ERM 206 INSERM, Faculte de Science de Luminy, Universite de Ia Mediterranee, Case 906, Parc Scien... more ERM 206 INSERM, Faculte de Science de Luminy, Universite de Ia Mediterranee, Case 906, Parc Scientifique de Luminy, F-13288 Marseille Cedex 9, 1FR57, France INSERM U435, Universite de Rennes I, Campus de Beaulieu, Avenue du General, Leclerc, 35042 Rennes Cedex, France MRC HGMP, Wellcome Trust Genome Campus, Hinxton CB10 ISB, UK Centre d’Immunologie INSERM-CNRS, Case 906, Parc Scientifique de Luminy, F-13288 Marseille Cedex 9, Faculte de Science de Luminy, Universite de la Mediterranee, IFR57, Marseille, France
supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-AL... more supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-ALL. Figure S2. Global flow chart of the patients Figure S3. Comparison of outcomes between LALA94 patients with central lab onco-genetic study performed (dotted line) and patients without (full line). Figure S4. Epigenetic histone marks. Figure S5. Kaplan-Meier graph for OS is shown for TAL1+ patients treated on LALA-94 vs. GRAALL-2003/2005 trials. Figure S6. TAL1 expression normalised to GAPDH by RTQ-PCR in 8 PDX treated with L-asparaginase (Rf. Figure 4H). Figure S7. (A) Correlation analysis between ASNS expression and ASNS promoter methylation ratio. (B) ASNS transcriptional expression normalized to GAPDH in T-ALL, in normal Bone Marrow (BM) (100%, 50%, 10% and 1%) and in normal Peripheral Blood Cells (PBL) (100%, 50%, 10% and 1. (C) comparison of ASNS transcriptional expression in non-sorted diagnostic sample, blast and non-blast sorted cells in two patients with a hypermethylated ASN...
Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depe... more Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depending on the underlying oncogenic events is a promising research area. TLX1- or TLX3-deregulated T-cell acute lymphoblastic leukemias (T-ALL; TLX1/3+) share an immature cortical phenotype and similar transcriptional signatures. However, their prognostic impacts differ, and inconsistent clinical outcome has been reported for TLX3. We therefore hypothesized that the overlapping transcriptional profiles of TLX1+ and TLX3+ T-ALLs would allow identification of candidate genes, which might determine their distinct clinical outcomes.Experimental Design:We compared TLX1+ and TLX3+ adult T-ALL outcome in the successive French national LALA-94 and GRAALL-2003/2005 multicentric trials and analyzed transcriptomic data to identify differentially expressed genes. Epigenetic regulation of asparagine synthetase (ASNS) and in vitro l-asparaginase sensitivity were evaluated for T-ALL cell lines and primar...
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-speci... more Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain–associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain–associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain–associated genes in preleukemic cells. Finally,...
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visual... more TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks Lepoivre et al. Lepoivre et al. BMC Bioinformatics 2012, 13:19
The high mortality rate in septic shock patients is likely due to environmental and genetic facto... more The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this reg...
Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition a... more Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes i...
Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortali... more Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortality rates. CD8 + T lymphocytes are responsible for the elimination of infected cells. Understanding the response of these cells to normal and high stimulatory conditions is important to propose better treatments and vaccine formulations for neonates. We have previously shown that human neonatal CD8 + T cells overexpress innate inflammatory genes and have a low expression of cytotoxic and cell signaling genes. To investigate the activation potential of these cells, we evaluated the transcriptome of human neonatal and adult naïve CD8 + T cells after TCR/CD28 signals ± IL-12. We found that in neonatal cells, IL-12 signals contribute to the adult-like expression of genes associated with cell-signaling, T-cell cytokines, metabolism, and cell division. Additionally, IL-12 signals contributed to the downregulation of the neutrophil signature transcription factor CEBPE and other immaturity related genes. To validate the transcriptome results, we evaluated the expression of a series of genes by RT-qPCR and the promoter methylation status on independent samples. We found that in agreement with the transcriptome, IL-12 signals contributed to the chromatin closure of neutrophil-like genes and the opening of cytotoxicity genes, suggesting that IL-12 signals contribute to the epigenetic reprogramming of neonatal lymphocytes. Furthermore, high expression of some inflammatory genes was observed in naïve and stimulated neonatal cells, in agreement with the high inflammatory profile of neonates to infections. Altogether our results point to an important contribution of IL-12 signals to the reprogramming of the neonatal CD8 + T cells.
