Publications
2021 |
Tottone, Luca; Lancho, Olga; Loh, Jui-Wan; Singh, Amartya; Kimura, Shunsuke; Roels, Juliette; Kuchmiy, Anna; Strubbe, Steven; Lawlor, Matthew A; da Silva-Diz, Victoria; Luo, Shirley; Gachet, Stéphanie; García-Prieto, Carlos A; Hagelaar, Rico; Esteller, Manel; Meijerink, Jules P P; Soulier, Jean; Taghon, Tom; Vlierberghe, Pieter Van; Mullighan, Charles G; Khiabanian, Hossein; Rocha, Pedro P; Herranz, Daniel A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Journal Article Blood cancer discovery, 2 , pp. 92–109, 2021, ISSN: 2643-3249. @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} } 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. |
2020 |
Buratin, Alessia; Paganin, Maddalena; Gaffo, Enrico; Molin, Anna Dal; Roels, Juliette; Germano, Giuseppe; Siddi, Maria Teresa; Serafin, Valentina; Decker, Matthias De; Gachet, Stéphanie; Durinck, Kaat; Speleman, Frank; Taghon, Tom; Kronnie, Geertruij Te; Vlierberghe, Pieter Van; Bortoluzzi, Stefania Large-scale circular RNA deregulation in T-ALL: unlocking unique ectopic expression of molecular subtypes. Journal Article Blood advances, 4 , pp. 5902–5914, 2020, ISSN: 2473-9537. @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} } 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. |
Billiet, Lore; Goetgeluk, Glenn; Bonte, Sarah; Munter, Stijn De; Cock, Laurenz De; Pille, Melissa; Ingels, Joline; Jansen, Hanne; Weening, Karin; Nieuwerburgh, Filip Van; Kerre, Tessa; Taghon, Tom; Leclercq, Georges; Vandekerckhove, Bart International journal of molecular sciences, 21 , 2020, ISSN: 1422-0067. @article{Billiet2020, title = {Human Thymic CD10+ PD-1+ Intraepithelial Lymphocyte Precursors Acquire Interleukin-15 Responsiveness at the CD1a– CD95+ CD28– CCR7– Developmental Stage}, author = {Lore Billiet and Glenn Goetgeluk and Sarah Bonte and Stijn De Munter and Laurenz De Cock and Melissa Pille and Joline Ingels and Hanne Jansen and Karin Weening and Filip Van Nieuwerburgh and Tessa Kerre and Tom Taghon and Georges Leclercq and Bart Vandekerckhove}, doi = {10.3390/ijms21228785}, issn = {1422-0067}, year = {2020}, date = {2020-11-01}, journal = {International journal of molecular sciences}, volume = {21}, abstract = {Human thymic CD8αα CD10 PD-1 αβ T cells selected through early agonist selection have been proposed as the putative thymic precursors of the human CD8αα intestinal intraepithelial lymphocytes (IELs). However, the progeny of these thymic precursor cells in human blood or tissues has not yet been characterized. Here, we studied the phenotypical and transcriptional differentiation of the thymic IEL precursor (IELp) lineage upon in vitro exposure to cytokines prominent in the peripheral tissues such as interleukin-15 (IL-15) and the inflammatory cytokines interleukin-12 (IL-12) and interleukin-18 (IL-18). We showed that only the CD1a fraction of the CD10 PD-1 IELp population was able to proliferate with IL-15, suggesting that this subset had acquired functionality. These cells downregulated PD-1 expression and completely lost CD10 expression, whereas other surface markers such as CD95 and CXCR3 remained highly expressed. RNA-seq analysis of the IL-15-cultured cells clearly showed induction of innate-like and effector genes. Induction of the cytotoxic machinery by the CD10 PD-1 population was acquired in the presence of IL-15 and was further augmented by inflammatory cytokines. Our data suggest that only the CD1a CD10 PD-1 population exits the thymus and survives in the periphery. Furthermore, PD-1 and CD10 expression is not an intrinsic property of this lineage, but rather characterizes a transient stage in differentiation. CD95 and CXCR3 expression combined with the absence of CD28, CCR7, and CD6 expression might be more powerful markers to define this lineage in the periphery.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human thymic CD8αα CD10 PD-1 αβ T cells selected through early agonist selection have been proposed as the putative thymic precursors of the human CD8αα intestinal intraepithelial lymphocytes (IELs). However, the progeny of these thymic precursor cells in human blood or tissues has not yet been characterized. Here, we studied the phenotypical and transcriptional differentiation of the thymic IEL precursor (IELp) lineage upon in vitro exposure to cytokines prominent in the peripheral tissues such as interleukin-15 (IL-15) and the inflammatory cytokines interleukin-12 (IL-12) and interleukin-18 (IL-18). We showed that only the CD1a fraction of the CD10 PD-1 IELp population was able to proliferate with IL-15, suggesting that this subset had acquired functionality. These cells downregulated PD-1 expression and completely lost CD10 expression, whereas other surface markers such as CD95 and CXCR3 remained highly expressed. RNA-seq analysis of the IL-15-cultured cells clearly showed induction of innate-like and effector genes. Induction of the cytotoxic machinery by the CD10 PD-1 population was acquired in the presence of IL-15 and was further augmented by inflammatory cytokines. Our data suggest that only the CD1a CD10 PD-1 population exits the thymus and survives in the periphery. Furthermore, PD-1 and CD10 expression is not an intrinsic property of this lineage, but rather characterizes a transient stage in differentiation. CD95 and CXCR3 expression combined with the absence of CD28, CCR7, and CD6 expression might be more powerful markers to define this lineage in the periphery. |
Roels, Juliette; Thénoz, Morgan; Szarzyńska, Bronisława; Landfors, Mattias; Coninck, Stien De; Demoen, Lisa; Provez, Lien; Kuchmiy, Anna; Strubbe, Steven; Reunes, Lindy; Pieters, Tim; Matthijssens, Filip; Loocke, Wouter Van; Erarslan-Uysal, Büşra; Richter-Pechańska, Paulina; Declerck, Ken; Lammens, Tim; Moerloose, Barbara De; Deforce, Dieter; Nieuwerburgh, Filip Van; Cheung, Laurence C; Kotecha, Rishi S; Mansour, Marc R; Ghesquière, Bart; Camp, Guy Van; Berghe, Wim Vanden; Kowalczyk, Jerzy R; Szczepański, Tomasz; Davé, Utpal P; Kulozik, Andreas E; Goossens, Steven; Curtis, David J; Taghon, Tom; Dawidowska, Małgorzata; Degerman, Sofie; Vlierberghe, Pieter Van Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Journal Article Blood cancer discovery, 1 , pp. 274–289, 2020, ISSN: 2643-3249. @article{Roels2020, title = {Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia.}, author = {Juliette Roels and Morgan Thénoz and Bronisława Szarzyńska and Mattias Landfors and Stien De Coninck and Lisa Demoen and Lien Provez and Anna Kuchmiy and Steven Strubbe and Lindy Reunes and Tim Pieters and Filip Matthijssens and Wouter Van Loocke and Büşra Erarslan-Uysal and Paulina Richter-Pechańska and Ken Declerck and Tim Lammens and Barbara De Moerloose and Dieter Deforce and Filip Van Nieuwerburgh and Laurence C Cheung and Rishi S Kotecha and Marc R Mansour and Bart Ghesquière and Guy Van Camp and Wim Vanden Berghe and Jerzy R Kowalczyk and Tomasz Szczepański and Utpal P Davé and Andreas E Kulozik and Steven Goossens and David J Curtis and Tom Taghon and Małgorzata Dawidowska and Sofie Degerman and Pieter Van Vlierberghe}, doi = {10.1158/2643-3230.BCD-20-0059}, issn = {2643-3249}, year = {2020}, date = {2020-11-01}, journal = {Blood cancer discovery}, volume = {1}, pages = {274--289}, abstract = {Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL. |
