Biology subjects

Carvalho, H. F.

Publications and source records attributed to Carvalho, H. F..

5 recordsLinked to original sources

bioRxiv2026

Unravelling the memory of the extracellular matrix using MASH-derived decellularized scaffolds

The use of decellularized diseased livers in regenerative medicine is a promising approach for eliminating organ shortages. Bioengineering studies have shown that ECM can impact cell physiology, inducing cell activation, function, and ECM deposition, which suggests that the ECM has a "memory" that is involved in the outcome after recellularization. However, the effect of diseased ECM memory on new cells in vitro and in vivo has not been thoroughly investigated. Since it has been increasingly recognized that liver ECM changes due to different factors, it is comprehensively that diseased ECM obtained from discarded organs will ensure a distinct environment and impact cell survival and physiology. Thus, we aimed at investigating the impact of the memory of diseased ECM obtained from metabolic dysfunction-associated steatohepatitis (MASH)-derived organs on steatohepatitis establishment. To address this aim, we explored decellularized ECM obtained from rats and humans with MASH in different contexts. First, MASH ECM was characterized and then submitted to transplantation to investigate whether a MASH-derived ECM could be used as a scaffold for transplantation and to promote steatohepatitis features in control animals. Histological analysis revealed that the MASH-ECM was completely recellularized after transplantation in both control and MASH recipient rats. However, steatosis and fibrosis were observed in MASH ECM after transplantation in both groups. Molecular analysis showed that MASH ECM stimulates de novo lipogenesis and fibrosis 30 days after transplantation. Untargeted metabolomic analysis revealed that cells grown on MASH ECM had a similar metabolic profile, even when transplanted into healthy or MASH recipient rats. In addition, we observed that MASH ECM promoted impaired lipid oxidation and mitochondrial dysfunction when transplanted into healthy recipients. Altered lipid turnover and inflammatory signaling were observed in MASH ECM transplanted in MASH recipients. In vitro analysis revealed that MASH ECM induced lipid accumulation in HepG2 cells after 10 days of culture. Calcium signalling experiments obtained from HepG2 cells cultured in MASH ECM showed a lower response to ATP, a reduced calcium signalling amplitude, and a distinct response profile than that observed in healthy ECM. On the other hand, a diseased human-derived ECM could still provide an environment that allows cell development. Taken together, our data showed that MASH ECM impacts cell metabolism, promoting steatohepatitis maintenance. In conclusion, our data confirm that diseased ECM memory can impact cell physiology contributing to disease progression.

physiology↗

bioRxiv2025

Bclaf1 biomolecular condensates protect nuclear PTK2 from ubiquitin-proteasome system promoting cardiomyocyte survival during oxidative stress

PTK2, a non-receptor tyrosine kinase, plays a critical role in regulating essential cellular functions, including cell survival, by reducing p53 levels and activating the PI3K/AKT pathway. However, the mechanism underlying PTK2 stabilization during stress remains unclear. In this study, we identified Bclaf1, a multifunctional protein known to stabilize partners, as a PTK2 interactor. Using advanced microscopy techniques we identified nuclear Bclaf1 biomolecular condensates containing PTK2 in cardiomyocytes under oxidative stress. While diffuse PTK2 in the nucleus was susceptible to ubiquitination, PTK2 sequestered in the Bclaf1 condensates was protected from the ubiquitin-proteasome system (UPS). The K926 residue was identified as a ubiquitination site on PTK2, and subsequent proteasome inhibition experiments confirmed the role of the UPS in PTK2 homeostasis. Furthermore, disrupting Bclaf1 biomolecular condensates lead to PTK2 degradation, subsequently increasing p53 levels and activating apoptosis. Our findings support the role of Bclaf1 in the formation of pro-survival nuclear condensates that sequester and stabilize PTK2, promoting cardiomyocyte survival during oxidative stress. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/636487v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@15377a9org.highwire.dtl.DTLVardef@d5325forg.highwire.dtl.DTLVardef@de0ac9org.highwire.dtl.DTLVardef@196325d_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefMoretto et al. demonstrated that Bclaf1 undergo liquid-liquid phase separation (LLPS) during doxorubicin (Dox) induced oxidative stress to generate membraneless organelles where PTK2 is sequestered and protected from the ubiquitin-proteasome system (UPS). The maintenance of PTK2 stability may favor the p53 and Mdm2 interaction, which results in p53 ubiquitination and degradation, promoting cell survival. Loss of Bclaf1 disrupts PTK2 stabilization, leading to the ubiquitination and degradation of this kinase and downstream upregulation of p53, increasing cell death. HighlightsO_LIBclaf1 undergoes LLPS to stabilize protein partners during stress. C_LIO_LIPTK2 inside the Bclaf1 biomolecular condensates is protected from the UPS to promote cardiomyocyte survival during dox-induced oxidative stress. C_LIO_LIThe PTK2 ubiquitination site, lysine 926, was identified and the action of the UPS on PTK2 proteostasis was confirmed. C_LIO_LIBclaf1 knockdown results in overall protein ubiquitination and in PTK2 ubiquitination and degradation, resulting in increased levels of p53 and PUMA. C_LI

cell biology↗

bioRxiv2021

Physiochemically distinct SU-8 surfaces tailor Xylella fastidiosa cell-surface holdfast and colonization

