cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3503477.v1
title: Impaired Autophagy in Macrophages Promotes Inflammatory Eye Disease

description: Autophagy is critical for maintaining cellular homeostasis. Organs such as the eye and brain are immunologically privileged. Here, we demonstrate that autophagy is essential for maintaining ocular immune privilege. Deletion of multiple autophagy genes in macrophages leads to an inflammation-mediated eye disease called uveitis that can cause blindness. Loss of autophagy activates inflammasome-mediated IL1B secretion that increases disease severity. Inhibition of caspase activity by gene deletion or pharmacological means completely reverses the disease phenotype. Of interest, experimental uveitis was also increased in a model of Crohn disease, a systemic autoimmune disease in which patients often develop uveitis, offering a potential mechanistic link between macrophage autophagy and systemic disease. These findings directly implicate the homeostatic process of autophagy in blinding eye disease and identify novel pathways for therapeutic intervention in uveitis.
DOI: 10.6084/m9.figshare.3503471
title: The secretome of MUSE cells contains factors that may play a role in regulation of stemness, apoptosis and immunomodulation

description: Mesenchymal stromal cells (MSCs) are a heterogeneous population, which contain several cell phenotypes: mesenchymal stem cells, progenitor cells, fibroblasts and other type of cells. Previously, we identified unique stem cells that we named multilineage-differentiating stress enduring (Muse) cells as one to several percent of MSCs of the bone marrow, adipose tissue and dermis. Among different cell populations in MSCs, Muse cells, positive for pluripotent surface marker SSEA-3, may represent cells responsible for pluripotent-like property of MSCs, since they express pluripotency genes, able to differentiated into triploblastic cells from a single cells and are self-renewable. MSCs release biologically active factors that have profound effects on local cellular dynamics. A thorough examination of MSC secretome seems essential for understanding the physiological functions exerted by these cells in our organism and also for rational cellular therapy design. In this setting, studies on secretome of Muse cells may shed light on pathways that are associated with their specific features. Our findings evidenced that secretomes of MSCs and Muse cells contain factors that regulate extracellular matrix remodeling, ox-redox activities and immune system. Muse cells appear to secrete factors that may preserve their stem cell features, allow survival under stress conditions and may contribute to their immunomodulation capacity. In detail, the proteins belonging to protein kinase A signaling, FXR/RXR activation and LXR/RXR activation pathways may play a role in regulation of Muse stem cell features. These last 2 pathways together with proteins associated with antigen presentation pathway and coagulation system may play a role in immunomodulation.
DOI: 10.6084/m9.figshare.3503471.v1
title: The secretome of MUSE cells contains factors that may play a role in regulation of stemness, apoptosis and immunomodulation

description: Mesenchymal stromal cells (MSCs) are a heterogeneous population, which contain several cell phenotypes: mesenchymal stem cells, progenitor cells, fibroblasts and other type of cells. Previously, we identified unique stem cells that we named multilineage-differentiating stress enduring (Muse) cells as one to several percent of MSCs of the bone marrow, adipose tissue and dermis. Among different cell populations in MSCs, Muse cells, positive for pluripotent surface marker SSEA-3, may represent cells responsible for pluripotent-like property of MSCs, since they express pluripotency genes, able to differentiated into triploblastic cells from a single cells and are self-renewable. MSCs release biologically active factors that have profound effects on local cellular dynamics. A thorough examination of MSC secretome seems essential for understanding the physiological functions exerted by these cells in our organism and also for rational cellular therapy design. In this setting, studies on secretome of Muse cells may shed light on pathways that are associated with their specific features. Our findings evidenced that secretomes of MSCs and Muse cells contain factors that regulate extracellular matrix remodeling, ox-redox activities and immune system. Muse cells appear to secrete factors that may preserve their stem cell features, allow survival under stress conditions and may contribute to their immunomodulation capacity. In detail, the proteins belonging to protein kinase A signaling, FXR/RXR activation and LXR/RXR activation pathways may play a role in regulation of Muse stem cell features. These last 2 pathways together with proteins associated with antigen presentation pathway and coagulation system may play a role in immunomodulation.
DOI: 10.6084/m9.figshare.3503390
title: Autophagy in <i>Saccharomyces cerevisiae</i> requires the monomeric GTP-binding proteins, Arl1 and Ypt6

