement
                   com plem ent activation                                                        6
                                                                                           complement activation                                                                      4                                                               2                                                    -1 3                                                                                       5
                                                                                                                                                                                           activation                                                    activation                                                 activation
   hum oral defense m echanism (sensu                              humoral defense mechanism (sensu                                                                                           humoral                                                       humoral                                                    humoral
                                                                                         6                                                                                             5                                                               3                                                   -1     4                                                                               4
                Vertebrata)                                                    Vertebrata)                                                                                                    defense                                                       defense                                                    defense
                         serine protease*                                                              4
                                                                                                     serine protease*                                                                3
                                                                                                                                                                                    serine protease*                                               serine protease*
                                                                                                                                                                                                                                                        3                                                  -1 serine6 protease*                                                               2

                           trypsin activity                                                           4
                                                                                                      trypsin activity                                                               3trypsin activity                                                trypsin activity
                                                                                                                                                                                                                                                        2                                                  -1 trypsin activity
                                                                                                                                                                                                                                                                                                                  6                                                                           2
                                                                                                                                                                                             actin                                                       actin                                                          actin
                       actin cytoskeleton                                                        actin5cytoskeleton                                                        -1         4                                                       -1 1                                                                  3                                                                                 5
                                                                                                                                                                                        cytoskeleton                                                cytoskeleton                                                    cytoskeleton
                                                                                                                                                                                         negative                                                    negative                                                        negative
  negative regulation of cell proliferation                                       -2      4
                                                                  negative regulation of cell proliferation                                                                -1          5                                                               5                                                              5                                                             -2            4
                                                                                                                                                                                    regulation of cell                                          regulation of cell                                              regulation of cell
                                                                                                                                                                                    regulation of cell                                          regulation of cell                                              regulation of cell
                 regulation of cell grow th                                                         6
                                                                                         regulation of cell grow th                                                        -1           6                                                  -4          5                                                             4                                                               -1           3
                                                                                                                                                                                          growth                                                     growth                                                          growth
                                                                                                                                                                                      innate immune                                               innate immune                                                   innate immune
                innate im m une response                                                      2
                                                                                     innate immune response                                                                            5                                                      -1                                                                    3                                                                         2
                                                                                                                                                                                         response                                                    response                                                        response
                               cell grow th                                                 -1           8cell grow th                                                    -2             7 cell growth                                     -4              cell growth
                                                                                                                                                                                                                                                             7                                             -1            5 growth
                                                                                                                                                                                                                                                                                                                         cell                                                       -2            4
                                                                                                                                                                                            glucose                                                     glucose                                                   glucose
                      glucose catabolism                                                   -3 glucose catabolism                                                      -5                                                                        -1 1                                                       -1                                                                       -2        1
                                                                                                                                                                                          catabolism                                                  catabolism                                                catabolism
                                                                                                                                                                                            steroid                                                     steroid                                                   steroid
                      steroid m etabolism                                                  -3 steroid metabolism
                                                                                                  2                                                                   -5                                                                    -3                                                       -5     1                                                                   -3            2
                                                                                                                                                                                         metabolism                                                  metabolism                                                metabolism
                                                                                                                                                                                             lipid                                                       lipid                                                     lipid
                        lipid biosynthesis                                                 -3     lipid biosynthesis                                                  -4                                                                     -1                                                      -5                                                                             -2        1
                                                                                                                                                                                        biosynthesis                                                biosynthesis                                              biosynthesis
                                                                                                                                                                                        carbohydrate                                               carbohydrate                                              carbohydrate
               carbohydrate m etabolism                                             -8       1
                                                                                     carbohydrate metabolism                                                    -8                  1                                                    -6        1                                                  -3 1                                                                 -6                     3
                                                                                                                                                                                         metabolism                                                  metabolism                                               metabolism
                                                                                                                                                                                         electron                                                    electron                                                  electron
                electron transport chain+                                           -9electron 1
                                                                                               transport chain+                                                           -3                                                                 -1                                                         -2 1                                                                   -5