SU-8 polymer is an excellent platform for diverse applications due to its high aspect ratio of micro/nanostructures fabrication and exceptional optical, chemical, and biocompatible properties. Although SU-8 has been often investigated for a variety of biological applications, how its surface properties influence both the interaction of bacterial cells with the substrate and its colonization is poorly understood. In this work, we tailor SU-8 nanoscale surface properties to investigate single cell motility, adhesion and successive colonization of a phytopathogenic bacteria, Xylella fastidiosa. Different surface properties of SU-8 thin films have been prepared using photolithography processing and oxygen plasma treatment. We found a significant difference in bacterial cell behavior and subsequent colonization on SU-8 as surface property changes. A larger density of carboxyl groups in hydrophilic plasma-treated SU-8 surfaces promotes faster cell motility in the earlier stage of the growth. The hydrophobic nature of pristine SU-8 surfaces has no trackable bacterial motility with 5 to 10 times more single cells adhered to surface than its plasma-treated counterpart. In fact, plasma-treated SU-8 samples suppressed bacterial adhesion, with surfaces showing less than 5% coverage. These results not only showcase that SU-8 surface properties can impact the bacterial behavior in a spatiotemporal manner, but also provide insights on the prominent ability of pathogens to evolve and adapt to different surface properties.

bioengineering↗

bioRxiv2021

Enviromic-based Kernels Optimize Resource Allocation with Multi-trait Multi-environment Genomic Prediction for Tropical Maize

Genomic prediction (GP) success is directly dependent on establishing a training population, where incorporating envirotyping data and correlated traits may increase the GP accuracy. Therefore, we aimed to design optimized training sets for multi-trait for multi-environment trials (MTMET). For that, we evaluated the predictive ability of five GP models using the genomic best linear unbiased predictor model (GBLUP) with additive + dominance effects (M1) as the baseline and then adding genotype by environment interaction (G x E) (M2), enviromic data (W) (M3), W+G x E (M4), and finally W+G x W (M5), where G x W denotes the genotype by enviromic interaction. Moreover, we considered single-trait multi-environment trials (STMET) and MTMET for three traits: grain yield (GY), plant height (PH), and ear height (EH), with two datasets and two cross-validation schemes. Afterward, we built two kernels for genotype by environment by trait interaction (GET) and genotype by enviromic by trait interaction (GWT) to apply genetic algorithms to select genotype:environment:trait combinations that represent 98% of the variation of the whole dataset and composed the optimized training set (OTS). Using OTS based on enviromic data, it was possible to increase the response to selection per amount invested by 142%. Consequently, our results suggested that genetic algorithms of optimization associated with genomic and enviromic data efficiently design optimized training sets for genomic prediction and improve the genetic gains per dollar invested.

genetics↗

bioRxiv2021

Reduction of genotyping marker density for genomic selection is not an affordable approach to long-term breeding in cross-pollinated crops

The selection of informative markers has been studied massively as an alternative to reduce genotyping costs for the genomic selection (GS) application. Low-density marker panels are attractive for GS because they decrease computational time-consuming and multicollinearity beyond more individuals can be genotyped with the same cost. Nevertheless, these inferences are usually made empirically using "static" training sets and populations, which are adequate only to predict a breeding programs initial cycles but might not for long-term cycles. Moreover, to the best of our knowledge, none of these inferences considered the inclusion of dominance into the GS models, which is particularly important to predict cross-pollinated crops. Therefore, that reveals an important and unexplored topic for allogamous long-term breeding. To achieve this goal, we employed two approaches: the former used empirical maize datasets, and the latter simulations of long-term breeding cycles of phenotypic and genomic recurrent selection (intrapopulation and reciprocal). Then, we observed the reducing marker density effect on populations (mean, the best genotypes performance, accuracy, additive variance) over cycles and models (additive, additive-dominance, specific combining ability (SCA)). Our results indicate that the markers reduction based on different linkage disequili brium (LD) levels is viable only within a cycle and brings a significant decrease in predictive ability over generations. Furthermore, in the long-term, regardless of the selection scheme adopted, the more makers, the better because they buffer LD losses caused by recombination over breeding cycles. Finally, regarding the accuracy, the additive-dominant models tend to outperform the additive ones and perform similar to the SCA.

genetics↗