Biology subjects

Martinez-Jimenez, C. P.

Publications and source records attributed to Martinez-Jimenez, C. P..

8 recordsLinked to original sources

bioRxiv2026

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

Current circadian omics analysis tools have been developed primarily for bulk time-series. However, heterogeneous single-cell datasets require analysis and interpretation of rhythmic programs across different cells, cell types, and biological conditions. In these datasets, cellular circadian phase is usually unobserved, and sample-level zeitgeber time provides temporal information but does not define the exact phase of every cell. Existing methods address only selected aspects of this problem and do not model how cell-level phase evidence informs gene-level rhythmic parameters and rhythm-state remodeling. Here we present scRhythmBayes, a new probabilistic algorithm for phase-resolved circadian analysis in heterogeneous single-cell transcriptomes. scRhythmBayes combines a seed-gene count likelihood with a stratum-aware circular prior to infer cell-level circadian phase, incorporates phase support into gene-level rhythmic modeling, and assigns posterior probabilities to interpretable rhythm-state categories, including rhythm gain, rhythm loss, amplitude remodeling and phase shifts. In heterogeneous simulations, scRhythmBayes achieved higher phase-recovery accuracy than existing phase-inference methods and maintained balanced performance across rhythmic gene detection, parameter recovery, and rhythm-state classification. Stress tests defined practical requirements for seed-gene support, zeitgeber anchoring, temporal sampling density, and cell number. In mouse liver, scRhythmBayes revealed distinct circadian phase occupancy and rhythm-state organization between periportal and pericentral hepatocytes, supporting a temporal dimension of liver zonation. It also identified cell-type-specific rhythmic markers that were largely distinct from conventional static markers, indicating that cellular identity includes temporal programs not captured by average expression. In human heart disease data, phase-coordination and phase-distribution analyses identified cell-type-selective temporal disorganization rather than uniform circadian disruption across the tissue. scRhythmBayes therefore provides a statistically grounded approach for resolving circadian organization across cells, genes, cell types and biological conditions.

bioinformatics↗

bioRxiv2024

Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability

The histone methylase Setdb1 plays a pivotal role in embryonic stem cell maintenance and developmental lineage specification. However, its function in adult stem cells remains elusive. Here we show that conditional inactivation of Setdb1 in Lgr5+ intestinal stem cells alters the transcriptional programs of the progeny cell types and results in increased cell-to-cell transcriptional variability. Loss of Setdb1 blocked differentiation towards the absorptive enterocyte lineage, while the secretory cell types were only marginally affected due to the activation of alternative developmental trajectories. Setdb1 inactivation did not affect global H3K9 methylation at large heterochromatin domains but led to altered distribution of transposase-accessible chromatin regions, aberrant exposure of transcription factor binding sites and premature activation of differentiation-specific genes. The results demonstrate that Setdb1 regulates intestinal stem cell differentiation by fine-tuning chromatin accessibility in open euchromatin regions thereby controlling transcriptional variability between cells.

cell biology↗

bioRxiv2022

Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue

In this study, we present a multiplexed version of deterministic barcoding in tissue (xDbit) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 mx50 m. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. Furthermore, the introduction of alignment markers allows seamless registration of images and spatial transcriptomic spot coordinates. Together with technological advances, we provide an open-source computational pipeline to transform raw sequencing data from xDbit experiments into the AnnData format. The functionality of xDbit was demonstrated by the acquisition of 18 spatially resolved transcriptomic datasets from five different murine organs, including cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of xDbit spatial transcriptomes allowed for in-depth characterization of the murine kidney.

genomics↗

bioRxiv2022

Coupling of oxytocin and cholecystokinin pathways in the hypothalamus is required for gut-to-brain homeostatic feeding control

Oxytocin-expressing paraventricular hypothalamic neurons (PVNOT neurons) integrate afferent signals from the gut including cholecystokinin (CCK) to adjust whole-body energy homeostasis. However, the molecular underpinnings by which PVNOT neurons orchestrate gut-to-brain feeding control remain unclear. Here, we show that mice undergoing selective ablation of PVNOT neurons fail to reduce food intake in response to CCK and develop hyperphagic obesity on chow diet. Notably, exposing wildtype mice to a high-fat/high-sugar (HFHS) diet recapitulates this insensitivity towards CCK, which is linked to diet-induced transcriptional and electrophysiological aberrations specifically in PVNOT neurons. Restoring OT pathways in DIO mice via chemogenetics or polypharmacology sufficiently re-establishes CCKs anorexigenic effects. Lastly, by single-cell profiling, we identify a specialized PVNOT neuronal subpopulation with increased {kappa}-opioid signaling under HFHS diet, which restrains their CCK-evoked activation. In sum, we here document a novel (patho)mechanism by which PVNOT signaling uncouples a gut-brain satiation pathway under obesogenic conditions.

neuroscience↗

bioRxiv2022

Single-cell metabolic profiling reveals subgroups of primary human hepatocytes showing heterogeneous responses to drug challenge.

Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes (PHHs) are the gold standard model for the assessment of drug efficacy, safety and toxicity in the early phases of drug development. Recent advances in single-cell genomics have shown liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. Here, we investigate the metabolic capacity of individual human hepatocytes in vitro, and assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. A phenotyping five-probe cocktail was used to identify four functional subgroups of hepatocytes that respond differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminished the drug-related metabolic capacity of hepatocytes. Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups lead to different and heterogeneous transcriptional responses.

cell biology↗

bioRxiv2021

Hepatocyte-specific activity of TSC22D4 triggers progressive NAFLD by impairing mitochondrial function

ObjectiveFibrotic organ responses have recently been identified as long-term complication in diabetes. Indeed, insulin resistance and aberrant hepatic lipid accumulation represent driving features of progressive non-alcoholic fatty liver disease (NAFLD), ranging from simple steatosis and non-alcoholic steatohepatitis (NASH) to fibrosis. Effective pharmacological regimens to stop progressive liver disease are still lacking to-date. MethodsBased on our previous discovery of transforming growth factor beta-like stimulated clone (TSC)22D4 as a key driver of insulin resistance and glucose intolerance in obesity and type 2 diabetes, we generated a TSC22D4-hepatocyte specific knockout line (TSC22D4-HepaKO) and exposed mice to control or NASH diet models. Mechanistic insights were generated by metabolic phenotyping and single cell liver sequencing. ResultsHepatic TSC22D4 expression was significantly correlated with markers of liver disease progression and fibrosis in both murine and human livers. Indeed, hepatic TSC22D4 levels were elevated in human NASH patients as well as in several murine NASH models. Specific genetic deletion of TSC22D4 in hepatocytes led to reduced liver lipid accumulation, improvements in steatosis and inflammation scores and decreased apoptosis in mice. Single cell RNA sequencing revealed a distinct gene signature identifying an upregulation of mitochondrial-related processes. An enrichment of genes involved in the TCA cycle, mitochondrial organization, and triglyceride metabolism underscored the hepatocyte-protective phenotype and overall decreased liver damage as seen in mouse models. ConclusionsTogether, our data uncover a new connection between targeted depletion of TSC22D4 and intrinsic metabolic processes in progressive liver disease. Cell-specific reduction of TSC22D4 improves hepatic steatosis, inflammation and promotes hepatocyte survival thus paving the way for further preclinical therapy developments.

physiology↗

bioRxiv2018

Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

How age-associated decline of immune function leads to increased cancer incidence is poorly understood. Here, we have characterized the cellular composition of the{gamma}{delta} T cell pool in peripheral lymph nodes (pLNs) upon ageing. We found that ageing has minimal cell-intrinsic effects on function and global gene expression of{gamma}{delta} T cells, and TCR{gamma}{delta} diversity remained stable. However, ageing altered TCR{delta} chain usage and clonal structure of{gamma}{delta} T cell subsets. Importantly, IL-17-producing{gamma}{delta} 17 T cells dominated the{gamma}{delta} T cell pool of aged mice - mainly due to the selective expansion of V{gamma}6+{gamma}{delta} 17 T cells and augmented{gamma}{delta} 17-polarisation of V{gamma}4+ T cells. Expansion of the{gamma}{delta} 17 T cell compartment was supported by increased Interleukin-7 expression in the T cell zone of old mice. In a Lewis lung cancer model, pro-tumourigenic V{gamma}6+{gamma}{delta}17 T cells were exclusively activated in the tumour-draining LN and their infiltration into the tumour correlated with increased tumour size in aged mice. Thus, upon ageing, substantial compositional changes of{gamma}{delta} T cell pool in a dysregulated pLN microenvironment promote tumour growth.

immunology↗

bioRxiv2018

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

Understanding male fertility requires an in-depth characterisation of spermatogenesis, the developmental process by which male gametes are generated. Spermatogenesis occurs continuously throughout a males reproductive window and involves a complex sequence of developmental steps, both of which make this process difficult to decipher at the molecular level. To overcome this, we transcriptionally profiled single cells from multiple distinct stages during the first wave of spermatogenesis, where the most mature germ cell type is known. This naturally enriches for spermatogonia and somatic cell types present at very low frequencies in adult testes. Our atlas, available as a shiny app (https://marionilab.cruk.cam.ac.uk/SpermatoShiny), allowed us to reconstruct the three main processes of spermatogenesis: spermatogonial differentiation, meiosis, and spermiogenesis. Additionally, we profiled the chromatin changes associated with meiotic silencing of the X chromosome, revealing a set of genes specifically and strongly repressed by H3K9me3 in the spermatocyte stage, but which escape post-meiotic silencing in spermatids.

developmental biology↗