Publications

@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}

}

@article{Ingels2022,

title = {Small-scale manufacturing of neoantigen-encoding messenger RNA for early-phase clinical trials.},

author = {Joline Ingels and Laurenz De Cock and Rupert L Mayer and Pam Devreker and Karin Weening and Kelly Heyns and Nele Lootens and Saskia De Smet and Marieke Brusseel and Stijn De Munter and Melissa Pille and Lore Billiet and Glenn Goetgeluk and Sarah Bonte and Hanne Jansen and Sandra Van Lint and Georges Leclercq and Tom Taghon and Björn Menten and Karim Vermaelen and Francis Impens and Bart Vandekerckhove},

doi = {10.1016/j.jcyt.2021.08.005},

issn = {1477-2566},

year  = {2022},

date = {2022-02-01},

journal = {Cytotherapy},

volume = {24},

pages = {213--222},

abstract = {Messenger RNA (mRNA) has become a promising tool in therapeutic cancer vaccine strategies. Owing to its flexible design and rapid production, mRNA is an attractive antigen delivery format for cancer vaccines targeting mutated peptides expressed in a tumor-the so-called neoantigens. These neoantigens are rarely shared between patients, and inclusion of these antigens in a vaccine requires the production of individual batches of patient-tailored mRNA. The authors have developed MIDRIX , a personalized mRNA-loaded dendritic cell vaccine targeting tumor neoantigens, which is currently being evaluated in a phase 1 clinical study in lung cancer patients. To facilitate this study, the authors set up a Good Manufacturing Practice (GMP)-compliant production process for the manufacture of small batches of personalized neoantigen-encoding mRNA. In this article, the authors describe the complete mRNA production process and the extensive quality assessment to which the mRNA is subjected. Validation runs have shown that the process delivers mRNA of reproducible, high quality. This process is now successfully applied for the production of neoantigen-encoding mRNA for the clinical evaluation of MIDRIX . To the authors' knowledge, this is the first time that a GMP-based production process of patient-tailored neoantigen mRNA has been described.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Kiekens2022,

title = {T-BET drives the conversion of human type 3 innate lymphoid cells into functional NK cells.},

author = {Laura Kiekens and Sigrid Wahlen and Eva Persyn and Zenzi De Vos and Tom Taghon and Bart Vandekerckhove and Georges Leclercq},

doi = {10.3389/fimmu.2022.975778},

issn = {1664-3224},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in immunology},

volume = {13},

pages = {975778},

abstract = {Type 3 innate lymphoid cells (ILC3s) are characterized by RORγt expression and they produce IL-22 upon activation. ILC3s play a role in maintenance of barrier integrity in the intestine. Under inflammatory conditions, the ILC composition of the mucosal tissues is altered due to a high degree of plasticity. It has been extensively demonstrated that both murine and human ILC3s convert into ILC1s to mediate appropriate immune responses. However, plasticity between human ILC3s and NK cells is less well documented. As T-BET and EOMES are key transcription factors in NK cell differentiation, we investigated whether ectopic T-BET or EOMES expression converts human ILC3s into NK cells. ILC3s with ectopic T-BET and EOMES expression downregulate RORγt expression, while T-BET-overexpressing ILC3s additionally upregulate EOMES expression. High E ctopic T-BET expression in ILC3s results in transdifferentiation towards CD94 NK cells, whereas ectopic EOMES overexpression results in dedifferentiation of ILC3s into CD94-CD117 cells but is ineffective in NK cell generation. Dedifferentiating ILC3s from both T-BET and EOMES overexpression cultures upregulate NK cell receptors, perforin and granzyme B. Finally, IL-22 secretion is completely blocked in transdifferentiating ILC3s with both T-BET and EOMES ectopic expression, whereas only T-BET overexpression increases IFN-γ secretion and cytotoxicity. Altogether, these findings demonstrate that human ILC3s can convert into functional NK cells, wherein T-BET, and not EOMES, is the main driver.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Roels2022,

