Biology subjects

Lopez, F.

Publications and source records attributed to Lopez, F..

10 recordsLinked to original sources

bioRxiv2026

Sustained epigenetic rejuvenation of serially engrafting human iPSC-derived HSCs

Hematopoietic stem cell (HSC) function declines with age, contributing to immunosenescence and inferior transplantation outcomes. Here, we generated iPSC-derived HSCs (iHSCs) from multiple adult donors and performed integrated epigenetic, transcriptional, telomeric, and functional analyses to see if they retain youthful identity across differentiation and serial transplantation. Longitudinal DNA methylation profiling revealed that, independent of donor age, epigenetic age was reset to near zero in iPSCs and remained under seven years across differentiation and transplantation. In contrast, hematopoietic identity was established through a two-phase process: directional remodeling during in vitro differentiation extinguished pluripotency programs and initiated hematopoietic regulatory networks, while long-term engraftment was associated with a second wave of promoter methylation differences that converged toward primary adult HSCs. Notably, methylation at age-associated sites and global entropy remained stable across both phases, and single-cell telomere analysis demonstrated restoration of telomere length in iHSCs compared to primary adult HSCs. Youthful epigenetic features were maintained through secondary transplantation. These findings demonstrate that long-term HSC identity can be achieved independently of epigenetic aging and establish a framework for evaluating rejuvenated stem cell-derived grafts in regenerative medicine.

cell biology↗

bioRxiv2026

PATIENT-DERIVED ORGANOIDS CAPTURE HISTOLOGICAL, MOLECULAR AND THERAPEUTIC HETEROGENEITY IN PHARYNGEAL AND LARYNGEAL SQUAMOUS CELL CARCINOMAS

BackgroundHead and neck squamous cell carcinoma (HNSCC) comprises a heterogeneous group of epithelial malignancies associated with poor survival ({approx}50%), limited therapeutic options, and a lack of predictive biomarkers. Concurrent chemoradiotherapy (CRT) remains the standard treatment for advanced disease; however, many patients fail to respond, develop resistance, or eventually relapse. The development of three-dimensional organoid technology has enabled the generation of patient-derived organoids (PDOs), offering a promising platform for personalized therapeutic testing. MethodsWe established a biobank of HNSCC PDOs from fresh laryngeal and pharyngeal tumor samples, including human papillomavirus-positive (HPV+) cases. Organoid formation and expansion rates were analyzed in relation to clinical parameters. Selected representative PDOs were histologically and molecularly characterized. Additionally, several models were exposed to cisplatin and radiation to evaluate treatment response, and a subset was assessed for tumorigenicity in subcutaneous mouse models. ResultsFifty-seven PDO models were successfully established, long-term expanded, and cryopreserved. Prior chemotherapy and/or radiotherapy was identified as an independent negative predictor of organoid outgrowth and expansion capacity compared with treatment-naive samples. Histological features, including differentiation grade and immunohistochemical markers, were largely preserved and strongly correlated with the original tumors. PDOs displayed heterogeneous responses to cisplatin and radiotherapy, with HPV-positive models showing greater sensitivity, consistent with clinical observations. Global transcriptomic profiling revealed molecular subtypes concordant with established HNSCC classifications and suggested an additional subtype characterized by low MYC and mTORC1 transcriptional activity. ConclusionHNSCC PDOs faithfully recapitulate tumor histology and molecular diversity, providing a robust platform to investigate tumor biology and therapeutic response.

cancer biology↗

bioRxiv2023

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

Extension of prostate cancer beyond the primary site into the surrounding organs by local invasion or nodal metastasis is associated with poor prognosis. The emergence and evolution of cancer clones at this early stage of expansion and spread has not been studied in detail. We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Using cancer cell fractions computed from single nucleotide variants and copy number alterations, we reconstructed the tumour phylogenies, which in turn allowed us to infer key molecular steps in the progression of prostate cancer in these individuals. We mapped the clonal composition of cancer sampled across the prostate in each individual and inferred the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes. Based on these data, we delineated the route of tumour progression and metastasis following the transformation of adenocarcinoma to amphicrine morphology, the molecular events leading to whole genome duplication associated with a single clonal expansion and identified putative driver events associated with local invasion and lymph node metastasis. We also correlated genomic changes associated with differences in morphology and identified putative driver events associated with spread to seminal vesicle invasion and lymph node metastasis. Taken together, these findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes associated with morphological transformation. Our results demonstrate the value of integrating multi-region sequencing with histopathological data to study tumour evolution and identify mechanisms of prostate cancer spread.

cancer biology↗

bioRxiv2022

Single-cell Spatial Explorer: Easy exploration of spatial and multimodal transcriptomics