Normal T-cell differentiation requires a complex regulatory network which supports a series of ma... more Normal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models. Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8-double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation. Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Ca...
Circulating plasma cells in 10 cases of reactive plasmacytosis had a shared phenotype with early ... more Circulating plasma cells in 10 cases of reactive plasmacytosis had a shared phenotype with early plasma cell (CD19+CD38+ CD138+ CD40+CD45+ CD11a+ CD49e−CD56−). In most cases, a minor subpopulation of CD28+ plasma cells was also detected. Reactive plasma cells were highly proliferative, suggesting the presence of circulating progenitors (plasmablasts). After CD138+ plasma cell removal, highly proliferative CD138− plasmablasts differentiated into CD138+ plasma cells within a few days. This differentiation, which was associated with increased CD38 and decreased HLA-DR expression, was further confirmed by a large increase in intracellular Ig content (associated with Ig secretion) and was concomitant with extensive secretion of interleukin-6 (IL-6). The addition of neutralizing anti–IL-6 and anti-CD126 (IL-6 receptor) monoclonal antibodies totally prevented Ig secretion and cell differentiation by inducing apoptosis of plasmablasts, which indicates that IL-6 is an essential survival fact...
Chemotherapeutic treatment for Canine transmissible venereal tumor (CTVT) commonly relies on vinc... more Chemotherapeutic treatment for Canine transmissible venereal tumor (CTVT) commonly relies on vincristine administration. Since the treatment outcomes can vary among CTVT cases, gaining insight into the tumor cell mechanisms influencing vincristine's potency should render veterinarians novel knowledge to enhance its therapeutic effect. This study aimed to attain such knowledge from a meta-analysis of CTVT mRNA sequencing (mRNA-seq) transcriptome data using Factor Analysis for Bicluster Acquisition (FABIA) biclustering. FABIA biclustering identified 459 genes consistently expressed among mRNA-seq transcription profiling of CTVT samples regressed by vincristine. These genes were also differentially expressed from those of progressive CTVT (FDR 0.001). Enrichment analysis illustrated the affiliation of these genes with "Antigen presentation" and "Lysosome" GO terms (FDR 0.05). Several genes in "Lysosome" term involved 5 cell mechanisms-antigen presentation, autophagy, cell-adhesion, lysosomal membrane permeabilization (LMP), and PI3K/mTOR signaling. This study integrated FABIA biclustering in CTVT transcriptome analysis to gain insight into cell mechanisms responsible for vincristine-sensitive characteristics of the tumor, in order to identify new molecular targets augmenting therapeutic effect of vincristine. Interestingly, the analysis indicated LMP targeting by lysosome destabilizing agent-siramesine as the promising vincristine's enhancer for future study. As far as we know, this is the first canine tumor transcriptomic meta-analysis applying FABIA biclustering for the betterment of future CTVT therapy. This study hereby provided an interesting manifestation to acquire such knowledge in other canine neoplasia.
Motivation While Python has become very popular in bioinformatics, a limited number of libraries ... more Motivation While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format. Results We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic featur...
Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depe... more Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depending on the underlying oncogenic events is a promising research area. TLX1- or TLX3-deregulated T-cell acute lymphoblastic leukemias (T-ALL; TLX1/3+) share an immature cortical phenotype and similar transcriptional signatures. However, their prognostic impacts differ, and inconsistent clinical outcome has been reported for TLX3. We therefore hypothesized that the overlapping transcriptional profiles of TLX1+ and TLX3+ T-ALLs would allow identification of candidate genes, which might determine their distinct clinical outcomes.Experimental Design:We compared TLX1+ and TLX3+ adult T-ALL outcome in the successive French national LALA-94 and GRAALL-2003/2005 multicentric trials and analyzed transcriptomic data to identify differentially expressed genes. Epigenetic regulation of asparagine synthetase (ASNS) and in vitro l-asparaginase sensitivity were evaluated for T-ALL cell lines and primar...
