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| Status |
Public on Dec 03, 2019 |
| Title |
Gene expression of fibroblasts carrying SAMHD1 mutations or not |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
In mammalian cells, the catabolic activity of the dNTP triphosphohydrolase SAMHD1 sets the balance and the concentrations of the four dNTPs. Deficiency of SAMHD1 leads to unequally increased pools and marked dNTP imbalance. Although it is documented that imbalanced dNTP pool expansion increases mutation frequency in cancer cells, it is not known if the SAMHD1-induced dNTP imbalance favors accumulation of somatic mutations in non-transformed cells. Here we have investigated how fibroblasts isolated from Aicardi Goutières Syndrome (AGS) patients with mutated SAMHD1 react to the constitutive pool imbalance characterized by a huge dGTP pool. We focused on the effects on dNTP pools, cell-cycle progression, dynamics and fidelity of DNA replication, efficiency of UV-induced DNA repair. AGS fibroblasts entered senescence prematurely or upregulated genes involved in G1/S transition and DNA replication. The normally growing AGS cells exhibited unchanged DNA replication dynamics and, when quiescent, faster rate of excision repair of UV-induced DNA damages than wildtype fibroblasts. To investigate if the lack of SAMHD1 affects DNA replication fidelity we compared de novo mutations in AGS and WT cells by exome next generation sequencing. Somatic variant analysis indicated a mutator phenotype suggesting that SAMHD1 is a caretaker gene whose deficiency is per se mutagenic promoting genome instability in non-transformed cells.
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| Overall design |
This experiment was designed to understand if mutations on SAMHD1 gene interfere with gene expression. We used one primary cell line as control (WT) and four primary cell line carrying SAMHD1 mutantions (AGS patients). The four AGS cell lines are named P1 (AGS282 carring the mutation R145X and R164X), P2 (AGS295 carring a deletion of exons 12-16), P3 (AGS165 carring the deletion of AA 120_123), P4 (AGS128 carring the mutation Q149X). Each cell line was tested in at least three biological replicates using one color design.
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| Contributor(s) |
Cagnin S, Rampazzo C, Pacchioni B, Millino C |
| Citation(s) |
31914608 |
| Submission date |
Aug 09, 2019 |
| Last update date |
Jan 13, 2020 |
| Contact name |
Gerolamo Lanfranchi |
| E-mail(s) |
stefano.cagnin@unipd.it
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| Phone |
+39-0498276219
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| Organization name |
University of Padova
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| Department |
CRIBI - Biotechnology Center and Biology Department
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| Lab |
Functional Genomics Lab
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| Street address |
Via U. Bassi, 58/B
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| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
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| Platforms (1) |
| GPL17077 |
Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version) |
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| Samples (16)
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| GSM4025450 |
Skin fibroblasts, Wild-type-replica4 |
| GSM4025451 |
Skin fibroblasts, Patient1-replica1 |
| GSM4025452 |
Skin fibroblasts, Patient1-replica2 |
| GSM4025453 |
Skin fibroblasts, Patient1-replica3 |
| GSM4025454 |
Skin fibroblasts, Patient2-replica1 |
| GSM4025455 |
Skin fibroblasts, Patient2-replica2 |
| GSM4025456 |
Skin fibroblasts, Patient2-replica3 |
| GSM4025457 |
Skin fibroblasts, Patient3-replica1 |
| GSM4025458 |
Skin fibroblasts, Patient3-replica2 |
| GSM4025459 |
Skin fibroblasts, Patient3-replica3 |
| GSM4025460 |
Skin fibroblasts, Patient4-replica1 |
| GSM4025461 |
Skin fibroblasts, Patient4-replica2 |
| GSM4025462 |
Skin fibroblasts, Patient4-replica3 |
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| Relations |
| BioProject |
PRJNA559555 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135652_RAW.tar |
198.7 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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