Immunoprecipitation Mass Spectrometry Research Articles

Synaptosomal-Associated Protein 25kDA (SNAP-25) Levels in Cerebrospinal Fluid: Implications for Alzheimer's Disease Diagnosis and Monitoring.

Synaptic degeneration has been linked to cognitive decline. The presynaptic protein, synaptosomal-associated protein 25kDA (SNAP-25), is crucial for synaptic transmission and has been suggested as a biomarker in Alzheimer's disease (AD). In the current study, we investigated the ability of SNAP-25 to differentiate between heterogenous dementia etiologies and whether SNAP-25 could be a staging marker in AD. SNAP-25 in the cerebrospinal fluid (CSF) from a retrospective (n=187) and a prospective (n=134) cohort was investigated with immunoprecipitation mass spectrometry (IP-MS) and single-molecule array (Simoa), respectively. Both cohorts consisted of healthy controls (HC) and patients with cognitive decline of different etiologies. CSF SNAP-25 concentration was higher in AD and non-neurodegenerative diseases (i.e., vascular dementia) compared with controls but did not differ between AD and non-AD neurodegenerative diseases. We found a trend toward an association between SNAP-25 and disease burden when comparing HC, mild cognitive impairment due to AD, and AD. CSF SNAP-25 concentrations were strongly associated with CSF phosphorylated tau (p-tau) concentrations, thus strengthening the link between synaptic dysfunction and tau pathophysiology in AD. Our initial findings suggest that SNAP-25 may be a potential biomarker for differentiating AD from dementia due to other etiologies. However, due to the significant association between SNAP-25 and p-tau proteins, the clinical utility of SNAP-25 as a diagnostic biomarker for AD may be limited, while SNAP-25 may be useful for monitoring disease progression or treatment response.

Neddylation of RhoA impairs its protein degradation and promotes renal interstitial fibrosis progression in diabetic nephropathy.

Diabetic nephropathy (DN) is a common and serious complication of diabetes, characterized by chronic fibro-inflammatory processes with an unclear pathogenesis. Renal fibrosis plays a significant role in the development and progression of DN. While recent research suggests that the neddylation pathway may influence fibrotic processes, its specific dysregulation in DN and the underlying mechanisms remain largely unexplored. This study identified the neddylation of RhoA as a novel post-translational modification that regulates its expression and promotes renal fibrosis in DN. We here demonstrated that two key components of the neddylation pathway-NEDD8-activating enzyme E1 subunit 1 (NAE1) and NEDD8-are significantly upregulated in human chronic kidney disease (CKD) specimens compared to healthy kidneys, implicating neddylation in CKD-associated fibrosis. Our findings further revealed that both pharmacological inhibition of neddylation using MLN4924 and genetic knockdown of NAE1 mitigate renal fibrosis in mouse models of streptozotocin-induced diabetes and unilateral ureteral obstruction (UUO). Immunoprecipitation-mass spectrometry (IP-MS) and subsequent function assays demonstrated a direct interaction between RhoA and NEDD8. Importantly, neddylation inhibition reduced RhoA protein expression, highlighting a potential therapeutic target. Additionally, a positive correlation was noted between elevated NEDD8 mRNA levels and RhoA mRNAexpression in human CKD specimens. RhoA overexpression counteracted the antifibrotic effects of neddylation inhibition, underscoring its critical role in fibrosis progression. Mechanistically, we unveiled that neddylation enhances RhoA protein stability by inhibiting its ubiquitination-mediated degradation, which subsequently activates the ERK1/2 pathway. Collectively, this study provides novel insights into NAE1-dependent RhoA neddylation as a key contributor to renal fibrosis in DN. The NAE1 protein mediates RhoA protein hyper-neddylation and subsequent stabilization of the RhoA protein, which, in turn, contributes to the development of renal fibrosis and inflammation through an ERK1/2-dependent mechanism. Consequently, targeting neddylation inhibition represents a viable therapeutic approach for the treatment of renal fibrosis in DN.

H4K12 lactylation-regulated NLRP3 is involved in cigarette smoke-accelerated Alzheimer-like pathology through mTOR-regulated autophagy and activation of microglia.