title = {Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development.},

author = {Juliette Roels and Jolien Van Hulle and Marieke Lavaert and Anna Kuchmiy and Steven Strubbe and Tom Putteman and Bart Vandekerckhove and Georges Leclercq and Filip Van Nieuwerburgh and Lena Boehme and Tom Taghon},

doi = {10.3389/fimmu.2022.960918},

issn = {1664-3224},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in immunology},

volume = {13},

pages = {960918},

abstract = {T cells are generated from hematopoietic stem cells through a highly organized developmental process, in which stage-specific molecular events drive maturation towards αβ and γδ T cells. Although many of the mechanisms that control αβ- and γδ-lineage differentiation are shared between human and mouse, important differences have also been observed. Here, we studied the regulatory dynamics of the E and ID protein encoding genes during pediatric human T cell development by evaluating changes in chromatin accessibility, histone modifications and bulk and single cell gene expression. We profiled patterns of ID/E protein activity and identified up- and downstream regulators and targets, respectively. In addition, we compared transcription of E and ID protein encoding genes in human versus mouse to predict both shared and unique activities in these species, and in prenatal versus pediatric human T cell differentiation to identify regulatory changes during development. This analysis showed a putative involvement of TCF3/E2A in the development of γδ T cells. In contrast, in αβ T cell precursors a pivotal pre-TCR-driven population with high ID gene expression and low predicted E protein activity was identified. Finally, in prenatal but not postnatal thymocytes, high HEB/TCF12 levels were found to counteract high ID levels to sustain thymic development. In summary, we uncovered novel insights in the regulation of E and ID proteins on a cross-species and cross-developmental level.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Persyn2022,

title = {TXNIP Promotes Human NK Cell Development but Is Dispensable for NK Cell Functionality.},

author = {Eva Persyn and Sigrid Wahlen and Laura Kiekens and Sylvie Taveirne and Wouter Van Loocke and Els Van Ammel and Filip Van Nieuwerburgh and Tom Taghon and Bart Vandekerckhove and Pieter Van Vlierberghe and Georges Leclercq},

doi = {10.3390/ijms231911345},

issn = {1422-0067},

year  = {2022},

date = {2022-01-01},

journal = {International journal of molecular sciences},

volume = {23},

abstract = {The ability of natural killer (NK) cells to kill tumor cells without prior sensitization makes them a rising player in immunotherapy. Increased understanding of the development and functioning of NK cells will improve their clinical utilization. As opposed to murine NK cell development, human NK cell development is still less understood. Here, we studied the role of thioredoxin-interacting protein (TXNIP) in human NK cell differentiation by stable TXNIP knockdown or overexpression in cord blood hematopoietic stem cells, followed by in vitro NK cell differentiation. TXNIP overexpression only had marginal effects, indicating that endogenous TXNIP levels are sufficient in this process. TXNIP knockdown, however, reduced proliferation of early differentiation stages and greatly decreased NK cell numbers. Transcriptome analysis and experimental confirmation showed that reduced protein synthesis upon TXNIP knockdown likely caused this low proliferation. Contrary to its profound effects on the early differentiation stages, TXNIP knockdown led to limited alterations in NK cell phenotype, and it had no effect on NK cell cytotoxicity or cytokine production. Thus, TXNIP promotes human NK cell differentiation by affecting protein synthesis and proliferation of early NK cell differentiation stages, but it is redundant for functional NK cell maturation.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Boehme2022,

title = {Development of γδ T cells in the thymus – A human perspective},

author = {Lena Boehme and Juliette Roels and Tom Taghon},

doi = {10.1016/j.smim.2022.101662},

issn = {1044-5323},

year  = {2022},

date = {2022-01-01},

volume = {61-64},

pages = {101662},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Persyn2022b,

title = {IRF2 is required for development and functional maturation of human NK cells.},

