Urinary peptidome analysis in CKD and IgA nephropathy.

Background: Chronic kidney disease (CKD) has emerged as a significant challenge to human health and economic stability in aging societies worldwide. Current clinical practice strategies remain insufficient for the early identification of kidney dysfunction, and the differential diagnosis of immunoglobulin A nephropathy (IgAN) predominantly relies on invasive kidney biopsy procedures. Methods: First, we assessed a case-control cohort to obtain urine samples from healthy controls and biopsy-confirmed CKD patients. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was applied to detect urinary peptide and then these urinary peptide profiles were used to construct diagnostic models to distinguish CKD patients from controls and identify IgAN patients from other nephropathy patients. Furthermore, we assessed the robustness of the diagnostic models and their reproducibility by applying different algorithms. Results: A rapid and accurate working platform for detecting CKD and its IgAN subtype based on urinary peptide pattern detected by MALDI-TOF MS was established. Naturally occurring urinary peptide profiles were used to construct a diagnostic model to distinguish CKD patients from controls and identify IgAN patients from other nephropathy patients. The performance of several algorithms was assessed and demonstrated that the robustness of the diagnostic models as well as their reproducibility were satisfactory. Conclusions: The present findings suggest that the CKD-related and IgAN-specific urinary peptides discovered facilitate precise identification of CKD and its IgAN subtype, offering a dependable framework for screening conditions linked to renal dysfunction. This will aid in comprehending the pathogenesis of nephropathy and identifying potential protein targets for the clinical management of nephropathy.

Evaluation of a two-test strategy for HIV screening in a low-prevalence setting and the indications for optimizing clinical management.

Objectives: To evaluate a two-test strategy for HIV screening in the low-prevalence population and to assess the feasibility of utilizing the optimal signal-to-cutoff (S/CO) threshold on the chemiluminescence immunoassay(CMIA) and an additional rapid test on the gold immune-chromatography assay (GICA) for screening positive patients and optimization of clinical management. Methods: We conducted a retrospective study of samples analyzed by the fourth-generation Architect HIV Ag/Ab combo assay (CMIA) in a large medical center between June 2017 and August 2020. Reactive samples underwent a second screening test using the rapid test GICA, followed by Western blot (WB) as the confirmatory test. Receiver operating characteristic (ROC) curve analysis was used to determine the optimal S/CO. We calculated sensitivity, specificity, and predictive value based on our population. The performance of the single-test strategy (CMIA) was compared with that of the two-test strategy (CMIA and GICA). Logistic regression was used to analyze the factors of clinical characteristics leading to false positive results. Results: A total of 220558 samples were screened by CMIA, and 429 patients met the inclusion criteria. Of these, CMIA produced 199 false-positive results with a median S/CO of 1.93(IQR1.45-3.68) and 230 positive results with a median S/CO of 455.1 (IQR169.3-709.7). The optimal S/CO of the single-test strategy was 8.82, which achieved a sensitivity of 100% and a positive predictive value (PPV) of 90.9%. The two-test strategy (CMIA and GICA) provided a sensitivity of 100% and a PPV of 98.7%, which best correlated with the confirmatory test WB. The combination of S/CO 8.82 on the CMIA assay and additional test results of GICA can be defined as four types used to interpret HIV serostatus. The false positive rate (FPR) was high in the female, the age≤18 group, the pre-operative patients, and the patients from the clinical departments of Pediatrics, Gynecology and Obstetrics, and Oncology, etc. Conclusions: The false positive rate is high in the low-prevalence setting by using CMIA. The two-test strategy (CMIA and GICA) is recommended for HIV screening in hospitals. Hopefully, the clinicians will be able to interpret HIV serostatus and facilitate clinical decision-making while waiting for the confirmatory results.

The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans.

Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.

Exploring the role of uterine fibroids in promotion of cardiovascular diseases by diabetes exposure: Findings from national health and nutrition examination survey 1999-2006.

