Publications

@article{Demoen2024,

title = {A dual role for PSIP1/LEDGF in T cell acute lymphoblastic leukemia.},

author = {Lisa Demoen and Filip Matthijssens and Lindy Reunes and Bruno Palhais and Béatrice Lintermans and Sara T'Sas and Igor Fijalkowski and Joachim Taminau and Muluembet Z. Akele and Siska Van Belle and Tom Taghon and Dieter Deforce and Filip Van Nieuwerburgh and Geert Berx and Panagiotis Ntziachristos and Zeger Debyser and Kaat Durinck and Tim Pieters and Steven Goossens and Pieter Van Vlierberghe},

doi = {10.1126/sciadv.ado6765},

issn = {2375-2548},

year  = {2024},

date = {2024-11-01},

journal = {Science advances},

volume = {10},

issue = {44},

pages = {eado6765},

abstract = {T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Current intensified therapeutic protocols coincide with severe side effects, and no salvage therapy is available for primary therapy-resistant or relapsed patients. This highlights the need to identify new therapeutic targets in T-ALL. PSIP1, dispensable for normal hematopoiesis, is a dependency factor in KMT2A -rearranged myeloid leukemia. Nonetheless, loss-of-function mutations suggest a tumor suppressor role for PSIP1 in T-ALL. Here, we demonstrate that the loss of Psip1 accelerates T-ALL initiation in mice which we correlated with reduced H3K27me3 binding. Contrastingly, loss of PSIP1 impaired cell proliferation in several T-ALL cell lines. In cell lines, PSIP1 down-regulation leads to a reduction of COX20, an assembly factor of the cytochrome c oxidase in the mitochondria, and to a reduction in mitochondrial respiration. This indicates that PSIP1 can exert a dual role in the context of T-ALL, either as a tumor suppressor gene during tumor initiation or as a dependency factor in tumor maintenance.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Yayon2024,

title = {A spatial human thymus cell atlas mapped to a continuous tissue axis.},

author = {Nadav Yayon and Veronika R. Kedlian and Lena Boehme and Chenqu Suo and Brianna T. Wachter and Rebecca T. Beuschel and Oren Amsalem and Krzysztof Polanski and Simon Koplev and Elizabeth Tuck and Emma Dann and Jolien Van Hulle and Shani Perera and Tom Putteman and Alexander V. Predeus and Monika Dabrowska and Laura Richardson and Catherine Tudor and Alexandra Y. Kreins and Justin Engelbert and Emily Stephenson and Vitalii Kleshchevnikov and Fabrizio De Rita and David Crossland and Marita Bosticardo and Francesca Pala and Elena Prigmore and Nana-Jane Chipampe and Martin Prete and Lijiang Fei and Ken To and Roger A. Barker and Xiaoling He and Filip Van Nieuwerburgh and Omer Ali Bayraktar and Minal Patel and E. Graham Davies and Muzlifah A. Haniffa and Virginie Uhlmann and Luigi D. Notarangelo and Ronald N. Germain and Andrea J. Radtke and John C. Marioni and Tom Taghon and Sarah A. Teichmann},

doi = {10.1038/s41586-024-07944-6},

issn = {1476-4687},

year  = {2024},

date = {2024-11-01},

journal = {Nature},

volume = {635},

issue = {8039},

pages = {708–718},

abstract = {T cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection (1). In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus-the Cortico-Medullary Axis-and used it to perform a spatially resolved analysis. Here, by applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions by the beginning of the the second trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall's corpuscles and identify divergence in the timing of medullary entry between CD4 and CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation and OrganAxis construction (TissueTag), which can be applied to any tissue.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{DeMunter2024,

title = {Knocking Out CD70 Rescues CD70-Specific NanoCAR T Cells from Antigen-Induced Exhaustion.},

author = {Stijn De Munter and Juliane L. Buhl and Laurenz De Cock and Alexander Van Parys and Willem Daneels and Eva Pascal and Lucas Deseins and Joline Ingels and Glenn Goetgeluk and Hanne Jansen and Lore Billiet and Melissa Pille and Julie Van Duyse and Sarah Bonte and Niels Vandamme and Jo Van Dorpe and Fritz Offner and Georges Leclercq and Tom Taghon and Erik Depla and Jan Tavernier and Tessa Kerre and Jarno Drost and Bart Vandekerckhove},

