Genomic and clinical characterization of B/T mixed phenotype acute leukemia reveals recurrent features and T-ALL like mutations

Acute leukemia of ambiguous lineage: Diagnosis, prognosis and treatment

Acute leukemias of ambiguous lineage (ALAL) are an infrequent subtype of acute leukemias without clear evidence of differentiation to a one single cell lineage. Despite their rarity constitute a recognized subgroup in the recent international classifications, such as the WHO (World Health Organization) classification. Their diagnosis require highly specialized flow cytometry technology, and also cytogenetics and molecular techniques. The low frequency of the disease has made it difficult to find the best therapeutic strategy, due both to the lack of prospective studies and randomized trials, and to the heterogeneity of the published retrospective studies on follow-up and treatment. The group of ALAL has bad prognosis, and usually requires intensive strategies that include consolidation with allogeneic stem cell transplant as part of the treatment. The objective of this review was to analyze diagnosis, treatment and prognosis of this rare subtype of leukemias.

Characteristics and outcome of pediatric mixed-phenotype acute leukemia treated with EORTC 58951 protocol: An observational study in Tunisia

BACKGROUND

Mixed phenotype acute leukemia (MPAL), also known as biphenotypic acute leukemia (BAL), is an uncommon subgroup of leukemia that exhibits features of both lymphoid and myeloid lineages.

OBJECTIVE

This study aims to analyze the clinical and biological features of MPAL and to evaluate the therapeutic approaches in children diagnosed with MPAL.

METHODS AND SETTINGS

It was a retrospective study that included children (age<18 years old) diagnosed with MPAL, based on the European Group for Immunological Characterization of Leukemia or the 2008/2016 WHO criteria, in the pediatric hematology department of Aziza Othmana Hospital in Tunisia, from 2006 to 2022.

RESULTS

Of 639 patients with acute leukemia, 10 (1.5%) were diagnosed with MPAL (10 of 639). The median age at diagnosis was 9 years old (range, 4-18 years) with a gender ratio of 1.5. The median initial leukocyte count was 28.3×10⁹/L (range, 1.6-143×10⁹/L). None of the patients had central nervous system involvement. Four patients (40%) had a T/Myeloid phenotype and 6 patients (60%) had a B/Myeloid phenotype. Cytogenetic abnormalities were seen in 7 cases (70%). The BCR-ABL fusion gene was detected in 2 patients (20%). None of the patients had a KMT2A rearrangement. All patients initially received acute lymphoblastic leukemia (ALL) chemotherapy using the EORTC 58951 protocol. Within these patients, one patient (10%) died during the induction phase and 9 (90%) achieved morphologic complete remission at the end of induction. Only one patient underwent allogeneic hematopoietic stem cell transplantation. Treatment-related mortality was 20% (2 cases). The median follow-up time was 38 months (1-202 months). The 3-year event-free and the 3-year overall survival rates for the entire group were 60%.

CONCLUSION

MPAL is rare and complex, with heterogeneous clinical and biological features. A literature review suggests that ALL chemotherapy is better for achieving a favorable prognosis than AML regimens.

Genomic Landscape of Mixed Phenotype Acute Leukemia Associated With Immunophenotypic Lineage Predominance: Impact on Diagnosis and Treatment

OBJECTIVES

Mixed phenotype acute leukemia (MPAL) often poses challenges in diagnosis and clinical management. This is the first study to assess the lineage/immunophenotype-genotype association and the significance of AML-myelodysplasia-related changes (MR, cytogenetic abnormalities and gene mutations, AML-MR-CG-Gene) in MPAL classification.

METHODS

We conducted a clinicopathologic and genomic evaluation of 25 MPAL cases by the WHO-HEM5/ICC classification criteria, except for retaining those MPAL cases with AML-MR-CG-Gene (Conditional-MPAL).

RESULTS

The majority of MPAL cases (22/25, 88%) showed distinct genotypes that overlapped with those of lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). The genomic profile of ALL-like and AML-like was associated with immunophenotypically lymphoid and myeloid lineage predominance, respectively. The lineage/immunophenotype-genotype association may provide a rationale to develop a lineage-immunophenotypically/biologically guided therapy selection. Additionally, 64% of MPAL cases carried AML-MR-CG-Gene, half of which were MPAL with lymphoid-lineage predominance and had ALL-like molecular signatures, and most of these patients responded well to the ALL-based induction regimens. These results support that Conditional-MPAL with AML-MR-CG-Gene may be better diagnosed as MPAL rather than AML-MR.

CONCLUSION

Genomic landscape of AML-like or ALL-like MPAL is associated with the immunophenotypic lineage predominance, and such association could impact treatment decisions and provide supporting evidence to refine MPAL diagnostic criteria in future studies.

An update on mixed phenotype acute leukemia

Mixed phenotype acute leukemias (MPALs) are a heterogeneous group of acute leukemias that show differentiation along more than one lineage. MPAL are rare and account for <5 % of all acute leukemias and demonstrate an inferior prognosis compared with standard acute lymphoblastic or myeloid leukemias. Historically, due to the limited understanding of its underlying pathogenesis, there were no well-established classification schemes, leading to difficulty in both diagnosis and treatment. With the advent of new nomenclature and algorithms, including the European Group for the Immunological Characterization of Leukemias (EGIL) scoring system, World Health Organization (WHO) tumor classification, and International Consensus Classification (ICC), these entities are better defined and there have been significant changes in clinical management. Additionally, an increasing variety of molecular and cytogenetic abnormalities have been recognized, which have improved the diagnostic classifications and may represent important potential therapeutic targets. However, due to its rarity, current evidence and recommendations on the clinical approach to MPAL are largely based on retrospective studies with relatively small cohorts, and it remains a diagnostic and therapeutic dilemma. In this review, we discuss the most updated classifications, genomic complexity, and diagnostic and therapeutic strategies for MPAL.

