Biology subjects

Martin, S. A.

Publications and source records attributed to Martin, S. A..

12 recordsLinked to original sources

bioRxiv2026

Biomarker Fidelity Score - A Quantitative Framework for Individual-Level Validation of Explainability Methods in 3D Alzheimer's Disease MRI Classification

Explainability methods applied to deep learning models for Alzheimer's disease neuroimaging produce attribution maps that vary substantially across methods and architectures, yet no validated quantitative framework exists for determining which method most faithfully localises attribution signal within established AD biomarker anatomy at the individual subject level. Existing validation approaches rely on group-level comparisons or qualitative visual inspection, leaving individual-level biomarker alignment uncharacterised. We introduce the Biomarker Fidelity Score (BFS), a quantitative tool measuring spatial overlap between individual-level 3D explainability attention maps and atlas-registered AD-relevant neuroimaging ROIs across thirteen anatomically defined structures including hippocampus, entorhinal cortex, amygdala, and parahippocampal gyrus. Five explainability methods (GradCAM++, Integrated Gradients, DeepSHAP, LRP, ScoreCAM) were benchmarked across three volumetric architectures (3D ResNet-18, DenseNet-121, Swin-UNETR) on 327 balanced ADNI-3 subjects. Integrated Gradients achieved the highest BFS across all architectures while GradCAM++ consistently showed the lowest biomarker alignment (all p<0.001, Friedman test). The complete BFS pipeline replicated these rankings without retraining on 207 independent OASIS-3 subjects, with maximum absolute difference of 0.0005 across all fifteen method-architecture combinations and Spearman rank correlation of 0.964 between cohort rankings. By offering an externally validated, individual-level, biomarker-grounded quantitative standard, BFS equips clinicians and AI developers with practical guidance for selecting trustworthy explainability methods in AD neuroimaging.

neuroscience↗

bioRxiv2026

Chaperone condensates buffer the heat shock response against pleiotropic inputs

Stress response pathways can be specific, dedicated to one stimulus, or pleiotropic, funneling distinct perturbations into a shared program. The heat shock response (HSR), the Hsf1-driven transcriptional program, has been linked to numerous stresses, suggesting it is pleiotropic. Here we find that high amplitude HSR activation is specific to heat shock in budding yeast. Heat shock activates the HSR through a condensate cascade in which orphan ribosomal proteins condense with Sis1 and Hsp70, titrating these chaperones away from their repressive interactions with Hsf1, triggering Hsf1 condensation with the transcriptional machinery, and activating HSR genes. Other stressors likewise drive Sis1 and Hsp70 condensation, redeploying Sis1 to stimulus-specific subcellular sites. However, chaperone condensation is not sufficient to activate the HSR. Sis1 and Hsp70 condense under conditions in which the HSR remains inactive, and Sis1 depletion increases HSR activation under all conditions except heat shock. These results suggest that chaperone condensates buffer the HSR, setting a threshold for activation and imparting specificity.

cell biology↗

bioRxiv2026

Bone microarchitecture and material properties decline differently across midlife for male and female F344 x BN F1 rats

While bone mineral density (BMD) remains the clinical standard for assessing age-related fracture risk, accumulating evidence indicates that bone quality, including matrix properties and microarchitecture, contributes to fracture susceptibility in ways not captured by BMD alone. As matrix-targeted therapeutics emerge, preclinical models that exhibit translationally relevant bone quality changes are needed. Here, we evaluated the Fischer 344 x Brown Norway (F344xBN) F1 rat, a strain characterized by hybrid vigor and non-pathological aging, as a model for studying matrix-related mechanisms of skeletal aging. Femurs from male and female rats aged 7, 15, and 22 months were analyzed to quantify age- and sex-dependent changes in bone microarchitecture, fracture resistance, and matrix properties. Microcomputed tomography analyses revealed sexually dimorphic aging trajectories. From 7 to 22 months, females exhibited moderate declines in trabecular microarchitecture and no change in cortical porosity, whereas males showed pronounced trabecular deterioration and increased cortical porosity. Whole-bone flexural testing demonstrated age-related declines in material properties that were not attributable to changes in geometry, while females maintained geometry-scaled bone strength. Both sexes exhibited reduced bone toughness with age. Raman spectroscopy identified matrix-level alterations in males by 15 months, whereas systemic markers of bone turnover remained unchanged across age or sex. Together, these findings indicate that males exhibit combined tissue-scale and whole-bone deterioration by midlife, while females exhibit declining fracture resistance preceding substantial cortical bone loss or overt matrix deterioration. These results support the F344xBN F1 rat as a translational model for investigating matrix-driven skeletal aging. Lay summaryF344 x BN F1 hybrid rats provide a healthy, matrix-driven skeletal aging model. This strain exhibits distinct aging trajectories dependent on sex. Strength and toughness decrease in both sexes by midlife. Fracture resistance declines in females prior to substantial bone loss.

