bims-tremyl 2022-02-06 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2022‒02‒06
twenty-four papers selected by
Paolo Gallipoli
Barts Cancer Institute, Queen Mary University of London

Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia.
Inhibition of BCL2A1 by STAT5 inactivation overcomes resistance to targeted therapies of FLT3-ITD/D835 mutant AML.
Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response.
Impact of frontline treatment approach on outcomes in patients with secondary AML with prior hypomethylating agent exposure.
MOLECULAR CHARACTERIZATION OF MUTANT TP53 ACUTE MYELOID LEUKEMIA AND HIGH-RISK MYELODYSPLASTIC SYNDROME.
Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13.
SIRT2 regulates proliferation and chemotherapy response of MLL-ENL-driven acute myeloid leukemia.
Clinical experience with venetoclax in patients with newly diagnosed, relapsed, or refractory acute myeloid leukemia.
Megakaryocytic emperipolesis as a dyshematopoietic feature in acute myeloid leukemia with inv(16).
CAR T cells redirected to cell surface GRP78 display robust anti-acute myeloid leukemia activity and do not target hematopoietic progenitor cells.
CDK19 regulates the proliferation of hematopoietic stem cells and acute myeloid leukemia cells by suppressing p53-mediated transcription of p21.
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia.
An oncogenic enhancer encodes selective selenium dependency in AML.
Analyzing the key gene expression and prognostics values for acute myeloid leukemia.
LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-κB signaling axis.
Non-T depleted haploidentical stem cell transplantation in AML patients achieving first complete remission after one versus two induction courses: a study from the ALWP/EBMT.
Translatome changes in acute myeloid leukemia cells post-exposure to pegcrisantaspase and venetoclax.
A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Epigenetic targeted therapy of stabilized BAP1 in ASXL1 gain-of-function mutated leukemia.
Myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T): Mayo-Moffitt collaborative study of 158 patients.
Antibody response to mRNA vaccination for COVID-19 in patients with AML receiving hypomethylating agents alone or with venetoclax.
Genetic and non-genetic mechanisms of inflammation may promote transformation in leukemia.
Epigenetic Achilles' heel of AML.
Decade-long leukaemia remissions with persistence of CD4+ CAR T cells.

Nat Cancer. 2021 Nov;2(11): 1204-1223

Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia.

Claudie Bosc, Estelle Saland, Aurélie Bousard, Noémie Gadaud, Marie Sabatier, Guillaume Cognet, Thomas Farge, Emeline Boet, Mathilde Gotanègre, Nesrine Aroua, Pierre-Luc Mouchel, Nathaniel Polley, Clément Larrue, Eléonore Kaphan, Muriel Picard, Ambrine Sahal, Latifa Jarrou, Marie Tosolini, Florian Rambow, Florence Cabon, Nathalie Nicot, Laura Poillet-Perez, Yujue Wang, Xiaoyang Su, Quentin Fovez, Jérôme Kluza, Rafael José Argüello, Céline Mazzotti, Hervé Avet-Loiseau, François Vergez, Jérôme Tamburini, Jean-Jacques Fournié, Ing S Tiong, Andrew H Wei, Tony Kaoma, Jean-Christophe Marine, Christian Récher, Lucille Stuani, Carine Joffre, Jean-Emmanuel Sarry.

Therapy resistance represents a major clinical challenge in acute myeloid leukemia (AML). Here we define a 'MitoScore' signature, which identifies high mitochondrial oxidative phosphorylation in vivo and in patients with AML. Primary AML cells with cytarabine (AraC) resistance and a high MitoScore relied on mitochondrial Bcl2 and were highly sensitive to venetoclax (VEN) + AraC (but not to VEN + azacytidine). Single-cell transcriptomics of VEN + AraC-residual cell populations revealed adaptive resistance associated with changes in oxidative phosphorylation, electron transport chain complex and the TP53 pathway. Accordingly, treatment of VEN + AraC-resistant AML cells with electron transport chain complex inhibitors, pyruvate dehydrogenase inhibitors or mitochondrial ClpP protease agonists substantially delayed relapse following VEN + AraC. These findings highlight the central role of mitochondrial adaptation during AML therapy and provide a scientific rationale for alternating VEN + azacytidine with VEN + AraC in patients with a high MitoScore and to target mitochondrial metabolism to enhance the sensitivity of AML cells to currently approved therapies.

DOI: https://doi.org/10.1038/s43018-021-00264-y
Transl Oncol. 2022 Feb 01. pii: S1936-5233(22)00016-X. [Epub ahead of print]18 101354

Inhibition of BCL2A1 by STAT5 inactivation overcomes resistance to targeted therapies of FLT3-ITD/D835 mutant AML.

Kotoko Yamatani, Tomohiko Ai, Kaori Saito, Koya Suzuki, Atsushi Hori, Sonoko Kinjo, Kazuho Ikeo, Vivian Ruvolo, Weiguo Zhang, Po Yee Mak, Bogumil Kaczkowski, Hironori Harada, Kazuhiro Katayama, Yoshikazu Sugimoto, Jered Myslinski, Takashi Hato, Takashi Miida, Marina Konopleva, Yoshihide Hayashizaki, Bing Z Carter, Yoko Tabe, Michael Andreeff.

