Biology subjects

King, C. D.

Publications and source records attributed to King, C. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Acute LINE-1 overexpression rewires the transcriptome, proteome and secretome of primary human fibroblasts

A large portion of eukaryotic genomes is composed of transposable elements, which are usually kept repressed in young, healthy cells but can be derepressed in response to cell senescence and organismal aging. LINE-1 (L1) is the most abundant TE in the human genome by percent coverage, and its derepression has been implicated in inflammaging responses. However, whether L1 transcription itself is sufficient to drive aging-associated molecular phenotypes in healthy cells has not been extensively explored. Here, we leverage a multi-omic approach combining transcriptomics, proteomics, and secretomics of primary human IMR-90 fibroblasts transiently overexpressing a human L1Hs element in order to define the systems-level consequences of L1 transcription. Intriguingly, transient L1Hs overexpression induced widespread remodeling of the transcriptome, proteome and secretome, impacting pathways related to cell cycle regulation and interferon signaling. Interrogation of multiple independent L1 elements revealed both shared and distinct cellular responses to acute expression. Thus, our findings demonstrate that acute L1 expression induces coordinated molecular remodeling extending beyond canonical retrotransposition-associated pathways, rather than simply mimicking senescence or triggering antiviral signaling. This study establishes a comprehensive multi-omics resource for investigating the impact of L1 transcription in human cells and highlights the need to consider individual transposable element families as distinct regulators of cellular state during aging and disease.

genomics↗

bioRxiv2026

Proprotein convertase activity regulates cumulus-oocyte-complex matrix integrity and cumulus cell migration during ovulation via a GDF9-dependent mechanism

Cumulus cells have well-established roles early in ovulation but the key molecules that drive their behavior in later stages, leading to follicle rupture, remain underexplored. Here, we observed that inhibition of proprotein convertases (PCSKs) via a pan-inhibitor (PCI) impaired follicular rupture and disrupted the cumulus matrix integrity within intact follicles. Reduced cumulus cell adherence to the cumulus-oocyte-complex (COC) matrix was also observed in isolated COCs and notably occurred late during the maturation window without affecting oocyte maturation. Visualization of PCSK transcript and protein expression, as well as selective inhibition of specific PCSKs, determined that the observed phenotype in COCs is likely attributed to PCSK5A inhibition. We conducted bulk RNA-sequencing and proteomics of PCI-treated COCs which revealed that PCSK inhibition caused dysregulation of extracellular matrix organization, cell migration/adhesion, and TGF-{beta} signaling pathways. Subsequent validation showed that this inhibition translated to disrupted matrix organization and altered migratory and adhesive behaviors in cumulus cells. The TGF-{beta} ligand GDF9 has a predicted PCSK cleavage site, and supplementation with GDF9 rescued matrix integrity suggesting its role as a downstream substrate of PCSKs to regulate matrix organization. Altogether, this study identified PCSK5A and GDF9 as key regulators of COC matrix integrity and cumulus cell migration during late ovulation. These findings highlight novel factors required for follicle rupture which can be leveraged for the development of fertility therapeutics and contraceptives.

cell biology↗

bioRxiv2026

Distinct fibroblast and perivascular senotypes define spatial niches that regulate fibrosis

Fibrotic conditions contribute to significant global morbidity and mortality. Yet the underlying processes that orchestrate fibrosis remain poorly understood due to the cellular and spatial complexity of the stromal, immune, and vascular compartments that regulate fibrotic disease progression. Senescent cells (SnCs) have been implicated in fibrosis, but their roles are unclear, as evidence indicates that they serve both pathogenic and reparative functions. Here, we show that fibrosis-associated SnCs contain functionally divergent senotypes that are organized into distinct spatial niches. Using integrated single-cell and spatial transcriptomics analyses and hierarchical factorization in a murine fibrosis model, we identify fibroblast and perivascular SnC subpopulations that upregulate diverse programs related to extracellular matrix (ECM) production, immune signaling, and vascular remodeling. Fibroblast senotypes localize to discrete microenvironments with distinct tissue architectures, including niches associated with fibrotic signaling, immune activity, and cartilage development. Perivascular SnCs occupy interfaces between fibrotic signaling and immune-active niches and upregulate vascular and fibrotic remodeling pathways. Depletion of pericyte-lineage SnCs increases vascular maturation and fibrotic ECM deposition, providing mechanistic validation of the beneficial role these SnCs play in vascular remodeling and fibrosis modulation. In addition, using a new web-based infrastructure to query our senotype gene signatures in public datasets, we demonstrate that these senotypes are conserved across different murine and human fibrotic conditions. These findings establish senescence as a spatially organized regulator of fibrosis and identify perivascular senescence as a link between vascular remodeling and fibrotic outcomes.

