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Cao X, Huber S, Ahari AJ, Traube FR, Seifert M, Oakes CC, Secheyko P, Vilov S, Scheller IF, Wagner N, Yépez VA, Blombery P, Haferlach T, Heinig M, Wachutka L, Hutter S, Gagneur J. Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes. Genome Med 2024; 16:70. [PMID: 38769532 PMCID: PMC11103968 DOI: 10.1186/s13073-024-01331-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/04/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their identification remains challenging. METHODS To address this issue, we generated the largest dataset to date of matched whole genome sequencing and total RNA sequencing of hematologic malignancies from 3760 patients spanning 24 disease entities. Taking advantage of our dataset size, we focused on discovering rare regulatory aberrations. Therefore, we called expression and splicing outliers using an extension of the workflow DROP (Detection of RNA Outliers Pipeline) and AbSplice, a variant effect predictor that identifies genetic variants causing aberrant splicing. We next trained a machine learning model integrating these results to prioritize new candidate disease-specific driver genes. RESULTS We found a median of seven expression outlier genes, two splicing outlier genes, and two rare splice-affecting variants per sample. Each category showed significant enrichment for already well-characterized driver genes, with odds ratios exceeding three among genes called in more than five samples. On held-out data, our integrative modeling significantly outperformed modeling based solely on genomic data and revealed promising novel candidate driver genes. Remarkably, we found a truncated form of the low density lipoprotein receptor LRP1B transcript to be aberrantly overexpressed in about half of hairy cell leukemia variant (HCL-V) samples and, to a lesser extent, in closely related B-cell neoplasms. This observation, which was confirmed in an independent cohort, suggests LRP1B as a novel marker for a HCL-V subclass and a yet unreported functional role of LRP1B within these rare entities. CONCLUSIONS Altogether, our census of expression and splicing outliers for 24 hematologic malignancy entities and the companion computational workflow constitute unique resources to deepen our understanding of rare oncogenic events in hematologic cancers.
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Affiliation(s)
- Xueqi Cao
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany
| | - Sandra Huber
- Munich Leukemia Laboratory (MLL), Munich, Germany
| | - Ata Jadid Ahari
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Franziska R Traube
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Marc Seifert
- Department of Haematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Polina Secheyko
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sergey Vilov
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Ines F Scheller
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Torsten Haferlach Leukämiediagnostik Stiftung, Munich, Germany
| | | | - Matthias Heinig
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Leonhard Wachutka
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany.
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Wang Q, Xu H, Yu W, Sun L, Zhao H, Shi X. Transformation of Severe Aplastic Anemia into Donor Cell Leukemia after Allogeneic Hematopoietic Stem Cell Transplantation: A Rare Case Report. AMERICAN JOURNAL OF CASE REPORTS 2024; 25:e943801. [PMID: 38632857 DOI: 10.12659/ajcr.943801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
BACKGROUND Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an important treatment for severe aplastic anemia (SAA). It is known that SAA can evolve into malignant clonal diseases, such as acute myeloblastic leukemia (AML) or myelodysplastic syndrome. However, the transformation of SAA into AML after allo-HSCT is a rare phenomenon. Here, we report a case of SAA transformed into AML after patient received human leucocyte antigen (HLA)-matched sibling peripheral blood stem cell transplantation. CASE REPORT A 51-year-old female patient presented with petechiae and fatigue and received a diagnosis of idiopathic SAA. The immunosuppressive therapy combined with umbilical cord blood transplantation failed for this patient. Then, she received HLA-matched sibling allogeneic peripheral blood stem cell transplantation (allo-PBSCT). However, 445 days after allo-PBSCT, the patient had a diagnosis of AML by bone marrow puncture. Donor-recipient chimerism monitoring and cytogenetic analysis confirmed that the leukemia was donor cell origin. Notably, a new HOXA11 mutation was detected in the peripheral blood of the patient after transplantation by whole-exome sequencing, which was the same gene mutation detected in the donor. The patient received 1 cycle of induction chemotherapy with azacytidine and achieved complete remission. However, the leukemia relapsed after 2 cycles of consolidation chemotherapy. Unfortunately, the patient died of leukemia progression 575 days after allo-HSCT. CONCLUSIONS The mechanism of how normal donor hematopoietic cells transform to leukemia in the host remains unclear. Donor cell leukemia provides a unique opportunity to examine genetic variations in donors and hosts with regards to the progression to malignancy.