physiology↗

bioRxiv2025

Intracellular aggregation of the transthyretin protein is limited by Hsp70 chaperones

Extracellular amyloid deposits are a hallmark feature of systemic protein aggregation diseases such as transthyretin amyloidosis (ATTR). However, emerging evidence suggests that extracellular transthyretin (TTR) aggregates are internalized and result in an intracellular stress response, including elevated Hsp70 levels. While ATTR research has predominantly focused on extracellular TTR amyloid, our understanding of TTR aggregation inside the cell is poorly explored. To better understand how intracellular chaperones impact intracellular TTR, we used a yeast model that expresses TTR fused eGFP (TTR-eGFP) within the cytoplasm. Since the Hsp70 chaperone family, and co-chaperones the J-domain proteins (JDPs) and Hsp110, act as a disaggregase in vitro, we asked how these molecular chaperones impact TTR aggregation intracellularly in vivo. TTR-eGFP forms detergent-soluble high molecular weight (HMW) aggregates in yeast that have biochemistry profiles similar to human patient TTR. While knockdown of the JDP, Sis1, and deletion of the Hsp110, Sse1, appear to slightly increase TTR-eGFP aggregation, the loss of two major yeast Hsp70s, Ssa1 and Ssa2, lead to a significant increase in the size of HMW species. Taken together, our data suggest that Hsp70s limit the formation of HMW TTR aggregates in the intracellular environment. Based on our results, it is possible that the age-related decline of protein homeostasis, including Hsp70s, may promote the intracellular aggregation of TTR.

biochemistry↗

bioRxiv2025

Stress granules and protein aggregates reveal intracellular resource competition

Stress granules are biomolecular condensates that form in response to environmental stress and disassemble once normal conditions are restored. However, when disassembly fails, stress granules can persist and solidify. While stress granule solidification has been well documented, the cellular mechanisms underlying the transition from reversible to persistent stress granules remain unclear. Persistent stress granules can seed the formation of pathological aggregates, such as TDP-43 in amyotrophic lateral sclerosis1, 2. Although amyloid and tau aggregates are hallmarks of Alzheimers disease, a subset of patients also develop TDP-43 deposits, suggesting a possible role for stress granule solidification in Alzheimers disease progression3-5. Despite theoretical models explaining why persistence and ensuing solidification occurs, strong in vivo evidence is lacking6. Here we show that competition for limited chaperone resources drive stress granule persistence. In the presence of TDP-43 aggregates or yeast amyloid proteins called prions, stress granule disassembly is slowed or halted disassembly. Using yeast prions as a model, we show that the addition of chaperones, specifically the AAA+ ATPase molecular chaperone, Hsp104, resulted in resumption of stress granule disassembly. Our results demonstrate that the competition for shared resources, such as molecular chaperones, can limit stress granule disassembly. We suspect that the presence of pathological aggregates results in resource competition within the aging brain, contributing to the persistence of stress granules and their subsequent solidification and aggregation.

cell biology↗

bioRxiv2025

Calbindin Stratifies Midbrain Dopaminergic Neurons Governing Distinct Aspects of Locomotion

Despite advances in delineating the molecular diversity and projection patterns of midbrain dopaminergic (DA) neurons, their specific contributions to locomotion and motor learning remain poorly defined. Here, we applied intersectional ablation and chemogenetic approaches to dissect the distinct roles of calbindin-expressing (CALB1+) and non-expressing (CALB1-) DA neurons in locomotion. Using newly engineered intersectional constructs, we ablated CALB1+ or CALB1- DA neurons in the mouse midbrain. Loss of either subtype led to pronounced deficits in the initiation and vigor of voluntary movements, as demonstrated by a reduction in peak speed, acceleration and deceleration of locomotor bouts. Notably, only CALB1- ablation disrupted locomotor learning. Beyond these functional effects, we observed that selective ablation of CALB1 DA neurons induced local microglial activation and was followed by a non-cell-autonomous loss of CALB1- DA neurons, suggesting that CALB1- neurons are more vulnerable to inflammation triggered by CALB1 neuron loss. We then confirmed these findings by performing acute inhibition of either population using inhibitory DREADD hM4Di. CALB1- DA neurons inhibition impaired the initial acquisition of locomotor learning, whereas inhibition of CALB1+ DA neurons disrupted the retention of acquired motor skills from previous days. Moreover, inhibition of CALB1+ DA neurons further impaired the initiation and amplitude of voluntary movements, as well as the velocity and acceleration/deceleration of locomotor bouts. Together, these findings provide causal evidence for functional specialization among molecularly distinct midbrain DA subtypes and reveal new aspects of mesostriatal circuit organization underlying locomotion and motor memory.