Objective: The relationship between uterine fibroids (UF) and cardiovascular diseases (CVDs) in the diabetes population seemed to remain undetermined in previous studies. This study aims to explore the association between UF and CVDs by using the database from the National Health and Nutrition Examination Survey (NHANES). To further evaluate the connection between UF and CVDs we also tested the potential differences due to diabetes exposure. Materials and methods: National Health and Nutrition Examination Survey data (1999-2006) were collected and used in this study. A total of 5,509 individuals were included and analyzed. The student's t-test and the chi-squared test were used to explore the demographic characteristic between UF and non-UF groups. Logistic regression analysis was performed to determine the odds ratios of UF and covariates. Results: Female participants were divided into UF (n = 694, 12.60%) and non-UF (n = 4,815, 87.40%) groups. The incidence of CVDs in UF patients (n = 245, 35.30%) were higher than non-UF individuals (n = 776, 16.12%) (p < 0.001). In addition, each subtype of CVDs were also different, which contains hypertension (33.29 vs. 15.31%, p < 0.001), heart failure (1.59 vs. 0.52%, p < 0.01), angina (2.59 vs. 0.62%, p < 0.001), heart attack (1.73 vs. 0.58%, p < 0.01) and coronary heart disease (1.44 vs. 0.54%, p < 0.01). The odds ratios of CVDs according to logistic regression were 2.840 (95% CI: 2.387-3.379) for UF patients (p < 0.001), while the odds ratios (ORs) were 1.438 (95% CI: 1.175-1.760) after taking account for the age, body mass index (BMI), diabetes, race, education, and annual family income (p < 0.001). In addition, secondary analysis indicated more adverse effects in by UF exposure on CVDs risk among non-diabetes individuals (OR = 1.389, 95% CI = 1.124-1.718, p < 0.01) than diabetes patients (p = 0.063). Conclusion: Overall, UFs were positively associated with CVDs, and this effect seems blunted by diabetes exposure.

Research progress on intervention effect and mechanism of protocatechuic acid on nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) has become a surge burden worldwide due to its high prevalence, with complicated deterioration symptoms such as liver fibrosis and cancer. No effective drugs are available for NALFD so far. The rapid growth of clinical demand has prompted the treatment of NAFLD to become a research hotspot. Protocatechuic acid (PCA) is a natural secondary metabolite commonly found in fruits, vegetables, grains, and herbal medicine. It is also the major internal metabolites of anthocyanins and other polyphenols. In the present manuscript, food sources, metabolic absorption, and efficacy of PCA were summarized while analyzing its role in improving NAFLD, as well as the mechanism involved. The results indicated that PCA could ameliorate NAFLD by regulating glucose and lipid metabolism, oxidative stress and inflammation, gut microbiota and metabolites. It was proposed for the first time that PCA might reduce NAFLD by enhancing the energy consumption of brown adipose tissue (BAT). However, the PCA administration mode and dose for NAFLD remain inconclusive. Fresh insights into the specific molecular mechanisms are required, while clinical trials are essential in the future. This review provides new targets and reasoning for the clinical application of PCA in the prevention and treatment of NAFLD.

Association Between Diet-Related Inflammation and COPD: Findings From NHANES III.

Background and Aims: Little is known about diet-related inflammation in chronic obstructive pulmonary disease (COPD). In this study, we aimed to explore the association between COPD and dietary inflammatory index (DII) scores in adults over 40 years old. Methods: Data were obtained from the 2013 to 2018 National Health and Nutrition Examination Survey (NHANES). In the present study, 9,929 participants were included and analyzed. The DII score was calculated and divided into tertiles. Logistic regression analysis was performed to determine the odds ratios of DII tertiles. Results: Participants were categorized into COPD (565, 5.69%) and non-COPD groups (9,364, 94.31%) according to interview information. COPD individuals had higher DII scores than non-COPD individuals (0.429 ± 1.809 vs. -0.191 ± 1.791, p < 0.001). The highest DII score tertile included 46.55% of COPD individuals was associated with lower family incomes and education and a higher smoking rate (p < 0.01). The odds ratios (95% CIs) of COPD according to logistic regression were 0.709 (0.512-0.982) for T1 and 0.645 (0.475-0.877) for T2 of the DII score (p = 0.011). Conclusion: Higher DII scores were positively correlated with COPD in participants over 40 years old. These results further support that diet can be used as an intervention strategy for COPD management.

