# Patent

## Title
TET2 as a new diagnostic and pronostic marker in hematopoietic neoplasms

## Abstract

The present invention concerns an in vitro method for diagnosing a myeloid tumor or a lymphoid tumor in a subject, which comprises the step of analyzing a biological sample from said subject by (i) detecting the presence of a mutation in the Ten Eleven Translocation protein family member 2 gene (TET2) coding for the polypeptide having the sequence SEQ ID NO:2, and/or (ii) analyzing the expression of the TET2 gene; wherein the detection of such a TET2 mutation, of the absence of expression of TET2 or of the expression of a truncated TET2 is indicative of a subject developing or predisposed to develop a myeloid tumor or a lymphoid tumor.

## Background
This application is a continuation-in-part of U.S. patent application Ser. No. 12/997,203, filed Dec. 9, 2010, which is a U.S. National Stage of PCT/EP2009/057295, filed Jun. 12, 2009, which claims the priority of European patent applications EP 08305255.5 and EP 09155169.7 filed on Jun. 12, 2008, and on Mar. 13, 2009, respectively, all of which are incorporated herein by reference in their entirety.


FIELD OF THE INVENTION
The present invention relates to genetic markers to diagnose myeloid neoplasms, more particularly to a new identified tumour suppressor gene, the Ten Eleven Translocation protein family member 2 gene (TET2). Genetic alterations of TET2 are useful to diagnose myeloid tumours, such as myelodysplastic/myeloproliferative syndromes, MDS, AML or MPD, and lymphoid tumours.
BACKGROUND OF THE INVENTION
Hematopoiesis is maintained by a hierarchical system where hematopoietic stem cells (HSCs) give rise to multipotent progenitors, which in turn differentiate into all types of mature blood cells. The molecular mechanisms controlling multipotentiality, self-renewal, quiescence and HSC commitment have been extensively studied. However, numerous issues remain to be addressed and important genes regulating these processes remain to be identified.
Myeloid malignancies include Acute Myeloid leukaemia (AML), Myeloproliferative disorders (MPDs), myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative syndromes that are all clonal stem-cell (HSC) or progenitor malignant disorders (TIU et al., Leukemia, vol. 21(8), p: 1648-57, 2007).
Several genetic mutations have been correlated to AML, and four groups are recognized: (i) the AML with recurrent genetic abnormalities AML t(8; 21)(q22; q22) with RUNX1-ETO fusion gene; AML with abnormal bone marrow eosinophils and inv(16)(p13; q22) or t(16; 16)(p13; q22) with CBFB/MYH11 rearrangement; acute promyelocytic leukaemia APL with t(15; 17)(q22; q12) PML/RARA; AML with 11q23 (MLL) abnormalities); (ii) AML with multilineage dysplasia following MDS or MDS/MPD or without antecedent of MDS or MPD; (iii) AML or MDS therapy related and (iv) other unclassified AML among that comprises the group of AML with normal karyotype which prognosis is based on molecular analysis of oncogenes such as mutations of FLT3-ITD or NPM1.
Myelodysplastic/myeloproliferative syndromes include four myeloid diseases grouped in 1999 by the WHO: chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia (JMML), atypical chronic myeloid leukemia (aCML) and unclassified myelodysplastic/myeloproliferative syndromes (U-MDS/MPS).
MDS include refractory anemia (RA), and refractory cytopenia with multilineage dysplasia (RCMD). MDS are characterized by ineffective hematopoiesis in one or more of the lineage of the bone marrow. Early MDS mostly demonstrate excessive apoptosis and hematopoietic cell dysplasia (CLAESSENS et al., Blood, vol. 99, p: 1594-601, 2002; CLASESSENS et al., Blood, vol. 105, p: 4035-42, 2005). In about a third of MDS patients, this ineffective hematopoiesis precedes progression to secondary AML (sAML). Although some molecular events associated with specific MDS subtypes (ELBERT et al., Nature, vol. 451(7176), p: 335-9, 2008) or disease transformation (BRAUN et al., Blood, vol. 107(3), p: 1156-65, 2006) have been identified, the underlying molecular defects are still poorly understood. No biological markers, except morphological features, are currently available for early diagnosis and prognosis.
MPDs, referred now as myeloproliferative neoplasms (MPN; TEFFERI & VARDIMAN, Leukemia, vol. 22, p: 14-22, 2008), are chronic myeloid diseases including chronic myelogenous leukaemia (CML), polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF) and idiopathic myelofibrosis (IMF). MPDs are characterized by an increased proliferation of one or several myeloid lineages. If most MPDs are sporadic diseases, familial cases of MPDs, for which the exact prevalence is unknown, have been reported (GILBERT, Baillieres Clin. Haematol., vol. 11, p: 849-858, 1998; KRALOVICS et al., Blood, vol. 102, p: 3793-3796, 2003; BELLANNE-CHANTELOT et al., Blood, vol. 108, p: 346-352, 2006). The clinical analysis of these familial cases has shown that they are phenotypically identical to sporadic cases. Nevertheless, MPD families are characterized by a clinical and genetic heterogeneity. First, MPD cases from a single family can either display the same subtype or different types of MPD (GILBERT, abovementioned, 1998; BELLANNE-CHANTELOT et al., abovementioned, 2006; RUMI et al., Cancer, vol. 107, p: 2206-2211, 2006). Second, about 6-15% of patients with PV and 3-5% of patients with ET are at risk of developing hematological complication after 15 years of evolution (FINAZZI & HARRISON, Semin. Hematol., vol. 42, p: 230-238, 2005; KILADJIAN et al., Blood, vol. 112, p: 1746, 2008; PASSAMONTI et al., Blood, vol. 111, p: 3383-3387, 2008; PASSAMONTI et al., Haematologica, vol. 93, p: 1645-1651, 2008).
MPDs, in both sporadic and familial cases, are commonly associated with an acquired constitutive kinase activity, as exemplified by the JAK2V617F mutation in Polycythemia Vera, in most PV cases and in half of ET and PMF cases (MORGAN & GILLIGAND, Annu. Rev. Med., vol. 59, p: 213-22, 2008; DELHOMMEAU et al., Cell Mol. Life. Sci., vol. 63(24), p: 2939-53, 2006, CAMPBELL & GREEN, N. Engl. J. Med., vol. 355(23), p: 2452-66, 2006; BELLANNE-CHANTELOT et al., above-mentioned, 2006; JAMES et al., Nature, vol. 434, p: 1144-1148, 2005; BAXTER et al., Lancet, vol. 365, p: 1054-1061, 2005; LEVINE et al., Blood, vol. 106, p: 3377-3379, 2005; KRALOVICS et al., N. Engl. J. Med., vol. 352, p: 1779-1790, 2005). MPDs frequently result from the expression of a constitutive tyrosine kinase protein:

    
    
        Through a fusion like BCR-ABL in CML, FIP1L1-PDGFRA in HES, TEL-PDGFRB in CMML with hypereosinophilia, ZNF198-FGFR1 in rare MPD coupled to lymphoid proliferation and PCM1-JAK2 in rare MPDs, AML and T cell lymphomas
        A limited or single nucleotide mutation i.e. JAK2 V617F (1849G>T), which recent discovery of in PV (98%), ET (75%), IMF (50%) and a few percent of CMML, MDS/MPD and U-MPD allows for a new MPD classification and diagnosis criteria and perspectives for treatment. In addition, KIT mutations are recurrent in systemic mast cell proliferation.
        Through activating mutations in the receptor for thrombopoietin receptor (MPL), especially of the tryptophan 515 (MPLW515K/L/A) (PIKMAN et al., PLoS Med, vol. 3(e270), 2006; CHALIGNÉ et al., Leukemia, vol. 22, p 1557-66, 2008).
        Marginal cases of CML presented with BCR/JAK2 rearrangement due to t(9; 22)(p24; q11).
    
    


The JAK2 gene on chromosome 9p encodes a tyrosine kinase that associates with type 1 cytokine receptors. The V617F mutation is predicted to disrupt the auto-inhibitory effect of the JH2 domain to constitutive activation of the kinase. Wild type JAK2 exerts a dominant negative effect on the activity of the mutated protein. Therefore the loss of WT JAK2 associated to the duplication of the mutated gene by mitotic recombination observed in most of MPD samples allows for a higher expression and activity of the mutated kinase.
However, several observations, such as the Polycythemia Vera co expressing the WT and mutated JAK2 and the characterization of secondary AML emerging from mutated MPD but lacking of JAK2 mutation in the blast phases indicate oncogenetic events earlier occurring before JAK2 mutation. Moreover, and as discussed previously, the MPD disease evolution is indeed highly variable within and between families. Thus, there is some evidence that there is at least one other mutation than JAK2 implicated in MPDs and, more specifically, their progression.
Lymphoid tumours consist of expansion of cells with lymphoid features. Acute lymphoblastic leukaemia/lymphoma are proliferation of cells blocked in lymphoid differentiation, from either T (T-cell acute lymphoblastic leukaemia; T-ALL) or B (B-cell precursor acute lymphoblastic leukaemia; BCP-ALL) origin. Some leukaemia lymphoma are from Natural Killer (NK) origin. Lymphoma involve expansion of more mature lymphoid cells (B or T). Some neoplasms are chronic, and can involve T cell (prolymphocytic leukaemia) or B cells (Chronic Lymphocytic Leukaemia). The classification of lymphoid neoplasm is based on anatomopathological analyses, differentiation markers and pathogenesis data (Swerdllow S. H., Campo E., Harris N. L., Jaffe E. S., Pileri S. A., Stein H., Thiele J. W., Vardiman J. W. (Eds): WHO classification of tumors of haematopoietc and lymphoid tissues. IARC: Lyon 2008). For example, Anaplasic large T-cell lymphoma are associated with NPM-ALK fusion oncogene (and variant thereof), follicular lymphoma are associated with BCL2 activation following t(14; 18)(q32; q21) chromosomal translocation, mantle cell lymphoma are associated with CCND1 activation following t(11; 14)(q13; q32) chromosomal translocation. Many lymphoma however lack any reliable molecular marker suggesting a pathophysiological mechanism. This is the case, in particular, for more than 50% of diffuse large B cell lymphomas (DLBCL), for most peripheral T-cell lymphomas (PTCL) and for a majority of non-follicular low grade lymphomas.
Therefore, there was an urgent need of a reliable diagnostic marker that allows to identify lymphoid and myeloid neoplasms, in particular MDS and MPD, and eventually to prognosticate their progression.
The Ten Eleven Translocation protein family contains three recently identified members, with unknown functions, characterized in that they share two highly conserved domains at their C-terminal end. As used herein, the expression “gene of the TET family” refers to members of the Ten Eleven Translocation family, TET1, TET2 or TET3, which have been recently identified (Lorsbach et al, Leukemia 2003).
Among them, TET1 is the only studied member, because it has been identified as a fusion partner with the protein mixed lineage leukemia (MLL) in two different and independent studies (ONO et al., Cancer Research, vol. 62(14), p: 4075-80, 2002 and LORSBACH et al., Leukemia, vol. 17(3), p: 637-41, 2003). This protein, also called LCX, or “leukemia associated protein with a CXXC domain in N-terminal region”, contains an α-helical coiled-coil region in its C-terminal region, region which is retained in the fusion MLL-TET1. On the contrary, the N-terminus CXXC domain of TET1 is not present in this protein fusion (Ono R, Cancer Research 2002). The two highly conserved carboxy terminal regions are included in the MLL-TET1 fusion (Lorsbach et al, Leukemia 2003). One conserved region is disrupted by the translocation; the other one is fused to MLL. Despite its description as an MLL fusion partner 7 years ago, functional and sequence analysis of the TET1 gene have been reported recently, after the priority date of the present application.
The MLL gene is located at human chromosome 11q23 and is found to be rearranged in a heterogenous group of lymphoid, myeloid and mixed lineage human leukemias. More than 70 loci have been described to be rearranged with the 11q23 chromosomal band and at least 50 of these have been cloned and characterized on a molecular level. Most of the MLL rearrangements map to a 8.3 kb base of the genes. The partners genes are always fused in frame to the 5′ part MLL and may include MLL itself. Amplifications of MLL have also been reported. The partner genes code for proteins with disparate functions. In the MLL fusion, they may provide transcriptional activation domains, chromatin modifier complex recruitment or dimerization/oligomerization motif. Indeed, the expression of an MLL-Beta-galactosidase (a bacterial protein able to tetramerize) or to dimerization domain is sufficient to induce leukemia in mouse models. Therefore, it is not possible to infer the function of a protein or its independent involvement in cellular transformation from its fusion to MLL (The versatile mixed lineage leukaemia gene MLL and its many associations in leukaemogenesis. Daser A, Rabbitts T H. Semin Cancer Biol. 2005 June; 15(3):175-88. Review. Chromosomal rearrangements leading to MLL gene fusions: clinical and biological aspects. Harper D P, Aplan P D. Cancer Res. 2008 Dec. 15; 68(24):10024-7.)
On the contrary, little is known about the TET2 protein, which is encoded by a gene located on the 4q24 chromosomal region, and the TET3 protein, which is encoded by a gene located on the 2p12 chromosomal region.
More specifically, the Ten Eleven Translocation oncogene number 2 (TET2) has been designated recently (Lorsbach et al, Leukemia 2003). The TET2 gene located on the chromosomal region 4q24, comprises 11 exons spread over >130 Kb and is normally widely expressed. This gene is referenced with the accession number ID 54790 (Locus ID NCBI) (SEQ ID NO:1), and its cDNA (Accession number NM_001127208, SEQ ID NO:39) is encoding a protein of 2002 amino acids (Accession number NP_001120680, SEQ ID NO:2).
The TET2 protein shares two highly conserved regions with a single orthologous Drosophila predicted protein. These regions are i) a 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444), and ii) a second 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922) (these regions are highlighted in FIG. 1). The predicted sequence of TET2 did not reveal any motif corresponding to an identified function.
Applicants report herein that one or both copies of the Ten Eleven Translocation 2 (TET2) gene are often inactivated/modified by acquired mutations in MPD, MDS and CMML but also in lymphoma. These events target the hematopoietic stem cell and indicate an important function for TET2 as a tumor suppressor gene in myeloid or lymphoid neoplasms.
SUMMARY OF THE INVENTION
In a first aspect, the present invention provides an in vitro method for diagnosing a myeloid tumour or a lymphoid tumour in a subject, which comprises the step of analyzing a biological sample from said subject by:

    
    
        (i) detecting the presence of a mutation in the Ten Eleven Translocation protein family member 2 gene (TET2) coding for the polypeptide having the sequence SEQ ID NO:2, and/or
        (ii) analyzing the expression of the TET 2 gene;
        wherein the detection of such a TET2 mutation, of the absence of expression of TET2 or of the expression of a truncated TET2 is indicative of a subject developing or predisposed to develop a myeloid tumour or a lymphoid tumour.
    
    


In a preferred embodiment, said subject is a mammal, preferably a human.
In another preferred embodiment, said myeloid cancer is selected in the group consisting of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), myeloproliferative disease (MPD) and myelodysplatic/myeloproliferative syndrome.
In still another preferred embodiment, said lymphoid tumour is selected in the group consisting of lymphoma and more preferentially of T cell lymphoma
Preferably, said mutation is detected on each copy of the TET2 gene coding for the polypeptide having the sequence SEQ ID NO:2 (encoded by the cDNA having the sequence SEQ ID NO:39) and is included in the group consisting of deletions, insertions and point mutations such as mutations affecting splice sites, missense mutation and nonsense mutations, preferably missense mutation and nonsense mutations.
In a more preferred aspect of the invention, the mutation is a deletion or an insertion which results in the absence of expression of the TET2 protein or in the expression of a truncated TET2 protein.
Even more preferably, this truncated TET2 protein does not comprise at least one of the two highly conserved regions shared by the other TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), or ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4), preferably the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
For example, these deletions or insertions can be selected in the group comprising or consisting of those disclosed in Table I in reference to SEQ ID NO:39 for nucleic acid position and to SEQ ID NO:2 for amino acid position.









TABLE I






Nucleotide Change
Consequence








del1264_1666
p.Glu135 FS



delC 1642
p.Ser261 FS



del1893_1896
p.Lys345FS



delC 2448
p.Gln530 FS



delA 2505
p.Thr549 FS



delC 2524
p. Pro555 FS



Ins 2540_2544
p.Leu560FS



delT 2685
p.Ser609 FS



delA 2815
p.Gln652FS



del 2834_2835
p.His658 FS



delA 2935
p.Glu692 FS



delT 2944
p.Leu699 STOP



delG 2994
p.Glu711 FS



delC 3009
p.His717 FS



insA 3009
p.His717 FS



del 3131_3137
p. Leu757 FS



insC 3151
p.Gln764 FS



delA 3166
p.Gln769 FS



delT3215
p.Phe785 FS



insA3350
p.Gln831FS



insT3995
p.Glu846 FS



delA3430
p.Asn857FS



insT 3465
p.Pro869 FS



insA 5757
p.Gln891 STOP



insCT 3581
pGly 908 FS



del CA 3756_3757
p.Gln966 FS



dupT 3914
p.Glu1026 STOP



delT 3998
p.Leu1046FS



delA 4130
p.Lys1090 FS



delG 4271
p.Glu1137 FS



delA4327
p.Asn1156 FS



delG 4527
p.Ala1223 FS



—
p.del 1237-1239



delG 4932
p.Glu1357 FS



insG 5119
p.Leu 1420 FS



delG 5133
p.Asp 1425 FS



insA 5177
p.Arg1440FS



dupA 5177
p.Arg1440FS



delC 5222
p.Leu1457 STOP



del5521_5524
pThr1554 FS



insA 5540
p.Tyr1560 FS



del 5583_5605
p.Pro1575FS



delT 5570
p.Leu1637 FS



del5828_5843
p.Met1656 FS



del6049_6050
p.Asp1830 FS



delC 6360
p.Gln1834 FS



del6396_6531
p.Val1846 FS



delA 6507
p.Thr1883 FS



insC 6507
p.Thr1883 FS



del6511_6512
p.Pro1885FS



DelC 6555
p.Leu1889FS



insC splice site
mutation of splice




site exon 8





Del: deletion;


ins: insertion;


FS: frame shift






In another more preferred aspect of the invention, the mutation is a missense mutation. Said mutation in the TET2 protein, preferably resulting from a mutation in the open reading frame of the TET2 gene, is preferably located in at least one of the two highly conserved regions shared by the TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), and ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4), and more preferably in the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). For example, these missense mutations can be selected in the group comprising or consisting of I1175V, L1197N, H1219Y, E1235V, C1271W, K1299E, L1340P, R1302G, G1370E, A1344E, N1387S, L1398P, V1417F, P1419R, H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F, preferably can be selected in the group comprising or consisting of L1197N, H1219Y, E1235V, C1271W, K1299E, L1340P, R1302G, G1370E, A1344E, N1387S, H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F, and more preferably in the group comprising or consisting of: H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F.
In another more preferred aspect of the invention, the mutation is a nonsense mutation. Said mutation resulting from a mutation in the open reading frame of the TET2 gene, is preferably located before or inside at least one of the two highly conserved regions shared by the TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), and ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4), and more preferably before or inside the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). For example, said nonsense mutations can be selected in the group comprising or consisting of Q232Stop, Q321Stop, S354Stop, Q417Stop, Q481Stop, R544Stop, R550Stop, Q557Stop, Q574Stop, Q593Stop, Q635Stop, Q642Stop, Q685Stop, L699Stop, Q743Stop, Q778Stop, S792Stop, Q886Stop, Q891Stop, Q916Stop, Q943Stop, Q963Stop, E1026Stop R1067Stop, R1216Stop, Y1225Stop, R1404Stop, Q1414Stop, Q1445Stop, L1457Stop, R1465Stop, K1491Stop, R1516Stop, Q1524Stop, Q1542Stop, N1624Stop, Y1724Stop, Y1751 Stop, L1819Stop, Q1834Stop and W1847Stop.
In another aspect of the invention, the mutation in the TET2 gene induces absence of expression or under-expression of the polypeptide having the sequence SEQ ID NO:2 and more preferably the absence of expression or under-expression of at least one of the two highly conserved regions shared by the TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), and ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4), more preferably of the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
In a second aspect, the present invention provides a kit for diagnosing myeloid cancer in a subject comprising at least one nucleic acid probe or oligonucleotide or at least one antibody, which can be used in a method as defined previously for detecting the presence of a mutation in the TET2 gene and/or analysing the expression of the TET2 gene.
In a preferred embodiment of the invention, said oligonucleotide is at least one PCR primer, and preferably a set of PCR primers.
More preferably, said set of primers is selected in the group comprising SEQ ID NO: 5 to SEQ ID NO: 38 (see examples).
In a third aspect, the present invention provides the use of a hypomethylating agent for treating a patient suffering from a myeloid or a lymphoid tumour, for which tumour, a TET2 mutation, an absence of TET2 expression or an expression of a truncated TET2 has been detected.
In a final aspect, the present invention provides a method for treating a subject suffering a myeloid or a lymphoid tumour, for which tumour, a TET2 mutation, an absence of TET2 expression or an expression of a truncated TET2 has been detected, said method comprising the step of administrating to said subject a therapeutically efficient amount of a hypomethylating agent.



