Nat Commun. 2023 Apr 25;14(1):2375. doi: 10.1038/s41467-023-38110-7.

ABSTRACT

GEnome-scale Metabolic models (GEMs) are powerful tools to predict cellular metabolism and physiological states in living organisms. However, due to our imperfect knowledge of metabolic processes, even highly curated GEMs have knowledge gaps (e.g., missing reactions). Existing gap-filling methods typically require phenotypic data as input to tease out missing reactions. We still lack a computational method for rapid and accurate gap-filling of metabolic networks before experimental data is available. Here we present a deep learning-based method - CHEbyshev Spectral HyperlInk pREdictor (CHESHIRE) - to predict missing reactions in GEMs purely from metabolic network topology. We demonstrate that CHESHIRE outperforms other topology-based methods in predicting artificially removed reactions over 926 high- and intermediate-quality GEMs. Furthermore, CHESHIRE is able to improve the phenotypic predictions of 49 draft GEMs for fermentation products and amino acids secretions. Both types of validation suggest that CHESHIRE is a powerful tool for GEM curation to reveal unknown links between reactions and observed metabolic phenotypes.

PMID:37185345 | DOI:10.1038/s41467-023-38110-7

mSystems. 2023 May 15:e0107322. doi: 10.1128/msystems.01073-22. Online ahead of print.

ABSTRACT

The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifier PXD033425 and PXD039416, respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined are a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm-surface-binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection.

PMID:37184670 | DOI:10.1128/msystems.01073-22

Elife. 2023 May 15;12:e88345. doi: 10.7554/eLife.88345. Online ahead of print.

ABSTRACT

Facioscapulohumeral muscular dystrophy (FSHD) is an incurable myopathy linked to over-expression of the myotoxic transcription factor DUX4. Targeting DUX4 is the leading therapeutic approach, however it is only detectable in 0.1-3.8% of FSHD myonuclei. How rare DUX4 drives FSHD and the optimal anti-DUX4 strategy is unclear. We combine stochastic gene expression with compartment models of cell states, building a simulation of DUX4 expression and consequences in FSHD muscle fibres. Investigating iDUX4 myoblasts, scRNAseq and snRNAseq of FSHD muscle we estimate parameters including DUX4 mRNA degradation, transcription and translation rates and DUX4 target gene activation rates. Our model accurately recreates the distribution of DUX4 and target gene positive cells seen in scRNAseq of FSHD myocytes. Importantly we show DUX4 drives significant cell death despite expression in only 0.8% of live cells. Comparing scRNAseq of unfused FSHD myocytes to snRNAseq of fused FSHD myonuclei, we find evidence of DUX4 protein syncytial diffusion and estimate its rate via genetic algorithms. We package our model into freely available tools, to rapidly investigate consequences of anti-DUX4 therapy.

PMID:37184373 | DOI:10.7554/eLife.88345

EMBO J. 2023 May 15:e112657. doi: 10.15252/embj.2022112657. Online ahead of print.

ABSTRACT

Correct nervous system development depends on the timely differentiation of progenitor cells into neurons. While the output of progenitor differentiation is well investigated at the population and clonal level, how stereotypic or variable fate decisions are during development is still more elusive. To fill this gap, we here follow the fate outcome of single neurogenic progenitors in the zebrafish retina over time using live imaging. We find that neurogenic progenitor divisions produce two daughter cells, one of deterministic and one of probabilistic fate. Interference with the deterministic branch of the lineage affects lineage progression. In contrast, interference with fate probabilities of the probabilistic branch results in a broader range of fate possibilities than in wild-type and involves the production of any neuronal cell type even at non-canonical developmental stages. Combining the interference data with stochastic modelling of fate probabilities revealed that a simple gene regulatory network is able to predict the observed fate decision probabilities during wild-type development. These findings unveil unexpected lineage flexibility that could ensure robust development of the retina and other tissues.

PMID:37184124 | DOI:10.15252/embj.2022112657

Elife. 2023 May 15;12:e82593. doi: 10.7554/eLife.82593. Online ahead of print.

