Published OnlineFirst September 28, 2018; DOI: 10.1158/2159-8290.CD-17-0831 RESEARCH ARTICLE Deletion 6q Drives T-cell Leukemia Progression by Ribosome Modulation Stéphanie Gachet 1 , 2 , Tiama El-Chaar 1 , 2 , David Avran 1 , 2 , 3 , Eulalia Genesca 1 , 2 , Frédéric Catez 4 , Samuel Quentin1 , 2 , 3 , Marc Delord 2 , Gabriel Thérizols 4 , Delphine Briot 1 , 2 , 3 , Godelieve Meunier 1 , 2 , Lucie Hernandez1 , 2 , Marika Pla 2 , 5 , Willem K. Smits 6 , Jessica G. Buijs-Gladdines 6 , Wouter Van Loocke 7 , Gerben Menschaert7 , Isabelle André-Schmutz 8 , Tom Taghon 7 , Pieter Van Vlierberghe 7 , Jules P. Meijerink 6 , André Baruchel2 , 9 , Hervé Dombret 2 , 10 , Emmanuelle Clappier 1 , 2 , 3 , Jean-Jacques Diaz 4 , Claude Gazin 11 , Hugues de Thé1 , 2 , François Sigaux 1 , 2 , 3 , and Jean Soulier 1 , 2 , 3 Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst September 28, 2018; DOI: 10.1158/2159-8290.CD-17-0831 ABSTRACT Deletion of chromosome 6q is a well-recognized abnormality found in poor- prognosis T-cell acute lymphoblastic leukemia (T-ALL). Using integrated genomic approaches, we identifi ed two candidate haploinsuffi cient genes contiguous at 6q14,SYNCRIP (encod- ing hnRNP-Q) and SNHG5 (that hosts snoRNAs), both involved in regulating RNA maturation and trans- lation. Combined silencing of both genes, but not of either gene alone, accelerated leukemogeneis in a Tal1/Lmo1/Notch1 -driven mouse model, demonstrating the tumor-suppressive nature of the two-gene region. Proteomic and translational profi ling of cells in which we engineered a short 6q deletion by CRISPR/Cas9 genome editing indicated decreased ribosome and mitochondrial activities, suggesting that the resulting metabolic changes may regulate tumor progression. Indeed, xenograft experiments showed an increased leukemia-initiating cell activity of primary human leukemic cells upon coextinction of SYNCRIP and SNHG5. Our fi ndings not only elucidate the nature of 6q deletion but also highlight the role of ribosomes and mitochondria in T-ALL tumor progression. SIGNIFICANCE: The oncogenic role of 6q deletion in T-ALL has remained elusive since this chromo- somal abnormality was fi rst identifi ed more than 40 years ago. We combined genomic analysis and functional models to show that the codeletion of two contiguous genes at 6q14 enhances malignancy through deregulation of a ribosome–mitochondria axis, suggesting the potential for therapeutic inter- vention. Cancer Discov; 8(12); 1614–31. ©2018 AACR. INTRODUCTION often associated with a worse prognosis. This is exemplifi ed by the considerable efforts that were developed over several The identifi cation of somatic genome aberrations in can- decades to understand and model oncogenesis for abnormali- cer cells has been a highly fruitful strategy to identify cancer ties such as monosomy 7 in myeloid malignancies or deletion genes, especially in hematopoietic malignancies. With the 6q in T-cell acute lymphoblastic leukemia (T-ALL). T-ALL is availability of massive sequencing tools, it is now relatively related to leukemic transformation of T-cell progenitors ( 2, easy to identify cancer genes from translocations, point muta- 3 ). In addition to a founding rearrangement that deregulates tions, or short insertion/deletions ( 1 ). However, the molecu- transcription factor genes and determines the oncogenic lar targets of large chromosomal losses or gains can remain subtype, such as TAL1/2, LMO1/2, TLX1/3 , and HOXA , the diffi cult to elucidate, and these types of abnormalities are T-ALL genome harbors a myriad of additional mutations, deletions, and duplications that collectively lead to overt leu- kemia ( 3–10 ). These have a particular impact on the cell cycle (CDKN2A/p16/ARF deletion), the Notch pathway (NOTCH1 1 INSERM UMR944 and CNRS UMR7212, Hôpital Saint-Louis, Paris, and FBXW7 mutations), and the JAK/STAT and PI3K/AKT France. 2 Institute of Hematology (IUH), Université Paris Diderot, pathways (IL7R and PTEN mutations). Deletion of the 3 Sorbonne Paris Cité, Paris, France. Hematology Laboratory APHP, Hôpital long arm of chromosome 6 (del6q) is a frequent karyotypic Saint-Louis, Paris, France. 4 Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard; Université abnormality in T-cell ALL and lymphoblastic lymphoma, Lyon 1, Lyon, France. 5 INSERM UMRS 940, Hôpital Saint-Louis, Paris, where it has been associated with an unfavorable prognosis France. 6 Department of Pediatric Oncology/Hematology, Princess ( 11–13 ). Although fi rst reported as a recurrent structural 7 Maxima Center for Pediatric Oncology, Utrecht, the Netherlands. Cancer abnormality in lymphoblastic leukemia in 1976, the under- Research Institute, Ghent University, Ghent, Belgium. 