Biology subjects

Gephart, M. H.

Publications and source records attributed to Gephart, M. H..

3 recordsLinked to original sources

bioRxiv2025

Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases

BackgroundNon-small cell lung cancer (NSCLC) patients with brain metastases (BMET) have a poor prognosis. Cerebrospinal fluid (CSF) is a source of cell free DNA (cfDNA) from the brain and its methylation and fragmentation properties may be an indicator of NSCLC-BMET. MethodsWe applied a nanopore single-molecule sequencing approach to characterize the fragmentation, methylation and hydroxymethylation patterns present in CSF-derived cfDNA from NSCLC-BMET patients (N=15). We compared the cancer cfDNA finding to non-cancer healthy controls (N=11) and their CSF cfDNA. We also compared the fragmentation patterns between CSF-derived cfDNA and plasma-derived cfDNA. ResultsWe observed enriched mono-nucleosome levels and significantly higher mono-/trinucleosome ratios in cancer patients. Comparison with plasma-derived cfDNA further confirmed the unique fragmentation features of CSF-derived cfDNA. Distinct methylation and hydroxymethylation patterns were observed between cancer and control CSF samples. We observed significantly lower degree of hydroxymethylation in cancer patients compared to healthy controls and the affected genes had different pathway profiles. ConclusionsCSF cfDNA in patients with NSCLC-BMET had a distinct profiles of DNA fragmentation, methylation and hydroxymethylation.

genomics↗

bioRxiv2025

Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence

Gliomas are among the most lethal cancers, with limited treatment options. To uncover hallmarks of therapeutic escape and tumor microenvironment (TME) evolution, we applied spatial proteomics, transcriptomics, and glycomics to 670 lesions from 310 adult and pediatric patients. Single-cell analysis shows high B7H3+ tumor cell prevalence in glioblastoma (GBM) and pleomorphic xanthoastrocytoma (PXA), while most gliomas, including pediatric cases, express targetable tumor antigens in less than 50% of tumor cells, potentially explaining trial failures. Longitudinal samples of isocitrate dehydrogenase (IDH)-mutant gliomas reveal recurrence driven by tumor-immune spatial reorganization, shifting from T-cell and vasculature-associated myeloid cell-enriched niches to microglia and CD206+ macrophage-dominated tumors. Multi-omic integration identified N-glycosylation as the best classifier of grade, while the immune transcriptome best predicted GBM survival. Provided as a community resource, this study opens new avenues for glioma targeting, classification, outcome prediction, and a baseline of TME composition across all stages.

cancer biology↗

bioRxiv2017

Recurrently Mutated Genes Differ between Leptomeningeal and Solid Lung Cancer Brain Metastases

PurposeBrain metastases from non-small cell lung cancer (NSCLC) engraft and grow either within the brain (solid) or diffusely on its surface (leptomeningeal disease; LMD). Routine clinical diagnostics have low sensitivity and provide no information about the underlying mutations. A recurrent mutation analysis of LMD and a comparison between solid and LMD NSCLC brain metastases have yet to be explored.\n\nExperimental DesignWe performed whole-exome sequencing (WES) on eight cerebrospinal fluid (CSF) specimens from NSCLC LMD patients. We compared our LMD sequencing data with a published data set of 26 NSCLC solid brain metastases to determine the relative mutation frequency. We then performed a retrospective chart review of an additional set of 44 NSCLC LMD patients to further evaluate LMD mutations and clinical prognosis.\n\nResultsSix (75%) LMD cases had mutations in EGFR, while none had KRAS mutations. Retrospective chart review revealed only 4 LMD cases (7.7%) with KRAS mutations, but 33 cases (63.5%) with EGFR mutations. TP53 was mutated in 4/8 LMD (50%) cases and 13/26 of solid metastasis (50%). The median interval for developing LMD from NSCLC was shorter in EGFR-mutant (16.3 mo) than wild-type (23.9 mo) patients (p = 0.017).\n\nConclusionsEGFR and TP53 mutations were frequent in LMD exomes (combined frequency 87.5%), suggesting that PCR-based mutation detection assays towards these two genes could be a useful complement to current diagnostics. Correlations of EGFR in LMD and KRAS in solid metastases suggest molecular distinctions or systemic treatment pressure underpinning differences in growth patterns within the brain.\n\nTranslational RelevanceLeptomeningeal disease is a diffuse, malignant, and incurable metastatic brain tumor that accounts for 5-10% of brain metastases. Patients with LMD do not undergo biopsy and their overall prognosis is poor (median survival 3 to 27 months), making it difficult to collect sufficient samples for recurrent mutation analysis. Standard diagnostic procedures (MRI and cytology) for LMD provide no genetic information. To understand the mutation landscape of LMD, we performed whole-exome sequencing on eight lung-derived LMD cases. We showed that mutations in EGFR occurred more frequently in LMD than solid brain metastases, but KRAS mutations were not present in LMD. Further, mutations in recurrent genes such as EGFR and TP53 could be reliably detected in CSF via droplet digital PCR. Targeted analysis of recurrent mutations thus presents a useful complement to the existing diagnostic toolkit, and differences in mutations between LMD and solid brain metastases suggest distinct molecular mechanisms for growth.

genomics↗