Acute Leukemia of Ambiguous Lineage: Diagnosis and Evaluation by Flow Cytometry

Acute leukemia of ambiguous lineage (ALAL) includes mixed-phenotype acute leukemia (MPAL), which exhibits immunophenotypic evidence of differentiation along more than one cell lineage, and acute undifferentiated leukemia (AUL), which lacks sufficient immunophenotypic differentiation along any cell lineage. This review provides an overview of ALAL, emphasizing the central role of flow cytometric analysis in its diagnostic workflow. It primarily focuses on MPAL, addressing updated classification and diagnostic criteria by the WHO-HEM5 and the ICC, including both genetically defined and phenotypically defined MPAL. The article provides a detailed review of the MPAL lineage assignment criteria with an illustrative description of a series of MPAL cases. Future studies are needed to reconcile the different criteria used in these two classifications. Continuously expanded molecular studies are expected to provide a genomic and lineage-associated framework for the classification of ALAL with clinical relevance in the diagnosis and therapy selection.

How to think about acute leukemia of ambiguous lineage

Classification of acute leukemia involves assigning lineage by resemblance of blasts to normal progenitor cells. This approach provides descriptive information that is useful for disease monitoring, provides clues to pathogenesis, and can help to select effective chemotherapeutic regimens. Acute leukemias of ambiguous lineage (ALAL) are those leukemias that either fail to show evidence of myeloid, B-lymphoid, or T-lymphoid lineage commitment or show evidence of commitment to more than 1 lineage, including mixed-phenotype acute leukemia (MPAL). The different treatment regimens for acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) make ALAL a challenge both diagnostically and therapeutically. Current classification criteria have reduced the reported incidence of mixed lineage leukemias by emphasizing fewer markers and categorizing some biphenotypic leukemias with recurrent cytogenetic abnormalities as other entities. Several recent studies have explored the genomic and epigenetic landscape of MPAL and emphasize the genomic heterogeneity of MPAL. Two classification proposals of myeloid malignancies recently been published and include International Consensus Classification and fifth edition of the World Health Organization Classification of Haematolymphoid Tumours. Our review aims to discuss the diagnostic challenges in the setting of classification updates, recent genomic studies, and therapeutic strategies in this poorly understood disease.

Measuring single-cell immune clonality to track haematological cancers

While paediatric blood cancers are deadly, modern medical advances have enabled clinicians to measure levels of residual cancer cells to manage therapeutic strategies for patients. However, blood cancers, including leukaemias and lymphomas, are highly heterogeneous and is comprised of complex clonal populations that can hinder efforts in detecting the cancer cells as well as managing treatments. Furthermore, the tumour microenvironment is comprised of heterogenous immune dynamics that may be different between patients. High-throughput sequencing has constributed to new discoveries in genetic and transcriptomic alterations underpinning cancer, including blood cancers, and has changed how patients are monitored and managed. Here we discuss the recent efforts using single-cell approach, particularly on efforts to track clonal heterogenity of paediatric blood cancer and the underlying immune response, highlighting avenues for novel biomarker discovery that may have significant impact on clinical oncology practice.

Effective treatment of relapsed/refractory CD19-positive B/T-type mixed-phenotype acute leukemia with blinatumomab: A case report

A 26-year-old man was diagnosed with B/T-type mixed-phenotype acute leukemia (MPAL-B/T) based on blasts being positive for CD19, cytoplasmic CD3, and cyCD79a, but negative for myeloperoxidase. Acute lymphoblastic leukemia-based chemotherapy was started, but the leukemia was refractory. He underwent cord blood transplantation with the conditioning regimen of total body irradiation plus cyclophosphamide and cytarabine with granulocyte-colony stimulating factor priming. Prophylaxis for graft versus host disease was performed with short-term methotrexate and cyclosporin. The leukemia relapsed in bone marrow 20 months later. At that time, he was treated with inotuzumab ozogamicin because the blasts expressed CD22 (75.4%), but this was ineffective. He was next administered blinatumomab with dexamethasone pretreatment, resulting in a complete remission (CR). He subsequently underwent human leukocyte antigen-haploidentical peripheral blood stem cell transplantation. He has still maintained a CR for 12 months. Blinatumomab might be a promising treatment and a bridge to stem cell transplantation even in relapsed/refractory CD19-expressing MPAL-B/T.

Fifth Edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues: Acute Lymphoblastic Leukemias, Mixed-Phenotype Acute Leukemias, Myeloid/Lymphoid Neoplasms With Eosinophilia, Dendritic/Histiocytic Neoplasms, and Genetic Tumor Syndromes

This manuscript represents a review of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia/lymphoblastic lymphoma), acute leukemias of ambiguous lineage, mixed-phenotype acute leukemias, myeloid/lymphoid neoplasms with eosinophilia and defining gene rearrangements, histiocytic and dendritic neoplasms, and genetic tumor syndromes of the 5th edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The diagnostic, clinicopathologic, cytogenetic, and molecular genetic features are discussed. The differences in comparison to the 4th revised edition of the World Health Organization classification of hematolymphoid neoplasms are highlighted.