Cigarette smoke (CS), an indoor environmental pollution, is an environmental risk factor for diverse neurological disorders. However, the neurotoxicological effects and mechanisms of CS on Alzheimer's disease (AD) progression remain unclear. We found that CS accelerated the progression of AD, including increasing β-amyloid (Aβ) plaque deposition and exacerbating cognitive decline. Mechanistically, CS exposure increased the levels of NOD-like receptor protein 3 (NLRP3), which impaired autophagic flux in microglia by activating the mammalian target of rapamycin (mTOR) signal. Metabolomics analysis revealed an upregulation of lactate levels and an increase in global protein lysine lactylation in the brain tissue of CS-exposed AD-transgenic mice. Immunoprecipitation-Mass Spectrometry and chromatin immunoprecipitation assays demonstrated that CS elevates H4K12 lactylation (H4K12la) levels, which accumulate at the promoter region of NLRP3, leading to the activation of its transcription. Via inhibiting lactate or NLRP3 activation, oxamate and MCC950 alleviates these CS-induced effects. Therefore, our data suggest that the CS-induced increase in lactate levels triggers NLRP3 transcriptional activation through H4K12la, which subsequently leads to mTOR-mediated autophagy dysfunction in microglia, promoting microglial activation and resulting in Aβ plaque accumulation in AD-transgenic mice. This provides a new mechanism and potential therapeutic target for AD associated with environmental factors.

Suppression of PCK1 attenuates neuronal injury and improves post-resuscitation outcomes.

Cardiac arrest (CA) is a critical medical emergency that can occur in both patients with preexisting conditions and otherwise healthy individuals. Despite successful resuscitation through cardiopulmonary resuscitation (CPR), many survivors are at significant risk of developing post-cardiac arrest syndrome (PCAS), a complex systemic response to CA that includes brain injury as a major component. Phosphoenolpyruvate carboxykinase 1 (PCK1), the first rate-limiting enzyme in gluconeogenesis, has been implicated in various diseases. However, its role in neuronal damage following CA/CPR remains unclear. To investigate the role of PCK1 in neuronal damage after CA/CPR, we established the CA/CPR animal model and hypoxia/re‑oxygenation (H/R) cell model, manipulated PCK1 expression both in vivo and in vitro. We found increased expression of PCK1 in cortical neurons after CA/CPR. In vivo PCK1 overexpression exacerbated brain injury after CA/CPR via augmenting neuroinflammation and neuronal apoptosis. RNA-sequencing suggested PCK1-OE disturbed the neuronal metabolism while immunoprecipitation/mass spectrometry (IP/MS) revealed that PCK1 contributed to the mitochondrial dysfunction via binding to Voltage-dependent anion-selective channel 1 (VDAC1) and promoting its oligomerization and cytochrome c release. Besides, we confirmed that 3-Mercaptopicolinic acid (3-MPA), the PCK1 inhibitor, could ameliorate the mitochondrial dysfunction and apoptosis of neurons both in vitro and in vivo. For the first time, we identified the detrimental role of PCK1 in post-CA brain injury. During CA/CPR, excessive PCK1 binds to VDAC1, promoting its oligomerization and cytochrome c release which leading to neuronal apoptosis and eventually PCAS. Utilization of 3-MPA during CPR could effectively improve the survival rate and prognosis of mice after CA, which may provide a novel strategy for CA/CPR treatment.

Ubiquitination of TFEB increased intestinal permeability to aggravate metabolic dysfunction-associated steatohepatitis.

Increased intestinal permeability exacerbates the development of metabolic dysfunction associated steatohepatitis (MASH), but the underlying mechanisms remain unclear. Autophagy is important for maintaining normal intestinal permeability. Here, we investigated the impact of intestinal transcription factor EB (TFEB), a key regulator of autophagy, in intestinal permeability and MASH progression. TFEB expression was analyzed in the proximal colon of 45 individuals with metabolic dysfunction associated steatotic liver disease and 23 healthy controls. We utilized immunoprecipitation-mass spectrometry toidentify TFEB-interacting proteins. Intestine-specific Tfeb knockout mice were generated by mating Tfebfl/fl mice with Villin-Cre mice. The mice were fed a high-fat, high-sucrose diet, and assessments were performed to evaluate intestinal permeability and MASH progression. Intestinal TFEB levels were reduced in MASH patients and negatively correlated with intestinal permeability and hepatic toxicity. Intestine-specific TFEB deficiency increased intestinal permeability and worsened MASH severity, whereas moderate TFEB overexpression conferred protective effects. Mechanistically, the E3 ligase TRIP12 promotes the ubiquitination and degradation of nuclear TFEB, thereby inhibiting autophagic flux to aggravate intestinal barrier impairment and subsequently promote MASH progression. Importantly, a peptide PT1 designed to block the TRIP12-TFEB interaction reduced MASH progression. The ubiquitination of TFEB plays a pivotal role in increasing intestinal permeability and promoting the progression of MASH by inhibiting autophagy. Intestinal TFEB may represent a novel therapeutic target for the treatment of MASH.

