Podcasts about pax5

In this episode, Karl Bacos joins us to discuss an interdisciplinary topic: PAX5 - a new player in T2D pathophysiology. Ask the Expert is a ~30 minute digital cafe experience where scientists and grad students can meet and exchange with thought leaders in the field of type 1 diabetes. Link below to sign up for a seat in the cafe!

Mutations in the autism-linked gene PAX5 underlie a range of traits, including developmental delay, intellectual disability, seizures and autism. The post Top autism candidate gene tied to newly identified syndrome appeared first on Spectrum | Autism Research News.

Mutations in the autism-linked gene PAX5 underlie a range of traits, including developmental delay, intellectual disability, seizures and autism.

Mutations in the autism-linked gene PAX5 underlie a range of traits, including developmental delay, intellectual disability, seizures and autism.

In this episode of the Epigenetics Podcast, we caught up with Dr. Hodaka Fujii, Professor of Biochemistry and Genome Biology at Hirosaki University Graduate School of Medicine and School of Medicine, to talk about his work on the development of locus-specific ChIP technologies. The goal of conventional chromatin immunoprecipitation (ChIP) assays is to find genomic locations of transcription factor binding or genome-wide profiles of histone tail modifications.  In contrast to that, the guest of this episode, Dr. Fujii, has developed methods such as insertional chromatin immunoprecipitation (iChIP) and engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to identify the factors that are binding to specific sites on the genome. In iChIP, LexA binding sites are inserted into the genomic region of interest. In parallel, the DNA-binding domain of LexA, fused with FLAG epitope tags and a nuclear localization signal, is expressed in the same cells. After crosslinking and chromatin preparation, the resulting chromatin is immunoprecipitated with an antibody against the tag. This allows proteins or RNA interacting with the region of interest to be analyzed with the appropriate downstream application. The enChIP takes a similar approach, but does not require insertion of the LexA binding sites. Instead, a FLAG-tagged dCas9 protein together with the respective guide RNA are used to target the region of the genome of interest. After the IP and the purification DNA, RNA, or proteins can be analyzed accordingly. The lack of the requirement of to insert the LexA binding sites into the genome makes enChIP much more straightforward than iChIP. In this interview, we discuss the story behind how Dr. Fujii got into the field of epigenetics, how he developed iChIP, and how the method was improved over the years. Furthermore, we discuss the development of enChIP and how this can be used as an alternate method to Hi-C.   References   Akemi Hoshino, Satoko Matsumura, … Hodaka Fujii (2004) Inducible Translocation Trap (Molecular Cell) DOI: 10.1016/j.molcel.2004.06.017 Akemi Hoshino, Hodaka Fujii (2009) Insertional chromatin immunoprecipitation: a method for isolating specific genomic regions (Journal of Bioscience and Bioengineering) DOI: 10.1016/j.jbiosc.2009.05.005 Toshitsugu Fujita, Hodaka Fujii (2013) Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR (Biochemical and Biophysical Research Communications) DOI: 10.1016/j.bbrc.2013.08.013 Toshitsugu Fujita, Miyuki Yuno, … Hodaka Fujii (2015) Identification of Non-Coding RNAs Associated with Telomeres Using a Combination of enChIP and RNA Sequencing (PLOS ONE) DOI: 10.1371/journal.pone.0123387 Toshitsugu Fujita, Miyuki Yuno, Hodaka Fujii (2016) Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins (Genes to Cells) DOI: 10.1111/gtc.12341 Toshitsugu Fujita, Miyuki Yuno, … Hodaka Fujii (2017) Identification of physical interactions between genomic regions by enChIP-Seq (Genes to Cells) DOI: 10.1111/gtc.12492 Toshitsugu Fujita, Fusako Kitaura, … Hodaka Fujii (2017) Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line (DNA Research) DOI: 10.1093/dnares/dsx023   Contact   Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com

Dr Xose Puente speaks with ecancertv at AACR2016 about his discoveries of mutations in non-coding regions driving tumourigensis in chronic lymphocytic leukaemia. Using a library of genomic data from CLL patients, Dr Puente's lab were able to determine point mutations outside of the coding regions of patients DNA that gave rise to altered gene expression. A single substitution in the 3' tail of Notch1, a cell cycle regulator, is reported as introducing a novel splicing site resulting in the deletion of 500 base pairs, including those which determine Notch1 persistence in healthy cells. Another mutation in an intragenic region results in down-regulation of Pax5, essential for B cell maturation. These results are among the first to indicate the clinical significance of non-coding DNA to cancer development.