bioengineering↗

bioRxiv2026

Individual variation in sound localization accuracy is correlated with the properties of eye movement-related eardrum oscillations (EMREOs)

Calibration of sound localization behavior in species with mobile eyes requires not only accurate visual input but also accurate oculomotor signals across the lifespan. The recent discovery of eye movement-related eardrum oscillations suggest that oculomotor signals may be incorporated into auditory processing at the level of the ear. One inference of this discovery is that individual variation in such signals might be correlated with individual variation in sound localization accuracy. Here, we tested this hypothesis in humans with normal hearing. We discovered that there is considerable variation in the accuracy of sound localization (here, saccades to sounds) even in normal individuals: median horizontal errors ranged from 2-6{degrees}, and median vertical errors could be as large as 36{degrees}. We separated the subject pool into groups with "good" performance (median vectorial error < 8{degrees}) vs "poor" performance (median vectorial error > 10{degrees}) and evaluated their respective EMREOs. The EMREOs differed across the two groups in both horizontal and vertical dimensions, in how saccade amplitude vs. initial eye position was encoded, and across time, with considerable individual variation in the "poor" group. These results are consistent with the interpretation that EMREOs are associated with underlying processes that ensure the accuracy of sound localization. HIGHLIGHTSO_LIThe accuracy of eye movements to look at sounds varied across individuals, with median errors spanning a greater than 10-fold range. This range is surprising given that the participants passed screening for normal hearing. C_LIO_LI"Good" vs "poor" sound localizers exhibited differences in their eye movement-related eardrum oscillations (EMREOs) C_LIO_LIEMREOs differed in both horizontal and vertical sensitivity, for both saccade amplitude and initial eye position, and the differences varied in timing with respect to saccade onset. C_LIO_LIWe interpret the results under the theory that poor sound localization may be a consequence of poor eye movement encoding, without which linking visual and auditory space is likely inaccurate. C_LI

neuroscience↗

bioRxiv2026

The human ovary exhibits dynamic molecular remodeling in the decades post-menopause

The human ovary is among the first organs to show age-related functional decline, resulting in menopause. Beyond this transition, the postmenopausal ovary is often regarded as quiescent and remains poorly characterized. We analyzed the proteomes of healthy, non-pathological ovaries using mass spectrometry (data-independent acquisition) from 28 postmenopausal women (50-75 years old), stratified into three age groups (50-59, 60-69, [≥]70). We quantified 5,812 protein groups and observed progressive age-associated shifts, with 117 proteins significantly altered in the [≥]70 vs 50-59 age comparison. Multivariate analysis demonstrated clear separation between 50-59 and [≥]70-year-old age cohorts, with protein signatures shifting from RNA/gene-regulatory functions in younger ovaries to metabolic, trafficking, and innate immune/complement pathways in older ovaries. Across differential abundance, multivariate modelling, and covariate-adjusted linear modelling, we identified a convergent set of age-associated proteins that were integrated into the 26-protein Buck Postmenopausal Ovary Molecular Signature (BuckPOMS), a consensus molecular signature capturing progressive extracellular matrix remodeling, inflammatory signaling, and loss of structural and keratin-associated proteins with age. Representative BuckPOMS proteins, including the secreted matrisome proteins WNT4 and Fibromodulin (FMOD), were validated by immunohistochemistry. Pathway enrichment further identified an increase in inflammatory and matrisome pathways, and increased abundance of damage-associated secretory factors decades following menopause. These data fundamentally shift the notion of the postmenopausal ovary as an inert organ and instead demonstrate active and continuous molecular remodeling that has potential relevance to tissue signaling and implications for womens health.

biochemistry↗

bioRxiv2026

Saccade-related sound pulses and phase-resetting contribute to eye movement-related eardrum oscillations (EMREOs)

