Luteolin Inhibits Lung Cancer Cell Migration by Negatively Regulating TWIST1 and MMP2 Through Upregulation of miR-106a-5p.

BACKGROUND: Luteolin, a common dietary flavonoid found in plants, has been shown to have anti-cancer properties. However, its exact mechanisms of action in non-small cell lung cancer (NSCLC) are still not fully understood, particularly its role in regulating broader genomic networks and specific gene targets. In this study, we aimed to elucidate the role of microRNAs (miRNAs) in NSCLC treated with luteolin, using A549 cells as a model system. MATERIALS AND METHODS: miRNA profiling was conducted on luteolin-treated A549 cells using Exiqon microarrays, with validation of selected miRNAs by qRT-PCR. Bioinformatic analysis identified the regulatory roles of miRNAs in biological processes and pathways following luteolin treatment. Computational algorithms were employed to identify potential target genes. A549 cells were transfected with miR-106a-5p mimic and inhibitor or their corresponding controls. The expression levels of 2 genes, twist basic helix-loop-helix transcription factor 1 (TWIST1) and matrix metallopeptidase 2 (MMP2), and cell migration were assessed. RESULTS: miRNA profiling identified 341 miRNAs, with 18 exhibiting significantly altered expression (P < 0.05). Subsequent qRT-PCR analysis confirmed altered expression of 6 selected miRNAs. KEGG and GO analyses revealed significant alterations in pathways and biological processes crucial for tumor biology. TWIST1 and MMP2, which both contain conserved miR-106a-5p binding sites, exhibited an inverse correlation with the expression levels of miR-106a-5p. Dual-luciferase reporter assays confirmed TWIST1 and MMP2 as direct targets of miR-106a-5p. Luteolin treatment led to a reduction in A549 cell migration, and this reduction was further amplified by the overexpression of miR-106a-5p. CONCLUSION: Luteolin inhibits A549 cell migration by modulating the miRNA landscape, shedding light on its mechanisms and laying the foundation for miRNA-based therapeutic approaches for NSCLC.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data.

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data.

OBJECTIVE: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins.

Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.

Genome-wide analyses based on a novel donkey 40K liquid chip reveal the gene responsible for coat color diversity in Chinese Dezhou donkey.

Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome-wide association analysis was performed for the differences in coat color traits between the Sanfen (n = 97) and Wutou (n = 108) strains using a novel donkey 40K liquid chip developed based on GenoBaits technology, to identify genomic regions and causal genes that could explain this variation. We also used FST and The cross-population composite likelihood ratio test (XPCLR) analyses to explore selected regions related to coat color differences. We identified one significant region on chromosome 15, with the most significant SNP located within the agouti signaling protein (ASIP) gene. At the same time, both FST and XPCLR methods detected the same selected region on chromosome 15, and ASIP was the gene with the strongest signal. ASIP and melanocortin 1 receptor (MC1R) control the ratio of eumelanin to pheomelanin through their protein activity. They are deeply involved in the process of melanosome organation and melanogenesis, thus affecting mammals' coat color variation. We used a range of genome-wide approach to identify the genetic basis of coat color variation in Dezhou donkeys. The results provide a supplement to the color variation study in Chinese donkeys at the genome-wide level, and preliminarily verified the reliability of the Molbreeding Donkey No. 1 40K liquid chip.

Dynamic processes of mindfulness-based alterations in pain perception.