author = {Eva Persyn and Sigrid Wahlen and Laura Kiekens and Wouter Van Loocke and Hannah Siwe and Els Van Ammel and Zenzi De Vos and Filip Van Nieuwerburgh and Patrick Matthys and Tom Taghon and Bart Vandekerckhove and Pieter Van Vlierberghe and Georges Leclercq},

doi = {10.3389/fimmu.2022.1038821},

issn = {1664-3224},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in immunology},

volume = {13},

pages = {1038821},

abstract = {Natural killer (NK) cells are cytotoxic and cytokine-producing lymphocytes that play an important role in the first line of defense against malignant or virus-infected cells. A better understanding of the transcriptional regulation of human NK cell differentiation is crucial to improve the efficacy of NK cell-mediated immunotherapy for cancer treatment. Here, we studied the role of the transcription factor interferon regulatory factor (IRF) 2 in human NK cell differentiation by stable knockdown or overexpression in cord blood hematopoietic stem cells and investigated its effect on development and function of the NK cell progeny. IRF2 overexpression had limited effects in these processes, indicating that endogenous IRF2 expression levels are sufficient. However, IRF2 knockdown greatly reduced the cell numbers of all early differentiation stages, resulting in decimated NK cell numbers. This was not caused by increased apoptosis, but by decreased proliferation. Expression of IRF2 is also required for functional maturation of NK cells, as the remaining NK cells after silencing of IRF2 had a less mature phenotype and showed decreased cytotoxic potential, as well as a greatly reduced cytokine secretion. Thus, IRF2 plays an important role during development and functional maturation of human NK cells.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Wahlen2022,

title = {The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency.},

author = {Sigrid Wahlen and Filip Matthijssens and Wouter Van Loocke and Sylvie Taveirne and Laura Kiekens and Eva Persyn and Els Van Ammel and Zenzi De Vos and Stijn De Munter and Patrick Matthys and Filip Van Nieuwerburgh and Tom Taghon and Bart Vandekerckhove and Pieter Van Vlierberghe and Georges Leclercq},

doi = {10.7554/eLife.80320},

issn = {2050-084X},

year  = {2022},

date = {2022-01-01},

journal = {eLife},

volume = {11},

abstract = {Natural killer (NK) cells are innate lymphocytes that eliminate virus-infected and cancer cells by cytotoxicity and cytokine secretion. In addition to circulating NK cells, distinct tissue-resident NK subsets have been identified in various organs. Although transcription factors regulating NK cell development and function have been extensively studied in mice, the role of RUNX2 in these processes has not been investigated, neither in mice nor in human. Here, by manipulating RUNX2 expression with either knockdown or overexpression in human haematopoietic stem cell-based NK cell differentiation cultures, combined with transcriptomic and ChIP-sequencing analyses, we established that RUNX2 drives the generation of NK cells, possibly through induction of IL-2Rβ expression in NK progenitor cells. Importantly, RUNX2 promotes tissue residency in human NK cells. Our findings have the potential to improve existing NK cell-based cancer therapies and can impact research fields beyond NK cell biology, since tissue-resident subsets have also been described in other lymphocyte subpopulations.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Lorenzi2021a,

title = {The RNA Atlas expands the catalog of human non-coding RNAs.},

author = {Lucia Lorenzi and Hua-Sheng Chiu and Francisco Avila Cobos and Stephen Gross and Pieter-Jan Volders and Robrecht Cannoodt and Justine Nuytens and Katrien Vanderheyden and Jasper Anckaert and Steve Lefever and Aidan P Tay and Eric J de Bony and Wim Trypsteen and Fien Gysens and Marieke Vromman and Tine Goovaerts and Thomas Birkballe Hansen and Scott Kuersten and Nele Nijs and Tom Taghon and Karim Vermaelen and Ken R Bracke and Yvan Saeys and Tim De Meyer and Nandan P Deshpande and Govardhan Anande and Ting-Wen Chen and Marc R Wilkins and Ashwin Unnikrishnan and Katleen De Preter and Jørgen Kjems and Jan Koster and Gary P Schroth and Jo Vandesompele and Pavel Sumazin and Pieter Mestdagh},

