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Bueno, C.

Publications and source records attributed to Bueno, C..

16 recordsLinked to original sources

CaMKII generates actin bundle morphology and mechanics distinct from canonical bivalent cross-linkers

Actin cross-linkers are essential modulators of the actin cytoskeleton, enabling structural diversity and dynamic remodeling. Among them, calcium/calmodulin-dependent protein kinase II (CaMKII) is unique in serving a dual role as a kinase and as a multivalent structural binder of actin in dendritic spines, where it plays a major role in supporting dendritic spine structure via its {beta} subunit. To understand the basis of the structural function of CaMKII, we quantified the morphology and mechanics of actin bundles formed by CaMKII and directly compared them with bundles assembled by the canonical bivalent cross-linkers -actinin and fascin. Using fluorescence microscopy, we measured contour length, straightness ratio, and persistence length across different cross-linker concentrations. Fascin generated progressively shorter, straighter, and stiffer bundles with increasing concentration, whereas -actinin bundles remained largely unchanged. In contrast, increasing CaMKII concentration reduced both bundle straightness and persistence length, revealing a unique concentration-dependent increase in bundle flexibility. To investigate the structural origins of these mechanical behaviors, we complemented the experiments with coarse-grained simulations of cross-linked actin bundles. Simulations revealed that CaMKII-generated bundles retained a substantially larger fraction of their curvature in their time-averaged configuration than bundles formed by -actinin or fascin, indicating that bundle mechanics are strongly influenced by organizational features beyond thermal bending fluctuations alone. CaMKII bundles displayed behavior consistent with additional structural complexity arising from their multivalent architecture and flexible linker domains. Together, our experimental and computational results identify CaMKII as a structurally and mechanically distinct actin cross-linker. We propose that the combination of multivalency and linker flexibility enables CaMKII to function as a molecular structural pivot, promoting flexible, adaptable actin assemblies that are mechanically compatible with the dynamic remodeling required for dendritic spine plasticity.

biophysics↗

The direct conversion of human somatic cells into neural-like cells involves a transition through a transient intermediate state.

BackgroundDirect conversion of human somatic cells into functional neurons could offer a faster way to generate patient-specific neurons for use in regenerative medicine, disease modelling, and drug development. Although it has been reported that neuronal direct reprogramming bypasses the intermediate pluripotent state, no reports have included time-lapse experiments, potentially overlooking transient intermediate states. Recent studies have shown that the conversion of human mesenchymal stromal cells (hMSCs) into neuron-like cells involves a transition through a transient intermediate state. Therefore, further research is needed to fully understand the process by which human somatic cells can become neurons without cell division. In this study we investigates whether direct neuronal reprogramming of human bone marrow-derived MSC (hBM-MSCs), dental pulp-derived MSC (hDP-MSCs), and adult human dermal fibroblasts (HDFa), involves a transient intermediate state, and sought to further validate the neuronal identity of hMSC-derived induced neurons. MethodsIn this study, we conducted time-lapse experiments to observe the transformation of hBM-MSCs, hDP-MSCs and HDFa, into neurons using a small-molecule-based direct reprogramming protocol. Cellular and ultrastructural changes were further characterized by confocal and electron microscopy. ResultsDirect conversion of hBM-MSCs, hDP-MSCs and HDFa into neuron-like cells occurred rapidly and in absence of cell division. Time-lapse analyses revealed that reprogramming proceeds through a transient intermediate state characterized by distinct morphological changes and dynamic nuclear remodelling. Furthermore, we found that neuron-like cells derived from hBM-MSCs and hDP-MSCs exhibit neuronal polarization, expressed specific neuronal and synaptic markers, formed interconnected cellular networks, and exhibited functional plasticity, providing further evidence that hMSCs can become functional neurons. ConclusionsThis study provides clear evidence that the direct neuronal reprogramming process involves a transition through an intermediate, transient state. Our findings also provide further evidence that hMSCs can become functional neurons. In summary, our work provides new insights into the direct neuronal reprogramming process, which is essential for advancing both developmental biology and regenerative medicine.

