Next-generation sequencing of urine specimens: A novel platform for genomic analysis in patients with non-muscle-invasive urothelial carcinoma treated with bacille Calmette-Guérin.
BACKGROUND
Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment.


METHODS
Forty-one cytology slides from patients with HR NMIUC treated with intravesical BCG were selected for this study. Histological confirmation was available for all cases. The specimens were subjected to NGS analysis with a customized targeted exome capture assay composed of 341 genes.


RESULTS
In this cohort, genomic alterations were successfully identified in all cytology samples. Mutations were detected down to a 2% allele frequency and chromosomal rearrangements including copy number alterations and gene fusions were identified. The most frequently altered genes included telomerase reverse transcriptase (TERT), tumor protein 53 (TP53), Erb-B2 receptor tyrosine kinase 2 (ERBB2), and chromatin remodeling genes such as lysine demethylase 6A (KDM6A) and AT-rich interaction domain 1A (ARID1A). For patients with matched tumor tissue, cytology specimens revealed all mutations detected in tissue as well as additional mutations, and this suggested that urine might more effectively capture the full genetic heterogeneity of disease than an individual cystectomy. Alterations in multiple genes correlated with clinical and histopathological features, including responses to BCG treatment, flat architecture versus papillary architecture, and smoking history.


CONCLUSIONS
Urine specimens can replace tissue as a substrate for NGS analysis of HR NMIUC. Several genomic alterations identified in urine specimens might be associated with histological features and clinical characteristics. Cancer Cytopathol 2017;125:416-26. © 2017 American Cancer Society.
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
Sasinya N
SN
Scott
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.
Irina
I
Ostrovnaya
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
Caroline M
CM
Lin
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
Nancy
N
Bouvier
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
Bernard H
BH
Bochner
Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
Gopakumar
G
Iyer
Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
David
D
Solit
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.|Marie Josée and Henry R. Kravis Center for Molecular Oncology, New York, New York.
Michael F
MF
Berger
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
Oscar
http://orcid.org/0000-0003-2089-6118
O
Lin
D000276:Adjuvants, Immunologic / Q000627:therapeutic use; D000283:Administration, Intravesical; D000368:Aged; D000369:Aged, 80 and over; D001500:BCG Vaccine / Q000627:therapeutic use; D002295:Carcinoma, Transitional Cell / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology / Q000652:urine; D004268:DNA-Binding Proteins; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056466:Histone Demethylases / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009361:Neoplasm Invasiveness; D009367:Neoplasm Staging; D009687:Nuclear Proteins / Q000235:genetics; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D017422:Sequence Analysis, DNA; D019098:Telomerase / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D001749:Urinary Bladder Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology / Q000652:urine; D014556:Urine / Q000166:cytology*
D000276:Adjuvants, Immunologic; D001500:BCG Vaccine; D004268:DNA-Binding Proteins; D056466:Histone Demethylases; D009687:Nuclear Proteins; D018719:Erb-b2 Receptor Tyrosine Kinases; D019098:Telomerase; D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53; C112476:ARID1A protein, human; C495901:TP53 protein, human; C523998:KDM6A protein, human; C508053:ERBB2 protein, human; C509186:TERT protein, human
bacille Calmette-Guérin (BCG); bladder cancer; next-generation sequencing; urine cytology