Complement Coagulation Cascade Research Articles

Identified a novel prognostic model of HCC basing on virus signature for guiding immunotherapy

Oncolytic viral immunotherapy is a cancer treatment that uses native or genetically modified viruses that selectively replicate and destroy tumor cells. In this study, we aimed to construct a virus-based prognostic model for risk assessment and prognosis prediction in patients with hepatocellular carcinoma (HCC) and determine the most appropriate virus as a candidate vector for oncolytic virus immunotherapy. Microbiome and RNA sequencing data and clinical information were obtained from The Cancer Genome Atlas, and viruses with prognostic value were identified (Deltabaculovirus, Sicinivirus, and Cytomegalovirus) to construct the prognostic model. Correlation analyses were performed to evaluate the predictive function of the viral signature. Bioinformatics analyses were conducted to explore the functional enrichment of viral expression in HCC. The risk score generated by this model could distinguish patients with different survival outcomes, have excellent reliability and accuracy, and could be used as an independent prognostic indicator. The high-risk score group showed significantly lower overall survival, and this trend was also observed in subgroups with different clinicopathological features. Furthermore, Deltabaculovirus positively correlated with amino acid metabolism, energy metabolism signaling pathways, peroxisomes, and complement coagulation cascades. In addition, Deltabaculovirus was significantly related to immune cell infiltration; therefore, patients with high Delta-baculovirus expression might respond better to HCC immunotherapy. Our study identified a promising predictive viral signature for assessing clinical prognosis and guiding immunotherapy in HCC. Deltabaculovirus might be a suitable viral vector for oncolytic virus immunotherapy.

Intranasal delivery of small extracellular vesicles reduces the progress of amyotrophic lateral sclerosis and the overactivation of complement-coagulation cascade and NF-ĸB signaling in SOD1G93A mice

Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by progressive motoneuron degeneration, and effective clinical treatments are lacking. In this study, we evaluated whether intranasal delivery of mesenchymal stem cell–derived small extracellular vesicles (sEVs) is a strategy for ALS therapy using SOD1G93A mice. In vivo tracing showed that intranasally-delivered sEVs entered the central nervous system and were extensively taken up by spinal neurons and some microglia. SOD1G93A mice that intranasally received sEV administration showed significant improvements in motor performances and survival time. After sEV administration, pathological changes, including spinal motoneuron death and synaptic denervation, axon demyelination, neuromuscular junction degeneration and electrophysiological defects, and mitochondrial vacuolization were remarkably alleviated. sEV administration attenuated the elevation of proinflammatory cytokines and glial responses. Proteomics and transcriptomics analysis revealed upregulation of the complement and coagulation cascade and NF-ĸB signaling pathway in SOD1G93A mouse spinal cords, which was significantly inhibited by sEV administration. The changes were further confirmed by detecting C1q and NF-ĸB expression using Western blots. In conclusion, intranasal administration of sEVs effectively delays the progression of ALS by inhibiting neuroinflammation and overactivation of the complement and coagulation cascades and NF-ĸB signaling pathway and is a potential option for ALS therapy.Graphical abstract

Exploring the “gene–metabolite” network of ischemic stroke with blood stasis and toxin syndrome by integrated transcriptomics and metabolomics strategy

A research model combining a disease and syndrome can provide new ideas for the treatment of ischemic stroke. In the field of traditional Chinese medicine, blood stasis and toxin (BST) syndrome is considered an important syndrome seen in patients with ischemic stroke (IS). However, the biological basis of IS-BST syndrome is currently not well understood. Therefore, this study aimed to explore the biological mechanism of IS-BST syndrome. This study is divided into two parts: (1) establishment of an animal model of ischemic stroke disease and an animal model of BST syndrome in ischemic stroke; (2) use of omics methods to identify differentially expressed genes and metabolites in the models. We used middle cerebral artery occlusion (MCAO) surgery to establish the disease model, and utilized carrageenan combined with active dry yeast and MCAO surgery to construct the IS-BST syndrome model. Next, we used transcriptomics and metabolomics methods to explore the differential genes and metabolites in the disease model and IS-BST syndrome model. It is found that the IS-BST syndrome model exhibited more prominent characteristics of IS disease and syndrome features. Both the disease model and the IS-BST syndrome model share some common biological processes, such as thrombus formation, inflammatory response, purine metabolism, sphingolipid metabolism, and so on. Results of the “gene–metabolite” network revealed that the IS-BST syndrome model exhibited more pronounced features of complement-coagulation cascade reactions and amino acid metabolism disorders. Additionally, the “F2 (thrombin)–NMDAR/glutamate” pathway was coupled with the formation process of the blood stasis and toxin syndrome. This study reveals the intricate mechanism of IS-BST syndrome, offering a successful model for investigating the combination of disease and syndrome.

