Matthew K Stein

JAK Pseudokinase Domain Variants Highlight nRTK VUSs Identified with Next-Generation Sequencing in Solid Tumor Patients

Non-receptor tyrosine kinase (nRTK) pathways are aberrantly activated in cancer, and mutations in nRTKs have potential therapeutic and prognostic importance. Consisting of 10 families, the 32 known human nRTKs each include a TKD made of N and C-terminal lobes necessary for catalytic activity, as well as varying regulatory regions including Src homology 2 (SH2) and 3 (SH3), and in the case of the Janus kinases a PSKD which is also bi-lobed [1]. Tumor profiling with NGS enables the entire coding sequence of numerous genes to be evaluated, thus facilitating the identification of novel nsSNPs in nRTKs. We reviewed advanced breast, colon and lung cancer patients treated at West Cancer Center (Memphis, Tennessee) from 2013 to 2015 who received tumor profiling including NGS with a 592 cancer-related gene panel from Caris Life Sciences (Phoenix, Arizona). Caris NGS searched 14 nRTKs: ABL1, ABL2, AKT1, AKT2, AKT3, BTK, JAK1, JAK2, JAK3, SRC, CDK4, CDK6, CDK12, PIK3CA. All mutations test-defined as either pathogenic (PATH) or nonsynonymous single nucleotide variants deemed variants of undetermined significance (VUS) were included. All variants had >99% detection confidence based upon allele frequency and amplicon coverage. In order to classify VUS, in silico analysis with PolyPhen-2 was utilized to predict pathogenicity [2]. Any VUS predicted-damaging with in silico analysis we denote VUSp. VUSs were then classified as occurring within or outside of the TKD; PSKD lesions were also detailed for JAK1–3. 346 patients (79 breast, 110 colon and 157 non-small cell lung cancer (NSCLC)) were identified. The cohort had a median age of 61 years (range 26–86). 58% were female; 62% were Caucasian and 35% African-American. 245 variants were found, with 200 VUS and 45 PATHs. PATHs were seen in 2 genes: PIK3CA (21 breast, 13 colon, 5 NSCLC) and AKT1 (6 breast). 168/346 (49%) patients had ≥1 nRTK lesion. 52/200 (26%) VUS were VUSp and spread amongst 48 patients (5 breast, 13 colon and 30 NSCLC). VUSp were found in 13/14 nRTKs (excluding AKT1) with median 3 (range 0– 10). The most numerous VUSp by gene were JAK3 (10), ABL1 (8), JAK2 (5), BTK (5) and CDK12 (5). By cancer type, the most-frequently mutated nRTKs were: SRC (2/2 VUS were VUSp) and ABL2 (1/5) in breast, ABL1 (5/10), JAK3 (3/27) and CDK12 (2/8) in colon, and JAK3 (6/20), BTK (5/ 8), ABL1 (3/12) and JAK2 (3/11) in NSCLC. Of 180 VUS with in silico results, 68% were outside of the TKD (29/122 VUSp), 23% TKD-restricted (13/42) and 9% in PSKD of JAK1–3 (11/16). Of note, 44 unique VUS were found in JAK1–3, with a total 18 VUSp (3 JAK1, 5 JAK2 and 10 JAK3). 12/18 JAK VUSp were NSCLC, including 9 PSKD, 2 FERM (4.1, Ezrin, Radixin,Moesin) and 1 TKD variants (Table 1). Comprised of 4 regions including N-terminal FERM and SH2 domains and C-terminal PSKD and TKD, the JAK family is known to harbor oncogenic mutations in myeloproliferative neoplasms (e.g. V617F in JAK2), other hematologic malignancies and several solid cancers [1].While described in all 4 domains, the majority of activating JAK mutations focus in the N-lobes of the PSKD and TKD, which normally form an autoinhibitory * Matthew K. Stein mkstein@westclinic.com

Correction to: Genomic landscape of small cell carcinoma of the breast contrasted to small cell carcinoma of the lung

In the original publication, the sixth author name was published incorrectly as Matthew Stein. The correct author name should read as Matthew K Stein.

Role Of Early Evaluation For Clonal Heterogeneity In Acute Myeloid Leukemia

A 67-year-old Caucasian male presented with a chief complaint of shortness of breath and fatigue. Initial laboratory evaluation revealed hyperleukocytosis with WBC count of 76,000/mcL and 83% blasts. He immediately received leukapheresis for respiratory symptoms. Bone marrow biopsy and peripheral blood flow cytometry confirmed a diagnosis of acute myeloid leukemia (AML) with normal cytogenetics. Fluorescence in-situ hybridization (FISH) study of the bone marrow was negative for t(8;21), t(15;17), inv(16) and abnormalities of Mixed Lineage Leukemia. Mutation analysis by PCR (Quest Diagnostics, AML Prognostic Panel) showed mutations in nucleophosmin (NPM1) gene and internal tandem duplication in the FMS-like Tyrosine Kinase 3 gene (FLT3-ITD) but wild-type for CCAAT/enhancer binding protein α gene (CEBPA). The patient received induction chemotherapy with cytarabine and idarubicin (7+3). Day-14bone marrow biopsy showed a hypocellular marrow with no morphologic evidence of residual AML. Cytogenetic analysis was unsuccessful due to lack of metaphases. Repeat mutational analysis was also completed on the day-14 bone marrow sample and was found to be positive for FLT3-ITD but negative for NPM1. The day-30 bone marrow biopsy showed evidence of residual AML with normal cytogenetics and 67% blasts. He subsequently underwent salvage chemotherapy with cladribine, cytarabine and filgrastrim (CLAG regimen). Despite salvage chemotherapy his follow-up 1Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 2Division of Hematology & Oncology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 3The West Cancer Center, Memphis, TN