Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer

Abstract

The genetic landscape of medullary thyroid cancer (MTC) is not yet fully understood, although some oncogenic mutations have been identified. To explore genetic profiles of MTCs, formalin-fixed, paraffin-embedded tumor tissues from MTC patients were assayed on the Ion AmpliSeq Cancer Panel v2. Eighty-four sporadic MTC samples and 36 paired normal thyroid tissues were successfully sequenced. We discovered 101 hotspot mutations in 18 genes in the 84 MTC tissue samples. The most common mutation was in the ret proto-oncogene, which occurred in 47 cases followed by mutations in genes encoding Harvey rat sarcoma viral oncogene homolog (N = 14), serine/threonine kinase 11 (N = 11), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (N = 6), mutL homolog 1 (N = 4), Kiesten rat sarcoma viral oncogene homolog (N = 3) and MET proto-oncogene (N = 3). We also evaluated anaplastic lymphoma kinase (ALK) rearrangement by immunohistochemistry and break-apart fluorescence in situ hybridization (FISH). Two of 98 screened cases were positive for ALK FISH. To identify the genomic breakpoint and 5’ fusion partner of ALK, customized targeted cancer panel sequencing was performed using DNA from tumor samples of the two patients. Glutamine:fructose-6-phosphate transaminase 1 (GFPT1)-ALK and echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusions were identified. Additional PCR analysis, followed by Sanger sequencing, confirmed the GFPT1-ALK fusion, indicating that the fusion is a result of intra-chromosomal translocation or deletion. Notably, a metastatic MTC case harboring the EML4-ALK fusion showed a dramatic response to an ALK inhibitor, crizotinib. In conclusion, we found several genetic mutations in MTC and are the first to identify ALK fusions in MTC. Our results suggest that the EML4-ALK fusion in MTC may be a potential driver mutation and a valid target of ALK inhibitors. Furthermore, the GFPT1-ALK fusion may be a potential candidate for molecular target therapy.

New drugs for medullary thyroid cancer: new promises?

“…So far, only a few non-RET molecular alterations have been detected in MTC, including primarily HRAS and KRAS mutations, as well as BRAF mutations (0-7%) (Moura et al 2015). In a recent study, also very few mutations in genes encoding KIT, MLH1, STK11, and MET were reported (Ji et al 2015). In addition, ALK rearrangements were found in 2 of 98 screened cases (Ji et al 2015).…”

“…In a recent study, also very few mutations in genes encoding KIT, MLH1, STK11, and MET were reported (Ji et al 2015). In addition, ALK rearrangements were found in 2 of 98 screened cases (Ji et al 2015). RAS mutations seem to be mutually exclusive with RET mutations and have been reported in different series to be present in approximately 0-81.3% of RET wild-type sporadic MTC (Moura et al 2015).…”

Treatment of advanced thyroid cancer with targeted therapies: ten years of experience

“…In addition, RAS and RET are mutually exclusive in MTC cases. A few anecdotal MTC cases harboring a RET or ALK rearrangement have been very recently described (Grubbs et al 2015, Ji et al 2015.…”

“…Despite the many genetic alterations that have been described for thyroid cancer and the most recent efforts to find other activated oncogenes, approximately 5-10% of PTCs, 50-60% of MTCs, and 10% of ATCs and PDTCs are still negative for all known genetic abnormalities (Soares et al 2011, Giordano et al 2014, Ji et al 2015.…”

Anaplastic large cell lymphoma: pathology, genetics, and clinical aspects

“…Although very rare, kinesin family member 5B (KIF5B), kinesin light chain 1 (KLC1), TFG, striatin (STRN), protein tyrosine phosphatase, non-receptor type 3 (PTPN3), Huntingtin interacting protein (HIP1), translocated promoter region protein (TPR), SEC31A, SQSTM1, DCTN1, and cysteine-rich transmembrane BMP regulator 1 (CRIM1) have also been reported to function as an ALK fusion partner in NSCLC. [100][101][102][103][104][105][106][107][108][109] After the discovery of EML4-ALK in NSCLC, ALK fusions were explored and identified in different epithelial tumors, including renal cancer, [110][111][112][113] 116 The frequencies of these fusions are 1-2% in thyroid cancer [120][121][122][123] and less than 1% in kidney and colon cancers. 112,118 Recent studies have revealed that approximately 10% of Spitz tumors harbor ALK fusions.…”