Kim Keersmaecker | KU Leuven (original) (raw)

Papers by Kim Keersmaecker

How ribosomes translate cancer

A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somat... more A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis – from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on “onco-ribosomes” as an Achilles’ heel of cancer cells and a promising target for further therapeutic intervention.

Several somatic ribosome defects have recently been discovered in cancer, yet their oncogenic mec... more Several somatic ribosome defects have recently been discovered in cancer, yet their oncogenic mechanisms remain poorly understood. Here we investigated the pathogenic role of the recurrent R98S mutation in ribosomal protein L10 (RPL10-R98S) found in T-ALL. The JAK-STAT signaling pathway is a critical controller of cellular proliferation and survival. A proteome screen revealed overexpression of several Jak-Stat signaling proteins in engineered RPL10-R98S mouse lymphoid cells, which we confirmed in hematopoietic cells from transgenic Rpl10-R98S mice and T-ALL xenograft samples. RPL10-R98S expressing cells displayed JAK-STAT pathway hyper-activation upon cytokine stimulation, as well as increased sensitivity to clinically used JAK-STAT inhibitors like pimozide. A mutually exclusive mutation pattern between RPL10-R98S and JAK-STAT mutations in T-ALL patients further suggests that RPL10-R98S functionally mimics JAK-STAT activation. Mechanistically, besides transcriptional changes, RPL10-R98S caused reduction of apparent programmed ribosomal frameshifting at several ribosomal frameshift signals in mouse and human Jak-Stat genes, as well as decreased Jak1 degradation. Of further medical interest, RPL10-R98S cells showed reduced proteasome activity and enhanced sensitivity to clinical proteasome inhibitors. Collectively, we describe modulation of the JAK-STAT cascade as a novel cancer-promoting activity of a ribosomal mutation, and expand the relevance of this cascade in leukemia.

The Notch1 gene is a major oncogenic driver and therapeutic target in T-cell acute lymphoblastic ... more The Notch1 gene is a major oncogenic driver and therapeutic target in T-cell acute lymphoblastic leukemia (T-ALL). However, inhibition of NOTCH signaling with γ-secretase inhibitors (GSIs) has shown limited antileukemic activity in clinical trials. Here we performed an expression-based virtual screening to identify highly active antileukemic drugs that synergize with NOTCH1 inhibition in T-ALL. Among these, withaferin A demonstrated the strongest cytotoxic and GSI-synergistic antileukemic effects in vitro and in vivo. Mechanistically, network perturbation analyses showed eIF2A-phosphorylation-mediated inhibition of protein translation as a critical mediator of the antileukemic effects of withaferin A and its interaction with NOTCH1 inhibition. Overall, these results support a role for anti-NOTCH1 therapies and protein translation inhibitor combinations in the treatment of T-ALL.

For many years, defects in the ribosome have been associated to cancer. Recently, somatic mutatio... more For many years, defects in the ribosome have been associated to cancer. Recently, somatic mutations and deletions affecting ribosomal protein genes were identified in a few leukemias and solid tumor types. However, systematic analysis of all 81 known ribosomal protein genes across cancer types is lacking. We screened mutation and copy number data of respectively 4926 and 7322 samples from 16 cancer types and identified six altered genes (RPL5, RPL11, RPL23A, RPS5, RPS20 and RPSA). RPL5 was located at a significant peak of heterozygous deletion or mutated in 11% of glioblastoma, 28% of melanoma and 34% of breast cancer samples. Moreover, patients with low RPL5 expression displayed worse overall survival in glioblastoma and in one breast cancer cohort. RPL5 knockdown in breast cancer cell lines enhanced G2/M cell cycle progression and accelerated tumor progression in a xenograft mouse model. Interestingly, our data suggest that the tumor suppressor role of RPL5 is not only mediated by its known function as TP53 or c-MYC regulator. In conclusion, RPL5 heterozygous inactivation occurs at high incidence (11-34%) in multiple tumor types, currently representing the most common somatic ribosomal protein defect in cancer, and we demonstrate a tumor suppressor role for RPL5 in breast cancer.