doi = {10.1158/2326-6066.CIR-23-0677},

issn = {2326-6074},

year  = {2024},

date = {2024-09-01},

journal = {Cancer immunology research},

volume = {12},

issue = {9},

pages = {1236–1251},

abstract = {CD70 is an attractive target for chimeric antigen receptor (CAR) T-cell therapy for the treatment of both solid and liquid malignancies. However, the functionality of CD70-specific CAR T cells is modest. We optimized a CD70-specific VHH-based CAR (nanoCAR). We evaluated the nanoCARs in clinically relevant models in vitro, using co-cultures of CD70-specific nanoCAR T cells with malignant rhabdoid tumor organoids, and in vivo, using a diffuse large B-cell lymphoma patient-derived xenograft (PDX) model. Although the nanoCAR T cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. We determined that fratricide was not causing this loss in efficacy but rather CD70 interaction in cis with the nanoCAR-induced exhaustion. Knocking out CD70 in nanoCAR T cells using CRISPR/Cas9 resulted in dramatically enhanced functionality in the diffuse large B-cell lymphoma PDX model. Through single-cell transcriptomics, we obtained evidence that CD70 knockout CD70-specific nanoCAR T cells were protected from antigen-induced exhaustion. In addition, we demonstrated that wild-type CD70-specific nanoCAR T cells already exhibited signs of exhaustion shortly after production. Their gene signature strongly overlapped with gene signatures of exhausted CAR T cells. Conversely, the gene signature of knockout CD70-specific nanoCAR T cells overlapped with the gene signature of CAR T-cell infusion products leading to complete responses in chronic lymphatic leukemia patients. Our data show that CARs targeting endogenous T-cell antigens negatively affect CAR T-cell functionality by inducing an exhausted state, which can be overcome by knocking out the specific target.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Billiet2024,

title = {ThymoSpheres culture: A model to study human polyclonal unconventional T cells.},

author = {Lore Billiet and Hanne Jansen and Melissa Pille and Lena Boehme and Guillem Sanchez Sanchez and Laurenz De Cock and Glenn Goetgeluk and Eva Pascal and Stijn De Munter and Lucas Deseins and Joline Ingels and Thomas Michiels and Robrecht De Vos and Amin Zolfaghari and Niels Vandamme and Jana Roels and Tessa Kerre and Ruslan I. Dmitriev and Tom Taghon and David Vermijlen and Bart Vandekerckhove},

doi = {10.1002/eji.202451265},

issn = {1521-4141},

year  = {2024},

date = {2024-09-01},

journal = {European journal of immunology},

pages = {e2451265},

abstract = {In vitro cultures remain crucial for studying the fundamental mechanisms of human T-cell development. Here, we introduce a novel in vitro cultivation system based on ThymoSpheres (TS): dense spheroids consisting of DLL4-expressing stromal cells and human hematopoietic precursor cells, in the absence of thymic epithelial cells. These spheroids are subsequently cultured at the air-liquid interphase. TS generate large numbers of mature T cells, are easy to manipulate, scalable, and can be repeatably sampled to monitor T-cell differentiation. The mature T cells generated from primary human hematopoietic precursor cells were extensively characterized using single-cell RNA and combined T-cell receptor (TCR) sequencing. These predominantly CD8α T cells exhibit transcriptional and TCR CDR3 characteristics similar to the recently described human polyclonal αβ unconventional T cell (UTC) lineage. This includes the expression of hallmark genes associated with agonist selection, such as IKZF2 (Helios), and the expression of various natural killer receptors. The TCR repertoire of these UTCs is polyclonal and enriched for CDR3-associated autoreactive features and early rearrangements of the TCR-α chain. In conclusion, TS cultures offer an intriguing platform to study the development of this human polyclonal UTC lineage and its inducing selection mechanisms.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{RuizPerez2024,

title = {TL1A and IL-18 synergy promotes GM-CSF-dependent thymic granulopoiesis in mice.},

author = {Mario Ruiz Pérez and Christian Maueröder and Wolf Steels and Bruno Verstraeten and Sahine Lameire and Wei Xie and Laura Wyckaert and Jelle Huysentruyt and Tatyana Divert and Ria Roelandt and Amanda Gonçalves and Riet De Rycke and Kodi Ravichandran and Bart N. Lambrecht and Tom Taghon and Georges Leclercq and Peter Vandenabeele and Peter Tougaard},

