Amino acid metabolism provides significant insight into the development and prevention of many viral diseases. Therefore, the present study aimed to compare the amino acid profiles of hand, foot, and mouth disease (HFMD) patients with those of healthy individuals and to further reveal the molecular mechanisms of HFMD severity. Using UPLC-MS/MS, we determined the plasma amino acid expression profiles of pediatric patients with HFMD (mild, n = 42; severe, n = 43) and healthy controls (n = 25). Brain tissues from CVA6-infected mice were examined using untargeted metabolomics. Several amino acids were significantly different between the three groups. Pathway analysis revealed that arginine, proline, and tryptophan metabolism are implicated in the pathogenesis of HFMD. A similar arginine depletion was observed in the brain tissues of CVA6-infected mice. Importantly, L-arginine supplementation improved the survival rate of CVA6-infected mice, inhibited virus multiplication, and reduced pathological autophagy associated with mTOR-autophagy pathway in the brain. Collectively, arginine, as the hub amino acid metabolite of the mammalian target of rapamycin (mTOR) signaling pathway affecting autophagy, plays an important role in the pathogenesis of severe HFMD. L-arginine supplementation may serve as a potential therapeutic option for critical patients with HFMD.

Aging can cause age-related diseases such as cancer, cardiovascular and neurodegenerative diseases. Cordycepin exerts anti-oxidation, anti-inflammatory and neuroprotective effects. However, the anti-aging effect of cordycepin is still unclear. This study aimed to investigate the anti-aging effect of cordycepin and unravel the underlying mechanism. Cordycepin prolonged the lifespan of C. elegans under normal and heat stress conditions, without effects on the normal growth and reproduction of C. elegans. Cordycepin also improved the locomotion ability, inhibited the deposition of aging pigment lipofuscin and alleviated the oxidative stress damage by decreasing the excessive accumulation of ROS and raising the antioxidant enzyme activities in C. elegans. The metabolomics study showed that cordycepin changed 19 metabolites including citric acid, linoleic acid, oleic acid, glutamic acid, pyruvic acid and so on. Transcriptomics study revealed that cordycepin up-regulated the gene expression of acox-1.2, acox-1.3, acox-1.4, acs-1, acs-15, acdh-1, acdh-4 and acdh-8 in C. elegans, suggesting that cordycepin prolonged its lifespan via regulating fatty acid degradation, fatty acid metabolism and so on. In summary, the current study demonstrated that cordycepin exerted the anti-aging effect on C. elegans by improving the antioxidant system and regulating the genes involved in fatty acid metabolism to inhibit the accumulation of linoleic acid and oleic acid. Therefore, cordycepin might be a promising agent for aging and age-related diseases.

Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilast's potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography (SD-OCT), and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilast's neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Müller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilast's potential to protect inner retinal neurons during damage and show promise for future clinical translation.

As a classic formula, Ermiao San (EMS) characterized by its less medicinal flavor and strong potency had been proven to be effective and safe in the treatment of rheumatoid arthritis (RA) during clinical experience and our previous research.

The therapeutic characteristics of multi-component and multi-target of traditional Chinese medicine prompted us to further investigated the effective compounds of EMS, and evaluated its potential mechanisms in treating RA.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS) was used to analyze the primary absorption components of EMS in rat serum, with secondary mass spectrometry used to assist in identifying the structures of the compounds. Open field experiments, H&E staining, safranin-O-turquoise staining, ELISA, and other methods were applied to verify the alleviating effects of EMS on exercise capacity, inflammation, and cartilage damage in CIA rats. The RA-FLS model was established using TNF-α, and observed the effects of EMS on cell migration and invasion were observed through wound healing and transwell assays. In addition, immunohistochemistry and western blotting were employed to investigate the PI3K/AKT/mTOR/HIF-1α pathway both in vivo and in vitro.

Seventeen compounds were identified in rat serum, which were considered as active ingredients involved in the improvement of RA by EMS. Furthermore, EMS demonstrated the outstanding anti-RA ability, as evidenced by the improvement in foot swelling and arthritis scores, alleviation of pathological changes in joint tissue, inhibition of inflammatory factors, and restoration of exercise ability. In vivo data showed that EMS reduced joint injury through the PI3K/AKT/mTOR/HIF-1α signaling pathway. In vitro studies indicated that TNF-α induced the expression of Glut1 and HK2 proteins, accelerated the glycolysis rate, and promoted migration and invasion of RA-FLS cells, leading to adverse outcomes. However, EMS regulated the expression of glycolysis-related molecules, HK2 and Glut1 through the PI3K/AKT/mTOR/HIF-1α pathway, thereby inhibiting inflammation, migration, and invasion of RA-FLS cells.

The beneficial effects of EMS in CIA rats can be attributed to the inhibition of glycolysis in synovial fibroblasts via the PI3K/AKT/mTOR/HIF-1α pathway. This finding further enriches our understanding of the mechanisms by which EMS contributes to the treatment of RA.

This study presents a comprehensive examination of the physiological adaptations of white shrimp (Penaeus vannamei) to low-salinity conditions and evaluates the effects of supplementing dietary glucose on disease resistance. Compared to the control group, shrimp cultured at a salinity of 4 psu exhibit significantly elevated expression levels of adenosine 5'-monophosphate-activated protein kinase (AMPK) in the hepatopancreas, which leads to increased energy expenditure and a corresponding reduction in resistance to infection by Vibrio alginolyticus. The suppression of AMPK via dsAMPK treatment markedly enhances disease resistance. Moreover, shrimp raised in low salinity conditions exhibit downregulation of mTOR-associated molecules, including Lipin-1 and hypoxia-inducible factor 1-α (HIF-1α), both of which are essential for immune regulation. Metabolic assessments revealed reduced ATP levels and disrupted ATP/AMP and ATP/ADP ratios, indicating energy imbalance under low salinity stress. Notably, supplementing the diet with 1 % glucose significantly increased glycogen reserves and ATP content, stabilized hemolymph glucose levels, and upregulated glycolysis-related genes, thereby optimizing energy metabolism and enhancing resilience to stress. This study underscores that AMPK activation in response to low salinity conditions leads to increased energy expenditure, which in turn lowers disease resistance. Furthermore, it underscores the critical role of strategic dietary management in maintaining energy homeostasis and improving disease resistance in white shrimp under stressful environmental conditions associated with climate change, offering valuable insights for aquaculture nutrition strategies.