Mindfulness-based processes have been shown to enhance attention and related behavioral responses, including analgesia, which is discussed as an effective method in the context of pain interventions. In the present review, we introduce the construct of mindfulness, delineating the concepts, factors, and processes that are summarized under this term and might serve as relevant components of the underlying mechanistic pathways in the field of pain. We also discuss how differences in factors such as definitions of mindfulness, study design, and strategies in mindfulness-based attention direction may need to be considered when putting the findings from previous studies into a whole framework. In doing so, we capitalize on a potential dynamic process model of mindfulness-based analgesia. In this respect, the so-called mindfulness-based analgesia may initially result from improved cognitive regulation strategies, while at later stages of effects may be driven by a reduction of interference between both cognitive and affective factors. With increasing mindfulness practice, pathways and mechanisms of mindfulness analgesia may change dynamically, which could result from adaptive coping. This is underlined by the fact that the neural mechanism of mindfulness analgesia is manifested as increased activation in the ACC and aINS at the beginner level while increased activation in the pINS and reduced activation in the lPFC at the expert level.

A novel model based on necroptosis to assess progression for polycystic ovary syndrome and identification of potential therapeutic drugs.

Background: Polycystic ovary syndrome (PCOS), a common endocrine and reproductive disorder, lacks precise diagnostic strategies. Necroptosis was found to be crucial in reproductive and endocrine disorders, but its function in PCOS remains unclear. We aimed to identify differentially diagnostic genes for necroptosis (NDDGs), construct a diagnostic model to assess the progression of PCOS and explore the potential therapeutic drugs. Methods: Gene expression datasets were combined with weighted gene co-expression network analysis (WGCNA) and necroptosis gene sets to screen the differentially expressed genes for PCOS. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct a necroptosis-related gene signatures. Independent risk analyses were performed using nomograms. Pathway enrichment of NDDGs was conducted with the GeneMANIA database and gene set enrichment analysis (GSEA). Immune microenvironment analysis was estimated based on ssGSEA algorithm analysis. The Comparative Toxicogenomics Database (CTD) was used to explore potential therapeutic drugs for NDDGs. The expression of NDDGs was validated in GSE84958, mouse model and clinical samples. Results: Four necroptosis-related signature genes, IL33, TNFSF10, BCL2 and PYGM, were identified to define necroptosis for PCOS. The areas under curve (AUC) of receiver operating characteristic curve (ROC) for training set and validation in diagnostic risk model were 0.940 and 0.788, respectively. Enrichment analysis showed that NDDGs were enriched in immune-related signaling pathways such as B cells, T cells, and natural killer cells. Immune microenvironment analysis revealed that NDDGs were significantly correlated with 13 markedly different immune cells. A nomogram was constructed based on features that would benefit patients clinically. Several compounds, such as resveratrol, tretinoin, quercetin, curcumin, etc., were mined as therapeutic drugs for PCOS. The expression of the NDDGs in the validated set, animal model and clinical samples was consistent with the results of the training sets. Conclusion: In this study, 4 NDDGs were identified to be highly effective in assessing the progression and prognosis of PCOS and exploring potential targets for PCOS treatment.

Elemental and spectral chemometric analyses of Octopus vulgaris beaks as reliable markers of capture location.

The high demand and economic relevance of cephalopods make them prone to food fraud, including related to harvest location. Therefore, there is a growing need to develop tools to unequivocally confirm their capture location. Cephalopod beaks are nonedible, making this material ideal for traceability studies as it can also be removed without a loss of commodity economic value. Within this context, common octopus (Octopus vulgaris) specimens were captured in five fishing areas along the Portuguese coast. Untargeted multi-elemental total X-ray fluorescence analysis of the octopus beaks revealed a high abundance of Ca, Cl, K, Na, S, and P, concomitant with the keratin and calcium phosphate nature of the material. We tested a suite of discrimination models on both elemental and spectral data, where the elements contributing most to discriminate capture location were typically associated with diet (As), human-related pressures (Zn, Se, and Mn), or geological features (P, S, Mn, and Zn). Among the six different chemometrics approaches used to classify individuals to their capture location according to their beaks' element concentration, classification trees attained a classification accuracy of 76.7%, whilst reducing the number of explanatory variables for sample classification and highlighting variable importance for group discrimination. However, using X-ray spectral features of the octopus beaks further improved classification accuracy, with the highest classification of 87.3% found with partial least-squares discriminant analysis. Ultimately, element and spectral analyses of nonedible structures such as octopus beaks can provide an important, complementary, and easily accessible means to support seafood provenance and traceability, whilst integrating anthropogenic and/or geological gradients.