Pathogenic variants of TUBB8 cause oocyte spindle defects by disrupting with EB1/CAKP5 interactions and potential treatment targeting microtubule acetylation through HDAC6 inhibition.

Numerous pathogenic variants causing human oocyte maturation arrest have been reported on the primate-specific TUBB8 gene. The main etiology is the dramatic reduction of tubulin α/β dimer, but still large numbers of variants remain unexplained. Using microinjection mRNA and genome engineering to reintroduce the conserved pathogenic missense variants into oocytes or in generating TUBB8 variant knock-in mouse models, we investigated that the human deleterious variants alter microtubule nucleation and spindle assembly during meiosis. Live-cell imaging and immunofluorescence were utilised to track the dynamic expression of microtubule plus end-tracking proteins in vivo and analysed microtubule nucleation or spindle assembly in vitro, respectively. Immunoprecipitation-mass spectrometry and ultramicro-quantitative proteomics were performed to identify the differential abundance proteins and affected interactome of TUBB8 protein. First, we observed a significant depletion of the EB1 signal upon microinjection of mutated TUBB8 mRNA (including R262Q, M300I, and D417N missense variants), indicating disruption of microtubule nucleation caused by these introduced TUBB8 missense variants. Mechanically, we demonstrated that the in vivo TUBB8-D417N missense variant diminished the affinity of EB1 and microtubules. It also harmed the interaction between microtubules and CKAP5/TACC3, which are crucial for initiating microtubule nucleation. Attenuated Ran-GTP pathway was also found in TUBB8-D417N oocytes, leading to disrupted spindle assembly. Stable microtubule was largely abolished on the spindle of TUBB8-D417N oocytes, reflected by reduced tubulin acetylation and accumulated HDAC6. More importantly, selective inhibition of HDAC6 by culturing TUBB8-D417N oocytes with Tubacin or Tubastatin A showed morphologically normal spindle and drastically recovered polar-body extrusion rate. These rescue results shed light on the strategy to treat meiotic defects in a certain group of TUBB8 mutated patients. Our study provides a comprehensive mechanism elucidating how TUBB8 missense variants cause oocyte maturation arrest and offers new therapeutic avenues for treating female infertility in the clinic.

YAP K236 acetylation facilitates its nucleic export and deprived the protection against cardiac hypertrophy in mice.

The subcellular localization of Yes-associated protein (YAP) is dynamically regulated by post-transcriptional modifications, critically influencing cardiac function. Despite its significance, the precise mechanism controlling YAP nuclear sequestration and its role in cardiac hypertrophy remain poorly defined. In this study, utilizing immunoprecipitation-mass spectrometry, we identified potential acetylation sites and interacting proteins of YAP. Co-immunoprecipitation and immunofluorescence assays were used to elucidate the protein interactions and subcellular colocalization. We found that YAP protected against ISO-induced pathological cardiac hypertrophy both in vivo and in vitro. During cardiac hypertrophy YAP acetylation increased while its nuclear accumulation reduced without altering Ser127 phosphorylation. Notably, lysine 236 was identified as a novel acetylation site on YAP. Acetylation at K236 facilitated YAP's nucleic export, suppressed the expression of target genes such as NRF1 and Cox IV, and counteracted YAP's anti-hypertrophic effects. Importantly, deacetylase SIRT6 was identified as a regulator of YAP deacetylation, disrupting the YAP with chaperone protein 14-3-3 interaction and inhibiting YAP's nuclear export, thereby facilitating cardiac protective role of YAP. This study identified YAP K236 acetylation as a key regulator of its nuclear retention in cardiomyocytes, with SIRT6-mediated deacetylation facilitating YAP's protective effects against cardiac hypertrophy. Targeting YAP acetylation may offer a promising therapeutic strategy for cardiac hypertrophy.

Histone lactylation-mediated overexpression of RASD2 promotes endometriosis progression via upregulating the SUMOylation of CTPS1.