Taveirne, Sylvie; Wahlen, Sigrid; Loocke, Wouter Van; Kiekens, Laura; Persyn, Eva; Ammel, Els Van; Mulder, Katrien De; Roels, Juliette; Tilleman, Laurentijn; Aumercier, Marc; Matthys, Patrick; Nieuwerburgh, Filip Van; Kerre, Tessa C C; Taghon, Tom; Vlierberghe, Pieter Van; Vandekerckhove, Bart; Leclercq, Georges The transcription factor ETS1 is an important regulator of human NK cell development and terminal differentiation. Journal Article Blood, 136 , pp. 288–298, 2020, ISSN: 1528-0020. @article{Taveirne2020, title = {The transcription factor ETS1 is an important regulator of human NK cell development and terminal differentiation.}, author = {Sylvie Taveirne and Sigrid Wahlen and Wouter Van Loocke and Laura Kiekens and Eva Persyn and Els Van Ammel and Katrien De Mulder and Juliette Roels and Laurentijn Tilleman and Marc Aumercier and Patrick Matthys and Filip Van Nieuwerburgh and Tessa C C Kerre and Tom Taghon and Pieter Van Vlierberghe and Bart Vandekerckhove and Georges Leclercq}, doi = {10.1182/blood.2020005204}, issn = {1528-0020}, year = {2020}, date = {2020-07-01}, journal = {Blood}, volume = {136}, pages = {288--298}, abstract = {Natural killer (NK) cells are important in the immune defense against tumor cells and pathogens, and they regulate other immune cells by cytokine secretion. Although murine NK cell biology has been extensively studied, knowledge about transcriptional circuitries controlling human NK cell development and maturation is limited. By generating ETS1-deficient human embryonic stem cells and by expressing the dominant-negative ETS1 p27 isoform in cord blood hematopoietic progenitor cells, we show that the transcription factor ETS1 is critically required for human NK cell differentiation. Genome-wide transcriptome analysis determined by RNA-sequencing combined with chromatin immunoprecipitation-sequencing analysis reveals that human ETS1 directly induces expression of key transcription factors that control NK cell differentiation (ie, E4BP4, TXNIP, TBET, GATA3, HOBIT, BLIMP1). In addition, ETS1 regulates expression of genes involved in apoptosis and NK cell activation. Our study provides important molecular insights into the role of ETS1 as an important regulator of human NK cell development and terminal differentiation.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } Natural killer (NK) cells are important in the immune defense against tumor cells and pathogens, and they regulate other immune cells by cytokine secretion. Although murine NK cell biology has been extensively studied, knowledge about transcriptional circuitries controlling human NK cell development and maturation is limited. By generating ETS1-deficient human embryonic stem cells and by expressing the dominant-negative ETS1 p27 isoform in cord blood hematopoietic progenitor cells, we show that the transcription factor ETS1 is critically required for human NK cell differentiation. Genome-wide transcriptome analysis determined by RNA-sequencing combined with chromatin immunoprecipitation-sequencing analysis reveals that human ETS1 directly induces expression of key transcription factors that control NK cell differentiation (ie, E4BP4, TXNIP, TBET, GATA3, HOBIT, BLIMP1). In addition, ETS1 regulates expression of genes involved in apoptosis and NK cell activation. Our study provides important molecular insights into the role of ETS1 as an important regulator of human NK cell development and terminal differentiation. |
Smedt, Renate De; Morscio, Julie; Reunes, Lindy; Roels, Juliette; Bardelli, Valentina; Lintermans, Beatrice; Loocke, Wouter Van; Almeida, Afonso; Cheung, Laurence C; Kotecha, Rishi S; Mansour, Marc R; Uyttebroeck, Anne; Vandenberghe, Peter; Starza, Roberta La; Mecucci, Cristina; Lammens, Tim; Roy, Nadine Van; Moerloose, Barbara De; Barata, João T; Taghon, Tom; Goossens, Steven; Vlierberghe, Pieter Van Targeting cytokine- and therapy-induced PIM1 activation in preclinical models of T-cell acute lymphoblastic leukemia and lymphoma. Journal Article Blood, 135 , pp. 1685–1695, 2020, ISSN: 1528-0020. @article{DeSmedt2020, title = {Targeting cytokine- and therapy-induced PIM1 activation in preclinical models of T-cell acute lymphoblastic leukemia and lymphoma.}, author = {Renate De Smedt and Julie Morscio and Lindy Reunes and Juliette Roels and Valentina Bardelli and Beatrice Lintermans and Wouter Van Loocke and Afonso Almeida and Laurence C Cheung and Rishi S Kotecha and Marc R Mansour and Anne Uyttebroeck and Peter Vandenberghe and Roberta La Starza and Cristina Mecucci and Tim Lammens and Nadine Van Roy and Barbara De Moerloose and João T Barata and Tom Taghon and Steven Goossens and Pieter Van Vlierberghe}, doi = {10.1182/blood.2019003880}, issn = {1528-0020}, year = {2020}, date = {2020-05-01}, journal = {Blood}, volume = {135}, pages = {1685--1695}, abstract = {T-cell acute lymphoblastic leukemia (T-ALL) and T-cell acute lymphoblastic lymphoma (T-LBL) are aggressive hematological malignancies that are currently treated with high-dose chemotherapy. Over the last several years, the search toward novel and less-toxic therapeutic strategies for T-ALL/T-LBL patients has largely focused on the identification of cell-intrinsic properties of the tumor cell. However, non-cell-autonomous activation of specific oncogenic pathways might also offer opportunities that could be exploited at the therapeutic level. In line with this, we here show that endogenous interleukin 7 (IL7) can increase the expression of the oncogenic kinase proviral integration site for Moloney-murine leukemia 1 (PIM1) in CD127+ T-ALL/T-LBL, thereby rendering these tumor cells sensitive to in vivo PIM inhibition. In addition, using different CD127+ T-ALL/T-LBL xenograft models, we also reveal that residual tumor cells, which remain present after short-term in vivo chemotherapy, display consistent upregulation of PIM1 as compared with bulk nontreated tumor cells. Notably, this effect was transient as increased PIM1 levels were not observed in reestablished disease after abrogation of the initial chemotherapy. Furthermore, we uncover that this phenomenon is, at least in part, mediated by the ability of glucocorticoids to cause transcriptional upregulation of IL7RA in T-ALL/T-LBL patient-derived xenograft (PDX) cells, ultimately resulting in non-cell-autonomous PIM1 upregulation by endogenous IL7. Finally, we confirm in vivo that chemotherapy in combination with a pan-PIM inhibitor can improve leukemia survival in a PDX model of CD127+ T-ALL. Altogether, our work reveals that IL7 and glucocorticoids coordinately drive aberrant activation of PIM1 and suggests that IL7-responsive CD127+ T-ALL and T-LBL patients could benefit from PIM inhibition during induction chemotherapy.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } T-cell acute lymphoblastic leukemia (T-ALL) and T-cell acute lymphoblastic lymphoma (T-LBL) are aggressive hematological malignancies that are currently treated with high-dose chemotherapy. Over the last several years, the search toward novel and less-toxic therapeutic strategies for T-ALL/T-LBL patients has largely focused on the identification of cell-intrinsic properties of the tumor cell. However, non-cell-autonomous activation of specific oncogenic pathways might also offer opportunities that could be exploited at the therapeutic level. In line with this, we here show that endogenous interleukin 7 (IL7) can increase the expression of the oncogenic kinase proviral integration site for Moloney-murine leukemia 1 (PIM1) in CD127+ T-ALL/T-LBL, thereby rendering these tumor cells sensitive to in vivo PIM inhibition. In addition, using different CD127+ T-ALL/T-LBL xenograft models, we also reveal that residual tumor cells, which remain present after short-term in vivo chemotherapy, display consistent upregulation of PIM1 as compared with bulk nontreated tumor cells. Notably, this effect was transient as increased PIM1 levels were not observed in reestablished disease after abrogation of the initial chemotherapy. Furthermore, we uncover that this phenomenon is, at least in part, mediated by the ability of glucocorticoids to cause transcriptional upregulation of IL7RA in T-ALL/T-LBL patient-derived xenograft (PDX) cells, ultimately resulting in non-cell-autonomous PIM1 upregulation by endogenous IL7. Finally, we confirm in vivo that chemotherapy in combination with a pan-PIM inhibitor can improve leukemia survival in a PDX model of CD127+ T-ALL. Altogether, our work reveals that IL7 and glucocorticoids coordinately drive aberrant activation of PIM1 and suggests that IL7-responsive CD127+ T-ALL and T-LBL patients could benefit from PIM inhibition during induction chemotherapy. |
