Biology subjects

Perez, E.

Publications and source records attributed to Perez, E..

13 recordsLinked to original sources

bioRxiv2025

Kazal-type serine protease inhibitors from Arabidopsis thaliana and Toxoplasma gondii exhibit antimicrobial activity against plant pathogens

Kazal-type serine protease inhibitors (KPIs) interfere with microbial proteases and have been associated with antimicrobial activity, yet their specific role in plant protection remains poorly understood. In this work, we evaluated the antimicrobial potential of recombinant Arabidopsis thaliana KPI (rAtKPI-1T), recombinant Toxoplasma gondii KPI (rTgPI-1), and two truncated versions of rTgPI-1 (rTgPI-1NT and rTgPI-1CT). Both rAtKPI-1T and rTgPI-1 exhibited inhibitory effects against Pseudomonas syringae DC3000, P. syringae (AvRpm1), and P. viridiflava in a concentration-dependent manner, with significant inhibition at 3.5 M. The lower MIC50 values obtained for rTgPI-1 and its truncated forms compared to rAtKPI-1T suggest a higher antibacterial potency. Binding and immunofluorescence assays further revealed that rAtKPI-1T, rTgPI-1, and rTgPI-1NT associated with bacterial surfaces, while rTgPI-1CT displayed weaker or transient interactions. In addition to their antibacterial activity, rTgPI-1NT and rTgPI-1CT also inhibited the germination of Botrytis cinerea conidia. Both truncated proteins significantly reduced germination after 6 and 9 hours of incubation, with rTgPI-1CT exerting a markedly stronger antifungal effect than rTgPI-1NT. These findings suggest that specific Kazal-type domains, particularly those in the C-terminal region, could play a critical role in suppressing early infection processes of necrotrophic fungi. Overall, this study demonstrates that rKPIs display distinct and complementary antimicrobial profiles mediated by microbial binding and protease inhibition. The contrasting activities of rTgPI-1NT and rTgPI-1CT highlight the value of domain-level analysis to discern functional contributions within multidomain KPIs. These results expand current knowledge on plant-derived protease inhibitors and underscore their potential as biotechnological tools for sustainable crop protection.

microbiology↗

bioRxiv2025

SteMClass: A Novel DNA Methylation-Based Classifier for iPSC In Vitro Differentiation States.

Human induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, disease modelling, and drug discovery, but most downstream applications require differentiation into specialised cell types not covered by current quality control assays. Here, we present "SteMClass", a proof-of-concept DNA methylation-based classifier that standardises iPSC differentiation state identification across protocols with one test. We curated a reference cohort of 15 iPSC lines differentiated into seven distinct states (n = 97), performed array-based DNA methylation profiling, and trained a random forest model to classify the eight distinct differentiation states. In nested cross-validation, SteMClass achieved a Brier score of 0.018, and on an independent cohort (n = 58) attained 96.5% accuracy (Cohens K = 0.959) with a 3% rejection rate. Applied to external data (n = 249), SteMClass achieved 85.1% overall accuracy (Cohens K = 0.687) with a 12.9% rejection rate. Among classified samples (n = 217), accuracy was 97.7% (Cohens K = 0.93). SteMClass is compatible with all Illumina methylation array versions, and accessible via an interactive web interface that supports classification and exploration of DNA methylation profiles. By providing a harmonised, single-assay framework for iPSC-derived differentiation state characterisation, SteMClass improves reproducibility and comparability across studies, paving the way for robust quality control standards and accelerating clinical translation.

cell biology↗

bioRxiv2025

Optimization of a Cannabis sativa micropropagation protocol (chemotype III) to preserve its cannabinoid profile

