Cancer therapy of subjects carrying mutations in a splicing factor gene

Abstract

The present invention is directed to SEL24 / MEN1703 for use in the treatment of a patient suffering from cancer and / or for use in increasing the overall survival of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in at least one gene associated with splicing.

Description

[0001] CANCER THERAPY OF SUBJECTS CARRYING MUTATIONS IN A SPLICING FACTOR GENE

[0002] Field of the Invention

[0003] The present invention lies in the field of cancer therapy. More specifically, it is directed to SEL24 / MEN1703 for use in the treatment of cancer of a patient that carries at least one mutation in a least one gene associated with splicing.

[0004] Background of the Invention

[0005] Myelodysplastic syndromes (MDS) are a genetically and clinically diverse group of clonal disorders of the progenitor cells or hematopoietic stem cells, which are comprised of chronic phases including myeloproliferative neoplasms, myelodysplastic disorders, chronic myelomonocytic leukemia, and acute stages, i.e., acute myeloid leukemia (AML). They are generally characterized by inefficient hematopoiesis and peripheral blood cytopenias. It is hypothesized that genetic alterations occurring at the level of a multipotent stem cell accelerate clonal evolution from MDS, often resulting in transformation to acute leukemia, although no specific disease-initiating defect has been identified to date.

[0006] To date various gene mutations acting as driver events have been identified with various frequencies across the spectrum of MDS and AML. Functional analysis of these genes could cluster them into pathways including DNA methylation, chromatin remodeling, RNA-splicing, cohesion complex, RAS family signaling, gene transcription, and DNA repair.

[0007] One of the major classes of driver mutations is mutations in splicing factor (SF) genes encoding for components of the splicing reaction-catalyzing spliceosomes. SF mutations are found in a substantial share of different MDS subtypes and in a significant number of primary AML cases, where these mutations occur in the same spots in MDS and AML. The most commonly observed mutations in MDS and AML occur in the ZRSR2, SF3B1 , SRSF2, and U2AF1 genes and include missense mutations as well as inactivating mutations (nonsense or frameshift).

[0008] It has been found that while SF3B1 mutations are typcially associated with increased survival, SRSF2 and U2AF1 are associated with shorter overall survival, increased AML progression and lower remission rate, respectively.

[0009] While various treatment options for MDS and in particular AML exist, there is thus need in the art for novel therapies that target the cancer subtypes characterized by SF mutations.

[0010] Summary of the Invention

[0011] The present invention is based on the inventors’ surprising finding that an AML patient subgroup having mutations in splicing factor genes respond particularly well to treatment with the oral, type I dual PIM / FLT3 inhibitor SEL24 / MEN1703 (5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H- 1 ,3, benzodiazole).

[0012] In a first aspect, the present invention is thus directed to a method for the treatment of cancer in a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), comprising administering a therapeutically effective amount of 5,6-Dibromo-4-nitro-2- (piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703) to said patient, wherein said patient carries at least one mutation in at least one gene associated with splicing.

[0013] The first aspect may also be formulated as SEL24 / MEN1703 for use in the treatment of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in at least one gene associated with splicing.

[0014] In a second aspect, the present invention is directed to a method for increasing the overall survival or improving the prognosis of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), comprising administering a therapeutically effective amount of 5, 6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703) to said patient, wherein said patient carries at least one mutation in at least one gene associated with splicing.

[0015] The second aspect may also be formulated as SEL24 / MEN1703 for use in increasing the overall survival or improving the prognosis of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in at least one gene associated with splicing.

[0016] In a third aspect, the present invention is directed to a method of treating a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), the method comprising:

[0017] (a) obtaining a biological sample from the subject;

[0018] (b) detecting in the biological sample at least one mutation in at least one gene associated with splicing and / or, if the cancer is MDS, detecting in the biological sample the presence of >5%, preferably >15% ring sideroblasts; and

[0019] (c) administering to the patient a therapeutically effective amount of 5,6-Dibromo-4-nitro-2- (piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703), thereby treating the cancer.

[0020] The third aspect may also be formulated as SEL24 / MEN1703 for use in a method of treating a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), the method comprising: (a) obtaining a biological sample from the subject;

[0021] (b) detecting in the biological sample at least one mutation in at least one gene associated with splicing and / or, if the cancer is MDS, detecting in the biological sample the presence of >5%, preferably >15% ring sideroblasts; and

[0022] (c) administering to the patient a therapeutically effective amount of 5,6-Dibromo-4-nitro-2- (piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703), thereby treating the cancer.

[0023] In an embodiment, the method of the third aspect comprises the following steps:

[0024] (a) obtaining a biological sample from the subject;

[0025] (b) detecting in the biological sample at least one mutation in at least one gene associated with splicing; and

[0026] (c) administering to the patient a therapeutically effective amount of 5,6-Dibromo-4-nitro-2- (piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703), thereby treating the cancer.

[0027] In a fourth aspect, the present invention is directed to a method of selecting a patient suffering from cancer for the treatment with 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703), wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), the method comprising:

[0028] (a) obtaining a biological sample from the subject;

[0029] (b) determining in the biological sample the presence or absence of at least one mutation in at least one gene associated with splicing and / or, if the cancer is MDS, determining the percentage of ring sideroblasts; and

[0030] (c) selecting the patient for the treatment with SEL24 / MEN1703 if at least one mutation in at least one gene associated with splicing is present in the biological sample and / or, if the cancer is MDS, the percentage of ring sideroblasts is >5%, preferably >15%.

[0031] In an embodiment, the method of the fourth aspect comprises the following steps:

[0032] (a) obtaining a biological sample from the subject;

[0033] (b) determining in the biological sample the presence or absence of at least one mutation in at least one gene associated with splicing; and

[0034] (c) selecting the patient for the treatment with SEL24 / MEN1703 if at least one mutation in at least one gene associated with splicing is present in the biological sample.

[0035] In various embodiments, said at least one gene associated with splicing is a splicing factor gene. The at least one mutation may cause a reduction or inhibition of splicing, or may result in a reduction or inhibition of splicing. In various embodiments, the patient carries said at least one mutation in any one or more splicing factor gene(s) selected from the SRSF2, SF3B1, U2AF1 and / or ZRSR2 gene(s). In a preferred embodiment, the patient carries said at least one mutation in any one or more splicing factor gene(s) selected from the SRSF2, U2AF1 and / or ZRSR2 gene(s).

[0036] In various embodiments, the patient carries said at least one mutation in the SRSF2 gene, for example at a position corresponding to amino acid position P95 of the SRSF2 gene product. Said at least one mutation may result in the amino acid substitution P95H, P95L, P95R, P96A or P95T, preferably P95H in the encoded protein.

[0037] In various embodiments, the patient carries said at least one mutation in the U2AF1 gene, for example at a position corresponding to amino acid position(s) S34 and / or Q157 of the U2AF1 gene product. Said at least one mutation may result in the amino acid substitution S34F in the encoded protein.

[0038] In various embodiments, the patient carries said at least one mutation in the ZRSR2 gene.

