Table 2 Categories of altered genes in CNE-2 single clone cells by macrophages-like cells during conditioned culture Accession No. Gene description NM_001012 Ribosomes This gene encodes a ribosomal protein that is a component of the 40S subunit. NM_002140.2 heterogeneous nuclear ribonucleoproteins (hnRNPs) NM_005174.2 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 (ATP5C1), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA NM_015937.3 Homo sapiens phosphatidylinositol glycan anchor biosynthesis, class T (PIGT), mRNA NM_018085.4 Homo sapiens importin 9 (IPO9) NM_000314.4 Homo sapiens phosphatase and tensin homolog (PTEN) NM_001033756.1 Homo sapiens vascular endothelial growth factor A (VEGFA), transcript variant 7, mRNA NM_003064.2 Homo sapiens secretory leukocyte peptidase inhibitor (SLPI) NM_002394.4 Homo sapiens solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 (SLC3A2), transcript variant 3 NM_005496.3 Homo sapiens structural maintenance of chromosomes 4 (SMC4), transcript variant 1 NM_006145.1 Homo sapiens DnaJ (Hsp40) homolog, subfamily B, member 1 (DNAJB1) NM_002306.2 Homo sapiens lectin, galactoside-binding, soluble, 3 (LGALS3), transcript variant 1 NM_020186.1 Homo sapiens ACN9 homolog (S. cerevisiae) (ACN9) NM_005347.2 Homo sapiens heat shock 70 kDa protein 5 (glucose-regulated protein,78 kDa) (HSPA5) NM_016639.1 Homo sapiens tumor necrosis factor receptor superfamily, member 12A (TNFRSF12A) NM_005348.3 Homo sapiens heat shock protein 90 kDa alpha (cytosolic), class A member 1 (HSP90AA1), transcript variant 2 NM_194247.2 Homo sapiens heterogeneous nuclear ribonucleoprotein A3 (HNRNPA3) NM_004148.3 Homo sapiens ninjurin 1 (NINJ1) NM_002337.1 Homo sapiens low density lipoprotein receptor-related protein associated protein 1 (LRPAP1) NM_001003703.1 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 (ATP5J), nuclear gene encoding mitochondrial protein, transcript variant 1 NM_004048.2 Homo sapiens beta-2-microglobulin (B2M) NM_000146.3 Homo sapiens ferritin, light polypeptide (FTL) NM_001105079.1 Homo sapiens fibrosin (FBRS), mRNA NM_001002.3 Homo sapiens ribosomal protein, large, P0 (RPLP0) transcript variant 1 NM_015134.2 Homo sapiens myosin phosphatase Rho interacting protein (MPRIP), transcript variant 1 NM_004888.3 Homo sapiens ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G1 (ATP6V1G1) NM_015161.1 Homo sapiens ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1) NM_001001973.1 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 (ATP5C1), nuclear gene encoding mitochondrial protein, transcript variant 1 NM_001997.3 Homo sapiens Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (FAU) NM_006196.2 Homo sapiens poly(rC) binding protein 1 (PCBP1) NM_000925.2 Homo sapiens pyruvate dehydrogenase (lipoamide) beta (PDHB) NR_003286.1 Homo sapiens 18S ribosomal RNA (LOC100008588) BAG64005.1 unnamed protein product NW_001838014.1 Homo sapiens chromosome 10 genomic contig, alternate assembly NT_007592.14 Homo sapiens chromosome 6 genomic contig, reference assembly NW_001839064.2 Homo sapiens chromosome 7 genomic contig, alternate assembly Cao et al. BMC Cancer 2010, 10:68 http://www.biomedcentral.com/1471-2407/10/68 niche microenvironments indeed, hence these niches might represent targets for treatments of cancer. Further understanding of the fate of cancer stem cells interfered by their particular microenvironment may bring out a new era for cancer treatment. A cancer stem cell is thought to be quiescent and should be in G0/G1 phase [30]. Non-SP cells cultured with macrophage-like cells could be arrested on G1/S thus slow down the cell cycle. It therefore indicated that the micro- environment had an effect on cell-cycle-specific change. On the other hand, the migration of the non-SP cells is enhanced through conditioned culture. Therefore, these results implied that non-SP cells showed more aggressive characteristics with response to microenvironment. Comprehensive analysis of gene expression using SSH revealed distinct differences between conditioned culture and non-conditioned culture cells. A few genes have been found to be evidently up-regulated in conditioned cultured non-SP cells. Genes such as ARMER, PCBP1 and PDHB were only expressed in conditioned cultured non-SP cells, which can be validated by Northern blot- ting analysis. ARMER is an apoptotic regulator in the Page 8 of 11 Alteration Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up