Linking cellular stress responses to systemic homeostasis

Partial mitochondrial involvement in the antiproliferative and immunostimulatory effects of PT-112

PT-112 is a novel small molecule exhibiting promising clinical activity in patients with solid tumors. PT-112 kills malignant cells by inhibiting ribosome biogenesis while promoting the emission of immunostimulatory signals. Accordingly, PT-112 is an authentic immunogenic cell death (ICD) inducer and synergizes with immune checkpoint inhibitors in preclinical models of mammary and colorectal carcinoma. Moreover, PT-112 monotherapy has led to durable clinical responses, some of which persisting after treatment discontinuation. Mitochondrial outer membrane permeabilization (MOMP) regulates the cytotoxicity and immunogenicity of various anticancer agents. Here, we harnessed mouse mammary carcinoma TS/A cells to test whether genetic alterations affecting MOMP influence PT-112 activity. As previously demonstrated, PT-112 elicited robust antiproliferative and cytotoxic effects against TS/A cells, which were preceded by the ICD-associated exposure of calreticulin (CALR) on the cell surface, and accompanied by the release of HMGB1 in the culture supernatant. TS/A cells responding to PT-112 also exhibited eIF2α phosphorylation and cytosolic mtDNA accumulation, secreted type I IFN, and exposed MHC Class I molecules as well as the co-inhibitory ligand PD-L1 on their surface. Acute cytotoxicity and HMGB1 release caused by PT-112 in TS/A cells were influenced by MOMP competence. Conversely, PT-112 retained antiproliferative effects and its capacity to drive type I IFN secretion as well as CALR, MHC Class I and PD-L1 exposure on the cell surface irrespective of MOMP defects. These data indicate a partial involvement of MOMP in the mechanisms of action of PT-112, suggesting that PT-112 is active across various tumor types, including malignancies with MOMP defects.

Computational strategies in systems-level stress response data analysis

Stress responses in biological systems arise from complex, dynamic interactions among genes, proteins, and metabolites. A thorough understanding of these responses requires examining not only changes in individual molecular components but also their organization into interconnected pathways and networks that collectively maintain cellular homeostasis. This review provides an overview of computational strategies designed to capture these multifaceted processes. First, we discuss the importance of data analysis in uncovering how stress adaptation unfolds, highlighting both classical approaches (e.g., ANOVA, t-tests) and more advanced methods (e.g., clustering, smoothing splines) that handle strong temporal dependencies. We then explore how enrichment analyses can contextualize these dynamic changes by linking regulated molecules to broader biological functions and processes. The latter half of the review focuses on network-based modeling techniques, emphasizing the construction and refinement of de novo networks to identify stress-specific regulatory networks. Pairwise approaches are discussed alongside advanced methods that include multi-omics data, literature knowledge, and machine learning. Finally, we address comparative network analyses, which facilitate cross-condition studies, revealing both conserved and distinct features that shape resilience. With continued advances in high-throughput experimentation and computational modeling, these methods will deepen our insights into how cells detect and counteract stress.

Hyperacute response proteins synthesized on γ-tubulin-FTO-MARK4 translation microdomains regulate cancer's acute stress response

Compared to normal cells, cancer cells are particularly resistant to stress, and their immediate response to stress is critical for subsequent adaptation, a major clinical challenge. With unbiased proteomics and transcriptomics, we identify a list of hyperacute response proteins (HARPs) translated from pre-existing mRNAs within 20 min of diverse stresses in several cancer cells, despite the known suppressed global translation in stress. HARP mRNAs are translated on microtubule-associated translation microdomains (MATMs) located on γ-tubulin, which host FTO and specialized distinct cytoskeletal ribosomes. FTO exits the nucleus immediately after stress and is activated by microtubule-associated kinase MARK4, demethylating a translation-inhibiting m6A mRNA methylation signature and facilitating compartmentalized HARP translation on MATMs, while non-HARP mRNAs remain inhibited. FTO or MARK4 inhibition suppresses HARP synthesis and increases apoptosis after various stresses, including chemotherapy. γ-tubulin, FTO, and MARK4 are therapeutic targets, as they comprehensively promote HARP translation, a potential Achilles' heel for cancer's resistance to physiologic or therapeutic stress.

Pathogenesis and Therapeutic Perspectives of Tubular Injury in Diabetic Kidney Disease: An Update

Diabetic kidney disease (DKD), a well-characterized microvascular complication associated with the progression of diabetes mellitus, has been identified as the leading etiological factor contributing to the global burden of end-stage kidney disease (ESKD). Historically, DKD research has predominantly centered on glomerular mechanisms; however, recent studies have increasingly emphasized the critical role of tubular dysfunction. Extensive evidence has elucidated the key pathological drivers of tubular injury in DKD, encompassing metabolic dysregulation, pro-inflammatory signaling pathways, diverse cellular stress responses, and epithelial-mesenchymal transition (EMT). Furthermore, emerging mechanistic studies reveal that autophagic flux impairment and epigenetic memory formation collaboratively drive cellular senescence in DKD. Regarding the treatment of DKD, various hypoglycemic drugs, as well as hypotensive drugs, and microcirculatory improvers have garnered significant attention. Recently, stem cell-based interventions and precision gene editing techniques have unveiled novel therapeutic paradigms for DKD, fundamentally expanding the treatment arsenal beyond conventional pharmacotherapy. This review synthesizes updated insights into the pathogenesis of tubular injury in DKD and highlights promising therapeutic strategies for managing this condition.

Metabolic switches in cell death regulation

The death of mammalian cells is generally regulated by a complex interplay amongst distinct molecular machineries that ultimately determines the kinetic and immunological consequences of the process. Recent data from Song et al. delineate a new metabolic circuitry through which apoptotic signals may actively suppress cell death via ferroptosis.

Hepatic Nuclear Factor Erythroid 2 Related Factor 1 Activity Promotes Host Defense in Endotoxemia and Bacterial Sepsis

BACKGROUND & AIMS

Sepsis and endotoxemia cause mortality by inducing organ dysfunction and damage. Liver defends against such insults by mediating metabolic adaptations that promote stress and damage control. The mechanisms underlying liver defenses may require coordinated actions between cellular and systemic stress-defense programming. Here, we investigated whether the stress-defending transcription factors nuclear factor erythroid 2 related factor-1 (Nrf1) and -2 (Nrf2) in hepatocytes protect against endotoxemia and sepsis.

METHODS

We used mice injected with Escherichia coli-derived lipopolysaccharide (endotoxemia), or E coli (sepsis). Hepatic Nrf1 and Nrf2 activity was examined, and we also genetically altered their activity and examined corresponding effects on survival, body temperature, cytokines and liver inflammation, liver gene and protein expression, and liver-related metabolism.

RESULTS

Hepatic Nrf1 and Nrf2 activity was reduced in endotoxemia and sepsis, and deficiency for hepatic Nrf1, but not Nrf2, promoted severe hypothermia and mortality. Conversely, increasing hepatic Nrf1 activity mitigated hypothermia and improved survival. These effects were linked to very-low-density lipoprotein (VLDL) secretion and triglyceride metabolism. In endotoxemia, hepatic Nrf1 deficiency reduced VLDL secretion, whereas increased hepatic Nrf1 activity enhanced VLDL secretion. Administering a VLDL secretion inhibitor, lomitapide, or inhibitor of circulating triglyceride hydrolysis, poloxamer 407, diminished protective effects of hepatic Nrf1 activity, whereas administering intralipid rescued the lomitapide-injected mice. Gene expression profiling indicates Nrf1 promotes this effect by regulating stress-defense programming.

