Biology subjects

Sierra, J.

Publications and source records attributed to Sierra, J..

9 recordsLinked to original sources

bioRxiv2025

The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function

Risdiplam and branaplam represent two classes of small-molecule splicing modulators that promote U1 snRNP recognition of weak non-canonical GA/GU-containing 5 splice sites (ss). We demonstrated that branaplam enhanced recognition of these 5 ss by reconstituted U1 snRNP in vitro, and that this effect depended on the ZnF domain of U1C and Helix H of U1 snRNA, but not U1A or U1-70K. In cells, depletion of U1C generally reduced compound-induced exon inclusion for most cassette exons. Interestingly, a subset of cassette exons became responsive to compound only upon U1C knockdown, supporting a model in which U1C stabilizes specific conformations at the 5 ss/U1 snRNA interface in a context-dependent manner that can either facilitate or hinder compound binding. Surprisingly, risdiplam shows no effect on weak 5 ss recognition in vitro, suggesting additional cellular factors are required for its activity.

biochemistry↗

bioRxiv2024

Apocarotenoid signaling regulates meristem activity and shapes shoot and root lateral organ formation in Arabidopsis

Plant carotenoids are precursors to phytohormones and signaling molecules, playing critical roles in plant development, an emerging area of research. This study investigates the function of the undefined apocarotenoid ACS1 signal in modulating plant development, particularly its impact on the morphologenesis of lateral organs and apical meristems. By modulating ACS1 levels under varying light conditions, we demonstrate its dynamic role in leaf and root development. Notably the characteristic radial leaf morphology of the clb5 mutant reverts to normal even days post-germination, demonstrating that ACS1 is not a toxic signal but rather a key component of a biogenic retrograde signaling pathway. Transcriptomic analysis of clb5 seedlings at different post-germination stages underscores the critical role of ACS1 during specific developmental window. The expression profile of this mutant correlates with a proplastid stage, where even the expression of most of the genes involved in plastid biogenesis are downregulated. Furthermore, ACS1 disrupts the expression of diverse developmentally important genes, including those participating in auxin transport and signaling, leading to impaired meristem maintenance and inhibiting leaf expansion. The effects of ACS1 extends beyond photosynthetic tissues, impacting shoot and apical root meristem organization. In particular, ACS1 affects columella cell pattering, disrupting normal gravitropic responses. These findings demonstrate that ACS1 dynamically regulates both leaf and root development, as well as meristem activity. This study provides new insights into the role of cis-carotenoids as retrograde signals, functioning very early in the plastid differentiation and emphasizes the significance of plastid retrograde signaling in plant growth and development.

plant biology↗

bioRxiv2024

Impact of adolescent high-fat diet and psychosocial stress on neuroendocrine stress responses and binge eating behavior in adult male Lewis rats

Childhood obesity is a multifactorial disease affecting more than 160 million adolescents worldwide. Adolescent exposure to obesogenic environments, characterized by access to high-fat diets and stress, precipitates maladaptive eating habits in adulthood such as binge eating. Evidence suggests a strong association between Western-like high-saturated-fat (WD) food consumption and dysregulated hormone fluctuations. However, few studies have explored the long-term impact of adolescent WD and psychosocial stress on brain and behavior. This longitudinal study aimed to investigate the impact of adolescent exposure to an obesogenic diet on stress resiliency and increased susceptibility for binge-like eating behaviors. Adolescent male Lewis rats were given WD (41% fat; n=40) or control diet (CD, 16% fat; n=38) for 4 weeks before undergoing a stress paradigm of predator exposure and social instability (CDE, WDE, CDU, WDU; n=16/group). Subjects were provided intermittent WD access (24 h/week) to evaluate binge eating-like behavior in adulthood. Fecal corticosterone and testosterone were measured at four timepoints throughout adolescence and adulthood. WD rats exhibited increased body weight (p = 0.0217) and elevated testosterone in mid-adolescence (p=0.0312) and blunted stress-induced corticosterone response in mid-late adolescence (CDE:WDE, p=0.028). Adolescent hormone levels were negatively correlated with bingeing and explained the variability between adult rats expressing hyperphagic and hypophagic behaviors. These results demonstrate that exposure to WD in adolescence disrupts hormone fluctuations and stress responsivity, with effects persisting into adulthood. This underscores the importance of addressing obesogenic environments early to mitigate their lasting impact on hormone regulation and stress responsiveness.