Microglia are a specialized type of neuroimmune cells that undergo morphological and molecular changes through multiple signaling pathways in response to pathological protein aggregates, neuronal death, tissue injury, or infections. Microglia express Trem2, which serves as a receptor for a multitude of ligands enhancing their phagocytic activity. Trem2 has emerged as a critical modulator of microglial activity, especially in many neurodegenerative disorders. Human TREM2 mutations are associated with an increased risk of developing Alzheimer disease (AD) and other neurodegenerative diseases. Trem2 plays dual roles in neuroinflammation and more specifically in disease-associated microglia. Most recent developments on the molecular mechanisms of Trem2, emphasizing its role in uptake and clearance of amyloid β (Aβ) aggregates and other tissue debris to help protect and preserve the brain, are encouraging. Although Trem2 normally stimulates defense mechanisms, its dysregulation can intensify inflammation, which poses major therapeutic challenges. Recent therapeutic approaches targeting Trem2 via agonistic antibodies and gene therapy methodologies present possible avenues for reducing the burden of neurodegenerative diseases. This review highlights the promise of Trem2 as a therapeutic target, especially for Aβ-associated AD, and calls for more mechanistic investigations to understand the context-specific role of microglial Trem2 in developing effective therapies against neurodegenerative diseases.

Diabetes mellitus (DM) and neuroendocrine tumors (NET) can exert unfavorable effects on each other prognosis. In this narrative review, we evaluated the effects of NET therapies on glycemic control and DM management and the effects of anti-diabetic therapies on NET outcome and management. For this purpose, we searched the PubMed, Science Direct, and Google Scholar databases for studies reporting the effects of NET therapy on DM as well as the effect of DM therapy on NET. The majority of NET treatments appear to impair glycaemic control, both inducing hypoglycemic or, more commonly, hyperglycemia and even new-onset DM. However, glucose metabolism imbalance can be effectively managed by modulating anti-diabetic therapy and adopting an appropriate nutritional approach. On the other hand, the effects of anti-diabetic treatment, like insulin, sulfonylureas, thiazolidinediones, ipeptidyl-peptidase-4 inhibitors, Glucagon-like peptide-1 receptor agonists, and Sodium-glucose cotransporter-2 inhibitors on NET are unclear. Recently, metformin has been investigated in patients with gastroenteropancreatic NET resulting in improved progression free survival suggesting a potential antineoplastic role. Finally, the management of DM in patients with NET is of great clinical relevance to correctly perform radiological procedures and even more functional imaging procedures, as well as to optimize the therapy and avoid treatment withdrawal or discontinuation. In conclusion, understanding the mechanisms underlying therapy-induced DM and implementing appropriate monitoring and management strategies of DM are essential for optimizing NET patient outcome and quality of life.

Modulating the excitatory amino acid transporter 3 (EAAT3) can be considered a novel approach for the treatment of multiple sclerosis (MS). EAAT3 plays a crucial role in regulating oxidative stress and oligodendrocyte function through its ability to transport cysteine, the rate-limiting building block in the synthesis of the antioxidant glutathione. Therefore, EAAT3 activation is hypothesised to improve oligodendrocyte health and relieve its differentiation block in MS, improving remyelination capacity. Using a cuprizone-induced demyelination model, the effects of EAAT3 overexpression by viral transduction of oligodendrocytes and pharmacological inhibition of EAAT3 were examined. Surprisingly, EAAT3 overexpression significantly hampered remyelination, while EAAT3 inhibition prevented demyelination and improved functional remyelination as assessed by visual evoked potentials and post mortem myelin basic protein fluorescent staining. Next, cellular mechanisms underlying these results were investigated. Consistent with the in vivo findings, post mortem gene expression analysis of the corpus callosum of cuprizone treated animals revealed a trend towards upregulation of oligodendrocyte lineage genes in response to EAAT3 inhibition, supporting its role in oligodendrocyte health and myelination processes. In vitro studies using the human oligodendroglioma (HOG) cell line demonstrated the beneficial effects of EAAT3 inhibition on cellular morphology, indicating potential roles in promoting oligodendrocyte maturation and myelination. In contrast, EAAT3 overexpression appears to hamper these processes. These findings suggest that, contrary to our initial hypothesis, EAAT3 inhibition could improve oligodendrocyte function and myelination processes, highlighting its potential as a therapeutic target for demyelinating disorders. Future studies should address the exact molecular mechanism through which this effect is obtained.

Periodontal ligament stem cells (PDLSCs) have been regarded as ideal candidates for tissue regeneration due to their excellent self-renewal and multipotent differentiation ability. Rapamycin (RAPA) is reported to play an important role in the regulation of biological properties of stem cells and a variety of physiological processes. This study investigates whether RAPA could ameliorate the senescence and accelerate the osteogenic differentiation of PDLSCs, particularly the regenerative potential in a rat calvarial bone defect model, and the underlying mechanisms involved. β-galactosidase staining, quantitative real-time polymerase chain reaction, and western blot analysis were performed to assess the effects of RAPA on senescent PDLSCs. The osteogenic differentiation ability of PDLSCs was detected by alkaline phosphatase staining and activity, Alizarin Red S staining, and gene and protein levels of osteogenesis-related markers. The underlying signaling pathways were investigated via RNA transcriptome sequencing analysis and WB tests. Calvarial bone defects in rat were treated with PDLSCs pre-incubated with or without RAPA and/or H2O2. The results showed that RAPA could enhance the osteogenic potentials of PDLSCs via PI3K/AKT signaling pathway, and reversed H2O2-induced senescence and osteogenic differentiation inhibition of PDLSCs. Moreover, calvarial defects transplanted with RAPA-treated PDLSCs showed significantly greater new bone formation compared with other groups, and also improved the H2O2-induced impairment of bone formation, whether by micro-computed tomography examination or by histological analysis. Collectively, RAPA was capable of promoting osteogenic differentiation of PDLSCs via PI3K/AKT signaling pathway in vitro, facilitating calvarial bone regeneration and reversing H2O2-induced impairment of osteogenic differentiation and cell senescence in PDLSCs.

