PubMed

Front Microbiol. 2023 Apr 18;14:1180319. doi: 10.3389/fmicb.2023.1180319. eCollection 2023.ABSTRACTMycorrhizal helper bacteria (MHB) can promote mycorrhizal fungal colonization and form mycorrhizal symbiosis structures. To investigate the effect of interactions between mycorrhizal beneficial microorganisms on the growth of blueberry, 45 strains of bacteria isolated from the rhizosphere soil of Vaccinium uliginosum were screened for potential MHB strains using the dry-plate confrontation assay and the bacterial extracellular metabolite promotion method. The results showed that the growth rate of mycelium of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was increased by 33.33 and 77.77% for bacterial strains L6 and LM3, respectively, compared with the control in the dry-plate confrontation assay. In addition, the extracellular metabolites of L6 and LM3 significantly promoted the growth of O. maius 143 mycelium with an average growth rate of 40.9 and 57.1%, respectively, the cell wall-degrading enzyme activities and genes of O. maius 143 was significantly increased. Therefore, L6 and LM3 were preliminarily identified as potential MHB strains. In addition, the co-inoculated treatments significantly increased blueberry growth; increased the nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activities in the leaves; and promoted nutrient uptake in blueberry. Based on the physiological, and 16S rDNA gene molecular analyses, we initially identified strain L6 as Paenarthrobacter nicotinovorans and LM3 as Bacillus circulans. Metabolomic analysis revealed that mycelial exudates contain large amounts of sugars, organic acids and amino acids, which can be used as substrates to stimulate the growth of MHB. In conclusion, L6 and LM3 and O. maius 143 promote each other's growth, while co-inoculation of L6 and LM3 with O. maius 143 can promote the growth of blueberry seedlings, providing a theoretical basis for further studies on the mechanism of ericoid mycorrhizal fungi-MHB-blueberry interactions. It laid the technical foundation for the exploitation of biocontrol strain resources and the development of biological fertilizer.PMID:37143547 | PMC:PMC10151510 | DOI:10.3389/fmicb.2023.1180319

Front Microbiol. 2023 Apr 18;14:1160702. doi: 10.3389/fmicb.2023.1160702. eCollection 2023.ABSTRACTThe outbreak of Bacterial blight (BB) caused by Xanthomonas oryzae (Xoo) generates substantial economic losses to agricultural production. Antibiotics application is a valuable measure to control this bacterial disease. However, microbial antibiotic resistance dramatically reduced antibiotic effectiveness. Identifying the resistance mechanism of Xoo to antibiotics and restoring antibiotic susceptibility is one of the crucial ways to solve this problem. This study employed a GC-MS-based metabolomic approach to reveal the differential metabolomics between a kasugamycin-susceptible Xoo strain (Z173-S) and a kasugamycin-resistant strain (Z173-RKA). The metabolic mechanism of kasugamycin (KA) resistance in Xoo by GC-MS showed that the downregulation of the pyruvate cycle (P cycle) is a crucial feature of Z173-RKA resistance to KA. This conclusion was confirmed by the decreased enzyme activities and the related gene transcriptional level in the P cycle. Furfural (an inhibitor of pyruvate dehydrogenase) can effectively inhibit the P cycle and increase the resistance of Z173-RKA to KA. Moreover, exogenous alanine can reduce the resistance of Z173-RKA to KA by promoting the P cycle. Our work seems to be the first exploration of the mechanism of KA resistance in Xoo by GC-MS-based metabonomics approach. These results provide a new idea for developing metabolic regulation to address KA resistance in Xoo.PMID:37143533 | PMC:PMC10151481 | DOI:10.3389/fmicb.2023.1160702

Front Vet Sci. 2023 Apr 18;10:1170573. doi: 10.3389/fvets.2023.1170573. eCollection 2023.ABSTRACTFor the purpose to improve meat quality, pigs were fed a normal diet (ND), a low protein diet (LPD) and a LPD supplemented with glycine (LPDG). Chemical and metabolomic analyses showed that LPD increased IMF deposition and the activities of GPa and PK, but decreased glycogen content, the activities of CS and CcO, and the abundance of acetyl-CoA, tyrosine and its metabolites in muscle. LPDG promoted muscle fiber transition from type II to type I, increased the synthesis of multiple nonessential amino acids, and pantothenic acid in muscle, which should contributed to the improved meat quality and growth rate. This study provides some new insight into the mechanism of diet induced alteration of animal growth performance and meat quality. In addition, the study shows that dietary supplementation of glycine to LPD could be used to improved meat quality without impairment of animal growth.PMID:37143503 | PMC:PMC10153625 | DOI:10.3389/fvets.2023.1170573