Radiochemical signature of radium-isotopes and some radiological hazard parameters in TENORM waste associated with petroleum production: A review study.

Large amounts of TENORM waste (produced water, scale, and sludge) are created in oilfields around the world, presenting radiological risks to employees, the public, and the environment since activity concentrations of radioactive substances were above the exemption levels accredited by several authorities. Using the activity concentration of the radium-isotopes (226Ra and 228Ra) in the waste, we determined the 'fingerprint' as a radiochemical signature and some relevant 'radiological hazard parameters' in this review. The majority of the reported residues take the form of radio-contaminated (produced water, scale, and sludge) generated in Egypt's oilfields or elsewhere include radium isotope activity concentrations (226,228Ra) that exceed the international exemption limit. The activity concentrations of 226Ra(238U-series) in produced water, scale, and sludge waste were 0.04-1,480 Bq/L, 1.1-2,015,000 Bq/kg, and 1-120,800 Bq/kg, respectively, whereas 228Ra (232Th-series) was 0.34-250 Bq/L, 1.8-1,428,000 Bq/kg, and 10-122,830 Bq/kg, respectively. The radioactivities of radium isotopes were found to be above the exemption values recognized by WHO, IAEA, IOGP, EC, and ICRP in 95, 82, and 58% of produced water, scale, and sludge waste, respectively. The 226Ra(238U)/228Ra(232Th) ratio, from the other hand, was estimated to be utilised as a 'radiochemical fingerprint', or signature in the reported TENORM residues. The radium isotopes ratio in produced water, scale, and sludge waste in Egypt's oilfields is 0.41-4.45 (av. 1.98 ± 1.37, coefficient of variation, COV %: ∼69%), 0.2-21.4 (av. 4.3 ± 4.7, ∼109%), and 1.4-52.2 (av. 9.6 ± 15.3, ∼159%), respectively. For produced water, scale, and sludge waste, the 226Ra/228Ra ratios are 0.12-9.1 (av. 1.43 ± 1.72, ∼120%), 0.2-159 (av. 7.78 ± 23.5, ∼302%), and 0.8-223.5 (av. 14.1 ± 45.4, ∼322%) in global oilfields. The radiological hazard parameters (Ig, Ia, E◦, EG, and ELCR) owing to radium isotopes or 222Rn in most scale and sludge residues, as well as a small percentage of produced water, are all over the allowed safe limits. Substantial differences in the radium isotopes ratio in the reported waste can be attributed to thier geological, chemical, physical, and/or operational constraints. However, from the different perspectives of remediation and/or radiation protection programs, these values can be employed as a guidance for organizations investing in oil and gas production.

Tongue diagnostic parameters-based diagnostic signature in coronary artery disease patients with clopidogrel resistance after percutaneous coronary intervention.

BACKGROUND: Credible diagnostic stratification remains a challenge for coronary artery disease patients with clopidogrel resistance after percutaneous coronary intervention. Tongue diagnostic parameters-based diagnostic signatures might predict clopidogrel resistance. METHODS: Clinical and tongue diagnostic parameters data were obtained from coronary artery disease patients with clopidogrel resistance after percutaneous coronary intervention patients and then analyzed. Tongue diagnostic parameters-based diagnostic signatures were developed through univariate and multivariate logistic regression analysis. The diagnostic prediction was assessed using a receiver operating characteristic curve. RESULTS: A total of 101 patients were consecutively identified. Then, tongue diagnostic parameters were identified as significantly associated with clopidogrel resistance diagnosis and were combined with risk factors to develop a model. The receiver operating characteristic curve analysis showed that tongue diagnostic parameters-based diagnostic signatures performed well in diagnosing clopidogrel resistance with an area under the receiver operating characteristic curve value of 0.819. CONCLUSIONS: This study identified a novel tongue diagnostic parameters-based diagnostic signature to reliably distinguish clopidogrel resistance diagnosis in coronary artery disease patients undergoing percutaneous coronary intervention. Further larger, multicenter prospective studies are desired to validate this model.