  Tyrosine kinase inhibitors (TKIs) are established drugs in the therapy of FLT3-ITD mutated acute myeloid leukemia (AML). However, acquired mutations, such as D835 in the tyrosine kinase domain (FLT3-ITD/D835), can induce resistance to TKIs. A cap analysis gene expression (CAGE) technology revealed that the gene expression of BCL2A1 transcription start sites was increased in primary AML cells bearing FLT3-ITD/D835 compared to FLT3-ITD. Overexpression of BCL2A1 attenuated the sensitivity to quizartinib, a type II TKI, and venetoclax, a selective BCL2 inhibitor, in AML cell lines. However, a type I TKI, gilteritinib, inhibited the expression of BCL2A1 through inactivation of STAT5 and alleviated TKI resistance of FLT3-ITD/D835. The combination of gilteritinib and venetoclax showed synergistic effects in the FLT3-ITD/D835 positive AML cells. The promoter region of BCL2A1 contains a BRD4 binding site. Thus, the blockade of BRD4 with a BET inhibitor (CPI-0610) downregulated BCL2A1 in FLT3-mutated AML cells and extended profound suppression of FLT3-ITD/D835 mutant cells. Therefore, we propose that BCL2A1 has the potential to be a novel therapeutic target in treating FLT3-ITD/D835 mutated AML.

Keywords:  AML; BCL2A1; CAGE; FLT3; Venetoclax

DOI:  https://doi.org/10.1016/j.tranon.2022.101354
Nat Cancer. 2021 May;2(5): 527-544

Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response.

Marina Scheller, Anne Kathrin Ludwig, Stefanie Göllner, Christian Rohde, Stephen Krämer, Sina Stäble, Maike Janssen, James-Arne Müller, Lixiazi He, Nicole Bäumer, Christian Arnold, Joachim Gerß, Maximilian Schönung, Christian Thiede, Christian Niederwieser, Dietger Niederwieser, Hubert Serve, Wolfgang E Berdel, Ulrich Thiem, Inga Hemmerling, Florian Leuschner, Christoph Plass, Matthias Schlesner, Judith Zaugg, Michael D Milsom, Andreas Trumpp, Caroline Pabst, Daniel B Lipka, Carsten Müller-Tidow.

Somatic mutations in DNA methyltransferase 3A (DNMT3A) are among the most frequent alterations in clonal hematopoiesis (CH) and acute myeloid leukemia (AML), with a hotspot in exon 23 at arginine 882 (DNMT3AR882). Here, we demonstrate that DNMT3AR882H-dependent CH and AML cells are specifically susceptible to the hypomethylating agent azacytidine (AZA). Addition of AZA to chemotherapy prolonged AML survival solely in individuals with DNMT3AR882 mutations, suggesting its potential as a predictive marker for AZA response. AML and CH mouse models confirmed AZA susceptibility specifically in DNMT3AR882H-expressing cells. Hematopoietic stem cells (HSCs) and progenitor cells expressing DNMT3AR882H exhibited cell autonomous viral mimicry response as a result of focal DNA hypomethylation at retrotransposon sequences. Administration of AZA boosted hypomethylation of retrotransposons specifically in DNMT3AR882H-expressing cells and maintained elevated levels of canonical interferon-stimulated genes (ISGs), thus leading to suppressed protein translation and increased apoptosis.

DOI: https://doi.org/10.1038/s43018-021-00213-9
J Hematol Oncol. 2022 Jan 29. 15(1): 12

Impact of frontline treatment approach on outcomes in patients with secondary AML with prior hypomethylating agent exposure.

Nicholas J Short, Sangeetha Venugopal, Wei Qiao, Tapan M Kadia, Farhad Ravandi, Walid Macaron, Courtney D Dinardo, Naval Daver, Marina Konopleva, Gautam Borthakur, Elizabeth J Shpall, Uday Popat, Richard E Champlin, Rohtesh Mehta, Gheath Al-Atrash, Betul Oran, Elias Jabbour, Guillermo Garcia-Manero, Ghayas C Issa, Guillermo Montalban-Bravo, Musa Yilmaz, Abhishek Maiti, Hagop Kantarjian.

  BACKGROUND: Treated secondary acute myeloid leukemia (ts-AML)-i.e., AML arising from a previously treated antecedent hematologic disorder-is associated with very poor outcomes. The optimal frontline treatment regimen for these patients is uncertain.METHODS: We retrospectively analyzed 562 patients who developed AML from preceding myelodysplastic syndrome or chronic myelomonocytic leukemia for which they had received a hypomethylating agent (HMA). Patients with ts-AML were stratified by frontline AML treatment with intensive chemotherapy (IC, n = 271), low-intensity therapy (LIT) without venetoclax (n = 237), or HMA plus venetoclax (n = 54).
RESULTS: Compared with IC or LIT without venetoclax, HMA plus venetoclax resulted in higher CR/CRi rates (39% and 25%, respectively; P = 0.02) and superior OS (1-year OS 34% and 17%, respectively; P = 0.05). The benefit of HMA plus venetoclax was restricted to patients with non-adverse risk karyotype, where HMA plus venetoclax resulted in a median OS of 13.7 months and 1-year OS rate of 54%; in contrast, for patients with adverse risk karyotype, OS was similarly dismal regardless of treatment approach (median OS 3-5 months). A propensity score analysis accounting for relevant clinical variables confirmed the significant OS benefit of HMA plus venetoclax, as compared with other frontline treatment approaches. In a landmark analysis, patients with ts-AML who underwent subsequent hematopoietic stem cell transplantation (HSCT) had superior 3-year OS compared to non-transplanted patients (33% vs. 8%, respectively; P = 0.003).
CONCLUSIONS: The outcomes of ts-AML are poor but may be improved with use of an HMA plus venetoclax-based regimen, followed by HSCT, particularly in those with a non-adverse risk karyotype.

