Patient cohorts
Detailed pathology reports were collected of all NMTC patients diagnosed in Nijmegen and surrounding hospitals between 2000 and 2016 (1544 patients). We selected 35 RAI-sensitive NMTC patients and 28 RAI-refractory NMTC patients that underwent total or near-total thyroidectomy and showed residual disease after primary surgery. Patients with confirmed nodal metastases prior to primary surgery also underwent a modified radical lymph node dissection. RAI ablation of residual thyroid tissue was performed 4–6 weeks after surgery. All patients included in this study had residual disease after primary surgery as demonstrated by diagnostic RAI scintigraphy. If indicated, patients were repeatedly treated with RAI to reach remission. RAI sensitivity was defined as a complete response to RAI therapy of histologically differentiated tumor lesions resulting in remission after the primary treatment by surgery and RAI ablation or (if indicated) after subsequent treatments with RAI for metastases with documented 131I uptake. Remission was defined as undetectable TSH stimulated Tg in the absence of anti-Tg antibodies and no evidence of loco-regional disease or distant metastasis on the whole-body iodide scans (WBS) and/or neck ultrasonographic examinations at 6–9 months after the last RAI treatment. The remission status was confirmed at the last follow-up visit. According to the RECIST criteria, RAI refractoriness was defined as either new evidence of recurrent loco-regional disease or distant metastasis after successful primary therapy or progressive disease at least 6 months after primary treatment by surgery and RAI treatment preferably supported by presence of metastases that do not accumulate 131I on the last post-therapy scan. Persistent disease was defined as detectable Tg and/or evidence of loco-regional disease or distant metastases. Of all selected NMTC patients, archived FFPE tissue specimens were collected for genetic, transcriptomic and protein analyses. Collection, storage and use of archival tissue and patient data were in compliance with the “Code of Proper Secondary Use of Human Tissue in the Netherlands” (http://www.fmwv.nl and www.federa.org). This study was approved by the Research Ethics Committee (CMO) under application 2015 − 1762 and followed the ethical guidelines of the CMO.
An independent cohort including eight consecutive newly diagnosed patients with NMTC (with and without metastases) that were therapy naïve and were planned to receive conventional primary treatment by surgery followed by RAI were included in which plasma insulin growth factor 2 (IGF2) concentrations were measured before surgery and 30 days after 131I radioactive iodide therapy. CMO application: 2017–3628; NL62671.091.17; ClinicalTrials.gov Identifier: NCT03397238. Their results were compared to those of six gender and aged matched healthy volunteers.
DNA and RNA isolation from FFPE tissues
For DNA isolation, 60 µm FFPE tissue slices were digested overnight at 56 °C in the presence of TET-lysis buffer (10 mM Tris/HCl pH 8.5, 1 mM EDTA pH 8.0, 0.01% Tween-20), 5% Chelex-100 (Bio-Rad, Hercules, CA, USA), 15 µg/mL GlycoBlue (Life Technologies, Carlsbad, CA, USA) and 400 µg proteinase K (Qiagen, Valencia, CA, USA), followed by inactivation at 95 °C for 10 minutes. For DNA isolation, the supernatant was transferred after centrifugation (20817 rcf), cooled on ice and precipitated in the presence of 100% EtOH and 1/33 volume 3M NaAc (pH 5.2). Pellets were washed with cold 70% EtOH, dissolved in 80 µL Tris-EDTA and DNA concentrations were determined using the Qubit Broad Range Kit (Thermo Fisher, Waltham, MA, USA). For RNA isolation, 60 µm FFPE tissue slices were digested overnight at 56 °C in the presence of 240 µl lysis buffer (Qiagen, Valencia, CA, USA) and 400 µg proteinase K. Next, supernatants were transferred after centrifugation (16,000 rpm) and mixed with RNA-Bee. Subsequently, RNA was isolated by phase separation with chloroform and precipitated by isopropanol, according to the manufacturer’s instructions (Thermo Fisher, Waltham, MA, USA).
Intratumoral mutation profiling
Somatic mutations in human NMTC tumor tissue were detected by our in-house Cancer Hotspot Panel based on single-molecule molecular inversion probes (smMIPs), as described previously (15). Isolated DNA from FFPE tissues with a tumor cell percentage of > 60% was subjected to library preparation and clinically relevant regions were sequenced of the following genes: AKT1, BIRC3, BRAF, CHEK2,CTNNB1, CXCR4, EGFR, ERBB2, EZH2, GNA11, GNAQ, GNAS, H3F3A, H3F3B, HRAS, IDH1, IDH2, JAK2, KIT, KRAS, MPL, MSH2, MYD88, NRAS, PDGFRA, PIK3CA, SF3B1, SLC7A8 and ZNF2.