Tracing tumorigenesis in a solid tumor model at single-cell resolution.

Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems.

Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT.

The competitive endogenous RNA (ceRNA) hypothesis suggests an intrinsic mechanism to regulate biological processes. However, whether the dynamic changes of ceRNAs can modulate miRNA activities remains controversial. Here, we examine the dynamics of ceRNAs during TGF-ß-induced epithelial-to-mesenchymal transition (EMT). We observe that TGFBI, a transcript highly induced during EMT in A549 cells, acts as the ceRNA for miR-21 to modulate EMT. We further identify FN1 as the ceRNA for miR-200c in the canonical SNAIL-ZEB-miR200 circuit in MCF10A cells. Experimental assays and computational simulations demonstrate that the dynamically induced ceRNAs are directly coupled with the canonical double negative feedback loops and are critical to the induction of EMT. These results help to establish the relevance of ceRNA in cancer EMT and suggest that ceRNA is an intrinsic component of the EMT regulatory circuit and may represent a potential target to disrupt EMT during tumorigenesis.

The intestinal microbiota associated with cardiac valve calcification differs from that of coronary artery disease.

BACKGROUND AND AIMS: Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical symptoms. Recently, increasing evidence suggests that intestinal bacteria play essential roles in cardiovascular disease (CVD). It is plausible that the gut microbiota is linked to the occurrence of different CVDs under similar risk factors. Thus, we aimed to explore the gut microbiomes in patients with VC or CAD and determine their underlying connections. METHODS: We collected samples from 119 subjects and performed 16S rRNA gene sequencing to analyze the gut microbiomes in VC and CAD patients and in control volunteers. RESULTS: The gut microbiomes of VC and CAD patients were significantly different in terms of beta-diversity. Bacteria from Veillonella dispar, Bacteroides plebeius and Fusobacterium were enriched in the VC group, while members of Collinsella aerofaciens, Megamonas, Enterococcus, Megasphaera, Dorea and Blautia were decreased. According to the association with dyslipidemia, seven operational taxonomic units (OTUs), including Parabacteroides distasonis, Megamonas, Fusobacterium, Bacteroides sp., Bacteroides plebeius, Lactobacillus and Prevotella copri, were regarded as potential pathogens for CVDs. Additionally, Prevotella copri might be a keystone of CVDs, especially in VC patients, while Collinsella aerofaciens is a possible keystone of CAD, based on the multi-correlations of these bacteria with other OTUs in microbial communities. CONCLUSIONS: Patients with VC and CAD suffer from different gut microbial dysbiosis. The gut microbiomes are associated with the clinical characteristics in these diseases and might be potential therapeutic targets.

Distinct shifts in the oral microbiota are associated with the progression and aggravation of mucositis during radiotherapy.

BACKGROUND AND PURPOSE: Oral mucositis remains one of the most common complications of radiation therapy for patients with head and neck cancer. This study aimed to investigate the dynamic shifts in the oral mucosal microbiota and their association with the progression and aggravation of mucositis in patients with nasopharyngeal carcinoma (NPC) undergoing radiotherapy. MATERIALS AND METHODS: In this study, oropharyngeal mucosa of patients were examined regularly, and sampled longitudinally in eight stages of their radiation treatment program: before radiation, and then after 10, 20, 30, 40, 50, 60, and 70 Gy. Based on 16S rRNA gene sequencing and bioinformatics analysis, the characteristics of dynamic variations in oral microbiota during their treatment were investigated. RESULTS: The results showed that the mucosal bacterial alpha diversity (richness and evenness) did not change significantly during the entire course of these patient treatments. Notwithstanding 20 genera were found to be significantly positively associated with their radiation dose, whereas 10 genera were negatively associated with it. Notably, two bacterial co-abundance groups (CAG 1 and 2) were identified and the majority of bacteria clustered within the CAG 2 were indeed periodontal disease-associated genera. Most strikingly, many of them, especially Prevotella, Fusobacterium, Treponema and Porphyromonas, showed obvious dynamic synchronous variations in their abundances throughout the course of radiation therapy, where their peaks frequently coincided with the onset of severe mucositis. CONCLUSION: Our results suggest that dysbiosis of oral mucosal microbiota may contribute to exacerbating the severity of mucositis in patients undergoing radiotherapy for nasopharyngeal carcinoma.