Several studies have demonstrated that LncRNAs can play major roles in cancer development. The cr... more Several studies have demonstrated that LncRNAs can play major roles in cancer development. The creation of a catalogue of LncRNAs expressed in T cell acute lymphoblastic leukemia (T-ALL) is thus of particular importance. However, this task is challenging as LncRNA expression is highly restricted in a time and space manner and may thus greatly differ between samples. We performed a systematic transcript discovery in RNA-Seq data obtained from TALL primary cells and cell lines. This led to the identification of 2560 novel LncRNAs. After the integration of these transcripts into a large compendium of LncRNAs (n=30478) containing both known LncRNAs and those previously described in T-ALLs, we then performed a systematic genomic and epigenetic characterization of these transcript models demonstrating that these novel LncRNAs share properties with known LncRNAs. Finally, we provide evidences that these novel transcripts could be enriched in LncRNAs with potential oncogenic effects and identified a subset of LncRNAs coregulated with TALL oncogenes. Overall, our study represents a comprehensive resource of LncRNAs expressed in TALL and might provide new cues on the role of lncRNAs in this type of leukemia.
Multiple myeloma (MM) is a malignancy characterized by a very slow proliferation of malignant pla... more Multiple myeloma (MM) is a malignancy characterized by a very slow proliferation of malignant plasma cells leading to their accumulation within the bone marrow. This suggests that resistance to apoptosis may play a critical role both in the pathogenesis and resistance to treatment of MM. Bcl-2 is a key protein for the regulation of apoptosis. However, it has been shown that this protein also regulates the state of proliferation. In the current study, we show that malignant plasma cells from both the bone marrow and peripheral blood express high levels of Bcl-2 and are slowly proliferating cells. In contrast, myeloma cells from extramedullary sites (ie pleural effusion, ascitis, mammary and gastric plasmacytoma) express Bcl-2 weakly while being highly proliferative. Normal non-dividing bone marrow plasma cells express high levels of Bcl-2 protein. In contrast, four highly proliferative reactive plasmacytosis express weak levels of Bcl-2. We conclude that there is an inverse correlation between Bcl-2 expression and the proliferation rate of both normal and malignant plasma cells. These data may be explained by the double function of Bcl-2, ie its well known function as an anti-apoptotic molecule and its intriguing function as an inhibitory molecule of cell proliferation.
In this study, we show that malignant plasma cells from patients with either primary (n = 12) or ... more In this study, we show that malignant plasma cells from patients with either primary (n = 12) or secondary (n = 15) plasma cell leukemia (PCL) do not express CD56 at all, neither in the bone marrow nor the peripheral blood in 81% of cases. On the other hand, multiple myeloma (MM) at diagnosis overexpress it in 63 of 94 (67%) cases (P = 0.0001). In three secondary PCL evaluated serially, CD56 was also lacking at diagnosis showing that CD56 is not downregulated at the end stage of the disease but rather not upregulated in this subset of patients. This last concept is strengthened by the observation that 29% of MM patients lacking CD56 or weakly expressing it at diagnosis present a detectable leukemic phase vs 11% only in CD56 + MM (P = 0.06). Forty percent of all the CD56 −/weak malignant plasma cell disorders present or develop a leukemic phase vs only 15% of CD56 + cases (P Ͻ 0.008). CD56 −/weak MM subset is also associated with a significantly less aggressive osteolytic potential (P = 0.012). We conclude that the lack or weak expression of CD56 is a characteristic feature of PCL but also delineates a special subset of MM at diagnosis mainly characterized by a lower osteolytic potential and a trend for malignant plasma cells to circulate in the peripheral blood more overtly.
In order to evaluate putative changes of major adhesion molecule expression on plasma cells (PCs)... more In order to evaluate putative changes of major adhesion molecule expression on plasma cells (PCs) associated with malignant transformation, tumor spreading, and immortalization, we have quantified and compared the expression of CD56, CD44, CD11a, CD49e, and CD45 RO/RA on normal PCs, malignant PCs from multiple myeloma patients in chronic phase, in accelerated phase with or without extramedullary progression, and from human myeloma cell lines. Plasma cell phenotype was defined with the use of two-color immunofluorescence in combination with B-B4 or anti-CD38 antibodies. We found that all the adhesion antigens were expressed on normal PCs. Malignancy was characterized by an overexpression of CD56, whereas extramedullary spreading was associated with a dramatic down expression of CD56. Although CD44 remained unchanged, the subpopulation of PCs expressing CD11a, CD49e, and CD45RA/RO were significantly reduced during malignancy, and each of these negative subpopulations increased during ...
