Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis

Table 1 References used in the definition of types of hematopoietic cells in the Kupffer cell fraction

No.	Reference
1	Tordjmann T, Soulie A, Guettier C, Schmidt M, Berthou C, Beaugrand M, Sasportes M. Perforin and granzyme B lytic protein expression during chronic viral and autoimmune hepatitis. Liver 1998; 18: 391-397
2	Lautenschlager I. Characteristics of the strongly Ia-positive cells in rat liver. Scand J Immunol 1984; 20: 333-338
3	Boisclair J, Dore M, Beauchamp G, Chouinard L, Girard C. Characterization of the inflammatory infiltrate in canine chronic hepatitis. Vet Pathol 2001; 38: 628-635
4	Ahlenstiel G, Woitas RP, Rockstroh J, Spengler U. CC-chemokine receptor 5 (CCR5) in hepatitis C--at the crossroads of the antiviral immune response? J Antimicrob Chemother 2004; 53: 895-898
5	Eis V, Luckow B, Vielhauer V, Siveke JT, Linde Y, Segerer S, De Lema GP, Cohen CD, Kretzler M, Mack M, Horuk R, Murphy PM, Gao JL, Hudkins KL, Alpers CE, Grone HJ, Schlondorff D, Anders HJ. Chemokine receptor CCR1 but not CCR5 mediates leukocyte recruitment and subsequent renal fibrosis after unilateral ureteral obstruction. J Am Soc Nephrol 2004; 15: 337-347
6	McCabe MJ Jr, Dias JA, Lawrence DA. Lead influences translational or posttranslational regulation of Ia expression and increases invariant chain expression in mouse B cells. J Biochem Toxicol 1991; 6: 269-276
7	Wilson KM, Labeta MO, Pawelec G, Fernandez N. Cell-surface expression of human histocompatibility leucocyte antigen (HLA) class II-associated invariant chain (CD74) does not always correlate with cell-surface expression of HLA class II molecules. Immunology 1993; 79: 331-335
8	Kiley SC, Parker PJ. Differential localization of protein kinase C isozymes in U937 cells: evidence for distinct isozyme functions during monocyte differentiation. J Cell Sci 1995; 108 (Pt 3): 1003-1016
9	Allen JN, Liao Z, Moore SA, Wewers MD. Changes in mononuclear phagocyte microtubules after endotoxin stimulation. II. Changes in microtubule composition. Am J Respir Cell Mol Biol 1997; 16: 127-132
10	Devergne O, Peuchmaur M, Humbert M, Navratil E, Leger-Ravet MB, Crevon MC, Petit MA, Galanaud P, Emilie D. In vivo expression of IL-1 beta and IL-6 genes during viral infections in human. Eur Cytokine Netw 1991; 2: 183-194
11	Thornton AJ, Ham J, Kunkel SL. Kupffer cell-derived cytokines induce the synthesis of a leukocyte chemotactic peptide, interleukin-8, in human hepatoma and primary hepatocyte cultures. Hepatology 1991; 14: 1112-1122
12	Manthey CL, Kossmann T, Allen JB, Corcoran ML, Brandes ME, Wahl SM. Role of Kupffer cells in developing streptococcal cell wall granulomas. Streptococcal cell wall induction of inflammatory cytokines and mediators. Am J Pathol 1992; 140: 1205-1214
13	Zhu XL, Zellweger R, Zhu XH, Ayala A, Chaudry IH. Cytokine gene expression in splenic macrophages and Kupffer cells following haemorrhage. Cytokine 1995; 7: 8-14
14	Loike JD, Kaback E, Silverstein SC, Steinberg TH. Lactate transport in macrophages. J Immunol 1993; 150: 1951-1958
15	Daberkow RL, White BR, Cederberg RA, Griffin JB, Zempleni J. Monocarboxylate transporter 1 mediates biotin uptake in human peripheral blood mononuclear cells. J Nutr 2003; 133: 2703-2706
16	Merezhinskaya N, Ogunwuyi SA, Mullick FG, Fishbein WN. Presence and localization of three lactic acid transporters (MCT1, -2, and -4) in separated human granulocytes, lymphocytes, and monocytes. J Histochem Cytochem 2004; 52: 1483-1493
17	Marra F, Valente AJ, Pinzani M, Abboud HE. Cultured human liver fat-storing cells produce monocyte chemotactic protein-1. Regulation by proinflammatory cytokines. J Clin Invest 1993; 92: 1674-1680