doi = {10.1038/s41423-024-01180-8},

issn = {2042-0226},

year  = {2024},

date = {2024-06-01},

journal = {Cellular & molecular immunology},

abstract = {Acute systemic inflammation critically alters the function of the immune system, often promoting myelopoiesis at the expense of lymphopoiesis. In the thymus, systemic inflammation results in acute thymic atrophy and, consequently, impaired T-lymphopoiesis. The mechanism by which systemic inflammation impacts the thymus beyond suppressing T-cell development is still unclear. Here, we describe how the synergism between TL1A and IL-18 suppresses T-lymphopoiesis to promote thymic myelopoiesis. The protein levels of these two cytokines were elevated in the thymus during viral-induced thymus atrophy infection with murine cytomegalovirus (MCMV) or pneumonia virus of mice (PVM). In vivo administration of TL1A and IL-18 induced acute thymic atrophy, while thymic neutrophils expanded. Fate mapping with Ms4a3-Cre mice demonstrated that thymic neutrophils emerge from thymic granulocyte-monocyte progenitors (GMPs), while Rag1-Cre fate mapping revealed a common developmental path with lymphocytes. These effects could be modeled ex vivo using neonatal thymic organ cultures (NTOCs), where TL1A and IL-18 synergistically enhanced neutrophil production and egress. NOTCH blockade by the LY411575 inhibitor increased the number of neutrophils in the culture, indicating that NOTCH restricted steady-state thymic granulopoiesis. To promote myelopoiesis, TL1A, and IL-18 synergistically increased GM-CSF levels in the NTOC, which was mainly produced by thymic ILC1s. In support, TL1A- and IL-18-induced granulopoiesis was completely prevented in NTOCs derived from Csf2rb (-/-)mice and by GM-CSFR antibody blockade, revealing that GM-CSF is the essential factor driving thymic granulopoiesis. Taken together, our findings reveal that TL1A and IL-18 synergism induce acute thymus atrophy while promoting extramedullary thymic granulopoiesis in a NOTCH and GM-CSF-controlled manner.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{DeConinck2024,

title = {Tet2 is a tumor suppressor in the preleukemic phase of T-cell acute lymphoblastic leukemia.},

author = {Stien De Coninck and Juliette Roels and Béatrice Lintermans and Sara T'Sas and Tom Taghon and David J. Curtis and Tim Pieters and Steven Goossens and Pieter Van Vlierberghe},

doi = {10.1182/bloodadvances.2023011970},

issn = {2473-9537},

year  = {2024},

date = {2024-06-01},

journal = {Blood advances},

volume = {8},

issue = {11},

pages = {2646–2649},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Stanulovic2024,

title = {The glutamate/aspartate transporter EAAT1 is crucial for T-cell acute lymphoblastic leukemia proliferation and survival.},

author = {Vesna S. Stanulović and Shorog Al Omair and Michelle A. C. Reed and Jennie Roberts and Sandeep Potluri and Taylor Fulton-Ward and Nancy Gudgeon and Emma L. Bishop and Juliette Roels and Tracey A. Perry and Sovan Sarkar and Guy Pratt and Tom Taghon and Sarah Dimeloe and Ulrich L. Günther and Christian Ludwig and Maarten Hoogenkamp},

doi = {10.3324/haematol.2023.283471},

issn = {1592-8721},

year  = {2024},

date = {2024-05-01},

journal = {Haematologica},

abstract = {T-cell acute lymphoblastic leukemia (T-ALL) is a cancer of the immune system. Approximately 20% of paediatric and 50% of adult T-ALL patients have refractory disease or relapse and die from the disease. To improve patient outcome new therapeutics are needed. With the aim to identify new therapeutic targets, we combined the analysis of T-ALL gene expression and metabolism to identify the metabolic adaptations that T-ALL cells exhibit. We found that glutamine uptake is essential for T-ALL proliferation. Isotope tracing experiments showed that glutamine fuels aspartate synthesis through the TCA cycle and that glutamine and glutamine-derived aspartate together supply three nitrogen atoms in purines and all but one atom in pyrimidine rings. We show that the glutamate-aspartate transporter EAAT1 (SLC1A3), which is normally expressed in the central nervous system, is crucial for glutamine conversion to aspartate and nucleotides and that T-ALL cell proliferation depends on EAAT1 function. Through this work, we identify EAAT1 as a novel therapeutic target for T-ALL treatment.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Ingels2024,

title = {Neoantigen-targeted dendritic cell vaccination in lung cancer patients induces long-lived T cells exhibiting the full differentiation spectrum.},

author = {Joline Ingels and Laurenz De Cock and Dieter Stevens and Rupert L. Mayer and Fabien Théry and Guillem Sanchez Sanchez and David Vermijlen and Karin Weening and Saskia De Smet and Nele Lootens and Marieke Brusseel and Tasja Verstraete and Jolien Buyle and Eva Van Houtte and Pam Devreker and Kelly Heyns and Stijn De Munter and Sandra Van Lint and Glenn Goetgeluk and Sarah Bonte and Lore Billiet and Melissa Pille and Hanne Jansen and Eva Pascal and Lucas Deseins and Lies Vantomme and Maarten Verdonckt and Ria Roelandt and Thomas Eekhout and Niels Vandamme and Georges Leclercq and Tom Taghon and Tessa Kerre and Floris Vanommeslaeghe and Annemieke Dhondt and Liesbeth Ferdinande and Jo Van Dorpe and Liesbeth Desender and Frederic De Ryck and Frank Vermassen and Veerle Surmont and Francis Impens and Björn Menten and Karim Vermaelen and Bart Vandekerckhove},