The development of single cell technologies yields large datasets of informations as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called spatial transcriptomics. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 6 human and murine tissues datasets.

bioinformatics↗

bioRxiv2021

Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single cell resolution

Early hematopoiesis is a continuous process in which hematopoietic stem and progenitor cells (HSPCs) gradually differentiate toward specific lineages. Aging and myeloid malignant transformation are characterized by changes in the composition and regulation of HSPCs. In this study, we used single cell RNA sequencing (scRNAseq) to characterize an enriched population of human hematopoietic stem and progenitor cells (HSPC) obtained from young and elderly healthy individuals. Based on their transcriptional profile, we identified changes in the proportions of progenitor compartments during aging, and differences in their functionality, as evidenced by gene set enrichment analysis. Trajectory inference revealed that altered gene expression dynamics accompanied cell differentiation, which could explain age-associated changes in hematopoiesis. Next, we focused on key regulators of transcription by constructing gene regulatory networks and detected regulons that were specifically active in elderly individuals. Using previous findings in healthy cells as a reference, we analyzed scRNA-seq data obtained from patients with myelodysplastic syndrome (MDS) and detected specific alterations of the expression dynamics of genes involved in erythroid differentiation in all patients with MDS such as TRIB2. In addition, the comparison between transcriptional programs and GRN regulating normal HSPCs and MDS HSPCs allowed identification of regulons that were specifically active in MDS cases such as SMAD1, HOXA6, POU2F2 and RUNX1 suggesting a role of these TF in the pathogenesis of the disease. In summary, we demonstrate that the combination of single cell technologies with computational analysis tools enable the study of a variety of cellular mechanisms involved in early hematopoiesis and can be used to dissect perturbed differentiation trajectories associated with aging and malignant transformation. Furthermore, the identification of abnormal regulatory mechanisms associated with myeloid malignancies could be exploited for personalized therapeutic approaches in individual patients.

genomics↗

bioRxiv2020

Geographic heterogeneity in Anopheles albimanus microbiota is lost within one generation of laboratory colonization

BackgroundResearch on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-collected mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings. MethodsUsing high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1 progeny of wild-caught adult Anopheles albimanus from four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed. ResultsResults showed geographical heterogeneity in both F1 larval internal (p=0.001; pseudo-F = 9.53) and cuticle surface (p=0.001; pseudo-F = 8.51) microbiota, and only F1 adult cuticle surface (p=0.001; pseudo-F = 4.5) microbiota, with a more homogenous adult internal microbiota (p=0.12; pseudo-F = 1.6) across collection sites. Overall, ASVs assigned to Leucobacter, Thorsellia, Chryseobacterium and uncharacterized Enterobacteriaceae, dominated F1 larval internal microbiota, while Acidovorax, Paucibacter, and uncharacterized Comamonadaceae, dominated the larval cuticle surface. F1 adults comprised a less diverse microbiota compared to larvae, with ASVs assigned to the genus Asaia dominating both internal and cuticle surface microbiota, and constituting at least 70% of taxa in each microbial niche. ConclusionsThese results suggest that location-specific heterogeneity in filed mosquito microbiota can be transferred to F1 progeny under normal laboratory conditions, but this may not last beyond the F1 larval stage without adjustments to maintain field-derived microbiota. Our findings provide the first comprehensive characterization of laboratory-colonized F1 An. albimanus progeny from field-derived mothers. This provides a background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.

microbiology↗

bioRxiv2020

The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors

Toll like receptors are key players in the innate immune system. Recent studies have suggested that they may impact the growth of pancreatic cancer, a disease with no cure. Among them, Toll like receptor-7 shows promise for therapy but may also promote tumor growth. Thus, we aimed to better understand the mechanism of action of Toll like receptor-7 ligands in pancreatic cancer, to open the door for clinical applications. In vitro, Toll like receptor-7 ligands strongly inhibit the proliferation and induce cell death by apoptosis of pancreatic cancer cells. In vivo, while Toll like receptor-7 agonists significantly delay the growth of aggressive tumors engrafted in immunodeficient mice, they instead surprisingly promote tumor growth and accelerate animal death in immunocompetent models. Molecular investigations revealed that Toll like receptor-7 agonists strongly increase the number of tumor-promoting macrophages to drive pancreatic tumorigenesis in immunocompetent mice. This is in stark contrast with Toll like receptor-7 ligands great potential to inhibit pancreatic cancer cell proliferation in vitro and tumor growth in vivo in immunosuppressed models. Collectively, our findings shine a light on the duality of action of Toll like receptor-7 agonists in experimental cancer models, and calls into question their use for pancreatic cancer therapy.

