List of secreted proteins from Rossetta (~2000)

Filter the secreted gene list based on DE (q< 0.05) in individual tissues (adipose, liver, islets, gastroc)

Sort the list based on fold-change

1.Liver gene list - 492. Islet gene list - 483. Adipose gene list - 494. Gastroc gene list -6

Create candidate gene list1. Select genes that are not DE in all other tissues (q>0.05 for same gene in all other tissues)2. Select genes that are more highly expressed in the origin than the target tissue (Average expression of the gene is higher in tissue of origin compared to other tissues (target tissues))

Use correlations, gene enrichment, and literature to identify testable candidates

TEST CASE: Time course B6 10 wk lean vs B6 10 wk obese

Simplified case: try to find genes originating from a single tissue of origin

Candidate genes and their fold change (obese/lean) from liver, adipose, islets, and gastroc

Liver Adipose Islet Gastroc

1 Apoa4- 10.03 Cd200r1- 4.83 C1ql3 - 12.9 Wisp1- 3.31

2 A1bg – 4.57 Mmp3 – 2.56 Pdyn - 3.65 1110018H23Rik – 1.99

3 AI 851790 – 3.96 Hapln3 – 2.28 Pappa2 - 3.1 1110017I16Rik – 1.48

4 Bche – 1.94 Il13 – 2.23 Cbln3 - 2.65 Cbln2 – 1.45

5 Wnt2 – 1.544 4930503L19Rik – 1.97

Svop - 2.44

6 Dnajc19 – 1.24 Xcl1 – 1.97 Serpini1- 2.19

7 Apoc3 – 1.2 Col28a1 – 1.92 Pycr2 - 2.07

8 Mmp27 – 1.79 Cart - 1.89

9 Ccl5 – 1.77 B230216G23Rik - 1.88

10 4732435N03Rik – 1.72

Prok2 - 1.75

Candidate genes and their fold change (obese/lean) from liver, adipose, islets, and gastroc

Liver Adipose Islet Gastroc

1 Serpina1b – 0.06 1700021K14Rik-0.31

Serpini -0.11 Ntf5 – 0.843

2 Itlh2 – 0.32 Id1 – 0.38 Pnliprp2 – 0.11 Ecm2 – 0.672

3 Serpina1b – 0.38 E030025L21Rik – 0.42

Cel- 0.12

4 Itlh2 – 0.5 Vwa2 – 0.43 Sycn – 0.12

5 Serpinf2 – 0.52 Megf6 – 0.45 Spink3 – 0.17

6 Cpn2 – 0.60 Gm1238- 0.45 Sema3e – 0.18

7 D030034A15Rik- 0.6

Cyp2j13 – 0.49 Reg1 – 0.19

8 Col4a4 – 0.49 Tac1 – 0.26

9 Cndp1 – 0.52 Sst – 0.26

10 Fbln1 - 0.57 Lgl2 – 0.26

Islets candidate genes

Pappalysin 2 (Pappa2)Member of the pregnancy-associated plasma protein-A family, has high similarity to a region of pappalysin 2 (human PAPPA2), which is a calcium ion-binding metalloendopeptidase that binds human PRG2 and cleaves human IGFBP5 between Ser-143 and Lys-144

Pappalysin 2 (Pappa2)

1. Location : Chromosome 1

2. Tissue of origin: Islets

3. In liver GO terms: glucose metabolic process, cellular lipid metabolic process,

glycolysis, lipid biosynthetic process, pentose-phosphate shunt Kegg pathway: pentose-phosphate pathway

Key metabolic correlates are: pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate mutase 1, pyruvate carboxylase, pyruvate dehydrogenase kinase- isoenzyme 1, 6-phosphogluconolactonase, stearoyl-Coenzyme A desaturase 2, fatty acid synthase, angiopoietin-like 3, SREBP cleavage activating protein, phosphatidylinositol 3-kinase, C2 domain containing- gamma polypeptide, apolipoprotein C-III, hexose-6-phosphate dehydrogenase, and 24-dehydrocholesterol reductase

