Biology subjects

Martinez, N.

Publications and source records attributed to Martinez, N..

13 recordsLinked to original sources

bioRxiv2025

Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7

Pseudouridines are abundant mRNA modifications that can impact splicing, translation, and stability to tune gene expression. PUS7 is one of the major mRNA pseudouridine synthase whose dysregulation leads to neurodevelopmental disorders and cancer, underscoring the critical function of PUS7-dependent pseudouridines. Beyond a short and degenerate consensus sequence, the molecular mechanisms underlying PUS7-mediated pseudouridylation remain unknown. A lack of targeted, high-throughput pseudouridine detection methods limits simultaneous interrogation of PUS7 regulatory features across many experimental conditions. We developed novel Nanopore sequencing tools, including Nano-Mod-Amp, to reveal pseudouridine stoichiometry, its RNA structural context, and dependence on PUS7 levels at specific sites across biological conditions. We identified a novel RNA structural signature that is associated with more efficient mRNA modification by PUS7. Pseudouridines are largely responsive to modulations in PUS7 protein levels, demonstrating the regulatory potential of varying PUS7 levels across cellular conditions. Conversely, PUS7 activity is also regulated in a cell-type specific manner, independent of PUS7 expression levels in a manner consistent with regulation by RNA structure and RNA binding proteins. Together, we developed Nanopore sequencing tools and uncovered new mechanisms of PUS7 regulation with a framework that can be applied to other RNA-modifying enzymes to query the regulation of the epitranscriptome. HighlightsO_LINanopore direct RNA sequencing identifies PUS7-dependent pseudouridines with stoichiometry. C_LIO_LINano-Mod-Amp quantifies PUS7-dependent pseudouridines at hundreds of sites in high-throughput. C_LIO_LIMPRAs define RNA sequence and structural features associated with modification by PUS7. C_LIO_LIIndividual PUS7 target pseudouridines are substoichiometric and poised for regulation. C_LIO_LIPUS7 activity is regulated by cell type in the absence of differences in PUS7 protein levels. C_LI

molecular biology↗

bioRxiv2025

A Spatially Coordinated Keratinocyte-Fibroblast Circuit Recruits MMP9+ Myeloid Cells to Drive IFN-I-Driven Inflammation in Photosensitive Autoimmunity

Photosensitivity is a hallmark of cutaneous lupus erythematosus (CLE) and dermatomyositis (DM), yet the mechanisms linking ultraviolet B (UVB) exposure to tissue-specific autoimmunity remain incompletely defined. Here, we use an integrative human-based approach, including single-cell RNA sequencing, spatial transcriptomics (seqFISH+), in vivo UVB provocation, and in vitro modeling, to uncover a spatially coordinated inflammatory circuit that underlies interferon-I (IFN-I)-amplified skin pathology. We identify MMP9+ CD14+ myeloid cells as central effectors of photosensitivity in both CLE and DM. These cells are markedly expanded in lesional skin, serve as the dominant source of IFN-{beta}, and colocalize with cytotoxic CD4+ T cells at the dermal-epidermal junction. Spatial transcriptomics further reveals a keratinocyte-fibroblast-myeloid axis, wherein keratinocytes activate discrete subsets of pro-inflammatory fibroblasts in the superficial dermis to produce monocyte-attracting chemokines, including CCL2, CCL19, CCL7, CCL8, and CXCL12, directing MMP9+ CD14+ cell recruitment toward the interface. In our in-vitro model, IFN-I-primed basal keratinocytes undergo heightened UVB-induced cell death and release membrane-associated cytokines such as TNF-, IL-1, which activate monocyte-derived dendritic cells (moDCs) and induce transcriptional programs mirroring those of MMP9+ CD14+ cells in vivo. In vivo, UVB irradiation of non-lesional DM skin, but not healthy controls, elicits rapid infiltration of these myeloid cells, confirming their disease-specific responsiveness to UVB. Finally, in a proof-of-concept clinical study, treatment with anifrolumab (anti-IFN-I receptor) blocked UVB-induced MMP9+ CD14+ infiltration and attenuated photosensitivity in CLE. Together, these findings define a multicellular inflammatory cascade linking keratinocyte injury, fibroblast chemotactic programming, and myeloid effector function in IFN-I-driven skin autoimmunity and nominate MMP9+ CD14+ cells as actionable targets in photosensitive dermatoses. Photosensitivity is central to cutaneous lupus erythematosus (CLE) and dermatomyositis (DM), but the mechanisms linking UVB exposure to tissue-specific autoimmunity are poorly defined. Using single-cell RNA sequencing, spatial transcriptomics, UVB provocation, and in vitro modeling, we identify MMP9+ CD14+ myeloid cells as critical mediators of photosensitivity. These cells expand significantly in lesional skin, produce IFN-{beta}, and colocalize with cytotoxic CD4+ T cells at the dermal-epidermal junction. Keratinocytes activate fibroblasts in the superficial dermis, prompting them to release chemokines (CCL2, CCL19, CCL7, CCL8, CXCL12) that recruit MMP9+ CD14+ cells. IFN-I-primed keratinocytes exposed to UVB release cytokines activating dendritic cells, mirroring in vivo responses. UVB irradiation of non-lesional DM skin rapidly recruits these myeloid cells. In a clinical proof-of-concept study, anti-IFN-I treatment with anifrolumab prevented UVB-induced myeloid infiltration and reduced photosensitivity. Thus, targeting MMP9+ CD14+ cells may offer therapeutic potential for managing photosensitive autoimmune skin conditions.

