| Literature DB >> 29600293 |
Cora Ballmann1, Anne Thiel1, Hannah E Korah1, Anna-Carinna Reis2, Wolfgang Saeger3, Stefanie Stepanow4, Karl Köhrer4, Guido Reifenberger5,6, Christiane B Knobbe-Thomsen5, Ulrich J Knappe7, Ute I Scholl1,8.
Abstract
Gain-of-function somatic mutations in the ubiquitin specific protease 8 (USP8) gene have recently been reported as a cause of pituitary adenomas in Cushing disease. Molecular diagnostic testing of tumor tissue may aid in the diagnosis of specimens obtained through therapeutic transsphenoidal surgery; however, for small tumors, availability of fresh tissue is limited, and contamination with normal tissue is frequent. We performed molecular testing of DNA isolated from single formalin-fixed and paraffin-embedded (FFPE) tissue sections of 42 pituitary adenomas from patients with Cushing disease (27 female patients and 15 male patients; mean age at surgery, 42.5 years; mean tumor size, 12.2 mm). By Sanger sequencing, we identified previously reported USP8 missense mutations in six tumors. Targeted next-generation sequencing (NGS) revealed known or previously undescribed missense mutations in three additional tumors (two with two different mutations each), with mutant allele frequencies as low as 3%. Of the nine tumors with USP8 mutations (mutation frequency, 21.4%), seven were from female patients (mutation frequency, 25.9%), and two were from male patients (mutation frequency, 13.3%). Mutant tumors were on average 11.4 mm in size, and patients with mutations were on average 43.9 years of age. The overall USP8 mutation frequency in our cohort was lower than in previously described cohorts, and we did not observe USP8 deletions that were frequent in other cohorts. We demonstrate that testing for USP8 variants can be performed from small amounts of FFPE tissue. NGS showed higher sensitivity for USP8 mutation detection than did Sanger sequencing. Assessment for USP8 mutations may complement histopathological diagnosis.Entities:
Keywords: FFPE; molecular diagnostic testing; ubiquitin specific protease
Year: 2018 PMID: 29600293 PMCID: PMC5838826 DOI: 10.1210/js.2017-00364
Source DB: PubMed Journal: J Endocr Soc ISSN: 2472-1972
Clinical Data and Experimental Results in the Investigated Corticotroph Adenoma Patient Cohort
| HYP No. | Sex | Age (y) | Size (mm) | Repli-G | Sanger Result | NGS Result | EGFR IHC |
|---|---|---|---|---|---|---|---|
| Cushing disease | |||||||
| 002 | F | 15 | 5 | Yes | WT | p.P720R | − |
| p.S716Y | |||||||
| 005 | F | 14 | 5 | Yes | WT | p.S716F | − |
| p.S718P | |||||||
| 006 | F | 36 | 13 | Yes | p.S718P | NA | − |
| 019 | M | 50 | 3 | Yes | WT | p.P720R | − |
| 024 | F | 51 | 13 | Yes | p.P720Q | NA | − |
| 026 | F | 46 | 6 | Yes | p.P720R | NA | − |
| 029 | F | 36 | 11 | Yes | p.P720R | p.P720R | − |
| 039 | F | 66 | 18 | Yes | p.P720Q | NA | − |
| 051 | M | 81 | 29 | No | p.P720R | NA | − |
| 001 | M | 34 | 8 | Yes | WT | WT | − |
| 003 | M | 21 | 50 | Yes | WT | WT | (+) |
| 004 | F | 48 | Below detection | Yes | WT | WT | − |
| 007 | F | 25 | 4 | Yes | WT | WT | − |
| 009 | F | 61 | 20 | Yes | WT | WT | − |
| 011 | F | 42 | 6 | Yes | WT | WT | − |
| 013 | F | 45 | Below detection | Yes | WT | WT | − |
| 015 | F | 56 | 3 (ultrasonography) | Yes | WT | WT | − |
| 016 | F | 30 | 14 | Yes | WT | WT | (+) |
| 017 | F | 43 | NA | Yes | WT | WT | − |
| 018 | F | 65 | 3 | Yes | WT | WT | − |
| 020 | F | 52 | 8 | Yes | WT | WT | − |
| 021 | F | 24 | 6 | Yes | WT | WT | − |
| 022 | F | 52 | 3 (surgery) | Yes | WT | WT | − |
| 023 | M | 57 | 28 | Yes | WT | WT | − |
| 025 | F | 42 | 26 | Yes | WT | WT | − |
| 027 | M | 52 | 30 | Yes | WT | WT | − |
| 028 | F | 36 | 9 | Yes | WT | WT | − |
| 030 | M | 36 | NA | Yes | WT | WT | − |
| 032 | F | 54 | 8 | Yes | WT | WT | − |
| 033 | M | 49 | 3 | Yes | WT | WT | − |
| 036 | F | 35 | 5 | Yes | WT | WT | − |
| 037 | M | 20 | 3 | Yes | WT | WT | − |
| 038 | M | 35 | 4 | Yes | WT | WT | − |
| 041 | M | 40 | 4 | Yes | WT | WT | − |
| 043 | F | 29 | 3 | Yes | WT | WT | − |
| 044 | M | 38 | 9 (ultrasonography) | Yes | WT | WT | − |
| 045 | F | 47 | Below detection | Yes | WT | WT | − |
| 046 | F | 47 | 7 | Yes | WT | WT | − |
| 047 | M | 44 | 24 | Yes | WT | WT | − |
| 050 | F | 35 | 16 | No | WT | WT | − |
| 053 | M | 32 | 8 | No | WT | WT | − |
| 055 | M | 64 | 36 | No | WT | WT | − |
| Silent corticotroph adenomas | No | ||||||
| 056 | M | 59 | 13 | No | WT | WT | − |
| 063 | M | 57 | 15 | No | WT | WT | − |
Abbreviations: F, female; IHC, immunohistochemistry; M, male; Repli-G, whole-genome amplification of DNA; NA, not available; −, no positivity by immunohistochemistry; (+), possible very weak positivity by immunohistochemistry.