BRIEF DESCRIPTION OF THE DRAWINGS
The FIG. 1 shows the protein sequence of TET2 (SEQ ID NO:2), highlighting the conserved regions between species (bold).
The FIG. 2 shows the sequence traces obtained by sequencing the PCR products obtained for samples obtained from two patients A and E, showing that the mutation only occurs in the tumoral and not in non-tumoral samples (NT), and Peripheral Blood Lymphocytes (PBL). R corresponds to the sequence obtained with the Reverse primer, and F corresponds to the one obtained with the Forward primer. WT corresponds to the sequence obtained in healthy individuals.
The FIG. 3 shows that in MDS samples, mutated TET2 is observed in immature CD34+ cells and is associated with in vivo expansion of the mutated clone. The FIG. 3a shows the sequencing histograms of sorted CD34+ cells. The FIG. 3b shows the PCR-RFLP analysis of DNA isolated from sorted MDS03 CD34+CD38− and CD34+CD38+ cells at RAEB1 phase. The FIG. 3c shows PCR-RFLP analysis of TET2. The FIG. 3d shows genotyping by PCR-RFLP.
The FIG. 4 shows that JAK2V617F-positive MPD hematopoietic stem cells with TET2 defects display enhanced NOD/SCID repopulating capacities. The FIG. 4a shows the percentage of human CD45-positive cells in mouse bone marrow. The FIG. 4b shows flow cytometric analysis of human cells present in NOD-SCID bone marrow.
The FIG. 5 shows the locations of some of the identified mutations of the TET2 gene distributed along the protein sequence Conserved regions are marked with gray stripes. Arrowheads indicate the location of exon boundaries. FS: Frame shift.
The FIG. 6 shows a schematic representation of the TET2 gene and protein showing the mutations identified in familial myeloproliferative neoplasms. Hatched boxes indicate exons. Truncating mutations are depicted as stars, missense mutations as inverted triangles. Conserved functional domains are depicted as boxes on the protein scheme. fs: frameshift.
The FIG. 7 shows the sequential study of TET2 and JAK2 in patient P4 (F3). Sequence electrophoregrams are shown for each TET2 mutation and for JAKV617F. The diagram on the left indicates time lapse from diagnosis (in years) and corresponding phenotype for each sample (white: ET; grey: PV; hatched: post-ET MF; black: AML).
The FIG. 8 shows the schematic representation of the clinical status of the twelve patients with at least one TET2 mutation. White boxes depict ET stages, grey, PV, crosswised hatching indicates myelofibrosis, either primary (left-slanting) or post-PV/ET (right-slanting) and AML are symbolized as black boxes. Above each arrowhead indicating a molecular analysis is annotated the TET2 corresponding mutation. Disease duration (in years) is indicated below the bars, the “zero” point indicating time of diagnosis. Time of death is symbolized as a vertical line, when appropriate, at the right end.
The FIG. 9 shows the TET2 and JAK2 genotypes in committed progenitors of patients P2, P3 and P4. Histograms show the fraction of clones harboring JAKV617F and two TET2 mutations (crosswised hatching), JAK2V617F and one TET2 mutation (white), wild type JAK2 and two TET2 mutations (light grey), JAK2V617F and wild type TET2 (grey) and no mutation in any of the two genes (black). Two samples were analyzed for patient P4, the corresponding stage is indicated below each bar. The numbers of analyzed clones are indicated.
The FIG. 10 shows the clinical status and TET2 genotypes in MDS patients. Whites boxes represent low/int-1 grade MDS, hatched boxes represent int-2/high grade MDS and grey boxes represent secondary AML.
The FIG. 11a shows partial structure of the Tet2 gene. For the Tet2LacZ “LacZ” allele, the location of the gene-trap cassette containing a splice acceptor and a beta-galactosidaseneomycin fusion gene is indicated (empty triangle). For the Tet2Lox “foxed” allele, loxP sites (black triangles) have been introduced in intron 10 and in the 30 untranslated region of exon 11.
The FIG. 11b shows the PCR analyses of Mx1−Cre-mediated exon 11 deletion in peripheral blood leukocytes (PBL), bone marrow (BM), spleen (Spl) and thymus (Th) cells from Mx1−Cre−Tet2Lox/Lox (hereafter named Tet2+/+) and Mx1−Cre+Tet2Lox/Lox (hereafter named Tet2−/−) animals 2 months after poly(dI:dC) injections (floxed allele: 305 bp; deleted allele: 237 bp).
The FIG. 11c shows quantitative RT-PCR analysis of expression of the murine Tet1, Tet2 and Tet3 genes in flow-sorted hematopoietic progenitors from Tet2+/+ and Tet2−/− animals (n=3 per genotype). Results are normalized with respect to Abl1 expression and represented relatively to expression in control mice samples. Tet2 RT-PCR assay spans the exon 10-11 boundary. LSK: Lin-Sca-1+c-Kit+; CMP: common myeloid progenitor; MEP: megakaryocyte-erythrocyte progenitor; GMP: granulocyte-macrophage progenitor.
The FIG. 11d shows quantitative RT-PCR analysis in Tet2LacZ/LacZ versus wild-type controls as in C (n=3 per genotype).
The FIG. 11e shows drop in 5-hydroxymethyl-cytosine (5hmC) in immature populations of Tet2-inactivated mice. Immunoblot analyses of increased quantity of genomic DNA from BM lineage (lin)-negative cells of Tet2+/+ and Tet2−/− mice 4 months after poly(dI:dC) induction using anti 5-methylcytosine-(5mC) antibody (left panel) and 5-hydroxymethyl-cytosine-(5hmC) antibody (right panel).
The FIG. 11f shows the quantification of the signal shown in FIG. 11e. 
The FIG. 12a shows the flow cytometrical analysis of hematopoietic stem and progenitor cells in the bone marrow of Tet2+/+ and Tet2−/− animals. Analysis was performed 4-6 months postinduction. Percentages within lineage—bone marrow cells (left panel), myeloid progenitor cells (MProg: lin-Sca-1-c-Kit+ cells; middle left panel), or within LSK cells (lin-Sca-1+c-Kit+ cells; middle right and right panel) are indicated.
The FIG. 12b shows the representation of the results exemplified in FIG. 12a as a percentage of lineage-negative hematopoietic progenitors. Data are presented as mean±SEM Tet2+/+ (n=6; white histogram) and Tet2−/− (n=6; black histogram) mice.
The FIG. 12c shows clonogenic activity of bone marrow (BM), spleen (Spl) and peripheral blood (PB) cells from Tet2+/+ (n=6; white circles) and Tet2−/− (n=6; black circles) mice 4-8 months postinduction in methylcellulose M3434 medium. Colonies were scored after 7 days and results are represented as mean colony number±SEM.
The FIG. 12d shows competitive bone marrow transplantation (BMT) assay. CD45.2+ donor BM cells isolated from Tet2+/+, Tet2LacZ/LacZ and Tet2−/− mice were transplanted into lethally irradiated CD45.1+ recipients, in equivalent number to wild-type competitor CD45.1+CD45.2+ BM cells. The percentage of donor chimerism (CD45.2+ cells) in the blood is given at the indicated time points post-BMT (n=2 mice per genotype).
The FIG. 12e shows the percentage of CD45.2+ donor chimerism in blood cells 20 weeks post-BMT; myelomonocytic cells (My; CD11b+Gr-1+), B cells (CD19+B220+) and T cells (CD4+ or CD8+). Values shown are mean±SEM (n=2 mice per genotype).
The FIG. 12f shows the representative flow cytometrical profiles of donor chimerism in blood subpopulations shown in (E) (host cells were electronically excluded with CD45.1).
The FIG. 12g shows LSK cells transplantation. CD45.2+ sorted-LSK cells isolated from Tet2-deficient or wild-type mice were transplanted into lethally irradiated CD45.1+ congenic recipients. The percentage of donor chimerism in the blood is given at the indicated time points post-BMT. Values shown are mean±SEM (n=2 mice per genotype).
The FIG. 12h shows the representative flow cytometrical analysis of donor chimerism in bone marrow subpopulations 16 weeks post-BMT (CD11b+Gr−1+ myelomonocytic cells; CD71+ erythroid cells; CD19+B220+ B cells).
The FIG. 13a White blood cell (WBC), red blood cell (RBC), hematocrit (Ht), hemoglobin (Hb), and platelet (Plt) counts in peripheral blood samples obtained from Tet2+/+, Tet2+/−, and Tet2−/− mice, performed 4-6 months post-induction.
The FIG. 13b shows spleen and liver weights of mutant and littermate control mice.
The FIG. 13c shows Von Willebrand staining on spleen sections from Tet2+/+ and Tet2−/− animals highlights megakaryocytic hyperplasia in Tet2−/− animals 4 months postinduction.
The FIG. 13d shows representative flow cytometrical analysis of the mature myeloid cells in the bone marrow, spleen, and blood of Tet2+/+ and Tet2−/− animals. Percentages of total cells are indicated. Lower panel: absolute number of cells from analysis shown in FIG. 13c. Tet2+/+ (n=10; white bars) and Tet2−/− (n=16; black bars) animals are represented as mean±SEM.
The FIG. 13e shows representative flow cytometrical analysis of the erythroid lineage in the bone marrow and spleen of Tet2+/+ and Tet2−/− animals. Percentage of total cells is indicated. Lower panel: absolute number of cells from analysis shown in (D). Tet2+/+ (n=10; white bars) and Tet2−/− (n=16; black bars) animals are represented as mean±SEM.
The FIG. 13f shows representative flow cytometry analysis of thymocytes in Tet2+/+ and Tet2−/− mice performed 4 months post-induction. Upper left panels: the percentages of total thymocytes are indicated. Upper right panels: the percentages of thymocytes precursors in Lineage-CD4−CD8− double-negative (DN) cells are represented. Lineage antibodies included antibodies against CD19, CD3ε, CD8, TCR-beta, NK-1.1, Ly-6G, and CD11b murine markers. Lower panels: the percentages of CD4−CD8− DN in total thymocytes and CD44+CD25− DN1 cells in DN precursor thymocytes from Tet2+/+ and Tet2−/− animals (n=3 per genotype) are represented as mean±SEM.
The FIG. 13g shows flow cytometrical analysis of B cells in the bone marrow of Tet2+/+ and Tet2−/− animals 4 months postinduction. Left panel: whole bone marrow. Right panel: gated on CD19+ cells (the frequencies are indicated as a percentage of CD19+ cells). Gates include pro- and pre-B precursor cells (B220low IgM−), immature B cells (B220low IgMhi) and mature B cells (B220low IgMhi). Lower panels indicate mean±SEM of eight animals per genotype.
The FIG. 13h shows flow cytometrical analysis of splenic B cells in Tet2+/+ and Tet2−/− animals. Lower panel indicate mean±SEM of ten animals per genotype.
The FIG. 14a shows Kaplan-Meier survival curve of Tet2LacZ/LacZ animals and wild-type littermate controls. Only animals that reached moribund state were considered.
The FIG. 14b shows representative picture of spleens observed in mutant Tet2LacZ/LacZ mouse compared with spleens from wild-type littermates.
The FIG. 14c shows hematoxylin-Eosin-Safran (HES) staining of bone marrow, spleen and liver sections from a 14-month-old moribund Tet2LacZ/LacZ animal.
The FIG. 14d shows reticulin staining of spleen from animal in FIG. 14c. 
The FIG. 14e shows flow cytometrical analysis of myelomonocytic, erythroid, B and T lymphoid lineages in the spleen of a 14-month-old moribund mutant Tet2LacZ/LacZ mouse. Of note, this animal displayed leukocytosis (69.1×106 WBC/mm3), anemia (1.76×106 RBC/mm3, 12.6% hematocrit, and 4.7 g hemoglobin/dl), thrombocytopenia (189×103 platelets/mm3) and hepatosplenomegaly (liver and spleen weights were 3960 and 2000 mg, respectively).
The FIG. 15a shows TET2 sequence in diagnostic and matched control samples. Vertical arrows indicate the sequence variations. Horizontal arrows hang over the frameshift mutations. The presence of the mutated TET2 sequences was confirmed by sub cloning the PCR product from patient 10. The [1893_1896 delAAGC] (on the left) was observed on 1/29 DNA molecules analyzed and the [4527 delG] (on the right) was observed on 2/18 DNA molecules analyzed.
The FIG. 15b shows genotype of CD34+ colonies from patient 8. Four erythroid lineage colonies were carrying the TET2 mutation.
The FIG. 15c shows genotyping of diagnostic and purified bone marrow fractions and CD34+ colonies from patient 2. Left panel: TET2 sequences at the lymphoma phase. Wild-type (WT) sequences are shown at the top. Node: nodal biopsy at diagnosis. Whole-blood sample was considered as normal matched DNA because it is devoid of IGH clonal marker. Right panel: TET2 sequences at the AML phase. BM: bone marrow nucleated cells. CD34−: negative fraction after CD34+ beads selection and CD34+: flow-sorted CD34+ population. Both mutations (frameshift [fs] and splice site mutation) are observed in all analyzed fractions. Bottom: Genotype of colonies obtained from single cells sorted on CD34 and CD38 expression. 4663+1G>A would have appeared first in the course of the disease. The cloning efficiency was extremely low (less than one colony out of 3000 seeded cells) and that colonies were small.
The FIG. 16a shows TET2 mutation status in flow-sorted subpopulations from blood samples from patient 27. The TET2 sequences in sorted subpopulations are shown on the right side of the picture. Both mutations are detected in the CD3− and CD34−CD3−CD19−CD14− populations, whereas only P761fs is observed as a trace (indicated by a star) in the other fractions.
The FIG. 16b shows a summary of results presented in FIG. 16a. 
The FIG. 16c shows the genotype of colonies obtained from sorted single CD34+ cells. 1 and 2 correspond to two successive blood samples at a 4-month interval. Only the P761fs mutation is observed in CD34+ (about 7%) and CD34+CD38− (2.2%) colonies. No P761fs positive colony was observed out of 40 CD34+CD38+ single-cell-derived colonies (data not shown).
The FIG. 16d presents single-cell analyses which shows the presence of both TET2 mutations in the same cell.
The FIG. 16e shows somatic mutations identified through exome analyses of patient 27.
The FIG. 16f shows the expression level of the mutated genes in normal tissues and tumor sample. Expression levels were normalized with respect to GUSB expression.



DETAILED DESCRIPTION OF THE INVENTION
The present invention is based on the discovery by the present inventors that the TET2 alleles are often genetically targeted by mutations and/or deletions in tumoral cells in patients suffering from lymphoid tumour or from myeloid tumour such as MPD, AML or MDS and can be considered as a bona fide tumor suppressor gene of human myeloid malignancies.
In a first aspect, the inventors report that, for sporadic cancer, the frequencies of TET2 mutation in unselected patient series were 12% in MPD, 18.5% in MDS, 24% in AML until 50% in CMML patients. Also, applicants demonstrated that TET2 is a tumor suppressor gene in myeloid malignant disorders, because mutated hematopoietic stem cells are endowed with a growth advantage leading to enhanced proliferation.
In a second aspect, the inventors demonstrated by an analysis of 61 familial MPD cases (i.e. PV, ET, and PMF) that anomalies of TET2 gene are found in 20% of the three major MPD phenotypes (PV, ET and PMF) with a higher prevalence in PMF (42%).
Among the TET2-positive patients diagnosed with PV or ET, 77% developed myelofibrosis (MF) suggesting that the presence of acquired events of TET2 influence the evolution of the disease. In four patients (3 PV and 1 ET), we were able to show that the TET2 defect preceded from one to 7 years the hematological complication. The patients with a defect in TET2 are prone to progress to MF. This highly suggested a possible link between the TET2 acquired mutations and the severity of the disease, more specifically between TET2 and the development of MF.
In a third aspect, the inventors report that, for sporadic cancer, the frequencies of TET2 mutation in patients suffering from T-cell lymphoid tumour was  ̃20%. Finally, the TET2 rearrangements were observed in patients suffering from B-cell lymphoid tumour.
Thus, in a first aspect of the invention, there is provided an in vitro method for diagnosing a myeloid tumour or a lymphoid tumour in a subject, which comprises the step of analyzing a biological sample from said subject by:

    
    
        (i) detecting the presence of a mutation in the Ten Eleven Translocation protein family member 2 gene (TET2) coding for the polypeptide having the sequence SEQ ID NO:2, and/or
        (ii) analyzing the expression of the TET2 gene;
        wherein, the detection of a TET2 mutation, of the absence of expression of TET2 or of the expression of a truncated TET2 is indicative of a subject developing or predisposed to develop a myeloid tumour or a lymphoid tumour.
    
