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Background: A retrospective study was conducted to explore the urinary expression of α 1-microglobulin (α1MG) and β2-microglobulin (β2MG) in patients with human immunodeficiency virus (HIV) infection, aiming to evaluate their predictive capability for renal injury., Method: One hundred and five male HIV-infected patients treated with Tenofovir (TDF) regimen (TDF+3TC or the third drug TDF/FTC+) were selected between March 1, 2021, and March 1, 2022, in Wuhan Jinyintan Hospital. Three months after TDF treatment, the renal function injury was evaluated with the standard creatinine clearance rate. The urinary levels of α1MG and β2MG were compared between the initiation of TDF treatment and three months thereafter. Spearman correlation was utilized to analyze the correlation between the urinary expression of α1MG and β2MG and renal injury in HIV patients. The logistic regression was used to analyze the predictive value of urinary α1MG and β 2-microglobulin expression in renal injury., Results: Up to the first follow-up, 29 (27.6%) cases of the 105 male HIV patients had varying degrees of renal function injury, including 14 (13.3%) mild injury, 9 (8.6%) moderate injury, and 6 (5.7%) severe injury cases. Patients with severe renal injury had the highest levels of urinary α1MG and β2MG expression while those with mild injury demonstrated higher levels compared to the non-injury group (P < 0.05). Spearman correlation analysis indicated that urinary α1MG and β2MG were positively correlated with renal impairment in HIV patients (Rho = -0.568, and -0.732; P < 0.001). The ROC curve analysis demonstrated that the area under the curve (AUC) for urine α1MG and β2MG in predicting kidney damage among HIV patients were 0.928, 0.916, and 0.889, respectively. The sensitivity values were 96.55%, 82.76%, and 89.66% while the specificity values were 84.07%, 94.51%, and 89.29% for urine α1MG and β2MG, respectively., Conclusion: The expression level of urinary α1MG and β2MG in HIV patients was significantly higher compared to normal people. Detection of these two indexes can enable early determination of renal injury and its severity in HIV patients., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Serum lactate dehydrogenase (LDH), carcinoembryonic antigen (CEA) and CYFRA21-1 are the commonly used biomarkers to identify patients with autoimmune pulmonary alveolar proteinosis (APAP). However, it is not clear which of the biomarkers is more sensitive to the severity of the patient's condition., Methods: APAP patients numbering 151 were enrolled in this study. All patients' severity was assessed through the severity and prognosis score of PAP (SPSP). According to the respective laboratory upper limits of serum levels of LDH, CEA and CYFRA21-1, APAP patients were divided into higher and lower-level groups. Patients were divided into five groups based on SPSP. 88 patients had completed six months of follow-up. We calculated sensitivity, specificity, and critical point of LDH, CEA and CYFRA21-1 between APAP patients and normal control group, and between grade 1-2 and 3-5 through receiving operating characteristics (ROC) curve., Results: Serum LDH, CEA and CYFRA21-1 levels of patients with PAP were higher and distinctly related to PaO 2 , FVC, FEV 1 , DLCO, HRCT scores and SPSP. The SPSP of patients in higher-level LDH, CEA and CYFRA21-1 groups were higher than those of corresponding lower-level groups. Based on SPSP results, the patients were divided into five groups (grade I, 20; grade II, 37; grade III, 40; grade IV, 38; grade V, 16). The serum level of CYFRA21-1 of patients with APAP in grade II was higher than that of patients in grade I and lower than that of patients in grade III. Serum CYFRA21-1 of patients with APAP after six months were higher than the baseline among the aggravated group. Serum LDH, CEA and CYFRA21-1 levels after six months among patients in the relieved group of patients with APAP were lower than the baseline. ROC correlating LDH, CEA and CYFRA21-1 values with APAP severity (between grade 1-2 and 3-5) showed an optimal cutoff of LDH of over 203 U/L (< 246 U/L), CEA of over 2.56 ug/L (< 10 ug/L), and CYFRA21-1 of over 5.57 ng/ml (> 3.3 ng/ml) (AUC: 0.815, 95% CI [0.748-0.882], sensitivity: 0.606, specificity: 0.877)., Conclusion: Serum CYFRA21-1 level was more sensitive in revealing the severity of APAP than LDH and CEA levels among mild to moderate forms of disease., (© 2021. The Author(s).)

Background: The occurrence of hypomagnesemia in patients with primary hyperparathyroidism (PHPT) has been noted previously; however, the association of hypomagnesemia and severity of primary hyperparathyroidism remains unknown. The present study aimed to evaluate the association of hypomagnesemia with biochemical and clinical manifestations in patients with PHPT., Methods: This was a retrospective study conducted at a tertiary hospital. We obtained data from 307 patients with PHPT from January 2010 through August 2020. Data on demographics, history, laboratory findings, bone densitometry findings, and clinical presentation and complications were collected and were compared in normal magnesium group vs hypomagnesemia group., Results: Among the 307 patients with PHPT included in our study, 77 patients (33/102 [32.4%] males and 44/205 [21.5%] females) had hypomagnesemia. Mean hemoglobin levels in the hypomagnesemia group were significantly lower than those in the normal magnesium group in both males and females. In contrast, patients with hypomagnesemia had a higher mean serum calcium and parathyroid hormone than individuals with normal magnesium. The typical symptoms of PHPT, such as nephrolithiasis, bone pain/fractures, polyuria, or polydipsia, were more common in the hypomagnesemia group. In addition, patients with hypomagnesemia had a higher prevalence of osteoporosis, anemia, and hypercalcemic crisis. Even after adjusting for potential confounders, including age, sex, body mass index, estimated glomerular filtration rate, and parathyroid hormone levels, these associations remained essentially unchanged., Conclusion: Biochemical and clinical evidence indicates that patients with PHPT with hypomagnesemia have more severe hyperparathyroidism than those without hypomagnesemia. In addition, PHPT patients with hypomagnesemia had a higher prevalence of osteoporosis, anemia, and hypercalcemic crisis., (© 2021. The Author(s).)

