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Medina, R.

Publications and source records attributed to Medina, R..

15 recordsLinked to original sources
bioRxiv2026

Transient Vascular Cell Integration and Intrinsic Media-Stimulated Endothelial Activation Reveal Diabetic Retinopathy Signatures in Human Retinal Organoids

Retinal organoids (ROs) model human retinogenesis but remain avascular and lack immune components, limiting their utility for studying vascular retinopathies. We generated vascular organoids (VOrs) from human pluripotent stem cells and evaluated their integration into developing ROs. Dissociated VOr cells (day 12 or day 30) were seeded onto 2D retinal neuroepithelium before 3D transition, followed by long-term culture to day 210. VOr derived cells migrated into ROs and transiently persisted. V30 ROs preserved retinal lamination, major neuronal subtypes and light evoked retinal ganglion cell responses comparable to non vascularised controls, whereas media-only ROs cultured in proangiogenic conditions showed structural disorganisation and reduced neuronal survival. Single-cell RNA sequencing revealed an endogenous, inflammatory endothelial-like population with partial endothelial-to-mesenchymal features and a perivascular fibroblast-like cluster in pro-angiogenic media only RO controls. The endothelial-like cell cluster was significantly enriched for genes upregulated in human retinal endothelial cells exposed to high glucose, indicating a diabetic retinopathy like transcriptional state. Microglia like and border associated macrophage populations were present across all conditions, with developmental shifts in morphology and marker expression. Our findings define conditions under which vascular cells can be incorporated into human ROs without disrupting retinal architecture, while uncovering an intrinsic capacity for inflammatory endothelial activation that partially recapitulates diabetic retinopathy. This work advances the engineering of vascularised, immunocompetent retinal models and highlights endogenous vascular immune programmes that must be considered when modelling retinal disease in vitro.

neuroscience↗
bioRxiv2026

Single-molecule m6A profiling reveals position-dependent mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis

The maternal-to-zygotic transition (MZT) requires coordinated clearance and deadenylation of maternally deposited mRNAs, yet the underlying molecular mechanisms remain poorly understood. N6-methyladenosine (m6A) has emerged as a key regulator of maternal mRNA fate, but prior studies have relied on population-averaged short-read methods that cannot resolve modification state, poly(A) tail length, or isoform identity on the same molecule. Here, we employ nanopore direct RNA sequencing on zebrafish embryos across MZT to resolve the interplay between m6A deposition, mRNA clearance, and poly(A) tail length dynamics at single-molecule resolution. We find that 78% of expressed maternal genes harbor m6A-modified isoforms, significantly exceeding prior bulk estimates. Within-isoform comparisons demonstrate that m6A promotes mRNA decay, with CDS m6A contributing more to maternal mRNA clearance than 3-UTR m6A. The positional context of m6A alone is sufficient to determine the temporal regulation of poly(A) tail lengths. CDS m6A constitutively suppresses tail length throughout MZT, while 3'-UTR m6A acquires shortening activity only after zygotic genome activation (ZGA). Transcriptomic analysis of ythdf2 knockout embryos reveals two unrecognized roles. Ythdf2 stabilizes m6A-marked maternal transcripts to set stoichiometry at MZT onset, and is also responsible for maintaining global poly(A) tail homeostasis prior to ZGA through an m6A-independent mechanism. Together, these findings define the single-molecule logic by which m6A modifications shape transcript fate during vertebrate MZT.

developmental biology↗
bioRxiv2026

Oxidative Stress Susceptibility, Complement Dysregulation, and Metabolic Reprogramming in CFH Y402H Patient-Derived Choriocapillaris Endothelial Cells

Age-related macular degeneration (AMD) is a leading cause of central vision loss. Immunofluorescence and gene expression studies in human donor eyes have shown that choriocapillaris endothelial cells (CECs) are lost before retinal pigment epithelium (RPE) degeneration, leaving extracellular matrix-filled empty lumens known as "ghost vessels." To investigate disease mechanisms, we generated CECs from patient-specific induced pluripotent stem cells (iPSCs) carrying the high-risk CFH Y402H variant and CRISPR-Cas9-corrected isogenic controls. The iPSC-derived CECs expressed canonical endothelial markers, formed fenestrations, maintained barrier function, and assembled capillary-like structures. Although baseline metabolism was preserved, Y402H CECs showed heightened sensitivity to hydroquinone-induced oxidative stress, with increased cytotoxicity and deposition of the complement membrane attack complex (C5b-9). RNA sequencing revealed oxidative stress-driven upregulation of lipid biosynthesis, mTORC signalling, endothelial-to-mesenchymal transition, and angiogenic pathways, alongside an imbalance in the complement pathway. These findings demonstrate that the CFH Y402H polymorphism increases CEC vulnerability to environmental stress, linking complement dysregulation and metabolic reprogramming to choriocapillaris dysfunction in AMD and highlighting CECs as a potential therapeutic target.

