Neurology · 2014 · 28 citations · 32 references
Life SciencesCell BiologyImmunologyAutoimmunityImmunopathologyNeuroimmunologyHelper T Cell SubsetsT Cell ActivationT Cell BiologyT Cell Receptor SignalingCd4 Positive T CellsCd4 T Cell ActivationCd4+ T Helper Cell ResponsesFlow Cytometry ImmunophenotypingMultiple Sclerosis ImmunopathogenesisMultiple Sclerosis ImmunopathologyNaive T CellsToll-like Receptor Signaling
OBJECTIVE: Our objective was to determine whether altered naive CD4 T-cell biology contributes to development of disease progression in secondary progressive multiple sclerosis (SPMS). METHODS: We compared the naive CD4 T-cell gene expression profiles of 19 patients with SPMS and 14 healthy controls (HCs) using a whole-genome microarray approach. We analyzed surface protein expression of critical genes by flow cytometry after T-cell receptor (TCR) stimulation of naive CD4 T cells isolated from HCs and patients with SPMS. RESULTS: Hierarchical clustering segregated patients with SPMS into 2 subgroups: SP-1, which had a short duration of relapsing-remitting multiple sclerosis (MS), and SP-2, which had a long duration of relapsing-remitting MS. SP-1 patients upregulated numerous immune genes, including genes within TCR and toll-like receptor (TLR) signaling pathways. SP-2 patients showed immune gene downregulation in comparison with HCs. We identified an SP-1-specific transcriptional signature of 3 genes (TLR4, TLR2, and chemokine receptor 1), and these genes had higher surface protein expression in SP-1 than in SP-2. After TCR stimulation for 48 hours, only SP-1 showed a progressive linear increase in TLR2 and TLR4 protein expression. CONCLUSIONS: Differences in naive CD4 T-cell biology, notably of TCR and TLR signaling pathways, identified patients with MS with more rapid conversion to secondary progression, a critical determinant of long-term disability in MS.
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Data clustering: 50 years beyond K-means
Anil K. Jain · Pattern Recognition Letters · 2009 · 9.2K citations
affy—analysis of <i>Affymetrix GeneChip</i> data at the probe level
Laurent Gautier, Leslie Cope, Benjamin M. Bolstad et al. · Bioinformatics · 2004 · 5.4K citations · Full text