ERM 206 INSERM, Faculte de Science de Luminy, Universite de Ia Mediterranee, Case 906, Parc Scien... more ERM 206 INSERM, Faculte de Science de Luminy, Universite de Ia Mediterranee, Case 906, Parc Scientifique de Luminy, F-13288 Marseille Cedex 9, 1FR57, France INSERM U435, Universite de Rennes I, Campus de Beaulieu, Avenue du General, Leclerc, 35042 Rennes Cedex, France MRC HGMP, Wellcome Trust Genome Campus, Hinxton CB10 ISB, UK Centre d’Immunologie INSERM-CNRS, Case 906, Parc Scientifique de Luminy, F-13288 Marseille Cedex 9, Faculte de Science de Luminy, Universite de la Mediterranee, IFR57, Marseille, France
supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-AL... more supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-ALL. Figure S2. Global flow chart of the patients Figure S3. Comparison of outcomes between LALA94 patients with central lab onco-genetic study performed (dotted line) and patients without (full line). Figure S4. Epigenetic histone marks. Figure S5. Kaplan-Meier graph for OS is shown for TAL1+ patients treated on LALA-94 vs. GRAALL-2003/2005 trials. Figure S6. TAL1 expression normalised to GAPDH by RTQ-PCR in 8 PDX treated with L-asparaginase (Rf. Figure 4H). Figure S7. (A) Correlation analysis between ASNS expression and ASNS promoter methylation ratio. (B) ASNS transcriptional expression normalized to GAPDH in T-ALL, in normal Bone Marrow (BM) (100%, 50%, 10% and 1%) and in normal Peripheral Blood Cells (PBL) (100%, 50%, 10% and 1. (C) comparison of ASNS transcriptional expression in non-sorted diagnostic sample, blast and non-blast sorted cells in two patients with a hypermethylated ASN...
Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depe... more Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depending on the underlying oncogenic events is a promising research area. TLX1- or TLX3-deregulated T-cell acute lymphoblastic leukemias (T-ALL; TLX1/3+) share an immature cortical phenotype and similar transcriptional signatures. However, their prognostic impacts differ, and inconsistent clinical outcome has been reported for TLX3. We therefore hypothesized that the overlapping transcriptional profiles of TLX1+ and TLX3+ T-ALLs would allow identification of candidate genes, which might determine their distinct clinical outcomes.Experimental Design:We compared TLX1+ and TLX3+ adult T-ALL outcome in the successive French national LALA-94 and GRAALL-2003/2005 multicentric trials and analyzed transcriptomic data to identify differentially expressed genes. Epigenetic regulation of asparagine synthetase (ASNS) and in vitro l-asparaginase sensitivity were evaluated for T-ALL cell lines and primar...
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-speci... more Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain–associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain–associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain–associated genes in preleukemic cells. Finally,...
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visual... more TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks Lepoivre et al. Lepoivre et al. BMC Bioinformatics 2012, 13:19
The high mortality rate in septic shock patients is likely due to environmental and genetic facto... more The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this reg...
Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition a... more Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes i...
Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortali... more Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortality rates. CD8 + T lymphocytes are responsible for the elimination of infected cells. Understanding the response of these cells to normal and high stimulatory conditions is important to propose better treatments and vaccine formulations for neonates. We have previously shown that human neonatal CD8 + T cells overexpress innate inflammatory genes and have a low expression of cytotoxic and cell signaling genes. To investigate the activation potential of these cells, we evaluated the transcriptome of human neonatal and adult naïve CD8 + T cells after TCR/CD28 signals ± IL-12. We found that in neonatal cells, IL-12 signals contribute to the adult-like expression of genes associated with cell-signaling, T-cell cytokines, metabolism, and cell division. Additionally, IL-12 signals contributed to the downregulation of the neutrophil signature transcription factor CEBPE and other immaturity related genes. To validate the transcriptome results, we evaluated the expression of a series of genes by RT-qPCR and the promoter methylation status on independent samples. We found that in agreement with the transcriptome, IL-12 signals contributed to the chromatin closure of neutrophil-like genes and the opening of cytotoxicity genes, suggesting that IL-12 signals contribute to the epigenetic reprogramming of neonatal lymphocytes. Furthermore, high expression of some inflammatory genes was observed in naïve and stimulated neonatal cells, in agreement with the high inflammatory profile of neonates to infections. Altogether our results point to an important contribution of IL-12 signals to the reprogramming of the neonatal CD8 + T cells.