Eye movement-related eardrum oscillations (EMREOs) appear to consist of a pulse of oscillation occurring in conjunction with saccades. However, this apparent pulse could occur either because there is an increase in energy at that frequency at the time of saccades (a true pulse), or because there is saccade-related phase resetting of ongoing energy at that frequency band, thus appearing like a pulse when averaged in the time domain across many trials. Here we conducted a spectral analysis at the individual trial level in humans performing a visually guided saccade task to determine whether the power at the EMREO frequency (30-45 Hz) is higher during saccades than during steady fixation. Although all subjects had easily identifiable EMREOs, we found that only 40% of participants showed a statistically significant increase in sound power in the EMREO frequency band associated with saccade onset, i.e. sound pulses at the individual trial level (in some cases, these power increases were sustained during eccentric fixation). In contrast, 97% of subjects showed statistically significant phase resetting at saccade onset. While both factors may contribute to the apparently pulse-like EMREO signal, phase resetting appears to be more reliably associated with EMREOs. The prevalence of phase resetting has implications for the underlying mechanism(s) producing EMREOs as well as functional consequences for how the ear might respond to incoming sound in an eye-position dependent fashion.

neuroscience↗

bioRxiv2026

Hearing sounds when the eyes move: A case study implicating the tensor tympani in eye movement-related peripheral auditory activity

Information about eye movements is necessary for linking auditory and visual information across space. Recent work has suggested that such signals are incorporated into processing at the level of the ear itself (Gruters, Murphy et al. 2018). Here we report confirmation that the eye movement signals that reach the ear can produce perceptual consequences, via a case report of an unusual participant with tensor tympani myoclonus who hears sounds when she moves her eyes. The sounds she hears could be recorded with a microphone in the ear in which she hears them (left), and occurred for large leftward eye movements to extreme orbital positions of the eyes. The sounds elicited by this participants eye movements were reminiscent of eye movement-related eardrum oscillations (EMREOs, (Gruters, Murphy et al. 2018, Brohl and Kayser 2023, King, Lovich et al. 2023, Lovich, King et al. 2023, Lovich, King et al. 2023, Abbasi, King et al. 2025, Sotero Silva, Kayser et al. 2025, King and Groh 2026, Leon, Ramos et al. 2026, Sotero Silva, Brohl et al. 2026)), but were larger and longer lasting than classical EMREOs, helping to explain why they were audible to her. Overall, the observations from this patient help establish that (a) eye movement-related signals specifically reach the tensor tympani muscle and that (b) when there is an abnormality involving that muscle, such signals can lead to actual audible percepts. Given that the tensor tympani contributes to the regulation of sound transmission in the middle ear, these findings support that eye movement signals reaching the ear have functional consequences for auditory perception. The findings also expand the types of medical conditions that produce gaze-evoked tinnitus, to date most commonly observed in connection with acoustic neuromas.

neuroscience↗

bioRxiv2025

Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale

The gut microbiome can regulate the strength of bone matrix but the specific changes in matrix function and composition are not yet understood. Here we introduce micropillar splitting to determine the fracture toughness of matrix at the cellular scale in concert with proteomic analysis of bone matrix when the gut microbiome was altered by oral antibiotics (ampicillin+neomycin). Male mice were divided into four groups (n = 3-4/group): (1) Unaltered (no alteration), (2) Continuous (alteration from 4-24 weeks), (3) Delayed (alteration from 16-24 weeks) and (4) Reconstituted (alteration from 1-16 weeks following by reconstitution). Micropillars (5 {micro}m diameter) were fabricated using focused ion beam milling on femur cross-sections in regions of matrix formed either before or after changes in the microbiome (16 weeks) (n = 4/group). Proteomics was used to identify differences in matrix protein composition. Micropillar fracture toughness differed by group (p < 0.001) and region (p < 0.001). Fracture toughness in the Unaltered group (1.34 {+/-} 0.32 MPa{surd}m, mean {+/-} SD) was substantially greater than the Continuous group (0.95 {+/-} 0.20) and the Delayed group (0.90 {+/-} 0.21) but not different from the Reconstituted group (1.22 {+/-} 0.25). Bone matrix formed from 16-24 weeks of age had lower fracture toughness than matrix formed before 16 weeks of age in all groups. Notably, micropillar splitting was substantially more precise than whole bone testing; whole bone notched 3-point bending tests did not detect differences in fracture toughness. Proteomics identified 46 extracellular matrix proteins that were differentially abundant between groups, including decreased abundance of Periostin (q < 0.001) and Emilin-1 (q < 0.001) in groups with impaired bone matrix. These findings demonstrate that modifications to the gut microbiome lead to changes in bone matrix throughout cortical bone volume and establish micropillar splitting as a high-precision approach for characterizing matrix material properties. Plain Language SummaryThis study investigated the effect of the gut microbiome on the brittleness of bone as a material. We used a new technique for measuring the brittleness of bone that involves making microscopic pillars on the bone surface and splitting them down the middle to measure a material property called fracture toughness. Mice with altered gut microbiomes had bone with reduced fracture toughness (by 35-40%). Restoration of an altered gut microbiome for two months reversed the effects. The effect of the microbiome on bone occurred throughout the whole bone and was not limited to regions of the bone formed after a change in the gut microbiome.

