bims-tremyl 2022-10-30 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2022–10–30
twenty-one papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Venetoclax-based salvage therapy in patients with relapsed/refractory acute myeloid leukemia previously treated with FLT3 or IDH1/2 inhibitors.
Prognostic impact of ASXL1 mutations in chronic phase chronic myeloid leukemia.
The m6A reader IGF2BP2 regulates glutamine metabolism and represents a therapeutic target in acute myeloid leukemia.
Antileukemic activity of YPN-005, a CDK7 inhibitor, inducing apoptosis through c-MYC and FLT3 suppression in acute myeloid leukemia.
Subtype-specific 3D genome alteration in acute myeloid leukaemia.
Efficacy and safety of CPX-351 versus 7 + 3 chemotherapy by European LeukemiaNet 2017 risk subgroups in older adults with newly diagnosed, high-risk/secondary AML: post hoc analysis of a randomized, phase 3 trial.
Understanding a high-risk acute myeloid leukemia by analyzing the interactome of its major driver mutation.
A cryptic transactivation domain of EZH2 binds AR and AR's splice variant, promoting oncogene activation and tumorous transformation.
Treatment options for acute myeloid leukemia patients aged <60 years.
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r.
A British Society for Haematology good practice paper: Recommendations for laboratory testing of UK patients with acute myeloid leukaemia.
Use of endpoints in phase III randomized controlled trials for acute myeloid leukemia over the last 15 years: a systematic review.
Immunogenicity of COVID-19 mRNA vaccines in patients with acute myeloid leukemia and myelodysplastic syndrome.
Combinatorial gene targeting in primary human hematopoietic stem and progenitor cells.
Comprehensive molecular characterization of a rare case of Philadelphia chromosome-positive acute myeloid leukemia.
Comparison of transplant outcomes between haploidentical transplantation and single cord blood transplantation in non-remission acute myeloid leukaemia: A nationwide retrospective study.
The co-evolution of the genome and epigenome in colorectal cancer.
IL-13/IL-4 signaling contributes to fibrotic progression of the myeloproliferative neoplasms.
Targeting UHRF1-SAP30-MXD4 axis for leukemia initiating cell eradication in myeloid leukemia.
Hoxa9/meis1-transgenic zebrafish develops acute myeloid leukaemia-like disease with rapid onset and high penetrance.
Phenotypic plasticity and genetic control in colorectal cancer evolution.

Leuk Lymphoma. 2022 Oct 26. 1-9

Venetoclax-based salvage therapy in patients with relapsed/refractory acute myeloid leukemia previously treated with FLT3 or IDH1/2 inhibitors.

Jan Philipp Bewersdorf, Rory M Shallis, Andriy Derkach, Aaron D Goldberg, Anthony Stein, Eytan M Stein, Guido Marcucci, Amer M Zeidan, Shai Shimony, Daniel J DeAngelo, Richard M Stone, Ibrahim Aldoss, Brian J Ball, Maximilian Stahl.

  FLT3, IDH1 and IDH2 inhibitors as well as venetoclax in combination with hypomethylating agents or low-dose cytarabine have expanded treatment options for patients with acute myeloid leukemia (AML). However, little data exist on the efficacy of venetoclax-based therapies in AML patients previously treated with FLT3 or IDH1/2 inhibitors. In this multicenter, retrospective cohort study, we included 44 patients who received venetoclax-based therapy after FLT3, IDH1 or IDH2 inhibitors. The overall response rate (ORR; composite of complete remission [CR]/CR with incomplete count recovery, partial remission, and morphologic leukemia free state) was 56.8% (18.2% CR) and a median overall survival of 9.2 months. While 6 out of 7 patients with IDH1 mutations who had previously been treated with ivosidenib responded to venetoclax-based therapy, FLT3-ITD mutations were associated with a lower response rate. Our data suggest that venetoclax can be an effective salvage therapy in patients previously treated with IDH1/2 or FLT3 inhibitors.

Keywords:  AML; Acute myeloid leukemia; outcomes; targeted agents; venetoclax

DOI:  https://doi.org/10.1080/10428194.2022.2136952
Blood Cancer J. 2022 Oct 28. 12(10): 144

Prognostic impact of ASXL1 mutations in chronic phase chronic myeloid leukemia.

Aram Bidikian, Hagop Kantarjian, Elias Jabbour, Nicholas J Short, Keyur Patel, Farhad Ravandi, Koji Sasaki, Ghayas C Issa.