doi = {10.1016/j.xcrm.2024.101516},

issn = {2666-3791},

year  = {2024},

date = {2024-05-01},

journal = {Cell reports. Medicine},

volume = {5},

issue = {5},

pages = {101516},

abstract = {Non-small cell lung cancer (NSCLC) is known for high relapse rates despite resection in early stages. Here, we present the results of a phase I clinical trial in which a dendritic cell (DC) vaccine targeting patient-individual neoantigens is evaluated in patients with resected NSCLC. Vaccine manufacturing is feasible in six of 10 enrolled patients. Toxicity is limited to grade 1-2 adverse events. Systemic T cell responses are observed in five out of six vaccinated patients, with T cell responses remaining detectable up to 19 months post vaccination. Single-cell analysis indicates that the responsive T cell population is polyclonal and exhibits the near-entire spectrum of T cell differentiation states, including a naive-like state, but excluding exhausted cell states. Three of six vaccinated patients experience disease recurrence during the follow-up period of 2 years. Collectively, these data support the feasibility, safety, and immunogenicity of this treatment in resected NSCLC.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{DeVos2024,

title = {HES6 knockdown in human hematopoietic precursor cells reduces their in vivo engraftment potential and their capacity to differentiate into erythroid cells, B cells, T cells and plasmacytoid dendritic cells.},

author = {Tamara De Vos and Nicole Oatman and Lena Boehme and Tom Putteman and Imke Velghe and Yana Van Droogenbroeck and Stijn De Munter and Michaela Cesnekova and Filip Van Nieuwerburgh and Bart Vandekerckhove and Jan Philippe and Tom Taghon},

doi = {10.3324/haematol.2023.283432},

issn = {1592-8721},

year  = {2024},

date = {2024-04-01},

journal = {Haematologica},

abstract = {Hematopoiesis is driven by molecular mechanisms that induce differentiation and proliferation of hematopoietic stem cells and their progeny. This involves the activity of various transcription factors, such as members of the Hairy/Enhancer of Split (HES) family, and important roles for both HES1 and HES4 have been shown in normal and malignant hematopoiesis. Here, we investigated the role of HES6 in human hematopoiesis using in vitro and in vivo models. Using bulk and scRNA-seq data, we show that HES6 is expressed during erythroid/megakaryocyte and pDC development, as well as in multipotent precursors and at specific stages of T- and B-cell development following preBCR and preTCR signalling, respectively. Consistently, knockdown of HES6 in cord blood-derived hematopoietic precursors in well-defined in vitro differentiation assays resulted in reduced differentiation of human hematopoietic precursors towards megakaryocytes, erythrocytes, pDCs, Band T-cells. In addition, HES6 knockdown HSPCs displayed reduced colony forming unit capacity in vitro and impaired potential to reconstitute hematopoiesis in vivo in a competitive transplantation assay. We demonstrate that loss of HES6 expression impacts cell cycle progression during erythroid differentiation and provide evidence for potential downstream target genes that impact these perturbations. Thus, our study uncovers new insights for a role of HES6 in human hematopoiesis.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Assatova2024,

title = {KLRG1 Cell Depletion As A Novel Therapeutic Strategy In Patients With Mature T-cell lymphoma Subtypes.},

author = {Bimarzhan Assatova and Robert Willim and Christopher Trevisani and Garrett Haskett and Khyati Maulik Kariya and Kusha Chopra and Sung Rye Park and Michael Yevgeniy Tolstorukov and Sean M. McCabe and Jessica Duffy and Abner Louissaint and Jani Huuhtanen and Dipabarna Bhattacharya and Satu Mustjoki and Min Jung Koh and Foster Powers and Elizabeth A. Morgan and Lei Yang and Brandy Pinckney and Matthew J. Cotton and Andrew Crabbe and Jessica Beth Ziemba and Ian Brain and Tayla B. Heavican-Foral and Javeed Iqbal and Ronald Nemec and Anna Baird Rider and Josie Germain Ford and Min Ji Koh and Nora Scanlan and David J. Feith and Thomas P. Loughran and Won Seog Kim and Jaehyuk Choi and Juliette Roels and Lena Boehme and Tom Putteman and Tom Taghon and Jeffrey A. Barnes and P. Connor Johnson and Eric D. Jacobsen and Steven A. Greenberg and David M. Weinstock and Salvia Jain},