Keywords:  Acute myeloid leukemia; Azacitidine; Chronic myelomonocytic leukemia; Decitabine; Myelodysplastic syndrome

DOI:  https://doi.org/10.1186/s13045-022-01229-z
Blood. 2022 Feb 02. pii: blood.2021014472. [Epub ahead of print]

MOLECULAR CHARACTERIZATION OF MUTANT TP53 ACUTE MYELOID LEUKEMIA AND HIGH-RISK MYELODYSPLASTIC SYNDROME.

Tim Grob, Adil Sa Al Hinai, Mathijs Arnoud Sanders, François Kavelaars, Melissa Rijken, Patrycja Gradowska, Bart J Biemond, Dimitri A Breems, Johan Maertens, Marinus van Marwijk Kooy, Thomas Pabst, Okke de Weerdt, Gert J Ossenkoppele, Arjan A van de Loosdrecht, Gerwin Huls, Jan J Cornelissen, H Berna Beverloo, Bob Löwenberg, Mojca Jongen-Lavrencic, Peter J M Valk.

Substantial heterogeneity within mutant TP53 AML and MDS-EB precludes the exact assessment of prognostic impact for individual patients. Here we performed in-depth clinical and molecular analysis of mutant TP53 AML and MDS-EB to dissect the molecular characteristics in detail and determine its impact on survival. We performed next-generation sequencing (NGS) on 2,200 AML/MDS-EB specimens and assessed the TP53 mutant allelic status (mono or bi-allelic), the number of TP53 mutations, mutant TP53 clone size, concurrent mutations, cytogenetics and mutant TP53 molecular minimal residual disease, and studied the associations of these characteristics with overall survival (OS). TP53 mutations were detected in 230 (10.5%) AML/MDS-EB patients with a median variant allele frequency (VAF) of 47%. Bi-allelic mutant TP53 status was observed in 174 (76%) patients. Multiple TP53 mutations were found in 49 (21%) patients. Concurrent mutations were detected in 113 (49%) patients. No significant difference in any of the aforementioned molecular characteristics of mutant TP53 were detected between AML and MDS-EB. Mutant TP53 patients have a very poor outcome (2-year OS, 12.8%), however no survival difference among AML and MDS-EB was observed. Importantly, none of the molecular characteristics were significantly associated with survival. In the majority of patients, TP53 mutations remained detectable in complete remission (CR) by deep sequencing (73%). Detection of residual mutant TP53 was not associated with survival. In conclusion, mutant TP53 AML and MDS-EB do not differ with respect to molecular characteristics and survival. Therefore, mutant TP53 AML/MDS-EB should be considered a distinct molecular disease entity.

DOI: https://doi.org/10.1182/blood.2021014472
Biotechniques. 2022 Feb 04.

Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13.

Subhash C Prajapati, Nicholas Dunham, Hao Fan, Francine E Garrett-Bakelman.

  Acute myeloid leukemia patients with FMS-like tyrosine kinase 3-internal tandem duplications and mixed lineage leukemia-protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these abnormalities and is used in CRISPR experiments to identify disease drivers. However, experimental observations may be biased or inconclusive in the absence of experimentally validated positive control genes. We validated sgRNAs for knockdown of TP53 for cell proliferation and for DCK knockdown and CDA upregulation for cytarabine resistance control genes in MOLM-13 cells. We have provided a detailed CRISPR protocol applicable to both gene knockdown or activation experiments and downstream leukemic phenotype analyses. Inclusion of these controls in CRISPR experiments will enhance the capacity to identify novel myeloid leukemia drivers in MOLM-13 cells.

Keywords:  CDA; CRISPR-Cas9; DCK; MOLM-13; acute myeloid leukemia; cytarabine; p53; proliferation; resistance

DOI:  https://doi.org/10.2144/btn-2021-0089
Biochem Biophys Res Commun. 2022 Jan 25. pii: S0006-291X(22)00107-3. [Epub ahead of print]596 36-42

SIRT2 regulates proliferation and chemotherapy response of MLL-ENL-driven acute myeloid leukemia.

Caiqing Hao, Xianyu Shao, Juan Song, Mengyuan Peng, Yimin Lao, Ryan Mack, Lei Zhang, Wei Wei, Na Liu, Tian Wang, Yuanyuan Wu, Lanyao Feng, Lijun Yin, Shouxin Wang, Xiaojian Sun, Saijuan Chen, Jiwang Zhang, Bing Li.

  Both MLL-AF9 and MLL-ENL leukemia fusion proteins drive oncogenic transformation of hematopoietic cells through their N-terminal DNA/histone binding mixed-lineage leukemia 1 domain and C-terminal fragment of AF9 or ENL containing an unstructured linker region and the ANC1 homology domain, which recruits transcription factors. Despite of their structural similarity, acute myeloid leukemia (AML) patients bearing MLL-ENL show more adverse outcomes compared to those with MLL-AF9. We recapitulated the clinical patterns of these two MLL-fusions driven AMLs using murine models and found that MLL-ENL AML cells showed slower cell cycle progression and more resistance to standard chemotherapy than MLL-AF9 cells. These phenotypes were primarily controlled by the linker regions of ENL and a highly conserved lysine residue K469 within. Substitution of K469 with an acetylated mimic glutamine abolished the ability of MLL-ENL to suppress proliferation and promote chemo-resistance. We showed that deacetylase Sirt2 might act as an upstream regulator of MLL-ENL. Deletion of Sirt2 promoted proliferation of AML cells with either MLL fusions. Importantly, loss of Sirt2 greatly enhanced the sensitivity of the MLL-ENL AML cells to chemo-treatment. Taken together, our study uncovered a unique regulatory role of Sirt2 in leukemogenesis and suggested targeting SIRT2 as a new way to sensitize MLL-ENL AML patience for chemotherapy.