ABSTRACT

Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate predictions of changes in protein stability by leveraging deep learning representations. RaSP performs on-par with biophysics-based methods and enables saturation mutagenesis stability predictions in less than a second per residue. We use RaSP to calculate ∼ 300 million stability changes for nearly all single amino acid changes in the human proteome, and examine variants observed in the human population. We find that variants that are common in the population are substantially depleted for severe destabilization, and that there are substantial differences between benign and pathogenic variants, highlighting the role of protein stability in genetic diseases. RaSP is freely available-including via a Web interface-and enables large-scale analyses of stability in experimental and predicted protein structures.

PMID:37184062 | DOI:10.7554/eLife.82593

Elife. 2023 May 15;12:e82675. doi: 10.7554/eLife.82675. Online ahead of print.

ABSTRACT

Many developmental processes depend on precise temporal control of gene expression. We have previously established a theoretical framework for regulatory strategies that can govern such high temporal precision, but experimental validation of these predictions was still lacking. Here, we use the time-dependent expression of a Wnt receptor that controls neuroblast migration in C. elegans as a tractable system to study a robust, cell-intrinsic timing mechanism in vivo. Single molecule mRNA quantification showed that the expression of the receptor increases non-linearly, a dynamic that is predicted to enhance timing precision over an unregulated, linear increase in timekeeper abundance. We show that this upregulation depends on transcriptional activation, providing in vivo evidence for a model in which the timing of receptor expression is regulated through an accumulating activator that triggers expression when a specific threshold is reached. This timing mechanism acts across a cell division that occurs in the neuroblast lineage, and is influenced by the asymmetry of the division. Finally, we show that positive feedback of receptor expression through the canonical Wnt pathway enhances temporal precision. We conclude that robust cell-intrinsic timing can be achieved by combining regulation and feedback of the timekeeper gene.

PMID:37184061 | DOI:10.7554/eLife.82675

Int J Fertil Steril. 2023 Apr 1;17(3):208-214. doi: 10.22074/ijfs.2022.546434.1249.

ABSTRACT

BACKGROUND: Semen hyperviscosity is a threatening cause of abnormal spermatozoa and infertility in men. We aimed to evaluate oxidative stress, antioxidants depletion and sperm apoptosis as main reasons for poor quality of spermatozoa in men with hyperviscous semen.

MATERIALS AND METHODS: In this cross-sectional study, ejaculate specimens were collected from fertile (n=102) and infertile men with hyperviscous semen (n=123) and without semen hyperviscosity (n=143). Total antioxidant capacity (TAC), glutathione (GSH), malondialdehyde (MDA), protein carbonyl (PC), 8-hydroxydeoxyguanosine (8-OHdG), and were measured in semen samples to estimate oxidative stress status. Gene expression pattern of BAX, CASPASE-9, CASPASE-3, and BCL2 was assessed to estimate sperm apoptosis.

RESULTS: The average of sperm count, normal morphology, normal motility, and sperm vitality in men with hyperviscous semen was significantly lower than infertile subjects without hyperviscous semen (P<0.01). Men with hyperviscous semen exhibited higher levels of PC (8.34 ± 1.03 nmol/mg vs. 6.01 ± 0.93 nmol/mg, P=0.008), MDA (1.14 ± 0.27 nmol/ ml vs. 0.89 ± 0.22 nmol/ml, P=0.031), 8-OHdG (259.71 ± 24.59 ng/ml vs. 197.13 ± 18.47 ng/ml, P=0.009), but lower TAC contents (1250.44 ± 66.23 μM/L vs. 1784.31 ± 89.87 μM/L, P=0.018) and GSH (3.82 ± 1.05 μM vs. 5.89 ± 0.87 μM, P=0.021) than men with non-viscous semen. The expression of BAX, CASPASE-3 and CASPASE-9 genes in men with hyperviscous semen was significantly increased by 1.39-fold (P=0.041), 1.47-fold (P=0.046), 1.29-fold (P=0.048), respectively, as compared with the infertile subjects without hyperviscous semen. However, BCL2 expression in infertile men without hyperviscous semen was higher compared to those with hyperviscous semen (1.36-fold, P=0.044).

