Amorphochlora amoebiformis
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ABSTRACT:
PROVIDER: PRJNA12808 | ENA |
REPOSITORIES: ENA
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Project description:Highly invasive integrin and protease-independent amoeboid migration is often employed by cancer cells at the invasive front, though little is known about the transcriptomic changes underlying the switch to an amoeboid migratory mode. Using a metastatic melanoma cell line expressing photoconvertible Dendra2 protein (WM983c-D2), tumour spheroids were cultured in 3D collagen matrices and imaged over time. Spheroids grown from WM983c-D2 cells generate cells of three distinct phenotypes: 1) compact, non-invading cells organised at the spheroid surface with no visual cell protrusions, hereafter termed ‘epithelial’; 2) cells still attached to the spheroid periphery that have commenced tumour escape, exhibiting cellular protrusions and an elongated phenotype, hereafter termed ‘escaping’; 3) singly migrating cells exhibiting a rounded phenotype and no lamellipodia consistent with amoeboid cell migration, hereafter termed 'amoeboid'. Individual amoeboid and escaping cells, as well as groups of epithelial cells at the spheroid edge were photoconverted and single cell sorted via FACS following enzymatic digestion of the collagen matrix. 10 Epithelial, 12 escaping and 13 amoeboid cells were subjected to scRNA-seq and differential expression analyses in order to identify changes in gene expression as melanoma cells convert from a non-invasive epithelial state to invasive amoeboid cells.
2022-05-21 | E-MTAB-11722 | biostudies-arrayexpress
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Project description:Dunaliella tertiolecta is an extremophilic, green alga from the Chlorophyte lineage. It is found in coastal marine environments around the world. D. tertiolecta can tolerate extremes of heat, light, pH, and salinity. D. tertiolecta is under development for the production biofuels and other bioproducts because it can produce large quantities of neutral lipids, and it can be grown in open raceway ponds using only the inputs of seawater and sunlight. This isolate of D. tertiolecta (UTEX LB 999) was found in Oslofjord, Norway in 1938. This accession includes an RNA-Seq analysis of D. tertiolecta cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.
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Project description:Amoeboid and mesenchymal migration of cancer cells both contribute to metastatic spreading of tumors. To characterize gene expression profiles underlying the different migratory modes, we performed RNA sequencing of HT1080 fibrosarcoma cells undergoing mesenchymal-amoeboid transition induced by either doxycycline-inducible constitutively active RhoA or dasatinib treatment. Cells were kept in three-dimensional collagen gels with or without induction for 48 hours. RNA was isolated with a modified Chomczynski protocol. RNA-seq libraries were constructed from DNase I treated, rRNA depleted total RNA and sequenced with Illumina 2000/2500 sequencers.
2019-07-29 | E-MTAB-6823 | biostudies-arrayexpress
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Project description:Invasion plasticity allows malignant cells to toggle between collective, mesenchymal and amoeboid phenotypes while traversing extracellular matrix (ECM) barriers. Current dogma holds that collective and mesenchymal invasion programs trigger the mobilization of proteinases that digest structural barriers dominated by type I collagen, while amoeboid activity allows cancer cells to marshal mechanical forces to traverse tissues independently of ECM proteolysis. Here, we use cancer spheroid-3-dimensional matrix models, single-cell RNA sequencing, and human tissue explants to identify the mechanisms controlling mesenchymal versus amoeboid invasion. Unexpectedly, collective/mesenchymal- and amoeboid-type invasion programs – though distinct – are each characterized by active tunneling through ECM barriers, with expression of matrix-degradative metalloproteinases. CRISPR/Cas9-mediated targeting of a single membrane-anchored collagenase, MMP14/MT1-MMP, ablates tissue-invasive activity while co-regulating cancer cell transcriptional programs. Though changes in matrix architecture, nuclear rigidity, and metabolic stress as well as the presence of cancer-associated fibroblasts are proposed to support amoeboid activity, none of these changes restore invasive activity of MMP14-targeted cancer cells. While a requirement for MMP14 is bypassed in low-density collagen hydrogels, invasion by the proteinase-deleted cells is associated with nuclear envelope and DNA damage, highlighting a proteolytic requirement for maintaining nuclear integrity. Nevertheless, when cancer cells confront explants of live human breast tissue, MMP14 is again required to support invasive activity. Corroborating these results, spatial transcriptomic and immunohistological analyses of human breast cancers identified MMP14 expression in tissue-infiltrating carcinoma cells that were further juxtaposed with proteolyzed type I collagen fragments, underlining the pathophysiologic importance of this proteinase in directing invasive activity in vivo.