Background: Histone lactylation is crucial in a variety of physiopathological processes, however, the function and mechanism of histone lactylation in endometriosis remain poorly understood. Therefore, the objective of this investigation was to illuminate the function and mechanism of histone lactylation in endometriosis. Methods: Immunohistochemistry was used to investigate the expression of histone lactylation. Cell Counting Kit-8 assay (CCK8), Transwell assay and endometriosis mouse models were used to investigate the effects of histone lactylation in vitro and in vivo. Transcriptomics and Immunoprecipitation-Mass Spectrometry (IP-MS), Western Blot, Co-Immunoprecipitation (Co-IP), quantitative reverse transcription polymerase chain reaction (qRT-PCR) and chromatin immunoprecipitation-qPCR (ChIP-qPCR) were used to explore the intrinsic mechanisms. Results: In this study, we found that histone lactylation was upregulated in endometriosis and could promote endometriosis progression both in vivo and in vitro. Mechanistically, histone lactylation H3K18la promoted the transcription of Ras homolog enriched in striatum (RASD2), and RASD2, in turn, increased the stability of CTP synthase 1 (CTPS1) by promoting the SUMOylation and inhibiting the ubiquitination of CTPS1, thereby promoting endometriosis progression. Conclusion: Overall, our findings indicated that histone lactylation could promote the progression of endometriosis through the RASD2/CTPS1 axis. This investigation uncovered a novel mechanism and identified prospective targets for endometriosis diagnosis and therapy.

Central control of dynamic gene circuits governs T cell rest and activation

The ability of cells to maintain distinct identities and respond to transient environmental signals requires tightly controlled regulation of gene networks1, 2–3. These dynamic regulatory circuits that respond to extracellular cues in primary human cells remain poorly defined. The need for context-dependent regulation is prominent in T cells, where distinct lineages must respond to diverse signals to mount effective immune responses and maintain homeostasis4, 5, 6, 7–8. Here we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify regulators that control expression of IL-2Rα, a canonical marker of T cell activation transiently expressed by pro-inflammatory effector T cells and constitutively expressed by anti-inflammatory regulatory T cells where it is required for fitness9, 10–11. Approximately 90% of identified regulators of IL-2Rα had effects that varied across cell types and/or stimulation states, including a subset that even had opposite effects across conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. MED12 — a component of the Mediator complex — serves as a dynamic orchestrator of key regulators, controlling expression of distinct sets of regulators in different T cell contexts. Immunoprecipitation–mass spectrometry revealed that MED12 interacts with the histone methylating COMPASS complex. MED12 was required for histone methylation and expression of genes encoding key context-specific regulators, including the rest maintenance factor KLF2 and the versatile regulator MYC. CRISPR ablation of MED12 blunted the cell-state transitions between rest and activation and protected from activation-induced cell death. Overall, this work leverages CRISPR screens performed across conditions to define dynamic gene circuits required to establish resting and activated T cell states.

Extrajunctional CLDN10 cooperates with LAT1 and accelerates clear cell renal cell carcinoma progression

Background & aimsIn addition to their adhesive properties, cell adhesion molecules such as claudins (CLDNs) exhibit signaling ability to organize diverse cellular events. Although the CLDN-adhesion signaling stimulates or inhibits cancer progression, the underlying mechanism remains poorly established. Here, we verified whether and how CLDN10 promotes intracellular signals and malignant phenotypes in clear cell renal cell carcinoma (ccRCC).MethodsWe developed a novel monoclonal antibody that specifically recognizes CLDN10. By immunohistochemistry using this antibody, the clinicopathological significance of aberrant CLDN10 expression in 165 ccRCC patients was determined. We next generated the ccRCC cells (786-O, ACHN, and OS-RC-2) expressing CLDN10, and compared their phenotypes with those of control cells. Immunoprecipitation-mass spectrometry was used to identify a CLDN10-interacting protein, followed by evaluation of its association with CLDN10 and loss-of-functions in ccRCC cells.ResultsHigh CLDN10 expression predicted poor outcome in ccRCC patients and represented an independent prognostic marker for cancer-specific survival. Cell surface CLDN10 promoted cell viability, proliferation, and migration of ccRCC cells, as well as their tumor growth. CLDN10 also activated mTOR signaling and expression of downstream targets, including MYC target genes. Notably, we found that CLDN10 forms a complex with an amino acid transporter, LAT1, and that CLDN10–LAT1 signaling facilitates malignant phenotypes in ccRCC cells. Structural prediction and immunoprecipitation analysis results strongly suggest an interaction between CLDN10-TM1 (transmembrane domain 1) and LAT1-TM4.ConclusionsWe conclude that CLDN10–LAT1 signaling drives ccRCC progression. Taken together with our previous findings on CLDN–Src-family kinases signaling, CLDNs propagate distinct intracellular signals depending on their association with different binding partners.

Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes.

Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear pores and disrupting transport. Using CRISPR-based microRaft, followed by gRNA identification (CRaft-ID), we discovered 55 RNA-binding proteins (RBPs) that influence CHMP7 localization, including SmD1, a survival of motor neuron (SMN) complex component. Immunoprecipitation-mass spectrometry (IP-MS) and enhanced crosslinking and immunoprecipitation (CLIP) analyses revealed CHMP7's interactions with SmD1, small nuclear RNAs, and splicing factor mRNAs in motor neurons (MNs). ALS induced pluripotent stem cell (iPSC)-MNs show reduced SmD1 expression, and inhibiting SmD1/SMN complex increased CHMP7 nuclear localization. Crucially, overexpressing SmD1 in ALS iPSC-MNs restored CHMP7's cytoplasmic localization and corrected STMN2 splicing. Our findings suggest that early ALS pathogenesis is driven by SMN complex dysregulation.

Consistent classification of amyloid status by fasted and non‐fasted plasma Aβ42/40 and Amyloid Probability Score

AbstractBackgroundIt is unknown whether fasting status affects classification of amyloid status by plasma Aβ42/40.MethodsThe cohort included 50 amyloid PET positive and 50 amyloid PET negative individuals enrolled in studies of memory and aging at the Knight Alzheimer Disease Research Center (ADRC). Included individuals had a non‐fasted plasma sample and an amyloid PET scan performed within 3 months of a fasted plasma sample. Non‐fasted samples were collected throughout the day. CSF was collected at approximately 8 am at the same session as the fasted plasma sample. Plasma Aβ42/40 was measured by an immunoprecipitation‐mass spectrometry (IPMS) assay at C2N Diagnostics. The classification accuracy of amyloid PET and CSF status was evaluated in the fasted and non‐fasted samples by logistic regression. Cut‐offs for amyloid positivity with the highest Youden index (combined sensitivity and specificity) were selected. The correlations of fasted and non‐fasted plasma Aβ42/40 and amyloid probability score (APS, a modeled value incorporating plasma Ab42/40, ApoE proteotype, and age) were evaluated.ResultsParticipants had an average age of 69.3 ± 8.3 years (mean ± standard deviation) and 94 of 100 were cognitively unimpaired. The average interval between collection of fasted and non‐fasted plasma samples was 1.8 ± 0.7 months. Classification accuracy of amyloid status based on fasted or non‐fasted samples (either plasma Aβ42/Aβ40 or APS) was almost identical: for amyloid PET status, ROC AUC 0.88 and 0.89 respectively; for CSF Ab42/40 status, ROC AUC 0.89 and 0.91 respectively. The APS cut‐off for amyloid PET status and CSF status was 16 for both fasted and non‐fasted samples; based on this cut‐off, 8 of 100 samples had discordance between fasted and non‐fasted plasma APS. The Spearman correlation between fasted and non‐fasted plasma for Ab42/40 was ρ=0.74 (0.64‐0.82) and for APS was ρ=0.87 (0.82‐0.91).ConclusionsMeasurements of plasma Aβ42/40 with an IPMS assay and the APS had high and consistent associations with amyloid PET and CSF Aβ42/40 status in fasted and non‐fasted samples. These results suggest that fasting status, and potentially the time of day that a sample is collected, does not significantly affect classification of amyloid status by plasma Aβ42/40 or APS.

The GPER is an important factor through which somatic cells regulate oocyte maternal mRNA translation and developmental competence.

The G protein-coupled estrogen receptor (GPER) plays a crucial role in various biological processes, but its regulation of oocyte meiosis remains unclear. In this study, we generated a Gper1 knockout in growing oocytes using Zp3-Cre, revealing that GPER is essential for oocyte maturation and embryo development. RNA-seq analysis indicated that GPER deficiency significantly altered the oocyte transcriptome and disrupted mRNA translation. Immunoprecipitation mass spectrometry revealed that GPER directly interacts with HSP90 and modulates the ERK1/2 and PI3K-AKT signaling pathways, which are vital for enhancing maternal mRNA translation and developmental potential. We also found that cumulus cell-derived GPER-positive vesicles and delivered to oocytes through a RAB11A-dependent pathway. RAB11A facilitates GPER recycling, preventing its degradation in late endosomes and promoting its plasma membrane localization. Moreover, epidermal growth factor (EGF) improves GPER expression in cumulus cells by upregulating RAB11A, thereby enhancing the exocytosis of recycling vesicles. Knockdown of Rab11a severely reduced GPER-positive vesicles in oocytes, impairing spindle morphogenesis and meiosis. Our findings highlight the critical role of somatic cell signals in regulating maternal mRNA translation and oocyte quality for embryonic development.

A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses.