Dr Hauer speaks at an EHA 2017 press conference about a mouse model of childhood leukaemia, based on exposure to common infections. For mice engineered to express pre-leukaemic genotype PAX5± and TEL-AML1, infection was found to be an essential trigger for disease progression.

Dr. Suzanne Cory discusses the 1999 publication that described how commitment to the B-lymphoid lineage depends on the transcription factor Pax5.

Die akute myeloische Leukämie (AML) ist aus genetischer Sicht eine sehr heterogene Erkrankung. Rezeptortyrosinkinasen (RTKs) wie FLT3 sind in der Leukämogenese von zentraler Bedeutung. Durch Mutationen aktivierte RTKs sind allerdings alleine nicht in der Lage eine AML zu induzieren. Die Kooperation mit anderen Mutationen ist hierfür notwendig. Zu den am häufigsten gemeinsam auftretenden Mutationen in der AML gehören NPM1- und FLT3-ITD- (internal tandem duplication) Mutationen. Klinische Daten zeigen, dass eine FLT3-ITD die gute Prognose von NPM1-mutierten (NPM1c+) Patienten in Abhängigkeit des FLT3-ITD-mRNA-Levels in negativer Weise beeinflusst. Dies lässt auf ein pathogenes Zusammenwirken beider Genmutationen in der AML schließen, welches im Rahmen dieser Arbeit untersucht wurde. Dazu wurde basierend auf der humanen AML-Zelllinie OCI-AML3 mittels stabiler, lentiviraler Transduktion das erste zelluläre Modellsystem etabliert, das die relevanten Genotypen (NPM1c+/FLT3-ITD; NPM1c+/FLT3-WT) sowie unterschiedliche Verhältnisse von FLT3-ITD zu FLT3-WT (ITD/WT) im NPM1-mutierten Hintergrund modelliert. Zunächst wurde die NPM1-Mutation sowie die Funktionalität des FLT3-WT- und FLT3-ITD-Rezeptors in den nativen und transgenen Zellen bestätigt. Mit Hilfe des Zellmodells konnte gezeigt werden, dass Zellen, die beide Mutationen tragen, in vitro wie auch in vivo einen Wachstumsvorteil besitzen. Dieser vergrößerte sich zudem mit zunehmendem ITD/WT-Verhältnis. Ab einem bestimmten ITD/WT-Verhältnis konnte dieser Wachstumsvorteil in vitro mit einem FLT3-Inhibitor über eine gewisse Dauer gehemmt werden. Diese Ergebnisse könnten auf ein Zusammenwirken der beiden Mutationen bei der Leukämogenese hinweisen und eine Ursache für die schlechteren Überlebenskurven von Patienten mit beiden Mutationen und zunehmender FLT3-ITD-Last darstellen. Der insgesamt jedoch nur schwach ausgeprägte Phänotyp des etablierten Zellmodells erfordert zum eindeutigen Nachweis der funktionellen Interaktion von NPM1- und FLT3-ITD Mutationen ein alternatives Modellsystem. In diesem Zellmodell zeigten Zellen, die den FLT3-WT-Rezeptor überexprimierten, ebenfalls einen schwachen Wachstumsvorteil gegenüber nativen Zellen mit endogener FLT3-WT-Expression. Neben aktivierenden FLT3-Mutationen wie einer ITD, führen auch hohe FLT3-WT-Expressionslevel zur konstitutiven Aktivierung der FLT3-Kinase und verschlechtern die Prognose der Patienten. Deshalb wurde in dieser Arbeit mit der Untersuchung der transkriptionellen Regulation von FLT3, als mögliche Ursache hoher FLT3-WT-Expressionslevel, begonnen. In silico wurden im proximalen FLT3-Promotor Bindestellen für die hämatopoetischen Transkriptionsfaktoren (TF) PAX5 und MYB identifiziert. Mit Hilfe des Dual-Luciferase® Reporter Assay Systems wurden PAX5 als schwacher Repressor und MYB als Aktivator des Flt3-Promotors bestätigt. Auch der Transkriptionsfaktor CEBPA verhielt sich auf gleiche Weise als Aktivator der Flt3-Promotoraktivität. Eine Punktmutation im CEBPA-Gen, die aus zwei AML-Fällen bekannt ist, führte zu einer erhöhten Flt3-Promotoraktivität. Die Identifizierung weiterer mutierter, FLT3-regulierender TF und ihre Korrelation mit der FLT3-Expression sollen zukünftig tiefere Einblicke in die transkriptionelle Regulierung von FLT3 als Ursache der FLT3-Überexpression in AML-Patienten gewähren. Für eine Reihe von in AML-Patienten gefundenen Mutationen ist deren Rolle in der Pathogenese der AML noch unbekannt. Dazu gehören Mutationen in den Rezeptortyrosinkinasen DDR1 und DDR2. In der vorliegenden Arbeit wurden DDR1- und DDR2-Mutationen stabil in Ba/F3 Zellen und transient in HEK-293T Zellen exprimiert, um ihr transformierendes Potential zu untersuchen und diese funktionell zu charakterisieren. Transgene, DDR1- und DDR2-exprimierende Ba/F3 Zellen zeigten keinen transformierenden Phänotyp. Weitere Untersuchungen zeigten eine konstitutive Phosphorylierung der extrazellulären DDR2-Mutanten (G222R, M291I) in HEK-293T Zellen und eine Adhäsion von Ba/F3 Zellen mit wildtypischem sowie mutiertem DDR1-Rezeptor in Anwesenheit des DDR-Liganden Kollagen. DDR1- und DDR2-Rezeptoren sind bisher vor allem in soliden Tumoren untersucht. Weitere funktionelle Analysen sind notwendig, um ihren Stellenwert bei der Entstehung von AML zu erfassen. Diese Arbeit zeigt, dass Rezeptortyrosinkinasen in der Leukämogenese auf unterschiedliche Weise eine wesentliche Rolle spielen können. Da Rezeptortyrosinkinasen zudem wichtige Zielmoleküle für therapeutische Ansätze darstellen, sind sie von besonderer Bedeutung.