Front Vet Sci. 2023 Apr 18;10:1153903. doi: 10.3389/fvets.2023.1153903. eCollection 2023.ABSTRACTINTRODUCTION: Allodynia, which can be induced by paclitaxel administration, is the presence of pain as a result of a stimulus that does not usually provoke pain. Many studies have investigated the analgesic efficacy of acupuncture, including laser acupuncture (LA) and electroacupuncture (EA). Although pain-related diseases are relatively common, few studies have analyzed the analgesic effects and mechanisms of LA combined with EA. The purpose of this study was to investigate the therapeutic effect and mechanism of manual acupuncture (MA), EA, LA, and combined therapy (LA + EA) in a paclitaxel-induced allodynia rat model.METHODS: A total of 56 rats were classified into eight groups: a normal (Nor, n = 7), a control (Con, n = 7), an MA (n = 7), an EA (n = 7), a 650-nm LA (650LA, n = 7), an 830-nm LA (830LA, n = 7), a 650-nm LA combined with EA (650LA + EA, n = 7), and an 830-nm LA combined with EA group (830LA + EA, n = 7). Allodynia was induced by intraperitoneal injection of 2 mg/kg of paclitaxel every other day for a total of four times except the Nor group. Acupuncture treatments were conducted at the points of Jungwan (CV12) and Joksamni (ST36) once every other day for 6 min, for a total of nine times. Withdrawal response reaction times and force intensity of the foot were measured before the start of the experiment, after the 4th paclitaxel administration (day 8), and after the 9th and last treatment (day 15). On the 16th day, mRNA and protein expression in the spinal nerves was assessed, and a metabolome analysis of the animals' feces was performed.RESULTS AND DISCUSSION: Our analyses show that 650LA + EA treatment resulted in an upregulation of protein expression related to pain relief and nerve regeneration, whereas 830LA + EA treatment led to significant changes in metabolomes. This study demonstrates that a combination treatment of EA and LA can suppress allodynia and promote upregulation of protein expression related to nerve regeneration and is effective in changing the intestinal microbiome. Further large-scale research is required to assess the exact mechanism underlying the therapeutic effect of this combination treatment in pain-related diseases.PMID:37143500 | PMC:PMC10151682 | DOI:10.3389/fvets.2023.1153903

J Intern Med. 2023 May 4. doi: 10.1111/joim.13648. Online ahead of print.ABSTRACTThe etiology of type 1 diabetes foreshadows the pancreatic islet beta-cell autoimmune pathogenesis that heralds the clinical onset of type 1 diabetes. Standardized and harmonized tests of autoantibodies against insulin (IAA), glutamic acid decarboxylase (GADA), islet antigen-2 (IA-2A) and ZnT8 transporter (ZnT8A) allowed children to be followed from birth until the appearance of a first islet autoantibody. In the Environmental Determinants of Diabetes in the Young (TEDDY) study, a multicenter (Finland, Germany, Sweden and the US) observational study, children were identified at birth for the type 1 diabetes high risk HLA haplogenotypes DQ2/DQ8, DQ2/DQ2, DQ8/DQ8 and DQ4/DQ8. The TEDDY study was preceded by smaller studies in Finland, Germany, Colorado, Washington and Sweden. The aims were to follow children at increased genetic risk to identify environmental factors that trigger the first-appearing autoantibody (etiology) and progress to type 1 diabetes (pathogenesis). The larger TEDDY study found that the incidence rate of the first-appearing autoantibody was split into two patterns. IAA first peaked already during the first year of life and tapered off by 3-4 years of age. GADA first appeared by 2-3 years of age to reach a plateau by about 4 years. Prior to the first-appearing autoantibody, genetic variants were either common or unique to either pattern. A split was also observed in whole blood transcriptomics, metabolomics, dietary factors and exposures such as gestational life events and early infections associated with prolonged shedding of virus. An innate immune reaction prior to the adaptive response cannot be excluded. Clarifying the mechanisms by which autoimmunity is triggered to either insulin or GAD65 is key to uncovering the aetiology of autoimmune type 1 diabetes. This article is protected by copyright. All rights reserved.PMID:37143363 | DOI:10.1111/joim.13648