Genomic heterogeneity within B/T mixed phenotype acute leukemia in a context of an immunophenotype

B/T mixed phenotype acute leukemia (MPAL) is a rare aggressive leukemia. Three cases of B/T MPAL were identified with comprehensive immunophenotypic, cytogenetic, and molecular studies. T-lineage predominant B/T MPAL shares a genetic signature with T-ALL whereas B/T lineage co-dominant B/T MPAL lacks such a T-ALL signature. All three patients were treated with lineage-matched-ALL therapy and alive at the last follow-up. Our study is the first to demonstrate molecular heterogeneity within B/T MPAL in a context of an immunophenotype of T-lineage versus B-lineage predominance. The implication of such a phenotype-genotype association on diagnostic classification is briefly discussed.

Superior sagittal sinus thrombosis in the course of mixed phenotype acute leukaemia treated with acute lymphoblastic leukaemia-like therapy-a case report

Mixed phenotype acute leukaemia (MPAL) is associated with worse overall survival, compared with other acute leukaemias in adults. Lack of clear treatment guidelines makes the therapy challenging. ALL-like induction and consolidation treatment followed by allo-HSCT is the preferred first-line treatment. We present a case of a 36-year-old woman diagnosed with MPAL (EGIL Myelo/B) with KMT2A rearrangement, treated with the PALG-ALL-7 (including PEG-asparaginase) protocol. On day 25 after the induction therapy initiation, numbness of limbs and dizziness were observed. Therefore, the imaging studies (CT and MRI) were performed and a diagnosis of thrombosis of superior sagittal sinus of the brain was established. Routinely performed blood coagulation tests showed prolonged APTT and PT, decreased antithrombin III activity and decreased free protein S concentration. LMWH treatment and substitutional therapy with antithrombin III were started, which resulted in a significant reduction in the thrombosis associated symptoms and improvement of the neurological status after 3 days. After induction and consolidation therapy, the patient obtained complete haematological remission and negative measurable residual disease. Six months after the diagnosis, allo-HSCT was successfully performed. During the 4 months follow-up, the patient remained MRD negative and thrombotic symptoms free. To the best of our knowledge, our communication has been the first report of such complication in an MPAL patient treated with PEG-asparaginase containing protocol in adults. We recommend increased vigilance in patients manifesting any mild neurological symptoms and early decision about the MRI study performance.

[Update on acute leukemia of ambiguous lineage in 2023 - Recommendations of the French Society for Childhood and Adolescent Cancer and Leukemia (SFCE)]

Acute leukemias of ambiguous lineage (ALAL) represent between 3 and 5% of childhood AL. This term encompasses many subtypes of AL that have been defined according to the immunophenotypic profile based on the expression of various lineage markers. This classification has been modified and enriched during the last decade thanks to the improvement of molecular biology techniques, which have led to reconsider the ontogenic proximity existing between certain forms of ALAL. This increasing diagnostic complexity justifies the establishment of a close communication between clinicians and biologists in the management of these rare forms of AL. Indeed, the initial classification remains the cornerstone of their management since it conditions the future choice of therapeutic protocol. Thus, with the notable exception of undifferentiated forms of AL or AUL (for acute undetermined leukemia), it is now accepted that ALAL benefit from a lymphoid-based therapy approach. As with the management of "classic" acute lymphoblastic leukemias (ALL), the evaluation of response to treatment will determine the modalities of therapeutic intensification. The objective of improving the prognosis of ALAL justifies, in the long term, their future inclusion in the international ALLTogether protocol while continuing in-depth molecular exploration of these patients to identify targeted therapies.

Treatment of Relapsed B/T-cell Mixed Phenotype Acute Leukemia With Blinatumomab

Here, we describe the treatment of a patient with relapsed/refractory B/T mixed phenotype acute leukemia (MPAL) using blinatumomab monotherapy, the first bispecific T cell engager (BiTE) approved by the FDA for relapsed/refractory B cell acute lymphoblastic leukemia (B-ALL). A 64-year-old man with a history of stage 3 chronic kidney disease and type 2 diabetes mellitus was discovered to have B/T MPAL on bone marrow biopsy during hospitalization for dyspnea due to pulmonary embolism. The patient achieved brief remission with blinatumomab treatment before succumbing to neutropenic sepsis. The lack of sufficient data to guide therapy in MPAL remains a challenge, highlighting the potential of new targeted approaches such as blinatumomab to improve outcomes in relapsed/refractory MPAL.

Acute leukemias with complex karyotype show a similarly poor outcome independent of mixed, myeloid or lymphoblastic immunophenotype: A study from the Bone Marrow Pathology Group

