Comparison of myeloid neoplasms with nonclassic 3q26.2/MECOM versus classic inv(3)/t(3;3) rearrangements reveals diverse clinicopathologic features, genetic profiles, and molecular mechanisms of MECOM activation

RUNX1::MECOM rearrangement in myeloid neoplasm post cytotoxic therapy following sarcoma treatment: a case presentation and review of the literature

OBJECTIVES

Myeloid neoplasms occurring after cytotoxic therapy (MN-pCT), previously termed therapy-related myelodysplastic neoplasia (MDS) or therapy-related acute myelogenous leukemia (AML), pose significant treatment challenges due to high resistance, poor chemotherapy tolerance, and relapse.

METHODS

We present a 73-year-old woman with therapy-related AML following treatment for myxofibrosarcoma, characterized by the rare RUNX1::MECOM fusion resulting from a t(3;21)(q26;q22) chromosomal translocation. We also review the current literature regarding cases of this rare translocation.

RESULTS

The patient, previously treated with chemotherapy and radiotherapy for sarcoma, was diagnosed with pancytopenia and hypoplastic bone marrow with increased blasts. Cytogenetic analysis confirmed RUNX1::MECOM fusion. Furthermore, we discuss the molecular mechanisms underlying MECOM rearrangements, specifically the role of the EVI1 oncogene. AML associated with MECOM rearrangements is associated with poor prognosis and resistance to conventional therapies. While allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains the only potential curative treatment, the high relapse rate limits its efficacy. Recent advancements in understanding the molecular drivers of MECOM-related AML suggest potential therapeutic strategies, including hypomethylating agents and novel combinations such as lenalidomide.

CONCLUSION

this case and literature review emphasizes the importance of long-term monitoring of cancer survivors treated with cytotoxic therapies, as well as awareness of rare translocations in MN-pCT.

The demographic characteristics and prognosis of acute myeloid leukemia with t(3;3)/inv(3) in the united states: a SEER-based study

Acute myeloid leukemia (AML) with t(3;3) (q21; q26.2) or inv(3) (q21; q26.2) is a rare subtype of acute myeloid leukemia with a poor prognosis. Research on the demographic characteristics and clinical outcomes of AML patients with t(3;3) (q21; q26.2) or inv(3) (q21; q26.2) is limited. All AML patients diagnosed with t(3;3) (q21; q26.2) or inv(3) (q21; q26.2) between 2000 and 2021 from SEER (Surveillance, Epidemiology, and End Results Program) database were included in this study. Survival analysis was performed using the Kaplan-Meier method. The log-rank test was used to analyze the significance of differences between overall survival (OS) and cancer-specific survival (CSS). Due to being a retrospective study, the limited amount of baseline characteristics available, and the missing information on treatments and recurrence, the provided dataset is not exactly representative for the US population. The median age of the total 90 AML patients with t(3;3) (q21; q26.2) or inv(3) (q21; q26.2) was 65(49-74) years old. Among them, 57.78% were married and non-Hispanic whites accounted for 74.44%. 84.44% of the patients received chemotherapy. The median OS was 8 months, and the median CSS was 10 months. The 5-year survival rate for OS was 15.29% (95%CI:7.98-24.78%), and 20.05% (95%CI:10.69-31.51%) for CSS. The OS and CSS of patients above 60 years were inferior to those of patients under 60 years. Single (never-married) patients had better OS and CSS than those with other marital status. Age and marital status at diagnosis were independent influencing factors for OS and CSS based on the multivariate COX regression analysis. AML with t(3;3) (q21; q26.2) or inv(3) (q21; q26.2) mostly occurs in adults and has poor clinical outcomes with worse OS and CSS, especially in the elderly.