While the clinical impact of mutations in the ABL1 gene on response to therapy in chronic phase chronic myeloid leukemia (CP-CML) is well established, less is known about how other mutations affect prognosis. In a retrospective analysis, we identified 115 patients with CML (71 chronic, 15 accelerated and 29 blast phase) where targeted next-generation sequencing of genes recurrently mutated in myeloid leukemias was performed. ASXL1 was the most frequently mutated gene in the chronic (14%) and accelerated phase (40%) CML patients, whereas RUNX1 (20%) was the most common mutation in blast phase. Compared with wild-type ASXL1, CP-CML with mutant ASXL1 was associated with worse event-free survival (EFS) (median of 32.8 vs 88.3 months; P = 0.002) and failure-free survival (median of 13.8 vs 57.8 months; P = 0.04). In a multivariate analysis, ASXL1 mutation was the only independent risk factor associated with worse EFS in chronic phase CML with a hazard ratio of 4.25 (95% CI 1.59-11.35, P = 0.004). In conclusion, mutations in ASXL1 are associated with worse outcomes when detected in chronic phase CML.

DOI: https://doi.org/10.1038/s41408-022-00742-1
Cancer Cell. 2022 Oct 26. pii: S1535-6108(22)00495-0. [Epub ahead of print]

The m6A reader IGF2BP2 regulates glutamine metabolism and represents a therapeutic target in acute myeloid leukemia.

Hengyou Weng, Feng Huang, Zhaojin Yu, Zhenhua Chen, Emily Prince, Yalin Kang, Keren Zhou, Wei Li, Jiacheng Hu, Chen Fu, Tursunjan Aziz, Hongzhi Li, Jingwen Li, Ying Yang, Li Han, Subo Zhang, Yuelong Ma, Mingli Sun, Huizhe Wu, Zheng Zhang, Mark Wunderlich, Sean Robinson, Daniel Braas, Johanna Ten Hoeve, Bin Zhang, Guido Marcucci, James C Mulloy, Keda Zhou, Hong-Fang Tao, Xiaolan Deng, David Horne, Minjie Wei, Huilin Huang, Jianjun Chen.

  N6-Methyladenosine (m6A) modification and its modulators play critical roles and show promise as therapeutic targets in human cancers, including acute myeloid leukemia (AML). IGF2BP2 was recently reported as an m6A binding protein that enhances mRNA stability and translation. However, its function in AML remains largely elusive. Here we report the oncogenic role and the therapeutic targeting of IGF2BP2 in AML. High expression of IGF2BP2 is observed in AML and associates with unfavorable prognosis. IGF2BP2 promotes AML development and self-renewal of leukemia stem/initiation cells by regulating expression of critical targets (e.g., MYC, GPT2, and SLC1A5) in the glutamine metabolism pathways in an m6A-dependent manner. Inhibiting IGF2BP2 with our recently identified small-molecule compound (CWI1-2) shows promising anti-leukemia effects in vitro and in vivo. Collectively, our results reveal a role of IGF2BP2 and m6A modification in amino acid metabolism and highlight the potential of targeting IGF2BP2 as a promising therapeutic strategy in AML.

Keywords:  GPT2; IGF2BP2; MYC; SLC1A5; acute myeloid leukemia; glutamine metabolism; leukemia stem cells; m(6)A modification; mitochondria oxygen consumption; targeted therapy

DOI:  https://doi.org/10.1016/j.ccell.2022.10.004
Heliyon. 2022 Oct;8(10): e11004

Antileukemic activity of YPN-005, a CDK7 inhibitor, inducing apoptosis through c-MYC and FLT3 suppression in acute myeloid leukemia.

Bon-Kwan Koo, Eun-Ji Choi, Eun-Hye Hur, Ju Hyun Moon, Ji Yun Kim, Han-Seung Park, Yunsuk Choi, Jung-Hee Lee, Kyoo-Hyung Lee, Eun Kyung Choi, Jinhwan Kim, Je-Hwan Lee.

  Acute myeloid leukemia (AML) is an aggressive blood cancer with a high rate of relapse associated with adverse survival outcomes, especially in elderly patients. An aberrant expression of cyclin dependent kinase 7 (CDK7) is associated with poor outcomes and CDK7 inhibition has showed antitumor activities in various cancers. We investigated the efficacy of YPN-005, a CDK7 inhibitor in AML cell lines, xenograft mouse model, and primary AML cells. YPN-005 effectively inhibited the proliferation of AML cells by inducing apoptosis and reducing phosphorylation of RNA polymerase II. The c-MYC expression decreased with treatment of YPN-005, and the effect of YPN-005 was negatively correlated with c-MYC expression. YPN-005 also showed antileukemic activities in primary AML cells, especially those harboring FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) mutation and in in vivo mouse model. Phosphorylated FLT3/Signal transducer and activator of transcription 5 (STAT5) was decreased and FLT3/STAT5 was downregulated with YPN-005 treatment. Our data suggest that YPN-005 has a role in treating AML by suppressing c-MYC and FLT3.