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Affiliation(s)
- Qianqian Wang
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Hong Xu
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Wei Yu
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Lingjie Sun
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Hongguo Zhao
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Xue Shi
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
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Ge Y, Hong M, Zhang Y, Wang J, Li L, Zhu H, Sheng Y, Wu WS, Zhang Z. miR-30e-5p regulates leukemia stem cell self-renewal through the Cyb561/ROS signaling pathway. Haematologica 2024; 109:411-421. [PMID: 37584287 PMCID: PMC10828755 DOI: 10.3324/haematol.2023.282837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023] Open
Abstract
Leukemia stem cells (LSC) represent a crucial and rare subset of cells present in acute myeloid leukemia (AML); they play a pivotal role in the initiation, maintenance, and relapse of this disease. Targeting LSC holds great promise for preventing AML relapse and improving long-term outcomes. However the precise molecular mechanisms governing LSC self-renewal are still poorly understood. Here, we present compelling evidence that the expression of miR-30e-5p, a potential tumor-suppressive microRNA, is significantly lower in AML samples than in healthy bone marrow samples. Forced expression of miR- 30e effectively inhibits leukemogenesis, impairs LSC self-renewal, and delays leukemia progression. Mechanistically, Cyb561 acts as a direct target of miR-30e-5p in LSC, and its deficiency restricts the self-renewal of LSC by activating reactive oxygen series signaling and markedly prolongs recipients' survival. Moreover, genetic or pharmacological overexpression of miR-30e-5p or knockdown of Cyb561 suppresses the growth of human AML cells. In conclusion, our findings establish the crucial role of the miR-30e-5p/Cyb561/ROS axis in finely regulating LSC self-renewal, highlighting Cyb561 as a potential therapeutic target for LSC-directed therapies.
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Affiliation(s)
- Yanwen Ge
- School of Life Sciences, Shanghai University, Shanghai, 200444
| | - Mei Hong
- School of Life Sciences, Shanghai University, Shanghai, 200444
| | - Yu Zhang
- School of Life Sciences, Shanghai University, Shanghai, 200444
| | - Jiachen Wang
- School of Life Sciences, Shanghai University, Shanghai, 200444
| | - Lei Li
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022
| | - Hongkai Zhu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011
| | - Yue Sheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011
| | - Wen-Shu Wu
- Division of Hematology/Oncology, Department of Medicine and University of Illinois Cancer Center, the University of Illinois at Chicago, IL 60612.
| | - Zhonghui Zhang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China; Shaoxing Institute of Technology, Shanghai University, Shaoxing, 312000.
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Hoxa11-mediated reduction of cell migration contributes to myeloid sarcoma formation induced by cooperation of MLL/AF10 with activating KRAS mutation in a mouse transplantation model. Neoplasia 2022; 29:100802. [PMID: 35500545 PMCID: PMC9065885 DOI: 10.1016/j.neo.2022.100802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/18/2022] [Indexed: 12/02/2022]
Abstract
Acute myeloid leukemia (AML) patients with MLL translocations (MLL-t) are frequently found to harbor N-/K-RAS activating mutations. Mouse models revealed that cooperating mutations accelerated leukemia development and myeloid sarcoma formation. The molecular mechanism of accelerated leukemia development and myeloid sarcoma formation is not clear. In this study, we demonstrate Hoxa10 accelerated leukemia development and are the first to show that Hoxa11 controls migration and retention of leukemia cell at extramedullary sites and is a key player in myeloid sarcoma formation.
The molecular mechanism of myeloid sarcoma (MS) formation remains nuclear. Our clinical and mouse model findings from a previous study revealed that cooperation of KMT2A (MLL) translocation (MLL-t) with activating N-/K-RAS mutations promoted MS formation in a shorter latency. To improve the understanding of MS formation, in this study, we performed imaging cell trafficking analysis and demonstrated that cells harboring cooperating mutations migrated more slowly to omental adipose tissues and more cells were retained in adipose tissues in vivo. Comparison of transcriptome profiling among three pairs of mouse MLL/AF10(OM-LZ) leukemia cell lines harboring activating and wild-type KRAS identified 77 differentially expressed genes (DEGs) with >1.5-fold change. Functional annotation of these 77 DEGs using Gene Ontology (GO) enrichment analysis followed by cluster analysis revealed that GO terms related to development/differentiation have the highest enrichment score. The roles of Hoxa10 and Hoxa11, two genes which mapped to this cluster, were further characterized. Silencing Hoxa10 and Hoxa11 in cells harboring cooperating mutations prolonged the survival and reduced MS formation, respectively, in the recipient mice. Data of imaging cell trafficking as well as competitive engraftment and clonal expansion analyses indicated that silencing or overexpressing Hoxa11 in mouse leukemia cells affected cell migration and retention in omental adipose tissue. Although silencing Hoxa11 in leukemia cells did not affect Cxcr4 expression, it resulted in increased transwell migration, motility in confined spaces 3 μm in size, and cell protrusion. Our results revealed that Hoxa10 plays an important role in survival and Hoxa11 contributes to MS formation in MLL-t acute myeloid leukemia with activating KRAS mutation.
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