Biology subjects

Ruiz-Cabello, J.

Publications and source records attributed to Ruiz-Cabello, J..

7 recordsLinked to original sources

bioRxiv2026

Sensitivity of Pulmonary 4D Flow MRI Biomarkers to Controlled Spatial and Temporal Degradation in a CFD Benchmark

Purpose: To quantify, in a computational fluid dynamics (CFD) benchmark, how spatial degradation, temporal acquisition and noise change the error of plane-based pulmonary-artery flow endpoints. Methods: Twenty-two historical, non-converged CFD simulations (11 geometry families) were voxelised at 2 mm with 80 frames per cycle. Simulations with numerical divergence were excluded, leaving 13 (7 families). Fields were degraded to 4 and 8 mm and with noise, plane waveforms were sampled at 20 phases with one-interval averaging, and errors were computed against the noise-free reference waveform on 66 geometric planes. Family-mean paired differences are reported with t-based 95% confidence intervals under an analysis plan fixed in advance. Results: Spatial degradation from 2 to 4 mm increased full-waveform nRMSE by 0.0032 [0.0021, 0.0043], in 7 of 7 families; cycle-mean flow bias accounted for 23% of the squared error, against 60% at 8 mm. With SNR scaled to voxel volume, the increase was not resolved (0.0002 [-0.0012, 0.0015]). Twenty-phase acquisition increased PI error (0.0223 [0.0214, 0.0233]) and diastolic-trough timing error (0.63 [0.52, 0.74] frames) more than spatial degradation, and its point estimates for these endpoints were larger with every recovery method; the nRMSE ordering and peak timing depended on the recovery method. The implementation of the downsampling operator mattered: an alternative, corner-aligned implementation of the same 4 mm degradation gave a larger spatial effect (nRMSE difference 0.0010 [0.0002, 0.0017]). Conclusion: In this benchmark, a 2 to 4 mm degradation produced a small, consistent, mostly shape-related nRMSE increase that depended on the noise model, whereas 20-phase acquisition changed PI error and trough timing more. The results describe benchmark behaviour, not clinical acquisition requirements.

bioengineering↗

bioRxiv2026

Biomarker-Aware Super-Resolution for 4D Flow MRI in a Synthetic Pulmonary-Artery Benchmark

Purpose: To evaluate, within a synthetic pulmonary-artery benchmark, whether biomarker-aware super-resolution improves hemodynamic endpoint fidelity in 4D flow MRI. Methods: A 3D residual channel attention network (RCAN) was trained on 22 CFD simulations from 11 pulmonary-artery geometries with 2x spatial degradation. The original primary comparison evaluated full biomarker-aware training against a combined divergence-temporal-regularization control across 14 matched seeds on a fixed six-case test set. Additional matched analyses subsequently separated divergence and adjacent-frame temporal-difference regularization and evaluated biomarker supervision in a controlled 2x2 design with a common reconstruction schedule. Results: In the original primary comparison, biomarker-aware training reduced PI error relative to the matched combined-regularization control (12.76 +/- 2.34% vs. 17.12 +/- 1.23%; paired difference -4.35 percentage points [95% CI -5.58, -3.09]; p = 0.0015). In the matched factorial analysis, biomarker supervision reduced PI error without (-2.235 percentage points [95% CI -3.514, -0.849]) and with (-4.125 percentage points [95% CI -5.392, -2.732]) combined regularization. PI improvement was not mirrored by uniformly improved reconstruction metrics: PSNR changed by -0.058 (p = 0.50) and +0.144 dB (p = 0.28), while SSIM decreased by 0.009 (p = 0.004) and 0.007 (p = 0.009), respectively. Divergence alone changed PI by +0.034 percentage points [95% CI -0.705, 0.809] while reducing DivRMS by 1.869 percentage points; temporal-difference regularization increased PI error by 1.562 percentage points [95% CI 0.594, 2.439]. Conclusion: Within this synthetic, fixed-case RCAN benchmark, biomarker supervision improved PI under both regularization conditions. PI improvement was not mirrored by uniformly improved reconstruction metrics. Temporal-difference - not divergence - regularization was the only isolated component associated with reproducible PI deterioration. These findings are configuration-specific and require geometry-independent and in vivo validation.