Keywords:  Acute myeloid leukemia (AML); Cyclin dependent kinase 7 (CDK7) inhibitor; FLT3; MCL1; c-MYC

DOI:  https://doi.org/10.1016/j.heliyon.2022.e11004
Nature. 2022 Oct 26.

Subtype-specific 3D genome alteration in acute myeloid leukaemia.

Jie Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Hiu-Yuen Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C Hardison, Sinisa Dovat, Leonidas C Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron D Viny, Ross L Levine, David Claxton, James R Broach, Hong Zheng, Feng Yue.

Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.

DOI: https://doi.org/10.1038/s41586-022-05365-x
J Hematol Oncol. 2022 Oct 26. 15(1): 155

Efficacy and safety of CPX-351 versus 7 + 3 chemotherapy by European LeukemiaNet 2017 risk subgroups in older adults with newly diagnosed, high-risk/secondary AML: post hoc analysis of a randomized, phase 3 trial.

Jorge E Cortes, Tara L Lin, Kobby Asubonteng, Stefan Faderl, Jeffrey E Lancet, Thomas Prebet.

  CPX-351 (Europe: Vyxeos® liposomal; United States: Vyxeos®) is a dual-drug liposomal encapsulation of daunorubicin and cytarabine in a synergistic 1:5 molar ratio. In a phase 3 study in older adults with newly diagnosed, high-risk/secondary AML, CPX-351 improved the remission frequency, overall survival, and post-transplant survival versus 7 + 3. This post hoc analysis evaluated the final 5-year follow-up outcomes according to the European LeukemiaNet 2017 risk classification. CPX-351-treated patients had a higher remission frequency (adverse risk: 41% vs 26%; intermediate risk: 58% vs 39%) and longer median overall survival (adverse risk: 7.59 vs 5.52 months; intermediate risk: 11.86 vs 7.75 months) and post-transplant survival (adverse risk: 43.14 vs 7.08 months; intermediate risk: not reached vs 13.57 months) versus 7 + 3, with outcomes generally poorer among patients with adverse-risk AML. The safety profile of CPX-351 among patients with adverse-risk or intermediate-risk AML was consistent with that of the overall study population. Early mortality was lower, and hospitalization length of stay per patient-year was shorter with CPX-351 versus 7 + 3 within the adverse-risk and intermediate-risk subgroups. The favorable outcomes observed with CPX-351 in this post hoc analysis are consistent with results for the overall study population and further support the use of CPX-351 in these patients.ClinicalTrials.gov Identifier: NCT01696084.

Keywords:  Acute myeloid leukemia; CPX-351; Chemotherapy; European LeukemiaNet 2017 risk subgroup; Post hoc

DOI:  https://doi.org/10.1186/s13045-022-01361-w
PLoS Genet. 2022 Oct 26. 18(10): e1010463

Understanding a high-risk acute myeloid leukemia by analyzing the interactome of its major driver mutation.

Claudia Chiriches, Nathalie Nicolaisen, Maria Wieske, Heba Elhaddad, Ecmel Mehmetbeyoglu, Caroline Alvares, Dörte Becher, Paul Hole, Oliver Gerhard Ottmann, Martin Ruthardt.

The WHO classifies t(6;9)-positive acute myeloid leukemia (AML) as a subgroup of high-risk AML because of its clinical and biological peculiarities, such as young age and therapy resistance. t(6;9) encodes the DEK/NUP214 fusion oncoprotein that targets only a small subpopulation of bone marrow progenitors for leukemic transformation. This distinguishes DEK/NUP214 from other fusion oncoproteins, such as PML/RARα, RUNX1/ETO, or MLL/AF9, which have a broad target population they block differentiation and increase stem cell capacity. A common theme among most leukemogenic fusion proteins is their aberrant localization compared to their wild-type counterparts. Although the actual consequences are widely unknown, it seems to contribute to leukemogenesis most likely by a sequester of interaction partners. Thus, we applied a global approach to studying the consequences of the aberrant localization of t(6;9)-DEK/NUP214 for its interactome. This study aimed to disclose the role of localization of DEK/NUP214 and the related sequester of proteins interacting with DEK/NUP214 for the determination of the biology of t(6;9)-AML. Here we show the complexity of the biological consequences of the expression of DEK/NUP214 by an in-depth bioinformatic analysis of the interactome of DEK/NUP214 and its biologically dead mutants. DEK/NUP214's interactome points to an essential role for aberrant RNA-regulation and aberrant regulation of apoptosis and leukocyte activation as a significant determinant of the phenotype of t(6;9)-AML. Taken together, we provide evidence that the interactome contributes to the aberrant biology of an oncoprotein, providing opportunities for developing novel targeted therapy approaches.