Case Report: Myeloid neoplasms with the t(3;12)(q26.2;p13.1)/MECOM-ETV6 translocation: report of two new cases and review of the literature

The MECOM (MDS1 and EVI1 complex locus) gene, located at 3q26.2, encodes an oncogenic transcription factor implicated in multiple signaling pathways. Rearrangements involving MECOM/3q26.2, including inversions, translocations, insertions and cryptic chromosomal changes, are observed in myeloid neoplasms and are associated with high-risk disease features and poor clinical outcomes. The translocation t(3;12)(q26.2;p13.1) is a rare genetic event, resulting in a fusion of the MECOM gene at 3q26.2 with the ETV6 gene at 12p13.1. To date, only 78 cases of hematologic neoplasms harboring t(3;12) have been reported in the English literature, primarily as case reports or case series. T(3;12) has been associated with abnormalities of chromosome 7, multiple hematopoietic lineage dysplasia, and poor prognosis. Given its rarity, studies on t(3;12) in myeloid neoplasms are limited. In this report, we present two additional cases exhibiting t(3;12), initially identified through routine karyotyping. The clinicopathological, cytogenetic and molecular genetic characteristics were summarized and discussed. A comprehensive review of partner genomic loci and genes mutated in myeloid neoplasms with MECOM rearrangement was conducted. The AF4 gene and the transcription elongation control pathways are proposed as potential therapeutic targets for MECOM-rearranged myeloid neoplasms.

Mechanisms of enhancer-driven oncogene activation

An aggressive subtype of acute myeloid leukemia (AML) is caused by enhancer hijacking resulting in MECOM overexpression. Several chromosomal rearrangements can lead to this: the most common (inv(3)/t(3;3)) results in a hijacked GATA2 enhancer, and there are several atypical MECOM rearrangements involving enhancers from other hematopoietic genes. The set of enhancers which can be hijacked by MECOM can also be hijacked by BCL11B. Enhancer deregulation is also a driver of oncogenesis in a range of other malignancies. The mechanisms of enhancer deregulation observed in other cancer types, including TAD boundary disruptions and the creation of de novo (super-) enhancers, may explain overexpression of MECOM or other oncogenes in AML without enhancer hijacking upon translocation. Gaining mechanistic insight in both enhancer deregulation and super-enhancer activity is critical to pave the way for new treatments for AML and other cancers that are the result of enhancer deregulation.

Complex Genetic Evolution and Treatment Challenges in Myeloid Neoplasms: A Case of Persistent t(2;3)(p15~23;q26)/MECOM Rearrangement, SF3B1 Mutation, and Transient TNIP1::PDGFRB Chimera

BACKGROUND/AIM

Myelodysplastic syndromes (MDSs) are clonal bone marrow disorders characterized by ineffective hematopoiesis. They are classified based on morphology and genetic alterations, with SF3B1 variants linked to favorable prognosis and MECOM rearrangements associated with poor outcomes. The combined effects of these alterations remain unclear. We report an MDS patient carrying both SF3B1 and MECOM alterations who developed transient eosinophilia accompanied by a TNIP1::PDGFRB chimera in a subset of MECOM-affected cells.

CASE REPORT

A 73-year-old woman was diagnosed with myeloid neoplasia with excess blasts and multilineage dysplasia (MDS-EB1). Six months later, SF3B1 mutations were identified, leading to a diagnosis of MDS-SF3B1. Despite azacitidine treatment, her condition worsened, showing hypercellular bone marrow and eosinophilia. Genetic analysis revealed a t(2;3)(p15~23;q26)/MECOM rearrangement and TNIP1::PDGFRB chimera. Imatinib eradicated eosinophilia and reduced TNIP1::PDGFRB-positive cells, but the MECOM-clone persisted. Subsequent treatments, including hydroxyurea, mercaptopurine, and low-dose cytarabine, were ineffective. FLT3 mutations and high EVI1 transcript levels were later detected. The patient succumbed to progressive disease.

CONCLUSION

This case highlights the complexity of MDS and the importance of genetic abnormalities in treatment planning. Persistent MECOM rearrangement and the TNIP1::PDGFRB chimera emphasize the need for further research into resistance mechanisms.

