Project description:Transcriptional profiling of different clam tissues (hemolymph and mantle) in response to QPX disease and temperautre Quahog Parasite Unknown (QPX) is a fatal protistan parasite that causes severe losses in the hard clam (Mercenaria mercenaria) fisheries along the northeastern coast of the US. Field and laboratory studies of QPX disease have demonstrated a major role for water temperature and M. mercenaria genetic origin in disease development. Infections are more likely to occur at cold temperatures, with clam stocks originating from southern states being more susceptible than clams from northern origin where disease is enzootic. Even though the influence of temperature on QPX infection have been examined in susceptible and resistant M. mercenaria at physiological and cellular scales, the underlying molecular mechanisms associated with host-pathogen interactions remain largely unknown. This study was carried out to explore the molecular changes in M. mercenaria in response to temperature and QPX infection on the transcriptomic level, and also to compare molecular responses between susceptible and resistant clam stocks. A M. mercenaria oligoarray (15K Agilent) platform was produced based on our previously generated transcriptomic data and was used to compare gene expression profiles in naive and QPX-infected susceptible (Florida stock) and resistant (Massachusetts) clams maintained at temperatures favoring disease development (13 °C) or clam healing (21 °C). In addition, transcriptomic changes reflecting focal (the site of infection, mantle) and systemic (circulating hemocytes) responses were also assessed using the oligoarray platform. Results revealed significant regulation of multiple biological pathways by temperature and QPX infection, mainly associated with immune recognition, microbial killing, protein synthesis, oxidative protection and metabolism. Alterations were widely systemic with most changes in gene expression revealed in hemocytes, highlighting the role of circulating hemocytes as the first line of defense against pathogenic stress. A large number of complement-related recognition molecules with fibrinogen or C1q domains were shown to be specially induced following QPX challenge, and the expression of these molecules was significantly higher in resistant clams as compared to susceptible ones. These highly variable immune proteins may be potent candidate molecular markers for future study of M. mercenaria resistance against QPX. Beyond the specific case of clam response to QPX, this study also provides insights into the primitive complement-like system in the hard clam. Three-condition interaction experiment (Temperature x clam/infection type x tissue type), 2 temperatures, 3 clam/infection types, 2 tissues, 3 biological replicates for each condition
Project description:The proteomic profile of sea cucumber was conducted to identify key proteins involved in stress resistance based on the iTRAQ technique, including heat, hypoxia and heat plus hypoxia stress.
Project description:Transcriptional profiling of different clam tissues (hemolymph and mantle) in response to QPX disease and temperautre Quahog Parasite Unknown (QPX) is a fatal protistan parasite that causes severe losses in the hard clam (Mercenaria mercenaria) fisheries along the northeastern coast of the US. Field and laboratory studies of QPX disease have demonstrated a major role for water temperature and M. mercenaria genetic origin in disease development. Infections are more likely to occur at cold temperatures, with clam stocks originating from southern states being more susceptible than clams from northern origin where disease is enzootic. Even though the influence of temperature on QPX infection have been examined in susceptible and resistant M. mercenaria at physiological and cellular scales, the underlying molecular mechanisms associated with host-pathogen interactions remain largely unknown. This study was carried out to explore the molecular changes in M. mercenaria in response to temperature and QPX infection on the transcriptomic level, and also to compare molecular responses between susceptible and resistant clam stocks. A M. mercenaria oligoarray (15K Agilent) platform was produced based on our previously generated transcriptomic data and was used to compare gene expression profiles in naive and QPX-infected susceptible (Florida stock) and resistant (Massachusetts) clams maintained at temperatures favoring disease development (13 °C) or clam healing (21 °C). In addition, transcriptomic changes reflecting focal (the site of infection, mantle) and systemic (circulating hemocytes) responses were also assessed using the oligoarray platform. Results revealed significant regulation of multiple biological pathways by temperature and QPX infection, mainly associated with immune recognition, microbial killing, protein synthesis, oxidative protection and metabolism. Alterations were widely systemic with most changes in gene expression revealed in hemocytes, highlighting the role of circulating hemocytes as the first line of defense against pathogenic stress. A large number of complement-related recognition molecules with fibrinogen or C1q domains were shown to be specially induced following QPX challenge, and the expression of these molecules was significantly higher in resistant clams as compared to susceptible ones. These highly variable immune proteins may be potent candidate molecular markers for future study of M. mercenaria resistance against QPX. Beyond the specific case of clam response to QPX, this study also provides insights into the primitive complement-like system in the hard clam.
2015-12-20 | GSE76182 | GEO
Project description:Transcriptome of Manila clam under hypoxia stress
| PRJNA478917 | ENA
Project description:RNA-seq of hard clam under salinity challenge
Project description:Adult Cardiac hypoxia as a crucial pathogenesis factor can induce detrimental effects on cardiac injury and dysfunction. The global transcriptome and translatome reflecting the cellular response to hypoxia have not yet been extensively studied in myocardium. In this study, adult rats were subjected to acute normobaric hypoxia at 10% oxygen with 10 min (mild hypoxia) and 30 min (severe hypoxia). Rat H9C2 cardiomyocytes were treated with the culture condition (1% O2, 94% N2, and 5% CO2) for mild hypoxia (8 hr) and severe hypoxia(24 hr). We then conducted RNA-seq and Ribo-seq in non-infarcted left ventricular myocardial tissues and H9C2 cells exposed to different periods of hypoxia stress in vivo and in vitro.