Keywords:  AML; Chemotherapy; MLL-ENL; Proliferation; SIRT2

DOI:  https://doi.org/10.1016/j.bbrc.2022.01.081
J Cancer Res Clin Oncol. 2022 Jan 31.

Clinical experience with venetoclax in patients with newly diagnosed, relapsed, or refractory acute myeloid leukemia.

Maximilian Fleischmann, Sebastian Scholl, Jochen J Frietsch, Inken Hilgendorf, Karin Schrenk, Jakob Hammersen, Florian Prims, Christian Thiede, Andreas Hochhaus, Ulf Schnetzke.

  BACKGROUND: Diagnosis of acute myeloid leukemia (AML) is associated with poor outcome in elderly and unfit patients. Recently, approval of the BCL-2 inhibitor venetoclax (VEN) in combination with hypo-methylating agents (HMA) led to a significant improvement of response rates and survival. Further, application in the relapsed or refractory (r/r) AML setting or in context of allogeneic stem cell transplantation (alloHSCT) seems feasible.METHODS AND PATIENTS: Fifty-six consecutive adult AML patients on VEN from January 2019 to June 2021 were analyzed retrospectively. Patients received VEN either as first-line treatment, as subsequent therapy (r/r AML excluding prior alloHSCT), or at relapse after alloHSCT. VEN was administered orally in 28-day cycles either combined with HMA or low-dose cytarabine (LDAC).
RESULTS: After a median follow-up of 11.5 (range 6.1-22.3) months, median overall survival (OS) from start of VEN treatment was 13.3 (2.2-20.5) months, 5.0 (0.8-24.3) months and 4.0 (1.5-22.1) months for first-line, subsequent line treatment and at relapse post-alloHSCT, respectively. Median OS was 11.5 (10-22.3) months from start of VEN when subsequent alloHSCT was carried out. Relapse-free survival (RFS) for the total cohort was 10.2 (2.2 - 24.3) months. Overall response rate (composite complete remission + partial remission) was 51.8% for the total cohort (61.1% for VEN first-line treatment, 52.2% for subsequent line and 42.8% at relapse post-alloHSCT). Subgroup analysis revealed a significantly reduced median OS in FLT3-ITD mutated AML with 3.4 (1.9-4.9) months versus 10.4 (0.8-24.3) months for non-mutated cases, (HR 4.45, 95% CI 0.89-22.13, p = 0.0002). Patients harboring NPM1 or IDH1/2 mutations lacking co-occurrence of FLT3-ITD showed a survival advantage over patients without those mutations (11.2 (5-24.3) months versus 5.0 (0.8-22.1) months, respectively, (HR 0.53, 95% CI 0.23 - 1.21, p = 0.131). Multivariate analysis revealed mutated NPM1 as a significant prognostic variable for achieving complete remission (CR) (HR 19.14, 95% CI 2.30 - 436.2, p < 0.05). The most common adverse events were hematological, with grade 3 and 4 neutropenia and thrombocytopenia reported in 44.6% and 14.5% of patients, respectively.
CONCLUSION: Detailed analyses on efficacy for common clinical scenarios, such as first-line treatment, subsequent therapy (r/r AML), and application prior to and post-alloHSCT, are presented. The findings suggest VEN treatment combinations efficacious not only in first-line setting but also in r/r AML. Furthermore, VEN might play a role in a subgroup of patients with failure to conventional chemotherapy as a salvage regimen aiming for potential curative alloHSCT.

Keywords:  AML; Hypo-methylating agents; Refractory; Relapse; Salvage therapy; Venetoclax

DOI:  https://doi.org/10.1007/s00432-022-03930-5
Blood. 2022 Feb 03. 139(5): 798

Megakaryocytic emperipolesis as a dyshematopoietic feature in acute myeloid leukemia with inv(16).

Xiu Qing Wang, Eric McGinnis.

DOI: https://doi.org/10.1182/blood.2021014251
Nat Commun. 2022 Jan 31. 13(1): 587

CAR T cells redirected to cell surface GRP78 display robust anti-acute myeloid leukemia activity and do not target hematopoietic progenitor cells.

Nikhil Hebbar, Rebecca Epperly, Abishek Vaidya, Unmesha Thanekar, Sarah E Moore, Masayuki Umeda, Jing Ma, Sagar L Patil, Deanna Langfitt, Sujuan Huang, Cheng Cheng, Jeffery M Klco, Stephen Gottschalk, M Paulina Velasquez.

Developing CAR T cells for acute myeloid leukemia (AML) has been hampered by a paucity of targets that are expressed on AML blasts and not on hematopoietic progenitor cells (HPCs). Here we demonstrate that GRP78 is expressed on the cell surface of primary AML blasts but not HPCs. To target GRP78, we generate T cell expressing a GRP78-specific peptide-based CAR, which show evidence of minimal fratricide post activation/transduction and antigen-dependent T cell differentiation. GRP78-CAR T cells recognize and kill GRP78-positive AML cells without toxicity to HPCs. In vivo, GRP78-CAR T cells have significant anti-AML activity. To prevent antigen-dependent T cell differentiation, we block CAR signaling and GRP78 cell surface expression post activation by using dasatinib during GRP78-CAR T cell manufacturing. This significantly improves their effector function in vitro and in vivo. Thus, targeting cell surface GRP78-positive AML with CAR T cells is feasible, and warrants further active exploration.

DOI: https://doi.org/10.1038/s41467-022-28243-6
Leukemia. 2022 Feb 02.