neuroscience↗

CAR-T cells targeting CCR9 and CD1a for the treatment of T cell acute lymphoblastic leukemia

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy characterized by high rates of induction failure and relapse, and effective targeted immunotherapies are lacking. Despite promising clinical progress with genome-edited CD7-directed CAR-T cells, which present significant logistical and regulatory issues, CAR-T cell therapy in T-ALL remains challenging due to the shared antigen expression between malignant and healthy T cells. This can result in CAR-T cell fratricide, T cell aplasia, and the potential for blast contamination during CAR-T cell manufacturing. Recently, CAR-T cells have been described that target non-pan-T antigens, absent on healthy T cells but expressed on specific T-ALL subsets. These antigens include CD1a (NCT05679895), which is expressed in cortical T-ALL, and CCR9. We show that CCR9 is expressed on >70% of T-ALL patients (132/180) and is maintained at relapse, with a safe expression profile in healthy hematopoietic and non-hematopoietic tissues. Further analyses showed that dual targeting of CCR9 and CD1a could benefit [~]86% of patients with T-ALL, with a greater blast coverage than single CAR-T cell treatments. We therefore developed, characterized, and preclinically validated a novel humanized CCR9-specific CAR with robust and specific antileukemic activity as a monotherapy in vitro and in vivo against cell lines, primary T-ALL samples, and patient-derived xenografts. Importantly, CCR9/CD1a dual-targeting CAR-T cells showed higher efficacy than single-targeting CAR-T cells, particularly in T-ALL cases with phenotypically heterogeneous leukemic populations. Dual CCR9/CD1a CAR-T therapy may prevent T cell aplasia and obviate the need for allogeneic transplantation and regulatory-challenging genome engineering approaches in T-ALL.

immunology↗

Integrative single-cell multi-omics of CD19CARpos and CARneg T cells suggest drivers of immunotherapy response in B-cell neoplasias

How phenotypic, clonal, and functional heterogeneity of CAR-T-cells impact clinical outcomes remain understudied. Here, we integrated clonal kinetics with transcriptomic heterogeneity resolved by single-cell omics to explore cellular dynamics response of both non-transduced (CARneg) and transduced (CARpos)T-cells. CARneg and CARposT-cells were longitudinally interrogated in the manufactured infusion product (IP) and in-vivo at CAR-T cell expansion peak in five B-ALL patients treated with CD19CAR-T-cells (varni-cel). Significant differences were found in the cellular dynamics between CARpos and CARnegT-cells in response to therapy. CARposT-cells in the IP exhibited a significant higher CD4:CD8 ratio than CARnegT-cells, and the CD4:CD8 CARposT-cell composition impacted therapy outcome as confirmed in a larger cohort of 24 varni-cel-treated B-ALL patients. Conversely, an inverted trend in the CD4:CD8 CARposT-cell ratio was consistently observed at the expansion peak, with clonally expanding CD8+ effector memory and cytotoxic T-cells being the most abundant populations. Expanded cytotoxic CARpos{gamma}{delta}T cells emerged at the expansion peak, and the extent of their in-vivo expansion positively correlated with treatment efficacy, which was validated in a large cohort of B-ALL patients (n=18) treated with varni-cell and B-cell lymphoma patients (n=58) treated with either lisa-cel or axi-cel. Our data provide insights into the complexity and diversity of T-cell responses following CAR-T cell therapy and suggest drivers of immunotherapy response.

immunology↗

Towards Generalizability and Robustness in Biological Object Detection in Electron Microscopy Images