Abstract 13568: Proteomic Analysis Reveals Protein Alterations in Drp1 Cardiac Knockout Mice With Circadian Rhythm Disruption

Introduction: Mitochondria dynamics are altered in circadian rhythm disruption, and dynamin-related protein 1 (Drp1) may be an important target. Methods: Wild-type and Drp1 cardiac-specific knockout mice were divided into normal circadian group and circadian disorder group, respectively. Normal circadian group mice were housed in a standard environment (12 hours of light/12 hours of darkness), while dark group mice were housed in a 24-hour dark environment. After 4 weeks, the cardiac tissues were analysed using Tandem Mass Tag proteomics. Differentially expressed proteins (DEPs) was identified. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Gene set enrichment analysis (GSEA) was performed to find enriched biological processes. Results: Compared with the WT/N group, the Drp1-/N group possessed a total of 176 DEPs. These proteins are widely involved in mitochondrial membrane and metabolism process. We identified several differentially expressed mitochondrial dynamics-related genes, including Drp1, using Western blotting. Compared with the WT/D group, the Drp1-/D group exhibited a total of 126 DEPs. GO and KEGG showed that the DEPs were mainly involved in response to stress, metabolic pathways. For Drp1 cKO mice, the protein changes caused by the circadian rhythm disorder were mainly concentrated in vitamin transport, complement coagulation cascades. Conclusions: This study may provide an insight into the myocardial protein changes caused by Drp1 cKO with circadian rhythm disruption, which may involve in terms such as metabolic pathways, complement coagulation, and vitamin transport.

Systematic investigation of the material basis, multiple mechanisms and quality control of Simiao Yong'an decoction combined with antibiotic in the treatment of sepsis

BackgroundSepsis is one of the major threats to human health with high mortality. Simiao Yong'an decoction (SMYAD) has the efficacy of anti-inflammation, improving coagulation and microcirculation, which is applicable for the clinical assistance treatment of sepsis. Yet, its material basis and relevant mechanisms are still vague. PurposeExplore the quality markers (Q-markers), biomarkers and potential mechanisms of SMYAD combined with imipenem/cilastatin sodium for anti-sepsis. MethodsLinear-Trap-LC/MSn was employed to profile the compounds in the extract and medicated serum of SMYAD. Then, the components and targets obtained from databases were applied to network pharmacology. Q-markers’ range was narrowed via the affinity of three times docking and determined as per its screening criteria. Also, the content of them was detected by HPLC. Next, cecal ligation and puncture (CLP) model was reproduced to observe the effect of SMYAD united antibiotic by survival rate, histopathology score, ELISA, western blot and qPCR. Finally, metabolomics based upon GC–MS was exerted to discover the differential endogenous metabolites, metabolic pathway and joint pathway of SMYAD combined with antibiotic for sepsis. ResultsThe 25 serum migrant ingredients derived from 113 chemical compounds of SMYAD were identified for the first time, and 6 components were determined as the Q-markers of SMYAD. The enrichment analysis indicated that the potential mechanism was mainly associated with the IL-17 signaling pathway, complement-coagulation cascades signaling pathway and VEGF signaling pathway. Then, SMYAD united antibiotic declined the mortality of septic rats, restored cytokine levels, ameliorated histopathological lesions and decreased the mRNA and protein expression of target proteins in a dose-dependent way. Furthermore, 8 differential metabolites were regarded as latent biomarkers related to the antiseptic effect of SMYAD united antibiotic, which were mainly involved in the Citrate cycle (TCA cycle) metabolic pathway. ConclusionsDifferent skeletons of compounds, including iridoids, phenylpropanoids, organic acids, triterpenes and others, were the main compositions of SMYAD. Among them, 6 components were determined as the Q-markers, which provided a basis for the construction of quality standards for this ancient classic formula. The combination therapy of SMYAD and antibiotic obviously ameliorated inflammatory reaction, coagulation dysfunction and microcirculation abnormalities for sepsis by inhibiting IL-17 signaling pathway, complement-coagulation cascades signaling pathway and VEGF signaling pathway.