Pappalysin 2 (Pappa2)

1. In Islets enriched for GO terms such as: oxidative phosphorylation, vesicle-mediated transport, cell redox homeostasis, purine ribonucleotide biosynthetic process, and transport

2. In Adipose enriched for GO terms such as: metabolic process, protein-DNA complex assembly, macromolecule localization, and protein transport

3. No enrichment in Gastroc

4. Substrate specificity of a metalloprotease of the pappalysin family revealed by an inhibitor and a product complex.

García-Castellanos R, Tallant C, Marrero A, Solà M, Baumann U, Gomis-Rüth FX.Departament de Biologia Estructural, Institut de Biologia Molecular de Barcelona, CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain.

Protein domains InterPro ID Description

IPR000436 Sushi/SCR/CCPIPR000800 Notch regionIPR006025 Peptidase M, neutral zinc metallopeptidases, zinc-binding siteIPR008754 Peptidase M43B, pregnancy-associated plasma-AIPR011936 Myxococcus cysteine-rich repeatIPR016060 Complement control module

Pappalysin 2 (Pappa2)

Resistance to age-dependent thymic atrophy in long-lived mice that are deficient in pregnancy-associated plasma protein A.Vallejo AN, Michel JJ, Bale LK, Lemster BH, Borghesi L, Conover CA.

Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15201, USA. andv26@pitt.edu

Pregnancy-associated plasma protein A (PAPPA) is a metalloproteinase that controls the tissue availability of insulin-like growth factor (IGF). Homozygous deletion of PAPPA in mice leads to lifespan extension. Since immune function is an important determinant of individual fitness, we examined the natural immune ecology of PAPPA(-/-) mice...

C1q-like 3; C1q-like; gliacolinC1q-like, binds to hsp47 (Serpinh1) and this binding requires the C1q-like domain, C1q-like domain can form homotrimers

Location: chromosome 2 (12923513-12932491)

Protein domains InterPro ID DescriptionIPR001073 Complement C1q proteinIPR008160 Collagen triple helix repeatIPR008983 Tumour necrosis factor-like

In Liver GO terms: metabolic process biosynthetic process cellular metabolic process Kegg pathway: Ribosome Complement and coagulation cascades Valine, leucine and isoleucine degradation

C1q-like 3; C1q-like; gliacolin

Disturbed secretion of mutant adiponectin associated with the metabolic syndrome.Kishida K, Nagaretani H, Kondo H, Kobayashi H, Tanaka S, Maeda N, Nagasawa A, Hibuse T, Ohashi K, Kumada M, Nishizawa H, Okamoto Y, Ouchi N, Maeda K, Kihara S, Funahashi T, Matsuzawa Y.

Department of Internal Medicine and Molecular Science, Graduate School of Medicine, B5, Osaka University, 2-2, Yamadaoka, Suita, 565-0871, Osaka, Japan.

Adiponectin, an adipocyte-derived protein, consists of collagen-like fibrous and complement C1q-like globular domains, and circulates in human plasma in a multimeric form…

C1q-like inhibits p53-mediated apoptosis and controls normal hematopoiesis during zebrafish embryogenesis.Mei J, Zhang QY, Li Z, Lin S, Gui JF.

State Key Laboratory of Freshwater Ecology and Biotechnology, Center for Developmental Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Wuhan 430072, China

C1q-like 3; C1q-like; gliacolin

WISP1 Int2 and ML ratio

Location: Chromosome 15 (+ strand) 66722954-66754761Mbps

Proteome short description: promotes osteoblast differentiation, likely involved in Wnt1 signaling; human WISP1 associated with breast gastric, and colon cancer

WNT1 inducible signaling pathway protein 1 (WISP-1)

KEGG pathway: skeletal development; regulation of cell growth; cell proliferation;