Comb Chem High Throughput Screen. 2023 May 4. doi: 10.2174/1386207326666230504124030. Online ahead of print.ABSTRACTINTRODUCTION: Cervical cancer is one of the malignant cancers with high mortality among women worldwide. Although vaccines and early detection have reduced cervical cancer mortality, it remains a malignancy with a high mortality rate in women.OBJECTIVE: We aimed to develop a novel integrated strategy that combines metabolomics with network pharmacology to explore the therapeutic mechanisms of naringin in cervical cancer. The mechanism of naringin intervention in cervical cancer was initially clarified by metabolomics and network pharmacology.METHODS: The method of LC-MS and network pharmacology for the detection and identification of potential biomarkers and the mechanisms of action of naringin was used. The metabolites were detected and identified based on ultra-high-performance liquid chromatography coupled with Quadrupole-Exactive Orbitrap MS (UHPLC-Q-Exactive Orbitrap MS) and followed by the network pharmacology analysis.RESULTS: In network pharmacology, naringin played a synergetic role through regulatory shared pathways, such as steroid hormone biosynthesis, sphingolipid signaling pathway and arachidonic acid metabolism, etc. Besides, the metabolomics analysis showed that 20 differential metabolites and 10 metabolic pathways were mainly involved in the therapeutic effect of naringin on cervical cancer. The result showed that naringin treatment for cervical cancer mainly occurs through the following metabolic pathways: amino acid metabolism and arachidonic acid metabolism.CONCLUSION: This work provided valuable information and a scientific basis for further studies of naringin in the treatment of cervical cancer.PMID:37143280 | DOI:10.2174/1386207326666230504124030

J Biol Chem. 2023 May 2:104774. doi: 10.1016/j.jbc.2023.104774. Online ahead of print.ABSTRACTMitochondria are signaling organelles implicated in cancer, but the mechanisms are elusive. Here, we show that Parkin, an E3 ubiquitin ligase altered in Parkinson's Disease (PD), forms a complex with the regulator of cell motility, Kindlin-2 (K2) at mitochondria of tumor cells. In turn, Parkin ubiquitinates Lys581 and Lys582 using Lys48 linkages, resulting in proteasomal degradation of K2 and shortened half-life from ∼5 h to ∼1.5 h. Loss of K2 inhibits focal adhesion turnover and β1 integrin activation, impairs membrane lamellipodia size and frequency, and inhibits mitochondrial dynamics, altogether suppressing tumor cell-ECM interactions, migration, and invasion. Conversely, Parkin does not affect tumor cell proliferation, cell cycle transitions or apoptosis. Expression of a Parkin ubiquitination-resistant K2 Lys581Ala/Lys582Ala double mutant is sufficient to restore membrane lamellipodia dynamics, correct mitochondrial fusion/fission, and preserve single-cell migration and invasion. In a 3D model of mammary gland developmental morphogenesis, impaired K2 ubiquitination drives multiple oncogenic traits of EMT, increased cell proliferation, reduced apoptosis and disrupted basal-apical polarity. Therefore, deregulated K2 is a potent oncogene and its ubiquitination by Parkin enables mitochondria-associated metastasis suppression.PMID:37142218 | DOI:10.1016/j.jbc.2023.104774

Environ Pollut. 2023 May 2:121766. doi: 10.1016/j.envpol.2023.121766. Online ahead of print.ABSTRACTLow dissolved oxygen (LO) in seawater negatively affects aquatic animals and has received considerable attention. However, there is still much to learn about how echinoderms, which are keystone species in benthic ecosystems, respond to hypoxic stress. Here, we detected differentially expressed metabolites (DEMs) in sea cucumber (Apositchopus japonicus) between normoxic conditions (NC group) and hypoxic conditions (2 mg L-1) for 3 and 7 days (i.e., LO3 and LO7 groups). A total of 156, 180, and 95 DEMs were found in the NC versus LO3, NC vs. LO7, and LO3 vs. LO7 comparisons, respectively. Amino acids were the most abundant class of DEMs, and "biosynthesis of amino acids" was an enriched pathway in all three comparisons. Most of the enriched metabolite sets under hypoxic stress were related to metabolism. As the duration of the hypoxia treatment extended, the metabolism-related process maintained an upward trend, and signaling pathways maintained a downward trend. Thus, metabolism-related processes are affected in hypoxia-stressed sea cucumber, and amino acid metabolism is the most important process for adaption to hypoxic conditions, potentially function in osmotic regulation and energy regulation. Our results shed light on the adaptative strategies of sea cucumber to challenging environmental conditions.PMID:37142211 | DOI:10.1016/j.envpol.2023.121766