description: Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in <i>Saccharomyces cerevisiae</i>, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-<i>trans-</i>Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress. Using established autophagy-specific assays we found that cells lacking either <i>ARL1</i> or <i>YPT6</i>, which exhibit synthetic lethality with one another, were unable to undergo autophagy at an elevated temperature, although autophagy proceeds normally at normal growth temperature; specifically, strains lacking one or the other of these genes are unable to construct the autophagosome because these 2 proteins are required for proper traffic of Atg9 to the phagophore assembly site (PAS) at the restrictive temperature. Using degron technology to construct an inducible <i>arl1</i>Δ <i>ypt6</i>Δ double mutant, we demonstrated that cells lacking both genes show defects in starvation-inducted autophagy at the permissive temperature. We also found Arl1 and Ypt6 participate in autophagy by targeting the Golgi-associated retrograde protein (GARP) complex to the PAS to regulate the anterograde trafficking of Atg9. Our data show that these 2 membrane traffic regulators have novel roles in autophagy.
DOI: 10.6084/m9.figshare.3503390.v1
title: Autophagy in <i>Saccharomyces cerevisiae</i> requires the monomeric GTP-binding proteins, Arl1 and Ypt6

description: Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in <i>Saccharomyces cerevisiae</i>, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-<i>trans-</i>Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress. Using established autophagy-specific assays we found that cells lacking either <i>ARL1</i> or <i>YPT6</i>, which exhibit synthetic lethality with one another, were unable to undergo autophagy at an elevated temperature, although autophagy proceeds normally at normal growth temperature; specifically, strains lacking one or the other of these genes are unable to construct the autophagosome because these 2 proteins are required for proper traffic of Atg9 to the phagophore assembly site (PAS) at the restrictive temperature. Using degron technology to construct an inducible <i>arl1</i>Δ <i>ypt6</i>Δ double mutant, we demonstrated that cells lacking both genes show defects in starvation-inducted autophagy at the permissive temperature. We also found Arl1 and Ypt6 participate in autophagy by targeting the Golgi-associated retrograde protein (GARP) complex to the PAS to regulate the anterograde trafficking of Atg9. Our data show that these 2 membrane traffic regulators have novel roles in autophagy.
DOI: 10.6084/m9.figshare.3503387
title: Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of <i>ATG5</i>

description: Melanoma is a paradigm of aggressive tumors with a complex and heterogeneous genetic background. Still, melanoma cells frequently retain developmental traits that trace back to lineage specification programs. In particular, lysosome-associated vesicular trafficking is emerging as a melanoma-enriched lineage dependency. However, the contribution of other lysosomal functions such as autophagy to melanoma progression is unclear, particularly in the context of metastasis and resistance to targeted therapy. Here we mined a broad spectrum of cancers for a meta-analysis of mRNA expression, copy number variation and prognostic value of 13 core autophagy genes. This strategy identified heterozygous loss of <i>ATG5</i> at chromosome band 6q21 as a distinctive feature of advanced melanomas. Importantly, partial <i>ATG5</i> loss predicted poor overall patient survival in a manner not shared by other autophagy factors and not recapitulated in other tumor types. This prognostic relevance of <i>ATG5</i> copy number was not evident for other 6q21 neighboring genes. Melanocyte-specific mouse models confirmed that heterozygous (but not homozygous) deletion of <i>Atg5</i> enhanced melanoma metastasis and compromised the response to targeted therapy (exemplified by dabrafenib, a BRAF inhibitor in clinical use). Collectively, our results support ATG5 as a therapeutically relevant dose-dependent rheostat of melanoma progression. Moreover, these data have important translational implications in drug design, as partial blockade of autophagy genes may worsen (instead of counteracting) the malignant behavior of metastatic melanomas.
DOI: 10.6084/m9.figshare.3503387.v1
title: Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of <i>ATG5</i>

