Detection of Critical Genes Associated with Overall Survival (OS) and Progression-Free Survival (PFS) in Reconstructed Canine B-Cell Lymphoma Gene Regulatory Network (GRN)

References

• MacEwen EG. Spontaneous tumors in dogs and cats: models for the study of cancer biology and treatment. Cancer Metastasis Rev 1990;9:125–136.
   PubMed Web of Science ®Google Scholar
• Jacobs RM, Messick JB, Valli VE. Hemolymphatic system. In: Tumors in Domestic Animals. Meuten DJ, (ed.). Ames, Iowa: Iowa State Press; 2002;138–143.
   Google Scholar
• McCaw DL, Chan AS, Stegner AL, Mooney B, Bryan JN, Turnquist SE, et al. Proteomics of canine lymphoma identifies potential cancer-specific protein markers. Clin Cancer Res 2007;13:2496–2503.
   PubMed Web of Science ®Google Scholar
• Vail DM ME, Young KM. Canine lymphoma and lymphoid leukemias. In: Withrow and MacEwen's Small Animal Clinical Oncology, Withrow SJ, Vail DM, Page RL, (eds.). Philadelphia: Elsevier Health Sciences; 2001;558–584.
   Google Scholar
• Mudaliar MAV, Haggart RD, Miele G, Sellar G, Tan KAL, Goodlad JR, et al. Comparative gene expression profiling identifies common molecular signatures of NF-κB activation in canine and human diffuse large B cell lymphoma (DLBCL). PLoS ONE 2013;8:e72591.
   Google Scholar
• Richards KL, Motsinger-Reif AA, Chen H-W, Fedoriw Y, Fan C, Nielsen DM, et al. Gene profiling of canine B-cell lymphoma reveals germinal center and postgerminal center subtypes with different survival times, modeling human DLBCL. Cancer Res 2013;73:5029–5039.
   PubMed Web of Science ®Google Scholar
• Emmert-Streib F, de Matos Simoes R, Mullan P, Haibe-Kains B, Dehmer M. The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks. Front Genet 2014;5.
   Google Scholar
• Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D. How to infer gene networks from expression profiles. Mol Syst Biol 2007;3.
   Google Scholar
• Blais A, Dynlacht BD. Constructing transcriptional regulatory networks. Genes Dev 2005;19:1499–1511.
   PubMed Web of Science ®Google Scholar
• Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim W-K, et al. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood 2010;115:975–984.
   PubMed Web of Science ®Google Scholar
• Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005;37:382–390.
   PubMed Web of Science ®Google Scholar
• Agnelli L, Forcato M, Ferrari F, Tuana G, Todoerti K, Walker BA, et al., The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma. Clin Cancer Res 2011;17:7402–7412.
   PubMed Web of Science ®Google Scholar
• Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004;20:307–315.
   PubMed Web of Science ®Google Scholar
• Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998;95:14863–14868.
   PubMed Web of Science ®Google Scholar
• Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein–protein interaction networks, with increased coverage and integration. Nucl Acids Res 2013;41:D808–D815.
   Google Scholar
• Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, et al. Michigan molecular interactions r2: from interacting proteins to pathways. Nucl Acids Res 2009;37:D642–D646.
   Google Scholar
• Zamani-Ahmadmahmudi M, Najafi A, Nassiri SM. Reconstruction of canine diffuse large b-cell lymphoma gene regulatory network: detection of functional modules and hub genes. J Comp Pathol 2015;152:119–130.
   PubMed Web of Science ®Google Scholar
• Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007;2:2366–2382.
   PubMed Web of Science ®Google Scholar
• Assenov Y, Ramírez F, Schelhorn S-E, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics 2008;24:282–284.
   PubMed Web of Science ®Google Scholar
• Mey U, Hitz F, Lohri A, Pederiva S, Taverna C, Tzankov A, et al. Diagnosis and treatment of diffuse large B-cell lymphoma. Swiss Med Wkly 2012;142:w13511.