A therapeutic strategy targeting the PI3K-AKT-mTOR pathway is widely seen as promising against prostate cancer (PCa) treatment. However, resistance to targeted inhibitors is still a major challenge. Herein we observed that the overexpression of TPD52 (isoform 3) in LNCaP, PCa cells confers resistance to mTOR inhibitors, specifically everolimus and rapamycin. This study demonstrates that TPD52 promotes the proliferation and survival of tumor cells treated with mTOR inhibitors by hyperactivating PI3K/AKT. Despite the inactivation of downstream targets like p70S6K and S6 upon mTOR inhibition, p4E-BP1 remained consistently high in TPD52 overexpressing LNCaP cells, suggesting activation of an alternative regulatory mechanism independent of mTOR. Furthermore, elevated c-Myc levels were correlated with overexpression of TPD52 and were linked to loss of PTEN expression further promoting drug resistance. Contrarily, silencing of TPD52 and c-Myc sensitized LNCaP cells to mTOR inhibitors by restoring PTEN levels and further downregulation of 4E-BP1. Above all, downregulation of both TPD52 and c-Myc enhanced the sensitivity of LNCaP-TPD52 cells facilitating apoptosis indicating a potential strategy to overcome resistance to mTOR inhibitors in PCa. Taken together, these findings underscore the role of TPD52 through c-Myc in conferring resistance to mTOR inhibitors and warrant further exploration of their molecular mechanisms in PCa treatment.

Tuberous Sclerosis Complex (TSC) is a genetic neurodevelopmental disorder associated with early onset epilepsy, intellectual disability and neuropsychiatric disorders. A hallmark of the disorder is cortical tubers, which are focal malformations of brain development containing dysplastic cells with hyperactive mTORC1 signaling. One barrier to developing therapeutic approaches and understanding the origins of tuber cells is the lack of a model system that recapitulates this pathology. To address this, we established a genetically mosaic cortical organoid system that models a somatic "second-hit" mutation, which is thought to drive the formation of tubers in TSC. With this model, we find that loss of TSC2 cell-autonomously promotes the differentiation of astrocytes, which exhibit features of a disease-associated reactive state. TSC2 -/- astrocytes have pronounced changes in morphology and upregulation of proteins that are risk factors for neurodegenerative diseases, such as clusterin and APOE. Using multiplexed immunofluorescence in primary tubers from TSC patients, we show that tuber cells with hyperactive mTORC1 activity also express reactive astrocyte proteins, and we identify a unique population of cells with expression profiles that match those observed in organoids. Together, this work reveals that reactive astrogliosis is a primary feature of TSC that arises early in cortical development. Dysfunctional glia are therefore poised to be drivers of pathophysiology, nominating a potential therapeutic target for treating TSC and related mTORopathies.

Vitiligo is a chronic autoimmune disorder with a multifactorial etiology, typically manifesting as localized or generalized hypopigmentation or depigmentation of the skin and mucous membranes. The pathogenesis of vitiligo is complex and significantly impacts patients' quality of life. Although traditional treatments such as hormone therapy, topical medications, and laser therapy can help control the disease to some extent, their outcomes remain unsatisfactory. Therefore, ongoing research is crucial to explore and develop novel treatment strategies while assessing their efficacy and safety. This review aims to classify and summarize various new candidate drugs for vitiligo currently undergoing clinical trials, providing a reference for clinical practice. Recent advancements in the understanding of the pathogenesis of vitiligo have facilitated the development of potential treatment strategies, such as Janus kinase inhibitors, cytokine blockers, and agents targeting tissue-resident memory or regulatory T cells. These emerging therapies offer hope to patients with vitiligo, though further investigation is needed to confirm their safety, efficacy, and optimal treatment regimens.

Diet influences macronutrient availability to cells, and although mechanisms of sensing dietary glucose and amino acids are well characterized, less is known about sensing lipids. We defined a nutrient signaling mechanism involving fatty acid-binding protein 5 (FABP5) and mechanistic target of rapamycin complex 1 (mTORC1) that is activated by the essential polyunsaturated fatty acid (PUFA) ω-6 linoleic acid (LA). FABP5 directly bound to the regulatory-associated protein of mTOR (Raptor) to enhance formation of functional mTORC1 and substrate binding, ultimately converging on increased mTOR signaling and proliferation. The amounts of FABP5 protein were increased in tumors and serum from triple-negative compared with those from receptor-positive breast cancer patients, which highlights its potential role as a biomarker that mediates cellular responses to ω-6 LA intake in this disease subtype.

Aging-related decreases in cardiac and skeletal muscle function are strongly associated with various comorbidities. Elamipretide (ELAM), a novel mitochondria-targeted peptide, has demonstrated broad therapeutic efficacy in ameliorating disease conditions associated with mitochondrial dysfunction across both clinical and pre-clinical models. Herein, we investigated the impact of 8-week ELAM treatment on pre- and post-measures of C57BL/6J mice frailty, skeletal muscle, and cardiac muscle function, coupled with post-treatment assessments of biological age and affected molecular pathways. We found that health status, as measured by frailty index, cardiac strain, diastolic function, and skeletal muscle force, is significantly diminished with age, with skeletal muscle force changing in a sex-dependent manner. Conversely, ELAM mitigated frailty accumulation and was able to partially reverse these declines, as evidenced by treatment-induced increases in cardiac strain and muscle fatigue resistance. Despite these improvements, we did not detect statistically significant changes in gene expression or DNA methylation profiles indicative of molecular reorganization or reduced biological age in most ELAM-treated groups. However, pathway analyses revealed that ELAM treatment showed pro-longevity shifts in gene expression, such as upregulation of genes involved in fatty acid metabolism, mitochondrial translation, and oxidative phosphorylation, and downregulation of inflammation. Together, these results indicate that ELAM treatment is effective at mitigating signs of sarcopenia and cardiac dysfunction in an aging mouse model, but that these functional improvements occur independently of detectable changes in epigenetic and transcriptomic age. Thus, some age-related changes in function may be uncoupled from changes in molecular biological age.