Dolens, Anne-Catherine; Durinck, Kaat; Lavaert, Marieke; der Meulen, Joni Van; Velghe, Imke; Medts, Jelle De; Weening, Karin; Roels, Juliette; Mulder, Katrien De; Volders, Pieter-Jan; Preter, Katleen De; Kerre, Tessa; Vandekerckhove, Bart; Leclercq, Georges; Vandesompele, Jo; Mestdagh, Pieter; Vlierberghe, Pieter Van; Speleman, Frank; Taghon, Tom Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development. Journal Article EMBO reports, 21 , pp. e49006, 2020, ISSN: 1469-3178. @article{Dolens2020, title = {Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development.}, author = {Anne-Catherine Dolens and Kaat Durinck and Marieke Lavaert and Joni Van der Meulen and Imke Velghe and Jelle De Medts and Karin Weening and Juliette Roels and Katrien De Mulder and Pieter-Jan Volders and Katleen De Preter and Tessa Kerre and Bart Vandekerckhove and Georges Leclercq and Jo Vandesompele and Pieter Mestdagh and Pieter Van Vlierberghe and Frank Speleman and Tom Taghon}, doi = {10.15252/embr.201949006}, issn = {1469-3178}, year = {2020}, date = {2020-05-01}, journal = {EMBO reports}, volume = {21}, pages = {e49006}, abstract = {γδ and αβ T cells have unique roles in immunity and both originate in the thymus from T-lineage committed precursors through distinct but unclear mechanisms. Here, we show that Notch1 activation is more stringently required for human γδ development compared to αβ-lineage differentiation and performed paired mRNA and miRNA profiling across 11 discrete developmental stages of human T cell development in an effort to identify the potential Notch1 downstream mechanism. Our data suggest that the miR-17-92 cluster is a Notch1 target in immature thymocytes and that miR-17 can restrict BCL11B expression in these Notch-dependent T cell precursors. We show that enforced miR-17 expression promotes human γδ T cell development and, consistently, that BCL11B is absolutely required for αβ but less for γδ T cell development. This study suggests that human γδ T cell development is mediated by a stage-specific Notch-driven negative feedback loop through which miR-17 temporally restricts BCL11B expression and provides functional insights into the developmental role of the disease-associated genes BCL11B and the miR-17-92 cluster in a human context.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } γδ and αβ T cells have unique roles in immunity and both originate in the thymus from T-lineage committed precursors through distinct but unclear mechanisms. Here, we show that Notch1 activation is more stringently required for human γδ development compared to αβ-lineage differentiation and performed paired mRNA and miRNA profiling across 11 discrete developmental stages of human T cell development in an effort to identify the potential Notch1 downstream mechanism. Our data suggest that the miR-17-92 cluster is a Notch1 target in immature thymocytes and that miR-17 can restrict BCL11B expression in these Notch-dependent T cell precursors. We show that enforced miR-17 expression promotes human γδ T cell development and, consistently, that BCL11B is absolutely required for αβ but less for γδ T cell development. This study suggests that human γδ T cell development is mediated by a stage-specific Notch-driven negative feedback loop through which miR-17 temporally restricts BCL11B expression and provides functional insights into the developmental role of the disease-associated genes BCL11B and the miR-17-92 cluster in a human context. |
Park, Jong-Eun; Botting, Rachel A; Conde, Cecilia Domínguez; Popescu, Dorin-Mirel; Lavaert, Marieke; Kunz, Daniel J; Goh, Issac; Stephenson, Emily; Ragazzini, Roberta; Tuck, Elizabeth; Wilbrey-Clark, Anna; Roberts, Kenny; Kedlian, Veronika R; Ferdinand, John R; He, Xiaoling; Webb, Simone; Maunder, Daniel; Vandamme, Niels; Mahbubani, Krishnaa T; Polanski, Krzysztof; Mamanova, Lira; Bolt, Liam; Crossland, David; de Rita, Fabrizio; Fuller, Andrew; Filby, Andrew; Reynolds, Gary; Dixon, David; Saeb-Parsy, Kourosh; Lisgo, Steven; Henderson, Deborah; Vento-Tormo, Roser; Bayraktar, Omer A; Barker, Roger A; Meyer, Kerstin B; Saeys, Yvan; Bonfanti, Paola; Behjati, Sam; Clatworthy, Menna R; Taghon, Tom; Haniffa, Muzlifah; Teichmann, Sarah A A cell atlas of human thymic development defines T cell repertoire formation. Journal Article Science (New York, N.Y.), 367 , 2020, ISSN: 1095-9203. @article{Park2020, title = {A cell atlas of human thymic development defines T cell repertoire formation.}, author = {Jong-Eun Park and Rachel A Botting and Cecilia Domínguez Conde and Dorin-Mirel Popescu and Marieke Lavaert and Daniel J Kunz and Issac Goh and Emily Stephenson and Roberta Ragazzini and Elizabeth Tuck and Anna Wilbrey-Clark and Kenny Roberts and Veronika R Kedlian and John R Ferdinand and Xiaoling He and Simone Webb and Daniel Maunder and Niels Vandamme and Krishnaa T Mahbubani and Krzysztof Polanski and Lira Mamanova and Liam Bolt and David Crossland and Fabrizio de Rita and Andrew Fuller and Andrew Filby and Gary Reynolds and David Dixon and Kourosh Saeb-Parsy and Steven Lisgo and Deborah Henderson and Roser Vento-Tormo and Omer A Bayraktar and Roger A Barker and Kerstin B Meyer and Yvan Saeys and Paola Bonfanti and Sam Behjati and Menna R Clatworthy and Tom Taghon and Muzlifah Haniffa and Sarah A Teichmann}, doi = {10.1126/science.aay3224}, issn = {1095-9203}, year = {2020}, date = {2020-02-01}, journal = {Science (New York, N.Y.)}, volume = {367}, abstract = {The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development. |
Loontiens, Siebe; Dolens, Anne-Catherine; Strubbe, Steven; de Walle, Inge Van; Moore, Finola E; Depestel, Lisa; Vanhauwaert, Suzanne; Matthijssens, Filip; Langenau, David M; Speleman, Frank; Vlierberghe, Pieter Van; Durinck, Kaat; Taghon, Tom PHF6 Expression Levels Impact Human Hematopoietic Stem Cell Differentiation. Journal Article Frontiers in cell and developmental biology, 8 , pp. 599472, 2020, ISSN: 2296-634X. @article{Loontiens2020, title = {PHF6 Expression Levels Impact Human Hematopoietic Stem Cell Differentiation.