doi = {10.1158/1078-0432.CCR-23-3504},

issn = {1557-3265},

year  = {2024},

date = {2024-01-01},

journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},

abstract = {Develop a novel therapeutic strategy for patients with subtypes of mature T-cell and NK-cell neoplasms. Primary specimens, cell lines, patient-derived xenograft models, commercially available and proprietary anti-KLRG1 antibodies were used for screening, target, and functional validation. Here we demonstrate that surface KLRG1 is highly expressed on tumor cells in subsets of patients with extranodal NK/T-cell lymphoma (ENKTCL), T-prolymphocytic leukemia (T-PLL) and gamma/delta T-cell lymphoma (G/D TCL). The majority of the CD8+/CD57+ or CD3-/CD56+ leukemic cells derived from patients with T- and NK-large granular lymphocytic leukemia (T-LGLL and NK-LGLL) respectively expressed surface KLRG1. The humanized afucosylated anti-KLRG1 monoclonal antibody (mAb208) optimized for mouse in vivo use depleted KLRG1+ TCL cells by mechanisms of ADCC, ADCP and CDC rather than apoptosis. mAb208 induced ADCC and ADCP of T-LGLL patient-derived CD8+/CD57+ cells ex vivo. mAb208 effected ADCC of subsets of healthy donor-derived KLRG1+ NK, CD4+, CD8+ Tem and TemRA cells while sparing KLRG1- naive and CD8+ Tcm cells. Treatment of cell line and TCL patient-derived xenografts with mAb208 or anti-CD47 mAb alone and in combination with the PI3K-δ/γ inhibitor, duvelisib extended survival. The depletion of macrophages in vivo antagonized mAb208 efficacy. Our findings suggest the potential benefit of a broader treatment strategy combining therapeutic antibodies with PI3Ki for the treatment of patients with mature T-cell and NK-cell neoplasms.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Tougaard2024,

title = {Type 1 immunity enables neonatal thymic ILC1 production.},

author = {Peter Tougaard and Mario R. Pérez and Wolf Steels and Jelle Huysentruyt and Bruno Verstraeten and Jessica Vetters and Tatyana Divert and Amanda Gonçalves and Ria Roelandt and Nozomi Takahashi and Sophie Janssens and Terkild B. Buus and Tom Taghon and Georges Leclercq and Peter Vandenabeele},

doi = {10.1126/sciadv.adh5520},

issn = {2375-2548},

year  = {2024},

date = {2024-01-01},

journal = {Science advances},

volume = {10},

issue = {3},

pages = {eadh5520},

abstract = {Acute thymic atrophy occurs following type 1 inflammatory conditions such as viral infection and sepsis, resulting in cell death and disruption of T cell development. However, the impact type 1 immunity has on thymic-resident innate lymphoid cells (ILCs) remains unclear. Single-cell RNA sequencing revealed neonatal thymic-resident type 1 ILCs (ILC1s) as a unique and immature subset compared to ILC1s in other primary lymphoid organs. Culturing murine neonatal thymic lobes with the type 1 cytokines interleukin-12 (IL-12) and IL-18 resulted in a rapid expansion and thymic egress of KLRG1 (+)CXCR6 (+)cytotoxic ILC1s. Live imaging showed the subcapsular thymic localization and exit of ILC1s following IL-12 + IL-18 stimulation. Similarly, murine cytomegalovirus infection in neonates resulted in thymic atrophy and subcapsular localization of thymic-resident ILC1s. Neonatal thymic grafting revealed that type 1 inflammation enhances the homing of cytokine-producing thymus-derived ILC1s to the liver and peritoneal cavity. Together, we show that type 1 immunity promotes the expansion and peripheral homing of thymic-derived ILC1s.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Liang2023b,

title = {Circulating IRF8-expressing CD123⁺CD127⁺ lymphoid progenitors: key players in human hematopoiesis.},

author = {Kai Ling Liang and Elisa Laurenti and Tom Taghon},

doi = {10.1016/j.it.2023.07.004},

issn = {1471-4981},

year  = {2023},

date = {2023-08-01},

journal = {Trends in immunology},

abstract = {Lymphopoiesis is the process in which B and T cells, and innate lymphoid cells (ILCs) develop from hematopoietic progenitors that exhibit early lymphoid priming. The branching points where lymphoid-primed human progenitors are further specified to B/T/ILC differentiation trajectories remain unclear. Here, we discuss the emerging role of interferon regulatory factor (IRF)8 as a key factor to bridge human lymphoid and dendritic cell (DC) differentiation, and the current evidence for the existence of circulating and tissue-resident CD123⁺CD127⁺ lymphoid progenitors. We propose a model whereby DC/B/T/ILC lineage programs in circulating CD123⁺CD127⁺ lymphoid progenitors are expressed in balance. Upon tissue seeding, the tissue microenvironment tilts this molecular balance towards a specific lineage, thereby determining in vivo lineage fates. Finally, we discuss the translational implication of these lymphoid precursors.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Billiet2023,

title = {Single-cell profiling identifies a novel human polyclonal unconventional T cell lineage.},