                                                                                                                                                                                     transport chain+                                           transport chain+                                          transport chain+
                             lyase activity                                         -8                  lyase activity                                               -6                   lyase activity                                      -2         1lyase activity                                  -2         lyase activity                                                 -2        1
                                                                                                                                                                                         lipid and fatty                                                 lipid and fatty                                            lipid and fatty
              lipid and fatty acid binding*                                         lipid-2 fatty acid binding*
                                                                                          and                                                                         -5                                                                        -1                                                         -1                                                                   -4
                                                                                                                                                                                          acid binding*                                                   acid binding*                                              acid binding*
                         dehydrogenase*                                             -9               2
                                                                                                     dehydrogenase*                                             -9                  dehydrogenase*                                       -5 dehydrogenase*
                                                                                                                                                                                                                                              1                                                       -3 dehydrogenase*
                                                                                                                                                                                                                                                                                                           1                                                              -7                  2
                                                                                                                                                                                            energy                                                      energy                                                           energy
                        energy pathw ays                                      -13                  1
                                                                                                   energy pathw ays                                             -8                  1                                                    -6                                                               -2         3                                                    -7                  2
                                                                                                                                                                                           pathways                                                    pathways                                                         pathways
         m ain pathw ays of carbohydrate                                                                                                                                             main pathways                                               main pathways                                                   main pathways
                                                                               -6
                                                            main pathw ays of carbohydrate metabolism                                                           -9                                                                           -2 1                                                         -2                                                               -6                 1
                   m etabolism                                                                                                                                                      of carbohydrate                                             of carbohydrate                                                 of carbohydrate
                                                                                                                                                                                      carboxylic acid                                            carboxylic acid                                                 carboxylic acid
              carboxylic acid m etabolism                                            -7
                                                                                    carboxylic 1 metabolism
                                                                                               acid                                                             -8                                                                        -5                                                          -4          1                                                             -3
                                                                                                                                                                                       metabolism                                                  metabolism                                                      metabolism
                                                                                                                                                                                            electron                                                    electron                                                         electron
                       electron transport                              -21                         2
                                                                                                 electron transport                                       -13                        3                                                   -6        2                                                  -3              6                                             -12                           3
                                                                                                                                                                                           transport                                                   transport                                                        transport
                                                                                                                                                                                        oxidative                                                   oxidative                                                       oxidative
               oxidative phosphorylation                                     -15     oxidative 1
                                                                                               phosphorylation                                                -10                                                                          -4     1                                                   -3          1                                                       -8                  1
                                                                                                                                                                                    phosphorylation                                             phosphorylation                                                 phosphorylation
                                                                                                                                                                                          fatty acid                                                  fatty acid                                                       fatty acid
                    fatty acid m etabolism                                          -8      fatty 1 metabolism
                                                                                                  acid                                                          -9                                                                        -5                                                    -7                                                                              -3            2
                                                                                                                                                                                        metabolism                                                  metabolism                                                      metabolism
generation of precursor m etabolites and                        generation of precursor metabolites and                                                                                generation of                                               generation of                                                   generation of
                                                                              -8                                                                                      -5                                                                     -2                                                       -3                                                                       -5
                 energy                                                          energy                                                                                                  precursor                                                   precursor                                                       precursor
                              peroxisom e                                             -6                 peroxisome                                              -7                       peroxisome                                     -5               peroxisome                                  -4             peroxisome                                                     -2
                                                                                                                                                                                      fatty acid beta-                                                fatty acid beta-                                            fatty acid beta-
                  fatty acid beta-oxidation                                          -7fatty acid beta-oxidation                                                      -5                                                                 -5                                                          -5                                                                         -3
                                                                                                                                                                                         oxidation                                                       oxidation                                                   oxidation
                                                                                                                                                                                     oxidoreductase                                                  oxidoreductase                                              oxidoreductase
                  oxidoreductase activity                       -27                                 6
                                                                                           oxidoreductase activity                                -21                                3                                              -9                   3                                      -8                     7                                        -14                                       8
                                                                                                                                                                                          activity                                                        activity                                                    activity
                           m itochondrion            -37                                              3mitochondrion                       -27                                          mitochondrion
                                                                                                                                                                                        4                                     -15                     1
                                                                                                                                                                                                                                                     mitochondrion                        -16                     mitochondrion
                                                                                                                                                                                                                                                                                                                       8                                -23                                       3