Computational identification of mutually exclusive transcriptional drivers dysregulating metastatic microRNAs in prostate cancer.

Androgen-ablation therapies, which are the standard treatment for metastatic prostate cancer, invariably lead to acquired resistance. Hence, a systematic identification of additional drivers may provide useful insights into the development of effective therapies. Numerous microRNAs that are critical for metastasis are dysregulated in metastatic prostate cancer, but the underlying molecular mechanism is poorly understood. We perform an integrative analysis of transcription factor (TF) and microRNA expression profiles and computationally identify three master TFs, AR, HOXC6 and NKX2-2, which induce the aberrant metastatic microRNA expression in a mutually exclusive fashion. Experimental validations confirm that the three TFs co-dysregulate a large number of metastasis-associated microRNAs. Moreover, their overexpression substantially enhances cell motility and is consistently associated with a poor clinical outcome. Finally, the mutually exclusive overexpression between AR, HOXC6 and NKX2-2 is preserved across various tissues and cancers, suggesting that mutual exclusivity may represent an intrinsic characteristic of driver TFs during tumorigenesis.

The Potential Effect of Oral Microbiota in the Prediction of Mucositis During Radiotherapy for Nasopharyngeal Carcinoma.

BACKGROUND: Oral mucositis is probably the most debilitating complication that can arise in treating a patient with head and neck cancer. Little is known about the impacts of oral microbiota on the initiation and progression of mucositis. METHODS: Based on 16S rRNA gene sequencing, dynamic changes in oral bacterial profile as well as correlations between the severity of mucositis and bacterial shifts during radiotherapy were investigated. FINDINGS: Our results revealed that bacterial community structure altered progressively during radiation therapy, in parallel with a marked increase in the relative abundance of some Gram-negative bacteria. Patients who eventually developed severe mucositis harbored a significantly lower bacterial alpha diversity and higher abundance of Actinobacillus during the phase of erythema - patchy mucositis. Accordingly, a random forest model for predicting exacerbation of mucositis was generated, which achieved a high predictive accuracy (AUC) of 0.89. INTERPRETATION: Oral microbiota changes correlate with the progression and aggravation of radiotherapy-induced mucositis in patients with nasopharyngeal carcinoma. Microbiota-based strategies can be used for the early prediction and prevention of the incidence of severe mucositis during radiotherapy.

Synergistic action of master transcription factors controls epithelial-to-mesenchymal transition.

Epithelial-to-mesenchymal transition (EMT) is a complex multistep process in which phenotype switches are mediated by a network of transcription factors (TFs). Systematic characterization of all dynamic TFs controlling EMT state transitions, especially for the intermediate partial-EMT state, represents a highly relevant yet largely unexplored task. Here, we performed a computational analysis that integrated time-course EMT transcriptomic data with public cistromic data and identified three synergistic master TFs (ETS2, HNF4A and JUNB) that regulate the transition through the partial-EMT state. Overexpression of these regulators predicted a poor clinical outcome, and their elimination readily abolished TGF-ß-induced EMT. Importantly, these factors utilized a clique motif, physically interact and their cumulative binding generally characterized EMT-associated genes. Furthermore, analyses of H3K27ac ChIP-seq data revealed that ETS2, HNF4A and JUNB are associated with super-enhancers and the administration of BRD4 inhibitor readily abolished TGF-ß-induced EMT. These findings have implications for systematic discovery of master EMT regulators and super-enhancers as novel targets for controlling metastasis.