Chromosomal region 1p22 is deleted in ⩾20% of multiple myeloma (MM) patients, suggesting the pres... more Chromosomal region 1p22 is deleted in ⩾20% of multiple myeloma (MM) patients, suggesting the presence of an unidentified tumor suppressor. Using high-resolution genomic profiling, we delimit a 58 kb minimal deleted region (MDR) on 1p22.1 encompassing two genes: ectopic viral integration site 5 (EVI5) and ribosomal protein L5 (RPL5). Low mRNA expression of EVI5 and RPL5 was associated with worse survival in diagnostic cases. Patients with 1p22 deletion had lower mRNA expression of EVI5 and RPL5, however, 1p22 deletion status is a bad predictor of RPL5 expression in some cases, suggesting that other mechanisms downregulate RPL5 expression. Interestingly, RPL5 but not EVI5 mRNA levels were significantly lower in relapsed patients responding to bortezomib and; both in newly diagnosed and relapsed patients, bortezomib treatment could overcome their bad prognosis by raising their progression-free survival to equal that of patients with high RPL5 expression. In conclusion, our genetic data restrict the MDR on 1p22 to EVI5 and RPL5 and although the role of these genes in promoting MM progression remains to be determined, we identify RPL5 mRNA expression as a biomarker for initial response to bortezomib in relapsed patients and subsequent survival benefit after long-term treatment in newly diagnosed and relapsed patients.

T-cell acute lymphoblastic leukemia (TALL) is an aggressive malignancy caused by the accumulation... more T-cell acute lymphoblastic leukemia (TALL) is an aggressive malignancy caused by the accumulation of genomic lesions that affect the development of T-cells. Since many years, it has been established that deregulated expression of transcription factors, impairment of the CDKN2A/2B cell cycle regulators and hyperactive NOTCH1 signaling play prominent roles in the pathogenesis of this leukemia. In the past decade, systematic screening of TALL genomes by high resolution copy number arrays and next-generation sequencing technologies has revealed that T-cell progenitors accumulate additional mutations affecting JAK/STAT signaling, protein translation and epigenetic control, providing novel attractive targets for therapy. In this review, we provide an update on our knowledge on TALL pathogenesis, on the opportunities for the introduction of targeted therapy and on the challenges that are still ahead.

Blood, 2015

Ribosomopathies are largely congenital diseases linked to defects in ribosomal proteins or biogen... more Ribosomopathies are largely congenital diseases linked to defects in ribosomal proteins or biogenesis factors. Some of these disorders are characterized by hypoproliferative phenotypes such as bone marrow failure and anemia early in life, followed by elevated cancer risks later in life. This transition from hypo-to hyperproliferation presents an intriguing paradox in the field of hematology known as "Dameshek's riddle." Recent cancer sequencing studies also revealed somatically acquired mutations and deletions in ribosomal proteins in T-cell acute lymphoblastic leukemia and solid tumors, further extending the list of ribosomopathies and strengthening the association between ribosomal defects and oncogenesis. In this perspective, we summarize and comment on recent findings in the field of ribosomopathies. We explain how ribosomopathies may provide clues to help explain Dameshek's paradox and highlight some of the open questions and challenges in the field. (Blood. 2015;125(9): 1377-1382

British Journal of Haematology, 2016

Diamond-Blackfan anaemia (DBA) is an inherited disease characterized by pure erythroid aplasia th... more Diamond-Blackfan anaemia (DBA) is an inherited disease characterized by pure erythroid aplasia that has been tagged as a 'ribosomopathy'. We report a multi-centre study focused on the analysis of rRNA processing of 53 Italian DBA patients using capillary electrophoresis analysis of rRNA maturation of the 40S and 60S ribosomal subunits. The ratio of 28S/18S rRNA was higher in patients with mutated ribosomal proteins (RPs) of the small ribosomal subunit. In contrast, patients with mutated RPs of the large ribosomal subunit (RPLs) had a lower 28S/18S ratio. The assay reported here would be amenable for development as a diagnostic tool.