Structural Variant Analysis of Complex Karyotype Myelodysplastic Neoplasia Through Optical Genome Mapping

Myelodysplastic neoplasia with complex karyotype (CK-MDS) poses significant clinical challenges and is associated with poor survival. Detection of structural variants (SVs) is crucial for diagnosis, prognostication, and treatment decision-making in MDS. However, the current standard-of-care (SOC) cytogenetic testing, relying on karyotyping, often yields ambiguous results in cases with CK. Here, SV detection by novel optical genome mapping (OGM) technique was explored in 15 CK-MDS cases, which collectively harbored 85 chromosomes with abnormalities reported by SOC. Additionally, OGM was utilized in the discovery of novel SVs. Altogether, OGM detected corresponding > 5 Mbp alterations for 73 out of 85 SOC reported abnormalities, resulting in an 86% concordance rate. OGM provided further specification of these abnormalities, revealing that 64% of the altered chromosomes were affected by multiple SVs or chromoanagenesis. Prominently, only 5% of missing chromosomes reported by SOC were true monosomies. In addition, OGM detected alterations in chromosomes not reported as abnormal by karyotyping in 93% of cases and provided clinically relevant gene-level information, such as SVs in TP53, MECOM, NUP98, IKZF1, and ETV6. Analysis of novel SVs revealed two previously unreported gene-fusions (SCFD1::ZNF592 and VPS8::LRBA), both confirmed by transcriptome sequencing. Furthermore, the repositioning of CCDC26 (8q24.21) was identified as a potential cause of inappropriate gene activation in two cases, affecting MECOM and SOX7, respectively. This study shows that OGM can significantly enhance the diagnostic analysis of SVs in CK-MDS and highlights the utility of OGM identifying novel SVs in complex cancer genomes.

Clinical significance of dynamic monitoring of EVI1 gene expression in pediatric acute myeloid leukemia

OBJECTIVE

To investigate the clinical significance of dynamic monitoring ecotropic virus integration site-1 (EVI1) expression in childhood acute myeloid leukemia (AML).

METHODS

A retrospective analysis was conducted on 113 pediatric AML patients of Wuhan Children's Hospital from 2014 to 2022. The correlation between EVI1 expression levels and clinical indicators including clinical characteristics, first complete remission (CR1), relapse, and overall survival (OS) was analyzed. Receiver operating characteristic (ROC) curve analysis was carried out to comprehend the influence of EVI1 expression on relapse.

RESULTS

A total of 78 AML children with EVI1 expression at initial diagnosis were eligible, divided into EVI1-positive (EVI1high) and EVI1-negative (EVI1low) groups. FAB classification (P = 0.047) and abnormal karyotype (P = 0.009) showed significant differences between the two groups. The proportion of EVI1high in individuals with complex and/or monomeric karyotypes was significantly higher than in other cases (P = 0.032). When completing the first induction therapy, the EVI1high group showed a significantly lower CR1 rate than the EVI1low group (P = 0.015). Among 51 cases with EVI1 expression dynamically monitored, those with EVI1 overexpression more than twice had significantly shorter OS (P < 0.05). Among 19 non-HSCT patients undergoing three EVI1 assessments during induction therapy, those with EVI1 overexpression over once had higher relapse rates (P = 0.045). In addition, EVI1 expression level ≥ 83.38% significantly predicted relapse (AUC = 0.833).

CONCLUSION

Aberrantly high expression of EVI1 in pediatric AML was associated with poor prognosis. Continuous and dynamic monitoring of EVI1 expression promotes prognostic evaluation. We add some insights into the impact of EVI1 on the AML patients' OS and survival.