8 U1163 INSERM, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, lying molecular targets of this chromosomal event remain France. 9 Hematology Pediatry Department, Robert Debré Hospital, Paris, elusive ( 14 ). France. 10 Hematology Department, Hôpital Saint-Louis, Paris, France. In our study, we used a large range of integrated genomic 11 Centre National de Recherche en Génomique Humaine (CNRGH), Insti- and functional analyses and identifi ed two genes simultane- tut de Biologie François Jacob, Direction de La Recherche Fondamentale, ously inactivated through del6q, the combined haploinsuf- CEA, Evry, France. fi ciency of which accelerates T-ALL progressionin vivo . By Note: Supplementary data for this article are available at Cancer Discovery Online (http://cancerdiscovery.aacrjournals.org/). using a genome-editing CRISPR/Cas9 approach, we precisely engineered a short del6q in human cells that enabled us S. Gachet, T. El-Chaar, D. Avran, and E. Genesca contributed equally to this article. to examine the proteomic and translatome profi le of the Corresponding Author: Jean Soulier, Hematology Department INSERM deleted cells. We found that the haploinsuffi ciency of these U944 and Hematology Laboratory, Hôpital Saint-Louis, 1, Av Claude velle- two genes, one encoding a ribonucleoprotein and the other faux, Paris, France. Phone: 33-1-53-72-40-41; Fax: 33-1-42-49-40-27; hosting noncoding small nucleolar RNA (snoRNA), deregu- E-mail: [email protected] lates cellular metabolism and ultimately affects the leukemia- doi: 10.1158/2159-8290.CD-17-0831 initiating cell (LIC) activity of human T-ALL cells through ©2018 American Association for Cancer Research. modulation of ribosomal functions. DECEMBER 2018 CANCER DISCOVERY | 1615 Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst September 28, 2018; DOI: 10.1158/2159-8290.CD-17-0831 RESEARCH ARTICLE Gachet et al. AB * TAL HOX HOXA TLX1 TLX3 Immature Case TL08 −4 −2 −1 0 +1 +2 +4 −40−2 −1 0 +1 +2 +4 −4 −2 −1 +1 +2 +4 p25.2 p24.3 p24.1 p22.3 p22.1 p21.32 p21.2 p12.3 p12.1 q12 q14.1 del6q q14.3 q16.1 q16.3 q22.1 q22.31 q22.33 q23.2 q24.1 q24.3 q25.2 q26 Chr. 6 Diag Xeno Relapse C 1032 1753 1815 1941 2120 2649 2775 9083 9160 9376 9027 TL05 TL06 TL04 TL11 TL14 TL02 TL03 TL08 TL10 TL17 TL25 TL27 335 1842 1950 2759 2787 8815 9963 10111 TL16 TL07 TL13 TL01 TL12 TL15 258 704 768 1632 1948 1949 2117 2322 2436 2486 2669 2720 2722 2760 2774 2788 2789 2794 2844 2846 9243 9323 9827 9938 10110 TL34 TL19 TL26 TL28 TL31 TL18 TL20 TL21 TL24 TL30 TL22 TL23 TL29 del6q NOTCH1 FBXW7 PTEN Mutated 6q deleted Wild-type Nondeleted Figure 1. Del6q is associated with the TAL1-related T-ALL subtype as a late chromosomal event. A, aCGH showing copy-number losses (green) and gains (red) for chromosome 6 in the first T-ALL cohort n( = 78 cases). Cases were ordered by oncogenic subtypes as described (4). The region of del6q is boxed. *, Association between del6q and TAL1-related subtype, P < 0.05 (Fisher test). B, Different-sized del6q were found in T-ALL samples from the same patient (TL08) at diagnosis and relapse and in a xenograft raised from the diagnosis sample; by contrast, a core of common events was found in this patient—i.e., SIL-TAL and CDKN2A deletion (not shown)—demonstrating late occurrence of del6q events. C, Co-occurring NOTCH1, FBXW7, and PTEN gene mutations in the TAL-R case cohorts (cases with available mutation data are shown). RESULTS and analyzed a total of 107 TAL1-related (TAL-R) cases from Del6q Is a Late Chromosomal Event in TAL1 three patient cohorts (4, 5, 15), in which del6q was detected in 34 Oncogene–Related T-ALL cases (32%). Del6q could be subclonal, and distinct del6q could be observed in the same sample, or in the diagnosis and relapse To identify tumor suppressor genes in this deletion, we ini- leukemia samples from the same patient, or in primary and tially screened deletion 6q by array comparative genomic hybrid- patient-derived xenografts (PDX; Supplementary Fig. S2; Fig. ization (aCGH) in a cohort of 78 primary T-ALL cases that were 1B). Additional, co-occurring mutations in NOTCH1/FBXW7 or previously characterized by large-scale expression profiling (ref. PTEN genes were often found, as previously reported in TAL-R 4; see flow chart of the study in Supplementary Fig. S1). Del6q cases, suggesting multistage oncogenesis (Fig. 1C; refs. 3, 7). was associated with the T-ALL subtype that is characterized by Collectively, these data indicate that del6q is strongly associated aberrant expression of the TAL1 oncogene (P = 0.032), suggest- with the TAL-R subtype in which it occurs as a late-stage