Pascal Kahlem - Academia.edu (original) (raw)

Papers by Pascal Kahlem

Gene Function & Disease, 2000

than one century after the discovery of trisomy 21, the molecular mechanisms under-Berlin-Dahlem,... more than one century after the discovery of trisomy 21, the molecular mechanisms under-Berlin-Dahlem, Germany lying the complex phenotype associated with Down syndrome (DS) remain unknown. Up to now, the molecular consequences of gene-dosage imbalance have been mainly investigated by the definition of DS critical regions, based on phenotype-genotype correlations established for rare cases of partial trisomy 21. Recently, the generation of trisomic mouse models has opened interesting possibilities for studying components of the DS phenotype, addressing in particular the cerebellar pathology. The complete DNA sequence, clone map, and gene catalogue of chromosome 21 offers new molecular tools for revisiting phenotype-genotype correlations and for dissecting the molecular bases of DS pathogenesis, using strategic technologies that will allow to define molecular profiles of trisomy 21.

Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie, 1995

Long QT syndrome (LQT) is an autosomal dominant cardiac disease characterized by ventricular arrh... more Long QT syndrome (LQT) is an autosomal dominant cardiac disease characterized by ventricular arrhythmia. A first locus for LQT has been identified on chromosome 11p15.5 (LQT1), closely linked to HRAS. To refine the location of LQT1, microsatellites were genotyped in 8 French families and the following order was determined: tel-HRAS-DRD4-D11S922-D11S4046- IGF2-INS-TH-D11S1318-D11S1323-D11S1338-D11S90 9-D11S1346-cen. By haplotype analysis, 12 crossing-over events were identified in affected and unaffected subjects, delineating the LQT1 candidate region to 7 cM. This new delineated localization between D11S1318 and D11S1323 is in a more centromeric region than previously thought and is 5 cM proximal to HRAS.

The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular c... more The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular characterization of all of its genes. Trisomy 21 is associated with Down's syndrome, the most common genetic cause of mental retardation in humans. The phenotype includes various organ dysmorphies, stereotypic craniofacial anomalies and brain malformations. Molecular analysis of congenital aneuploidies poses a particular challenge because the aneuploid region contains many protein-coding genes whose function is unknown. One essential step towards understanding their function is to analyse mRNA expression patterns at key stages of organism development. Seminal works in flies, frogs and mice showed that genes whose expression is restricted spatially and/or temporally are often linked with specific ontogenic processes. Here we describe expression profiles of mouse orthologues to HSA21 genes by a combination of large-scale mRNA in situ hybridization at critical stages of embryonic and brain development and in silico (computed) mining of expressed sequence tags. This chromosome-scale expression annotation associates many of the genes tested with a potential biological role and suggests candidates for the pathogenesis of Down's syndrome.

Background: Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developm... more Background: Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular challenge, because the aneuploid region of Chr21 contains many genes of unknown function. Subcellular localization of human Chr21 proteins may contribute to further understanding of the functions and regulatory mechanisms of the genes that code for these proteins. Following this idea, we used a transfected-cell array technique to perform a rapid and cost-effective analysis of the intracellular distribution of Chr 21 proteins.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008

Integration of biological data of various types and development of adapted bioinformatics tools r... more Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both generation of new bioinformatics tools and experimental validation of computational predictions. With the aim of bridging

Proceedings of the National Academy of Sciences, 1996

Many proteins contain reiterated glutamine residues, but polyglutamine of excessive length may re... more Many proteins contain reiterated glutamine residues, but polyglutamine of excessive length may result in human disease by conferring new properties on the protein containing it. One established property of a glutamine residue, depending on the nature of the flanking residues, is its ability to act as an amine acceptor in a transglutaminase-catalyzed reaction and to make a glutamyl-lysine cross-link with a neighboring polypeptide. To learn whether glutamine repeats can act as amine acceptors, we have made peptides with variable lengths of polyglutamine flanked by the adjacent amino acid residues in the proteins associated with spinocerebellar ataxia type 1 (SCA1), Machado-Joseph disease (SCA3), or dentato-rubral pallidoluysian atrophy (DRPLA) or those residues adjacent to the preferred cross-linking site of involucrin, or solely by arginine residues. The polyglutamine was found to confer excellent substrate properties on any soluble peptide; under optimal conditions, virtually all the glutamine residues acted as amine acceptors in the reaction with glycine ethyl-ester, and lengthening the sequence of polyglutamine increased the reactivity of each glutamine residue. In the presence of transglutaminase, peptides containing polyglutamine formed insoluble aggregates with the proteins of brain extracts and these aggregates contained glutamyl-lysine cross-links. Repeated glutamine residues exposed on the surface of a neuronal protein should form cross-linked aggregates in the presence of any transglutaminase activated by the presence of Ca 2؉ .