DOI: https://doi.org/10.1371/journal.pgen.1010463
Nucleic Acids Res. 2022 Oct 27. pii: gkac861. [Epub ahead of print]

A cryptic transactivation domain of EZH2 binds AR and AR's splice variant, promoting oncogene activation and tumorous transformation.

Jun Wang, Kwang-Su Park, Xufen Yu, Weida Gong, H Shelton Earp, Gang Greg Wang, Jian Jin, Ling Cai.

Enhancer of Zeste Homolog 2 (EZH2) and androgen receptor (AR) are crucial chromatin/gene regulators involved in the development and/or progression of prostate cancer, including advanced castration-resistant prostate cancer (CRPC). To sustain prostate tumorigenicity, EZH2 establishes non-canonical biochemical interaction with AR for mediating oncogene activation, in addition to its canonical role as a transcriptional repressor and enzymatic subunit of Polycomb Repressive Complex 2 (PRC2). However, the molecular basis underlying non-canonical activities of EZH2 in prostate cancer remains elusive, and a therapeutic strategy for targeting EZH2:AR-mediated oncogene activation is also lacking. Here, we report that a cryptic transactivation domain of EZH2 (EZH2TAD) binds both AR and AR spliced variant 7 (AR-V7), a constitutively active AR variant enriched in CRPC, mediating assembly and/or recruitment of transactivation-related machineries at genomic sites that lack PRC2 binding. Such non-canonical targets of EZH2:AR/AR-V7:(co-)activators are enriched for the clinically relevant oncogenes. We also show that EZH2TAD is required for the chromatin recruitment of EZH2 to oncogenes, for EZH2-mediated oncogene activation and for CRPC growth in vitro and in vivo. To completely block EZH2's multifaceted oncogenic activities in prostate cancer, we employed MS177, a recently developed proteolysis-targeting chimera (PROTAC) of EZH2. Strikingly, MS177 achieved on-target depletion of both EZH2's canonical (EZH2:PRC2) and non-canonical (EZH2TAD:AR/AR-V7:co-activators) complexes in prostate cancer cells, eliciting far more potent antitumor effects than the catalytic inhibitors of EZH2. Overall, this study reports a previously unappreciated requirement for EZH2TAD for mediating EZH2's non-canonical (co-)activator recruitment and gene activation functions in prostate cancer and suggests EZH2-targeting PROTACs as a potentially attractive therapeutic for the treatment of aggressive prostate cancer that rely on the circuits wired by EZH2 and AR.

DOI: https://doi.org/10.1093/nar/gkac861
Front Oncol. 2022 ;12 897220

Treatment options for acute myeloid leukemia patients aged <60 years.

Giuseppe Visani, Martina Chiarucci, Sara Paolasini, Federica Loscocco, Alessandro Isidori.

  Treatment of acute myeloid leukemia (AML) has changed over the last few years, after the discovery of new drugs selectively targeting AML blasts. Although 3/7 remains the standard of care for most AML patients, several new targeted agents (such as FLT3 inhibitors, CPX-351, gemtuzumab ozogamicin, BCL-2 inhibitor, and oral azacitidine), either as single agents or combined with standard chemotherapy, are approaching clinical practice, starting a new era in AML management. Moreover, emerging evidence has demonstrated that high-risk AML patients might benefit from both allogeneic stem cell transplant and maintenance therapy, providing new opportunities, as well as new challenges, for treating clinicians. In this review, we summarize available data on first-line therapy in young AML patients focusing on targeted therapies, integrating established practice with new evidence, in the effort to outline the contours of a new therapeutic paradigm, that of a "total therapy", which goes beyond obtaining complete remission.

Keywords:  AML - acute myeloid leukemia; allogeneic stem cell transplantation; induction; target therapy; young

DOI:  https://doi.org/10.3389/fonc.2022.897220
BMC Bioinformatics. 2022 Oct 28. 23(1): 448

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r.

Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, Maxime Bucci, Karine Celli-Lebras, Matthieu Duchmann, Romane Joudinaud, Laurène Fenwarth, Olivier Nibourel, Laure Goursaud, Raphael Itzykson, Hervé Dombret, Mathilde Hunault, Claude Preudhomme, Mikaël Salson.