Top News aus der Medizinischen Forschung vom 23.01.2008, Billrothhaus

We have demonstrated, that an acute leukemia with a predominantly myeloid phenotype can be propagated by a progenitor with lymphoid characteristics in a mouse model of the t(10;11) (p13;q14) translocation. Mice transplanted with bone marrow retrovirally engineered to express the leukemia specific CALM/AF10 fusion gene consistently developed an acute leukemia with a short latency. The leukemia showed characteristic myeloid features such as the presence of myeloid marker positive cells infiltrating multiple hematopoietic and non-hematopoietic organs, the positivity of blasts for myeloid specific histochemical stainings and the depletion of the lymphoid compartment in lymphoid organs. Apart from the major population of cells expressing myeloid but not lymphoid markers (M population), a smaller population of cells expressing myeloid markers as well as the lymphoid marker B220 ( B/M population) and a smaller population expressing only the B220 marker (B population) could be detected in all mice. We determined that the frequency of leukemia propagating cells was the highest in the B population and that this population could give rise to the other two populations of cells, namely the B/M and the M populations. This indicated that the leukemic stem cell candidate for the myeloid leukemia in this model of CALM/AF10 induced transformation is a B220 + cell. Further characterization of these candidate LSCs revealed the presence of D-JH rearrangements and the absence of Pax5 transcription. These cells were characterised as being CD43 + /AA4.1 + /HSA low-pos/CD19 -/FLT3R + /IL-7R low-neg c-kit low-neg and expressing the early B cell factor (EBF) transcripts as well as transcripts for the myeloperoxidase (MPO) gene,bearing a resemblance to Pax5 knockout preBI cells. These findings indicate that the leukemia-propagating cell in a subset of acute myeloid leukemias could be a cell with lymphoid characteristics. The fact that this progenitor cell expressed markers different from those expressed by the bulk leukemic population but could still propagate the leukemia raises the interesting possibility of selectively targeting these cells using novel therapeutic strategies that aim to eliminate these LSCs.