Correlating aberrant miRNA levels with imported malaria during the blood stage is required to better understand the in vivo biological and molecular processes that are involved in the response to Plasmodium falciparum infection and to find new biomarkers and diagnosis tools. We used a parallel microarray-based approach to investigate an integrated view of how the host miRNA expression profile changes in response to P. falciparum infection in whole blood obtained from six subjects with adult imported falciparum malaria (AIFM) and six normal subjects. We first investigated the functions of 1007 significantly differentially expressed genes from microarrays and predicted 56 putative pathways participating in malaria pathogenesis, which reflected systemic changes in the host under falciparum infection. Then, we validated the in silico-predicted targets of 50 differentially modulated miRNAs (7 upregulated and 43 downregulated) by examining the actual mRNA expression of these particular genes in our gene expression profile database; putative target gene sets were grouped into functional categories to investigate the roles of differentially expressed miRNAs. We considered 36 intersecting putative pathways, most of which were involved in multiple immune response processes, such as cell defense response, immune response, TNF signaling pathway, and T cell receptor signaling pathway, which may actually be regulated by differentially expressed miRNAs. Additionally, we identified five enriched upregulated miRNA sets (miR-3135b, miR-6780b-5p, miR-1246, miR-6126, and miR-3613-5p) as potential blood biomarkers of immunopathological status and prediction of early host responses, disease prognosis, and severe outcomes in AIFM., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Background: Recently, a series of studies have been conducted to investigate the association of the common biochemical biomarkers, such as serum lactate and creatinine, with clinical outcomes in cardiac arrest patients treated with extracorporeal membrane oxygenation (ECMO), however, the results were not consistent and the sample size of primary studies is limited. In the present study, we performed a systematic review and meta-analysis to summarize the associations., Methods: Relevant studies in English databases (PubMed, ISI web of science, and Embase) and Chinese databases (Wanfang and CNKI) up to January 2018 were systematically searched. Crude ORs or HRs from the included studies were extracted and pooled to summarize the associations of lactate and creatinine with clinical outcomes including survival and neurological outcomes in ECMO treated cardiac arrest patients., Results: 17 papers containing 903 cases were included in the present meta-analysis study. After pooling all the eligible studies, we identified the significant associations of high lactate level with poor survival (N=13, OR=1.335, 95%CI=1.167-1.527, P<0.001) and poor neurological outcome (N=2, HR=1.058, 95%CI=1.020-1.098, P=0.002) in CA patients treated with ECMO and a slight significant association of high creatinine with poor survival was also found (N=7, OR=1.010, 95%CI=1.002-1.018, P=0.015)., Conclusions: High serum lactate level was associated with poor survival and poor neurological outcome in CA patients treated with ECMO. Further well-designed studies with larger sample size should be conducted to confirm the results., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Objectives: The purpose of this study was to determine the diagnostic and prognostic values of serum KL-6 levels in Chinese patients with interstitial lung disease (ILDs)., Methods: A total of 1084 subjects including 373 cases of ILDs, 584 cases of non-ILD pulmonary diseases, and 127 healthy individuals were recruited from three clinical centers in China between January 2011 and December 2013. A total of 106 patients undergoing treatments for ILDs in Shanghai Pulmonary Hospital between January 2011 and December 2013 were enrolled. Baseline and posttreatment serum KL-6 levels were determined., Results: Serum KL-6 levels in patients with ILDs were significantly higher than those in patients with non-ILD pulmonary diseases or in healthy individuals (1492.09 ± 2230.08 U/mL vs 258.67 ± 268.73 U/mL or 178.73 ± 71.17 U/mL, all P < 0.05). At the cut-off value of 500 U/mL, the sensitivity and specificity of serum KL-6 as a diagnostic marker for ILDs was 77.75% and 94.51%, respectively. The Kappa value was 0.743 (P < 0.001). The area below the receiver operating characteristic curve was 0.922 with a 95% Confidence interval of 0.904-0.941 (P < 0.001). The posttreatment serum KL-6 levels significantly reduced in patients with improved ILDs, whereas markedly increased in patients with exacerbated ILDs (All P < 0.05)., Conclusions: Serum KL-6 levels might be a promising diagnostic biomarker for ILDs in Chinese patients. The prognostic value of serum KL-6 levels for ILDs remains to be verified by large-scaled studies., (© 2015 John Wiley & Sons Ltd.)

RNA binding motif 3 (RBM3) is a highly conserved cold-induced RNA binding protein that is transcriptionally up-regulated in response to harsh stresses. Featured as RNA binding protein, RBM3 is involved in mRNA biogenesis as well as stimulating protein synthesis, promoting proliferation and exerting anti-apoptotic functions. Nowadays, accumulating immunohistochemically studies have suggested RBM3 function as a proto-oncogene that is associated with tumor progression and metastasis in various cancers. Moreover, emerging evidences have also indicated that RBM3 is equally effective in neuroprotection. In the present review, we provide an overview of current knowledge concerning the role of RBM3 in various cancers and neuroprotection. Additionally, its potential roles as a promising diagnostic marker for cancer and a possible therapeutic target for neuro-related diseases are discussed.

Increased p66Shc expression has been associated with diabetic nephropathy (DN). However, whether p66Shc can serve as a potential biomarker for tubular oxidative injury in DN is unknown. We measured the expression of p66Shc in peripheral blood monocytes (PBMs) and renal biopsy tissues from DN patients and then analysed the relationship between p66Shc expression and the clinical characteristics of patients with DN. Patients were divided into 4 groups (class IIa, class IIb, class III and the control group). qPCR, Western blotting and immunohistochemistry were performed. The results showed that both p66Shc and p-p66Shc expression significantly increased in PBMs and kidney tissues of DN patients. Moreover, Spearman's correlation and multiple regression analyses were carried out. A positive relationship between the p66Shc expression and oxidative stress was found. p66Shc and oxidative stress were significant predictors of the degree of tubular damage. In addition, p66Shc expression was positively correlated with the concentrations of β-NAG, UACR and 8-OHdG, low-density lipoprotein and blood glucose levels, and duration of diabetes in patients with DN from class IIa to class III. These data indicated that increased expression of p66Shc may serve as a therapeutic target and a novel biomarker of DN.

While high-throughput technologies are expected to play a critical role in clinical translational research for complex disease diagnosis, the ability to accurately and consistently discriminate disease phenotypes by determining the gene and protein expression patterns as signatures of different clinical conditions remains a challenge in translational bioinformatics. In this study, we propose a novel feature selection algorithm: Multi-Resolution-Test (MRT-test) that can produce significantly accurate and consistent phenotype discrimination across a series of omics data. Our algorithm can capture those features contributing to subtle data behaviors instead of selecting the features contributing to global data behaviors, which seems to be essential in achieving clinical level diagnosis for different expression data. Furthermore, as an effective biomarker discovery algorithm, it can achieve linear separation for high-dimensional omics data with few biomarkers. We apply our MRT-test to complex disease phenotype diagnosis by combining it with state-of-the-art classifiers and attain exceptional diagnostic results, which suggests that our method's advantage in molecular diagnostics. Experimental evaluation showed that MRT-test based diagnosis is able to generate consistent and robust clinical-level phenotype separation for various diseases. In addition, based on the seed biomarkers detected by the MRT-test, we design a novel network marker synthesis (NMS) algorithm to decipher the underlying molecular mechanisms of tumorigenesis from a systems viewpoint. Unlike existing top-down gene network building approaches, our network marker synthesis method has a less dependence on the global network and enables it to capture the gene regulators for different subnetwork markers, which will provide biologically meaningful insights for understanding the genetic basis of complex diseases.