Nardosinone and aurantio-obtusin, two medicine food homology natural compounds, are anti-influenza agents as indicated by transcriptome signature reversion.

BACKGROUND: Medicine food homology (MFH) refers to food that can be used as medicine, and compounds isolated from MFH materials are valuable in novel drug discovery due to their good safety. Transcriptome signature reversion (TSR) is an attractive method for discovering drugs through transcriptional reverse matching; namely, the changes in transcriptional signatures induced by compounds are matched to a certain disease. This strategy can be used to discover anti-influenza agents among MFH natural compounds. PURPOSE: MFH natural compounds with anti-influenza activities were identified through analyses of the reversal in the expression of multiple informative genes followed by in vitro evaluation of the cytopathic effect (CPE) caused by influenza infection and relative quantification of the nucleoprotein (NP) gene in viral RNA (vRNA). The combined effect of active compounds was determined through network-based separation score prediction followed by quantification of the viral hemagglutinin (HA) level. METHODS: The transcriptome profiles of 4 lung or airway cell lines infected with 7 influenza virus strains were analyzed by robust rank aggregation (RRA) to identify informative genes in the signature of influenza virus infection. The identified informative genes were then matched to a transcriptomic profile library of MFH natural compounds. The anti-influenza activities of MFH natural compounds with negative enrichment scores (ESs) were evaluated in vitro using a CPE assay and relative quantification of the NP gene in the vRNA in the supernatant and cytoplasm to identify anti-influenza agents. The effects of combinations of active compounds were analyzed using network-based calculations followed by confirmation through bioassays for quantifying the viral HA levels. RESULTS: Among the 159 MFH natural compounds, 54 compounds had negative ESs, as determined through TSR, and the anti-influenza activities of nardosinone and aurantio-obtusin were confirmed by bioassays. The half-maximal effective concentrations (EC50) of nardosinone and aurantio-obtusin were 4.3-84.4 µM and 31.9-113.6 µM, respectively. The separation score between the informative genes with expression that was negatively regulated by nardosinone and aurantio-obtusin in the human protein-protein interaction (PPI) network was calculated to be 0.10, which indicated that the two compounds potentially exert a synergistic effect, and this effect was confirmed by the finding that the combination indexes (CIs) were calculated to equal 0.86 at inhibition level of 50% and 0.44 at inhibition level of 90%. CONCLUSION: The TSR analysis and in vitro evaluation identified nardosinone and aurantio-obtusin as anti-influenza agents. Their antiviral activities were exerted by reversing the expression of multiple informative genes of the host cells. The separation analysis between the informative genes that were reversely regulated by nardosinone and aurantio-obtusin indicated that their combination may exert a synergistic effect, which was confirmed in vitro.

Deciphering hepatocellular carcinoma pathogenesis and therapeutics: a study on anoikis, ceRNA regulatory network and traditional Chinese medicine.