The ETV6-MECOM fusion protein promotes EMT-related properties by repressing the transactivation activity of E-cadherin promoter in K562 leukemia cells

The ETV6-MECOM fusion gene, produced by the rare and recurrent chromosomal translocation t(3; 12) (q26; p13), is associated with high mortality and short survival in myeloid leukemia. However, its function and underlying mechanisms in leukemia progression remain unknown. In this study, leukemia-stable K562 cells expressing the ETV6-MECOM fusion protein were used to investigate the effects of the ETV6-MECOM oncoprotein. K562-ETV6-MECOM cells were undifferentiated and had reduced colony formation, increased cell migration and invasion, and increased sphere number and diameter in a spheroid formation assay, presenting epithelial-to-mesenchymal transition (EMT) traits. The expression of E-cadherin, a hallmark of EMT, was significantly downregulated at the transcriptional and translational level in K562-ETV6-MECOM cells to explore the mechanistic basis of EMT. Stepwise truncation, DNA sequence deletion, mutation analysis for E-cadherin promoter transactivation, and a dual luciferase assay indicated that the regulatory region of ETV6-MECOM is located in the DNA motif -1116 TTAAAA-1111 of E-cadherin promoter. Moreover, a chromatin immunoprecipitation assay showed that this oncoprotein binds to the DNA motif -1116 TTAAAA-1111 with the anti-EVI1 antibody. Although ETV6-MECOM upregulated the expressions of EMT master regulators, including SNAIL, SLUG, ZEB2, and TWIST2, their knockdown had no effect on EMT-related properties. However, overexpression of E-cadherin eliminated EMT traits in the presence of the ETV6-MECOM oncoprotein. These data confirmed that the ETV6-MECOM oncoprotein, not SNAIL, SLUG, ZEB2, or TWIST2, plays a critical role in inducing EMT traits in leukemia K562 cells. ETV6-MECOM induces EMT-related properties by downregulating the transcriptional expression of E-cadherin and repressing its transactivation activity by binding to its core motif -1116TTAAAA-1111 in leukemia K562 cells. These findings could contribute to the development of a therapeutic target for patients with myeloid leukemia characterized by ETV6-MECOM.

Cytogenetics in the management of myelodysplastic neoplasms (myelodysplastic syndromes, MDS): Guidelines from the groupe francophone de cytogénétique hématologique (GFCH)

Myelodysplastic neoplasms (MDS) are clonal hematopoietic neoplasms. Chromosomal abnormalities (CAs) are detected in 40-45% of de novo MDS and up to 80% of post-cytotoxic therapy MDS (MDS-pCT). Lately, several changes appeared in World Health Organization (WHO) classification and International Consensus Classification (ICC). The novel 'biallelic TP53 inactivation' (also called 'multi-hit TP53') MDS entity requires systematic investigation of TP53 locus (17p13.1). The ICC maintains CA allowing the diagnosis of MDS without dysplasia (del(5q), del(7q), -7 and complex karyotype). Deletion 5q is the only CA, still representing a low blast class of its own, if isolated or associated with one additional CA other than -7 or del(7q) and without multi-hit TP53. It represents one of the most frequent aberrations in adults' MDS, with chromosome 7 aberrations, and trisomy 8. Conversely, translocations are rarer in MDS. In children, del(5q) is very rare while -7 and del(7q) are predominant. Identification of a germline predisposition is key in childhood MDS. Aberrations of chromosomes 5, 7 and 17 are the most frequent in MDS-pCT, grouped in complex karyotypes. Despite the ever-increasing importance of molecular features, cytogenetics remains a major part of diagnosis and prognosis. In 2022, a molecular international prognostic score (IPSS-M) was proposed, combining the prognostic value of mutated genes to the previous scoring parameters (IPSS-R) including cytogenetics, still essential. A karyotype on bone marrow remains mandatory at diagnosis of MDS with complementary molecular analyses now required. Analyses with FISH or other technologies providing similar information can be necessary to complete and help in case of karyotype failure, for doubtful CA, for clonality assessment, and for detection of TP53 deletion to assess TP53 biallelic alterations.

