Chromosome 5 and 7 abnormalities are observed in myeloid malignancies, including MDS and both de-novo and secondary AML. Chromosome 5, one of the largest human chromosomes, spans 181 million base pairs, representing ~6% of total cellular DNA. It includes numerous intra-chromosomal duplications and 923 protein-coding genes. Despite its size, chromosome 5 has among the lowest gene densities due to gene-poor regions that are evolutionarily conserved in vertebrates, implying functional importance [1]. Chromosome 7 includes 160 million base pairs, representing over 5% of the genome, and contains 1,455 genes [2]. Aberrations within these chromosomes may involve loss of chromosomal material leading to unbalanced deletions, such as interstitial deletion of the short (p) or long (q) arms (described as deletion 5q or del(5q) when involving chromosome 5q). Complete loss of a chromosome (monosomy 5 or 7) or loss of genetic material due to structural aberrations, such as unbalanced translocations with a known partner chromosome, additional material of unknown origin, and isochromosome formation, are also observed [3].

MDS and AML are heterogeneous diseases characterized by somatic gene mutations and chromosomal abnormalities, including balanced genetic abnormalities, such as reciprocal translocations, and unbalanced chromosomal abnormalities, leading to material gain or loss through deletion or aneuploidy. Identifying these genetic abnormalities is crucial for diagnostic sub-classification, predicting therapeutic responses, and guiding treatment choices [4–6]. Outcomes depend on patient-specific factors, leukemia genetics, and treatment intensity. In this review, we explore the implications of chromosome 5 and 7 alterations within the context of the myeloid malignancies in which they appear and describe the testing methods available to detect these chromosomal changes.

Since the identification of the association between chromosome 5 deletions and myeloid diseases in 1974 [7], extensive research has been conducted to identify commonly deleted regions (CDRs) to characterize the genes involved in leukemogenesis and identify potential therapeutic targets in MDS and AML. Deletions in 5q result in the loss of large chromosome segments, representing ~2% of the haploid genome [8]. Given the substantial size of the deleted regions, identifying key genes with leukemogenic potential is challenging. Despite intensive efforts, no somatic mutations of single candidate tumor suppressor genes have been identified [9]. No single genomic aberration comprehensively explains clone inception or progression to AML. Genes on 5q exhibiting haploinsufficiency in AML are involved in signal transduction, DNA repair, and cell cycle control [10]. Similarly, in myeloid malignancies with –7/del(7q), genes critical to DNA damage response, DNA replication, and chromatin regulation are deleted [11].

Chromosome 5 deletions in myeloid malignancies

Two distinct regions of 5q are commonly deleted in MDS and AML. The distal CDR (CDR-1), located at 5q33, is associated with 5q– syndrome, an MDS entity [12]. These cases have an isolated interstitial deletion of the long arm of chromosome 5, including bands q31-q33, and exhibit a low blast count (<5%) [5]. Single-nucleotide polymorphism array (SNP-A) karyotyping in patients with 5q– syndrome revealed that the CDR-1 boundaries lie between the genes encoding SH3 domain and tetratricopeptide repeats 2 proximally and glycine receptor alpha 1 distally, covering ~2.9 Mb, with deletions between 5q32 and 5q33.2 [13]. The proximal and terminal regions of the long arm are consistently retained, with the commonly retained region (CRR) ending at 5q14.2 proximally and beginning at 5q34 distally [14]. The proximal CDR (CDR-2) centers on bands 5q31.2 and 5q31.3, spanning ~1.92 Mb [14]. This CDR is associated with aggressive MDS and AML and a poor prognosis (Fig. 1). These 5q deletions frequently co-occur with additional cytogenetic abnormalities, most commonly del(7q) and/or a complex karyotype (defined by the presence of three or more chromosomal aberrations) [7, 9,].

Figure 1. CDRs and CCRs of chromosome 5q associated with MDS and AML. The distal CDR (CDR-1) is located at 5q33 and is associated with the deletion of RPS14 and 5q– syndrome. The proximal CDR (CDR-2) at 5q31 encompasses genes, including EGR1, CSNK1A1, and G3BP1, and is associated with aggressive MDS and AML. CRRs are shown in green. This figure was created with BioRender.com.
Abbreviations: MDS, myelodysplastic syndrome; CDR, commonly deleted region; CRR, commonly retained region; RPS14, ribosomal protein S14; EGR1, early growth response 1; CSNK1A1, casein kinase 1 alpha 1; G3BP1, G3BP stress granule assembly factor 1; NPM1, nucleophosmin 1; DDX41, DEAD-box helicase 41.