doi = {10.1038/s41587-021-00936-1},

issn = {1546-1696},

year  = {2021},

date = {2021-11-01},

journal = {Nature biotechnology},

volume = {39},

pages = {1453--1465},

abstract = {Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are derived almost exclusively from small and polyadenylated RNAs. Here we present a more comprehensive atlas of the human transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues and cell lines. We report thousands of previously uncharacterized RNAs, increasing the number of documented ncRNAs by approximately 8%. To infer functional regulation by known and newly characterized ncRNAs, we exploited pre-mRNA abundance estimates from total RNA sequencing, revealing 316 microRNAs and 3,310 long non-coding RNAs with multiple lines of evidence for roles in regulating protein-coding genes and pathways. Our study both refines and expands the current catalog of human ncRNAs and their regulatory interactions. All data, analyses and results are available for download and interrogation in the R2 web portal, serving as a basis for future exploration of RNA biology and function.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Strubbe2021,

title = {Modeling of human T cell development in vitro as a read-out for hematopoietic stem cell multipotency.},

author = {Steven Strubbe and Tom Taghon},

doi = {10.1042/BST20210144},

issn = {1470-8752},

year  = {2021},

date = {2021-11-01},

journal = {Biochemical Society transactions},

volume = {49},

pages = {2113--2122},

abstract = {Hematopoietic stem cells (HSCs) reside in distinct sites throughout fetal and adult life and give rise to all cells of the hematopoietic system. Because of their multipotency, HSCs are capable of curing a wide variety of blood disorders through hematopoietic stem cell transplantation (HSCT). However, due to HSC heterogeneity, site-specific ontogeny and current limitations in generating and expanding HSCs in vitro, their broad use in clinical practice remains challenging. To assess HSC multipotency, evaluation of their capacity to generate T lymphocytes has been regarded as a valid read-out. Several in vitro models of T cell development have been established which are able to induce T-lineage differentiation from different hematopoietic precursors, although with variable efficiency. Here, we review the potential of human HSCs from various sources to generate T-lineage cells using these different models in order to address the use of both HSCs and T cell precursors in the clinic.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Moirangthem2021,

title = {A DL-4- and TNFα-based culture system to generate high numbers of nonmodified or genetically modified immunotherapeutic human T-lymphoid progenitors.},

author = {Ranjita Devi Moirangthem and Kuiying Ma and Sabrina Lizot and Anne Cordesse and Juliette Olivré and Corinne de Chappedelaine and Akshay Joshi and Agata Cieslak and John Tchen and Nicolas Cagnard and Vahid Asnafi and Antonio Rausell and Laura Simons and Julien Zuber and Tom Taghon and Frank J T Staal and Françoise Pflumio and Emmanuelle Six and Marina Cavazzana and Chantal Lagresle-Peyrou and Tayebeh Soheili and Isabelle André},

doi = {10.1038/s41423-021-00706-8},

issn = {2042-0226},

year  = {2021},

date = {2021-07-01},

journal = {Cellular & molecular immunology},

volume = {18},

pages = {1662--1676},

abstract = {Several obstacles to the production, expansion and genetic modification of immunotherapeutic T cells in vitro have restricted the widespread use of T-cell immunotherapy. In the context of HSCT, delayed naïve T-cell recovery contributes to poor outcomes. A novel approach to overcome the major limitations of both T-cell immunotherapy and HSCT would be to transplant human T-lymphoid progenitors (HTLPs), allowing reconstitution of a fully functional naïve T-cell pool in the patient thymus. However, it is challenging to produce HTLPs in the high numbers required to meet clinical needs. Here, we found that adding tumor necrosis factor alpha (TNFα) to a DL-4-based culture system led to the generation of a large number of nonmodified or genetically modified HTLPs possessing highly efficient in vitro and in vivo T-cell potential from either CB HSPCs or mPB HSPCs through accelerated T-cell differentiation and enhanced HTLP cell cycling and survival. This study provides a clinically suitable cell culture platform to generate high numbers of clinically potent nonmodified or genetically modified HTLPs for accelerating immune recovery after HSCT and for T-cell-based immunotherapy (including CAR T-cell therapy).},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Kiekens2021,