neuroscience↗

bioRxiv2024

Shifts in Naturalistic Behaviors Induced by Early Social Isolation Stress are Associated with Adult Binge-like Eating in Female Rats

Binge eating (BE) is a highly pervasive maladaptive coping strategy in response to severe early life stress such as emotional and social neglect. BE is described as repeated episodes of uncontrolled eating and is tightly linked with comorbid mental health concerns. Despite social stressors occurring at a young age, the onset of BE typically does not occur until adulthood providing an interval for potential therapeutic intervention. Currently, our knowledge of longitudinal noninvasive digital biomarkers predictive of BE needs further development. Monitoring longitudinal impacts of adolescent social isolation stress on naturalistic behaviors in rats will enable the identification of noninvasive digital markers of disease progression to predict adult eating strategies. Recognizing adolescent naturalistic behaviors shaped by social stress informs our understanding of the underlying neurocircuits most effected. This study aimed to monitor and identify longitudinal behavioral shifts to enhance predictive capabilities in a rat model of social isolation stress-induced BE. We placed Paired (n=12) and Socially Isolated (SI, n=12) female rats in observational home cages weekly for seven weeks to evaluate the effect of SI on 10 naturalistic behaviors. All 10 naturalistic behaviors were simultaneously detected and tracked using Noldus Ethovision XT automated recognition software. Composite phenotypic z-scores were calculated by standardizing all 10 behaviors. When transitioning into adulthood, all rats underwent conventional emotionality testing and were exposed to a Western-like high fat diet (WD, 43% kcal from fat) to evaluate BE. Longitudinal assessments revealed SI-induced shifts in adolescent phenotypic z-scores and that sniffing, unsupported rearing, jumping, and twitching were the most susceptible to SI. SI increased emotionality compared to the Paired controls. Finally, we identified adolescent twitching as a digital biomarker of adult WD consumption. This study employed novel approaches to identify early life predictive biomarkers of adult eating strategies and laid a foundation for future investigations.

neuroscience↗

bioRxiv2024

Tumor microenvironment noise-induced polarization: the main challenge in macrophages' immunotherapy for cancer.

Disturbance of epigenetic processes can lead to altered gene function and malignant cellular transformation. In particular, changes in the epigenetic landscape are a central topic in cancer biology. The initiation and progression of cancer are now recognized to involve both epigenetic and genetic alterations. In this paper, we study the epigenetic mechanism (related to the tumor microenvironment) responsible for increasing tumor-associated macrophages that promote the occurrence and metastasis of tumor cells, support tumor angiogenesis, inhibit T cell-mediated anti-tumor immune response, and lead to tumor progression. We show that the tumor benefits from the macrophages high degree of plasticity and larger epigenetic basins corresponding to phenotypes that favor cancer development through a process that we call noise-induced polarization. Moreover, we propose a mechanism to promote the appropriate epigenetic stability for immunotherapies involving macrophages, which includes p53 and APR-246 (eprenetapopt). Our results show that a combination therapy may be necessary to ensure the proper epigenetic stability of macrophages, which otherwise will contribute to cancer progression. On the other hand, we conclude that macrophages may remain in the anti-tumoral state in types of cancer that exhibit less TP53 mutation, like colorectal cancer; in these cases, macrophages immunotherapy may be more suitable. We finally mention the relevance of the epigenetic potential (Waddingtons landscape) as the backbone for our study, which encapsulates the biological information of the system.

cancer biology↗

bioRxiv2023

Human Placenta-Derived Mesenchymal Stem Cells Stimulate Neuronal Regeneration By Promoting Axon Growth And Restoring Neuronal Activity