Larger 5q deletions (median size, 71.4 Mb) also occur and often extend across the proximal and/or telomeric extremes of the q arm, encompassing both CDR-1 and CDR-2. These occur in high-risk MDS and AML, with nearly all affected patients also exhibiting mutations in the CRRs [14]. Other chromosomal defects, including 7q deletions (20% of cases), may co-occur. Unbalanced rearrangements involving 5q are more prevalent in AML than in MDS [15]. The larger 5q deletions (>70 Mb) are associated with tumor protein p53 gene (TP53) deletions [16] because of the deletion or uniparental disomy of 17p [14]. Copy-neutral loss of heterozygosity (CN-LOH) of 17p occurs in ~20% of del(5q) AML cases, all spanning TP53, with most also exhibiting TP53 mutations on the remaining allele [14]. Complex karyotypes with 5q and 7q abnormalities but without del(17p) frequently show CN-LOH of 17p, which may remain undetected unless examined using SNP-A [17]. LOH at 17p only appears in patients whose 5q deletion affects the centromeric and telomeric regions, particularly at band 5q13. Deletion size and CRR involvement influence survival in MDS, with smaller lesions exhibiting lower transformation rates than those affecting the extremes of 5q. Loss of 5q13.3 (within the centromeric CRR) is hypothesized to precede TP53 mutations, conferring a proliferative advantage to the dysplastic clone. Consequently, larger deletions correlate with additional cytogenetic abnormalities and TP53 mutation, contributing to more severe disease in MDS and AML. These findings suggest that the loss of additional genes in the proximal or centromeric extremes of 5q may drive increased genomic instability, favoring AML transformation [14]. Graubert, et al. [18] utilized total exonic resequencing and array comparative genomic hybridization to evaluate all 28 genes in the 5q31.2 region in 46 patients with MDS. None of the del(5q) samples harbored mutations in the remaining wild-type chromosome, and no cytogenetically silent microdeletions were detected in non-del(5q) samples, confirming that loss of one copy of the 5q32.1 genes in de-novo MDS predominantly occurs via large cytogenetic deletions affecting numerous genes. This finding reinforces the pathogenic role of haploinsufficiency of multiple 5q genes in myeloid neoplasms.

Candidate genes in the pathogenesis of del(5q) in myeloid malignancies

Early growth response 1 (EGR1), a gene located on chromosome 5, functions as a tumor suppressor in various cancers, including breast cancer, fibrosarcoma, and glioblastoma. In mouse models, EGR1 mediates cellular responses to growth factors, mitogens, and stress, acting as a direct transcriptional regulator of tumor suppressor genes, including TP53, transforming growth factor beta, and phosphatase and tensin homolog [19]. EGR1-knockout mouse embryonic fibroblasts bypass senescence and become immortalized, suggesting a gatekeeper role in p53-dependent growth regulation [20]. Heterozygous and homozygous loss of EGR1, coupled with alkylating agent-induced secondary mutations, leads to myeloid neoplasms in mice [21]. EGR1 was universally deleted in a large cohort of 1,200 patients with MDS or AML with del(5q) [15]. Indicating that loss of EGR1 function contributes to the pathogenesis of these myeloid neoplasms by permitting uncontrolled cell growth and impairing cellular differentiation and apoptosis.

Hosono, et al. [22] employed SNP-A and next-generation sequencing (NGS) to investigate pathogenic molecular features in patients with MDS and AML with del(5q), either as the sole abnormality or part of a complex karyotype. Several genes, including those encoding casein kinase 1 alpha 1 (CSNK1A1) and G3BP stress granule assembly factor 1 (G3BP1) within the distal CDR (5q31.1–5q33.1), and DEAD-box helicase 41 (DDX41) within CRR-2, were frequently mutated and exhibited consistent haploinsufficiency in deletion cases. Low expression or mutations in G3BP1 or DDX41 are associated with poor survival. CSNK1A1 is a putative tumor suppressor, whereas G3BP1 regulates p53 activity. DDX41 is involved in RNA splicing, and germline mutations in this gene predispose individuals to MDS and AML.

Chromosome 5 and/or 7 deletions are also found in therapy-related AML (t-AML) following prolonged azathioprine treatment [23, 24], presumably owing to defective DNA mismatch repair, leading to leukemic clone formation. Microsatellite instability occurs in patients with t-AML and those >60 yrs old (but not in younger patients with de-novo AML) and is associated with chromosome 5 and/or 7 abnormalities. This provides functional evidence for DNA mismatch repair defects in t-AML [24]. Deficient expression of the MutS homolog 2 gene (MSH2), involved in DNA mismatch repair, is observed in adult AML cases, predominantly in patients aged >60 yrs and those with t-AML, and is associated with TP53 mutations and microsatellite instability. Therefore, defective DNA mismatch repair because of reduced MSH2 expression may play a key role in leukemogenesis, particularly in older patients and those with prior chemotherapy exposure [25].