CONCLUSIONS

Mortality in endotoxemia and sepsis is exacerbated by impaired hepatic Nrf1 activity. Interventions increasing hepatic Nrf1 activity promote liver defenses that protect against sepsis-associated hypothermia and mortality.

Dual Modulation of Autophagy and Apoptosis as Anticancer Mechanism of Action of Khaya grandiofoliola in Colon Carcinoma Cells

Khaya grandiofoliola (Kh) is a medicinal plant with therapeutic properties. Studies have reported on the general bioactivity and anticancer potentials of the plant, but no investigations have yet investigated its anticancer mechanism of action. This study presents the first examination of the anticancer mechanism of action of the methanolic extract of Kh, alongside phytochemical profiling of its anticancer constituents. We conducted in vitro investigations into the mechanism of action of Kh and performed bioactivity-guided fractionation, with subsequent identification of its anticancer phytochemicals using HPLC and GC-MS, respectively. Kh posed a potent antiproliferative effect against colon carcinoma cells and an antioxidant property at low microgram levels. Furthermore, the treatment of Kh in Caco-2 cells led to the accumulation of p62 puncta, indicating inhibition of autophagic flux degradation. Kh impacts microtubule, induced G1 arrest, and late apoptosis induction in Caco-2 cells. Phytochemicals belonging to sesquiterpene alcohols were found most abundant in the Kh bioactive fractions. The identified phytochemicals are potential inducers of apoptosis, autophagy flux inhibition, and G1-phase arrest. Our findings suggest that the anticancer property of Kh is mediated through the dual modulation of autophagy and apoptosis. Further studies are needed to isolate the active compounds responsible for these effects and further elucidate the underlying molecular mechanisms.

Impact of radiation therapy on the immunological tumor microenvironment

External beam radiation therapy (RT) is a cornerstone of modern cancer management, being utilized in both curative and palliative settings due to its safety, efficacy, and widespread availability. A primary biological effect of RT is DNA damage, which leads to significant cytostatic and cytotoxic effects. Importantly, malignant cells possess a limited capacity for DNA repair compared to normal cells, and when combined with irradiation techniques that minimize damage to healthy tissues, this creates an advantageous therapeutic window. However, the clinical effectiveness of RT also appears to involve both direct and indirect interactions between RT and non-transformed components of the tumoral ecosystem, particularly immune cells. In this review, we describe the molecular and cellular mechanisms by which irradiated cancer cells modify the immunological tumor microenvironment and how such changes ultimately impact tumor growth.

Role of Fibroblast Growth Factors in Neurological Disorders: Insight into Therapeutic Approaches and Molecular Mechanisms

In the last few decades, the incidence and progression of neurological disorders have consistently increased, which mainly occur due to environmental pollution, genetic abnormalities, and modern lifestyles. Several case reports suggested that these factors enhanced oxidative stress, mitochondrial dysfunction, inflammation, and apoptosis, leading to neurological disease. The pathophysiology of neurological disorders is still not understood, mainly due to the diversity within affected populations. Existing treatment options primarily provide symptomatic relief but frequently come with considerable side effects, including depression, anxiety, and restlessness. Fibroblast growth factors (FGFs) are key signalling molecules regulating various cellular functions, including cell proliferation, differentiation, electrical excitability, and injury responses. Hence, several investigations claimed a relationship between FGFs and neurological disorders, and their findings indicated that they could be used as therapeutic targets for neurological disorders. The FGFs are reported to activate various signalling pathways, including Ras/MAPK/PI3k/Akt, and downregulate the GSK-3β/NF-κB pathways responsible for anti-oxidant, anti-inflammatory, and anti-apoptotic effects. Therefore, researchers are interested in developing novel treatment options for neurological disorders. The emergence of unreported FGFs contributes to our understanding of their involvement in these conditions and encourages further exploration of innovative therapeutic approaches. All the data were obtained from published articles using PubMed, Web of Science, and Scopus databases using the search terms Fibroblast Growth Factor, PD, HD, AD, ALS, signalling pathways, and neurological disorders.

Acetylation and deacetylation dynamics in stress response to cancer and infections

In response to stress stimuli, cells have evolved various mechanisms to integrate internal and external signals to achieve dynamic homeostasis. Lysine acetyltransferase (KATs) and deacetyltransferase (KDACs) are the key modulators of epigenetic modifications, enabling cells to modulate cellular responses through the acetylation and deacetylation of both histone and nonhistone proteins. Understanding the signaling pathways involved in cellular stress response, along with the roles of KATs and KDACs may pave the way for the development of novel therapeutic strategies. This review discusses the molecular mechanisms of acetylation and deacetylation in stress responses related to tumorigenesis, viral and bacterial infections. In tumorigenesis section, we focused on the tumor cells' intrinsic and external molecules and signaling pathways regulated by acetylation and deacetylation modification. In viral and bacterial infections, we summarized the update research on acetylation and deacetylation modification in viral and bacterial infections, which systematical introduction on this topic is not too much. Additionally, we provide an overview of current therapeutic interventions and clinical trials involving KAT and KDAC inhibitors in the treatment of cancer, as well as viral and bacterial infection-related diseases.

Passiflora incarnate extract attenuates neuronal loss and memory impairment in stressed rats

The present study investigated the protective effects of hydroalcoholic Passiflora incarnate extract on memory, anxiety-like behaviors, inflammatory factors, and cell density in the brain following stress. This study randomly divided 40 adult Wistar rats into 5 groups: control, normal saline, stress, stress + Passiflora incarnata, and Passiflora incarnata groups. For 21 consecutive days, the stress group and the Passiflora incarnata + stress group were exposed to immobilizing stress for 2 h each day. The Passiflora incarnata and the stress + Passiflora incarnata groups were gavaged with Passiflora incarnata extract half an hour before stress for 21 days. One day after the last stress, the Barnes and elevated plus maze were used to measure learning, memory, and anxiety-like behavior, respectively. Additionally, the MDA (malondialdehyde), TNF-α, IL-1, and gamma-glutamyl transferase (GGT) factors in the serum, as well as the cell density in the hippocampus, amygdala, and prefrontal regions, were investigated. The results of the Barnes maze showed that immobility stress increases the number of errors and the distance traveled to reach the target hole. Administering Passiflora incarnata extract prior to stress led to fewer errors and a shorter distance covered to reach the target hole. The use of Passiflora incarnata before stress in the elevated plus maze reduced anxiety-like behaviours (less frequent entries into the open arm, reduced duration of time in the open arm) compared to the stress group. The stress group caused a significant enhance in MDA, TNF-α, and IL-1 and a decrease in GGT, while treatment with Passiflora incarnata significantly improved these factors than the stress group. The immobility stress caused a significant decrease in cell density in the hippocampus, amygdala, and prefrontal region, and treatment with Passiflora incarnata increased cell density in these areas than the stress animals. In conclusion, Passiflora incarnata improves learning and memory impairment, anxiety-like behaviors, inflammatory factors, and damage caused by stress in the hippocampus, amygdala, and prefrontal areas.

