Project description:Elucidating the genetic control of development of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were studied along a leaf developmental gradient to compare development between C3 and C4. C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid were studied along the same developmental gradient and will aid in identifying regulatory elements involved in C3 and C4 leaf development.
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:Synovial Sarcomas (SS) are characterized by the presence of the SS18::SSX fusion gene, which protein product induce chromatin changes through remodeling of the BAF complex (BRG1/BRM-associated factor complex), which leads to widespread alterations in gene expression that drive tumor development and progression. However, there are no comprehensive studies that integrate multi-omics approaches to fully understand the heterogeneity and molecular subtypes of SS. To elucidate the genomic events that drive phenotypic diversity in SS, we performed RNA and targeted DNA sequencing on 91 tumors from 55 patients. Our results were verified by proteomic analysis, public gene expression cohorts and single-cell RNA sequencing. Transcriptome profiling identified three distinct SS subtypes resembling the known histological subtypes: SS subtype I and was characterized by hyperproliferation, evasion of immune detection and a poor prognosis. SS subtype II and was dominated by a vascular-stromal component and had a significantly better outcome. SS Subtype III was characterized by biphasic differentiation, increased genomic complexity and immune suppression mediated by checkpoint inhibition, and poor prognosis despite good responses to neoadjuvant therapy. Chromosomal abnormalities were an independent significant risk factor for metastasis. KRT8 was identified as a key component for epithelial differentiation in biphasic tumors, potentially controlled by OVOL1 regulation. Our multi-omics analysis revealed biological and genetic variability between these subtypes, including key transcriptome patterns and secondary genomic events such as copy number alterations, could be associated with long-term outcomes. Our findings explain the histological grounds for SS classification and indicate that a significantly larger proportion of patients have high risk tumors (corresponding to SS subtype I) than previously believed.