The nucleophosmin 1 gene (NPM1), which encodes nucleophosmin, a chaperone protein that shuttles between the nucleus and cytoplasm, is located at 5q35. NPM1 has roles in TP53 regulation, ribosome biogenesis, and maintaining genomic stability [26]. NPM1 is the most frequently mutated gene in AML, occurring in ~30% of cases, including at least 50% of AML with a normal karyotype [27]. NPM1 is lost in 10% of MDS cases because of large 5q deletions and is associated with a poor clinical course and increased likelihood of progression to AML [28, 29]. NPM1 haploinsufficiency is hypothesized to offer a proliferative advantage to myeloid clones [30]. Mice heterozygous for NPM1 have an increased rate of spontaneous malignancy, with 75% developing myeloid and lymphoid neoplasms [31]. NPM1 knockout is embryonically lethal. Conditional NPM1-knockout mice develop an MDS-like phenotype with aging, whereas combined heterozygous knockout of NPM1 and TP53 results in myeloid leukemia in >90% of mice. NPM1 loss appears to cause an MDS-like phenotype, which promotes AML when TP53 is lost [32]. Therefore, aneuploidy with loss of chromosome 5 and/or 7 in the context of mutated TP53 may promote genetic instability because of NPM1 loss, promoting transformation to AML.

Chromosome 7 deletions in myeloid malignancies

The CDR in –7/del(7q) myeloid neoplasms is located in the 7q22 region [11, 33]. Mapping with SNP-A and whole-genome sequencing has identified deletion of 7q21.13–36.3 in >70% of cases and deletions of 7q31.33, 7q34, and 7q35–7q36.1 in over 90% of cases. These areas comprise 304 genes, including those encoding sterile alpha motif domain-containing 9 (SAMD9), cut-like homeobox 1 (CUX1), dedicator of cytokinesis 4 (DOCK4), cullin 1 (CUL1), enhancer of zeste 2 polycomb-repressive complex 2 subunit (EZH2), lysine methyltransferase 2C (KMT2C), and LUC7-like 2, pre-mRNA splicing factor (LUC7L2) [11] (Fig. 2). Analyses of somatic mutations in chromosome 7 in cases with –7/del(7q) have identified 16 recurrently mutated genes. EZH2 mutations are the most common (5% of cases) and are associated with hemizygous deletion of EZH2 on one allele and EZH2 mutation on the other in 16% of cases. In isolated –7/del(7q), the most recurrently mutated genes are those encoding Tet methylcytosine dioxygenase 2 (TET2), DNA methyltransferase 3 alpha (DNMT3A), ASXL transcriptional regulator 1 (ASXL1), RUNX family transcription factor 1 (RUNX1), and serine and arginine-rich splicing factor 2 (SRSF2), and EZH2. In contrast, in –7/del(7q) associated with a complex karyotype, TP53 is the most commonly mutated (57%), followed by del(5q) (>50%) and del(17p) (25%) [11].

Figure 2. CDRs of chromosome 7q associated with MDS and AML. The CDR on chromosome 7q spans 7q21.13–7q36.3, with regions corresponding to bands 7q31.33, 7q34, and 7q35–7q36.1 deleted in the majority of cases [¹⁵]. Genes of interest in the pathogenesis of –7/del(7q) myeloid neoplasms include SAMD9/SAMD9L, CUX1, and EZH2. This figure was created with BioRender.com.
Abbreviations: MDS, myelodysplastic syndrome; CDR, commonly deleted region; SAMD9/SAMD9L, sterile alpha motif domain-containing 9/sterile alpha motif domain-containing 9-like; CUX1, cut-like homeobox 1; EZH2, enhancer of zeste 2 polycomb-repressive complex 2 subunit.

Candidate genes in the pathogenesis of deletion 7 in myeloid malignancies

The genes within the CDRs have been analyzed to elucidate leukemogenesis associated with –7/del(7q). Theories include LOH, haploinsufficiency of tumor suppressor genes, and somatic rescue of suppressive germline variants located within the deleted regions. Additionally, tumor suppressor genes may modulate genes on other chromosomes through downstream pathways or compensatory mechanisms [11].

Mori, et al. [11] used NGS to analyze clonal hierarchy and define the initial molecular events in the pathogenesis of –7/del(7q). These events varied based on associated genomic complexity. In the majority of isolated –7/del(7q) cases, the chromosome 7 abnormality was secondary, and mutations in ASXL1 or TET2 were the most common dominant somatic alterations. Conversely, in del(7q) myeloid neoplasms with complex karyotypes, 73% exhibited dominant TP53 mutations. Single-cell DNA sequencing indicated loss of chromosome 7 as a secondary event following DNMT3A and TET2 mutations in a case of AML with isolated –7 and subsequent to TP53 mutation and del(5q) in another case with subclonal del(7q). This suggests that –7/del(7q) may not be a primary event in leukemogenesis and can occur secondary to other genomic defects.