Construction of lncRNA prognostic model related to cuproptosis in esophageal carcinoma.

Background: Esophageal carcinoma (ESCA) is one of the most prevalent malignant tumors in the world. The prognosis of patients has significantly improved with the development of surgery, targeted therapy and immunotherapy. But the 5-year survival rate of ESCA patients is still incredibly low. Cuproptosis is a type of mitochondrial cell death induced by copper. It is unclear how cuproptosis-related lncRNAs (CRLs) affect ESCA prognosis. Methods: In this study, we obtained the clinical data of ESCA patients, the transcriptome data from TCGA and identified CRLs by co-expression analysis, lasso regression, and cox regression analysis, to build a prognostic model. Then we validated the prognostic model using the Kaplan-Meier curve, cox regression analysis, and ROC, to create a nomogram based on risk score to forecast the prognosis of ESCA. Next, the immune escape of the CRLs was examined using the TIDE algorithm to assess its sensitivity to possible ESCA medications. Results: To predict the prognosis of ESCA patients, we created a predictive model using 6 CRLs (AC034199.1, AC125437.1, AC107032.2, CTBP1-DT, AL024508.1, and AC008610.1), validated by the Kaplan-Meier and ROC curves. The model has a higher diagnostic value compared to other clinical features. The 6 CRLs expressed high in TCGA and ESCA specimens. Enrichment analysis revealed CRLs largely contributed to the interaction between cytokines and their receptors as well as complement coagulation cascades. The immunity escape analysis demonstrated that immunotherapy had a worse effect in the low-risk group than in the high-risk group. Additionally, we screened out potential antineoplastic drugs according to the results of the immunoassay and obtained 5 drugs, including CP-466722, crizotinib, MS-275, KIN001-135, and CP-466722. Conclusion: The prognosis of patients with ESCA can be correctly predicted by the 6 CRLs chosen from this investigation. It lays the groundwork for more investigation into the ESCA mechanism and the identification of novel therapeutic targets.

Abstract 4977: Development of small molecule inhibitors of protein interaction with glycosaminoglycans

Abstract Glycosaminoglycans (GAGs), such as heparan sulfate and chondroitin sulfate, are an important component of the tumor microenvironment (TME). These carbohydrates are attached to proteoglycans at the surface of tumor cells and play a vital role in malignant transformation. Heparan sulfate (HS) glycosaminoglycans have been demonstrated to play a pleiotropic role in regulating the activity of important cellular receptors and downstream signaling pathways, and are implicated in cancer cell proliferation, angiogenesis, invasion, and metastasis. Heparinase, an endoglycosidase that specifically cleaves heparan sulfate side chains of heparan sulfate proteoglycans is expressed in several sarcoma subtypes. We measured heparinase activity in several cell lines and found that A673, CHP100, CHLA9 and RD-ES Ewing’s sarcoma cell lines have significantly higher levels of heparinase activity compared to the heparinase-deficient CHO-K1 psgD-677 cell line. Interference with heparinase or heparin sulfate function(s) may represent a therapeutic approach in sarcoma. To this end, we tested these cell lines by measuring cell growth using a cell viability assay, in the presence or absence of GTC3300P, a small molecule inhibitor of protein interaction with glycosaminoglycan. We demonstrate that the Ewing’s sarcoma cell lines exhibit potent and significant inhibition in cell growth in vitro, in the presence of drug. Western blot analysis shows induction of cleaved Poly-ADP Ribose Polymerase (PARP), yH2AX, as well as cleaved caspase-3, known markers of apoptosis and down regulation of mTORC1 targets such as phospho-S6 (p-S6), in Ewing’s sarcoma. Apoptosis was confirmed by the induction of sub-G1 population in Ewing’s sarcoma by cell cycle analysis. Previous reports have indicated that heparinase activity is strongly implicated in cell migration and invasion and is associated with tumor metastasis, angiogenesis and inflammation. This was confirmed by LC-MS/MS proteomics and bioinformatics (gene ontology and gene set enrichment) analysis of these multiple cell lines, which identified alterations in numerous biomarkers in these pathways, including multiple ribosomal protein subunits, spliceosomes components, and complement coagulation cascade. We further conducted a cell migration assay and demonstrate that GTC3300 significantly inhibits cell migration in Ewing’s sarcoma cell lines, but not in heparinase-deficient psg677 cells. Taken together our data strongly suggests that targeting protein interaction with glycosaminoglycans including heparan sulfate in Ewing’s sarcoma represents a novel approach and merits further investigation Citation Format: Tahir N. Sheikh, Elgilda Musi, Alex J. Rai, Gary K. Schwartz. Development of small molecule inhibitors of protein interaction with glycosaminoglycans. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4977.

