Biology subjects

Chen, L. M.

Publications and source records attributed to Chen, L. M..

9 recordsLinked to original sources

bioRxiv2025

Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

This study aimed to evaluate diffusion parameters derived from diffusion tensor imaging (DTI) and spherical mean technique (SMT) for detecting region-specific, fine-grained tissue damage and white matter (WM) tract disruptions following spinal cord injury (SCI). Diffusion MRI data were acquired from the cervical spinal cord of monkeys before and after a unilateral dorsal column lesion at the C5 level, using a 9.4T scanner. Parametric maps derived from DTI and SMT effectively detected regional fiber damage around 16 weeks post-injury. Post-mortem silver staining served as the ground truth for assessing region-specific fiber damage. Diffusion MRI maps aligned well with histological measures and captured the severity of WM damage at the lesioned segment (in an order of dorsal > ventral > lateral WM tracts) and along the dorsal column tract across segments (in an order of lesion center > rostral > caudal). Among the diffusion parameters, fractional anisotropy (FA), axonal volume fraction (Vax), radial diffusivity (RD), and extra axonal transverse diffusivity (Dex) showed most significant changes at and around the lesion site where severe tissue damage occurred. FA, Vax, and axial diffusivity (AD) exhibited marked changes in dorsal column proximal to the lesion center, where moderate axonal damage occurred. Additionally, AD and FA showed the greatest sensitivity (true positive rate) and specificity (true negative rate) to mild fiber disruption and demyelination in regions distal to the lesion. Overall, FA provided the highest sensitivity and specificity for detecting fiber degeneration and demyelination, while Vax demonstrated the strongest spatial correlation with histologic markers of regional fiber damage. The combination of DTI and SMT thus offers reliable biomarkers for assessing SCI.

neuroscience↗

bioRxiv2025

Early Detection of Neuroinflammation and White Matter Damage Following Dorsal Spinal Nerve Root Sectioning in a Nonhuman Primate Model

PurposeDorsal rhizotomy, or spinal dorsal nerve root lesioning, is a surgical procedure used to treat intractable nerve pain by selectively severing sensory afferent nerve roots. This study aimed to evaluate whether multiparametric MRI, including diffusion tensor imaging (DTI), quantitative magnetization transfer (qMT), and chemical exchange saturation transfer (CEST), can sensitively detect structural and biochemical changes in the intact spinal cord following a focal dorsal nerve root section in a non-human primate model. MethodsIn four squirrel monkeys, unilateral dorsal nerve roots at cervical segments C4 and C5 were surgically transected. MRI data were collected using a 9.4 T scanner with a custom saddle-shaped transmit-receive quadrature coil before and one week after lesioning. DTI-derived fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD); qMT-derived pool size ratio (PSR); and CEST and nuclear Overhauser enhancement (NOE) effects were quantified across seven spinal cord regions of interest (ROIs). CEST and NOE effects were extracted using five-pool Lorentzian fitting of Z-spectra. ResultsAt the lesioned dorsal nerve root bundles, FA, PSR, and NOE (-1.6 ppm) values decreased, while RD and CEST (3.5 ppm) increased, consistent with fiber degeneration, demyelination, and inflammation. Similar, though less pronounced, changes were observed in the dorsal root entry zone, particularly within the first week post-lesion. ConclusionMultiparametric MRI enables region-specific detection of early spinal cord pathology as soon as one week following dorsal nerve root injury. These findings support its potential as a noninvasive tool for monitoring secondary degeneration due to spinal nerve damage and for evaluating outcomes of therapeutic interventions.

neuroscience↗

bioRxiv2023

Small volume blood-brain barrier opening in macaques with a 1 MHz ultrasound phased array

