bims-tremyl 2022-06-19 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2022–06–19
27 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Enasidenib vs conventional care in mutant-IDH2 relapsed/refractory acute myeloidleukemia: a randomized, phase 3 trial.
Prediction of complete remission and survival in acute myeloid leukemia using supervised machine learning.
Phase II Study of Venetoclax Added to Cladribine Plus Low-Dose Cytarabine Alternating With 5-Azacitidine in Older Patients With Newly Diagnosed Acute Myeloid Leukemia.
Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression.
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia.
Rise of the Clones: Myelodysplastic Syndrome  to Secondary Acute Myeloid Leukemia.
Protein Kinase C Epsilon Overexpression Is Associated With Poor Patient Outcomes in AML and Promotes Daunorubicin Resistance Through p-Glycoprotein-Mediated Drug Efflux.
Targeting the Leukemic stem cell protein machinery by inhibition of mitochondrial pyrimidine synthesis.
Prognostic Impact and Phenotype of Residual Acute Myeloid Leukemia Stem Cells.
A dynamic 3-factor survival model for acute myeloid leukemia that accounts for response to induction chemotherapy.
Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia.
Macaque Clonal Hematopoiesis Model Demonstrates Expansion of TET2-Disrupted Clones and Utility for Testing Interventions.
Outcomes and molecular profile of oligomonocytic CMML support its consideration as the first stage in the CMML continuum.
Clinicopathologic spectrum of myeloid neoplasms with concurrent myeloproliferative neoplasm driver mutations and SRSF2 mutations.
TET2-mutant clonal hematopoiesis and risk of gout.
Memory-like NK cells armed with a neoepitope-specific CAR exhibit potent activity against NPM1 mutated acute myeloid leukemia.
Azacitidine and its role in the upfront treatment of acute myeloid leukemia.
Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation.
Transcriptional plasticity drives leukemia immune escape.
Identification of an Epi-metabolic dependency on EHMT2/G9a in T-cell acute lymphoblastic leukemia.
Blinatumomab Is Associated with Favorable Outcomes in Patients With B-cell Lineage Acute Lymphoblastic Leukemia and Positive Measurable Residual Disease at a Threshold of 10-4 and Higher.
Hematopoietic stem cell regeneration through paracrine regulation of the Wnt5a/Prox1 signaling axis.
Differentiation and prognostic stratification of acute myeloid leukemia by serum-based spectroscopy coupling with metabolic fingerprints.
Calreticulin mutant myeloproliferative neoplasms induce MHC-I skewing, which can be overcome by an optimized peptide cancer vaccine.
HLA-haploidentical transplantation for relapsed/refractory AML: better LFS with BM than with PBSC in patients ≥ 55 years of age.
CLASP2 safeguards hematopoietic stem cell properties during mouse and fish development.
Signatures of copy number alterations in human cancer.

Blood. 2022 Jun 17. pii: blood.2021014901. [Epub ahead of print]

Enasidenib vs conventional care in mutant-IDH2 relapsed/refractory acute myeloidleukemia: a randomized, phase 3 trial.

Stéphane de Botton, Pau Montesinos, Andre Schuh, Cristina Papayannidis, Paresh Vyas, Andrew H Wei, Hans Beier Ommen, Sergey Semochkin, Hee-Je Kim, Richard A Larson, Jamie Koprivnikar, Olga Frankfurt, Felicitas R Thol, Jörg Chromik, Jenny L Byrne, Arnaud Pigneux, Xavier Thomas, Olga Salamero, María-Belén Vidriales, Vadim A Doronin, Hartmut Döhner, Amir T Fathi, Eric Laille, Xin Yu, Maroof Hasan, Patricia Martín-Regueira, Courtney D DiNardo.

This open-label, randomized, phase 3 trial (NCT02577406) compared enasidenib, an oral IDH2 inhibitor, with conventional care regimens (CCR) in patients aged ≥60 years with late-stage, mutant-IDH2 acute myeloid leukemia (AML) relapsed/refractory (R/R) to 2 or 3 prior AML-directed therapies. Patients were first preselected to a CCR (azacitidine, intermediate-dose cytarabine, low-dose cytarabine, or supportive care), and then randomized (1:1) to enasidenib 100 mg/day or CCR. The primary endpoint was overall survival (OS). Secondary endpoints included event-free survival (EFS), time to treatment failure (TTF), overall response rate (ORR), hematologic improvement (HI), and transfusion independence (TI). Overall, 319 patients were randomized to enasidenib (n=158) or CCR (n=161). Median age was 71 years. Median (range) enasidenib exposure was 142 days (3-1270) and CCR was 36 days (1-1166). One enasidenib (0.6%) and 20 CCR (12%) patients received no randomized treatment, and 30% and 43%, respectively, received subsequent AML-directed therapies during follow-up. Median OS with enasidenib vs CCR was 6.5 vs 6.2 months (HR [hazard ratio] 0.86; P=.23); 1-year survival was 37.5% vs 26.1%. Enasidenib meaningfully improved EFS (median 4.9 months, vs 2.6 months with CCR; HR 0.68; P=.008), TTF (median 4.9 vs 1.9 months, HR 0.53; P<.001), ORR (40.5% vs 9.9%; P<.001), HI (42.4% vs 11.2%), and RBC-TI (31.7% vs 9.3%). Enasidenib safety was consistent with prior reports. The primary study endpoint was not met but OS was confounded by early dropout and subsequent AML-directed therapies. Enasidenib provided meaningful benefits in EFS, TTF, ORR, HI, and RBC-TI in this heavily pretreated older mutant-IDH2 R/R AML population.

DOI: https://doi.org/10.1182/blood.2021014901
Haematologica. 2022 Jun 16.

Prediction of complete remission and survival in acute myeloid leukemia using supervised machine learning.

Jan-Niklas Eckardt, Christoph Röllig, Klaus Metzeler, Michael Kramer, Sebastian Stasik, Julia-Annabell Georgi, Peter Heisig, Karsten Spiekermann, Utz Krug, Jan Braess, Dennis Görlich, Cristina M Sauerland, Bernhard Woermann, Tobias Herold, Wolfgang E Berdel, Wolfgang Hiddemann, Frank Kroschinsky, Johannes Schetelig, Uwe Platzbecker, Carsten Müller-Tidow, Tim Sauer, Hubert Serve, Claudia Baldus, Kerstin Schäfer-Eckart, Martin Kaufmann, Stefan Krause, Mathias Hänel, Christoph Schliemann, Maher Hanoun, Christian Thiede, Martin Bornhäuser, Karsten Wendt, Jan Moritz Middeke.

