cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1632161.v1
title: Role of stress-activated OCT4A in the cell fate decisions of embryonal carcinoma cells treated with etoposide

description: Tumor cellular senescence induced by genotoxic treatments has recently been found to be paradoxically linked to the induction of “stemness.” This observation is critical as it directly impinges upon the response of tumors to current chemo-radio-therapy treatment regimens. Previously, we showed that following etoposide (ETO) treatment embryonal carcinoma PA-1 cells undergo a p53-dependent upregulation of OCT4A and p21Cip1 (governing self-renewal and regulating cell cycle inhibition and senescence, respectively). Here we report further detail on the relationship between these and other critical cell-fate regulators. PA-1 cells treated with ETO display highly heterogeneous increases in OCT4A and p21Cip1 indicative of dis-adaptation catastrophe. Silencing OCT4A suppresses p21Cip1, changes cell cycle regulation and subsequently suppresses terminal senescence; p21Cip1-silencing did not affect OCT4A expression or cellular phenotype. SOX2 and NANOG expression did not change following ETO treatment suggesting a dissociation of OCT4A from its pluripotency function. Instead, ETO-induced OCT4A was concomitant with activation of AMPK, a key component of metabolic stress and autophagy regulation. p16ink4a, the inducer of terminal senescence, underwent autophagic sequestration in the cytoplasm of ETO-treated cells, allowing alternative cell fates. Accordingly, failure of autophagy was accompanied by an accumulation of p16ink4a, nuclear disintegration, and loss of cell recovery. Together, these findings imply that OCT4A induction following DNA damage in PA-1 cells, performs a cell stress, rather than self-renewal, function by moderating the expression of p21Cip1, which alongside AMPK helps to then regulate autophagy. Moreover, this data indicates that exhaustion of autophagy, through persistent DNA damage, is the cause of terminal cellular senescence.
DOI: 10.6084/m9.figshare.1632160.v1
title: Epithelial morphological reversion drives Profilin-1-induced elevation of p27<sup>kip1</sup> in mesenchymal triple-negative human breast cancer cells through AMP-activated protein kinase activation

description: Profilin-1 (Pfn1) is an important regulator of actin polymerization that is downregulated in human breast cancer. Previous studies have shown Pfn1 has a tumor-suppressive effect on mesenchymal-like triple-negative breast cancer cells, and Pfn1-induced growth suppression is partly mediated by upregulation of cell-cycle inhibitor p27<sup>kip1</sup> (p27). In this study, we demonstrate that Pfn1 overexpression leads to accumulation of p27 through promoting AMPK activation and AMPK-dependent phosphorylation of p27 on T198 residue, a post-translational modification that leads to increased protein stabilization of p27. This pathway is mediated by Pfn1-induced epithelial morphological reversion of mesenchymal breast cancer through cadherin-mediated restoration of adherens junctions. These findings not only elucidate a potential mechanism of how Pfn1 may inhibit proliferation of mesenchymal breast cancer cells, but also highlight a novel pathway of cadherin-mediated p27 induction and therefore cell-cycle control in cells.
DOI: 10.6084/m9.figshare.1632156
title: RNase J depletion leads to massive changes in mRNA abundance in <i>Helicobacter pylori</i>

description: Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen <i>Helicobacter pylori</i>, an exo- and endoribonuclease RNase J is essential for growth. To explore the role of RNase J in <i>H. pylori</i>, we identified its putative targets at a global scale using next generation RNA sequencing. We found that strong depletion for RNase J led to a massive increase in the steady-state levels of non-rRNAs. mRNAs and RNAs antisense to open reading frames were most affected with over 80% increased more than 2-fold. Non-coding RNAs expressed in the intergenic regions were much less affected by RNase J depletion. Northern blotting of selected messenger and non-coding RNAs validated these results. Globally, our data suggest that RNase J of <i>H. pylori</i> is a major RNase involved in degradation of most cellular RNAs.
DOI: 10.6084/m9.figshare.1632156.v1
title: RNase J depletion leads to massive changes in mRNA abundance in <i>Helicobacter pylori</i>

description: Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen <i>Helicobacter pylori</i>, an exo- and endoribonuclease RNase J is essential for growth. To explore the role of RNase J in <i>H. pylori</i>, we identified its putative targets at a global scale using next generation RNA sequencing. We found that strong depletion for RNase J led to a massive increase in the steady-state levels of non-rRNAs. mRNAs and RNAs antisense to open reading frames were most affected with over 80% increased more than 2-fold. Non-coding RNAs expressed in the intergenic regions were much less affected by RNase J depletion. Northern blotting of selected messenger and non-coding RNAs validated these results. Globally, our data suggest that RNase J of <i>H. pylori</i> is a major RNase involved in degradation of most cellular RNAs.
DOI: 10.6084/m9.figshare.1632152
title: The polyadenylation complex of <i>Trypanosoma brucei:</i> Characterization of the functional poly(A) polymerase

