title: Enrichment strategies in glycomics-based lung cancer biomarker development.
abstract: OBJECTIVE
  There is a need to identify better glycan biomarkers for diagnosis, early detection, and treatment monitoring in lung cancer using biofluids such as blood. Biofluids are complex mixtures of proteins dominated by a few high abundance proteins that may not have specificity for lung cancer. Therefore, two methods for protein enrichment were evaluated; affinity capturing of IgG and enrichment of medium abundance proteins, thus allowing us to determine which method yields the best candidate glycan biomarkers for lung cancer.
  
  
  METHODS
  N-glycans isolated from plasma samples from 20 cases of lung adenocarcinoma and 20 matched controls were analyzed using nLC-PGC-chip-TOF-MS (where PGC is porous-graphitized carbon). N-glycan profiles were obtained for five different fractions: total plasma, isolated IgG, IgG-depleted plasma, and the bound and flow-through fractions of protein enrichment.
  
  
  RESULTS
  Four glycans differed significantly (false discovery rate, FDR < 0.05) between cases and controls in whole unfractionated plasma, while four other glycans differed significantly by cancer status in the IgG fraction. No significant glycan differences were observed in the other fractions.
  
  
  CONCLUSIONS
  These results confirm that the N-glycan profile in plasma of lung cancer patients is different from healthy controls and appears to be dominated by alterations in relatively abundant proteins.
authors: Department of Chemistry, University of California Davis, Davis, CA 95616, USA. lruhaak@ucdavis.edu
authors: L Renee
authors: LR
authors: Ruhaak
authors: Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA.
authors: Uyen Thao
authors: UT
authors: Nguyen
authors: Department of Chemistry, University of California Davis, Davis, CA, USA.|Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA.
authors: Carol
authors: C
authors: Stroble
authors: Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA.
authors: Sandra L
authors: SL
authors: Taylor
authors: Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, WA, USA.
authors: Ayumu
authors: A
authors: Taguchi
authors: Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, WA, USA.|Department of Clinical Cancer Prevention - Research, Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors: Samir M
authors: SM
authors: Hanash
authors: Department of Chemistry, University of California Davis, Davis, CA, USA.
authors: Carlito B
authors: CB
authors: Lebrilla
authors: Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA.
authors: Kyoungmi
authors: K
authors: Kim
authors: Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA.
authors: Suzanne
authors: S
authors: Miyamoto
mesh_terms: D000230:Adenocarcinoma / Q000378:metabolism*; D000077192:Adenocarcinoma of Lung; D014408:Biomarkers, Tumor / Q000378:metabolism*; D016022:Case-Control Studies; D005260:Female; D054794:Glycomics / Q000379:methods*; D006031:Glycosylation; D006801:Humans; D008175:Lung Neoplasms / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D010865:Pilot Projects; D011134:Polysaccharides / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D011134:Polysaccharides
keywords: Biomarker; Mass spectrometry; N-glycan; Nonsmall cell lung cancer; Protein enrichment
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