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R. Marke et al.
multipotent progenitors.49 At different stages of T-lineage differentiation and development, IKZF1 is engaged by set- ting thresholds for (pre-)T-cell receptor-controlled check- points as well as T-cell activation downstream of inter- leukin-2 receptor signaling.50,51 In B-cell progenitors, Ikzf1 is required to induce Rag1 and Rag2 expression, and medi- ates chromatin accessibility during immunoglobulin gene rearrangement and allelic exclusion at the Igk locus.12,32,52 During pre-B-cell differentiation, IKZF1 regulates the tran- scription of genes implicated in pre-B-cell receptor signal- ing, cell survival, stromal-cell adhesion and B-cell commit- ment, such as Pax5, Foxo1 and Ebf1.12,32,53 Many of those regulatory activities during B-lineage differentiation are navigated by super-enhancer networks controlled by IKZF1 and other B-cell master transcription factors.54 Besides regulating expression of B-lymphoid genes, IKZF1 is actively involved in repression of a lineage-inappropri- ate transcriptional program normally prevalent in epithe- lial and mesenchymal precursors.54
To further delineate the function of the individual zinc- fingers within the DNA-binding domain of IKZF1 in B- lymphopoiesis, Ikzf1 mouse mutants have been generated with targeted deletion of exon 4, which encodes zinc-fin- ger 1 (Ikzf1ΔF1/ΔF1), or exon 6 encoding zinc-finger 4 (Ikzf1ΔF4/ΔF4).37 Germline deletion of either exon 4 or 6 results in decreased B-cell precursors with a stronger developmen- tal block in Ikzf1ΔF1/ΔF1 mice, especially at the pre-B-cell stage.37 In contrast, the fraction of large pre-B cells is strong- ly increased in Ikzf1ΔF4/ΔF4 mice as compared to wild-type control animals. Interestingly, deletion of zinc-finger 4, but not zinc-finger 1, accelerates the onset of BCR-ABL1-medi- ated B-cell leukemia.37,55 Conditional deletion of exon 5 (Ikzf1E5Δ/Δ), which encodes zinc-fingers 2 and 3, at the stage of common lymphoid progenitors also results in an expan- sion of large pre-B cells within the bone marrow compart- ment, which is followed by a subsequent block in the tran- sition to small pre-B cells.56 These findings indicate that N- terminal zinc-fingers 2, 3 and 4 of IKZF1 limit cell prolifer- ation and survival at the time of active pre-B-cell receptor signaling, while zinc-fingers 1, 2 and 3 are absolutely required for the transition to the pre-B-cell stage.
IKZF1 gene lesions drive leukemia development and relapse
In the past decade, complementary genome-wide approaches have been employed to identify the genetic drivers implicated in the pathogenesis of ALL. Those stud- ies revealed that the IKZF1 gene, which is located on chro- mosome band 7p12.2, is recurrently affected by different types of genetic alterations in BCP-ALL. Analysis of copy number alterations has demonstrated that IKZF1 gene deletions are present in about 15% of cases of childhood BCP-ALL and 40%-50% of adult patients with BCP- ALL.57-60 These deletions frequently involve the whole gene (DEL1-8) that results in loss of expression of wild- type IKZF1, as well as focal deletions that alter the func- tion of IKZF1, such as the dominant-negative isoform IK6 (DEL4-7). Other common variants include deletions affecting exons 2-3, exons 2-7 and exons 4-8.61 In most cases these are monoallelic IKZF1 deletions where one functional copy of IKZF1 is retained, although biallelic deletions are also observed in a fraction of BCP-ALL cases.62,63 In addition, IKZF1 function is compromised by insertions, frameshift and missense mutations, which rep- resent ~7% of IKZF1 alterations in BCP-ALL.63
Furthermore, rare in-frame gene fusions involving IKZF1 have been identified by RNA sequencing in BCP-ALL, including IKZF1-NUTM1, IKZF1-SETD5 and the recipro- cal SETD5-IKZF1.64 However, it remains to be established whether these IKZF1 gene fusions are pathogenic and contribute to leukemia development.
An interesting feature is the strongly increased preva- lence of IKZF1 deletions and mutations in high-risk BCP- ALL cases with an activated tyrosine kinase profile, partic- ularly BCR-ABL1-positive ALL (~85%),65 and BCR-ABL1- like ALL (~70%), which is characterized by a range of genetic alterations driving cytokine receptor and kinase signaling.3,66-68 Similarly, IKZF1 deletions and mutations are highly abundant in chronic myeloid leukemia that has progressed to lymphoid blast crises, but IKZF1 alterations are virtually absent in chronic-phase and myeloid blast cri- sis chronic myeloid leukemia.65,69,70 IKZF1 deletions are also rarely detected in ETV6-RUNX1-positive BCP-ALL (3%), TCF3-rearranged (~3%) and MLL-rearranged (~5%) B-cell ALL.58,71,72 The distribution of IKZF1 deletions among the remaining subtypes, including hyperdiploid and B- other leukemia, ranges from 15%-20%.72
IKZF1 acts as a critical tumor suppressor in mouse T- lymphoid malignancies,43,46,47 but IKZF1 gene lesions are not very prevalent in T-ALL. Copy number alterations and mutations affecting the IKZF1 gene can be detected in ~4% of T-ALL.58,65,71,73 Notably, IKZF1 alterations occur in ~13% of early T-cell precursor ALL, a high-risk subtype of T-ALL characterized by recurrent mutations activating tyrosine kinases (FLT3, JAK1, JAK3) and cytokine signaling (IL7R).74 IKZF1 alterations have also been reported in myeloproliferative neoplasms,75 and both pediatric and adult acute myeloid leukemia harbor IKZF1 deletions that affect its function.76,77 Thus, the tumor suppressive activity of IKZF1 is not uniquely restricted towards the lymphoid lineage and extends to a broader range of hematologic malignancies.
Besides its critical role in the pathogenesis of leukemia, IKZF1 alterations are also associated with adverse progno- sis in BCP-ALL.3,4,78 even within the high-risk group of BCR-ABL1-positive ALL.79,80 Notably, the occurrence and prognostic impact of IKZF1 alterations is not restricted to high-risk cases, but is also observed in standard-risk B-ALL subtypes,72 including high hyperploidy.81 Indeed, IKZF1 deletion represents one of the strongest independent pre- dictors of poor treatment outcome in childhood BCP- ALL.71,72,82 Similar data have been reported in adult BCP- ALL, where loss-of-function gene deletions of IKZF1 pre- dict poor treatment outcome in BCR-ABL1-negative cases.83-86 Interestingly, the presence of other co-occurring gene lesions may either enhance or negate the prognostic value of IKZF1 deletions. For instance, focal deletions affecting both transcriptional regulator BTG1 and IKZF1 represent a high-risk group with a worse outcome than those with IKZF1 alterations alone.48 On the other hand, the BCP-ALL subtype characterized by deregulation of transcription factors ERG and DUX4 has a favorable out- come, despite the presence of IKZF1 deletions in approxi- mately 40% of these patients.64,87-90 An explanation for this latter observation remains elusive.
Genetic alterations that cooperate with IKZF1 deletions in B-cell precursor acute lymphoblastic leukemia There is accumulating evidence that recurrent chromo- somal aberrations present in BCP-ALL, such as BCR-ABL1
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haematologica | 2018; 103(4)