CDK19 regulates the proliferation of hematopoietic stem cells and acute myeloid leukemia cells by suppressing p53-mediated transcription of p21.

Zihao Zhang, Yukai Lu, Yan Qi, Yang Xu, Song Wang, Fang Chen, Mingqiang Shen, Mo Chen, Naicheng Chen, Lijing Yang, Shilei Chen, Fengchao Wang, Yongping Su, Mengjia Hu, Junping Wang.

The cell cycle progression of hematopoietic stem cells (HSCs) and acute myeloid leukemia (AML) cells is precisely controlled by multiple regulatory factors. However, the underlying mechanisms are not fully understood. Here, we find that cyclin-dependent kinase 19 (CDK19), not its paralogue CDK8, is relatively enriched in mouse HSCs, and its expression is more significantly increased than CDK8 after proliferative stresses. Furthermore, SenexinB (a CDK8/19 inhibitor) treatment impairs the proliferation and self-renewal ability of HSCs. Moreover, overexpression of CDK19 promotes HSC function better than CDK8 overexpression. Using CDK19 knockout mice, we observe that CDK19-/- HSCs exhibit similar phenotypes to those of cells treated with SenexinB. Interestingly, the p53 signaling pathway is significantly activated in HSCs lacking CDK19 expression. Further investigations show that CDK19 can interact with p53 to inhibit p53-mediated transcription of p21 in HSCs and treatment with a specific p53 inhibitor (PFTβ) partially rescues the defects of CDK19-null HSCs. Importantly, SenexinB treatment markedly inhibits the proliferation of AML cells. Collectively, our findings indicate that CDK19 is involved in regulating HSC and AML cell proliferation via the p53-p21 pathway, revealing a new mechanism underlying cell cycle regulation in normal and malignant hematopoietic cells.

DOI: https://doi.org/10.1038/s41375-022-01512-5
Nat Cancer. 2021 Mar;2(3): 340-356

Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia.

Mari Hashimoto, Yoriko Saito, Ryo Nakagawa, Ikuko Ogahara, Shinsuke Takagi, Sadaaki Takata, Hanae Amitani, Mikiko Endo, Hitomi Yuki, Jordan A Ramilowski, Jessica Severin, Ri-Ichiroh Manabe, Takashi Watanabe, Kokoro Ozaki, Akiko Kaneko, Hiroshi Kajita, Saera Fujiki, Kaori Sato, Teruki Honma, Naoyuki Uchida, Takehiro Fukami, Yasushi Okazaki, Osamu Ohara, Leonard D Shultz, Makoto Yamada, Shuichi Taniguchi, Paresh Vyas, Michiel de Hoon, Yukihide Momozawa, Fumihiko Ishikawa.

Aggressive therapy-resistant and refractory acute myeloid leukemia (AML) has an extremely poor outcome. By analyzing a large number of genetically complex and diverse, primary high-risk poor-outcome human AML samples, we identified specific pathways of therapeutic vulnerability. Through drug screens followed by extensive in vivo validation and genomic analyses, we found inhibition of cytosolic and mitochondrial anti-apoptotic proteins XIAP, BCL2 and MCL1, and a key regulator of mitosis, AURKB, as a vulnerability hub based on patient-specific genetic aberrations and transcriptional signatures. Combinatorial therapeutic inhibition of XIAP with an additional patient-specific vulnerability eliminated established AML in vivo in patient-derived xenografts (PDXs) bearing diverse genetic aberrations, with no signs of recurrence during off-treatment follow-up. By integrating genomic profiling and drug-sensitivity testing, this work provides a platform for a precision-medicine approach for treating aggressive AML with high unmet need.

DOI: https://doi.org/10.1038/s43018-021-00177-w
Cell Stem Cell. 2022 Jan 27. pii: S1934-5909(22)00003-0. [Epub ahead of print]

An oncogenic enhancer encodes selective selenium dependency in AML.

Kenneth Eagle, Yajian Jiang, Xiangguo Shi, Minhua Li, Nikolaus P Obholzer, Tianyuan Hu, Monika W Perez, Jošt Vrabič Koren, Ayumi Kitano, Joanna S Yi, Charles Y Lin, Daisuke Nakada.

  Deregulation of transcription is a hallmark of acute myeloid leukemia (AML) that drives oncogenic expression programs and presents opportunities for therapeutic targeting. By integrating comprehensive pan-cancer enhancer landscapes with genetic dependency mapping, we find that AML-enriched enhancers encode for more selective tumor dependencies. We hypothesized that this approach could identify actionable dependencies downstream of oncogenic driver events and discovered a MYB-regulated AML-enriched enhancer regulating SEPHS2, a key component of the selenoprotein production pathway. Using a combination of patient samples and mouse models, we show that this enhancer upregulates SEPHS2, promoting selenoprotein production and antioxidant function required for AML survival. SEPHS2 and other selenoprotein pathway genes are required for AML growth in vitro. SEPHS2 knockout and selenium dietary restriction significantly delay leukemogenesis in vivo with little effect on normal hematopoiesis. These data validate the utility of enhancer mapping in target identification and suggest that selenoprotein production is an actionable target in AML.

Keywords:  AML; MYB; SEPHS2; enhancer; hematopoiesis; hematopoietic stem cell; leukemia stem cell; selenium; selenocysteine

DOI:  https://doi.org/10.1016/j.stem.2022.01.003
Transl Cancer Res. 2020 Nov;9(11): 7284-7298

Analyzing the key gene expression and prognostics values for acute myeloid leukemia.

Lingling Shi, Yan Huang, Xunjun Huang, Weijie Zhou, Jie Wei, Donghong Deng, Yongrong Lai.