Achievement of complete remission (CR) signifies a crucial milestone in the therapy of acute myeloid leukemia (AML) while refractory disease is associated with dismal outcomes. Hence, accurately identifying patients at risk is essential to individually tailor treatment concepts to disease biology. We used nine machine learning (ML) models to predict CR and 2-year overall survival (OS) in a large multi-center cohort of 1383 AML patients who received intensive induction therapy using clinical, laboratory, cytogenetic and molecular genetic data and validated our results on an external multicenter cohort. Our ML models autonomously selected predictive features both including established markers of favorable or adverse risk as well as identifying markers of so-far controversial relevance. De novo AML, extramedullary AML, double-mutated (dm) CEBPA, mutations of CEBPA-bZIP, NPM1, FLT3-ITD, ASXL1, RUNX1, SF3B1, IKZF1, TP53, U2AF1, t(8;21), inv(16)/t(16;16), del(5)/del(5q), del(17)/del(17p), normal or complex karyotypes, age and hemoglobin at initial diagnosis were statistically significant markers predictive of CR, while t(8;21), del(5)/del(5q), inv(16)/t(16;16), del(17)/del(17p), dmCEBPA, CEBPA-bZIP, NPM1, FLT3-ITD, DNMT3A, SF3B1, U2AF1, TP53, age, white blood cell count, peripheral blast count, serum LDH and Hb at initial diagnosis as well as extramedullary manifestations were predictive for 2-year OS. For prediction of CR and 2-year OS, AUROCs ranged between 0.77 - 0.86 and 0.63 and 0.74, respectively in our test set and 0.71 - 0.80 and 0.65 - 0.75 in the external validation cohort. We demonstrate the feasibility of ML for risk stratification in AML as a model disease for hematologic neoplasms using a scalable and reusable ML framework. Our study illustrates the clinical applicability of ML as a decision support system in hematology.

DOI: https://doi.org/10.3324/haematol.2021.280027
J Clin Oncol. 2022 Jun 15. JCO2102823

Phase II Study of Venetoclax Added to Cladribine Plus Low-Dose Cytarabine Alternating With 5-Azacitidine in Older Patients With Newly Diagnosed Acute Myeloid Leukemia.

Tapan M Kadia, Patrick K Reville, Xuemei Wang, Caitlin R Rausch, Gautam Borthakur, Naveen Pemmaraju, Naval G Daver, Courtney D DiNardo, Koji Sasaki, Ghayas C Issa, Maro Ohanian, Guillermo Montalban-Bravo, Nicholas J Short, Nitin Jain, Alessandra Ferrajoli, Kapil N Bhalla, Elias Jabbour, Koichi Takahashi, Rashmi Malla, Kelly Quagliato, Rashmi Kanagal-Shamanna, Uday R Popat, Michael Andreeff, Guillermo Garcia-Manero, Marina Y Konopleva, Farhad Ravandi, Hagop M Kantarjian.

PURPOSE: The combination of venetoclax and 5-azacitidine (5-AZA) for older or unfit patients with acute myeloid leukemia (AML) improves remission rates and survival compared with 5-AZA alone. We hypothesized that the addition of venetoclax to cladribine (CLAD)/low-dose araC (low-dose cytarabine [LDAC]) alternating with 5-AZA backbone may further improve outcomes for older patients with newly diagnosed AML.
METHODS: This is a phase II study investigating the combination of venetoclax and CLAD/LDAC alternating with venetoclax and 5-AZA in older (≥ 60 years) or unfit patients with newly diagnosed AML. The primary objective was composite complete response (CR) rate (CR plus CR with incomplete blood count recovery); secondary end points were overall survival, disease-free survival (DFS), overall response rate, and toxicity.
RESULTS: A total of 60 patients were treated; median age was 68 years (range, 57-84 years). By European LeukemiaNet, 23%, 33%, and 43% were favorable, intermediate, and adverse risk, respectively. Fifty-six of 60 evaluable patients responded (composite CR: 93%) and 84% were negative for measurable residual disease. There was one death (2%) within 4 weeks. With a median follow-up of 22.1 months, the median overall survival and DFS have not yet been reached. The most frequent grade 3/4 nonhematologic adverse events were febrile neutropenia (n = 33) and pneumonia (n = 14). One patient developed grade 4 tumor lysis syndrome.
CONCLUSION: Venetoclax and CLAD/LDAC alternating with venetoclax and 5-AZA is an effective regimen among older or unfit patients with newly diagnosed AML. The rates of overall survival and DFS are encouraging. Further study of this non-anthracycline-containing backbone in younger patients, unfit for intensive chemotherapy, as well as comparisons to standard frontline therapies is warranted.

DOI: https://doi.org/10.1200/JCO.21.02823
Blood Cancer Discov. 2022 Jun 16. OF1-OF16

Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression.

Andrew J Menssen, Ajay Khanna, Christopher A Miller, Sridhar Nonavinkere Srivatsan, Gue Su Chang, Jin Shao, Joshua Robinson, Michele O'Laughlin, Catrina C Fronick, Robert S Fulton, Kimberly Brendel, Sharon E Heath, Raya Saba, John S Welch, David H Spencer, Jacqueline E Payton, Peter Westervelt, John F DiPersio, Daniel C Link, Matthew J Schuelke, Meagan A Jacoby, Eric J Duncavage, Timothy J Ley, Matthew J Walter.

Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression.
SIGNIFICANCE: Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML. See related article by Guess et al., p. 316 (33). See related commentary by Romine and van Galen, p. 270.

DOI: https://doi.org/10.1158/2643-3230.BCD-21-0155
Blood. 2022 06 16. pii: blood.2021015325. [Epub ahead of print]

Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia.

Atsushi Tanaka, Taizo A Nakano, Masaki Nomura, Hiromi Yamazaki, Jan Philipp Bewersdorf, Roger Mulet-Lazaro, Simon Hogg, Bo Liu, Alex Penson, Akihiko Yokoyama, Weijia Zang, Marije Havermans, Miho Koizumi, Yasutaka Hayashi, Hana Cho, Akinori Kanai, Stanley C Lee, Muran Xiao, Yui Koike, Yifan Zhang, Miki Fukumoto, Yumi Aoyama, Tsuyoshi Konuma, Hiroyoshi Kunimoto, Toshiya Inaba, Hideaki Nakajima, Hiroaki Honda, Hiroshi Kawamoto, Ruud Delwel, Omar Abdel-Wahab, Daichi Inoue.

Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 drive inv(3)/t(3;3) myeloid leukemias via structural rearrangement of an enhancer which upregulates transcription of EVI1. Here we identify a novel, previously unannotated oncogenic RNA-splicing derived isoform of EVI1 which is frequently present in inv(3)/t(3;3) AML and directly contributes to leukemic transformation. This EVI1 isoform is generated by oncogenic mutations in the core RNA splicing factor SF3B1, which is mutated in >30% of inv(3)/t(3;3) myeloid neoplasm patients and thereby represents the single most commonly co-occurring genomic alteration in inv(3)/t(3;3) patients. SF3B1 mutations are statistically uniquely enriched in inv(3)/t(3;3) myeloid neoplasm patients and patient-derived cell lines compared with other forms of AML and promote mis-splicing of EVI1 generating an in-frame insertion of six amino acids at the 3' end of the second Zinc finger domain of EVI1. Expression of this EVI1 splice variant enhanced the self-renewal of hematopoietic stem cells and introduction of mutant SF3B1 in mice bearing the humanized inv(3)(q21q26) allele resulted in generation of this novel EVI1 isoform in mice and hastened leukemogenesis in vivo. The mutant SF3B1 spliceosome depends upon an exonic splicing enhancer within EVI1 exon 13 to promote usage of a cryptic branch point and aberrant 3' splice site within intron 12 resulting in the generation of this isoform. These data provide a mechanistic basis for the frequent co-occurrence of SF3B1 mutations as well as new insights into the pathogenesis of myeloid leukemias harboring inv(3)/t(3;3).