    


Recent evidence indicate that proteins of the TET family encode enzymes responsible for the conversion of 5-methylcytosine to 5-hydroxymethylcytosine (TAHILIANI et al., Sciencexpress, 2009), thus have potential roles in CpG demethylation and epigenetic regulation. Moreover, this reference established that the conserved TET domains, where most TET2 mutations are observed, are implicated in this activity.
Concomitantly, several works have established, in the last years, a role for hypomethylating agents in MDS (ITZYKSON & FENAUX, Current Opinion in Hematology, vol. 16, p: 77-83, 2009).
The results of the inventors now suggest that the observed efficiency of hypomethylating agent in some MDS potentially results from a demethylation defect in MDS with TET2 mutations.
Thus, the results of the inventors further suggest the use of hypomethylating agent on subjects suffering from lymphoid or myeloid tumour, such as MDS, for which tumour, a TET2 mutation, an absence of TET2 expression or an expression of a truncated TET2 has been detected.
Consequently and according to a preferred embodiment, the detection of a TET2 mutation, of the absence of expression of TET2 or of the expression of a truncated TET2 is indicative of a subject developing a myeloid tumour or a lymphoid tumour suffering from a demethylation defect, which subject can be advantageously treated with a hypomethylating agent, such as azacytidine (AZA).
Preferably, the method of the invention is dedicated to diagnose myeloid tumours.
In fact, the inventors have established that the frequency of TET2 mutations in patients suffering from myeloid tumor or from lymphoid tumour is greater than 10%.
The present invention furthermore provides a method for detection of the presence or absence of cells that have the potential to evolve to invasive myeloid neoplasms or to invasive lymphoid tumours, although those cells are not detectable as a lesion or precursor by conventional means.
As used herein, the term “subject” refers to a mammal, preferably a human.
Said subject may be a healthy, but the method of the invention is particularly useful for testing a subject thought to develop or to be predisposed to developing a myeloid cancer (i.e., myeloid tumour) or a lymphoid tumour. In that case, the method of the invention enables to confirm that said subject develops or is predisposed for developing a myeloid cancer (i.e., a myeloid tumour) or a lymphoid tumour.
More preferably, said lymphoid tumour is selected in the group consisting of lymphoma such as T- or B-cell lymphoma, and more preferentially of T cell lymphoma.
Still more preferably, said myeloid cancer (i.e., myeloid tumour) is selected in the group consisting of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), myeloproliferative disorders (MPD) and myelodysplatic/myeloproliferative syndrome. Advantageously, said myeloid cancer is a myelodysplatic/myeloproliferative syndrome, and preferably a chronic myelomonocytic leukemia (CMML).
According to a preferred embodiment, the method of the invention is for diagnosing a myelofibrosis (MF) in a subject, wherein said subject is suffering from polycythemia vera (PV) or from thrombocythemia (ET), and wherein the detection of a TET2 mutation or TET2 under-expression is indicative of a subject developing or predisposed to develop a myelofibrosis (MF).
According to still another preferred embodiment, the subject is suffering from myelodysplastic syndrome (MDS), and the detection of a TET2 mutation or TET2 under-expression is indicative of a subject with a good prognosis.
As used herein a good prognosis corresponds to a patient suffering from MDS and having a reduced risk of developing an AML.
In fact, the inventors have established that five-year survival was significantly increased in TET2 mutated patients suffering from MDS compared to unmutated patients (p<0.05).
As used herein, the expression “biological sample” refers to solid tissues such as, for example, a lung biopsy; buccal swab, fluids and excretions such as for example, sputum, induced sputum, blood, serum, plasma, urine. Preferably, said biological sample is a bone marrow sample.
In this aspect of the invention, the method comprises the step of detecting the presence of a mutation in the TET2 gene coding for the polypeptide having the sequence SEQ ID NO:2.
As used herein, the term “mutations” correspond to any modification in the sequence of the original nucleic acid sequence. These mutations comprise small-scale mutations, or large scale mutations. Small scale mutations are those affecting a gene in one or a few nucleotides, including point mutations, insertions or deletions of one or more extra nucleotides in the DNA. Point mutations can be silent, missense and nonsense mutation. Large scale mutation in the genomic structure, such as gene duplications, deletions, or mutations whose effect is to juxtapose previously separate pieces of DNA, potentially bringing together separate genes to form functionally distinct fusion genes. These last mutations include chromosomal translocations, interstitial deletions, chromosomal inversions and loss of heterezygosity.
Preferably, only a biological sample containing cells including genomic DNA (or optionally RNA) from the subject to be tested is required.
Preferably, this detecting step is realized on each allele of the TET2 gene. In fact, the diagnosis is more reliable when the mutation is detected on each allele of the TET2 coding for the polypeptide having the sequence SEQ ID NO:2.
In a particular embodiment, the in vitro method of the invention aims to detect mutation included in the group consisting of deletions, insertions and point mutations such as mutations affecting splice sites, missense mutation and nonsense mutations, preferably missense mutation and nonsense mutations.
The inventors have established that the existence of such mutations is associated with myeloid or lymphoid cancer. Moreover, the inventors observed that the polypeptidic C-terminal domain of the TET2 protein is preferentially targeted by the deleterious mutations in the studied patients (see examples).
For deletion or insertion, said deletion or insertion preferably results in the absence of expression of the TET2 protein or in the expression of a truncated TET2 protein, which truncated TET2 protein does not comprise at least one of the two highly conserved regions shared by the other TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), or ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). More preferably, said truncated TET2 protein does not comprise the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
For example, these deletions or insertions can be selected in those disclosed in table 1.
Other example of those mutations can be selected in those disclosed in table 1a below:








TABLE 1a





Nucleotide change
Consequence







c.3087C > T
p.Gln743X


c.[2202delG(+)4663 + 1G > A]
p.Glu448fs


c.5406C > T
p.Arg1516X


c.3506C > T
p.Gln886X


c.4814 + 2T > G
—


c.5116C > G
p.Pro1419Arg


c.[3192C > T(+)3628_3629insCATA]
p.[Gln778X(+)Asn923fs]


c.5193C > T
p.Gln1445X


c.6564delT
p.Tyr1902fs


c.5523_5524insA
p.Glu1555fs


c.4815-2delA
—


c.[3747C > T] + [5331A > T]
[p.Gln963X] + [p.Lys1491X]


c.[1700_1701insT(+)3606C > T]
p.[Asn281fs(+)Gln916X]


c.6553C > T
p.Ser1898Phe


c.[1805delC(+)3602delT]
p.[Ser315fs(+)Leu914fs]


c.5100C > T
p.Gln1414X


c.[5053T > C(+)5253C > T]
p.[Leu1398Pro(+)Arg1465X]


c.2636C > T
p.Gln593X


c.1511delC
p.Ser217fs


c.[2301C > T(+)3142delC]
p.[Gln481X(+)Pro761fs]









and preferably said mutation is selected in the group consisting of: p.Glu448fs, p.Gln1445X and p.[Gln481X(+)Pro761fs].
In another more preferred aspect of the invention, the missense mutation, resulting from a mutationin the open reading frame of the TET2 gene, is preferably located in at least one of the two highly conserved regions shared by the TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), and ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
As an example, said missense mutations are selected in the group comprising or consisting of I1175V, L1197N, H1219Y, E1235V, C1271W, K1299E, L1340P, R1302G, G1370E, A1344E, N1387S, L1398P, V1417F, P1419R, H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F; preferably in the group comprising or consisting of I1175V, L1197N, H1219Y, E1235V, C1271W, K1299E, L1340P, R1302G, G1370E, A1344E, N1387S, H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F.
More preferably, said missense mutation is located in the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). Even more preferably, said missense mutations are selected in the group comprising or consisting of H1868R, G1869W, L1872P, I1873T, R1896M, and S1898F, as an example I1873T, R1896M, and S1898F.
For nonsense mutation, said nonsense mutation, preferably resulting from the introduction of a stop mutation in the open reading frame of the TET2 gene, is preferably located before at least one of the two highly conserved regions shared by the TET2 protein corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), or ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
Also, said nonsense mutation can result in the introduction of a stop mutation inside at least one of the two highly conserved regions shared by the TET2 protein corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), or ii) the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
As an example, said nonsense mutations are selected in the group comprising or consisting of Q232Stop, Q321Stop, S354Stop, Q417Stop, Q481Stop, R544Stop, R550Stop, Q557Stop, Q574Stop, Q593Stop, Q635Stop, Q642Stop, Q685Stop, L699Stop, Q743Stop, Q778Stop, S792Stop, Q886Stop, Q891Stop, Q916Stop, Q943Stop, Q963Stop, E1026Stop R1067Stop, R1216Stop, Y1225Stop, R1404Stop, Q1414Stop, Q1445Stop, L1457Stop, R1465Stop, K1491Stop, R1516Stop, Q1524Stop, Q1542Stop, N1624Stop, Y1724Stop, Y1751Stop, L1819Stop, Q1834Stop and W1847Stop; preferably in the group comprising or consisting of Q321Stop, S354Stop, Q481Stop R544Stop, Q557Stop, R1216Stop, Q1445Stop and Y1724Stop.
More preferably, said nonsense mutation, resulting from the introduction of a stop mutation in the open reading frame of the TET2 gene, is located in the TET2 protein before the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). As an example, said nonsense mutation is selected in the group comprising or consisting of Q232Stop, Q321Stop, S354Stop, Q417Stop, Q481Stop, R544Stop, R550Stop, Q557Stop, Q574Stop, Q593Stop, Q635Stop, Q642Stop, Q685Stop, L699Stop, Q743Stop, Q778Stop, S792Stop, Q886Stop, Q891Stop, Q916Stop, Q943Stop, Q963Stop, E1026Stop R1067Stop, R1216Stop, Y1225Stop, R1404Stop, Q1414Stop, Q1445Stop, L1457Stop, R1465Stop, K1491Stop, R1516Stop, Q1524Stop, Q1542Stop, N1624Stop, Y1724Stop, Y1751 Stop, L1819Stop, and Q1834Stop.
Also, said nonsense mutation, preferably resulting from the introduction of a stop mutation in the open reading frame of the TET2 gene, is preferably located in TET2 protein inside the 80 amino acid region located near the carboxyterminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4). As an example, said nonsense mutation is W1847Stop.
Typical techniques for detecting the presence of a mutation may include restriction fragment length polymorphism, hybridization techniques, DNA sequencing, exonuclease resistance, microsequencing, solid phase extension using ddNTPs, extension in solution using ddNTPs, oligonucleotide ligation assays, methods for detecting single nucleotide polymorphisms such as dynamic allele-specific hybridization, ligation chain reaction, mini-sequencing, DNA “chips”, allele-specific oligonucleotide hybridization with single or dual-labelled probes merged with PCR or with molecular beacons, and others.
Advantageously, the alteration is detected on the cDNA or DNA of the TET2 gene by either PCR and sequencing, SNP-array or CGH, all of them being well known for the skilled person.
In molecular biology and bioinformatics, a SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. The basic principles of SNP array are the same as the DNA microarray. These are the convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA capture. The three mandatory components of the SNP arrays are: i) the array that contains immobilized nucleic acid sequences or target; ii) one or more labeled Allele specific oligonucleotide (ASO) probes; and iii) a detection system that records and interprets the hybridization signal (see in Sheils, O., Finn, S, and O'Leary J. (2003) “Nucleic acid microarray: an overview.” Current Diagnostic Pathology. 9:155-158).
Comparative genomic hybridization (CGH) is a molecular cytogenetic method of screening a tumor for genetic changes. The alterations are classified as DNA gains and losses and reveal a characteristic pattern that includes mutations at chromosomal and subchromosomal levels. The method is based on the hybridization of fluorescently labeled tumor DNA (frequently fluorescein (FITC)) and normal DNA (frequently rhodamine or Texas Red) to normal human metaphase preparations. Using epifluorescence microscopy and quantitative image analysis, regional differences in the fluorescence ratio of gains/losses vs. control DNA can be detected and used for identifying abnormal regions in the genome. CGH will detect only unbalanced chromosomes changes. Structural chromosome aberrations such as balanced reciprocal translocations or inversions can usually not be detected, as they do not systematically change the copy number (Emanuel B S, Saitta S C. From microscopes to microarrays: dissecting recurrent chromosomal rearrangements. Nat Rev Genet. 2007 November; 8(11):869-83. Review).
In another preferred embodiment of the invention, the method comprises the step of analyzing the expression of the TET family member 2 gene (TET2).
According to the results obtained by the inventors, the absence of expression or the under-expression of the TET2 gene or protein or the expression of a truncated TET2 protein as disclosed previously is associated with myeloid cancer.
Methods for analyzing the expression of a gene are well known for the man skilled in the art.
In a particular embodiment of the invention, the expression of the TET2 gene is assessed by analyzing the expression of mRNA transcript or mRNA precursors, such as nascent RNA, of said gene.
Such analysis can be assessed by preparing mRNA/cDNA from cells in a biological sample from a subject, and hybridizing the mRNA/cDNA with a reference polynucleotide. The prepared mRNA/cDNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction analyses, such as quantitative PCR (TAQMAN), and probes arrays such as GENECHIPTM DNA Arrays (AFFYMETRIX).
Advantageously, the analysis of the expression level of mRNA transcribed from the TET2 gene involves the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in U.S. Pat. No. 4,683,202), ligase chain reaction (BARANY, Proc. Natl. Acad. Sci. USA, vol. 88, p: 189-193, 1991), self sustained sequence replication (GUATELLI et al., Proc. Natl. Acad. Sci. USA, vol. 87, p: 1874-1878, 1990), transcriptional amplification system (KWOH et al., 1989, Proc. Natl. Acad. Sci. USA, vol. 86, p: 1173-1177, 1989), Q-Beta Replicase (LIZARDI et al., Biol. Technology, vol. 6, p: 1197, 1988), rolling circle replication (U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. As used herein, amplification primers are defined as being a pair of nucleic acid molecules that can anneal to 5′ or 3′ regions of a gene (plus and minus strands, respectively, or vice-versa) and contain a short region in between. In general, amplification primers are from about 10 to 30 nucleotides in length and flank a region from about 50 to 200 nucleotides in length. Under appropriate conditions and with appropriate reagents, such primers permit the amplification of a nucleic acid molecule comprising the nucleotide sequence flanked by the primers.
In another particular embodiment, the expression of the TET2 gene is assessed by analyzing the expression of the TET2 protein translated from said gene.
Such analysis can be assessed using an antibody (e.g., a radio-labeled, chromophore-labeled, fluorophore-labeled, or enzyme-labeled antibody), an antibody derivative (e.g., an antibody conjugate with a substrate or with the protein or ligand of a protein of a protein/ligand pair (e.g., biotin-streptavidin)), or an antibody fragment (e.g., a single-chain antibody, an isolated antibody hypervariable domain, etc.) which binds specifically to the TET2 protein. Said analysis can be assessed by a variety of techniques well known by one of skill in the art including, but not limited to, enzyme immunoassay (EIA), radioimmunoassay (RIA), Western blot analysis and enzyme linked immunoabsorbant assay (ELISA).
Polyclonal antibodies can be prepared by immunizing a suitable animal, such as mouse, rabbit or goat, with the TET2 protein (SEQ ID NO:2) or a fragment thereof (e.g., at least 10 or 15 amino acids). The antibody titer in the immunized animal can be monitored over time by standard techniques, such as with an ELISA using immobilized polypeptide. At an appropriate time after immunization, e.g., when the specific antibody titers are highest, antibody producing cells can be obtained from the animal and used to prepare monoclonal antibodies (mAb) by standard techniques, such as the hybridoma technique originally described by KOHLER and MILSTEIN (Nature, vol. 256, p: 495-497, 1975), the human B cell hybridoma technique (KOZBOR et al., Immunol., vol. 4, p: 72, 1983), the EBV—hybridoma technique (COLE et al., In Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., p: 77-96, 1985) or trioma techniques. The technology for producing hybridomas is well known (see generally Current Protocols in Immunology, COLIGAN et al. ed., John Wiley & Sons, New York, 1994). Hybridoma cells producing the desired monoclonal antibody are detected by screening the hybridoma culture supernatants for antibodies that bind the polypeptide of interest, e.g., using a standard ELISA.
As previously mentioned, mutations in the TET2 gene may trigger the absence of expression or the under-expression of the TET2 protein.
As used herein, the “under-expression” of a polypeptide occurs when the transcription and/or the translation of the gene is affected by the mutation, leading to an expression level in a biological sample that is lower than the standard error of the assay employed to assess expression, and is preferably at least 20% inferior to the normal level of expression of said gene, preferably at least 50% inferior to the normal level of expression of said gene, and most preferably at least 100% inferior to the normal level of expression of said gene.
Therefore, the method of the invention may comprise comparing the level of expression of the TET2 gene in a biological sample from a subject with its expression level in a control (i.e., normal expression level). A significantly lower level of expression of said gene in the biological sample of a subject as compared to the normal expression level is an indication that the patient may develop a myeloid neoplasm.
As used herein, a “control” corresponds preferably to a control sample comprising non-tumoral cells. Preferably, said control corresponds to peripheral blood leukocytes (PBL), and most preferably to a peripheral blood leukocyte immortalized with Epstein Barr Virus.
Thus, the “normal” level of expression of the TET2 gene is the level of expression of said gene in a biological sample of non-tumoral cell. Preferably, said normal level of expression is assessed in a control sample and preferably, the average expression level of said gene in several control samples.
Analyzing the normal expression of the TET2 gene may be assessed by any of a wide variety of well-known methods for detecting expression of a transcribed nucleic acid or translated protein as previously described.
In a preferred embodiment of the invention, said mutation in the TET2 gene induces absence of expression or under-expression of the two highly conserved regions shared by the TET proteins and corresponding to i) the 310 amino acid region located near the center of the protein TET2 (amino acids 1134 to amino acid 1444, SEQ ID NO:3), and ii) the 80 amino acid region located near the carboxy-terminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4), and more preferably of the 80 amino acid region located near the carboxy-terminal end of the protein TET2 (corresponding to amino acid 1843 until amino acid 1922, SEQ ID NO:4).
In a second aspect, the present invention refers to a kit for diagnosing myeloid cancer or lymphoid cancer in a subject comprising at least one nucleic acid probe or oligonucleotide or at least one antibody, which can be used in a method as defined in the present in invention, for detecting the presence of a mutation in the TET2 gene and/or analysing the expression of the TET2 gene.
Preferably, the oligonucleotide is at least one PCR primer, preferably a set of PCR primers is provided, which allows to amplify the TET2 gene or a fragment thereof. The skilled person readily provides such an oligonucleotide or set of PCR primers which allows to amplify a region of the TET2 gene, provided that the nucleic acid sequence of TET2 is well known (Accession number NM_001127208, SEQ ID NO:39) (Current Protocols in Molecular Biology; edited by Fred M. Ausubel et al., supra).
In a preferred embodiment, the kit comprises at least one PCR primer selected in the group comprising SEQ ID NO:5 to SEQ ID NO: 38 (see examples and sequence listing) for detecting the presence of a mutation in the TET2 gene and/or analysing the expression of said gene.
As used herein, the term “kit” refers to any delivery system for delivering materials. In the context of reaction assays, such delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., oligonucleotides, enzymes, etc. in the appropriate containers) and/or supporting materials (e.g., buffers, written instructions for performing the assay etc.) from one location to another. For example, kits include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and/or supporting materials. As used herein, the term “fragmented kit” refers to delivery systems comprising two or more separate containers that each contains a subportion of the total kit components. The containers may be delivered to the intended recipient together or separately. For example, a first container may contain an enzyme for use in an assay, while a second container contains oligonucleotides. The term “fragmented kit” is intended to encompass kits containing Analyte specific reagents (ASR's) regulated under section 520(e) of the Federal Food, Drug, and Cosmetic Act, but are not limited thereto. Indeed, any delivery system comprising two or more separate containers that each contains a subportion of the total kit components are included in the term “fragmented kit.” In contrast, a “combined kit” refers to a delivery system containing all of the components of a reaction assay in a single container (e.g., in a single box housing each of the desired components). The term “kit” includes both fragmented and combined kits.
The present kits can also include one or more reagents, buffers, hybridization media, nucleic acids, primers, nucleotides, probes, molecular weight markers, enzymes, solid supports, databases, computer programs for calculating dispensation orders and/or disposable lab equipment, such as multi-well plates, in order to readily facilitate implementation of the present methods. Enzymes that can be included in the present kits include nucleotide polymerases and the like. Solid supports can include beads and the like whereas molecular weight markers can include conjugatable markers, for example biotin and streptavidin or the like.
In one embodiment, the kit is made up of instructions for carrying out the method described herein for diagnosing a myeloid cancer or a lymphoid cancer in a subject. The instructions can be provided in any intelligible form through a tangible medium, such as printed on paper, computer readable media, or the like.
Still a further aspect of the present invention refers to the use, for diagnosing myeloid or lymphoid cancer, of the abovementioned kit comprising at least one nucleic acid probe or oligonucleotide or at least one antibody, which can be used in a method as defined for detecting the presence of a mutation in the TET2 gene and/or analysing the expression of the TET2 gene.
Advantageously, myeloid cancer is selected in the group consisting of myelodysplastic syndrome, acute myeloid leukemia, myeloproliferative disease and myelodysplatic/myeloproliferative syndrome.
Still advantageously, said lymphoid cancer is selected in the group consisting of lymphoma such as T- or B-cell lymphoma, and more preferentially of T-cell lymphoma.
In still another aspect, the invention relates to the use of a hypomethylating agent for treating a patient suffering from a myeloid or a lymphoid tumour, for which tumour, a TET2 mutation, an absence of TET2 expression or an expression of a truncated TET2 has been detected.
Preferably, said myeloid tumour is not a MDS.
Hypomethylating agent are well known from the skilled person and include, as an example, azacytidine.
In a final aspect, the invention relates to a method for treating a subject suffering a myeloid or a lymphoid tumour, for which tumour, a TET2 mutation, an absence of TET2 expression or an expression of a truncated TET2 has been detected, said method comprising the step of administrating to said subject a therapeutically efficient amount of hypomethylating agent.
Preferably, said myeloid tumour is not a MDS.
Preferably said hypomethylating agent is azacytidine.
A therapeutically efficient amount of hypomethylating agent can be simply determined by the skilled person. As an example of therapeutically efficient amount of azacytidine for treating lymphoid or myeloid tumour, one can cite the regimen which is disclosed in FENAUX et al. (Blood, vol. 110, 817, 2007) which is incorporated herein by reference.
In the following, the invention is described in more detail with reference to amino acid sequences, nucleic acid sequences and the examples. Yet, no limitation of the invention is intended by the details of the examples. Rather, the invention pertains to any embodiment which comprises details which are not explicitly mentioned in the examples herein, but which the skilled person finds without undue effort.
Examples
1. Identification of Tet2 Gene Mutation in MDS, MPD and in AML
We identified 6 patients suffering from myeloid cancer (AML (nAML1, nAML2, nAML3) or MDS (MDS01, MDS02, and MDS03)) and harboring an acquired chromosomal translocation associated with a genomic deletion in the vicinity of the chromosome 4 breakpoint at 4q24. These deletions were homozygous in one instance and heterozygous in the other cases and could indicate the location of a tumor suppressor gene in that region.
FISH analyses first permit to narrow the commonly deleted region in these patients to a  ̃500 kb interval (data not shown). Computer and RT-PCR assisted analyses uncovered the structure of a single gene, Ten Eleven Translocation (TET2) lying in this region (FIG. 1).
TET2 gene comprises 11 exons spread over 150 Kb. The predicted TET2 protein, encoded by exons 3 to 11, belongs to a three-member family (TET family) in human and mouse. Proteins of the TET family share two highly conserved regions with a single orthologous Drosophila protein in their central and carboxy-terminal part (FIG. 1).
The FIG. 1 shows the protein sequence of TET2 (SEQ ID NO:2), highlighting the conserved regions between species (bold).
For TET2, a translational initiation codon situated at the 5′ end of exon 3 (Nucleotides 862-864 of the cDNA or 27-29 of Exon 3) was predicted to allow for the synthesis of a 2002 amino acids protein (FIG. 1). An alternative ATG situated in exon 2 (nucleotides 798-800 of the cDNA or 111-113 of Exon 2) will direct the synthesis of 21 more amino acids. Additional starts are not excluded.
TET2 transcript is widely expressed (ONO et al., abovementioned, 2002; LORSBACH et al., abovementioned, 2003), and as suggested by available data, the expression of TET2 was confirmed in human bone marrow and blood tissues by RT-PCR (data not shown). More specifically, TET2 transcripts were detected in umbilical cord blood CD34+ cells, in granulocytes from healthy controls, and in hematopoietic cell lines.
Finally, of these six patients, five harbored a deletion on one chromosome 4 whereas both copies were deleted in MDS01.
The involvement of the same 4q24 region was also found by using a different approach in MPD. Analysis of CD34+CD38− multipotent progenitors, CD34+CD38+ committed progenitors, and mature cells, led us to identify two subsets of JAK2 V617F MPD at diagnosis with distinct kinetics of hematopoietic expansion (DUPONT et al., Blood, vol. 110(3), p: 1013-21, 2007). The first subset is characterized by a late expansion of the malignant clone; i.e. downstream of the committed progenitor. In contrast, the second subset of patients had an early expansion of the clone, upstream of the committed progenitor. We hypothesized that the second subset of patients had a molecular defect able to promote the early expansion of the malignant clone. Five patients from this second subset (MPD01 to MPD05) were analyzed using high-resolution CGH and SNP arrays to compare presumed clonal cells (granulocytes) versus polyclonal cells (peripheral blood mononuclear cells or lymphocytes) DNA. One primary myelofibrosis (PMF) patient (MPD01) and one polycythemia vera (PV) patient (MPD04) exhibited a large acquired loss-of-heterozygosity (LOH) without copy number modification (uniparental disomy; UPD (20)) ranging from q22 to qter of chromosome 4. The third patient (MPD05) demonstrated an acquired deletion located in the 4q24 region. This 325 kb deletion in MPD05 was included in the 4q24 LOH region of patients MPD01 and MPD04 and contained TET2 as a single candidate gene. This region was normal in the two other studied MPD samples (MPD02 and MPD03).
As the 4q24 region is affected in patients suffering from myeloid neoplasms, and as TET2 localized in this region, the integrity of the TET2 gene might be affected in these patients. Moreover, loss of the two copies of TET2 in patient MDS01 and recurrent loss of one copy in 8 other patients with MDS, MPD or AML designated TET2 as a candidate tumor suppressor gene.
PCR on the TET2 gene was thus performed in order to detect alterations of the TET2 gene in these patients. Importantly, both alleles were analysed in order to detect bi-allelic modifications.
2. Experimental Procedure to Detect Alterations of the Tet2 Gene
2.1. Primers Used for the Identification of TET2 Mutations or Deletions (Table 2)