Bioinformatics analysis of haploinsufficiency within the 7q21–7q36 CDR in –7/del(7q) cases identified 199 haploinsufficient genes, including tumor suppressors, genes involved in DNA damage response, DNA replication, and chromatin regulation. CUX1 and EZH2 exhibited haploinsufficiency in >90% of cases and were associated with lethality in knockout mice. Expression analysis of genes outside the defined CDRs on chromosome 7 helped identify 19 significantly upregulated genes and seven downregulated genes, including a tumor suppressor gene (ribosomal protein S6 kinase A1) and two oncogenes (lysosomal protein transmembrane 4 beta and Ras homolog family member C). These findings suggest impaired DNA damage repair may contribute to the genesis of myeloid neoplasms with –7/del(7q) and align with the known association of –7/del(7q) in AML with genotoxic exposure (i.e., t-AML) [11].

Mono- or biallelic EZH2 mutations at 7q35 are among the most frequent mutations in myeloid malignancies with chromosome 7 deletions, affecting 10% of MDS and t-AML). EZH2 encodes a methyltransferase that acts as an epigenetic regulator and contributes to gene silencing via histone modification [34]. Somatic EZH2 mutations confer an unfavorable prognosis, including the risk of transformation to AML [35]. Biallelic mutations are often associated with CN-LOH of the distal portion of 7q, suggesting that EZH2 haploinsufficiency may promote leukemogenesis. However, EZH2 deletion in mice resulted in T-cell leukemia rather than myeloid neoplasms [36]. EZH2 mutations are commonly associated with TET2 mutations in myeloid neoplasms. In in-vitro TET2- or RUNX1-knockdown models, the incidence of aggressive myeloid disease increased when EZH2 was deleted, suggesting that additional loss of EZH2 contributes to myeloid neoplasia development [37].

CUX1, located at 7q22.1, encodes a homeobox transcription factor and is implicated in –7/del(7q) malignancies and may fiunction as a role as a haploinsufficient tumor suppressor. CUX1^–/– mice do not survive past weaning and exhibit myeloid hyperplasia [38, 39].

SAMD9 and SAMD9L (SAMD9-like), at 7q21.2, encode endosomal proteins crucial for endosomal trafficking, including cytokine receptor metabolism. Mutations in SAMD9/SAMD9L are associated with hereditary diseases predisposing to MDS with monosomy 7 [40, 41]. Germline gain-of-function (GOF) mutations have been identified in children and adolescents with inherited bone marrow failure syndromes and MDS [42]. The transcription factor EVI1, frequently associated with therapy-resistant myeloid malignancies bearing inv(3)/t(3;3) abnormalities [43], suggests that haploinsufficiency of SAMD9L at 7q21 and over-function of EVI1 may cooperatively promote myeloid leukemogenesis [40].

Karyotyping

ELN prognostic groups are defined on conventional karyotypic analysis, which is mandated in the diagnostic evaluation of AML [4]. Giemsa staining of metaphase chromosomes after short-term culture (G-banding) enables detection of numerical changes and structural variations (SVs), including deletions, translocations, inversions, and duplications (Fig. 3A). This method requires dividing cells, and failure rates for AML samples can reach up to 20% [44]. While G-banding offers a comprehensive view of the chromosome complement of the cell, its resolution is limited—deletions <5–10 Mb and rare events such as mosaicism may be missed. Furthermore, this technique cannot detect CN-LOH or acquired segmental uniparental disomy.

Figure 3. Examples of chromosome abnormalities via karyotyping and FISH. (A) Karyotype of AML with a monosomal karyotype, with losses of multiple chromosomes, including monosomy 7. (B) del(5q) in a case of AML. FISH using a dual color probe set for EGR1 (5q31) and D5S23 (5p15.2) (one orange signal for EGR1 and two green signals for D5S23).
Abbreviations: EGR1, early growth response 1; D5S23, human D5S23 control region on 5p.