author = {Lore Billiet and Laurenz De Cock and Guillem Sanchez Sanchez and Rupert L. Mayer and Glenn Goetgeluk and Stijn De Munter and Melissa Pille and Joline Ingels and Hanne Jansen and Karin Weening and Eva Pascal and Killian Raes and Sarah Bonte and Tessa Kerre and Niels Vandamme and Ruth Seurinck and Jana Roels and Marieke Lavaert and Filip Van Nieuwerburgh and Georges Leclercq and Tom Taghon and Francis Impens and Björn Menten and David Vermijlen and Bart Vandekerckhove},

doi = {10.1084/jem.20220942},

issn = {1540-9538},

year  = {2023},

date = {2023-06-01},

journal = {The Journal of experimental medicine},

volume = {220},

issue = {6},

abstract = {In the human thymus, a CD10+ PD-1+ TCRαβ+ differentiation pathway diverges from the conventional single positive T cell lineages at the early double-positive stage. Here, we identify the progeny of this unconventional lineage in antigen-inexperienced blood. These unconventional T cells (UTCs) in thymus and blood share a transcriptomic profile, characterized by hallmark transcription factors (i.e., ZNF683 and IKZF2), and a polyclonal TCR repertoire with autoreactive features, exhibiting a bias toward early TCRα chain rearrangements. Single-cell RNA sequencing confirms a common developmental trajectory between the thymic and blood UTCs and clearly delineates this unconventional lineage in blood. Besides MME+ recent thymic emigrants, effector-like clusters are identified in this heterogeneous lineage. Expression of Helios and KIR and a decreased CD8β expression are characteristics of this lineage. This UTC lineage could be identified in adult blood and intestinal tissues. In summary, our data provide a comprehensive characterization of the polyclonal unconventional lineage in antigen-inexperienced blood and identify the adult progeny.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Guo2023,

title = {RNA helicase DHX15 exemplifies a unique dependency in acute leukemia.},

author = {Hao Guo and Jin Xu and Peiqi Xing and Qilong Li and Donghai Wang and Chao Tang and Bruno Palhais and Juliette Roels and Jiaxu Liu and Sa Pan and Jinyan Huang and Zhaoqi Liu and Ping Zhu and Tom Taghon and Guoliang Qing and Pieter Van Vlierberghe and Hudan Liu},

doi = {10.3324/haematol.2022.282066},

issn = {1592-8721},

year  = {2023},

date = {2023-03-01},

journal = {Haematologica},

abstract = {RNA-binding proteins (RBPs) have emerged as essential regulators to control gene expression and modulate multiple cancer traits. T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy derived from transformation of T-cell progenitors that normally undergo discrete steps of differentiation in the thymus. Yet implications of essential RBPs during T-cell neoplastic transformation remain largely unclear. Systematic evaluation of RBPs identifies RNA helicase DHX15, which facilitates the disassembly of spliceosome and release of lariat introns, as a T-ALL dependency factor. Functional analysis using multiple murine T-ALL models demonstrates the essential importance of DHX15 in tumor cell survival and leukemogenesis. Moreover, single-cell transcriptomics reveals that DHX15 depletion in T-cell progenitors hinders burst proliferation during CD4-CD8-(DN)-to-CD4+CD8+(DP) transition. Mechanistically, abrogation of DHX15 perturbs RNA splicing and leads to diminished levels of SLC7A6 and SLC38A5 transcripts due to intron retention, thereby suppressing glutamine import and mTORC1 activity. We further propose a DHX15 signature modulator drug ciclopirox and demonstrate prominent anti-T-ALL efficacy. Collectively, we here highlight the functional contribution of DHX15 to leukemogenesis through regulation of established oncogenic pathways. These findings also suggest a promising therapeutic approach that splicing perturbation by targeting spliceosome disassembly may achieve considerable anti-tumor efficacy.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Provez2023,

title = {Pre-Clinical Evaluation of the Hypomethylating Agent Decitabine for the Treatment of T-Cell Lymphoblastic Lymphoma.},

author = {Lien Provez and Tom Putteman and Mattias Landfors and Juliette Roels and Lindy Reunes and Sara T'Sas and Wouter Van Loocke and Béatrice Lintermans and Stien De Coninck and Morgan Thenoz and Wouter Sleeckx and Natalia Maćkowska-Maślak and Tom Taghon and Marc R Mansour and Nadine Farah and Koen Norga and Peter Vandenberghe and Rishi S Kotecha and Steven Goossens and Sofie Degerman and Renate De Smedt and Pieter Van Vlierberghe},