title = {T-BET and EOMES Accelerate and Enhance Functional Differentiation of Human Natural Killer Cells.},

author = {Laura Kiekens and Wouter Van Loocke and Sylvie Taveirne and Sigrid Wahlen and Eva Persyn and Els Van Ammel and Zenzi De Vos and Patrick Matthys and Filip Van Nieuwerburgh and Tom Taghon and Pieter Van Vlierberghe and Bart Vandekerckhove and Georges Leclercq},

doi = {10.3389/fimmu.2021.732511},

issn = {1664-3224},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in immunology},

volume = {12},

pages = {732511},

abstract = {T-bet and Eomes are transcription factors that are known to be important in maturation and function of murine natural killer (NK) cells. Reduced T-BET and EOMES expression results in dysfunctional NK cells and failure to control tumor growth. In contrast to mice, the current knowledge on the role of T-BET and EOMES in human NK cells is rudimentary. Here, we ectopically expressed either T-BET or EOMES in human hematopoietic progenitor cells. Combined transcriptome, chromatin accessibility and protein expression analyses revealed that T-BET or EOMES epigenetically represses hematopoietic stem cell quiescence and non-NK lineage differentiation genes, while activating an NK cell-specific transcriptome and thereby drastically accelerating NK cell differentiation. In this model, the effects of T-BET and EOMES are largely overlapping, yet EOMES shows a superior role in early NK cell maturation and induces faster NK receptor and enhanced CD16 expression. T-BET particularly controls transcription of terminal maturation markers and epigenetically controls strong induction of KIR expression. Finally, NK cells generated upon T-BET or EOMES overexpression display improved functionality, including increased IFN-γ production and killing, and especially EOMES overexpression NK cells have enhanced antibody-dependent cellular cytotoxicity. Our findings reveal novel insights on the regulatory role of T-BET and EOMES in human NK cell maturation and function, which is essential to further understand human NK cell biology and to optimize adoptive NK cell therapies.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Ingels2021,

title = {Treatment of a patient with severe cytomegalovirus (CMV) infection after haploidentical stem cell transplantation with donor derived CMV specific T cells.},

author = {Joline Ingels and Saskia De Smet and Kelly Heyns and Nele Lootens and Jonas Segaert and Tom Taghon and Georges Leclercq and Karim Vermaelen and Evelyne Willems and Etienne Baudoux and Tessa Kerre and Frédéric Baron and Bart Vandekerckhove},

doi = {10.1080/17843286.2020.1752446},

issn = {2295-3337},

year  = {2021},

date = {2021-01-01},

journal = {Acta clinica Belgica},

volume = {76},

pages = {482--486},

abstract = {Cytomegalovirus (CMV) infection is one of the most common complications in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients. The classic antiviral treatments have shown clinical efficacy but are often associated with drug resistance. Reconstitution of CMV-specific cellular immunity is essential in controlling CMV infection; therefore, adoptive transfer of CMV-specific T cells is a promising treatment option. We treated a patient with a multidrug resistant CMV infection after haploidentical HSCT with CMV-specific T cells. The T cells were derived from the HSCT donor who was CMV seropositive. We generated the T cells by a short-term Good Manufacturing Practice (GMP) grade protocol in which a leukapheresis product of the HSCT donor was stimulated with the immunodominant antigen pp65 and interferon-γ secreting cells were isolated. A total of 5 × 10  T cells were administered to the patient within 30 hours after leukapheresis. The patient was closely monitored for reconstitution of antiviral T cell immunity and viral replication after adoptive T cell transfer. We observed an in vivo expansion of both CD4 and CD8 CMV-specific T cells associated with a significant decrease in viral burden and clinical improvement. This case report further supports the feasibility and effectiveness of adoptive donor T cell transfer for the treatment of drug resistant CMV infections after allo-HSCT.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Lorenzi2021,

