PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data.

Proteomics offers a robust method for quantifying proteins and elucidating their roles in cellular functions, surpassing the insights provided by transcriptomics. The Clinical Proteomic Tumor Analysis Consortium database, enriched with comprehensive cancer proteomics data including phosphorylation and ubiquitination profiles, alongside transcriptomics data from the Genomic Data Commons, allow for integrative molecular studies of cancer. The ProteoCancer Analysis Suite (PCAS), our newly developed R package and Shinyapp, leverages these resources to facilitate in-depth analyses of proteomics, phosphoproteomics, and transcriptomics, enhancing our understanding of the tumor microenvironment through features like immune infiltration and drug sensitivity analysis. This tool aids in identifying critical signaling pathways and therapeutic targets, particularly through its detailed phosphoproteomic analysis. To demonstrate the functionality of the PCAS, we conducted an analysis of GAPDH across multiple cancer types, revealing a significant upregulation of protein levels, which is consistent with its important biological and clinical significance in tumors, as indicated in our prior research. Further experiments were used to validate the findings performed using the tool. In conclusion, the PCAS is a powerful and valuable tool for conducting comprehensive proteomic analyses, significantly enhancing our ability to uncover oncogenic mechanisms and identify potential therapeutic targets in cancer research.

Identifying and assessing a prognostic model based on disulfidptosis-related genes: implications for immune microenvironment and tumor biology in lung adenocarcinoma.

Introduction: Lung cancer, with the highest global mortality rate among cancers, presents a grim prognosis, often diagnosed at an advanced stage in nearly 70% of cases. Recent research has unveiled a novel mechanism of cell death termed disulfidptosis, which is facilitated by glucose scarcity and the protein SLC7A11. Methods: Utilizing the least absolute shrinkage and selection operator (LASSO) regression analysis combined with Cox regression analysis, we constructed a prognostic model focusing on disulfidptosis-related genes. Nomograms, correlation analyses, and enrichment analyses were employed to assess the significance of this model. Among the genes incorporated into the model, CHRNA5 was selected for further investigation regarding its role in LUAD cells. Biological functions of CHRNA5 were assessed using EdU, transwell, and CCK-8 assays. Results: The efficacy of the model was validated through internal testing and an external validation set, with further evaluation of its robustness and clinical applicability using a nomogram. Subsequent correlation analyses revealed associations between the risk score and infiltration of various cancer types, as well as oncogene expression. Enrichment analysis also identified associations between the risk score and pivotal biological processes and KEGG pathways. Our findings underscore the significant impact of CHRNA5 on LUAD cell proliferation, migration, and disulfidptosis. Conclusion: This study successfully developed and validated a robust prognostic model centered on disulfidptosis-related genes, providing a foundation for predicting prognosis in LUAD patients.

Constructing and Evaluating a Mitophagy-Related Gene Prognostic Model: Implications for Immune Landscape and Tumor Biology in Lung Adenocarcinoma.

Mitophagy, a conserved cellular mechanism, is crucial for cellular homeostasis through the selective clearance of impaired mitochondria. Its emerging role in cancer development has sparked interest, particularly in lung adenocarcinoma (LUAD). Our study aimed to construct a risk model based on mitophagy-related genes (MRGs) to predict survival outcomes, immune response, and chemotherapy sensitivity in LUAD patients. We mined the GeneCards database to identify MRGs and applied LASSO/Cox regression to formulate a prognostic model. Validation was performed using two independent Gene Expression Omnibus (GEO) cohorts. Patients were divided into high- and low-risk categories according to the median risk score. The high-risk group demonstrated significantly reduced survival. Multivariate Cox analysis confirmed the risk score as an independent predictor of prognosis, and a corresponding nomogram was developed to facilitate clinical assessments. Intriguingly, the risk score correlated with immune infiltration levels, oncogenic expression profiles, and sensitivity to anticancer agents. Enrichment analyses linked the risk score with key oncological pathways and biological processes. Within the model, MTERF3 emerged as a critical regulator of lung cancer progression. Functional studies indicated that the MTERF3 knockdown suppressed the lung cancer cell proliferation and migration, enhanced mitophagy, and increased the mitochondrial superoxide production. Our novel prognostic model, grounded in MRGs, promises to refine therapeutic strategies and prognostication in lung cancer management.

Homocysteine Modulates Social Isolation-Induced Depressive-Like Behaviors Through BDNF in Aged Mice.