   BACKGROUND: Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data.
RESULTS: Our algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software.
CONCLUSION: FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r . The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.

Keywords:  Alignment-free; Cancer; High-throughput sequencing; Sequence analysis

DOI:  https://doi.org/10.1186/s12859-022-04983-6
Br J Haematol. 2022 Oct 24.

A British Society for Haematology good practice paper: Recommendations for laboratory testing of UK patients with acute myeloid leukaemia.

Priyanka Mehta, Nick Telford, Chris Wragg, Richard Dillon, Sylvie Freeman, Damian Finnegan, Angela Hamblin, Mhairi Copland, Steve Knapper.



Keywords:  cytogenetics; flow cytometry; leukaemia diagnosis; molecular genetics; myeloid leukaemia

DOI:  https://doi.org/10.1111/bjh.18516
Leuk Lymphoma. 2022 Oct 25. 1-10

Use of endpoints in phase III randomized controlled trials for acute myeloid leukemia over the last 15 years: a systematic review.

Moazzam Shahzad, Sibgha Gull Chaudhary, Ezza Tariq, Ali Hassan Mushtaq, Iqra Anwar, Nausheen Ahmed, Rajat Bansal, Forat Lutfi, Ramesh Balusu, Haitham Abdelhakim, Abdulraheem Yacoub, Peiman Hematti, Anurag K Singh, Joseph P McGuirk, Muhammad Umair Mushtaq.

  We systematically evaluated the primary and secondary endpoints used in acute myeloid leukemia (AML) phase III randomized controlled trials (RCTs). We included 238 phase III AML RCTs in the past 15 years that reported 279 primary endpoints and 657 secondary endpoints. Overall survival (OS), progression-free survival (PFS), event-free survival (EFS), and complete remission (CR) were primary endpoints in 120 (43%), 34 (12%), 30 (11%), and 41 (15%) studies, respectively. OS (12.5%), PFS (13.2%), CR (14%), safety (11%), and EFS (9%) were commonly reported secondary endpoints. Among primary endpoints, a higher use of OS (OR 2.03, 95%CI 1.10-3.75, p = 0.023) and lower use of PFS (OR 0.25, 95%CI 0.12-0.52, p < 0.001) was observed from 2014 to 2021 compared to 2006-2013; CR was frequently used in relapsed/refractory compared to frontline RCTs (OR 2.20, 95%CI 1.11-4.38, p = 0.025); EFS was frequently used in frontline compared to relapsed/refractory AML RCTs (OR 10.11, 95%CI 1.34-76.34, p = 0.025). A higher trend in the use of clinically meaningful and objective endpoint of OS over the last 15 years.

Keywords:  Acute myeloid leukemia; endpoints; outcomes; phase III randomized clinical trials

DOI:  https://doi.org/10.1080/10428194.2022.2136947
Leuk Lymphoma. 2022 Oct 25. 1-9

Immunogenicity of COVID-19 mRNA vaccines in patients with acute myeloid leukemia and myelodysplastic syndrome.

David C Helfgott, Sabrina Racine-Brzostek, Kelsey J Short, Zhen Zhao, Paul Christos, Itzel Nino, Tina Niu, Jorge Contreras, Ellen K Ritchie, Pinkal Desai, Michael Samuel, Gail J Roboz.

  Immunocompromised patients are susceptible to complications from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The mRNA vaccines BNT162b2 and mRNA-1273 are effective in immunocompetent adults, but have diminished activity in immunocompromised patients. We measured anti-spike SARS-CoV-2 antibody (anti-S) response, avidity, and surrogate neutralizing antibody activity in COVID-19 vaccinated patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Anti-S was induced in 89% of AML and 88% of MDS patients, but median levels were significantly lower than in healthy controls. SARS-CoV-2 antibody avidity and neutralizing activity from AML patients were significantly lower than controls. Antibody avidity was significantly greater in patients after mRNA-1273 versus BNT162b2; there were trends toward higher anti-S levels and greater neutralizing antibody activity after mRNA-1273 vaccination. Patients with AML and MDS are likely to respond to COVID-19 mRNA vaccination, but differences in anti-S levels, avidity, and neutralizing antibody activity may affect clinical outcomes and require further study.

Keywords:  COVID-19 vaccine immunogenicity; infectious complications of neoplasia; myeloid leukemias and dysplasias; the humoral immune response

DOI:  https://doi.org/10.1080/10428194.2022.2131414
Sci Rep. 2022 Oct 28. 12(1): 18169

Combinatorial gene targeting in primary human hematopoietic stem and progenitor cells.

Alexandra Bäckström, David Yudovich, Kristijonas Žemaitis, Ludvig Nilsén Falck, Agatheeswaran Subramaniam, Jonas Larsson.