bioengineering↗

bioRxiv2026

Membrane surface geometry is a determinant of mitochondrial electron transfer and cellular adaptation

Energy conversion in living organisms relies on biological membranes that facilitate electron transfer between oxidoreductases. In mitochondria, this process is mediated by the electron transport chain embedded in the inner mitochondrial membrane (IMM). Under various physiological and genetic conditions, mitochondrial matrix Na+ levels increase, reducing IMM fluidity through the formation of ternary coordination adducts between Na+ and phospholipids. These adducts impair ubiquinone (CoQ) transfer between respiratory complexes, thereby promoting mitochondrial reactive oxygen species (mtROS) production and activating the hypoxic adaptive pathway. Here, we show that modifying solely the ionic subatomic interaction with phospholipids is sufficient to prevent initiation of this pathway. Compound A (CA) outcompetes Na+ for phospholipid binding without impairing CoQ transfer, thereby preventing mtROS production and hypoxic adaptation. This divergence arises from the penta-coordinate complexes formed by CA with phospholipids, in contrast to the trigonal adducts formed by Na+. This structural distinction preserves IMM fluidity because CA:phospholipid assemblies adopt a less angular configuration. These findings establish membrane-surface geometry, modulated by ion:phospholipid interactions, as an unexpected determinant of membrane biology, mitochondrial energy conversion, redox signalling, and cellular adaptation, with profound implications for physiology and disease.

biochemistry↗

bioRxiv2025

Mitochondrial genetics defines anti-tumour immunity through mitochondrial ROS and PD-1 signalling

As central players in cell metabolism, mitochondria influence numerous aspects of health and disease, including the initiation and progression of cancer. Although mitochondrial DNA (mtDNA) mutations have been extensively documented in human cancers for decades, the functional impact of mitochondrial haplogroups on tumour biology remains largely unexplored. Here, we investigate the role of mitochondrial variability in tumour biology using conplastic mouse strains, which are animal models with identical nuclear genomes but different mtDNA haplotypes. We showed that the physiologically relevant variation in mitochondrial ROS (mROS) generation, associated with specific clusters of mtDNA single nucleotide polymorphisms (SNPs), modulated immune responses within the tumour microenvironment and altered tumour growth. We observed strain-dependent differences in the abundance of multiple immune subsets and in PD-1 expression in tumour-infiltrating lymphocytes (TILs). In addition, mtDNA haplotypes influenced cancer progression by modulating tumour angiogenesis through an mROS-independent mechanism. These findings connect nucleo-mitochondrial genetic variability to tumour progression, de novo vessel formation and anti-tumour immunity. Tumour immunotherapies should incorporate the spatial and temporal dynamics of cancer evolution and consider mitochondrial genetics as a targetable layer influencing treatment efficacy.

cancer biology↗

bioRxiv2024

Energy scarcity and impaired mitochondrial translation induce perinuclear stress granule clustering

Many proteins linked to amyotrophic lateral sclerosis and fronto-temporal dementia (ALS-FTD) change their cellular location and coalesce in cytoplasmic inclusion bodies in the disease state; yet the factors that govern protein relocation and organization remain unclear. Here, we show that inhibition of glycolysis and mitochondrial protein synthesis causes many proteins involved in ALS-FTD to change location, and form a novel structure comprising a ring of stress granules encircling the aggresome, a focal microtubule-based structure beside the nucleus. A perinuclear ring of stress granules also forms in activated microglia of mice exposed to the glycolytic inhibitor, 2-Deoxy-D-glucose. We propose that the new arrangement increases the risk of the stress granules merging and converting from the liquid phase to the insoluble inclusion characteristic of ALS-FTD. Thus, our findings suggest that that compromised nutrient and energy metabolism can precipitate a molecular cascade that ultimately leads to the pathological hallmark of ALS-FTD the perinuclear inclusion body. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/578399v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@b32d48org.highwire.dtl.DTLVardef@161f848org.highwire.dtl.DTLVardef@f35c66org.highwire.dtl.DTLVardef@1375508_HPS_FORMAT_FIGEXP M_FIG C_FIG Inhibition of glycolysis and mitochondrial protein synthesis induces translocation of a swathe of ALS-FTD related proteins in primary human fibroblasts. The relocated proteins form concentric cytoplasmic rings (CCR) comprising stress granules, the Golgi and the aggresome, beside the nucleus. A perinuclear ring of stress granules forms in the mouse brain following intermittent nutrient restriction, with the glucose analog 2DG. The CCR is potentially a key intermediate step in the formation of pathological inclusions and so perturbed nutrient and energy metabolism encompassing impaired mitochondrial translation could precipitate the ALS-FTD disease cascade.