FISH

FISH uses fluorescently labeled DNA probes to interrogate chromosomal sequences of interest and can identify gene fusions, deletions, or aneuploidies using various probe designs, including deletion/duplication probe sets or whole-chromosome paints [45]. In AML, prognostically significant abnormalities routinely targeted by FISH include recurrent translocations (e.g., RUNX1::RUNX1 partner transcriptional co-repressor 1, core-binding factor subunit beta::myosin heavy chain 11) and gene fusions, and myelodysplasia-related chromosome abnormalities [e.g., del(5q)/add(5q), –7/del(7q), and –17/add(17p)/del(17p)] [4]. FISH can be performed on non-dividing interphase cells, making it applicable when karyotyping fails [46]. Deletion/duplication probe sets can help detect del(5q) and monosomy 5 (Fig. 3B). 5q deletions are detectable with FISH probes targeting 5q31.2 (EGR1) and 5q33.1 (ribosomal protein S14 [RPS14]), corresponding to CDR-2 and CDR-1, respectively, with a concurrent 5p probe enabling monosomy 5 detection [47]. EGR1 FISH is more sensitive than G-band karyotyping for detecting del(5q) in MDS (6%). Therefore, FISH studies for del(5q) are recommended in cases with insufficient cell growth or <20 normal metaphases in karyotyping and when rapid results are needed to guide treatment choice (e.g., lenalidomide for 5q– syndrome) [46].

Probes targeting the 7q CDR, including 7q22 and 7q36, have been used to identify del(7q) and a centromeric probe for monosomy 7 in MDS and AML [48]. FISH studies have helped detect a high monosomy 7 rate in cytogenetically normal MDS and AML cases. The frequency of occult monosomy 7 was up to 30% [49, 50]. MDS patients with monosomy 7 detected using FISH are more likely to progress to AML [49].

SNP-A

Newer genomic technologies such as chromosome arrays and NGS give more precise characterization of chromosomal abnormalities. SNP-A enables high-resolution whole-genome scanning for unbalanced defects, such as deletions, by assessing individual base pairs. Fragmented single-stranded DNA is fluorescently labeled and hybridized to a microarray chip containing hundreds of thousands of unique nucleotide probes. The fluorescence intensity measured at each probe location helps quantify gene dosage and highlights cryptic changes, such as small deletions. SNP-A can identify CN-LOH, which is undetectable with metaphase karyotyping and common in myeloid malignancies [51]. CN-LOH may result in the duplication of oncogenic mutations in genes such as Janus kinase 2, KIT proto-oncogene, receptor tyrosine kinase, and FMS-related receptor tyrosine kinase 3 (FLT3), with concurrent loss of the normal allele, or loss of tumor suppressor genes such as c-CBL and TET2 [52]. When applied to MDS and AML cases with del(5q), SNP-A has facilitated precise breakpoint identification and revealed additional cryptic lesions in >50% of cases and retention of chromosome 5q material in marker chromosomes [14]. In AML cases with a normal karyotype, SNP-A has revealed chromosomal rearrangements in 32% of cases and CN-LOH in 23% [51]. The presence and number of abnormal SNP lesions were independent predictors of poorer overall survival (OS) in MDS and AML [53].

The resolution of SNP-A is limited by the finite number of probes, and smaller CNVs or SNPs may be missed because of probe spacing. As SNP-A uses a reference genome, variants that are absent in the reference genome may be overlooked, and population-specific variations under-represented. Furthermore, SNP-A can be expensive, and high-throughput analysis of large datasets requires substantial resources and bioinformatics experience. Thus, SNP-A is not routinely used in diagnostic practice to analyze chromosome 5 and 7 integrity.

NGS

In NGS, nucleic acids are fragmented and attached to a solid surface (library preparation), and the entire library is sequenced simultaneously, generating large quantities of complex data consisting of short DNA reads. Bioinformatics software is used to annotate variants. NGS offers higher resolution than karyotyping and FISH and does not require dividing cells or prior knowledge of abnormalities. NGS is primarily used in AML diagnostics to screen targeted panels covering a limited number of driver gene mutations, including in FLT3, NPM1, DNMT3A, and TP53, as recommended by international guidelines [4, 54]. Of the 36 genes currently recommended for screening by the ELN-2022 guidelines, four are located on chromosomes 5 and 7, including NPM1 and EZH2 at 7q36.1 within the 7q CDR. Another important gene in myeloid neoplasms is the B-Raf proto-oncogene, serine/threonine kinase gene (BRAF), located at 7q34 within the 7q22–q34 CDR [11]. This gene encodes a Raf family serine/threonine protein kinase that regulates the mitogen-activated protein kinase/extracellular signal-regulated kinase pathway, which affects cell division and differentiation. BRAF mutations in AML are associated with poor prognosis regardless of clonal burden and are enriched in MDS-related AML (AML-MR) [55]. Detection of these mutations by NGS may indicate the presence of 5q or 7q deletions. Mate-pair sequencing (MPseq), an NGS variant involving a unique library preparation method with circularization of long input DNA (2–5 kb), enables paired-end sequencing of reads that map 2–5 kb apart in the genome and facilitates whole-genome sequencing optimized for the detection of SVs and CNVs [56]. MPseq allows comprehensive CNV evaluation of a sample in a single assay. The reduced sequencing depth makes it more cost-effective than traditional NGS [57]. MPseq demonstrates utility in high-resolution detection and improved characterization of chromosome 5 and 7 abnormalities, genomic complexity, and TP53 mutation detection in AML [58] but does not improve risk stratification [59].

