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Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023; 10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
Our current understanding of human hematopoiesis has undergone significant transformation throughout the years, challenging conventional views. The evolution of high-throughput technologies has enabled the accumulation of diverse data types, offering new avenues for investigating key regulatory processes in blood cell production and disease. In this review, we will explore the opportunities presented by these advancements for unraveling the molecular mechanisms underlying normal and abnormal hematopoiesis. Specifically, we will focus on the importance of enhancer-associated regulatory networks and highlight the crucial role of enhancer-derived transcription regulation. Additionally, we will discuss the unprecedented power of single-cell methods and the progression in using in vitro human blood differentiation system, in particular induced pluripotent stem cell models, in dissecting hematopoietic processes. Furthermore, we will explore the potential of ever more nuanced patient profiling to allow precision medicine approaches. Ultimately, we advocate for a multiparameter, regulatory network-based approach for providing a more holistic understanding of normal hematopoiesis and blood disorders.
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Affiliation(s)
- Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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Ho NI, Huis In 't Veld LGM, van Eck van der Sluijs J, Heuts BMH, Looman MWG, Kers-Rebel ED, van den Dries K, Dolstra H, Martens JHA, Hobo W, Adema GJ. Saponin-based adjuvants enhance antigen cross-presentation in human CD11c + CD1c + CD5 - CD163 + conventional type 2 dendritic cells. J Immunother Cancer 2023; 11:e007082. [PMID: 37612044 PMCID: PMC10450066 DOI: 10.1136/jitc-2023-007082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Adjuvants are key for effective vaccination against cancer and chronic infectious diseases. Saponin-based adjuvants (SBAs) are unique among adjuvants in their ability to induce robust cell-mediated immune responses in addition to antibody responses. Recent preclinical studies revealed that SBAs induced cross-presentation and lipid bodies in otherwise poorly cross-presenting CD11b+ murine dendritic cells (DCs). METHOD Here, we investigated the response of human DC subsets to SBAs with RNA sequencing and pathway analyses, lipid body induction visualized by laser scanning microscopy, antigen translocation to the cytosol, and antigen cross-presentation to CD8+ T cells. RESULTS RNA sequencing of SBA-treated conventional type 1 DC (cDC1) and type 2 DC (cDC2) subsets uncovered that SBAs upregulated lipid-related pathways in CD11c+ CD1c+ cDC2s, especially in the CD5- CD163+ CD14+ cDC2 subset. Moreover, SBAs induced lipid bodies and enhanced endosomal antigen translocation into the cytosol in this particular cDC2 subset. Finally, SBAs enhanced cross-presentation only in cDC2s, which requires the CD163+ CD14+ cDC2 subset. CONCLUSIONS These data thus identify the CD163+ CD14+ cDC2 subset as the main SBA-responsive DC subset in humans and imply new strategies to optimize the application of saponin-based adjuvants in a potent cancer vaccine.
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Affiliation(s)
- Nataschja I Ho
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lisa G M Huis In 't Veld
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jesper van Eck van der Sluijs
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Maaike W G Looman
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Esther D Kers-Rebel
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Koen van den Dries
- Radboud Technology Center Microscopy, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Harry Dolstra
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Willemijn Hobo
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gosse J Adema
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Nijmegen Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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Heuts BMH, Arza-Apalategi S, Alkema SG, Tijchon E, Jussen L, Bergevoet SM, van der Reijden BA, Martens JHA. Inducible MLL-AF9 Expression Drives an AML Program during Human Pluripotent Stem Cell-Derived Hematopoietic Differentiation. Cells 2023; 12:cells12081195. [PMID: 37190104 DOI: 10.3390/cells12081195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
A t(9;11)(p22;q23) translocation produces the MLL-AF9 fusion protein, which is found in up to 25% of de novo AML cases in children. Despite major advances, obtaining a comprehensive understanding of context-dependent MLL-AF9-mediated gene programs during early hematopoiesis is challenging. Here, we generated a human inducible pluripotent stem cell (hiPSC) model with a doxycycline dose-dependent MLL-AF9 expression. We exploited MLL-AF9 expression as an oncogenic hit to uncover epigenetic and transcriptomic effects on iPSC-derived hematopoietic development and the transformation into (pre-)leukemic states. In doing so, we observed a disruption in early myelomonocytic development. Accordingly, we identified gene profiles that were consistent with primary MLL-AF9 AML and uncovered high-confidence MLL-AF9-associated core genes that are faithfully represented in primary MLL-AF9 AML, including known and presently unknown factors. Using single-cell RNA-sequencing, we identified an increase of CD34 expressing early hematopoietic progenitor-like cell states as well as granulocyte-monocyte progenitor-like cells upon MLL-AF9 activation. Our system allows for careful chemically controlled and stepwise in vitro hiPSC-derived differentiation under serum-free and feeder-free conditions. For a disease that currently lacks effective precision medicine, our system provides a novel entry-point into exploring potential novel targets for personalized therapeutic strategies.