Haematologica, Mar 1, 2015

CORRESPONDENCE Kim De Keersmaecker, Campus Gasthuisberg O&N4, box 602, Herestraat 49, 3000 Leuven... more CORRESPONDENCE Kim De Keersmaecker, Campus Gasthuisberg O&N4, box 602, Herestraat 49, 3000 Leuven. Kim.dekeersmaecker@med.kuleuven.be WORD COUNTS: Text (excl refs; max 1500): 1352 # references (max 20): 20 Cancer studies have historically focused on changes in the transcriptome of tumor cells to reveal the molecular pathways responsible for cellular transformation. In the last 20 years, however, it has become clear that deregulation of translation also plays a crucial role in cancer development and progression. Major players in cancer biology, such as the PI3K pathway, tumor suppressor protein p53 and MYC, can deregulate expression of components of the translation machinery and can influence the spectrum of mRNAs which are most efficiently translated in the cell. In addition, somatic lesions affecting ribosome biogenesis, translation initiation and elongation factors have been described in a wide variety of human

Haematologica the Hematology Journal, 2008

Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTC... more Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTCH1 signaling with γ-secretase inhibitors causes cell cycle block, but only after treatment for several days. We further documented the effects of γ-secretase inhibitor treatment on T-cell acute lymphoblastic leukemia cell lines and tested whether combining γ-secretase inhibitors with other anti-cancer drugs offers a therapeutic advantage.

Haematologica, 2005

Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymp... more Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) has been identified by molecular characterization of recurrent chromosomal aberrations and more subtle genetic defects. When reviewing the current list of oncogenes and tumor suppressor genes, it becomes clear that these can be grouped into four classes of mutations, which are involved in: (i) cell cycle deregulation; (ii) impaired differentiation; (iii) proliferation and survival advantage and (iv) unlimited self-renewal capacity. Based on recent studies of T-ALL, we can speculate that at least these four different mutations are required for the development of T-ALL. In this review we summarize our current insights into the molecular pathogenesis of T-ALL, and we discuss how these molecular findings provide new directions for future research and novel therapeutic strategies in T-ALL. Acute Lymphoblastic Leukemia • Molecular Basis of Disease © F e r r a t a S t o r t i F o u n d a t i o n haematologica/the hematology journal | 2005; 90(8) | 1117 | Genetics of T-ALL Genetics of T-ALL haematologica/the hematology journal | 2005; 90(8) | 1121 | © F e r r a t a S t o r t i F o u n d a t i o n K. De Keersmaecker et al. | 1122 | haematologica/the hematology journal | 2005; 90(8) © F e r r a t a S t o r t i F o u n d a t i o n © F e r r a t a S t o r t i F o u n d a t i o n

Haematologica

Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTC... more Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTCH1 signaling with gamma-secretase inhibitors causes cell cycle block, but only after treatment for several days. We further documented the effects of gamma-secretase inhibitor treatment on T-cell acute lymphoblastic leukemia cell lines and tested whether combining gamma-secretase inhibitors with other anti-cancer drugs offers a therapeutic advantage. The effect of gamma-secretase inhibitor treatment and combinations of gamma-secretase inhibitors with chemotherapy or glucocorticoids was assessed on T-cell acute lymphoblastic leukemia cell lines. We sequenced NOTCH1 in T-cell acute lymphoblastic leukemia cases with ABL1 fusions and tested combinations of gamma-secretase inhibitors and the ABL1 inhibitor imatinib in a T-cell acute lymphoblastic leukemia cell line. gamma-secretase inhibitor treatment for 5-7 days reversibly inhibited cell proliferation, caused cell cycle block in sensitive T...