A micropropagation protocol was developed using axillary buds of the Charlies Dream variety of Cannabis sativa (chemotype III, THC<<CBD), under the hypothesis that clonal propagation preserves the CBD/{Delta}9-THC profile between donor and micropropagated plants. The effects of plant growth regulators BAP and TDZ (0.5, 1, 2.5 M) in MS medium with or without vitamin supplementation (MS vs. MSS) were determined. The progress in the growth of the axillary buds was evaluated by analyzing the shoot length, the number of shoots per explant, and the foliar area of the shoots. The role of naphthaleneacetic acid (NAA) and indolebutyric acid (IBA) in the rooting process was also evaluated in vitro and ex vitro. Resins were extracted from dried flowers of donor and micropropagated plants using cold ethanol treatment. The CBD and {Delta}9-THC contents were analyzed by GC/MS. The results show that vitamin supplementation in the MS medium did not improve any of the growth parameters evaluated. However, significant differences were observed when comparing TDZ and BAP. At 15 days post-initiation of micropropagation (dpim) from axillary buds, the explants treated with 0.5 and 1 M TDZ showed a greater number of shoots per explant and larger foliar area, compared to those treated with any concentration of BAP. However, by 30 dpim, explants treated with BAP showed an improved performance, reaching shoot numbers and foliar area values similar to those observed with TDZ. It is worth mentioning that no differences were observed in the shoot length at all concentrations analyzed for both hormones. Likewise, the explants grown in 2.5 M TDZ showed greater callus production and vitrification. The effects of supplementation with the hormone gibberellin (7 {micro}M) or exposure of the shoots to red light were also evaluated. The results indicated that combining these treatments with BAP at 0.5 and 1 {micro}M significantly enhanced shoot elongation compared to combinations with TDZ at the same concentrations. On the other hand, in vitro rooting was unsuccessful. However, direct rooting in soil was observed, and root length was further enhanced when shoots were pretreated with 2.5 M IBA. The CBD/{Delta}9-THC ratio remained stable between donor and micropropagated plants, supporting the development of standardized micropropagation protocols. Our results confirm that clonal micropropagation is a reliable method to preserve cannabinoid profiles in C. sativa.

plant biology↗

bioRxiv2025

EWS-FLI1 Expression in Human Embryonic MSCs Leads to Transcriptional Reprograming, Defective DNA Damage Repair and Ewing Sarcoma

Ewing sarcoma (ES) is an aggressive bone and soft tissue neoplasm characterized by EWSR1/ETS rearrangements and whose cellular origin remains unclear. EWS-FLI1 expression in human pediatric mesenchymal stem cells (hpMSCs) induces a quantitatively and qualitatively different transcriptional response than its expression in human adult MSCs (haMSCs), but fails to form tumors in vivo. ES cells have early developmental lineage signatures distinct from postnatal MSCs. Here, we have generated MSCs from experimental teratomas out of human embryonic stem cells (heSCs). Transduction of these human embryonic mesenchymal stem cells (heMSCs) with EWS-FLI1 results in the acquisition of an ES transcriptome, although the oncogene does not preferentially bind to promoters, but to intronic and intergenic microsatellites with >10 CA dinucleotides and GGAA repeats, respectively. In heMSCs, EWS-FLI1 directly regulates BRCA1 expression, although EWS-FLI1-expressing cells show defects in DNA damage repair. Xenografting of EWS-FLI1-transduced heMSCs resulted in the formation of tumors expressing characteristic ES markers. In summary, EWS-FLI1 enforces an aberrant transcriptome and endows in vivo transforming capacity when expressed in an undifferentiated early heMSC. Our approach represents an innovative experimental method for understanding critical aspects of the biology of developmental tumors, from leukemia to sarcomas, in which few (even single) genetic alterations are able to transform a fetal stem cell.

cancer biology↗

bioRxiv2024

Key roles of the zona pellucida and perivitelline space in promoting gamete fusion and fast block to polyspermy inferred from the choreography of spermatozoa in mice oocytes

Mammalian fertilization is still lacking a comprehensive understanding of gamete fusion and block to polyspermy mechanisms. One reason is that they are highly dynamic processes involving transient events that can only be revealed and characterized by direct observation. To extend while challenging existing knowledge, this study applies real time brightfield and confocal imaging to inseminated ZP-intact mouse oocytes and statistical analyses to establish an accurate dynamic picture of the cascade of events leading to fusion and prevention of polyspermy in conditions as close to physiology as possible. These observations allow to characterize the roles of the different components of the oocyte (i.e. zona pellucida (ZP), perivitelline space (PVS), oocyte plasma membrane (OPM)) and the spermatozoon (i.e. head, flagellum) in promoting fertilization and preventing polyspermy. The kinetics we have determined challenge dogmas by showing that: (i) the first sperm is not necessarily the one that fertilizes in mice pointing to the existence of other post-penetration fertilization factors, (ii) the ZP block resulting from the cortical reaction is too slow to contribute to the prevention of polyspermy in mice. On the other hand, it evidences that the ZP directly contributes to polyspermy block in two other ways: (a) as a naturally effective entry barrier for the spermatozoon (independent of any block caused by fertilization), (b) as an effective exit barrier for components released by the OPM, which may contribute to a fast PVS block to polyspermy through the neutralizing of unwanted spermatozoa in the PVS. Moreover, our observations reveal that the ZP plays a key role in fertilization itself by channeling the flagellar oscillations of spermatozoa in the PVS to make them conducive to fusion.