Mixed phenotype acute leukemia (MPAL) is a heterogenous group of acute leukemias characterized by leukemic blasts that express markers of multiple lineages. The revised 4th edition WHO classification of MPAL excludes AML with myelodysplasia related changes (AML-MRC), including those with complex karyotype (CK), from a diagnosis of MPAL. Abnormal karyotype is frequent in MPAL with the reported rate of CK in MPAL ranging from 19% to 32%. Due its rarity, the clinical and genetic features of MPAL with CK remain poorly characterized. This study aims to further characterize the genetic features of MPAL with CK in comparison to cases of AML and ALL with CK. Cases of de novo MPAL, AML, and B- and T-ALL patients with CK were collected from 8 member institutions of the Bone Marrow Pathology Group. We found no significant difference in overall survival between MPAL with CK compared to AML and ALL with CK. AML with CK was more strongly associated with TP53 mutations, however the presence of TP53 mutations conferred a worse prognosis regardless of lineage. ALL with CK seems to show increased IKZF1 mutation rates which is known to confer a worse prognosis in ALL. Additionally, MPAL with CK showed similarly poor outcomes regardless of whether a lymphoid or myeloid chemotherapy regimen is chosen. Our results suggest that acute leukemias with complex karyotype show a similarly poor outcome regardless of lineage differentiation and that mutation in TP53 confers a poor prognosis in all lineages. Our results support the exclusion of immunophenotypic MPAL with CK from MPAL and appear to confirm the approach proposed in the revised 4th edition WHO to include them as AML with myelodysplasia-related changes and similar myelodysplasia-related AML categories of newer classifications.

Integrative genomic and transcriptomic profiling reveals distinct molecular subsets in adult mixed phenotype acute leukemia

Mixed phenotype acute leukemia (MPAL) is a subtype of leukemia in which lymphoid and myeloid markers are co-expressed. Knowledge regarding the genetic features of MPAL is lacking due to its rarity and heterogeneity. Here, we applied an integrated genomic and transcriptomic approach to explore the molecular characteristics of 176 adult patients with MPAL, including 86 patients with T-lymphoid/myeloid MPAL (T/My MPAL-NOS), 42 with Ph+ MPAL, 36 with B-lymphoid/myeloid MPAL (B/My MPAL-NOS), 4 with t(v;11q23), and 8 with MPAL, NOS, rare types. Genetically, T/My MPAL-NOS was similar to B/T MPAL-NOS but differed from Ph+ MPAL and B/My MPAL-NOS. T/My MPAL-NOS exhibited higher CEBPA, DNMT3A, and NOTCH1 mutations. Ph+ MPAL demonstrated higher RUNX1 mutations. B/T MPAL-NOS showed higher NOTCH1 mutations. By integrating next-generation sequencing and RNA sequencing data of 89 MPAL patients, we defined eight molecular subgroups (G1-G8) with distinct mutational and gene expression characteristics. G1 was associated with CEBPA mutations, G2 and G3 with NOTCH1 mutations, G4 with BCL11B rearrangement and FLT3 mutations, G5 and G8 with BCR::ABL1 fusion, G6 with KMT2A rearrangement/KMT2A rearrangement-like features, and G7 with ZNF384 rearrangement/ZNF384 rearrangement-like characteristics. Subsequently, we analyzed single-cell RNA sequencing data from five patients. Groups G1, G2, G3, and G4 exhibited overexpression of hematopoietic stem cell disease-like and common myeloid progenitor disease-like signatures, G5 and G6 had high expression of granulocyte-monocyte progenitor disease-like and monocyte disease-like signatures, and G7 and G8 had common lymphoid progenitor disease-like signatures. Collectively, our findings indicate that integrative genomic and transcriptomic profiling may facilitate more precise diagnosis and develop better treatment options for MPAL.

The Role of PHF6 in Hematopoiesis and Hematologic Malignancies

Epigenetic regulation of gene expression represents an important mechanism in the maintenance of stem cell function. Alterations in epigenetic regulation contribute to the pathogenesis of hematological malignancies. Plant homeodomain finger protein 6 (PHF6) is a member of the plant homeodomain (PHD)-like zinc finger family of proteins that is involved in transcriptional regulation through the modification of the chromatin state. Germline mutation of PHF6 is the causative genetic alteration of the X-linked mental retardation Borjeson-Forssman-Lehmann syndrome (BFLS). Somatic mutations in PHF6 are identified in human leukemia, such as adult T-cell acute lymphoblastic leukemia (T-ALL, ~ 38%), pediatric T-ALL (~ 16%), acute myeloid leukemia (AML, ~ 3%), chronic myeloid leukemia (CML, ~ 2.5%), mixed phenotype acute leukemia (MPAL, ~ 20%), and high-grade B-cell lymphoma (HGBCL, ~ 3%). More recent studies imply an oncogenic effect of PHF6 in B-cell acute lymphoblastic leukemia (B-ALL) and solid tumors. These data demonstrate that PHF6 could act as a double-edged sword, either a tumor suppressor or an oncogene, in a lineage-dependent manner. However, the underlying mechanisms of PHF6 in normal hematopoiesis and leukemogenesis remain largely unknown. In this review, we summarize current knowledge of PHF6, emphasizing the role of PHF6 in hematological malignancies. Epigenetic regulation of PHF6 in B-ALL. PHF6 maintains a chromatin structure that is permissive to B-cell identity genes, but not T-cell-specific genes (left). Loss of PHF6 leads to aberrant expression of B-cell- and T-cell-specific genes resulting from lineage promiscuity and binding of T-cell transcription factors (right).

