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NTRK Gene Amplification in Patients with Metastatic Cancer

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NTRK Gene Amplification in Patients with Metastatic Cancer Precision and Future Medicine 2017;1(3):129-137 ORIGINAL https://doi.org/10.23838/pfm.2017.00142 ARTICLE pISSN: 2508-7940 · eISSN: 2508-7959 NTRK gene amplification in patients with metastatic cancer 1 2 1 1 1 Su Jin Lee *, Nayoung1 K. D. Kim1 *, Se-Hoon Lee1 *, Seung Tae Kim1 , Se Hoon Park2, Joon Oh Park3 , Young Suk Park ,3 Ho Yeong Lim , 1Won Ki Kang1, Woong Yang Park , Hee Jin Bang , Kyoung-Mee Kim , Keunchil Park , Jeeyun Lee 1 Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Korea 2 Samsung Genome Institute, Samsung Medical Center, Seoul, Korea 3 Department of Pathology, Sungkyunkwan University School of Medicine, Seoul, Korea Received: July 3, 2017 Revised: August 2, 2017 Accepted: August 3, 2017 ABSTRACT Purpose: Neurotropic tropomyosin receptor kinase (NTRK) fusions have been identi- Corresponding author: Jeeyun Lee fied in a variety of cancers, and tyrosine kinase inhibitors targeting the tropomyosin re- Division of Hematology- ceptor kinase (TRK) receptor are currently in clinical trials. However, no reports are Oncology, Department of available on the effects ofNTRK gene amplification. Medicine, Samsung Medical Methods: Samples from patients enrolled in the sequencing program were analyzed Center, Sungkyunkwan using a next-generation sequencing (NGS) cancer panel. For cases in which NTRK am- University School of Medicine, plification (defined as ≥4.0 copies) was identified, panTRK immunohistochemical 81 Irwon-ro, Gangnam-gu, (IHC) staining of tissue microarrays was performed. Seoul 06351, Korea Results: A total of 1,250 tumor specimens collected between February 2014 and Janu- Tel: +82-2-3410-1779 ary 2016 were analyzed using the NGS cancer panel. NTRK amplification was detected E-mail: [email protected] in 28 cases of various types of cancer. Among 27 cases, only four were positive for pan- TRK IHC. These four cases were melanoma, sarcoma, lung cancer, and gastric cancer. We found that 2.2% of cancer patients showed NTRK amplification using NGS cancer panel and NTRK amplification resulted in protein overexpression in 14.8% of these pa- tients. Conclusion: Patients with NTRK amplification and increased TRK protein expression may be considered for inclusion in clinical trials for NTRK inhibitors. Keywords: NGS cancer panel; NTRK gene amplification; TRK immunohistochemistry INTRODUCTION This is an Open Access article Tropomyosin receptor kinase (TRK) is a receptor in the tyrosine kinase family that is activated by distributed under the terms of the neurotrophins, a family of nerve growth factors [1-4]. Three members of the TRK family have Creative Commons Attribution been described: TRKA, TRKB, and TRKC, encoded by neurotropic tropomyosin receptor kinase 1 Non-Commercial License (http:// creativecommons.org/licenses/ (NTRK1), NTRK2, and NTRK3, respectively. Trk family members play important roles in nervous by-nc/4.0/). system development through regulation of cell proliferation, differentiation, apoptosis, and sur- Copyright © 2017 Sungkyunkwan University School of Medicine 129 NTRK amplification in cancer vival of neurons in both the central and peripheral nervous clinicopathologic characteristics. system. Trk receptors are expressed not only in the nervous system, but also in many other non-neuronal cell types and Targeted exome sequencing tissues, including monocytes, lung, bone, and pancreatic β Genomic DNA was extracted, and a SureSelect customized -cells [5,6]. kit (Agilent Technologies, Santa Clara, CA, USA) was used to In 1982, the first NTRK1 gene fusion was identified in a co- capture 83 or 379 cancer-related genes, depending on the lon cancer specimen; it contained sequence from tropomyo- sequencing panel version. An Illumina HiSeq 2500 (Illumina, sin 3 (TPM3; non-muscle tropomyosin) [7,8]. Subsequently, San Diego, CA, USA) was used for sequencing, and 100-bp NTRK1 fusions have been detected at a frequency of 12% in paired-end reads were obtained. The sequencing reads were papillary thyroid cancers, with TPM3-NTRK1 being the most aligned to the human genome reference sequence (hg19) us- common gene rearrangement [9-11]. In addition, TRKC and ing BWA-mem (v0.7.5), SAMTOOLS (v0.1.18), Picard (v1.93), very recently TRKB have also been shown to form oncogenic and GATK (v3.1.1) for sorting SAM/BAM files, duplicate mark- chimeras in multiple tumor types [12,13]. Aside from gene ing, and local realignment, respectively. Local realignment fusions, only an in-frame deletion of NTRK1 in acute myeloid and base recalibration were carried out using dbSNP137, leukemia and a splice variant of NTRK1 in neuroblastoma Mills indels, HapMap, and Omni. Single nucleotide variants have been