bioengineering↗

bioRxiv2025

Alzheimer's disease risk factor APOE4 exerts dimorphic effects on female bone

Individuals diagnosed with Alzheimers disease (AD) are at an increased risk of bone fractures. Conversely, a diagnosis of osteoporosis in women is the earliest known predictor for AD. However, mechanisms responsible for the coupled decline in cognitive and skeletal health remain unclear. Proteomic analysis of cortical bone from aged mice revealed neurological disease-associated proteins that are highly enriched in aged mouse bones, including apolipoprotein E (Apoe) and amyloid precursor protein. Further, Apoe localized specifically to bone-embedded osteocytes with expression twice as high in aged female bone as in young or male counterparts. In humans, APOE allele variants carry differing AD risk with age. To investigate APOE allelic roles in bone, we utilized a humanized APOE knock-in mouse model that expresses either the protective APOE2, the neutral APOE3, or the AD risk factor APOE4, and analyzed bone and hippocampus from the same mice. APOE4 exerted strong sex-specific effects on the bone transcriptome and proteome, relative to APOE2 or APOE3. Interestingly, the APOE4-associated perturbation in the female bone proteome was more pronounced than the corresponding alterations observed in the hippocampus. APOE4 protein causes bone fragility in females, but not males, even without changes in cortical bone structure. These bone quality deficits arose from suppression of osteocyte perilacunocanalicular remodeling. We find that APOE4 is a new molecular culprit capable of disrupting osteocyte maintenance of bone quality as early as midlife in a manner that disproportionately affects females. These findings highlight osteocytes as potential targets for early diagnosis of age-related cognitive impairment, and treatment for bone fragility, in females.

molecular biology↗

bioRxiv2025

γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response

Immune-stromal crosstalk governs tissue fibrosis, which is marked by dysregulated extracellular matrix (ECM) production and aberrant vasculature. Here, we investigate how {gamma}{delta} T cell interactions with stromal cells shape fibrosis in the foreign body response. During the acute reaction, type-1 ({gamma}{delta}IFN{gamma}) and type-17 ({gamma}{delta}17) effector subsets accumulated at the implant. While {gamma}{delta}IFN{gamma} decreased as fibrosis progressed, activated {gamma}{delta}17 persisted as dominant interleukin-17 producers. The {gamma}{delta}17 increased with aging and high-fat diet, both factors associated with chronic inflammation and fibrosis. Co-culture with {gamma}{delta}17 stimulated fibroblast expression of collagen genes and intercellular communication inference linked {gamma}{delta} T cell ligands to activation of ECM remodeling and vascular development programs in fibroblasts and endothelial cells. Finally, genetic deletion of {gamma}{delta} T cells altered expression of ECM components and increased vessel size within the fibrotic matrix. Altogether, our findings implicate {gamma}{delta} T cells in regulating stromal behavior to modulate composition and vascularity of fibrotic tissues.

immunology↗

bioRxiv2025

Tau oligomers modulate synapse fate by eliciting progressive bipartite synapse dysregulation and synapse loss