                              m etabolism           -40                                                   11
                                                                                                         metabolism            -41                                                        metabolism
                                                                                                                                                                                          8                                  -17                          3
                                                                                                                                                                                                                                                          metabolism                    -19                           metabolism
                                                                                                                                                                                                                                                                                                                        9                           -24                                                   8



                                                                                      PST                                                                RMA-CT                                                        RMA-Anova                                                        MAS5-CT                                                   MAS5-Anova
Electron transport, electron transport chain, oxidative phosphorylation, energy pathways




                   PST                 ACO2
                                       ACOX1
                   ATP5A1              ATP5C1               RMA-CT
                   ATP5B               ATP5F1
                   ATP5D               CAT                   ACADL
                   COX6A1              COX5A                 ACADSB
                   COX8A               COX6C                 CABC1
                   CYB5                DLD                   NDUFB5
                   DHCR24              ETFA
                   ECHS1               GBE1
                   ETFDH               MAOA
                   MRPS30              NDUFS1
                   NDUFAB1             PP
                   NDUFB2              PPARG
                   NDUFB3              SDHA
                   SLC25A3             SLC25A5
                   UQCRH               UQCRB
                                       UQCRC2
Comparing oxidative phosphorylation genes from muscle with fat




                                                          Intersection of PST and RMA-CT
                                                         PST Only




                                 Patti: Curr Opin Clin Nutr Metab Care, Volume 7(4).July 2004.383-390
Complement activation, defense response, immune response, humoral
          defense mechanism, innate immune response




             PST                        RMA-CT

             BF                          CCL5
             C1QG           C1R          CD24
             CD14           C1S          CD74
             CD53           CLU          CFH
             CD83           CTSS         COLEC12
             FTH1           CXCL12       CYBB
             HRMT1L2        FCGRT        LSP1
             IFI30          INHBB        LYZ
             IL2RB          SPON2        TNFAIP6
             IL6ST
             SERPING1
             SQSTM1
               Functional prioritization and analysis of HT datasets
                                     GeneGo: Metacore
                                        “Whole genome” datasets
                               1 – 10,000 statistically significant datapoints




                                                                             P-values
                            P-values




Ontologies of cellular                   Signaling, metabolic
processes, diseases                      pathways and maps

                                                                                 Biological networks: protein interactions and
                                                                                 metabolic transformations
 Process, pathway, map specific networks; expanded
 Interaction space around particular catagories
                                                                                  Prioritization of subnetworks:
                                                                                  - Relevance to data
                                                                                  - Relevance to processes
                                                                                  - Relevance to disease, tissue, organelle etc.
 Small, customized datasets connected via physical
                                                                                  - Relevanve to pathways
 and functional interactions; signature networks                                   p-values, z-score, g-score
                 Homologs changed in human or rat

Enrichment in Signaling, metabolic and regulatory pathways and processes


Human     Rat

                        Pathways affected in insulin resistance or
                        reversed by TZD treatment
               Pathways relevant to genes decreased in Human Insulin Resistance OR
                     reversed by Rosiglitazone treatment of Zucker Fatty Rats



                             Map Name                                  Map Folder              p-value      Expressed   All        Ratio
1 Citric acid cycle (citrate cycle; Krebs cycle)             Amino acid metabolism               4.68E-14          17         19   89.47%

2 Propionate metabolism. Part II                             Carbohydrate metabolism             2.40E-13          20         27   74.07%

