Effect of depletion of IMPDH1 and IMPDH2 on gene expression after DNA damage in HeLa cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE265772 | GEO | 2024/07/24
REPOSITORIES: GEO
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Project description:Ribonucleotides serve important cellular functions as energy carriers, signaling molecules and building blocks of RNA. In eukaryotes, rRNA and tRNA synthesis in the nucleolus accounts together for over 90% of all RNA molecules. In many cancers, high proliferation rates correlated with elevation of rRNA and tRNA levels4 and nucleolar hypertrophy. However, the metabolic changes that lead to the increased nucleolar transcription and in turn foster tumorigenesis are incompletely understood. Here we show that in the highly lethal brain cancer glioblastoma (GBM), inosine monophosphate dehydrogenase-2 (IMPDH2), the rate-limiting enzyme for de novo guanine nucleotide biosynthesis, is overexpressed. This leads to increased rRNA and tRNA synthesis and stabilization of the oncogenic GTP-binding protein nucleostemin, and enlarged and malformed nucleoli. Pharmacological or genetic inactivation of IMPDH2 reverses these malignant effects and inhibits GBM cell proliferation, whereas untransformed glia cells are unaffected. Impairment of IMPDH2 activity triggers nucleolar stress and growth arrest of GBM cells even in the absence of functional p53. Our results have uncovered upregulation of IMPDH2 as a prerequisite for aberrant nucleolar function and translational capacity in GBM. This GTP metabolic reprogramming constitutes a primary event in gliomagenesis and has implications for GBM treatment and possible malignant transformation in other cancers.
2019-07-30 | GSE124727 | GEO
Project description:Physiological changes in GTP levels in live cells have never been considered a regulatory step of RAC1 activation because GTP concentrations determined by chromatography or mass spectrometry were shown to be substantially higher than the RAC1 GTP dissociation constant (RAC1-GTP Kd) determined in vitro. Here, using a combination of genetically engineered intracellular GTP sensors, recently generated by us, and RAC1 activity reporter, we demonstrate that fluctuations in GTP levels within the range of RAC1-GTP Kd, correlate with changes in RAC1 activity in live cells. We further demonstrate that RAC1 co-localize in protrusions of invading cells with the de novo guanylate biosynthesis enzymes including rate-limiting inosine monophosphate dehydrogenase 2 (IMPDH2) and guanosine monophosphate synthase (GMPS). This colocalization is partly driven by direct interaction of RAC1 with the Bateman domain of IMPDH2. Substitution of endogenous IMPDH2 with the IMPDH2 mutants incapable of binding RAC1 did not affect total intracellular GTP levels but suppressed RAC1 activity. Accordingly, targeting of IMPDH2 away from the plasma membrane did not alter total intracellular GTP pools but decreased local GTP levels in cell protrusions, downregulated RAC1 activity and decreased cell invasion. These data provide previously unrecognized mechanistic insight into the regulation of RAC1 activity by local GTP pools in live cells.
2021-11-04 | PXD028540 | Pride
Project description:Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use a mouse model of AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that AMPD deficiency in mice primarily leads to hippocampal dentate gyrus degeneration despite causing a generalized reduction of brain GTP levels. Remarkably, we uncover that neurodegeneration resistant regions of the hippocampus accumulate micron sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis. In contrast, IMPDH2 filaments are barely detectable in the dentate gyrus, which show a progressively neuroinflammation and neurodegeneration. Furthermore, using a human AMPD2 neural cell culture model, we show that blocking IMPDH2 polymerization with a dominant negative IMPDH2 variant impairs AMPD2 deficient neural progenitor growth. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation caused by AMPD2 deficiency, providing resistance to neurodegeneration. This data opens the possibility of exploring the involvement of IMPDH2 assembly as a therapeutic intervention for neurodegeneration.