  Background: Acute myeloid leukemia (AML) is one of the first tumor types sequenced at the whole genome level. However, numbers of the mutated genes expression levels, functions, and prognostics values still unclear.Methods: To most ordinary mutated genes were analyzed via cancer virtual cohort discovery analysis platform (CVCDAP), and further investigated the mutational conversions, variant allele frequencies (VAF), driver genes, and potential druggable mutated genes in AML. The top mutated gene mRNA expression levels and the relationship between gene expression levels and prognosis for AML patients were performed by Gene Expression Profiling Interactive Analysis (GEPIA). Moreover, we used the UALCAN dataset to confirm the association between gene expression levels and prognosis for AML patients. Enrichment functions of the top mutated genes of AML were analyzed through Metascape. Finally, the role of these defined genes in cancer pathways and potential drug targets were analyzed by gene set cancer analysis (GSCALite).
Results: The top 20 mutated genes for AML included FLT3, HPS3, ABCA6, PCLO, SLIT2, and other ones. Compared to normal control samples, NPM1 and GABRB3 were significantly downregulated in AML samples, but TP53, DNMT3A, HPS3, FLT3, SENP6, and RUNX1 were significantly overexpressed (all these genes P value <0.01). Overexpression of FLT3 and PCLO indicated a poor prognosis, but the overexpression of SLIT3 functioned as a protector for AML via GEPIA. HSP3 indicates the favorable factor for AML, but overexpression of ABCA6 (P=0.066) may act as the adverse factor by UALCAN analysis. Enrichment function analysis shows the functions of defining genes, including negative regulation of cell differentiation, small GTPase mediated signal transduction, and immune system process. Finally, these genes participate in apoptosis, cell cycle, PI3K/AKT, and RAS/MAPK signaling pathway, and FLT3 is sensitive to 5-Fluorouracil, Methotrexate, ATRA. DNMT3A and IDH2 are resistant to Trametinib. RUNX1 and TP53 were sensitive to I-BET-762 and Tubastatin A.
Conclusions: Present study showed overexpression of FLT3, ABCA6, and PCLO indicated the poor prognosis of AML, but overexpression of SLIT3 and HSP3 functioned as an AML protector. There are several drugs and small molecules that target the top 20 mutated genes in AML.

Keywords:  Acute myeloid leukemia (AML); bioinformatics analysis; top mutated genes

DOI:  https://doi.org/10.21037/tcr-20-3177
Nat Cancer. 2021 Nov;2(11): 1170-1184

LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-κB signaling axis.

Guojin Wu, Yixiang Xu, Robbie D Schultz, Heyu Chen, Jingjing Xie, Mi Deng, Xiaoye Liu, Xun Gui, Samuel John, Zhigang Lu, Hisashi Arase, Ningyan Zhang, Zhiqiang An, Cheng Cheng Zhang.

Leukocyte immunoglobulin-like receptor B (LILRB), a family of immune checkpoint receptors, contributes to acute myeloid leukemia (AML) development, but the specific mechanisms triggered by activation or inhibition of these immune checkpoints in cancer is largely unknown. Here we demonstrate that the intracellular domain of LILRB3 is constitutively associated with the adaptor protein TRAF2. Activated LILRB3 in AML cells leads to recruitment of cFLIP and subsequent NF-κB upregulation, resulting in enhanced leukemic cell survival and inhibition of T-cell-mediated anti-tumor activity. Hyperactivation of NF-κB induces a negative regulatory feedback loop mediated by A20, which disrupts the interaction of LILRB3 and TRAF2; consequently the SHP-1/2-mediated inhibitory activity of LILRB3 becomes dominant. Finally, we show that blockade of LILRB3 signaling with antagonizing antibodies hampers AML progression. LILRB3 thus exerts context-dependent activating and inhibitory functions, and targeting LILRB3 may become a potential therapeutic strategy for AML treatment.

DOI: https://doi.org/10.1038/s43018-021-00262-0
Bone Marrow Transplant. 2022 Feb 01.

Non-T depleted haploidentical stem cell transplantation in AML patients achieving first complete remission after one versus two induction courses: a study from the ALWP/EBMT.

Arnon Nagler, Myriam Labopin, Xiao-Jun Huang, Didier Blaise, William Arcese, Mercedes Colorado Araujo, Gerard Socié, Edouard Forcade, Fabio Ciceri, Jonathan Canaani, Sebastian Giebel, Eolia Brissot, Jaime Sanz Caballer, Ali Bazarbachi, Ibrahim Yakoub-Agha, Mohamad Mohty.

There are no data indicating whether the number of induction courses needed to achieve first complete remission (CR1) is of prognostic significance in Haploidentical transplantation (HaploSCT). We compared transplantation outcomes of adults with AML that underwent HaploSCT in CR1, achieved following one or two induction courses. A total of 635 patients were included: 469 (74%) with 1 and 166 (26%) with two induction chemotherapy courses. A total of 429 (91.5%) and 151 (91%) patients had de novo AML and 40 (8.5%) and 15 (9%) had secondary AML (p = 0.84). Engraftment rates were 97.2 and 97.6%. Day 180 incidence of acute GVHD II-IV and III-IV was similar in both induction groups (31.1 and 34.8%, and 10 and 10.6 %), as was 2-4 year total and extensive chronic GVHD (33.7 and 36.5 %, and 12.2 and 12.1%), respectively. Two-year relapse incidence (RI) was higher while leukemia-free survival (LFS), overall survival (OS) and GVHD-free, relapse-free survival (GRFS) were inferior for patients achieving CR1 with 2 vs 1 course and were 29.1% vs 15.1%, 88 (p = 0.001), 56.2% vs 66.9% (p = 0.03), 58.8% vs 72.2% (p = 0.044) and 44% vs 55.6% (p = 0.013), respectively. Non-relapse mortality (NRM) did not differ, 18% vs 14.6% 90 (p = 0.25). These results were confirmed by multivariate analysis.