doi = {10.3390/cancers15030647},

issn = {2072-6694},

year  = {2023},

date = {2023-01-01},

journal = {Cancers},

volume = {15},

abstract = {T-cell lymphoblastic lymphoma (T-LBL) is a rare and aggressive lymphatic cancer, often diagnosed at a young age. Patients are treated with intensive chemotherapy, potentially followed by a hematopoietic stem cell transplantation. Although prognosis of T-LBL has improved with intensified treatment protocols, they are associated with side effects and 10-20% of patients still die from relapsed or refractory disease. Given this, the search toward less toxic anti-lymphoma therapies is ongoing. Here, we targeted the recently described DNA hypermethylated profile in T-LBL with the DNA hypomethylating agent decitabine. We evaluated the anti-lymphoma properties and downstream effects of decitabine, using patient derived xenograft (PDX) models. Decitabine treatment resulted in prolonged lymphoma-free survival in all T-LBL PDX models, which was associated with downregulation of the oncogenic MYC pathway. However, some PDX models showed more benefit of decitabine treatment compared to others. In more sensitive models, differentially methylated CpG regions resulted in more differentially expressed genes in open chromatin regions. This resulted in stronger downregulation of cell cycle genes and upregulation of immune response activating transcripts. Finally, we suggest a gene signature for high decitabine sensitivity in T-LBL. Altogether, we here delivered pre-clinical proof of the potential use of decitabine as a new therapeutic agent in T-LBL.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Liang2023,

title = {Intrathymic dendritic cell-biased precursors promote human T cell lineage specification through IRF8-driven transmembrane TNF.},

author = {Kai Ling Liang and Juliette Roels and Marieke Lavaert and Tom Putteman and Lena Boehme and Laurentijn Tilleman and Imke Velghe and Valentina Pegoretti and Inge Van de Walle and Stephanie Sontag and Jolien Vandewalle and Bart Vandekerckhove and Georges Leclercq and Pieter Van Vlierberghe and Claude Libert and Filip Van Nieuwerburgh and Roman Fischer and Roland E Kontermann and Klaus Pfizenmaier and Gina Doody and Martin Zenke and Tom Taghon},

doi = {10.1038/s41590-022-01417-6},

issn = {1529-2916},

year  = {2023},

date = {2023-01-01},

journal = {Nature immunology},

abstract = {The cross-talk between thymocytes and thymic stromal cells is fundamental for T cell development. In humans, intrathymic development of dendritic cells (DCs) is evident but its physiological significance is unknown. Here we showed that DC-biased precursors depended on the expression of the transcription factor IRF8 to express the membrane-bound precursor form of the cytokine TNF (tmTNF) to promote differentiation of thymus seeding hematopoietic progenitors into T-lineage specified precursors through activation of the TNF receptor (TNFR)-2 instead of TNFR1. In vitro recapitulation of TNFR2 signaling by providing low-density tmTNF or a selective TNFR2 agonist enhanced the generation of human T cell precursors. Our study shows that, in addition to mediating thymocyte selection and maturation, DCs function as hematopoietic stromal support for the early stages of human T cell development and provide proof of concept that selective targeting of TNFR2 can enhance the in vitro generation of T cell precursors for clinical application.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}

@article{Lambrechts2023,

title = {In Vitro Model Systems to Study Human T Cell Development.},

author = {Nina Lambrechts and Kai Ling Liang and Imke Velghe and Steven Strubbe and Anne-Catherine Dolens and Tom Taghon},

doi = {10.1007/978-1-0716-2740-2_21},

issn = {1940-6029},

year  = {2023},

date = {2023-01-01},

journal = {Methods in molecular biology (Clifton, N.J.)},

volume = {2580},

pages = {335--354},

abstract = {Not only is human T cell development characterized by unique changes in surface marker expression, but it also requires specific growth factors and conditions to mimic and study T cell development in vitro. In this chapter, we provide an overview of the specific aspects that need attention when performing T cell differentiation cultures with human hematopoietic and T cell progenitors.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{VandeWalle2023,

title = {Identification and Purification of Human T Cell Precursors.},

author = {Inge Van de Walle and Nina Lambrechts and Anaïs Derveeuw and Marieke Lavaert and Juliette Roels and Tom Taghon},

doi = {10.1007/978-1-0716-2740-2_20},

issn = {1940-6029},

year  = {2023},

date = {2023-01-01},

journal = {Methods in molecular biology (Clifton, N.J.)},

volume = {2580},

pages = {315--333},

abstract = {During their development, human T cells undergo similar genomic changes and pass through the same developmental checkpoints as developing thymocytes in the mouse. The difference between both species, however, is that some of these developmental stages are characterized by different phenotypic markers, and as a result, evidence emerges that the molecular regulation of human T cell development subtly differs from the mouse (Taghon et al., Curr Top Microbiol Immunol 360:75-97, 2021; Haddad et al., Immunity 24:217-230, 2006; Hao et al., Blood 111:1318-1326, 2008; Taghon and Rothenberg, Semin Immunopathol 30:383-398, 2008). In this chapter, we describe in detail how the different stages of human T cell development can be characterized and isolated using specific surface markers.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Pille2023,