GO terms: insulin-like growth factor binding

Tissue of origin- Gastroc

WISP1 protein domains

Wisp 1This gene encodes a member of the WNT1 inducible signaling pathway (WISP) protein subfamily, which belongs to the connective tissue growth factor (CTGF) family. WNT1 is a member of a family of cysteine-rich, glycosylated signaling proteins that mediate diverse developmental processes. The CTGF family members are characterized by four conserved cysteine-rich domains: insulin-like growth factor-binding domain, von Willebrand factor type C module, thrombospondin domain and C-terminal cystine knot-like domain. This gene may be downstream in the WNT1 signaling pathway that is relevant to malignant transformation. It is expressed at a high level in fibroblast cells, and overexpressed in colon tumors. The encoded protein binds to decorin and biglycan, two members of a family of small leucine-rich proteoglycans present in the extracellular matrix of connective tissue, and possibly prevents the inhibitory activity of decorin and biglycan in tumor cell proliferation. It also attenuates p53-mediated apoptosis in response to DNA damage through activation of the Akt kinase. It is 83% identical to the mouse protein at the amino acid level. Alternative splicing of this gene generates 2 transcript variants.

Abstract of interestThe CCN family: a new stimulus package.Brigstock DR.

Department of Surgery, The Ohio State University, Columbus, Ohio 43212, USA. brigstocd@pediatrics.ohio-state.edu

The CCN family comprises cysteine-rich 61 (CYR61/CCN1), connective tIssue growth factor (CTGF/CCN2), nephroblastoma overexpressed (NOV/CCN3), and Wnt-induced secreted proteins-1 (WISP-1/CCN4), -2 (WISP-2/CCN5) and -3 (WISP-3/CCN6). These proteins stimulate mitosis, adhesion, apoptosis, extracellular matrix production, growth arrest and migration of multiple cell types. Many of these activities probably occur through the ability of CCN proteins to bind and activate cell surface integrins. Accumulating evidence supports a role for these factors in endocrine pathways and endocrine-related processes. To illustrate the broad role played by the CCN family in basic and clinical endocrinology, this Article highlights the relationship between CCN proteins and hormone action, skeletal growth, placental angiogenesis, IGF-binding proteins and diabetes-induced fibrosis.

Interleukin 13 (IL13)Interleukin 13, a cytokine that modulates B-cell IgE switching, regulates thymocyte development and inflammatory responses; human IL13 may be therapeutic for AIDS, diabetes, rheumatoid arthritis, asthma, and some cancers

Location: chromosome 11 (53444825-53448204)

Tissue of origin – AdiposeIn Liver, islets, and gastroc- no enrichment for GO terms or keggpathways

Interleukin 13 (IL13)

Apoa4Apolipoprotein A-IV, involved in cholesterol transport, lipid homeostasis, and regulation of feeding behavior; human APOA4 is linked to cardiovascular pathology in NIDDM diabetes and senile systemic amyloidosis, but may be protective in atherosclerosis

Location: Chromosome 9 (46048926-46051541)

Apoa4

Tissue of origin- LiverIn IsletsGO term-localization establishment of localization transport vesicle-mediated

transport cellular localization establishment of protein localization protein localization establishment of cellular localization protein transport macromolecule localization secretion by cell

In Adipose GO terms-macromolecule localization protein localization protein transport

establishment of protein localization regulation of multicellular organism growth

1110018H23 Rik• Location: chromosome17 (+ strand):25257721-25262158Mbps • neuronal pentraxin II-like (e=0.0,score=864,100% ID over 431aa

[query=1362nt], +1 frame, blastx,Mus musculus) • Protein containing a pentaxin family domain, has low similarity to serum

amyloid P component (human APCS), which regulates the classical complement pathway that is associated with primary idiopathic amyloidosis and Alzheimer's disease

• Protein domains: 1) Pentaxin; 2)Concanavalin A-like lectin/glucanase, subgroup

• Homologues in human; chimpanzee; cattle; dog, domestic; rat based on AA and NT BLAST

• GO terms: defense response; physiological process; detection of biotic stimulus; antigen binding