Biology subjects

Jackson, M. S.

Publications and source records attributed to Jackson, M. S..

6 recordsLinked to original sources

bioRxiv2026

Retest Reliability of Task-related fMRI BOLD Signals during Sequential Decision Making

IntroductionFunctional magnetic resonance imaging (fMRI) is widely used to study neural processes of behavior, but evaluations of test-retest reliability (TRR) of task-related blood-oxygen-level-dependent (BOLD) responses are scarce for many cognitive tasks. Such information is particularly important for longitudinal and intervention research. The ability to learn associations between choices and outcomes across decision stages is crucial for daily behavior. We assessed the measurement reliability of behavioral performance and fMRI BOLD signals during value-based sequential decision making to evaluate the TRR of task-relevant regions for future research on non-invasive brain stimulations. MethodsTwenty healthy adults (22 to 40 years) completed two task-fMRI sessions, at least 2 weeks apart. During scanning, participants performed two variants of a three-stage Markov decision task with conditions varied in temporal contingency (immediate vs. delayed) and magnitude of choice outcomes (high vs. low). Both sessions were conducted under sham tDCS via a focal 3 x 1 montage targeting left dorsolateral prefrontal cortex (DLPFC). TRR was assessed using intraclass correlation coefficients (ICC) with a two-way mixed-effects consistency model for decision performance and task-related fMRI signals at voxel level and summarized in key regions defined by the extended Human Connectome Project atlas (HCPex). ResultsDecision performance was lower with delayed than immediate outcomes (p < 0.001). Higher outcome magnitude improved performance (p < 0.001). Decision performance increased across learning bins (p < 0.001). The behavioral TRR was in the moderate to good level (ICC(3,1) = 0.744 for accuracy; ICC(3,1) = 0.788 for reaction time). At the whole-brain level, contrasting brain activities in delayed with immediate condition revealed suprathreshold cluster peaks in several frontal-parietal (e.g., orbitofrontal, bilateral dorsolateral prefrontal, and medial parietal cortices) and striatal regions (e.g., bilateral putamen). Voxel-wise ICCs revealed variable but often moderate-to-good TRR across task-relevant regions, with stronger reliability in several striatal, orbitofrontal, and left dorsolateral prefrontal parcels, and more variable reliability across anterior cingulate and medial prefrontal parcels. ConclusionThese results from a 2-session tDCS sham-sham stimulation study establish the validity of using the three-stage Markov decision task in future studies about intervention effects on the frontal-parietal-striatal network.

neuroscience↗

bioRxiv2025

Standardized pipeline for establishing, expanding, and differentiating airway and alveolar organoids from human BAL fluid

Lung organoids are versatile experimental models, but their broader use in studying human disease is limited by the scarcity of starting material and the complexity of current methods. To align organoid technology with common clinical practice, we developed airway and alveolar organoids using cells obtained from patients bronchoalveolar lavage (BAL) fluid. Building on existing techniques, we showed that BAL is a reliable, accessible source of primary human epithelial cells, yielding airway and alveolar organoids within 10 days. Organoids can then be expanded over many passages for downstream analysis. Our streamlined methods do not require cell sorting or other complex procedures, all cells are derived from a single patient, and media are based on serum-free, chemically-defined formulations. Here, we present detailed protocols for organoid establishment, standardized passaging and phenotyping, and differentiation of both airway and alveolar models. We provide a time course of BAL-derived airway organoid differentiation at air-liquid interface, and we demonstrate proof of principle for differentiation of BAL-derived alveolar organoids in 3D culture. These methods can be readily adapted to generate and characterize organoids from lung tissue, tracheobronchial specimens, or other primary cells from humans or mice, expanding the potential to use lung organoids for disease modeling. NEW AND NOTEWORTHYWe provide streamlined protocols to generate both airway and alveolar epithelial organoids from a single, clinical BAL specimen. From standardized specimen collection to organoid plating to passaging and differentiation, we show that rare, primary epithelial cells in BAL can give rise to all the major airway and alveolar cell types. Our serum-free, feeder-free, sorting-free methods offer a simplified starting point for using patient-derived organoids to model lung disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/682184v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@e0abe2org.highwire.dtl.DTLVardef@349f9aorg.highwire.dtl.DTLVardef@da4b0eorg.highwire.dtl.DTLVardef@175a97f_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Standardized pipeline for BAL organoids. Created in BioRender. C_FIG

cell biology↗

bioRxiv2023

The influence of marker number and sequencing depth on the ability to identify mismatch repair deficient tumours.

