
==== Front
Neurooncol Adv
Neurooncol Adv
noa
Neuro-Oncology Advances
2632-2498
Oxford University Press US

10.1093/noajnl/vdae090.023
vdae090.023
Final Category: Basic Science Leptomeningeal Disease
AcademicSubjects/MED00300
AcademicSubjects/MED00310
BSLM-13 EXTRACTION AND WHOLE TRANSCRIPTOME SEQUENCING OF CELL FREE RNA FROM HUMAN CEREBROSPINAL FLUID: A METHOD TO IDENTIFY BIOMARKERS OF BRAIN HEALTH AND DISEASE
Garcia Maxine Umeh Stanford Universtiy, Stanford/CA, USA

Taiwo Rukayat Stanford Universtiy, Stanford/CA, USA

Barisano Giuseppe Stanford Universtiy, Stanford/CA, USA

Spiliotopoulos Elias Oregon Health and Science University, Portland, OR, USA

Herrick Daniel Stanford Universtiy, Stanford/CA, USA

Godfrey Bryanna Stanford Universtiy, Stanford/CA, USA

Trinh Thy Stanford Universtiy, Stanford/CA, USA

Lee Seunghyun sh1231@stanford.edu, Stanford/CA, USA

Perez Pablo Nunez Stanford Universtiy, Stanford/CA, USA

Ngo Thuy Oregon Health and Science University, Portland, OR, USA

Gephart Melanie Hayden Stanford Universtiy, Stanford/CA, USA

8 2024
02 8 2024
02 8 2024
6 Suppl 1 2024 SNO/ASCO CNS Metastases Conference i8i8
© The Author(s) 2024. Published by Oxford University Press, the Society for Neuro-Oncology and the European Association of Neuro-Oncology.
2024
https://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Abstract

BACKGROUND

Brain biopsy carries a morbidity risk of ~5%, which has significantly limited samples available for research, hindering our understanding and treatment of brain metastases (BrM) and Leptomeningeal Disease (LMD). However, cerebrospinal fluid (CSF) – which circulates the CNS, significantly interfacing with brain tumor tissues and carries tumor cell-free nucleic acids and LMD cells – provides a critically understudied biospecimen to understand BrM/LMD biology. We previously found brain tumor-specific cell-free DNA (cfDNA) in CSF, even when not detectable in blood; and showed that the mutant fraction of cfDNA mirrored treatment response and disease progression. Expanding to study CSF cell-free mRNA (cfRNA) allowed us to extend from mutation-driven cancers (e.g., BRAF/melanoma, EGFR/lung cancer) to investigate the transcriptional profiles of not only cancer, but also brain-resident cells.

METHODS

We have banked, and have ready-access to, 300+ CSF samples from patients with brain tumors and LMD, many of whom were treated at Stanford Hospital (2012 – 2023). We then leveraged a combination of total RNA extraction and whole transcriptome RNA sequencing to interrogate gene expression patterns present in CSF cfRNA. A method we term CSF-Seq.

RESULTS

CSF-Seq has revealed expression profiles in LMD CSF not found in CSF of non-LMD cancers, like gliomas, and non-cancer controls, like hydrocephalous. Importantly, CSF-Seq accurately recapitulates our previous panel-based qPCR method, demonstrating upregulated cancer-associated genes like CEACAM6 and MUC1 in breast and lung LMD, and ubiquitous expression of brain-associated genes, like MBP, across all CSF samples. This demonstrates our ability to retrieve well-established, validated target genes, while positioning us to discover novel gene signatures in LMD.

CONCLUSION

These results serve as a starting point for identifying key gene expression signatures associated with development of LMD and BrM progression. Further investigation focused on tumor-brain crosstalk, and gene signatures associated with response to treatment, will provide promising targets for therapeutic advancement.
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