Introduction: Hepatocellular carcinoma (HCC) is responsible for approximately 90% of liver malignancies and is the third most common cause of cancer-related mortality worldwide. However, the role of anoikis, a programmed cell death mechanism crucial for maintaining tissue equilibrium, is not yet fully understood in the context of HCC. Methods: Our study aimed to investigate the expression of 10 anoikis-related genes (ARGs) in HCC, including BIRC5, SFN, UBE2C, SPP1, E2F1, etc., and their significance in the disease. Results: Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we discovered that these ARGs are involved in important processes such as tissue homeostasis, ion transport, cell cycle regulation, and viral infection pathways. Furthermore, we found a significant correlation between the prognostic value of five ARGs and immune cell infiltrates. Analysis of clinical datasets revealed a strong association between BIRC5 expression and HCC pathological progression, including pathological stage, T stage, overall survival (OS), and race. By constructing a competing endogenous RNA (ceRNA) network and using molecular docking, we identified ten bioactive compounds from traditional Chinese medicine (TCM) that could potentially modulate BIRC5. Subsequent in vitro experiments confirmed the influence of platycodin D, one of the identified compounds, on key elements within the ceRNA network. Discussion: In conclusion, our study presents a novel framework for an anoikis-centered prognostic model and an immune-involved ceRNA network in HCC, revealing potential regulatory targets. These insights contribute to our understanding of HCC pathology and may lead to improved therapeutic interventions.

Systematic transcriptome analysis reveals molecular mechanisms and indications of bupleuri radix.

Pharmacogenomic analysis based on drug transcriptomic signatures is widely used to identify mechanisms of action and pharmacological indications. Despite accumulating reports on the efficacy of medicinal herbs, related transcriptome-level analyses are lacking. The aim of the present study was to elucidate the underlying molecular mechanisms of action of Bupleuri Radix (BR), a widely used herbal medicine, through a systematic transcriptomic analysis. We analyzed the drug-responsive transcriptome profiling of A549 lung cancer cell line after treating them with multiple doses of BR water (W-BR) and ethanol (E-BR) extracts and their phytochemicals. In vitro validation experiments were performed using both A549 and the immortalized human keratinocyte line HaCaT. Pathway enrichment analysis revealed the anti-cancer effects of BR treatment via inhibition of cell proliferation and induction of apoptosis. Enhanced cell adhesion and migration were observed with the W-BR but not with the E-BR. Comparison with a disease signature database validated an indication of the W-BR for skin disorders. Moreover, W-BR treatment showed the wound-healing effect in skin and lung cells. The main active ingredients of BR showed only the anti-cancer effect of the E-BR and not the wound healing effect of the W-BR, suggesting the need for research on minor ingredients of BR.

Comprehensive bioinformatics analysis to identify a novel cuproptosis-related prognostic signature and its ceRNA regulatory axis and candidate traditional Chinese medicine active ingredients in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is the most ordinary histological subtype of lung cancer, and regulatory cell death is an attractive target for cancer therapy. Recent reports suggested that cuproptosis is a novel copper-dependent modulated form of cell death dependent on mitochondrial respiration. However, the role of cuproptosis-related genes (CRGs) in the LUAD process is unclear. In the current study, we found that DLD, LIAS, PDHB, DLAT and LIPA1 in 10 differentially expressed CRGs were central genes. GO and KEGG enrichment results showed that these 10 CRGs were mainly enriched in acetyl-CoA biosynthetic process, mitochondrial matrix, citrate cycle (TCA cycle) and pyruvate metabolism. Furthermore, we constructed a prognostic gene signature model based on the six prognostic CRGs, which demonstrated good predictive potential. Excitedly, we found that these six prognostic CRGs were significantly associated with most immune cell types, with DLD being the most significant (19 types). Significant correlations were noted between some prognostic CRGs and tumor mutation burden and microsatellite instability. Clinical correlation analysis showed that DLD was related to the pathological stage, T stage, and M stage of patients with LUAD. Lastly, we constructed the lncRNA UCA1/miR-1-3p/DLD axis that may play a key role in the progression of LUAD and screened nine active components of traditional Chinese medicine (TCM) that may regulate DLD. Further, in vitro cell experiments and molecular docking were used to verify this. In conclusion, we analyzed the potential value of CRGs in the progression of LUAD, constructed the potential regulatory axis of ceRNA, and obtained the targeted regulatory TCM active ingredients through comprehensive bioinformatics combined with experimental validation strategies. This work not only provides new insights into the treatment of LUAD but also includes a basis for the development of new immunotherapy drugs that target cuproptosis.