neuroscience↗

bioRxiv2025

Hsp70 chaperones, Ssa1 and Ssa2, limit poly(A) binding protein aggregation

Molecular chaperones play a central role in maintaining protein homeostasis. The highly conserved Hsp70 family of chaperones have major functions in folding of nascent peptides, protein refolding, and protein aggregate disassembly. In yeast, loss of two Hsp70 proteins, Ssa1 and Ssa2, is associated with decreased cellular growth and shortened lifespan. While heterologous or mutant temperature sensitive proteins form anomalous large cytoplasmic inclusions in ssa1{Delta}ssa2{Delta} strains, it is unclear how endogenous wildtype proteins behave and are regulated in the presence of limiting Hsp70s. Using the wildtype yeast Poly A binding protein (Pab1), which is involved in mRNA binding and forms stress granules (SGs) upon heat shock, Pab1 forms large inclusions in approximately half of ssa1{Delta}ssa2{Delta} cells in the absence of stress. Overexpression of Ssa1, Hsp104, and Sis1 almost completely limits the formation of these large inclusions in ssa1{Delta}ssa2{Delta}, suggesting that excess Ssa1, Hsp104 and Sis1 can each compensate for the lower levels of Ssa proteins. Upon heat shock, SGs also form in cells whether large Pab1 inclusions are present or not. Surprisingly, cells containing only SGs disassemble faster than wildtype, whereas cells with both large inclusions disassemble slower albeit completely. We suspect that disassembly of these large inclusions is linked to the elevated heat shock response and elevated Hsp104 and Sis1 levels in ssa1{Delta}ssa2{Delta} strains. We also observed that wildtype cultures grown to saturation also form large Pab1-GFP inclusions. These inclusions can be partially rescued by overexpression of Ssa1. Taken together, our data suggests that Hsp70 not only plays a role in limiting unwanted protein aggregation in normal cells, but as cells age, the depletion of active Hsp70 possibly underlies the age-related aggregation of endogenous proteins.

cell biology↗

bioRxiv2023

Microtubule-associated proteins MAP7 and MAP7D1 promote DNA double strand break repair in the G1 cell cycle phase.

The DNA-damage response is a complex signalling network that guards genomic integrity. The microtubule cytoskeleton is involved in the repair of DNA double-strand breaks; however, little is known about which cytoskeleton-related proteins are involved in DNA repair and how. Using quantitative proteomics, we discovered that microtubule associated proteins MAP7 and MAP7D1 interact with several DNA repair proteins including DNA double-strand break repair proteins RAD50, BRCA1 and 53BP1. We observed that downregulation of MAP7 and MAP7D1 leads to increased phosphorylation of p53 after {gamma}- irradiation. Moreover, we determined that the downregulation of MAP7D1 leads to a strong G1 arrest and that the downregulation of MAP7 and MAP7D1 in cells arrested in G1 negatively affects DNA repair, recruitment of RAD50 to chromatin and localisation of 53BP1 to the sites of damage. These findings describe for the first time a novel function of MAP7 and MAP7D1 in cell cycle regulation and cellular response to DNA double-strand breaks.