[0039] In various embodiments, the patient carries said at least one mutation in both, the SRSF2 and the U2AF1 genes. In various other embodiments, the patient carries said at least one mutation in both, the SRSF2 and ZRSR2 genes. In still various further embodiments, the patient carries said at least one mutation in both, the U2AF1 and ZRSR2 genes. In some embodiments, the patient may also carry at least one mutation in all three of the SRSF2, U2AF1 and ZRSR2 genes.

[0040] In various embodiments, the patient carries, in addition to the at least one mutation in any one or more of the SRSF2, U2AF1 and ZRSR2 gene(s), one or more additional mutations in any one or more of the RUNX1, BCOR, STAG2, EZH2, KMT2A, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s). Preferably, the patient carries, in addition to the at least one mutation in any one or more of the SRSF2, U2AF1 and ZRSR2 gene(s), one or more additional mutations in any one or more of the RUNX1, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s).

[0041] In various embodiments, the patient carries at least one mutation in the SRSF2 gene and at least one mutation in any one of more of the RUNX1, IDH1, IDH2, TET2, and ASXL1 gene(s), preferably the IDH1 and / or / D / 72 genes.

[0042] In various embodiments, the patient carries at least one mutation in the U2AF1 gene and at least one mutation in any one of more of the DNMT3A, RUNX1, TET2 and ASXL1 gene(s), and preferably no mutation in the IDH1 gene.

[0043] In various embodiments, the patient further carries at least one mutation in any one or more of the LUC7L2, and PRPF8 gene(s). In various embodiments, SEL24 / MEN1703 is administered at a daily dose of about 50 mg to about 150 mg, wherein a daily dose of 125 mg is particularly preferred.

[0044] In various embodiments, SEL24 / MEN1703 is administered orally.

[0045] In various embodiments, the cancer treated may be AML, optionally secondary, relapsed, or refractory AML. The cancer treated may also be CS-AML.

[0046] In various embodiments, the cancer treated may be MDS with ring sideroblasts (RS).

[0047] In various embodiments, the biological sample may be a bone marrow aspirate / biopsy sample or a blood sample comprising cells. The biological sample may be obtained by any standard procedure known to the skilled person. The presence (and the percentage, respectively) of ring sideroblasts is typically determined in bone marrow aspirates.

[0048] In various embodiments, the absence or presence of the at least one mutation in at least one gene associated with splicing in the biological sample, more specifically in the cells comprised in the biological sample, may be detected using next generation sequencing (NGS), preferably NGS of gDNA (obtained from the sample) or cDNA prepared from RNA (obtained from the sample). However, any other commonly established method may be used as well.

[0049] Brief Description of the Drawings

[0050] Figure 1 shows product-limit survival probability estimates for two patient groups treated with the same doses of SEL24 / MEN1703 (125 mg), wherein the first group of patients carries the wt SRSF2 gene and the second group of patients carries a mutant SRSF2 gene.

[0051] Figure 2 shows product-limit survival probability estimates for two patient groups treated with the same doses of SEL24 / MEN1703 (125 mg), wherein the first group of patients carries the wt spliceosome genes SRSF2, U2AF1 and ZRSR2 and the second group of patients carries mutations in at least one of the SRSF2, U2AF1 and ZRSR2 genes.

[0052] Detailed Description

[0053] 1. Definitions

[0054] As used in the specification and the claims, the singular forms of “a” and “an” also include the corresponding plurals unless the context clearly dictates otherwise.

[0055] The term “at least one”, as used herein, means one or more, i.e. 1 , 2, 3, 4, 5, 6, 7, 8, 9 or more of the referenced species. Similarly, “one or more”, as used herein, relates to at least one and comprises 1 , 2, 3, 4, 5, 6, 7, 8, 9 or more. In connection with a given species, the term does not relate to the total number of molecules, but rather to the type of species. “At least one compound”, for example, thus means that one type of compound or two or more different types of compounds may be present. In connection with amounts, the term relates to the total amount of the referenced species.

[0056] Numeric values specified without decimal places here refer to the full value specified with one decimal place, i.e., for example, 99 % means 99.0 %, unless otherwise defined.

[0057] The term “about” in the context of the present invention denotes an interval of accuracy that a person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically indicates a deviation from the indicated numerical value of ±10% and preferably ±5%.

[0058] It needs to be understood that the term “comprising” is not limiting. For the purposes of the present invention, the term “consisting of’ is considered to be a preferred embodiment of the term “comprising”. If hereinafter a group is defined to comprise at least a certain number of embodiments, this is also meant to encompass a group which preferably consists of these embodiments only.

[0059] The term “SEL24 / MEN1703” (alternatively referred to herein as “MEN”, “Men”, “men” or “Men1703”) as used herein means the compound 5,6-dibromo-4-nitro-2-(piperidin-4-yl)-1 -(propan-2-yl)-1 H-1 ,3- benzodiazole, in the form of the free base or a pharmaceutically acceptable salt thereof (such as the HCI-salt). The free base form has the CAS-number 1616359-00-2, whereas the HCI-salt form has the CAS-number 2769008-22-0. The compound is a dual pan-PIM / FLT3 inhibitor, which has inter alia been shown to inhibit the growth of a broad panel of AML cell lines in xenograft models. The rationale for the development of this dual inhibitor was that PIM kinases are deemed to be majordrivers of the resistance to FLT3-inhibitors. SEL24 / MEN1703 is characterized in more detail e.g., in Czardybon et al., 2018. International patent publication WO 2014 / 096388 discloses SEL24 / MEN1703 as Compound 26A therein and characterizes SEL24 / MEN1703 as dual pan-PIM / FLT3 inhibitor, see Table 1A of WO 2014 / 096388.

[0060] The term “treatment” as used herein refers to clinical intervention in order to cure or ameliorate a disease, prevent recurrence of a disease, alleviate symptoms of a disease, diminish any direct or indirect pathological consequences of a disease, achieve a stabilized (i.e., not worsening) state of disease, prevent metastasis, decrease the rate of disease progression, and / or prolong survival as compared to expected survival if not receiving treatment.

[0061] The term “relapsed or recurrent AML” as used herein means that the AML has come back after treatment (using a different drug, optionally a drug combination, as the combination of the present invention) and remission.

[0062] The term “refractory AML” as used herein means that the leukemia did not respond to previous treatment (using a different drug, optionally a drug combination, as the combination of the present invention). The term “secondary AML” also abbreviated (sAML) refers to AML arising either after a prior hematologic disorder, such as myelodysplastic syndrome (MDS) or a myeloproliferative neoplasm (MPN), or after exposure to cytotoxic agents or radiation therapy. In total, sAML accounts for 10% to 30% of all AML cases. Most cases (60%-85%) of sAML progress from antecedent MDS, while therapy-related (tAML) accounts for 15% to 40% of all sAML cases. The proportion of AML patients with sAML increases with age. Before age 40, therapy-related AML (tAML) and AML with an antecedent hematologic disorder each constitute about 3% of all AML cases; after age 40, the prevalence of tAML and AML with an antecedent hematologic disorder increase to approximately 10% and 20% of all AML cases, respectively. Across multiple studies, sAML has been associated with inferior outcomes, including lower remission rates and shortened overall survival (OS), compared with de novo AML. The term “CS-AML” refers to the AML subtype of the chromatin-spliceosome group according to the genomic classification of Papaemmanuil E. et al., Genomic Classification and Prognosis in Acute Myeloid Leukemia. N. Engl. J. Med. 2016;374:2209-2221 . doi: 10.1056 / NEJMoa1516192.