DOI: https://doi.org/10.1182/blood.2021015325
Blood Cancer Discov. 2022 Jun 16. OF1-OF3

Rise of the Clones: Myelodysplastic Syndrome  to Secondary Acute Myeloid Leukemia.

Kyle A Romine, Peter van Galen.

SUMMARY: Myelodysplastic syndrome (MDS) describes a family of blood disorders driven by the clonal expansion of mutated blood cells that can evolve into secondary acute myeloid leukemia (sAML). Two new studies use single-cell and deep sequencing to elucidate the progression of MDS to AML, revealing discrete clonal architectures and the driving role of signaling mutations.

DOI: https://doi.org/10.1158/2643-3230.BCD-22-0046
Front Oncol. 2022 ;12 840046

Protein Kinase C Epsilon Overexpression Is Associated With Poor Patient Outcomes in AML and Promotes Daunorubicin Resistance Through p-Glycoprotein-Mediated Drug Efflux.

Rachael Nicholson, Ana Catarina Menezes, Aleksandra Azevedo, Adam Leckenby, Sara Davies, Claire Seedhouse, Amanda Gilkes, Steve Knapper, Alex Tonks, Richard L Darley.

  The protein kinase C (PKC) family of serine/threonine kinases are pleiotropic signaling regulators and are implicated in hematopoietic signaling and development. Only one isoform however, PKCϵ, has oncogenic properties in solid cancers where it is associated with poor outcomes. Here we show that PKCϵ protein is significantly overexpressed in acute myeloid leukemia (AML; 37% of patients). In addition, PKCϵ expression in AML was associated with a significant reduction in complete remission induction and disease-free survival. Examination of the functional consequences of PKCϵ overexpression in normal human hematopoiesis, showed that PKCϵ promotes myeloid differentiation, particularly of the monocytic lineage, and decreased colony formation, suggesting that PKCϵ does not act as an oncogene in hematopoietic cells. Rather, in AML cell lines, PKCϵ overexpression selectively conferred resistance to the chemotherapeutic agent, daunorubicin, by reducing intracellular concentrations of this agent. Mechanistic analysis showed that PKCϵ promoted the expression of the efflux pump, P-GP (ABCB1), and that drug efflux mediated by this transporter fully accounted for the daunorubicin resistance associated with PKCϵ overexpression. Analysis of AML patient samples also showed a link between PKCϵ and P-GP protein expression suggesting that PKCϵ expression drives treatment resistance in AML by upregulating P-GP expression.

Keywords:  P-glycoprotein (ABCB1 protein); acute myeloid leukemia; daunorubicin; drug resistance; protein kinase C epsilon

DOI:  https://doi.org/10.3389/fonc.2022.840046
EMBO Mol Med. 2022 Jun 13. e16171

Targeting the Leukemic stem cell protein machinery by inhibition of mitochondrial pyrimidine synthesis.

Elisa Donato, Andreas Trumpp.

Acute Myeloid Leukemia is one of the most aggressive blood cancers with a high frequency of relapse. While standard chemotherapy is able to target rapidly proliferating immature blasts, it fails to eradicate slowly proliferating Leukemic Stem Cells. Therefore, new therapeutic strategies that efficiently target LSCs are urgently needed. Recent studies suggest that LSCs have particular metabolic vulnerabilities, which would open the possibility of a therapeutic window with limited off-target effects on the normal hematopoietic system. In this issue of EMBO Molecular Medicine, So and colleagues investigate the mechanism of action of AG636, a new potent inhibitor of de novo pyrimidine synthesis, and discovered an unexpected link to AML protein translation essential for LSC function.

DOI: https://doi.org/10.15252/emmm.202216171
Clin Lab. 2022 Jun 01. 68(6):

Prognostic Impact and Phenotype of Residual Acute Myeloid Leukemia Stem Cells.

Samiha Jaddaoui, Hanaa Bencharef, Mouna Lamchahab, Asmaa Quessar, Bouchra Oukkache.

BACKGROUND: Leukemia stem cells (LSCs) have been demonstrated to be more therapy-resistant than leukemic blast cells reflecting measurable residual disease (MRD). CD34+CD38- cell frequency is an independent factor for relapse prediction and could therefore be used in the future to improve MRD assessment in acute myeloid leukemia (AML). This protocol is designed to enable accurate and reproducible immunophenotypic detection of measurable residual stem cell disease necessary for proper therapeutic decision and report their prognostic value in AML patients.
METHODS: Fifty-four Novo AML adult patients diagnosed in the onco-hematology service of the "20 August 1953" Hospital in Casablanca. We analyzed phenotype and frequency of CD45dim CD34+CD38- cells in bone marrow samples from patients with AML and non-myeloid malignancies using six-color flow cytometry and a simple one-tube essay.
RESULTS: For evaluation of leukemic stem cells, our gate strategy was based on the selection of CD34+CD38 - stem cells and leukemia associated immunophenotype approach. Positivity of CD123 or/and aberrant expression of primitive markers CD117 and HLA DR on stem cells discriminate leukemia stem cells from normal hematopoietic stem cells. We reported a statistically significant difference between expressions of primitive markers (CD117 and HLA DR) on leukemic stem cells. In addition, the frequency of LSCs after complete remission in post-induction was persistent in 50% of AML patients.
CONCLUSIONS: Overall, we show that CD34+CD38-CD123+ as a basic phenotype, with aberrant phenotype detection of HLA DR and CD117 markers on stem cells, contributes to detecting LSCs which indicates the poor prognosis.

DOI: https://doi.org/10.7754/Clin.Lab.2021.210821
Am J Hematol. 2022 Jun 15.

A dynamic 3-factor survival model for acute myeloid leukemia that accounts for response to induction chemotherapy.

Ayalew Tefferi, Naseema Gangat, Aref Al-Kali, Hassan Alkhateeb, Mithun Shah, Mrinal S Patnaik, Michelle A Elliott, William J Hogan, Mark R Litzow, Christopher C Hook, Abhishek Mangaonkar, David Viswanatha, Dong Chen, Animesh Pardanani, Rhett P Ketterling, Courtney D DiNardo, Tapan M Kadia, Farhad Ravandi, Koji Sasaki, Kebede H Begna.

