Table 4 Review of gene signatures previously published for MSCs and comparison with the proposed MSC lineage signature of 489 genes
Reference | Organism | Cells types in contrast | DE features | Statistical significance threshold | Observations | Overlap of the proposed MSCs lineage signature with other studies |
|---|---|---|---|---|---|---|
Tsai et al. 2007 | Human | Four MSC types (BM, AF, AM and CB) vs 6 whole sampled tissues (brain, heart, lung, liver, kidney, and muscle) | 47 genes commonly UP in MSCs, forming a core signature | >4-fold change (p < 0.000005) | Human U133A GeneChip (Affymetrix) 22,000 probe sets that span 14,500 genes | 21 genes in the MSC lineage signature: ACTN1, ADAM9, ANXA5, CALU, CAV1, CTGF, KDELR3, MCFD2, NNMT, NT5E (CD73), LOX, LOXL2, PHLDA1, PLOD2, S100A11, SERPINE1, SMURF2, TAGLN, TIMP1, TPM4, UAP1 |
Kubo et al. 2009 | Human | BM-MSC vs differentiated cells (FIB included) | 148 genes UP in BM-MSC | >2-fold change | Affymetrix Human Genome U133 plus 2.0. 54,000 probe sets / 38,500 genes. Differentiated cells include FIB, osteoblasts, adipocytes and chondrocytes. | 14 genes in the MSC lineage signature: ADAMTS5, CCND1, FHL2, GDF15, IGFBP3, LOX, LOXL2, MAP4K4, MCFD2, SH3RF1, SLC16A4, SMURF2, UGCG, VEGFC |
Jääger et al. 2012 [41] | Human | AD-MSC or FIB vs their lineage derived cells | 211 genes UP versus cells differentiate to 3 lineages | ANOVA (1% FDR) | AD-MSC and FIB were in vitro differentiated towards osteogenic, chondrogenic and adipogenic lineages. | 16 genes in the MSC lineage signature: CRISPLD2, HTRA1, IGFBP5, LAMB1, MARCKS, NNMT, PSAT1, REXO2, RPS27L, S100A11, SARS, SERPINF1, TMEM165, TMEM47, VAMP3, WARS |
Jääger et al. 2012 [41] | Human | AD-MSC or FIB vs their lineage derived cells | 333 genes DOWN versus cells differentiate to 3 lineages | ANOVA (1% FDR) | AD-MSC and FIB were in vitro differentiated towards osteogenic, chondrogenic and adipogenic lineages. | 38 genes in the MSC lineage signature: ACTN1, ADAM9, ANXA5, ARF4, C1R, C1S, CALU, CAV1, CCND1, CD63, CKAP4, CLIC4, CORO1C, CTGF, CYB5A, DDAH1, DDR2, DSP, ELL2, FRMD6, FTL, HEG1, HEXA, HNMT, IER3IP1, ISLR, KDELR3, LAMA4, LAMC1, LASP1, LMO7, MYH9, NRP1, NUPR1, PTRF, SERPINE1, SRPX, TUBB6 |
Jääger et al. 2012 [41] | Human | AD-MSC or FIB vs their lineage derived cells | genes UP or DOWN in distinct contrasts versus cells differentiate to 3 lineages | ANOVA (1% FDR) | AD-MSC and FIB were in vitro differentiated towards osteogenic, chondrogenic and adipogenic lineages. | 10 genes in the MSC lineage signature: IGFBP3, MT1E, MYOF, NAV1, NTM, PDLIM7, PTPN21, RHOC, SH2D4A, TPM1 |
Pedemonte et al. 2007 [30] | Mouse | BM-MSCs vs any given tissue or cell type of the 12 included (brain, heart, skeletal muscle, liver, kidney, lung, dendritic cells, ESCs, MEFs, NSCs, HSCs, T-cells) | 403 genes (translated into 249 human orthologs) | F-test p < 0.0001 | Affymetrix Mouse Genome 430 2.0 arrays, covering 39,000 transcripts. 7 BM-MSC samples against 486 publicly available samples from different origins. | 54 orthologs genes in the MSC lineage signature: ADAMTS5, ANTXR1, ANXA2, ASNS, BGN, C6orf89, CALD1, CDC42EP3, CNN3, COL3A1, COL4A1, COL5A1, COL5A2, COL6A3, CSRP1, DAP, DBN1, DDR2, DKK3, DPYSL3, ERRFI1, FGF7, FSTL1, FZD2, GJA1, GPR124, HTRA1, KDELR3, LGALS1, LOX, MMP2, MRC2, NID2, NNMT, NUPR1, OSMR, PDGFRB, PHLDA3, PLOD2, PLS3, POSTN, PSAT1, PYCR1, RCN1, RHOC, RNASE4, TNFRSF12A, TPBG, TPM4, TSPAN6, SERPINF1, SERPINH1, SNAI2, SPARC |