}, author = {Siebe Loontiens and Anne-Catherine Dolens and Steven Strubbe and Inge Van de Walle and Finola E Moore and Lisa Depestel and Suzanne Vanhauwaert and Filip Matthijssens and David M Langenau and Frank Speleman and Pieter Van Vlierberghe and Kaat Durinck and Tom Taghon}, doi = {10.3389/fcell.2020.599472}, issn = {2296-634X}, year = {2020}, date = {2020-01-01}, journal = {Frontiers in cell and developmental biology}, volume = {8}, pages = {599472}, abstract = {Transcriptional control of hematopoiesis involves complex regulatory networks and functional perturbations in one of these components often results in malignancies. Loss-of-function mutations in , encoding a presumed epigenetic regulator, have been primarily described in T cell acute lymphoblastic leukemia (T-ALL) and the first insights into its function in normal hematopoiesis only recently emerged from mouse modeling experiments. Here, we investigated the role of PHF6 in human blood cell development by performing knockdown studies in cord blood and thymus-derived hematopoietic precursors to evaluate the impact on lineage differentiation in well-established models. Our findings reveal that levels differentially impact the differentiation of human hematopoietic progenitor cells into various blood cell lineages, with prominent effects on lymphoid and erythroid differentiation. We show that loss of PHF6 results in accelerated human T cell development through reduced expression of and its downstream target genes. This functional interaction in developing thymocytes was confirmed using a -deficient zebrafish model that also displayed accelerated developmental kinetics upon reduced or notch1 activation. In summary, our work reveals that appropriate control of expression is important for normal human hematopoiesis and provides clues towards the role of in T-ALL development.}, keywords = {}, pubstate = {epublish}, tppubtype = {article} } Transcriptional control of hematopoiesis involves complex regulatory networks and functional perturbations in one of these components often results in malignancies. Loss-of-function mutations in , encoding a presumed epigenetic regulator, have been primarily described in T cell acute lymphoblastic leukemia (T-ALL) and the first insights into its function in normal hematopoiesis only recently emerged from mouse modeling experiments. Here, we investigated the role of PHF6 in human blood cell development by performing knockdown studies in cord blood and thymus-derived hematopoietic precursors to evaluate the impact on lineage differentiation in well-established models. Our findings reveal that levels differentially impact the differentiation of human hematopoietic progenitor cells into various blood cell lineages, with prominent effects on lymphoid and erythroid differentiation. We show that loss of PHF6 results in accelerated human T cell development through reduced expression of and its downstream target genes. This functional interaction in developing thymocytes was confirmed using a -deficient zebrafish model that also displayed accelerated developmental kinetics upon reduced or notch1 activation. In summary, our work reveals that appropriate control of expression is important for normal human hematopoiesis and provides clues towards the role of in T-ALL development. |
Zhou, Yalu; Han, Cuijuan; Wang, Eric; Lorch, Adam H; Serafin, Valentina; Cho, Byoung-Kyu; Diaz, Blanca Gutierrez T; Calvo, Julien; Fang, Celestia; Khodadadi-Jamayran, Alireza; Tabaglio, Tommaso; Marier, Christian; Kuchmiy, Anna; Sun, Limin; Yacu, George; Filip, Szymon K; Jin, Qi; Takahashi, Yoh-Hei; Amici, David R; Rendleman, Emily J; Rawat, Radhika; Bresolin, Silvia; Paganin, Maddalena; Zhang, Cheng; Li, Hu; Kandela, Irawati; Politanska, Yuliya; Abdala-Valencia, Hiam; Mendillo, Marc L; Zhu, Ping; Palhais, Bruno; Vlierberghe, Pieter Van; Taghon, Tom; Aifantis, Iannis; Goo, Young Ah; Guccione, Ernesto; Heguy, Adriana; Tsirigos, Aristotelis; Wee, Keng Boon; Mishra, Rama K; Pflumio, Francoise; Accordi, Benedetta; Basso, Giuseppe; Ntziachristos, Panagiotis Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia. Journal Article Cancer discovery, 10 , pp. 1388–1409, 2020, ISSN: 2159-8290. @article{Zhou2020, title = {Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia.}, author = {Yalu Zhou and Cuijuan Han and Eric Wang and Adam H Lorch and Valentina Serafin and Byoung-Kyu Cho and Blanca T Gutierrez Diaz and Julien Calvo and Celestia Fang and Alireza Khodadadi-Jamayran and Tommaso Tabaglio and Christian Marier and Anna Kuchmiy and Limin Sun and George Yacu and Szymon K Filip and Qi Jin and Yoh-Hei Takahashi and David R Amici and Emily J Rendleman and Radhika Rawat and Silvia Bresolin and Maddalena Paganin and Cheng Zhang and Hu Li and Irawati Kandela and Yuliya Politanska and Hiam Abdala-Valencia and Marc L Mendillo and Ping Zhu and Bruno Palhais and Pieter Van Vlierberghe and Tom Taghon and Iannis Aifantis and Young Ah Goo and Ernesto Guccione and Adriana Heguy and Aristotelis Tsirigos and Keng Boon Wee and Rama K Mishra and Francoise Pflumio and Benedetta Accordi and Giuseppe Basso and Panagiotis Ntziachristos}, doi = {10.1158/2159-8290.CD-19-1436}, issn = {2159-8290}, year = {2020}, date = {2020-01-01}, journal = {Cancer discovery}, volume = {10}, pages = {1388--1409}, abstract = {Splicing alterations are common in diseases such as cancer, where mutations in splicing factor genes are frequently responsible for aberrant splicing. Here we present an alternative mechanism for splicing regulation in T-cell acute lymphoblastic leukemia (T-ALL) that involves posttranslational stabilization of the splicing machinery via deubiquitination. We demonstrate there are extensive exon skipping changes in disease, affecting proteasomal subunits, cell-cycle regulators, and the RNA machinery. We present that the serine/arginine-rich splicing factors (SRSF), controlling exon skipping, are critical for leukemia cell survival. The ubiquitin-specific peptidase 7 (USP7) regulates SRSF6 protein levels via active deubiquitination, and USP7 inhibition alters the exon skipping pattern and blocks T-ALL growth. The splicing inhibitor H3B-8800 affects splicing of proteasomal transcripts and proteasome activity and acts synergistically with proteasome inhibitors in inhibiting T-ALL growth. Our study provides the proof-of-principle for regulation of splicing factors via deubiquitination and suggests new therapeutic modalities in T-ALL. SIGNIFICANCE: Our study provides a new proof-of-principle for posttranslational regulation of splicing factors independently of mutations in aggressive T-cell leukemia. It further suggests a new drug combination of splicing and proteasomal inhibitors, a concept that might apply to other diseases with or without mutations affecting the splicing machinery. .}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } Splicing alterations are common in diseases such as cancer, where mutations in splicing factor genes are frequently responsible for aberrant splicing. Here we present an alternative mechanism for splicing regulation in T-cell acute lymphoblastic leukemia (T-ALL) that involves posttranslational stabilization of the splicing machinery via deubiquitination. We demonstrate there are extensive exon skipping changes in disease, affecting proteasomal subunits, cell-cycle regulators, and the RNA machinery. We present that the serine/arginine-rich splicing factors (SRSF), controlling exon skipping, are critical for leukemia cell survival. The ubiquitin-specific peptidase 7 (USP7) regulates SRSF6 protein levels via active deubiquitination, and USP7 inhibition alters the exon skipping pattern and blocks T-ALL growth. The splicing inhibitor H3B-8800 affects splicing of proteasomal transcripts and proteasome activity and acts synergistically with proteasome inhibitors in inhibiting T-ALL growth. Our study provides the proof-of-principle for regulation of splicing factors via deubiquitination and suggests new therapeutic modalities in T-ALL. SIGNIFICANCE: Our study provides a new proof-of-principle for posttranslational regulation of splicing factors independently of mutations in aggressive T-cell leukemia. It further suggests a new drug combination of splicing and proteasomal inhibitors, a concept that might apply to other diseases with or without mutations affecting the splicing machinery. . |