CONCLUSION: Hyperviscous semen is markedly associated with depletion of seminal plasma antioxidants, sperm membrane lipid peroxidation, DNA and protein oxidation, and sperm apoptosis. Antioxidant therapy might be considered as a valuable strategy to protect sperm cells against oxidative damage in cases with seminal fluid hyperviscosity.

PMID:37183848 | DOI:10.22074/ijfs.2022.546434.1249

Am J Chin Med. 2023 May 15:1-25. doi: 10.1142/S0192415X23500398. Online ahead of print.

ABSTRACT

Several functional gastrointestinal disorders (FGIDs) have overlapping symptoms, and, consequently, developing treatment strategies based on symptomatology poses a challenge for the clinical management of complex FGIDs. The significant overlap in the symptoms of FGIDs caused by the shared pathophysiological mechanisms is both a challenge and an excellent target for therapeutic development, since treatment strategies focused on shared pathophysiological mechanisms can treat the associated underlying diseases rather than just alleviating the primary symptoms. Owing to its multi-targeted approach, traditional Chinese medicine (TCM) has garnered immense interest worldwide; however, the quality of the data demonstrating its effectiveness is generally weak. Additionally, the causal link between the intrinsic mechanisms of action of TCM and its clinical benefits remains obscure. Systems biology is characterized by holistic and dynamic research, which corresponds to the holistic, multi-targeted, and syndrome-based approach of TCM. Therefore, high-throughput analysis techniques can be employed to describe and comprehend the genesis and progression of diseases, as well as the impacts of TCM on the organism, which may aid in elucidating the pathogenic mechanisms of the diseases as well as the mechanism of action of TCM.

PMID:37183682 | DOI:10.1142/S0192415X23500398

Aging Cell. 2023 May 14:e13862. doi: 10.1111/acel.13862. Online ahead of print.

ABSTRACT

Sarcopenia, the age-related decline in muscle function, places a considerable burden on health-care systems. While the stereotypic hallmarks of sarcopenia are well characterized, their contribution to muscle wasting remains elusive, which is partly due to the limited availability of animal models. Here, we have performed cellular and molecular characterization of skeletal muscle from the African killifish-an extremely short-lived vertebrate-revealing that while many characteristics deteriorate with increasing age, supporting the use of killifish as a model for sarcopenia research, some features surprisingly reverse to an "early-life" state in the extremely old stages. This suggests that in extremely old animals, there may be mechanisms that prevent further deterioration of skeletal muscle, contributing to an extension of life span. In line with this, we report a reduction in mortality rates in extremely old killifish. To identify mechanisms for this phenomenon, we used a systems metabolomics approach, which revealed that during aging there is a striking depletion of triglycerides, mimicking a state of calorie restriction. This results in the activation of mitohormesis, increasing Sirt1 levels, which improves lipid metabolism and maintains nutrient homeostasis in extremely old animals. Pharmacological induction of Sirt1 in aged animals was sufficient to induce a late life-like metabolic profile, supporting its role in life span extension in vertebrate populations that are naturally long-lived. Collectively, our results demonstrate that killifish are not only a novel model to study the biological processes that govern sarcopenia, but they also provide a unique vertebrate system to dissect the regulation of longevity.

PMID:37183563 | DOI:10.1111/acel.13862

Eur J Neurol. 2023 May 14. doi: 10.1111/ene.15866. Online ahead of print.

ABSTRACT

BACKGROUND: Vitamin D is considered to play a role in multiple sclerosis (MS) etiopathogenesis. We recently identified a polymorphism in the CYP24A1 gene, rs2762943, that was associated with an increased MS risk. CYP24A1 encodes a protein involved in the catabolism of the active form of vitamin D. We investigated the immunological effects of carrying the rs2762943 risk allele, and its role as genetic modifier.

METHODS: Serum levels of 25-hydroxyvitamin D (25OHD) and 1,25-dihydroxyvitamin D (1,25(OH)2 D) were measured in a cohort of 167 MS patients. In a subgroup of patients, expression levels of MHC class II and co-stimulatory molecules were determined by flow cytometry, and serum levels of proinflammatory (IFNG, GM-CSF, CXCL13) and anti-inflammatory (IL-10) cytokines and neurofilament light chain were measured by single-molecule array assays. The effect of the rs2762943 polymorphism on disease activity and disability measures was evaluated in 340 MS patients.

