Similar Datasets
Project description:The two most common melanoma histopathologic subtypes, superficial spreading (SSM) and nodular melanoma (NM), are believed to represent sequential phases of linear progression from radial to vertical growth. Studies suggest, however, that SSM and NM are biologically distinct. We utilized an integrative genomic approach to examine the possibility that SSM and NM are the result of independent pathways characterized by unique molecular alterations. Cell lines including SSM, NM, metastatic melanoma, and melanocyte controls were evaluated for copy number changes and differential mRNA expression using single nucleotide polymorphism array (SNP 6.0, Affymetrix) and gene array (U133A 2.0, Affymetrix). Data sets were integrated to identify copy number alterations that correlated with gene expression, and array results were validated using immunohistochemistry on human tissue microarrays (TMAs) and an external data set. The functional effect of genomic deletion was assessed by lentiviral overexpression. Integrative genomics revealed 8 genes in which NM/SSM-specific copy number alterations were correlated with NM/SSM differential gene expression (P<0.05, Spearman’s rank). Pathways analysis of differentially expressed genes (N=114) showed enrichment for metabolic-related processes. SSM-specific genomic deletions (DIS3, MTAP, G3BP2, SEC23IP, USO1) were verified in an expanded panel of cell lines, and forced overexpression of MTAP in SSM resulted in reduced cell growth. Metabolism-related gene ALDH7A1 was verified as overexpressed in NM using human TMAs.The identification of recurrent genomic deletions in SSM not present in NM challenges the linear model of melanoma progression and supports the unique molecular classification of SSM and NM.
2010-12-01 | GSE22301 | GEO
Project description:The two most common melanoma histopathologic subtypes, superficial spreading (SSM) and nodular melanoma (NM), are believed to represent sequential phases of linear progression from radial to vertical growth. Studies suggest, however, that SSM and NM are biologically distinct. We utilized an integrative genomic approach to examine the possibility that SSM and NM are the result of independent pathways characterized by unique molecular alterations. Cell lines including SSM, NM, metastatic melanoma, and melanocyte controls were evaluated for copy number changes and differential mRNA expression using single nucleotide polymorphism array (SNP 6.0, Affymetrix) and gene array (U133A 2.0, Affymetrix). Data sets were integrated to identify copy number alterations that correlated with gene expression, and array results were validated using immunohistochemistry on human tissue microarrays (TMAs) and an external data set. The functional effect of genomic deletion was assessed by lentiviral overexpression. Integrative genomics revealed 8 genes in which NM/SSM-specific copy number alterations were correlated with NM/SSM differential gene expression (P<0.05, Spearman’s rank). Pathways analysis of differentially expressed genes (N=114) showed enrichment for metabolic-related processes. SSM-specific genomic deletions (DIS3, MTAP, G3BP2, SEC23IP, USO1) were verified in an expanded panel of cell lines, and forced overexpression of MTAP in SSM resulted in reduced cell growth. Metabolism-related gene ALDH7A1 was verified as overexpressed in NM using human TMAs.The identification of recurrent genomic deletions in SSM not present in NM challenges the linear model of melanoma progression and supports the unique molecular classification of SSM and NM. Gene expression profiling using Affymetrix U133A 2.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP).
2010-12-01 | E-GEOD-22301 | biostudies-arrayexpress
Project description:We reported transcriptional characterization of BMDCs stimulated by filter-sterilized spent medium of Parabacteroides goldsteinii ASF519 (ASF519 SSM) alone or in comination with zymosan. We identified that ASF519 SSM-induced differentially expressed genes have a wide association with the regulation of immune functions, cell communication, apoptosis. We observed that ASF519 SSM induced transcriptomic changes towards immune tolerance, such as a dramatic induction of tolerogenic Il10, lipocalin-2(Lcn2) and indoleamine 2, 3-dioxygenases (Ido1/2), and a reduction of the co-stimulatory molecule Cd40 and inflammatory cytokines, including Il12b, Il23a, and Il1f9 (or Il-36 gamma).
2021-04-07 | GSE171658 | GEO
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls.
2010-10-21 | GSE22305 | GEO
Project description:Hydrogenimonas sp. SSM-sur55 genome sequencing
| PRJDB9990 | ENA
Project description:Skeletal muscle subsarcolemmal mitochondria (SSM) and intermyofibrillar mitochondria subpopulations have distinct metabolic activity and sensitivity, though the mechanisms that localize SSM to peripheral areas of muscle fibers are poorly understood. A protein interaction study and complexome profiling identified PERM1 interacts with the MICOS-MIB complex. Ablation of Perm1 in mice reduced muscle force, decreased mitochondrial membrane potential and complex I activity, and reduced the numbers of SSM in skeletal muscle. We demonstrate PERM1 interacts with the intracellular adaptor protein ankyrin B (ANKB) that connects the cytoskeleton to the plasma membrane. In addition, we discovered a C-terminal transmembrane helix that anchors PERM1 into the outer mitochondrial membrane. We conclude PERM1 functions in the MICOS-MIB complex and acts as an adapter to connect the mitochondria with the sarcolemma via ANKB.