Cell therapy is a cutting-edge medical approach that involves the use of cells to treat various diseases and conditions. It harnesses the remarkable regenerative and reparative abilities of cells to restore or replace damaged tissues and promote healing. In the last decades, mesenchymal stem cells (MSCs) have become the cornerstone of cellular therapy due to their unique characteristics. Specifically human placenta-derived mesenchymal stem cells (hPMSCs) are highlighted for their unique features, including ease to isolate, non-invasive techniques for large scale cell production, significant immunomodulatory capacity, and a high ability to migrate to injuries. Researchers are exploring innovative techniques to overcome the low regenerative capacity of Central Nervous System (CNS) neurons, with one promising avenue being the development of tailored mesenchymal stem cell therapies capable of promoting neural repair and recovery. In this context, we have evaluated hPMSCs as candidate for CNS lesion regeneration using a skillful co-culture model system. Indeed, we have demonstrated the hPMSCs ability to stimulate damaged rat-retina neurons regeneration by promoting axon growth and restoring neuronal activity both under normoxia and hypoxia conditions. With our model we have obtained neuronal regeneration values of 10-12% and axonal length per neuron rates of 19.99{+/-}0.77, m/neuron. To assess whether the regenerative capabilities of hPMSCs are contact-dependent effects or it is mediated through paracrine mechanisms, we carried out transwell co-culture and conditioned medium experiments confirming the role of secreted factors in axonal regeneration. It was found that hPMSCs produce brain derived, nerve growth factors (BDNF, NGF) and Neurotrophin-3, involved in the process of neuronal regeneration and restoration of their physiological activity of neurons. The capability to access axonal physiology is crucial for studying information processing among neurons in healthy and diseased states. We confirm the success of our treatment using the patch clamp technique to study ionic currents in individual isolated living cells, confirming that in our model the regenerated neurons are electrophysiologically active.

cell biology↗

bioRxiv2023

GENERATION OF FUNCTIONAL NEURONS FROM ADULT HUMAN MUCOSAL OLFACTORY ENSHEATHING GLIA BY DIRECT LINEAGE CONVERSION

A recent approach to promote central nervous system (CNS) regeneration after injury or disease is direct conversion of somatic cells to neurons. This is achieved by transduction of viral vectors that express neurogenic transcription factors. In this work we propose adult human mucosal olfactory ensheathing glia (hmOEG) as a candidate for direct reprogramming to neurons due to its accessibility and to its well-characterized neuro-regenerative capacity. After induction of hmOEG with the single neurogenic transcription factor NEUROD1, the cells under study exhibited morphological and immunolabeling neuronal features, fired action potentials and expressed glutamatergic and GABAergic markers. In addition, after engraftment of transduced hmOEG cells in mouse hippocampus, these cells showed specific neuronal labeling. Thereby, if we add to the neuro-regenerative capacity of hmOEG cultures the conversion to neurons of a fraction of their population through reprogramming techniques, the engraftment of hmOEG and hmOEG induced neurons could be a procedure to enhance neural repair after central nervous system injury.

neuroscience↗

bioRxiv2021

Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto full-length proteins with precise control over chain length and modification site. A series of semi-synthetic ADP-ribosylated histone proteins are prepared which demonstrate that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. Importantly, we found ALC1 selectively remodels activated substrates within heterogeneous nucleosome populations and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a method that is broadly applicable to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.

biochemistry↗

bioRxiv2018

Spatio-temporal regulation of Dachsous proteins expressed during Drosophila development

Transcriptional regulation is one of the main mechanisms involved in tissue morphogenesis to give rise to functional organs with characteristic shapes. The Drosophila dachsous (ds) gene plays a key role in tissue development and tumorigenesis by controlling planar cell polarity (PCP), tissue growth, patterning and mitochondrial activity, among other processes. Disturbance of ds expression during Drosophila development results in alterations of the function and morphology of a wide range of embryonic and larval tissues. Similarly, in humans, mutations in the DCHS1 gene cause severe congenital malformations due to a global impairment affecting the normal formation of many tissues and organs. However, the transcriptional mechanism governing the expression of ds gene remains poorly understood. Here, we perform transcriptional analysis of ds expression and identify novel embryonic Ds proteins not expressed in larvae. The comparative analysis of Ds proteins and the exon expression pattern in/of two regulatory alleles such as dsD36 and ds38K further suggests the existence of specific transcriptional ds variants at different stages. Furthermore, a search for regulatory elements that control the spatial and temporal pattern of ds revealed the presence of cis-regulatory elements located in the intronic regions, which regulate the expression of these Ds proteins. Finally, using the Drosophila wing as model to perform a functional analysis, we show that wing growth and PCP are differentially regulated by Ds proteins expressed in different regions of wing disc. The present findings reveal that the complex regulation of the ds gene ensures the expression of specific Ds protein isoforms at different developmental stages in order to activate the cell-specific molecular programs required for tissue morphogenesis.

genetics↗