RESULTS: Compared to non-carriers, carriers of the rs2762943 risk allele were characterized by reduced levels of 1,25(OH)2 D (p=0.0001), and elevated levels of IFNG (p=0.03) and GM-CSF (p=0.008), whereas no significant differences were observed for the other markers. The presence of the rs2762943 risk allele had no significant impact on disease activity and disability outcomes during follow-up. However, risk allele carriers were younger at disease onset (p=0.04).

CONCLUSIONS: These findings suggest that the CYP24A1 rs2762943 polymorphism plays a more important role on MS susceptibility than on disease prognosis, and is associated with lower 1,25(OH)2 D levels and heightened pro-inflammatory environment in MS patients.

PMID:37183562 | DOI:10.1111/ene.15866

Phys Chem Chem Phys. 2023 May 15. doi: 10.1039/d2cp05611a. Online ahead of print.

ABSTRACT

Insights into the structures, functions and dynamics of Cordyceps militaris (C. militaris) sugar transporters are necessary for understanding their versatile metabolic capability for fungal growth. The sequence-function relationship study of 85 C. militaris sugar transporters showed that there is a gap between phylogenetic-based subfamily classification and their functions. Beyond protein sequences, structural modeling and principal component analysis of the structural ensemble revealed the different folds of the Car and Org subfamilies. Performing channel detection and network analysis found that the Alp and Hex subfamilies can be specifically distinguished from others by the betweenness of channel residues. Signature dynamics analysis further suggested that the Hex subfamily demonstrates different dynamics, with high flexibility at the H1 region in TM11. Furthermore, the H1 region as an allosteric site was examined by network parameter calculations that guided allosteric pathways between this region and the channel cavity. Together with gene expression data of C. militaris, e.g., Hex06741 in the Hex subfamily, it was promisingly expressed when sugar utilization was altered. This work demonstrates an in silico framework for investigating C. militaris sugar transporters as an example case study of the allosteric activity of the Hex subfamily and can facilitate sugar transporter engineering design that can further optimize the preferable sugar utilization and fermentation process of C. militaris.

PMID:37183444 | DOI:10.1039/d2cp05611a

Virol Sin. 2023 May 12:S1995-820X(23)00055-X. doi: 10.1016/j.virs.2023.05.007. Online ahead of print.

ABSTRACT

Chikungunya virus (CHIKV) is a re-emerging mosquito-transmitted RNA virus causing joint and muscle pain. To better understand how CHIKV rewires the host cell and usurps host cell functions, we generated a systematic CHIKV-human protein-protein interaction map and revealed several novel connections that will inform further mechanistic studies. One of these novel interactions, between the viral protein E1 and STIP1 homology and U-box containing protein 1 (STUB1), was found to mediate ubiquitination of E1 and degrade E1 through the proteasome. Capsid associated with G3BP1, G3BP2 and AAA+ ATPase valosin-containing protein (VCP). Furthermore, VCP inhibitors blocked CHIKV infection, suggesting VCP could serve as a therapeutic target. Further work is required to fully understand the functional consequences of these interactions. Given that CHIKV proteins are conserved across alphaviruses, many virus-host protein-protein interactions identified in this study might also exist in other alphaviruses. Construction of interactome of CHIKV provides the basis for further studying the function of alphavirus biology.

PMID:37182691 | DOI:10.1016/j.virs.2023.05.007

Neurosci Lett. 2023 May 12:137297. doi: 10.1016/j.neulet.2023.137297. Online ahead of print.