p38 mediated ACSL4 phosphorylation drives stress-induced esophageal squamous cell carcinoma growth through Src myristoylation

The comprehension of intricate molecular mechanisms underlying how external stimuli promote malignancy is conducive to cancer early prevention. Esophageal squamous cell carcinoma (ESCC) is considered as an external stimuli (hot foods, tobacco, chemo-compounds) induced cancer, characterized by stepwise progression from hyperplasia, dysplasia, carcinoma in situ and invasive carcinoma. However, the underlying molecular mechanism governing the transition from normal epithelium to neoplastic processes in ESCC under persistent external stimuli has remained elusive. Herein, we show that a positive correlation between p38 and ERK1/2 activation during the progression of ESCC. We identify that phosphorylation of ACSL4 at T679 by p38 enhances its enzymatic activity, resulting in increased production of myristoyl-CoA (C14:0 CoA). This subsequently promotes Src myristoylation and activates downstream ERK signaling. Our results partially elucidate the role of ACSL4 in mediating stress-induced signaling pathways that activate growth cascades and contribute to tumorigenesis.

Adverse Outcome Pathway-Based Strategies to Mitigate Ag2Se Quantum Dot-Induced Neurotoxicity

Silver selenide quantum dots (Ag2Se QDs) show great advantages in tumor imaging due to their excellent optical performance and good biocompatibility. However, the ultrasmall particle size of Ag2Se QDs allows them to cross the blood-brain barrier, thus potentially affecting the central nervous system. Therefore, risk assessment and response strategies for Ag2Se QDs are important. The adverse outcome pathway (AOP) framework makes it possible to develop risk management strategies based on toxicity mechanisms. In this study, using the AOP framework, we constructed causal mechanism relationship diagrams at different biological levels of Ag2Se QD neurotoxicity. In this framework, excess mitochondrial reactive oxygen species (mtROS) triggered Nod-like receptor protein 3 (NLRP3) inflammasome activation in microglia was molecular initiation event (MIE). Proinflammatory mediator secretion and microglia activation were key events (KEs) at the cellular level. Neuroinflammation and neuronal damage were KEs at the organ/tissue level. Altered hippocampal physiology was the adverse outcome (AO) at the individual level. Based on the established AOP framework, further studies confirmed that mtROS-activated nuclear-factor-E2-related factor 2 (Nrf2)/PTEN-induced kinase 1 (PINK1)- mitophagy contributed to weaken the MIE. Molecular docking-assisted molecular biology experiments demonstrated that quercetin (Qu) enhanced this process. This article emphasizes the importance of the AOP in the risk management of nanomaterials. Furthermore, this paper guides the use of natural small-molecule drugs as a strategy to mitigate nanomaterial-induced neurotoxicity.

Distinct immune responses to proton and photon radiotherapy: implications for anti-PD-L1 combination therapy in colorectal cancer

BACKGROUND

Ionizing radiation can influence the antitumor immune response, either activating or suppressing the immune system depending on the tumor type and radiotherapy modality. While photon radiation (RT) combined with immunotherapy (IT) is widely studied in clinical trials, proton radiation (PT) combined with IT has not been thoroughly investigated in clinical or preclinical studies despite its radiobiological advantages. This study aims to explore the immune effects of a hypofractionated PT scheme compared to RT and its efficacy with anti-PD-L1 immunotherapy.

METHODS

Balb/c mice bearing subcutaneous CT26 colon tumors were treated with RT or PT, delivered with 3 × 8 Gy. Seven days post-treatment, transcriptomic analysis and immune response assessments to characterize lymphoid cells, myeloid cells, and PD-L1 expression were performed. Tumor growth was monitored to evaluate the efficacy of combining RT or PT with anti-PD-L1 IT.

RESULTS

The RNA sequencing analysis demonstrated an overexpression of genes involved in the interferon type I pathway after both RT and PT. Tumor microenvironment analysis showed enhanced immune cell infiltration in tumors after both treatments. Immunoactivating cells infiltration was observed, with LT CD8 + cells infiltration after both RT and PT, more significantly after RT. NK and TAM1 cells infiltrated only after RT. Immunosuppressive cell populations were induced by PT, including MDSCs, while Tregs infiltrated both RT and PT treated tumors. PD-L1 expression was significantly induced only by RT. The combination of anti-PD-L1 with RT or PT resulted in tumor growth delay compared to RT or PT alone, with a significant survival benefit observed only after the combination of RT and IT.

CONCLUSIONS

This study demonstrates that hypofractionated RT and PT induced both similar and significantly distinct immune responses. PT triggers a stronger immunosuppressive response than RT. Optimizing the combination of PT with IT, including dose, fractionation, and sequencing is crucial for improving treatment efficacy.

Serum starvation induces cytosolic DNA trafficking via exosome and autophagy-lysosome pathway in microglia

The imbalance of microglial homeostasis is highly associated with age-related neurological diseases, where cytosolic endogenous DNA is also likely to be found. As the main medium for storing biological information, endogenous DNA could be localized to cellular compartments normally free of DNA when cells are stimulated. However, the intracellular trafficking of endogenous DNA remains unidentified. In this study, we demonstrated that nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), as the components of endogenous DNA, undergo different intracellular trafficking under conditions of microglial homeostasis imbalance induced by serum starvation. Upon detecting various components of endogenous DNA in the cytoplasmic and extracellular microglia, we found that cytosolic nDNA primarily exists in a free form and undergoes degradation through the autophagy-lysosome pathway. In contrast, cytosolic mtDNA predominantly exists in a membrane-wrapped form and is trafficked through both exosome and autophagy-lysosome pathways, with the exosome pathway serving as the primary one. When the autophagy-lysosome pathway was inhibited, there was an increase in exosomes. More importantly, the inhibition of the autophagy-lysosome pathway resulted in enhanced trafficking of mtDNA through the exosome pathway. These findings unveiled the crosstalk between these two pathways in the trafficking of microglial cytosolic DNA and thus provide new insights into intervening in age-related neurological diseases.

Nicotine-Induced Endoplasmic Reticulum Stress and Airway Smooth Muscle Cell Proliferation Is Mediated by α7nAChR and Chaperones-RIC-3 and TMEM35

Nicotine exposure in the context of smoking or vaping worsens airway function. Although nicotinic acetylcholine receptors (nAChRs) are commonly thought to exert effects through the peripheral nervous system, we previously showed that airway smooth muscle (ASM) expresses them, particularly α7 subtype nAChR (α7nAChR), with functional effects on contractility and metabolism. However, the mechanisms of nAChR regulation and downstream effects in ASM are not fully understood. Using ASM cells from people without asthma versus people with mild to moderate asthma, we tested the hypothesis that nAChR-specific endoplasmic reticulum (ER) chaperones, resistance to inhibitors of cholinesterase 3 (RIC-3) and transmembrane protein 35A (TMEM35A) promote cell surface localization of α7nAChR with downstream influence on its functionality: effects exacerbated by inflammation. We found that mild to moderate asthma and exposure to proinflammatory cytokines relevant to asthma promote chaperone and α7nAChR expression in ASM. Downstream, ER stress was linked to nicotine/α7nAChR signaling, where RIC-3 and TMEM35 regulate nicotine-induced ER stress, intracellular Ca2+ regulation, and ASM cell proliferation. Overall, our data highlight the importance α7nAChR chaperones in mediating and modulating nicotine effects in ASM toward airway contractility and remodeling.