The current study was approached with the assumption that response to induction chemotherapy, in acute myeloid leukemia (AML), overshadows pre-treatment risk variables in predicting survival and therefore be used as an anchor for a simplified risk model. We considered 759 intensively-treated patients with AML, not promyelocytic: median age 60 years; primary 66%, secondary 25%, and therapy-related 9%; European LeukemiaNet cytogenetic risk category favorable 8%, intermediate 61%, and adverse 31%. Complete remission with (CR) or without (CRi) count recovery was achieved in 608 (80%) patients. After a median follow-up of 22 months, 503 deaths, 272 relapses, and 257 allogeneic hematopoietic stem cell transplants (AHSCTs) were recorded. Multivariable analysis identified failure to achieve CR/CRi (HR 3.8, 95% CI 3.1-4.8), adverse karyotype (2.2, 1.8-2.8), and age >55 years (2.1, 1.6-2.7) as main risk factors for survival. HR-weighted scoring resulted in four-tiered risk stratification: low (0 points; N=183), intermediate-1 (1 point; N=331), intermediate-2 (2 points; N=117), and high (≥3 points; N=128), with respective median survival (5-year rate) not reached (68%), 34 (37%), 13 (20%), and 5 (5%) months (p <0.001). FLT3-ITD mutation was associated with inferior survival in intermediate-1 (p=0.004) and TP53 in intermediate-2 (p=0.06) and high (p=0.02) risk disease; the latter was fully accounted for by the close association between TP53 mutation and complex/monosomal karyotype while the observations regarding FLT3-ITD were not affected by treatment with midostaurin. AHSCT had a favorable impact on survival, most apparent in intermediate-1 (p<0.001), intermediate-2 (p=0.03), and high (p=0.01) risk disease. The proposed 3-factor survival model offers a novel prototype that is amenable to further enhancement by molecular information and was validated in an external cohort of 1,032 intensively-treated AML patients. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/ajh.26630
Leukemia. 2022 Jun 14.

Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia.

Yue Wei, Rashmi Kanagal-Shamanna, Hong Zheng, Naran Bao, Pamela Pennington Lockyer, Caleb A Class, Faezeh Darbaniyan, Yue Lu, Kevin Lin, Hui Yang, Guillermo Montalban-Bravo, Irene Ganan-Gomez, Kelly A Soltysiak, Kim-Anh Do, Simona Colla, Guillermo Garcia-Manero.

Loss-of-function TET2 mutations are recurrent somatic lesions in chronic myelomonocytic leukemia (CMML). KDM6B encodes a histone demethylase involved in innate immune regulation that is overexpressed in CMML. We conducted genomic and transcriptomic analyses in treatment naïve CMML patients and observed that the patients carrying both TET2 mutations and KDM6B overexpression constituted 18% of the cohort and 42% of patients with TET2 mutations. We therefore hypothesized that KDM6B overexpression cooperated with TET2 deficiency in CMML pathogenesis. We developed a double-lesion mouse model with both aberrations, and discovered that the mice exhibited a more prominent CMML-like phenotype than mice with either Tet2 deficiency or KDM6B overexpression alone. The phenotype includes monocytosis, anemia, splenomegaly, and increased frequencies and repopulating activity of bone marrow (BM) hematopoietic stem and progenitor cells (HSPCs). Significant transcriptional alterations were identified in double-lesion mice, which were associated with activation of proinflammatory signals and repression of signals maintaining genome stability. Finally, KDM6B inhibitor reduced BM repopulating activity of double-lesion mice and tumor burden in mice transplanted with BM-HSPCs from CMML patients with TET2 mutations. These data indicate that TET2 deficiency and KDM6B overexpression cooperate in CMML pathogenesis of and that KDM6B could serve as a potential therapeutic target in this disease.

DOI: https://doi.org/10.1038/s41375-022-01605-1
Blood. 2022 Jun 17. pii: blood.2021014875. [Epub ahead of print]

Macaque Clonal Hematopoiesis Model Demonstrates Expansion of TET2-Disrupted Clones and Utility for Testing Interventions.

Tae-Hoon Shin, Yifan Zhou, Shirley Chen, Stefan Cordes, Max Z Grice, Xing Fan, Byung-Chul Lee, Aisha A AlJanahi, So Gun Hong, Kelli L Vaughan, Julie A Mattison, Steven G Kohama, Margarete Alice Fabre, Naoya Uchida, Selami Demirci, Marcus A F Corat, Jean-Yves Métais, Katherine R Calvo, Manuel Buscarlet, Hannah Natanson, Kathy L McGraw, Alan F List, Lambert Busque, John F Tisdale, George S Vassiliou, Kyung-Rok Yu, Cynthia E Dunbar.

Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error-corrected sequencing of 56 human CH/myeloid malignancy genes we identified natural CH driver mutations in aged rhesus macaques matching genes somatically mutated in human CH, with DNMT3A mutations being the most frequent. A CH model in young adult macaques was generated via autologous transplantation of CRISPR/Cas9-mediated gene-edited hematopoietic stem and progenitor cells (HSPCs), targeting the top human CH genes with loss-of-function (LOF) mutations. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 LOF mutations, compared to minimal expansion of clones bearing other mutations. Although the blood counts of these CH macaques were normal, their bone marrows were hypercellular and myeloid-predominant. TET2-disrupted myeloid colony-forming units isolated from these animals showed a distinct hyperinflammatory gene expression profile compared to WT. In addition, mature macrophages purified from the CH macaques showed elevated NLRP3 inflammasome activity and increased interleukin (IL)-1b and IL-6 production. The model was used to test the impact of IL-6 blockage by tocilizumab, documenting a slowing of TET2 mutated expansion, suggesting that interruption of the IL-6 axis may remove the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and give insights into potential therapeutic interventions.

DOI: https://doi.org/10.1182/blood.2021014875
Blood Adv. 2022 Jun 16. pii: bloodadvances.2022007359. [Epub ahead of print]

Outcomes and molecular profile of oligomonocytic CMML support its consideration as the first stage in the CMML continuum.

Xavier Calvo, David Roman-Bravo, Nieves Garcia-Gisbert, Juan Jose Rodríguez-Sevilla, Sara Garcia-Avila, Lourdes Florensa, Joan Gibert, Concepción Fernández-Rodríguez, Marta Salido, Anna Puiggros, Blanca Espinet, Luis Colomo, Beatriz Bellosillo, Ana Ferrer, Leonor Arenillas.

Oligomonocytic chronic myelomonocytic leukemia (OM-CMML) patients are currently classified into the different categories of the 2017 WHO MDS classification. However recent data support considering OM-CMML as a specific subtype of chronic myelomonocytic leukemia (CMML) given their similar clinical, genomic and immunophenotypic profiles. The main purpose of our study was to provide survival outcome data of a well-annotated series of 42 patients with OM-CMML and to compare them to 162 patients with CMML, 120 with dysplastic type (D-CMML) and 42 with proliferative type (P-CMML). OM-CMML showed significantly longer overall survival (OS) and acute myeloid leukemia-free survival than CMML patients considered as a whole group, and when compared to D-CMML and P-CMML, respectively. Moreover, gene mutations associated with increased proliferation (i.e.: ASXL1 and RAS-pathway mutations) were identified as independent adverse prognostic factors for OS in our series. We found that at a median follow-up of 53.47 months, 29.3% of our OM-CMML patients progressed to D-CMML, and at a median follow-up of 46.03 months, 28.6% of our D-CMML progressed to P-CMML. These data support the existence of an evolutionary continuum among OM-CMML, D-CMML and P-CMML. In this context, we observed that harboring more than 3 mutated genes, ASXL1 mutations and a peripheral blood monocyte percentage above 20% significantly predicted shorter time of progression of OM-CMML into overt CMML. These variables were also detected as independent adverse prognostic factors for OS in OM-CMML. These data support the consideration of OM-CMML as the first evolutionary stage within the proliferative continuum of CMML.