Focused ultrasound blood-brain barrier (BBB) opening is a promising tool for targeted delivery of therapeutic agents into the brain. The volume of opening determines the extent of therapeutic administration and sets a lower bound on the size of targets which can be selectively treated. We tested a custom 1 MHz array transducer optimized for cortical regions in the macaque brain with the goal of achieving small volume openings. We integrated this device into a magnetic resonance image guided focused ultrasound system and demonstrated twelve instances of small volume BBB opening with average opening volumes of 59 {+/-} 37 mm3 and 184 {+/-} 2 mm3 in cortical and subcortical targets, respectively. We developed real-time cavitation monitoring using a passive cavitation detector embedded in the array and characterized its performance on a bench-top flow phantom mimicking transcranial BBB opening procedures. We monitored cavitation during in-vivo procedures and compared cavitation metrics against opening volumes and safety outcomes measured with FLAIR and susceptibility weighted MR imaging. Our findings show small BBB opening at cortical targets in macaques and characterize the safe pressure range for 1 MHz BBB opening. Additionally, we used subject-specific simulations to investigate variance in measured opening volumes and found high correlation (R2 = 0.8577) between simulation predictions and observed measurements. Simulations suggest the threshold for 1 MHz BBB opening was 0.53 MPa. This system enables BBB opening for drug delivery and gene therapy to be targeted to more specific brain regions.

bioengineering↗

bioRxiv2022

Enrichment and application of bacterial sialic acids containing polymers from the extracellular polymeric substances of Candidatus Accumulibacter

Pseudaminic and legionaminic acids are a subgroup of nonulosonic acids (NulOs) unique to bacterial species. There is a lack of advances in the study of these NulOs due to their complex synthesis and production. Recently, it was seen that "Candidatus Accumulibacter" can produce Pse or Leg analogues as part of its extracellular polymeric substances (EPS). In order to employ a "Ca. Accumulibacter" enrichment as production platform for bacterial sialic acids, it is necessary to determine which fractions of the EPS of "Ca. Accumulibacter" contain NulOs and how to enrich and/or isolate them. We extracted the EPS from granules enriched with "Ca. Accumulibcater" and used size-exclusion chromatography to separate them into different molecular weight fractions. This separation resulted in two high molecular weight (> 5,500 kDa) fractions dominated by polysaccharides, with a NulO content up to 4 times higher than the extracted EPS. This suggests that NulOs in "Ca. Accumulibacter" are likely located in high molecular weight polysaccharides. Additionally, it was seen that the extracted EPS and the NulO-rich fractions can bind and neutralize histones. This suggest that they can serve as source for sepsis treatment drugs, although further purification needs to be evaluated. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/508216v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1f59ff7org.highwire.dtl.DTLVardef@d933fcorg.highwire.dtl.DTLVardef@1e3ff78org.highwire.dtl.DTLVardef@1994948_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINulOs in "Ca. Accumulibacter" are likely located in high molecular weight polysaccharides. C_LIO_LISize exclusion chromatography allows to obtain high molecular weight polysaccharide-rich fractions enriched with NulOs. C_LIO_LIEPS and the NulOs-rich fractions can serve as source for sepsis treatment drugs. C_LI

microbiology↗

bioRxiv2020

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.

genomics↗

bioRxiv2020

Recording the age of RNA with deamination

Transcriptional programs implemented by cells often consist of complex temporal features, but current approaches to single-cell RNA sequencing only provide limited information about the dynamics of gene expression. Here, we present RNA timestamps, a method for inferring the age of individual RNAs in a sequencing-based readout by leveraging RNA editing. Timestamped RNAs include a RNA reporter motif that accumulates A to I edits over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we are able to infer when in the past the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events, with no prior knowledge. Finally, we apply this method to cluster single cells according to the times at which a particular transcriptional program was activated. RNA timestamps thus suggest a new approach for incorporating temporal information into RNA sequencing workflows.

synthetic biology↗

bioRxiv2019

Slide-seq: A Scalable Technology for Measuring Genome-Wide Expression at High Spatial Resolution

The spatial organization of cells in tissue has a profound influence on their function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. Here, we introduce Slide-seq, a highly scalable method that enables facile generation of large volumes of unbiased spatial transcriptomes with 10 {micro}m spatial resolution, comparable to the size of individual cells. In Slide-seq, RNA is transferred from freshly frozen tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the spatial locations of the RNA to be inferred by sequencing. To demonstrate Slide-seqs utility, we localized cell types identified by large-scale scRNA-seq datasets within the cerebellum and hippocampus. We next systematically characterized spatial gene expression patterns in the Purkinje layer of mouse cerebellum, identifying new axes of variation across Purkinje cell compartments. Finally, we used Slide-seq to define the temporal evolution of cell-type-specific responses in a mouse model of traumatic brain injury. Slide-seq will accelerate biological discovery by enabling routine, high-resolution spatial mapping of gene expression. One Sentence SummarySlide-seq measures genome-wide expression in complex tissues at 10-micron resolution.