cell biology↗

bioRxiv2024

Comparison of spatial transcriptomics technologies across six cancer types

Spatial biology experiments integrate the molecular and histological landscape of tissues to provide a previously inaccessible view of tissue biology, unlocking the architecture of complex multicellular tissues. Within spatial biology, spatial transcriptomics platforms are among the most advanced, allowing researchers to characterize the expression of thousands of genes across space. These new technologies are transforming our understanding of how cells are organized in space and communicate with each other to determine emergent phenotypes. This is particularly important in cancer research, as tumor evolution is shaped not only by the genetic properties of cancer cells but also by how they interact with the tumor microenvironment and their spatial organization. While many platforms can generate spatial transcriptomics profiles, it is still unclear in which context each platform better suits the needs of its users. Here we compare the results obtained using 5 different spatial transcriptomics (VISIUM, VISIUM CytAssist, VisiumHD, Xenium, and CosMx) and one spatial proteomics (VISIUM CytAssist) platforms across serial sections of 6 FFPE samples from primary human tumors covering some of the most common forms of the disease (lung, breast, colorectal, bladder, lymphoma and ovary). We observed that the VISIUM platform with CytAssist chemistry yielded superior data quality than manual VISIUM. On the other hand, Xenium consistently produced more reliable results for in situ platforms, with better gene clustering and fewer false positives than CosMx. Importantly, these platform-based variations didnt significantly affect cell type identification. VisiumHD offers the best options of both worlds, with subcellular resolution and whole-transcriptome coverage, albeit with some limitations that need to be accounted for in downstream analyses. Finally, by comparing VISIUM protein profiles with the spatial transcriptomics data from all four platforms on each sample, we identified several genes with mismatched RNA and protein expression patterns, highlighting the importance of multi-omics profiling to reveal the true biology of human tumors.

genomics↗

bioRxiv2022

LincRNA-Cox2 regulates smoke-induced inflammation in murine macrophages

Cigarette smoke (CS) exposure is a risk factor for many chronic diseases including chronic obstructive pulmonary disease (COPD), however the mechanism by which smoke exposure can alter homeostasis and bring about chronic inflammation is poorly understood. Here, we showcase a novel role for smoke in regulating long noncoding RNAs (lncRNAs), showing that it activates lincRNA-Cox2, which we previously characterized as functional in inflammatory regulation. Exposing lincRNA-Cox2 murine models to smoke in vivo confirmed lincRNA-Cox2 as a regulator of inflammatory gene expression in response to smoke both systemically and within the lung. We also report that lincRNA-Cox2 negatively regulates genes in smoked bone marrow derived macrophages exposed to LPS stimulation. In addition to the effects on lncRNAs, we also report dysregulated transcription and splicing of inflammatory protein-coding genes in the bone marrow niche following CS exposure in vivo. Collectively, this work provides insights into how innate immune signaling from gene expression to splicing is altered following in vivo exposure to CS and highlights an important new role for lincRNA-Cox2 in regulating immune genes following smoke exposure.

immunology↗

bioRxiv2022

An early decline in ETPs reflects reduced pre-thymic progenitors and altered signals from the thymus microenvironment