Genomic Landscape of Mixed-Phenotype Acute Leukemia

Mixed-phenotype leukemia (MPAL) is a type of acute leukemia in which the blast population shows mixed features of myeloid, T-lymphoid, and/or B-lymphoid differentiation. MPALs are rare and carry a poor prognosis, thus, often pose both a diagnostic and therapeutic challenge. Conventionally, the diagnosis of MPAL requires either a single blast population with a lineage-defining phenotypic expression of multiple lineages (myeloid, B-cell and/or T-cell) (biphenotypic) or two distinct blast populations that each independently satisfy criteria for designation as AML, B-ALL, and/or T-ALL (bilineage). Given the rarity of MPAL, minimal studies have been performed to describe the genomic landscape of these neoplasms. IRB approval was obtained. Central MCC database was searched for any patient with a diagnosis of acute undifferentiated leukemia (AUL), acute leukemia of ambiguous lineage (ALAL), and MPAL. All patient diagnoses were manually reviewed by a hematopathologist to confirm the diagnosis of MPAL. Genomic and molecular data were collated from the EMR and bioinformatically from MCC genomics repositories. Twenty-eight patients with MPAL were identified. Thirteen were female and 15 were male. Average age was 56 years old (range = 28-81). Ten cases were biclonal and 18 were biphenotypic. Diagnoses were as follows: B/myeloid (n = 18), T/myeloid (n = 9), and T/B (n = 1). Cytogenetic analysis (Karyotype +/- FISH) was available for 27 patients. The most frequent recurrent abnormalities were complex karyotype (n = 8), BCR/ABL1 translocation (n = 6), Del 5q/-5 (n = 4), Polysomy 21 (n = 4). Mutational analysis was available for 18 patients wherein mutations were detected in 45 unique genes. The most frequently mutated genes were TP53 (7), RUNX1 (6), WT1 (4), MLL2 (3), FLT3 (3), CBL (2), ASXL1 (2), TET2 (2), MAP3K6 (2), MLL (2), and MAP3K1 (2). Targetable or potentially targetable biomarkers were found in 56% of cases. Overall survival was 19.5 months (range = 0-70 m). Ten patients were treated with an allogeneic stem cell transplant and had superior outcome (p = 0.0013). In one the largest series of MPAL cases to date, we corroborate previous findings with enriched detection of RUNX1 and FLT3-ITD mutations along with discovery of unreported mutations (MAP3K) that may be amenable to therapeutic manipulation. We also report the frequent occurrence of AML with MDS-related changes (AML-MRC)-defining cytogenetic abnormalities (26%). Finally, we show that those patients that received stem cell transplant had a better overall survival. Our findings support the need to genomically profile MPAL cases to exploit opportunities for targeted therapies in this orphan disease with dismal prognosis.

Mixed-Phenotype Acute Leukemia: Clinical Diagnosis and Therapeutic Strategies

Mixed-phenotype acute leukemia (MPAL) comprises a heterogenous group of leukemias that are genetically, immunophenotypically, and clinically, diverse. Given the rarity of the disease, the diagnosis and treatment of MPAL is extremely challenging. Recent collaborative efforts have made significant progress in understanding the complex genomic landscape of MPAL. Some retrospective studies support starting ALL-type induction followed by an allogeneic stem cell transplant(allo-sct) in the first complete remission; however, due to the inherent bias of retrospective data and small case series, a prospective validation of AML- and ALL-based regimen, and the incorporation of targeted therapies based on genetics and immunophenotype are warranted. The prognosis of adults and children with MPAL varies; this justifies modulating the intensity of therapy, including the use of allo-sct as a consolidation strategy.

MEF2C opposes Notch in lymphoid lineage decision and drives leukemia in the thymus

Rearrangements that drive ectopic MEF2C expression have recurrently been found in patients with human early thymocyte progenitor acute lymphoblastic leukemia (ETP-ALL). Here, we show high levels of MEF2C expression in patients with ETP-ALL. Using both in vivo and in vitro models of ETP-ALL, we demonstrate that elevated MEF2C expression blocks NOTCH-induced T cell differentiation while promoting a B-lineage program. MEF2C activates a B cell transcriptional program in addition to RUNX1, GATA3, and LMO2; upregulates the IL-7R; and boosts cell survival by upregulation of BCL2. MEF2C and the Notch pathway, therefore, demarcate opposite regulators of B- or T-lineage choices, respectively. Enforced MEF2C expression in mouse or human progenitor cells effectively blocks early T cell differentiation and promotes the development of biphenotypic lymphoid tumors that coexpress CD3 and CD19, resembling human mixed phenotype acute leukemia. Salt-inducible kinase (SIK) inhibitors impair MEF2C activity and alleviate the T cell developmental block. Importantly, this sensitizes cells to prednisolone treatment. Therefore, SIK-inhibiting compounds such as dasatinib are potentially valuable additions to standard chemotherapy for human ETP-ALL.

ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells

Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.

B/T mixed phenotype acute leukemia with high hyperdiploidy and lineage switch to B-cell acute leukemia

Acute leukemias are often of myeloid or lymphoid origin. However, some acute leukemias revealed an undefined differentiation into a single lineage. Mixed phenotype acute leukemia (MPAL) is an uncommon diagnosis were blasts can share B/T/myeloid phenotype. Here, we report a rare case of a 17-year-old Moroccan female diagnosed with B/T mixed phenotype acute leukemia and a high hyperdiploid karyotype who relapsed after one year of complete remission with a lineage switch to B-cell acute lymphoblastic leukemia. This case report corroborates the disclosed findings about the high occurence of abnormal karyotypes and poor prognosis of MPAL.

TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes

Ahmed and colleagues recently described a novel hybrid lymphocyte expressing both a B and T cell receptor, termed double expresser (DE) cells. DE cells in blood of type 1 diabetes (T1D) subjects were present at increased numbers and enriched for a public B cell clonotype. Here, we attempted to reproduce these findings. While we could identify DE cells by flow cytometry, we found no association between DE cell frequency and T1D status. We were unable to identify the reported public B cell clone, or any similar clone, in bulk B cells or sorted DE cells from T1D subjects or controls. We also did not observe increased usage of the public clone VH or DH genes in B cells or in sorted DE cells. Taken together, our findings suggest that DE cells and their alleged public clonotype are not enriched in T1D. This Matters Arising paper is in response to Ahmed et al. (2019), published in Cell. See also the response by Ahmed et al. (2021), published in this issue.

PHF6 Mutations in Hematologic Malignancies

Next generation sequencing has uncovered several genes with associated mutations in hematologic malignancies that can serve as potential biomarkers of disease. Keeping abreast of these genes is therefore of paramount importance in the field of hematology. This review focuses on PHF6, a highly conserved epigenetic transcriptional regulator that is important for neurodevelopment and hematopoiesis. PHF6 serves as a tumor suppressor protein, with PHF6 mutations and deletions often implicated in the development of T-lymphoblastic leukemia and less frequently in acute myeloid leukemia and other myeloid neoplasms. PHF6 inactivation appears to be an early event in T-lymphoblastic leukemogenesis, requiring cooperating events, including NOTCH1 mutations or overexpression of TLX1 and TLX3 for full disease development. In contrast, PHF6 mutations tend to occur later in myeloid malignancies, are frequently accompanied by RUNX1 mutations, and are often associated with disease progression. Moreover, PHF6 appears to play a role in lineage plasticity within hematopoietic malignancies, with PHF6 mutations commonly present in mixed phenotype acute leukemias with a predilection for T-lineage marker expression. Due to conflicting data, the prognostic significance of PHF6 mutations remains unclear, with a subset of studies showing no significant difference in outcomes compared to malignancies with wild-type PHF6, and other studies showing inferior outcomes in certain patients with mutated PHF6. Future studies are necessary to elucidate the role PHF6 plays in development of T-lymphoblastic leukemia, progression of myeloid malignancies, and its overall prognostic significance in hematopoietic neoplasms.

Update on Acute Leukemias of Ambiguous Lineage

Acute leukemias of ambiguous lineage are a heterogenous group of diseases that include acute undifferentiated leukemias and mixed-phenotype acute leukemias (MPALs). These leukemias pose a challenge for pathologists and clinicians alike in diagnosis, treatment, and further management. Recent genetic characterization has provided insights into their underlying biology and classification, and has offered potential for targeted therapies. This article addresses diagnosis of MPALs with examples of the most common pitfalls, recent comprehensive molecular studies, and advancement in treatment and follow-up modalities.

BACH2-mediated FOS confers cytarabine resistance via stromal microenvironment alterations in pediatric ALL

Acute lymphoblastic leukemia (ALL) is an aggressive hematological cancer that mainly affects children. Relapse and chemoresistance result in treatment failure, underlining the need for improved therapies. BTB and CNC homology 2 (BACH2) is a lymphoid-specific transcription repressor recognized as a tumor suppressor in lymphomas, but little is known about its function and regulatory network in pediatric ALL (p-ALL). Herein, we found aberrant BACH2 expression at new diagnosis not only facilitated risk stratification of p-ALL but also served as a sensitive predictor of early treatment response and clinical outcome. Silencing BACH2 in ALL cells increased cell proliferation and accelerated cell cycle progression. BACH2 blockade also promoted cell adhesion to bone marrow stromal cells and conferred cytarabine (Ara-C)-resistant properties to leukemia cells by altering stromal microenvironment. Strikingly, we identified FOS, a transcriptional activator competing with BACH2, as a novel downstream target repressed by BACH2. Blocking FOS by chemical compounds enhanced the effect of Ara-C treatment in both primary p-ALL cells and pre-B-ALL-driven leukemia xenografts and prolonged the survival of tumor-bearing mice. These data highlight an interconnected network of BACH2-FOS, disruption of which could render current chemotherapies more effective and offer a promising therapeutic strategy to overcome Ara-C resistance in p-ALL.

Mixed Phenotype Acute Leukemia: Current Approaches to Diagnosis and Treatment

PURPOSE OF REVIEW

Mixed phenotype acute leukemia (MPAL) is a rare subtype of acute leukemia with features of both acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). The review examines current definitions and controversies in classification of MPAL, new insights into genomic drivers and pathogenesis, recent evidence to support treatment recommendations, and opportunities for future research.

RECENT FINDINGS

Recent collaborative efforts have made progress in understanding the genomic landscape and optimal therapy for MPAL. The preponderance of retrospective data supports beginning therapy with ALL directed regimens. Differences in prognosis for adult and children with MPAL have led to divergent approaches for therapy intensity, including use of stem cell transplantation consolidation. MPAL remains a challenging leukemia to understand, research, and treat due to low incidence, shifting and subjective approaches to classification, and innate biological heterogeneity. Ongoing research hopes to surmount these obstacles through prospective studies within large cooperative groups to provide new insight into targetable biology and further refine optimal therapy.

Plant homeodomain finger protein 6 in the regulation of normal and malignant hematopoiesis

PURPOSE OF REVIEW

Even though an increasing amount of sequencing data on the leukemia genome has highlighted a tumor-suppressive function for plant homeodomain finger protein 6 (PHF6), its role in the hematopoietic system remained elusive until recently. The purpose of this review is to describe the role of PHF6 in normal hematopoiesis and leukemogenesis based on recent findings from knockout mouse models.