2024-01-16 | GSE253045 | GEO
Project description:Nuclear metabolism and DNA damage response are intertwined processes, but the precise molecular connections remain elusive. Here, we delve into this crosstalk using as a model triple-negative breast cancer (TNBC), a subtype often prone to DNA damage accumulation. We reveal that the de novo purine synthesis enzyme Inosine monophosphate dehydrogenase 2 (IMPDH2) is enriched on chromatin in TNBC when compared to other subtypes. IMPDH2 chromatin localization is DNA damage dependent and IMPDH2 repression leads to DNA damage accumulation. On chromatin, IMPDH2 interacts and modulates Poly [ADP-ribose] polymerase 1 (PARP1) activity by controlling nuclear availability of nicotinamide adenine dinucleotide (NAD+) -a shared metabolic cofactor- to fine-tune the DNA damage response. However, when IMPDH2 is restricted to the nucleus, it depletes nuclear NAD+, leading to PARP1 cleavage and cell death. Our study identifies a non-canonical nuclear role for IMPDH2 that act as convergence point of nuclear metabolism and DNA damage response. # Contributed equally *Corresponding authors: sara.sdelci@crg.eu; marta.garciacao@crg.eu
2024-09-16 | GSE271269 | GEO
Project description:Recent studies have highlighted the critical role of metabolism in the response to DNA damage. However, the precise metabolic interactions that are set in motion to tune this fundamental process remain largely unknown. In this study, we investigated the role of nuclear metabolism in the DNA damage response using triple-negative breast cancer as a model. By comparing the chromatin-associated proteome of different breast cancer subtypes, we observed that the purine synthesis enzyme Inosine monophosphate dehydrogenase 2 (IMPDH2) is enriched in the chromatin of triple-negative breast cancer cells, which are often prone to DNA damage accumulation. Downregulation, depletion, or inhibition of IMPDH2 leads to accumulation of DNA damage. IMPDH2 chromatin localization is DNA damage dose dependent and happens at a late stage of the DNA damage repair. On chromatin, IMPDH2 interacts with PARP1. The enzymatic function of IMPDH2, which consumes NAD+, modulates PARP1 activity, thus mediating a pondered DNA damage response. However, forcing the nuclear localization of exogenous IMPDH2 provokes a dramatic NAD+ depletion that results in PARP1 cleavage and consequent cytoplasmic translocation, which mediates apoptosis. Our study identifies a moonlighting role for IMPDH2 in the control of nuclear ATP and NAD+ level, which fine-tune the activation of PARP1 and regulates the DNA damage response.
2024-11-28 | PXD043522 | Pride
Project description:Prostate cancer is the commonest male cancer in Europe and the USA. The androgen receptor is a key transcription factor contributing to the development of all stages of the disease. In addition, other transcription factors have been associated with poor prognosis in prostate cancer, amongst which c-Myc is a well-established oncogene in many other cancers. We have previously reported that a role for the androgen receptor in prostate cancer is to promote glycolysis and anabolic metabolism. Many of these metabolic pathways are also c-Myc-regulated in other cancers. In this study we report that de novo purine biosynthesis is a c-Myc-dependent pathway in prostate cancer cells as determined by commensurate changes in the levels of enzymes in the pathway in response to siRNA knockdown of c-Myc and inducible overexpression of c-Myc. In addition c-Myc is recruited to the promoters of genes in the pathway as determined by chromatin immunoprecipitation. Using immunohistochemistry and real-time transcript detection we show that two enzymes (PAICS and IMPDH2) within the pathway are overexpressed in prostate cancers. An inhibitor of IMPDH2 reduces cell proliferation and significantly reduces the levels of guanosine triphosphate within treated cells. This imposes nucleolar stress on cells as determined by significant reductions in the levels of guanine nucleotide binding protein-like 3 (GNL3). In addition the levels of c-Myc, p53 and the androgen receptor are affected and the expression of tumour suppressive microRNA-34b is increased. Combining the IMPDH2 inhibitor with anti-androgens results in a combinatorial inhibition of cell proliferation. In conclusion we propose using enzymes within the de novo purine biosynthesis as cancer biomarkers and applying drugs to alter the flux through this pathway may represent an effective means of stratifying patients for therapy and sensitising some to AR-targeted therapies. Total RNA of three biological replicates for each condition was extracted using the RNeasy kit (Qiagen), conditions are: 5 h vehicle, 5 h Doxycycline, 12 h vehicle, 12 h Doxycyline
2016-03-17 | E-GEOD-51384 | biostudies-arrayexpress
Project description:Cell cycle and metabolism are two major outputs controlled by circadian rhythm in many organisms. Here we show that the three processes were linked through inosine 5'-phosphate dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis. We using adult zebrafish as a model system,we applied a genome-wide transcriptome approach that allowed us to investigate circadian gene expression. The whole-genome transcriptome profiles of adult brain in time-series were assayed on Agilent zebrafish microarrays. We used a similar statistical method to identify zebrafish circadian genes (ZCOG) as our previous study in larval zebrafish. Three isoforms of impdh show strong circadian oscillations in different tissues of zebrafish. impdh1a contributes to the ocular development and pigment synthesis, impdh2 promotes and impdh1b delays the development. By limiting the GTP required by DNA synthesis, impdh2 contributes to the daily rhythm of S phase in cell cycle. Multiple enzymes in the de novo purine synthesis pathway show the same circadian oscillations with peaks similar to impdh2. The circadian expression of this pathway is conserved in mouse liver. In summary, we show that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is critical for gating cell cycle in circadian rhythm.
