Examination of the interaction between NCoA coactivator proteins in the regulation of transcription

Die Mitglieder der NCoA-Koaktivator-Familie fungieren als Koaktivatoren für verschiedene Transkriptionsfaktoren, wie z.B. nukleäre Hormonrezeptoren und STAT-Proteine. NCoA-Proteine rekrutieren sekundäre Koaktivatoren, die durch die Modifikation des Chromatins die Transkriptionsaktivierung ermöglichen. Vorhergehende Studien postulierten die Dimerisierung von NCoA-Proteinen über die aminoterminalen bHLH/PAS-Domänen und die Rekrutierung von Paaren von NCoA-Proteinen, konnten jedoch eine direkte Interaktion nicht nachweisen. In unserer Arbeitsgruppe konnte gezeigt werden, dass die PAS-B-Domäne von NCoA-1 ein LXXLL-Motiv in der Transaktivierungsdomäne von STAT6 binden kann. Im Rahmen dieser Arbeit sollte untersucht werden, ob eine Interaktion von Mitgliedern der NCoA-Proteinfamilie über die PAS-B-Domäne und eigene LXXLL-Motive vermittelt werden kann und welche physiologische Bedeutung die Interaktion von NCoA-Proteinen hat. Die Interaktion endogener NCoA-Proteine konnte in zwei verschiedenen Zelllinien nachgewiesen werden. Es konnte gezeigt werden, dass die PAS-B-Domänen aller drei NCoA-Familienmitglieder mit allen Volllängen-NCoA-Proteinen interagieren können und für eine solche Interaktion ausreichend sind. Dabei interagieren die PAS-B-Domänen spezifisch mit einer Region in der CBP-Interaktions-Domäne (CID/AD1) von NCoA-1, die zwei LXXLL-Motive und den vollständigen Bereich, der die Interaktion mit CBP vermittelt, enthält. Es zeigte sich, dass sich die Bindungsmotivspezifität der NCoA-1-PAS-B-Domäne von den Bindungsmotivspezifitäten der PAS-B-Domänen von NCoA-2 und NCoA-3 unterscheidet. Ebenso zeigten sich unterschiedliche Bindungsmotivspezifitäten für die Interaktion mit der CID/AD1 von NCoA-3, die nur mit der PAS-B-Domäne von NCoA-1 interagierte. Eine physiologische Bedeutung der charakterisierten PAS-B/CID/AD1-Interaktion auf die Bildung und Rekrutierung von Koaktivator-Komplexen wurde mittels Überexpressions-Experimenten untersucht, in denen dominant negative Effekte erwartet wurden. So führte die Überexpression der PAS-B-Domäne bzw. die Kompetition mit der CID/AD1 zur Inhibition der Interaktion von NCoA-1 mit dem Koaktivator CBP und dem Transkriptionsfaktor STAT6. Außerdem führte die stabile Überexpression der PAS-B-Domänen von NCoA-1 und NCoA-3 zu einer veränderten Expression des natürlichen endogenen Androgen-Rezeptor-Zielgenes PSA. Die in dieser Arbeit identifizierte Interaktion von NCoA-Proteinen stellt einen neuen und, zu den bisher bekannten Modellen der Koaktivator-Rekrutierung, ergänzenden Mechanismus dar. Dies gilt sowohl für eine postulierte inter- und intramolekulare Interaktion von NCoA-1 bei der STAT6-vermittelten Transkriptionsaktivierung, als auch für die durch nukleäre Hormonrezeptoren geforderte Rekrutierung von Paaren von NCoA-Proteinen. Zusammenfassend können die in dieser Arbeit erhaltenen Ergebnisse dabei helfen, das Verständnis der dynamischen Rekrutierung von Koaktivatoren bzw. Koaktivator-Komplexen und damit der Regulation der Genexpression, weiter zu verbessern.The members of the NCoA coactivator family function as coactivators for different transcription factors, like nuclear hormone receptors or STAT proteins. NCoA proteins recruit secondary coactivators, which in turn modify the chromatin, thus enabling the activation of transcription. Previous studies postulated dimerization of NCoA proteins through the aminoterminal bHLH/PAS domains and the recruitment of NCoA protein pairs, but a direct interaction has not yet been proven. Our group showed that the PAS-B domain of NCoA-1 binds to an LXXLL motif in the transactivation domain of STAT6. The aim of this work was, to examine whether an interaction of members of the NCoA protein family is mediated through the PAS-B domain and their own LXXLL motifs and to determine the physiological importance of an interaction between NCoA proteins. The interaction of endogenous NCoA proteins was detected in two different cell lines. It was shown that the PAS-B domains of all three NCoA family members are able to interact with all full-length NCoA proteins and that these domains are sufficient for these interactions. The PAS-B domains interact specifically with a region in the CBP interaction domain (CID/AD1) of NCoA-1, which contains two LXXLL motifs and the complete region, which mediates the interaction with CBP. Further analysis revealed that the binding motif specificity of the NCoA-1 PAS-B domain differs from the binding motif specificities of the PAS-B domains of NCoA-2 and NCoA-3. Likewise, different binding motif specificities were detected for the interaction with the CID/AD1 of NCoA-3, which interacted only with the PAS-B domain of NCoA-1. The physiological importance of the characterized PAS-B/CID/AD1 interaction for the formation and the recruitment of coactivator complexes was examined with overexpression experiments. Overexpression of the PAS-B domain and competition with the CID/AD1 led to inhibition of the interaction between NCoA-1 with the coactivator CBP or the transcription factor STAT6, respectively. Furthermore, stable overexpression of the PAS-B domain of NCoA-1 and NCoA-3 led to an altered expression of the natural endogenous androgen receptor target gene PSA. The identified interaction of NCoA proteins suggests a new and complementary mechanism for the known models of coactivator recruitment. This can be considered for the postulated inter- and intramolecular interaction of NCoA-1 in the STAT6 mediated transcriptional activation, as well as for the nuclear hormone receptor mediated recruitment of NCoA protein pairs. In summary, the results of this work can help to improve the understanding of the dynamic recruitment of coactivators and coactivator complexes and in turn the regulation of gene expression