TABLE 2





SEQ ID


Amplified
Length of


NO
Tm (° C.)
Sequences
region
amplicon



















5
60.9
TGAACTTCCCACATTAGCTGGT
106374235-
955


6
60.7
GAAACTGTAGCACCATTAGGCATT
106375189



 


7
62.0
CAAAAGGCTAATGGAGAAAGACGTA
106374894-
836


8
62.0
GCAGAAAAGGAATCCTTAGTGAACA
106375729



 


9
63.0
GCCAGTAAACTAGCTGCAATGCTAA
106375458-
843


10
62.3
TGCCTCATTACGTTTTAGATGGG
106376300



 


11
60.0
GACCAATGTCAGAACACCTCAA
106376065-
867


12
60.9
TTGATTTTGAATACTGATTTTCACCA
106376931



 


13
60.5
TTGCAACATAAGCCTCATAAACAG
106376703-
788


14
60.9
ATTGGCCTGTGCATCTGACTAT
106377490



 


15
62.1
GCAACTTGCTCAGCAAAGGTACT
106377284-
781


16
62.3
TGCTGCCAGACTCAAGATTTAAAA
106378064



 


17
60.1
ATACTACATATAATACATTCTAATTCCCTCACTG
106381631-
495


18
61.5
TGTTTACTGCTTTGTGTGTGAAGG
106382125



 


19
61.7
CATTTCTCAGGATGTGGTCATAGAAT
106383324-
286


20
61.5
CCCAATTCTCAGGGTCAGATTTA
106383609



 


21
60.1
AGACTTATGTATCTTTCATCTAGCTCTGG
106383864-
599


22
60.1
ACTCTCTTCCTTTCAACCAAAGATT
106384462



 


23
60.0
ATGCCACAGCTTAATACAGAGTTAGAT
106400093-
362


24
60.9
TGTCATATTGTTCACTTCATCTAAGCTAAT
106400454



 


25
61.1
GATGCTTTATTTAGTAATAAAGGCACCA
106402226-
354


26
61.5
TTCAACAATTAAGAGGAAAAGTTAGAATAATATTT
106402579



 


27
61.7
TGTCATTCCATTTTGTTTCTGGATA
106410076-
361


28
60.5
AAATTACCCAGTCTTGCATATGTCTT
106410436



 


29
63.0
CTGGATCAACTAGGCCACCAAC
106413052-
774


30
63.0
CCAAAATTAACAATGTTCATTTTACAATAAGAG
106413825



 


31
61.1
GCTCTTATCTTTGCTTAATGGGTGT
106415516-
748


32
60.5
TGTACATTTGGTCTAATGGTACAACTG
106416263



 


33
60.5
AATGGAAACCTATCAGTGGACAAC
106416016-
1107


34
60.2
TATATATCTGTTGTAAGGCCCTGTGA
106417122



 


35
62.0
CAGAGCTTTCTGGATCCTGACAT
106416670-
535


36
60.3
GCCCACGTCATGAGAACTATACTAC
106417204



 


37
66
TCTAAGCTCAGTCTACCACCCATCCATA
106416118-
570


38
66.7
TGCTCGCTGTCTGACCAGACCTCAT
106416671









2.2. PCR
PCR were performed in 20 μL starting from 25-50 ng of DNA on APPLIED BIOSYSTEM PCR 9700.
For each sample: 17 PCR were used to detect the mutations/deletions localized on the TET2 gene. The mix was prepared as below:












mix *1


















10X
2



dNTP 25 mM
0.15



O1 100 pmol/μl
0.1



O2 100 pmol/μl
0.1



hot star (5 U/μl)
0.2



Water
15.5-16.5



DNA sample (25 ng/μl)
1-2









We use the following PCR cycles conditions:















15′
94° C.
1 cycle 


20 s
94° C.
2 cycles


20 s
56° C.



30 s
72° C.



20 s
94° C.
2 cycles


20 s
54° C.



30 s
72° C.



20 s
94° C.
2 cycles


20 s
52° C.



30 s
72° C.



20 s
94° C.
37 cycles 


20 s
50° C.



30 s
72° C.



10′
72° C.
1 cycle 









2.3. Sequencing of the PCR Products
Finally, the PCR products sequencing was realized by EUROFINS MWG Biotech (France, 9, rue de la Laponie, 91967 Les Ulis cedex) or by “Département des services commun de l'Institut Cochin” (Plate forme transcriptomique, Hôpital Cochin/Bat G. Roussy/3ème étage, 27 rue du Fg St Jacques, 75014 Paris) with the kit Big Dye terminator V1.1 and 3130 XL sequencing machines (both from APPLIED BIOSYSTEMS).
3. Mutations of the Tet2 Gene in Patients Suffering from MDS or AML with Heterozygous 4q24 Deletion
3.1. In Tumoral Cells
TET2 gene integrity was checked on the 4q24 “intact” copy of the 8 above-mentioned patients harboring the heterozygous acquired chromosomal translocation associated with a genomic deletion in the vicinity of the chromosome 4 breakpoint at 4q24.
To identify potential mutations of the TET2 gene in these alleles, the sequence of the eight coding exons and of their splice sites in the DNA extracted from bone marrow samples of 8 patients having a 4q24 rearrangement was investigated by PCR as described previously.
Table 3 discloses the status of both alleles of the TET2 genes in patients suffering from MPD, MDS or AML and having a 4q24 deletion on one allele:







TABLE 3







discloses the status of both alleles of the TET2


genes in patients suffering from MPD, MDS


or AML and having a 4q24 deletion on one allele:












Patient
Copy 1
Copy2
Disease







nAML1
R1896M
Deletion
AML



nAML2
I1873T
Deletion
AML



nAML3
Deletion
Unknown
AML



MDS01
Deletion
Deletion
RA



MDS02
FS after L560 (Exon 3)
Deletion
RA



MDS03
N1624Stop (Exon 11)
Deletion
RA



MPD01
Q557Stop
Q557Stop
PMF



MPD04
Deletion
Deletion
PV




(1237 to 1239)
(1237 to 1239)




MPD05
Deletion
Wild type
PV










Comparison of the sequence obtained from the patients with the wild type counterpart identified nucleotide changes in 6 patients (Table 3). Changes were not attributable to identified polymorphisms. Patient nAML1 and nAML2 harbored single nucleotide changes, leading to an I1873T in patient nAML2 and to R1896M in patient nAML1. Patient MDS03 exhibited a CAG to TAG changes, introducing a stop codon instead of N1624. Patient MPD01 exhibited a single nucleotide change, introducing a stop codon instead of NQ557. Patient MDS02 had a 4 base pair insertion, leading to a stop codon 6 amino acids after L560. Patient MPD04 had an in frame 9-nucleotide deletion. No notable nucleotide changes were observed in DNA of patient nAML3. Patient MDS01 harbors a bi-allelic deletion of the TET2 gene.
3.2. In Non-Tumoral Cells of the Patients
To confirm that the observed changes were somatically acquired, we analyzed DNA from non-tumoral samples when available.
In patient nAML2, the T to C change was not observed in DNA from EBV-transformed B cell population (FIG. 2). In patient nAML1, the analyses of a sample obtained after auto-bone marrow transplantation demonstrated an inversed ratio between the wild type G and the mutated T, when compared to the diagnosis sample (data not shown). Similarly, the signal corresponding to the mutated T is almost absent in DNA extracted from stimulated PBL from patient MDS03 (FIG. 2). This analysis has also shown the absence of mutation for MPD04 or of deletion for MPD05 in non-tumoral cells (data not shown). This analysis has further shown that a small amount of residual wild-type sequence is detected in peripheral mononuclear cells from patient MPD01 (data not shown).
The FIG. 2 shows the sequence traces obtained by sequencing of PCR on samples obtained from the two patients nAML2 and MDS03, and showing that the mutation only occurs in the tumoral (R: reverse primer and F: forward primer) and in non-tumoral samples (NT or PBL).
Taken together, these results demonstrate that the two copies of the TET2 gene is targeted in patients suffering from diverse myeloid neoplasm, and this through two different events, a chromosomal translocation associated with a deletion and point mutations, establishing TET2 as a tumor suppressor gene.
4. Alteration of the Tet2 Gene in Patients Suffering from MDS or AML without Cytogentically Detectable 4q24 Deletion
To establish whether mutation of TET2 could also occurs independently of a chromosomal abnormality, DNA from bone marrow samples of 309 additional patients with different subtypes of MDS (n=81), sAML (n=21), CMML (n=9), JAK2V617F positive MPD (n=181), and JAK2V617F negative MPD (n=17) without known 4q24 abnormality was analyzed by PCR as previously described.
Table 4 discloses the status of the identified TET2 defect in patients suffering from MDS or AML:







TABLE 4







discloses the status of the identified TET2 defect 


in patients suffering from MDS or AML:











Patient
TET2 defect
Disease







sAML2
S1898F
sAMLII



sAML4
FS (Exon3)
sAMLII



sAML5
FS (Exon11)
sAMLII



sAML6
FS (Exon11)/Q891stop
sAMLII



sAML7
Q943Stop
sAMLII



MDS04
K1299E/R544Stop
RA



MDS07
No amplification Ex11
RA



MDS30
FS (Exon3)
RA



MDS09
FS (Exon3)
RARS



MDS35
Y1225Stop Exon6
RARS



MDS10
Y1724Stop/Q321Stop
RCMD-RS



MDS28
FS (Exon3)
RCMD-RS



MDS18
FS (Exon11)
RAEB1



MDS27
FS (Exon3)/FS (Exon3)
RAEB1



MDS33
FS (Exon4)
RAEB1



MDS39
L1872P
RAEB1



MDS40
FS (Exon11)
RAEB1



MDS42
L1872P/I1873T
RAEB1




Mutation of splice





acceptor




MDS34
Site Exon5
RAEB2



MDS41
FS (Exon11)
RAEB2



CMML01
Q685Stop
CMML



CMML02
FS (Exon3)/R1067Stop
CMML







RA, refractory anemia;



RARS, refractory anemia with ringed sideroblasts;



RARS-T, RARS with thrombocytosis;



RAEB, refractory anemia with excess blasts;



RAEB1: blasts 5-9%;



RAEB2: blasts 10-19%;



AML, acute myeloid leukemia;



FAB, French American British classification;



del, deletion;



FS, frame shift;



ND, not done.



All MDS/AML tested (22/27) were negative for JAK2V617F.



MDS03 was studied at the RAEB1 and RAEB2 phases.



Two successive samples of patient MDS34 were analyzed.



Selected patients analyzed during the initial part of the study appear in bold.













TABLE 5







discloses the status of the identified TET2 defect 


in patients suffering from MPD:













JACK2 and


Patient
TET2 defect
Disease
MPL status





MPD18
R1216stop
PV
JAK2V617F


MPD20
FS Ex11
PV
JAK2V617F


MPD35
S354stop
ET
JAK2V617F


MPD43
FS Ex3/R550stop
post ET MF
JAK2V617F


MPD45
FS Ex3
PV
JAK2V617F


MPD69
FS Ex7/FS Ex11
PV
JAK2V617F


MPD74
FS Ex3
PMF
WT


MPD81
FS Ex6
ET
JAK2V617F


MPD86
FS Ex5/R1404stop
PV
JAK2V617F


MPD89
FS Ex10
PV
JAK2V617F


MPD92
R1302G
PMF
JAK2V617F


MPD96
W1847stop
ET
JAK2V617F


MPD99
FS Ex3
ET
JAK2V617F


MPD120
FS Ex3
PV
JAK2V617F


MPD130
FS Ex3
ET
JAK2V617F


MPD132
FS Ex3
PV
JAK2V617F


MPD133
G1869W
ET
JAK2V617F


MPD142
FS Ex3
PV
JAK2V617F


MPD149
FS Ex6
ET
JAK2V617F


MPD158
FS Ex3
PV
JAK2V617F


MPD163
Q1542stop
ET
MPLW515L


MPD164
FS Ex3
PMF
JAK2V617F


MPD183
FS Ex7/Q635stop
PV
JAK2V617F


MPD200
FS Ex3/FS Ex11
ET
WT





PMF, primary myelofibrosis,


PV, polycythemia vera,


ET, essential thrombocythemia.


WT: negative for JAK2V617F and MPL515 mutations.


FS, frame shift.