ReDisX, a machine learning approach, rationalizes rheumatoid arthritis and coronary artery disease patients uniquely upon identifying subpopulation differentiation markers from their genomic data.

Diseases originate at the molecular-genetic layer, manifest through altered biochemical homeostasis, and develop symptoms later. Hence, symptomatic diagnosis is inadequate to explain the underlying molecular-genetic abnormality and individual genomic disparities. The current trends include molecular-genetic information relying on algorithms to recognize the disease subtypes through gene expressions. Despite their disposition toward disease-specific heterogeneity and cross-disease homogeneity, a gap still exists in describing the extent of homogeneity within the heterogeneous subpopulation of different diseases. They are limited to obtaining the holistic sense of the whole genome-based diagnosis resulting in inaccurate diagnosis and subsequent management. Addressing those ambiguities, our proposed framework, ReDisX, introduces a unique classification system for the patients based on their genomic signatures. In this study, it is a scalable machine learning algorithm deployed to re-categorize the patients with rheumatoid arthritis and coronary artery disease. It reveals heterogeneous subpopulations within a disease and homogenous subpopulations across different diseases. Besides, it identifies granzyme B (GZMB) as a subpopulation-differentiation marker that plausibly serves as a prominent indicator for GZMB-targeted drug repurposing. The ReDisX framework offers a novel strategy to redefine disease diagnosis through characterizing personalized genomic signatures. It may rejuvenate the landscape of precision and personalized diagnosis and a clue to drug repurposing.

A prognostic six-gene expression risk-score derived from proteomic profiling of the metastatic colorectal cancer secretome.

The necessity to accurately predict recurrence and clinical outcome in early stage colorectal cancer (CRC) is critical to identify those patients who may benefit from adjuvant chemotherapy. Here, we developed and validated a gene-based risk-score algorithm for patient stratification and personalised treatment in early stage disease based on alterations in the secretion of metastasis-related proteins. A quantitative label-free proteomic analysis of the secretome of highly and poorly metastatic CRC cell lines with different genetic backgrounds revealed 153 differentially secreted proteins (fold-change >5). These changes in the secretome were validated at the transcriptomic level. Starting from 119 up-regulated proteins, a six-gene/protein-based prognostic signature composed of IGFBP3, CD109, LTBP1, PSAP, BMP1, and NPC2 was identified after sequential discovery, training, and validation in four different cohorts. This signature was used to develop a risk-score algorithm, named SEC6, for patient stratification. SEC6 risk-score components showed higher expression in the poor prognosis CRC subtypes: consensus molecular subtype 4 (CMS4), CRIS-B, and stem-like. High expression of the signature was also associated with patients showing dMMR, CIMP+ status, and BRAF mutations. In addition, the SEC6 signature was associated with lower overall survival, progression-free interval, and disease-specific survival in stage II and III patients. SEC6-based risk stratification indicated that 5-FU treatment was beneficial for low-risk patients, whereas only aggressive treatments (FOLFOX and FOLFIRI) provided benefits to high-risk patients in stages II and III. In summary, this novel risk-score demonstrates the value of the secretome compartment as a reliable source for the retrieval of biomarkers with high prognostic and chemotherapy-predictive capacity, providing a potential new tool for tailoring decision-making in patient care.

Identification of Pinelliae Rhizoma and its counterfeit species based on enzymatic signature peptides from toxic proteins.