Metasilicate-based alkaline mineral water improves the growth performance of weaned piglets by maintaining gut-liver axis homeostasis through microbiota-mediated secondary bile acid pathway

Weaning stress causes substantial economic loss in the swine industry. Moreover, weaning-induced intestinal barrier damage and dysfunction of the gut-liver axis are associated with reduced growth performance in piglets. Metasilicate-based alkaline mineral water (AMW) has shown potential therapeutic effects on gastrointestinal disorders; however, the mechanisms involved and their overall effects on the gut-liver axis have not been explored. Here, sodium metasilicate (SMS) was used to prepare metasilicate-based AMW (basal water + 500 mg/L SMS). A total of 240 newly weaned piglets were allocated to the Control and SMS groups (6 replicate pens per group and 20 piglets per pen) for a 15-day trial period. Histopathological evaluations were conducted using hematoxylin and eosin staining. To analyze the composition of the gut microbiota, 16S rRNA PacBio SMRT Gene Full-Length Sequencing was performed. Western blotting and immunofluorescence were employed to assess protein expression levels. Our results indicated that metasilicate-based AMW effectively alleviated weaning-induced colonic or liver morphological injury and inflammatory response, as well as liver cholesterol metabolism disorders. Further analysis showed that metasilicate-based AMW promoted deoxycholic acid (DCA) biosynthesis by increasing the abundance of Lactobacillus_delbrueckii in the colon (P < 0.001). This consequently improved weaning-induced colon and liver injury and dysfunction through the DCA-secondary bile acid (SBA) receptors (SBAR)-nuclear factor-kappaB (NF-κB)/NOD-like receptor family pyrin domain-containing 3 (NLRP3) pathways. Growth performance parameters, including final body weight (P = 0.034) and average daily gain (P < 0.001), in the SMS group were significantly higher than those in the Control group. Therefore, metasilicate-based AMW maintains gut-liver axis homeostasis by regulating the microbiota-mediated SBA-SBAR pathway in piglets under weaning stress. Our research provides a new strategy for mitigating stress-induced gut-liver axis dysfunction in weaned piglets.

Yeast cells experience chronological life span extension under prolonged glucose starvation

Budding yeast, Saccharomyces cerevisiae, is an ideal model organism for genetic research due to its similarity in life cycle and cellular structure to higher eukaryotes as well as its ease of cultivation and manipulation in the laboratory. Yeast cells benefit from being cultured in calorie-restricted media, which can be achieved by reducing glucose concentration from 2 % to 0.5 %. Cell metabolism depends on glucose and therefore, affects the physiology of the cell. This study aimed to investigate the effects of long-term glucose starvation on the lifespan of yeast cells by culturing in both standard and glucose-starved conditions. In this investigation yeast cells (BY4743 strain) were cultured in glucose-restricted YPD media (0.5 percent dextrose) to assess lifespan, growth-proliferation, autophagy, apoptosis, mtDNA abundance. The findings revealed that prolonged glucose restriction significantly extended chronological lifespan in yeast (p < 0.05). In order to decipher how starved yeast live chronologically longer, we tested mitochondrial association and found that calorie deprivation lowered the rate of mtDNA spontaneous mutation and increased mtDNA abundance which is a suggestive sign of mitobiogenesis. Furthermore, cells cultured on glucose-restricted media led to more autophagosome formation but less cell death. These results suggested that glucose restriction can enhance lifespan by improving overall cellular conditions. These findings may serve as a foundation for future research in aging, cancer and diabetes.

Single-Cell Sequencing and Transcriptome Analysis Explored Changes in Midnolin-Related Immune Microenvironment and Constructed Combined Prognostic Model for Pancreatic Cancer

Background

Pancreatic cancer has one of the worst prognoses of any malignant tumor. The value of MIDN, midnolin-related genes and midnolin-related immune infiltrating cells (MICs) in the prognosis of pancreatic cancer remains unknown.

Methods

Single-cell analysis were used to identify midnolin-related genes. Immune cell infiltration was obtained using CIBERSORT. The prognostic midnolin-related genes were identified through the utilization of Cox regression and the least absolute selection operator (LASSO) approach. The combined prognostic model was created using multifactorial Cox regression analysis. Survival analyses, immune microenvironment assessments, drug sensitivity checks were performed to evaluate the combined model performance. Finally, cellular experiments were carried out to confirm MIDN significance in pancreatic cancer.

Results

The combined model was constructed based on MIDN expression, prognostic model of 10 midnolin-related genes and M1 cell infiltration. Most immune checkpoint-related genes were expressed at greater levels in the low-risk group, suggesting a greater chance of immunotherapy's benefits. The most significant model gene, MIDN, was shown to have a function by cellular tests. In pancreatic cancer, MIDN knockdown drastically decreased pancreatic cancer cell lines' activity, proliferation, and invasive potential.

Conclusion

The combined model helped assess the prognosis of pancreatic cancer and offered fresh perspectives on immunotherapy in particular.

Functional Specialization of S-Adenosylmethionine Synthases Links Phosphatidylcholine to Mitochondrial Function and Stress Survival

S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. Humans and many other organisms express multiple SAM synthases. Evidence in Caenorhabditis elegans , which possesses four SAM synthase genes, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we show that SAMS-1 contributes to a variety of intermediary metabolic pathways, whereas SAMS-4 is more important to generate SAM for methylation reactions. We demonstrate that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and may induce mitophagy. We propose a mechanistic model where reduced SAM from SAMS-1 acts through PC to impact mitochondria, thereby enhancing survival during heat stress.

Mitochondrial DNA leakage: underlying mechanisms and therapeutic implications in neurological disorders

Mitochondrial dysfunction is a pivotal instigator of neuroinflammation, with mitochondrial DNA (mtDNA) leakage as a critical intermediary. This review delineates the intricate pathways leading to mtDNA release, which include membrane permeabilization, vesicular trafficking, disruption of homeostatic regulation, and abnormalities in mitochondrial dynamics. The escaped mtDNA activates cytosolic DNA sensors, especially cyclic gmp-amp synthase (cGAS) signalling and inflammasome, initiating neuroinflammatory cascades via pathways, exacerbating a spectrum of neurological pathologies. The therapeutic promise of targeting mtDNA leakage is discussed in detail, underscoring the necessity for a multifaceted strategy that encompasses the preservation of mtDNA homeostasis, prevention of membrane leakage, reestablishment of mitochondrial dynamics, and inhibition the activation of cytosolic DNA sensors. Advancing our understanding of the complex interplay between mtDNA leakage and neuroinflammation is imperative for developing precision therapeutic interventions for neurological disorders.