Machine learning approaches have the potential for meaningful impact in the biomedical field. However, there are often challenges unique to biomedical data that prohibits the adoption of these innovations. For example, limited data, data volatility, and data shifts all compromise model robustness and generalizability. Without proper tuning and data management, deploying machine learning models in the presence of unaccounted for corruptions leads to reduced or misleading performance. This study explores techniques to enhance model generalizability through iterative adjustments. Specifically, we investigate a detection tasks using electron microscopy images and compare models trained with different normalization and augmentation techniques. We found that models trained with Group Normalization or texture data augmentation outperform other normalization techniques and classical data augmentation, enabling them to learn more generalized features. These improvements persist even when models are trained and tested on disjoint datasets acquired through diverse data acquisition protocols. Results hold true for transformerand convolution-based detection architectures. The experiments show an impressive 29% boost in average precision, indicating significant enhancements in the models generalizibality. This underscores the models capacity to effectively adapt to diverse datasets and demonstrates their increased resilience in real-world applications.

bioengineering↗

The nuclei of human adult stem cells can move within the cell and generate cellular protrusions to contact other cells

Despite a considerable interest in understanding the mechanisms regulating nucleus structure, chromatin organization and nuclear positioning over decades, the exact significance of the variety of morphologies and positioning that cell nuclei can adopt and their relationship in cellular function is still far from being clearly understood. In this study, we examined the functional significance of the variety of morphologies and positioning that cell nuclei of human bone marrow-derived mesenchymal stem cells can adopt during neural-like differentiation. Here, we show that after neural induction, human bone marrow-derived mesenchymal stem cells enter an intermediate cellular state in which the nuclei are observed to be able to move within the cells, switching shapes and positioning and even generating cellular protrusions as they attempt to contact the cells around them. These findings suggest that changes in nuclear positioning are due to the fact that human cell nuclei somehow sensing their environment.

cell biology↗

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

Long-range interactions between regulatory elements and promoters are key in gene transcriptional control; however, their study requires large amounts of starting material, which is not compatible with clinical scenarios nor the study of rare cell populations. Here we introduce low input capture Hi-C (liCHi-C) as a cost-effective, flexible method to map and robustly compare promoter interactomes at high resolution. As proof of its broad applicability, we implement liCHi-C to study normal and malignant human hematopoietic hierarchy in clinical samples. We demonstrate that the dynamic promoter architecture identifies developmental trajectories and orchestrates transcriptional transitions during cell-state commitment. Moreover, liCHi-C enables the identification of new disease-relevant cell types, genes and pathways potentially deregulated by non-coding alterations at distal regulatory elements. Finally, we show that liCHi-C can be harnessed to uncover genome-wide structural variants, resolve their breakpoints and infer their pathogenic effects. Collectively, our optimized liCHi-C method expands the study of 3D chromatin organization to unique, low-abundance cell populations, and offers an opportunity to uncover novel factors and regulatory networks involved in disease pathogenesis.

genomics↗

Binucleated cells generated by nuclear movement during neural transdifferentiation from human bone marrow-derived mesenchymal cells

Although it has been reported that bone marrow-derived cells (BMDCs) can transdifferentiate into neural cells, the findings are considered unlikely. It has been argued that the rapid neural transdifferentiation of BMDCs reported in culture studies is actually due to cytotoxic changes induced by the media. While transplantation studies indicated that BMDCs can form new neurons, it remains unclear whether the underlying mechanism is transdifferentiation or BMDCs-derived cell fusion with the existing neuronal cells. Cell fusion has been put forward to explain the presence of gene-marked binucleated neurons after gene-marked BMDCs transplantation. In the present study, we demostrated that human BMDCs can rapidly adopt a neural-like morphology through active neurite extension and binucleated human BMDCs can form with independence of any cell fusion events. We also showed that BMDCs neural transdifferentiation involves the formation of intermediate cells which can then redifferentiate into neural-like cells, redifferentiate back to the mesenchymal fate or even repeatedly switch lineages without cell division. Furthermore, we have discovered that nuclei from intermediate cells rapidly move within the cell, adopting different morphologies and even forming binucleated cells. Therefore, our results provide a stronger basis for rejecting the idea that BMDCs neural transdifferentiation is merely an artefact.