DOI: https://doi.org/10.1182/bloodadvances.2022007359
Mod Pathol. 2022 Jun 11.

Clinicopathologic spectrum of myeloid neoplasms with concurrent myeloproliferative neoplasm driver mutations and SRSF2 mutations.

Mehrnoosh Tashakori, Joseph D Khoury, Mark J Routbort, Keyur P Patel, Sa A Wang, Chi Young Ok, Siba El-Hussein, Rashmi Kanagal-Shamanna, Rajyalakshmi Luthra, Shimin Hu, Pei Lin, Naveen Pemmaraju, Prithviraj Bose, Srdan Verstovsek, Carlos E Bueso-Ramos, L Jeffrey Medeiros, Sanam Loghavi.

Myeloproliferative neoplasms (MPNs) are frequently associated with classic driver mutations involving JAK2, MPL or CALR. SRSF2 is among the most frequently mutated splicing genes in myeloid neoplasms and SRSF2 mutations are known to confer a poor prognosis in patients with MPNs. In this study, we sought to evaluate the clinicopathologic spectrum of myeloid neoplasms harboring concurrent MPN-driver mutations and SRSF2 mutations. The study cohort included 27 patients, 22 (82%) men and five (19%) women, with a median age of 71 years (range, 51-84). These patients presented commonly with organomegaly (n = 15; 56%), monocytosis (n = 13; 48%), morphologic dysplasia (n = 11; 41%), megakaryocytic hyperplasia and/or clustering (n = 10; 37%) and bone marrow fibrosis >MF-1 (17/22; 77%). About one third of patients either initially presented with acute myeloid leukemia (AML) or eventually progressed to AML. Eighteen (68%) patients had a dominant clone with SRSF2 mutation and nine (33%) patients had a dominant clone with a classic MPN-associated driver mutation. Our data suggest that the presence of an SRSF2 mutation preceding the acquisition of a MPN driver mutations is not a disease-defining alteration nor is it restricted to any specific disease entity within the spectrum of myeloid neoplasms. In summary, patients with myeloid neoplasms associated with concurrent SRSF2 and classic MPN driver mutations have clinical and morphologic features close to that of classic MPNs often with frequent dysplasia and monocytosis.

DOI: https://doi.org/10.1038/s41379-022-01118-3
Blood. 2022 Jun 17. pii: blood.2022015384. [Epub ahead of print]

TET2-mutant clonal hematopoiesis and risk of gout.

Mridul Agrawal, Abhishek Niroula, Pierre Cunin, Marie McConkey, Veronica Kovalcik, Peter G Kim, Waihay J Wong, Lachelle D Weeks, Amy E Lin, Peter G Miller, Christopher J Gibson, Aswin Sekar, Inga-Marie Schaefer, Donna Neuberg, Richard M Stone, Alexander G Bick, Md Mesbah Uddin, Gabriel K Griffin, Siddhartha Jaiswal, Pradeep Natarajan, Peter A Nigrovic, Deepak A Rao, Benjamin L Ebert.

Gout is a common inflammatory arthritis caused by precipitation of monosodium urate (MSU) crystals in individuals with hyperuricemia. Acute flares are accompanied by secretion of pro-inflammatory cytokines, including interleukin-1 beta (IL-1B). Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition predisposing to hematologic cancers and cardiovascular disease. CHIP is associated with elevated IL-1B, thus we investigated CHIP as a risk factor for gout. To test the clinical association between CHIP and gout, we analyzed whole exome sequencing data from 177,824 individuals in the MGB Biobank (MGBB) and UK Biobank (UKB). In both cohorts, the frequency of gout was higher among individuals with CHIP than without CHIP (MGBB, CHIP with variant allele fraction [VAF] ≥2%: OR, 1.69; 95% CI, 1.09-2.61; P=0.0189; UKB, CHIP with VAF ≥10%: OR, 1.25; 95% CI, 1.05-1.50; P=0.0133). Moreover, individuals with CHIP and a VAF ≥10% had an increased risk of incident gout (UKB: HR, 1.28; 95% CI, 1.06-1.55; P=0.0107). In murine models of gout pathogenesis, animals with Tet2 knockout hematopoietic cells had exaggerated IL-1B secretion and paw edema upon administration of MSU crystals. Tet2 knockout macrophages elaborated higher levels of IL-1B in response to MSU crystals in vitro, and this was ameliorated through genetic and pharmacologic Nlrp3 inflammasome inhibition. These studies show that TET2-mutant CHIP is associated with an increased risk of gout in humans and that MSU crystals lead to elevated IL-1B levels in Tet2 knockout murine models. We identify CHIP as an amplifier of NLRP3-dependent inflammatory responses to MSU crystals in gout patients.

DOI: https://doi.org/10.1182/blood.2022015384
Proc Natl Acad Sci U S A. 2022 Jun 21. 119(25): e2122379119

Memory-like NK cells armed with a neoepitope-specific CAR exhibit potent activity against NPM1 mutated acute myeloid leukemia.

Han Dong, James Dongjoo Ham, Guangan Hu, Guozhu Xie, Juliana Vergara, Yong Liang, Alaa Ali, Mubin Tarannum, Hannah Donner, Joanna Baginska, Yasmin Abdulhamid, Khanhlinh Dinh, Robert J Soiffer, Jerome Ritz, Laurie H Glimcher, Jianzhu Chen, Rizwan Romee.

  Acute myeloid leukemia (AML) remains a therapeutic challenge, and a paucity of tumor-specific targets has significantly hampered the development of effective immune-based therapies. Recent paradigm-changing studies have shown that natural killer (NK) cells exhibit innate memory upon brief activation with IL-12 and IL-18, leading to cytokine-induced memory-like (CIML) NK cell differentiation. CIML NK cells have enhanced antitumor activity and have shown promising results in early phase clinical trials in patients with relapsed/refractory AML. Here, we show that arming CIML NK cells with a neoepitope-specific chimeric antigen receptor (CAR) significantly enhances their antitumor responses to nucleophosphmin-1 (NPM1)-mutated AML while avoiding off-target toxicity. CIML NK cells differentiated from peripheral blood NK cells were efficiently transduced to express a TCR-like CAR that specifically recognizes a neoepitope derived from the cytosolic oncogenic NPM1-mutated protein presented by HLA-A2. These CAR CIML NK cells displayed enhanced activity against NPM1-mutated AML cell lines and patient-derived leukemic blast cells. CAR CIML NK cells persisted in vivo and significantly improved AML outcomes in xenograft models. Single-cell RNA sequencing and mass cytometry analyses identified up-regulation of cell proliferation, protein folding, immune responses, and major metabolic pathways in CAR-transduced CIML NK cells, resulting in tumor-specific, CAR-dependent activation and function in response to AML target cells. Thus, efficient arming of CIML NK cells with an NPM1-mutation-specific TCR-like CAR substantially improves their innate antitumor responses against an otherwise intracellular mutant protein. These preclinical findings justify evaluating this approach in clinical trials in HLA-A2+ AML patients with NPM1c mutations.