Haematologica, 2005

Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymp... more Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) has been identified by molecular characterization of recurrent chromosomal aberrations and more subtle genetic defects. When reviewing the current list of oncogenes and tumor suppressor genes, it becomes clear that these can be grouped into four classes of mutations, which are involved in: (i) cell cycle deregulation; (ii) impaired differentiation; (iii) proliferation and survival advantage and (iv) unlimited self-renewal capacity. Based on recent studies of T-ALL, we can speculate that at least these four different mutations are required for the development of T-ALL. In this review we summarize our current insights into the molecular pathogenesis of T-ALL, and we discuss how these molecular findings provide new directions for future research and novel therapeutic strategies in T-ALL.

Molecular Pathology Library, 2010

Page 1. Introduction Precursor T-cell lymphoblastic leukemias and lymphomas represent 15% of chil... more Page 1. Introduction Precursor T-cell lymphoblastic leukemias and lymphomas represent 15% of childhood acute lymphoblastic leukemias (ALLs) and one third of pediatric non-Hodgkin lympho-mas, respectively. T-cell ALLs ...

PLoS ONE, 2012

With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently ... more With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.

Nature Cell Biology, 2010

Molecular Cell, 2008

Genetic alterations causing constitutive tyrosine kinase activation are observed in a broad spect... more Genetic alterations causing constitutive tyrosine kinase activation are observed in a broad spectrum of cancers. Thus far, these mutant kinases have been localized to the plasma membrane or cytoplasm, where they engage proliferation and survival pathways. We report that the NUP214-ABL1 fusion is unique among these because of its requisite localization to the nuclear pore complex for its transforming potential. We show that NUP214-ABL1 displays attenuated transforming capacity as compared to BCR-ABL1 and that NUP214-ABL1 preferentially transforms T cells, which is in agreement with its unique occurrence in T cell acute lymphoblastic leukemia. Furthermore, NUP214-ABL1 differs from BCR-ABL1 in subcellular localization, initiation of kinase activity, and signaling and lacks phosphorylation on its activation loop. In addition to delineating an unusual mechanism for kinase activation, this study provides new insights into the spectrum of chromosomal translocations involving nucleoporins by indicating that the nuclear pore context itself may play a central role in transformation.

How ribosomes translate cancer

A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somat... more A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis – from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on “onco-ribosomes” as an Achilles’ heel of cancer cells and a promising target for further therapeutic intervention.

Several somatic ribosome defects have recently been discovered in cancer, yet their oncogenic mec... more Several somatic ribosome defects have recently been discovered in cancer, yet their oncogenic mechanisms remain poorly understood. Here we investigated the pathogenic role of the recurrent R98S mutation in ribosomal protein L10 (RPL10-R98S) found in T-ALL. The JAK-STAT signaling pathway is a critical controller of cellular proliferation and survival. A proteome screen revealed overexpression of several Jak-Stat signaling proteins in engineered RPL10-R98S mouse lymphoid cells, which we confirmed in hematopoietic cells from transgenic Rpl10-R98S mice and T-ALL xenograft samples. RPL10-R98S expressing cells displayed JAK-STAT pathway hyper-activation upon cytokine stimulation, as well as increased sensitivity to clinically used JAK-STAT inhibitors like pimozide. A mutually exclusive mutation pattern between RPL10-R98S and JAK-STAT mutations in T-ALL patients further suggests that RPL10-R98S functionally mimics JAK-STAT activation. Mechanistically, besides transcriptional changes, RPL10-R98S caused reduction of apparent programmed ribosomal frameshifting at several ribosomal frameshift signals in mouse and human Jak-Stat genes, as well as decreased Jak1 degradation. Of further medical interest, RPL10-R98S cells showed reduced proteasome activity and enhanced sensitivity to clinical proteasome inhibitors. Collectively, we describe modulation of the JAK-STAT cascade as a novel cancer-promoting activity of a ribosomal mutation, and expand the relevance of this cascade in leukemia.

