Biology subjects

Aldabe, R.

Publications and source records attributed to Aldabe, R..

5 recordsLinked to original sources

bioRxiv2025

In-depth 3D Exploration of Autosomal Dominant Polycystic Kidney Disease Through Light Sheet Fluorescence Microscopy

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most prevalent genetic kidney disorder. Animal preclinical studies are one of the main tools to study this disease, often through either 2D histology imaging for high-resolution analysis or CT or MRI for full kidney segmentation. As an alternative to these modalities, we propose the use of Light Sheet Fluorescence Microscopy (LSFM) for high-resolution 3D imaging of healthy and ADPKD-induced mouse kidneys, enabling a detailed volumetric morphological analysis of the diseases effects. In a mouse ADPKD model, ex vivo imaging of the kidneys was performed through LSFM, after which a combination of machine learning and other processing techniques allowed us to perform an in-depth image analysis. This includes the segmentation of key structures, such as the full kidney volume and, within it, its internal cavities, cortex, glomeruli, and cysts, complemented by texture analysis of tubular structures in the cortical area. Pathological kidneys exhibited significant volume enlargement and increased internal cavities due to cystogenesis. While glomerular count remained stable, their spatial distribution was altered, showing increased interglomerular distances and show-casing the deformations produced by the disease. The texture analysis of tubules from the cortex region identified Local Binary Pattern (LBP) uniformity and porosity as key biomarkers of tissue deformation, which could be used as markers to further evaluate the development of the disease. These findings underscore the potential of LSFM imaging as a powerful tool for detailed ADPKD characterization and treatment assessment.

bioengineering↗

bioRxiv2024

SAM-based Automatic Workflow for Histology Cyst Segmentation in Autosomal Dominant Polycystic Kidney Disease

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a genetic disorder characterized by the development of numerous cysts in the kidneys, ultimately leading to significant structural alterations and renal failure. Detailed investigations of this disease frequently utilize histological analyses of kidney sections across various stages of ADPKD progression. In this paper, we introduce an automated workflow leveraging the Segment Anything Model (SAM) neural network, complemented by a series of post-processing steps, to autonomously segment cysts in histological images. This approach eliminates the need for manual annotations or preliminary training phases and enables precise quantification of cystic changes over entire kidney sections. Application of this method to sequential histology images across the development timeline of ADPKD in mice demonstrated a notable increase in the proportion of diseased tissue from 8 to 12 weeks and from 12 to 16 weeks, with the cysts appearing progressively lighter. Our workflow not only surpasses the performance of the existing Cystanalyser tool but also offers enhanced flexibility and accuracy in full-image segmentation. The developed workflow is made publicly accessible to facilitate its adoption as an efficient tool for rapid and reliable cyst segmentation in histological studies.

bioinformatics↗

bioRxiv2023

Protective Role of RIPK1 Scaffolding against HDV-Induced Hepatocyte cell death and the Significance of Cytokines in Mice

Hepatitis delta virus (HDV) infection represents the most severe form of human viral hepatitis; however, the mechanisms underlying its pathology remain incompletely understood. We recently developed an HDV mouse model by injecting adeno-associated viral vectors (AAV) containing replication-competent HBV and HDV genomes. This model replicates many features of human infection, including liver injury. Notably, the extent of liver damage can be diminished with anti-TNF- treatment. In the present study, we found that TNF- is mainly produced by macrophages. Downstream of the TNF- receptor (TNFR), the receptor-interacting serine/threonine-protein kinase 1 (RIPK1) serves as a cell fate regulator, playing roles in both cell survival and death pathways. In this study, we explored the function of RIPK1 and other host factors in HDV-induced cell death. We determined that the scaffolding function of RIPK1, and not its kinase activity, offers partial protection against HDV-induced apoptosis. A reduction in RIPK1 expression in hepatocytes through Cas9-mediated gene editing significantly intensifies HDV-induced damage. Contrary to our expectations, the protective effect of RIPK1 was not linked to TNF- or macrophage activation, as their absence did not alter the extent of damage. Intriguingly, in the absence of RIPK1, macrophages confer a protective role. However, in animals unresponsive to type-I IFNs, RIPK1 downregulation did not exacerbate the damage, suggesting RIPK1s role in shielding hepatocytes from type-I IFN-induced cell death. Interestingly, while the damage extent is similar between IFNAR KO and WT mice in terms of transaminase elevation, their cell death mechanisms differ. In conclusion, our findings reveal that HDV-induced type-I IFN production is central to inducing hepatocyte death, and RIPK1s scaffolding function offers protective benefits. Thus, type-I IFN together with TNF-, contribute to HDV-induced liver damage. These insights may guide the development of novel therapeutic strategies to mitigate HDV-induced liver damage and halt disease progression. Author summaryHepatitis D is the most aggressive form of viral hepatitis. Our manuscript underscores the complexity of HDV-induced liver damage, where both viral and host factors play significant roles. Previously, we demonstrated that pharmacological inhibition of TNF- reduced HDV-induced liver damage. This result was corroborated in the present study using TNF--deficient mice. Moreover, we reported that the expression of the HDV antigen might have a cytotoxic effect, and HDV replication induces a strong activation of the innate immune system, accompanied by a substantial production of IFN-{beta}. In this study, we discovered that RIPK1, a molecule described as a cell fate modulator acting downstream of TNF-, plays a protective role during HDV replication. Contrary to our expectations, neither TNF- nor macrophages, the primary producers of TNF-, contributed to this protective effect. Instead, it seems type I IFN was involved. Interestingly, the role of type I IFN in HBV-induced liver damage has recently been proposed. Furthermore, our data reveals that several mechanisms of hepatocyte death are at play simultaneously during HDV replication, with apoptosis being one of them. Additional studies are needed to identify other mechanisms involved. Finally, these findings suggest that therapies targeting TNF- and type-I IFN, or those increasing RIPK1 levels, might be effective in preventing or treating HDV-induced liver damage.

pathology↗

bioRxiv2023

NatB-dependent acetylation protects procaspase-8 from UBR4-mediated degradation and is required for full induction of the extrinsic apoptosis pathway

N-terminal acetyltransferase B (NatB) is a major contributor to the N-terminal acetylome and is implicated in several key cellular processes including apoptosis and proteostasis. However, the molecular mechanisms linking NatB-mediated N-terminal acetylation to apoptosis and its relationship with protein homeostasis remain elusive. In this study, we generated mouse embryonic fibroblasts (MEFs) with an inactivated catalytic subunit of NatB (Naa20-/-) to investigate the impact of NatB deficiency on apoptosis regulation. Through quantitative N-terminomics, label-free quantification, and targeted proteomics, we demonstrated that NatB does not influence the proteostasis of all its substrates. Instead, our focus on putative NatB-dependent apoptotic factors revealed that NatB-mediated acetylation serves as a protective shield against UBR4 and UBR1 Arg/N-recognin-mediated degradation. Notably, Naa20-/- MEFs exhibited reduced responsiveness to extrinsic pro-apoptotic stimuli, a phenotype that was partially reversible upon UBR4 Arg/N-recognin silencing and consequent inhibition of procaspase-8 degradation. Collectively, our results shed light on how the interplay between NatB-mediated acetylation and the Arg/N-degron pathway impacts apoptosis regulation, providing new perspectives in the field including in therapeutic interventions.

biochemistry↗

bioRxiv2023

Evaluating possible maternal effect lethality of Naa10 knockout mice, and modulation of phenotypes for embryonic and neonatal lethality by genetic background and environment

Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/ymale mice on the inbred genetic background in this different animal facility.

genetics↗