BackgroundSynapse function is critical for cognition, and synapse loss is highly correlated with cognitive decline in Alzheimers disease and related dementias. Tau oligomers, which accumulate in the brain in Alzheimers disease, can acutely inhibit synaptic plasticity and cause synapse loss. Coordinated presynaptic and postsynaptic function is essential for effective synaptic transmission, and both compartments can be dysregulated by pathogenic tau. However, the series of pathophysiological events triggered by tau oligomers to cause the dysfunction and deterioration of presynaptic terminals and postsynaptic sites remain unclear. MethodsWe developed a proximity labeling tool to map the postsynaptic proteome by fusing PSD-95 with APEX2 (APEX2-PSD-95) which was expressed in human induced pluripotent stem cell (iPSC)-derived neurons. We used APEX2-PSD-95 to map the dynamic changes in the postsynaptic proteome with precise temporal resolution after an acute exposure of human iPSC-derived neurons to recombinant tau oligomers for 30 min. Leveraging immunocytochemistry, electrophysiology and electron microscopy, we further delineated the impact of the acute tau oligomer exposure on presynaptic and postsynaptic compartments over time for up to 14 days. ResultsThe brief exposure of human iPSC-derived neurons to tau oligomers caused a progressive deterioration of synapses, marked by both presynaptic and postsynaptic dysregulation. Postsynaptic proteome mapping revealed an immediate tau oligomer-triggered downregulation of the postsynaptic actin motor proteins Myosin-Va and Myosin-10, which coincided with impaired AMPA receptor (AMPAR) trafficking during synaptic plasticity. This was followed 24 hours later by the upregulation of disease-related proteins, including GSK3{beta}, at postsynaptic sites. The loss of PSD-95-labeled postsynaptic sites at 7 days after tau oligomer exposure preceded the loss of Synapsin-labeled presynaptic terminals at 14 days. The postsynaptic sites that remained exhibited a long-term downregulation of postsynaptic AMPAR levels and sustained synaptic plasticity impairment. Moreover, the remaining presynaptic terminals contained less clusters of vesicles at the presynaptic active zone which was associated with reduced vesicle release probability at synapses. ConclusionOur findings reveal the series of events underlying tau oligomer-induced bipartite synapse deterioration. The progressive decline of synapses involves the emergence of two synapse fates. One synapse fate involves the persistent weakening of both presynaptic and postsynaptic function, and the other results in synaptic loss.

neuroscience↗

bioRxiv2025

A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways

During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Though Alu elements are often studied for their mutagenic potential, there is increasing appreciation for their contributions to other biological functions, including pro-inflammatory signaling and mitochondrial dysfunction. However, a comprehensive analysis of Alu-driven molecular changes remains to be conducted, and Alus potential contributions to aging features remain incompletely characterized. Here, we show that overexpression of an AluJb transposon in human primary IMR-90 fibroblasts leads to large-scale alterations across the transcriptome, cellular proteome, and secretome. Functional genomics analyses reveal alterations in aging pathways, broadly, and mitochondrial metabolism, proteostasis, cell cycle, and extracellular matrix pathways, more specifically. Our results demonstrate that Alu transcriptional upregulation is sufficient to drive widespread disruptions to cellular homeostasis that mirror aging-associated alterations.

genomics↗

bioRxiv2025

Age-Dependent Increase and Dysregulation of the Splicing Machinery in Acute Myeloid Leukemia of Older Patients

Acute myeloid leukemia (AML) is characterized by age-related resistance to therapy and poor outcomes. Initial remission rates vary from 30-80% with current therapies, but relapses are common. The 5-year survival is 30% overall but less than 10% for those 60 years of age or older. Resistance to current therapies is the central clinical challenge. This study investigated how age influences the AML proteome in patients with increasing age. We analyzed bone marrow or leukapheresis samples from 14 AML patients, including 9 older ([≥] 66 years) and 5 younger ([≤] 58 years) individuals, using proteomic technologies (Data-Independent Acquisitions, DIA-MS). We identified 4,471 protein groups, of which 889 exhibited significant changes and regulation between the two age groups. Proteins upregulated in older patients were predominantly associated with DNA transcription and translation, while downregulated proteins were linked to metabolic, catabolic, and extracellular matrix or structural processes. Significant changes in older samples affected the splicing machinery. Significant alterations in several of these factors, suggests either dysregulated or elevated splicing activity and reduced transcription initiation factor activity in older AML patients. Our study provides novel insights into molecular changes during AML arising in the older adult, highlighting the importance of age-specific therapeutic strategies. Statement of Significance of the StudyThis study is significant as it investigates a devastating and highly aggressive cancer, acute myeloid leukemia (AML), which often presents in patients with very low 5-year survival rates (32%), however which is even lower in patients over 60 years old (10%). This study really focuses on the complications and severe outcome in older patients which is not well understood. This is particularly relevant as older AML patients often do not respond to the available treatments. Understanding the pathways and protein profiles that are dysregulated in older AML patients compared to younger AML patients may in the future help to develop more customized therapeutic interventions or allow for some precision treatments. AML patients were stratified into cohort groups by age (older vs younger) and the proteomic profiling highlighted the particularly strong dysregulation of the splicing machinery in the older AML patients. While alternative splicing is often observed in cancers, here the emphasis is pointed to the fact that the dysregulation of the spliceosome and other pathways are greatly exacerbated in the older AML patients, likely leading to even worse outcomes and poor response to treatments in the older patients.