immunology↗

bioRxiv2025

Taxonomic Diversity of Ants (Formicidae) in Forest Fragments of Tropical Dry Forest in Atlantico, Colombia

This study provides the first taxonomic diversity analysis of ants in the department of Atlantico, Colombia, documenting 6.75% of the countrys known ant species, 29.5% of its genera, and 63.3% of its subfamilies. We report the first record of Leptogenys volcanica in the Colombian Caribbean and expand the known distribution of 19 species within Atlantico. Our results show marked differences in species composition among forest fragments. El Morro exhibited the highest taxonomic distinctness (TD), supporting a community composed of more distantly related species. In contrast, Uninorte, an isolated urban fragment, had the lowest TD value, suggesting a more taxonomically clustered community and potentially acting as a diversity sink. Nesting values indicate that El Morro functions as a biodiversity reservoir, while the species composition of Los Charcones appears shaped by past land-use changes. The dominance of Myrmicinae and Formicinae aligns with patterns observed in other tropical dry forests. Although fragmentation was not directly assessed, patterns of alpha, beta, and taxonomic distinctness suggest that isolation and land use may influence community composition. El Morro emerges as a key fragment for regional conservation. Enhancing habitat connectivity could help mitigate biodiversity loss in these fragmented landscapes. This study provides a critical baseline for future research on ant ecology and conservation in the Caribbean region of Colombia.

ecology↗

bioRxiv2025

UCP1 Mitigates Hepatic Steatosis and Fibrosis Independent of Cold Exposure

Non-shivering thermogenesis by brown adipose tissue (BAT) is a promising target for anti-obesity therapies, making its regulatory mechanisms of significant translational interest. While cold-induced BAT thermogenesis (CIT) is well characterized, certain high-calorie diets can also activate BAT in the absence of cold, a process known as diet-induced thermogenesis (DIT). Despite its potential relevance to modern human diets and lifestyles, the mechanisms and physiological relevance underlying DIT remain poorly understood. Here, we show that DIT reduces adiposity and protects against hepatic steatosis and fibrosis in males but not female mice. Moreover, adipose tissue-specific ablation of uncoupling protein 1 (UCP1) reveals that BAT is the primary mediator of DIT but that non-adipocyte UCP1 also contributes to body weight regulation. Transcriptome analysis suggests that DIT is triggered by intrinsic metabolic stress, distinguishing it from CIT, which is driven by sympathetic tone. Finally, BAT-specific arteriovenous metabolomics identifies glucose as the predominant circulating fuel for DIT. These findings uncover distinct molecular and metabolic features of DIT, highlighting opportunities to harness BAT activity for treating obesity and metabolic diseases without requiring cold exposure.

physiology↗

bioRxiv2025

Demographic history explains mitochondrial genome capture and mitonuclear discordance among South American collared Tropidurus lizards

Mitonuclear discordance--evolutionary discrepancies between mitochondrial and nuclear DNA phylogenies--can arise from various factors, including introgression, incomplete lineage sorting, recent or ancient demographic fluctuations, sex-biased dispersal asymmetries, among others. Understanding this phenomenon is crucial for accurately reconstructing evolutionary histories, as failing to account for discordance can lead to misinterpretations of species boundaries, phylogenetic relationships, and historical biogeographic patterns. We investigate the evolutionary drivers of mitonuclear discordance in the Tropidurus spinulosus species group, which contains nine species of lizards inhabiting open tropical and subtropical environments in South America. Using a combination of population genetic and phylogenomic approaches applied to mitochondrial and nuclear data, we identified different instances of gene flow that occurred in ancestral lineages of extant species. Our results point to a complex evolutionary history marked by prolonged isolation between species, demographic fluctuations, and potential episodes of secondary contact with genetic admixture. These conditions likely facilitated mitochondrial genome capture while diluting signals of nuclear introgression. Furthermore, we found no strong evidence supporting incomplete lineage sorting or natural selection as primary drivers of the observed mitonuclear discordance. Therefore, the unveiled patterns are most consistent with neutral demographic processes, coupled with ancient mitochondrial introgression, as the main factors underlying the mismatch between nuclear and mitochondrial phylogenies in this system. Future research could further explore the role of other demographic processes, such as asymmetric sex-biased dispersal, in shaping these complex evolutionary patterns.

