GEO DataSets

(Submitter supplied) D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) is a necessary enzyme for de novo L-serine biosynthesis via the phosphorylated pathway. We demonstrated previously that Phgdh is expressed exclusively by neuroepithelium and radial glia in developing mouse brain and later mainly by astrocytes. Mutations in the human PHGDH gene cause serine deficiency disorders (SDD) associated with severe neurological symptoms such as congenital microcephaly, psychomotor retardation, and intractable seizures. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2874

Platform:

GPL1261

8 Samples

Download data: CEL, CHP, EXP

Analysis of embryonic head tissue lacking D-3-phosphoglycerate dehydrogenase (Phgdh). Mutations in human PHGDH gene cause serine deficiency disorders like congenital microcephaly and psychomotor retardation. Results provide insight into the pathogenesis of SDD.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE8555

8 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) Live hepatocyte-specific Phgdh KO (LKO) mice were generated by introducing Albumin-Cre transgene into Phgdh flox/flox (Floxed) mice. LKO mice exhibited mild obesity and impaired glucose intolerance at 30 weeks old.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

12 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify genes that are regulated by activiating transcription factor (ATF3) in the cellular response to serine deprivation. Serine biosynthesis is crucial for cancer cells to proliferate and survival under serine-limiting conditions. We found that ATF3 expression induced by serine deprivation supports cancer cell growth. This RNA-seq study is thus designed to understand how ATF3 regulates serine biosynthesis in cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Serine synthesis is crucial for tumor growth and survival, but its regulatory mechanism in cancer remains elusive. Here, using integrative metabolomics and transcriptomics analyses, we show a heterogeneity between metabolite and transcript profiles. Specifically, the level of serine in HCC tissues is increased, whereas the expression of phosphoglycerate dehydrogenase (PHGDH), the first rate-limiting enzyme in serine biosynthesis pathway, is dramatically downregulated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

54 Samples

Download data: TXT

(Submitter supplied) RNAseq data from C57BL/6 bone marrow-derived macrophages that were stimulated with IL-4 in the presence or absence of the PHGDH inhibitor CBR-5884.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: GTF

(Submitter supplied) HCT116 cells (WT or PHGDH KO) were harvested and mRNA were extracted for high-throughput sequencing

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) Here, we demonstrate that virus-infected macrophages display decreased expression of serine synthesis pathway (SSP) enzymes. Suppressing the SSP key enzyme phosphoglycerate dehydrogenase (PHGDH) by genetic approaches enhanced IFN-b-mediated antiviral innate immunity in vitro and in vivo. To further explore its mechanism, we used high-throughput sequencing technology (RNA-seq) to assess gene expression in PHGDH-deficiency BMDMs and RAW264.7 macrophages.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

12 Samples

Download data: TXT

(Submitter supplied) Since bone metastatic breast cancer is an incurable disease, causing significant morbidity and mortality, understanding of the underlying molecular mechanisms would be highly valuable. Here, we describe in vitro and in vivo evidence for the importance of serine biosynthesis in the metastasis of breast cancer to bone. We first characterized the bone metastatic propensity of the MDA-MB-231(SA) cell line variant as compared to the parental MDA-MB-231 cells by radiographic and histological observations in the inoculated mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9987

2 Samples

Download data: CEL

(Submitter supplied) Here we show under glucose deficiency PHGDH is phosphorylated by p38 at Ser371, which promotes the cytosol-localized PHGDH translocation into the nucleus. Meanwhile, AMPK concurrently phosphorylates PHGDH-Ser55 and selectively increases PHGDH catalytic activity against malate oxidation, thus pushing the reduction of NAD+ towards NADH generation. In the nucleus, the altered PHGDH activity positively regulates NADH/NAD+ ratio and thus restricts NAD+ level, and thereby leads to repression of NAD+-dependent PARP1 activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

12 Samples

Download data: XLSX

(Submitter supplied) L-Ser deficiency leads to growth arrest, tissue malformation and embryonic lethality in mice. However, the molecular mechanism by which L-Ser deficiency impairs basic cellular function remains largely unexplored. We used microarrays to identify genes differentially expressed in KO-MEFs cultured with presence or absence of L-Ser, and tried to understand the underlying mechanism of growth-arrested phenotype of KO mice/MEFs elicited by L-Ser deficiency.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3643

Platform:

GPL1355

24 Samples

Download data: CEL

Analysis of forebrains of animals treated with up to 500 mg/kg D-serine for 96 hours. D-serine is involved in many physiological processes through its interaction with the glycine binding site of the NMDA receptor. Results provide insight into the impact of D-serine exposure on neuronal functions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 6 dose sets

Platform:

GPL1355

Series:

GSE10748

24 Samples

Download data: CEL

(Submitter supplied) Cancer-associated mutations in the spliceosome gene create a neomorphic protein that produces aberrant mRNA splicing in hundreds of genes, but the ensuing biologic and therapeutic consequences of this missplicing are not well understood. Here we provide evidence that aberrant splicing by mutant alters the transcriptome, proteome, and metabolome of human cells, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15456

8 Samples

Download data: BED, GTF

(Submitter supplied) Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process. Metabolic heterogeneity has also been observed, yet its role for cancer progression is less explored. Here, we discover that loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301

19 Samples

Download data: TXT