Genetic material is commonly lost from chromosomes 5 and 7 in MDS [16, 60]. Deletion of 5q, 7q, or monosomy 7 are defining cytogenetic abnormalities in the WHO classification and recognized by the International Consensus Classification (ICC) as sufficient for the diagnosis of MDS/AML or AML with MDS-related cytogenetic abnormalities in the absence of other recurrent genetic abnormalities or gene mutations [4, 5]. These chromosomal defects are also present in other myeloid malignancies, including myeloproliferative neoplasms (MPN) and MDS/MPN albeit at lower frequencies [16, 60].

Chromosome 5 and 7 deletions in MDS

Interstitial chromosome 5q deletion is the most common karyotypic abnormality in de-novo MDS, occurring in up to 20% of cases and chromosome 7 abnormalities in 10% [61]. Chromosome 5 and 7 abnormalities may appear as the sole abnormality or as part of a complex karyotype [61]. Detection of these is important as they provide critical prognostic information regarding outcomes and the risk of transformation to AML [62]. The cytogenetic risk classification system identifies five groups: very good, good, intermediate, poor, and very poor [62, 63].

Deletion 5q confers a good prognosis, with a median survival of 4.8 yrs, and a low risk of evolution to AML [63]. Although monosomy 5 is not specifically addressed in the MDS prognostic scoring system, patient survival is worse than that of patients with sole del(5q) [64]. Deletion 7q alone is of intermediate risk, with a 2.7-yr median survival. Monosomy 7 with or without del(7q) confers a poor risk, with a 1.5-yr survival and a median survival of 1.7 yrs for the 25% of cases that evolve to AML [63]. Monosomy 7 is associated with a high rate of progression to AML relative to del(7q) [63, 65], and the presence of chromosome 7 anomalies is a potential indicator of leukemic evolution in MDS [66].

5q– syndrome

5q deletion was the first chromosomal deletion associated with a specific hematological phenotype [7]. The WHO has now names this entity “myelodysplastic neoplasm with low blasts and 5q deletion.” Deletion of 5q frequently is the sole cytogenetic abnormality in patients with 5q– syndrome. Patients are predominantly female and present with refractory macrocytic anemia and thrombocytosis. The bone marrow exhibits erythroid hyperplasia, small megakaryocytes with non-lobated nuclei, and relatively preserved granulocytic activity (Fig. 4). The WHO criteria include <5% blasts, absence of Auer rods, no more than one other cytogenetic abnormality, and absence of –7/del(7q). Notably, most patients with MDS and del(5q) do not meet these criteria for “MDS with isolated del(5q).” Patients respond to lenalidomide therapy but some are transfusion-dependent. The prognosis is generally favorable, with low rates of transformation to AML.

Figure 4. Bone marrow morphology of a myelodysplastic neoplasm with low blasts and isolated del(5q). (A) Bone marrow aspirate showing a small megakaryocyte with a non-lobated eccentric nucleus (Romanowsky staining, 1,000×). (B) Section of the bone marrow trephine showing megakaryocytic hyperplasia with a predominance of characteristic small forms with hypolobated nuclei (hematoxylin and eosin staining, 400×).

Additional CNVs involving other chromosomes, including 17p, are rare in del(5q), as are large areas of CN-LOH [14]. Other leukemia-associated mutations, such as in the NRAS proto-oncogene, GTPase gene (NRAS), and FLT3, are also uncommon [13]. Therefore, the favorable prognosis for patients with 5q– syndrome may relate to their relative genetic stability. The consistent clinical phenotype of 5q– syndrome suggests that the loss of one or more genes within CDR-1 is pathogenic. This area includes 40 genes encoding proteins and microRNAs, with numerous genes encoding hematopoietic growth factors and receptors [12]. Studies using Sanger and NGS technologies, SNP-A, and gene expression profiling have failed to identify a tumor suppressor gene on 5q with both alleles inactivated, supporting the notion that haploinsufficiency for one or more genes on 5q contributes to the molecular pathophysiology of MDS [67]. Functional studies using RNA interference have identified critical genes. Research using short hairpin RNAs targeting RPS14 demonstrated that partial loss of RPS14 function results in anemia because of reduced erythroid production, whereas RPS14 overexpression in MDS patient-derived hematopoietic cells rescued the phenotype [68]. The erythroid defect was analogous to that observed in Diamond–Blackfan anemia, a congenital bone marrow failure syndrome caused by heterozygous mutations in ribosomal proteins [69]. Defective ribosomal biogenesis may induce high p53 expression by interfering with the ubiquitin ligase mouse double minute 2 homolog, which targets p53 for proteasomal destruction [70]. Bone marrow-derived CD34-positive stem cells from patients with 5q– syndrome show marked downregulation of the microRNAs miR-145 and miR-146a. Loss of one allele of these microRNAs results in increased megakaryocyte production and megakaryocytic dysplasia via activation of the nuclear factor kappa-light-chain-enhancer of activated B cells pathway. MicroRNA-145 and RPS14 co-localize within 1 Mb in CDR-1; thus, their combined loss may be sufficient to explain the clinical features of 5q– syndrome [10].