Table 5 discloses the status of the identified TET2 defect in patients suffering from MPD:
Obvious abnormalities of TET2 coding sequence were observed in 45 patients, resulting in conserved amino acid substitution, generation of in frame stop codons, or frame shifts (Tables 4 and 5). In one additional patient (MDS07), amplification of the 5′ part of exon 11 only resulted in trace amounts of PCR fragment despite the use of several conditions and primers pairs (data not shown), which was attributed to an uncharacterized structural genomic rearrangement affecting this region. Defects of TET2 were observed in all types of MDS (22/111) and BCR-ABL negative MPDs associated with JAK2 V617F (21/181), or MPL W515L/K (1/6) or devoid of these mutations (2/11).
The results demonstrate that TET2 defects can be identified in unselected diverse myeloid disorders with a high prevalence (46/309=17%). As an example, patient MDS04 showed two changes leading to K1299D and R544Stop. Patient MDS10 had two stop mutations, Y1724Stop and Q321Stop. Patient sAML2 had a point mutation leading to S1898F. These observed mutations may result in a partial or total loss of function of the TET2 protein. It can be anticipated that other defects such as deletions of the TET2 gene might have been missed and thus the estimated the frequency of TET2 defects in these malignancies would be underestimated.
Overall, in 19/55 of the patients with TET2 defects, two different mutations were detected, likely targeting both copies of TET2. This point was confirmed by sequencing individual molecules after subcloning of the PCR fragments obtained from patient MDS42. A single defect was observed in 35/55 samples suggesting that TET2 haploinsufficiency may play a role in these malignancies.
5. Tet2 Mutations Target Early Progenitors in MDS
MDS are myeloid malignancies originating from a HSC. If the mutations observed in TET2 are causative, they should also be observed in the HSC. To investigate this, we first analyzed the presence of the TET2 defects in CD34+ cells, which include HSC and hematopoietic progenitors, from 4 MDS patients (MDS03, MDS09, MDS28, MDS35).
The FIG. 3a shows the sequencing histograms of sorted CD34+ cells from patient MDS03 at RAEB1 and RAEB2 phases. Sequences observed in unsorted bone marrow sample and of wild-type control are shown for comparison purposes. Asterisks indicate the mutated nucleotide.
The FIG. 3b shows the PCR-RFLP analysis of DNA isolated from sorted MDS03 CD34+CD38− and CD34+CD38+ cells at RAEB1 phase. Amplified fragments were digested using Tas1 and size-fractionated by agarose migration. The proportion of mutated TET2 mutated was evaluated by measuring the intensities of the mutated (mut) or wild-type (wt) signals relative to that of the signal generated by both alleles (wt+mut). Undigested (−) and digested (+). (ctl) correspond to PCR products from control DNA. MW: molecular weight.
The FIG. 3c shows the PCR-RFLP analysis of TET2 directly performed from sorted CD34+CD38− and CD34+CD38+ cells from MDS09 patient using BseLI endonuclease.
The FIG. 3d shows the genotyping by PCR-RFLP using BseLI of sorted CD34+CD38− and CD34+CD38+ cells from patient MDS09 grown at one cell per well. Annotations are as in b. The histograms represent the fraction of clones with wild-type (gray) or mutated (black) TET2. Note the absence of wild-type fragment in CD34+CD38+ clones indicated by asterisks.
In all cases, the mutated TET2 sequence could be detected (FIG. 3). In one of these patients (MDS03), CD34+ cells could be analyzed at refractory anemia with excess of blasts 1 (RAEB1) and RAEB2 phases. Interestingly, the wild-type sequence was detected at the RAEB1 phase, but not at the RAEB2 phase (FIG. 3a), suggesting expansion of TET2 mutated progenitors with the disease progression.
We next fractionated the CD34+ from these four patients into CD34+CD38− (corresponding to HSC and multipotent progenitors) and CD34+CD38+ (corresponding to more mature progenitors) cell populations using CD34-PeCy5 and CD38-FITC antibodies (IMMUNOTECH) using a FACSDiva cell sorter (BECTON DICKINSON). In two patients (MDS03 and MDS09), PCR-RFLP analysis was used to distinguish mutated and wild-type TET2 sequences. The mutated TET2 burden increased in both patients from CD34+CD38− to CD34+CD38+ cells (16% to 54% in MDS03, and 26% to 48% in MDS09) (FIG. 3b, c). Further analysis was performed at the cellular level, by seeding single hematopoietic progenitors from MDS09.
Sorted CD34+CD38− cells from MDS09 bone marrow were seeded at one cell per well on a confluent layer of the MS5 cell line in MEM alpha medium supplemented with 10% FBS (STEM CELL TECHNOLOGIES), and a cocktail of early cytokines (thrombopoietin (Tpo) interleukin-3 (IL3), FLT3-L, Stem Cell factor (SCF) and interleukin-6 (IL6)). CD34+CD38+ cells were also seeded at one cell per well using the same combination of “late” cytokines (SCF, IL3, erythropoietin (Epo) and granulocyte-colony stimulating factor (G-CSF)) as used in methylcellulose cultures (DUPONT et al., abovementioned, 2007). After three weeks (CD34+CD38−) or 10 days (CD34+CD38+), individual clones were collected for further genotyping.
The results show that TET2 mutation was identified in 8 out of 32 (25%) and 18 out of 30 (60%) clones derived from CD34+CD38− and CD34+CD38+ cells, respectively (FIG. 3d). Interestingly, the wild-type copy of TET2 was not always amplified from clones bearing a mutated TET2, suggesting its loss in a minority of the cells.
For the two other patients (MDS28, MDS35), the increase in TET2 mutation burden from CD34+CD38− to CD34+CD38+ samples was evaluated with the sequence graphs. To be more accurate, the amplified fragments from MDS28 samples were subcloned and individual bacterial clones were sequenced. The mutated copy was barely detectable in the CD34+CD38+ population of MDS28 whereas it represented 32% of TET2 sequences in the CD34+CD38− population (data not shown). These data indicate that TET2 mutations target a CD34+CD38− cell and that in MDS TET2 mutated burden increases from immature to mature progenitors, suggesting a selective advantage of the mutated cells during early phases of hematopoietic differentiation.
In three sAML samples (sAML2, sAML4, sAML5), TET2 mutations were also found in CD34+ cells (data not shown). When analyzed, in sAML4, sAML5 sorted cells, no marked changes in the mutated TET2 burden were observed between CD34+ C38− and CD34+CD38+ populations.
6. Prevalence and Prognosis Impact of Tet2 Mutations in MDS
So as to establish the prevalence and prognosis impact of TET2 mutations in MDS, we retrospectively analyzed TET 2 mutations and their prognosis value, in 204 MDS and AML post MDS enrolled in GFM multicenter trials (41 RA/RCMD/MDS-U/5q-, 18 RCMD, 28 RARS/RCMD-RS/RARS-T, 43 RAEB 1, 32 RAEB 2, 44 AML post MDS). TET2 mutations analysis was realized as described previously and the results are presented in table 6.







TABLE 6







discloses the status of the identified TET2 defect 


in patients suffering from MDS or AML:









Disease
Nucleotide change
Consequence





MDS02 G04
delA 3166
p.Gln769 FS


MDS 04
c.4755A > G +
p.[Lys1299Glu] +



c.2490C > T
[Arg544X]


MDS01 A08
insT 3465
p.Pro869 FS


MDS01 A11
c.5071 C > T
p.Arg1404 STOP


MDS02 C01
delT 2685 + insA 3009
p.Ser609 FS +




p.His717 FS


MDS01 B03
insA 5540
p.Tyr1560 FS


MDS01 B11
c.2913C > T
p.Gln685 STOP


sAML1

del/wt


MDS 07

No amplification of 5′




Exon 11


MDS01 C08
delC 6360
p.Gln1834 FS


MDS01 C09
c.3532C > T + insA 5757
p.Cys1633 FS +




p.Gln891 STOP


MDS01 D01
c.6475T > C
p.Leu1872Pro


MDS02 H02
c.4384A > G +
p.Ile1175Val +



c.4625C > G
p.Tyr1255 STOP


sAML2

Ser1898Phe


MDS01 D06
del 2834_2835
p.His658 FS


MDS 10

p.Gln530 FS +




p.Tyr1724 STOP


MDS02 C12
delT 2685 + c.6316T > G
p.Ser609 FS +




p.Leu1819 STOP


MDS02 D01
delC 3009
p.His717 FS


MDS 01

del/del


MDS 02

del/p.Arg581 FS


MDS01 E02
c.5730C > T
del/Gln1624 STOP


MDS02 D04
delT 2944
p.Leu699 STOP


MDS01 E06
insC 3151 + p.5406C > T
p.Gln764 FS +




Arg1516 STOP


MDS01 E07
c.6475T > C +
p.Leu1872Pro +



c.6478T > C
p.Ile1873Thr


MDS01 E08
delC 2448 + delA 4130
p.Gln530 FS +




p.Lys1090 FS


MDS01 F02
p.6360C > T
p.Gln1834 STOP


MDS01 F04
delG 2994
p.Glu711 FS


MDS02 E01
c.6114T > G + insT
p.Tyr1751 STOP +



splice site
mutation of splice




site exon 8


MDS01 F06
p.3688C > T +
p.Gln943 STOP +



delA 6507
p.Thr1883 FS


MDS01 G01
delG 4271 +
p.Glu1137 FS +



c.6478T > C
p.Ile1873Thr


MDS01 G03
p.3688C > T
p.Gln943 STOP


nAML2
c.6478T > C
del/p.Ile1873Thr


MDS01 G05
delC 5222
p.Leu1457 STOP


MDS02 F11
dupT 3914
p.Glu1026 STOP


MDS01 G06
delA 2935 +
p.Glu692 FS +



del5828_5843
p.Met1656 FS


MDS02 A12
p.4969G > A +
p.Gly 1370 Glu +



del6396_6531
p.Val1846 FS


MDS01 G7/8
g.4366-1G > T
mutation of splice




acceptor site exon5


MDS02 E10
insCT 3581
pGly 908 FS


MDS02 H12
delG 4932 +
p.Glu1357 FS +



del5521_5524
pThr1554 FS


MDS02 G03
insC 3151 +
p.Gln764 FS +



insC 6507
p.Thr1883 FS


MDS02 G01
delG 5133 +
p.Asp 1425 FS +



del6511_6512
p.Pro1885FS


MDS02 G07
p.5253C > T
p.Arg1465 STOP


MDS02 C07
c.4561A > T
p.Glu1234Val


MDS02 B07
c.2109C > T
p.Gln417 STOP


nAML1
c.6547G > T
del/p.Arg1896Met


MDS02 E11
c.2784C > T +
p.Gln642 STOP +



p.5253C > T
p.Arg1465 STOP


MDS01 H05
c.4515C > T
p.His1219 Tyr


MDS02 H06
del1264_1666
p.Glu135 FS


MDS02 B08
delA4327 +
p.Asn1156 FS +



c.5020A > G
Asn 1387Ser


MDS02 D10
insC 3151 +
p.Gln764 FS +



c.4891C > A
p.Ala1344 Glu


MDS02 B02
delT 5570 + insC
p.Leu1637 FS + mutation



splice site
of splice site exon 8


MDS01 F01
insT3995 +
p.Glu846 FS +



c.4059A > T
p.Arg1067 STOP


MDS02 B11
c.4673C > G +
p.Cys1271 Trp +



Del6049_6050
p.Asp1830 FS


MDS01 E09
insG 5119
p.Leu 1420 FS


MDS
c.5430C > T
p.Gln1524STOP


MDS
c.5177dupA
p.Arg1440FS


MDS
c.5583_5605 del
p.Pro1575FS


MDS
c.5310A > G
p.Lys1197Arg


MDS
c.2375C > A
p.Ser792STOP









We found 59 mutations of the TET2 gene by direct sequencing of exons 3 to 11 (27 frameshifts, 21 nonsense and 11 missense mutations in conserved domains) in 43/204 pts (Table 6). The frequencies according to the WHO subtypes were 21.8% in RA, 5.2% in RCMD, 21.4% in RARS/RARS-T/RCMD-RS, 34.9% in RAEB 1, 15.6% in RAEB 2, 19% in AML post MDS. Other anomalies of the 4q24 region were found including a deletion in 1/46 pts analyzed by CGH and 3 LOH in 3/22 patients analyzed by SNP arrays and 2 deletions in 5/23 pts analyzed SNP arrays. Thus, the overall prevalence of 4q24 anomalies was 21.6% patients (44/204). 20 patients had two anomalies of TET2 identified by direct sequencing (17 patients), or sequencing plus SNP array (3 patients), indicating that the two copies of the gene were targeted in 43.5% of mutated patients.
Then, univariate and multivariate survival analyses were conducted with Cox hazard proportional model so as to establish the prognosis impact of TET2 mutations. Comparison between the 43 patients with TET2 coding sequence mutations and unmutated patients found no significant differences in initial characteristics for sex, age, previous exposure to chemo or radiotherapy, Hb level, WBC count, ANC, plt count, % bone marrow blasts, multilineage dysplasia, WHO and FAB subtypes, karyotype and IPSS.
The analysis revealed that five-year survival (Kaplan-Meier curve) was significantly increased in TET2 mutated patients compared to unmutated patients (p<0.05).
7. Rearrangement of the Tet2 Gene in Patients Suffering from MPD with 4q24 Abnormality Detected by SNP or CGH Arrays Analyses
Among 35 MPD samples, 4 patients had a LOH by SNP arrays and were analyzed for mutations within TET2 gene on both alleles. In 3 of the 4 samples a clear mutation or deletion was observed.
Table 7 discloses the status of both alleles of the TET2 genes in patients suffering from MPD:







TABLE 7







discloses the status of both alleles of the TET2 


genes in patients suffering from MPD:












Patient
Copy 1
Copy2
Disease







IGR-1
Q557Stop
LOH
PMF



IGR-2
Deletion 1237-1239
LOH
PV



IGR-3
whole gene deletion
No abnormality
PV



IGR-4
unknown
LOH
ET







In table 7, “PMF” stands for Primitive Myelofibrosis, “PV” for polycythemia Vera, “EV” for Essential Thrombocytosis. All these diseases are Class II MPDs.