Ixodes scapularis ticks transmit several medically important pathogens including Anaplasma phagocytophilum to humans and animals. In this study, we provide evidence that A. phagocytophilum modulates autophagy molecules for its survival in tick cells. qRT-PCR analysis revealed that A. phagocytophilum infection results in the upregulation of tyrosine phosphatase, shp-2, and serine/threonine-protein kinase, mTOR, in ticks and tick cells. RNAi-mediated knockdown of shp-2 or functional blocking with SHP-2 inhibitor resulted in significantly increased bacterial burden and reduced phospho-mTOR levels in A. phagocytophilum-infected tick cells. In addition, treatment of A. phagocytophilum-infected tick cells with rapamycin (mTOR inhibitor) resulted in significantly increased bacterial burden and reduced phospho-mTOR levels. Furthermore, expression of autophagy molecules such as atg14 and ulk1 were noted to be upregulated in both A. phagocytophilum-infected unfed ticks and tick cells. RNAi-mediated silencing of atg14 or ulk1 affected bacterial growth in tick cells. Collectively, these results not only indicate distinct host and pathogen responses in tick-A. phagocytophilum interactions but also suggest that this bacterium modulates autophagy molecules for its survival in ticks.

The CNC-bZIP family member NRF3 (NFE2L3) has received limited attention since its discovery. However, recent research has gradually revealed its biological functions, such as involvement in the regulation of cell differentiation, lipid metabolism, and malignant cell proliferation. Under physiological conditions, NRF3 is anchored to the endoplasmic reticulum within the cytoplasm and is biologically inactive. Upon cellular exposure to microenvironmental stresses such as oxidative stress, NRF3 translocates to the nucleus, binds to DNA, and acts as a transcription factor by inducing or repressing the expression of various genes. In terms of tumor regulation, NRF3 exhibits a dual role. It can function as a tumor suppressor to prevent the malignant progression of tumor tissues, protecting the organism from harm. Conversely, current research indicates that NRF3 plays a tumor-promoting role in most tumor tissues. NRF3 enhances the proliferation, migration and invasion of tumor cells by regulating cell cycle-related proteins and enhancing proteasome assembly to degrade tumor suppressors. Studies correlating NRF3 expression with clinical tumor features have found that elevated NRF3 expression is often associated with poor prognoses in various cancers, with patients exhibiting higher NRF3 expression typically having lower survival rates. Several studies suggest that NRF3 could serve as a clinical diagnostic and prognostic marker for tumors. Finally, from the clinical perspective, exploring the feasibility of inhibiting NRF3 activity in tumor treatment provides new insights for the development of NRF3-targeted oncological therapies.

Delineating the shared genetic architecture of type 2 diabetes with muscle mass and function and frailty is essential for unraveling the common etiology and developing holistic therapeutic strategies for these co-existing conditions.

In this genome-wide pleiotropic association study, we performed multi-level pairwise trait pleiotropic analyses using genome-wide association study summary statistics from up to 461,026 European ancestry individuals to dissect the shared genetic factors and causal relationships of type 2 diabetes and seven glycemic traits with four muscle mass- and function-related phenotypes and the frailty index.

We first identified 27 pairs with significant genetic correlations through the linkage disequilibrium score regression and high-definition likelihood analysis. Then we determined 79 pleiotropic loci and 109 pleiotropic genes across linkage pairs via the pleiotropic analysis under the composite null hypothesis (PLACO), the colocalization, and the Multi-marker Analysis of GenoMic Annotation (MAGMA) analyses. We subsequently performed transcriptome-wide association study (TWAS) analyses using joint-tissue imputation, refined by gene-based integrative fine-mapping through a conditional TWAS approach, and identified 44 unique causal shared genes across 13 tissues in linkage pairs, including eight druggable genes (ABO, AOC1, FTO, GCKR, MTOR, POLK, PPARG, and APEH), with MTOR and PPARG categorized as clinically actionable. Two-sample Mendelian randomization analysis supported bidirectional causality between diabetes and frailty index and unidirectional causal effects of muscle phenotypes on glycemic profiles.

Our findings highlight the common genetic underpinnings between type 2 diabetes and muscle loss and frailty and inform drug targets with pleiotropic effects on both of these aging-related challenges.

Spermine (SPM) and spermidine (SPD) are polyamines found in all organisms, and their concentrations can be regulated by ingestion. We demonstrated that yeast-fermented garlic (YF) extract significantly increased autophag flux in OUMS-36T-1 and HeLa cells expressing the fluorescent probe (GFP-LC3-RFP-LC3ΔG). YF-induced increase of autophagy occurred independently of mTORC1 signaling, and RNA-sequencing analysis revealed that EGR1 was the most significantly altered gene in YF-treated OUMS-36T-1 cells. YF-treated EGR1-deficient HAP1 cells displayed reduced autophagic flux (p < 0.05). YF-induced increasing of autophagic flux occurred via a specific SPM/SPD ratio. HAP1 cells treated with equivalent amounts of SPD or SPM as that found in YF did not increase autophagic flux (p > 0.05); however, treatment with SPD and SPM in the same ratio as that found in YF increased autophagic flux (p < 0.05). This specific SPM/SPD ratio reduced MG132-induced proteostress via EGR1-dependent pathways (p < 0.05). Thus, the SPM/SPD balance may regulate autophagy via EGR1-dependent pathways, and controlling this balance may provide a strategy to maintain cellular homeostasis.

Losing muscle functions due to reducing muscle mass and quality is one of the main features of cancer cachexia that impairs patients' quality of life and decrease their survival. This study aimed to investigate the synergistic effects of resistance training and resveratrol supplementation on cachexia induced by CT26 tumors in male mice. Forty-eight mice were divided into eight groups randomly: healthy sedentary vehicle (HSV), healthy exercise vehicle (HEV), healthy sedentary resveratrol (HSR), healthy exercise resveratrol (HER), CT-26 tumor-bearing sedentary vehicle (TSV), CT-26 tumor-bearing exercise vehicle (TEV), CT-26 tumor-bearing sedentary resveratrol (TSR) and CT-26 tumor-bearing exercise resveratrol (TER). Training groups performed ladder climbing with weights tied to their tails, for six weeks. Resveratrol-treated groups received 50 mg/kg daily by gavage. The results showed muscle weight, and mTORC1 phosphorylation decreased in TSV compared to the HSV group. mTORC1 phosphorylation was increased in TER compared to TSV, TEV, and TSR. In addition, AMPK phosphorylation was more elevated in HER compared to HSV, HEV, and HSR. LC3BII/I ratio was higher in TSV than HSV group. Tumor volume was increased in all groups, with the lowest increase in TER group. In tumor tissue, mTORC1 phosphorylation was decreased in TER than in TSV, TEV, and TSR groups; AMPK phosphorylation and LC3BII/I ratio were increased in TSV than in TEV, TSR, and TER groups. In conclusion, the synergistic effect of resistance training and resveratrol supplementation is the most effective in reducing tumor volume. These advantages were mostly in line with molecular findings.