3 TCA                                                        Amino acid metabolism               3.30E-13          15         16   93.75%

4 Cholesterol Biosynthesis                                   Steroid metabolism                  4.99E-12          17         22   77.27%

5 Leucune, isoleucine and valine metabolism.p.2              Amino acid metabolism               8.71E-12          18         25   72.00%

6 Propionate metabolism p.2                                  Carbohydrate metabolism             1.32E-11          15         18   83.33%

7 Fatty acid oxidation IV                                    Lipid metabolism                    6.83E-11          21         36   58.33%

8 Peroxisomal branched chain fatty acid oxidation            Lipid metabolism                    7.22E-09          13         18   72.22%

9 Glycolysis and gluconeogenesis                             Carbohydrate metabolism             1.28E-08          29         77   37.66%

10 Fatty acid oxidation III                                  Lipid metabolism                    1.10E-07          14         24   58.33%

11 Mitochondrial long chain fatty acid beta-oxidation        Lipid metabolism                    1.13E-07          12         18   66.67%

12 Fatty acid oxidation II                                   Lipid metabolism                    2.22E-07          14         25   56.00%

13 Ubiquinone metabolism                                     Vitamin and cofactor metabolism     6.71E-07          24         67   35.82%

14 Isoleucine and valine metabolism                          Amino acid metabolism               7.96E-07          18         42   42.86%

15 Propionate metabolism p.1                                 Carbohydrate metabolism             6.36E-06           8         11   72.73%

16 Ubiquinone biosynthesis                                   Vitamin and Cofactor Metabolism     6.63E-06          24         75   32.00%

17 Leucine and lysine metabolism                             Amino acid metabolism               6.93E-06          19         52   36.54%

18 Ketone bodies metabolism                                  Lipid metabolism                    7.04E-06          10         17   58.82%

19 PPAR regulation of lipid metabolism                       Regulation of lipid metabolism      9.47E-06          13         28   46.43%

20 Mitochondrial ketone bodies biosynthesis and metabolism   Lipid metabolism                    1.27E-05           7          9   77.78%
Glycolysis and gluconeogenesis

                                 PGM1
                                 phosphoglucomutase




                                 FBP1: Fructose-1,6-
                                 bisphosphatase 1




                                 PEPCK:
                                 phosphoenolpyruvate
                                 carboxykinase 1

                                 PDHA1, PDHB
                                 pyruvate dehydrogenase
                                 (lipoamide)

                                 DLD: dihydrolipoyl
                                 dehydrogenase
TCA Cycle




            ACO2: aconitase 2




            SDHD: succinate
            dehydrogenase complex




            SUCLG2: succinate-CoA
            ligase, GDP-forming, beta
            subunit



            DLD: dihydrolipoamide
            dehydrogenase
                                    Downregulated in
                                  Human insulin resistance




Upregulated after TZD treatment
              Rat
Mitochondrial long chain fatty acid beta-oxidation




                                     ECHS1: enoyl Coenzyme A hydratase, short
                                     chain, 1, mitochondrial

                                     HCDH: Medium and Short chain 3-
                                     hydroxyacyl-CoA dehydrogenase

                                     HADHA/HADHB: hydroxyacyl-Coenzyme A
                                     dehydrogenase/3-ketoacyl-Coenzyme A
                                     thiolase/enoyl-Coenzyme A hydratase
                                     (trifunctional protein)
PPAR regulation of lipid metabolism
                 Homologs changed in human or rat

Enrichment in Signaling, metabolic and regulatory pathways and processes


Human     Rat




                        Pathways affected in insulin resistance that are
                        reversed by TZD treatment
      Pathways relevant to genes decreased in Human Insulin Resistance AND
            reversed by Rosiglitazone treatment of Zucker Fatty Rats



                             Map Name                              Map Folder             p-value     Expressed   All       Ratio
1 Fatty acid oxidation I                                 Lipid metabolism                  9.74E-09           6     19       31.58%