Chromosome 5 and 7 deletions occur frequently, with each present in 5–15% of cases of de-novo AML [71–74]. In half of these cases, chromosome 5 and 7 abnormalities co-occur and represent the most common chromosomal abnormalities to co-segregate [8]. The relative frequency of these abnormalities increases with age, prior chemotherapeutic exposure, and a history of myeloid disease [73, 74].

t-AML

t-AML is increasing in incidence, representing 10%–15% of all AML cases, and occurs more commonly in older patients [73]. Two types of t-AML with distinct cytogenetic profiles are recognized: those caused by alkylating agents or ionizing radiation and those induced by topoisomerase II inhibitors [75]. Alkylating agent-related t-AML accounts for 75% of cases and typically presents with cytopenia and multilineage dysplasia 4–7 yrs after exposure to the mutagen [76].

The prevalence of chromosome 5 or 7 abnormalities in t-AML is estimated at 20%–30%, with 70%–80% harboring unbalanced chromosomal deletions of either chromosome [77]. del(5q) in t-AML is frequently associated with additional changes, usually in the context of a complex or monosomal karyotype [78, 79]. TP53 mutation is found in 80% of del(5q) but is not significantly associated with del(7q) or cases with balanced chromosomal translocations [79]. TP53 mutations in t-AML are associated with a highly complex genetic profile (mean number of genomic alterations, 7.5) and genomic instability [78]. Chromosome 5 and/or 7 deletions, TP53 mutation, and a complex karyotype are hallmarks of alkylator-associated t-AML.

AML, myelodysplasia-related (AML-MR)

AML-MR describes a subset of AML with features overlapping with those of MDS [5]. AML-MR represents up to 50% of adult AML and is most common age >60 yrs [80, 81]. These cases may arise following a history of MDS or MDS/MPN, or de novo and genetic characteristics, rather than clinical history, have the highest biological relevance [4, 5, 78, 82]. The most frequent abnormalities are a complex karyotype, del(5q), del(7q), or monosomy 7 [4, 5]. The increase in chromosome 5 and 7 abnormalities with age likely reflects a complex interplay between aging-related genetic changes, prior therapy, and myeloid disease progression.

AML with complex karyotype (AML-CK)

Chromosome 5 and 7 abnormalities often co-exist and in association with other chromosomal abnormalities in the context of a complex or monosomal karyotype. AML-CK is defined by the presence of three or more unrelated chromosomal aberrations and the absence of favorable cytogenetic rearrangements. AML-CK comprises 10%–12% of AML, and its incidence increases with age [83]. The median number of chromosomal aberrations ranges from 6 to 10, show a non-random pattern, with a relative paucity of balanced translocations and a predominance of monosomies, deletions, and unbalanced translocations, leading to loss of chromosome material, resulting in a hypodiploid karyotype [83–86]. Approximately 80% of patients show loss of genomic material from 5q, and 50% have 7q deletions and 17p abnormalities andthese abnormalities often co-occur [73, 83]. In AML, –7/del(7q) may be the sole abnormality or as part of a complex karyotype. In contrast –5/del(5q) tends to occur only as part of the complex karyotyp; however the chromosome is rarely lost entirely and parts of the chromosome are frequently found in marker and/or ring chromosomes [83]. However, the net result is still loss of chromosome 5 material, primarily from 5q.

AML with monosomal karyotype

AML with monosomal karyotype (AML-MK) is defined by the presence of at least two autosomal monosomies or a single autosomal monosomy in combination with at least one structural abnormality [87]. AML-MK comprises 20%–30% of cases in patients aged >60 yrs (cf <5% in <30 yrs) and is more common with preceding MDS or t-AML [71, 87]. Chromosome 5 and 7 abnormalities are frequently observed with AML-MK. Monosomy 5 occurs in 55% and –7 in 45% of adult AML cases, commonly in association with other changes, including del(12p), del(17p), –18/del(18q), –20/del(20q) and inv(3)/t(3;3), a complex karyotype, and MDS-related cytogenetic abnormalities [88]. NPM1 and FLT3 mutations are less frequent in AML-MK, whereas TP53 alterations occur in 70% of patients [88]. Furthermore, they appear to be more frequent in patients with both complex and monosomal karyotypes than in those with a complex karyotype alone [89].