[0063] The term “MDS with ring sideroblasts” or “MDS with RS” or “MDS-RS” refers to a lower risk MDS characterized by the presence of ring sideroblasts (RS), which are erythroid precursors with abnormal perinuclear mitochondrial iron accumulation. MDS-RS is diagnosed as an MDS with single or multilineage dysplasia (MDS-RS-SLD / MLD), <5% bone marrow (BM) blasts, <1 % peripheral blood blasts and >15% BM RS (>5% in the presence of SF3B1 mutations).

[0064] The terms “splicing related gene” or “gene associated with splicing”, as used interchangeably herein, relate to genes that encode splicing factors, as defined herein below, or other components involved in the splicing of mRNA, in particular all proteins and RNA molecules (snRNA) forming or involved in forming the spliceosomes. The term thus does not only include the protein splicing factors but also the nucleic acid molecules involved in gene splicing, i.e., the small nuclear RNAs (snRNAs) that are involved in assembling the spliceosome. The terms do, however, not include the mRNA that is spliced or the gene encoding the mRNA that is spliced.

[0065] The term “splicing factor (SF)”, as used herein, relates to a protein that is involved in the removal of introns from strings of messenger RNAs so that the exons are directly bound to each other. SF genes encode for components of the spliceosomes. Spliceosomes are nuclear structures composed of five small nuclear RNAs (snRNA) and approximately 150 proteins, which catalyze the splicing reaction. The complex removes non-coding sequences (introns) from precursor messenger RNA and ligates coding sequences (exons) in order to form mature mRNA transcripts through early and late steps. Early steps involve recognition of the 5' and 3' exon / intron junctions and late steps recall all the spliceosome together. The information to define the splicing regions are included in short and conserved sequences at the 5' splice site (SS), the 3'SS, and the branch site (BS). Many genes in humans are spliced into two or more transcripts with altered sequences through a process called alternative splicing. The proteins involved in the splicing comprise, among others, the family of serine-arginine rich (SR) proteins, such as SRSF6 and SRSF2. SR proteins have versatile functions such as regulating pre-mRNA splicing, RNA stability, and translation. Known SF proteins include, without limitation, SRSF6, ZRS2, U2AF1 L4, SF1 , U2AF2, U2AF1 , SRSF2, SF3A1 , SF3B1 , SF3B3, PRFP8, and LUC7L2. Several splicing factors are recurrently mutated in cancer, including splicing factor 3B, subunit 1 (SF3BT), serine / arginine-rich splicing factor 2 (SRSF2), U2 small nuclear RNA auxiliary factor 1 (U2AF1) and zinc finger, RNA-binding motif and serine / arginine-rich 2 (ZRSR2). These spliceosomal mutations have been discovered across a broad range of tumor types, including myelodysplastic syndromes (MDS), chronic lymphocytic leukemia (CLL), uveal melanoma (UVM), lung adenocarcinoma (LUAD), breast invasive carcinoma (BRCA) and others.

[0066] The term “SRSF2 mutation”, as used herein, means a mutation in the serine / arginine-rich splicing factor 2 gene, which encodes the corresponding protein. The SRSF2 gene is located on chromosome 17q25.2 and encodes a member of the serine / arginine (SR)-rich family of pre-mRNA splicing components. It contains an RNA recognition motif (RRM) for binding RNA and an arginine and serine domain for binding other proteins. The arginine and serine domain is enriched in SR residues facilitating the interaction between SR and SF. SRSF2 mutations on a protein level occur almost exclusively at proline 95 and alter binding affinity of the RRM motif. SRSF2 mutations have been found in 28-47% of patients with CMML and about 14% of patients with MDS and have been associated with increased age, higher levels of hemoglobin, and normal cytogenetics. SRSF2 mutations are almost never sole mutations. In CMML, SRSF2 mutations are often found with TET2 mutations, while in AML they are typically associated with RUNX1 , IDH2, and ASXL1 mutations. Pooled meta-analysis studies of MDS patients have shown that patients with SRSF2 mutations predict for a worse survival and an increased risk for AML transformation and have no prognostic effects in CMML. As noted above, a preferred SRSF2 mutation is at least one mutation in the SRSF2 gene resulting in an amino acid substitution at position 95 of the SRSF2 protein. The amino acid at position 95 in the wild-type SRSF2 protein is a proline. Accordingly, in the preferred embodiment, the proline at position 95 is substituted by a different amino acid, wherein the substitution can be selected from P95H, P95L, P95R, P96A and P95T.

[0067] The term “U2AF1 mutation”, as used herein, means a mutation in the U2-complex auxiliary factor 1 gene (U2AF1 , 21q22.3) which encodes a 35-kDa protein (alias U2AF35) of the U2-spliceosome responsible for recognition of the terminal 30 AG dinucleotide in pre-messenger RNA introns. The protein has four major domains including two zinc finger regions, a serine-arginine (SR) domain, and an U2AF-homology domain. The U2AF1 unit forms a complex by heterodimerization with the 65-Kda protein called U2AF2 in order to bind the polypyrimidine tract upstream the 30SS and recognize the branch point and the AG dinucleotide of the 30SS. Mutations in the U2AF1 gene corresponding to amino acid position S34 (often resulting in the amino acid substitution S34F) and Q157 are found in about 11 % of patients with MDS and in 4% of patients with AML. Mutations are associated with a worse survival and are associated with an increased risk of AML transformation. U2AF1 mutations result in the production of neomorphic phenotypes by chancing splicing patterns for many RNA downstream genes. These changes are lineage-specific and seem to influence the division of erythroid progenitors and subsequently change the differentiation trajectory of granulocytes and monocytes.

[0068] The term “ZRSR2 mutation”, as used herein, relates to a mutation in the zinc finger, RNA-binding motif and serine / arginine-rich a gene located on chromosome Xp22.2, which is mutated in about 5% of patients with MDS, predominantly males. The protein is another member of the SR-rich family of SF, and the gene encodes a component of the U2 auxiliary factor heterodimer which is responsible for the recognition of the 30 splice acceptor site. The nature of the mutations resembles loss-of-function mutations. Out-of-frame insertions and deletions, nonsense, missense, and splice site mutations have all been detected. No mutation hotspots have been observed and the mutations scatter across the entire coding region. In terms of splicing abnormalities, ZRSR2 mutations cause abnormal splicing via intron retention of U12-depedent introns.