Deciphering the role of skin aging in pigmentary disorders

Skin aging is a complex biological process involving intrinsic and extrinsic factors. Skin aging contains alterations at the tissue, cellular, and molecular levels. Currently, there is increasing evidence that skin aging occurs not only in time-dependent chronological aging but also plays a role in skin pigmentary disorders. This review provides an in-depth analysis of the impact of skin aging on different types of pigmentary disorders, including both hyperpigmentation disorders such as melasma and senile lentigo and hypopigmentation disorders such as vitiligo, idiopathic guttate hypomelanosis and graying of hair. In addition, we explore the mechanisms of skin aging on pigmentation regulation and suggest several potential therapeutic approaches for skin aging and aging-related pigmentary disorders.

Unremodeled GPI-anchored proteins at the plasma membrane trigger aberrant endocytosis

The plasma membrane has a complex organization that includes the polarized distribution of membrane proteins and lipids. Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are ubiquitously expressed in eukaryotes and represent a functionally diverse, extensively remodeled, ER-derived group of proteins critical for the organization and function of the plasma membrane. Little is known about how the transport of incompletely remodeled GPI-APs to the plasma membrane affects cell function. Here, we investigated how failure to remodel mannose 2 (Man2) of the GPI moiety impacted endocytic activity on the plasma membrane. We find that Man2 unremodeled GPI-APs increased membrane disorder and generated a stress response that triggered abnormal ubiquitin- and clathrin-dependent endocytosis. The resulting stress-induced endocytosis disrupted the trafficking repertoire of a subset of plasma membrane proteins, which were redirected, via the multivesicular body, to numerous small vacuoles for degradation. Our findings highlight the critical importance of GPI-AP Man2 remodeling for maintaining the integrity and homeostasis of the plasma membrane.

Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells

Cell stress adaptation plays a key role in normal development and in various diseases including cancer. Caspases are activated in response to cell stress, and growing evidence supports their function in non-apoptotic cellular processes. A role for effector caspases in promoting stress-induced cytoprotective autophagy was demonstrated in Drosophila, but has not been explored in the context of human cells. We found a functionally conserved role for effector caspase 3 (CASP3) and caspase 7 (CASP7) in promoting starvation or proteasome inhibition-induced cytoprotective autophagy in human breast cancer cells. The loss of CASP3 and CASP7 resulted in an increase in PARP1 cleavage, reduction in LC3B and ATG7 transcript levels, and a reduction in H2AX phosphorylation, consistent with a block in autophagy and DNA damage-induced stress response pathways. Surprisingly, in non-lethal cell stress conditions, CASP7 underwent non-canonical processing at two calpain cleavage sites flanking a PARP1 exosite, resulting in stable CASP7-p29/p30 fragments. Expression of CASP7-p29/p30 fragment(s) could rescue H2AX phosphorylation in the CASP3 and CASP7 double knockout background. Strikingly, yet consistent with these phenotypes, the loss of CASP3 and CASP7 exhibited synthetic lethality with BRCA1 loss. These findings support a role for human caspases in stress adaptation through PARP1 modulation and reveal new therapeutic avenues for investigation.

PEBP1 amplifies mitochondrial dysfunction-induced integrated stress response

Mitochondrial dysfunction is involved in numerous diseases and the aging process. The integrated stress response (ISR) serves as a critical adaptation mechanism to a variety of stresses, including those originating from mitochondria. By utilizing mass spectrometry-based cellular thermal shift assay (MS-CETSA), we uncovered that phosphatidylethanolamine-binding protein 1 (PEBP1), also known as Raf kinase inhibitory protein (RKIP), is thermally stabilized by stresses which induce mitochondrial ISR. Depletion of PEBP1 impaired mitochondrial ISR activation by reducing eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and subsequent ISR gene expression, which was independent of PEBP1's role in inhibiting the RAF/MEK/ERK pathway. Consistently, overexpression of PEBP1 potentiated ISR activation by heme-regulated inhibitor (HRI) kinase, the principal eIF2α kinase in the mitochondrial ISR pathway. Real-time interaction analysis using luminescence complementation in live cells revealed an interaction between PEBP1 and eIF2α, which was disrupted by eIF2α S51 phosphorylation. These findings suggest a role for PEBP1 in amplifying mitochondrial stress signals, thereby facilitating an effective cellular response to mitochondrial dysfunction. Therefore, PEBP1 may be a potential therapeutic target for diseases associated with mitochondrial dysfunction.

Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

The cellular stress response (CSR) is a conserved mechanism that protects cells from -environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-h recovery period. RNA sequencing revealed the conserved activation of canonical HSR pathways, including the unfolded protein response, alongside the -enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell-line-specific variations were observed, with HepG2 cells exhibiting significantly higher ex-pression levels of certain genes compared to other cell lines under stress conditions, as well as greater fold changes in gene expression relative to its control conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

Bionanoparticles with In Situ Nitric Oxide Release for Precise Modulation of ER-TRPV1 Ion Channels in Multimodal Killing of Glioblastoma

Glioblastoma (GBM) with highly immunosuppressive tumor microenvironment is a significant factor contributing to its treatment resistance and low survival rate. The activation of the transient receptor potential vanilloid 1 (TRPV1) ion channel, which is overexpressed on the endoplasmic reticulum (ER) of GBM cells, governs the control of multi-organelle stress pathway branches to inhibit GBM expansion. Precise modulation of ER-TRPV1 is considered an effective strategy for inhibition of GBM. As an effective intracellular and extracellular second messenger, nitric oxide (•NO) activates the TRPV1 ion channel through nitrosylation of cysteine residues. However, the short lifespan and limited effective range of •NO makes it challenging to achieve precise regulation of ER-TRPV1. Herein, a biomimetic upconversion nanoassembly (M-UCN-T) is constructed, which encapsulates an organic •NO donor and is coated with homologous tumor-targeting cell membrane and ER-targeting peptide. In response to near-infrared light and glutathione, M-UCN-T releases •NO in situ to activate the ER-TRPV1 ion channels. This study developed a •NO-targeted release nanoplatform with stepwise targeting functions, which allow for the precise modulation of ER-TPRV1 in GBM through in situ release of •NO. This approach induces multi-organelle stress signaling pathways, ultimately resulting in multi-modal killing of tumor cells.

Histone lactylation in macrophage biology and disease: from plasticity regulation to therapeutic implications

Epigenetic modifications have been identified as critical molecular determinants influencing macrophage plasticity and heterogeneity. Among these, histone lactylation is a recently discovered epigenetic modification. Research examining the effects of histone lactylation on macrophage activation and polarization has grown substantially in recent years. Evidence increasingly suggests that lactate-mediated changes in histone lactylation levels within macrophages can modulate gene transcription, thereby contributing to the pathogenesis of various diseases. This review provides a comprehensive analysis of the role of histone lactylation in macrophage activation, exploring its discovery, effects, and association with macrophage diversity and phenotypic variability. Moreover, it highlights the impact of alterations in macrophage histone lactylation in diverse pathological contexts, such as inflammation, tumorigenesis, neurological disorders, and other complex conditions, and demonstrates the therapeutic potential of drugs targeting these epigenetic modifications. This mechanistic understanding provides insights into the underlying disease mechanisms and opens new avenues for therapeutic intervention.