RECENT FINDINGS

In a mouse model, the loss of Phf6 enhanced the bone marrow repopulating capacity of hematopoietic stem cells (HSCs) during serial transplantations without transforming hematopoietic cells, whereas donor mice, which lacked Phf6 expression in the hematopoietic system, did not show any apparent phenotypes in the steady-state. Mechanistically, Phf6 activates effectors in the tumor necrosis factor α (Tnfα) pathway. Therefore, a Phf6 deficiency attenuates the expression of the effectors and confers resistance against Tnfα-mediated growth inhibition to HSCs. Moreover, the loss of Phf6 promoted the development of leukemia induced by aberrant TLX3 expression or an active NOTCH mutation.

SUMMARY

Phf6 restricts the self-renewal of HSCs by governing the Tnfα pathway. Phf6 fulfills a tumor-suppressive function, and its loss synergizes with leukemic lesions to promote the onset of hematological malignancies.

A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis

Classification of acute lymphoblastic and myeloid leukemias (ALL and AML) remains heavily based on phenotypic resemblance to normal hematopoietic precursors. This framework can provide diagnostic challenges for immunophenotypically heterogeneous immature leukemias, and ignores recent advances in understanding of developmental multipotency of diverse normal hematopoietic progenitor populations that are identified by transcriptional signatures. We performed transcriptional analyses of a large series of acute myeloid and lymphoid leukemias and detected significant overlap in gene expression between cases in different diagnostic categories. Bioinformatic classification of leukemias along a continuum of hematopoietic differentiation identified leukemias at the myeloid/T-lymphoid interface, which shared gene expression programs with a series of multi or oligopotent hematopoietic progenitor populations, including the most immature CD34+CD1a−CD7− subset of early thymic precursors. Within these interface acute leukemias (IALs), transcriptional resemblance to early lymphoid progenitor populations and biphenotypic leukemias was more evident in cases originally diagnosed as AML, rather than T-ALL. Further prognostic analyses revealed that expression of IAL transcriptional programs significantly correlated with poor outcome in independent AML patient cohorts. Our results suggest that traditional binary approaches to acute leukemia categorization are reductive, and that identification of IALs could allow better treatment allocation and evaluation of therapeutic options.

Optimal therapeutic strategies for mixed phenotype acute leukemia

PURPOSE OF REVIEW

Mixed phenotype acute leukemia (MPAL) encompasses a rare group of clinically, immunophenotypically, and genetically diverse leukemias. Diagnosing and treating these patients remains challenging. In recent years, systematic efforts have been made to better define the genetic landscape of MPAL. These insights allow better understanding of the pathophysiology of MPAL, have the potential for a more biologically meaningful classification and may promote targeted, novel approaches to treat these leukemias.

RECENT FINDINGS

Recent studies suggest that MPALs originate in a multipotent primitive cell, demonstrate large genetic diversity and include subgroups that may benefit from targeted therapy. Recent data support the use of ALL-type induction followed by allogeneic stem cell transplantation in first remission for most adults. Novel targeted approaches hold promise for treatment of MPAL; however, some may unpredictably select for clonal expansion of cells from a different lineage than observed at presentation.

SUMMARY

A biologically and genetically driven classification of MPAL may yield more accurate prognosis and potentially direct therapy in patients with MPAL. Prospective efforts that incorporate targeted approaches based on genetics and immunophenotype are warranted.

Diagnostic workup of acute leukemias of ambiguous lineage

Acute leukemias of ambiguous lineage (ALAL) comprise acute undifferentiated leukemias (AUL) and mixed-phenotype acute leukemias (MPAL). In the revised fourth edition of the World Health Organization (WHO) classification provided further refinements to the diagnostic criteria for ALAL. Molecular characterization of MPALs using comprehensive next-generation sequencing (NGS) has provided insights into their underlying biology and enabled a deeper understanding of ALAL classification. This review addresses the various components of pathologic assessment to establish a diagnosis of ALAL, and to further subclassify individual cases as AUL or MPAL, with an emphasis on the most up-to-date revisions to diagnostic criteria. In addition, key issues related to the detection of minimal residual disease (MRD) in ALALs and MPALs, and recently uncovered novel molecular diagnostic findings that may be helpful in better distinguishing various types of MPALs from each other, and from their "non-mixed" phenotypic correlates, are also discussed.

Acute Leukemias of Ambiguous Lineage: Clarification on Lineage Specificity

Acute leukemias of ambiguous lineage (ALAL) include acute undifferentiated leukemia and mixed-phenotype acute leukemia (MPAL). This article provides an overview of the diagnosis of ALAL and focuses on the data accounting for the current lineage-assignment criteria for blasts harboring more than one lineage-associated marker. In addition, the currently known molecular data are reviewed, which show that MPAL-associated gene mutations, methylation signatures, and expression profiles are a mixture of those seen in both acute myeloid leukemia and acute lymphoblastic leukemia. Finally, the prognosis and current treatments of MPAL are briefly discussed.