[0069] The term “RUNX1 mutation”, as used herein, relates to a mutation in the Runt-related transcription factor

[0070] 1 gene, which encodes the RUNX1 transcription factor also known as acute myeloid leukemia 1 protein (AML1) or core-binding factor subunit alpha-2 (CBFA2). RUNX1 regulates the differentiation of hematopoietic stem cells into mature blood cells. RUNX proteins form a heterodimeric complex with CBFp which confers increased DNA binding and stability to the complex. Chromosomal translocations involving the RUNX1 gene are associated with several types of leukemia including M2 AML. Mutations in RUNX1 are also implicated in cases of breast cancer.

[0071] The terms “IDH1 and / or IDH2 mutation” as used herein means a mutation in the “isocitrate dehydrogenase 1 ” gene or the “isocitrate dehydrogenase 2” gene, which encode the corresponding isocitrate dehydrogenases. IDH1 mutations are heterozygous, typically involving an amino acid substitution in the active site of the enzyme in codon 132. These mutations primarily occur in cells that can become cancerous, such as those in brain and bone tumors. The mutation results in a loss of normal enzymatic function and the abnormal production of 2-hydroxyglutarate (2-HG), causing widespread changes in histone and DNA methylation and potentially promoting tumorigenesis. To date it has become clear that mutations in IDH1 and its homologue IDH2 are among the most frequent mutations in diffuse gliomas.

[0072] The term “TET2 mutation”, as used herein, relates to a mutation in the Tet methylcytosine dioxygenase

[0073] 2 (TET2) gene. It resides at chromosome 4q24, in a region showing recurrent microdeletions and copyneutral loss of heterozygosity in patients with diverse myeloid malignancies. The TET2 protein catalyzes the conversion of the modified DNA base methylcytosine to 5-hydroxymethylcytosine.

[0074] The term “DNMT3A mutation”, as used herein, relates to a mutation in the DNMT3A gene encoding the DNA (cytosine-5)-methyltransferase 3A (DNMT3A) which catalyzes the transfer of methyl groups to specific CpG structures in DNA. This gene is frequently mutated in cancer, being one of 127 frequently mutated genes identified in the Cancer Genome Atlas project. DNMT3A mutations are most commonly seen in AML where they occur in just over 25% of cases sequenced. These mutations most often occur at position R882 in the protein and this mutation may cause loss of function. DNMT3A mutations are associated with poor overall survival.

[0075] The term “ASXL1 mutation”, as used herein, relates to a mutation in the additional sex combs like 1 (ASXL1) gene. The gene encodes a chromatin-binding protein required for normal determination of segment identity in the developing embryo. The protein is a member of the polycomb group of proteins, which are necessary for the maintenance of stable repression of homeotic and other loci. Mutations in this gene have been found to be associated with myelodysplastic syndromes and chronic myelomonocytic leukemia.

[0076] The term “BCOR mutation”, as used herein, relates to a mutation in the BCL6 corepressor (BCOR) gene. The gene encodes a corepressor that is a component of a variant Polycomb repressive complex 1 . The term “STAG2 mutation”, as used herein, relates to a mutation in the STAG2 gene. The protein encoded by this gene is a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. The term “EZH2 mutation”, as used herein, relates to a mutation in the Enhancer Of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2) gene. The protein encoded by this gene is a member of the Polycomb-group (PcG) family. The term “KMT2A mutation”, as used herein, relates to a mutation in the Lysine Methyltransferase 2A (KMT2A) gene, in particular a partial tandem duplication (PTD) of the gene. The protein encoded by this gene is a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The afore-mentioned mutations in these genes and genes, respectively, are amongst other genes part of a definition of a genomic subgroup of AML, namely AML with mutated chromatin, RNA-splicing genes, or both (see Papaemmanuil E. et al., supra).

[0077] The term “LUC7L2 mutation”, as used herein, relates to a mutation in the Luc7-like 2 gene located on chromosome 7q34. It is a common target of gene deletions given the frequency of deletion of the long arm of chromosome 7 [del(7q)] and monosomy 7 in myeloid malignancies. The gene encodes a protein with a C2H2-type zinc finger, a coiled-coil region, and an SR domain. To date the function of LUC7L2 is not well characterized and the majority of what is known about the protein is based on observations of its ortholog splicing factor LUC7 which is involved in recruitment and interaction of SF. LUC7L2 mutations can be hemizygous, heterozygous, and homozygous. LUC7L2 mutations have been associated with shorter survival in patients with -7 / del7q compared to patients with normal LUC7L2 expression.

[0078] The term “PRPF8 mutation”, as used herein, is a mutation in the pre-mRNA processing factor 8 gene located on chromosome 17p13.3 and has been found to be affected by somatic mutations or hemizygous deletions. A majority of patients (50%) with PRPF8 mutations and del(17p) were found to be AML patients with poor prognosis. PRPF8 alterations were found to correlate with increased RS and myeloblasts. A subsequent analysis of a large cohort showed that PRPF8 mutations were common and found in 4% (65 / 1700) of patients with MDS and AML. Mutations are mainly missense, nonsense, frameshift, and splice site mutations, and showed a strong association with dismal prognosis.

[0079] The term “SF3B1 mutation”, as used herein, relates to a mutation in the splicing factor 3B, subunit 1 gene (chromosome 2q33.1), which encodes a core component of the U2 nuclear ribonucleoprotein, which recognizes the 30SS at intron-exon junctions. Mutations are located preferentially in four consecutive HEAT (Huntington elongation factor 3 protein phosphatase 2A, and the yeast PI3-kinase TOR1) domains of the C-terminal region, with the lysine to glutamic acid substitution at codon 700 (K700E) accounting for more than 50% of all mutant cases. Other common hotspot mutations involve the conserved amino acids 622, 625, 662, and 666. Studies in murine models have shown that homozygous mutations of the SF3B1 gene are incompatible with life.

[0080] The term “wherein said patient carries at least one mutation in at least one gene”, as used herein, means that the patient has at least one mutation in a gene, i.e., at least one mutation at the genomic level, wherein the mutation is in particular present in the genome of a cancer cell of said patient, i.e., in an MDS or AML cell.

[0081] 2. Description of the present invention

[0082] The present invention is based on the surprising finding that SEL24 / MEN1703 treatment can significantly increase overall survival (OS) in patients affected by mutations in the spliceosome genes SRSF2, U2AF1 and ZRSR2 relative to those patients treated that had no mutations in these genes. This is particularly surprising since mutations in these genes have previously been found to correlate with a poor prognosis and shorter overall survival (Visconte et al., Cancers (2019), 11 , 1844) and a higher rate of progression from MDS to AML (Damm et al., Blood (2012) 1 19 (14): 3211-3218).

[0083] The invention is thus directed to methods for the treatment of cancer, in particular hematologic malignancies, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), by administration of 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or salt thereof (SEL24 / MEN1703), in particular the hydrochloride salt, to a patient afflicted by such a cancer, wherein the patient carries at least one mutation in at least one gene associated with splicing, preferably a splicing factor gene.