2 Fatty acid synthesis I                                 Lipid metabolism                  1.38E-08           6     20       30.00%

3 Tryptophan metabolism                                  Aminoacid metabolism              1.44E-08           7     34       20.59%

4 Fatty acid oxidation IV                                Lipid metabolism                  2.20E-08           7     36       19.44%

5 Fatty acid oxidation III                               Lipid metabolism                  4.66E-08           6     24       25.00%

6 Leucune, isoleucine and valine metabolism.p.2          Aminoacid metabolism              6.09E-08           6     25       24.00%

7 Propionate metabolism p.2                              Carbohydrates metabolism          3.70E-07           5     18       27.78%

8 n-6 Polyunsaturated fatty acid biosynthesis            Lipid metabolism                  6.77E-07           7     58       12.07%

9 n-3 Polyunsaturated fatty acid biosynthesis            Lipid metabolism                  6.77E-07           7     58       12.07%

10 Regulation of fatty acid synthesis: NLTP and EHHADH   Regulation of lipid metabolism    6.83E-07           4         9    44.44%

11 Tryptophan metabolism                                 Aminoacid metabolism              1.76E-06           5     24       20.83%

12 Fatty acid oxidation II                               Lipid metabolism                  2.18E-06           5     25       20.00%

13 Propionate metabolism. Part II                        Carbohydrates metabolism          3.27E-06           5     27       18.52%

14 Lysine metabolism                                     Aminoacid metabolism              5.16E-06           6     51       11.76%

15 Leucine and lysine metabolism                         Aminoacid metabolism              5.79E-06           6     52       11.54%

16 Mitochondrial unsaturated fatty acid beta-oxidation   Lipid metabolism                  7.11E-06           4     15       26.67%

17 Peroxisomal branched chain fatty acid oxidation       Lipid metabolism                  1.56E-05           4     18       22.22%

18 Mitochondrial long chain fatty acid beta-oxidation    Lipid metabolism                  1.56E-05           4     18       22.22%

19 Citric acid cycle (citrate cycle; Krebs cycle)        Aminoacid metabolism              1.96E-05           4     19       21.05%

20 Isoleucine and valine metabolism                      Aminoacid metabolism              3.11E-05           5     42       11.90%
Fatty acid synthesis 1




                         FASN: fatty acid synthase




                         ECHS1: enoyl Coenzyme A
                         hydratase, short chain, 1,
                         mitochondrial


                         HADHA/HADHB: hydroxyacyl-
                         Coenzyme A dehydrogenase/3-
                         ketoacyl-Coenzyme A
                         thiolase/enoyl-Coenzyme A
                         hydratase (trifunctional protein)

                         HSD17B4: hydroxysteroid (17-
                         beta) dehydrogenase 4
Regulation of fatty acid synthesis




                                     SCP2: sterol carrier protein 2




                                     ECHS1: Enoyl-CoA hydratase,
                                     mitochondrial precursor
Family members with catalase deficiency had an aggregate frequency of 12·7% diabetes (types 1 and 2).
                                                             Goth and Eaton, Lancet 356:1820, 2000
              Electron Transport and Oxidative Stress


•   NO inhibition of mitochondrial electron transfer at cytochrome oxidase and at the
    ubiquinone–cytochrome b region of the respiratory chain leads to increased 02-
    production. Poderoso JJ et al, Arch Biochem Biophys 328: 85, 1996

•   Partial inhibition of the electron transport chain by NO may initially cause oxidative
    stress rather than ATP depletion, and subsequently induce irreversible changes in
    electron transport function providing the basis for a cycle of damage. Jacobson et al,
    J Neurochem 95: 388, 2005




     Mitochondrial                                                       Inflammatory
     Oxidative                          Oxidative Stress                 Response
     Phosphorylation
                 Homologs changed in human or rat

Enrichment in Signaling, metabolic and regulatory pathways and processes


Human     Rat




                        Pathways affected in insulin resistance that are
                        not reversed by TZD treatment
             Pathways relevant to genes decreased in Human Insulin Resistance BUT
                 NOT reversed by Rosiglitazone treatment of Zucker Fatty Rats