Targeting class I histone deacetylase 2 in MYC amplified group 3 medulloblastoma

Introduction: Medulloblastoma (MB) is the most frequent malignant brain tumor in children. Four subgroups with distinct genetic, epigenetic and clinical characteristics have been identified. Survival remains particularly poor in patients with Group 3 tumors harbouring a MYC amplification. We herein explore the molecular mechanisms and translational implications of class I histone deacetylase (HDAC) inhibition in MYC driven MBs. Material and Methods: Expression of HDACs in primary MB subgroups was compared to normal brain tissue. A panel of MB cell lines, including Group 3 MYC amplified cell lines, were used as model systems. Cells were treated with HDAC inhibitors (HDACi) selectively targeting class I or IIa HDACs. Depletion of HDAC2 was performed. Intracellular HDAC activity, cellular viability, metabolic activity, caspase activity, cell cycle progression, RNA and protein expression were analyzed. Results: HDAC2 was found to be overexpressed in MB subgroups with poor prognosis (SHH, Group 3 and Group 4) compared to normal brain and the WNT subgroup. Inhibition of the enzymatic activity of the class I HDACs reduced metabolic activity, cell number, and viability in contrast to inhibition of class IIa HDACs. Increased sensitivity to HDACi was specifically observed in MYC amplified cells. Depletion of HDAC2 increased H4 acetylation and induced cell death. Simulation of clinical pharmacokinetics showed time-dependent on target activity that correlated with binding kinetics of HDACi compounds. Conclusions: We conclude that HDAC2 is a valid drug target in patients with MYC amplified MB. HDACi should cover HDAC2 in their inhibitory profile and timing and dosing regimen in clinical trials should take binding kinetics of compounds into consideration

Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN‐amplified neuroblastoma

Here we sought metabolic alterations specifically associated with MYCN amplification as nodes to indirectly target the MYCN oncogene. Liquid chromatography-mass spectrometry-based proteomics identified seven proteins consistently correlated with MYCN in proteomes from 49 neuroblastoma biopsies and 13 cell lines. Among these was phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in de novo serine synthesis. MYCN associated with two regions in the PHGDH promoter, supporting transcriptional PHGDH regulation by MYCN. Pulsed stable isotope-resolved metabolomics utilizing C-13-glucose labeling demonstrated higher de novo serine synthesis in MYCN-amplified cells compared to cells with diploid MYCN. An independence of MYCN-amplified cells from exogenous serine and glycine was demonstrated by serine and glycine starvation, which attenuated nucleotide pools and proliferation only in cells with diploid MYCN but did not diminish these endpoints in MYCN-amplified cells. Proliferation was attenuated in MYCN-amplified cells by CRISPR/Cas9-mediated PHGDH knockout or treatment with PHGDH small molecule inhibitors without affecting cell viability. PHGDH inhibitors administered as single-agent therapy to NOG mice harboring patient-derived MYCN-amplified neuroblastoma xenografts slowed tumor growth. However, combining a PHGDH inhibitor with the standard-of-care chemotherapy drug, cisplatin, revealed antagonism of chemotherapy efficacy in vivo. Emergence of chemotherapy resistance was confirmed in the genetic PHGDH knockout model in vitro. Altogether, PHGDH knockout or inhibition by small molecules consistently slows proliferation, but stops short of killing the cells, which then establish resistance to classical chemotherapy. Although PHGDH inhibition with small molecules has produced encouraging results in other preclinical cancer models, this approach has limited attractiveness for patients with neuroblastoma

Human iPSC modelling of a familial form of atrial fibrillation reveals a gain of function of I-f and I-CaL in patient-derived cardiomyocytes

Aims: Atrial fibrillation (AF) is the most common type of cardiac arrhythmias, whose incidence is likely to increase with the aging of the population. It is considered a progressive condition, frequently observed as a complication of other cardiovascular disorders. However, recent genetic studies revealed the presence of several mutations and variants linked to AF, findings that define AF as a multifactorial disease. Due to the complex genetics and paucity of models, molecular mechanisms underlying the initiation of AF are still poorly understood. Here we investigate the pathophysiological mechanisms of a familial form of AF, with particular attention to the identification of putative triggering cellular mechanisms, using patient's derived cardiomyocytes (CMs) differentiated from induced pluripotent stem cells (iPSCs). Methods and results: Here we report the clinical case of three siblings with untreatable persistent AF whose whole-exome sequence analysis revealed several mutated genes. To understand the pathophysiology of this multifactorial form of AF we generated three iPSC clones from two of these patients and differentiated these cells towards the cardiac lineage. Electrophysiological characterization of patient-derived CMs (AF-CMs) revealed that they have higher beating rates compared to control (CTRL)-CMs. The analysis showed an increased contribution of the If and ICaL currents. No differences were observed in the repolarizing current IKr and in the sarcoplasmic reticulum calcium handling. Paced AF-CMs presented significantly prolonged action potentials and, under stressful conditions, generated both delayed after-depolarizations of bigger amplitude and more ectopic beats than CTRL cells. Conclusions: Our results demonstrate that the common genetic background of the patients induces functional alterations of If and ICaL currents leading to a cardiac substrate more prone to develop arrhythmias under demanding conditions. To our knowledge this is the first report that, using patient-derived CMs differentiated from iPSC, suggests a plausible cellular mechanism underlying this complex familial form of AF

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells

Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond

Targeting class I histone deacetylase 2 in MYC amplified group 3 medulloblastoma

Introduction: Medulloblastoma (MB) is the most frequent malignant brain tumor in children. Four subgroups with distinct genetic, epigenetic and clinical characteristics have been identified. Survival remains particularly poor in patients with Group 3 tumors harbouring a MYC amplification. We herein explore the molecular mechanisms and translational implications of class I histone deacetylase (HDAC) inhibition in MYC driven MBs. Material and Methods Expression of HDACs in primary MB subgroups was compared to normal brain tissue. A panel of MB cell lines, including Group 3 MYC amplified cell lines, were used as model systems. Cells were treated with HDAC inhibitors (HDACi) selectively targeting class I or IIa HDACs. Depletion of HDAC2 was performed. Intracellular HDAC activity, cellular viability, metabolic activity, caspase activity, cell cycle progression, RNA and protein expression were analyzed. Results: HDAC2 was found to be overexpressed in MB subgroups with poor prognosis (SHH, Group 3 and Group 4) compared to normal brain and the WNT subgroup. Inhibition of the enzymatic activity of the class I HDACs reduced metabolic activity, cell number, and viability in contrast to inhibition of class IIa HDACs. Increased sensitivity to HDACi was specifically observed in MYC amplified cells. Depletion of HDAC2 increased H4 acetylation and induced cell death. Simulation of clinical pharmacokinetics showed time-dependent on target activity that correlated with binding kinetics of HDACi compounds. Conclusions: We conclude that HDAC2 is a valid drug target in patients with MYC amplified MB. HDACi should cover HDAC2 in their inhibitory profile and timing and dosing regimen in clinical trials should take binding kinetics of compounds into consideration. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0201-7) contains supplementary material, which is available to authorized users

p160/SRC/NCoA coactivators form complexes via specific interaction of their PAS-B domain with the CID/AD1 domain