mTOR plays a pivotal role in cancer growth control upon amino acid response. Recently, CDK inhibitor P27KIP1 has been reported as a noncanonical inhibitor of mTOR signaling in MEFs, via unclear mechanisms. Here, we find that P27KIP1 degradation via E3 ligase TRIM21 is inhibited by human micropeptide hSPAR through its C-terminus (hSPAR-C), causing P27KIP1's cytoplasmic accumulation in breast cancer cells. Furthermore, hSPAR/hSPAR-C also serves as an inhibitor of glutamine transporter SLC38A2 expression and thereby decreases the cellular glutamine levels specifically in cancer cells. The resultant glutamine deprivation sequentially triggers translocation of cytoplasmic P27KIP1 to lysosomes, where P27KIP1 disrupts the Ragulator complex and suppresses mTORC1 assembly. Administration of hSPAR or hSPAR-C significantly impedes breast cancer cell proliferation and tumor growth in xenograft models. These findings define hSPAR as an intrinsic control factor for cellular glutamine levels and as a novel tumor suppressor inhibiting mTORC1 assembly.

Time-restricted feeding (TRF) is a distinct regimen of intermittent fasting advocated for health improving. Although nighttime TRF (NRF) in rodents is analogous to daytime TRF (DRF) in humans and has health benefits, the effects of DRF on rodent's health remain uncertain. The adverse health effects of DRF in rodents are primarily attributed to its implementation-induced temporal shift in the expression of circadian rhythm-related genes. However, studies also demonstrate the health-beneficial effect of restricted feeding itself on metabolic homeostasis, particularly in periphery tissues. Moreover, the direct effects of DRF on aging progression in rodents are underexplored, highlighting a gap in current research. To explore the overall health effects of long-term DRF in rodents, especially its influence on aging progression, we investigated the impact of long-term DRF on mice under a progeric aging condition. Results showed that both 4-h and 8-h DRF regimens exerted positive effects on aging retardation; these effects were manifested as improved physical and memory capacities, enhanced liver and kidney functions, and reduced oxidative damage and inflammatory response. These DRF regimens also lowered the manifestation of aging-related markers in peripheral tissues, with decreased SA-β-gal staining and p16 expression. Mechanistically, DRF regimens, especially DRF8, upregulated AMPK signaling and downregulated mTORC1 signaling. Interestingly, the health benefits of DRF are similar to those of metformin intervention. In conclusion, our study demonstrates for the first time that DRF effectively counteracts oxidative stress-induced aging progression in mice, supporting the viewpoint that TRF as a promising strategy for preventing aging and aging-related disorders.

Breast cancer is a multifaceted and prevalent malignancy, impacting a considerable proportion of women globally. Numerous signaling pathways intricately regulate cellular functions such as growth, proliferation, and survival. Among the various regulators, lncRNAs have emerged as significant players despite their inability to encode proteins. An expanding body of literature underscores the pivotal roles lncRNAs play in cancer biology, particularly in the context of breast cancer. Autophagy, the cellular process dedicated to the degradation and recycling of cellular components, is now recognized as a crucial factor in cancer initiation and progression. The interplay between lncRNAs, various signaling pathways, and autophagy in the pathophysiology of breast cancer remains an active area of investigation. Researchers have identified specific lncRNAs that are dysregulated in breast cancer patients, influencing the modulation of key signaling pathways. Using experimental methodologies and bioinformatics approaches, multiple lncRNAs have been elucidated, providing deeper insights into their contributions to breast cancer pathogenesis and metastatic processes. In summary, the pathophysiological landscape of breast cancer is characterized by the complex interactions involving lncRNA-mediated autophagy. This understanding paves the way for identifying novel therapeutic targets, prognostic markers, and diagnostic markers, ultimately contributing to improved treatment outcomes in breast cancer management.

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease primarily affecting elderly individuals aged >65 years and has a poor prognosis. No effective treatment is currently available for IPF. The two antipulmonary fibrosis drugs nintedanib and pirfenidone approved by the FDA in the United States have somewhat decelerated IPF progression. However, the side effects of these drugs can lead to poor patient tolerance and compliance with the medications. Researchers have recently developed various methods for IPF treatment, such as gene silencing and pathway inhibitors, which hold great promise in IPF treatment. Nevertheless, the nonselectivity and nonspecificity of drugs often affect their efficacies. Drug delivery systems (DDS) are crucial for delivering drugs to specific target tissues or cells, thereby minimizing potential side effects, enhancing drug bioavailability, and reducing lung deposition. This review comprehensively summarizes the current state of DDS and various delivery strategies for IPF treatment (e.g., nano-delivery, hydrogel delivery, and biological carrier delivery) to completely expound the delivery mechanisms of different drug delivery carriers. Subsequently, the advantages and disadvantages of different DDS are fully discussed. Finally, the challenges and difficulties associated with the use of different DDS are addressed so as to accelerate their rapid clinical translation.

Neurodegenerative disorders are straining public health worldwide. During neurodegenerative disease progression, aberrant neuronal network activity, bioenergetic impairment, adaptive neural plasticity impairment, dysregulation of neuronal Ca2+ homeostasis, oxidative stress, and immune inflammation manifest as characteristic pathological changes in the cellular milieu of the brain. There is no drug for the treatment of neurodegenerative disorders, and therefore, strategies/treatments for the prevention or treatment of neurodegenerative disorders are urgently needed. Intermittent fasting (IF) is characterized as an eating pattern that alternates between periods of fasting and eating, requiring fasting durations that vary depending on the specific protocol implemented. During IF, depletion of liver glycogen stores leads to the production of ketone bodies from fatty acids derived from adipocytes, thereby inducing an altered metabolic state accompanied by cellular and molecular adaptive responses within neural networks in the brain. At the cellular level, adaptive responses can promote the generation of synapses and neurons. At the molecular level, IF triggers the activation of associated transcription factors, thereby eliciting the expression of protective proteins. Consequently, this regulatory process governs central and peripheral metabolism, oxidative stress, inflammation, mitochondrial function, autophagy, and the gut microbiota, all of which contribute to the amelioration of neurodegenerative disorders. Emerging evidence suggests that weight regulation significantly contributes to the neuroprotective effects of IF. By alleviating obesity-related factors such as blood-brain barrier dysfunction, neuroinflammation, and β-amyloid accumulation, IF enhances metabolic flexibility and insulin sensitivity, further supporting its potential in mitigating neurodegenerative disorders. The present review summarizes animal and human studies investigating the role and underlying mechanisms of IF in physiology and pathology, with an emphasis on its therapeutic potential. Furthermore, we provide an overview of the cellular and molecular mechanisms involved in regulating brain energy metabolism through IF, highlighting its potential applications in neurodegenerative disorders. Ultimately, our findings offer novel insights into the preventive and therapeutic applications of IF for neurodegenerative disorders.