Hydrogel Elastic Energy: A Stressor Triggering an Adaptive Stress-Mediated Cell Response

The crosstalk between the cells and the extracellular matrix (ECM) is bidirectional and consists of a pushing/pulling stretch exerted by the cells and a mechanical resistance counteracted by the surrounding microenvironment. It is widely recognized that the stiffness of the ECM, its viscoelasticity, and its overall deformation are the most important traits influencing the response of the cells. Here these three parameters are combined into a concept of elastic energy, which in biological terms represents the mechanical feedback that cells perceive when the ECM is deformed. It is shown that elastic energy is a stress factor that influences the response of cells in three-dimensional (3D) cultures. Strikingly, the higher the elastic energy of the matrix and thus the mechanical feedback, the higher the stress state of the cells, which correlates with the formation of G3BP-mediated stress granules. This condition is associated with an increase in alkaline phosphatase (ALP) activity but a decrease in gene expression and is mediated by the nuclear translocation of Yes-associated protein (YAP). This work supports the importance of considering the elastic energy as mechano-controller in regulating cellular stress state in 3D cultures.

Proteomic analysis of human iPSC-derived sympathetic neurons identifies proteostasis collapse as a molecular signature following subtoxic rotenone exposure

Rotenone is a toxic isoflavone and an inhibitor of the mitochondrial respiratory chain. Rotenone is commonly used due to its piscicidal and pesticidal properties. The peripheral nervous system (PNS) lacks protective barriers and is exposed to many environmental substances due to its long-reaching structure. A causal association between rotenone and human PNS dysfunction is currently a subject of investigation. Here, we treated human induced pluripotent stem cell (iPSC)-derived peripheral sympathetic neurons with a subtoxic dose of rotenone (10 µg/L) that is considered safe for human health and is permitted for environmental use. Indeed, no overt toxicity was observed in the human peripheral neurons and neurite morphology was intact in the treated neurons. Surprisingly, we detected significant changes in the proteome of rotenone-exposed sympathetic neurons with a signature of protein homeostasis (proteostasis) collapse. Screening the proteostasis modules of protein translation, proteolysis, and chaperones, revealed severe perturbations in clusters of autophagy regulators. Our proteomic profiling reveals compromised proteostasis as a consequence of low-dose non-toxic exposure to rotenone, which can disrupt the ability of the PNS to cope with proteotoxic stress. Exposed individuals may have varying degrees of tolerance to such vulnerabilities but they may eventually progress into peripheral neuropathies.

Chronic unpredictable stress induces anxiety-like behavior and oxidative stress, leading to diminished ovarian reserve

Chronic stress can adversely affect the female reproductive endocrine system, potentially leading to disorders and impairments in ovarian function. However, current research lacks comprehensive understanding regarding the biochemical characteristics and underlying mechanisms of ovarian damage induced by chronic stress. We established a stable chronic unpredictable stress (CUS)-induced diminished ovarian reserve (DOR) animal model. Our findings demonstrated that prolonged CUS treatment over eight weeks resulted in increased atresia follicles in female mice. This atresia was accompanied by decreased AMH and increased FSH levels. Furthermore, we observed elevated levels of corticosterone both in the peripheral blood and within the ovary. Additionally, we detected abnormalities in ATP metabolism within the ovarian tissue. CUS exposure led to oxidative stress in the ovaries, fostering a microenvironment characterized by oxidative damage to mouse ovarian granulosa cells (mGCs) and heightened levels of reactive oxygen species. Furthermore, CUS prompted mGCs to undergo apoptosis via the mitochondrial pathway. These findings indicate a direct association between the fundamental physiological alterations leading to DOR and the oxidative phosphorylation processes within mGCs. The diminished ATP production by mGCs, triggered by CUS, emerges as a pivotal indicator of CUS-induced DOR. Our study establishes an animal model to investigate the impact of chronic stress on ovarian reserve function and sheds light on potential mechanisms underlying this phenomenon.

Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

The cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying more uniquely expressed genes and elevated expression levels (fold changes) of shared genes under stress conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

A functional approach to homeostatic regulation

In this work, we present a novel modeling framework for understanding the dynamics of homeostatic regulation. Inspired by engineering control theory, this framework incorporates unique features of biological systems. First, biological variables often play physiological roles, and taking this functional context into consideration is essential to fully understand the goals and constraints of homeostatic regulation. Second, biological signals are not abstract variables, but rather material molecules that may undergo complex turnover processes of synthesis and degradation. We suggest that the particular nature of biological signals may condition the type of information they can convey, and their potential role in shaping the dynamics and the ultimate purpose of homeostatic systems. We show that the dynamic interplay between regulated variables and control signals is a key determinant of biological homeostasis, challenging the necessity and the convenience of strictly extrapolating concepts from engineering control theory in modeling the dynamics of homeostatic systems. This work provides a simple, unified framework for studying biological regulation and identifies general principles that transcend molecular details of particular homeostatic mechanisms. We show how this approach can be naturally applied to apparently different regulatory systems, contributing to a deeper understanding of homeostasis as a fundamental process in living systems.

Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation.

Programmed cell death: molecular mechanisms, biological functions, diseases, and therapeutic targets

Programmed cell death represents a precisely regulated and active cellular demise, governed by a complex network of specific genes and proteins. The identification of multiple forms of programmed cell death has significantly advanced the understanding of its intricate mechanisms, as demonstrated in recent studies. A thorough grasp of these processes is essential across various biological disciplines and in the study of diseases. Nonetheless, despite notable progress, the exploration of the relationship between programmed cell death and disease, as well as its clinical application, are still in a nascent stage. Therefore, further exploration of programmed cell death and the development of corresponding therapeutic methods and strategies holds substantial potential. Our review provides a detailed examination of the primary mechanisms behind apoptosis, autophagy, necroptosis, pyroptosis, and ferroptosis. Following this, the discussion delves into biological functions and diseases associated dysregulated programmed cell death. Finally, we highlight existing and potential therapeutic targets and strategies focused on cancers and neurodegenerative diseases. This review aims to summarize the latest insights on programmed cell death from mechanisms to diseases and provides a more reliable approach for clinical transformation.

The danger theory of immunity revisited

The danger theory of immunity, introduced by Polly Matzinger in 1994, posits that tissue stress, damage or infection has a decisive role in determining immune responses. Since then, a growing body of evidence has supported the idea that the capacity to elicit cognate immune responses (immunogenicity) relies on the combination of antigenicity (the ability to be recognized by T cell receptors or antibodies) and adjuvanticity (additional signals arising owing to tissue damage). Here, we discuss the molecular foundations of the danger theory while focusing on immunologically relevant damage-associated molecular patterns, microorganism-associated molecular patterns, and neuroendocrine stress-associated immunomodulatory molecules, as well as on their receptors. We critically evaluate patient-relevant evidence, examining how cancer cells and pathogenic viruses suppress damage-associated molecular patterns to evade immune recognition, how intestinal dysbiosis can reduce immunostimulatory microorganism-associated molecular patterns and compromise immune responses, and which hereditary immune defects support the validity of the danger theory. Furthermore, we incorporate the danger hypothesis into a close-to-fail-safe hierarchy of immunological tolerance mechanisms that also involve the clonal deletion and inactivation of immune cells.