Keywords:  CAR-NK cells; NPM1 mutation; TCR-like CAR; acute myeloid leukemia; memory-like NK cells

DOI:  https://doi.org/10.1073/pnas.2122379119
Expert Opin Pharmacother. 2022 Jun 13. 1-12

Azacitidine and its role in the upfront treatment of acute myeloid leukemia.

Omar Raslan, Alejandro Garcia-Horton.

   INTRODUCTION: Acute myeloid leukemia (AML) predominantly affects elderly population. This poses challenges in management, as patients are frequently not candidates for intensive therapy given comorbidities or frailty. Currently, azacitidine (AZA), either as monotherapy or in combination regimens, is the backbone treatment in this group of patients.
AREAS COVERED: We review the mechanism of action, pharmacology, clinical efficacy, and safety of AZA. It reviews current combination therapies of AZA with other targeted therapies for the treatment of newly diagnosed AML.
EXPERT OPINION: AZA is a cornerstone for the treatment of patients considered ineligible for intensive chemotherapy induction, but better results and therapies are required for these patients. AZA has shown synergistic properties when combined with other medications. Its safety profile and few drug interactions make it a suitable medication to use as backbone. Newer therapies are being combined with AZA, demonstrating safety and in cases, improved responses, and survival. AZA/venetoclax has emerged as the standard of care for patients who are ineligible for intensive chemotherapy. Doublet and triplet combinations are increasingly being studied. With the results observed in elderly patients, the intensive chemotherapy paradigm might be put to test in younger populations, with AZA combinations being at the forefront.

Keywords:  AML; Azacitidine; acute myeloid leukemia; de novo; gilteritinib; venetoclax

DOI:  https://doi.org/10.1080/14656566.2022.2082284
BMC Biol. 2022 Jun 15. 20(1): 141

Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation.

Olivia Cypris, Julia Franzen, Joana Frobel, Philipp Glück, Chao-Chung Kuo, Stephani Schmitz, Selina Nüchtern, Martin Zenke, Wolfgang Wagner.

   BACKGROUND: DNA methylation is involved in the epigenetic regulation of gene expression during developmental processes and is primarily established by the DNA methyltransferase 3A (DNMT3A) and 3B (DNMT3B). DNMT3A is one of the most frequently mutated genes in clonal hematopoiesis and leukemia, indicating that it plays a crucial role for hematopoietic differentiation. However, the functional relevance of Dnmt3a for hematopoietic differentiation and hematological malignancies has mostly been analyzed in mice, with the specific role for human hematopoiesis remaining elusive. In this study, we therefore investigated if DNMT3A is essential for hematopoietic differentiation of human induced pluripotent stem cells (iPSCs).
RESULTS: We generated iPSC lines with knockout of either exon 2, 19, or 23 and analyzed the impact of different DNMT3A exon knockouts on directed differentiation toward mesenchymal and hematopoietic lineages. Exon 19-/- and 23-/- lines displayed an almost entire absence of de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation efficiency was only slightly reduced in exon 19-/- and rather increased in exon 23-/- lines, while there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A-/- iHPCs recapitulate some DNA methylation patterns of acute myeloid leukemia (AML) with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed growth advantage of exon 23-/- iHPCs in a syngeneic competitive differentiation assay.
CONCLUSIONS: Our results demonstrate that iPSCs with homozygous knockout of different exons of DNMT3A remain capable of mesenchymal and hematopoietic differentiation-and exon 23-/- iHPCs even gained growth advantage-despite loss of almost the entire de novo DNA methylation. Partial recapitulation of DNA methylation patterns of AML with DNMT3A mutations by our DNMT3A knockout iHPCs indicates that our model system can help to elucidate mechanisms of clonal hematopoiesis.

Keywords:  CRISPR/Cas9; DNA methylation; DNMT3A; Epigenetics; Hematopoietic differentiation; Induced pluripotent stem cells; Mesenchymal differentiation

DOI:  https://doi.org/10.1186/s12915-022-01343-x
Blood Cancer Discov. 2022 Jun 16. pii: bloodcandisc.BCD-21-0207-E.2021. [Epub ahead of print]

Transcriptional plasticity drives leukemia immune escape.

Kenneth Eagle, Taku Harada, Jeremie Kalfon, Monika W Perez, Yaser Heshmati, Jazmin Ewers, Jost Vrabic Koren, Joshua M Dempster, Guillaume Kugener, Vikram R Paralkar, Charles Y Lin, Neekesh V Dharia, Kimberly Stegmaier, Stuart H Orkin, Maxim Pimkin.

Relapse of acute myeloid leukemia (AML) after allogeneic bone marrow transplantation has been linked to immune evasion due to reduced expression of major histocompatibility complex class II (MHC-II) proteins through unknown mechanisms. We developed CORENODE, a computational algorithm for genome-wide transcription network decomposition, that identified a transcription factor (TF) tetrad, consisting of IRF8, MYB, MEF2C and MEIS1, regulating MHC-II expression in AML cells. We show that reduced MHC-II expression at relapse is transcriptionally driven by combinatorial changes in the expression of these TFs, where MYB and IRF8 play major opposing roles, acting independently of the IFN-gamma/CIITA pathway. Beyond the MHC-II genes, MYB and IRF8 antagonistically regulate a broad genetic program responsible for cytokine signaling and T-cell stimulation that displays reduced expression at relapse. A small number of cells with altered TF abundance and silenced MHC-II expression are present at the time of initial leukemia diagnosis, likely contributing to eventual relapse.

DOI: https://doi.org/10.1158/2643-3230.BCD-21-0207
Cell Death Dis. 2022 Jun 17. 13(6): 551

Identification of an Epi-metabolic dependency on EHMT2/G9a in T-cell acute lymphoblastic leukemia.

Anna Montanaro, Samuel Kitara, Elisa Cerretani, Matteo Marchesini, Chiara Rompietti, Luca Pagliaro, Andrea Gherli, Angela Su, Maria Laura Minchillo, Mariafrancesca Caputi, Rodanthi Fioretzaki, Bruno Lorusso, Linda Ross, Gabriela Alexe, Elena Masselli, Marina Marozzi, Federica Maria Angela Rizzi, Roberta La Starza, Cristina Mecucci, Yan Xiong, Jian Jin, Angela Falco, Birgit Knoechel, Franco Aversa, Olivia Candini, Federico Quaini, Paolo Sportoletti, Kimberly Stegmaier, Giovanni Roti.

Genomic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in acute lymphoblastic leukemia (ALL), suggesting new opportunities for therapeutic interventions. In this study, we identified G9a/EHMT2 as a potential target in T-ALL through the intersection of epigenome-centered shRNA and chemical screens. We subsequently validated G9a with low-throughput CRISPR-Cas9-based studies targeting the catalytic G9a SET-domain and the testing of G9a chemical inhibitors in vitro, 3D, and in vivo T-ALL models. Mechanistically we determined that G9a repression promotes lysosomal biogenesis and autophagic degradation associated with the suppression of sestrin2 (SESN2) and inhibition of glycogen synthase kinase-3 (GSK-3), suggesting that in T-ALL glycolytic dependent pathways are at least in part under epigenetic control. Thus, targeting G9a represents a strategy to exhaust the metabolic requirement of T-ALL cells.

