User:Matthew Whiteside/Notebook/Malaria Microarray/2009/01/22

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Entry title
Malaria Task1.1

Searched ArrayExpress and Geo. Human studies that may be relevant:


 * 1) Paper1 pmid=16988231
 * 2) Paper2 pmid=17579077
 * 3) Paper3 pmid=15838786

Other studies with no assoc paper (GEO id):
 * 1) GDS1971[ACCN] Comparison of Gabonese children with uncomplicated & severe malaria
 * 2) GSE9861 Cerebral malaria - incubation of infected erythrocytes with brain endothelial cells.

Other studies likely not relevant:
 * 1) Paper1 pmid=17981117

Also checked cibex - nada.

Malaria Task 2.1

Search for mouse datasets

GEO:

Datasets with papers: // Rationale: Male mice display increased fatality to plasmodium infection. Reversed when castrated. Experimental Setup: Gonadectomized mice / non, m & F, infected with Plasmodium chabaudi. Expression measured in WBC extracted from spleens over 14 day timecourse. 48 samples. Control is day 0. Analysis: Compared survival. Identified differentially expressed genes. Compared Ab response.
 * 1) cernetich2006 pmid=16714546

Results: Observed differences in survival, health. INF-gamma primary indicator between M & F responses. Also difference in degree of Th response. //Rationale: Compare resistant and susceptible mouse strains. Look for markers of susceptibility. Experimental Setup: Create F2 crosses between res / sus strains. Recombinant strains that are resistant were isolated AcB55 and AcB61. These strains were compare against susceptible controls (87% of genome same as control). 14 array samples. RNA isolated from splene (noticed differences in spleens from control) Analysis: Identified genes diff-expressed in both recomb strains.Identified genes involved in: i) erythroid-specific genes or proteins involved in iron metabolism and (ii) genes involved in cell cycle, DNA replication and protein synthesis.
 * 1) minoo2003 pmid=14595440

Results: Linkage analysis identified erythroid-assoc pyruvate kinase. Recomb mice homozygous mutation - deficiency. Showed that this pyruvate deficiency is associated with lower parasite load. //Rationale: Compare transcriptional response in brain to Fatal Cerebral malaria (FCM) and Non-cerebral malaria (NCM): two different parasite strains. Experimental setup: PbA - CM parasite strain. PbK - NCM strain. Control: uninfected mice. All mice same genetic background. 2 timepoint measured. RNA extracted from brain. Analysis: Differential expression of genes in infected mice (both parasite strains). Differential expression of genes in infected mice with different parasite strains. GO ORA and functional annotation ORA on differentially-expressed genes.
 * 1) mui2008 pmid=18299338

Results: Identified novel pathways involved: IFN, MHC, Apoptosis and cell proliferation. Showed through RT-PCR that magnitude of response is different in FCM. //Rationale: study molecular basis of lung dysfunction associated severe malaria. Experimental setup: RNA isolated from lungs of mice infected with PbA. Control: uninfected. 2 time points. Analysis: 300 genes differentially-expressed. GO ORA analysis. Network picture showing cytokine change in infected mouse lung. Hub analysis? Many other wetlab analyses performed to assess damage. These other analyses also tested differences in mouse strain.
 * 1) lovegrove2008 pmid=18483551

Results:THBS-1 is identified hub. binds CD36, involved in CD36-mediated cytoadherance in the lung. CD36 -/- mice have increased lung injury (not increased pathogen load). //Rationale: Look for differences in transcriptional response in two distinct mouse strains susceptible to PbA-caused CM. Then tested whether depletion of CD25+ Treg cells was protective in two strains with heterogeneous responses. Experimental setup: 4 samples. RNA from brains of uninfected / infected in two mouse strains. Analysis: Compared differentially-expressed genes between strains. Many additional wetlab experiments characterizing CM infection in strains.
 * 1) randall2008 pmid=18474652

Results: Showed that Treg depletion is protective in mice with hetergeneous responses. Did not elucidate responses. //Rationale: Compare expression of CM-res and CM-sus mice strains (no cross-breeding, distinct genetic backgrounds in these mice). Experimental setup: 64 samples. B6 (CM-sus) Balb/C (CM-res) mice. time course data over 6 days. Mice infected with PbA. Analysis: Identified 1100 differentially expressed genes. Hierarchical clustering distinguished between early CM-sus, late CM-sus, and all CM-res. Same with PCA analysis. GO ORA analysis on genes differentially expressed between CM-res & CM-sus. Showed DE genes in gene intx network, displayed network with hubs clearly visable. Identified hubs known to be assoc with CM. Showed that apoptotic pathways were up-reg in CM-sus. Performed Transcription Factor Binding Site ORA for up-reg genes. Identified IRF, IRF-1, IRF-7, and ISRE as highly enriched promoter sites (INF-response). Confirmed INF up-reg using RT-PCR.
 * 1) lovegrove2007 pmid=17991715

Results: CM-sus highly enriched in processes involved in inflammation, immunity, and apoptosis (Function, Network and TFBS analysis).

//Rationale: Simultaneously measure host and pathogen responses in CM-res and CM-sus mice strains. Experimental setup: Isolate total RNA from brain, liver, lung, spleen. Run on PbA and mice arrays. Can detect pathogen RNA from organ tissue. Do this for CM-sus and CM-res mice strains (heterogeneous genetic background). 13 samples. small time course (0,3,6 days).
 * 1) lovegrove2006 pmid=17118208

Analysis: Identified 2268 DE genes (vs baseline uninfected). Hierarchical clustering of Pearson for each tissue & day. GO ORA analysis. Did something similar for pathogen data. Also looked at previously-annotated PbA PPI subnetworks that were OR in DE genes. Used linear model to detect DE at baseline between CM-res & CM-sus (608 genes), as well as during infection 2 point time course (607 genes). Performed cluster and GO ORA for these DE gene between mice strains. Identified pathways OR in DE expressed gene from linear model. Included pyruvate metabolism, p38 MAPK signalling and platelet-derived growth factor (PDGF) signalling. Show STAT1 network with Liver day 0 DE genes between strains (one example that is OR in DE genes). Did similar analysis for PbA expression. Found DE between tissues and strains when clustered data. GO ORA was performed on the clustered genes.

Results: Parasites display a unique transcriptional signature in each tissue, and lung appears to be reservoir for metabolically active parasites. CM-res & CM-sus have distinct parasite and organ-specific transcriptional profiles. DE mouse genes were related to humoral immune response, complement activation, or cell-cell interactions. PbA displayed DE of genes related to biosynthetic activities.

Datasets without papers:
 * 1) NK Response in mice.
 * 2) * RNA isolated from whole blood in C57BL/6 mice, infected / non with Plasmodium chabaudi. Noted increased expression of NK-related genes, and presence of NK cells in blood. 36 samples.
 * 3) * Followup - RNA isolated from NK-cells. 10 samples. Observed cell proliferation expression signature in NK cells. Indicate early response to P. chabaudi infection of the blood is marked by a primary wave of interferon with a subsequent response by NK cells.