Summary of Study ST003065
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001911. The data can be accessed directly via it's Project DOI: 10.21228/M8Q148 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003065 |
| Study Title | Investigative needle core biopsies for multi-omics in Glioblastoma |
| Study Summary | Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and 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 role of investigative biopsies – tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses (‘Multi-omics”) has yet to be defined. Here we adapt stereotactic needle core biopsy tissue for highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics. Biopsy tissue was obtained from a single patient with recurrent GBM during one procedure. In a second patient, we analyzed multi-regional core biopsies to decipher spatial 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 highlighted immune cell associated metabolic pathways and poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. 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 process and tumor immune microenvironment and could be of potential value in evaluating treatment responses. |
| Institute | Brigham and Women's Hospital |
| Department | Department of Neurosurgery |
| Laboratory | Nathalie Y.R. Agar |
| Last Name | Stopka |
| First Name | Sylwia |
| Address | 60 Fenwood Rd |
| sstopka@bwh.harvard.edu | |
| Phone | 617-525-9746 |
| Submit Date | 2024-02-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | imzML |
| Analysis Type Detail | MALDI |
| Release Date | 2025-02-03 |
| Release Version | 1 |
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Collection:
| Collection ID: | CO003173 |
| Collection Summary: | Biopsy Core Four underwent a preservation process, being rapidly frozen on dry ice. For MALDI MSI the core was then cryo-sectioned into 10 µm-thick slices. |
| Sample Type: | Brain |