Lavaert, Marieke; Valcke, Brecht; Vandekerckhove, Bart; Leclercq, Georges; Liang, Kai Ling; Taghon, Tom Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty. Journal Article Frontiers in immunology, 11 , pp. 1659, 2020, ISSN: 1664-3224. @article{Lavaert2020, title = {Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty.}, author = {Marieke Lavaert and Brecht Valcke and Bart Vandekerckhove and Georges Leclercq and Kai Ling Liang and Tom Taghon}, doi = {10.3389/fimmu.2020.01659}, issn = {1664-3224}, year = {2020}, date = {2020-01-01}, journal = {Frontiers in immunology}, volume = {11}, pages = {1659}, abstract = {The thymus is the organ where subsets of mature T cells are generated which subsequently egress to function as central mediators in the immune system. While continuously generating T cells even into adulthood, the thymus does undergo involution during life. This is characterized by an initial rapid decrease in thymic cellularity during early life and by a second age-dependent decline in adulthood. The thymic cellularity of neonates remains low during the first month after birth and the tissue reaches a maximum in cellularity at 6 months of age. In order to study the effect that this first phase of thymic involution has on thymic immune subset frequencies, we performed multi-color flow cytometry on thymic samples collected from birth to 14 years of age. In consideration of the inherent limitations posed by conventional flow cytometry analysis, we established a novel computational analysis pipeline that is adapted from single-cell transcriptome sequencing data analysis. This allowed us to overcome technical effects by batch correction, analyze multiple samples simultaneously, limit computational cost by subsampling, and to rely on KNN-graphs for graph-based clustering. As a result, we successfully identified rare, distinct and gradually developing immune subsets within the human thymus tissues. Although the thymus undergoes early involution from infanthood onwards, our data suggests that this does not affect human T-cell development as we did not observe significant alterations in the proportions of T-lineage developmental intermediates from birth to puberty. Thus, in addition to providing an interesting novel strategy to analyze conventional flow cytometry data for the thymus, our work shows that the early phase of human thymic involution mainly limits the overall T cell output since no obvious changes in thymocyte subsets could be observed.}, keywords = {}, pubstate = {epublish}, tppubtype = {article} } The thymus is the organ where subsets of mature T cells are generated which subsequently egress to function as central mediators in the immune system. While continuously generating T cells even into adulthood, the thymus does undergo involution during life. This is characterized by an initial rapid decrease in thymic cellularity during early life and by a second age-dependent decline in adulthood. The thymic cellularity of neonates remains low during the first month after birth and the tissue reaches a maximum in cellularity at 6 months of age. In order to study the effect that this first phase of thymic involution has on thymic immune subset frequencies, we performed multi-color flow cytometry on thymic samples collected from birth to 14 years of age. In consideration of the inherent limitations posed by conventional flow cytometry analysis, we established a novel computational analysis pipeline that is adapted from single-cell transcriptome sequencing data analysis. This allowed us to overcome technical effects by batch correction, analyze multiple samples simultaneously, limit computational cost by subsampling, and to rely on KNN-graphs for graph-based clustering. As a result, we successfully identified rare, distinct and gradually developing immune subsets within the human thymus tissues. Although the thymus undergoes early involution from infanthood onwards, our data suggests that this does not affect human T-cell development as we did not observe significant alterations in the proportions of T-lineage developmental intermediates from birth to puberty. Thus, in addition to providing an interesting novel strategy to analyze conventional flow cytometry data for the thymus, our work shows that the early phase of human thymic involution mainly limits the overall T cell output since no obvious changes in thymocyte subsets could be observed. |
Lavaert, Marieke; Liang, Kai Ling; Vandamme, Niels; Park, Jong-Eun; Roels, Juliette; Kowalczyk, Monica S; Li, Bo; Ashenberg, Orr; Tabaka, Marcin; Dionne, Danielle; Tickle, Timothy L; Slyper, Michal; Rozenblatt-Rosen, Orit; Vandekerckhove, Bart; Leclercq, Georges; Regev, Aviv; Vlierberghe, Pieter Van; Guilliams, Martin; Teichmann, Sarah A; Saeys, Yvan; Taghon, Tom Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Journal Article Immunity, 52 , pp. 1088–1104.e6, 2020, ISSN: 1097-4180. @article{Lavaert2020a, title = {Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.}, author = {Marieke Lavaert and Kai Ling Liang and Niels Vandamme and Jong-Eun Park and Juliette Roels and Monica S Kowalczyk and Bo Li and Orr Ashenberg and Marcin Tabaka and Danielle Dionne and Timothy L Tickle and Michal Slyper and Orit Rozenblatt-Rosen and Bart Vandekerckhove and Georges Leclercq and Aviv Regev and Pieter Van Vlierberghe and Martin Guilliams and Sarah A Teichmann and Yvan Saeys and Tom Taghon}, doi = {10.1016/j.immuni.2020.03.019}, issn = {1097-4180}, year = {2020}, date = {2020-01-01}, journal = {Immunity}, volume = {52}, pages = {1088--1104.e6}, abstract = {During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis. |
Roels, Juliette; Kuchmiy, Anna; Decker, Matthias De; Strubbe, Steven; Lavaert, Marieke; Liang, Kai Ling; Leclercq, Georges; Vandekerckhove, Bart; Nieuwerburgh, Filip Van; Vlierberghe, Pieter Van; Taghon, Tom Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development. Journal Article Nature immunology, 21 , pp. 1280–1292, 2020, ISSN: 1529-2916. @article{Roels2020a, title = {Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development.}, author = {Juliette Roels and Anna Kuchmiy and Matthias De Decker and Steven Strubbe and Marieke Lavaert and Kai Ling Liang and Georges Leclercq and Bart Vandekerckhove and Filip Van Nieuwerburgh and Pieter Van Vlierberghe and Tom Taghon}, doi = {10.1038/s41590-020-0747-9}, issn = {1529-2916}, year = {2020}, date = {2020-01-01}, journal = {Nature immunology}, volume = {21}, pages = {1280--1292}, abstract = {The development of TCRαβ and TCRγδ T cells comprises a step-wise process in which regulatory events control differentiation and lineage outcome. To clarify these mechanisms, we employed RNA-sequencing, ATAC-sequencing and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics show clear stage specificity and reveal that human T cell-lineage commitment is marked by GATA3- and BCL11B-dependent closing of PU.1 sites. A temporary increase in H3K27me3 without open chromatin modifications is unique for β-selection, whereas emerging γδ T cells, which originate from common precursors of β-selected cells, show large chromatin accessibility changes due to strong T cell receptor (TCR) signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ-lineage cells that support their effector functions and reveal gene-specific mechanisms that define mature T cells. This resource provides a framework for studying gene regulatory mechanisms that drive normal and malignant human T cell development.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } The development of TCRαβ and TCRγδ T cells comprises a step-wise process in which regulatory events control differentiation and lineage outcome. To clarify these mechanisms, we employed RNA-sequencing, ATAC-sequencing and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics show clear stage specificity and reveal that human T cell-lineage commitment is marked by GATA3- and BCL11B-dependent closing of PU.1 sites. A temporary increase in H3K27me3 without open chromatin modifications is unique for β-selection, whereas emerging γδ T cells, which originate from common precursors of β-selected cells, show large chromatin accessibility changes due to strong T cell receptor (TCR) signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ-lineage cells that support their effector functions and reveal gene-specific mechanisms that define mature T cells. This resource provides a framework for studying gene regulatory mechanisms that drive normal and malignant human T cell development. |
