Biology subjects

Mankame, S.

Publications and source records attributed to Mankame, S..

4 recordsLinked to original sources

bioRxiv2026

Patient-Derived Glioma Models Preserve Tumor Heterogeneity and Identify Stearoyl-CoA Desaturase1 (SCD1) as a Candidate Biomarker for Precision Immunotherapy

Background: Pediatric and adult brain tumors, including glioblastoma, astrocytoma, ependymoma, and medulloblastoma, remain associated with poor prognosis despite advances in surgery, radiation, and chemotherapy. Therapeutic resistance, tumor heterogeneity, and treatment-related toxicity highlight the need for clinically relevant models that enable precision medicine and immunotherapy development. Methods: Freshly dispersed tumors (FDTs), low-passage patient-derived brain tumor (PBT) spheroid lines, and matched patient-derived xenograft (PDX) models were established from patients with primary brain tumors. Models were characterized using single-cell and bulk RNA sequencing, whole-exome sequencing, multiparameter flow cytometry, and immunohistochemistry. PBTs were compared with matched FDTs to evaluate model fidelity. Results: PBT lines were established in approximately 68% of cases and retained key patient-specific genomic alterations, including IDH1, MGMT, TP53, and PTEN, with expression of therapeutically relevant targets, including IL13R2, EGFR, HER2, WNT1, JAK1/2, and NOTCH1-4. Gene expression profiles of PBTs closely correlated with matched FDTs (R = 0.38, P = 0.0038). PBT and PDX models preserved intratumoral heterogeneity and non-clonal populations, enabling identification of therapy-resistant subclones during in vitro selection. Molecular analyses identified Stearoyl-CoA Desaturase1 (SCD1) as an overexpressed biomarker across glioma PBTs and matched patient tumors. Ingenuity Pathway Analysis identified SCD1 as an upstream regulator of EGFR-, TP53-, and CYCS-associated signaling networks implicated in tumor progression and immune suppression. Conclusions: Clinically relevant PBT and matched PDX models recapitulate molecular, transcriptional, and histopathological characteristics of primary brain tumors. These platforms provide tools for biomarker discovery, therapeutic testing, and precision immunotherapy development, while identifying SCD1 as a biomarker and therapeutic target in glioma.

cancer biology↗

bioRxiv2025

Cell-Free DNA Reveals the Longitudinal Effects of Temozolomide Treatment and Host Co-Culture in Glioblastoma Models

Glioblastoma (GBM) is a highly aggressive brain tumor with limited options for longitudinal monitoring. We evaluated the potential of cell-free DNA (cfDNA) as a real-time biomarker of tumor burden under tightly controlled conditions. We measured the cfDNA release dynamics, fragmentation sizes, and variant allele frequencies (VAF) in patient-derived GBM cell cultures. Time series of cfDNA were collected and analyzed in treatment-naive monocultures, during temozolomide (TMZ) treatment, and in co-culture with normal human astrocyte (NHA) cells. Longitudinal collection of media from individual cultures demonstrated that cfDNA yield increased, indicating the ability to use cfDNA to track tumor burden over time. Using a co-culture system, we deconvoluted cfDNA admixtures by analyzing yield, fragment size patterns, and cell line-specific variants. The exclusive detection of NHA- and GBM-specific mutations confirmed the distinct contributions of each cell type. Finally, TMZ treatment of GBM cells prompted an increase in cfDNA yield and VAF, suggesting that the effects of therapy could be measured using cfDNA. These findings support cfDNA as a non-invasive biomarker for real-time monitoring of GBM progression and treatment response, with clinical potential as a liquid biopsy tool in glioblastoma management. KEY POINTSO_LIcfDNA yield and variant allele frequencies (VAFs) correlate with GBM tumor burden. C_LIO_LIcfDNA properties can be used to differentiate between cell types in a mixed population. C_LIO_LITMZ treatment increases cfDNA yield and VAFs, reflecting treatment response. C_LI IMPORTANCE OF THE STUDYThis study highlights the potential of cell-free DNA (cfDNA) as a non-invasive biomarker for monitoring glioblastoma (GBM) progression and treatment response. By utilizing in-vitro models, we demonstrate that cfDNA yield, fragmentation patterns, and variant allele frequencies (VAFs) can effectively identify treatment-induced changes, such as those induced by temozolomide (TMZ) treatment, providing insights into therapeutic response. These results have significant translational implications, as cfDNA could serve as a real-time liquid biopsy tool for monitoring GBM progression, assessing treatment efficacy, and identifying early signs of treatment resistance in clinical settings. The ability to track tumor dynamics non-invasively holds great promise for improving GBM patient management and guiding personalized therapeutic approaches.