Normal T-cell differentiation requires a complex regulatory network which supports a series of ma... more Normal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models. Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8-double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation. Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Ca...
Circulating plasma cells in 10 cases of reactive plasmacytosis had a shared phenotype with early ... more Circulating plasma cells in 10 cases of reactive plasmacytosis had a shared phenotype with early plasma cell (CD19+CD38+ CD138+ CD40+CD45+ CD11a+ CD49e−CD56−). In most cases, a minor subpopulation of CD28+ plasma cells was also detected. Reactive plasma cells were highly proliferative, suggesting the presence of circulating progenitors (plasmablasts). After CD138+ plasma cell removal, highly proliferative CD138− plasmablasts differentiated into CD138+ plasma cells within a few days. This differentiation, which was associated with increased CD38 and decreased HLA-DR expression, was further confirmed by a large increase in intracellular Ig content (associated with Ig secretion) and was concomitant with extensive secretion of interleukin-6 (IL-6). The addition of neutralizing anti–IL-6 and anti-CD126 (IL-6 receptor) monoclonal antibodies totally prevented Ig secretion and cell differentiation by inducing apoptosis of plasmablasts, which indicates that IL-6 is an essential survival fact...
Chemotherapeutic treatment for Canine transmissible venereal tumor (CTVT) commonly relies on vinc... more Chemotherapeutic treatment for Canine transmissible venereal tumor (CTVT) commonly relies on vincristine administration. Since the treatment outcomes can vary among CTVT cases, gaining insight into the tumor cell mechanisms influencing vincristine's potency should render veterinarians novel knowledge to enhance its therapeutic effect. This study aimed to attain such knowledge from a meta-analysis of CTVT mRNA sequencing (mRNA-seq) transcriptome data using Factor Analysis for Bicluster Acquisition (FABIA) biclustering. FABIA biclustering identified 459 genes consistently expressed among mRNA-seq transcription profiling of CTVT samples regressed by vincristine. These genes were also differentially expressed from those of progressive CTVT (FDR 0.001). Enrichment analysis illustrated the affiliation of these genes with "Antigen presentation" and "Lysosome" GO terms (FDR 0.05). Several genes in "Lysosome" term involved 5 cell mechanisms-antigen presentation, autophagy, cell-adhesion, lysosomal membrane permeabilization (LMP), and PI3K/mTOR signaling. This study integrated FABIA biclustering in CTVT transcriptome analysis to gain insight into cell mechanisms responsible for vincristine-sensitive characteristics of the tumor, in order to identify new molecular targets augmenting therapeutic effect of vincristine. Interestingly, the analysis indicated LMP targeting by lysosome destabilizing agent-siramesine as the promising vincristine's enhancer for future study. As far as we know, this is the first canine tumor transcriptomic meta-analysis applying FABIA biclustering for the betterment of future CTVT therapy. This study hereby provided an interesting manifestation to acquire such knowledge in other canine neoplasia.
Motivation While Python has become very popular in bioinformatics, a limited number of libraries ... more Motivation While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format. Results We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic featur...
Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depe... more Purpose:Biological explanation for discrepancies in patient-related response to chemotherapy depending on the underlying oncogenic events is a promising research area. TLX1- or TLX3-deregulated T-cell acute lymphoblastic leukemias (T-ALL; TLX1/3+) share an immature cortical phenotype and similar transcriptional signatures. However, their prognostic impacts differ, and inconsistent clinical outcome has been reported for TLX3. We therefore hypothesized that the overlapping transcriptional profiles of TLX1+ and TLX3+ T-ALLs would allow identification of candidate genes, which might determine their distinct clinical outcomes.Experimental Design:We compared TLX1+ and TLX3+ adult T-ALL outcome in the successive French national LALA-94 and GRAALL-2003/2005 multicentric trials and analyzed transcriptomic data to identify differentially expressed genes. Epigenetic regulation of asparagine synthetase (ASNS) and in vitro l-asparaginase sensitivity were evaluated for T-ALL cell lines and primar...