Drobna, Monika; Szarzyńska, Bronisława; Jaksik, Roman; Sędek, Łukasz; Kuchmiy, Anna; Taghon, Tom; Vlierberghe, Pieter Van; Szczepański, Tomasz; Witt, Michał; Dawidowska, Małgorzata hsa-miR-20b-5p and hsa-miR-363-3p Affect Expression of PTEN and BIM Tumor Suppressor Genes and Modulate Survival of T-ALL Cells In Vitro Journal Article Cells, 9 , 2020, ISSN: 2073-4409. @article{Drobna2020, title = {hsa-miR-20b-5p and hsa-miR-363-3p Affect Expression of PTEN and BIM Tumor Suppressor Genes and Modulate Survival of T-ALL Cells In Vitro}, author = {Monika Drobna and Bronisława Szarzyńska and Roman Jaksik and Łukasz Sędek and Anna Kuchmiy and Tom Taghon and Pieter Van Vlierberghe and Tomasz Szczepański and Michał Witt and Małgorzata Dawidowska}, doi = {10.3390/cells9051137}, issn = {2073-4409}, year = {2020}, date = {2020-01-01}, journal = {Cells}, volume = {9}, abstract = {T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis indicated their potential involvement in the regulation of apoptosis. Here, we aimed to test the hypothesis on the pro-tumorigenic roles of these miRNAs in T-ALL cells in vitro. We demonstrate, for the first time, that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster, when upregulated in T-ALL cells in vitro, protect leukemic cells from apoptosis, enhance proliferation, and contribute to growth advantage. We show, using dual luciferase reporter assays, Ago2-RNA immunoprecipitation, RT-qPCR, and Western blots, that the oncogenic effects of these upregulated miRNAs might, at least in part, be mediated by the downregulation of two important tumor suppressor genes, and , targeted by both miRNAs. Additionally, we demonstrate the cooperative effects of these two miRNAs by simultaneous inhibition of both miRNAs as compared to the inhibition of single miRNAs. We postulate that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster might serve as oncomiRs in T-ALL, by contributing to post-transcriptional repression of key tumor suppressors, and .}, keywords = {}, pubstate = {published}, tppubtype = {article} } T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis indicated their potential involvement in the regulation of apoptosis. Here, we aimed to test the hypothesis on the pro-tumorigenic roles of these miRNAs in T-ALL cells in vitro. We demonstrate, for the first time, that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster, when upregulated in T-ALL cells in vitro, protect leukemic cells from apoptosis, enhance proliferation, and contribute to growth advantage. We show, using dual luciferase reporter assays, Ago2-RNA immunoprecipitation, RT-qPCR, and Western blots, that the oncogenic effects of these upregulated miRNAs might, at least in part, be mediated by the downregulation of two important tumor suppressor genes, and , targeted by both miRNAs. Additionally, we demonstrate the cooperative effects of these two miRNAs by simultaneous inhibition of both miRNAs as compared to the inhibition of single miRNAs. We postulate that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster might serve as oncomiRs in T-ALL, by contributing to post-transcriptional repression of key tumor suppressors, and . |
Bonte, Sarah; Munter, Stijn De; Goetgeluk, Glenn; Ingels, Joline; Pille, Melissa; Billiet, Lore; Taghon, Tom; Leclercq, Georges; Vandekerckhove, Bart; Kerre, Tessa T-cells with a single tumor antigen-specific T-cell receptor can be generated in vitro from clinically relevant stem cell sources Journal Article Oncoimmunology, 9 , pp. 1727078, 2020, ISSN: 2162-4011. @article{Bonte2020, title = {T-cells with a single tumor antigen-specific T-cell receptor can be generated in vitro from clinically relevant stem cell sources}, author = {Sarah Bonte and Stijn De Munter and Glenn Goetgeluk and Joline Ingels and Melissa Pille and Lore Billiet and Tom Taghon and Georges Leclercq and Bart Vandekerckhove and Tessa Kerre}, doi = {10.1080/2162402X.2020.1727078}, issn = {2162-4011}, year = {2020}, date = {2020-01-01}, journal = {Oncoimmunology}, volume = {9}, pages = {1727078}, abstract = {Chimeric antigen receptor (CAR) T-cells have shown great promise in the treatment of B-cell malignancies. For acute myeloid leukemia (AML), however, the optimal target surface antigen has yet to be discovered. Alternatively, T-cell receptor (TCR)-redirected T-cells target intracellular antigens, marking a broader territory of available target antigens. Currently, adoptive TCR T-cell therapy uses peripheral blood lymphocytes for the introduction of a transgenic TCR. However, this can cause graft-versus-host disease, due to mispairing of introduced and endogenous TCR chains. Therefore, we started from hematopoietic stem and progenitor cells (HSPC), that do not express a TCR yet, isolated from healthy donors, patients in remission after chemotherapy and AML patients at diagnosis. Using the OP9-DL1 in vitro co-culture system and agonist selection, TCR-transduced HSPC develop into mature tumor antigen-specific T-cells with only one TCR. We show here that this approach is feasible with adult HSPC from clinically relevant sources, albeit with slower maturation and lower cell yield compared to cord blood HSPC. Moreover, cryopreservation of HSPC does not have an effect on cell numbers or functionality of the generated T-cells. In conclusion, we show here that it is feasible to generate TA-specific T-cells from HSPC from adult healthy donors and patients and we believe these T-cells could be of use as a very valuable form of patient-tailored T-cell immunotherapy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chimeric antigen receptor (CAR) T-cells have shown great promise in the treatment of B-cell malignancies. For acute myeloid leukemia (AML), however, the optimal target surface antigen has yet to be discovered. Alternatively, T-cell receptor (TCR)-redirected T-cells target intracellular antigens, marking a broader territory of available target antigens. Currently, adoptive TCR T-cell therapy uses peripheral blood lymphocytes for the introduction of a transgenic TCR. However, this can cause graft-versus-host disease, due to mispairing of introduced and endogenous TCR chains. Therefore, we started from hematopoietic stem and progenitor cells (HSPC), that do not express a TCR yet, isolated from healthy donors, patients in remission after chemotherapy and AML patients at diagnosis. Using the OP9-DL1 in vitro co-culture system and agonist selection, TCR-transduced HSPC develop into mature tumor antigen-specific T-cells with only one TCR. We show here that this approach is feasible with adult HSPC from clinically relevant sources, albeit with slower maturation and lower cell yield compared to cord blood HSPC. Moreover, cryopreservation of HSPC does not have an effect on cell numbers or functionality of the generated T-cells. In conclusion, we show here that it is feasible to generate TA-specific T-cells from HSPC from adult healthy donors and patients and we believe these T-cells could be of use as a very valuable form of patient-tailored T-cell immunotherapy. |