[0084] In various embodiments, the cancer treated may be AML, including relapsed or recurrent AML, refractory AML, secondary AML, and / or therapy-related AML. The AML treated may thus be an aggressive form of AML that did not respond well to other treatments or is relapsed / recurrent AML or AML that developed from MDS progression.

[0085] Since it has been found that the treatment of the specific patient subgroup that has mutations in splicing related genes surprisingly results in an increase in overall survival relative to patients that lack the corresponding mutations in splicing related genes, it can be concluded that SEL24 / MEN1703 treatment is particularly effective for those patients in which the cancer is at least partly driven by mutations in splicing related genes, in particular those disclosed herein.

[0086] The present invention thus also features a method for increasing overall survival in a patient afflicted by a cancer, in particular hematologic malignancies, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), and carrying at least one mutation in at least one splicing related gene relative to a patient that lacks said at least one mutation in at least one splicing related gene, comprising administering 5, 6-Dibromo-4-nitro-2-(piperidin-4-yl)-1 -(propan-2 -yl)-1 H-1 ,3, benzodiazole or salt thereof (SEL24 / MEN1703) to said patient.

[0087] The administration of 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1 -(propan-2-yl)-1 H-1 ,3, benzodiazole or salt thereof (SEL24 / MEN1703) is typically carried out in therapeutically effective doses, for examples those defined herein below.

[0088] The increase in overall survival (OS) may be an increase of at least 5%, preferably at least 10%, more preferably at least 15% or 20% or 25% relative to the reference value. While it is generally desirable that OS is increased relative to the reference, i.e. a patient without the mutations in splicing related genes, in various embodiments, the object of the invention may be achieved by increasing overall survival to the same level as the reference, in particular in those cases where the mutation causes a worse prognosis and shorter overall survival relative to patients without the mutation. It is apparent that under such circumstances increasing OS to the same level as that of a patient with a similar treatment that lacks these mutations is already advantageous.

[0089] The invention also relates to the corresponding uses, i.e. SEL24 / MEN1703 for use in the treatment of cancer, in particular hematologic malignancies, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), in a patient and / or for increasing overall survival in a patient afflicted by a cancer, in particular hematologic malignancies, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), wherein said patient carries at least one mutation in at least one gene associated with splicing by administration of SEL24 / MEN1703, typically in a therapeutically effective amount or amount sufficient to achieve the desired effect, to said patient.

[0090] The invention also relates to a method of selecting a patient suffering from cancer for the treatment with 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703), wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), the method comprising:

[0091] (a) obtaining a biological sample from the subject;

[0092] (b) determining in the biological sample the presence or absence of at least one mutation in at least one gene associated with splicing; and

[0093] (c) selecting the patient for the treatment with SEL24 / MEN1703 if at least one mutation in at least one gene associated with splicing is present in the biological sample. Yet further, the invention relates to a method of selecting a patient suffering from cancer for the treatment with 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703), wherein the cancer is myelodysplastic syndrome (MDS), the method comprising:

[0094] (a) obtaining a biological sample from the subject;

[0095] (b) determining in the biological sample the percentage of ring sideroblasts; and

[0096] (c) selecting the patient for the treatment with SEL24 / MEN1703 if the percentage of ring sideroblasts is >5%, preferably >15%.

[0097] All following embodiments are similarly applicable to the inventive methods and uses and compounds for use.

[0098] The patient is preferably a human patient.

[0099] In various embodiments, said at least one gene associated with splicing is at least one splicing factor gene, i.e., a gene encoding a splicing factor. These splicing factors are typically proteins involved in gene splicing in particular those involved in the assembly, formation, and function of the spliceosome. The mutation typically results in a modulation of the normal splicing activity so that it becomes abnormal. Accordingly, all mutations in splicing related genes referred to herein, typically impair splicing in that they cause total or partial loss-of-function or result in aberrant splicing. The splicing activity may, for example, by reduced or inhibited to certain extent. While there are a multitude of mutations in splicing related genes and splicing factors that are known or hypothesized to play a role in cancer development, cancer progression, severity of the disease, resistance to treatments, and prognosis known in the field, in various embodiments, the at least one mutation in at least one gene associated with splicing is in at least one of the splicing factors genes SRSF2, SF3B1, U2AF1 and ZRSR2, preferably SRSF2, U2AF1 and ZRSR2.

[0100] It has been found by genotyping data analysis that the at least one mutation in at least one of the SRSF2, U2AF1 and ZRSR2 genes occurs in a certain percentage of AML patients and have generally been correlated to a poor prognosis in particular reduced overall survival in MDS / AML patients.

[0101] In various embodiments, the patient treated by the methods and uses of the invention is a patient carrying at least one mutation in the SRSF2 gene. Said mutation may be in the codon encoding P95 of the mature protein and may be a mutation resulting in the amino acid substitution P95H. As described above, it is known that SRSF2 mutations occur almost exclusively at positions corresponding to the encoded proline 95 and alter binding affinity of the RRM motif. The mature protein may have the sequence as given in Uniprot databank entry Q01130-1 (entry version 255 of 2 Oct 2024). The positional numbering may thus be according to the sequence given in said databank entry. The patients carrying at least one mutation in the SRSF2 gene may comprise additional mutations in other splicing related genes, in particular other splicing factor genes. These other genes may be U2AF1 and / or ZRSR2. In further embodiments, these other genes may be selected from any one or more of the RUNX1, IDH1, IDH2, TET2, and ASXL1 gene(s), such as the RUNX1, IDH2, and ASXL1 gene(s). In some embodiments, the patient may carry at least one mutation in the IDH1 and / or / D / 2 gene(s).

[0102] In various embodiments, the patient treated by the methods and uses of the invention is a patient carrying at least one mutation in the U2AF1 gene. Said mutation may be in the codon encoding amino acids S34 and / or Q157. The mutation in the codon encoding S34 may be a mutation resulting in the amino acid substitution S34F. The positional numbering is based on the mature protein which may have the sequence as given in Uniprot databank entry Q01081-1 (entry version 247 of 2 Oct 2024). The positional numbering may thus be according to the sequence given in said databank entry.

[0103] The patients carrying at least one mutation in the U2AF1 gene may comprise additional mutations in other splicing related genes, in particular other splicing factor genes. These other genes may be SRSF2 and / or ZRSR2. In further embodiments, these other genes may be selected from any one or more of the DNMT3A, RUNX1, TET2 and ASXL1 gene(s). In some embodiments, the patient may not have a mutation in the IDH1 gene.

[0104] In various embodiments, the patient treated by the methods and uses of the invention is a patient carrying at least one mutation in the ZRSR2 gene. Said mutation may be a loss-of-function mutations, such as those caused by out-of-frame insertions and deletions, nonsense, missense, and splice site mutations. The mature protein may have the sequence as given in Uniprot databank entry Q15696 (entry version 199 of 2 Oct 2024).

[0105] The patient treated according to the methods and uses of the invention may have at least one mutation in at least two of the genes SRSF2, U2AF1 and ZRSR2, or even in all three of SRSF2, U2AF1 and ZRSR2 genes.