description: The generation of mature mRNA in the protozoan parasite <i>Trypanosoma brucei</i> requires coupled polyadenylation and <i>trans</i> splicing. In contrast to other eukaryotes, we still know very little on components, mechanisms, and dynamics of the 3′ end-processing machinery in trypanosomes. To characterize the catalytic core of the polyadenylation complex in <i>T. brucei</i>, we first identified the poly(A) polymerase [Tb927.7.3780] as the major functional, nuclear-localized enzyme in trypanosomes. In contrast, another poly(A) polymerase, encoded by an intron-containing gene [Tb927.3.3160], localizes mainly in the cytoplasm and appears not to be functional in general 3′ end processing of mRNAs. Based on tandem-affinity purification with tagged CPSF160 and mass spectrometry, we identified ten associated components of the trypanosome polyadenylation complex, including homologues to all four CPSF subunits, Fip1, CstF50/64, and Symplekin, as well as two hypothetical proteins. RNAi-mediated knockdown revealed that most of these factors are essential for growth and required for both <i>in vivo</i> polyadenylation and <i>trans</i> splicing, arguing for a general coupling of these two mRNA-processing reactions.
DOI: 10.6084/m9.figshare.1632150
title: Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in <i>Drosophila melanogaster</i>

description: In vertebrates, TFEB (transcription factor EB) and MITF (microphthalmia-associated transcription factor) family of basic Helix-Loop-Helix (bHLH) transcription factors regulates both lysosomal function and organ development. However, it is not clear whether these 2 processes are interconnected. Here, we show that Mitf, the single TFEB and MITF ortholog in <i>Drosophila</i>, controls expression of vacuolar-type H<sup>+</sup>-ATPase pump (V-ATPase) subunits. Remarkably, we also find that expression of <i>Vha16-1</i> and <i>Vha13</i>, encoding 2 key components of V-ATPase, is patterned in the wing imaginal disc. In particular, <i>Vha16-1</i> expression follows differentiation of proneural regions of the disc. These regions, which will form sensory organs in the adult, appear to possess a distinctive endolysosomal compartment and Notch (N) localization. Modulation of Mitf activity in the disc in vivo alters endolysosomal function and disrupts proneural patterning. Similar to our findings in <i>Drosophila</i>, in human breast epithelial cells we observe that impairment of the <i>Vha16-1</i> human ortholog <i>ATP6V0C</i> changes the size and function of the endolysosomal compartment and that depletion of TFEB reduces ligand-independent N signaling activity. Our data suggest that lysosomal-associated functions regulated by the TFEB-V-ATPase axis might play a conserved role in shaping cell fate.
DOI: 10.6084/m9.figshare.1632152.v2
title: The polyadenylation complex of <i>Trypanosoma brucei:</i> Characterization of the functional poly(A) polymerase

description: The generation of mature mRNA in the protozoan parasite <i>Trypanosoma brucei</i> requires coupled polyadenylation and <i>trans</i> splicing. In contrast to other eukaryotes, we still know very little on components, mechanisms, and dynamics of the 3′ end-processing machinery in trypanosomes. To characterize the catalytic core of the polyadenylation complex in <i>T. brucei</i>, we first identified the poly(A) polymerase [Tb927.7.3780] as the major functional, nuclear-localized enzyme in trypanosomes. In contrast, another poly(A) polymerase, encoded by an intron-containing gene [Tb927.3.3160], localizes mainly in the cytoplasm and appears not to be functional in general 3′ end processing of mRNAs. Based on tandem-affinity purification with tagged CPSF160 and mass spectrometry, we identified ten associated components of the trypanosome polyadenylation complex, including homologues to all four CPSF subunits, Fip1, CstF50/64, and Symplekin, as well as two hypothetical proteins. RNAi-mediated knockdown revealed that most of these factors are essential for growth and required for both <i>in vivo</i> polyadenylation and <i>trans</i> splicing, arguing for a general coupling of these two mRNA-processing reactions.
DOI: 10.6084/m9.figshare.1632150.v1
title: Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in <i>Drosophila melanogaster</i>