The application of global gene expression profiling allows to obtain detailed molecular fingerprints of underlying gene expression in any cell of interest. In this work gene expression profiles were generated from a comprehensive cohort of leukemia patients and healthy donors referred to and diagnosed in the Laboratory for Leukemia Diagnostics, Munich, Germany, which is a nation-wide reference center for the diagnosis of hematologic malignancies. Thoroughly characterized clinical samples were analyzed by high-density microarrays interrogating the expression status of more than 33,000 transcripts. In one specific aspect of this work the potential application of gene expression signatures for the prediction and classification of specific leukemia subtypes was assessed. Today the diagnosis and subclassification of leukemias is based on a controlled application of various techniques including cytomorphology, cytogenetics, fluorescence in situ hybridization, multiparameter flow cytometry, and PCR-based methods. The diagnostic procedure is performed according to a specific algorithm, but is time-consuming, cost-intensive, and requires expert knowledge. Based on a very low number of candidate genes it is demonstrated in this work that prognostically relevant acute leukemia subtypes can be classified using microarray technology. Moreover, in an expanded analysis including 937 patient samples representing 12 distinct clinically relevant acute and chronic leukemia subtypes and healthy, non-leukemia bone marrow specimens a diagnostic prediction accuracy of ~95% was achieved. Thus, given these results it can be postulated that the occurring patterns in gene expression would be so robust that they would allow to predict the leukemia subtype using global gene expression profiling technology. This finding is further substantiated through the demonstration that reported differentially expressed genes from the literature, namely pediatric gene expression signatures representing various acute lymphoblastic leukemia (ALL) subtypes, can be used to independently predict the corresponding adult ALL subtypes. Furthermore, it could be demonstrated that microarrays both confirm and reproduce data from standard diagnostic procedures, but also provide very robust results. Parameters such as partial RNA degradation, shipment time of the samples, varying periods of storage of the samples, or target preparations at different time points from either bone marrow or peripheral blood specimens by different operators did not dramatically influence the diagnostic gene expression signatures. In another major aspect of this work gene expression signatures were examined in detail to obtain new insights into the underlying biology of acute promyelocytic leukemia (APL) and t(11q23)/MLL leukemias. In APL, microarrays led to a deeper understanding of morphological and clinical characteristics. Firstly, genes which have a functional relevance in blood coagulation were found to be differentially expressed when APL was compared to other acute myeloid leukemia (AML) subtypes. Secondly, a supervised pairwise comparison between the two different APL phenotypes, M3 and its variant M3v, for the first time revealed differentially expressed genes encoding for biological functions and pathways such as granulation and maturation. With respect to 11q23 leukemias it could be demonstrated that leukemias with rearrangements of the MLL gene are characterized by a common specific gene expression signature. Additionally, in unsupervised and supervised data analysis algorithms ALL and AML cases with t(11q23)/MLL segregated according to the lineage, i.e., myeloid or lymphoid, respectively. This segregation could be explained by a highly differing transcriptional program. Through the use of biological network analyses essential regulators of early B cell development, PAX5 and EBF, were shown to be associated with a clear B-lineage commitment in lymphoblastic t(11q23)/MLL leukemias. Also, the influence of the different MLL translocation partners on the transcriptional program was directly assessed. But interestingly, gene expression profiles did not reveal a clear distinct pattern associated with one of the analyzed partner genes. Taken together, the identified molecular expression pattern of MLL fusion gene samples and biological networks revealed new insights into the aberrant transcriptional program in t(11q23)/MLL leukemias. In addition, a series of analyses was targeted to obtain new insights into the underlying biology in heterogeneous B-lineage leukemias not positive for BCR/ABL or MLL gene rearrangements. It could be demonstrated that the genetically more heterogeneous precursor B-ALL samples intercalate with BCR/ABL-positive cases, but their profiles were clearly distinct from T-ALL and t(11q23)/MLL cases. In conclusion, various unsupervised and supervised data analysis strategies demonstrated that defined leukemia subtypes can be characterized on the basis of distinct gene expression signatures. Specific gene expression patterns reproduced the taxonomy of this hematologic malignancy, provided new insights into different disease subtypes, and identified critical pathway components that might be considered for future therapeutic intervention. Based on these results it is now further possible to develop a one-step diagnostic approach for the diagnosis of leukemias using a customized microarray.