DOI: https://doi.org/10.1038/s41419-022-05002-5
Am J Hematol. 2022 Jun 17.

Blinatumomab Is Associated with Favorable Outcomes in Patients With B-cell Lineage Acute Lymphoblastic Leukemia and Positive Measurable Residual Disease at a Threshold of 10-4 and Higher.

Elias J Jabbour, Nicholas J Short, Nitin Jain, Nadya Jammal, Jeffrey Jorgensen, Sa Wang, Xuemei Wang, Maro Ohanian, Yesid Alvarado, Tapan Kadia, Koji Sasaki, Rebecca Garris, Guillermo Garcia-Manero, Farhad Ravandi, Hagop M Kantarjian.

The presence of measurable residual disease (MRD) is the strongest predictor of relapse in acute lymphoblastic leukemia (ALL). We conducted a prospective, single-arm, phase II study in adults with B-cell ALL with MRD ≥1x10-4 after ≥3 months from the start of frontline therapy or one month from any salvage therapy. Blinatumomab was administered at a standard dosing of 28 micrograms daily as a continuous infusion for up to five cycles and up to 4 additional maintenance cycles. Thirty-seven patients with a median age of 43 years (range, 22-84 years) were treated. Twenty-seven patients (73%) were treated in first complete remission (CR) and 10 patients (27%) in second CR and beyond. Eighteen patients (49%) had Philadelphia-chromosome positive ALL and received concomitant tyrosine kinase inhibitor therapy. Twenty-three patients (62%) had a baseline MRD ≥10-3 . A median of three cycles (range, 1-9 cycles) were administered. Overall, 27 patients (73%) achieved MRD-negative remission. With a median follow-up of 31 months (range, 5-70 months), the estimated 3-year relapse-free survival (RFS) rate was 63% (95% confidence interval [CI], 43%-77%) and overall survival (OS) rate 67% (95% CI, 46%-81%). These rates were 51% (95% CI, 27%-70%) and 61% (95% CI, 36%-78%) in patients with baseline MRD ≥1x10-3 , and 83% (95% CI, 45%-95%) and 77% (95% CI, 32%-95%) in patients with baseline MRD <10-3 , respectively. The rates of adverse events were consistent with previous studies of blinatumomab. In summary, blinatumomab induced MRD negativity in most patients and resulted in high rates of RFS and OS. This study is registered at www.clinicaltrials.gov as #NCT02458014. Funding provided by Amgen Inc. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/ajh.26634
J Clin Invest. 2022 Jun 15. pii: e155914. [Epub ahead of print]132(12):

Hematopoietic stem cell regeneration through paracrine regulation of the Wnt5a/Prox1 signaling axis.

Qiqi Lin, Limei Wu, Srinivas Chatla, Fabliha A Chowdhury, Neha Atale, Jonathan Joseph, Wei Du.

  The crosstalk between the BM microenvironment (niche) and hematopoietic stem cells (HSCs) is critical for HSC regeneration. Here, we show that in mice, deletion of the Fanconi anemia (FA) genes Fanca and Fancc dampened HSC regeneration through direct effects on HSCs and indirect effects on BM niche cells. FA HSCs showed persistent upregulation of the Wnt target Prox1 in response to total body irradiation (TBI). Accordingly, lineage-specific deletion of Prox1 improved long-term repopulation of the irradiated FA HSCs. Forced expression of Prox1 in WT HSCs mimicked the defective repopulation phenotype of FA HSCs. WT mice but not FA mice showed significant induction by TBI of BM stromal Wnt5a protein. Mechanistically, FA proteins regulated stromal Wnt5a expression, possibly through modulating the Wnt5a transcription activator Pax2. Wnt5a treatment of irradiated FA mice enhanced HSC regeneration. Conversely, Wnt5a neutralization inhibited HSC regeneration after TBI. Wnt5a secreted by LepR+CXCL12+ BM stromal cells inhibited β-catenin accumulation, thereby repressing Prox1 transcription in irradiated HSCs. The detrimental effect of deregulated Wnt5a/Prox1 signaling on HSC regeneration was also observed in patients with FA and aged mice. Irradiation induced upregulation of Prox1 in the HSCs of aged mice, and deletion of Prox1 in aged HSCs improved HSC regeneration. Treatment of aged mice with Wnt5a enhanced hematopoietic repopulation. Collectively, these findings identified the paracrine Wnt5a/Prox1 signaling axis as a regulator of HSC regeneration under conditions of injury and aging.

Keywords:  Cell Biology; Hematology; Hematopoietic stem cells

DOI:  https://doi.org/10.1172/JCI155914
FASEB J. 2022 Jul;36(7): e22416

Differentiation and prognostic stratification of acute myeloid leukemia by serum-based spectroscopy coupling with metabolic fingerprints.

Zhengwei Duan, Yang Chen, Minlu Ye, Lijing Xiao, Yanxin Chen, Yingping Cao, Yi Peng, Jingling Zhang, Yu Zhang, Ting Yang, Wuping Liu, Shangyuan Feng, Jianda Hu.

  Acute myeloid leukemia (AML) is a heterogeneous disease characterized by complex molecular and cytogenetic abnormalities. New approaches to predict the prognosis of AML have increasingly attracted attention. There were 98 non-M3 AML cases and 48 healthy controls were enrolled in the current work. Clinically routine assays for cytogenetic and molecular genetic analyses were performed on the bone marrow samples of patients with AML. Meanwhile, metabolic profiling of these AML subjects was also performed on the serum samples by combining Ag nanoparticle-based surface-enhanced Raman spectroscopy (SERS) with proton nuclear magnetic resonance (NMR) spectroscopy. Although most of the routine biochemical test showed no significant differences between the M0-M2 and M5 groups, the metabolic profiles were significantly different either between AML subtypes or between prognostic risk subgroups. Specific SERS bands were screened to serve as potential markers for AML subtypes. The results demonstrated that the classification models for M0-M2 and M5 shared two bands (i.e., 1328 and 741 cm-1 ), all came from nucleic acid signals. Furthermore, Metabolic profiles provided various differential metabolites responsible for different AML subtypes, and we found altered pathways mainly included energy metabolism like glycolysis, pyruvate metabolism, and metabolisms of nucleic acid bases as well as specific amino acid metabolisms. It is concluded that integration of SERS and NMR provides the rational and could be reliable to reveal AML differentiation, and meanwhile lay the basis for experimental and clinical practice to monitor disease progression and prognostic evaluation.

Keywords:  acute myeloid leukemia; metabolic profiling; nuclear magnetic resonance; prognosis; surface-enhanced Raman scattering

DOI:  https://doi.org/10.1096/fj.202200487R
Sci Transl Med. 2022 Jun 15. 14(649): eaba4380

Calreticulin mutant myeloproliferative neoplasms induce MHC-I skewing, which can be overcome by an optimized peptide cancer vaccine.