BACKGROUND: Pinelliae Rhizoma (PR), a toxic medication, with long history, is commonly used for eliminating phlegm. Due to the shortage of wild resources and the relative lacking of cultivation technology, it is often confused with its counterfeit species in the market, such as Typhonii Rhizoma (TR), Arisaematis Rhizoma (AR) and tubers of Typhonium flagelliforme (TF) and Pinellia pedatisecta (PP). PURPOSE: It was aimed to screen signature enzymatic peptides from toxic proteins to identify PR and its four counterfeit species. STUDY DESIGN: A comparative proteogenomics strategy based on open-source transcriptome data was applied for screening signature peptides from toxic proteins, which were applied for species authentication of PR and its counterfeit species. METHODS: Firstly, the open-source transcriptome data was used for constructing the annotated protein database, which was used for peptides identification. Secondly, the toxicity of different fractions of PR were evaluated by the rat peritoneal inflammation model. Furthermore, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to profile the main proteins bands of five species, whose sequences were identified based on the in-gel digestion experiment by using ultra-high-performance liquid chromatography/quadrupole-Orbitrap mass spectrometry. Finally, the label-free proteomic analysis was performed to character the proteins and screen the signature peptides of five species, which were validated in commercially available products by dynamic multi reaction monitor (DMRM). RESULTS: The results in this study confirmed that protein was the main toxic components of PR. Both Pinellia ternata agglutinin (PTA) and trypsin inhibitor (TI) like proteins are the main proteins, which were characterized by proteomic analysis based on four annotated protein database. Meanwhile, seven signature peptides from toxic proteins were screened and validated with good repeatability and specificity in commercial products. CONCLUSION: Seven signature enzymatic peptides from toxic protein screened by the comparative proteogenomics strategy based on open-source transcriptome data achieved good identification ability of PR and its four counterfeit species.

Integrative transcriptional characterization of cell cycle checkpoint genes promotes clinical management and precision medicine in bladder carcinoma.

Background: The aberrant regulation of cell cycle is significantly correlated with cancer carcinogenesis and progression, in which cell cycle checkpoints control phase transitions, cell cycle entry, progression, and exit. However, the integrative role of cell cycle checkpoint-related genes (CRGs) in bladder carcinoma (BC) remains unknown. Methods: The transcriptomic data and clinical features of BC patients were downloaded from The Cancer Genome Atlas (TCGA), used to identify CRGs correlated with overall survival (OS) by univariate Cox regression analysis. Then, the multivariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses further developed a prognostic CRG signature, which was validated in three external datasets retrieved from Gene Expression Omnibus (GEO). The receiver operating characteristic curve (ROC) analysis was conducted for evaluating the performance of the CRG signature in prognosis prediction. RNA sequencing (RNA-Seq) was performed to explore the expression difference in the identified CRGs between tumor and normal tissue samples from 11 BC patients in the local cohort. Ultimately, genomic profiles and tumor microenvironment (TME), and the Genomics of Drug Sensitivity in Cancer (GDSC) were investigated to guide precision treatment for BC patients with different CRG features. Results: The novel constructed 23-CRG prognostic signature could stratify BC patients into high-risk and low-risk groups with significantly different outcomes (median OS: 13.64 vs. 104.65 months). Notably, 19 CRGs were the first to be identified as being associated with BC progression. In three additional validation datasets (GSE13507, GSE31684, and GSE32548), higher CRG scores all indicated inferior survival, demonstrating the robust ability of the CRG signature in prognosis prediction. Moreover, the CRG signature as an independent prognostic factor had a robust and stable risk stratification for BC patients with different histological or clinical features. Then, a CRG signature-based nomogram with a better performance in prognostic prediction [concordance index (C-index): 0.76] was established. Functional enrichment analysis revealed that collagen-containing extracellular matrix (ECM), and ECM-related and MAPK signaling pathways were significantly associated with the signature. Further analysis showed that low-risk patients were characterized by particularly distinctive prevalence of FGFR3 (17.03% vs. 6.67%, p < 0.01) and POLE alterations (7.97% vs. 2.50%, p < 0.05), and enrichment of immune infiltrated cells (including CD8+ T cells, CD4+ naïve T cells, follicular helper T cells, Tregs, and myeloid dendritic cells). RNA-seq data in our local cohort supported the findings in the differentially expressed genes (DEGs) between tumor and normal tissue samples, and the difference in TME between high-risk and low-risk groups. Additionally, CRG signature score plus FGFR3 status divided BC patients into four molecular subtypes, with distinct prognosis, TME, and transcriptomic profiling of immune checkpoint genes. Of note, CRG signature score plus FGFR3 status could successfully distinguish BC patients who have a higher possibility of response to immunotherapy or chemotherapy drugs. Conclusions: The CRG signature is a potent prognostic model for BC patients, and in combination with FGFR3 alterations, it had more practical capacity in the prediction of chemotherapy and immunotherapy response, helping guide clinical decision-making.