ABSTRACT

Physical exercise is beneficial for preventing Alzheimer's disease (AD) and cognitive decline through several mechanisms, including suppression of neuroinflammation and neuronal loss in the hippocampus. Despite these exercise-induced benefits in AD pathology, less attention has been paid to the importance of maintaining exercise and the consequences of detraining. This study aimed to investigate the effects of early exercise intervention and detraining on age-related cognitive decline and its protective mechanisms using senescence-accelerated mouse prone 8 (SAMP8). These mice were divided to four groups: no-exercise (No-Ex, n = 9), 4 months (4M)-detraining (n = 11), 2 months (2M)-detraining (n = 11), and long-term exercise (LT-Ex, n = 13). Age-related cognitive decline was prevented in the LT-Ex group compared with the No-Ex group through the suppression of neuronal loss, enhanced brain-derived neurotrophic factor (BDNF), and inhibition of neuroinflammation corresponding to reduced M1 and increased M2 microglia in the hippocampus. No significant differences were observed in cognitive function between the detraining and No-Ex groups. However, the 2M-detraining group showed increased BDNF positive area in the CA1 region and the enhancement of anti-inflammatory M2 phenotype microglia. In contrast, no statistically beneficial exercise-induced changes in the hippocampus were observed in the 4M-detrainig group. These results showed that early exercise intervention prevented age-related cognitive deficits in AD progression by suppressing neuronal loss and neuroinflammation in the hippocampus. Exercise-induced benefits, including the anti-inflammation in the hippocampus, may be retained after exercise cessation, even if exercise-induced beneficial effects decline in a time-dependent manner.

PMID:37182575 | DOI:10.1016/j.neulet.2023.137297

Lancet Healthy Longev. 2023 May 11:S2666-7568(23)00057-0. doi: 10.1016/S2666-7568(23)00057-0. Online ahead of print.

ABSTRACT

BACKGROUND: Physical exercise is effective at attenuating ageing-related physical decline in general, but evidence of its benefits for older adults in residential care, who often have functional dependency, multimorbidity, and polypharmacy, is inconclusive. We aimed to establish the effects of exercise interventions on the physical function of this population.

METHODS: For this systematic review and network meta-analysis, we searched PubMed, Web of Science, Cochrane Library, Rehabilitation & Sports Medicine Source, and SPORTDiscus to identify randomised controlled trials assessing the effects of exercise interventions (vs usual care) on physical function (ie, functional independence, physical performance, and other related measures, such as muscle strength, balance, or flexibility) in adults aged 60 years or older living in residential care. Relevant studies published in English or Spanish up to Jan 12, 2023, were included in the systematic review. The quality of studies was assessed using the Tool for the Assessment of Study Quality and Reporting in Exercise (TESTEX) score. A network meta-analysis was performed for physical function-related outcomes reported in at least ten studies, with subanalyses for specific intervention (ie, exercise type, training volume, and study duration) and participant (eg, having cognitive impairment or dementia, pre-frail or frail status, and being functionally dependent) characteristics. The study protocol was registered on PROSPERO (CRD42021247809).

FINDINGS: 147 studies (11 609 participants, with mean ages ranging from 67 years [SD 9] to 92 years [2]) were included in the systematic review, and were rated as having overall good quality (median TESTEX score 9 [range 3-14]). In the meta-analysis (including 105 studies, n=7759 participants), exercise interventions were associated with significantly improved overall physical function, with a standardised mean difference [SMD] of 0·13 (95% credible interval [CrI] 0·04-0·21), which was confirmed in all analysed subpopulations. The strongest association was observed with 110-225 min per week of exercise, and the greatest improvements were observed with 170 min per week (SMD 0·36 [95% CrI 0·20-0·52]). No significant differences were found between exercise types. Subanalyses showed significant improvements for almost all analysed physical function-related outcomes (Barthel index, five-times sit-to-stand test, 30-s sit-to-stand test, knee extension, hand grip strength, bicep curl strength, Short Physical Performance Battery, 6-min walking test, walking speed, Berg balance scale, and sit-and-reach test). Large heterogeneity was found between and within studies in terms of population and intervention characteristics.

INTERPRETATION: Exercise interventions are associated with improved physical function in older adults in residential care, and should, therefore, be routinely promoted in long-term care facilities.

FUNDING: None.

TRANSLATION: For the Spanish translation of the abstract see Supplementary Materials section.