With a steep increase in the incidence of type 1 and 2 diabetes globally, diabetic nephropathy (DN) has now become the leading cause of renal failure in the world. There are no suitable biomarkers for the diagnosis of early stages of DN. In recent years, tremendous efforts are being made worldwide to delineate the role of micro RNAs in the pathogenesis of DN. Circulating miRNAs in serum, plasma, urine and other body fluids, which reflect a response to various pathophysiological stresses, are being investigated in the context of diabetic nephropathy. Delineation of the changes in miRNA levels in patients with DN may lead to a better understanding of the progression of the disease. We present here an exhaustive survey of the miRNA literature, highlighting various studies performed over the last decade. The aim is to assess if changes in various miRNAs could correlate with the progression of diabetic nephropathy. Based on the survey, we found that miRNA-377, miRNA-192, miRNA-216/217 and miRNA-144 are increased in body fluids of patients with DN, while miRNA-21 and miRNA-375 are decreased. Overall, there are a very few miRNAs that are kidney specific, and although significant differences were observed in the urinary excretion of certain miRNAs, they were not correlative to their levels in the blood or plasma. Thus, it is completely plausible that urine-specific miRNAs could serve as novel biomarkers for the diagnosis of early stages of diabetic nephropathy., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Background: Sepsis, a common deadly systemic infection caused by a variety of pathogens, has some clinical symptoms similar to the systemic inflammatory response syndrome (SIRS), a whole-body non-infectious inflammatory reaction to severe insults, such as burn, trauma, hypotensive shock and so on. Treatment of sepsis depends mainly on anti-microbial, while remedy for SIRS might require steroids that could possibly enhance the spread of microbes. Unfortunately, it is very difficult to distinguish these two completely different serious conditions without blood culture, which takes days to grow and identify causative pathogens. We examined a biomarker, serum decoy receptor 3 (DcR3), was evaluated for its utility in the differential diagnosis between sepsis and SIRS., Methods: Serum DcR3 level in 118 healthy controls, 24 sepsis patients and 43 SIRS patients, was quantitatively measured by enzyme-linked immunosorbent assay (ELISA)., Results: The serum DcR3 was significantly increased in sepsis patients compared with SIRS patients and healthy controls (6.11±2.58 ng/ml vs 2.62±1.46 ng/ml, and 0.91±0.56 ng/ml, respectively, p<0.001). The areas under the receiver operating characteristic curve of DcR3 for the normal vs. SIRS, normal vs. sepsis and SIRS vs. sepsis were 0.910 (0.870-0.950), 0.992 (0.984-1.000) and 0.896 (0.820-0.973), respectively. In addition, the DcR3 exhibited a positive correlation coefficient with APACHE II score, a most commonly used index for the severity of sepsis (r=0.556, p=0.005)., Conclusion: The serum DcR3 has a potential to serve as a new biomarker for sepsis with its high specificity and sensitivity., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Peritoneal fibrosis is a common complication of long-term peritoneal dialysis, and contributes to encapsulating peritoneal sclerosis and eventually peritoneal ultrafiltration failure, which restricts the wide application of peritoneal dialysis. Therefore, the prevention and treatment of peritoneal fibrosis is important to maintain peritoneal membrane integrity and prolong peritoneal dialysis treatment. Unfortunately, neither specific biomarkers nor effective therapies are available for peritoneal fibrosis in the clinic up to now. Emerging evidence suggests that extracellular microRNAs in body fluids are promising biomarkers for the diagnosis of diseases. microRNAs were reported to be involved in multiple fibrotic diseases and the serum levels of specific microRNAs were correlated with the degree of fibrosis. Moreover, extracellular microRNAs were found in peritoneal fluids and ascites. Based on these findings, here we present our hypothesis that extracellular microRNAs associated with peritoneal epithelial-to-mesenchymal transition and fibrosis could potentially be detected in peritoneal dialysis effluent, and serve as novel biomarkers for early assessment and diagnosis of peritoneal fibrosis., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Background: Biomarkers for neurodegenerative diseases are essential to facilitate disease diagnosis. Application of proteomics has greatly hastened the search for novel biomarkers. In this study, new potential biomarkers were discovered, and a diagnostic pattern was established for idiopathic Parkinson's disease (PD) by using proteomic technology., Methods: Serum proteins from PD patients and controls were captured by magnetic bead-based weak cation exchange. The molecular weight of the proteins in bead-binding fraction was detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Biomarker Wizard 3.1 and Biomarker Patterns Software were used for data analysis and constructing a model of biomarkers. A blinded testing set was used to validate the model., Results: A total of 17 discriminating m/z peaks related to PD were identified. The model based on the 5 biomarkers generated an excellent separation between PD and healthy controls with 98.36% for the sensitivity and 83.05% for the specificity. Blind test data demonstrated the model could recognize patients with PD with a sensitivity of 85.0% and a specificity of 70.0%., Conclusions: The preliminary data suggested a potential application of MALDI-TOF-MS combined with magnetic beads. The model comprising 5 promising biomarkers can differentiate individuals with PD and the healthy subjects precisely., (Copyright © 2011 S. Karger AG, Basel.)

Aim: To study the potential value and specificity of plasma miR-216a as a marker for pancreatic injury., Methods: Two rat models were applied in this article: L-arginine-induced acute pancreatitis was used as one model to explore the potential value of plasma miR-216a for detection of pancreatic injury; nonlethal sepsis induced in rats by single puncture cecal ligation and puncture (CLP) was used as the other model to evaluate the specificity of plasma miR-216a compared with two commonly used markers (amylase and lipase) for acute pancreatitis. Plasmas were sampled from rats at indicated time points and total RNA was isolated. Real-Time Quantitative reverse transcriptase-polymerase chain reaction was used to quantify miR-216a in plasmas., Results: In the acute pancreatitis model, among five time points at which plasmas were sampled, miR-216a concentrations were significantly elevated 24 h after arginine administration and remained significantly increased until 48 h after operation (compared with 0 h time point, P < 0.01, Kruskal-Wallis Test). In the CLP model, plasma amylase and lipase, two commonly used biomarkers for acute pancreatitis, were significantly elevated 24 h after operation (compared with 0 h time point, P < 0.01 and 0.05 respectively, Pairwise Bonferroni corrected t-tests), while miR-216a remained undetectable among four tested time points., Conclusion: Our article showed for the first time that plasma miR-216a might serve as a candidate marker of pancreatic injury with novel specificity.

Abstract The advent of immunotherapy, a groundbreaking advancement in cancer treatment, has given rise to the prominence of the tumor microenvironment (TME) as a critical area of research. The clinical implications of an improved understanding of the TME are significant and far-reaching. Radiomics has been increasingly utilized in the comprehensive assessment of the TME and cancer prognosis. Similarly, the advancement of pathomics, which is based on pathological images, can offer additional insights into the panoramic view and microscopic information of tumors. The combination of pathomics and radiomics has revolutionized the concept of a “digital biopsy”. As genomics and transcriptomics continue to evolve, integrating radiomics with genomic and transcriptomic datasets can offer further insights into tumor and microenvironment heterogeneity and establish correlations with biological significance. Therefore, the synergistic analysis of digital image features (radiomics, pathomics) and genetic phenotypes (genomics) can comprehensively decode and characterize the heterogeneity of the TME as well as predict cancer prognosis. This review presents a comprehensive summary of the research on important radiomics biomarkers for predicting the TME, emphasizing the interplay between radiomics, genomics, transcriptomics, and pathomics, as well as the application of multiomics in decoding the TME and predicting cancer prognosis. Finally, we discuss the challenges and opportunities in multiomics research. In conclusion, this review highlights the crucial role of radiomics and multiomics associations in the assessment of the TME and cancer prognosis. The combined analysis of radiomics, pathomics, genomics, and transcriptomics is a promising research direction with substantial research significance and value for comprehensive TME evaluation and cancer prognosis assessment.

Abstract Background Bowen's disease is a cutaneous squamous cell carcinoma (CSCC) in situ. If left untreated, BD may progress to invasive CSCC. CSCC is one of the most common cutaneous carcinoma in the elderly and the advanced, metastasis CSCC usually have a poor outcomes. However, the mechanisms of invasion and metastasis from Bowen’s disease to CSCC is complicated and still unclear. Objectives The aim of this study was to explore the biomarkers and molecular alterations in Bowen’s disease development process via analyzing the proteomics changes in tissues of CSCC, Bowen disease and healthy skin. Methods A total of 7 individuals with CSCC (5 for proteomics study and 2 for validation), 7 individuals with Bowen disease (5 for proteomics study and 2 for validation) and 7 healthy controls (5 for proteomics study and 2 for validation) presented to the Department of Dermatology, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College between January 2021 and December 2021 were enrolled. The proteomics analysis was performed to screen differentially expressed proteins/gens (DEPs/DEGs) in the lesions of CSCC, Bowen disease and healthy skin tissues. The transcriptomic data (GSE32628) of CSCC was selected and downloaded from the GEO database. The common DEGs in our proteomics results and GSE32628 between CSCC and healthy skin tissues were selected. And then, the common DEGs which significantly up or down-regulated between CSCC and Bowen disease in our proteomics results were further screened to identify using Western blot methods in the validation group. CSCC A431 cells were transfected with SERPINB1 small interfering RNA (si-SERPINB1) or small interfering RNA negative control (si-NC). To explore the effect of SERPINB1 silencing on migration and invasion ability of A431 cells. Results A total of 501 proteins were differentially expressed between the CSCC and healthy skin tissues, with 332 up-regulated and 169 down-regulated at least 1.5-fold with a P value

Kidney dysfunction is particularly important in systemic organ injuries caused by aging. Metabolomics are utilized in this study to explore the mechanism of kidney dysfunction during aging by the identification of metabolites and the characterization of metabolic pathways. We analyzed the serum biochemistry and kidney histopathology of male Kunming mice aged 3 months and 24 months and found that the aged mice had inflammatory lesions, aggravated fibrosis, and functional impairment. A high-resolution untargeted metabolomics analysis revealed that the endogenous metabolites in the kidneys and urine of the mice were significantly changed by 25 and 20 metabolites, respectively. A pathway analysis of these differential metabolites revealed six key signaling pathways, namely, D-glutamine and D-glutamate metabolism, purine metabolism, the citrate cycle [tricarboxylic acid (TCA) cycle], histidine metabolism, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism. These pathways are involved in amino acid metabolism, carbohydrate metabolism, and nucleotide metabolism, and these can lead to immune regulation, inflammatory responses, oxidative stress damage, cellular dysfunction, and bioenergy disorders, and they are closely associated with aging and kidney insufficiency. We also screened nine types of sensitive metabolites in the urine as potential biomarkers of kidney dysfunction during the aging process to confirm their therapeutic targets in senior-induced kidney dysfunction and to improve the level of risk assessment for senile kidney injury.