Mathieu Gigoux, Morten O Holmström, Roberta Zappasodi, Joseph J Park, Stephane Pourpe, Cansu Cimen Bozkus, Levi M B Mangarin, David Redmond, Svena Verma, Sara Schad, Mariam M George, Divya Venkatesh, Arnab Ghosh, David Hoyos, Zaki Molvi, Baransel Kamaz, Anna E Marneth, William Duke, Matthew J Leventhal, Max Jan, Vincent T Ho, Gabriela S Hobbs, Trine Alma Knudsen, Vibe Skov, Lasse Kjær, Thomas Stauffer Larsen, Dennis Lund Hansen, R Coleman Lindsley, Hans Hasselbalch, Jacob H Grauslund, Thomas L Lisle, Özcan Met, Patrick Wilkinson, Benjamin Greenbaum, Manuel A Sepulveda, Timothy Chan, Raajit Rampal, Mads H Andersen, Omar Abdel-Wahab, Nina Bhardwaj, Jedd D Wolchok, Ann Mullally, Taha Merghoub.

The majority of JAK2V617F-negative myeloproliferative neoplasms (MPNs) have disease-initiating frameshift mutations in calreticulin (CALR), resulting in a common carboxyl-terminal mutant fragment (CALRMUT), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALRMUT-specific T cells are rare in patients with CALRMUT MPN for unknown reasons. We examined class I major histocompatibility complex (MHC-I) allele frequencies in patients with CALRMUT MPN from two independent cohorts. We observed that MHC-I alleles that present CALRMUT neoepitopes with high affinity are underrepresented in patients with CALRMUT MPN. We speculated that this was due to an increased chance of immune-mediated tumor rejection by individuals expressing one of these MHC-I alleles such that the disease never clinically manifested. As a consequence of this MHC-I allele restriction, we reasoned that patients with CALRMUT MPN would not efficiently respond to a CALRMUT fragment cancer vaccine but would when immunized with a modified CALRMUT heteroclitic peptide vaccine approach. We found that heteroclitic CALRMUT peptides specifically designed for the MHC-I alleles of patients with CALRMUT MPN efficiently elicited a CALRMUT cross-reactive CD8+ T cell response in human peripheral blood samples but not to the matched weakly immunogenic CALRMUT native peptides. We corroborated this effect in vivo in mice and observed that C57BL/6J mice can mount a CD8+ T cell response to the CALRMUT fragment upon immunization with a CALRMUT heteroclitic, but not native, peptide. Together, our data emphasize the therapeutic potential of heteroclitic peptide-based cancer vaccines in patients with CALRMUT MPN.

DOI: https://doi.org/10.1126/scitranslmed.aba4380
Am J Hematol. 2022 Jun 13.

HLA-haploidentical transplantation for relapsed/refractory AML: better LFS with BM than with PBSC in patients ≥ 55 years of age.

Frédéric Baron, Myriam Labopin, Johanna Tischer, Fabio Ciceri, Anna Maria Raiola, Didier Blaise, Simona Sica, Jan Vydra, Renato Fanin, Friedrich Stölzel, Alessandro Busca, Jose Luis Diez-Martin, Yener Koc, Arnon Nagler, Mohamad Mohty.

  The best stem cell source for T-cell replete HLA-haploidentical transplantation with post-transplant cyclophosphamide (PTCy) remains to be determined. In this EBMT retrospective study we analyzed the impact of stem cell source on leukemia-free survival (LFS) in adult patients with primary refractory or relapsed acute myeloid leukemia (AML) given grafts from HLA-haploidentical donors with PTCy as graft-versus-host disease (GVHD) prophylaxis. A total of 668 patients (249 bone marrow (BM) and 419 peripheral blood stem cells (PBSC) recipients) met the inclusion criteria. The use of PBSC was associated with a higher incidence of grade II-IV (HR = 1.59, P = 0.029) and grade III-IV (HR = 2.08, P = 0.013) acute GVHD. There was a statistical interaction between patient age and the impact of stem cell source for LFS (P < 0.01). In multivariate Cox models, among patients <55 years, the use of PBSC versus BM resulted in comparable LFS (HR = 0.82, P = 0.2). In contrast, in patients ≥55 years of age, the use of PBSC versus BM was associated with higher non-relapse mortality (NRM) (HR = 1.7, P = 0.01), lower LFS (HR = 1.37, P = 0.026) and lower overall survival (OS) (HR = 1.33, P = 0.044). In conclusions, our data suggest that in patients ≥55 years of age with active AML at HLA-haploidentical transplantation, the use of BM instead of PBSC as stem cell source results in lower NRM and better LFS. In contrast among younger patients, the use of PBSC results in at least a comparable LFS. This article is protected by copyright. All rights reserved.

Keywords:  AML; BM; HLA-haploidentical; PBSC; PTCy; acute myeloid leukemia; bone marrow; peripheral blood stem cells; post-transplant cyclophosphamide; refractory; relapsed

DOI:  https://doi.org/10.1002/ajh.26627
Cell Rep. 2022 Jun 14. pii: S2211-1247(22)00739-2. [Epub ahead of print]39(11): 110957

CLASP2 safeguards hematopoietic stem cell properties during mouse and fish development.

Anna Klaus, Thomas Clapes, Laurent Yvernogeau, Sreya Basu, Bart Weijts, Joris Maas, Ihor Smal, Niels Galjart, Catherine Robin.

  Hematopoietic stem cells (HSCs) express a large variety of cell surface receptors that are associated with acquisition of self-renewal and multipotent properties. Correct expression of these receptors depends on a delicate balance between cell surface trafficking, recycling, and degradation and is controlled by the microtubule network and Golgi apparatus, whose roles have hardly been explored during embryonic/fetal hematopoiesis. Here we show that, in the absence of CLASP2, a microtubule-associated protein, the overall production of HSCs is reduced, and the produced HSCs fail to self-renew and maintain their stemness throughout mouse and zebrafish development. This phenotype can be attributed to decreased cell surface expression of the hematopoietic receptor c-Kit, which originates from increased lysosomal degradation in combination with a reduction in trafficking to the plasma membrane. A dysfunctional Golgi apparatus in CLASP2-deficient HSCs seems to be the underlying cause of the c-Kit expression and signaling imbalance.

Keywords:  CLASP2; CP: Developmental biology; Golgi integrity; c-Kit; embryonic aorta; hematopoietic stem cells; hemogenic endothelium; intra-aortic hematopoietic clusters; mouse; post-translational regulation; zebrafish

DOI:  https://doi.org/10.1016/j.celrep.2022.110957
Nature. 2022 Jun 15.

Signatures of copy number alterations in human cancer.

Christopher D Steele, Ammal Abbasi, S M Ashiqul Islam, Amy L Bowes, Azhar Khandekar, Kerstin Haase, Shadi Hames-Fathi, Dolapo Ajayi, Annelien Verfaillie, Pawan Dhami, Alex McLatchie, Matt Lechner, Nicholas Light, Adam Shlien, David Malkin, Andrew Feber, Paula Proszek, Tom Lesluyes, Fredrik Mertens, Adrienne M Flanagan, Maxime Tarabichi, Peter Van Loo, Ludmil B Alexandrov, Nischalan Pillay.

Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.

DOI: https://doi.org/10.1038/s41586-022-04738-6