The Notch1 gene is a major oncogenic driver and therapeutic target in T-cell acute lymphoblastic ... more The Notch1 gene is a major oncogenic driver and therapeutic target in T-cell acute lymphoblastic leukemia (T-ALL). However, inhibition of NOTCH signaling with γ-secretase inhibitors (GSIs) has shown limited antileukemic activity in clinical trials. Here we performed an expression-based virtual screening to identify highly active antileukemic drugs that synergize with NOTCH1 inhibition in T-ALL. Among these, withaferin A demonstrated the strongest cytotoxic and GSI-synergistic antileukemic effects in vitro and in vivo. Mechanistically, network perturbation analyses showed eIF2A-phosphorylation-mediated inhibition of protein translation as a critical mediator of the antileukemic effects of withaferin A and its interaction with NOTCH1 inhibition. Overall, these results support a role for anti-NOTCH1 therapies and protein translation inhibitor combinations in the treatment of T-ALL.

For many years, defects in the ribosome have been associated to cancer. Recently, somatic mutatio... more For many years, defects in the ribosome have been associated to cancer. Recently, somatic mutations and deletions affecting ribosomal protein genes were identified in a few leukemias and solid tumor types. However, systematic analysis of all 81 known ribosomal protein genes across cancer types is lacking. We screened mutation and copy number data of respectively 4926 and 7322 samples from 16 cancer types and identified six altered genes (RPL5, RPL11, RPL23A, RPS5, RPS20 and RPSA). RPL5 was located at a significant peak of heterozygous deletion or mutated in 11% of glioblastoma, 28% of melanoma and 34% of breast cancer samples. Moreover, patients with low RPL5 expression displayed worse overall survival in glioblastoma and in one breast cancer cohort. RPL5 knockdown in breast cancer cell lines enhanced G2/M cell cycle progression and accelerated tumor progression in a xenograft mouse model. Interestingly, our data suggest that the tumor suppressor role of RPL5 is not only mediated by its known function as TP53 or c-MYC regulator. In conclusion, RPL5 heterozygous inactivation occurs at high incidence (11-34%) in multiple tumor types, currently representing the most common somatic ribosomal protein defect in cancer, and we demonstrate a tumor suppressor role for RPL5 in breast cancer.

Chromosomal region 1p22 is deleted in ⩾20% of multiple myeloma (MM) patients, suggesting the pres... more Chromosomal region 1p22 is deleted in ⩾20% of multiple myeloma (MM) patients, suggesting the presence of an unidentified tumor suppressor. Using high-resolution genomic profiling, we delimit a 58 kb minimal deleted region (MDR) on 1p22.1 encompassing two genes: ectopic viral integration site 5 (EVI5) and ribosomal protein L5 (RPL5). Low mRNA expression of EVI5 and RPL5 was associated with worse survival in diagnostic cases. Patients with 1p22 deletion had lower mRNA expression of EVI5 and RPL5, however, 1p22 deletion status is a bad predictor of RPL5 expression in some cases, suggesting that other mechanisms downregulate RPL5 expression. Interestingly, RPL5 but not EVI5 mRNA levels were significantly lower in relapsed patients responding to bortezomib and; both in newly diagnosed and relapsed patients, bortezomib treatment could overcome their bad prognosis by raising their progression-free survival to equal that of patients with high RPL5 expression. In conclusion, our genetic data restrict the MDR on 1p22 to EVI5 and RPL5 and although the role of these genes in promoting MM progression remains to be determined, we identify RPL5 mRNA expression as a biomarker for initial response to bortezomib in relapsed patients and subsequent survival benefit after long-term treatment in newly diagnosed and relapsed patients.

T-cell acute lymphoblastic leukemia (TALL) is an aggressive malignancy caused by the accumulation... more T-cell acute lymphoblastic leukemia (TALL) is an aggressive malignancy caused by the accumulation of genomic lesions that affect the development of T-cells. Since many years, it has been established that deregulated expression of transcription factors, impairment of the CDKN2A/2B cell cycle regulators and hyperactive NOTCH1 signaling play prominent roles in the pathogenesis of this leukemia. In the past decade, systematic screening of TALL genomes by high resolution copy number arrays and next-generation sequencing technologies has revealed that T-cell progenitors accumulate additional mutations affecting JAK/STAT signaling, protein translation and epigenetic control, providing novel attractive targets for therapy. In this review, we provide an update on our knowledge on TALL pathogenesis, on the opportunities for the introduction of targeted therapy and on the challenges that are still ahead.