description: Melanoma is a paradigm of aggressive tumors with a complex and heterogeneous genetic background. Still, melanoma cells frequently retain developmental traits that trace back to lineage specification programs. In particular, lysosome-associated vesicular trafficking is emerging as a melanoma-enriched lineage dependency. However, the contribution of other lysosomal functions such as autophagy to melanoma progression is unclear, particularly in the context of metastasis and resistance to targeted therapy. Here we mined a broad spectrum of cancers for a meta-analysis of mRNA expression, copy number variation and prognostic value of 13 core autophagy genes. This strategy identified heterozygous loss of <i>ATG5</i> at chromosome band 6q21 as a distinctive feature of advanced melanomas. Importantly, partial <i>ATG5</i> loss predicted poor overall patient survival in a manner not shared by other autophagy factors and not recapitulated in other tumor types. This prognostic relevance of <i>ATG5</i> copy number was not evident for other 6q21 neighboring genes. Melanocyte-specific mouse models confirmed that heterozygous (but not homozygous) deletion of <i>Atg5</i> enhanced melanoma metastasis and compromised the response to targeted therapy (exemplified by dabrafenib, a BRAF inhibitor in clinical use). Collectively, our results support ATG5 as a therapeutically relevant dose-dependent rheostat of melanoma progression. Moreover, these data have important translational implications in drug design, as partial blockade of autophagy genes may worsen (instead of counteracting) the malignant behavior of metastatic melanomas.
DOI: 10.6084/m9.figshare.3503378
title: Quantitative chemical proteomics profiling of <i>de novo</i> protein synthesis during starvation-mediated autophagy

description: Autophagy is an intracellular degradation mechanism in response to nutrient starvation. Via autophagy, some nonessential cellular constituents are degraded in a lysosome-dependent manner to generate biomolecules that can be utilized for maintaining the metabolic homeostasis. Although it is known that under starvation the global protein synthesis is significantly reduced mainly due to suppression of MTOR (mechanistic target of rapamycin serine/threonine kinase), emerging evidence demonstrates that <i>de novo</i> protein synthesis is involved in the autophagic process. However, characterizing these <i>de novo</i> proteins has been an issue with current techniques. Here, we developed a novel method to identify newly synthesized proteins during starvation-mediated autophagy by combining bio-orthogonal noncanonical amino acid tagging (BONCAT) and isobaric tags for relative and absolute quantitation (iTRAQ<sup>TM</sup>). Using bio-orthogonal metabolic tagging, L-azidohomoalanine (AHA) was incorporated into newly synthesized proteins which were then enriched with avidin beads after a click reaction between alkyne-bearing biotin and AHA's bio-orthogonal azide moiety. The enriched proteins were subjected to iTRAQ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Via the above approach, we identified and quantified a total of 1176 proteins and among them 711 proteins were found to meet our defined criteria as <i>de novo</i> synthesized proteins during starvation-mediated autophagy. The characterized functional profiles of the 711 newly synthesized proteins by bioinformatics analysis suggest their roles in ensuring the prosurvival outcome of autophagy. Finally, we performed validation assays for some selected proteins and found that knockdown of some genes has a significant impact on starvation-induced autophagy. Thus, we think that the BONCAT-iTRAQ approach is effective in the identification of newly synthesized proteins and provides useful insights to the molecular mechanisms and biological functions of autophagy.
DOI: 10.6084/m9.figshare.3503378.v1
title: Quantitative chemical proteomics profiling of <i>de novo</i> protein synthesis during starvation-mediated autophagy