Social isolation is an unpleasant experience associated with an increased risk of mental disorders. Exploring whether these experiences affect behaviors in aged people is particularly important, as the elderly is very likely to suffer from periods of social isolation during their late-life. In this study, we analyzed the depressive-like behaviors, plasma concentrations of homocysteine (Hcy), and brain-derived neurotropic factor (BDNF) levels in aged mice undergoing social isolation. Results showed that depressive-like behavioral performance and decreased BDNF level were correlated with increased Hcy levels that were detected in 2-month isolated mice. Elevated Hcy induced by high methionine diet mimicked the depressive-like behaviors and BDNF downregulation in the same manner as social isolation, while administration of vitamin B complex supplements to reduce Hcy alleviated the depressive-like behaviors and BDNF reduction in socially isolated mice. Altogether, our results indicated that Hcy played a critical role in social isolation-induced depressive-like behaviors and BDNF reduction, suggesting the possibility of Hcy as a potential therapeutic target and vitamin B intake as a potential value in the prevention of stress-induced depression.

Physicochemical property and antioxidant activity of polysaccharide from the seed cakes of Camellia oleifera Abel.

Seed cake refers to the food by-product of Camellia oleifera Abel, and its insufficient utilization can cause serious environment pollution and resource waste. This study aimed to investigate antioxidant activities of the polysaccharide from the seed cakes of Camellia oleifera Abel (COCP) in vitro and in vivo. The physicochemical property of COCP was also determined. COCP was characterized to be an acidic glycoprotein and mainly consisted of rhamnose (Rha), arabinose (Ara), galactose (Gal), glucose (Glc), xylose (Xyl), mannose (Man), and galacturonic acid (Gal-UA). COCP exhibited the polysaccharide's characteristic absorption in the Fourier transform infrared (FT-IR) spectroscopy and showed as sheet-like structures with a smooth surface under the scanning electron microscope (SEM). COCP exerted good scavenging activities on ABTS, DPPH, and OH radicals, with IC50 values of 2.94, 2.24, and 5.09 mg/ml, respectively. COCP treatment improved learning and memory abilities of D-galactose-induced aging mice. Significant decreases were found in the levels of alanine transaminase (ALT), aspartate aminotransferase (AST), creatinine (CRE), blood urea nitrogen (BUN), creatine kinase (CK), and lactate dehydrogenase (LDH) in serum, as aging mice were supplemented with COCP. Aging mice showed obviously higher malondialdehyde (MDA) contents and lower superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities in serum, brain, liver, kidney, and heart. The phenomena were noticeably reversed when mice were treated with COCP. Results indicated that COCP exerted excellent antioxidant activities in vitro and in vivo, which support its potential application as a natural antioxidant in food and medicine industries.

Claudin-5 relieves cognitive decline in Alzheimer's disease mice through suppression of inhibitory GABAergic neurotransmission.

Alzheimer's disease (AD) is characterized by progressive cognitive decline, which is considered as the most common form of dementia in the elderly. Recently, it is suggested that impaired cerebrovascular function may precede the onset of AD. Claudin-5, which is the most enriched tight junction protein, has been reported to prevent the passage of damaging material at the blood-brain barrier. However, whether claudin-5 impacts AD has no direct evidence. We found a decrease level of claudin-5 in the hippocampus of AD and elder mice. And intravenous injection of claudin-5 improved learning and memory ability in these mice, while knockout of the protein led to impaired learning and memory and long-term potentiation in adult control mice. Furthermore, the effects of claudin-5 are mediated by suppressing inhibitory GABAergic neurotransmission. Our results suggest benefit effects of claudin-5 on learning and memory, which may provide a new treatment strategy for AD.

Knockdown of astrocytic TREM2 in the hippocampus relieves cognitive decline in elderly male mice.

With the lengthening of the human lifespan, an increasing proportion of the population is subject to age-related cognitive impairments, making it important to investigate ways to confront the effects of aging. Triggering receptor expressed on myeloid cells 2 (TREM2) is an innate immune receptor that is expressed mainly on the surfaces of microglia. Previous studies have found a significant positive correlation between age and TREM2 levels. An increased concentration of soluble TREM2 in cerebrospinal fluid was also found in Alzheimer's disease (AD) patients. Although TREM2 is more highly expressed in microglia than in astrocytes, little attention has been focused on astrocytic TREM2, and the precise role of astrocytic TREM2 in the aging process remains unknown. In this study, we injected TREM2 shRNA into the hippocampal CA1 region to specifically knock down the expression of this protein in astrocytes. We found that TREM2 shRNA injection can improve learning and memory ability in elderly mice, as demonstrated by improved learning ability and memory performance in the Morris water maze (MWM) test, an increased freezing duration in the contextual fear conditioning test, a higher preference ratio in the novel object recognition (NOR) test and a higher alternation rate in the T-maze test. Knocking down astrocytic TREM2 can also rescue impaired long-term potentiation (LTP) induction in the hippocampal CA1 of elderly mice through a presynaptic mechanism. Our results suggest that decreased astrocytic TREM2 levels have beneficial effects on learning and memory ability in elderly mice, which may provide new insight into the pathological mechanism and potential targets of age-related dementia.

