Profiling of Sarcomas from Archival Tissues [lp-WGS]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE243377 | GEO | 2024/06/21
REPOSITORIES: GEO
Similar Datasets
Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS) and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).
2024-06-21 | GSE243380 | GEO
Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS) and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).
2024-06-21 | GSE243379 | GEO
Project description:Profiling of Sarcomas from Archival Tissues [lp-WGS]
| PRJNA1018219 | ENA
Project description:This study was designed to investigate the RNA sequencing profile of mouse myeloid sarcomas in comparison to their matched whole bone marrow acute myeloid leukemia specimens. The goal was to determine gene set profiles that are different between the two phenotypes in the same primary genetic driver of AML mutation in mice to further investigate the results demonstrated in the patient derived specimens.
2024-05-18 | GSE264700 | GEO
Project description:Sarcomas are rare, difficult to treat, mesenchymal lineage tumours that disproportionately affect children and young adults. Immunologically-based therapies have improved outcomes for numerous adult cancers, however, such approaches have proven ineffective for the majority of individuals with advanced sarcomas. Clinically relevant, immunologically-competent, and transplantable pre-clinical sarcoma models are needed in order to test and develop novel immunologically-based therapies for sarcoma. Herein we show that Cre- lox P-mediated simultaneous activation of Kras G12D , and deletion Trp53, in the hindlimb muscles of C57Bl/6 mice results in the development of highly penetrant, rapid onset undifferentiated pleomorphic sarcomas (UPS). The latter represents a model one of the most common human sarcoma subtypes both histologically and genetically. Furthermore, cell lines derived from the UPS tumors induced in C57Bl/6 mice can be transplanted into the hindlimbs or lungs of naïve, immune competent syngeneic mice. Immunological characterization of both the spontaneous and transplanted UPS tumours demonstrates an immunologically- ‘quiescent’ microenvironment, characterized by a paucity of lymphocytes and spontaneous adaptive immune pathways in addition to dense macrophage infiltrates. UPS cell line induced tumours demonstrate mildly increased lymphocytic infiltrates as compared with the spontaneous UPS tumours, furthermore, growth of transplanted UPS was unaltered in lymphocyte deficient hosts. Despite expression of PD-1 on the tumour infiltrating lymphocytes, UPS tumours were resistant to immunological checkpoint blockade. This syngeneic transplantable UPS model that recapitulates many of the immunological features of human UPS will prove invaluable for the preclinical development and evaluation of novel immunotherapeutic approaches for targeting sarcomas.
2021-06-24 | GSE174540 | GEO
Project description:Undifferentiated pleomorphic sarcoma (UPS) and related tumors are the most common type of soft tissue sarcoma. However, this spectrum of tumors has different etiologies with varying rates of metastasis and survival. Two dermal-based neoplasms in this class of pleomorphic sarcomas, atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS), are challenging to differentiate at initial biopsy but vary significantly in prognosis. We performed single-cell transcriptomics on five AFX and PDS biopsy specimens as well as both single-cell and spatial transcriptomics on one PDS excision specimen to better characterize these tumors. The top differential genes between AFX and PDS were predictive of overall survival in 17 other cancers included in the Human Protein Atlas. Of these genes, COL6A3 and BGN predicted overall survival and metastasis-free survival in independent cohorts of 46 and 38 UPS tumors, respectively. COL6A3 was most predictive of overall survival in UPS patients and outperformed an established sarcoma prognostic gene panel at predicting metastasis in UPS.
2024-11-10 | GSE281529 | GEO
Project description:Undifferentiated pleomorphic sarcoma (UPS) and related tumors are the most common type of soft tissue sarcoma. However, this spectrum of tumors has different etiologies with varying rates of metastasis and survival. Two dermal-based neoplasms in this class of pleomorphic sarcomas, atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS), are challenging to differentiate at initial biopsy but vary significantly in prognosis. We performed single-cell transcriptomics on five AFX and PDS biopsy specimens as well as both single-cell and spatial transcriptomics on one PDS excision specimen to better characterize these tumors. The top differential genes between AFX and PDS were predictive of overall survival in 17 other cancers included in the Human Protein Atlas. Of these genes, COL6A3 and BGN predicted overall survival and metastasis-free survival in independent cohorts of 46 and 38 UPS tumors, respectively. COL6A3 was most predictive of overall survival in UPS patients and outperformed an established sarcoma prognostic gene panel at predicting metastasis in UPS.
2024-11-08 | GSE281096 | GEO
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-01 | GSE256158 | GEO
Project description:Background: Undifferentiated pleomorphic sarcoma (UPS), used to be called malignant fibrous histiocytoma (MFH), is a malignant soft tissue tumor of uncertain origin, and is characterized by morphology. UPS often share similar morphological characters with other sarcomas, especially Leiomyosarcoma. Leiomyosarcoma (LMS) is another malignant soft tissue sarcoma with complex genomic abnormalities, origin from smooth muscle. As a result, development of gene signature and/or biomarkers distinguishing UPS and LMS will definitely help the pathologist to precisely diagnose those patients. However, in the past, UPS was reported to be indistinguishable with LMS by genomic profiles. Methods and Results: In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases. Overall, UPS was undistinguished with LMS by 3SEQ data, however, when we stratified LMS into three subtypes, UPS was shown to share similar expression pattern with Subtype II LMS, but had distinct molecular expression patterns with Subtype I and Subtype III LMS. Additional Immunohistochemistry staining by using LMS Subtype I and Subtype II markers validated that UPSs were positive for Subtype II marker ARL4C, but negative for Subtype I marker LMOD1. Furthermore, CD4 was shown to be significantly more highly expressed in UPS than LMS in both mRNA and protein levels. Conclusion: This study first reported that UPS shared similar gene expression pattern with subtype II LMS and UPS recapitulated the expression profiles of subtype II LMS. In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases. In order to explore the molecular differences between UPS and LMS, We analyzed the expression data by SAMseq to identify the genes which were significantly differently expressed between UPS and LMS, between UPS and each LMS subtype.
2015-05-19 | E-GEOD-53844 | biostudies-arrayexpress
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-15 | GSE261169 | GEO