Abstract Background Plakophilins (PKPs) are widely involved in gene transcription, translation, and signal transduction, playing a crucial role in tumorigenesis and progression. However, the function and potential mechanism of PKP1/2/3 in ovarian cancer (OC) remains unclear. It’s of great value to explore the expression and prognostic values of PKP1/2/3 and their potential mechanisms, immune infiltration in OC. Methods The expression levels, prognostic values and genetic variations of PKP1/2/3 in OC were explored by various bioinformatics tools and databases, and PKP2/3 were selected for further analyzing their regulation network and immune infiltration. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) enrichment were also conducted. Finally, the expression and prognosis of PKP2 were validated by immunohistochemistry. Results The expression level and prognosis of PKP1 showed little significance in ovarian cancer, and the expression of PKP2/3 mRNA and protein were upregulated in OC, showing significant correlations with poor prognosis of OC. Functional enrichment analysis showed that PKP2/3 and their correlated genes were significantly enriched in adaptive immune response, cytokine receptor activity, organization of cell–cell junction and extracellular matrix; KEGG analysis showed that PKP2/3 and their significantly correlated genes were involved in signaling pathways including cytokine-mediated signaling pathway, receptor signaling pathway and pathways in cancer. Moreover, PKP2/3 were correlated with lymphocytes and immunomodulators. We confirmed that high expression of PKP2 was significantly associated with advanced stage, poor differentiation and poor prognosis of OC patients. Conclusion Members of plakophilins family showed various degrees of abnormal expressions and prognostic values in ovarian cancer. PKP2/3 played crucial roles in tumorigenesis, aggressiveness, malignant biological behavior and immune infiltration of OC, and can be regarded as potential biomarker for early diagnosis and prognosis evaluation in OC.

Abstract Background Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberrant levels of circulating small non-coding RNAs (small ncRNAs) are potential diagnostic or prognostic markers for lung cancer. We aimed to identify plasma small ncRNA pairs that could be used for early screening and detection of lung adenocarcinoma (LAC). Results A panel of seven small ncRNA pair ratios could differentiate patients with LAC or benign lung disease from high-risk controls with an area under the curve (AUC) of 100.0%, a sensitivity of 100.0% and a specificity of 100.0% at the training stage (which included 50 patients with early-stage LAC, 35 patients with benign diseases and 29 high-risk controls) and an AUC of 90.2%, a sensitivity of 91.5% and a specificity of 80.4% at the validation stage (which included 44 patients with early-stage LAC, 32 patients with benign diseases and 51 high-risk controls). The same panel could distinguish LAC from high-risk controls with an AUC of 100.0%, a sensitivity of 100.0% and a specificity of 100.0% at the training stage and an AUC of 89.5%, a sensitivity of 85.4% and a specificity of 83.3% at the validation stage. Another panel of five small ncRNA pair ratios (different from the first) was able to differentiate LAC from benign disease with an AUC of 82.0%, a sensitivity of 81.1% and a specificity of 78.1% in the training cohort and an AUC of 74.2%, a sensitivity of 70.4% and a specificity of 72.7% in the validation cohort. Conclusions Several small ncRNA pair ratios were identified as markers capable of discerning patients with LAC from those with benign lesions or high-risk control individuals.

Background: Expression levels of transmembrane protein 41A (TMEM41A) are related to the progression of malignant tumors. However, the association between TMEM41A expression and endometrial carcinoma (EC) remains unclear. This study aims to identify the roles of TMEM41A expression in the prognosis of patients with EC and its correlation with EC progression. Methods: The TMEM41A expression and its correlation with the survival of patients with EC were assessed. Cox regression analysis was used to identify the prognostic factors, while nomograms were used to examine the association between the prognostic factors and the survival of patients with EC. Finally, the link between TMEM41A level and immune microenvironment and RNA modifications was investigated in EC. Results: TMEM41A was overexpressed in EC. TMEM41A overexpression could diagnose the EC and evaluate the poor prognosis of patients. Overexpression of TMEM41A was associated with clinical stage, age, weight, histological subtype, tumor grade, and survival status of patients with EC. Clinical stage, age, tumor grade, radiotherapy, and TMEM41A overexpression were factors of poor prognosis in patients with EC. The nomograms revealed the correlation between the TMEM41A level and survival time of patients with EC at 1, 3, and 5 years. Furthermore, TMEM41A overexpression was significantly correlated with the level of the stromal score, immune score, estimate score, NK CD56 bright cells, iDC, NK cells, eosinophils, pDC, T cells, TReg, cytotoxic cells, mast cells, Th17 cells, neutrophils, aDC, NK CD56 dim cells, TFH, Th2 cells, CD8 T cells, macrophages, immune cell markers, and RNA modifications. Conclusions: TMEM41A is overexpressed in EC tissues and is associated with the prognosis, immune microenvironment, and RNA modification. Our preliminary studies indicate that overexpression of TMEM41A can potentially serve as a biomarker for EC treatment. [ABSTRACT FROM AUTHOR]

Metabolomics has been reported as an efficient tool to screen biomarkers that are related to esophageal cancer. However, the metabolic biomarkers identifying malignant degrees and therapeutic efficacy are still largely unknown in the disease. Here, GC-MS-based metabolomics was used to understand metabolic alteration in 137 serum specimens from patients with esophageal cancer, which is approximately two- to fivefold as many plasma specimens as the previous reports. The elevated amino acid metabolism is in sharp contrast to the reduced carbohydrate as a characteristic feature of esophageal cancer. Comparative metabolomics showed that most metabolic differences were determined between the early stage (0-II) and the late stage (III and IV) among the 0-IV stages of esophageal cancer and between patients who received treatment and those who did not receive treatment. Glycine, serine, and threonine metabolism and glycine were identified as the potentially overlapped metabolic pathway and metabolite, respectively, in both disease progress and treatment effect. Glycine, fructose, ornithine, and threonine can be a potential array for the evaluation of disease prognosis and therapy in esophageal cancer. These results highlight the means of identifying previously unknown biomarkers related to esophageal cancer by a metabolomics approach. [ABSTRACT FROM AUTHOR]

The identification of ante- and post-mortem burns is challenging in forensic pathology. In this study, microarray analysis was used to detect the mRNA expression profiles in the skin of an experimental burn mouse model; the results were validated using RT-qPCR. Differentially expressed mRNAs (DE-mRNAs) were assessed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our results revealed that mRNA expression of 501 genes was significantly different, of which 273 were upregulated and 228 were downregulated in ante-mortem burned mice skin. The expression levels of eight random mRNAs were consistent when measured using the microarray assay-based method and RT-qPCR. Genes from different functional categories and signalling pathways were enriched, including interleukin-20 binding, type IV hypersensitivity, negative regulation of acute inflammatory response, sensory organ development, endocytosis, neuroactive ligand-receptor interaction, and Jak-STAT signalling pathway. Only five of the eight mRNAs exhibited consistent changes in expression between burned skin samples of mice and human autopsy specimens. Our findings showed that DE-mRNAs revealed using microarray are potential biomarkers of ante-mortem burns. However, DE-mRNAs identified from experimental animal models cannot be directly extended to autopsy specimens without careful validation. [ABSTRACT FROM AUTHOR]