cell biology↗

bioRxiv2024

Activation of HIF2 leads to vascular remodeling and inflammation, coronary thrombosis and arterial dilation, recapitulating cardiac involvement of Kawasaki disease.

Backgroundglobal deletion of Vhl leads to vascular defects and early lethality, precluding the study of VHL/HIF signaling during coronary formation and homeostasis. Hypoxia pathway has been associated with cardiovascular diseases involving inflammation and vascular remodeling like atherosclerosis, but its role in Kawasaki Disease (KD) remains unknown. Coronary dilatation and vessel rupture are the most serious complications of KD, while the molecular mechanisms underlying these cardiac events remain poorly understood. Here we aim to determine the function of VHL/HIF pathway in the development of cardiovascular defects and its role in KD. MethodsWe generated a new mouse model to genetically hyperactivate hypoxia pathway in progenitors contributing to coronary vessels and cardiac fibroblasts (Vhl/Wt1). We characterized the model by means of echocardiography, magnetic resonance imaging, histological analysis and molecular approaches. Human cardiac tissue from KD individuals suffering fatal coronary aneurysm were screened for HIF signaling and inflammatory markers by immunohistochemistry. Resultsconditional Vhl KO do not undergo developmental abnormalities but displays cardiomegaly and epicardial vascular defects, with cardiac hypertrophy and progressive coronary diameter increase, as well as pericardial hemorrhage and systemic inflammation early after birth. Histological characterization reveals inflammation of coronary arteries, vascular remodeling with elastin breaks and dilatation, increased perivascular fibrosis and smooth muscle cells death, together with high incidence of intracoronary thrombus formation. In addition, the mutants display vascular calcification and severe cardiac inflammation and interstitial hemorrhages, dying suddenly between 15-20 weeks of age due to vessel rupture. Simultaneous elimination of HIF2 and VHL prevents the cardiovascular abnormalities displayed by single cVhl KO, highlighting the essential role of HIF2 in coronary instability and vascular inflammation. Histological characterization of human cardiac samples shows positive signal for HIF1 and specially HIF2, in the coronary lesions and its surroundings in regions with high inflammatory infiltration, confirming the activation of hypoxia signaling in KD patients with cardiovascular complications. ConclusionsOur data demonstrate the importance of HIF2 signaling in the development of coronary inflammation and vascular remodeling and provide new evidences connecting low oxygen tensions with cardiovascular lesions occurring during the onset of the most severe cases of KD. Furthermore, the Vhl/Wt1 mouse generated recapitulates cardiac features of KD with critical heart complications, providing a new platform to uncover unknown aspects of KD pathogenesis.

pathology↗

bioRxiv2020

HAP-multitag, a PET and positive MRI contrast nanotracer for the longitudinal characterization of vascular calcifications in atherosclerosis

Vascular microcalcifications are associated with atherosclerosis plaque instability and, therefore, to increased mortality. Because of this key role, several imaging probes have been developed for their in vivo identification. Among them [18F]FNa is the gold standard, showing a large uptake in the whole skeleton. Here, we push the field towards the combined anatomical and functional early characterization of atherosclerosis. For that, we have developed HAP-multitag, a bisphosphonate-functionalized 68Ga magnetic nanoparticle showing high affinity towards most common calcium salts present in microcalcifications, particularly hydroxyapatite. We characterized this interaction in vitro and in vivo, showing a massive uptake in the atherosclerotic lesion identified by PET and positive contrast MRI. In addition, this accumulation was found to be dependent on the calcification progression, with a maximum uptake in the microcalcification stage. These results confirmed the ability of HAP-multitag to identify vascular calcifications by PET/(T1)MRI during the vulnerable stages of the plaque progression.

bioengineering↗