Project description:In this study, we identified and validated a molecular classification of hepatocellular carcinoma (HCC) patients based on 42 fatty acid degradation (FAD) genes. The F1 subtype was characterized by the lowest expression of FAD genes, whereas F3 subtype had the highest expression levels, and F2 had the intermediate expression levels of FAD genes. We characterized the immune microenvironment in HCC patients from different FAD subtypes. To further explore the immune landscape of HCC, we generated the Nras-driven HCC model (belonging to the F1 subtype) and the Akt1-driven HCC model (belonging to the F3 subtype) by hydrodynamic tail vein injection (HTVi) of oncogenes together with the sleeping beauty transposase. The tumor tissues were resected from the liver 14 weeks after the hydrodynamic delivery of the plasmids, isolated for single cells, and prepared for scRNA-seq.
Project description:Embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination appears to promote an epigenetic reprogramming of the male germ line that is associated with transgenerational adult-onset disease states. Transgenerational effects on the embryonic day 16 (E16) testis demonstrated reproducible changes in the testis transcriptome for multiple generations (F1-F3). The expression of 196 genes was found to be influenced, with the majority of gene expression being decreased or silenced. Dramatic changes in the gene expression of methyltransferases during gonadal sex determination were observed in the F1 and F2 vinclozolin generation (E16) embryonic testis, but the majority returned to control-generation levels by the F3 generation. The most dramatic effects were on the germ-line-associated Dnmt3A and Dnmt3L isoforms. Observations demonstrate that an embryonic exposure to vinclozolin appears to promote an epigenetic reprogramming of the male germ line that correlates with transgenerational alterations in the testis transcriptome in subsequent generations. Experiment Overall Design: E16 Testis RNA samples from F1, F2, F3 generation control groups are compared to F1, F2, F3 generation vinclozolin treated groups
Project description:The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals. The current study was designed to investigate the actions of direct fetal exposure on the F1 generation rat sperm DMRs compared to the F3 transgenerational sperm DMRs. The F1 generation DMRs were found to be fewer in number and for the most part distinct from the F3 generation epimutations. Therefore, the direct exposure induced F1 generation DMRs appear to promote alterations in germ cell development that lead to the programming of the F3 generation epimutations, but are distinct between the generations.
Project description:Elucidating the genetic control of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were at maturity to compare expression between C3 and C4 in leaves, stems, and roots. Their F1 hybrid leaf was studied at maturity and will aid in identifying regulatory elements involved in C3 and C4 leaf development. Two C3 Atriplex prostrata x C4 Atriplex rosea F3 hybrids (F3003 and F3036) were sequenced at a mature leaf stage.
Project description:Stress and glucocorticoid exposure during pregnancy alters neurodevelopment and behavior in offspring, and these effects extend multiple generations through a paternal lineage. The epigenetic mechanisms that govern this transgenerational transmission are unclear. We hypothesized that maternal exposure to multiple courses of sGC in late pregnancy would result in altered miRNA levels in germs cells of male guinea pigs across three generations. Further, our behavioral data indicate that F2 females exhibit altered behaviors following sGC exposure. Thus, we evaluated the miRNA profile of F2 female prefrontal cortex to determine the mechanisms responsible for these behavioral changes and to compare these data to our germ cell miRNA analysis. We used miRNA microarray to evaluate the miRNA levels in F1-F3 germ cells and F2 female PFC in guinea pigs that were exposed to control and F0 prenatal sGC exposure. We identified no significant changes to miRNA levels in both F1-F3 germ cells and F2 PFC from guinea pigs in the sGC group.
Project description:Analysis of the effect of diet and ageing in the liver at gene expression level. The hypothesis tested in the present study was that dietary energy would be associated positively with the magnitude of age-related changes in the expression of the liver transcriptome and that such effects would accumulate between generations. Results provide insight into the realtionship between diet across generations and ageing. Total RNA obtained from livers of D90 or D456 females in the F1 and F3 generation, following a 6 hour fast.
Project description:The variability in the prognosis of hepatocellular carcinoma (HCC) patients suggests that HCC may comprise several distinctive biological phenotypes. These phenotypes may result from different neoplastic pathways during the tumorigenesis and/or from a different cell of origin. Here we address if the transcriptional characteristics of the HCC would provide insight into the cellular origin of the tumors. We integrated gene expression data from rat fetal hepatoblasts and adult hepatocytes, HCC from mouse models, and human HCC. The HCC patients who shared gene expression patterns with fetal hepatoblasts showed extremely poor prognosis when compared with those lacking the hepatoblast signature. The gene expression program that distinguishes this novel subtype from the rest of HCC includes well known markers of hepatic oval cells, suggesting that HCC in this subtype may arise from hepatic progenitor cells. Two independent gene network analyses of the gene expression signature characteristic for the tumors sharing the hepatoblast expression patterns revealed that activation of AP-1 transcription factors might play key roles in tumor development in the newly identified HCC subtype. In addition, by applying hepatoblast-specific and genome-wide global signatures, HCC patients were further stratified into three distinct subgroups with a significant association with overall survival and recurrence. Total RNAs from 19 normal livers were pooled and used as the reference for all microarray experiments. To obtain gene expression profile data from 49 human HCC, 20 µg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA. At least two hybridizations were carried out for each tissue using a dye-swap strategy to eliminate dye labeling bias.
Project description:LSL-KrasG12D mice were backcrossed with FVB/N mice and primary keratinocytes were harvested were from F1 and F3 and transduced in vitro with a Cre adenovirus to express a single mutant Kras allele. When cultures were harvested and transplanted on athymic hosts large squamous papilloma formed within 3 weeks but only from F3 keratinocyte cultures