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Affiliation(s)
- Branco M H Heuts
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Saioa Arza-Apalategi
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Sinne G Alkema
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Esther Tijchon
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Laura Jussen
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Saskia M Bergevoet
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Bert A van der Reijden
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Joost H A Martens
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
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Arza-Apalategi S, Heuts BMH, Dooijes MTM, Gilissen D, van der Heijden AJP, Jansen JH, Martens JHA, van der Reijden BA. High expression of an intragenic long noncoding RNA misinterpreted as high FTO oncogene expression in NPM1 mutant acute myeloid leukemia. Leukemia 2023; 37:901-904. [PMID: 36807648 DOI: 10.1038/s41375-023-01844-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Affiliation(s)
- Saioa Arza-Apalategi
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
| | - Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Meike T M Dooijes
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Daan Gilissen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Adrian J P van der Heijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
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Tijchon E, Yi G, Mandoli A, Smits JGA, Ferrari F, Heuts BMH, Wijnen F, Kim B, Janssen-Megens EM, Schuringa JJ, Martens JHA. The acute myeloid leukemia associated AML1-ETO fusion protein alters the transcriptome and cellular progression in a single-oncogene expressing in vitro induced pluripotent stem cell based granulocyte differentiation model. PLoS One 2019; 14:e0226435. [PMID: 31869378 PMCID: PMC6927605 DOI: 10.1371/journal.pone.0226435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by recurrent mutations that affect normal hematopoiesis. The analysis of human AMLs has mostly been performed using end-point materials, such as cell lines and patient derived AMLs that also carry additional contributing mutations. The molecular effects of a single oncogenic hit, such as expression of the AML associated oncoprotein AML1-ETO on hematopoietic development and transformation into a (pre-) leukemic state still needs further investigation. Here we describe the development and characterization of an induced pluripotent stem cell (iPSC) system that allows in vitro differentiation towards different mature myeloid cell types such as monocytes and granulocytes. During in vitro differentiation we expressed the AML1-ETO fusion protein and examined the effects of the oncoprotein on differentiation and the underlying alterations in the gene program at 8 different time points. Our analysis revealed that AML1-ETO as a single oncogenic hit in a non-mutated background blocks granulocytic differentiation, deregulates the gene program via altering the acetylome of the differentiating granulocytic cells, and induces t(8;21) AML associated leukemic characteristics. Together, these results reveal that inducible oncogene expression during in vitro differentiation of iPS cells provides a valuable platform for analysis of aberrant regulation in disease.
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Affiliation(s)
- Esther Tijchon
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Guoqiang Yi
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Amit Mandoli
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Jos G. A. Smits
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Francesco Ferrari
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Branco M. H. Heuts
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Falco Wijnen
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Bowon Kim
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Eva M. Janssen-Megens
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Jan Jacob Schuringa
- Department of Hematology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Joost H. A. Martens
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, the Netherlands
- * E-mail:
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