Objective: Multi-modal functional magnetic resonance imaging (fMRI) can be used to make predictions about individual behavioral and cognitive traits based on brain connectivity networks. Methods: To take advantage of complementary information from multi-modal fMRI, we propose an interpretable multi-modal graph convolutional network (MGCN) model, incorporating both fMRI time series and functional connectivity (FC) between each pair of brain regions. Specifically, our model learns a graph embedding from individual brain networks derived from multi-modal data. A manifold-based regularization term is enforced to consider the relationships of subjects both within and between modalities. Furthermore, we propose the gradient-weighted regression activation mapping (Grad-RAM) and the edge mask learning to interpret the model, which is then used to identify significant cognition-related biomarkers. Results: We validate our MGCN model on the Philadelphia Neurodevelopmental Cohort to predict individual wide range achievement test (WRAT) score. Our model obtains superior predictive performance over GCN with a single modality and other competing approaches. The identified biomarkers are cross-validated from different approaches. Conclusion and Significance: This paper develops a new interpretable graph deep learning framework for cognition prediction, with the potential to overcome the limitations of several current data-fusion models. The results demonstrate the power of MGCN in analyzing multi-modal fMRI and discovering significant biomarkers for human brain studies. [ABSTRACT FROM AUTHOR]

Non-small-cell lung cancer (NSCLC) is one of the most devastating diseases worldwide. The study is aimed at identifying reliable prognostic biomarkers and to improve understanding of cancer initiation and progression mechanisms. RNA-Seq data were downloaded from The Cancer Genome Atlas (TCGA) database. Subsequently, comprehensive bioinformatics analysis incorporating gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and the protein-protein interaction (PPI) network was conducted to identify differentially expressed genes (DEGs) closely associated with NSCLC. Eight hub genes were screened out using Molecular Complex Detection (MCODE) and cytoHubba. The prognostic and diagnostic values of the hub genes were further confirmed by survival analysis and receiver operating characteristic (ROC) curve analysis. Hub genes were validated by other datasets, such as the Oncomine, Human Protein Atlas, and cBioPortal databases. Ultimately, logistic regression analysis was conducted to evaluate the diagnostic potential of the two identified biomarkers. Screening removed 1,411 DEGs, including 1,362 upregulated and 49 downregulated genes. Pathway enrichment analysis of the DEGs examined the Ras signaling pathway, alcoholism, and other factors. Ultimately, eight prioritized genes (GNGT1, GNG4, NMU, GCG, TAC1, GAST, GCGR1, and NPSR1) were identified as hub genes. High hub gene expression was significantly associated with worse overall survival in patients with NSCLC. The ROC curves showed that these hub genes had diagnostic value. The mRNA expressions of GNGT1 and NMU were low in the Oncomine database. Their protein expressions and genetic alterations were also revealed. Finally, logistic regression analysis indicated that combining the two biomarkers substantially improved the ability to discriminate NSCLC. GNGT1 and NMU identified in the current study may empower further discovery of the molecular mechanisms underlying NSCLC's initiation and progression. [ABSTRACT FROM AUTHOR]

Adipose-derived stem cells (ADSCs) have been documented as possible candidates for skin rejuvenation. However, the effects of ADSC-derived exosomes on photoaged skin remain to be fully elucidated. This study was aimed at determining the antiaging effects of ADSC-derived exosomes on photoaged skin. Human ADSCs were isolated from the adipose tissue of healthy women and cultured in vitro. Then, exosomes were extracted from the cultured ADSCs, purified by ultracentrifugation, and verified by examination of cell morphology using transmission electron microscopy and the identification of specific biomarkers. Meanwhile, the optimal exosome concentration and treatment time were selected. The photoaged skin model was created by subjecting Sprague-Dawley rats to ultraviolet B radiation. Exosomes were injected into the photoaged skin in a single therapeutic dose. The thickness of the epidermis and dermis was observed by HE staining. The relative mRNA expression of type I collagen, type III collagen, and matrix metalloproteinases (MMP-1 and MMP-3) was determined by real-time PCR. In the rat model of photoaged skin, the injected exosomes markedly decreased the epidermal thickness and increased the dermal thickness of the photoaged skin 7 days after treatment. Moreover, the proportion of the stratum corneum of the epidermis was decreased. Furthermore, real-time RT-PCR showed that the mRNA expression of type I collagen was increased and that of type III collagen, MMP-1, and MMP-3 was decreased. Our results demonstrate that ADSC-derived exosome treatment could significantly improve skin photodamage and that ADSC-derived exosomes may be a potential agent for photoaged skin treatment. [ABSTRACT FROM AUTHOR]

Bipolar disorder (BD) is a common and debilitating mental disorder. Bipolar depression is the main episode of BD. Furthermore, there are no objective biomarkers available for diagnosing the disorder. In this research, a Nuclear Magnetic Resonance (NMR) spectroscopy based on a metabonomics technique was used to analyze serum samples from 37 patients with bipolar depression and 48 healthy control participants to determine potential biomarkers for bipolar depression. In total, seven different metabolites were identified that could effectively distinguish patients from healthy controls. The metabolites indicated that disturbances of amino acid and energy metabolisms might be involved in the pathogenesis of BD. Finally, a panel consisting of four potential biomarkers (lactate, trimethylamine oxide, N-acetyl glycoprotein, and α-glucose) was identified, which showed a higher combined diagnostic ability with an area under the curve of 0.893. Our findings may contribute to the development of an objective method for diagnosing bipolar depression. [ABSTRACT FROM AUTHOR]

Background Previous studies have demonstrated that microRNA-204 (miR-204) is involved in atherosclerosis and vascular calcification. However, the value of miR-204 as the predictive biomarker for cardiovascular disease (CVD) remains unclear. We aimed to evaluate the association between the circulating miR-204 level and ten-year CVD risk based on the Framingham risk score (FRS). Methods In this retrospective study, we enrolled 194 consecutive patients with type 2 diabetes mellitus (T2DM) without CVD in Beijing Anzhen Hospital between January 2015 and September 2016. We used the FRS to evaluate the risk of CVD for each patient. Circulating miR-204 levels were measured by quantitative real-time polymerase chain reaction. Results Circulating miR-204 levels were significantly lower in the group of patients (0.49 ± 0.13) at high risk of CVD (FRS > 20%) than in the low (FRS < 10%) and intermediate (FRS: 10%-20%) risk groups (0.87 ± 0.19 and 0.75 ± 0.25, respectively; P < 0.001). FRS was negatively correlated with miR-204 levels (r = -0.421, P < 0.001). According to multivariate logistic analyses, reduced miR-204 level was independently associated with an increased risk of CVD after adjusting for conventional risk factors (OR = 0.876, 95% CI: 0.807-0.950, P = 0.001). Receiver-operating characteristic curve analysis showed that the circulating miR-204 level can predict the high risk of CVD with higher specificity than the traditional risk factor of high systolic blood pressure or the protective factor of high-density lipoprotein cholesterol. Conclusions Our study demonstrated that patients with lower circulating miR-204 levels were at high risk for CVD. After adjustment for potential confounders, miR-204 was independently associated with CVD in patients with T2DM. [ABSTRACT FROM AUTHOR]

Head and neck cancer is the sixth most common malignancy around the world, and 90% of cases are squamous cell carcinomas. In this study, we performed a systematic investigation of the immunogenomic landscape to identify prognostic biomarkers for head and neck squamous cell carcinoma (HNSCC). We analyzed the expression profiles of immune‐related genes (IRGs) and clinical characteristics by interrogating RNA-seq data from 527 HNSCC patients in the cancer genome atlas (TCGA) dataset, including 41 HPV+ and 486 HPV− samples. We found that differentially expressed immune genes were closely associated with patient prognosis in HNSCC by comparing the differences in gene expression between cancer and normal samples and performing survival analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the biological functions of the differentially expressed immunogenomic prognosis-related genes. Two additional cohorts from the Oncomine database were used for validation. 65, 56 differentially expressed IRGs was associated with clinical prognosis in total and HPV- samples, respectively. Furthermore, we extracted 10, 11 prognosis-related IRGs from 65, 56 differentially expressed IRGs, respectively. They were significantly correlated with clinical prognosis and used to construct the prognosis prediction models. The multivariable ROC curves (specifically, the AUC) were used to measure the accuracy of the prognostic models. These genes were mainly enriched in several gene ontology (GO) terms related to immunocyte migration and receptor and ligand activity. KEGG pathway analysis revealed enrichment of pathways related to cytokine−cytokine receptor interactions, which are primarily involved in biological processes. In addition, we identified 63 differentially expressed transcription factors (TFs) from 4784 differentially expressed genes, and 16 edges involving 18 nodes were formed in the regulatory network between differentially expressed TFs and the high-risk survival-associated IRGs. B cell and CD4 T cell infiltration levels were significantly negatively correlated with the expression of prognosis-related immune genes regardless of HPV status. In conclusion, this comprehensive analysis identified the prognostic IRGs as potential biomarkers, and the model generated in this study may enable an accurate prediction of survival. [ABSTRACT FROM AUTHOR]