neuroscience↗

Phyllochron duration and changes through rice development shape the vertical leaf size profile

O_LIWell-irrigated aerobic rice (Oryza sativa L.) plants are often shorter with smaller leaves, and the leaf appearance rate is slower in well-irrigated than in flooded environments. This observation questions the functional relationship between the leaf appearance rate, which is correlated with the apical cell production rate, and leaf length that is in turn correlated with the leaf division zone length. C_LIO_LIMeristem size, blade size, and appearance were monitored for all leaves from leaf 6 on the main stem of rice plants in field experiments using two varieties, two watering systems, and three sowing dates. C_LIO_LILeaf blade and division zone lengths were correlated in all leaves of the main stem of rice plants. New stable linear relationships were found between the leaf division zone growth duration and internal cell production rate, which changed after leaf 11. These stable relationships imply a stable link between the rates of cell production in the stem apex and leaf meristem, explaining the vertical leaf size profile. C_LIO_LIOverall, faster leaf appearance leads to shorter leaves and organs in rice because of a functional link, which is counterbalanced by additional acclimation in transplanted plants. C_LI

plant biology↗

A comprehensive single-cell expression atlas of human AML leukemia-initiating cells unravels the contribution of HIF pathway and its therapeutic potential

Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML), and is driven by rare therapy-resistant leukemia-initiating stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling keeps cells in a quiescent and metabolically relaxed state, desensitizing them to chemotherapy. This suggests the hypothesis that hypoxia contributes to AML-LSC function and chemoresistance and is a therapeutic target to sensitize AML-LSCs to chemotherapy. Here, we provide a comprehensive single-cell expression atlas (119,000 cells) of AML cells and AML-LSCs in paired diagnostic-relapse samples from risk-stratified patients with AML. The HIF/hypoxia pathway is attenuated in AML-LSCs compared with differentiated AML cells, but is enhanced when compared with healthy hematopoietic cells. Accordingly, chemical inhibition cooperates with standard-of-care chemotherapy to impair leukemogenesis, substantially eliminating AML-LSCs. These findings support the HIF pathway as a stem cell regulator in human AML, and reveal avenues for combinatorial targeted and chemotherapy-based approaches to specifically eliminate AML-LSCs.

cancer biology↗

A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines

A prion-like RNA-binding protein, CPEB3, can regulate local translation in dendritic spines. CPEB3 monomers repress translation, whereas CPEB3 aggregates activate translation of its target mRNAs. However, the CPEB3 aggregates, as long-lasting prions, may raise the problem of unregulated translational activation. Here, we propose a computational model of the complex structure between CPEB3 RNA-binding domain (CPEB3-RBD) and small ubiquitin-like modifier protein 2 (SUMO2). Free energy calculations suggest that the allosteric effect of CPEB3-RBD/SUMO2 interaction can amplify the RNA-binding affinity of CPEB3. Combining with previous experimental observations on the SUMOylation mode of CPEB3, this model suggests an equilibrium shift of mRNA from binding to deSUMOylated CPEB3 aggregates to binding to SUMOylated CPEB3 monomers in basal synapses. This work shows how a burst of local translation in synapses can be silenced following a stimulation pulse, and explores the CPEB3/SUMO2 interplay underlying the structural change of synapses and the formation of long-term memories.

molecular biology↗

Transplanting increases the leaf production rate in rice, consequently modifying plant development and growth