J Ethnopharmacol. 2023 May 2:116557. doi: 10.1016/j.jep.2023.116557. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: The traditional Chinese herbal formula, Xiang-lian Pill (XLP), is commonly prescribed for ulcerative colitis (UC) patients to relieve their clinical symptom. Nonetheless, the underlying cellular and molecular mechanisms of XLP's anti-UC effect remain incompletely understood.AIM OF THE STUDY: To evaluate the therapeutic effect and elucidate the possible working mechanisms of XLP in UC treatment. The major active component of XLP was also characterized.MATERIALS AND METHODS: Colitis was induced in C57BL/6 mice with 3% dextran sulfate sodium (DSS) dissolved in drinking water for 7 consecutive days. The UC mice were grouped and treated with XLP (3640 mg/kg) or vehicle orally during the procedure of DSS induction. Mouse body weight, disease activity index (DAI) score and colon length were recorded. Histopathological changes and inflammatory cell infiltration were evaluated by pathological staining and flow cytometric analysis (FACS). Network pharmacology, bioinformatic analysis, widely targeted and targeted metabolomics analysis were performed to screen the potential effective ingredients and key targets. Bone marrow derived macrophages (BMDMs), peripheral blood mononuclear cells (PBMCs), RAW264.7 and THP-1 cells were used to dissect the anti-inflammatory effect of XLP.RESULTS: Oral administration of XLP ameliorated DSS induced mouse colitis, as evidenced by reduced DAI and colonic inflammatory destruction. FACS results demonstrated that XLP treatment effectively restored immune tolerance in colon, inhibited the generation of monocyte derived macrophages and skewed macrophage polarization into M2 phenotype. Network pharmacology analysis suggested that innate effector modules related to macrophage activation comprise the major targets of XLP, and the counter-regulatory STAT1/PPARγ signaling possibly serves as the critical downstream pathway. Subsequent experiments unveiled an imbalance of STAT1/PPARγ signaling in monocytes derived from UC patients, and validated that XLP suppressed LPS/IFN-γ induced macrophage activation (STAT1 mediated) but facilitated IL-4 induced macrophage M2 polarization (PPARγ dependent). Meanwhile, our data showed that quercetin served as the major component of XLP to recapitulate the regulatory effect on macrophages.CONCLUSION: Our findings revealed that quercetin serves as the major component of XLP that regulates macrophage alternative activation via tipping the balance of STAT1/PPARγ, which provides a mechanistic explanation for the therapeutic effect of XLP in UC treatment.PMID:37142141 | DOI:10.1016/j.jep.2023.116557

Sci Total Environ. 2023 May 2:163889. doi: 10.1016/j.scitotenv.2023.163889. Online ahead of print.ABSTRACTSalinity and heavy metal pollution seriously affect plant growth. Tamarix hispida (T. hispida) has the potential to remediate soil saline-alkali and heavy metal pollution. In this study, the response mechanisms of T. hispida under NaCl, CdCl2 (Cd) and combined CdCl2 and NaCl (Cd-NaCl) stresses were explored. Overall, the antioxidant system showed changes under the three stresses. The addition of NaCl inhibited the absorption of Cd2+. However, there were obvious differences in the transcripts and metabolites identified among the three stress responses. Interestingly, the number of DEGs was greatest under NaCl stress (929), but the number of differentially expressed metabolites (DEMs) was lowest (48), with 143 and 187 DEMs identified under Cd and Cd-NaCl stress, respectively. It is worth noting that both DEGs and DEMs were enriched in the linoleic acid metabolism pathway under Cd stress. In particular, the content of lipids changed significantly under Cd and Cd-NaCl stress, suggesting that maintaining normal lipid synthesis and metabolism may be an important way to improve the Cd tolerance of T. hispida. Flavonoids may also play an important role in the response to NaCl and Cd stress. These results provide a theoretical basis for cultivating plants with improved salt and cadmium repair abilities.PMID:37142042 | DOI:10.1016/j.scitotenv.2023.163889