cancer biology↗

bioRxiv2019

Co-occurrence of kdr mutations V1016I and F1534C in pyrethroid-resistant Aedes aegypti (Diptera: Culicidae) populations from Costa Rica

Aedes aegypti (Linnaeus, 1762) is considered the most important mosquito vector species for several arboviruses (e.g., dengue, chikungunya, Zika) in Costa Rica. The main strategy for the control and prevention of Aedes-borne diseases relies on insecticide-based vector control. However, the emergence of insecticide resistance in the mosquito populations present a big threat for the prevention actions. The characterization of the mechanisms driving the insecticide resistance in Ae. aegypti are vital for decision making in vector control programs. Therefore, we analyzed the voltage-gated sodium channel gene for the presence of the V1016I and F1534C kdr mutations in pyrethroid-resistant Ae. aegypti populations from Puntarenas and Limon provinces, Costa Rica. The CDC bottle bioassays showed that both Costa Rican Ae. aegypti populations were resistant to permethrin and deltamethrin. In the case of kdr genotyping, results revealed the co-occurrence of V1016I and F1534C mutations in permethrin and deltamethrin-resistant populations, as well as the fixation of the 1534C allele. Therefore, our findings make an urgent call to expand the knowledge about the insecticide resistance status and mechanisms in the Costa Rican populations of Ae. aegypti which must be a priority to develop an effective resistance management plan.

genetics↗

bioRxiv2019

Pyrethroid exposure alters Anopheles albimanus microbiota and resistant mosquitoes harbor more insecticide-metabolizing bacteria

A deeper understanding of the mechanisms underlying insecticide resistance is needed to mitigate its threat to malaria vector control. Building upon our earlier identified associations between mosquito microbiota and insecticide resistance, we demonstrate for the first time, type-specific effects of pyrethroid exposure on internal and cuticle surface bacteria in adult progeny of field-collected Anopheles albimanus. In contrast, larval cuticle surface--but not internal--bacteria were affected by pyrethroid exposure. Being over five-folds more abundant in pyrethroid resistant adults, as compared to susceptible or non-insecticide-exposed mosquitoes, Klebsiella (alphacypermethrin), Pantoea and Asaia (permethrin) were identified as potential markers of pyrethroid resistance in An. albimanus. We also show for the first time that An. albimanus larvae and adult cuticles harbor more diverse bacterial communities than their internal microbial niches. Our findings indicate insecticide selection pressures on mosquito microbiota, and support the hypothesis of an undescribed microbe-mediated mechanism of insecticide metabolism in mosquitoes.

microbiology↗

bioRxiv2019

High prevalence and diversity of Extended-Spectrum β-Lactamase and emergence of Carbapenemase producing Enterobacteriaceae spp in wildlife in Catalonia

In wildlife, most of the studies focused on antimicrobial resistance (AMR) describe Escherichia coli as the principal indicator of the selective pressure. In the present study, new species of Enterobacteriaceae with a large panel of cephalosporin resistant (CR) genes have been isolated from wildlife in Catalonia. A total of 307 wild animals were examined to determine CR enterobacteria prevalence, AMR phenotypes and common carbapenem and CR gene expression. The overall prevalence of CR-phenotype was 13% (40/307): 17.3% in wild mammals (18/104) and 11.5% in wild birds (22/191) (p<0.01)). Hedgehogs presented the largest prevalence with 13.5% (14/104) of the mammal specimens, followed by raptors with 7.3% (14/191) of the total bird specimens. Although CR E. coli was obtained most frequently (45%), other CR-Enterobacteriaceae spp like Klebsiella pneumoniae (20%), Citrobacter freundii (15%), Enterobacter cloacae (5%), Proteus mirabilis (5%), Providencia spp (5%) and Serratia marcescens (2.5%) were isolated. A high diversity of CR genes was identified among the isolates, with 50% yielding blaO_SCPCAPCMYC_SCPCAP-2, 23% blaO_SCPCAPSHVC_SCPCAP-12, 20% blaO_SCPCAPCMYC_SCPCAP-1 and 18% blaO_SCPCAPCTX-MC_SCPCAP-15. Additionally, new CR-gene variants and resistance to carbapenems associated to OXA-48 were found. Most of the CR isolates, principally K. pneumoniae and C. freundii, were multiresistant with co-resistance to fluoroquinolones, tetracycline, sulphonamides and aminoglycosides. This study describes for the first time in wildlife a high prevalence of Enterobacteriaceae spp harbouring a large variety of carbapenem and CR genes frequently associated to nosocomial human infections. Implementation of control measures to reduce the impact of anthropogenic pressure in the environment is urgently needed.

microbiology↗