The IV subfamily of receptor-like cytoplasmic kinase (RLCK-IV), known as calcium-binding receptor-like cytoplasmic kinases (CRCKs), plays a vital role in plant signal transduction, particularly in coordinating growth and responses to abiotic stresses. However, our comprehension of CRCK genes in Populus deltoides, a species characterized as fast-growing and pest-resistant but with drought intolerance, is limited. Here, we identify 6 members of the CRCK subfamily on a genome-wide scale in P. deltoides, denoted as PdeCRCK1-PdeCRCK6. An evolutionary and structural analysis revealed highly conserved kinase catalytic domains across all PdeCRCKs, characterized by calmodulin (CaM)-binding sites and serine (Ser)/threonine (Thr) phosphorylation sites. The cis-acting elements of promoters indicated the presence of responsive elements for plant hormones, abiotic stresses, and transcription factor binding sites, which is supported by the distinct transcriptional expression patterns of PdeCRCKs under abscisic acid (ABA), polyethylene glycol (PEG), and mannitol treatments. A transient overexpression of PdeCRCK3/5/6 in tobacco (Nicotiana benthamiana) leaves indicated their involvement in reactive oxygen species (ROS) scavenging, polyamine gene synthesis, and ABA signaling pathway modulation. Immunoprecipitation-Mass Spectrometry (IP-MS) and a yeast two-hybrid (Y2H) assay showed that PdeCRCK6 interacted with AAA-type ATPase proteins and ubiquitin, suggesting its potential function in being involved in chloroplast homeostasis and the 26S ubiquitin protease system. Taken together, these findings offer a comprehensive analysis of the RLCK-IV subfamily members in P. deltoides, especially laying a foundation for revealing the potential mechanism of PdeCRCK6 in response to osmotic stresses and accelerating the molecular design breeding of drought tolerance in poplar.

Inhibition of the E3 ligase UBR5 stabilizes TERT and protects vascular organoids from oxidative stress

BackgroundExcessive oxidative stress is known to cause endothelial dysfunction and drive cardiovascular diseases (CVD). While telomerase reverse transcriptase (TERT) shows protective effects against oxidative stress in rodents and is associated to human flow-mediated dilation in CVD, its regulatory mechanisms in human vascular systems under pathological oxidative stress require further investigation.MethodsHuman induced pluripotent stem cells (hiPSCs) were used to create vascular organoids (VOs). These VOs and human umbilical vein endothelial cells (HUVECs) were subjected to oxidative stress through both hydrogen peroxide (H2O2) and oxidized low-density lipoprotein (oxLDL) models. The effects of TERT overexpression by inhibition of the ubiquitin protein ligase E3 component N-recognin 5 (UBR5) on reactive oxygen species (ROS)-induced vascular injury and cellular senescence were assessed using neovascular sprouting assays, senescence-associated β-galactosidase (SA-β-Gal) staining, and senescence-associated secretory phenotype (SASP) assays.ResultsROS significantly impaired VO development and endothelial progenitor cell (EPC) angiogenesis, evidenced by reduced neovascular sprouting and increased senescence markers, including elevated SA-β-Gal activity and SASP-related cytokine levels. Overexpression of TERT counteracted these effects, restoring VO development and EPC function. Immunoprecipitation-mass spectrometry identified UBR5 as a critical TERT regulator, facilitating its degradation. Inhibition of UBR5 stabilized TERT, improving VO angiogenic capacity, and reducing SA-β-Gal activity and SASP cytokine levels.ConclusionsInhibiting UBR5 stabilizes TERT, which preserves EPC angiogenic capacity, reduces VO impairment, and delays endothelial cell senescence under oxidative stress. These findings highlight the potential of targeting UBR5 to enhance vascular health in oxidative stress-related conditions.Graphical

KPNB1-ATF4 induces BNIP3-dependent mitophagy to drive odontoblastic differentiation in dental pulp stem cells