Poult Sci. 2023 Apr 12;102(7):102718. doi: 10.1016/j.psj.2023.102718. Online ahead of print.ABSTRACTApproaches for the diagnosis of wooden breast (WB) myopathy in live birds are urgently required before applying intervention strategies to reduce occurrence and severity for the poultry industry. The objective of this study was to characterize the serum metabolic profiles in male broilers affected by WB and to identify biomarkers related to this myopathy. Broilers were categorized into normal (CON) and WB groups based on gross scoring and histological evaluation. Gas chromatography-mass spectrometry-based metabolomics, multivariate analysis, and orthogonal partial least squares discriminant analysis revealed a clear separation between CON and WB. A total of 73 significantly different (P < 0.05) metabolites with 17 upregulated and 56 downregulated were identified, which were mainly involved in pathways of alanine, aspartate, and glutamate metabolism, carbohydrate metabolism, and taurine and hypotaurine metabolism. By using the nested cross-validation function of random forest analysis, 9 significantly altered (P < 0.05) metabolites (cerotinic acid, arabitol, phosphoenolpyruvate, terephthalic acid, cis-gondoic acid, N-acetyl-d-glucosamine, 4-hydroxymandelic acid, caffeine, and xanthurenic acid) were identified as biomarkers with an excellent discriminant performance for WB myopathy. Collectively, this study provides new insights for a deeper understanding of the pathogenesis and provides metabolites as biomarkers for diagnostic utilization of WB myopathy.PMID:37141813 | DOI:10.1016/j.psj.2023.102718

J Magn Reson. 2023 Apr 26;352:107462. doi: 10.1016/j.jmr.2023.107462. Online ahead of print.ABSTRACTNMR is a key technology for metabolomics because of its robustness and reproducibility. Herein we discuss practical considerations that extend the utility of NMR spectroscopy. First, the long T1 spin relaxation times of small molecules limits high-throughput data acquisition because most experimental time is lost while waiting for signal recovery. In principle, the addition of a small amount of commercially-available paramagnetic gadolinium chelate allows cost-effective and efficient high-throughput mixture analysis with correct concentration determination. However, idle time caused by slow temperature regulation during sample exchanges, poses a next constraint. We show how, with proper care, NMR sample scanning times can be reduced additionally by a factor of two. Lastly, we describe how equidistant bucketing is a simple and fast procedure for metabolomic fingerprinting. The combination of these advancements help to make NMR metabolomics more versatile than it is today.PMID:37141802 | DOI:10.1016/j.jmr.2023.107462

Semin Immunol. 2023 May 2;67:101767. doi: 10.1016/j.smim.2023.101767. Online ahead of print.NO ABSTRACTPMID:37141767 | DOI:10.1016/j.smim.2023.101767

Food Chem. 2023 Apr 28;422:136231. doi: 10.1016/j.foodchem.2023.136231. Online ahead of print.ABSTRACTAn integrated metabolomics approach based on UPLC-QTOF-MS and HS-SPME-GC-orbitrap-MS was performed to investigate the dynamic changes of metabolite profiling in chickpeas, red speckled kidney beans, and mung beans during soaking. There were 23, 23, 16 non-volatile metabolites, and 18, 21, 22 volatile metabolites were identified as differential metabolites in chickpeas, red speckled kidney beans, and mung beans during soaking, respectively. These metabolites mainly included flavonoids, lysophosphatidylcholines (LPCs), lysophosphatidylethanolamines (LPEs), fatty acids, alcohols, aldehydes, and esters. The key time points responsible for the significant changes in metabolites and quality of the three pulses were 4, 8, and 24 h of soaking. Results revealed that the variations of some metabolites could attribute to oxidation and hydrolysis reactions. These results contribute to a better understanding of how soaking affects pulses quality, and provide useful information for determining soaking time according to nutritional and sensory requirements of their final products or dishes.PMID:37141754 | DOI:10.1016/j.foodchem.2023.136231