Blood, 2015

Ribosomopathies are largely congenital diseases linked to defects in ribosomal proteins or biogen... more Ribosomopathies are largely congenital diseases linked to defects in ribosomal proteins or biogenesis factors. Some of these disorders are characterized by hypoproliferative phenotypes such as bone marrow failure and anemia early in life, followed by elevated cancer risks later in life. This transition from hypo-to hyperproliferation presents an intriguing paradox in the field of hematology known as "Dameshek's riddle." Recent cancer sequencing studies also revealed somatically acquired mutations and deletions in ribosomal proteins in T-cell acute lymphoblastic leukemia and solid tumors, further extending the list of ribosomopathies and strengthening the association between ribosomal defects and oncogenesis. In this perspective, we summarize and comment on recent findings in the field of ribosomopathies. We explain how ribosomopathies may provide clues to help explain Dameshek's paradox and highlight some of the open questions and challenges in the field. (Blood. 2015;125(9): 1377-1382

British Journal of Haematology, 2016

Diamond-Blackfan anaemia (DBA) is an inherited disease characterized by pure erythroid aplasia th... more Diamond-Blackfan anaemia (DBA) is an inherited disease characterized by pure erythroid aplasia that has been tagged as a 'ribosomopathy'. We report a multi-centre study focused on the analysis of rRNA processing of 53 Italian DBA patients using capillary electrophoresis analysis of rRNA maturation of the 40S and 60S ribosomal subunits. The ratio of 28S/18S rRNA was higher in patients with mutated ribosomal proteins (RPs) of the small ribosomal subunit. In contrast, patients with mutated RPs of the large ribosomal subunit (RPLs) had a lower 28S/18S ratio. The assay reported here would be amenable for development as a diagnostic tool.

Haematologica, Mar 1, 2015

CORRESPONDENCE Kim De Keersmaecker, Campus Gasthuisberg O&N4, box 602, Herestraat 49, 3000 Leuven... more CORRESPONDENCE Kim De Keersmaecker, Campus Gasthuisberg O&N4, box 602, Herestraat 49, 3000 Leuven. Kim.dekeersmaecker@med.kuleuven.be WORD COUNTS: Text (excl refs; max 1500): 1352 # references (max 20): 20 Cancer studies have historically focused on changes in the transcriptome of tumor cells to reveal the molecular pathways responsible for cellular transformation. In the last 20 years, however, it has become clear that deregulation of translation also plays a crucial role in cancer development and progression. Major players in cancer biology, such as the PI3K pathway, tumor suppressor protein p53 and MYC, can deregulate expression of components of the translation machinery and can influence the spectrum of mRNAs which are most efficiently translated in the cell. In addition, somatic lesions affecting ribosome biogenesis, translation initiation and elongation factors have been described in a wide variety of human

Haematologica the Hematology Journal, 2008

Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTC... more Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTCH1 signaling with γ-secretase inhibitors causes cell cycle block, but only after treatment for several days. We further documented the effects of γ-secretase inhibitor treatment on T-cell acute lymphoblastic leukemia cell lines and tested whether combining γ-secretase inhibitors with other anti-cancer drugs offers a therapeutic advantage.