title = {Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs.},

author = {Lucia Lorenzi and Hua-Sheng Chiu and Francisco Avila Cobos and Stephen Gross and Pieter-Jan Volders and Robrecht Cannoodt and Justine Nuytens and Katrien Vanderheyden and Jasper Anckaert and Steve Lefever and Aidan P Tay and Eric J de Bony and Wim Trypsteen and Fien Gysens and Marieke Vromman and Tine Goovaerts and Thomas Birkballe Hansen and Scott Kuersten and Nele Nijs and Tom Taghon and Karim Vermaelen and Ken R Bracke and Yvan Saeys and Tim De Meyer and Nandan P Deshpande and Govardhan Anande and Ting-Wen Chen and Marc R Wilkins and Ashwin Unnikrishnan and Katleen De Preter and Jørgen Kjems and Jan Koster and Gary P Schroth and Jo Vandesompele and Pavel Sumazin and Pieter Mestdagh},

doi = {10.1038/s41587-021-00996-3},

issn = {1546-1696},

year  = {2021},

date = {2021-01-01},

journal = {Nature biotechnology},

volume = {39},

pages = {1467},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}

@article{Ferrua2021,

title = {Thymic Epithelial Cell Alterations and Defective Thymopoiesis Lead to Central and Peripheral Tolerance Perturbation in MHCII Deficiency.},

author = {Francesca Ferrua and Ileana Bortolomai and Elena Fontana and Dario Di Silvestre and Rosita Rigoni and Genni Enza Marcovecchio and Elena Draghici and Francesca Brambilla and Maria Carmina Castiello and Gloria Delfanti and Despina Moshous and Capucine Picard and Tom Taghon and Victoria Bordon and Ansgar S Schulz and Catharina Schuetz and Silvia Giliani and Annarosa Soresina and Andrew R Gennery and Sara Signa and Blachy J Dávila Saldaña and Ottavia M Delmonte and Luigi D Notarangelo and Chaim M Roifman and Pietro Luigi Poliani and Paolo Uva and Pier Luigi Mauri and Anna Villa and Marita Bosticardo},

doi = {10.3389/fimmu.2021.669943},

issn = {1664-3224},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in immunology},

volume = {12},

pages = {669943},

abstract = {Major Histocompatibility Complex (MHC) class II (MHCII) deficiency (MHCII-D), also known as Bare Lymphocyte Syndrome (BLS), is a rare combined immunodeficiency due to mutations in genes regulating expression of MHCII molecules. MHCII deficiency results in impaired cellular and humoral immune responses, leading to severe infections and autoimmunity. Abnormal cross-talk with developing T cells due to the absence of MHCII expression likely leads to defects in thymic epithelial cells (TEC). However, the contribution of TEC alterations to the pathogenesis of this primary immunodeficiency has not been well characterized to date, in particular in regard to immune dysregulation. To this aim, we have performed an in-depth cellular and molecular characterization of TEC in this disease. We observed an overall perturbation of thymic structure and function in both MHCII mice and patients. Transcriptomic and proteomic profiling of murine TEC revealed several alterations. In particular, we demonstrated that impairment of lymphostromal cross-talk in the thymus of MHCII mice affects mTEC maturation and promiscuous gene expression and causes defects of central tolerance. Furthermore, we observed peripheral tolerance impairment, likely due to defective Treg cell generation and/or function and B cell tolerance breakdown. Overall, our findings reveal disease-specific TEC defects resulting in perturbation of central tolerance and limiting the potential benefits of hematopoietic stem cell transplantation in MHCII deficiency.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{DeDecker2021,

title = {HES1 and HES4 have non-redundant roles downstream of Notch during early human T-cell development.},

author = {Matthias De Decker and Marieke Lavaert and Juliette Roels and Laurentijn Tilleman and Bart Vandekerckhove and Georges Leclercq and Filip Van Nieuwerburgh and Pieter Van Vlierberghe and Tom Taghon},