TP53-mutated AML

The transcription factor p53 is pivotal in normal hematopoiesis, and aberrations are early events in myeloid leukemogenesis. TP53, on the short arm of chromosome 17 (17p), can lose functionality through deletion of chromosome 17 or 17p, or through gene mutation. TP53 mutations may result in LOF or GOF and have been detected in founding clones in clonal hematopoiesis of indeterminate potential, MDS, AML with a complex karyotype, and t-AML [82, 90]. Most TP53-mutant cases exhibit complex karyotypes, and in ~50%, TP53 mutations occur without other AML-associated gene mutations. “AML with TP53 mutations, chromosomal aneuploidies, or both” occurs in up to 15% of cases, are generally older patients, and have an association with chromosome 5 and/or 7 deletions in a complex karyotype [82]. Pitel et al. used mate-pair sequencing (MPseq) to explore the relationships among 5q and 7q deletions, genomic complexity, and TP53 mutations in MDS and AML [56]. They demonstrated that del(5q) and, particularly, del(5q)/(7q) subtypes showed higher genomic complexity than AML-MK and del(7q) subtypes. Cases with del(5q)/(7q) exhibited significantly higher genome-wide copy number gains and losses and SVs (median, 14.0, 24.0, and 60.0, respectively) than those with a normal karyotype. TP53 deletions were identified in 55% of del(5q)/(7q), 44% of del(5q) cases, and only 9% of those with del(7q), with no deletions found in AML with a normal karyotype. Monoallelic and biallelic TP53 SNVs were significantly increased in del(5q) and del(5q)/(7q) cases and rare in del(7q) and normal karyotype cases [22, 78, 82]. A history of prior myeloid disorder or chemotherapy, increasing age, and the presence of chromosome 5 and/or 7 abnormalities imply the probable presence of TP53 mutation in AML.

Chromosome 5 and 7 abnormalities in pediatric AML

Chromosome 5 and 7 abnormalities are also highly prevalent in pediatric AML, particularly when they evolve from a prior bone marrow disorder [91]. Chromosome 7 deletions are commonly implicated in bone marrow failure syndromes, such as Fanconi anemia, severe congenital neutropenia, Shwachman–Diamond syndrome, and aplastic anemia [92, 93]. Germline SAMD9/9L and GATA-binding protein 2 mutations have been reported in pediatric MDS with –7 [94]. Complex and monosomal karyotypes are less common in pediatric patients.

Prognostic impact of chromosome 5 and 7 abnormalities in MDS and AML

Karyotype and mutation status are the most important independent prognostic factors of AML and determine the likelihood of achieving complete remission, relapse risk, and OS [4, 71, 72, 82, 95]. Therefore, guidelines mandate cytogenetic analysis at diagnosis to stratify patients into risk groups [4, 96]. The ELN-2022 AML classification includes del(5q), –5, and –7, as well as complex and monosomal karyotypes, monosomy 17/abnormal 17p, and mutated TP53 in the adverse risk category.

AML clinical trials have shown that chromosome 5 abnormalities [del(5q), add(5q), and –5] or monosomy 7 are associated with a low complete remission rate (53%–58%) and a 10-yr OS of 0%–12%. Deletion of 7q is less adverse, with a 10-yr OS of 26%–30% [95]. Most chromosome 5 and 7 abnormalities occur in the context of a complex karyotype, and additional cytogenetic abnormalities likely adversely influence the outcome [72]. Evidence suggests that chromosome 7 deletion is a highly unfavorable prognostic factor conferring a worse prognosis than a complex karyotype without –7/del(7q) [11]. A monosomal karyotype also confers a dismal prognosis, which may be partly attributed to monosomy 7 [87]. TP53 mutations, which frequently co-occur with complex and monosomal karyotypes involving chromosomes 5 and 7, further adversely impact prognosis [15, 82]. Current guidelines recommend offering allogeneic HSCT to patients with unfavorable-risk AML [4]. However, long-term outcomes remain poor, with few achieving long-term survival [97].

Chromosome 5 and 7 deletions are prevalent in MDS and AML, involving large genomic areas that encompass numerous genes. These deletions are markers of increased genomic complexity, aneuploidy, TP53 mutations, and adverse risk; therefore, their identification is crucial for prognostic stratification and treatment planning. Currently, testing relies on karyotyping and FISH; however, emerging laboratory techniques promise enhanced resolution, accuracy, and high-throughput genomic characterization of leukemic cells.

None.

Kendrick TS reviewed the literature and wrote the manuscript; Buic D, Fuller KA, and Erber WN created the figures and reviewed the manuscript. All authors have read and approved the final manuscript.

None declared.

Kendrick TS received a WA Cancer and Palliative Care Network (WACPCN) Cancer Fellowship.