Project description:The production of Manila clam (Ruditapes philippinarum) is seriously threatened by the protistan parasite Perkinsus olseni. We characterized and compared gene expression of Manila clam haemocytes in response to P. olseni in a time-course (10 h, 24 h, 8 d) controlled laboratory challenge (LC), representing the first steps of infection, and in a more complex infection in the wild (WI) using a validated oligo-microarray containing 11,232 mostly annotated transcripts. Several immune-genes involved in NIK/NF-kappaB signalling, toll-like receptor signalling and apoptosis were activated at LC-10 h. However, down-regulation of others like lysozyme, histones, cathepsins and heat shock proteins indicated signals of immunodepression, which appeared exacerbated at LC-24 h, where only down-regulated genes were detected. A rebound of haemocytes activity occurred at LC-8 d as shown by up-regulation of genes involved in cytoskeleton organization and cell survival. WI showed a more complex picture and several immune-relevant processes, including cytoskeleton organization, cell survival, apoptosis, encapsulation, cell redox- and lipid- homeostasis were activated, involving the main mechanism of host response. Our results provide useful information, including potential biomarkers, to develop strategies for controlling Manila clam perkinsosis.
Project description:Mechanisms regulating the gene expression program at different hypoxia severity levels in patient tumors are not understood. We aimed to determine microRNA (miRNA) regulation of this program at defined hypoxia levels from moderate to severe in prostate cancer. Biopsies from 95 patients were used, where 83 patients received the hypoxia marker pimonidazole before prostatectomy. Forty hypoxia levels were extracted from pimonidazole-stained histological sections and correlated with miRNA and gene expression profiles determined by RNA-sequencing and Illumina bead arrays. This identified miRNAs associated with moderate (n=7) and severe (n=28) hypoxia and predicted their target genes. Scores of miRNAs or target genes showed prognostic significance, as validated in external cohort of 417 patients. The target genes showed enrichment of gene sets for cell proliferation and MYC activation at all hypoxia levels and PTEN inactivation at severe hypoxia. This was confirmed by RT-qPCR for MYC and PTEN, by Ki67-immunohistochemistry, and by gene set analysis in an external cohort. To assess whether miRNA regulation occurred within the predicted hypoxic regions, a method to quantify co-localization of multiple histopathology parameters at defined hypoxia levels was applied. A high Ki67-proliferation index co-localized significantly with hypoxia at all levels. The co-localization index was strongly associated with poor prognosis. Absence of PTEN-staining co-localized significantly with severe hypoxia. Scores for miRNAs correlated with the co-localization index for Ki67-staining and hypoxia, consistent with miRNA regulation within the overlapping regions. This was confirmed by showing miR-210-3p expression within severe hypoxia by in situ hybridization. Cell line experiments (22Rv1, PC3) were conducted to determine whether miRNAs and target genes were regulated directly by hypoxia. Most of them were hypoxia-unresponsive, and probably regulated by other mechanisms such as MYC activation. In conclusion, cancer cells residing within moderate and severe hypoxic regions in aggressive prostate tumors in patients exhibit different proliferative gene expression programs regulated by miRNAs.
Project description:Mechanisms regulating the gene expression program at different hypoxia severity levels in patient tumors are not understood. We aimed to determine microRNA (miRNA) regulation of this program at defined hypoxia levels from moderate to severe in prostate cancer. Biopsies from 95 patients were used, where 83 patients received the hypoxia marker pimonidazole before prostatectomy. Forty hypoxia levels were extracted from pimonidazole-stained histological sections and correlated with miRNA and gene expression profiles determined by RNA-sequencing and Illumina bead arrays. This identified miRNAs associated with moderate (n=7) and severe (n=28) hypoxia and predicted their target genes. Scores of miRNAs or target genes showed prognostic significance, as validated in external cohort of 417 patients. The target genes showed enrichment of gene sets for cell proliferation and MYC activation at all hypoxia levels and PTEN inactivation at severe hypoxia. This was confirmed by RT-qPCR for MYC and PTEN, by Ki67-immunohistochemistry, and by gene set analysis in an external cohort. To assess whether miRNA regulation occurred within the predicted hypoxic regions, a method to quantify co-localization of multiple histopathology parameters at defined hypoxia levels was applied. A high Ki67-proliferation index co-localized significantly with hypoxia at all levels. The co-localization index was strongly associated with poor prognosis. Absence of PTEN-staining co-localized significantly with severe hypoxia. Scores for miRNAs correlated with the co-localization index for Ki67-staining and hypoxia, consistent with miRNA regulation within the overlapping regions. This was confirmed by showing miR-210-3p expression within severe hypoxia by in situ hybridization. Cell line experiments (22Rv1, PC3) were conducted to determine whether miRNAs and target genes were regulated directly by hypoxia. Most of them were hypoxia-unresponsive, and probably regulated by other mechanisms such as MYC activation. In conclusion, cancer cells residing within moderate and severe hypoxic regions in aggressive prostate tumors in patients exhibit different proliferative gene expression programs regulated by miRNAs.