2013-10-01 | GSE51277 | GEO
Project description:Many studies in yeast have observed correlations between changes in phosphorylated adenosine and guanosine nucleotide concentrations, and changes in cell physiology or gene expression. Evidence for a causal relationship is however sparse. To investigate this further under controlled conditions, we have developed strains of S. cerevisiae containing inducible pathways which increase use of ATP or GTP. Analysis of the transcriptional response following induction of these strains during continuous culture in chemostats allowed the effects of specifically increasing the demand for each purine nucleotide triphosphate to be determined independently of growth rate and nutritional changes.
2018-08-23 | E-MTAB-5174 | biostudies-arrayexpress
Project description:Prostate cancer is the commonest male cancer in Europe and the USA. The androgen receptor is a key transcription factor contributing to the development of all stages of the disease. In addition, other transcription factors have been associated with poor prognosis in prostate cancer, amongst which c-Myc is a well-established oncogene in many other cancers. We have previously reported that a role for the androgen receptor in prostate cancer is to promote glycolysis and anabolic metabolism. Many of these metabolic pathways are also c-Myc-regulated in other cancers. In this study we report that de novo purine biosynthesis is a c-Myc-dependent pathway in prostate cancer cells as determined by commensurate changes in the levels of enzymes in the pathway in response to siRNA knockdown of c-Myc and inducible overexpression of c-Myc. In addition c-Myc is recruited to the promoters of genes in the pathway as determined by chromatin immunoprecipitation. Using immunohistochemistry and real-time transcript detection we show that two enzymes (PAICS and IMPDH2) within the pathway are overexpressed in prostate cancers. An inhibitor of IMPDH2 reduces cell proliferation and significantly reduces the levels of guanosine triphosphate within treated cells. This imposes nucleolar stress on cells as determined by significant reductions in the levels of guanine nucleotide binding protein-like 3 (GNL3). In addition the levels of c-Myc, p53 and the androgen receptor are affected and the expression of tumour suppressive microRNA-34b is increased. Combining the IMPDH2 inhibitor with anti-androgens results in a combinatorial inhibition of cell proliferation. In conclusion we propose using enzymes within the de novo purine biosynthesis as cancer biomarkers and applying drugs to alter the flux through this pathway may represent an effective means of stratifying patients for therapy and sensitising some to AR-targeted therapies.
2016-03-17 | GSE51384 | GEO
Project description:Cell cycle and metabolism are two major outputs controlled by circadian rhythm in many organisms. Here we show that the three processes were linked through inosine 5'-phosphate dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis. We using adult zebrafish as a model system,we applied a genome-wide transcriptome approach that allowed us to investigate circadian gene expression. The whole-genome transcriptome profiles of adult brain in time-series were assayed on Agilent zebrafish microarrays. We used a similar statistical method to identify zebrafish circadian genes (ZCOG) as our previous study in larval zebrafish. Three isoforms of impdh show strong circadian oscillations in different tissues of zebrafish. impdh1a contributes to the ocular development and pigment synthesis, impdh2 promotes and impdh1b delays the development. By limiting the GTP required by DNA synthesis, impdh2 contributes to the daily rhythm of S phase in cell cycle. Multiple enzymes in the de novo purine synthesis pathway show the same circadian oscillations with peaks similar to impdh2. The circadian expression of this pathway is conserved in mouse liver. In summary, we show that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is critical for gating cell cycle in circadian rhythm. Adult zebrafish were sacrificed and dissected at 4h intervals starting at CT0 in both LD and DD conditions for 12 time points. Total RNA of individual zebrafish brain was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturerM-bM-^@M-^Ys instruction. Microarrays were manufactured by Agilent Technologies (Agilent Technologies, Palo Alto, CA), containing 43,603 probes for zebrafish whole-genome transcriptional profiling.
2013-10-01 | E-GEOD-51277 | biostudies-arrayexpress