genomics↗

bioRxiv2018

A novel, biologically-informed polygenic score reveals role of mesocorticolimbic insulin receptor gene network on impulsivity and addiction

ImportanceActivation of brain insulin receptors occurs on mesocorticolimbic regions, modulating reward sensitivity and inhibitory control. Variations in the functioning of this mechanism likely associate with individual differences in the risk for related psychopathologies (attention-deficit hyperactivity disorder, addiction), an idea that agrees with the high comorbidity between insulin resistant states and psychiatric conditions. While genetic studies comprise an interesting tool to explore neurobiological mechanisms in community samples, the conventional genome-wide association studies and polygenic risk score methodologies completely ignore the fact that genes operate in networks, and code for precise biological functions in specific tissues.\n\nObjectiveWe propose a novel, biologically informed genetic score reflecting the mesocorticolimbic insulin receptor-related gene network, and investigate if it predicts dopamine-related psychopathology (impulsivity and addiction) in community samples.\n\nDesignBirth cohort (Maternal Adversity, Vulnerability and Neurodevelopment, MAVAN) and adult cohort (Study of Addiction, Genes and Environment, SAGE).\n\nSettingGeneral community.\n\nParticipants212 4-year-old children (MAVAN), and 1626 adults (SAGE).\n\nExposureThe biologically informed, mesocorticolimbic specific, insulin receptor polygenic score was created based on levels of co-expression with the insulin receptor in striatum and prefrontal cortex, and calculated in the two samples using the genotype data (Psychip/Psycharray).\n\nMain outcomechildhood impulsivity in the Information Sampling task, and risk for early addiction onset.\n\nResultsThe insulin receptor polygenic score showed improved prediction of childhood impulsivity in boys and risk for early addiction onset in males in comparison to conventional polygenic risk scores for attention-deficit hyperactivity disorder or addiction.\n\nConclusions and relevanceThis novel genomic approach reveals insulin action as a relevant biological process involved in the risk for dopamine-related psychopathology.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSConsidering the modulation of mesocorticolimbic dopaminergic pathways by insulin through the action on its receptors (IR), we investigated if a novel, region specific polygenic score on the IR-related gene network (ePRS-IR) is associated with dopamine-related behaviors (impulsivity and addiction).\n\nFindingsThe ePRS-IR showed improved prediction of childhood impulsivity and risk for early addiction onset in comparison to conventional polygenic risk scores for ADHD or addiction.\n\nMeaningThis novel genomic approach reveals insulin action as a biological process involved in the risk for dopamine-related psychopathology.

neuroscience↗

bioRxiv2017

PRS-on-Spark: a novel, efficient and flexible approach for generating polygenic risk scores

MotivationPolygenic risk scores describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of the variance than single nucleotide polymorphisms alone. However, there is little consensus on the optimal data input for generating polygenic risk scores and existing approaches largely preclude the use of imputed posterior probabilities and strand-ambiguous SNPs.\n\nResultsWe developed PRS-on-Spark (PRSoS) a polygenic risk score software implemented in Apache Spark and Python that accommodates a variety of data input (e.g., observed genotypes, imputed genotypes, or imputed posterior probabilities) and strand-ambiguous SNPs. We show that PRSoS is flexible and efficient and computes polygenic risk scores at a range of p-value thresholds more quickly than existing software (PRSice). We also show that the use of imputed posterior probabilities and the inclusion of strand-ambiguous SNPs increases the proportion of variance explained by polygenic risk scores for major depression.\n\nAvailability and ImplementationPRSoS is written in Apache Spark and Python and is freely available (see https://github.com/MeaneyLab/PRSoS).

bioinformatics↗