description: Autophagy is an intracellular degradation mechanism in response to nutrient starvation. Via autophagy, some nonessential cellular constituents are degraded in a lysosome-dependent manner to generate biomolecules that can be utilized for maintaining the metabolic homeostasis. Although it is known that under starvation the global protein synthesis is significantly reduced mainly due to suppression of MTOR (mechanistic target of rapamycin serine/threonine kinase), emerging evidence demonstrates that <i>de novo</i> protein synthesis is involved in the autophagic process. However, characterizing these <i>de novo</i> proteins has been an issue with current techniques. Here, we developed a novel method to identify newly synthesized proteins during starvation-mediated autophagy by combining bio-orthogonal noncanonical amino acid tagging (BONCAT) and isobaric tags for relative and absolute quantitation (iTRAQ<sup>TM</sup>). Using bio-orthogonal metabolic tagging, L-azidohomoalanine (AHA) was incorporated into newly synthesized proteins which were then enriched with avidin beads after a click reaction between alkyne-bearing biotin and AHA's bio-orthogonal azide moiety. The enriched proteins were subjected to iTRAQ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Via the above approach, we identified and quantified a total of 1176 proteins and among them 711 proteins were found to meet our defined criteria as <i>de novo</i> synthesized proteins during starvation-mediated autophagy. The characterized functional profiles of the 711 newly synthesized proteins by bioinformatics analysis suggest their roles in ensuring the prosurvival outcome of autophagy. Finally, we performed validation assays for some selected proteins and found that knockdown of some genes has a significant impact on starvation-induced autophagy. Thus, we think that the BONCAT-iTRAQ approach is effective in the identification of newly synthesized proteins and provides useful insights to the molecular mechanisms and biological functions of autophagy.
DOI: 10.6084/m9.figshare.3503183
title: Dataset lamdaDNA.xlsx

description: We treated lamda DNA by non thermal atmospheric pressure plasma jet for varying duration altering the treatment medium.
DOI: 10.6084/m9.figshare.3503138
title: Western blotting analyses of S6K isoforms expression modulation in human prostate cancer cell line PC3-luc

description: Figure 1 of S6Ks isoforms contribute to viability, migration, docetaxel resistance and tumor formation of prostate cancer cells article in BMC Cancer journal.<br>Western blotting analyses of S6K isoforms expression modulation in human prostate cancer cell line PC3-luc transduced with lentiviruses pLKO.1-shRNAs against S6K1 and S6K2 and with retroviruses carrying pBABE construction. S6K1 antibody detects both p85-S6K1 and p70-S6K1 proteins.
DOI: 10.6084/m9.figshare.3503138.v2
title: Western blotting analyses of S6K isoforms expression modulation in human prostate cancer cell line PC3-luc

description: Figure 1 of S6Ks isoforms contribute to viability, migration, docetaxel resistance and tumor formation of prostate cancer cells article in BMC Cancer journal.<br>Western blotting analyses of S6K isoforms expression modulation in human prostate cancer cell line PC3-luc transduced with lentiviruses pLKO.1-shRNAs against S6K1 and S6K2 and with retroviruses carrying pBABE construction. S6K1 antibody detects both p85-S6K1 and p70-S6K1 proteins.
DOI: 10.6084/m9.figshare.3503126
title: An efficient method to genotype the polymorphisms of cholinergic nicotinic receptor subunit genes and their associations with COPD onset risk

description: <b>Background:</b> Single-nucleotide polymorphisms (SNPs) in the cholinergic nicotinic receptor subunit genes on chromosome 15q25.1, including <i>CHRNA3</i>, <i>CHRNB4</i> and <i>CHRNA5</i>, are well-established biomarkers of chronic obstructive pulmonary disease (COPD) and lung cancer. Thus, there is great demand for a rapid, easy and inexpensive method to detect these variations for purpose of risk prediction in large populations. <b>Aim of the Study:</b> The aim of this study was to establish an accurate and efficient method for genotyping <i>CHRN</i> SNPs and testing their association with age at onset of COPD in Chinese population as well as the clinical stage in COPD patients. <b>Materials and Methods:</b> We designed a method to specifically genotype 5 SNPs of <i>CHRN</i> genes based on a modified high-resolution melt (HRM) method and then validated the genotyping results by direct sequencing of 120 samples. We further used the HRM method to genotype these 5 SNPs in 1,013 COPD patients. <b>Results:</b> Requiring little time, few material costs and only a simplified protocol, the modified HRM method could accurately distinguish the genotypes of <i>CHRN</i> SNPs, demonstrating kappa coefficients &gt;0.96 based on the results from direct sequencing. Furthermore, the data showed that the GG genotype of SNP rs56218866 was associated with a significantly earlier age of COPD onset than A (AA+AG) genotypes (61.0 ± 8.93 vs. 67.8 ± 9.88; <i>P</i> = 0.031), which was not found for the other SNPs. No significant association was observed between the COPD stages and any of the above SNPs. <b>Conclusion:</b> A simple, rapid and efficient HRM method was introduced for <i>CHRN</i> SNP genotyping and a suggestion that the SNP rs56218866A&gt;G is associated with early-onset COPD in a Chinese population was found.
DOI: 10.6084/m9.figshare.3503045
title: Input file and metadata for sage-grouse chick survival analysis