In Asia, direct sowing and water savings are major trends in previously transplanted and flooded irrigated rice systems because of the higher cost of wages and increasing water shortage. Previous experiments showed that the leaf appearance rate varies between aerobic and flooded cropping systems. This study aimed to further understand how the planting method affects the development rate, flowering time, and yield of lowland irrigated rice crops. A two-year experiment was undertaken at the International Rice Research Institute, Philippines, using three contrasting rice varieties and three planting methods (transplanted, wet direct-seeded, and dry direct-seeded; at a density of 25 plants m-2) in a field submerged in 3-5 cm water from two weeks after the transplanting date. The effect of the planting method was similar in the three varieties, mostly without interaction between the two factors. In 2013, the leaf number of seedlings grown in seedling trays was two leaves behind that of direct-seeded plants at the time of transplanting. However, the young transplanted plants recovered quickly; produced new leaves at a faster rate (with a shorter phyllochron); reached panicle initiation, flag-leaf emergence and flowering time 1 week later; and developed more leaves compared to the direct-seeded plants. In 2014, growing in the nursery induced no delay in leaf appearance due to temperatures lower than those in 2013; therefore, the planting method did not affect the leaf appearance rate. Thus, plant development was primarily delayed by the density stress in the seedling trays under warm temperatures; however, the transplanted rice plants had lower plastochron duration than the direct-seeded plants, which made up for the initial delay in leaf appearance. In both years and at similar plant density, the transplanted plants produced more tillers bearing larger upper leaves that led to a higher leaf area index; however, grain yields were similar for the transplanted and direct-seeded crops. Highlights- In seedling trays, leaf appearance stopped at the appearance of the fourth leaf. - After transplanting, leaf appearance resumed at a faster rate than in direct-seeded plants. - Transplanted plants had delayed panicle initiation and flowering time, more tillers, and more and larger leaves per tiller, but similar grain yield compared to direct-seeded plants at similar planting density.

plant biology↗

Differentiation of human adult-derived stem cells towards a neural lineage involves a de-differentiation event prior to re-differentiation to neural phenotypes

Although it has been reported that mesenchymal stem cells isolated from adult tissues can be induced to overcome their mesenchymal fate and transdifferentiate into neural cells, the findings and their interpretation have been challenged. The main argument against this process is that the cells rapidly adopt neuron-like morphologies through retraction of the cytoplasm rather than active neurite extension. In this study, we examined the sequence of biological events during neural differentiation of human periodontal ligament-derived stem cells (hPDLSCs), human bone marrow-derived stem cells (hBMSCs) and human dental pulp-derived stem cells (hDPSCs) by time-lapse microscopy. We have demonstrated that hPDLSCs, hBMSCs and hDPSCs can directly differentiate into neuron-like cells without passing through a mitotic stage and that they shrink dramatically and change their morphology to that of neuron-like cells through active neurite extension. Furthermore, we observed micronuclei movement and transient cell nuclei lobulation concurrent to in vitro neurogenesis from hBMSCs and hDPSCs. Our results demonstrate that the differentiation of hPDLSCs, hBMSCs and hDPSCs towards a neural lineage occurs through a de-differentiation step followed by re-differentiation to neural phenotypes, and therefore we definitively confirm that the rapid acquisition of the neural phenotype is via a differentiation trait.

neuroscience↗

OpenAWSEM with Open3SPN2: a fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMMs Custom Forces software framework. By utilizing GPUs, we achieve more than a 100-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a CPU. We showcase the benefits of OpenMMs Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsens early Nobel prize winning experiments [1] by using OpenMMs Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology. Author summaryThe cells most important pieces of machinery are large complexes of proteins often along with nucleic acids. From the ribosome, to CRISPR-Cas9, to transcription factors and DNA-wrangling proteins like the SMC-Kleisins, these complexes allow organisms to replicate and enable cells to respond to environmental cues. Computer simulation is a key technology that can be used to connect physical theories with biological reality. Unfortunately, the time and length scales accessible to molecular simulation have not kept pace with our ambition to study the cells molecular factories. Many simulation codes also unfortunately remain effectively locked away from the user community who need to modify them as more of the underlying physics is learned. In this paper, we present OpenAWSEM and Open3SPN2, two new easy-to-use and easy to modify implementations of efficient and accurate coarse-grained protein and DNA simulation forcefields that can now be run hundreds of times faster than before, thereby making studies of large biomolecular machines more facile.