doi = {10.3324/haematol.2019.226126},

issn = {1592-8721},

year  = {2021},

date = {2021-01-01},

journal = {Haematologica},

volume = {106},

pages = {130--141},

abstract = {In both mouse and human, Notch1 activation is the main initial driver to induce T-cell development in hematopoietic progenitor cells. The initiation of this developmental process coincides with Notch1-dependent repression of differentiation towards other hematopoietic lineages. Although well described in mice, the role of the individual Notch1 target genes during these hematopoietic developmental choices is still unclear in human, particularly for HES4 since no orthologous gene is present in the mouse. Here, we investigated the functional capacity of the Notch1 target genes HES1 and HES4 to modulate human Notch1-dependent hematopoietic lineage decisions and their requirement during early T-cell development. We show that both genes are upregulated in a Notch-dependent manner during early T-cell development and that HES1 acts as a repressor of differentiation by maintaining a quiescent stem cell signature in CD34+ hematopoietic progenitor cells. While HES4 can also inhibit natural killer and myeloid cell development like HES1, it acts differently on the T- versus B-cell lineage choice. Surprisingly, HES4 is not capable of repressing B-cell development, the most sensitive hematopoietic lineage with respect to Notch-mediated repression. In contrast to HES1, HES4 promotes initiation of early T-cell development, but ectopic expression of HES4, or HES1 and HES4 combined, is not sufficient to induce T-lineage differentiation. Importantly, knockdown of HES1 or HES4 significantly reduces human T-cell development. Overall, we show that the Notch1 target genes HES1 and HES4 have non-redundant roles during early human T-cell development which may relate to differences in mediating Notch-dependent human hematopoietic lineage decisions.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Bonte2021,

title = {In vitro OP9-DL1 co-culture and subsequent maturation in the presence of IL-21 generates tumor antigen-specific T cells with a favorable less-differentiated phenotype and enhanced functionality.},

author = {Sarah Bonte and Stijn de Munter and Lore Billiet and Glenn Goetgeluk and Joline Ingels and Hanne Jansen and Melissa Pille and Laurenz de Cock and Karin Weening and Tom Taghon and Georges Leclercq and Bart Vandekerckhove and Tessa Kerre},

doi = {10.1080/2162402X.2021.1954800},

issn = {2162-402X},

year  = {2021},

date = {2021-01-01},

journal = {Oncoimmunology},

volume = {10},

pages = {1954800},

abstract = {T cell receptor (TCR)-redirected T cells target intracellular antigens such as Wilms' tumor 1 (WT1), a tumor-associated antigen overexpressed in several malignancies, including acute myeloid leukemia (AML). For both chimeric antigen receptor (CAR)- and TCR-redirected T cells, several clinical studies indicate that T cell subsets with a less-differentiated phenotype (e.g. stem cell memory T cells, T ) survive longer and mediate superior anti-tumor effects as opposed to more terminally differentiated T cells. Cytokines added during and culture of T cells play an important role in driving the phenotype of T cells for adoptive transfer. Using the OP9-DL1 co-culture system, we have shown previously that we are able to generate , starting from clinically relevant stem cell sources, T cells with a single tumor antigen (TA)-specific TCR. This method circumvents possible TCR chain mispairing and unwanted toxicities that might occur when introducing a TA-specific TCR in peripheral blood lymphocytes. We now show that we are able to optimize our culture protocol, by adding IL-21 during maturation, resulting in generation of TA-specific T cells with a less-differentiated phenotype and enhanced anti-tumor effects. We believe the favorable T -like phenotype of these generated T cells preludes superior persistence and anti-tumor efficacy. Therefore, these TA-specific T cells could be of use as a valuable new form of patient-tailored T cell immunotherapy for malignancies for which finding a suitable CAR-T target antigen is challenging, such as AML.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tottone2021,