BackgroundDifferentiating dental pulp stem cells (DPSCs) into odontoblasts is a critical process for tooth self-repair and dentine‒pulp engineering strategies in the clinic. However, the mechanism underlying the regulation of DPSC odontoblastic differentiation remains largely unknown. Here, we demonstrated that BCL-2 interacting protein 3 (BNIP3)-dependent mitophagy is associated with importin subunit beta-1 (KPNB1)-activating transcription factor 4 (ATF4), which promotes DPSC odontoblastic differentiation.MethodsThe key genes involved in DPSC odontogenic differentiation were identified via bioinformatics. Stable silencing or overexpression of BNIP3 was performed to investigate its impact on DPSC differentiation in vitro (n ≥ 3). To explore the role of BNIP3 in vivo, tooth root fragments loaded with the hydrogel-transfected DPSC complex were implanted into nude mice (n ≥ 6). Dual-luciferase reporter assays and chromatin immunoprecipitation (ChIP) polymerase chain reaction (PCR) were conducted to explore the binding site of ATF4 to the BNIP3 promoter (n ≥ 3). Mitochondrial function experiments were performed to investigate the impact of ATF4-BNIP3 on mitochondria (n ≥ 3). Immunoprecipitation (IP) mass spectrometry (MS) was used to investigate the interaction between ATF4 and its binding protein, KPNB1. Plasmids containing wild-type (WT)/mutant (MUT)-nuclear localization signal (NLS) forms of ATF4 were constructed to determine the specific amino acid residues recognized by KPNB1 and their effects on DPSC odontoblastic differentiation (n ≥ 3).ResultsCompared with those in the control group, the levels of autophagy and mitophagy, especially BNIP3-dependent mitophagy, were greater in the DPSC odontoblastic differentiation group (P < 0.05). Genetic silencing or overexpression of BNIP3 demonstrated that BNIP3 expression was positively correlated with the transition of DPSCs into odontoblasts both in vitro and in vivo (P < 0.05). ATF4 regulates the expression of BNIP3 by directly binding to approximately −1292 to −1279 bp and approximately −1185 to −1172 bp within the BNIP3 promoter region, which is associated with mitophagy and mitochondrial reactive oxygen species (mtROS) levels (P < 0.05). Moreover, ATF4 increased mitophagy, mitochondrial function, and cell differentiation potential via BNIP3 (P < 0.05). Mechanistically, KPNB1 is a novel interacting protein of ATF4 that specifically recognizes amino acids (aa) 280–299 within ATF4 to control its translocation into the nucleus and subsequent transcription and differentiation processes (P < 0.05).ConclusionsWe reported that the critical role of KPNB1/ATF4/BNIP3 axis-dependent mitophagy could provide new cues for the regeneration of the dental pulp‒dentin complex in DPSCs.Graphical

S100A4 targets PPP1CA/IL-17 to inhibit the senescence of sheep endometrial epithelial cells.

Gonadotropin-releasing hormone (GnRH) is commonly used in animal reproduction and production, but it was previously reported that GnRH decreases the embryo implantation rate during artificial insemination or embryo transfer in sheep. In addition to the finding that GnRH can target S100A4 to inhibit endometrial epithelial cells proliferation, it was also found that endometrial cells were in poor condition and experienced cell death in S100A4 knockout mice, but the mechanism is unclear. The protein PPP1CA, which interacts with S100A4, was detected by immunoprecipitation-mass spectrometry of overexpression and knockdown of S100A4 and PPP1CA. The effect of S100A4 and PPP1CA on cell senescence was detected by Galactosidase staining. To further reveal the mechanism effect of S100A4 and PPP1CA on cell senescence, transcriptome sequencing was conducted. Additionally, in vivo experiments were performed to assess PPP1CA protein expression in the endometrial tissue of S100A4 knockout mice. S100A4 inhibited cell senescence by activating PPP1CA, while PPP1CA overexpression suppressed the activation of the IL-17 signaling pathway. Inhibition of the IL-17 signaling pathway inhibited the senescence of endometrial cells. S100A4 can target the PPP1CA/IL-17 signaling pathway and inhibit endometrial epithelial cell senescence.

Plasma pTau217 ratio predicts continuous regional brain tau accumulation in amyloid-positive early Alzheimer's disease.

This study examines whether phosphorylated plasma Tau217 ratio (pTau217R) can predict tau accumulation in different brain regions, as measured by positron emission tomography (PET) standardized uptake value ratio (SUVR), for staging Alzheimer's disease (AD). Plasma pTau217R was measured using immunoprecipitation-mass spectrometry. Models for predicting tau PET SUVR, developed with 144 early AD individuals using [18F]MK6240, were validated in two validation sets, VS1 (98 early AD) and VS2 (47 preclinical/early AD with a different tracer, flortaucipir (Tauvid)), all amyloid-beta positive (Aβ+). The pTau217R-based model predicted tau levels up to an SUVR of 2 in multiple brain regions, effectively assessing tau status at different tau levels with receiver operating characteristic (ROC) curve areas of 0.84-0.95 in VS1 and 0.71-0.88 in VS2 (using a different tracer). It reduced PET scan needs by 65% while maintaining 95% sensitivity. PTau217R reliably predicts regional tau accumulation in early AD, reducing reliance on tau PET scans and broadening its clinical application. NCT03887455 (ClarityAD) HIGHLIGHTS: Developed a model using plasma pTau217R to predict tau levels across brain regions. pTau217R model outperformed models based on clinical, MRI, and other blood biomarkers. The model reliably predicted tau levels exceeding tau positivity and higher thresholds. Screening with pTau217R could reduce tau PET scans by 65% at 95% sensitivity. pTau217R model aids in disease staging and monitoring in early AD.

