title: Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes.
abstract: BACKGROUND
  Melanoma is the major cause of skin cancer deaths and melanoma incidence doubles every 10 to 20 years. However, little is known about melanoma pathway aberrations. Here we applied the robust Gene Identification Signature Paired End diTag (GIS-PET) approach to investigate the melanoma transcriptome and characterize the global pathway aberrations.
  
  
  METHODS
  GIS-PET technology directly links 5' mRNA signatures with their corresponding 3' signatures to generate, and then concatenate, PETs for efficient sequencing. We annotated PETs to pathways of KEGG database and compared the murine B16F1 melanoma transcriptome with three non-melanoma murine transcriptomes (Melan-a2 melanocytes, E14 embryonic stem cells, and E17.5 embryo). Gene expression levels as represented by PET counts were compared across melanoma and melanocyte libraries to identify the most significantly altered pathways and investigate the expression levels of crucial cancer genes.
  
  
  RESULTS
  Melanin biosynthesis genes were solely expressed in the cells of melanocytic origin, indicating the feasibility of using the PET approach for transcriptome comparison. The most significantly altered pathways were metabolic pathways, including upregulated pathways: purine metabolism, aminophosphonate metabolism, tyrosine metabolism, selenoamino acid metabolism, galactose utilization, nitrobenzene degradation, and bisphenol A degradation; and downregulated pathways: oxidative phosphorylation, ATPase synthesis, TCA cycle, pyruvate metabolism, and glutathione metabolism. The downregulated pathways concurrently indicated a slowdown of mitochondrial activities. Mitochondrial permeability was also significantly altered, as indicated by transcriptional activation of ATP/ADP, citrate/malate, Mg++, fatty acid and amino acid transporters, and transcriptional repression of zinc and metal ion transporters. Upregulation of cell cycle progression, MAPK, and PI3K/Akt pathways were more limited to certain region(s) of the pathway. Expression levels of c-Myc and Trp53 were also higher in melanoma. Moreover, transcriptional variants resulted from alternative transcription start sites or alternative polyadenylation sites were found in Ras and genes encoding adhesion or cytoskeleton proteins such as integrin, beta-catenin, alpha-catenin, and actin.
  
  
  CONCLUSIONS
  The highly correlated results unmistakably point to a systematic downregulation of mitochondrial activities, which we hypothesize aims to downgrade the mitochondria-mediated apoptosis and the dependency of cancer cells on angiogenesis. Our results also demonstrate the advantage of using the PET approach in conjunction with KEGG database for systematic pathway analysis.
authors.affiliation: Genome Institute of Singapore, Genome #02-01, Singapore. chiukp@gis.a-star.edu.sg
authors.forename: Kuo Ping
authors.initials: KP
authors.lastname: Chiu
authors.forename: Pramila
authors.initials: P
authors.lastname: Ariyaratne
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Adrian
authors.initials: A
authors.lastname: Tan
authors.forename: Patrick
authors.initials: P
authors.lastname: Ng
authors.forename: Edison Tak-Bun
authors.initials: ET
authors.lastname: Liu
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Wing-Kin Ken
authors.initials: WK
authors.lastname: Sung
mesh_terms: D000818:Animals; D017209:Apoptosis / Q000235:genetics; D053898:Biosynthetic Pathways / Q000235:genetics; D004195:Disease Models, Animal; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D008543:Melanins / Q000096:biosynthesis* / Q000235:genetics; D008545:Melanoma / Q000235:genetics* / Q000473:pathology; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D012680:Sensitivity and Specificity; D012878:Skin Neoplasms / Q000235:genetics* / Q000473:pathology; D014407:Tumor Cells, Cultured
chemical_list: D008543:Melanins; D012333:RNA, Messenger