DOI: https://doi.org/10.1038/s41409-021-01537-x
Exp Hematol. 2022 Jan 29. pii: S0301-472X(22)00036-4. [Epub ahead of print]

Translatome changes in acute myeloid leukemia cells post-exposure to pegcrisantaspase and venetoclax.

Bandish Kapadia, Amol C Shetty, Dominique Bollino, Binny Bhandary, Rena G Lapidus, Kanwal Mahmood, Anup Mahurkar, Ronald B Gartenhaus, Richard L Eckert, Ashkan Emadi.

  The clinical outcomes of patients with AML treated with available therapy remains unsatisfactory. We recently reported that the BCL-2 inhibitor, venetoclax, synergized with pegcrisantaspase (PegC) and demonstrated remarkable in vivo efficacy in a preclinical model of AML with complex karyotype. Ven-PegC combination blocks synthesis of proteins in AML cells by inhibiting cap-dependent translation of mRNA. To further explore the impact of Ven-PegC on protein translation, we used polysome profiling and high-throughput RNA-seq to characterize Ven-PegC dependent changes to the translatome. Here we report that the translation of five mRNAs, including two microRNAs, one rRNA, and two mitochondrial genes was altered after exposure to all three treatments (Ven, PegC and Ven-PegC). We focused our translatome validation studies on six additional genes related to translational efficiency that were modified by Ven-PegC. Notably, Ven-PegC treatment increased the RNA translation and protein level of Tribbles homolog 3 (TRIB3), eukaryotic translation initiation factor 3 subunit C (eIF3C), doublesex and mab-3 related transcription factor 1 (DMRT1), salt inducible kinase 1 (SIK1). We validated the observed changes in gene/protein expression in vitro and confirmed our cell line-based studies in the bone marrow of an AML PDX model after Ven-PegC treatment. These results support examining alterations in the translatome post-chemotherapy to offer insight into drug mechanism of action and to inform future therapeutic decisions.

Keywords:  Ven-PegC; acute myeloid leukemia; asparaginase; glutamine; pegcrisantaspase; translatome; venetoclax

DOI:  https://doi.org/10.1016/j.exphem.2022.01.006
Nat Cancer. 2020 Nov;1(11): 1054-1065

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.

Roeland Lameris, Adam Shahine, Daniel G Pellicci, Adam P Uldrich, Stephanie Gras, Jérôme Le Nours, Richard W J Groen, Jana Vree, Scott J J Reddiex, Sergio M Quiñones-Parra, Stewart K Richardson, Amy R Howell, Sonja Zweegman, Dale I Godfrey, Tanja D de Gruijl, Jamie Rossjohn, Hans J van der Vliet.

Antibody-mediated modulation of major histocompatibility complex (MHC) molecules, or MHC class I-like molecules, could constitute an effective immunotherapeutic approach. We describe how single-domain antibodies (VHH), specific for the human MHC class I-like molecule CD1d, can modulate the function of CD1d-restricted T cells and how one VHH (1D12) specifically induced strong type I natural killer T (NKT) cell activation. The crystal structure of the VHH1D12-CD1d(α-GalCer)-NKT T-cell receptor (TCR) complex revealed that VHH1D12 simultaneously contacted CD1d and the type I NKT TCR, thereby stabilizing this interaction through intrinsic bispecificity. This led to greatly enhanced type I NKT cell-mediated antitumor activity in in vitro, including multiple myeloma and acute myeloid leukemia patient-derived bone marrow samples, and in vivo models. Our findings underscore the versatility of VHH molecules in targeting composite epitopes, in this case consisting of a complexed monomorphic antigen-presenting molecule and an invariant TCR, and represent a generalizable antitumor approach.

DOI: https://doi.org/10.1038/s43018-020-00111-6
Nat Cancer. 2021 May;2(5): 515-526

Epigenetic targeted therapy of stabilized BAP1 in ASXL1 gain-of-function mutated leukemia.

Lu Wang, Noah Warren Birch, Zibo Zhao, Carson Meredith Nestler, Alexander Kazmer, Anthony Shilati, Alisha Blake, Patrick Alexander Ozark, Emily Jane Rendleman, Didi Zha, Caila Ann Ryan, Marc Alard Jonathan Morgan, Ali Shilatifard.

Mutations of ASXL1, encoding a component of the BAP1 histone H2A deubiquitinase complex, occur in human myeloid neoplasms and are uniformly associated with poor prognosis. However, the precise molecular mechanisms through which ASXL1 mutations alter BAP1 activity and drive leukemogenesis remain unclear. Here we demonstrate that cancer-associated frameshift mutations in ASXL1, which were originally proposed to act as destabilizing loss-of-function mutations, in fact encode stable truncated gain-of-function proteins. Truncated ASXL1 increases BAP1 protein stability, enhances BAP1 recruitment to chromatin and promotes the expression of a pro-leukemic transcriptional signature. Through a biochemical screen, we identified BAP1 catalytic inhibitors that inhibit truncated-ASXL1-driven leukemic gene expression and impair tumor progression in vivo. This study represents a breakthrough in our understanding of the molecular mechanisms of ASXL1 mutations in leukemia pathogenesis and identifies small-molecular catalytic inhibitors of BAP1 as a potential targeted therapy for leukemia.