molecular biology↗

Electrochemotherapy with bleomycin associated with doxorubicin induces tumor regression and decreases the proliferative index in canine cutaneous squamous cell carcinomas

Canine cutaneous squamous cell carcinoma (cSCC) is the most common skin cancer in dogs, and due to its low metastatic rate, local treatments such as electrochemotherapy (ECT) promote disease control or even complete remission and increase the survival time in most cases. This study aimed to evaluate the expression of BAX, Bcl-2, and Ki67 and clinical parameters in dogs with cSCC subjected to ECT. A prospective clinical nonrandomized study was performed in dogs with naturally occurring cSCC treated with ECT. Eighteen lesions (from 11 dogs) were selected, independent of breed, sex and age. The ECT protocol consisted of bleomycin plus doxorubicin followed by electric pulses characterized by 8 biphasic electric pulses lasting 100 ms, 1 Hz and 1000 V/cm. Among the 18 lesions, the lesion volume significantly decreased after treatment (p=0.04). The tumor size at D0 had no impact on survival time or prognosis (P>0.05). A decreased mitotic index was observed at compared with D0 (P=0.019). We also observed more intratumoral necrosis at D21 compared to D0 (P=0.041). The median expression level of Ki67 was 277.96 at D0 and 193.92 at D21. Thus, tumor samples had a lower proliferative index after ECT (D21) (P=0.031). The survival times of subjects with Ki67 values lower and higher than the Ki67 median value were not significantly different (P>0.05). Regarding apoptotic markers, there was no significant difference in BAX or Bcl-2 expression between D0 and D21 (P>0.05) or in overall survival between subjects with different levels of apoptotic markers. Furthermore, a positive correlation was observed between BAX and Bcl-2 before ECT (D0) (P=0.0379, r=0.5067). In conclusion, there was no change in BAX and Bcl-2 protein expression levels in response to ECT at the time points evaluated, and ECT was able to reduce tumor volume and cellular proliferation in cSCC.

cancer biology↗

Nuclear polymorphism and non-proliferative adult neurogenesis in human neural crest-derived cells.

Self-renewal and lineage regulation of neural stem cells in the adult mammalian brain (aNSCs) are still far from been understood. Although previous studies have reported that some aNSCs in neurogenic niches showed irregular nuclei, their functional significance remains elusive. We used neural crest-derived human periodontal ligament stem cells (hPDLSCs) as an in vitro cell model of neurogenesis to investigate the functional significance of nuclear polymorphisms. Here, we show that hPDLSCs-derived neurons are not directly generated through cell division from stem cells. In fact, the cell shape of neural precursors is reset and start their neuronal development as round spheres. The hPDLSCs-derived neurons gradually adopted a complex morphology by forming several processes, that grew and arborized, adquiring dendritic-like and axonal-like identities, giving rise to a variety of neuron-like morphologies. To our knowledge, this article provides the first observation of these morphological events during in vitro neurogenesis and neuron polarization in human aNCSCs, and we have discovered a transient cell nuclei lobulation coincident to in vitro neurogenesis, without being related to cell proliferation. We observed that small DNA containing structures move within the cell to specific directions and temporarily form lobed nuclei. Morphological analysis also reveals that neurogenic niches in the adult mouse brain contains cells with nuclear shapes highly similar to those observed during in vitro neurogenesis from hPDLSCs. Our results provide strong evidence that neuronal differentiation from aNSCs may also occur during in vivo adult mammalian neurogenesis without being related to cell proliferation. In addition, we demonstrate that hPDLSCs-derived neurons display a sequence of morphologic development highly similar to those observed in primary neuronal cultures derived from rodent brains during neurogenesis, providing strong evidence that it is possible to reproduce neurogenic processes and obtain neurons from hPDLSCs. Beyond the central nervous system, the presence of lobed nuclei has been reported in most blood and immune cells, but the functional significance of multilobed nuclear structures is not yet stablished. Our results suggest that multilobed nuclear structures is associated to nuclear movement within the cell.

neuroscience↗