Cell Biology↗
bioRxiv2024

SeqTagger, a rapid and accurate tool to demultiplex direct RNA nanopore sequencing datasets

Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding of multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, are not compatible with newer RNA chemistry flowcells and the latest-generation GPU cards. To overcome these limitations, we introduce SeqTagger, a rapid and robust method that can demultiplex direct RNA sequencing datasets with 99% precision and 95% recall. We demonstrate the applicability of SeqTagger in both RNA002/R9.4 and RNA004/RNA chemistries and show its robust performance both for long and short RNA libraries, including custom libraries that do not contain standard poly-(A) tails, such as Nano-tRNAseq libraries. Finally, we demonstrate that increasing the multiplexing up to 96 barcodes yields highly accurate demultiplexing models. SeqTagger can be executed in a standalone manner or through the MasterOfPores NextFlow workflow. The availability of an efficient and simple multiplexing strategy improves the cost-effectiveness of this technology and facilitates the analysis of low-input biological samples.

genomics↗
bioRxiv2024

Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures

Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 rRNA modifications. Previous works have shown that some rRNA modification types can be dynamically regulated; however, how and when the mammalian rRNA modification landscape is remodeled remains largely unexplored. Here, we employ direct RNA nanopore sequencing to chart the human and mouse rRNA epitranscriptome across tissues, developmental stages, cell types and disease. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner, including previously unannotated modified sites. We demonstrate that rRNA modification patterns can be used for tissue and cell type identification, which we hereby term epitranscriptomic fingerprinting. We then explore rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that epitranscriptomic fingerprinting accurately classifies clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers.

molecular biology↗
bioRxiv2024

Novel introductions of human-origin H3N2 Influenza viruses in Swine, Chile

Influenza A virus (IAV) continuously threatens animal and public health globally, with swine serving as a crucial reservoir for viral reassortment and evolution. In Chile, H1N2 and H3N2 subtypes were introduced in the swine population before the H1N1 2009 pandemic, and the H1N1 was introduced from the H1N1pdm09 by successive reverse zoonotic events. Here, we report two novel introductions of IAV H3N2 human-origin in Chilean swine during 2023. Our study reveals a closer relationship between recent human seasonal H3N2 and novel swine strains. Interestingly, one strain maintains all the genes from the original human virus, but the other strain is already a reassortment of human H3N2 and an H1N2 previously observed on the farm. Observing global IAV sequences, a similar pattern was identified in the USA confirming the reverse zoonotic potential of current seasonal human H3N2 strains. These results highlight the importance of ongoing surveillance and reinforce biosecurity in swine farms. These findings raise questions about their potential impact on viral dynamics in the swine population and public health, underscoring the need for further investigation into the origin and evolutionary dynamics of this emerging swine H3N2 reassortant virus.

microbiology↗
bioRxiv2023

De novo basecalling of m6A modifications at single molecule and single nucleotide resolution

RNA modifications hold pivotal roles in shaping the fate and function of RNA molecules. Although nanopore sequencing technologies have proven successful at transcriptome-wide detection of RNA modifications, current algorithms are limited to predicting modifications at a per-site level rather than within individual RNA molecules. Herein, we introduce m6ABasecaller, an innovative method enabling direct basecalling of m6A modifications from raw nanopore signals within individual RNA molecules. This approach facilitates de novo prediction of m6A modifications with precision down to the single nucleotide and single molecule levels, without the need of paired knockout or control conditions. Using the m6ABasecaller, we find that the median transcriptome-wide m6A modification stoichiometry is [~]10-15% in human, mouse and zebrafish. Furthermore, we show that m6A modifications affect polyA tail lengths, exhibit a propensity for co-occurrence within the same RNA molecules, and show relatively consistent stoichiometry levels across isoforms. We further validate the m6ABasecaller by treating mESC with increasing concentrations of STM2457, a METTL3 inhibitor as well as in inducible METTL3 knockout systems. Overall, this work demonstrates the feasibility de novo basecalling of m6A modifications, opening novel avenues for the application of nanopore sequencing to samples with limited RNA availability and for which control knockout conditions are unavailable, such as patient-derived samples.

molecular biology↗
bioRxiv2023

N6-methyladenosine modification is not a general trait of viral RNA genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with a high rate of false positives. Here, we addressed the presence of m6A in CHIKV and DENV RNAs. For this, we combined m6A-seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we found no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery did not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection had no effect on the m6A machinerys localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.

microbiology↗
bioRxiv2023

Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes.

Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sub-genome sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of P. eurystomum and of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. pyriforme, and P. sphaericum. Our findings demonstrate the utility of a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called homologizer, when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

evolutionary biology↗
bioRxiv2023

Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites

The biological relevance and dynamics of mRNA modifications have been extensively studied in the past few years, revealing their key roles in major cellular processes, such as cellular differentiation or sex determination. However, whether rRNA modifications are dynamically regulated, and under which conditions, remains largely unclear. Here, we performed a systematic characterization of bacterial rRNA modification dynamics upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant rRNA modification changes, we developed NanoConsensus, a novel pipeline that integrates the estimates from multiple RNA modification detection algorithms, predicting differentially modified rRNA sites with very low false positive rates and high replicability. We showed that NanoConsensus is robust across RNA modification types, stoichiometries and coverage, and outperforms all individual algorithms tested. Using this approach, we identified multiple rRNA modifications that are lost upon the presence of antibiotics, showing that rRNA modification profiles are altered in an antibiotic-specific manner. We found that significantly altered rRNA modified sites upon antibiotic exposure are located in the vicinity of the A and P-sites of the ribosome, possibly contributing to antibiotic resistance. We then systematically examined whether loss of antibiotic-sensitive rRNA modifications may be sufficient to confer antibiotic resistance, finding that depletion of some rRNA modification enzymes guiding dysregulated rRNA modifications confers increased antibiotic resistance. Altogether, our work reveals that rRNA modification profiles can be rapidly altered in response to environmental exposures, and that nanopore sequencing can accurately identify dysregulated rRNA modifications, contributing to the mechanistic dissection of antibiotic resistance. Moreover, we provide a novel, robust workflow to study rRNA modification dynamics in any species using nanopore sequencing in a scalable and reproducible manner.

microbiology↗
bioRxiv2020

Decoding ribosomal RNA modification dynamics at single molecule resolution

A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify and quantify RNA modifications present in native RNA molecules. First, we show that each RNA modification type results in a distinct and characteristic base-calling error signature, which we validate using a battery of genetic strains lacking either pseudouridine (Y) or 2-O-methylation (Nm) modifications. We then demonstrate the value of these signatures for de novo prediction of Y modifications transcriptome-wide, confirming known Y-modified sites as well as uncovering novel Y sites in mRNAs, ncRNAs and rRNAs, including a previously unreported Pus4-dependent Y modification in yeast mitochondrial rRNA, which we validate using orthogonal methods. To explore the dynamics of pseudouridylation across environmental stresses, we treat the cells with oxidative, cold and heat stresses, finding that yeast ribosomal rRNA modifications do not change upon environmental exposures, contrary to the general belief. By contrast, our method reveals many novel heat-sensitive Y-modified sites in snRNAs, snoRNAs and mRNAs, in addition to recovering previously reported sites. Finally, we develop a novel software, nanoRMS, which we show can estimate per-site modification stoichiometries from individual RNA molecules by identifying the reads with altered current intensity and trace profiles, and quantify the RNA modification stoichiometry changes between two conditions. Our work demonstrates that Y RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

molecular biology↗
bioRxiv2020

Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms in the 2014-15 influenza season

The 2014-15 influenza season saw the emergence of an H3N2 antigenic drift variant that formed the 3C.2a HA clade. Whole viral genomes were sequenced from nasopharyngeal swabs of 94 patients with confirmed influenza A virus infection and primary human nasal epithelial cell cultures used to efficiently isolate H3N2 viruses. The isolates were classified by HA clade and the presence of a new set of co-selected mutations in NA (a glycosylation site, NAg+) and PB1-F2 (H75P). The NA and PB1-F2 mutations were present in a subset of clade 3C.2a viruses (NAg+F2P) which dominated during the subsequent influenza seasons. In human nasal epithelial cell cultures, a virus with the novel NAg+F2P genotype replicated less well compared to a virus with the parental genotype. Retrospective analyses of clinical data showed that NAg+F2P genotype viruses were associated with increased cough and shortness of breath in infected patients.

microbiology↗
bioRxiv2018

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native upper respiratory tract (URT) microbiome likely plays a role, yet the effects of influenza infection on the URT microbiome are largely unknown. We performed a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable \"heathy ecostate\" communities both within and between individuals. In contrast, infected patients and ferrets exhibited large changes in bacterial community composition over time and between individuals. The \"unhealthy\" ecostates of infected individuals progressed towards the \"healthy ecostate\" over time, coinciding with viral clearance and recovery. Blooms of Pseudomonas were a statistically associated constant in the disturbed microbiomes of infected individuals. The dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.\n\nOne Sentence SummaryDynamics of the upper respiratory tract microbiome during influenza A virus infection

microbiology↗
bioRxiv2017

Neuronal Inhibition Of The Autophagy Nucleation Complex Extends Lifespan In Post-Reproductive C. elegans

Autophagy is a ubiquitous catabolic process, which causes cellular bulk degradation of cytoplasmic components and thereby regulates cellular homeostasis. Inactivation of autophagy has been linked with detrimental effects to cells and organisms. The antagonistic pleiotropy theory postulates that fitness promoting genes during youth are harmful during aging (Williams 1957). On this basis we examined genes mediating post-reproductive longevity using an RNA interference screen. From this screen we identified 30 novel regulators of post-reproductive longevity including pha-4. Through downstream analysis of pha-4 we identify that genes governing the early stages of autophagy up until the stage of vesicle nucleation, such as bec-1, strongly extend both lifespan and healthspan. Further, our data demonstrates that the improvements in health and longevity are mediated through the neurons - resulting in reduced neurodegeneration and sarcopenia. We propose that autophagy switches from advantageous to harmful in the context of an age-associated dysfunction.

molecular biology↗