description: In vertebrates, TFEB (transcription factor EB) and MITF (microphthalmia-associated transcription factor) family of basic Helix-Loop-Helix (bHLH) transcription factors regulates both lysosomal function and organ development. However, it is not clear whether these 2 processes are interconnected. Here, we show that Mitf, the single TFEB and MITF ortholog in <i>Drosophila</i>, controls expression of vacuolar-type H<sup>+</sup>-ATPase pump (V-ATPase) subunits. Remarkably, we also find that expression of <i>Vha16-1</i> and <i>Vha13</i>, encoding 2 key components of V-ATPase, is patterned in the wing imaginal disc. In particular, <i>Vha16-1</i> expression follows differentiation of proneural regions of the disc. These regions, which will form sensory organs in the adult, appear to possess a distinctive endolysosomal compartment and Notch (N) localization. Modulation of Mitf activity in the disc in vivo alters endolysosomal function and disrupts proneural patterning. Similar to our findings in <i>Drosophila</i>, in human breast epithelial cells we observe that impairment of the <i>Vha16-1</i> human ortholog <i>ATP6V0C</i> changes the size and function of the endolysosomal compartment and that depletion of TFEB reduces ligand-independent N signaling activity. Our data suggest that lysosomal-associated functions regulated by the TFEB-V-ATPase axis might play a conserved role in shaping cell fate.
DOI: 10.6084/m9.figshare.1632152.v1
title: <b>The polyadenylation complex of</b><i><b>Trypanosoma brucei</b></i><b>: characterization of the functional poly(A) polymerase</b>

description: ABSTRACTThe generation of mature mRNA in the protozoan parasite <i>Trypanosoma brucei</i> requires coupled polyadenylation and <i>trans</i> splicing. In contrast to other eukaryotes, we still know very little on components, mechanisms, and dynamics of the 3′ end-processing machinery in trypanosomes. To characterize the catalytic core of the polyadenylation complex in <i>T. brucei</i>, we first identified the poly(A) polymerase [Tb927.7.3780] as the major functional, nuclear-localized enzyme in trypanosomes. In contrast, another poly(A) polymerase, encoded by an intron-containing gene [Tb927.3.3160], localizes mainly in the cytoplasm and appears not to be functional in general 3′ end processing of mRNAs. Based on tandem-affinity purification with tagged CPSF160 and mass spectrometry, we identified ten associated components of the trypanosome polyadenylation complex, including homologues to all four CPSF subunits, Fip1, CstF50/6;4, and Symplekin, as well as two hypothetical proteins. RNAi-mediated knockdown revealed that most of these factors are essential for growth and required for both <i>in vivo</i> polyadenylation and <i>trans</i> splicing, arguing for a general coupling of these two mRNA-processing reactions.
DOI: 10.6084/m9.figshare.1632141
title: DNA methylation profiling to assess pathogenicity of <i>BRCA1</i> unclassified variants in breast cancer

description: Germline pathogenic mutations in <i>BRCA1</i> increase risk of developing breast cancer. Screening for mutations in <i>BRCA1</i> frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate <i>BRCA1</i>-mutated from <i>BRCA1</i>-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 <i>BRCA1</i> pathogenic mutation carriers, 65 BRCAx (<i>BRCA1</i>-wild type), 38 <i>BRCA1</i> test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (<i>BACH2, C8orf31,</i> and <i>LOC654342</i>) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G&gt;A (IVS 19-12 G&gt;A) (<i>P</i>&gt;0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of <i>BRCA1</i> variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity.
DOI: 10.6084/m9.figshare.1632141.v1
title: DNA methylation profiling to assess pathogenicity of <i>BRCA1</i> unclassified variants in breast cancer

description: Germline pathogenic mutations in <i>BRCA1</i> increase risk of developing breast cancer. Screening for mutations in <i>BRCA1</i> frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate <i>BRCA1</i>-mutated from <i>BRCA1</i>-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 <i>BRCA1</i> pathogenic mutation carriers, 65 BRCAx (<i>BRCA1</i>-wild type), 38 <i>BRCA1</i> test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (<i>BACH2, C8orf31,</i> and <i>LOC654342</i>) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G&gt;A (IVS 19-12 G&gt;A) (<i>P</i>&gt;0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of <i>BRCA1</i> variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity.
DOI: 10.6084/m9.figshare.1632139
title: Lactic acid demineralization of green crab (<i>Carcinus maenas</i>) shells: effect of reaction conditions and isolation of an unusual calcium complex

description: Chitin and chitosan are potentially useful and environmentally friendly biopolymers with a wide range of value-added applications. Effective and green technologies for isolation of these materials are potentially important. Here, we report the use of lactic acid for the demineralization of green crab shells. Green crab shells and lactic acid, produced during cheese making, are two waste streams that could be tapped for large-scale chitin and chitosan processing. We have studied the effect of concentration and temperature on the demineralization of green crab shells. An unusual calcium lactate/lactic acid complex was also isolated and crystallographically characterized. The results have implications not only for the use of weak acids in the isolation of chitin and chitosan but also for the use of lactic acid as a solvent in green chemistry.
DOI: 10.6084/m9.figshare.1632139.v1
title: Lactic acid demineralization of green crab (<i>Carcinus maenas</i>) shells: effect of reaction conditions and isolation of an unusual calcium complex