title = {The Wiskott–Aldrich syndrome protein is required for positive selection during T-cell lineage differentiation},

author = {Melissa Pille and John Avila and Guillem Sanchez Sanchez and Guillem Sanchez Sanchez and Guillem Sanchez Sanchez and Guillem Sanchez Sanchez and Glenn Goetgeluk and Glenn Goetgeluk and Stijn De Munter and Stijn De Munter and Hanne Jansen and Lore Billiet and Karin Weening and Haipeng Xue and Sarah Bonte and Sarah Bonte and Joline Ingels and Joline Ingels and Laurenz De Cock and Laurenz De Cock and Eva Pascal and Eva Pascal and Lucas Deseins and Lucas Deseins and Tessa Kerre and Tessa Kerre and Tom Taghon and Tom Taghon and Georges Leclercq and Georges Leclercq and David Vermijlen and David Vermijlen and David Vermijlen and David Vermijlen and Brian Davis and Bart Vandekerckhove and Bart Vandekerckhove},

url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.1188099/full},

doi = {10.3389/fimmu.2023.1188099},

issn = {1664-3224},

year  = {2023},

date = {2023-01-01},

journal = {Frontiers in Immunology},

volume = {14},

publisher = {Frontiers Media S.A.},

abstract = {The Wiskott–Aldrich syndrome (WAS) is an X-linked primary immune deficiency caused by a mutation in the WAS gene. This leads to altered or absent WAS protein (WASp) expression and function resulting in thrombocytopenia, eczema, recurrent infections, and autoimmunity. In T cells, WASp is required for immune synapse formation. Patients with WAS show reduced numbers of peripheral blood T lymphocytes and an altered T-cell receptor repertoire. In vitro, their peripheral T cells show decreased proliferation and cytokine production upon aCD3/aCD28 stimulation. It is unclear whether these T-cell defects are acquired during peripheral activation or are, in part, generated during thymic development. Here, we assessed the role of WASp during T-cell differentiation using artificial thymic organoid cultures and in the thymus of humanized mice. Although CRISPR/Cas9 WAS knockout hematopoietic stem and progenitor cells (HSPCs) rearranged the T-cell receptor and differentiated to T-cell receptor (TCR)+ CD4+ CD8+ double-positive (DP) cells similar to wild-type HSPCs, a partial defect in the generation of CD8 single-positive (SP) cells was observed, suggesting that WASp is involved in their positive selection. TCR repertoire analysis of the DP and CD8+ SP population, however, showed a polyclonal repertoire with no bias toward autoreactivity. To our knowledge, this is the first study of the role of WASp in human T-cell differentiation and on TCR repertoire generation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DrobnaSledzinska2022,

title = {Multiomics to investigate the mechanisms contributing to repression of PTPRC and SOCS2 in pediatric T-ALL: Focus on miR-363-3p and promoter methylation.},

author = {Monika Drobna-Śledzińska and Natalia Maćkowska-Maślak and Roman Jaksik and Maria Kosmalska and Bronisława Szarzyńska and Monika Lejman and Łukasz Sędek and Tomasz Szczepański and Tom Taghon and Pieter Van Vlierberghe and Michał Witt and Małgorzata Dawidowska},

doi = {10.1002/gcc.23085},

issn = {1098-2264},

year  = {2022},

date = {2022-07-01},

journal = {Genes, chromosomes & cancer},

abstract = {T-cell acute lymphoblastic leukemia (T-ALL) is a heterogeneous and aggressive malignancy arising from T-cell precursors. MiRNAs are implicated in negative regulation of gene expression and when aberrantly expressed contribute to various cancer types, including T-ALL. Previously we demonstrated the oncogenic potential of miR-363-3p overexpression in a subgroup of T-ALL patients. Here, using combined proteomic and transcriptomic approaches, we show that miR-363-3p enhances cell growth of T-ALL in vitro via inhibition of PTPRC and SOCS2, which are implicated in repression of the JAK-STAT pathway. We propose that overexpression of miR-363-3p is a novel mechanism potentially contributing to overactivation of JAK-STAT pathway. Additionally, by combining the transcriptomic and methylation data of T-ALL patients, we show that promoter methylation may also contribute to downregulation of SOCS2 expression and thus potentially to JAK-STAT activation. In conclusion, we highlight aberrant miRNA expression and aberrant promoter methylation as mechanisms, alternative to mutations of JAK-STAT-related genes, which might lead to the upregulation of JAK-dependent signaling in T-ALL.},

keywords = {},

pubstate = {aheadofprint},

tppubtype = {article}

}