[0106] In all the above embodiments, the patient may carry at least one mutation in at least one further splicing related gene selected from RUNX1, BCOR, STAG2, EZH2, KMT2A, IDH1, IDH2, TET2, DNMT3A, ASXL1, LUC7L2, PRPF8 and SF3B1, for example in at least one further splicing related gene selected from RUNX1, IDH1, IDH2, TET2, DNMT3A, and ASXL1 and / or in at least one further splicing related gene selected from LUC7L2, PRPF8 and SF3B1.

[0107] In various embodiments, the patient may have a mutation in the SRSF2 gene but not in any one of the U2AF1, ZRSR2, RUNX1, IDH1, IDH2, TET2, DNMT3A, ASXL1, LUC7L2, PRPF8 and SF3B1 genes, for example not in the U2AF1, ZRSR2, RUNX1, IDH1 orlDH2 gene. In various embodiments, the patient has a mutation in the SRSF2 gene but not in the U2AF1 gene. In various embodiments, the patient has a mutation in the SRSF2 gene but not in the ZRSR2 gene. In various embodiments, the patient has a mutation in the SRSF2 gene but not in the IDH1 gene. In various embodiments, the patient has a mutation in the SRSF2 gene but not in the / D / 72 gene.

[0108] In various embodiments, the patient may have a mutation in the U2AF1 gene but not in any one of the SRSF2, ZRSR2, RUNX1, IDH1, IDH2, TET2, DNMT3A, ASXL1, LUC7L2, PRPF8 and SF3B1 genes, for example not in the SRSF2, ZRSR2, RUNX1, IDH1 orlDH2 gene. In various embodiments, the patient has a mutation in the U2AF1 gene but not in the SRSF2 gene. In various embodiments, the patient has a mutation in the U2AF1 gene but not in the ZRSR2 gene. In various embodiments, the patient has a mutation in the U2AF1 gene but not in the IDH1 gene. In various embodiments, the patient has a mutation in the U2AF1 gene but not in the IDH2 gene.

[0109] In various embodiments, the patient may have a mutation in the ZRSR2 gene but not in any one of the SRSF2, U2AF1, RUNX1, IDH1, IDH2, TET2, DNMT3A, ASXL1, LUC7L2, PRPF8 and SF3B1 genes, for example not in the SRSF2, ZRSR2, RUNX1, IDH1 or IDH2 gene. In various embodiments, the patient has a mutation in the ZRSR2 gene but not in the SRSF2 gene. In various embodiments, the patient has a mutation in the ZRSR2 gene but not in the U2AF1 gene. In various embodiments, the patient has a mutation in the ZRSR2 gene but not in the IDH1 gene. In various embodiments, the patient has a mutation in the ZRSR2 gene but not in the IDH2 gene.

[0110] In various embodiments, SEL24 / MEN1703 is administered in an amount of about 50 mg to about 150 mg, preferably in an amount of about 50 mg, about 55 mg, about 60 mg, about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about 90 mg, about 95 mg, about 100 mg, about 105 mg, about 110 mg, about 115 mg, about 120 mg, about 125 mg, about 130 mg, about 135 mg, about 140 mg, about 145 mg, or about 150 mg, most preferably in an amount of about 100 mg, about 105 mg, about 110 mg, about 115 mg, about 120 mg or about 125 mg, wherein an amount of 125 mg is particularly preferred. It may be preferred that the dosage form comprising SEL24 / MEN1703 is a once-a- day dosage form. It is further preferred that the dosage form comprising SEL24 / MEN1703 is an oral dosage form.

[0111] A dosage form for use according to the present invention may be formulated for oral, buccal, nasal, rectal, topical, transdermal, or parenteral application. Oral application is particularly preferred. Parenteral application includes intravenous, intramuscular, or subcutaneous administration. A dosage form of the present invention may also be designated as formulation or pharmaceutical composition.

[0112] In general, a pharmaceutical composition according to the present invention can comprise various pharmaceutically acceptable excipients which will be selected depending on which functionality is to be achieved for the composition. A “pharmaceutically acceptable excipient” in the meaning of the present invention can be any substance used for the preparation of pharmaceutical dosage forms, including coating materials, film-forming materials, fillers, disintegrating agents, release-modifying materials, carrier materials, diluents, binding agents, and other adjuvants. Typical pharmaceutically acceptable excipients include substances like sucrose, mannitol, sorbitol, starch and starch derivatives, lactose, and lubricating agents such as magnesium stearate, disintegrants and buffering agents.

[0113] The term “carrier” denotes pharmaceutically acceptable organic or inorganic carrier substances with which the active ingredient is combined to facilitate the application. Suitable pharmaceutically acceptable carriers include, for instance, water, salt solutions, alcohols, oils, preferably vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, surfactants, perfume oil, fatty acid monoglycerides and diglycerides, petroethral fatty acid esters, hydroxymethyl-cellulose, polyvinylpyrrolidone and the like. The pharmaceutical compositions can be sterilized and if desired, mixed with auxiliary agents, like lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavoring, and / or aromatic substances and the like which do not deleteriously react with the active compound.

[0114] If liquid dosage forms are considered for the present invention, these can include pharmaceutically acceptable emulsions, solutions, suspensions, and syrups containing inert diluents commonly used in the art such as water. These dosage forms may contain e.g., microcrystalline cellulose for imparting bulk, alginic acid or sodium alginate as a suspending agent, methylcellulose as a viscosity enhancer and sweeteners / flavoring agents.

[0115] For parenteral application, particularly suitable vehicles consist of solutions, preferably oily or aqueous solutions, as well as suspensions, emulsions, or implants. Pharmaceutical formulations for parenteral administration are particularly preferred and include aqueous solutions in water-soluble form. Additionally, suspensions may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.

[0116] For injectable preparations, sterile injectable aqueous or oleaginous suspensions can for example be formulated according to the known art using suitable dispersing agents, wetting agents and / or suspending agents. A sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent. Among the acceptable vehicles and solvents that can be used are water and isotonic sodium chloride solution. Sterile oils are also conventionally used as solvent or suspending medium.

[0117] Suppositories for rectal administration of a pharmaceutical composition of the present invention can be prepared by e.g. mixing the compound with a suitable non-irritating excipient such as cocoa butter, synthetic triglycerides and polyethylene glycols which are solid at room temperature but liquid at rectal temperature such that they will melt in the rectum and release the active agent from said suppositories. For administration by inhalation, the pharmaceutical composition according to the present invention may be conveniently delivered in the form of an aerosol spray from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0118] Oral dosage forms may be liquid or solid and include e.g., tablets, troches, pills, capsules, powders, effervescent formulations, dragees and granules. Pharmaceutical preparations for oral use can be obtained as solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and / or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. The oral dosage forms may be formulated to ensure an immediate release of the active agent or a sustained release of the active agent.

[0119] The present invention also relates to the following embodiments lists.