description: Input file and metadata to estimate pre-fledging chick survival of Greater sage-grouse broods in central Nevada from 2005-2012.
DOI: 10.6084/m9.figshare.3503126.v1
title: An efficient method to genotype the polymorphisms of cholinergic nicotinic receptor subunit genes and their associations with COPD onset risk

description: <b>Background:</b> Single-nucleotide polymorphisms (SNPs) in the cholinergic nicotinic receptor subunit genes on chromosome 15q25.1, including <i>CHRNA3</i>, <i>CHRNB4</i> and <i>CHRNA5</i>, are well-established biomarkers of chronic obstructive pulmonary disease (COPD) and lung cancer. Thus, there is great demand for a rapid, easy and inexpensive method to detect these variations for purpose of risk prediction in large populations. <b>Aim of the Study:</b> The aim of this study was to establish an accurate and efficient method for genotyping <i>CHRN</i> SNPs and testing their association with age at onset of COPD in Chinese population as well as the clinical stage in COPD patients. <b>Materials and Methods:</b> We designed a method to specifically genotype 5 SNPs of <i>CHRN</i> genes based on a modified high-resolution melt (HRM) method and then validated the genotyping results by direct sequencing of 120 samples. We further used the HRM method to genotype these 5 SNPs in 1,013 COPD patients. <b>Results:</b> Requiring little time, few material costs and only a simplified protocol, the modified HRM method could accurately distinguish the genotypes of <i>CHRN</i> SNPs, demonstrating kappa coefficients &gt;0.96 based on the results from direct sequencing. Furthermore, the data showed that the GG genotype of SNP rs56218866 was associated with a significantly earlier age of COPD onset than A (AA+AG) genotypes (61.0 ± 8.93 vs. 67.8 ± 9.88; <i>P</i> = 0.031), which was not found for the other SNPs. No significant association was observed between the COPD stages and any of the above SNPs. <b>Conclusion:</b> A simple, rapid and efficient HRM method was introduced for <i>CHRN</i> SNP genotyping and a suggestion that the SNP rs56218866A&gt;G is associated with early-onset COPD in a Chinese population was found.
DOI: 10.6084/m9.figshare.3503045.v1
title: Input file and metadata for sage-grouse chick survival analysis

description: Input file and metadata to estimate pre-fledging chick survival of Greater sage-grouse broods in central Nevada from 2005-2012.
DOI: 10.6084/m9.figshare.3503021
title: dbAnthro.csv

description: A flat comma-separated-value file created by combining data from 560 nutritional anthropometry surveys from 34 countries between August 1992 and October 2006.<br>Columns in the file are:<br>age (age in months)sex (1 = male. 2 = female)weight (weight in kg)height (height in cm)muac (MUAC in mm)oedema (1 = present, 2 = absent)countryCode (four letter code identifying country of origin)haz (HAZ, WGS 2006 reference)waz (WAZ, WGS 2006 reference)whz (WHZ, WGS 2006 reference)<br><br>
DOI: 10.6084/m9.figshare.3503021.v1
title: dbAnthro.csv

description: A flat comma-separated-value file created by combining data from 560 nutritional anthropometry surveys from 34 countries between August 1992 and October 2006.<br>Columns in the file are:<br>age (age in months)sex (1 = male. 2 = female)weight (weight in kg)height (height in cm)muac (MUAC in mm)oedema (1 = present, 2 = absent)countryCode (four letter code identifying country of origin)haz (HAZ, WGS 2006 reference)waz (WAZ, WGS 2006 reference)whz (WHZ, WGS 2006 reference)<br><br>