Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [scRNA-seq]
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ABSTRACT:
PROVIDER: PRJNA1213849 | ENA |
REPOSITORIES: ENA
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Project description:Glioblastoma, IDH wild type (GBM) is a primary brain cancer with a poor prognosis and few effective therapies. The ability to investigate the tumor and its microenvironment during treatment would greatly enhance understanding of disease response, progression and impact of therapeutics. Stereotactic needle core biopsies are routine surgical procedures performed primarily for tumor diagnosis. Use of these biopsies for investigations into tumor and microenvironmental responses to treatment is rarely performed but holds great potential to support therapeutic monitoring and understanding of tumor evolution. However, it is unclear whether needle core biopsies are sufficient for multi-omics analysis and tumor models. Here we test the depth of data generation possible from stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analyses including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance and quantify intra and inter-sample heterogeneity. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft (PDX) models in a separate patient cohort. Dataset integration across modalities highlighted spatially mapped immune cell associated metabolic pathways, revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome, and validated inferred cell-cell ligand receptor interactions. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data and PDX models, provide data rich insight into a patient’s disease process and tumor immune microenvironment and can be of value in evaluating treatment responses.
2025-04-28 | GSE287630 | GEO
Project description:Glioblastoma, IDH wild type (GBM) is a primary brain cancer with a poor prognosis and few effective therapies. The ability to investigate the tumor and its microenvironment during treatment would greatly enhance understanding of disease response, progression and impact of therapeutics. Stereotactic needle core biopsies are routine surgical procedures performed primarily for tumor diagnosis. Use of these biopsies for investigations into tumor and microenvironmental responses to treatment is rarely performed but holds great potential to support therapeutic monitoring and understanding of tumor evolution. However, it is unclear whether needle core biopsies are sufficient for multi-omics analysis and tumor models. Here we test the depth of data generation possible from stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analyses including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance and quantify intra and inter-sample heterogeneity. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft (PDX) models in a separate patient cohort. Dataset integration across modalities highlighted spatially mapped immune cell associated metabolic pathways, revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome, and validated inferred cell-cell ligand receptor interactions. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data and PDX models, provide data rich insight into a patient’s disease process and tumor immune microenvironment and can be of value in evaluating treatment responses.
2025-04-28 | GSE287629 | GEO
Project description:Glioblastoma, IDH wild type (GBM) is a primary brain cancer with a poor prognosis and few effective therapies. The ability to investigate the tumor and its microenvironment during treatment would greatly enhance understanding of disease response, progression and impact of therapeutics. Stereotactic needle core biopsies are routine surgical procedures performed primarily for tumor diagnosis. Use of these biopsies for investigations into tumor and microenvironmental responses to treatment is rarely performed but holds great potential to support therapeutic monitoring and understanding of tumor evolution. However, it is unclear whether needle core biopsies are sufficient for multi-omics analysis and tumor models. Here we test the depth of data generation possible from stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analyses including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance and quantify intra and inter-sample heterogeneity. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft (PDX) models in a separate patient cohort. Dataset integration across modalities highlighted spatially mapped immune cell associated metabolic pathways, revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome, and validated inferred cell-cell ligand receptor interactions. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data and PDX models, provide data rich insight into a patient’s disease process and tumor immune microenvironment and can be of value in evaluating treatment responses.
2025-04-28 | GSE287631 | GEO
Project description:Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [Spatial Transcriptomics]
| PRJNA1213852 | ENA
Project description:Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [BulkRNA-seq]
| PRJNA1213848 | ENA
Project description:Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis with few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both our understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The adaptation of stereotactic biopsy tissue for complex and integrated investigative multi-modal molecular analyses (‘Multi-omics”) in the context of GBM regional heterogeneity is not routinely performed, Most of the tissue is consumed with standard of care clinical testing and the amount and quality of remaining cells, particularly in the context of recurrent GBMs that have failed previous treatments, has not previously been shown to be amenable to complex analyses. Here we performed highly resolved multi-modal analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonal analysis, and immunopeptidomics on needle biopsy cores obtained from a single patient during the same procedure. In a second patient, we analyzed multi-regional core biopsies to decipher spatially associated tissue and genomic variance. Finally in a separate cohort of patients we investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models. Dataset integration across modalities showed good correspondence between spatial modalities and revealed tumor and immune cell associated metabolic profiles and cell signalling pathways. In conclusion, stereotactic needle biopsy cores are of sufficient quality for the purposes of investigative biopsy and can generate multi-omics data, providing data rich insight into a patient’s disease to interrogate the tumor immune microenvironment.
2025-05-06 | PXD046857 | Pride
Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes
2011-10-31 | GSE32518 | GEO
Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.
2011-10-31 | E-GEOD-32518 | biostudies-arrayexpress
Project description:Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account. Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes
2008-09-09 | GSE12072 | GEO
Project description:Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle core biopsies. 158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples.
2016-03-09 | GSE72220 | GEO