title = {A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia.},

author = {Luca Tottone and Olga Lancho and Jui-Wan Loh and Amartya Singh and Shunsuke Kimura and Juliette Roels and Anna Kuchmiy and Steven Strubbe and Matthew A Lawlor and Victoria da Silva-Diz and Shirley Luo and Stéphanie Gachet and Carlos A García-Prieto and Rico Hagelaar and Manel Esteller and Jules P P Meijerink and Jean Soulier and Tom Taghon and Pieter Van Vlierberghe and Charles G Mullighan and Hossein Khiabanian and Pedro P Rocha and Daniel Herranz},

doi = {10.1158/2643-3230.BCD-20-0201},

issn = {2643-3249},

year  = {2021},

date = {2021-01-01},

journal = {Blood cancer discovery},

volume = {2},

pages = {92--109},

abstract = {Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the promoter in multiple hematopoietic populations, including T-cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced levels in T-ALL cells. Moreover, PE-null mice show reduced levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Strubbe2021a,

title = {A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair.},

author = {Steven Strubbe and Marieke De Bruyne and Ulrich Pannicke and Elien Beyls and Bart Vandekerckhove and Georges Leclercq and Elfride De Baere and Victoria Bordon and Anne Vral and Klaus Schwarz and Filomeen Haerynck and Tom Taghon},

doi = {10.3389/fimmu.2021.674226},

issn = {1664-3224},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in immunology},

volume = {12},

pages = {674226},

abstract = {Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the gene in a T B NK SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.},

keywords = {},

pubstate = {epublish},

tppubtype = {article}

}

@article{Buratin2020,

title = {Large-scale circular RNA deregulation in T-ALL: unlocking unique ectopic expression of molecular subtypes.},

author = {Alessia Buratin and Maddalena Paganin and Enrico Gaffo and Anna Dal Molin and Juliette Roels and Giuseppe Germano and Maria Teresa Siddi and Valentina Serafin and Matthias De Decker and Stéphanie Gachet and Kaat Durinck and Frank Speleman and Tom Taghon and Geertruij Te Kronnie and Pieter Van Vlierberghe and Stefania Bortoluzzi},

doi = {10.1182/bloodadvances.2020002337},

issn = {2473-9537},

year  = {2020},

date = {2020-12-01},

journal = {Blood advances},

volume = {4},

pages = {5902--5914},

abstract = {Circular RNAs (circRNAs) are stable RNA molecules that can drive cancer through interactions with microRNAs and proteins and by the expression of circRNA encoded peptides. The aim of the study was to define the circRNA landscape and potential impact in T-cell acute lymphoblastic leukemia (T-ALL). Analysis by CirComPara of RNA-sequencing data from 25 T-ALL patients, immature, HOXA overexpressing, TLX1, TLX3, TAL1, or LMO2 rearranged, and from thymocyte populations of human healthy donors disclosed 68 554 circRNAs. Study of the top 3447 highly expressed circRNAs identified 944 circRNAs with significant differential expression between malignant T cells and normal counterparts, with most circRNAs displaying increased expression in T-ALL. Next, we defined subtype-specific circRNA signatures in molecular genetic subgroups of human T-ALL. In particular, circZNF609, circPSEN1, circKPNA5, and circCEP70 were upregulated in immature, circTASP1, circZBTB44, and circBACH1 in TLX3, circHACD1, and circSTAM in HOXA, circCAMSAP1 in TLX1, and circCASC15 in TAL-LMO. Backsplice sequences of 14 circRNAs ectopically expressed in T-ALL were confirmed, and overexpression of circRNAs in T-ALL with specific oncogenic lesions was substantiated by quantification in a panel of 13 human cell lines. An oncogenic role of circZNF609 in T-ALL was indicated by decreased cell viability upon silencing in vitro. Furthermore, functional predictions identified circRNA-microRNA gene axes informing modes of circRNA impact in molecular subtypes of human T-ALL.},

keywords = {},

pubstate = {ppublish},

tppubtype = {article}

}