   PubMed Web of Science ®Google Scholar
• Floratos A, Smith K, Ji Z, Watkinson J, Califano A. geWorkbench: an open source platform for integrative genomics. Bioinformatics 2010;26:1779–1780.
   PubMed Web of Science ®Google Scholar
• Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004;20:93–99.
   PubMed Web of Science ®Google Scholar
• Schroder MS, Culhane AC, Quackenbush J, Haibe-Kains B. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics 2011;27:3206–3208.
   PubMed Web of Science ®Google Scholar
• Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, et al. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med 2004;350:1828–1837.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl Acids Res 2009;37:1–13.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009;4:44–57.
   PubMed Web of Science ®Google Scholar
• Zhang A, Ohshima K, Sato K, Kanda M, Suzumiya J, Shimazaki K, et al. Prognostic clinicopathologic factors, including immunologic expression in diffuse large B-cell lymphomas. Pathol Int 1999;49:1043–1052.
   PubMed Web of Science ®Google Scholar
• P Drillenburg VJW. CD44 expression predicts disease outcome in localized large B cell lymphoma. Leukemia 1999;13:1448–1455.
   PubMed Web of Science ®Google Scholar
• Thorstenson YR, Shen P, Tusher VG, Wayne TL, Davis RW, Chu G et al. Global analysis of ATM polymorphism reveals significant functional constraint. Am J Hum Genet 2001;69:396–412.
   PubMed Web of Science ®Google Scholar
• Krenacs L, Himmelmann AW, Quintanilla-Martinez L, Fest T, Riva A, Wellmann A et al. Transcription factor B-cell-specific activator protein (BSAP) is differentially expressed in B cells and in subsets of B-cell lymphomas. Blood 1998;92:1308–1316.
   PubMed Web of Science ®Google Scholar
• Møller MB, Kania PW, Ino Y, Gerdes AM, Nielsen O, Louis DN et al. Frequent disruption of the RB1 pathway in diffuse large B cell lymphoma: prognostic significance of E2F-1 and p16INK4A. Leukemia 2000;14:898–904.
   Google Scholar
• Ichikawa A, Kinoshita T, Watanabe T, Kato H, Nagai H, Tsushita K et al. Mutations of the p53 gene as a prognostic factor in aggressive B-cell lymphoma. N Engl J Med 1997;337:529–534.
   PubMed Web of Science ®Google Scholar
• Gascoyne RD, Adomat SA, Krajewski S, Krajewska M, Horsman DE, Tolcher AW et al. Prognostic significance of Bcl-2 protein expression and Bcl-2 gene rearrangement in diffuse aggressive non-Hodgkin's lymphoma. Blood 1997;90:244–251.
   PubMed Web of Science ®Google Scholar
• Shaffer AL, Yu X, He Y, Boldrick J, Chan EP, Staudt LM. BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity 2000;13:199–212.
   PubMed Web of Science ®Google Scholar
• Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI et al. Leukemia Molecular Profiling P. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002;346:1937–1947.
   PubMed Web of Science ®Google Scholar
• Nojima H. G1 and S-phase checkpoints, chromosome instability, and cancer. Methods Mol Biol 2004;280:3–49.
   PubMedGoogle Scholar
• Gladkikh A, Potashnikova D, Korneva E, Khudoleeva O, Vorobjev I. Cyclin D1 expression in B-cell lymphomas. Exp Hematol 2010;38:1047–1057.
   PubMed Web of Science ®Google Scholar
• Krieger S, Gauduchon J, Roussel M, Troussard X, Sola B. Relevance of cyclin D1b expression and CCND1 polymorphism in the pathogenesis of multiple myeloma and mantle cell lymphoma. BMC Cancer 2006;6:238.
   Google Scholar
• Simpson JF, Quan DE, O'Malley F, Odom-Maryon T, Clarke PE. Amplification of CCND1 and expression of its protein product, cyclin D1, in ductal carcinoma in situ of the breast. Am J Pathol 1997;151:161–168.