Background: Junction plakoglobin (JUP) is an important cell-cell junction protein. Recently, its deregulation has been correlated with the initiation and progression of various malignancies. Our aim was to investigate the expression of JUP in oral squamous cell carcinoma (OSCC) and its correlation with prognosis and to further study the effects of JUP on the proliferation, apoptosis, migration and invasion of OSCC cells.Methods: We detected JUP expression in 273 OSCC specimens using immunohistochemistry. We assessed the correlation of JUP expression with clinicopathologic parameters and patient survival by Cox regression. Then, expression levels of JUP in normal oral keratinocytes (NOKs) and OSCC cell lines were detected by Western blotting and quantitative real-time PCR (qPCR). Next, we used HSC3 cells to study the effect of JUP on tumor cell proliferation, apoptosis, migration, and invasion by using cell counting kit-8, flow cytometry, and transwell assays, respectively.Results: Cox regression showed that high expression of JUP was related to the poor prognosis of OSCC patients. Western blotting and qPCR assays showed that the expression level of JUP in OSCC cell lines was higher than that in NOKs. Overexpression of JUP promoted the proliferation, metastasis, and invasion of HSC3 cells and inhibited apoptosis, while the opposite was observed after JUP knockdown.Conclusion: This study initially revealed that JUP was overexpressed in OSCC, and that JUP promoted the proliferation, migration, and invasion of OSCC cells and inhibited apoptosis. Moreover, high expression of JUP could be used as a potential prognostic marker of OSCC. [ABSTRACT FROM AUTHOR]

Maternal one-carbon metabolism during pregnancy is crucial for fetal development and programming by DNA methylation. However, evidence on one-carbon biomarkers other than folate is lacking. We, therefore, investigated whether maternal plasma methyl donors, that is, choline, betaine and methionine, are associated with birth outcomes. Blood samples were obtained from 115 women during gestation (median 26·3 weeks, 90 % range 22·7–33·0 weeks). Plasma choline, betaine, methionine and dimethylglycine were measured using HPLC-tandem MS. Multivariate linear and logistic regression models were used to estimate the association between plasma biomarkers and birth weight, birth length, the risk of small-for-gestational-age and large-for-gestational-age (LGA). Higher level of maternal betaine was associated with lower birth weight (–130·3 (95 % CI –244·8, –15·9) per 1 sd increment for log-transformed betaine). Higher maternal methionine was associated with lower risk of LGA, and adjusted OR, with 95 % CI for 1 sd increase in methionine concentration was 0·44 (95 % CI 0·21, 0·89). Stratified analyses according to infant sex or maternal plasma homocysteine status showed that reduction in birth weight in relation to maternal betaine was only limited to male infants or to who had higher maternal homocysteine status (≥5·1 µmol/l). Higher maternal betaine status was associated with reduced birth weight. Maternal methionine was inversely associated with LGA risk. These findings are needed to be replicated in future larger studies. [ABSTRACT FROM AUTHOR]

Background: Long non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Yet, their mechanisms in coronary artery disease (CAD) are not well understood. Methods: The expression profile of genes associated to CAD was reannotated into the lncRNA-mRNA biphasic profile. The target microRNA data were used to design a global CAD triple network. Thereafter, we conducted a functional enrichment analysis and clustering using the triple network from the level of topology analyses. The expression of four non-coding RNAs (ncRNAs) was measured by qRT-PCR and the risk of CAD was calculated by nomogram. The prognostic value of three ncRNAs was evaluated using receiver operating characteristic (ROC) curve. Results: A CAD lncRNA-miRNA-mRNA network was constructed which included 15 mRNAs, 3 miRNAs, 19 edges and one lncRNA. Nomogram showed that four ncRNAs were the risk of CAD. After RT-PCR validation in four ncRNAs between CAD and non-CAD samples, only three ncRNAs had significant meaning for further analysis. ROC curve showed that TWF1 presented an area under curve (AUC) of 0.862, the AUC of hsa -miR-142-3p was 0.856 and hsa -miR126-5p was 0.822. After the pairwise comparison, we found that TWF1 had significant statistical significance (PTWF1–142 < 0.05 and PTWF1–126 < 0.01). The results of functional enrichment analysis of interacting gene and microRNA showed that the shared lncRNA TWF1 may be a new factor for CAD. Conclusions: This investigation on the regulatory networks of lncRNA-miRNA-mRNA in CAD suggests that a novel lncRNA, lncRNA TWF1 is a risk factor for CAD, and expands our understanding into the mechanisms involved in the pathogenesis of CAD. [ABSTRACT FROM AUTHOR]

Objective. This study aims to reveal the regulation network of lncRNAs-miRNAs-mRNA in endometrial carcinoma (EC), to investigate the underlying mechanisms of EC occurrence and progression, to screen prognostic biomarkers. Methods. RNA-seq and miRNA-seq data of endometrial carcinoma were downloaded from the TCGA database. Edge.R package was used to screen differentially expressed genes. A database was searched to determine differentially expressed lncRNA-miRNA and miRNA-mRNA pairs, to construct the topological network of ceRNA, and to elucidate the key RNAs that are for a prognosis of survival. Results. We screened out 2632 mRNAs, 1178 lncRNAs and 189 miRNAs that were differentially expressed. The constructed ceRNA network included 97 lncRNAs, 20 miRNAs and 73 mRNAs. Analyzing network genes for associations with prognosies revealed 169 prognosis-associated RNAs, including 92 lncRNAs, 16miRNAs and 61 mRNAs. Conclusion. Our results reveal new potential mechanisms underlying the carcinogenesis and progression of endometrial carcinoma. [ABSTRACT FROM AUTHOR]

Manglietia patungensis Hu is an endangered plant native to China. Knowledge of its genetic diversity and structure would aid its conservation. This study assessed nine natural populations of M . patungensis using two methods: inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Using 10 ISSR primer pairs, 334 bands were generated, and 10 SRAP primer pairs generated 276 bands. The percent of polymorphic bands (91.32% and 93.48%), Nei's genetic diversity (0.3448 and 0.3323), and Shannon's information index (0.5075 and 0.4935) revealed a high level of genetic diversity at the species level. Total heterozygosity was 0.3439 by ISSR and 0.3281 by SRAP. The mean heterozygosity was 0.2323 by ISSR and 0.2521 by SRAP. The coefficient of genetic differentiation among natural populations was 0.3245 by ISSR and 0.2316 by SRAP. These data indicated higher levels of genetic diversity of M . patungensis within, rather than among, populations. Estimates of gene flow among natural populations were 1.0411 and 1.0589, which implied a certain amount of gene exchange among populations. A Mantel test revealed no significant correlation between genetic and geographic distance. ISSR and SRAP markers are both effective for genetic diversity research in M. Patungensis . Based on these results, conservation of M . patungensis should be performed both in situ and ex situ. [ABSTRACT FROM AUTHOR]