2026-02-01 | GSE313573 | GEO
Project description:Invasion plasticity allows malignant cells to toggle between collective, mesenchymal and amoeboid phenotypes while traversing extracellular matrix (ECM) barriers. Current dogma holds that collective and mesenchymal invasion programs trigger the mobilization of proteinases that digest structural barriers dominated by type I collagen, while amoeboid activity allows cancer cells to marshal mechanical forces to traverse tissues independently of ECM proteolysis. Here, we use cancer spheroid-3-dimensional matrix models, single-cell RNA sequencing, and human tissue explants to identify the mechanisms controlling mesenchymal versus amoeboid invasion. Unexpectedly, collective/mesenchymal- and amoeboid-type invasion programs – though distinct – are each characterized by active tunneling through ECM barriers, with expression of matrix-degradative metalloproteinases. CRISPR/Cas9-mediated targeting of a single membrane-anchored collagenase, MMP14/MT1-MMP, ablates tissue-invasive activity while co-regulating cancer cell transcriptional programs. Though changes in matrix architecture, nuclear rigidity, and metabolic stress as well as the presence of cancer-associated fibroblasts are proposed to support amoeboid activity, none of these changes restore invasive activity of MMP14-targeted cancer cells. While a requirement for MMP14 is bypassed in low-density collagen hydrogels, invasion by the proteinase-deleted cells is associated with nuclear envelope and DNA damage, highlighting a proteolytic requirement for maintaining nuclear integrity. Nevertheless, when cancer cells confront explants of live human breast tissue, MMP14 is again required to support invasive activity. Corroborating these results, spatial transcriptomic and immunohistological analyses of human breast cancers identified MMP14 expression in tissue-infiltrating carcinoma cells that were further juxtaposed with proteolyzed type I collagen fragments, underlining the pathophysiologic importance of this proteinase in directing invasive activity in vivo.
2026-02-01 | GSE313572 | GEO
Project description:Microglia, the resident immune cells of the central nervous system (CNS), have two distinct phenotypes in the developing brain: amoeboid form, known to be amoeboid microglial cells (AMC) and ramified form, known to be ramified microglial cells (RMC) alongside several intermediate forms. The AMC are characterized by being proliferative, phagocytic and migratory whereas the RMC are quiescent and exhibit a slow turnover rate. The AMC transform into RMC with advancing age, and this transformation is indicative of the gradual shift in the microglial functions. Both AMC and RMC respond to CNS inflammation, and they become hypertrophic when they are activated by trauma, infection or neurodegenerative stimuli. The molecular mechanisms and functional significance of morphological transformation of microglia during normal development and in disease conditions is not clear. It is hypothesized that AMC and RMC are functionally regulated by a specific set of genes encoding various signaling molecules and transcription factors. To address this, we carried out cDNA microarray analysis using lectin-labeled AMC and RMC isolated from frozen tissue sections of the corpus callosum of 5-day and 4-week old rat brain respectively, by laser capture microdissection (LCM). The global gene expression profiles of both microglial phenotypes were compared and the differentially expressed genes in AMC and RMC were clustered based on their functional annotations. This genome wide comparative analysis helps in identifying genes that are specific to AMC and RMC. The novel and specific molecules identified in both microglial phenotypes can be targeted for therapeutic purposes in developing and adult brain diseases. We used microarrays to identify the genes specific to amoeboid and ramified microglia. RNA was isolated from the laser-captured amoeboid and ramified microglia from the corpus callosum of 5-day and 4-week old rat brain. The RNA was hybridised onto Affymetrix Rat 230 2.0 array.
2011-06-11 | E-GEOD-29885 | biostudies-arrayexpress
Project description:Genome of the amoeboid chlorarachniophyte Amorphochlora moebiformis
| PRJDB20813 | ENA