[0120] List of embodiments A:

[0121] A1 . 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703) for use in the treatment of a patient suffering from cancer and / or for use in increasing the overall survival of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in at least one gene associated with splicing, wherein said at least one gene associated with splicing is a splicing factor gene, and wherein said at least one mutation results in a reduction or inhibition of splicing.

[0122] A2. SEL24 / MEN1703 for use according to A1 , wherein the patient carries said at least one mutation in any one or more of the SRSF2, SF3B1, U2AF1 and ZRSR2 gene(s), preferably in any one or more of the SRSF2, U2AF1 and ZRSR2 gene(s).

[0123] A3. SEL24 / MEN1703 for use according to A1 or A2, wherein the patient carries said at least one mutation in the SRSF2 gene. A4. SEL24 / MEN1703 for use according to A3, wherein the patient carries said at least one mutation in the SRSF2 gene at a position corresponding to amino acid position P95, preferably wherein the at least one mutation in the SRSF2 gene results in the amino acid substitution P95H in the encoded protein.

[0124] A5. SEL24 / MEN1703 for use according to any one of A1 to A4, wherein the patient carries said at least one mutation in the U2AF1 gene.

[0125] A6. SEL24 / MEN1703 for use according to A5, wherein the patient carries said at least one mutation in the U2AF1 gene at a position corresponding to amino acid position(s) S34 and / or Q157, preferably wherein the at least one mutation in the U2AF1 results in the amino acid substitution S34F in the encoded protein.

[0126] A7. SEL24 / MEN1703 for use according to any one A1 to A6, wherein the patient carries said at least one mutation in the ZRSR2 gene.

[0127] A8. SEL24 / MEN1703 for use according to any one of A1 to A7, wherein the patient carries said at least one mutation in (1) the SRSF2 and the U2AF1 genes, (2) the SRSF2 and ZRSR2 genes, (3) the U2AF1 and ZRSR2 genes, or (4) the SRSF2, U2AF1 and ZRSR2 genes.

[0128] A9. SEL24 / MEN1703 for use according to any one of A1 to A8, wherein the patient carries one or more additional mutations in any one or more of the RUNX1, BCOR, STAG2, EZH2, KMT2A, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s), preferably in any one or more of the RUNX1, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s).

[0129] A10. SEL24 / MEN1703 for use according to any one of A1 to A9, wherein the patient

[0130] (1) carries at least one mutation in the SRSF2 gene and at least one mutation in any one of more of the RUNX1, IDH1, IDH2, TET2, and ASXL1 gene(s), preferably the IDH1 and / or IDH2 genes; and / or

[0131] (2) carries at least one mutation in the U2AF1 gene and at least one mutation in any one of more of the DNMT3A, RUNX1, TET2 and ASXL1 gene(s), and preferably no mutation in the IDH1 gene.

[0132] A11 . SEL24 / MEN1703 for use according to any one of A1 to A10, wherein the patient further carries at least one mutation in any one or more of the LUC7L2 and PRPF8 gene(s).

[0133] A12. SEL24 / MEN1703 for use according to any one of A1 to A11 , wherein

[0134] (1) SEL24 / MEN1703 is administered at a daily dose of about 50 mg to about 150 mg; preferably of about 125 mg; and / or

[0135] (2) SEL24 / MEN1703 is administered orally; and / or

[0136] (3) the cancer is AML, optionally secondary, relapsed, or refractory AML. List of embodiments B:

[0137] B1 . 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703) for use in the treatment of a patient suffering from cancer and / or for use in increasing the overall survival of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in any one or more of the SRSF2, SF3B1, U2AF1 and ZRSR2 gene(s), wherein the at least one mutation in the SRSF2 gene is at a position corresponding to amino acid position P95.

[0138] B2. SEL24 / MEN1703 for use according to B1 , wherein said at least one mutation results in a reduction or inhibition of splicing.

[0139] B3. SEL24 / MEN1703 for use according to B1 or B2, wherein the patient carries said at least one mutation in any one or more of the SRSF2, U2AF1 and ZRSR2 gene(s), wherein the at least one mutation in the SRSF2 gene is at a position corresponding to amino acid position P95.

[0140] B4. SEL24 / MEN1703 for use according to any one of B1 to B3, wherein the at least one mutation in the SRSF2 gene results in the amino acid substitution P95H, P95L, P95R, P96A or P95T in the encoded protein.

[0141] B5. SEL24 / MEN1703 for use according to any one of B1 to B4, wherein the patient carries said at least one mutation in the U2AF1 gene.

[0142] B6. SEL24 / MEN1703 for use according to B5, wherein the patient carries said at least one mutation in the U2AF1 gene at a position corresponding to amino acid position(s) S34 and / or Q157, preferably wherein the at least one mutation in the U2AF1 results in the amino acid substitution S34F in the encoded protein.

[0143] B7. SEL24 / MEN1703 for use according to any one of B1 to B6, wherein the patient carries said at least one mutation in the ZRSR2 gene.

[0144] B8. SEL24 / MEN1703 for use according to any one of B1 to B7, wherein the patient carries said at least one mutation in (1) the SRSF2 and the U2AF1 genes, (2) the SRSF2 and ZRSR2 genes, (3) the U2AF1 and ZRSR2 genes, or (4) the SRSF2, U2AF1 and ZRSR2 genes.

[0145] B9. SEL24 / MEN1703 for use according to any one B1 to B8, wherein the patient carries one or more additional mutations in any one or more of the RUNX1, BCOR, STAG2, EZH2, KMT2A, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s), preferably in any one or more of the RUNX1, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s). B10. SEL24 / MEN1703 for use according to any one of B1 to B9, wherein the patient

[0146] (1) carries at least one mutation in the SRSF2 gene and at least one mutation in any one of more of the RUNX1, IDH1, IDH2, TET2, and ASXL1 gene(s), preferably the IDH1 and / or IDH2 genes; and / or

[0147] (2) carries at least one mutation in the U2AF1 gene and at least one mutation in any one of more of the DNMT3A, RUNX1, TET2 and ASXL1 gene(s), and preferably no mutation in the IDH1 gene.

[0148] B11 . SEL24 / MEN1703 for use according to any one of B1 to B10, wherein the patient further carries at least one mutation in any one or more of the LUC7L2 and PRPF8 gene(s).

[0149] B12. SEL24 / MEN1703 for use according to any one of B1 to B11 , wherein

[0150] (1) SEL24 / MEN1703 is administered at a daily dose of about 50 mg to about 150 mg; preferably of about 125 mg; and / or

[0151] (2) SEL24 / MEN1703 is administered orally; and / or

[0152] (3) the cancer is AML, optionally secondary, relapsed, or refractory AML.

[0153] Examples

[0154] Example 1

[0155] Methods

[0156] Genomic profiling was performed on samples (bone marrow aspirate / biopsy) from 54 cancer patients suffering from acute myeloid leukemia (AML), who received 125 mg of SEL24 / MEN1703.