Haematologica, 2005

Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymp... more Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) has been identified by molecular characterization of recurrent chromosomal aberrations and more subtle genetic defects. When reviewing the current list of oncogenes and tumor suppressor genes, it becomes clear that these can be grouped into four classes of mutations, which are involved in: (i) cell cycle deregulation; (ii) impaired differentiation; (iii) proliferation and survival advantage and (iv) unlimited self-renewal capacity. Based on recent studies of T-ALL, we can speculate that at least these four different mutations are required for the development of T-ALL. In this review we summarize our current insights into the molecular pathogenesis of T-ALL, and we discuss how these molecular findings provide new directions for future research and novel therapeutic strategies in T-ALL. Acute Lymphoblastic Leukemia • Molecular Basis of Disease © F e r r a t a S t o r t i F o u n d a t i o n haematologica/the hematology journal | 2005; 90(8) | 1117 | Genetics of T-ALL Genetics of T-ALL haematologica/the hematology journal | 2005; 90(8) | 1121 | © F e r r a t a S t o r t i F o u n d a t i o n K. De Keersmaecker et al. | 1122 | haematologica/the hematology journal | 2005; 90(8) © F e r r a t a S t o r t i F o u n d a t i o n © F e r r a t a S t o r t i F o u n d a t i o n

Haematologica

Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTC... more Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTCH1 signaling with gamma-secretase inhibitors causes cell cycle block, but only after treatment for several days. We further documented the effects of gamma-secretase inhibitor treatment on T-cell acute lymphoblastic leukemia cell lines and tested whether combining gamma-secretase inhibitors with other anti-cancer drugs offers a therapeutic advantage. The effect of gamma-secretase inhibitor treatment and combinations of gamma-secretase inhibitors with chemotherapy or glucocorticoids was assessed on T-cell acute lymphoblastic leukemia cell lines. We sequenced NOTCH1 in T-cell acute lymphoblastic leukemia cases with ABL1 fusions and tested combinations of gamma-secretase inhibitors and the ABL1 inhibitor imatinib in a T-cell acute lymphoblastic leukemia cell line. gamma-secretase inhibitor treatment for 5-7 days reversibly inhibited cell proliferation, caused cell cycle block in sensitive T...

Haematologica, 2005

Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymp... more Over the past 20 years, a large number of genes involved in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) has been identified by molecular characterization of recurrent chromosomal aberrations and more subtle genetic defects. When reviewing the current list of oncogenes and tumor suppressor genes, it becomes clear that these can be grouped into four classes of mutations, which are involved in: (i) cell cycle deregulation; (ii) impaired differentiation; (iii) proliferation and survival advantage and (iv) unlimited self-renewal capacity. Based on recent studies of T-ALL, we can speculate that at least these four different mutations are required for the development of T-ALL. In this review we summarize our current insights into the molecular pathogenesis of T-ALL, and we discuss how these molecular findings provide new directions for future research and novel therapeutic strategies in T-ALL.

Molecular Pathology Library, 2010

Page 1. Introduction Precursor T-cell lymphoblastic leukemias and lymphomas represent 15% of chil... more Page 1. Introduction Precursor T-cell lymphoblastic leukemias and lymphomas represent 15% of childhood acute lymphoblastic leukemias (ALLs) and one third of pediatric non-Hodgkin lympho-mas, respectively. T-cell ALLs ...

PLoS ONE, 2012

With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently ... more With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.

Nature Cell Biology, 2010

Molecular Cell, 2008

Genetic alterations causing constitutive tyrosine kinase activation are observed in a broad spect... more Genetic alterations causing constitutive tyrosine kinase activation are observed in a broad spectrum of cancers. Thus far, these mutant kinases have been localized to the plasma membrane or cytoplasm, where they engage proliferation and survival pathways. We report that the NUP214-ABL1 fusion is unique among these because of its requisite localization to the nuclear pore complex for its transforming potential. We show that NUP214-ABL1 displays attenuated transforming capacity as compared to BCR-ABL1 and that NUP214-ABL1 preferentially transforms T cells, which is in agreement with its unique occurrence in T cell acute lymphoblastic leukemia. Furthermore, NUP214-ABL1 differs from BCR-ABL1 in subcellular localization, initiation of kinase activity, and signaling and lacks phosphorylation on its activation loop. In addition to delineating an unusual mechanism for kinase activation, this study provides new insights into the spectrum of chromosomal translocations involving nucleoporins by indicating that the nuclear pore context itself may play a central role in transformation.