PMID- 27997540 OWN - NLM STAT- MEDLINE DCOM- 20170523 LR - 20181113 IS - 1549-1676 (Electronic) IS - 1549-1277 (Print) IS - 1549-1277 (Linking) VI - 13 IP - 12 DP - 2016 Dec TI - IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study. PG - e1002200 LID - 10.1371/journal.pmed.1002200 [doi] LID - e1002200 AB - BACKGROUND: Pediatric acute lymphoblastic leukemia (ALL) is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL) represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment. METHODS AND FINDINGS: We performed whole genome sequencing on paired pre-treatment (diagnostic) and post-treatment (remission) samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R) signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146) of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX). Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome. To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we expressed wild-type and mutant IL7R signaling molecules in two steroid-sensitive T-ALL cell lines (SUPT1 and P12 Ichikawa cells) using inducible lentiviral expression constructs. We found that expressing mutant IL7R, JAK1, or NRAS, or wild-type NRAS or AKT, specifically induced steroid resistance without affecting sensitivity to vincristine or L-asparaginase. In contrast, wild-type IL7R, JAK1, and JAK3, as well as mutant JAK3 and mutant AKT, had no effect. We then performed a functional study to examine the mechanisms underlying steroid resistance and found that, rather than changing the steroid receptor's ability to activate downstream targets, steroid resistance was associated with strong activation of MEK-ERK and AKT, downstream components of the IL7R signaling pathway, thereby inducing a robust antiapoptotic response by upregulating MCL1 and BCLXL expression. Both the MEK-ERK and AKT pathways also inactivate BIM, an essential molecule for steroid-induced cell death, and inhibit GSK3B, an important regulator of proapoptotic BIM. Importantly, treating our cell lines with IL7R signaling inhibitors restored steroid sensitivity. To address clinical relevance, we treated primary T-ALL cells obtained from 11 patients with steroids either alone or in combination with IL7R signaling inhibitors; we found that including a MEK, AKT, mTOR, or dual PI3K/mTOR inhibitor strongly increased steroid-induced cell death. Therefore, combining these inhibitors with steroid treatment may enhance steroid sensitivity in patients with ALL. The main limitation of our study was the modest cohort size, owing to the very low incidence of T-ALL. CONCLUSIONS: Using an unbiased sequencing approach, we found that specific mutations in IL7R signaling molecules underlie steroid resistance in T-ALL. Future prospective clinical studies should test the ability of inhibitors of MEK, AKT, mTOR, or PI3K/mTOR to restore or enhance steroid sensitivity and improve clinical outcome. FAU - Li, Yunlei AU - Li Y AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. FAU - Buijs-Gladdines, Jessica G C A M AU - Buijs-Gladdines JG AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. FAU - Cante-Barrett, Kirsten AU - Cante-Barrett K AUID- ORCID: 0000-0003-0418-8445 AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. FAU - Stubbs, Andrew P AU - Stubbs AP AD - Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. FAU - Vroegindeweij, Eric M AU - Vroegindeweij EM AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. FAU - Smits, Willem K AU - Smits WK AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. FAU - van Marion, Ronald AU - van Marion R AD - Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands. FAU - Dinjens, Winand N M AU - Dinjens WN AD - Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands. FAU - Horstmann, Martin AU - Horstmann M AD - Research Institute Children's Cancer Center Hamburg, Hamburg, Germany. AD - Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. AD - Co-operative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany. FAU - Kuiper, Roland P AU - Kuiper RP AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. AD - Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. FAU - Buijsman, Rogier C AU - Buijsman RC AUID- ORCID: 0000-0002-2757-2899 AD - Netherlands Translational Research Center, Oss, The Netherlands. FAU - Zaman, Guido J R AU - Zaman GJ AD - Netherlands Translational Research Center, Oss, The Netherlands. FAU - van der Spek, Peter J AU - van der Spek PJ AD - Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. FAU - Pieters, Rob AU - Pieters R AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. FAU - Meijerink, Jules P P AU - Meijerink JP AD - Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands. AD - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. LA - eng PT - Journal Article DEP - 20161220 PL - United States TA - PLoS Med JT - PLoS medicine JID - 101231360 RN - 0 (Antineoplastic Agents) RN - 0 (IL7 protein, human) RN - 0 (Interleukin-7) RN - 0 (Steroids) SB - IM CIN - Overcoming Steroid Resistance in T Cell Acute Lymphoblastic Leukemia. MH - Adolescent MH - Antineoplastic Agents/*pharmacology MH - Child MH - Child, Preschool MH - *Drug Resistance, Neoplasm MH - Exome MH - Gene Expression Regulation, Neoplastic/*drug effects MH - *Genome MH - Humans MH - Interleukin-7/*genetics/metabolism MH - Mutation MH - Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy/etiology/*genetics MH - Sequence Analysis, DNA MH - Steroids/*pharmacology PMC - PMC5172551 COIS- RCB and GJRZ are founders and shareholders of Netherlands Translational Research Center B.V. The other authors have declared that no competing interests exist. EDAT- 2016/12/21 06:00 MHDA- 2017/05/24 06:00 PMCR- 2016/12/20 CRDT- 2016/12/21 06:00 PHST- 2016/08/03 00:00 [received] PHST- 2016/11/11 00:00 [accepted] PHST- 2016/12/21 06:00 [entrez] PHST- 2016/12/21 06:00 [pubmed] PHST- 2017/05/24 06:00 [medline] PHST- 2016/12/20 00:00 [pmc-release] AID - PMEDICINE-D-16-02492 [pii] AID - 10.1371/journal.pmed.1002200 [doi] PST - epublish SO - PLoS Med. 2016 Dec 20;13(12):e1002200. doi: 10.1371/journal.pmed.1002200. eCollection 2016 Dec.