Patient IGR-2 harbored a 9 base pair in frame deletion lead to the loss of three amino acids, P1237, L1238, S1239. As shown by SNP analyses and by the analyses of the sequence traces, patients IGR-1 and IGR-2 had lost the other TET2 copy. None of the mutations were observed in non-tumoral cells of the patients. These data establish that inactivation TET2 participates to the development of MPD.
Systematic sequencing of TET2 genes in 17 other patients revealed two patients with a stop codon on one allele (IGR17: S354Stop, IGR-18:R1216Stop) and one patient with one nucleotide deletion leading to a frameshift in exon 11.
8. Analysis of the Acquisition of the Tet2 Rearrangement
Recent evidence indicate that JAK2V617F may not be the initiating event in some MPDs. Therefore we used MPD samples to evaluate the relative roles of TET2 defects and JAK2V617F mutation in these diseases and to gain insight into the sequence of the acquisition of the mutations. We first analyzed hematopoietic progenitors from five MPD patients with mutations in both genes, like the patient IGR2.
For MPD samples, Immature CD34+CD38− cells were seeded at one cell per well for four to six weeks in conditions permitting simultaneous B, NK and granulocytic differentiations (lympho-myeloid differentiation) as described (DUPONT et al., abovementioned, 2007), whereas more mature CD34+CD38+ cells were grown in erythroid/granulocytic methylcellulose assays. Individual clones were collected for analysis of B, NK, and granulocytic differentiation by flow cytometry, and genotyping. CD34+CD38+ cells were seeded at 1,500 to 3,000 cells per culture dish in 2% standard methylcellulose supplemented with 37% FBS (STEM CELL TECHNOLOGIES), and a cocktail of cytokines as described (DUPONT et al., abovementioned, 2007)). Individual colonies grown from burst-forming units-erythroid (BFU-E) and colony-forming units-granulocyte/macrophage (CFU-GM) were picked on day 14. The obtained clones were analyzed for the presence of both molecular defects.
The results have shown that in all patients tested, sequence analyses revealed that both TET2 and JAK2 defects were present in clones derived from lympho-myeloid progenitors (data not shown). Interestingly the JAK2V617F mutation was not observed in the absence of TET2 defect whereas TET2 mutation could be observed in the absence of JAK2V617F. These results demonstrate that, as in MDS, the TET2 mutation is present in immature progenitors of MPD patients and indicate that TET2 defects precede JAK2 mutation during the evolution of the disease.
To further define the role of the TET2 mutations in the amplification of the malignant clone, we compared the genotype of colonies derived from immature (CD34+CD38−) progenitors to that of erythroid and granulocytic colonies derived from committed (CD34+CD38+) progenitors.
The results shown that in three MPD patients (MPD01, MPD04, MPD35), almost all the colonies at different stages of hematopoietic differentiation harbored a TET2 mutation, suggesting that the TET2 mutated clone expanded at early steps of hematopoiesis (data not shown). In 2 other patients (MPD05, MPD20), most immature progenitors were wild-type whereas most committed progenitors were mutated for TET2. Within JAK2 wild-type progenitors from these two patients, we observed an increase in the proportion of clones with TET2 defects from the immature (2/37 and 0/34, respectively) to the committed (10/23 and 9/54, respectively) progenitor stage. Taken together, our results indicate that the selective advantage of the TET2 mutated clone at early differentiation steps is independent of the JAK2V617F mutation.
Overall, these data from MPD samples demonstrate that TET2 defects (i) occur at early steps of hematopoietic differentiation and that (ii) they may precede the occurrence of the JAK2V617F mutation and (iii) they give a selective advantage to the clone as it proceeds to myeloid differentiation.
9. Engraftment and Proliferation of Tet2 Mutated Cells In Vivo
We reasoned that loss of function of TET2 could confer a growth advantage to the hematopoietic stem cells. To demonstrate that the TET2 mutations occur in a HSCs with NOD-SCID repopulating capacity, we used a xenotransplantation assay by injecting, into NOD-SCID mice, CD34+ cells isolated from JAK2V617F MPD patients with TET2 mutations.
CD34+ cells (1 to 10×105 cells) from JAK2V617F MPD patients with TET2 mutations were injected intravenously into sub-lethally irradiated (3.5 Gy) NOD-SCID mice, previously treated with 200 μg of anti-CD122 antibody (JAMES et al., Blood, vol. 112(6), p: 2429-36, 2008). Bone marrow was obtained with heparinized syringue from the right femur at 3, 6 and 12 weeks after transplantation and mice were sacrificed at week 15. Human cell engraftment was evaluated by the sum of human leukocytes (CD45+) and erythroid populations (CD45−CD36+ and CD45−CD36−GlycophorinA+), as assessed by flow cytometry. Bone marrow cells were seeded in culture dish and 96-well plates for methylcellulose and long-term culture-initiating cell (LTC-IC) assays, respectively allowing the selective growth of human cells as described in JAMES et al. (abovementioned, 2008). Individual colonies were subsequently picked and genotyped.
We first compared the kinetics of chimerism after transplantation of CD34+ cells from these JAK2V617F MPD patients with TET2 mutations and from three JAK2V617F MPD devoid of TET2 defects (MPD09, MPD11, MPD27).
The FIG. 4a shows the percentage of human CD45-positive cells in mouse bone marrow monitored at 3, 6, 12, and 15 weeks post-transplant. MPD01 and MPD04 are patients with TET2 defects whereas MPD09, MPD11, and MPD27 are control patients devoid of identified TET2 defect.
The FIG. 4b shows the flow cytometric analysis of human cells present in NOD-SCID bone marrow 15 weeks after transplantation with 3×105 CD34+ cells from patients MPD04 and MPD09. The percentages of human CD45 (hCD45)-positive myeloid and lymphoid cells were determined using anti-CD45-PC7, anti-CD33-APC, and anti-CD19-PE antibodies.
The results show that human cells from the three patients devoid of TET2 mutation disappeared with time (FIG. 4a).
In contrast, the percentage of human cells in the bone marrow of mice engrafted with cells from the two TET2 mutated patients increased with time (FIG. 4a). In these mice, differentiation was skewed toward myeloid progenitor expansion, at the expense of lymphoid progenitors, as judged from CD33 and CD19 antigen flow cytometry analyses (FIG. 4b) unlike what is observed with normal HSCs wherein lymphoid differentiation is favored (ROBERT-RICHARD et al., Haematologica, vol. 17(3), p: 637-41, 2003).
Human cells present in the mouse bone marrow 15 weeks after transplantation (W15) were tested in in vitro progenitor and LTC-IC assays, and analyzed for the presence of TET2 and JAK2 mutations. The TET2 defects were found in pooled W15 CFU-derived colonies from both MPD01 and MPD04 samples, and in all individual human LTC-IC and progenitors present in the mice (data not shown). The results were compared with progenitor assays performed immediately before engraftment (D0). All colonies arising from patients' committed progenitor cells (D0 CFU) harbored TET2 mutation.
These results demonstrate that TET2 mutation occurs in a HSC. Interestingly, the results have further shown that the proportion of progenitor cells carrying only the TET2 mutation increased upon transplantation at the expense of cells carrying both TET2 and JAK2V617F mutations. These cells are thought to reflect the original HSC population. Therefore, these observations indicate that TET2 mutated HSCs with a wild-type JAK2 are more numerous than the TET2/JAK2 double mutant HSCs, further establishing the mutation of TET2 as a “pre-JAK2V617F” event in these patients.
Therefore our data are compatible with the hypothesis that TET2 defects endow the HSC with a selective engraftment advantage independently of JAK2V617F.
10. Positions of the Identified Mutations on the Tet2 Gene
We report that the inactivation of TET2 is a common early event in human MDS, MPD and sAML and that the frequencies of TET2 mutation in unselected patient series were 15/81=18.5% in MDS, 2/9=22% in CMML, 24/198=12% in MPD and 5/21=24% in sAML. It must be noticed that in these analyses we did not consider amino acid changes occurring outside of the conserved domains. Sequencing of the TET2 gene using the couples of primers identified in table 1 permits to identify a number of mutations in the TET2 gene (FIG. 5).
The FIG. 5 shows the locations of some of the identified mutations of the TET2 gene distributed along the protein sequence.
Mapping of the identified TET2 mutations on the TET2 sequence suggest an essential role for the carboxy terminal conserved region (amino acids in position 1860 to the position 1950) in the function of the protein.
Finally, the detection of acquired genetic defects targeting the two TET2 copies in 19 of the 55 patients with TET2 alteration establishes this gene as a bona fide tumor suppressor gene of human myeloid malignancies. TET2 defects are observed in both MDS and MPD, which are two distinct myeloid diseases. It is therefore likely that their characteristic clinical and biological phenotypes require at least another additional cooperating event. In MPD samples with both TET2 and JAK2 mutations, TET2 mutations likely occur first in the natural history of the disease, preceding the occurrence of JAK2V617F mutation.
11. Identification of Tet2 Gene Mutations in Familial MPD
Families with at least 2 affected patients with MPD were collected through a national network as previously described (BELANNE-CHANTELOT et al., abovementioned, 2006). The diagnoses of MPD were reviewed based on the 2008 World Health Organization criteria.1 All participants gave their written informed consent.
In a first step, we analyzed 15 probands of families compatible with an autosomal dominant inheritance, in search for a constitutional event that would account for these familial cases. Elected probands mostly suffered from PV or ET. In a second step, the analysis was extended to patients with hematological complications and to relatives of patients with TET2 variants.
Altogether, we analyzed 61 patients for mutations in the 6009 bp coding sequence of the TET2 gene from 42 MPD families (40 European, 2 African: families F3 and F4) including at least two available affected patients with MPDs. Thirty-four patients displayed a simple phenotype consisting of either PV (15), ET (12) or PMF (7) with no observed hematological evolution of the disease after a follow-up period of 12 years. Twenty-seven other patients had experienced an evolution in their MPD phenotype: PV evolving into myelofibrosis (post PV MF, 5) or into AML (12); ET evolving into MF (4) or AML (5), or PMF turning into AML (1).
The analysis was performed by polymerase chain reaction (PCR) on genomic DNA extracted from buccal swabs after heating at 95° C. for 10 minutes to release genomic DNA. Purified PCR products were sequenced using the BIGDYE TERMINATOR chemistry (APPLIED BIOSYSTEMS) and run on an APPLIED BIOSYSTEMS 3100 capillary sequencer.
The JAK2V617F mutational status was determined as previously reported in BELANNE-CHANTELOT et al. (abovementioned, 2006).
The whole coding region of the TET2 gene was sequenced as described previously. Two multiplex PCRs were set up to estimate the copy number of each TET2 exon using the quantitative multiplex PCR of short fluorescent fragments (QMPSF) method (CHARBONNIER et al., Cancer Res., vol. 60, p: 2760-2763, 2000). Two additional primer pairs amplifying short sequences of either the F9 or the DSCR1 gene were used as internal controls. PCR products were separated by capillary electrophoresis using a DNA genetic analyzer (ABI 3100). The analysis is based on the comparison of the peak heights generated from the tested DNA sample and the control DNA. The quantitative estimation of the height of peaks was determined using commercially available analysis software (GENEMAPPER VERSION 4.0, APPLIED BIOSYSTEMS).
Table 8 shows the TET2 mutations identified in 12 MPD patients.







TABLE 8







shows the TET2 mutations identified in 12 MPD patients.









TET2



















Proteic


Patients
Phenotype
Evolution
JAK2
Location
Nucleotide change
change





P1 (F1)
PV
MF
95
Exon 11
c.5695delC
p.Leu1899fs


P2 (F2)
PV
MF
63
Intron 7
c.3954 + 2T > A
p.?


P3 (F2)
PV

49-82
Exon 3
c.3138delT
pLeu1046fs


P4 (F3)
ET
PV > MF > AML
23-47
Exon 3
c.1648C > T
p.Arg550X






Exon 3
c.2570delA
p.Asn857fs


P5 (F3)
ET
MF > AML
 0
Exon 3
C2058A > T
p.Arg686Ser


P6 (F4)
ET
AML
 0
Exon 3
C1955delA
p.Gln652fs






Exon 3
c.2490dupA
p.Gln831fs


P7 (F4)
ET

39
Intron 4
c.3500 + 3A > C
p.?


P8
ET
MF
90
All
c.1.4999_5014del16
p.0






exons




P9
PMF

36
Exon 3
c.694C < T
p.Gln574X






Exon 11

p.Leu1667fs


P10
PMF

33
Exon 3
c.4019T < C
p.Gln232X


P11
PMF

66
Exon 8
c.5603A < G
p.Leu1340Pro


P12
PV
MF
78-96
Exon 11

p.His1868Arg









Patients were initially diagnosed with the phenotype indicated in the second column and subsequently had a hematological evolution shown in the third column. When measured in several samples, the JAK2V617F allele burden is indicated as a range.
The FIG. 6 is a schematic representation of the TET2 gene and protein showing the mutations identified in this study. Hatched boxes indicate exons. Truncating mutations are depicted as stars, missense mutations as inverted triangles. Conserved functional domains are depicted as boxes on the protein scheme. fs: frameshift.
Following this analysis, we identified a complete deletion of TET2 in one patient and a total of 39 point variants. Examination of these variants showed that 15 of them, identified in 12 patients, were deleterious heterozygous mutations. They were distributed as one deletion of the entire gene, 11 truncating (3 nonsense mutations, 6 out-of-frame insertions/deletions and 2 splice site mutations) and 3 missense mutations (FIG. 6, Table 8).
Furthermore, all three missense mutations were absent from 165 control individuals of ethnically matched populations, thus confirming their deleterious effect. Two, p.Leu1340Pro and p.His1868Arg, were located in the highly conserved TET2 functional domains (1134-1444 and 1842-1921). Truncating mutations seemed to be randomly distributed along the coding sequence (FIG. 6).
In patients P4, P6 and P9 two TET2 mutations were identified. For the former, multiple allele specific amplifications of the two mutations located in exon 3 showed that these two molecular events occurred on different alleles leading to the biallelic inactivation of TET2 (data not shown). The observation of such a biallelic inactivation of TET2 in these patients meets the criteria of the classical two-hit recessive model of carcinogenesis and supports the hypothesis that TET2 acts as a tumor suppressor gene.
Twenty-five other variants identified on the coding sequence of TET2 and the short nearby intronic regions were polymorphisms. Seven were substitutions in non-coding regions (intronic or 3′UTR), one was a variation in an intronic short tandem repeat, 4 were silent variations in the coding sequence and 13 were missense polymorphisms. They were all classified as polymorphisms on the basis of their presence in public databases, the fact that they were found in asymptomatic family members, or their identification in control populations. It is of interest to note that none of the missense polymorphisms were located in either one of the functional domains.
12. Tet2 Mutations were Sequentially Acquired in a Patient with Two Mutations
Seven blood samples were available for patient P4 from family F3, throughout the last three steps of her evolution: PV, MF and AML. Sequencing these samples allowed us to determine the temporality of the clinical and molecular events.
The FIG. 7 shows the sequential study of TET2 and JAK2 in patient P4 (F3). Sequence electrophoregrams are shown for each TET2 mutation and for JAKV617F. The diagram on the left indicates time lapse from diagnosis (in years) and corresponding henotype for each sample (white: ET; grey: PV; hatched: post-ET MF; black: AML).
The results show that JAK2V617F and the TET2 p.Arg550X mutation were already present in the first sample, when the patient suffered from PV. The second mutation, p.Asn857fs was detectable in the second sample, 7 years later and 5 months before the diagnosis of MF. This sequential analysis has shown that the burden of each of these mutations grew in time, concomitantly with the development of the disease.
Finally, TET2 mutations were found in similar proportions in JAK2V617F positive and negative patients suggesting that molecular events in both genes may arise independently of each other.
13. Tet2 Molecular Events were Mainly Observed in Patients with PMF or Patients with PV or ET Who Secondarily Evolved Towards a Hematological Transformation
Altogether, 12 patients were found carrying at least one TET2 mutation. They account for 20% of all MPD patients tested.
The FIG. 8 shows the schematic representation of the clinical status of these twelve patients with at least one TET2 mutation. White boxes depict ET stages, grey, PV, crosswised hatching indicates myelofibrosis, either primary (left-slanting) or post-PV/ET (right-slanting) and AML are symbolized as black boxes. Above each arrowhead indicating a molecular analysis is annotated the TET2 corresponding mutation. Disease duration (in years) is indicated below the bars, the “zero” point indicating time of diagnosis. Time of death is symbolized as a vertical line, when appropriate, at the right end.
This analysis shows that these TET2 defects were identified in patients diagnosed with the three main MPD phenotypes: PV (4/32), ET (5/21) and PMF (3/8). No TET2 mutation was observed in relatives with rare hematological phenotypes, including de novo AML and systemic mastocytosis (data not shown). All patients with a TET2 defect but two were positive for the JAK2V617F mutation. The allele burden varied from 33 to 95% (Table 6). The negative cases were ET patients who developed very active AML and died rapidly (P5 and P6, data not shown). We should note that the two patients, P3 and P7, who had not developed post-PV or post-ET MF at the time of examination, were characterized by a high level of JAK2V617F allele burden (82 and 39% respectively, Table 6).
Altogether, our results established that 20% of the JAK2V617F positive patients were found mutated for TET2 (10/49) vs. 17% among the JAK2V617F negative patients (2/12).
All patients carrying a TET2 mutation but two had either a myelofibrosis that occurred at onset or was acquired secondarily after PV or ET, or a secondary AML. Hence 29% (10/34) of patients with PMF or hematological complication after PV or ET were found mutated in TET2 compared to 7.4% (2/27) of patients without any diagnosed haematological complications after a mean time of disease duration of 12 years. Both patients with TET2 mutations and presenting PV or ET without hematological transformations had nevertheless an active course of the disease.
No correlation can be done between the clinical presentation, the hematological data or even the course of the disease in patients and the type and location of mutations or between patients with a single heterozygous TET2 mutation and patients with two. As shown on FIG. 8, TET2 mutations were found at different times in the evolution of the disease for each patient from the time of diagnosis (P9) to 20 years later (P8); the time to progression was also variable [1-16 years].
14. Tet2 Mutations were Present in Early Hematopoietic Progenitors and were Acquired Independently from JAK2V617F
Three patients were available for analysis of their progenitor cells, patient P4 from family F3 and patients P2 and P3 from F2. Blood progenitor cells were available for the former at two different steps of her disease during the PV stage and the blast phase after MF.
The FIG. 9 disclosed TET2 and JAK2 genotypes in committed progenitors of patients P2, P3 and P4. Histograms show the fraction of clones harboring JAKV617F and two TET2 mutations (crosswised hatching), JAK2V617F and one TET2 mutation (white), wild type JAK2 and two TET2 mutations (light grey), JAK2V617F and wild type TET2 (grey) and no mutation in any of the two genes (black). Two samples were analyzed for patient P4, the corresponding stage is indicated below each bar. The numbers of analyzed clones are indicated.
The results show that eight years after diagnosis, during the PV stage, endogenous erythroid colonies already carried the p.Arg550X mutation (5/29) but p.Asn857fs was never observed (0/29, FIG. 9).
Nine years later, after leukemic transformation, all genotyped Burst forming unit-erythroid (BFU-E) and all colony forming unit-granulocyte macrophage (CFU-GM), but 2, carried JAK2V617F and both TET2 mutations (FIG. 9). The progenitor analysis therefore confirmed the temporality of these events: in patient P4, p.Arg550X was first acquired in the earliest stages of the disease; and the latest stages were characterized by the presence of both p.Arg550X and p.Asn857fs. Interestingly, two CFU-GM carried both TET2 mutations in the absence of JAK2V617F. For patient P2, colonies were found with either both JAK2 and TET2 mutations, the sole JAK2V617F or none (FIG. 9). This was an indication that for this patient the TET2 mutation occurred in clones already mutated for JAK2. All BFU-E and CFU-GM from patient P3 diagnosed with PV carried both JAK2 and TET2 mutations and did not allow concluding on the temporality of JAK2 and TET2 events.
15. Tet2 Molecular Events were Mainly Observed in Patients with CMML
The nature and frequency of somatic mutations in TET2 was also studied in bone-marrow or peripheral blood collected from 88 patients with CMML1 (n=70) or CMML2 (n=18) according to the WHO criteria and 14 acute blastic transformation of a previously identified CMML. Patients signed their informed consent according to current ethical regulations. Patients with CMML in chronic phase were newly diagnosed (n=43) or known for hematopoietic disease and followed up every 3 months for therapeutic abstention, supportive cares or cytotoxic treatment, in most cases with Hydroxyurea (n=45).
Blood and bone-marrow samples were collected on EDTA and mononuclear cells were selected by Fycoll Hypaque. DNA was extracted using commercial kits (QIAGEN). Polymerase chain reaction (PCR) and direct sequencing reaction were performed using standard conditions with gene-specific primers designed to amplify coding sequences spanning from exon 3 to exon 11 of TET2 gene as described previously. For each PCR reaction, 20 ng of genomic DNA was used for PCR amplification followed by magnetic bead purification and bidirectional sequencing using ABI 3300 capillary sequencers (AGENCOURT BIOSCIENCE). Mutation Surveyor (SOFTGENETICS) was used to detect nonsense and missense mutations located in conserved regions spanning from 1134-1444 and 1842-1921 and sequences were reviewed manually to detect frameshift mutations. TET2 abnormalities were numbered according to FM 992369 EMBL nucleotide sequence database.
The mutations identified in TET2 are listed in table 10.











TABLE 10







Nucleotide change




Patient
WHO
in TET2
Exon
Consequence



















2
CMML1
c.4453G > A
5
W1198STOP


4
CMML1
c.5214C > T;
10 & 11
R1452 STOP;




Ins 5537 (A)

Y1560FS


5
CMML1
c.4942G > A
9
G1361S


15
CMML1
c.4500C > A;
 6 & 10
R1214W;




Del 5118_21

L1420FS




(TTAT)




18
CMML1
delT 4172;
3 & 9
F1104FS,




c.5011A > T

D1384V


19
CMML1
del 5362_5365;
10 & 11
G1501FS;




c.6441G > A

G1860R


20
CMML1
c.2631C > T
3
Q591 STOP


21
CMML1
Del 6507 (A)
11 
T1883FS


22
CMML1
c.2961C > T
3
Q701 STOP


23
CMML1
c.1818G > T;
3 & 9
E320 STOP;




c.4936G > A

R1359H


24
CMML1
c.4515C > T
6
H1219Y


25
CMML1
c.4663n +
 6 & 11
Mutation splice




1 G > A;

donor site exon




Del 6424_33

6 + L1855FS


26
CMML1
ins 2468_9 (AA)
3
K536FS


28
CMML1
c.1272C > A;
3 & 8
Q138 STOP,




c.4814n-

Mutation splice




1 G > A

receptor site






exon 8


31
CMML1
Ins 3151 (C);
3 & 5
Q764FS;




c.4390T > G

I1175S


32
CMML1
c.3675C > T
3
Q939 STOP


35
CMML1
delG 4754;
 7 & 11
K1298FS;




dup 6569_6573

M1570FS




(GAGA)




39
CMML1
delA 3874;
3 & 8
K1008FS;




del 4830_31

S1324FS




(TC)




40
CMML1
c.2208A > T;
3 & 4
K450 STOP;




del 4347 (A)

I1163FS


41
CMML1
c.6478T > C
11 
I1873T


42
CMML1
ins 1921 (A);
3 & 3
S354FS;




ins 2703 (G)

L615FS


44
CMML1
ins 3995 (T);
3 & 3
E846FS;




c.4059 A > T

R1067 STOP


17
CMML2
c.2814C > T
3
Q652 STOP


30
CMML2
Ins 4293 (A);
 4 & 11
G1145FS;




c.6510A > G

T1884A


34
CMML2
delT 4277;
 4 & 11
I1139FS;




c.6598G > T

G1913V


38
CMML2
c.4936G > C
9
R1359S


14
TA
c.3235C > A
3
S792 STOP


29
TA
c.2490C > T;
 3 & 10
R544 STOP;




Del 5334 (G)

E1492FS


1
CMML1
c.5043n-
10 & 11
Mutation splice




1G > A;

receptor site




Dup 6575_6579

exon ex10;




(GAGCA)

M1907FS


7
CMML1
c.4439T > G
5
C1193W


8
CMML1
c.4726G > T
7
C1289F


9
CMML1
c.5100C > T
10 
Q1414 STOP


11
CMML1
Del 6023 (G)
11 
L1721FS


12
CMML1
Del 1921 (C)
3
S354 STOP


16
CMML1
c.4827G > T;
 8 & 10
E1323 STOP;




Ins 5178 (A)