Transcriptional activation involves the ordered recruitment of coactivators via direct interactions between distinct binding domains and recognition motifs. The p160/SRC/NCoA coactivator family comprises three members (NCoA-1, -2 and -3), which are organized in multiprotein coactivator complexes. We had identified the PAS-B domain of NCoA-1 as an LXXLL motif binding domain. Here we show that NCoA family members are able to interact with other full-length NCoA proteins via their PAS-B domain and they specifically interact with the CBP-interaction domain (CID/AD1) of NCoA-1. Peptide competition, binding experiments and mutagenesis of LXXLL motifs point at distinct binding motif specificities of the NCoA PAS-B domains. NMR studies of different NCoA-1-PAS-B/LXXLL peptide complexes revealed similar although not identical binding sites for the CID/AD1 and STAT6 transactivation domain LXXLL motifs. In mechanistic studies, we found that overexpression of the PAS-B domain is able to disturb the binding of NCoA-1 to CBP in cells and that a CID/AD1 peptide competes with STAT6 for NCoA-1 in vitro. Moreover, the expression of an endogenous androgen receptor target gene is affected by the overexpression of the NCoA-1 or NCoA-3 PAS-B domains. Our study discloses a new, complementary mechanism for the current model of coactivator recruitment to target gene promoters

Using droplet digital PCR to analyze MYCN and ALK copy number in plasma from patients with neuroblastoma

The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients. Our ddPCR protocol accurately discriminated between MYCN and ALK amplification, gain and normal diploid status in a large panel of neuroblastoma cell lines, and discrepancies with reported MYCN and ALK status were detected, including a high-level MYCN amplification in NB-1, a MYCN gain in SH-SY5Y, a high-level ALK amplification in IMR-32 and ALK gains in BE(2)-C, Kelly, SH-SY5Y and LAN-6. MYCN and ALK status were also reliably determined from cell-free DNA derived from medium conditioned by the cell lines. MYCN and ALK copy numbers of subcutaneous neuroblastoma xenograft tumors were accurately determined from cell-free DNA in the mouse blood plasma. In a final validation step, we accurately distinguished MYCN and ALK copy numbers of the corresponding primary tumors using retrospectively collected blood plasma samples from 10 neuroblastoma patients. Our data justify the further development of molecular disease characterization using cell-free DNA in blood plasma from patients with neuroblastoma. This expanded molecular diagnostic palette may improve monitoring of disease progression including relapse and metastatic events as well as therapy success or failure in high-risk neuroblastoma patients

Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival

The number of long-term survivors of high-risk neuroblastoma remains discouraging, with 10-year survival as low as 20%, despite decades of considerable international efforts to improve outcome. Major obstacles remain and include managing resistance to induction therapy, which causes tumor progression and early death in high-risk patients, and managing chemotherapy-resistant relapses, which can occur years after the initial diagnosis. Identifying and validating novel therapeutic targets is essential to improve treatment. Delineating and deciphering specific functions of single histone deacetylases in neuroblastoma may support development of targeted acetylome-modifying therapeutics for patients with molecularly defined high-risk neuroblastoma profiles. We show here that HDAC11 depletion in MYCN-driven neuroblastoma cell lines strongly induces cell death, mostly mediated by apoptotic programs. Genes necessary for mitotic cell cycle progression and cell division were most prominently enriched in at least two of three time points in whole-genome expression data combined from two cell systems, and all nine genes in these functional categories were strongly repressed, including CENPA, KIF14, KIF23 and RACGAP1. Enforced expression of one selected candidate, RACGAP1, partially rescued the induction of apoptosis caused by HDAC11 depletion. High-level expression of all nine genes in primary neuroblastomas significantly correlated with unfavorable overall and event-free survival in patients, suggesting a role in mediating the more aggressive biological and clinical phenotype of these tumors. Our study identified a group of cell cycle-promoting genes regulated by HDAC11, being both predictors of unfavorable patient outcome and essential for tumor cell viability. The data indicate a significant role of HDAC11 for mitotic cell cycle progression and survival of MYCN-amplified neuroblastoma cells, and suggests that HDAC11 could be a valuable drug target