[0157] For the profiling, DNA and RNA extractions were performed using Maxwell CSC blood Kit for DNA and RNA, following the manufacture’s instruction (Maxwell Technology, California, US). Briefly, nucleic acids were purified using the Maxwell CSC Blood DNA and RNA Kit. gDNA and RNA were bound to paramagnetic particles in the first well of a prefilled cartridge, and samples were moved by a Maxwell CSC Instrument through the wells of the cartridge in order to perform washing and purification of nucleic acids. Libraries were generated using AmpliSeq Myeloid Panel (Thermo Fisher Scientific, Massachusetts, US). 10 ng of total RNA from samples were converted into cDNA using the superscript IV Vilo (Thermo Fisher). DNA target amplification was performed using the primer pool from the AmpliSeq Myeloid Panel (Thermo Fisher). Obtained amplicons were partially digested, and sampleindexing barcodes were added to each sample. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, California, US), amplified, and finally equalized at a concentration of 100 pM using Library Equalize Kit (Thermo Fisher). Library pools were then diluted to 25-60 pM, and the library templating was performed on the Ion 530™ Chip using the Ion Chef™ Instrument. Finally, libraries were sequenced on IONS5 (Thermo Fisher). The genomic and transcript analysis were performed with Ion Reporter software (Thermo Fisher) applying the last release of Myeloid workflow.

[0158] The relationship between next generation sequencing (NGS) results and efficacy was examined. Post- hoc, exploratory analyses were performed using Kaplan-Meier methods to estimate the survival distribution function of OS, without adjustment for multiple testing. Hazard ratios and 95% Cl were calculated using a Cox regression model. P-values were obtained using a log-rank test.

[0159] Results As noted above, genomic profiling was performed on samples from 54 patients who received 125 mg of SEL24 / MEN1703 to assess potential relationships between genomic alterations in the AML cells and efficacy of SEL24 / MEN1703. Among these, 10 patients harbored SRSF2- mutated tumors, and 15 had tumors with mutations in spliceosome genes (SRSF2, U2AF1, and ZRSR2). In patients with SRSF2- mutated tumors, the median Overall Survival (mOS) was 7.03 months vs 2.6 months in patients with SRSF2-WT tumors (HR, 0.32; 95% Cl, 0.12-0.85; log-rank test P-value=0.018). In patients with spliceosome-mutated tumors, the mOS was 6.08 months vs 2.53 months in patients with spliceosome WT tumors (HR, 0.40; 95% Cl, 0.17-0.94; log-rank test P-value=0.03). The results are shown in Figures 1 (for the SRSF2-mutated tumors vs. SRSF2-WT tumors) and 2 (for the spliceosome-mutated tumors vs. the spliceosome WT tumors), respectively .

Claims

Claims1 . 5,6-Dibromo-4-nitro-2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 ,3, benzodiazole or a salt thereof (SEL24 / MEN1703) for use in the treatment of a patient suffering from cancer and / or for use in increasing the overall survival of a patient suffering from cancer, wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), and wherein said patient carries at least one mutation in at least one gene associated with splicing.

2. SEL24 / MEN1703 for use according to claim 1 , wherein said at least one gene associated with splicing is a splicing factor gene.

3. SEL24 / MEN1703 for use according to claim 1 or 2, wherein said at least one mutation results in a reduction or inhibition of splicing.

4. SEL24 / MEN1703 for use according to any one of claims 1 to 3, wherein the patient carries said at least one mutation in any one or more of the SRSF2, SF3B1, U2AF1 and ZRSR2 gene(s), preferably in any one or more of the SRSF2, U2AF1 and ZRSR2 gene(s).

5. SEL24 / MEN1703 for use according to any one of claims 1 to 4, wherein the patient carries said at least one mutation in the SRSF2 gene.

6. SEL24 / MEN1703 for use according to claim 5, wherein the patient carries said at least one mutation in the SRSF2 gene at a position corresponding to amino acid position P95, preferably wherein the at least one mutation in the SRSF2 gene results in the amino acid substitution P95H in the encoded protein.

7. SEL24 / MEN1703 for use according to any one of claims 1 to 6, wherein the patient carries said at least one mutation in the U2AF1 gene.

8. SEL24 / MEN1703 for use according to claim 7, wherein the patient carries said at least one mutation in the U2AF1 gene at a position corresponding to amino acid position(s) S34 and / or Q157, preferably wherein the at least one mutation in the U2AF1 results in the amino acid substitution S34F in the encoded protein.

9. SEL24 / MEN1703 for use according to any one of claims 1 to 8, wherein the patient carries said at least one mutation in the ZRSR2 gene.

10. SEL24 / MEN1703 for use according to any one of claims 1 to 9, wherein the patient carries said at least one mutation in (1) the SRSF2 and the U2AF1 genes, (2) the SRSF2 and ZRSR2 genes, (3) the U2AF1 and ZRSR2 genes, or (4) the SRSF2, U2AF1 and ZRSR2 genes.1 1 . SEL24 / MEN1703 for use according to any one of claims 1 to 10, wherein the patient carries one or more additional mutations in any one or more of the RUNX1, BCOR, STAG2, EZH2, KMT2A, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s), preferably in any one or more of the RUNX1, IDH1, IDH2, TET2, DNMT3A and ASXL1 gene(s).

12. SEL24 / MEN1703 for use according to any one of claims 1 to 11 , wherein the patient(1) carries at least one mutation in the SRSF2 gene and at least one mutation in any one of more of the RUNX1, IDH1, IDH2, TET2, and ASXL1 gene(s), preferably the IDH1 and / or IDH2 genes; and / or(2) carries at least one mutation in the U2AF1 gene and at least one mutation in any one of more of the DNMT3A, RUNX1, TET2 and ASXL1 gene(s), and preferably no mutation in the IDH1 gene.

13. SEL24 / MEN1703 for use according to any one of claims 1 to 12, wherein the patient further carries at least one mutation in any one or more of the LUC7L2 and PRPF8 gene(s).

14. SEL24 / MEN1703 for use according to any one of claims 1 to 13, wherein(1) SEL24 / MEN1703 is administered at a daily dose of about 50 mg to about 150 mg; preferably of about 125 mg; and / or(2) SEL24 / MEN1703 is administered orally; and / or(3) the cancer is AML, optionally secondary, relapsed, or refractory AML.

15. A method of selecting a patient suffering from cancer forthe treatment with 5,6-Dibromo-4-nitro- 2-(piperidin-4-yl)-1-(propan-2-yl)-1 H-1 , 3, benzodiazole or a salt thereof (SEL24 / MEN1703), wherein the cancer is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), the method comprising:(a) obtaining a biological sample from the subject;(b) determining in the biological sample the presence or absence of at least one mutation in at least one gene associated with splicing and / or, if the cancer is MDS, determining the percentage of ring sideroblasts;(c) selecting the patient for the treatment with SEL24 / MEN1703 if at least one mutation in at least one gene associated with splicing is present in the biological sample and / or, if the cancer is MDS, the percentage of ring sideroblasts is >5%, preferably >15%.

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