Munter, Stijn De; Parys, Alexander Van; Bral, Layla; Ingels, Joline; Goetgeluk, Glenn; Bonte, Sarah; Pille, Melissa; Billiet, Lore; Weening, Karin; Verhee, Annick; der Heyden, Jose Van; Taghon, Tom; Leclercq, Georges; Kerre, Tessa; Tavernier, Jan; Vandekerckhove, Bart Rapid and Effective Generation of Nanobody Based CARs using PCR and Gibson Assembly. Journal Article International journal of molecular sciences, 21 , 2020, ISSN: 1422-0067. @article{DeMunter2020, title = {Rapid and Effective Generation of Nanobody Based CARs using PCR and Gibson Assembly.}, author = {Stijn De Munter and Alexander Van Parys and Layla Bral and Joline Ingels and Glenn Goetgeluk and Sarah Bonte and Melissa Pille and Lore Billiet and Karin Weening and Annick Verhee and Jose Van der Heyden and Tom Taghon and Georges Leclercq and Tessa Kerre and Jan Tavernier and Bart Vandekerckhove}, doi = {10.3390/ijms21030883}, issn = {1422-0067}, year = {2020}, date = {2020-01-01}, journal = {International journal of molecular sciences}, volume = {21}, abstract = {Recent approval of chimeric antigen receptor (CAR) T cell therapy by the European Medicines Agency (EMA)/Federal and Drug Administration (FDA) and the remarkable results of CAR T clinical trials illustrate the curative potential of this therapy. While CARs against a multitude of different antigens are being developed and tested (pre)clinically, there is still a need for optimization. The use of single-chain variable fragments (scFvs) as targeting moieties hampers the quick generation of functional CARs and could potentially limit the efficacy. Instead, nanobodies may largely circumvent these difficulties. We used an available nanobody library generated after immunization of llamas against Cluster of Differentiation (CD) 20 through DNA vaccination or against the ectodomain of CD33 using soluble protein. The nanobody specific sequences were amplified by PCR and cloned by Gibson Assembly into a retroviral vector containing two different second-generation CAR constructs. After transduction in T cells, we observed high cell membrane nanoCAR expression in all cases. Following stimulation of nanoCAR-expressing T cells with antigen-positive cell lines, robust T cell activation, cytokine production and tumor cell lysis both in vitro and in vivo was observed. The use of nanobody technology in combination with PCR and Gibson Assembly allows for the rapid and effective generation of compact CARs.}, keywords = {}, pubstate = {epublish}, tppubtype = {article} } Recent approval of chimeric antigen receptor (CAR) T cell therapy by the European Medicines Agency (EMA)/Federal and Drug Administration (FDA) and the remarkable results of CAR T clinical trials illustrate the curative potential of this therapy. While CARs against a multitude of different antigens are being developed and tested (pre)clinically, there is still a need for optimization. The use of single-chain variable fragments (scFvs) as targeting moieties hampers the quick generation of functional CARs and could potentially limit the efficacy. Instead, nanobodies may largely circumvent these difficulties. We used an available nanobody library generated after immunization of llamas against Cluster of Differentiation (CD) 20 through DNA vaccination or against the ectodomain of CD33 using soluble protein. The nanobody specific sequences were amplified by PCR and cloned by Gibson Assembly into a retroviral vector containing two different second-generation CAR constructs. After transduction in T cells, we observed high cell membrane nanoCAR expression in all cases. Following stimulation of nanoCAR-expressing T cells with antigen-positive cell lines, robust T cell activation, cytokine production and tumor cell lysis both in vitro and in vivo was observed. The use of nanobody technology in combination with PCR and Gibson Assembly allows for the rapid and effective generation of compact CARs. |
2019 |
Coninck, Stien De; Berx, Geert; Taghon, Tom; Vlierberghe, Pieter Van; Goossens, Steven ZEB2 in T-cells and T-ALL. Journal Article Advances in biological regulation, 74 , pp. 100639, 2019, ISSN: 2212-4934. @article{DeConinck2019, title = {ZEB2 in T-cells and T-ALL.}, author = {Stien De Coninck and Geert Berx and Tom Taghon and Pieter Van Vlierberghe and Steven Goossens}, doi = {10.1016/j.jbior.2019.100639}, issn = {2212-4934}, year = {2019}, date = {2019-12-01}, journal = {Advances in biological regulation}, volume = {74}, pages = {100639}, abstract = {The identification of the rare but recurrent t(2; 14)(q22; q32) translocation involving the ZEB2 locus in T-cell acute lymphoblastic leukemia, suggested that ZEB2 is an oncogenic driver of this high-risk subtype of leukemia. ZEB2, a zinc finger E-box homeobox binding transcription factor, is a master regulator of cellular plasticity and its expression is correlated with poor overall survival of cancer patients. Recent loss- and gain-of-function in the mouse revealed important roles of ZEB2 during different stages of hematopoiesis, including the T-cell lineage. Here, we summarize the roles of ZEB2 in T-cells, their development, and malignant transformation to T-ALL.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } The identification of the rare but recurrent t(2; 14)(q22; q32) translocation involving the ZEB2 locus in T-cell acute lymphoblastic leukemia, suggested that ZEB2 is an oncogenic driver of this high-risk subtype of leukemia. ZEB2, a zinc finger E-box homeobox binding transcription factor, is a master regulator of cellular plasticity and its expression is correlated with poor overall survival of cancer patients. Recent loss- and gain-of-function in the mouse revealed important roles of ZEB2 during different stages of hematopoiesis, including the T-cell lineage. Here, we summarize the roles of ZEB2 in T-cells, their development, and malignant transformation to T-ALL. |
Bonnardel, Johnny; T'Jonck, Wouter; Gaublomme, Djoere; Browaeys, Robin; Scott, Charlotte L; Martens, Liesbet; Vanneste, Bavo; Prijck, Sofie De; Nedospasov, Sergei A; Kremer, Anna; Hamme, Evelien Van; Borghgraef, Peter; Toussaint, Wendy; Bleser, Pieter De; Mannaerts, Inge; Beschin, Alain; van Grunsven, Leo A; Lambrecht, Bart N; Taghon, Tom; Lippens, Saskia; Elewaut, Dirk; Saeys, Yvan; Guilliams, Martin Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche. Journal Article Immunity, 51 , pp. 638–654.e9, 2019, ISSN: 1097-4180. @article{Bonnardel2019, title = {Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche.}, author = {Johnny Bonnardel and Wouter T'Jonck and Djoere Gaublomme and Robin Browaeys and Charlotte L Scott and Liesbet Martens and Bavo Vanneste and Sofie De Prijck and Sergei A Nedospasov and Anna Kremer and Evelien Van Hamme and Peter Borghgraef and Wendy Toussaint and Pieter De Bleser and Inge Mannaerts and Alain Beschin and Leo A van Grunsven and Bart N Lambrecht and Tom Taghon and Saskia Lippens and Dirk Elewaut and Yvan Saeys and Martin Guilliams}, doi = {10.1016/j.immuni.2019.08.017}, issn = {1097-4180}, year = {2019}, date = {2019-10-01}, journal = {Immunity}, volume = {51}, pages = {638--654.e9}, abstract = {Macrophages are strongly adapted to their tissue of residence. Yet, little is known about the cell-cell interactions that imprint the tissue-specific identities of macrophages in their respective niches. Using conditional depletion of liver Kupffer cells, we traced the developmental stages of monocytes differentiating into Kupffer cells and mapped the cellular interactions imprinting the Kupffer cell identity. Kupffer cell loss induced tumor necrosis factor (TNF)- and interleukin-1 (IL-1) receptor-dependent activation of stellate cells and endothelial cells, resulting in the transient production of chemokines and adhesion molecules orchestrating monocyte engraftment. Engrafted circulating monocytes transmigrated into the perisinusoidal space and acquired the liver-associated transcription factors inhibitor of DNA 3 (ID3) and liver X receptor-α (LXR-α). Coordinated interactions with hepatocytes induced ID3 expression, whereas endothelial cells and stellate cells induced LXR-α via a synergistic NOTCH-BMP pathway. This study shows that the Kupffer cell niche is composed of stellate cells, hepatocytes, and endothelial cells that together imprint the liver-specific macrophage identity.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } Macrophages are strongly adapted to their tissue of residence. Yet, little is known about the cell-cell interactions that imprint the tissue-specific identities of macrophages in their respective niches. Using conditional depletion of liver Kupffer cells, we traced the developmental stages of monocytes differentiating into Kupffer cells and mapped the cellular interactions imprinting the Kupffer cell identity. Kupffer cell loss induced tumor necrosis factor (TNF)- and interleukin-1 (IL-1) receptor-dependent activation of stellate cells and endothelial cells, resulting in the transient production of chemokines and adhesion molecules orchestrating monocyte engraftment. Engrafted circulating monocytes transmigrated into the perisinusoidal space and acquired the liver-associated transcription factors inhibitor of DNA 3 (ID3) and liver X receptor-α (LXR-α). Coordinated interactions with hepatocytes induced ID3 expression, whereas endothelial cells and stellate cells induced LXR-α via a synergistic NOTCH-BMP pathway. This study shows that the Kupffer cell niche is composed of stellate cells, hepatocytes, and endothelial cells that together imprint the liver-specific macrophage identity. |
de Bock, Charles E; Down, Michelle; Baidya, Kinsha; Sweron, Bram; Boyd, Andrew W; Fiers, Mark; Burns, Gordon F; Molloy, Timothy J; Lock, Richard B; Soulier, Jean; Taghon, Tom; Vlierberghe, Pieter Van; Cools, Jan; Holst, Jeff; Thorne, Rick F T-cell acute lymphoblastic leukemias express a unique truncated FAT1 isoform that cooperates with NOTCH1 in leukemia development. Journal Article Haematologica, 104 , pp. e204–e207, 2019, ISSN: 1592-8721. @article{Bock2019, title = {T-cell acute lymphoblastic leukemias express a unique truncated FAT1 isoform that cooperates with NOTCH1 in leukemia development.}, author = {Charles E de Bock and Michelle Down and Kinsha Baidya and Bram Sweron and Andrew W Boyd and Mark Fiers and Gordon F Burns and Timothy J Molloy and Richard B Lock and Jean Soulier and Tom Taghon and Pieter Van Vlierberghe and Jan Cools and Jeff Holst and Rick F Thorne}, doi = {10.3324/haematol.2018.198424}, issn = {1592-8721}, year = {2019}, date = {2019-05-01}, journal = {Haematologica}, volume = {104}, pages = {e204--e207}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } |
Habets, Roger A; de Bock, Charles E; Serneels, Lutgarde; Lodewijckx, Inge; Verbeke, Delphine; Nittner, David; Narlawar, Rajeshwar; Demeyer, Sofie; Dooley, James; Liston, Adrian; Taghon, Tom; Cools, Jan; de Strooper, Bart Safe targeting of T cell acute lymphoblastic leukemia by pathology-specific NOTCH inhibition. Journal Article Science translational medicine, 11 , 2019, ISSN: 1946-6242. @article{Habets2019, title = {Safe targeting of T cell acute lymphoblastic leukemia by pathology-specific NOTCH inhibition.}, author = {Roger A Habets and Charles E de Bock and Lutgarde Serneels and Inge Lodewijckx and Delphine Verbeke and David Nittner and Rajeshwar Narlawar and Sofie Demeyer and James Dooley and Adrian Liston and Tom Taghon and Jan Cools and Bart de Strooper}, doi = {10.1126/scitranslmed.aau6246}, issn = {1946-6242}, year = {2019}, date = {2019-05-01}, journal = {Science translational medicine}, volume = {11}, abstract = {Given the high frequency of activating mutations in T cell acute lymphoblastic leukemia (T-ALL), inhibition of the γ-secretase complex remains an attractive target to prevent ligand-independent release of the cytoplasmic tail and oncogenic NOTCH1 signaling. However, four different γ-secretase complexes exist, and available inhibitors block all complexes equally. As a result, these cause severe "on-target" gastrointestinal tract, skin, and thymus toxicity, limiting their therapeutic application. Here, we demonstrate that genetic deletion or pharmacologic inhibition of the presenilin-1 (PSEN1) subclass of γ-secretase complexes is highly effective in decreasing leukemia while avoiding dose-limiting toxicities. Clinically, T-ALL samples were found to selectively express only PSEN1-containing γ-secretase complexes. The conditional knockout of in developing T cells attenuated the development of a mutant NOTCH1-driven leukemia in mice in vivo but did not abrogate normal T cell development. Treatment of T-ALL cell lines with the selective PSEN1 inhibitor MRK-560 effectively decreased mutant NOTCH1 processing and led to cell cycle arrest. These observations were extended to T-ALL patient-derived xenografts in vivo, demonstrating that MRK-560 treatment decreases leukemia burden and increased overall survival without any associated gut toxicity. Therefore, PSEN1-selective compounds provide a potential therapeutic strategy for safe and effective targeting of T-ALL and possibly also for other diseases in which NOTCH signaling plays a role.}, keywords = {}, pubstate = {ppublish}, tppubtype = {article} } Given the high frequency of activating mutations in T cell acute lymphoblastic leukemia (T-ALL), inhibition of the γ-secretase complex remains an attractive target to prevent ligand-independent release of the cytoplasmic tail and oncogenic NOTCH1 signaling. However, four different γ-secretase complexes exist, and available inhibitors block all complexes equally. As a result, these cause severe "on-target" gastrointestinal tract, skin, and thymus toxicity, limiting their therapeutic application. Here, we demonstrate that genetic deletion or pharmacologic inhibition of the presenilin-1 (PSEN1) subclass of γ-secretase complexes is highly effective in decreasing leukemia while avoiding dose-limiting toxicities. Clinically, T-ALL samples were found to selectively express only PSEN1-containing γ-secretase complexes. The conditional knockout of in developing T cells attenuated the development of a mutant NOTCH1-driven leukemia in mice in vivo but did not abrogate normal T cell development. Treatment of T-ALL cell lines with the selective PSEN1 inhibitor MRK-560 effectively decreased mutant NOTCH1 processing and led to cell cycle arrest. These observations were extended to T-ALL patient-derived xenografts in vivo, demonstrating that MRK-560 treatment decreases leukemia burden and increased overall survival without any associated gut toxicity. Therefore, PSEN1-selective compounds provide a potential therapeutic strategy for safe and effective targeting of T-ALL and possibly also for other diseases in which NOTCH signaling plays a role. |