cell biology↗

bioRxiv2022

Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida

The liver is a multitasking organ with essential functions for vertebrate health spanning metabolism and immunity. In contrast to mammals, our understanding of liver cellular heterogeneity and its role in regulating immunological status remains poorly defined in fishes. Addressing this knowledge gap, we generated a transcriptomic atlas of 47,432 nuclei isolated from the liver of Atlantic salmon (Salmo salar L.) contrasting control fish with those challenged with a pathogenic strain of Aeromonas salmonicida, a problematic bacterial pathogen in global aquaculture. We identified the major liver cell types and their sub-populations, revealing poor conservation of many hepatic cell marker genes utilized in mammals, while identifying novel heterogeneity within the hepatocyte, lymphoid, and myeloid lineages. This included polyploid hepatocytes, multiple T cell populations including {gamma}{delta} T cells, and candidate populations of monocytes/macrophages/dendritic cells. A dominant hepatocyte population radically remodeled its transcriptome following infection to activate the acute phase response and other defense functions, while repressing routine functions such as metabolism. These defense-specialized hepatocytes showed strong activation of genes controlling protein synthesis and secretion, presumably to support the release of acute phase proteins into circulation. The infection response further involved up-regulation of numerous genes in an immune-cell specific manner, reflecting functions in pathogen recognition and killing, antigen presentation, phagocytosis, regulation of inflammation, B cell differentiation and T cell activation. Overall, this study greatly enhances our understanding of the multifaceted role played by liver cells in immune defense and metabolic remodeling following infection and provides many novel cell-specific marker genes to empower future studies of this organ in fishes.

immunology↗

bioRxiv2022

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

BackgroundInfectious Salmonid Anaemia virus (ISAV) is an orthomyxovirus responsible of large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon (Salmo salar) is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus. ResultsThree different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post infection) and RNA sequenced. The transcriptomes of Infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes our results suggest that other processes such as ubiquitination or ribosomal processing are important during early infection to ISAV. Moreover, the comparison between resistant and susceptible have also highlighted some interesting genes related to ubiquitination, intracellular transport or the inflammasome. ConclusionsAtlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An early immune response was observed in the head kidney, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.

genomics↗

bioRxiv2021

Targeted therapy for LIMD1-deficient non-small cell lung cancer subtypes.

An early event in lung oncogenesis is loss of the tumour suppressor gene LIMD1 (LIM domains containing 1); this encodes a scaffold protein, which suppresses tumourigenesis via a number of different mechanisms. Approximately 45% of non-small cell lung cancers (NSCLC) are deficient in LIMD11, yet this subtype of NSCLC has been overlooked in preclinical and clinical investigations. Defining therapeutic targets in these LIMD1 loss-of-function patients is difficult due to a lack of druggable targets, thus alternative approaches are required. To this end, we performed the first drug repurposing screen to identify compounds that confer synthetic lethality with LIMD1 loss in NSCLC cells. PF-477736 was shown to selectively target LIMD1 deficient cells in vitro through inhibition of multiple kinases, inducing cell death via apoptosis. Furthermore, PF-477736 was effective in treating LIMD1-/- tumors in subcutaneous xenograft models, with no significant effect in LIMD1+/+ cells. We have identified a novel drug tool with significant preclinical characterization that serves as an excellent candidate to explore and define LIMD1-deficient cancers as a new therapeutic subgroup of critical unmet need. Significance StatementHere we provide the first proof-of-concept data validating the scope for development of a targeted therapy against the non-small cell lung cancers (NSCLC) subtypes deficient in expression of the LIMD1 tumor suppressor gene. Approximately 45% of NSCLC are deficient in LIMD11 representing at least 1.2 million lung cancer patients worldwide; yet this subtype has been ignored in preclinical and clinical investigations with no targeted therapies available. This seminal study applied synthetic lethality drug screening to target the loss/reduction of LIMD1 in lung cancer and normal cell lines, identifying and validating the multi-kinase inhibitor PF-477736 as a selectively cytotoxic compound towards LIMD1 deficient cells. This study provides rationale for further investigation into targeting LIMD1 loss in lung cancer, thereby addressing a critical unmet need for therapeutic approached to targeting LIMD1-deficent cancer subtypes.

cancer biology↗

bioRxiv2020

Loss of coiled-coil protein Cep55 impairs abscission processes and results in p53-dependent apoptosis in developing cortex

To produce a brain of normal size and structure, embryonic neural stem cell (NSCs) must tightly regulate their cell divisions. Cerebral cortex NSCs undergo a polarized form of cytokinesis whose regulation is poorly understood. Cytokinetic abscission severs the daughter cells and is mediated by the midbody at the apical membrane. Here we elucidate the role of the coiled-coil midbody protein Cep55 in NSC abscission and brain development. A knockout of Cep55 in mice causes microcephaly with reduced NSCs and neurons, but relatively normal body size. Fixed and live analyses show NSCs lacking Cep55 have decreased but not eliminated ESCRT recruitment, and have abnormal abscission and higher rates of failure. P53-mediated apoptosis is greatly increased in the brain, but not other tissues, and p53 knockout partly rescues brain size. Thus, loss of Cep55 causes abscission defects and failures in multiple cell types, but the secondary p53 response and apoptosis is brain-specific.

developmental biology↗