cancer biology↗

bioRxiv2025

The critical role of the ZBP1-NINJ1 axis and IRF1/IRF9 in ethanol-induced cell death, PANoptosis, and alcohol-associated liver disease

Innate immunity provides the critical first line of defense against infection and sterile triggers. Cell death is a key component of the innate immune response to clear pathogens, but excessive or aberrant cell death can induce inflammation, cytokine storm, and pathology, making it a central molecular mechanism in inflammatory diseases. Alcohol-associated liver disease (ALD) is one such inflammatory disease, but the specific innate immune mechanisms driving pathology in this context remain unclear. Here, by leveraging RNAseq and tissue expression in clinical samples, we identified increased expression of the innate immune sensor Z-DNA binding protein (ZBP1) in patients with ALD. We discovered that ZBP1 expression correlated with ALD progression in patients, and that ethanol induced ZBP1-dependent lytic cell death, PANoptosis, in immune (macrophages, monocytes, Kupffer cells) and non-immune cells (hepatocytes). Mechanistically, the interferon regulatory factors (IRFs) IRF9 and IRF1 upregulated ZBP1 expression, allowing ZBP1 to sense Z-NAs through its Z2 domain and drive PANoptosis signaling, cell membrane rupture through NINJ1, and DAMP release. Furthermore, the expressions of ZBP1 and NINJ1 were upregulated in both liver and serum samples from patients with ALD. In mouse models of chronic and acute ALD, ZBP1-deficient mice were significantly protected from disease pathology and liver damage. Overall, our findings establish the critical role of the ZBP1-NINJ1 axis regulated by IRFs in driving inflammatory cell death, PANoptosis, in liver cells, suggesting that targeting these molecules will have therapeutic potential in ALD and other inflammatory conditions.

immunology↗

bioRxiv2023

Amyloid β accelerates age-related proteome-wide protein insolubility.

Loss of proteostasis is a highly conserved feature of aging across model organisms and typically results in the accumulation of insoluble protein aggregates. Protein insolubility is a central feature of major age-related neurodegenerative diseases, including Alzheimers Disease (AD), where hundreds of insoluble proteins associate with aggregated amyloid beta (A{beta}) in senile plaques. Moreover, proteins that become insoluble during aging in model organisms are capable of accelerating A{beta} aggregation in vitro. Despite the connection between aging and AD risk, therapeutic approaches to date have overlooked aging-driven protein insolubility as a contributory factor. Here, using an unbiased proteomics approach, we questioned the relationship between A{beta} and age-related protein insolubility. We demonstrate that A{beta} expression drives proteome-wide protein insolubility in C. elegans and this insoluble proteome closely resembles the insoluble proteome driven by normal aging, suggesting the possibility of a vicious feedforward cycle of aggregation in the context of AD. Importantly, using human genome-wide association studies (GWAS), we show that the CIP is replete with biological processes implicated not only in neurodegenerative diseases but also across a broad array of chronic, age-related diseases (CARDs). This provides suggestive evidence that age-related loss of proteostasis could play a role in general CARD risk. Finally, we show that the CIP is enriched with proteins that modulate the toxic effects of A{beta} and that the gut-derived metabolite, Urolithin A, relieves A{beta} toxicity, supporting its use in clinical trials for dementia and other age-related diseases.