                            Map Name                                                Map Folder               p-value     Expressed       All       Ratio
1 EGFR signaling via PIP3                                              Growth and differentiation             4.14E-05               8     27       29.63%

2 Propionate metabolism p.1                                            Carbohydrates metabolism               1.22E-04               5     11       45.45%

3 Estrogen receptor signaling pathway                                  Growth and differentiation             4.58E-04               8     37       21.62%

4 Leukotriene 4 biosynthesis and metabolism                            Lipid metabolism                       1.66E-03           12        88       13.64%

5 Role of PBX in fibroblasts signaling pathways                        Growth and differentiation             1.66E-03               6     26       23.08%

6 Receptors. Part B. INSR- pleckstrin homology proteins interactions   Growth and differentiation             2.00E-03               7     36       19.44%

7 PPAR Pathway                                                         Transcription factors                  2.73E-03               8     48       16.67%

8 Propionate metabolism. Part I                                        Carbohydrates metabolism               3.12E-03               8     49       16.33%

9 p38-MAPK cascade activation via IGF1R and EGFR                       Growth and differentiation             3.23E-03               7     39       17.95%

10 Ligand-Dependent Transcription of Retinoid-Target genes             Regulation of transcription            4.62E-03           14       125       11.20%

11 Notch Signaling Pathway                                             Growth and differentiation             5.68E-03               7     43       16.28%

12 Polyamine metabolism                                                Metabolism of mediators                7.66E-03           13       119       10.92%

13 Leucune, isoleucine and valine metabolism.p.2                       Aminoacid metabolism                   7.76E-03               5     25       20.00%

14 A2B receptor: action via G-protein alpha s (map 1)                  G-proteins/GPCR                        8.01E-03               8     57       14.04%

15 RAB5A regulation pathway                                            G-proteins/RAS-group                   8.85E-03               3         9    33.33%

16 Ligand- dependent and ligand-independent activation of estrogen
receptors                                                              Regulation of transcription            9.43E-03               4     17       23.53%

17 A2B Receptor: Action via G-alpha s. (map 2)                         G-proteins/GPCR                        1.09E-02               8     60       13.33%

18 Propionate metabolism p.2                                           Carbohydrates metabolism               1.16E-02               4     18       22.22%

19 Pleckstrin homology proteins interactions. Part VIII                Second messenger-mediated signaling    1.16E-02               4     18       22.22%

20 dCTP/dUTP metabolism                                                Nucleotides metabolism                 1.17E-02               7     49       14.29%
Estrogen receptor signaling pathway
Notch signaling pathway
                           Summary

• Several coordinately regulated pathways in human insulin resistance are
reversed by rosiglitazone treatment of insulin-resistant Zucker fatty rats

• Oxidative stress resulting from depressed electron transport/oxidative
phosphorylation may be a mechanism for insulin resistance, which is
synonymous with the proposed paradigm for other diseases associated with
aging: atherosclerosis and Alzheimer‟s disease.

• Novel pharmacological targets include Estrogen receptor and Notch
signaling pathways

• Pathway and network analysis can illuminate potentially important
molecular targets for treatment of Type 2 DM
                    Acknowledgments
                    NIDDK Genomics Core Lab
Joe Lee    David Stiles   Jun Lu      Weiping Chen     George Poy

  Experimental Diabetes, Metabolism, and Nutrition Section, NIDDK
              Samuel W. Cushman       Desmond Hunt     Xiaoli Chen

Laboratory of Experimental and Computational Biology, NCI-Frederick
               Igor A. Sidorov   Dimiter S. Dimitrov

   The Lundberg Laboratory for Diabetes Research, Sahlgrenska
             University Hospital, Göteborg, Sweden
                     Ivan Nagaev     Ulf Smith

                             Genego
                           Yuri Nikolsky

				
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