Molecular signatures of organic particulates as tracers of emission sources.

Chemical signature of airborne particulates and deposition dusts is subject of study since decades. Usually, three complementary composition markers are investigated, namely, (i) specific organic compounds; (ii) concentration ratios between congeners, and (iii) percent distributions of homologs. Due to its intrinsic limits (e.g., variability depending on decomposition and gas/particle equilibrium), the identification of pollution sources based on molecular signatures results overall restricted to qualitative purposes. Nevertheless, chemical fingerprints allow drawing preliminary information, suitable for successfully approaching multivariate analysis and valuing the relative importance of sources. Here, the state-of-the-art is presented about the molecular fingerprints of non-polar aliphatic, polyaromatic (PAHs, nitro-PAHs), and polar (fatty acids, organic halides, polysaccharides) compounds in emissions. Special concern was addressed to alkenes and alkanes with carbon numbers ranging from 12 to 23 and ≥ 24, which displayed distinct relative abundances in petrol-derived spills and exhausts, emissions from microorganisms, high vegetation, and sediments. Long-chain alkanes associated with tobacco smoke were characterized by a peculiar iso/anteiso/normal homolog fingerprint and by n-hentriacontane percentages higher than elsewhere. Several concentration ratios of PAHs were identified as diagnostic of the type of emission, and the sources of uncertainty were elucidated. Despite extensive investigations conducted so far, the origin of uncommon molecular fingerprints, e.g., alkane/alkene relationships in deposition dusts and airborne particles, remains quite unclear. Polar organics resulted scarcely investigated for pollution apportioning purposes, though they looked as indicative of the nature of sources. Finally, the role of humans and living organisms as actual emitters of chemicals seems to need concern in the future.

A nucleotide signature for the identification of Pinelliae Rhizoma (Banxia) and its products.

BACKGROUND: Ensuring the authenticity of raw materials is a key step prior to producing Chinese patent medicines. Pinellia ternata (Thunb.) Breit. is the botanical origin of Pinelliae Rhizoma (Banxia), a traditional Chinese medicine used to treat cough, insomnia, nausea, inflammation, epilepsy, and so on. Unfortunately, authentic Pinelliae Rhizoma is often adulterated by morphologically indistinguishable plant material due to the insufficient regulatory procedures of processed medicinal plant products. Thus, it is important to develop a molecular assay based on species-specific nucleotide signatures and primers to efficiently distinguish authentic Pinelliae Rhizoma from its adulterants. METHODS AND RESULTS: The ITS2 region of 67 Pinelliae Rhizoma and its common adulterants were sequenced. Eight single nucleotide polymorphisms within a 28-43 bp stretch of ITS2 were used to develop six primer pairs to amplify these species-specific regions. We assayed 56 Pinelliae Rhizoma products sold on the Chinese market, including medicinal slices, powder and Chinese patent medicines, which revealed that about 66% of products were adulterated. The most common adulterants were Pinellia pedatisecta (found in 57% of the assayed products), Arisaema erubescens (9%), Typhonium giganteum (2%) and Typhonium flagelliforme (2%). CONCLUSIONS: A severe adulteration condition was revealed in the traditional medicine market. The species-specific nucleotide assays developed in this study can be applied to reliably identify Pinelliae Rhizoma and its adulterants, aiding in the authentication and quality control of processed products on the herbal market.