genomics↗

bioRxiv2025

Chalcogen derivatives for the treatment of African trypanosomiasis: biological evaluation of thio and seleno- semicarbazones and their azole derivatives

Human African Trypanosomiasis (HAT) is caused by Trypanosoma brucei. Drug therapy remains challenging due to drug resistance and/or toxicity. New drugs are needed. Using thiosemicarbazones as a starting point, we employed a S to Se isosteric replacement strategy to design 44 analogs which were evaluated against T. brucei in vitro. Compounds were divided into eleven groups of four derivatives corresponding to thio-, selenosemicarbazones, and their cyclic counterparts, thio- and selenazoles. We selected three groups which contained a total of six derivatives that inhibited parasite growth by >70%. Then, we investigated the mechanism of action of these compounds, performing quantitative assays to measure their inhibition of the T. brucei cathepsin L-like protease (TbrCATL) and DPPH antioxidant activities. The lead compound (SeO3) showed antioxidant capacity and the best activity against T. brucei (EC50 = 0.47 {micro}M). Nevertheless, its toxicity should be improved. We also predicted the interactions of these compounds with TbrCATL utilizing molecular dynamics. We demonstrate that the Se derivatives are more active than their S analogues, and that the selenazole ring decreases Se-associated toxicity. Also, thio- and selenosemicarbazones are more potent against TbrCATL than the cyclic derivatives. We conclude that TbrCATL inhibition should be combined with antioxidant activity to obtain active compounds against T. brucei.

microbiology↗

bioRxiv2023

Recombinant chimeric Horsepox Virus (TNX-801) is attenuated relative to Vaccinia Virus Strains in Human Primary Cell Lines and in Immunocompromised Mice

Recombinant chimeric Horsepox virus (TNX-801) is a preclinical vaccine in development against Monkeypox and smallpox. In this brief report, we investigated the potential phenotypic differences in in vitro and in vivo models between TNX-801 and older VACV-based vaccine strains (VACV-IHD, VACV-Lis, VACV-NYC) used in the eradication of smallpox virus. TNX-801 displayed a small plaque phenotype ([~]1-2 mm) in both BSC-40 and Vero-E6 cells and yielded >10- to 100-fold lower infectious titers than the VACV strains in multiple-step replication kinetics. Growth kinetics in primary human cell lines from two main routes of poxvirus transmission, respiratory and dermal tracts, yielded [~]10- to 119-fold lower infectious titers of TNX-801. Intranasal infection of immunocompromised mice (C56BL/6 Ifnar-/-/Ifngr-/-) with VACV strains at 6.0 and 5.0 log10 PFU produced uniform lethal disease. In contrast, TNX-801 at 8.0 log10 PFU was unable to produce any clinical disease in mice. These data demonstrate that TNX-801 is >10- to 1,000-fold more attenuated than older VACV-based smallpox vaccines in human primary cell lines and immunocompromised mice.

microbiology↗

bioRxiv2023

Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans

We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster. In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.

evolutionary biology↗

bioRxiv2022

Growth hormone remodels the 3D-structure of the mitochondria of inflammatory macrophages and promotes metabolic reprogramming

Macrophages are a heterogeneous population of innate immune cells that support tissue homeostasis through their involvement in tissue development and repair, and pathogen defense. Emerging data reveal that metabolism may control macrophage polarization and function and, conversely, phenotypic polarization may drive metabolic reprogramming. Here, using biochemical analysis, correlative cryogenic fluorescence microscopy and cryo-focused ion-beam scanning electron microscopy, we demonstrate that growth hormone (GH) functions as a metabolic modulator to reprogram inflammatory GM-CSF-primed monocyte-derived macrophages (GM-MO). We found that exogenous treatment of GM-MO with recombinant human GH suppressed glycolysis, lactate production and non-mitochondrial respiration, and enhanced mitochondrial oxidative phosphorylation. Likewise, GH treatment augmented mitochondrial volume and altered mitochondrial dynamics, including the remodeling of the inner membrane to increase the density of cristae. Our data demonstrate that GH likely serves a modulatory role in the metabolism of inflammatory macrophages and suggest that metabolic reprogramming of macrophages should be considered a new target to intervene in multiple inflammatory diseases.