Gene fusion analysis
DNA/RNA was isolated from punched tumor tissue with a tumor cell percentage of > 50%. Gene fusion analysis was performed by Next Generation Sequencing (Archer FusionPlex CTL Panel) and data were analyzed by Archer Analysis software (version 5). Relevant fusions of the following target genes were sequenced: ALK (5'; exons 2, 4, 6, 10, 16–23, intron 19), AXL (3'; exons 18–20), BRAF ( 5'; exons 7–11, 3'; exons 7, 8, 10), CCND1 (5'; exons 1–4, 3'; exons 1, 2, 4), FGFR1 (5'; exons 2, 8–10, 17, 3'; exon 17), FGFR2 (5'; exons 2, 5, 7–10, 3'; exon 17), FGFR3 (5'; exons 3, 5, 8–10, 3'; exon 17, intron 17), MET (5'; exons 2, 4–6, 13, 14, 16, 17, 21, 3'; exon 2), NRG1 (5'; exons 1, 2, 3, 6), NTRK1 (5'; exons 2, 4, 6, 8, 10–13), NTRK2 (5'; exons 5, 7, 9, 11–17), NTRK3 (5'; exons 4, 7, 10, 13–16), PPARG (5'; exons 1, 2, 3, 5), RAF1 (5'; exons 4–7, 9–12), RET (5'; exons 2, 4, 6, 8, 9–14), ROS1 (5'; exons 2, 4, 7, 31–37), THADA (3'; exons 24–30, 36, 37). In addition, the FusionPlex-CTL hotspot panel also detects mutations in BRAF (exon 11, 15), HRAS, NRAS (exon 2 and 3, codon 12, 13, 61), KRAS (exon 2, 3 and 4, codon 12, 13, 61 and 146) and the EGFRvIII variant.
TERT promoter mutation analysis
TERT promoter mutations C228A, C228T (at position − 124 from translation start site) and C250T (-146 from translation start site) were detected by conventional PCR followed by Sanger sequencing. The TERT promoter region was amplified by the following M13-sequence extended primers: forward 5’- TGT-AAA-ACG-ACG-GCC-AGT-CCC-TTC-ACC-TTC-CAG-CTC-3’ and reverse 5’-CAG-GAA-ACA-GCT-ATG-ACC-AGC-GCT-GCC-TGA-AAC-TCG − 3’. DNA was amplified by AmpliTaq PCR 360 Gold Master Mix (Thermo Fisher, Waltham, MA, USA) and the following PCR program: 95 °C for 10 minutes followed by 95 °C for 30 seconds, 58 °C for 30 seconds and 72 °C for 1 minute (38 cycles) and a final step of 72 °C for 7 minutes. Subsequently, Sanger sequencing was performed with M13 primers and TERT promoter mutations were called by Sanger chromatogram software (Sequencher 4.8, Gene Codes Corp., Ann Arbor, MI, USA).
FFPE compatible RNA sequencing
Isolated RNA obtained from FFPE tissues with a tumor cell percentage of > 80% was processed for RNA sequencing by DNAse treatment, RNA demodification, RNA fragmentation (if necessary), first and second-strand cDNA synthesis and library preparation according to the Ovation SoLo RNA-Seq System (NuGEN, San Carlos, CA, USA). Subsequently, RNA sequencing was performed by Illumina NextSeq500 and analysis of the data was performed by the Centre for Molecular and Biomolecular Informatics (CMBI). STAR, a standard aligner that makes use of a reference genome (GRCh38), was selected for the alignment of the sequences. To quantify the alignments made in STAR the tool HTSeq was utilized. This produced “counts.txt” files that are easy to import into DESeq2, a package to carry out differential gene expression analysis. Raw RNA sequencing data are deposited in the GEO database under accession number GSE112202.
Plasma measurements
Plasma IGF2 and IGFBP2 concentrations were measured by ELISA according to manufacturer’s instructions (R&D Systems, Inc. Minneapolis, USA).
Statistical methods
Statistical significance was tested with Student’s T test, Mann Whitney U test, Wilcoxon matched-pairs signed rank test, when appropriate. P-values below 0.05 were considered statistically significant. For RNA sequencing data a false discovery rate of 0.05 was incorporated. All statistical tests were performed using GraphPad Prism 5.0.