Age-related thymus involution results in decreased T-cell production, contributing to increased susceptibility to pathogens. Elucidating mechanisms underlying involution will inform strategies to restore thymopoiesis. The thymus is colonized by circulating bone marrow (BM)-derived thymus seeding progenitors (TSPs) that differentiate into early T-cell progenitors (ETPs). We find ETP cellularity declines as early as 3 months (3MO) in mice. This initial ETP reduction could reflect changes in pre-thymic progenitors and/or thymic stromal niches. We demonstrate that the number of functional TSP/ETP niches is not reduced with age. Instead, the number of pre-thymic BM and circulating lymphoid progenitors is substantially reduced by 3MO, although their intrinsic ability to seed and differentiate in the thymus is maintained. Additionally, Notch signaling in BM progenitors and ETPs declines by 3MO, indicating defective niche quality contributes to the reduction in ETPs. Together, these findings indicate that diminished BM lymphopoiesis and thymic stromal support contribute to the initial decline in ETPs, setting the stage for progressive thymus involution. Summary statementThe number of early T-cell progenitors declines by 3 months of age in mice. This decline reflects a sharp drop in circulating thymus seeding progenitors, fewer bone marrow lymphoid progenitors, and reduced Notch signaling in both bone marrow and thymus.

immunology↗

bioRxiv2020

Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis

Metaproteomics is as a promising technique for studying the human gut microbiota, because it can reveal the taxonomic profile and also shed light on the functional role of the microbial community. Nevertheless, methods for extracting proteins from stool samples continue to evolve, in the pursuit of optimal protocols for moistening and dispersing the stool sample and for disrupting microbial cells which are two critical steps for ensuring good protein recovery. Here, we evaluated different stool sample processing and microbial cell disruption methods for metaproteomic analyses of human gut microbiota. An unsupervised principal component analysis showed that different methods produced similar human gut microbial taxonomic profiles. An unsupervised two-way hierarchical clustering analysis identified the microbial taxonomic signatures associated with each method. Proteobacteria and Bacteroidetes identification was favored by moistening the stool samples during processing and by disrupting cells with medium-sized glass beads. Ascomycota identification was enhanced by using large-sized glass beads during sample processing for stool dispersion. Euryarchaeota identification was improved with a combination of small and medium-sized glass beads for cell disruption. Assessments of the relative abundance of Firmicutes, Actinobacteria and Spirochaetes improved when ultrasonication was performed before cell disruption with glass beads. The latter method also increased the overall number of identified proteins. Taxonomic and protein functional analyses of metaproteomic data derived from stool samples from six healthy individuals showed common taxonomic profiles. We also detected certain proteins involved in microbial functions relevant to the host and related mostly to particular taxa, such as B12 biosynthesis and short chain fatty acid production carried out mainly by members in the Prevotella genus and the Firmicutes phylum, respectively. Finally, in this metaproteomic study we identified several human proteins, mostly related to the anti-microbial response, which could contribute to determining the beneficial and detrimental relationships between gut microbiota and human cells in particular human diseases.

microbiology↗

bioRxiv2020

BAG3-dependent autophagy maintains sarcomere function in cardiomyocytes

The association between reduced myofilament force-generating capacity (Fmax) and heart failure (HF) is clear, however the underlying molecular mechanisms are poorly understood. Here, we show the Fmax decrease arises from impaired BAG3-mediated sarcomere turnover. Myofilament BAG3 decreased in human HF and predicted the extent of Fmax decrease. This relationship was confirmed using BAG3+/- mice, which had reduced Fmax and increased myofilament ubiquitination, suggesting impaired protein turnover. We show cardiac BAG3 operates via the chaperone-assisted selective autophagy complex (CASA), conserved from skeletal muscle, and confirm sarcomeric CASA localization is BAG3/proteotoxic stress-dependent. To determine if increasing BAG3 expression in HF would restore sarcomere proteostasis/Fmax, HF mice were treated with AAV9/BAG3. Gene therapy fully restored Fmax after four weeks and decreased ubiquitination. Using mass spectrometry, we identified several sarcomere proteins with increased ubiquitination in HF and four that decreased with AAV9/BAG3. Our findings indicate BAG3-mediated sarcomere turnover is required for myofilament functional maintenance.

physiology↗

bioRxiv2019

Evaluation of copy number burden in specific epilepsy types from a genome-wide study of 18,564 subjects

Rare and large copy number variants (CNVs) around known genomic hotspots are strongly implicated in epilepsy etiology. But it remains unclear whether the observed associations are specific to an epilepsy phenotype, and if additional risk signal can be found outside hotspots. Here, we present the largest CNV burden and first CNV breakpoint level association analysis in epilepsy to date with 11,246 European epilepsy cases and 7,318 ancestry-matched controls. We studied five epilepsy phenotypes: genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, epileptic encephalopathy, and unclassified epilepsy. We discovered novel epilepsy-associated CNV loci and further characterized the CNV burden enrichment among phenotype-specific epilepsies. Finally, we provide evidence for deletion burden outside of known hotspot regions and show that CNVs play a significant role in the genetic architecture of lesional focal epilepsies.