PLoS ONE, 2010

It is essential to understand the network of transcription factors controlling self-renewal of hu... more It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells. We initially identified putative direct downstream targets of OCT4 by employing CHIPon-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes. A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Overexpression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells. In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.

Neuroscience Letters, 2000

We have analyzed the size of the expanded poly(CAG) associated with juvenile Huntington disease i... more We have analyzed the size of the expanded poly(CAG) associated with juvenile Huntington disease in the cerebra and the cerebella of five patients. The expanded poly(CAG) was always longer in the cerebrum than in the cerebellum, but the difference in size varied from patient to patient. Except for one patient who possessed an unusually large expansion, very little heterogeneity of size was detected within the cerebrum or within the cerebellum. The larger size of the expanded poly(CAG) in cerebrum must therefore have resulted from a single expansion event that took place early in cerebral development. In both cerebrum and cerebellum, the size of the expanded allele of gray matter was identical to that of white matter. We conclude that most if not all neurons and glia of cerebrum are descended from a common bipotent precursor, which segregated early in neurogenesis from the lineage leading to cerebellar neurons and glia.

Nature Genetics, 1994

UK PubMed Central (UKPMC) is an archive of life sciences journal literature.

Molecular Systems Biology, 2006

... H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, R... more ... H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J ... S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A ...

Journal of Clinical Investigation, 2004

Damage to DNA, the prime target of anticancer therapy, triggers programmed cellular responses. In... more Damage to DNA, the prime target of anticancer therapy, triggers programmed cellular responses. In addition to apoptosis, therapy-mediated premature senescence has been identified as another drug-responsive program that impacts the outcome of cancer therapy. Here, we discuss whether induction of senescence is a beneficial or, rather, a detrimental consequence of the therapeutic intervention.

Gene Function & Disease, 2000

than one century after the discovery of trisomy 21, the molecular mechanisms under-Berlin-Dahlem,... more than one century after the discovery of trisomy 21, the molecular mechanisms under-Berlin-Dahlem, Germany lying the complex phenotype associated with Down syndrome (DS) remain unknown. Up to now, the molecular consequences of gene-dosage imbalance have been mainly investigated by the definition of DS critical regions, based on phenotype-genotype correlations established for rare cases of partial trisomy 21. Recently, the generation of trisomic mouse models has opened interesting possibilities for studying components of the DS phenotype, addressing in particular the cerebellar pathology. The complete DNA sequence, clone map, and gene catalogue of chromosome 21 offers new molecular tools for revisiting phenotype-genotype correlations and for dissecting the molecular bases of DS pathogenesis, using strategic technologies that will allow to define molecular profiles of trisomy 21.

Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie, 1995

Long QT syndrome (LQT) is an autosomal dominant cardiac disease characterized by ventricular arrh... more Long QT syndrome (LQT) is an autosomal dominant cardiac disease characterized by ventricular arrhythmia. A first locus for LQT has been identified on chromosome 11p15.5 (LQT1), closely linked to HRAS. To refine the location of LQT1, microsatellites were genotyped in 8 French families and the following order was determined: tel-HRAS-DRD4-D11S922-D11S4046- IGF2-INS-TH-D11S1318-D11S1323-D11S1338-D11S90 9-D11S1346-cen. By haplotype analysis, 12 crossing-over events were identified in affected and unaffected subjects, delineating the LQT1 candidate region to 7 cM. This new delineated localization between D11S1318 and D11S1323 is in a more centromeric region than previously thought and is 5 cM proximal to HRAS.