Background information During embryonic development, cell death transforms the solid embryonic cell mass into a hollow structure (cavitation), which allows the surviving cells to differentiate into varied tissues and organs around the cavity. This process can be partly reproduced with embryonic stem cells. However, it is unknown if adult stem cell masses have the same ability to cavitate and then differentiate into organs. In this study, we assessed the capacity of human dental pulp stem cells (DPSCs)-derived spheroids to mimic the above-mentioned cavitation and spontaneous differentiation in vitro. Results DPSCs were able to form large-sized spheroids on matrigel in osteogenic medium. Inside the spheroids, cells in the centre showed positive stain to stem cell markers, alkaline phosphatase and STRO-1. Hypoxia and massive cell death were observed in the core of the spheroids. Cavities were formed when the spheroids were cultivated in the osteogenic medium for about 14 days. After 28 days of cultivation, the surviving cells around the cavity spontaneously differentiated into neuronal (28.8%), vascular (33.3%), osteogenic (46.7%) and cartilaginous (72.0%) tissues under the osteogenic medium only. In contrast, when DPSCs-formed cell sheets were folded into giant-sized lumps and cultivated under the same conditions, the folded cell sheets became an entire lumenal structure and failed to differentiate into neuronal, osteogenic and cartilaginous cells. Marker analysis showed that cavitation-related molecules BMP7 and FGF3 expressed on the wall of the cavity in the spheroids, suggesting that the cavitation was functional, whereas cavitation-related molecules were absent in the folded cell sheets. Conclusions DPSC-derived spheroids can mimic the developmental process of cell survival, cavitation and spontaneous multi-differentiation on matrigel under certain conditions. This work allows for functional studies to investigate organ regeneration with human DPSCs in vitro. [ABSTRACT FROM AUTHOR]

Background: Several prospective cohort and case-control studies reported the inconsistent association between biospecimen composition of C20 and C22 long-chain (LC) n-3 polyunsaturated fatty acid (PUFA) and colorectal cancer (CRC) risk. The aim of the present study was to investigate the association of biospecimen LC n-3 PUFA with CRC risk based on prospective cohort and case-control studies. Methods and Results: Cochrane Library, PubMed, and EMBASE database were searched up to February 2014 for eligible studies. Risk ratios (RRs) or odds ratios (ORs) from prospective and case-control studies were combined using a random-effects model in the highest vs. lowest categorical analysis. Nonlinear dose-response relationships were assessed using restricted cubic spline regression models. Difference in tissue composition of LC n-3 PUFA between cases and noncases was analyzed as standardized mean difference (SMD). Three prospective cohort studies and 8 case-control studies were included in the present study, comprising 60,627 participants (1,499 CRC cases and 59,128 noncases). Higher biospecimen LC n-3 PUFA was significantly associated with a lower risk of CRC in case-control (pooled OR: 0.76; 95% CI: 0.59, 0.97; I2 = 10.00%) and prospective cohort studies (pooled RR: 0.70; 95% CI: 0.55, 0.88; I2 = 0.00%), respectively. A significant dose-response association was found of biospecimen C20:5n-3 (P for nonlinearity  = 0.02) and C22:6n-3 (P for trend  = 0.01) with CRC risk, respectively. Subjects without CRC have significantly higher biospecimen compositions of C20:5n-3 (SMD: 0.27; 95%: 0.13, 0.41), C22:6n-3 (SMD: 0.23; 95%: 0.11, 0.34) and total LC n-3 PUFA (SMD: 0.22; 95% CI: 0.07, 0.37) compared with those with CRC. Conclusions: The present evidence suggests human tissue compositions of LC n-3 PUFA may be an independent predictive factor for CRC risk, especially C20:5n-3 and C22:6n-3. This needs to be confirmed with more large-scale prospective cohort studies. [ABSTRACT FROM AUTHOR]

Background: Alzheimer-associated neuronal thread protein (AD7c-NTP) has been reported to have high diagnostic accuracy in patients with Alzheimer's disease (AD). Objective: To determine the diagnostic accuracy of urinary AD7c-NTP for the diagnosis of AD in patients with suspected AD. Methods: We searched MEDLINE (January 1950 to date) and other electronic databases (from inception to date) for diagnostic accuracy studies that compared urinary AD7c-NTP to the standard clinical diagnosis of AD. We conducted citation searches and screened the reference lists of included studies. Studies were assessed for methodological quality using QUADAS. Summary receiver operating characteristic curves were used to summarize overall test performance. Result: Nine studies met our inclusion criteria. The summary estimates of the urinary AD7c-NTP assay for probable or possible AD were as follows: SEN, 0.87 (95%CI: 0.80-0.91); SPE, 0.89 (95%CI: 0.87-0.91); PLR, 8.13 (95% CI: 6.60-10.02); and NLR, 0.15 (95% CI: 0.10-0.22). The four summary estimates of urinary AD7c-NTP assay for probable AD were 0.89 (95% CI: 0.86-0.92), 0.90 (95% CI: 0.88-0.92), 8.88 (95% CI: 7.09-11.12), and 0.12 (95% CI: 0.09-0.16), with no obvious heterogeneity. Conclusion: Urinary AD7c-NTP is a sensitive and specific test for the diagnosis of probable AD. However, whether urinary AD7c-NTP can be used as an early marker is still unknown. [ABSTRACT FROM AUTHOR]

Background: Primary small cell carcinoma of the esophagus (SCCE) is a highly aggressive disease characterized by early dissemination and poor prognosis. Because of the rarity of this disease, few previous studies have investigated the biomarkers associated with its prognosis. Leucine-rich repeat-containing G-protein coupled receptor 5 (Lgr5) is a stem cell marker and a member of the canonical Wnt-signaling cascade. However, the clinical role of Lgr5 in SCCE remains unknown. Methods: Tissue sections were obtained from 44 patients diagnosed with SCCE and expression of Lgr5 was examined by immunohistochemistry. The correlations between Lgr5 expression, and clinical parameters and prognostic significance were evaluated. Results: Lgr5 was expressed in SCCE cancer tissues. High Lgr5 expression was significantly correlated with lymph node metastasis (p = 0.003), late stage (p = 0.003) and unfavorable response to chemotherapy (p = 0.013) according to RECIST 1.0 criteria. Patients with higher Lgr5 expression levels had shorter overall survival times than those with lower expression levels. Conclusions: These results demonstrated that overexpression of Lgr5 was significantly correlated with lymph node metastasis, tumor stage, and response to chemotherapy. Furthermore, high levels of Lgr5 expression appeared to be associated with poorer survival in patients with SCCE. [ABSTRACT FROM AUTHOR]

Serum glial fibrillary acidic protein (GFAP) has been reported to have high diagnosis accuracy for differentiating intracerebral hemorrhage (ICH) from ischemic stroke (IS) in patients within acute phase of stroke symptom onset. Our purpose was to perform a systematic review and diagnostic meta-analysis to evaluate the valuation of serum GFAP in the early identification of ICH and IS. We searched MEDLINE, EMBASE and other electronic databases for diagnostic accuracy studies that compared serum GFAP with standard clinical diagnosis of ICH and IS in patients with symptoms of acute stroke. All publication years were included through to April 2013. The sensitivity (SEN), specificity (SPE), and positive and negative likelihood ratios (PLR and NLR, respectively) of serum GFAP for differentiating ICH and IS were pooled using a bivariate meta-analysis. Summary receiver operating characteristic curves were used to summarize overall test performance. A total of five trials met our inclusion criteria. The summarized estimates of serum GFAP for the differentiation of ICH and IS within 24 h of symptom onset were as follows: SEN, 81.1 % (95 % CI, 72.6–87.5 %); SPE, 95.2 % (95 % CI 82.1–98.9 %); PLR, 16.945 (95 % CI 4.173–68.803); NLR, 0.198 (95 % CI 0.133–0.296), significant heterogeneity was present. The four summary estimates of serum GFAP for patients within 1–6 h of symptom onset were 81.1 % (95 % CI 72.5–88.0 %), 97.0 % (95 % CI 94.3–98.4 %), 26.786 (95 % CI 13.979–51.324), 0.191 (95 % CI 0.126–0.291), respectively, with no obvious heterogeneity. Serum GFAP is a sensitive and specific test for differentiating ICH and IS in patients within 1–6 h of acute stroke symptom onset. [ABSTRACT FROM AUTHOR]