PMID:37182530 | DOI:10.1016/S2666-7568(23)00057-0

EBioMedicine. 2023 May 12;92:104596. doi: 10.1016/j.ebiom.2023.104596. Online ahead of print.

ABSTRACT

BACKGROUND: Birt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin (FLCN) gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harbor FLCN alteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated.

METHODS: To elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles with FLCN variants and RNA expression profiles between BHD-associated renal tumours and sporadic renal tumours.

FINDINGS: RNA-seq analysis revealed that BHD-associated renal tumours and sporadic renal tumours have totally different expression profiles. Sporadic ChRCCs were clustered into two distinct clusters characterized by L1CAM and FOXI1 expressions, molecular markers for renal tubule subclasses. Increased mitochondrial DNA (mtDNA) copy number with fewer variants was observed in BHD-associated renal tumours compared to sporadic ChRCCs. Cell-of-origin analysis using WGS data demonstrated that BHD-associated renal tumours and sporadic ChRCCs may arise from different cells of origin and second hit FLCN alterations may occur in early third decade of life in BHD patients.

INTERPRETATION: These data further our understanding of renal tumourigenesis of these two different types of renal tumours with similar histology.

FUNDING: This study was supported by JSPS KAKENHI Grants, RIKEN internal grant, and the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research.

PMID:37182269 | DOI:10.1016/j.ebiom.2023.104596

STAR Protoc. 2023 May 12;4(2):102293. doi: 10.1016/j.xpro.2023.102293. Online ahead of print.

ABSTRACT

The Size-Exclusion Chromatography Analysis Toolkit (SECAT) elucidates protein complex dynamics using co-fractionated bottom-up mass spectrometry (CF-MS) data. Here, we present a protocol for the network-centric analysis and interpretation of CF-MS profiles using SECAT. We describe the technical steps for preprocessing, scoring, semi-supervised machine learning, and quantification, including common pitfalls and their solutions. We further provide guidance for data export, visualization, and the interpretation of SECAT results to discover dysregulated proteins and interactions, supporting new hypotheses and biological insights. For complete details on the use and execution of this protocol, please refer to Rosenberger et al. (2020).1.

PMID:37182203 | DOI:10.1016/j.xpro.2023.102293

iScience. 2023 Apr 13;26(5):106666. doi: 10.1016/j.isci.2023.106666. eCollection 2023 May 19.

ABSTRACT

Cytotoxic T lymphocytes (CTLs) control tumors via lysis of antigen-presenting targets or through secretion of cytokines such as interferon-γ (IFNG), which inhibit tumor cell proliferation. Improved understanding of CTL interactions within solid tumors will aid the development of immunotherapeutic strategies against cancer. In this study, we take a systems biology approach to compare the importance of cytolytic versus IFNG-mediated cytostatic effects in a murine melanoma model (B16F10) and to dissect the contribution of immune checkpoints HAVCR2, LAG3, and PDCD1/CD274 to CTL exhaustion. We integrated multimodal data to inform an ordinary differential equation (ODE) model of CTL activities inside the tumor. Our model predicted that CTL cytotoxicity played only a minor role in tumor control relative to the cytostatic effects of IFNG. Furthermore, our analysis revealed that within B16F10 melanomas HAVCR2 and LAG3 better characterize the development of a dysfunctional CTL phenotype than does the PDCD1/CD274 axis.

PMID:37182110 | PMC:PMC10173735 | DOI:10.1016/j.isci.2023.106666

Heliyon. 2023 Apr 26;9(5):e15652. doi: 10.1016/j.heliyon.2023.e15652. eCollection 2023 May.

ABSTRACT

Wumei Bolus is a traditional Chinese medicine prescription, first appeared in Shennong Bencao Jing. Modern pharmacology believes that Wumei Bolus has antibacterial, antitussive, sedative, antiviral and anti-tumor effects, and plays a therapeutic role by acting on multi-target/multi-pathway. Moreover, it has great advantages in digestive system diseases, such as repairing the damaged gastrointestinal mucosa and improving the inflammatory environment.

AIM OF THE STUDY: This review aimed to evaluate the efficacy and safety of prescriptions based on the Wumei Bolus treating ulcerative colitis (UC).