The CRISPR/Cas9 system offers enormous versatility for functional genomics but many applications have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, to establish a paradigm for multiplexed gene editing in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs), we used co-delivery of lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The fluorescent markers allow for tracking of either single- or double-edited cells, and we could achieve robust double knockout of the cell surface molecules CD45 and CD44 with an efficiency of ~ 70%. As a functional proof of concept, we demonstrate that this system can be used to model gene dependencies for cell survival, by simultaneously targeting the cohesin genes STAG1 and STAG2. Moreover, we show combinatorial effects with potential synergy for HSPC expansion by targeting the Aryl Hydrocarbon Receptor (AHR) in conjunction with members of the CoREST complex. Taken together, our traceable multiplexed CRISPR/Cas9 system enables studies of genetic dependencies and cooperation in primary HSPCs, and has important implications for modelling polygenic diseases, as well as investigation of the underlying mechanisms of gene interactions.

DOI: https://doi.org/10.1038/s41598-022-23118-8
Cold Spring Harb Mol Case Stud. 2022 Oct;pii: a006218. [Epub ahead of print]8(6):

Comprehensive molecular characterization of a rare case of Philadelphia chromosome-positive acute myeloid leukemia.

Mara W Rosenberg, Samantha L Savage, Christopher A Eide, Anna Reister Schultz, Rachel J Cook, Richard D Press, Carole Rempfer, Garrett Eickelberg, Beth Wilmot, Shannon K McWeeney, Jeffrey W Tyner, Brian J Druker, Cristina E Tognon.

  The Philadelphia chromosome (Ph) resulting from the t(9;22) translocation generates the oncogenic BCR::ABL1 fusion protein that is most commonly associated with chronic myeloid leukemia (CML) and Ph-positive (Ph+) acute lymphoblastic leukemia (ALL). There are also rare instances of patients (≤1%) with newly diagnosed acute myeloid leukemia (AML) that harbor this translocation (Paietta et al., Leukemia 12: 1881 [1998]; Keung et al., Leuk Res 28: 579 [2004]; Soupir et al., Am J Clin Pathol 127: 642 [2007]). AML with BCR::ABL has only recently been provisionally classified by the World Health Organization as a diagnostically distinct subtype of AML. Discernment from the extremely close differential diagnosis of myeloid blast crisis CML is challenging, largely relying on medical history rather than clinical characteristics (Arber et al., Blood 127: 2391 [2016]). To gain insight into the genomic features underlying the evolution of AML with BCR::ABL, we identified a patient presenting with a high-risk myelodysplastic syndrome that acquired a BCR::ABL alteration after a peripheral blood stem cell transplant. Serial samples were collected and analyzed using whole-exome sequencing, RNA-seq, and ex vivo functional drug screens. Persistent subclones were identified, both at diagnosis and at relapse, including an SF3B1p.Lys700Glu mutation that later cooccurred with an NRASp.Gly12Cys mutation. Functional ex vivo drug screening performed on primary patient cells suggested that combination therapies of ABL1 with RAS or PI3K pathway inhibitors could have augmented the patient's response throughout the course of disease. Together, our findings argue for the importance of genomic profiling and the potential value of ABL1 inhibitor-inclusive combination treatment strategies in patients with this rare disease.

Keywords:  acute myeloid leukemia; leukemia

DOI:  https://doi.org/10.1101/mcs.a006218
Br J Haematol. 2022 Oct 25.

Comparison of transplant outcomes between haploidentical transplantation and single cord blood transplantation in non-remission acute myeloid leukaemia: A nationwide retrospective study.

Kensuke Matsuda, Takaaki Konuma, Kyoko Fuse, Masayoshi Masuko, Koji Kawamura, Masahiro Hirayama, Naoyuki Uchida, Kazuhiro Ikegame, Atsushi Wake, Tetsuya Eto, Noriko Doki, Shigesaburo Miyakoshi, Masatsugu Tanaka, Satoshi Takahashi, Makoto Onizuka, Koji Kato, Takafumi Kimura, Tatsuo Ichinohe, Nobuyuki Takayama, Hikaru Kobayashi, Hirohisa Nakamae, Yoshiko Atsuta, Junya Kanda, Masamitsu Yanada.