1.Analysis of somatic mutation patterns is widely used to infer exposure to exogenous and endogenous mutagenic influences. This raises the question of the amount of sequence data required to detect factors of interest. A common use of mutation pattern analysis is the identification of increased microsatellite instability to uncover mismatch repair (MMR) defects in tumours and normal tissues. Here we explore the effects of sequencing depth and the number of loci analysed on the ability to detect MMR deficiency using artificial neural networks and publicly available amplicon sequencing data from colorectal tumours on 24 short quasi monomorphic microsatellites (up to 12 bp in length, PMID 31471937) split in a training (99 samples) and a test set (95 samples). We show that, at a sequencing depth of 200, pairs mononucleotide repeats can achieve discrimination between MMR proficient and deficient colorectal tumours similar to that obtained with the full 24 marker panel, with accuracies above 97% and ROC AUCs in excess of 99% in the test set. Our results indicate that for short monomorphic microsatellites considering the length distribution of the different alleles at each locus, representing these distributions as two-dimensional structures and including convolutional layers in the network can facilitate discrimination between MMR deficient and proficient tumour material. They also indicate that, despite the limitations imposed by amplification, sequencing accuracy and the limited divergence time between the sequences from one locus, high depth sequencing can be used to identify MMR deficiency from a limited number of loci. However, they also suggest that, for a fixed total number of reads per sample, increasing sensitivity by increasing the number of targets is more efficient than by increasing per target sequencing depth. These results are of interest for screening large numbers of samples and for assessing the impact MMR deficiency in different areas of the genome.

genetics↗

bioRxiv2022

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed by computational detection tools. During the last decade, a plethora of such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools were used and detected over 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were empirically validated using three orthogonal methods. Generally, tool-specific precision values are high and similar (median of 98.8%, 96.3%, and 95.5% for qPCR, RNase R, and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant tool differentiators. Furthermore, we demonstrate the complementarity of tools through the increase in detection sensitivity by considering the union of highly-precise tool combinations while keeping the number of false discoveries low. Finally, based on the benchmarking results, recommendations are put forward for circRNA detection and validation.

genomics↗

bioRxiv2018

A molecular inversion probe and sequencing-based microsatellite instability assay for high throughput cancer diagnostics and Lynch syndrome screening

BackgroundClinical guidelines recommend microsatellite instability (MSI) and BRAF V600E testing of all colorectal cancers (CRCs) to screen for Lynch syndrome (LS), a hereditary predisposition to cancer. MSI is also associated with response to immunotherapy. However, uptake of MSI testing is poor and current assays are not suitable for high throughput diagnostics.\n\nWe aimed to develop a cheap and scalable sequencing assay for MSI classification, which is robust to variables in clinical samples and simultaneously tests for BRAF V600E to streamline the LS screening pipeline.\n\nMethods24 short (7-12bp) microsatellites and the BRAF V600E locus were amplified in multiplex using single molecule molecular inversion probes (smMIPs) and sequenced using the Illumina MiSeq platform. Reads were aligned to reference genome hg19. An MSI classifier was trained from 98 CRCs and validated in 99 independent CRCs collected in pathology laboratories in Edinburgh, Spain and Newcastle.\n\nResultsThe smMIP-based MSI assay has 100% accuracy for MSI status relative to MSI Analysis System (Promega). MSI classification is reproducible (100% concordance) and is robust to sample variables, detecting less than 5% MSI-high content in template DNA and giving reliable classification from sequencing only 75 DNA molecules per marker. BRAF V600E was detected with mutant allele frequencies down to 1.7%.\n\nConclusionsOur short microsatellite, smMIP-based, MSI assay provides a cheap and fully automatable assessment of MSI status and BRAF mutation. It is readily scalable to high throughput cancer diagnostics, and is suitable both as a companion diagnostic for immunotherapy and for streamlined LS screening.

cancer biology↗

bioRxiv2018

A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours

Somatic mutations in mononucleotide repeats are commonly used to assess the mismatch repair status of tumours. Current tests focus on repeats with a length above 15bp, which tend to be somatically more unstable than shorter ones. These longer repeats also have a substantially higher PCR error rate and tests that use capillary electrophoresis for fragment size analysis often require expert interpretation. In this communication, we present a panel of 17 short repeats (length 7-12bp) for sequence-based microsatellite instability (MSI) testing. Using a simple scoring procedure that incorporates the allelic distribution of the mutant repeats, and analysis of two cohort of tumours totalling 209 samples, we show that this panel is able to discriminate between MMR proficient and deficient tumours, even when constitutional DNA is not available. In the training cohort, the method achieved 100% concordance with fragment analysis, while in the testing cohort, 4 discordant samples were observed (corresponding to 97% concordance). Of these, 2 showed discrepancies between fragment analysis and immunohistochemistry and one was reclassified after re-testing using fragment analysis. These results indicate that our approach offers the option of a reliable, scalable routine test for MSI.

genomics↗