description: Chitin and chitosan are potentially useful and environmentally friendly biopolymers with a wide range of value-added applications. Effective and green technologies for isolation of these materials are potentially important. Here, we report the use of lactic acid for the demineralization of green crab shells. Green crab shells and lactic acid, produced during cheese making, are two waste streams that could be tapped for large-scale chitin and chitosan processing. We have studied the effect of concentration and temperature on the demineralization of green crab shells. An unusual calcium lactate/lactic acid complex was also isolated and crystallographically characterized. The results have implications not only for the use of weak acids in the isolation of chitin and chitosan but also for the use of lactic acid as a solvent in green chemistry.
DOI: 10.6084/m9.figshare.1629376
title: Provenance of the Ordovician–lower Silurian Tumblagooda Sandstone, Western Australia

description: Detrital zircon U–Pb ages and heavy mineral assemblages provide conflicting evidence of the provenance of the Ordovician–lower Silurian Tumblagooda Sandstone, a fluvial to shallow marine, red-bed succession over 2000 m thick, within the northern Perth and Southern Carnarvon basins in Western Australia. Tourmaline composition indicates a main provenance from interior continental terranes dominated by ‘Li-poor granitoids, pegmatites and aplites’ and ‘Ca-poor metapelites, metapsammites and quartz-tourmaline rocks,’ akin to the Yilgarn Craton to the east of outcrop of the Tumblagooda Sandstone. Other possible source areas include orogens mostly to the south but lack tourmaline analyses for comparison. Taking into account the lack of garnets—a conspicuous component of the adjacent Proterozoic Northampton Inlier—the limited zircon data are compatible with the Albany–Fraser and Pinjarra orogens along the southern and western margins of Australia and/or terranes in or adjacent to East Africa and/or Antarctica, as ultimate source regions with a minor contribution from the Yilgarn Craton, as with other Phanerozoic strata in Western Australia. Whereas the textural and mineralogical maturity of the sandstone could be explained by derivation from such regions, it is more likely that the source was relatively local and that the sediment passed through several phases of reworking. The main source of ilmenite and hematite, by comparison, may have been mafic–ultramafic rocks and/or banded iron formations within the Archean Yilgarn Craton to the east or the Pilbara Craton to the northeast, mobilised by acidic meteoric waters. Iron oxides forming the earliest cements may have been derived from the oxidation of detrital hematite and ilmenite grains concentrated along some bedding laminae or transported in solution from beyond the zone of deposition. Whereas the detrital iron oxides most likely come from the craton to the east of outcrop of the Tumblagooda Sandstone, the sand grains appear to have originally come from a relatively local orogenic source.
DOI: 10.6084/m9.figshare.1629376.v1
title: Provenance of the Ordovician–lower Silurian Tumblagooda Sandstone, Western Australia

description: Detrital zircon U–Pb ages and heavy mineral assemblages provide conflicting evidence of the provenance of the Ordovician–lower Silurian Tumblagooda Sandstone, a fluvial to shallow marine, red-bed succession over 2000 m thick, within the northern Perth and Southern Carnarvon basins in Western Australia. Tourmaline composition indicates a main provenance from interior continental terranes dominated by ‘Li-poor granitoids, pegmatites and aplites’ and ‘Ca-poor metapelites, metapsammites and quartz-tourmaline rocks,’ akin to the Yilgarn Craton to the east of outcrop of the Tumblagooda Sandstone. Other possible source areas include orogens mostly to the south but lack tourmaline analyses for comparison. Taking into account the lack of garnets—a conspicuous component of the adjacent Proterozoic Northampton Inlier—the limited zircon data are compatible with the Albany–Fraser and Pinjarra orogens along the southern and western margins of Australia and/or terranes in or adjacent to East Africa and/or Antarctica, as ultimate source regions with a minor contribution from the Yilgarn Craton, as with other Phanerozoic strata in Western Australia. Whereas the textural and mineralogical maturity of the sandstone could be explained by derivation from such regions, it is more likely that the source was relatively local and that the sediment passed through several phases of reworking. The main source of ilmenite and hematite, by comparison, may have been mafic–ultramafic rocks and/or banded iron formations within the Archean Yilgarn Craton to the east or the Pilbara Craton to the northeast, mobilised by acidic meteoric waters. Iron oxides forming the earliest cements may have been derived from the oxidation of detrital hematite and ilmenite grains concentrated along some bedding laminae or transported in solution from beyond the zone of deposition. Whereas the detrital iron oxides most likely come from the craton to the east of outcrop of the Tumblagooda Sandstone, the sand grains appear to have originally come from a relatively local orogenic source.