2021-11-16 | PXD025745 | Pride
Project description:Corneal epithelial cells derived from hPSCs provides an important cells source for the construction of the in vitro preclinical models aimed for ophthalmic drugs tests. However, the recent differentiation protocols lack the optimal culturing conditions that hinder the robustness and the quality of cells as well as the scale-up application of cells production. Here we introduce a simplified, yet efficient small molecules-based corneal induction method (SSM-CI) for the generation of corneal epithelial cells from hPSCs. SSM-CI provides the advantage of minimization the cells culturing time and steps using only two defined xenobiotic-free and serum-free culturing mediums in combination with the TGFß pathway, Wnt/ß-catenin pathway signaling chemical inhibitors, and human bFGF growth factor for a period of 25 days. Compared to both conventional human corneal epithelial cell line (HCE-T) as well as the human primary corneal epithelial cells (hPCEpC), human embryonic stem cells derived corneal epithelial cells generated by SSM-CI has highly expressed major differentiation as well as maturation markers such as PAX6 and CK12. RNA-seq analysis indicated the genuine diversion of hPSCs into the corneal epithelium lineage where corneal progenitor and adult corneal epithelial phenotypes were significantly upregulated. Furthermore, despite the inhibition of TGF-β and Wnt/β-catenin at the early stage of differentiation, an upregulation of the TGF-β and Wnt/β-catenin pathways related transcripts we noticed in the late stage which indicated the necessity of these pathways in the generation of mature corneal epithelial cells. Moreover, there was a shift in gene signatures associated with the metabolic characteristics of mature corneal epithelial cells where a decrease of glycolysis related transcripts and an increase in fatty acid oxidation related one was noticed. That was also corresponded by the overexpression of metabolic enzymes and transporters related transcripts that were mainly responsible for the metabolism of fatty acids. Thus SSM-CI provide a comprehensive method for the generation of functional corneal epithelial cells that has the potential for the employment in future preclinical models.
2022-01-15 | GSE193514 | GEO
Project description:Sahaj Samadhi Meditation (SSM), a mantra-based effortless-transcending meditation, and Sudarshan Kriya Yoga (SKY), a rhythmic cyclical breathing practice, are taught by the Art of Living Foundation and practised together under a standardised daily protocol. Short-term studies have linked such practices to reduced pro-inflammatory gene expression and improved immune indices, but whether sustained multi-year practice produces a stable transcriptional phenotype has not been established. We profiled whole blood gene expression in 30 long-term Art of Living practitioners and 30 non-practitioner controls recruited from the same community. Practitioners followed the standard regimen of SSM for 20 minutes twice daily and SKY for approximately 25 minutes once daily, sustained for at least 10 years (mean 15.8, range 10-26 years). Because diet, alcohol, tobacco and socio-economic background strongly confound the blood transcriptome, all participants were vegetarian, abstained from alcohol, tobacco and recreational drugs, and came from a comparable socio-economic and geographic setting; the groups were matched on age, sex, body mass index and lifestyle, and differed by design only in the presence of a sustained meditation practice. Every practitioner followed both components daily, so these data characterize the combined SSM and SKY protocol rather than either practice in isolation. The dataset provides a lifestyle-matched reference for the transcriptional correlates of sustained practice, for comparison against signatures of chronic stress and against short-term mind body intervention datasets.
2026-09-30 | GSE348248 | GEO
Project description:The global transcriptome of the wild type Lactobacillus acidophilus NCFM strain (NCK56) was measured during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate. Oligoarray hybridization experiments were performed to compare the differential transcriptional profiles of the NCK56 at the early-log (OD600nm 0.3-0.5) phase when cultured in semi-synthetic medium (SSM, Barrangou et al., 2003 PNAS. 100:8957-8962, supplemented with a range of 1% (w/v) carbohydrates, at 37 M-BM-0C and harvested by centrifugation and flash freezing. A total of 12 NCK56 cultures were prepared by growing in SSM supplemented with each one of the 12 tested carbohydrates. Each culture was grown in fresh carbohydrate supplemented SSM with a 1% inoculum from an overnight culture for a total of five subcultured passages. Aliquots of cells were collected at OD600nm of 0.3-0.5 (early log-phase) for total RNA extraction and cDNA synthesis. Labeled cDNA samples from NCK56 were coupled with mono-reactive Cy3 and Cy5 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), for two technical replicates on each carbohydrate (e.g. cy3-GOS and cy5-GOS). Comparative hybridizations were performed on samples representing two different carbohydrate cultures at same growth phases labeled with either cy3 or cy5 using a loop design for 12 hybridizations.
2012-12-20 | E-GEOD-35968 | biostudies-arrayexpress