Epigenetically centered evolution in an example of myeloid malignancy
Authors: josé adélaide, nathalie cervera, nadine carbuccia, séverine garnier, arnaud guille, marie‐joelle mozziconnaci, raynier devillier, max chaffanet, norbert vey, daniel birnbaum, véronique gelsi‐boyer
Journal: American Journal of Hematology (2016)

To the Editor: In 2014, a 26-year-old man presented with tri-cytopenia discovered on a systematic blood test. Bone marrow analysis showed a component of myeloblasts with an erythroid proliferation of 13% and 58% respectively, and concluded to M6 acute myeloid leukemia (AML) according to the FAB criteria. It would now be classified as a myelodysplastic syndrome with excess of blasts according to the updated 4th edition of the WHO classification 1. Immunophenotypic findings were consistent with morphology, and karyotype analysis of the bone marrow showed a t(X;12)(p11;q24) in all mitoses studied. The patient achieved complete remission following conventional 3 + 7 induction chemotherapy followed by three cycles of high-dose cytarabine consolidation. Four months later, the patient presented multilineage dysplasia and cytogenetic relapse. Three months later the patient presented with AML with 20% marrow blasts. He received four cycles of azacytidine, had no response and was allografted with refractory disease from a haploidentical sibling donor. Despite transplant rejection, cytological remission was obtained for 10 months with the persistence of a minor clone with t(X;12). Unfortunately in 2016, a relapse occurred with 45% of bone marrow blasts with the t(X;12). The patient was appropriately informed and asked to consent in writing, in compliance with French and European regulations. Molecular characterization was done by targeted next generation sequencing (tNGS) using a panel of 106 genes, as already used to define M6 AML 2, and by aCGH. At diagnosis, tNGS revealed a mutation in BCORL1 (splice site mutation, variant allele frequency/VAF = 4.3), DNMT3A (R882H, VAF =38.4), and STAG2 (L871fs, VAF = 70.9) genes. At AML relapse, tNGS analysis revealed the same mutations in BCORL1 (VAF = 46.4), DNMT3A (VAF = 33.6), and STAG2 (VAF = 58.3) and an additional mutation in SETD2 (R1710H, VAF = 3.7). No abnormality in NPM1, TP53, spliceosome, and signaling genes was noted. No molecular abnormalities were detected during complete remission. In both 2014 (diagnosis) and 2016 (relapse) samples, array-comparative genomic hybridization (aCGH) showed that the t(X;12) actually resulted in two deletions. One at Xp11 deleted BCOR (Fig. 1a) and the other at 12q24 deleted a small region from SETD1B to SBNO1 (Fig. 1b). aCGH also revealed a gain at 17q21.31 targeting few loci, including the KANSL1/KIAA1267 gene (Fig. 1c). Molecular analysis thus showed that the translocation resulted in two hits in a single event, as it is sometimes the case 3, 4. The first hit deleted BCOR. In a male patient this deletion completely inactivates this gene. The second deleted 12q24 gene(s); the identification of the actual target of this deletion is more difficult because several genes were affected but SETD1B appears as a good candidate (although the 12q24 deletion is rare we found two other cases by examining the aCGH results of a series of myeloproliferative disorders, and they contained SETDB1—data not shown). Zooming in the 2014 aCGH profile shows the BCOR deletion on chromosome arm Xp (a), the 12q24 deletion (b), and the KANSL1 gain on chromosome arm 17q (c). (d) Proposed representation of the disease evolution. After a translocation as first event mutations of STAG2 and DNMT3A trigger the disease. Gain of KANSL1 may occur at this step or later. A clone with a BCORL1 mutation develops, potentially followed by a clone with a SETD2 mutation. (e) Possible mechanism responsible for the AML, comprising acetylation at lysine 16 of histone H4 by the MSL complex, loss of methylation of histone H3 and loss of polycomb PRC1 complex regulation, and leading to changes in expression of genes (possibly HOX genes). The VAF and stability of the DNMT3A and STAG2 mutations suggest they were present early in the malignant clone, while the BCORL1 mutation became important at relapse. Evolution of the disease may be represented as in Fig. 1d. The combination of the translocation with the mutations led us to hypothesize a possible epigenetically centered mechanism of leukemogenesis based on a cooperation that generates hyperacetylation of histones at leukemogenic loci (Fig. 1e). Deletion of SETD1B and mutation in SETD2 would compromise KMT2 and KMT3 lysine methyltransferase protein complexes, respectively, while gain of KANSL1, if accompanied by overexpression of the protein, would enhance lysine acetyltransferase (KAT) complexes such as the MSL (Male Specific Lethal) complex. Regulation of KAT by polycomb repressor complex one (PRC1) would be compromised by the inactivation of BCOR and BCORL1 X-linked genes, STAG2 X-linked gene encoding a cohesin component, and DNMT3A. The X chromosome is clearly a weak spot in this case. As a matter of fact, the histone acetyltransferase MSL complex, which contains KAT8/MOF/MYST1 and KANSL1 5, is important for dosage compensation regulating mammalian chromosome X 6, 7. If and how these two observations are connected remains unknown. In AML, it seems crucial to determine whether KMT (e.g., MLL) or KAT (e.g., MYST) complexes are altered. The same complexes may be altered in different ways. For example, KANSL1 gene inactivating mutations have been found in Down syndrome related AML 8. If the mechanism we propose here is proven to drive some cases of AML it may have impact on treatment: rather than inhibitors of histone deacetylases, drugs targeting histone acetylases could be efficient 9. VGB, MJM, RD, and NV recruited the patient and collected the samples and the biological annotations. JA, NCe, NCa, SG did the experimental work, while AG did the bioinformatic analyses. MC and DB supervised the aCGH and NGS experiments and the analyses. VGB and DB wrote the paper. Authors thank the IPC/CRCM Tumour Bank, that operates under authorization # AC-2007-33 granted by the French Ministry of Research (Ministère de la recherche et de l'Enseignement Supérieur). The project was approved by the IPC Institutional Review Board (Comité d'Orientation Stratégique, COS). José Adélaide1, Nathalie Cervera1, Nadine Carbuccia1, Séverine Garnier1, Arnaud Guille1, Marie-joelle Mozziconnaci2, Raynier Devillier3,4, Max Chaffanet1, Norbert Vey3,4, Daniel Birnbaum1, Véronique Gelsi-Boyer1,2,3* 1Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire, UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725, Marseille, France 2Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France 3Aix-Marseille Université, Marseille, France 4Département d'Hématologie, Institut Paoli-Calmettes, Marseille, France