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| Status |
Public on Dec 27, 2012 |
| Title |
Expression data from brain, liver and spleen of Npc1-/- mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Niemann-Pick Type C (NPC) disease is a rare, genetic, lysosomal disorder with progressive neurodegeneration. Poor understanding of the pathophysiology and lack of blood-based diagnostic markers are major hurdles in the treatment and management of NPC and several additional neurological, lysosomal disorders. To identify disease severity correlates, we undertook whole genome expression profiling of sentinel organs, brain, liver, and spleen of Balb/c Npc1-/- mice (Npc1nih)relative to Npc1+/- at an asymptomatic stage, as well as early- and late-symptomatic stages. Unexpectedly, we found prominent up regulation of innate immunity genes with age-dependent change in their expression, in all three organs. We shortlisted a set of 12 secretory genes whose expression steadily increased with age in both brain and liver, as potential plasma correlates for the neurological disease. Ten were innate immune genes with eight ascribed to lysosomes. Several are known to be elevated in diseased organs of murine models of other lysosomal diseases including Gaucher’s disease, Sandhoff disease and MPSIIIB. We validated the top candidate lysozyme, in the plasma of Npc1-/- as well as Balb/c Npc1nmf164 mice (bearing a point mutation closer to human disease mutants) and show its reduction in response to an emerging therapeutic. We further established elevation of innate immunity in Npc1-/- mice through multiple functional assays including inhibition of bacterial infection as well as cellular analysis and immunohistochemistry.
We used microarrays on the diseased organs, brain, liver and spleen of the Npc1-/- mice to unserstand the molecular changes occur during the progression of NPC diseases. From the data, we have identified 12 potential genes which can be potentially developed as blood-based biomarker. We have also discovered up regulation of innate iimunity genes in all three organs of Npc1-/- mice and functionally validated them in liver and spleen.
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| Overall design |
Brain from 11 female Npc1−/− and 16 control female mice (Npc1+/+ and Npc1+/−) from 6 age groups (20-25, 37-40, 54-55, 59-62, 67-71 and 81-84 days) were surgically harvested. Liver and spleen from 6 Npc1-/- and 6 Npc1+/- female mice from three age group ( 20-25, 54-55 and 67-71 days) were surgically harvested. Organs were kept in RNA later and stored at -20 °C until used. RNA was isolated and Affymetrix mouse 430 2.0 array hybridizations were performed by ‘UCLA Clinical Microarray Core’, UCLA, Los Angeles, CA, USA. Subsequent raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Data from Npc1-/- mice from all age groups were compared to control mice (Npc1+/- and/or Npc1-/- mice) from all age groups separately for brain, liver and spleen. 'Matrix Table1' corrsponds for brain, 'Matrix Table2' corresponds for liver and 'Matrix Table3' corresponds for spleen. Thresholds for selecting significant genes were set at a relative difference ³1.5-fold, absolute difference ³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.
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| Contributor(s) |
Alam S, Shin J, Tamez P, Haldar K |
| Citation(s) |
23094108 |
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| Submission date |
Jul 24, 2012 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Md Suhail Alam |
| E-mail(s) |
salam@nd.edu
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| Phone |
574-631-3227
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| Organization name |
University of Notre Dame
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| Department |
Center for Rare and Neglected Diseases/Biological Sciences
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| Lab |
Haldar lab
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| Street address |
103 Galvin, University of Notre Dame, IN
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| City |
Notre Dame |
| State/province |
IN Indiana |
| ZIP/Postal code |
46545 |
| Country |
USA |
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| Platforms (1) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
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| Samples (51)
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| Relations |
| BioProject |
PRJNA171263 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39621_Matrix_Table_1_Brain.txt.gz |
5.9 Mb |
(ftp)(http) |
TXT |
| GSE39621_Matrix_Table_2_Liver.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE39621_Matrix_Table_3_Spleen.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE39621_RAW.tar |
182.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
| Processed data are available on Series record |
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