  Allogeneic haematopoietic stem cell transplantation (HSCT) is a potentially curative treatment for some patients with acute myeloid leukaemia (AML) who are refractory to chemotherapy. Cord blood transplantation (CBT) is a reasonable option in such cases because of its rapid availability. Recently, a growing number of human leucocyte antigen (HLA)-haploidentical related donor HSCTs (haplo-HSCTs) have been performed, although its effectiveness remains undetermined. Using the Japanese nationwide transplantation registry data, we identified 2438 patients aged ≥16 years who received CBT or haplo-HSCT as their first transplant for non-remission AML between January 2008 and December 2018. After 2:1 propensity score matching, 918 patients in the CBT group and 459 patients in the haplo-HSCT group were selected. In this matched cohort, no significant difference in overall survival (OS) was observed between the CBT and haplo-HSCT groups (hazard ratio [HR] of haplo-HSCT to CBT 1.02, 95% confidence interval [CI] 0.89-1.16). Similarly, no significant difference in the cumulative incidence of relapse (HR 1.09, 95% CI 0.93-1.28) or non-relapse mortality (HR 0.94, 95% CI 0.76-1.18). Subgroup analysis showed that CBT was significantly associated with preferable OS in patients receiving myeloablative conditioning. Our data showed comparable outcomes between haplo-HSCT and CBT recipients with non-remission AML.

Keywords:  acute myeloid leukaemia; cord blood transplantation; haploidentical transplantation; non-remission

DOI:  https://doi.org/10.1111/bjh.18530
Nature. 2022 Oct 26.

The co-evolution of the genome and epigenome in colorectal cancer.

Timon Heide, Jacob Househam, George D Cresswell, Inmaculada Spiteri, Claire Lynn, Maximilian Mossner, Chris Kimberley, Javier Fernandez-Mateos, Bingjie Chen, Luis Zapata, Chela James, Iros Barozzi, Ketevan Chkhaidze, Daniel Nichol, Vinaya Gunasri, Alison Berner, Melissa Schmidt, Eszter Lakatos, Ann-Marie Baker, Helena Costa, Miriam Mitchinson, Rocco Piazza, Marnix Jansen, Giulio Caravagna, Daniele Ramazzotti, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Trevor A Graham, Andrea Sottoriva.

Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.

DOI: https://doi.org/10.1038/s41586-022-05202-1
Blood. 2022 Oct 25. pii: blood.2022017326. [Epub ahead of print]

IL-13/IL-4 signaling contributes to fibrotic progression of the myeloproliferative neoplasms.

Johanna Melo-Cardenas, Lavanya Bezavada, Jeremy Chase Crawford, Sandeep Gurbuxani, Anitria Cotton, Guolian Kang, Jeffrey Michael Gossett, Christian Marinaccio, Rona Singer Weinberg, Ronald Hoffman, Anna Rita Migliaccio, Yan Zheng, Marta Derecka, Ciro R Rinaldi, John D Crispino.

Myelofibrosis (MF) is a disease associated with high unmet medical needs since allogeneic stem cell transplantation is not an option for most patients and JAK inhibitors are generally effective for only 2-3 years and do not delay disease progression. MF is characterized by the presence of dysplastic megakaryocytic hyperplasia and progression to fulminant disease, which is associated with progressively increasing marrow fibrosis. Despite evidence of an inflammatory milieu in MF that contributes to disease progression, the specific factors that promote megakaryocyte growth are poorly understood. Here, we analyzed changes in the cytokine profiles of MF mouse models before and after development of fibrosis coupled with analysis of bone marrow populations by scRNA-seq. We found high IL-13 levels in the bone marrow of MF mice. IL-13 promoted the growth of mutant megakaryocytes and induced the surface expression of TGF-b and collagen biosynthesis. Analysis of samples from patients with myelofibrosis similarly revealed elevated levels of IL-13 in plasma and increased IL-13 receptor expression by marrow megakaryocytes. In vivo, IL-13 overexpression promoted disease progression while reducing IL-13/IL-4 signaling reduced several features of the disease including fibrosis. Lastly, we found an increase in the numbers of marrow T cells and mast cells, which are known sources of IL-13. Together, our data demonstrate that IL-13 is involved in disease progression in MF and that inhibition of the IL-13/IL-4 signaling pathway might serve as a novel therapeutic target to treat MF.

DOI: https://doi.org/10.1182/blood.2022017326
Cell Res. 2022 Oct 27.

Targeting UHRF1-SAP30-MXD4 axis for leukemia initiating cell eradication in myeloid leukemia.