DOI: https://doi.org/10.1038/s43018-021-00199-4
Blood Cancer J. 2022 Feb 01. 12(2): 26

Myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T): Mayo-Moffitt collaborative study of 158 patients.

Abhishek A Mangaonkar, Terra L Lasho, Rhett P Ketterling, Kaaren K Reichard, Naseema Gangat, Aref Al-Kali, Kebede H Begna, Animesh Pardanani, Najla H Al Ali, Chetasi Talati, David Sallman, Eric Padron, Mrinal M Patnaik, Ayalew Tefferi, Rami Komrokji.

The current World Health Organization (WHO) classification of myeloid malignancies includes myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T) as a distinct entity. Previous literature on predictors of survival was based on the provisional category of refractory anemia with ring sideroblast and thrombocytosis (RARS-T), which was not subject to MDS/MPN-RS-T exclusionary criteria such as PB blast% ≥1, BM blast% ≥5 or cytogenetic abnormalities such as t(3;3)(q21.2;q26.2), inv(3)(q21.23q26.2) or isolated del(5q). We examined overall (OS) and leukemia-free (LFS) survival and its predictors, among 158 patients with WHO-defined MDS/MPN-RS-T. In univariate analysis, age ≥70 years (P = 0.006), hemoglobin (Hb) ≤10 g/dL (P = 0.03) and abnormal karyotype (excluding -Y, P = 0.008) were associated with shortened OS, which was otherwise not affected by either ASXL1 (P = 0.7), SF3B1 (P = 0.4) or JAK2 V617F (P = 0.7) mutations; in multivariable analysis, Hb ≤ 10 g/dL (P = 0.03) and abnormal karyotype (P = 0.001) remained significant, and thus allowed the development of an operational survival model with low (0 risk factors, median OS 10.5 years), intermediate (1 risk factor, median OS 4.8 years) and high risk (2 risk factors, median OS 1.4 years) categories (P = 0.0009). Comparison of MDS/MPN-RS-T (n = 158) and MDS/MPN-U with BM RS ≥ 15% (MDS/MPN-U-RS; n = 25) did not reveal significant differences in frequency of thrombosis, OS, or LFS, although SF3B1 mutation frequency was higher in the former (93% versus 59%; P = 0.0005). These data suggest limited survival impact for molecular abnormalities and the morphological distinction between MDS/MPN-RS-T and MDS/MPN-U-RS.

DOI: https://doi.org/10.1038/s41408-022-00622-8
Blood Adv. 2022 Feb 02. pii: bloodadvances.2021006949. [Epub ahead of print]

Antibody response to mRNA vaccination for COVID-19 in patients with AML receiving hypomethylating agents alone or with venetoclax.

Anna Candoni.

DOI: https://doi.org/10.1182/bloodadvances.2021006949
Cell Stem Cell. 2022 Feb 03. pii: S1934-5909(22)00006-6. [Epub ahead of print]29(2): 184-186

Genetic and non-genetic mechanisms of inflammation may promote transformation in leukemia.

Paresh Vyas.

Non-genetic mechanisms of transformation are still relatively understudied and poorly understood. In this issue of Cell Stem Cell, Muto et al. provide preclinical evidence that loss of TRAF6 expression promotes transformation through a MYC-dependent mechanism that may be modulated by environmental inflammatory signals.

DOI: https://doi.org/10.1016/j.stem.2022.01.006
Nat Cancer. 2021 May;2(5): 481-483

Epigenetic Achilles' heel of AML.

Koki Ueda, Ulrich Steidl.

DOI: https://doi.org/10.1038/s43018-021-00212-w
Nature. 2022 Feb 02.

Decade-long leukaemia remissions with persistence of CD4+ CAR T cells.

J Joseph Melenhorst, Gregory M Chen, Meng Wang, David L Porter, Changya Chen, McKensie A Collins, Peng Gao, Shovik Bandyopadhyay, Hongxing Sun, Ziran Zhao, Stefan Lundh, Iulian Pruteanu-Malinici, Christopher L Nobles, Sayantan Maji, Noelle V Frey, Saar I Gill, Lifeng Tian, Irina Kulikovskaya, Minnal Gupta, David E Ambrose, Megan M Davis, Joseph A Fraietta, Jennifer L Brogdon, Regina M Young, Anne Chew, Bruce L Levine, Donald L Siegel, Cécile Alanio, E John Wherry, Frederic D Bushman, Simon F Lacey, Kai Tan, Carl H June.

The adoptive transfer of T lymphocytes reprogrammed to target tumour cells has demonstrated potential for treatment of various cancers1-7. However, little is known about the long-term potential and clonal stability of the infused cells. Here we studied long-lasting CD19-redirected chimeric antigen receptor (CAR) T cells in two patients with chronic lymphocytic leukaemia1-4 who achieved a complete remission in 2010. CAR T cells remained detectable more than ten years after infusion, with sustained remission in both patients. Notably, a highly activated CD4+ population emerged in both patients, dominating the CAR T cell population at the later time points. This transition was reflected in the stabilization of the clonal make-up of CAR T cells with a repertoire dominated by a small number of clones. Single-cell profiling demonstrated that these long-persisting CD4+ CAR T cells exhibited cytotoxic characteristics along with ongoing functional activation and proliferation. In addition, longitudinal profiling revealed a population of gamma delta CAR T cells that prominently expanded in one patient concomitant with CD8+ CAR T cells during the initial response phase. Our identification and characterization of these unexpected CAR T cell populations provide novel insight into the CAR T cell characteristics associated with anti-cancer response and long-term remission in leukaemia.

DOI: https://doi.org/10.1038/s41586-021-04390-6