   PubMed Web of Science ®Google Scholar
• Schraml P, Kononen J, Bubendorf L, Moch H, Bissig H, Nocito A, et al. Tissue microarrays for gene amplification surveys in many different tumor types. Clin Cancer Res 1999;5:1966–1975.
   PubMed Web of Science ®Google Scholar
• Ok CY, Xu-Monette ZY, Tzankov A, O'Malley DP, Montes-Moreno S, Visco C, et al. Prevalence and clinical implications of cyclin D1 expression in diffuse large B-cell lymphoma (DLBCL) treated with immunochemotherapy: a report from the International DLBCL Rituximab-CHOP Consortium Program. Cancer 2014;120:1818–1829.
   PubMed Web of Science ®Google Scholar
• Vela-Chávez T, Adam P, Kremer M, Bink K, Bacon CM, Menon G et al. Cyclin D1 positive diffuse large B-cell lymphoma is a post-germinal center-type lymphoma without alterations in the CCND1 gene locus. Leuk Lymphoma 2011;52:458–466.
   Google Scholar
• Lucioni M, Novara F, Riboni R, Fiandrino G, Nicola M, Kindl S, et al. CD5(−) diffuse large B-cell lymphoma with peculiar cyclin D1+ phenotype. Pathologic and molecular characterization of a single case. Hum Pathol 2011;42:1204–1208.
   PubMed Web of Science ®Google Scholar
• Juskevicius D, Ruiz C, Dirnhofer S, Tzankov A. Clinical, morphologic, phenotypic, and genetic evidence of cyclin D1-positive diffuse large B-cell lymphomas with CYCLIN D1 gene rearrangements. Am J Surg Pathol 2014;38:719–727.
   PubMed Web of Science ®Google Scholar
• Siddon AJ, Torres R, Rinder HM, Smith BR, Howe JG, Tormey CA. Normalized CCND1 expression has prognostic value in mantle cell lymphoma. Br J Haematol 2012;158:551–553.
   PubMed Web of Science ®Google Scholar
• Hein S, Mahner S, Kanowski C, Löning T, Jänicke F, Milde-Langosch K. Expression of Jun and Fos proteins in ovarian tumors of different malignant potential and in ovarian cancer cell lines. Oncol Rep 2009;22:177–183.
   PubMed Web of Science ®Google Scholar
• Mahner S, Baasch C, Schwarz J, Hein S, Wolber L, Janicke F, et al. C-Fos expression is a molecular predictor of progression and survival in epithelial ovarian carcinoma. Br J Cancer 2008;99:1269–1275.
   PubMed Web of Science ®Google Scholar
• Bland KI, Konstadoulakis MM, Vezeridis MP, Wanebo HJ. Oncogene protein co-expression. Value of Ha-ras, c-myc, c-fos, and p53 as prognostic discriminants for breast carcinoma. Ann Surg 1995;221:706–720.
   PubMed Web of Science ®Google Scholar
• Mathas S, Hinz M, Anagnostopoulos I, Krappmann D, Lietz A, Jundt F, et al. Aberrantly expressed c-Jun and JunB are a hallmark of Hodgkin lymphoma cells, stimulate proliferation and synergize with NF-kappa B. EMBO J 2002;21:4104–4113.
   PubMed Web of Science ®Google Scholar
• Tzankov A, Pehrs AC, Zimpfer A, Ascani S, Lugli A, Pileri S, et al.. Prognostic significance of CD44 expression in diffuse large B cell lymphoma of activated and germinal centre B cell-like types: a tissue microarray analysis of 90 cases. J Clin Pathol 2003;56:747–752.
   PubMed Web of Science ®Google Scholar
• Kiupel M, Teske E, Bostock D. Prognostic factors for treated canine malignant lymphoma. Vet Pathol 1999;36:292–300.
   PubMed Web of Science ®Google Scholar