To study the problem of male sterility of cattle-yak and improve the yak crossbreeding, this study obtained the testicular Sertoli cells of yak and cattle-yak and compared the differences in transcriptome levels between the two bovine species. The testicular tissues of 3 healthy male cattle-yaks and 3 F1 generation male yaks were collected at the age of 24 months. The Sertoli cells were isolated after enzymatic digestion, differential adhesion and starvation treatment. DATA-4 and SOX9 immunofluorescence staining were used to identify the cell type. Sertoli cells were subjected to transcriptome sequencing, GO analysis, KEGG analysis and differentially expressed gene were validated by RT-qPCR and Western blotting.

The study successfully isolated and purified Sertoli cells of yak and cattle-yak. The transcriptome sequencing data were compared, analyzed and annotated. Compared to yak Sertoli cells, 6592 differentially expressed genes were identified, with 3007 genes upregulated and 3585 genes downregulated in cattle-yak Sertoli cells. GO analysis suggested that the upregulated genes might be mainly involved in processes such as translation, peptide biosynthetic process, amide biosynthetic process, peptide metabolic process, ribosome, cytoplasmic part, structural constituent of ribosome, structural molecule activity, endomembrane system, protein kinase activity, and phosphotransferase activity. The downregulated genes appeared to be primarily involved in protein phosphorylation, phosphorylation, endomembrane system, protein kinase activity, and phosphotransferase activity. KEGG analysis compared differential genes across 316 pathways, with 8 pathways showing significant enrichment. The upregulated pathways were potentially enriched in cattle-yak Sertoli cells, including ribosome, thermogenesis, and oxidative phosphorylation, while the downregulated pathways seemed to be significantly enriched in adherens junction, mTOR signaling pathway, AMPK signaling pathway, FoxO signaling pathway, and focal adhesion. Compared with yak Sertoli cells, ISOC2, RPL27A and FISI were highly expressed in cattle-yak, as confirmed by RT-qPCR analysis. PDPN, SORBS2, TF, PLSCR1, TJP2, KIF2C, ITGA3, SMTNL2, DSP, ADGRG1, DDR1, GSK3A, RBBP6, ZC3H15 and Claudin 11 showed low expression levels in cattle-yak.

Compared with yak Sertoli cells, the expression of genes related to protein activation, cell function, and membranous organelle composition in cattle-yak Sertoli cells appeared to be abnormal. The potential defects in cattle-yak Sertoli cells may hinder the creation of a suitable environment for spermatogenesis, which could be one of the factors contributing to male cattle-yak sterility. Claudin-11 might be a potentially important gene for further research into cattle-yak male sterility.

Clear cell renal cell carcinoma (ccRCC) is the predominant human renal cancer with surging incidence and fatality lately. Hyperactivation of hypoxia-inducible factor (HIF) and mammalian target of rapamycin (mTOR) signaling are the common signatures in ccRCC. Herein, we employed spontaneous ccRCC model to demonstrate the indispensability of an underappreciated Ser/Thr kinase, CDKL3, in the initiation and progression of ccRCC. Ablation of CDKL3 does not affect normal kidney, but abrogates Akt-mTOR hyperactivity and thoroughly prevents the formation and growth of the HIF-agitated ccRCC in vivo. Remarkable clinical correlations also supported the oncogenic role of CDKL3. Mechanism-wise, cytosolic CDKL3 unexpectedly behaves as the adaptor to physically potentiate mTORC2-dependent Akt activation without functioning through kinase activity. And mTORC2 can phosphorylate and stabilize CDKL3 to form a positive feedback loop to sustain the cancer-favored Akt-mTOR overactivation. Together, we revealed the pathological importance and molecular mechanism of CDKL3-mediated Akt-mTOR axis in ccRCC initiation and progression.

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we develop paired imaging and sequencing methods to construct large-scale, multi-modal genotype-phenotypes maps in tissue with pooled genetic perturbations. Using imaging, we identify genetic perturbations in individual cells while simultaneously measuring their gene expression and subcellular morphology. Using single-cell sequencing, we measure transcriptomic responses to the same genetic perturbations. We apply this approach to study hundreds of genetic perturbations in the mouse liver. Our study reveals regulators of hepatocyte zonation and liver unfolded protein response, as well as distinct pathways that cause hepatocyte steatosis. Our approach enables new ways of interrogating the genetic basis of complex cellular and organismal physiology and provides crucial training data for emerging machine-learning models of cellular function.

Vascular smooth muscle cells(VSMCs) phenotypic switching under hyperglycemic conditions accelerates atherosclerotic progression. Notch receptor 3(NOTCH3), a critical stabilizer of VSMC homeostasis implicated in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) pathogenesis, ensures vascular integrity; however, its interplay with RAN Binding Protein 1(RANBP1) during pathological hyperglycemia remains uncharacterized. We hypothesize that hyperglycemia-induced autophagic dysregulation is mechanistically governed by theNotch receptor 3 (NOTCH3)/RANBP1 axis, proliferative capacity, and apoptotic signaling in high glucose (HG)-stimulated VSMCs. The aim of this study was to elucidate the regulatory mechanisms of autophagy in VSMCs under HG conditions, with a focus on the NOTCH3/RANBP1 axis and its implications for vascular health.