Pretreatment with 4-methylumbilliferon improves anxiety-like behaviors and memory impairment in stressed rats via modulation of neuronal cell death and oxidative stress

This work was done to investigate the ameliorating impact of 4-methylumbilliferon (4-MU) on spatial learning and memory dysfunction and restraint stress (STR)-induced anxiety-like behaviors in male Wistar rats and the underlying mechanisms. Thirty-two animals were assigned into 4 cohorts: control, 4-MU, STR, and STR+4-MU. Animals were exposed to STR for 4 h per day for 14 consecutive days or kept in normal conditions (healthy animals without exposure to stress). 4-MU (25 mg/kg) was intraperitoneally administered once daily to STR rats before restraint stress for 14 consecutive days. The behavioral tests were performed through Morris water maze tests and elevated-plus maze to examine learning/memory function, and anxiety levels, respectively. The levels of the antioxidant defense biomarkers (GPX, SOD) and MDA as an oxidant molecule in the brain tissues were measured using commercial ELISA kits. Neuronal loss or density of neurons was evaluated using Nissl staining. STR exposure could cause significant alterations in the levels of the antioxidant defense biomarkers (MDA, GPX, and SOD) in the prefrontal cortex and hippocampus, induce anxiety, and impair spatial learning and memory function. Treatment with 4-MU markedly reduced anxiety levels and improved spatial learning and memory dysfunction via restoring the antioxidant defense biomarkers to normal values and reducing MDA levels. Moreover, more intact cells with normal morphologies were detected in STR-induced animals treated with 4-MU. 4-MU could attenuate the STR-induced anxiety-like behaviors and spatial learning and memory dysfunction by reducing oxidative damage and neuronal loss in the prefrontal cortex and hippocampus region. Taken together, our findings provide new insights regarding the potential therapeutic effects of 4-MU against neurobehavioral disorders induced by STR.

The Human Mitochondrial Genome Encodes for an Interferon-Responsive Host Defense Peptide

The mitochondrial DNA (mtDNA) can trigger immune responses and directly entrap pathogens, but it is not known to encode for active immune factors. The immune system is traditionally thought to be exclusively nuclear-encoded. Here, we report the identification of a mitochondrial-encoded host defense peptide (HDP) that presumably derives from the primordial proto-mitochondrial bacteria. We demonstrate that MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c) is a mitochondrial-encoded amphipathic and cationic peptide with direct antibacterial and immunomodulatory functions, consistent with the peptide chemistry and functions of known HDPs. MOTS-c targeted E. coli and methicillin-resistant S. aureus (MRSA), in part, by targeting their membranes using its hydrophobic and cationic domains. In monocytes, IFNγ, LPS, and differentiation signals each induced the expression of endogenous MOTS-c. Notably, MOTS-c translocated to the nucleus to regulate gene expression during monocyte differentiation and programmed them into macrophages with unique transcriptomic signatures related to antigen presentation and IFN signaling. MOTS-c-programmed macrophages exhibited enhanced bacterial clearance and shifted metabolism. Our findings support MOTS-c as a first-in-class mitochondrial-encoded HDP and indicates that our immune system is not only encoded by the nuclear genome, but also by the co-evolved mitochondrial genome.

Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging

Loss of proteostasis is a hallmark of aging that underlies many age-related diseases. Different cell compartments experience distinctive challenges in maintaining protein quality control, but how aging regulates subcellular proteostasis remains underexplored. Here, by targeting the misfolding-prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we established transgenic sensors to examine subcellular proteostasis in Drosophila. Analysis of detergent-insoluble and -soluble levels of compartment-targeted FlucDM variants indicates that thermal stress, cold shock, and pro-longevity inter-organ signaling differentially affect subcellular proteostasis during aging. Moreover, aggregation-prone proteins that cause different neurodegenerative diseases induce a diverse range of outcomes on FlucDM insolubility, suggesting that subcellular proteostasis is impaired in a disease-specific manner. Further analyses with FlucDM and mass spectrometry indicate that pathogenic tauV337M produces an unexpectedly complex regulation of solubility for different FlucDM variants and protein subsets. Altogether, compartment-targeted FlucDM sensors pinpoint a diverse modulation of subcellular proteostasis by aging regulators.

Trial watch: anticancer vaccination with dendritic cells

Dendritic cells (DCs) are critical players at the intersection of innate and adaptive immunity, making them ideal candidates for anticancer vaccine development. DC-based immunotherapies typically involve isolating patient-derived DCs, pulsing them with tumor-associated antigens (TAAs) or tumor-specific antigens (TSAs), and utilizing maturation cocktails to ensure their effective activation. These matured DCs are then reinfused to elicit tumor-specific T-cell responses. While this approach has demonstrated the ability to generate potent immune responses, its clinical efficacy has been limited due to the immunosuppressive tumor microenvironment. Recent efforts have focused on enhancing the immunogenicity of DC-based vaccines, particularly through combination therapies with T cell-targeting immunotherapies. This Trial Watch summarizes recent advances in DC-based cancer treatments, including the development of new preclinical and clinical strategies, and discusses the future potential of DC-based vaccines in the evolving landscape of immuno-oncology.

Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics

The emergence of perturbation transcriptomics provides a new perspective for drug discovery, but existing analysis methods suffer from inadequate performance and limited applicability. In this work, we present PertKGE, a method designed to deconvolute compound-protein interactions from perturbation transcriptomics with knowledge graph embedding. By considering multi-level regulatory events within biological systems that share the same semantic context, PertKGE significantly improves deconvoluting accuracy in two critical "cold-start" settings: inferring targets for new compounds and conducting virtual screening for new targets. We further demonstrate the pivotal role of incorporating multi-level regulatory events in alleviating representational biases. Notably, it enables the identification of ectonucleotide pyrophosphatase/phosphodiesterase-1 as the target responsible for the unique anti-tumor immunotherapy effect of tankyrase inhibitor K-756 and the discovery of five novel hits targeting the emerging cancer therapeutic target aldehyde dehydrogenase 1B1 with a remarkable hit rate of 10.2%. These findings highlight the potential of PertKGE to accelerate drug discovery.

Proteomic analysis reveals molecular changes following genetic engineering in Chlamydomonas reinhardtii

BACKGROUND

Chlamydomonas reinhardtii is gaining recognition as a promising expression system for the production of recombinant proteins. However, its performance as a cellular biofactory remains suboptimal, especially with respect to consistent expression of heterologous genes. Gene silencing mechanisms, position effect, and low nuclear transgene expression are major drawbacks for recombinant protein production in this model system. To unveil the molecular changes following transgene insertion, retention, and expression in this species, we genetically engineered C. reinhardtii wild type strain 137c (strain cc-125 mt+) to express the fluorescent protein mVenus and subsequently analysed its intracellular proteome.

RESULTS

The obtained transgenic cell lines showed differences in abundance in more than 400 proteins, with multiple pathways altered post-transformation. Proteins involved in chromatin remodelling, translation initiation and elongation, and protein quality control and transport were found in lower abundance. On the other hand, ribosomal proteins showed higher abundance, a signal of ribosomal stress response.

CONCLUSIONS

These results provide new insights into the modifications of C. reinhardtii proteome after transformation, highlighting possible pathways involved in gene silencing. Moreover, this study identifies multiple protein targets for future genetic engineering approaches to improve the prospective use of C. reinhardtii as cell biofactory for industrial applications.

Agricultural insect pests as models for studying stress-induced evolutionary processes

Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.