Ketamine reverses the impaired fear memory extinction and accompanied depressive-like behaviors in adolescent mice.

Post-traumatic stress disorder (PTSD) is a chronic and disabling condition arising after exposure to a severe traumatic event, which affects approximately eight percent of the population. The underlying neurobiology of PTSD, however, has only been partially understood. The exploration of fear memory and its extinction has been the subject to increase our understanding of PTSD. Our previous studies have already found that adolescent mice exhibited impaired fear memory extinction with accompanied depressive-like behaviors. Considering the relationship between ketamine and its rapid antidepressant function, we hypothesis that ketamine can facilitate the fear memory extinction so as to exhibit an antidepressant effects. In this study, to evaluate our hypothesis, we intraperitoneal (i.p.) injection of ketamine in adolescent mice and found that ketamine exhibited a rapid antidepressant effect and facilitated the fear memory extinction. Moreover, ketamine can also reverse the accompanied depressive-like behaviors and restore long-term potentiation (LTP) induction in extinction process, which involved the presynaptic mechanism. Our results suggest that ketamine exhibited an antidepressant effect in FST and facilitated the fear memory extinction via presynaptic-mediated synaptic plasticity, which may provide new strategy for treatment of PTSD.

Impaired fear memory extinction during adolescence is accompanied by the depressive-like behaviors.

Fear is the emotion that is best understood in terms of brain mechanisms. And the management of fear memories is important when facing mental health disorders such as post-traumatic stress. Adolescence is a transitional stage of physical and psychological human development and the ability to deal with the fear memory in adolescence may be a potent factor for developing mental disorders in adulthood. However, little is known about the direct relationship between the ability to deal with the fear memory and appearance of depressive-like behaviors. To assess this, we used a model of associative learning to induce the fear memories and evaluated the depressive-related behaviors in the fear memory extinction process and its underlying cellular mechanisms from adolescent and adult mice. We found that, compared with adult mice, the adolescent mice exhibited impaired fear memory extinction in contextual fear conditioning extinction process. Meanwhile, impaired fear memory extinction was accompanied by more immobility time in forced swimming test, which was used to assess the depressive-like state. Consistent with this, we observed that long-term potentiation (LTP) induction in the hippocampal CA1 region of adolescent mice persistently larger in extinction process in adolescent mice, which was involved the presynaptic mechanism. Together, our results suggest that adolescent mice exhibited a disability to extinct the fear memory, and that this may lead to the depressive-like behaviors via presynaptic-mediated synaptic plasticity. These findings may give us a new insight in the knowledge of some mental disorders caused by persistent unpleasant memories.

Roflumilast ameliorates cognitive impairment in APP/PS1 mice via cAMP/CREB/BDNF signaling and anti-neuroinflammatory effects.

Phosphodiesterase type 4 (PDE4) inhibitors can prevent the breakdown of the second messenger cyclic adenosine monophosphate (cAMP) and improve cognitive performances in several animal models of cognition. However, the clinical development of PDE4 inhibitors has been seriously hampered by severe side effects, such as vomiting and nausea. In this study, we investigated the effect and mechanism of roflumilast, an FDA-approved PDE4 inhibitor for treatment of chronic obstructive pulmonary disease (COPD), on learning and memory abilities in the APP/PS1 mouse model of Alzheimer's disease (AD). APP/PS1 transgenic mice received 3 intragastric doses of roflumilast (0.1, 0.2 and 0.4 mg/kg) daily for 3 weeks followed by behavioral tests. Chronic administration of roflumilast significantly improved the learning and memory abilities of APP/PS1 transgenic mice in the novel object recognition task, Morris water maze, and the step-down passive avoidance task. In addition, roflumilast increased the cAMP, phosphorylated cAMP response-element binding protein (p-CREB) and brain-derived neurotrophic factor (BDNF) levels, and reduced the nuclear translocation of nuclear factor-kappa B (NF-κB) p65, and proinflammatory cytokine (IL-6, TNF-a and IL-1ß) levels in the hippocampus of APP/PS1 transgenic mice. In conclusion, these findings suggest that roflumilast can enhance cognitive function in APP/PS1 transgenic mice, which may be related to its stimulation of the cAMP/CREB/BDNF pathway and anti-neuroinflammatory effects.

Nicotine contributes to the neural stem cells fate against toxicity of microglial-derived factors induced by Aß via the Wnt/ß-catenin pathway.