Abstract: Alkane-degrading bacteria are crucial in the bioremediation of petroleum contamination from soil and groundwater. The alkane monooxygenase (alkB) gene encoding the Alk enzyme involved in aerobic degradation is a potentially functional gene biomarker for the detection of alkane-degrading bacteria. This study describes a denaturing gradient gel electrophoresis (DGGE) assay to facilitate the rapid and sensitive detection of alkB genes in wastewater from oilfield. The results showed that the presence of a considerable genetic diversity of alkB genes in the wastewater as evidenced by a total of 13 unique DNA bands detected. These alkB genes belong to nine genera, including Acinetobacter, Alcanivorax, Acidisphaera, Burkholderia, Geobacillus, Marinobacter, Mycobacterium, Pseudomonas, Rhodococcus and Xanthobacter. The abundance of alkane-degrading bacteria and total bacteria was calculated to range from 1.46 × 103 to 9.89 × 104 cell ml−1 and from 1.18 × 104 to 6.29 × 105 cells ml−1, respectively. The distribution of alkane-degrading bacteria was positively correlated with the environmental temperature and the specific types of n-alkanes in the wastewaters. Our results suggest that alkB-based DGGE methods could describe the diverse alkane-degrading bacteria in oil-degrading community, which may improve the understanding of the treatment for oil-polluted wastewater. [Copyright &y& Elsevier]

International Journal of Paediatric Dentistry 2012; 22: 363-368 Background. Effective caries control and management requires identification of susceptible children for timely intervention. Streptococcus mutans ( S. mutans) is an important biomarker of caries risk. Aim. This study aimed to comparatively evaluate the validities of a novel immunoassay and a conventional culture-based assay in detecting salivary S. mutans in a paediatric cohort. Methods. 190 children aged 3-4 years were recruited. The abundance of S. mutans in their saliva samples was analysed with three assay systems viz. a conventional culture-based assay (Dentocult SM), a novel immunoassay system (Saliva-Check MUTANS) based on monoclonal antibody technology and a Taqman real-time PCR assay taken as a gold standard. Results. The novel immunoassay accurately differentiated saliva samples with high (≥5 × 105 CFU/mL) and low (<5 × 105 CFU/mL) S. mutans levels. The sensitivity/specificity was 97.6%/90.6%. The conventional culture-based assay reached a reasonably high sensitivity/specificity (92.8%/81.3%) in identifying children with moderate (≥104 CFU/mL) S. mutans level. Its sensitivity/ specificity in selecting children with high (≥105 CFU/mL) and very high (>106 CFU/mL) S. mutans levels were not sufficient (78.7%/79.8% and 25.8%/91.8%, respectively). Conclusion. The monoclonal antibody-based immunoassay accurately and rapidly determines S. mutans abundance in saliva and could be useful for chairside assessment of children's caries risk. [ABSTRACT FROM AUTHOR]

The snow alga Chlamydomonas nivalis is a model species of microalgae for the investigation of cell response mechanism and adaptation ability in natural habitats in polar regions and similar extreme environments. The alteration of fatty acids in cellular lipids is known to play a vital role for cell survival and reproduction under various stress conditions. In the present work, an integrated approach of gas chromatography/mass spectrometry (GC/MS) coupled with multivariate statistical analysis was developed to investigate the fatty acid profiles and identify the biomarkers in response to NaCl stress. The data of fatty acid profiles between the control and NaCl-stress group was classified by orthogonal projection on latent structure discriminant analysis (OPLS-DA) and hierarchical cluster analysis (HCA); six of fatty acids (C16:0, C16:3, C18:0, C18:1, C18:2, and C18:3) were identified as biomarkers. These biomarkers showed a regulatory role by decreasing the degree of lipid unsaturation (DLU), providing an expected function in reducing membrane fluidity and permeability for enhancing the tolerance to higher salinity. This is the first report to demonstrate the fatty acid biomarkers in microalgae as the physiological regulators corresponding to the response and adaptation to NaCl stress based on an integrated approach at the lipidomic level. [ABSTRACT FROM AUTHOR]

Mutations in isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) have been shown to be present in most World Health Organization grade 2 and grade 3 gliomas in adults. These mutations are associated with the accumulation of 2-hydroxyglutarate (2HG) in the tumor. Here we report the noninvasive detection of 2HG by proton magnetic resonance spectroscopy (MRS). We developed and optimized the pulse sequence with numerical and phantom analyses for 2HG detection, and we estimated the concentrations of 2HG using spectral fitting in the tumors of 30 subjects. Detection of 2HG correlated with mutations in IDH1 or IDH2 and with increased levels of D-2HG by mass spectrometry of the resected tumors. Noninvasive detection of 2HG may prove to be a valuable diagnostic and prognostic biomarker. [ABSTRACT FROM AUTHOR]

Abstract: Neopicrorhiza scrophulariiflora Pennel (Hong) (Scrophulariaceae) is an endangered medicinal plant, endemic to the Eastern Himalayas and the Hengduan Mountains. Levels of genetic variation and genetic structure of seven populations of N. scrophulariiflora in China were studied using inter-simple sequence repeat (ISSR) markers. Thirteen primers amplified 82 total loci from 7 populations composed of 136 individuals. All 82 loci were polymorphic, showing a percentage of polymorphic bands (PPB) of 100%, indicating considerable genetic variation at the species level. In contrast, a low level of genetic diversity within populations was detected with a mean PPB of 30.56%. In addition, Nei’s genetic diversity analysis (0.4073) and Shannon’s diversity index (0.5917) revealed similar genetic structure. High levels of genetic differentiation (Gst = 0.6955) and restricted gene flow (Nm = 0.2198) among populations were also detected. Anthropologic impacts, together with clonal propagation, genetic drift and geographical isolation might be the reasons which had shaped the genetic structure of this species. [Copyright &y& Elsevier]

Background: Biomarkers for neurodegenerative diseases are essential to facilitate disease diagnosis. Application of proteomics has greatly hastened the search for novel biomarkers. In this study, new potential biomarkers were discovered, and a diagnostic pattern was established for idiopathic Parkinson's disease (PD) by using proteomic technology. Methods: Serum proteins from PD patients and controls were captured by magnetic bead-based weak cation exchange. The molecular weight of the proteins in bead-binding fraction was detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Biomarker Wizard 3.1 and Biomarker Patterns Software were used for data analysis and constructing a model of biomarkers. A blinded testing set was used to validate the model. Results: A total of 17 discriminating m/z peaks related to PD were identified. The model based on the 5 biomarkers generated an excellent separation between PD and healthy controls with 98.36% for the sensitivity and 83.05% for the specificity. Blind test data demonstrated the model could recognize patients with PD with a sensitivity of 85.0% and a specificity of 70.0%. Conclusions: The preliminary data suggested a potential application of MALDI-TOF-MS combined with magnetic beads. The model comprising 5 promising biomarkers can differentiate individuals with PD and the healthy subjects precisely. Copyright © 2011 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Background: Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tumor profiles challenge current machine learning methodologies for its small number of samples and large or even huge number of variables (genes). This naturally calls for the use of an effective feature selection in microarray data classification. Methods: We propose a novel feature selection method: multi-resolution independent component analysis (MICA) for large-scale gene expression data. This method overcomes the weak points of the widely used transform-based feature selection methods such as principal component analysis (PCA), independent component analysis (ICA), and nonnegative matrix factorization (NMF) by avoiding their global feature-selection mechanism. In addition to demonstrating the effectiveness of the multi-resolution independent component analysis in meaningful biomarker discovery, we present a multi-resolution independent component analysis based support vector machines (MICASVM) and linear discriminant analysis (MICA-LDA) to attain high-performance classifications in low-dimensional spaces. Results: We have demonstrated the superiority and stability of our algorithms by performing comprehensive experimental comparisons with nine state-of-the-art algorithms on six high-dimensional heterogeneous profiles under cross validations. Our classification algorithms, especially, MICA-SVM, not only accomplish clinical or near-clinical level sensitivities and specificities, but also show strong performance stability over its peers in classification. Software that implements the major algorithm and data sets on which this paper focuses are freely available at https://sites.google.com/site/heyaumapbc2011/. Conclusions: This work suggests a new direction to accelerate microarray technologies into a clinical routine through building a high-performance classifier to attain clinical-level sensitivities and specificities by treating an input profile as a 'profile-biomarker'. The multi-resolution data analysis based redundant global feature suppressing and effective local feature extraction also have a positive impact on large scale 'omics' data mining. [ABSTRACT FROM AUTHOR]