Association Between Dry Eye Disease with Anxiety and Depression Among Medical Sciences Students in Qassim Region: Cortisol Levels in Tears as a Stress Biomarker

Purpose

This study aimed to investigate the relationships between anxiety, depression, and ocular surface health. Cortisol levels were detected in human tears, and their relationship with anxiety levels was determined using a validated questionnaire.

Patients and Methods

In total, 112 participants were recruited for this study. All participants were healthy medical students at the Qassim University. Each participant signed an informed consent form after receiving detailed information about the study. Visual acuity examination, TBUT, Shirmer1 test were performed. Participants were asked to fill out three questionnaires: Taylor Manifest Anxiety Scale, Beck Depression Inventory, and The Ocular Surface Disease Index. Tear samples were extracted from the Schirmer strips and cortisol level was measured using ELISA kits.

Results

A total of 112 college students were included in the study, 58.9% of whom were females. The mean age was 21.9 ± 1.7 years. Subjective reported symptoms of anxiety levels were significantly correlated with depression scores, the OSDI, and reduced Schirmer test measurements. Moreover, cortisol levels detected in tears were positively associated with higher anxiety scores (r=0.328, P<0.05).

Conclusion

Ocular surface health is associated with symptoms of anxiety and depression. The use of tears to measure cortisol levels could be an interesting way to serve as an anxiety biomarker.

Integrating Vascular Phenotypic and Proteomic Analysis in an Open Microfluidic Platform

This research introduces a vascular phenotypic and proteomic analysis (VPT) platform designed to perform high-throughput experiments on vascular development. The VPT platform utilizes an open-channel configuration that facilitates angiogenesis by precise alignment of endothelial cells, allowing for a 3D morphological examination and protein analysis. We study the effects of antiangiogenic agents─bevacizumab, ramucirumab, cabozantinib, regorafenib, wortmannin, chloroquine, and paclitaxel─on cytoskeletal integrity and angiogenic sprouting, observing an approximately 50% reduction in sprouting at higher drug concentrations. Precise LC-MS/MS analyses reveal global protein expression changes in response to four of these drugs, providing insights into the signaling pathways related to the cell cycle, cytoskeleton, cellular senescence, and angiogenesis. Our findings emphasize the intricate relationship between cytoskeletal alterations and angiogenic responses, underlining the significance of integrating morphological and proteomic data for a comprehensive understanding of angiogenesis. The VPT platform not only advances our understanding of drug impacts on vascular biology but also offers a versatile tool for analyzing proteome and morphological features across various models beyond blood vessels.

Leveraging diverse cellular stress patterns for predicting clinical outcomes and therapeutic responses in patients with multiple myeloma

Tumour microenvironment harbours diverse stress factors that affect the progression of multiple myeloma (MM), and the survival of MM cells heavily relies on crucial stress pathways. However, the impact of cellular stress on clinical prognosis of MM patients remains largely unknown. This study aimed to provide a cell stress-related model for survival and treatment prediction in MM. We incorporated five cell stress patterns including heat, oxidative, hypoxic, genotoxic, and endoplasmic reticulum stresses, to develop a comprehensive cellular stress index (CSI). Then we systematically analysed the effects of CSI on survival outcomes, clinical characteristics, immune microenvironment, and treatment sensitivity in MM. Molecular subtypes were identified using consensus clustering analysis based on CSI gene profiles. Moreover, a prognostic nomogram incorporating CSI was constructed and validated to aid in personalised risk stratification. After screening from five stress models, a CSI signature containing nine genes was established by Cox regression analyses and validated in three independent datasets. High CSI was significantly correlated with cell division pathways and poor clinical prognosis. Two distinct MM subtypes were identified through unsupervised clustering, showing significant differences in prognostic outcomes. The nomogram that combined CSI with clinical features exhibited good predictive performances in both training and validation cohorts. Meanwhile, CSI was closely associated with immune cell infiltration level and immune checkpoint gene expression. Therapeutically, patients with high CSI were more sensitive to bortezomib and antimitotic agents, while their response to immunotherapy was less favourable. Furthermore, in vitro experiments using cell lines and clinical samples verified the expression and function of key genes from CSI. The CSI signature could be a clinically applicable indicator of disease evaluation, demonstrating potential in predicting prognosis and guiding therapy for patients with MM.

RNA G-quadruplexes and stress: emerging mechanisms and functions

RNA G-quadruplexes (rG4s) are noncanonical secondary structures formed by guanine-rich sequences that are found in different regions of RNA molecules. These structures have been implicated in diverse biological processes, including translation, splicing, and RNA stability. Recent studies have suggested that rG4s play a role in the cellular response to stress. This review summarizes the current knowledge on rG4s under stress, focusing on their formation, regulation, and potential functions in stress response pathways. We discuss the molecular mechanisms that regulate the formation of rG4 under different stress conditions and the impact of these structures on RNA metabolism, gene expression, and cell survival. Finally, we highlight the potential therapeutic implications of targeting rG4s for the treatment of stress-related diseases through modulating cell survival.

Changing the gravity vector direction by inverted culture enhances radiation-induced cell damage

In recent years, it has become clear that the cytotoxicity of γ-irradiation of cells is increased under microgravity conditions. However, there has been no study of the effect of the gravity vector direction, rather than the magnitude, on γ-ray-induced cytotoxicity. Therefore, in this study, we inverted cultures of human bronchial epithelium BEAS-2B cells and human lung cancer A549 cells in order to change the gravity vector direction by 180° with respect to the cells and observed the cellular response to radiation in this state. We found that cells in inverted culture showed increased irradiation-induced production of reactive oxygen species and decreased expression of the antioxidant protein thioredoxin-1 compared to cells in normal culture. Furthermore, the DNA damage response was delayed in γ-irradiated cells in inverted culture, and the number of unrepaired DNA sites was increased, compared to irradiated cells in normal culture. γ-Ray-induced cell death and the number of G2-M arrested cells were increased in inverted culture, in accordance with the decreased capacity for DNA repair. Our findings suggest that the gravity vector direction, as well as its magnitude, alters the cellular response to radiation.

Hypothalamic circuits and aging: keeping the circadian clock updated

Over the past century, age-related diseases, such as cancer, type-2 diabetes, obesity, and mental illness, have shown a significant increase, negatively impacting overall quality of life. Studies on aged animal models have unveiled a progressive discoordination at multiple regulatory levels, including transcriptional, translational, and post-translational processes, resulting from cellular stress and circadian derangements. The circadian clock emerges as a key regulator, sustaining physiological homeostasis and promoting healthy aging through timely molecular coordination of pivotal cellular processes, such as stem-cell function, cellular stress responses, and inter-tissue communication, which become disrupted during aging. Given the crucial role of hypothalamic circuits in regulating organismal physiology, metabolic control, sleep homeostasis, and circadian rhythms, and their dependence on these processes, strategies aimed at enhancing hypothalamic and circadian function, including pharmacological and non-pharmacological approaches, offer systemic benefits for healthy aging. Intranasal brain-directed drug administration represents a promising avenue for effectively targeting specific brain regions, like the hypothalamus, while reducing side effects associated with systemic drug delivery, thereby presenting new therapeutic possibilities for diverse age-related conditions.