Bioinformatics analysis was performed on NOTCH3 sequencing data, including weighted gene co-expression network analysis (WGCNA), screening of differentially expressed genes (DEGs), and construction of a protein-protein interaction (PPI) network, to identify the key gene, RANBP1. In vitro experiments, including cell counting kit-8 (CCK-8) assays, quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting (WB), and flow cytometry, were conducted to examine the effects of NOTCH3 knockdown combined with RANBP1 overexpression on glucose-induced autophagy marker expression and cell viability in VSMCs.

NOTCH3 knockdown suppressed VSMC proliferation and induced apoptosis, and the cell cycle was stopped at the S phase. Analysis of VSMC sequencing data revealed 38 overlapping genes between the turquoise module and DEGs, 11 (HPF1, RANBP1, CRNKL1, LGALS3, RDX, ECM1, CXCL5, PA2G4, CENPS, ZNF830, and HIST1H4L) of which were significantly underexpressed in VSMC samples with si-NOTCH3. In a dose-dependent manner, HG therapy altered the expression of autophagy-related markers, upregulated NOTCH3, and downregulated phosphorylated mammalian target of rapamycin (p-mTOR). Downregulation of NOTCH3 aggravated the effects of HG on cell viability and autophagy, whereas overexpression of RANBP1 reversed these effects, suggesting an offsetting effect on HG-induced autophagy.

On the basis of sequencing technology, bioinformatics analysis and cell experiments, we conclude that the RANBP1/NOTCH3 axis is essential for the control of autophagy and survival of VSMCs under hyperglycemic stress and could provide new insight for the clinical treatment of VSMC-related diseases.

The mechanistic target of rapamycin (mTOR) pathway plays a critical role in cell growth and metabolic homeostasis. The ribosomal protein S6 kinases S6K1 and S6K2 are the major effectors of the mTOR pathway key to translation efficiency, but the underlying regulatory mechanisms remain largely unclear. In this study, we searched for mTOR regulators and found that the splicing factor SRRM2 modulates the levels of S6K1 and S6K2, thereby activating the mTOR-S6K pathway. Interestingly, SRRM2 facilitates the expression of S6K2 by modulating alternative splicing, and enhances the stability of the S6K1 protein by regulating the E3 ubiquitin ligase WWP2. Moreover, SRRM2 is highly expressed in colorectal cancer (CRC) tissues and is associated with a poor prognosis. SRRM2 promotes CRC growth in vitro and in vivo. Combined, these data reveal an oncogenic role of SRRM2 in CRC through activating the mTOR-S6K pathway by two different approaches, further suggesting SRRM2 as a potential therapeutic target for CRC.

Chronic heart failure (CHF) is the final stage of heart disease and is caused by various factors. Unfortunately, CHF has a poor prognosis and a high mortality rate. Recent studies have found that aging is a significant risk factor for the development of CHF and that cellular senescence plays a vital role in its development. This article reviews different types of cellular senescence, mitochondrial dysfunction in senescent cells, autophagy in senescent cells, and senescence-associated secretory phenotype (SASP), and epigenetic regulation, to provide new perspectives on the research and treatment of CHF.

Phosphatase and Tensin Homolog (PTEN) is a dual-specific protein and lipid phosphatase that regulates AKT and downstream signaling of the mechanistic target of rapamycin (mTOR). PTEN functions as a tumor suppressor gene whose mutations result in PTEN Hamartoma Tumor Syndrome (PHTS) characterized by increased cancer risk and neurodevelopmental comorbidity. Here, we generated a novel neuron-specific Pten knock-out mouse model (Syn-Cre/Pten HOM) to test the ability of pharmacologic mTOR inhibition to rescue Pten mutation-associated disease phenotypes in vivo and in vitro. We found that treatment with the mTOR inhibitor, everolimus, increased the survival of Syn-Cre/Pten HOM mice while some neurologic phenotypes persisted. Transcriptomic analyses revealed that in contrast to mice harboring a neuron-specific deletion of the Tuberous Sclerosis Complex 2 gene (Syn-Cre/Tsc2 KO), genes that are under AKT regulation were significantly increased in the Syn-Cre/Pten HOM mice. In addition, genes associated with synapse, extracellular matrix, and myelination were broadly increased in Syn-Cre/Pten HOM mouse neocortex. These findings were confirmed by immunostaining of cortical sections in vivo, which revealed excessive immunoreactivity of myelin basic protein and perineuronal nets (PNN), the specialized extracellular matrix surrounding fast-spiking parvalbumin (PV) interneurons. We also detected increased expression of Synapsin I/PSD95 positive synapses and network hyperactivity phenotypes in Syn-Cre/Pten HOM mice neurons compared to wild-type (WT) neurons in vitro. Strikingly, everolimus treatment rescued the number of synapses and network hyperactivity in the Syn-Cre/Pten HOM mice cortical neuron cultures. Taken together, our results revealed in vivo and in vitro molecular and neuronal network mechanisms underlying neurological phenotypes of PHTS. Notably, pharmacologic mTOR inhibition by everolimus led to successful downstream signaling rescue, including mTOR complex 1 (mTORC1) site-specific suppression of S6 phosphorylation, correlating with phenotypic rescue found in our novel neuron-specific Syn-Cre/Pten HOM mice.

The incidence of gastric cancer remains high and poses a serious threat to human health. Recent comprehensive investigations into amino acid metabolism and immune system components within the tumor microenvironment have elucidated the functional interactions between tumor cells, immune cells, and amino acid metabolism. This study reviews the characteristics of amino acid metabolism in gastric cancer, with a particular focus on the metabolism of methionine, cysteine, glutamic acid, serine, taurine, and other amino acids. It discusses the relationship between these metabolic processes, tumor development, and the body's anti-tumor immunity, and analyzes the importance of targeting amino acid metabolism in gastric cancer for chemotherapy and immunotherapy.

Cardiac hypertrophy allows post-mitotic cardiomyocytes to meet increased hemodynamic demands but can predispose the heart to adverse clinical outcomes. Despite its central role in cardiac adaptation, the translational control mechanisms that drive cardiac hypertrophy are poorly understood. In this study, we elucidate the relative contributions of the various translational control mechanisms operant during homeostasis and hypertrophic growth.