immunology↗

bioRxiv2021

ImPartial: Partial Annotations for Cell Instance Segmentation

Segmenting noisy multiplex spatial tissue images constitutes a challenging task, since the characteristics of both the noise and the biology being imaged differs significantly across tissues and modalities; this is compounded by the high monetary and time costs associated with manual annotations. It is therefore imperative to build algorithms that can accurately segment the noisy images based on a small number of annotations. Recently techniques to derive such an algorithm from a few scribbled annotations have been proposed, mostly relying on the refinement and estimation of pseudo-labels. Other techniques leverage the success of self-supervised denoising as a parallel task to potentially improve the segmentation objective when few annotations are available. In this paper, we propose a method that augments the segmentation objective via self-supervised multi-channel quantized imputation, meaning that each class of the segmentation objective can be characterized by a mixture of distributions. This approach leverages the observation that perfect pixel-wise reconstruction or denoising of the image is not needed for accurate segmentation, and introduces a self-supervised classification objective that better aligns with the overall segmentation goal. We demonstrate the superior performance of our approach for a variety of cancer datasets acquired with different highly-multiplexed imaging modalities in real clinical settings. Code for our method along with a benchmarking dataset is available at https://github.com/natalialmg/ImPartial.

bioengineering↗

bioRxiv2020

Interrogation of SLFN11 in pediatric sarcomas uncovers an unexpected biological role and a novel therapeutic approach to overcoming resistance to replicative stress

Pediatric sarcomas represent a heterogeneous group of malignancies that exhibit variable response to DNA damaging chemotherapy. Schlafen family member 11 protein (SLFN11) increases sensitivity to replicative stress, and SLFN11 gene silencing has been implicated as a common mechanism of drug resistance in tumors in adults. We found SLFN11 to be widely expressed in our cohort of pediatric sarcomas. In sarcoma cell lines, protein expression strongly correlated with response to the PARP inhibitor talazoparib (TAL) and the topoisomerase I inhibitor irinotecan (IRN), with SLFN11 knockout resulting in significant loss of sensitivity in vitro and in vivo. However, SLFN11 expression was not associated with favorable outcomes in a retrospective analysis of our patient cohort; instead, the protein was retained and promoted tumor growth and evasion. Furthermore, we show that pediatric sarcomas develop resistance to TAL and IRN through impaired intrinsic apoptosis, and that resistance can be reversed by selective inhibition of BCL-XL. Statement of SignificanceThe role of SLFN11 in pediatric sarcomas has not been thoroughly explored. In contrast to its activity in adult tumors, SLFN11 did not predict favorable outcomes in pediatric patients, was not silenced, and promoted tumor growth. Resistance to replicative stress in SLFN11-expressing sarcomas was reversed by selective inhibition of BCL-XL.

cancer biology↗

bioRxiv2020

Metformin enhances anti-mycobacterial responses by educating immunometabolic circuits of CD8+ T cells

Diabetic patients taking metformin have lower risk for Mycobacterium tuberculosis (Mtb) infection, progression from infection to tuberculosis (TB) disease, TB morality and TB recurrence. However, a detailed mechanistic understanding of metformins protective immunological benefits on host resistance to TB is lacking. In this study, using mass cytometry we show that metformin treatment expands memory-like antigen-inexperienced CD8+CXCR3+ T cells in naive mice, and in healthy and diabetic humans. Metformin-educated CD8+ T cells have increased (i) mitochondrial mass, oxidative phosphorylation, and fatty acid oxidation; (ii) survival capacity; and (iii) anti-mycobacterial properties. CD8+ T cells from CXCR3-/- mice did not exhibit metformin-mediated metabolic programming. In BCG-vaccinated mice and guinea pigs, metformin enhanced immunogenicity and protective efficacy against Mtb challenge. Collectively, our results demonstrate an important role of CD8+ T cells in metformin-derived host metabolic-fitness towards Mtb infection.

immunology↗

bioRxiv2018

Active Learning of Cortical Connectivity from Two-Photon Imaging Data

Understanding how groups of neurons interact within a network is a fundamental question in system neuroscience. Instead of passively observing the ongoing activity of a network, we can typically perturb its activity, either by external sensory stimulation or directly via techniques such as two-photon optogenetics. A natural question is how to use such perturbations to identify the connectivity of the network efficiently. Here we introduce a method to infer sparse connectivity graphs from in-vivo, two-photon imaging of population activity in response to external stimuli. A novel aspect of the work is the introduction of a recommended distribution, incrementally learned from the data, to optimally refine the inferred network.. Unlike existing system identification techniques, this \"active learning\" method automatically focuses its attention on key undiscovered areas of the network, instead of targeting global uncertainty indicators like parameter variance. We show how active learning leads to faster inference while, at the same time, provides confidence intervals for the network parameters. We present simulations on artificial small-world networks to validate the methods and apply the method to real data. Analysis of frequency of motifs recovered show that cortical networks are consistent with a small-world topology model.

neuroscience↗