Trials. 2023 May 4;24(1):308. doi: 10.1186/s13063-023-07317-w.ABSTRACTBACKGROUND: Major depressive disorder (MDD) with atypical features, namely depression with atypical features (AFD), is one of the most common clinical specifiers of MDD, closely associated with bipolar disorder (BD). However, there is still a lack of clinical guidelines for the diagnosis, treatment, and prognosis of AFD. Our study mainly focuses on three issues about how to identify AFD, what is the appropriate individualized treatment for AFD, and what are the predictive biomarkers of conversion to BD.METHODS: The Study of Individualized Diagnosis and Treatment for Depression with Atypical Features (iDoT-AFD) is a multicenter, prospective, open-label study consisting of a 12-week randomized controlled trial (RCT) and a continued follow-up until 4 years or reaching the study endpoint. It is enrolling 480 patients with AFD (120 per treatment arm), 100 patients with BD, and 100 healthy controls (HC). Multivariate dimension information is collected including clinical features, cognitive function, kynurenine pathway metabolomics, and multimodal magnetic resonance imaging (MRI) data. Firstly, multivariate informatics analyses are performed to recognize patients with AFD from participants including the first-episode and recurrent atypical depression, patients with BD, and patients with HC. Secondly, patients with atypical depression are randomly allocated to one of the four treatment groups including "single application of selective serotonin reuptake inhibitor (SSRI) or serotonin-noradrenaline reuptake inhibitor (SNRI)", "SSRI/SNRI combined with mood stabilizer," "SSRI/SNRI combined with quetiapine (≥ 150 mg/day)," or "treatment as usual (TAU)" and then followed up 12 weeks to find out the optimized treatment strategies. Thirdly, patients with atypical depression are followed up until 4 years or switching to BD, to explore the risk factors of conversion from atypical depression to BD and eventually build the risk warning model of conversion to BD.DISCUSSION: The first enrolment was in August 2019. The iDoT-AFD study explores the clinical and biological markers for the diagnosis, treatment, and prognosis of AFD and further provides evidence for clinical guidelines of AFD.TRIAL REGISTRATION: ClinicalTrials.gov NCT04209166. Registered on December 19, 2019.PMID:37143128 | DOI:10.1186/s13063-023-07317-w

Chin Med. 2023 May 4;18(1):48. doi: 10.1186/s13020-023-00750-8.ABSTRACTBACKGROUND: Cold-dampness Syndrome (RA-Cold) and Hot-dampness Syndrome (RA-Hot) are two distinct groups of rheumatoid arthritis (RA) patients with different clinical symptoms based on traditional Chinese medicine (TCM) theories and clinical empirical knowledge. However, the biological basis of the two syndromes has not been fully elucidated, which may restrict the development of personalized medicine and drug discovery for RA diagnosis and therapy.METHODS: An integrative strategy combining clinical transcriptomics, phenomics, and metabolomics data based on clinical cohorts and adjuvant-induced arthritis rat models was performed to identify novel candidate biomarkers and to investigate the biological basis of RA-Cold and RA-Hot.RESULTS: The main clinical symptoms of RA-Cold patients are joint swelling, pain, and contracture, which may be associated with the dysregulation of T cell-mediated immunity, osteoblast differentiation, and subsequent disorders of steroid biosynthesis and phenylalanine metabolism. In contrast, the main clinical symptoms of RA-Hot patients are fever, irritability, and vertigo, which may be associated with various signals regulating angiogenesis, adrenocorticotropic hormone release, and NLRP3 inflammasome activation, leading to disorders of steroid biosynthesis, nicotinamide, and sphingolipid metabolism. IL17F, 5-HT, and IL4I1 were identified as candidate biomarkers of RA-Cold, while S1P and GLNS were identified as candidate biomarkers of RA-Hot.CONCLUSIONS: The current study presents the most comprehensive metabonomic and transcriptomic profiling of serum, urine, synovial fluid, and synovial tissue samples obtained from RA-Cold and RA-Hot patients and experimental animal models to date. Through the integration of multi-omics data and clinical independent validation, a list of novel candidate biomarkers of RA-Cold and RA-Hot syndromes were identified, that may be useful in improving RA diagnosis and therapy.PMID:37143094 | DOI:10.1186/s13020-023-00750-8

