title: Identification of multiple DNA copy number alterations including frequent 8p11.22 amplification in conjunctival squamous cell carcinoma.
abstract: OBJECTIVE
  Little is known about the molecular alterations that drive formation and growth of conjunctival squamous cell carcinoma (cSCC). We therefore sought to identify genetic changes that could be used as diagnostic markers or therapeutic targets.
  
  
  METHODS
  The DNA extracted from 10 snap-frozen cSCC tumor specimens and 2 in situ carcinomas was analyzed using array-based comparative genomic hybridization (aCGH), and further examined with NanoString and quantitative PCR.
  
  
  RESULTS
  The number of regions of DNA loss ranged from 1 to 23 per tumor, whereas gains and amplifications ranged from 1 to 15 per tumor. Most large regions of chromosomal gain and loss were confirmed by NanoString karyotype analysis. The commonest alteration was amplification of 8p11.22 in 9 tumors (75%), and quantitative PCR analysis revealed 100-fold or greater overexpression of ADAM3A mRNA from 8p11.22 locus. In addition, recurring losses were observed at 14q13.2 and 22q11.23, both lost in 5 (42%) of the 12 tumors, and at 12p13.31, lost in 4 (33%) of the 12 samples. Of the eight loci associated with the DNA damage repair syndrome xeroderma pigmentosum, three showed loss of at least one allele in our aCGH analysis, including XPA (9q22.33, one tumor), XPE/DDB2 (11p11.2, one tumor) and XPG/ERCC5 (13q33.1, three tumors).
  
  
  CONCLUSIONS
  Conjunctival SCC contains a range of chromosomal alterations potentially important in tumor formation and growth. Amplification of 8p11.22 and overexpression of ADAM3A suggests a potential role for this protease. Our findings also suggest that defects in DNA repair loci are important in sporadic cSCC.
authors.affiliation: Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States.
authors.forename: Laura
authors.initials: L
authors.lastname: Asnaghi
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Hind
authors.initials: H
authors.lastname: Alkatan
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Alka
authors.initials: A
authors.lastname: Mahale
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Maha
authors.initials: M
authors.lastname: Othman
authors.affiliation: Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Saeed
authors.initials: S
authors.lastname: Alwadani
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Hailah
authors.initials: H
authors.lastname: Al-Hussain
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Sabah
authors.initials: S
authors.lastname: Jastaneiah
authors.affiliation: Microarray Core Facility, Sidney Kimmel Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States.
authors.forename: Wayne
authors.initials: W
authors.lastname: Yu
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
authors.forename: Azza
authors.initials: A
authors.lastname: Maktabi
authors.affiliation: King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States.
authors.forename: Deepak P
authors.initials: DP
authors.lastname: Edward
authors.affiliation: Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States.
authors.forename: Charles G
authors.initials: CG
authors.lastname: Eberhart
mesh_terms: D051722:ADAM Proteins / Q000378:metabolism; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism; D002898:Chromosomes, Human, Pair 8; D055028:Comparative Genomic Hybridization / Q000379:methods; D003230:Conjunctival Neoplasms / Q000235:genetics* / Q000378:metabolism; D056915:DNA Copy Number Variations / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D005784:Gene Amplification; D005819:Genetic Markers / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; D005819:Genetic Markers; D051722:ADAM Proteins
keywords: NanoString assay; array CGH; conjunctiva squamous cell carcinoma (cSCC)