systems biology↗

bioRxiv2023

β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain

Loss of proteostasis is a hallmark of aging and Alzheimer disease (AD). Here, we identify {beta}-hydroxybutyrate ({beta}HB), a ketone body, as a regulator of protein solubility in the aging brain. {beta}HB is a small molecule metabolite which primarily provides an oxidative substrate for ATP during hypoglycemic conditions, and also regulates other cellular processes through covalent and noncovalent protein interactions. We demonstrate {beta}HB-induced protein insolubility across in vitro, ex vivo, and in vivo mouse systems. This activity is shared by select structurally similar metabolites, is not dependent on covalent protein modification, pH, or solute load, and is observable in mouse brain in vivo after delivery of a ketone ester. Furthermore, this phenotype is selective for pathological proteins such as amyloid-{beta}, and exogenous {beta}HB ameliorates pathology in nematode models of amyloid-{beta} aggregation toxicity. We have generated a comprehensive atlas of the {beta}HB-induced protein insolublome ex vivo and in vivo using mass spectrometry proteomics, and have identified common protein domains within {beta}HB target sequences. Finally, we show enrichment of neurodegeneration-related proteins among {beta}HB targets and the clearance of these targets from mouse brain, likely via {beta}HB-induced autophagy. Overall, these data indicate a new metabolically regulated mechanism of proteostasis relevant to aging and AD.

physiology↗

bioRxiv2023

Dicarboxylic acid supplementation protects from acute kidney injury via stimulation of renal peroxisomal activity

IntroductionLysine succinylation is a post-translational modification associated with the control of several diseases, including acute kidney injury (AKI). It is suggested that hypersuccinylation favors peroxisomal fatty acid oxidation (FAO) instead of mitochondrial. In addition, the medium-chain fatty acids (MCFAs) dodecanedioic acid (DC12) and octanedioic acid (DC8), upon FAO, generate succinyl-CoA, resulting in hypersuccinylation. DC8 is convenient, inexpensive, easily administered, and efficient. We believe this study could be translated in the future to clinical settings, which would highly benefit patients at high risk of AKI. Methods and ResultsTo test the protective roles of MCFAs during AKI, mice were fed with control, 10% DC12, or 10% DC8 diet, then, subjected to either ischemic-AKI, or cisplatin-AKI models. Supplementation was provided until sacrifice. Biochemical, histologic, genetic, and proteomic analysis were performed, the latter involving a lysine-succinylome-based analysis. Both DC8 and DC12 prevented the rise of AKI markers in mice that underwent renal injury. However, DC8 was even more protective against AKI than DC12. Finally, succinylome analysis evidenced that the kidneys of DC8-fed mice showed an extensive succinylation of peroxisomal activity-related proteins, and a decline in mitochondrial FAO, in comparison to control-fed mice. ConclusionDC8 supplementation drives renal protein hypersuccinylation, promoting a shift from mitochondrial to peroxisomal FAO, and protecting against AKI. Significance StatementLysine succinylation of proteins is shown to control several diseases, including acute kidney injury (AKI). Here we show that mice supplemented with the medium-chain fatty acid octanedioic acid successfully presented a high level of succinylation and were protected from both ischemia-reperfusion- and cisplatin-induced AKI. Moreover, our study demonstrates that peroxisomal activity was increased while mitochondrial activity was preserved, suggesting that the metabolism of diet-obtained medium-chain fatty acids by peroxisomes is renoprotective.

pathology↗

bioRxiv2023

Simultaneous neuronal expression of human amyloid-β and Tau genes drives global phenotypic and multi-omic changes in C. elegans

Alzheimers disease (AD) and Alzheimers related diseases (ADRD) are prevalent age-related neurodegenerative disorders characterized by the accumulation of amyloid-{beta} (A{beta}) plaques and Tau neurofibrillary tangles. The nematode Caenorhabditis elegans (C. elegans) serves as an invaluable model organism in diseases of old age-due to its rapid aging. Here we performed an unbiased systems analysis of a C. elegans strain expressing both A{beta} and Tau proteins within neurons. We set out to determine if there was a phenotypic interaction between A{beta} and Tau. In addition, we were interested in determining the temporal order of the phenotypic and multi-omic (geromic) outcomes. At an early stage of adulthood, we observed reproductive impairments and mitochondrial dysfunction consistent with disruptions in mRNA transcript abundance, protein solubility, and metabolite levels. Notably, the expression of these neurotoxic proteins exhibited a synergistic effect, leading to accelerated aging. Our findings shed light on the close relationship between normal aging and ADRD. Specifically, we demonstrate alterations to metabolic functions preceding age-related neurotoxicity, offering a resource for the development of new therapeutic strategies.

systems biology↗