A combination of immunofluorescence and single myocyte protein synthesis assays were used to dissect the single-cardiomyocyte mechanisms of translational control under basal and hypertrophic conditions in isolated adult rat cardiomyocytes. Translational control mechanism were examined in a mouse model of acute hypertrophic phenylephrine (PE) stimulation prior to overt cardiac growth.

We observed strikingly heterogeneous activity of mTORC1, the master regulator of translation, across cardiomyocytes both in situ and ex vivo. Heterogeneous mTORC1 activity drove heterogeneous protein synthesis, with translation primarily controlled via canonical mTORC1-dependent 4EBP1 phosphorylation at Thr36/Thr45/Thr69 under baseline conditions. Hypertrophic PE stimulation recruited more cardiomyocytes into a high mTORC1 activity state. PE induced a switch in 4EBP1 phosphorylation by increasing mTORC1-dependent phosphorylation at Thr36/Thr45, but not Thr69. Further, PE induced a novel mTORC1-independent, but MEK-ERK-dependent, pathway driving 4EBP1 phosphorylation at Ser64 in both isolated cardiomyocytes and in vivo. Ribosome biogenesis was also observed within hours upon hypertrophic stimulation, while the mTORC1-S6K-eEF2K-eEF2 pathway was not found to be a major driver of protein translation.

Protein synthesis is heterogeneous across cardiomyocytes driven by heterogeneous mTORC1 activity. MEK-ERK signaling directly controls 4EBP1 phosphorylation to augment translation during cardiac hypertrophy and challenges the canonical model of translation initiation.

Hepatocellular carcinoma (HCC) poses a substantial global health burden, with poor prognosis and high mortality rates. Dysregulated lipid metabolism has emerged as a critical driver of HCC progression. While mTORC1 signaling is known to promote lipid synthesis in HCC, the regulatory mechanisms governing mTORC1 remain largely unclear. Here, we demonstrate that mTORC1 inhibition significantly reduces lipogenesis in HCC and uncover a regulatory axis involving the transcription factor ATF3 and the leucine-arginine transporter SLC7A7. Transcriptomic analysis of HCC patients reveals an inverse correlation between ATF3 expression and lipid synthesis, a finding corroborated by experimental validation. Mechanistically, ATF3 suppresses mTORC1 signaling, thereby inhibiting lipid biosynthesis, with SLC7A7 identified as a key intermediary in this process. Specifically, ATF3 binds to the enhancer region of SLC7A7, driving its transcriptional activation and subsequently restraining mTORC1 activity. Functional assays in ATF3-overexpressing and -knockdown HCC cell lines further confirm ATF3's role as a tumor suppressor. Our study identifies a novel ATF3-SLC7A7-mTORC1 regulatory axis that attenuates lipogenesis and tumorigenesis in HCC, establishing a critical link between lipid metabolism and hepatocarcinogenesis. These findings offer new insights into potential therapeutic targets for the treatment of HCC.

Metabolic reprogramming within the tumor microenvironment (TME) plays a critical role in driving drug resistance in gastrointestinal cancers (GI), particularly through the pathways of fatty acid oxidation and glycolysis. Cancer cells often rewire their metabolism to sustain growth and reshape the TME, creating conditions such as nutrient depletion, hypoxia, and acidity that impair antitumor immune responses. Immune cells within the TME also undergo metabolic alterations, frequently adopting immunosuppressive phenotypes that promote tumor progression and reduce the efficacy of therapies. The competition for essential nutrients, particularly glucose, between cancer and immune cells compromises the antitumor functions of effector immune cells, such as T cells. Additionally, metabolic by-products like lactate and kynurenine further suppress immune activity and promote immunosuppressive populations, including regulatory T cells and M2 macrophages. Targeting metabolic pathways such as fatty acid oxidation and glycolysis presents new opportunities to overcome drug resistance and improve therapeutic outcomes in GI cancers. Modulating these key pathways has the potential to reinvigorate exhausted immune cells, shift immunosuppressive cells toward antitumor phenotypes, and enhance the effectiveness of immunotherapies and other treatments. Future strategies will require continued research into TME metabolism, the development of novel metabolic inhibitors, and clinical trials evaluating combination therapies. Identifying and validating metabolic biomarkers will also be crucial for patient stratification and treatment monitoring. Insights into metabolic reprogramming in GI cancers may have broader implications across multiple cancer types, offering new avenues for improving cancer treatment.

Autophagy related genes (ATGs) play essential roles in maintaining cellular functions, although biological and pathological alterations of ATG phenotypes remain poorly understood. To address this knowledge gap, we utilized the single-cell sequencing technology to elucidate the transcriptomic atlas of ATGs in lung diseases, with a focus on lung epithelium and lymphocytes. This study conducted a comprehensive investigation into RNA profiles of ATGs in the lung tissues obtained from healthy subjects and patients with different lung diseases through single-cell RNA sequencing (scRNA-seq), including COVID-19 related acute lung damage, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), systemic sclerosis (SSC), and lung adenocarcinoma (LUAD). Our findings revealed significant variations of ATGs expression across lung epithelial cell subsets, e.g., over-expression of MAPK8 in basal cells, ATG10 in club cells, and BCL2 in a goblet cell subset. The changes of autophagy-related pathways varied between lung epithelial and lymphocyte subsets. We identified the disease-associated changes in ATG expression, including significant alterations in BCL2, BCL2L1, PRKCD, and PRKCQ in inflammatory lung diseases (COPD and IPF), and MAP2K7, MAPK3, and RHEB in lung cancer (LUAD), as compared to normal lung tissues. Key ligand-receptor pairs (e.g., CD6-ALCAM, CD99-CD99) and signaling pathways (e.g., APP, CD74) might serve as biomarkers for lung diseases. To evaluate ATGs responses to external challenges, we examined ATGs expression in different epithelial cell lines exposed to cigarette smoking extract (CSE), lysophosphatidylcholine (lysoPC), lipopolysaccharide (LPS), and cholesterol at various doses and durations. Notable changes were observed in CFLAR, EIF2S1, PPP2CA, and PPP2CB in A549 and H1299 against CSE and LPS. The heterogeneity of ATGs expression was dependent on cell subsets, pathologic conditions, and challenges, as well as varied among cellular phenotypes, functions, and behaviors, and the severity of lung diseases. In conclusion, our data might provide new insights into the roles of ATGs in epithelial biology and pulmonary disease pathogenesis, with implications for disease progression and prognosis.