functionally characterized as oncogenic to date and indels were identified using Mutect (v1.1.4) and Pindel [14-18]. However, no reports are available on the effects of (v0.2.4), respectively. ANNOVAR was used to annotate the de- NTRK gene amplification (defined as ≥ 4.0 copies). tected variants. Only variants with an allele frequency > 1% In the past several years, DNA sequencing technology has were included in the results. Copy number variation was cal- evolved dramatically. Next-generation DNA sequencing culated for the targeted sequencing regions by dividing read (NGS) has brought genome sequencing to clinical laborato- depth per exon by the normal reads per exon using an in- ries. The huge reduction in sequencing cost and the increase house reference. Translocations in the target region were in sequencing efficiency, and the incomparable sequencing identified using an in-house algorithm (in preparation). throughput, sensitivity, and accuracy all make NGS the most promising technology for cancer genomics and personalized PanTRK immunohistochemistry cancer therapy. In this study, we investigated the prevalence For tissue microarray construction, all H&E stained slides of NTRK gene amplification using targeted sequencing and were reviewed and the representative area was carefully se- analyzed the association between gene amplification and lected and marked on all paraffin blocks. A 3-mm tissue core TRK protein expression. was taken from the representative region of each tumor specimen using Accumax (ISU Abxis, Seoul, Korea). Immuno- METHODS histochemistry (IHC) was performed under various condi- tions using five primary antibodies; panTRK (C17F1) from Patients Cell Signaling (Danvers, MA, USA) was identified as a highly This investigation was conducted in accordance with the ethi- sensitive and specific primary antibody and was adopted for cal standards of the Declaration of Helsinki as well as national screening [19]. Mild cytoplasmic or membranous staining and international guidelines, and was approved by the Insti- was considered to indicate a weakly positive result, and tutional Review Board at Samsung Medical Center, Seoul, Ko- moderate to strong cytoplasmic staining was considered to rea. Between October 2013 and January 2016, 1,250 patients indicate a positive result. with gastrointestinal cancer, lung cancer, and rare forms of cancer were prospectively enrolled in the NEXT-1, VIKTORY Statistical analysis (NCT#02299648), or LUNG PERSEQ (NCT#02299622) trials at Student t-test was used to compare the means of continuous Samsung Medical Center that employed targeted sequenc- variables between the TRK-IHC-positive and -negative groups. ing (other cancer panels, such as Ion Torrent [Thermo Fisher, P values < 0.05 were considered statistically significant. All Waltham, MA, USA], were excluded from this analysis). Pa- statistical analyses were performed using SPSS software ver- tient inclusion criteria were as follows: age ≥18 years, sion 18.0 (SPSS Inc., Chicago, IL, USA). pathologically confirmed cancer, and availability of resec- tion/biopsies of the primary or metastatic site and data on 130 http://pfmjournal.org Su Jin Lee, et al. RESULTS common site of metastases was a non-regional/distant lymph node (LN; n= 14) followed by lung, liver, peritoneal seeding, Patients’ characteristics bone, pleura, pancreas, and brain. Baseline characteristics Between October 2013 and January 2016, 1,250 patients with are listed in Table 1 and individual patients’ information, with gastrointestinal cancer, lung cancer, or rare cancers were pro- concomitant genetic aberrations, are also shown in Table 2. spectively enrolled in the NEXT-1, VIKTORY (NCT#02299648), The median NTRK copy number of all patients was 4.95 or LUNG PERSEQ (NCT#02299622) trials using targeted se- (range, 4.2 to 7.8). quencing at Samsung Medical Center, Seoul, Korea. Among these 1,250 samples, we identified 28 cases with NTRK am- Identification of panTRK IHC-positive cases plification (2.2%), defined as ≥ 4.0 copies (Fig. 1). Of 28 cas- Tissue staining with TRK IHC was performed for 27 of the 28 es, almost all cases were NTRK1-amplified except for two cases (tissue was not available for the remaining case). Four cases of NTRK3 amplification and one case ofNTRK2 ampli- of the 27 cases (14.8%) were positive for TRK IHC (Fig. 2), and fication. The median age was 59 years (range, 23 to 74 years), these four cases were all NTRK1-amplified. The first was a and 60% of patients were male. These cases included lung patient with acral melanoma, with an NTRK copy number of cancer (n= 6), gastric cancer (n= 5), biliary tract cancer (n= 3), 6 and moderate to strong cytoplasmic TRK IHC staining. The melanoma (n= 3), sarcoma (n= 3), pancreatic cancer (n= 2), second was a patient with sarcoma, with an NTRK copy num- hepatocellular
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