18	Guc D, Gulati P, Lemercier C, Lappin D, Birnie GD, Whaley K. Expression of the components and regulatory proteins of the alternative complement pathway and the membrane attack complex in normal and diseased synovium. Rheumatol Int 1993; 13: 139-146
19	Schwaeble W, Huemer HP, Most J, Dierich MP, Strobel M, Claus C, Reid KB, Ziegler-Heitbrock HW. Expression of properdin in human monocytes. Eur J Biochem 1994; 219: 759-764
20	Yamanouchi S, Kuwahara K, Sakata A, Ezaki T, Matsuoka S, Miyazaki J, Hirose S, Tamura T, Nariuchi H, Sakaguchi N. A T cell activation antigen, Ly6C, induced on CD4+ Th1 cells mediates an inhibitory signal for secretion of IL-2 and proliferation in peripheral immune responses. Eur J Immunol 1998; 28: 696-707
21	Manoussaka MS, Smith RJ, Conlin V, Toomey JA, Brooks CG. Fetal mouse NK cell clones are deficient in Ly49 expression, share a common broad lytic specificity, and undergo continuous and extensive diversification in vitro. J Immunol 1998; 160: 2197-2206
22	Wrammert J, Kallberg E, Agace WW, Leanderson T. Ly6C expression differentiates plasma cells from other B cell subsets in mice. Eur J Immunol 2002; 32: 97-103
23	Katz P, Whalen G, Kehrl JH. Differential expression of a novel protein kinase in human B lymphocytes. Preferential localization in the germinal center. J Biol Chem 1994; 269: 16802-16809
24	Valent P, Ashman LK, Hinterberger W, Eckersberger F, Majdic O, Lechner K, Bettelheim P. Mast cell typing: demonstration of a distinct hematopoietic cell type and evidence for immunophenotypic relationship to mononuclear phagocytes. Blood 1989; 73: 1778-1785
25	Titos E, Claria J, Planaguma A, Lopez-Parra M, Villamor N, Parrizas M, Carrio A, Miquel R, Jimenez W, Arroyo V, Rivera F, Rodes J. Inhibition of 5-lipoxygenase induces cell growth arrest and apoptosis in rat Kupffer cells: implications for liver fibrosis. FASEB J 2003; 17: 1745-1747
26	Titos E, Claria J, Planaguma A, Lopez-Parra M, Gonzalez-Periz A, Gaya J, Miquel R, Arroyo V, Rodes J. Inhibition of 5-lipoxygenase-activating protein abrogates experimental liver injury: role of Kupffer cells. J Leukoc Biol 2005; 78: 871-878
27	Sawano A, Iwai S, Sakurai Y, Ito M, Shitara K, Nakahata T, Shibuya M. Flt-1, vascular endothelial growth factor receptor 1, is a novel cell surface marker for the lineage of monocyte-macrophages in humans. Blood 2001; 97: 785-791
28	Coppola S, Narciso L, Feccia T, Bonci D, Calabro L, Morsilli O, Gabbianelli M, De Maria R, Testa U, Peschle C. Enforced expression of KDR receptor promotes proliferation, survival and megakaryocytic differentiation of TF1 progenitor cell line. Cell Death Differ 2006; 13: 61-74
29	Fernandez Pujol B, Lucibello FC, Zuzarte M, Lutjens P, Muller R, Havemann K. Dendritic cells derived from peripheral monocytes express endothelial markers and in the presence of angiogenic growth factors differentiate into endothelial-like cells. Eur J Cell Biol 2001; 80: 99-110
30	Bowling WM, Flye MW, Qiu YY, Callery MP. Inhibition of phosphatidylinositol-3'-kinase prevents induction of endotoxin tolerance in vitro. J Surg Res 1996; 63: 287-292
31	Capodici C, Hanft S, Feoktistov M, Pillinger MH. Phosphatidylinositol 3-kinase mediates chemoattractant-stimulated, CD11b/CD18-dependent cell-cell adhesion of human neutrophils: evidence for an ERK-independent pathway. J Immunol 1998; 160: 1901-1909
32	Bracke M, Nijhuis E, Lammers JW, Coffer PJ, Koenderman L. A critical role for PI 3-kinase in cytokine-induced Fcalpha-receptor activation. Blood 2000; 95: 2037-2043
33	Zweifel M, Breu K, Matozan K, Renner E, Welle M, Schaffner T, Clavien PA. Restoration of hepatic mast cells and expression of a different mast cell protease phenotype in regenerating rat liver after 70%-hepatectomy. Immunol Cell Biol 2005; 83: 587-595