Cheng-Long Hu, Bing-Yi Chen, Zijuan Li, Tianbiao Yang, Chun-Hui Xu, Ruirui Yang, Peng-Cheng Yu, Jingyao Zhao, Ting Liu, Na Liu, Bin Shan, Qunling Zhang, Junhong Song, Ming-Yue Fei, Li-Juan Zong, Jia-Ying Zhang, Ji-Chuan Wu, Shu-Bei Chen, Yong Wang, Binhe Chang, Dan Hou, Ping Liu, Yilun Jiang, Xiya Li, Xinchi Chen, Chu-Han Deng, Yi-Yi Ren, Roujia Wang, Jiacheng Jin, Kai Xue, Ying Zhang, Meirong Du, Jun Shi, Ling-Yun Wu, Chun-Kang Chang, Shuhong Shen, Zhu Chen, Sai-Juan Chen, Xiaolong Liu, Xiao-Jian Sun, Mingyue Zheng, Lan Wang.

Aberrant self-renewal of leukemia initiation cells (LICs) drives aggressive acute myeloid leukemia (AML). Here, we report that UHRF1, an epigenetic regulator that recruits DNMT1 to methylate DNA, is highly expressed in AML and predicts poor prognosis. UHRF1 is required for myeloid leukemogenesis by maintaining self-renewal of LICs. Mechanistically, UHRF1 directly interacts with Sin3A-associated protein 30 (SAP30) through two critical amino acids, G572 and F573 in its SRA domain, to repress gene expression. Depletion of UHRF1 or SAP30 derepresses an important target gene, MXD4, which encodes a MYC antagonist, and leads to suppression of leukemogenesis. Further knockdown of MXD4 can rescue the leukemogenesis by activating the MYC pathway. Lastly, we identified a UHRF1 inhibitor, UF146, and demonstrated its significant therapeutic efficacy in the myeloid leukemia PDX model. Taken together, our study reveals the mechanisms for altered epigenetic programs in AML and provides a promising targeted therapeutic strategy against AML.

DOI: https://doi.org/10.1038/s41422-022-00735-6
Open Biol. 2022 Oct;12(10): 220172

Hoxa9/meis1-transgenic zebrafish develops acute myeloid leukaemia-like disease with rapid onset and high penetrance.

Wei Wang, Hongji Li, Mengling Huang, Xue Wang, Wei Li, Xiaoqing Qian, Lili Jing.

  HOXA9 and MEIS1 are co-expressed in over 50% of acute myeloid leukaemia (AML) and play essential roles in leukaemogenesis, but the mechanisms involved are poorly understood. Diverse animal models offer valuable tools to recapitulate different aspects of AML and link in vitro studies to clinical trials. We generated a double transgenic zebrafish that enables hoxa9 overexpression in blood cells under the draculin (drl) regulatory element and an inducible expression of meis1 through a heat shock promoter. After induction, Tg(drl:hoxa9;hsp70:meis1) embryos developed a preleukaemic state with reduced myeloid and erythroid differentiation coupled with the poor production of haematopoietic stem cells and myeloid progenitors. Importantly, most adult Tg(drl:hoxa9;hsp70:meis1) fish at 3 months old showed abundant accumulations of immature myeloid precursors, interrupted differentiation and anaemia in the kidney marrow, and infiltration of myeloid precursors in peripheral blood, resembling human AML. Genome-wide transcriptional analysis also confirmed AML transformation by the transgene. Moreover, the dihydroorotate dehydrogenase (DHODH) inhibitor that reduces leukaemogenesis in mammals effectively restored haematopoiesis in Tg(drl:hoxa9;hsp70:meis1) embryos and improved their late survival. Thus, Tg(drl:hoxa9;hsp70:meis1) zebrafish is a rapid-onset high-penetrance AML-like disease model, which provides a novel tool to harness the unique advantages of zebrafish for mechanistic studies and drug screening against HOXA9/MEIS1 overexpressed high-risk AML.

Keywords:  acute myeloid leukaemia; hoxa9; meis1; myeloid malignancy; transgenic zebrafish model

DOI:  https://doi.org/10.1098/rsob.220172
Nature. 2022 Oct 26.

Phenotypic plasticity and genetic control in colorectal cancer evolution.

Jacob Househam, Timon Heide, George D Cresswell, Inmaculada Spiteri, Chris Kimberley, Luis Zapata, Claire Lynn, Chela James, Maximilian Mossner, Javier Fernandez-Mateos, Alessandro Vinceti, Ann-Marie Baker, Calum Gabbutt, Alison Berner, Melissa Schmidt, Bingjie Chen, Eszter Lakatos, Vinaya Gunasri, Daniel Nichol, Helena Costa, Miriam Mitchinson, Daniele Ramazzotti, Benjamin Werner, Francesco Iorio, Marnix Jansen, Giulio Caravagna, Chris P Barnes, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Andrea Sottoriva, Trevor A Graham.

Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.

DOI: https://doi.org/10.1038/s41586-022-05311-x