cancer biology↗

bioRxiv2023

Low frequency optogenetic deep brain stimulation of nucleus accumbens dopamine D1 or D2 receptor-containing neurons attenuates cocaine seeking selectively in male rats in part by reversing synaptic plasticity deficits

BackgroundClinically, deep brain stimulation (DBS) utilizes relatively high frequencies (>100 Hz). In preclinical models, 160 Hz stimulation of the nucleus accumbens in rodents prevents relapse of drug seeking. However, the ability of varied frequencies of accumbens DBS to attenuate drug seeking, and the neuronal subtype specificity of this effect, is unclear. MethodsThe present study examined the effect of DBS in the nucleus accumbens on neuronal plasticity and cocaine-primed reinstatement of cocaine seeking behavior in rats. ResultsElectrical DBS of the accumbens shell attenuated cocaine primed reinstatement across a range of frequencies in male rats, including as low as 12 Hz. The majority of nucleus accumbens neurons are medium spiny neurons (MSNs), which can be differentiated in terms of projections and effects on cocaine-related behaviors by expression of dopamine D1 receptors (D1DRs) or D2DRs. In slice electrophysiology experiments, 12 Hz electrical stimulation evoked long term potentiation (LTP) in eYFP labeled D1DR-MSNs and D2DR-MSNs from cocaine naive male and female rats. However, in rats that self-administered cocaine and underwent extinction training, a paradigm identical to our reinstatement experiments, electrical DBS only elicited LTP in D2DR-MSNs from male rats; this effect was replicated by optical stimulation in rats expressing Cre-dependent ChR2 in D2DR-MSNs. Low-frequency optogenetic-DBS in D1DR-containing or D2DR-containing neurons attenuated cocaine-primed reinstatement of cocaine seeking in male but not female rats. ConclusionsThese results suggest that administering DBS in the nucleus accumbens shell at lower frequencies effectively, but sex-specifically, suppresses cocaine craving, perhaps in part by reversing synaptic plasticity deficits selectively in D2DR-MSNs.

neuroscience↗

bioRxiv2022

High frequency DBS-like optogenetic stimulation of nucleus accumbens dopamine D2 receptor-containing neurons attenuates cocaine reinstatement in male rats

BackgroundPrevious work indicated that deep brain stimulation (DBS) of the nucleus accumbens shell in male rats attenuated reinstatement of cocaine seeking, an animal model of craving. However, the potential differential impact of DBS on specific populations of neurons to drive the suppression of cocaine seeking is unknown. Medium spiny neurons in the nucleus accumbens are differentiated by expression of dopamine D1 receptors (D1DRs) or D2DRs, activation of which promotes or inhibits cocaine-related behaviors, respectively. The advent of transgenic rat lines expressing Cre recombinase selectively in D1DR-containing or D2DR-containing neurons, when coupled with Cre-dependent virally mediated gene transfer of channelrhodopsin (ChR2), enabled mimicry of DBS in a selective subpopulation of neurons during complex tasks. HypothesisWe tested the hypothesis that high frequency DBS-like optogenetic stimulation of D1DR-containing neurons in the accumbens shell would potentiate, whereas stimulation of D2DR-containing neurons in the accumbens shell would attenuate, cocaine-primed reinstatement of cocaine seeking. ResultsResults indicated that high frequency, DBS-like optogenetic stimulation of D2DR-containing neurons attenuated reinstatement of cocaine seeking in male rats, whereas DBS-like optogenetic stimulation of D1DR-containing neurons did not alter cocaine-primed reinstatement. Surprisingly, DBS-like optogenetic stimulation did not alter reinstatement of cocaine seeking in female rats. In rats which only expressed eYFP, intra-accumbens optogenetic stimulation did not alter cocaine reinstatement relative to sham stimulation, indicating that the effect of DBS-like stimulation to attenuate cocaine reinstatement is mediated specifically by ChR2 rather than consequent to prolonged light delivery. ConclusionsThese results suggest that DBS of the accumbens attenuates cocaine-primed reinstatement in male rats through the selective manipulation of D2DR-containing neurons.

neuroscience↗