The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular c... more The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular characterization of all of its genes. Trisomy 21 is associated with Down's syndrome, the most common genetic cause of mental retardation in humans. The phenotype includes various organ dysmorphies, stereotypic craniofacial anomalies and brain malformations. Molecular analysis of congenital aneuploidies poses a particular challenge because the aneuploid region contains many protein-coding genes whose function is unknown. One essential step towards understanding their function is to analyse mRNA expression patterns at key stages of organism development. Seminal works in flies, frogs and mice showed that genes whose expression is restricted spatially and/or temporally are often linked with specific ontogenic processes. Here we describe expression profiles of mouse orthologues to HSA21 genes by a combination of large-scale mRNA in situ hybridization at critical stages of embryonic and brain development and in silico (computed) mining of expressed sequence tags. This chromosome-scale expression annotation associates many of the genes tested with a potential biological role and suggests candidates for the pathogenesis of Down's syndrome.

Background: Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developm... more Background: Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular challenge, because the aneuploid region of Chr21 contains many genes of unknown function. Subcellular localization of human Chr21 proteins may contribute to further understanding of the functions and regulatory mechanisms of the genes that code for these proteins. Following this idea, we used a transfected-cell array technique to perform a rapid and cost-effective analysis of the intracellular distribution of Chr 21 proteins.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008

Integration of biological data of various types and development of adapted bioinformatics tools r... more Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both generation of new bioinformatics tools and experimental validation of computational predictions. With the aim of bridging

Proceedings of the National Academy of Sciences, 1996

Many proteins contain reiterated glutamine residues, but polyglutamine of excessive length may re... more Many proteins contain reiterated glutamine residues, but polyglutamine of excessive length may result in human disease by conferring new properties on the protein containing it. One established property of a glutamine residue, depending on the nature of the flanking residues, is its ability to act as an amine acceptor in a transglutaminase-catalyzed reaction and to make a glutamyl-lysine cross-link with a neighboring polypeptide. To learn whether glutamine repeats can act as amine acceptors, we have made peptides with variable lengths of polyglutamine flanked by the adjacent amino acid residues in the proteins associated with spinocerebellar ataxia type 1 (SCA1), Machado-Joseph disease (SCA3), or dentato-rubral pallidoluysian atrophy (DRPLA) or those residues adjacent to the preferred cross-linking site of involucrin, or solely by arginine residues. The polyglutamine was found to confer excellent substrate properties on any soluble peptide; under optimal conditions, virtually all the glutamine residues acted as amine acceptors in the reaction with glycine ethyl-ester, and lengthening the sequence of polyglutamine increased the reactivity of each glutamine residue. In the presence of transglutaminase, peptides containing polyglutamine formed insoluble aggregates with the proteins of brain extracts and these aggregates contained glutamyl-lysine cross-links. Repeated glutamine residues exposed on the surface of a neuronal protein should form cross-linked aggregates in the presence of any transglutaminase activated by the presence of Ca 2؉ .

PLoS ONE, 2010

It is essential to understand the network of transcription factors controlling self-renewal of hu... more It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells. We initially identified putative direct downstream targets of OCT4 by employing CHIPon-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes. A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Overexpression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells. In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.

Neuroscience Letters, 2000

We have analyzed the size of the expanded poly(CAG) associated with juvenile Huntington disease i... more We have analyzed the size of the expanded poly(CAG) associated with juvenile Huntington disease in the cerebra and the cerebella of five patients. The expanded poly(CAG) was always longer in the cerebrum than in the cerebellum, but the difference in size varied from patient to patient. Except for one patient who possessed an unusually large expansion, very little heterogeneity of size was detected within the cerebrum or within the cerebellum. The larger size of the expanded poly(CAG) in cerebrum must therefore have resulted from a single expansion event that took place early in cerebral development. In both cerebrum and cerebellum, the size of the expanded allele of gray matter was identical to that of white matter. We conclude that most if not all neurons and glia of cerebrum are descended from a common bipotent precursor, which segregated early in neurogenesis from the lineage leading to cerebellar neurons and glia.

Nature Genetics, 1994

UK PubMed Central (UKPMC) is an archive of life sciences journal literature.

Molecular Systems Biology, 2006

... H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, R... more ... H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J ... S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A ...

Journal of Clinical Investigation, 2004

Damage to DNA, the prime target of anticancer therapy, triggers programmed cellular responses. In... more Damage to DNA, the prime target of anticancer therapy, triggers programmed cellular responses. In addition to apoptosis, therapy-mediated premature senescence has been identified as another drug-responsive program that impacts the outcome of cancer therapy. Here, we discuss whether induction of senescence is a beneficial or, rather, a detrimental consequence of the therapeutic intervention.