PHF6 and DNMT3A mutations are enriched in distinct subgroups of mixed phenotype acute leukemia with T-lineage differentiation

The genetic aberrations that drive mixed phenotype acute leukemia (MPAL) remain largely unknown, with the exception of a small subset of MPALs harboring BCR -ABL1 and MLL translocations. We performed clinicopathologic and genetic evaluation of 52 presumptive MPAL cases at Memorial Sloan Kettering Cancer Center. Only 29 out of 52 (56%) cases were confirmed to be bona fide MPAL according to the 2016 World Heath Organization classification. We identified PHF6 and DNMT3A mutations as the most common recurrent mutations in MPAL, each occurring in 6 out of 26 (23%) cases. These mutations are mutually exclusive of each other and BCR-ABL1/MLL translocations. PHF6- and DNMT3A-mutated MPAL showed marked predilection for T-lineage differentiation (5/6 PHF6 mutated, 6/6 DNMT3A mutated). PHF6-mutated MPAL occurred in a younger patient cohort compared with DNMT3A-mutated cases (median age, 27 years vs 61 years, P < .01). All 3 MPAL cases with both T- and B-lineage differentiation harbored PHF6 mutations. MPAL with T-lineage differentiation was associated with nodal or extramedullary involvement (9/15 [60%] vs 0, P = .001) and a higher relapse incidence (78% vs 22%, P = .017) compared with those without T-lineage differentiation. Sequencing studies on flow-cytometry-sorted populations demonstrated that PHF6 mutations are present in all blast compartments regardless of lineage differentiation with high variant allele frequency, implicating PHF6 as an early mutation in MPAL pathogenesis. In conclusion, PHF6 and DNMT3A mutations are the most common somatic alterations identified in MPAL and appear to define 2 distinct subgroups of MPAL with T-lineage differentiation with inferior outcomes.

Clinical, immunophenotypic, and genomic findings of acute undifferentiated leukemia and comparison to acute myeloid leukemia with minimal differentiation: a study from the bone marrow pathology group

Acute undifferentiated leukemia is a rare type of acute leukemia that shows no evidence of differentiation along any lineage. Clinical, immunophenotypic and genetic data is limited and it is uncertain if acute undifferentiated leukemia is biologically distinct from acute myeloid leukemia with minimal differentiation, which also shows limited myeloid marker expression and has been reported to have a poor prognosis. We identified 92 cases initially diagnosed as acute undifferentiated leukemia or acute myeloid leukemia with minimal differentiation from pathology databases of nine academic institutions with available diagnostic flow cytometric data, cytogenetic findings, mutational and clinical data. Outcome analysis was performed using Kaplan Meier test for the 53 patients who received induction chemotherapy. Based on cytogenetic abnormalities (N = 30) or history of myelodysplastic syndrome (N = 2), 32 cases were re-classified as acute myeloid leukemia with myelodysplasia related changes. The remaining 24 acute undifferentiated leukemia patients presented with similar age, blood counts, bone marrow cellularity, and blast percentage as the remaining 30 acute myeloid leukemia with minimal differentiation patients. Compared to acute myeloid leukemia with minimal differentiation, acute undifferentiated leukemia cases were characterized by more frequent mutations in PHF6 (5/15 vs 0/19, p = 0.016) and more frequent expression of TdT on blasts (p = 0.003) while acute myeloid leukemia with minimal differentiation cases had more frequent CD123 expression (p = 0.042). Outcome data showed no difference in overall survival, relapse free survival, or rates of complete remission between acute undifferentiated leukemia and acute myeloid leukemia with minimal differentiation groups (p > 0.05). Acute myeloid leukemia with myelodysplasia-related changes patients showed shorter survival when censoring for bone marrow transplant as compared to acute undifferentiated leukemia (p = 0.03) and acute myeloid leukemia with minimal differentiation (p = 0.002). In this largest series to date, the acute undifferentiated leukemia group shows distinct characteristics from acute myeloid leukemia with minimal differentiation, including more frequent PHF6 mutations and expression of TdT.

Genetic Testing in the Diagnosis and Biology of Acute Leukemia

OBJECTIVES

The 2017 Workshop of the Society for Hematopathology/European Association for Haematopathology examined the role of molecular genetics in the diagnosis and biology of acute leukemia.

METHODS

Acute leukemias were reviewed in two sessions: "Genetic Testing in Diagnosis of Acute Leukemias" (53 cases) and "Genetics Revealing the Biology of Acute Leukemias" (41 cases).

RESULTS

Cases included acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemia of ambiguous lineage. Many cases demonstrated genetic alterations of known diagnostic, prognostic, and/or therapeutic significance, while others exhibited alterations that illuminated disease biology. The workshop highlighted the complexity of acute leukemia diagnosis and follow-up, while illustrating advantages and pitfalls of molecular genetic testing.

CONCLUSIONS

Our understanding of the molecular genetics of acute leukemias continues to grow rapidly. Awareness of the potential complexity of genetic architecture and environment is critical and emphasizes the importance of integrating clinical information with morphologic, immunophenotypic, and molecular genetic evaluation.

Targeting steroid resistance in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is characterized by a variable response to steroids during induction and/or consolidation therapy. Notably, recent work suggested that these differences in glucocorticoid sensitivity might, at least in part, be mediated by hyperactivation of specific oncogenic pathways such as RAS/MEK/ERK, PI3K/AKT and IL7R/JAK/STAT. In this review, we elaborate on putative associations between aberrant signaling, therapy resistance, incidence of relapse and clinical outcome in human T-ALL. Furthermore, we emphasize that this potential association with clinical parameters might also be mediated by the tumor microenvironment as a result of increased sensitivity of leukemic T-cells towards cytokine induced signaling pathway activation. With this in mind, we provide an overview of small molecule inhibitors that might have clinical potential for the treatment of human T-ALL in the near future as a result of their ability to overcome steroid resistance thereby potentially increasing survival rates in this aggressive hematological neoplasm.