Recent studies have demonstrated that the molecules secreted from microglias play important roles in the cell fate determination of neural stem cells (NSCs), and nicotinic acetylcholine receptor agonist treatment could reduce neuroinflammation in some neurodegenerative disease models, such as Alzheimer's disease (AD). However, it is not clear how nicotine plays a neuroprotective role in inflammation-mediated central nervous diseases, and its possible mechanisms in the process remain largely elusive. The aim of this study is to improve the survival microenvironment of NSCs co-cultured with microglias in vitro by weakening inflammation that mediated by accumulation of ß-amyloid peptide (Aß). The viability, proliferation, differentiation, apoptosis of NSCs and underlying mechanisms associated with Wnt signaling pathway were investigated. The results showed that Aß could directly damage NSCs. Furthermore, concomitant to elevated levels of TNF-α, IL-1ß derived from microglias, the NSCs had been damaged more severely with the upregulation of Axin 2, p-ß-catenin and the downregulation of ß-catenin, p-GSK-3ß, microtubule-associated protein-2, choline acetyltransferase. However, addition of 10 µmol/L nicotine before microglias treated with Aß was beneficial to protect the NSCs against neurotoxicity of microglial-derived factors induced by Aß, which partially rescued proliferation, differentiation and inhibited apoptosis of NSCs via activation of Wnt/ß-catenin pathway. Taken together, these data imply that low concentration nicotine attenuates NSCs injury induced by microglial-derived factors via Wnt signaling pathway. Thus, treatment with nicotinic acetylcholine receptor agonist provides a promising research field for neural stem cell fate and therapeutic intervention in neuroinflammation diseases.

Huperzine A protects neural stem cells against Aß-induced apoptosis in a neural stem cells and microglia co-culture system.

OBJECTIVES: This study aims to explore whether Huperzine A (HupA) could protect neural stem cells against amyloid beta-peptide Aß induced apoptosis in a neural stem cells (NSCs) and microglia co-culture system. METHODS: Rat NSCs and microglial cells were isolated, cultured and identified with immunofluorescence Assays (IFA). Co-culture systems of NSCs and microglial cells were employed using Transwell Permeable Supports. The effects of Aß1-42 on NSCs were studied in 4 groups using co-culture systems: NSCs, Aß+NSCs, co-culture and Aß+co-culture groups. Bromodeoxyuridine (BrdU) incorporation and flow cytometry were utilized to assess the differences of proliferation, differentiation and apoptosis of NSCs between the groups. LQ test was performed to assess the amounts of IL-6, TNF-α and MIP-α secreted, and flow cytometry and Western blotting were used to assess apoptosis of NSCs and the expressions of Bcl-2 and Bax in each group. RESULTS: IFA results showed that isolated rat NSCs were nestin-positive and microglial cells were CD11b/c-positive. Among all the groups, the Aß+co-culture group has the lowest BrdU expression level, the lowest MAP2-positive, ChAT-positive cell counts and the highest NSC apoptosis rate. Smaller amounts of IL-6, TNF-α and MIP-α were being secreted by microglial cells in the HupA+Aß+co-culture group compared with those in the Aß+ co-culture group. Also the Bcl-2: Bax ratio was much higher in the HupA+Aß+co-culture group than in the Aß+co-culture group. CONCLUSIONS: HupA inhibits cell apoptosis through restraining microglia's inflammatory response induced by Aß1-42.

Social Isolation During Adolescence Strengthens Retention of Fear Memories and Facilitates Induction of Late-Phase Long-Term Potentiation.

Social isolation during the vulnerable period of adolescence produces emotional dysregulation that often manifests as abnormal behavior in adulthood. The enduring consequence of isolation might be caused by a weakened ability to forget unpleasant memories. However, it remains unclear whether isolation affects unpleasant memories. To address this, we used a model of associative learning to induce the fear memories and evaluated the influence of isolation mice during adolescence on the subsequent retention of fear memories and its underlying cellular mechanisms. Following adolescent social isolation, we found that mice decreased their social interaction time and had an increase in anxiety-related behavior. Interestingly, when we assessed memory retention, we found that isolated mice were unable to forget aversive memories when tested 4 weeks after the original event. Consistent with this, we observed that a single train of high-frequency stimulation (HFS) enabled a late-phase long-term potentiation (L-LTP) in the hippocampal CA1 region of isolated mice, whereas only an early-phase LTP was observed with the same stimulation in the control mice. Social isolation during adolescence also increased brain-derived neurotrophic factor (BDNF) expression in the hippocampus, and application of a tropomyosin-related kinase B (TrkB) receptor inhibitor ameliorated the facilitated L-LTP seen after isolation. Together, our results suggest that adolescent isolation may result in mental disorders during adulthood and that this may stem from an inability to forget the unpleasant memories via BDNF-mediated synaptic plasticity. These findings may give us a new strategy to prevent mental disorders caused by persistent unpleasant memories.