R1440FS


27
CMML1
insG 2703;
 3 & 10
L615FS;




ins 5125_26 (AA)

K1422FS


33
CMML1
Ins of 2950_85
3
L718FS




(dup)




36
CMML1
c.4638G > A;
5 & 8
C1193Y;




c.4825T > C

L1322P


37
CMML1
c.6414C > T;
11 & 11
Q1852 STOP;




c.6496A > C

E1879A


43
CMML1
del 3859 (A)
3
N1000FS


46
CMML1
del 1264_66
3
E135FS




(AAA)




3
CMML2
c.4431C > T
5
Q1191 STOP


6
CMML2
c.5070C > T
10 
R1404 STOP


10
CMML2
Del 2655_2658
5
N598FS




(CAAA)




13
CMML2
Ins 5602_5606
11 
S1582FS




(TCCAA)




45
CMML2
c.2784 C > T;
 3 & 10
Q642 STOP;




c.5253 C > T

R1465 STOP









The results revealed that a mutated status of TET2 gene was detected in 44 out of the 88 (50%) patients. Among the 43 patients studied at diagnostic, a mutated status of TET2 gene was identified in 18 cases (42%). Such a mutated status was identified in 26 of the 45 patients (58%) studies along the course of the disease. These results thus suggest that TET2 mutation prevalence is higher in CMML than in any other studied myeloid disease.
Moreover, it must be noticed that two distinct mutations in TET2 sequence, suggesting a bi-allelic alteration of the gene, were identified in 18 out of the 44 (40%) mutated patients with a chronic phase CMML, including 5 out of the 18 (27%) patients whose mutations was identified at diagnosis, and 13 out of the 26 (50%) mutated patients studied along the course of the disease. Altogether, 69 mutations in TET2 were identified, including 33 frameshift mutations, 19 nonsense mutations, 14 missense mutations and 3 mutations in a splice site. These mutations most frequently involved exon 3 (22 events), exon 10 (9 events) and exon 11 (10 events).
An analysis of overall survival was performed in 40 of the 43 patients whose TET2 status was determined at diagnosis with an at least two months follow-up and indicated a lower 1-year overall survival in patients with the 16 patients of this cohort with TET2 mutation, but the difference did not reach significance. When overall survival analysis was limited to the 29 patients with a CMML1 according to the WHO classification and an at least two months follow-up, the difference was then significant (p<0.01). None of the other tested parameters includes age, sex and FAB classification did affect survival. Finally, the results established that TET2 mutation was associated in the 29 patients with CMML1 with a trend to significantly lower survival.
16. Alteration of the Tet2 Gene in Patients Suffering from Lymphoid Cancer
CGH analyses of 157 patients suffering from B-cell lymphoma showed the loss of a whole chromosome 4 in 2 cases, a partial deletion of chromosome 4q sequences deleting the TET2 gene in 4 cases and loss of the upstream side of TET2 associated with duplication of the downstream side of TET2 in one case. These rearrangements were found in diffuse large B-cell lymphomas (107 cases), whereas no rearrangement could be found in follicular lymphomas (50 cases).
We have analyzed 93 patients for variation within the coding sequence of TET2. They were 33 T cell lymphoma and 60 B cell lymphoma.
14 mutations were observed in 10 samples from T-cell lymphomas, including 10 frame shifts and 2 non-sense and 2 missense mutations.
Table 9 shows the TET2 mutations identified in 10 T-cell lymphomas patients. disease







TABLE 9







shows the TET2 mutations identified in 


10 T-cell lymphomas patients.











Amino acid


disease
Nucleotide changes
consequences





T-lymphoma
c.3215delT
p.Phe785FS


T-lymphoma
c.[1893_1896delAAGC] +
p.[Lys345FS] +



[4527delG]
[Ala1223FS]


T-lymphoma
c.[2505delA] +
p.[Thr549FS] +



[2524delC]
[Pro555FS]


T-lymphoma
c.6564C > T
p.Tyr1902


T-lymphoma
c.5523_5524insA
p.Glu1555fs


T-lymphoma
c.[3131_3137delCCAGACT] +
p.[Leu757FS] +



[5109G > T]
[Val1417Phe]


T-lymphoma
c.[3747C > T] +
p.[Gln963STOP] +



[5331A > T]
[Lys1491STOP]


T-lymphoma
c.3756_3757del CA
p.Gln966 FS


T-lymphoma
c.1642delC
p.Ser261 FS


(LAI)









Thus, these results established that the frequencies of TET2 mutation in patients suffering from T-cell lymphoid tumour is 30%.
17. Tet2 Inactivation Results in Pleiotropic Hematopoietic Abnormalities in Mouse and is a Recurrent Event During Human Lymphomagenesis
To investigate the role of TET2 during hematopoiesis, two mouse models in which the 5-hydroxy-methylation function of Tet2 is impaired were engineered. In addition, the status of TET2 coding sequences in various human mature lymphoid malignancies was investigated.
17.1. Experimental Procedures
Generation of the Tet2LacZ and Tet2floxed Alleles and Animal Analyses
Gene-trap mouse embryonic stem cell clone (SIGTR ES cell line AN0709: Tet2Gt(AN0709)Wtsi, herein named Tet2LacZ) carrying a beta-galactosidase-neomycin (beta-geo) resistance fusion cassette in Tet2 gene were obtained from UC Davis Mutant Mouse Regional Resource Center (mmrrc.org) to generate gene-trap mouse line and the insertion of the beta-geo cassette in intron 9 of Tet2 was routinely genotyped on tail DNA by multiplexed polymerase chain reaction (PCR) using 5′-CAGCCAGGAAGACACTTACC-3′ (SEQ ID NO:40) and 5′-GACACCGATCTTGCTGGTTG-3′(SEQ ID NO:41) primers into intron 9 to detect wild-type Tet2 allele and 5′-CGCCTTGCAGCACATCCC-3′(SEQ ID NO:42) and 5′GGCCTTCCTGTAGCCAGC-3′(SEQ ID NO:43) primers into the beta-galactosidase sequence (and after the splicing donor site) to detect gene-trap allele (Tet2LacZ/LacZ).
Mice harboring Tet2 allele with exon 11 flanked by two loxP sites introduced in intron 10 and in the 30 untranslated region of exon 11 (Tet2Lox/Lox; “floxed allele”) were generated by the Clinique de la Souris (Strasbourg, France) and intercrossed with mice expressing Cre recombinase under the control of the type I interferon-inducible Mx1 murine promoter (transgene referred as Mx1−Cre). PCR on tail DNA using 5′-GGCAGAGGCATGTTGAATGA-3′(SEQ ID NO:44) and 5′-TAGACAAGCCCTGCAAGCAAA-3′(SEQ ID NO:45) primers allowed distinguishing between wild-type and foxed allele. The Tet2Lox allele was backcrossed into C57BL/6 background for at least six generations using speed-congenics (Harlan Laboratories) prior to analysis.
Acute inactivation of Tet2 in 6- to 10-week-old Mx1−Cre+Tet2Lox/Lox was performed by intraperitoneal injections (three injections every other day) of 800 mg poly(I:C)-LMW (InvivoGen, San Diego). Induction of Cre recombinase and efficient excision of floxed allele was confirmed by multiplex PCR using 5′-GGCAGAGGCATGTTGAATGA-3′(SEQ ID NO:46), 5′-TAGACAAGCCCTGCAAGCAAA-3′(SEQ ID NO:47) and 5′-GTGTCCCACGGTTACACACG-3′(SEQ ID NO:48) primers that discriminated between floxed and deleted allele, respectively 305 and 237 bp. Therefore, the following nomenclature was used: Mx1−Cre+Tet2Lox/Lox=Tet2−/−, Mx1−Cre−Tet2Lox/Lox=Tet2+/+.
Competitive transplantations were performed by transplanting equal numbers of total bone marrow cells from CD45.1−CD45.2+ Tet2-deficient and CD45.1+CD45.2+ wild-type animals into lethally irradiated CD45.1+CD45.2− recipients. For LSK cells transplantation, LSK cells were purified by flow cytometry from Tet2-deficient animals and 4000 LSK cells supplemented with 1 3 106 total bone marrow cells from wild-type were injected to lethally irradiated recipients. Expression of CD45.1 and CD45.2 was followed by flow cytometry on blood cells every month and animals were analyzed at 4 months after transplantation.
Animal experiments were conducted according to the Institut Gustave Roussy Institutional guidelines and authorized by the Direction Départementale des Services Vétérinaires du Val de Marne.
Patient Samples Collection
Lymph node, peripheral blood, and bone marrow samples from the patients were obtained with their informed consent and the approval of the local Research Ethics Committees (Centre Henri Becquerel, Pitié-Salpétrière, and Cochin hospitals). Additional information on patient samples is available in Table 11.
Flow Cytometry, Cell Sorting, and Purification
Total white blood cells, obtained from peripheral blood after lysis of red blood cells, and single-cell suspensions from bone marrow, spleen and thymus were stained in toto in PBS supplemented with 2% fetal bovine serum (FBS) with fluorochrome-conjugated mouse antibodies raised against specific markers of hematopoietic lineages (BD Biosciences PharMingen, except otherwise mentioned). Additional information on antibody clones is available in Supplemental Methods. Viability of cells was confirmed by using the Sytox Blue (Invitrogen) viability marker. Flow cytometric analysis and cell sorting were performed using a FACSCantoII Flow Cytometer (BD Biosciences) and a MoFlow (Becton Dickinson) or a FACSAriaIII (BD Biosciences), respectively.
Immunophenotypic data were analyzed using the FlowJo Version 7.2.4 software (TreeStar).
For human samples, bone marrow or peripheral blood mononuclear cells, lymphocytes, and granulocytes were isolated and stored in liquid nitrogen as viable cells in FBS with 10% dimethyl-sulfoxide (DMSO, Sigma). Patients were selected on DNA availability. Their clinical and biological characteristics are summarized in Table 11. Diagnoses were made by standard International criteria. Cells were purified using Miltenyi beads according the manufacturer instructions. When mentioned, cells were sorted after labeling with PE-CD34 and APC-CD38 antibodies (Immunotech) using a FACSDiva cell sorter (Becton Dickinson).
In Vitro Clonogenic Assays
Sorted CD34+ cells were seeded at one cell per well on methylcellulose in MEM alpha medium supplemented with 10% FBS (Stem Cell Technologies), and a cocktail of early cytokines (thrombopoietin [TPO], interleukin [IL-3], Flt3-L, Stem Cell Factor [SCF], erythropoietin [EPO], granulocyte-colony stimulating factor [G-CSF], granulocyte/macrophage-colony stimulating factor [GMCSF] and IL-6). After 2 weeks, individual clones were collected for further genotyping.
For patient 2, total mononuclear cells were seeded in 2% standard methylcellulose supplemented with 25% FBS (Stem Cell Technologies), and a cocktail of cytokines as described.
Nucleic Acid Methods
DNA and RNA were extracted using commercial kits (QIAGEN or Roche). Polymerase chain reaction (PCR) and direct sequencing reaction were performed using standard conditions with primers available upon request. Nucleotide sequences were compared to wild-type human genomic sequence present in the databases (genome.ucsc.edu). All observed mutations were scored on both strands. Additional information on exome sequencing is available in Supplemental Experimental Procedures.
In Vitro Differentiation Assays
LSKs (5 3 102), total BM (5 3 104), and spleen cells (5 3 104) isolated from mutant or control mice were cultured in methylcellulose-based medium (MethoCult M3434; StemCell Technologies) and scored for CFUs (colony-forming units) using combined scoring for burst-forming unit erythroids (BFU-Es), CFUmegakaryocytes (CFU-Mks), CFU-granulocyte macrophages (CFU-GMs), and CFU-granulocyte erythroid macrophage megakaryocytes (CFU-GEMMs) after 7 days. All live colonies were counted for each of the two 35 mm dishes plated per sample.
Quantitative PCR
cDNA was synthesized from total RNA purified (using the RNeasy microkit, QIAgen) from sorted LSK, common myeloid progenitor (CMP), megakaryocyte-erythrocyte progenitor (MEP), and granulocyte-macrophage progenitor (GMP) populations using the Superscript II reverse transcriptase (Invitrogen).
TaqMan probes were purchased from Applied Biosystems (Tet1: Mm01169089; Tet2 [exon 9-10]: Mm00524395_m1; Tet2 [exon 10-11]: Mm01312907; Tet3, Mm01184936; Abl1, Mm00802038). Tet2 (exon 3-4) transcript were detected using the following primers; Primer1: 5′-agaatcagatactcctggtgaacaaa-3′(SEQ ID NO:49), Primer2: 5′-cctagatgggtataataaggagcttcat-3′(SEQ ID NO:50), Probe: 5′ FAM-tctggattgcatccttcacatttgccat-3′TAM(SEQ ID NO:51). Tet2-LacZ fusion transcript was detected using the following primers and probe: Primer1 (Tet2 exon 9): 5′-cccacagagaccagcagaaca-3′(SEQ ID NO:52), Primer2 (LacZ): 5′-tgcgttcttcttctttggttttc-3′ (SEQ ID NO:53), Probe: 5′FAM-cctgggaccactgtactgccatttgg-3′TAM (SEQ ID NO:54). The expression level of each gene was assessed by qRT-PCR with an ABI PRISM 7500 and calculated following the DDCt method; each sample was analyzed in triplicate and normalized with Abl1 and GusB expression (Applied Biosystems Mm00802038_g1 and Mm03003537_s1, respectively).
Statistical and Quantification Analyses
Results are expressed as mean values±SEM. Statistical significance of differences between the results was assessed using a 2-tailed unpaired Student's t test, performed using Prism (GraphPad software, version 5.03). p values <0.05 were considered statistically significant. Quantification of the 5mC and 5hmC signals was performed by dot-blotting DNA and using antibodies from Eurogentec (1/500 dilution) and Active Motif (1/10,000 dilution) respectively. Signal was quantified using GelEval (FrogDance software, version 1.32).
Accession Numbers
Microarray procedures and data have been deposited in the European Bioinformatics Institute (EBI) database with the following accession number: E-TABM-1161.
17.2. Murine Models of Tet2 Inactivation
To investigate the role of Tet2 during hematopoiesis, two Tet2-deficient mouse lines were generated. One was derived from a gene-trap ES clone (SIGTR ES cell line AN0709) in which a beta-galactosidase-neomycin cassette was inserted in Tet2 intron 9 (Tet2LacZ allele), thus leading to the expression of a Tet2-beta Gal fusion transcript (FIG. 11a). A conditional knockout allele of Tet2 in which the coding sequences of the last exon of Tet2 are surrounded by loxP sites were also generated (Tet2Lox). After Cre recombination, this allele results in the loss of the last 490 carboxy-terminal (Ct) amino acids of Tet2. In both models, TET2 is predicted to lose the conserved Ct homology region of the double-stranded b-helix-2OG-Fe(II)-dependent dioxygenase domain. The two alleles were backcrossed for at least six generations into the C57BL/6 background, and then intercrossed to obtain homozygous animals.
Mice bearing the conditional Tet2 allele and the interferon inducible Cre transgene (Mx1−Cre) were intercrossed to obtain a cohort of Mx1−Cre+Tet2Lox/Lox (hereafter named Tet2−/−) and control Mx1−Cre−Tet2Lox/Lox (hereafter named Tet2+/+) animals that were injected with poly(dI-dC) to induce Cre expression and acute inactivation of Tet2 in adult animals. Full excision was observed in bone marrow and thymus (FIG. 11b) and correlated with loss of normal Tet2 mRNA expression in purified hematopoietic stem (Lineage−Sca-1+c-Kit+: LSK cells) and progenitor populations (FIG. 11c). Tet2LacZ/LacZ animals were obtained at a Mendelian ratio, were fertile and appeared normal (data not shown). Tet2LacZ/LacZ progenitors showed a 20%-50% residual expression of a normal Tet2 mRNA compared to wild-type progenitors, suggesting that the Tet2LacZ allele is an hypomorph allele (FIG. 11d). Importantly, Tet1 and Tet3 expression levels remained unchanged in progenitors from both models (FIGS. 11c and 11d). Quantification of mC and 5hmC in Tet2−/− lineage− cells revealed a marked reduction of 5hmC compared to Tet2+/+ (FIGS. 11e and 11f). Using a similar approach, no significant change in 5hmC level was detected in Tet2LacZ/LacZ lineage-cells (data not shown). Together these data confirmed the inactivation of Tet2 in these models and indicate that loss of Tet2 during adult hematopoiesis is not compensated by increased transcription of Tet1 and Tet3.
17.3. Tet2 Controls Hematopoietic Stem and Progenitor Cells Homeostasis
Analysis of the hematopoietic compartments in these animals showed an amplification of the LSK compartment in 4- to 6-month-old animals in both Tet2 inactivation models (FIGS. 12a and 12b). Heterozygous animals also presented increased LSK in both models (data not shown).
Within this compartment, CD34+Flt3− short-term stem cells and to a lesser extent CD34−Flt3− long-term stem cells were amplified.
Notably, absolute numbers of CD150+CD48− LSK cells were slightly increased (FIG. 12a). The absolute number of common myeloid progenitors (CMP) and megakaryocyte-erythrocyte progenitors (MEP) was increased, whereas the granulocyte-macrophage progenitor (GMP) population remained stable in Tet2−/− animals compared with controls (data not shown). Bone marrow cells from Tet2−/− animals presented a functional increase in methylcellulose colony forming progenitors (FIG. 12c). Of note, the average number of cells per colony was higher in Tet2-deficient cell cultures compared with controls.
Culture of purified LSK cells from some Tet2−/− animals 12 months after induction also produced an increased number of cells presenting a decreased differentiation toward CD11b+Gr1+ myeloid cells and a higher maintenance of the immature c-Kit+Sca1+ phenotype compared with controls (data not shown). The amplitude of this phenotype was variable among animals. Similar results were obtained from genetrap animals (data not shown).
To demonstrate the cell-autonomous nature of this property, total bone marrow or purified LSK cells were transplanted from both Tet2-deficient models (CD45.2+CD45.1−) in competition with wild-type cells (CD45.2+CD45.1+) into wild-type CD45.2−CD45.1+ recipients. Homozygous Tet2-deficient cells from both models efficiently reconstitute all hematopoietic lineages for over 16 weeks, indicating that amplified LSK cells are functional (FIGS. 12d-12h). In both myeloid and lymphoid lineages, the contribution of Tet2-deficient cells progressively increased over that of wild-type cells. An amplification of the LSK compartment was observed in some recipient animals (data not shown).
Together, these data showed that Tet2 inactivation resulted in a phenotypic and functional amplification and a competitive advantage of hematopoietic stem and progenitor cells indicating cell-autonomous control of their homeostasis by Tet2.
17.4. Tet2 Inactivation Induces Alteration of Several Mature Hematopoietic Lineages
To further characterize the consequences of Tet2 inactivation on mature hematopoietic lineages, a cohort of Tet2−/−, Tet2LacZ/LacZ animals and their respective controls for disease development were followed. Four-month-old Tet2−/− and Tet2LacZ/LacZ animals present a modest increase in white blood cell counts, a decrease in erythroid and platelets counts, and a significant hepatosplenomegaly compared with controls (FIGS. 13a and 13b). Histopathological analysis showed an alteration of the normal splenic architecture with significant expansion of the red pulp and infiltration of the lymphoid follicles with admixed maturing myeloid, immature erythroid, and maturing megakaryocytic elements (FIG. 13c). Interestingly, analysis of the liver showed that Tet2−/− animals presented a diffuse infiltration of the sinusoids with an admixture of lymphoid and trilineage myeloid elements with some focused perivascular infiltrations (data not shown).
Flow cytometrical analysis confirmed an amplification of myeloid cells in both models with a marked increase in a myelomonocytic CD11b+Gr1− population in the peripheral blood and spleen (FIG. 13d). Alteration of the erythroid lineage was observed in the bone marrow with a significant increase in CD71+Ter119− proerythroblasts and a decrease in the number of CD71lowTer119+ late erythroblasts (FIG. 13e). Splenic erythropoiesis was also visible with an increase in the number of CD71+Ter119+ erythroid cells (FIG. 13e). Tet2-deficient splenocytes could form multilineages colonies in methylcellulose colony-forming assays confirming extramedullar hematopoiesis (FIG. 12c and data not shown). Similar abnormalities were observed in the gene-trap model (data not shown).
Lymphoid lineages were also affected with a global increase in the number of immature double-negative (DN) CD4−CD8− T cell progenitors in the thymus, more particularly, CD44+CD25− DN1 cells (FIG. 13f). The B cell lineage was also altered with a decreased number of bone marrow B220+IgM− pre- and pro-B cells and B220+IglowM mature B cells (FIG. 13g) associated with an increase in the number of splenic B cells (FIG. 13h). Of note, heterozygous Tet2LacZ/wt animals present similar abnormalities of the myeloid, erythroid and B cell lineages (data not shown). Also, both lymphoid and myeloid lineage alterations were observed in recipients of Tet2-deficient cells (data not shown), indicating that differentiation abnormalities are cell autonomous.
With age, some Tet2LacZ/wt and Tet2LacZ/LacZ animals developed a lethal phenotype associated with important weight loss, high white blood cell counts, anemia, thrombocytopenia, and massive hepatosplenomegaly (FIGS. 14a and 14b; data not shown). Histopathological analysis of moribund animals showed complete effacement of the spleen architecture and massive perivascular as well as interstitial infiltration of the liver with myeloid elements (FIG. 14c). A moderate fibrosis, assessed by increased reticulin fiber staining on tissue sections, was observed in the spleen and liver but not the bone marrow (FIG. 14d). Flow cytometrical analysis confirmed the myeloid and erythroid lineage hyperplasia with abnormal myelomonocytic differentiation revealed by a striking amplification of the CD11b+Gr1− population visible in younger Tet2-deficient animals (FIG. 14e). Importantly, the disease was transplantable to secondary recipients, which succumbed with a shorter latency and a similar phenotype (data not shown). To date, Tet2−/− animals did not develop lethal disorders with a follow-up of over 15 months.
Together, these results show that Tet2 inactivation in mice results in pleiotropic alterations of the immature and mature hematopoietic compartments including both lymphoid and myeloid lineages (data not shown). With time, Tet2 inactivation leads to bona fide myeloid malignancies with differentiation abnormalities reminiscent of human CMML.
17.5. TET2 is Mutated in Human Lymphoid Malignancies
Based on these results indicating that TET2 controls both self-renewal and/or proliferation of early progenitors and also late steps of both myeloid and lymphoid hematopoietic differentiation, it was investigated whether human lymphoid malignancies could also present TET2 mutations. Supporting this hypothesis, two of six patients presenting myeloid malignancies and initially investigated for TET2 alterations, concomitantly suffered from lymphomas (Delhommeau et al., 2009; Viguié et al., 2005). Therefore, the entire coding sequence of TET2 in a series of human lymphoid malignancies was resequenced. No nucleotide changes inducing truncation or aminoacid changes in the catalytic domain of TET2 were observed in chronic lymphocytic leukemias (CLLs) (n=75), plasma cell neoplasms (PCNs) (n=22), and leukemic or disseminated T cell neoplasms (n=45) [including T cell prolymphocytic leukemia (TPLL), T cell large granular lymphocytic leukemias (TGLLs), and adult T cell lymphoma/leukemia HTLV1+ (ATLL HLTV1)]. In a series of 301 B cell lymphoma and 177 T cell lymphoma samples, TET2 mutations were observed in 2.0% of B cell and 11.9% of T cell lymphomas and in up to a third of the angioimmunoblastic T cell lymphoma (AITL) samples. The mutations were mainly insertion/deletions, generating frameshifts and nonsense mutations, as seen for myeloid malignancies (Table 11). Of note, five of these patients had a known history of successive haematological malignancies, as shown in Table 12 below:







TABLE 12







Patients with multiple diseases



















BM

Time of


Patient
Diagnosis
ge
Cytogenetics
tage
infiltration
Associated
associated

















2
GCB
7
normal
V
no
RAEB then
5 months after



DLBCL




AMLFAB 5a
B-cell lymphoma's


14
AITL
2
N.D.
V
yes
Myelofibrosis
4 years before








then RAEB
T-cell lymphoma's


15
AITL
6
del
V
yes
Sideroblastic
3 years before





(20)(q12)


anemia
T-cell lymphoma's


18
PCTL,
6
t(6; 15)(q21;
II
no
Hodgkin
6 years before



NOS

q23)


lymphoma
T-cell lymphoma's


21
PCTL,
3
hyper
V
yes
Tcutaneous
8 years before



NOS

ploidy with del


lymphoma
T-cell lymphoma's





(6q)


then THRBCL





GCB DLBCL: Germinal center B-cell like diffuse large B-cell lymphoma,


AITL: Angioimmunoblastic T-cell lymphoma,


PCTL-NOS: Peripheral T-cell lymphoma, not otherwise specified,


RAEB: Refractory anemia with excess blasts,


AML: Acute myeloid leukemia,


TCRBCL: T-cell-rich B-cell lymphoma.


BM: Bone marrow.






T-lymphoma samples by DNA micro-arrays, including nine TET2 wild-type and ten TET2 mutated samples were also analyzed.
The analysis revealed that one of the mutated samples also exhibited a small genomic deletion of chromosome 4q including the TET2 locus (data not shown). Therefore, as for myeloid malignancies, TET2 genomic abnormalities are less frequent than TET2 mutations but may occur in conjunction.
Matched nontumoral DNA samples were available for 13 patients with TET2 mutations (FIG. 15a, Table 11). The TET2 sequences were wild-type in two patients (patients 5 and 6). The mutated TET2 sequence detected in the lymphoma cells was clearly observed in the nontumoral DNA samples of five patients (patients 3, 4, 13, 15 and 26). In two of them (patients 3 and 15), this might be due to the presence of tumor cells, as judged by PCR analyses for TCR or IgH clonality or the presence of IGH-BCL2 fusion transcript (data not shown). Trace of the mutated TET2 sequence was suspected in six matched samples (patients 2, 10, 16, 17, 20, and 21) of which three (patients 2, 10, and 16) were devoid of tumor cells. Mutations observed in patients 17, 20, and 25 have been described as acquired in myeloid malignancies.
Together the mutated TET2 sequences were observed in the matched sample despite the absence of detectable circulating tumor cells in five samples (patients 2, 4, 10, 13, and 16). In two of these samples (patients 4 and 13), the estimated burden of mutated sequences was comparable to the wild-type sequence.
Two hypotheses could account for these observations: either the mutation was germline transmitted, or the mutation was acquired and had endowed the clone with a growth advantage over wild-type progenitors, leading to a skewed hematopoiesis.
17.6. TET2 Mutations are Detected in CD34+ Cells with Myeloid Potential
To test the hypothesis that TET2 mutations may arise in early hematopoietic progenitors in patients presenting lymphomas, three patients for which viable cells were available were analyzed.
Patient 8 was diagnosed with an AITL and carried a Q1445X mutation. Blood mononuclear cells were grown in a colony assay supporting myeloid differentiation. Of the 11 colonies that grew out, 5 showed only a wild-type TET2 allele and 6 showed both Q1445X and wild-type alleles (FIG. 15b). These results demonstrate the acquired nature of the TET2 mutation in this patient and also indicate its presence in progenitor cells with myeloid colony-forming potential.
Patient 2 was initially diagnosed with a B cell lymphoma carrying two TET2 mutations [(E448fs; 4663+1G>A: splice site mutation)] that were barely detectable in blood sample (FIG. 15c). Five months after treatment, the patient developed an MDS that rapidly evolved into AML. Viable bone marrow cells were available only at the AML phase. DNA was extracted from whole bone marrow cells, purified CD34− and CD34+ fractions.
In every DNA samples, both TET2 mutations were observed at seemingly variable ratios with respect to the wild-type sequence.
DNA was extracted from 28 colonies grown in myeloid conditions in vitro, from single CD34+ cells. Six colonies showed only wild type TET2 sequences, 14 colonies presented both TET2 mutations, and 8 colonies carried only the splice site mutation (FIG. 15c). These data demonstrate the presence of TET2 mutations in both the lymphoma and the AML cells, confirmed their acquired nature. Taken together, these observations suggest that the TET2 mutated clone had invaded the bone marrow and was at the origin of both the lymphoid and myeloid type malignancies.
Patient 27 was diagnosed with a T cell lymphoma. Bone marrow aspirate examination was cytologically normal. Two TET2 mutations (P761fs and Q481X) in the CD34−CD3−CD19−CD14− cell fraction (the remaining fraction after successive exclusion of the CD3+, CD19+ and CD14+ cell fractions from the blood sample) were observed, which were absent in the other fractions (FIGS. 16a and 16b). In vitro colonies assay of sorted CD34+ cells showed the presence of P761fs in 6 of 84 (about 7%) colonies, whereas the stop mutation was not observed (FIG. 16c). This fraction remained stable, since a similar analysis showed 6 out of 93 (about 6.5%) colonies with the P761 fs mutation 4 months later.
Of the 45 colonies obtained from cultures of Lineage-CD34+CD38− sorted cells, only one carried the P761fs (FIG. 16c).
These results show the acquired nature of the TET2 mutations in this patient and indicate the presence of a TET2 mutation on one copy in a small fraction of hematopoietic progenitors with myeloid differentiation potential.
Taken together, these results show the presence of TET2 mutations in B and T cell lymphomas. Detailed analysis of three patients indicated that lymphoma cells carried one somatic mutation originally acquired in an hematopoietic stem cell. During T cell maturation/differentiation, a second TET2 mutation may occur, leading to the total loss of TET2 function in lymphoma cells.
To investigate the sequence of events occurring during tumor development, the tumor cells from patient 27 were further analyzed. SNP microarray analyses showed several acquired abnormalities, including an LOH of the long arm of chromosome 7 and a duplication of the long arm of chromosome 4 (data not shown).
FISH analyses confirmed the presence of an additional copy of the TET2 locus in 20% of the nuclei in blood sample (data not shown). Sequencing of the PCR products obtained from single cells, sorted in individual wells from the fraction enriched in CD34−CD3−CD19−CD14− tumor cells, confirmed the simultaneous presence of both TET2 mutations in 6/10 assays (FIG. 16d). A fragment spanning the two mutations from the same tumor population was PCR-amplified, and the PCR products were subcloned using T/A vectors. Sequencing of individual bacterial colonies showed that a given mutation was always associated with a wild-type sequence at the other position. The P761fs/Q481 wt combination was observed 24/42 times (57%) and the P761 wt/Q481X combination 18/42 times (43%) (data not shown). No wild-type fragment was sequenced from these vectors, indicating that all three TET2 copies present in the tumor cells were mutated.
The observed ratio between both mutations indicated that the duplicated copy carried the P761fs mutation. In addition, these data indicate that the flow-sorted CD34−CD3−CD19−CD14− fraction contained essentially tumor cells.
17.7. Additional Genetic Alterations are Associated with TET2 Mutations
To identify additional genetic alterations in lymphomas, an exome sequencing approach was used to investigate DNA from the CD34−CD3−CD19−CD14− (tumor) and CD3+ (matched control) fractions. For each fraction, exonic DNA was captured using the SureSelect oligonucleotides (Agilent) and sequenced to generate 115600653 and 90633228 reads, from tumor and matched control libraries, respectively.
It was first confirmed the presence of both TET2 mutations in the tumor population at a ratio of 184/339 reads (54%) for P761fs and 140/389 reads (36%) for the Q481X, consistent with the duplication of the P761fs mutation (FIG. 16e). The two mutations were observed at very low frequencies in the CD3+ fraction (8/228 reads (4%) and 6/256 (2%) reads, respectively). It was next looked for sequence variations, with respect to the human reference sequence, that were present only in the tumor population.
Variations in seven genes (IGSF21, CRIM1, CLSTN2, MCCC2, PLZF, ZC3H10, and ZNF774) were validated by Sanger analysis (FIG. 16e).
Quantitative RT-PCR was then used to analyze the expression profile of the mutated genes in RNA from normal human brain, bone marrow, peripheral lymphocytes, and in flow-sorted tumor cells from patient 27 (FIG. 16f). CLSTN2 expression was observed in brain, but not in normal PBL, thymus, or bonemarrow nor inpatient's tumor samples (data not shown). The lack of detectable expression of CLSTN2 in the hematopoietic system suggests that the CLSTN2 mutation could be a passenger rather than a causal mutation. The transcription of ZNF774, CRIM1, and IGSF21 was not detected in normal blood cells and/or in the tumor sample, but was observed in the bone marrow and/or thymus, questioning their role in the transformation process. Finally, the presence of the mutations in the CD34+-derived colonies of the patient was investigated. Mutations in PLZF and CRIM1 were identified in eight of eight CD34+-derived colonies with the TET2 P761 fs mutation. The ZNF774 mutation was observed in six of eight TET2 mutated colonies tested, suggesting that it occurred later in the transformation process than the three others (i.e., TET2, PLZF, and CRIM1). ZNF774, PLZF, and CRIM1 mutations were not observed in 65 TET2 wild-type CD34+ colonies, suggesting that they did not occur independently of the TET2 P761fs mutation.














TABLE 11





TET2





TET2



mutated





mutation
Tumor


patients
Sample
Diagnosis
Mutation Type
Nucleotide change
Consequence
presence
presence2







 1
node
DLBCL
Nonsense
c.3087C > T
p.Gln743X
ND
ND


 2*
node
DLBCL
Frameshift and
c.[2202delG(+)4663 + 1G > A]
p.Glu448fs
Trace
No





splice






 3*
node
DLBCL
Nonsense
c.5406C > T
p.Arg1516X
Yes
Yes


 4*
node
DLBCL
Nonsense
c.3506C > T
p.Gln886X
Yes
No


 5*
node
DLBCL
Splice
c.4814 + 2T > G
—
No
No


 6*
node
FL
Missense
c.5116C > G
p.Pro1419Arg
No
No


 7
node
AITL
Nonsense +
c.[3192C > T(+)3628_3629insCATA]
p.[Gln778X(+)Asn923fs]
ND
ND





Frameshift






 8
blood
AITL
Nonsense
c.5193C > T
p.Gln1445X
ND
ND


 9
node
AITL
Frameshift
c.3215delT
p.Phe785fs
ND
ND


10*
node
AITL
Frameshift × 2
c.[1893_1896delAAGC] + [4527delG]
[p.Lys345fs] + [p.Ala1223fs]
Trace
No


11
node
AITL
Frameshift
c.6564delT
p.Tyr1902fs
ND
ND


12
node
AITL
Frameshift × 2
c.[2505delA] + [2524delC]
[p.Thr549fs] + [p.Pro555fs]
ND
ND


13*
node
AITL
Frameshift
c.5523_5524insA
p.Glu1555fs
Yes
No


14
node
AITL
Frameshift
c.3756_3757del CA
p.Gln966fs
ND
ND


15*
node
AITL
Frameshift
c.1642delC
p.Ser261fs
Yes
Yes


16*
node
AITL
Splice
c.4815-2delA
—
Trace
No


17*
node
PCTL, NOS
Frameshift +
c.[3131_3137delCCAGACT] +
[p.Leu757fs] + [p.Val1417Phe]
Trace
Yes





missense
[5109G > T]





18
node
PCTL, NOS
Nonsense × 2
c.[3747C > T] + [5331A > T]
[p.Gln963X] + [p.Lys1491X]
ND
ND


19
node
PCTL, NOS
Frameshift +
c.[1700_1701insT(+)3606C > T]
p.[Asn281fs(+)Gln916X]
ND
ND





nonsense






20*
node
PCTL, NOS
Missense
c.6553C > T
p.Ser1898Phe
Trace
Yes


21*
node
PCTL, NOS
Frameshift × 2
c.[1805delC(+)3602delT]
p.[Ser315fs(+)Leu914fs]
Trace
Yes


22
node
PCTL, NOS
Nonsense
c.5100C > T
p.Gln1414X
ND
ND


23
skin
Sezary
Missense +
c.[5053T > C(+)5253C > T]
p.[Leu1398Pro(+)Arg1465X]
ND
ND





Nonsense






24
blood
Sezary
Nonsense
c.2636C > T
p.Gln593X
ND
ND


25
node
TLBL
missense
c.6745C > T
p.Pro1962Leu
ND
ND


26*
node
Unspecified T-
Frameshift
c.1511delC
p.Ser217fs
Yes
NA




lymphoma







27
blood
Unspecified T-
Frameshift +
c.[2301C > T(+)3142delC]
p.[Gln481X(+)Pro761fs]
ND
ND




lymphoma
nonsense





*Matched DNA available


1Diagnosis and remission samples correspond respectively with whole blood and cytapheresis samples


2Clonality analysis (TCR/IgH rearrangement or BCL2-IGH transcript)


ND: Not Determined

## Claims

1. A method of treating a subject having a myeloid tumour or a lymphoid tumour, wherein the tumour comprises:
cells having a mutated TET2 gene encoding a frameshift at Leu757 or Glu448 in the resulting TET2 protein expressed by the tumour; or
cells having a mutated TET2 gene having
a nonsense mutation that encodes Gln963Stop, Gln593Stop, Gln778Stop, Gln886Stop, Gln1445Stop, Gln778Stop and a frameshift at Asn923, Gln916Stop and a frameshift at Asn281, or a frameshift at Ser315 and Leu914 in the resulting TET2 protein expressed by the tumour;


the method comprising:
detecting in a biological sample from the subject the presence of the mutated TET2 gene and/or the resulting TET2 protein expressed by the tumour; and
administering to the subject a therapeutically efficient amount of a hypomethylating agent.

2. The method according to claim 1, wherein said subject is in need of confirmation of having myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), myeloproliferative disease (MPD) or myelodysplastic/myeloproliferative syndrome.

3. The method according to claim 1, wherein said subject is in need of confirmation of having myelodysplastic/myeloproliferative syndrome.

4. The method according to claim 1, wherein said subject is in need of confirmation of having lymphoma.

5. The method according to claim 1, wherein said subject is a mammal.

6. The method according to claim 1, wherein the frameshift and/or mutation is detected on one or both allele of the TET2 gene coding for the polypeptide having the sequence SEQ ID NO:2.

7. The method of claim 1, wherein the detecting comprises using a kit comprising at least one nucleic acid probe, oligonucleotide, or antibody.