Several studies have demonstrated that LncRNAs can play major roles in cancer development. The cr... more Several studies have demonstrated that LncRNAs can play major roles in cancer development. The creation of a catalogue of LncRNAs expressed in T cell acute lymphoblastic leukemia (T-ALL) is thus of particular importance. However, this task is challenging as LncRNA expression is highly restricted in a time and space manner and may thus greatly differ between samples. We performed a systematic transcript discovery in RNA-Seq data obtained from TALL primary cells and cell lines. This led to the identification of 2560 novel LncRNAs. After the integration of these transcripts into a large compendium of LncRNAs (n=30478) containing both known LncRNAs and those previously described in T-ALLs, we then performed a systematic genomic and epigenetic characterization of these transcript models demonstrating that these novel LncRNAs share properties with known LncRNAs. Finally, we provide evidences that these novel transcripts could be enriched in LncRNAs with potential oncogenic effects and identified a subset of LncRNAs coregulated with TALL oncogenes. Overall, our study represents a comprehensive resource of LncRNAs expressed in TALL and might provide new cues on the role of lncRNAs in this type of leukemia.
Multiple myeloma (MM) is a malignancy characterized by a very slow proliferation of malignant pla... more Multiple myeloma (MM) is a malignancy characterized by a very slow proliferation of malignant plasma cells leading to their accumulation within the bone marrow. This suggests that resistance to apoptosis may play a critical role both in the pathogenesis and resistance to treatment of MM. Bcl-2 is a key protein for the regulation of apoptosis. However, it has been shown that this protein also regulates the state of proliferation. In the current study, we show that malignant plasma cells from both the bone marrow and peripheral blood express high levels of Bcl-2 and are slowly proliferating cells. In contrast, myeloma cells from extramedullary sites (ie pleural effusion, ascitis, mammary and gastric plasmacytoma) express Bcl-2 weakly while being highly proliferative. Normal non-dividing bone marrow plasma cells express high levels of Bcl-2 protein. In contrast, four highly proliferative reactive plasmacytosis express weak levels of Bcl-2. We conclude that there is an inverse correlation between Bcl-2 expression and the proliferation rate of both normal and malignant plasma cells. These data may be explained by the double function of Bcl-2, ie its well known function as an anti-apoptotic molecule and its intriguing function as an inhibitory molecule of cell proliferation.
In this study, we show that malignant plasma cells from patients with either primary (n = 12) or ... more In this study, we show that malignant plasma cells from patients with either primary (n = 12) or secondary (n = 15) plasma cell leukemia (PCL) do not express CD56 at all, neither in the bone marrow nor the peripheral blood in 81% of cases. On the other hand, multiple myeloma (MM) at diagnosis overexpress it in 63 of 94 (67%) cases (P = 0.0001). In three secondary PCL evaluated serially, CD56 was also lacking at diagnosis showing that CD56 is not downregulated at the end stage of the disease but rather not upregulated in this subset of patients. This last concept is strengthened by the observation that 29% of MM patients lacking CD56 or weakly expressing it at diagnosis present a detectable leukemic phase vs 11% only in CD56 + MM (P = 0.06). Forty percent of all the CD56 −/weak malignant plasma cell disorders present or develop a leukemic phase vs only 15% of CD56 + cases (P Ͻ 0.008). CD56 −/weak MM subset is also associated with a significantly less aggressive osteolytic potential (P = 0.012). We conclude that the lack or weak expression of CD56 is a characteristic feature of PCL but also delineates a special subset of MM at diagnosis mainly characterized by a lower osteolytic potential and a trend for malignant plasma cells to circulate in the peripheral blood more overtly.
In order to evaluate putative changes of major adhesion molecule expression on plasma cells (PCs)... more In order to evaluate putative changes of major adhesion molecule expression on plasma cells (PCs) associated with malignant transformation, tumor spreading, and immortalization, we have quantified and compared the expression of CD56, CD44, CD11a, CD49e, and CD45 RO/RA on normal PCs, malignant PCs from multiple myeloma patients in chronic phase, in accelerated phase with or without extramedullary progression, and from human myeloma cell lines. Plasma cell phenotype was defined with the use of two-color immunofluorescence in combination with B-B4 or anti-CD38 antibodies. We found that all the adhesion antigens were expressed on normal PCs. Malignancy was characterized by an overexpression of CD56, whereas extramedullary spreading was associated with a dramatic down expression of CD56. Although CD44 remained unchanged, the subpopulation of PCs expressing CD11a, CD49e, and CD45RA/RO were significantly reduced during malignancy, and each of these negative subpopulations increased during ...
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Papers by Denis Puthier