Methods Mol Biol. 2023;2644:193-209. doi: 10.1007/978-1-0716-3052-5_12.ABSTRACTCellular health, functionality, response to environment, and other variables affecting cell, tissue, or organ viability are reflected in the cellular proteomes and metabolomes. These "omic" profiles are in constant flux even during normal cellular functioning, to maintain cellular homeostasis, in response to small environmental changes and maintenance of optimal cell viability. However proteomic "fingerprints" can also provide insight into cellular ageing, response to disease, adjustment to environmental changes, and other variables that impact cellular viability. A variety of proteomic methods can be used to determine qualitative and quantitative proteomic change. In this chapter, we will focus on a labeling method called isobaric tags for relative and absolute quantification (iTRAQ), which is frequently used to identify and quantify proteomic expression changes in cells and tissues.PMID:37142923 | DOI:10.1007/978-1-0716-3052-5_12

Cell Death Dis. 2023 May 5;14(5):306. doi: 10.1038/s41419-023-05806-z.ABSTRACTThe major underlying cause for the high mortality rate in colorectal cancer (CRC) relies on its drug resistance, to which intratumor heterogeneity (ITH) contributes substantially. CRC tumors have been reported to comprise heterogeneous populations of cancer cells that can be grouped into 4 consensus molecular subtypes (CMS). However, the impact of inter-cellular interaction between these cellular states on the emergence of drug resistance and CRC progression remains elusive. Here, we explored the interaction between cell lines belonging to the CMS1 (HCT116 and LoVo) and the CMS4 (SW620 and MDST8) in a 3D coculture model, mimicking the ITH of CRC. The spatial distribution of each cell population showed that CMS1 cells had a preference to grow in the center of cocultured spheroids, while CMS4 cells localized at the periphery, in line with observations in tumors from CRC patients. Cocultures of CMS1 and CMS4 cells did not alter cell growth, but significantly sustained the survival of both CMS1 and CMS4 cells in response to the front-line chemotherapeutic agent 5-fluorouracil (5-FU). Mechanistically, the secretome of CMS1 cells exhibited a remarkable protective effect for CMS4 cells against 5-FU treatment, while promoting cellular invasion. Secreted metabolites may be responsible for these effects, as demonstrated by the existence of 5-FU induced metabolomic shifts, as well as by the experimental transfer of the metabolome between CMS1 and CMS4 cells. Overall, our results suggest that the interplay between CMS1 and CMS4 cells stimulates CRC progression and reduces the efficacy of chemotherapy.PMID:37142595 | DOI:10.1038/s41419-023-05806-z

Nat Commun. 2023 May 4;14(1):2581. doi: 10.1038/s41467-023-38335-6.ABSTRACTMany signaling and other genes known as "hidden" drivers may not be genetically or epigenetically altered or differentially expressed at the mRNA or protein levels, but, rather, drive a phenotype such as tumorigenesis via post-translational modification or other mechanisms. However, conventional approaches based on genomics or differential expression are limited in exposing such hidden drivers. Here, we present a comprehensive algorithm and toolkit NetBID2 (data-driven network-based Bayesian inference of drivers, version 2), which reverse-engineers context-specific interactomes and integrates network activity inferred from large-scale multi-omics data, empowering the identification of hidden drivers that could not be detected by traditional analyses. NetBID2 has substantially re-engineered the previous prototype version by providing versatile data visualization and sophisticated statistical analyses, which strongly facilitate researchers for result interpretation through end-to-end multi-omics data analysis. We demonstrate the power of NetBID2 using three hidden driver examples. We deploy NetBID2 Viewer, Runner, and Cloud apps with 145 context-specific gene regulatory and signaling networks across normal tissues and paediatric and adult cancers to facilitate end-to-end analysis, real-time interactive visualization and cloud-based data sharing. NetBID2 is freely available at https://jyyulab.github.io/NetBID .PMID:37142594 | DOI:10.1038/s41467-023-38335-6

Nat Commun. 2023 May 4;14(1):2587. doi: 10.1038/s41467-023-38304-z.ABSTRACTMulti-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.PMID:37142589 | DOI:10.1038/s41467-023-38304-z