34	Pemberton AD, Brown JK, Wright SH, Knight PA, Miller HR. The proteome of mouse mucosal mast cell homologues: the role of transforming growth factor beta1. Proteomics 2006; 6: 623-631
35	Schwartz LB. Analysis of MC(T) and MC(TC) mast cells in tissue. Methods Mol Biol 2006; 315: 53-62
36	Henningsson F, Yamamoto K, Saftig P, Reinheckel T, Peters C, Knight SD, Pejler G. A role for cathepsin E in the processing of mast-cell carboxypeptidase A. J Cell Sci 2005; 118: 2035-2042
37	Chen ZQ, He SH. Cloning and expression of human colon mast cell carboxypeptidase. World J Gastroenterol 2004; 10: 342-347
38	Lagasse E, Clerc RG. Cloning and expression of two human genes encoding calcium-binding proteins that are regulated during myeloid differentiation. Mol Cell Biol 1988; 8: 2402-2410
39	Bhardwaj RS, Zotz C, Zwadlo-Klarwasser G, Roth J, Goebeler M, Mahnke K, Falk M, Meinardus-Hager G, Sorg C. The calcium-binding proteins MRP8 and MRP14 form a membrane-associated heterodimer in a subset of monocytes/macrophages present in acute but absent in chronic inflammatory lesions. Eur J Immunol 1992; 22: 1891-1897
40	Ryckman C, Vandal K, Rouleau P, Talbot M, Tessier PA. Proinflammatory activities of S100: proteins S100A8, S100A9, and S100A8/A9 induce neutrophil chemotaxis and adhesion. J Immunol 2003; 170: 3233-3242
41	Yoshimoto T, Suzuki H, Yamamoto S, Takai T, Yokoyama C, Tanabe T. Cloning and expression of arachidonate 12-lipoxygenase cDNA from porcine leukocytes. Adv Prostaglandin Thromboxane Leukot Res 1991; 21A: 29-32
42	Gu JL, Natarajan R, Ben-Ezra J, Valente G, Scott S, Yoshimoto T, Yamamoto S, Rossi JJ, Nadler JL. Evidence that a leukocyte type of 12-lipoxygenase is expressed and regulated by angiotensin II in human adrenal glomerulosa cells. Endocrinology 1994; 134: 70-77
43	Nakamura M, Ueda N, Kishimoto K, Yoshimoto T, Yamamoto S, Ishimura K. Immunocytochemical localization of platelet-type arachidonate 12-lipoxygenase in mouse blood cells. J Histochem Cytochem 1995; 43: 237-244
44	Kaminski WE, Jendraschak E, Baumann K, Kiefl R, Fischer S, Marcus AJ, Broekman MJ, von Schacky C. Human mononuclear cells express 12-LX: coordinated mRNA regulation with 5-LX and FLAP genes. Blood 1996; 87: 331-340
45	Takenaga K, Nakamura Y, Sakiyama S. Expression of a calcium binding protein pEL98 (mts1) during differentiation of human promyelocytic leukemia HL-60 cells. Biochem Biophys Res Commun 1994; 202: 94-101
46	Yancopoulos GD, Oltz EM, Rathbun G, Berman JE, Smith RK, Lansford RD, Rothman P, Okada A, Lee G, Morrow M. Isolation of coordinately regulated genes that are expressed in discrete stages of B-cell development. Proc Natl Acad Sci USA 1990; 87: 5759-5763
47	Quelo I, Jurdic P. Differential regulation of the carbonic anhydrase II gene expression by hormonal nuclear receptors in monocytic cells: identification of the retinoic acid response element. Biochem Biophys Res Commun 2000; 271: 481-491
48	Baron WF, Pan CQ, Spencer SA, Ryan AM, Lazarus RA, Baker KP. Cloning and characterization of an actin-resistant DNase I-like endonuclease secreted by macrophages. Gene 1998; 215: 291-301
49	Kitabatake Y, Kawamura S, Yamashita M, Okuyama K, Takayanagi M, Ohno I. The expression of mRNA for calcitonin gene-related peptide receptors in a mucosal type mast cell line, RBL-2H3. Biol Pharm Bull 2004; 27: 896-898
50	Makino Y, Nakamura H, Ikeda E, Ohnuma K, Yamauchi K, Yabe Y, Poellinger L, Okada Y, Morimoto C, Tanaka H. Hypoxia-inducible factor regulates survival of antigen receptor-driven T cells. J Immunol 2003; 171: 6534-6540
51	Frank M. MAL, a proteolipid in glycosphingolipid enriched domains: functional implications in myelin and beyond. Prog Neurobiol 2000; 60: 531-544

The reference numbers correspond to the numbers in Figure 5 in the supplementary data.