Cytogenetics in the management of acute myeloid leukemia and histiocytic/dendritic cell neoplasms: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH)

Genetic data are becoming increasingly essential in the management of hematological neoplasms as shown by two classifications published in 2022: the 5th edition of the World Health Organization Classification of Hematolymphoid Tumours and the International Consensus Classification of Myeloid Neoplasms and Acute Leukemias. Genetic data are particularly important for acute myeloid leukemias (AMLs) because their boundaries with myelodysplastic neoplasms seem to be gradually blurring. The first objective of this review is to present the latest updates on the most common cytogenetic abnormalities in AMLs while highlighting the pitfalls and difficulties that can be encountered in the event of cryptic or difficult-to-detect karyotype abnormalities. The second objective is to enhance the role of cytogenetics among all the new technologies available in 2023 for the diagnosis and management of AML.

AML classification in the year 2023: How to avoid a Babylonian confusion of languages

In parallel to the 5th edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO 2022), an alternative International Consensus Classification (ICC) has been proposed. To evaluate the impact of the new classifications on AML diagnoses and ELN-based risk classification, we analyzed 717 MDS and 734 AML non-therapy-related patients diagnosed according to the revised 4th WHO edition (WHO 2017) by whole genome and transcriptome sequencing. In both new classifications, the purely morphologically defined AML entities decreased from 13% to 5%. Myelodysplasia-related (MR) AML increased from 22% to 28% (WHO 2022) and 26% (ICC). Other genetically-defined AML remained the largest group, and the abandoned AML-RUNX1 was mainly reclassified as AML-MR (WHO 2022: 77%; ICC: 96%). Different inclusion criteria of AML-CEBPA and AML-MR (i.a. exclusion of TP53 mutated cases according to ICC) were associated with differences in overall survival. In conclusion, both classifications focus on more genetics-based definitions with similar basic concepts and a large degree of agreement. The remaining non-comparability (e.g., TP53 mutated AML) needs additional studies to definitely answer open questions on disease categorization in an unbiased way.

3q26.2/MECOM Rearrangements by Pericentric Inv(3): Diagnostic Challenges and Clinicopathologic Features

MECOM rearrangement (MECOM-R) resulting from 3q26.2 aberrations is often associated with myeloid neoplasms and inferior prognosis in affected patients. Uncommonly, certain 3q26.2/MECOM-R can be subtle/cryptic and consequently overlooked by karyotyping. We identified 17 acute myeloid leukemia (AML) patients (male/female: 13/4 with a median age of 67 years, range 42 to 85 years) with a pericentric inv(3) leading to MECOM-R, with breakpoints at 3p23 (n = 11), 3p25 (n = 3), 3p21 (n = 2) and 3p13 (n = 1) on 3p and 3q26.2 on 3q. These pericentric inv(3)s were overlooked by karyotyping initially in 16 of 17 cases and later detected by metaphase FISH analysis. Similar to the patients with classic/paracentric inv(3)(q21q26.2), patients with pericentric inv(3) exhibited frequent cytopenia, morphological dysplasia (especially megakaryocytes), -7/del(7q), frequent NRAS (n = 6), RUNX1 (n = 5) and FLT-3 (n = 4) mutations and dismal outcomes (median overall survival: 14 months). However, patients with pericentric inv(3) more frequently had AML with thrombocytopenia (n = 15, 88%), relative monocytosis in peripheral blood (n = 15, 88%), decreased megakaryocytes (n = 11, 65%), and lower SF3B1 mutation. We conclude that AML with pericentric inv(3) shares some similarities with AML associated with classic/paracentric inv(3)/GATA2::MECOM but also shows certain unique features. Pericentric inv(3)s are often subtle/cryptic by chromosomal analysis. A reflex FISH analysis for MECOM-R is recommended in myeloid neoplasms showing -7/del(7q).