Alternative production of pro-death Bax∆2 protein via ribosomal frameshift in Alzheimer’s disease

Pro-death Bax family member, Bax∆2, forms protein aggregates in Alzheimer’s disease neurons and causes stress granule-mediated neuronal death. Production of Bax∆2 originated from two events: alternative splicing of Bax exon 2 and a microsatellite mutation (a deletion from poly guanines, G8 to G7). Each event alone leads to a reading frameshift and premature termination. While Bax exon 2 alternative splicing is common in Alzheimer’s brains, the G7 mutation is not, which is inconsistent with the high Bax∆2 protein levels detected in clinical samples. Here, we report an alternative mechanism to produce Bax∆2 protein in the absence of the G7 mutation. Using dual-tag systems, we showed that a ribosomal frameshift (RFS) can compensate the lack of G7 mutation in translating Bax∆2 protein. Intriguingly, the microsatellite poly G repeat is neither essential nor the site for the RFS. However, disruption of the poly G sequence impaired the RFS, potentially due to alteration of the local RNA structure. Using immunoprecipitation-mass spectrometry, we pinpointed the RFS site at 15 base pairs upstream of the microsatellite. These results uncover an alternative mechanism for generating functional Bax∆2-subfamily isoforms, highlighting the production plasticity of Bax family isoforms and unveiling potential new therapeutic targets for Alzheimer’s disease.

NRF3-mediated mitochondrial superoxide promotes cardiomyocyte apoptosis and impairs cardiac functions by suppressing Pitx2

Abstract Background Myocardial infarction (MI) elicits mitochondria reactive oxygen species (ROS) production and cardiomyocyte apoptosis. Nrf3 (Nuclear factor erythroid 2-related factor 3) has an established role in regulating redox signaling and tissue homeostasis. Herein, we aimed to uncover the exact role and potential mechanism of Nrf3 in injury-induced cardiac remodeling. Methods Global (Nrf3-KO) and cardiomyocyte-specific (NRF3△CM) Nrf3 knockout mice were subjected to MI or ischemia/reperfusion (I/R) injury, followed by functional and histopathological analysis. Primary neonatal mice (NMVMs) and rat (NRVMs) ventricular myocytes as well as cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) were used to detect the possible impact of Nrf3 on cardiomyocyte apoptosis and mitochondrial ROS production. Chromatin immunoprecipitation sequencing and immunoprecipitation–mass spectrometry analysis were used to uncover potential targets of Nrf3. MitoPQ administration and cardiomyocyte-specific AAV vector were used to further confirm the in vivo relevance of the identified signal pathways. Results Increased level of Nrf3 was observed in cardiomyocytes within border zone of infarcted human heart and murine cardiac tissues post-MI. Both global and cardiomyocyte-specific Nrf3 knockout significantly decreased injury-induced mitochondrial ROS production and cardiomyocyte apoptosis, consequently improving cardiac functions. Additionally, cardiac-specific Nrf3 overexpression reversed the cardiac phenotypes observed in Nrf3-KO mice. Functional studies showed that Nrf3 promoted NMVM, NRVM and hiPSC-CM apoptosis by increasing mitochondrial ROS production. Critically, restoring mitochondrial ROS using MitoParaquat blunted the beneficial effects of Nrf3 deletion on cardiac functions and remodeling. Mechanistically, the cardiac redox regulator paired-like homeodomain transcription factor 2 (Pitx2) was identified as one of the main target genes of Nrf3. Specifically, Nrf3 binds to Pitx2 gene promoter where it increases Pitx2 gene promoter DNA methylation through recruiting heterogeneous nuclear ribonucleoprotein K and DNA-methyltransferase 1 complex, thereby inhibiting Pitx2 expression. Importantly, cardiomyocyte-specific knockdown of Pitx2 blunted the beneficial effects of Nrf3 deletion on cardiac functions and remodeling. Conclusions Nrf3 promotes injury-induced cardiomyocyte apoptosis and deteriorates cardiac functions by increasing mitochondrial ROS production via suppressing Pitx2 expression. Targeting Nrf3-Pitx2-mitochondrial ROS signal axis could represent novel therapeutics for treating MI patients.Graphic Abstract