MATERIALS AND METHODS: In this meta-analysis, we searched CNKI, Wanfang Database, VIP, Pubmed, Web of Science (WOS) with language restrictions of Chinese and English for articles published from the establishment of the database to Dec 2022. This meta-analysis controlled randomized controlled trials (RCTs) assessing the efficacy and safety of Wumei Bolus against ulcerative colitis and using RevMan 5.4 and Stata 15.0to analyze information from the compliant studies.

RESULTS: The search incorporated 3145 results (1617 cases assigned into Wumei Bolus group and 1528 cases assigned into control group), from which 37 studies fulfilled our inclusion criteria and were included. The outcomes of this meta-analysis showed that compared to the control group, the Experiment group was significantly more effective (RR = 1.24，95%CI [1.20，1.28])and lower adverse reactions (RR = 0.32, 95%CI [0.20, 0.53]). According to the subgroup analysis, The results showed that the RR = 1.23 and 95%CI [1.16, 1.30] in the group treated with Wumei Bolus alone and the group treated with Western medicine with RR = 1.25 and 95%CI [1.20, 1.30], indicating that the efficacy of Wumei Bolus in the treatment of UC was better and the difference was statistically significant (P < 0.00001). The results showed that compared with the control group, the experimental group had more advantages in reducing inflammatory factors whether TNF-α or IL-8 (TNF-α:SMD = -4.44, 95%CI [-5.75, -3.14]; IL-8: SMD = -3.02, 95%CI [-4.06, -1.97]) and improving TCM symptoms and reduced TCM syndrome points (SMD = -3.82, 95%CI [-4.30, -3.34]). There was significant association of the basic treatment of Wumei Bolus improving clinical efficacy, reducing serum pro-inflammatory factors, improving symptoms, and reducing adverse reactions in UC patients. These results were statistically significant (P < 0.00001).

CONCLUSIONS: The prescriptions based on the Wumei Bolus is greatly related to reducing serum pro-inflammatory factors, improving symptoms, improving clinical efficacy and reducing adverse reactions in the treatment of UC compared to conventional western medicine and improve the total clinical effective rate.

PMID:37180938 | PMC:PMC10172760 | DOI:10.1016/j.heliyon.2023.e15652

Oxid Med Cell Longev. 2023 May 3;2023:9864037. doi: 10.1155/2023/9864037. eCollection 2023.

NO ABSTRACT

PMID:37180759 | PMC:PMC10171981 | DOI:10.1155/2023/9864037

Front Pharmacol. 2023 Apr 26;14:1113007. doi: 10.3389/fphar.2023.1113007. eCollection 2023.

ABSTRACT

The two most common reasons for attrition in therapeutic clinical trials are efficacy and safety. We integrated heterogeneous data to create a human interactome network to comprehensively describe drug behavior in biological systems, with the goal of accurate therapeutic candidate generation. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multiscale therapeutic discovery, repurposing, and design was enhanced by integrating drug side effects, protein pathways, protein-protein interactions, protein-disease associations, and the Gene Ontology, and complemented with its existing drug/compound, protein, and indication libraries. These integrated networks were reduced to a "multiscale interactomic signature" for each compound that describe its functional behavior as vectors of real values. These signatures are then used for relating compounds to each other with the hypothesis that similar signatures yield similar behavior. Our results indicated that there is significant biological information captured within our networks (particularly via side effects) which enhance the performance of our platform, as evaluated by performing all-against-all leave-one-out drug-indication association benchmarking as well as generating novel drug candidates for colon cancer and migraine disorders corroborated via literature search. Further, drug impacts on pathways derived from computed compound-protein interaction scores served as the features for a random forest machine learning model trained to predict drug-indication associations, with applications to mental disorders and cancer metastasis highlighted. This interactomic pipeline highlights the ability of Computational Analysis of Novel Drug Opportunities to accurately relate drugs in a multitarget and multiscale context, particularly for generating putative drug candidates using the information gleaned from indirect data such as side effect profiles and protein pathway information.

PMID:37180722 | PMC:PMC10169664 | DOI:10.3389/fphar.2023.1113007