genetics↗

bioRxiv2019

Aggregation-prone peptides modulate interferon gamma functionality in naturally occurring protein nanoparticles

Efficient protocols for the production of recombinant proteins are indispensable for the development of the biopharmaceutical sector. Approximately 400 recombinant protein-based biopharmaceuticals have been approved in recent decades, with steady growth projected in the coming years. During the expression of a heterologous gene, the protein quality control network is overcome by the disruption in protein homeostasis, leading to protein aggregation. This phenomenon has been described in all expression systems analyzed to date, including prokaryotic and eukaryotic host cells. These protein aggregates have long been considered inert protein clumps devoid of biological activity and their study has largely been neglected. However, in recent years, the classic view of protein aggregates has completely changed with the recognition that these aggregates are a valuable source of functional recombinant proteins. In this study, bovine interferon-gamma (rBoIFN-{gamma}) was engineered to enhance the formation of protein aggregates by the addition of aggregation-prone peptides (APPs) in the generally recognized as safe (GRAS) bacterial Lactococcus lactis expression system. The L6K2, HALRU and CYOB peptides were selected to assess their intrinsic aggregation capability to nucleate protein aggregation. These APPs enhanced the tendency of the resulting protein to aggregate at the expense of the total protein yield. However, fine physicochemical characterization of the resulting intracellular protein nanoparticles (NPs), the protein released from these protein NPs, and the protein purified from the soluble cell fraction indicated that the compactability of protein conformations is directly related to the biological activity of variants of IFN-{gamma}, which is used here as a model protein with therapeutic potential.\n\nImportanceThe demand for recombinant proteins in the pharmaceutical industry is steadily increasing. Emerging novel protein formulations, including naturally occurring protein NPs, might be an alternative to soluble variants for fine analysis at the biophysical level. Such analyses are important to address safety about biological molecules.\n\nThis study analyzes the effect of aggregation-prone peptides (APPs) on the improvement of the production of naturally occurring protein nanoparticles (NPs) of interferon gamma (IFN-{gamma}) in the generally recognized as safe (GRAS) Lactococcus lactis expression system. In addition, the fine physico-chemical characterization of the resulting proteins, either obtained from the soluble or insoluble cell fractions, indicates that the selected engineered proteins embedded in the protein NPs show higher compactability than their soluble protein counterparts. Conformational compactability is directly related to the biological performance of the recombinant IFN-{gamma}.

microbiology↗

bioRxiv2018

Within-host recombination in structural proteins of the Foot-and-Mouth Disease Virus

Although recombination is known to occur in FMDV, it is considered only a minor determinant of virus sequence diversity. This is because recombination appears to be highly suppressed at phylogenetic scales; inter-serotypic recombination events are rare; and in those a mosaic structure is present whereby recombination only occurs almost exclusively in non-structural proteins. Here we show that co-inoculation of closely related strains in buffaloes results over time in extensive within-host recombination in the genomic region coding for structural proteins. This enables us to directly estimate recombination rates for the first time. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Thanks to the features of our experimental setup, we are also able to build a high-resolution map of effective within-host recombination in the capsid-coding region. We find that the linkage disequilibrium pattern inside VP1 points to a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although those intra-host results are not immediately transportable to a phylogenetic setting, they force us to reconsider the relevance of recombination and epistasis, suggesting that they must play a major and so far underappreciated role in the molecular evolution of the virus at all time scales.\n\nAuthor summaryRecombination in the capsid-coding region of the Foot-and-Mouth Disease virus genome is highly suppressed at phylogenetic scales. However, the role of recombination in the intra-host dynamics of the virus is not known. In our experiment, a co-infection of African buffaloes with closely related FMDV strains results in a population structure of the intra-host viral swarm, allowing us to detect recombination events. For structural protein-coding sequences, the swarm dynamics is driven by extensive within-host recombination. During the acute infection phase, we infer intra-host recombination rates of 0.1 per base per year, comparable to the typical mutation rate of the virus. The recombination map reveals two linkage blocks within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between blocks. Our findings support a major role for recombination and epistasis in the intra-host evolution of FMDV.

microbiology↗