Atypical adenoma.
Studied tissue from recurrence, age and tumor size at first surgery are given.
Crooke cell adenoma.
Ectopic, sinus cavernosus (patient 2 in Knappe et al. [25]).
Primer Sequences
| Primer | Sequence 5′ > 3′ | Product Size (bp) |
|---|---|---|
| USP8_F | AGCCACAGATTCCTGCTGAG | 124 |
| USP8_R | ACTGTTGGAGTTACTGTTGGCT | |
| USP8big_F | AAAGCCAAGCCACAGATTCC | 234 |
| USP8big_R | TCCCTGACACTAACATACTGACA | |
| USP8bigadap_F | TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAAGCCAAGCCACAGATTCC | 301 |
| USP8bigadap_R | GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCCCTGACACTAACATACTGACA |
Used for NGS.
Figure 1.USP8 variants in corticotroph adenomas identified by Sanger sequencing. Sanger sequences of pituitary adenomas demonstrate USP8 variants in six tumors. Encoded protein sequences are shown in one-letter code, with mutant amino acids in red. The variant in HYP29 appears to be homozygous or hemizygous. Reverse sequence is shown as reverse complement. Fwd, forward; rev, reverse.
Identified USP8 Variants
| rs No. or COSMIC No. | Chromosomal Position | Nucleotide Change | Amino Acid Change |
|---|---|---|---|
| rs672601311 | 15:50490450 | C>G | P720R |
| rs672601307 | 15:50490443 | C>T | S718P |
| Identified in this study | 15:50490438 | C>A | S716Y |
| COSM416905 | 15:50490450 | C>A | P720Q |
| rs753615462 | 15:50490438 | C>T | S716F |
Chromosomal position refers to GRCh38.p7. Amino acid change refers to NP_005145.3.
Abbreviations: COSMIC number, catalog of somatic mutations in cancer database identifier, provided for variants without unique Single Nucleotide Polymorphism database identifier; Rs number, reference single-nucleotide polymorphism in Single Nucleotide Polymorphism database build 150.
Figure 2.USP8 variants in corticotroph adenomas identified by NGS. Shown are variant allele frequencies of four tumors with USP8 variants detected by NGS. Frequencies were determined in the CLC Workbench program. A 98.5% mutant allele frequency in HYP029 confirms homozygosity or hemizygosity of the variant. HYP002 and HYP005 show two USP8 variants each.
Figure 3.NGS reads in tumors with two concurrent USP8 variants. Analysis of mutant reads using Integrative Genomics Viewer demonstrates two variants on independent alleles or independent tumor subpopulations for HYP002 and two variants on the same allele for HYP005.
Figure 4.Clinical characteristics of individuals with USP8-mutant or WT tumors. Upper panels show sex distribution among mutant and WT tumors. Lower panel shows size and age in mutant and WT tumors (line, median; box, interquartile range; whiskers, 1.5x interquartile range). No significant differences were observed for either characteristic shown (see text for statistical analysis).
Figure 5.EGFR immunohistochemistry. HYP050 is shown as a representative EGFR-negative WT tumor. The positive control represents a glioblastoma. All mutant tumors stained negative for EGFR; representative pictures are shown. Some tumors showed very weak EGFR positivity of connective tissue, as demonstrated for HYP051. Scale bars, 100 µm.