Biology subjects

Tejada-Martinez, D.

Publications and source records attributed to Tejada-Martinez, D..

4 recordsLinked to original sources

bioRxiv2025

A CAR-T Cell-Based Strategy for Eliminating Pathogenic Microglia in ALS

Neurodegenerative diseases are defined by the propagation of neuroinflammation, driven in part by disease-associated microglia (DAM) that amplify inflammatory signaling and hasten neurodegeneration. Strategies to selectively eliminate DAM to attenuate disease progression remain elusive. Using existing datasets in combination with multiplexed immunofluorescence analysis of post-mortem ALS tissues, we identified the urokinase-type plasminogen activator receptor (uPAR) as a novel surface marker of DAM. uPAR protein is markedly elevated in IBA1/CD68 microglia within ALS-affected regions of both sporadic and familial cases, with negligible expression in unaffected areas or control tissues. These uPAR-high microglia drive neurite retraction in iPSC-derived neurons. To target these cells, we engineered 3rd-generation CAR-T cells expressing an anti-uPAR single-chain variable fragment, enabling specific recognition and elimination of uPAR-expressing microglia. Target specificity was assessed in human microglia C20 cells driven into a pathogenic state by poly(IC) or IFN{gamma} stimulation, which resulted in robust surface uPAR expression alongside phagocytic (CD68) and antigen-presenting (CD80) markers. uPAR-CAR-T cells induced antigen-dependent cytolysis of uPAR-high microglia, reducing their viability by over 80% while sparing resting microglia and neurons in a mixed culture system. These results position uPAR-directed CAR-T cells as a viable immunotherapeutic approach to selectively disrupt disease-amplifying microglial subsets and modify the trajectories of neuroinflammatory diseases. One Sentence SummaryCAR-T cells targeting uPAR selectively ablate pathogenic microglia while sparing neurons, enabling precision immunotherapy for ALS.

neuroscience↗

bioRxiv2022

Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells

Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where [~]3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that [~]750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in [~]3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks.

genomics↗

bioRxiv2021

Positive selection and enhancer evolution shaped lifespan and body mass in great apes

Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on ~1,550 genes previously described as tumor suppressors, oncogenes, ageing genes in addition to a novel Build of the CellAge database of cell-senescence genes (version 2), herein presented for the first time. Specifically, we analyzed dN/dS rates, positive selection, gene expression (RNA-seq) and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan and body mass we identified 67 genes that in primates co-evolved with those traits. Further, we identified 6 genes, important for immunity, neurodevelopment and telomere maintenance (including TERF2), under positive selection in the great ape ancestor. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that ~8% of the longevity genes are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel "ape-specific" enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus (SVAs). In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.

genomics↗

bioRxiv2019

A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease

Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses. We observed that genes promoting cell senescence tend to be overexpressed with age in human tissues and are also significantly overrepresented in anti-longevity and tumour-suppressor gene databases. By contrast, genes inhibiting cell senescence overlapped with pro-longevity genes and oncogenes. Furthermore, an evolutionary analysis revealed a strong conservation of senescence-associated genes in mammals, but not in invertebrates. Using the CellAge genes as seed nodes, we also built protein-protein interaction and co-expression networks. Clusters in the networks were enriched for cell cycle and immunological processes. Network topological parameters also revealed novel potential senescence-associated regulators. We then used siRNAs and observed that of 26 candidates tested, 19 induced markers of senescence. Overall, our work provides a new resource for researchers to study cell senescence and our systems biology analyses provide new insights and novel genes regarding cell senescence.

systems biology↗