Gene pathway analysis of the endometrium at the start of the window of implantation in women with unexplained infertility and unexplained recurrent pregnancy loss: is unexplained recurrent pregnancy loss a subset of unexplained infertility?

This study aims to understand differences/similarities in the genetic profile of the endometrium at the start of window of implantation (WOI) in women with unexplained infertility (UI) and unexplained recurrent pregnancy loss (uRPL). Differentially expressed genes (DEGs) from the endometrium were evaluated using gene expression array and pathway enrichment analysis was performed to analyse gene expression pathways involved in both conditions. We found 2,171 genes arranged in 117 pathways and 730 genes arranged in 33 pathways differentially expressed in endometrium of patients in UI and uRPL, respectively. Complement-coagulation cascades, morphine addiction pathway, and PI3K-Akt signalling pathway were predominantly differentially expressed in UI. Cancer pathways, NF-κB signalling pathway, and actin cytoskeleton regulation pathway showed significant changes in uRPL. Forty-eight percent of DEGs and 84% of differentially expressed pathways in uRPL were found in the endometrium of UI patients. Unexpected close association in gene expression pathways between UI and uRPL is observed supporting the hypothesis ‘uRPL is a clinical subset of UI’. Yet 100% DEGs overlap wasn’t found suggesting the endometrium has still some different gene expression patterns at start of WOI in UI and uRPL. Lastly, diagnostic tools may be developed for uRPL because more specific genes-pathways are involved compared with UI, which shows broader genetic expression profile.

Abstract 1154: Multi-omic analysis classifies colorectal cancer into distinct angiogenic and immunogenic subtypes based on anatomical laterality

Abstract Background: Colorectal cancer is a heterogeneous disease of tumors from distinct anatomical and embryological sources. According to GLOBOCAN2020, it is the second leading cause of cancer-related mortality1. Methodology: Utilising NIH-GDC2 datasets, we applied Bioinformatic algorithms to categorize LCRC and RCRC based on multi-omic variables. Mutational analysis was done using STRING v11.53. Kaplan-Meier were plotted. Transcriptome data was accessed using Bioconductor4 package TCGABiolinks5 and annotated as ‘Left’ or ‘Right’ based on tissue of origin. DE analysis was performed using DESeq6. DEGs were analyzed using Enrichr7 for signaling pathways. Further, differential methylation analysis was performed. Results: Tumors from left and right sides represent early Stage IIA non-metastatic cancers largely. Mutational analysis showed dissimilar genes in left vs right-sided tumors. CSMD1, CDH23, PCDH15, DSCAM, CDH9, and NRXN1 formed unique hubs within LCRC network while FLNC, CACNA1H, KMT2B, KMT2D, FAT4 and BRAF formed hubs in RCRC network. LCRC-specific genes were cadherins and EMT based, while RCRC-specific genes were related to lymphocytic invasion and epigenetic markers. TTN (p-value=4.61e-2) and ABCA13 (p-value=4.78e-2) significantly influenced OS in LCRC while SOX11 (p-value=4.12e-2) influenced OS in RCRC. For transcriptomic analysis, we obtained 766 DE genes at p-adjusted value <= 0.01, |log2 FC| > 1. Enrichr KEGG pathway analysis highlighted neuroactive ligand-receptor interaction (OR=3.11) and complement-coagulation cascade (OR=6.07) activity in LCRC. Platelet interaction with cancer cells have been demonstrated8 to have therapeutic potential in CRCs. NK cell mediated cytotoxicity (OR=4.33) and antigen processing-presentation (OR=6.95) were enriched in RCRC. Mean methylation analysis showed higher values in RCRC than LCRC (p-value=1.5e-05). Differential methylation gave 998 hypo- and 45 hyper-methylated genes in RCRC and LCRC respectively. RCRC evidently has an underlying hypermethylated biology when compared to LCRC. RCRCs are dependent on immune-regulated biology explaining rationale of immunotherapy. Right colon develops from midgut and is supplied by SMA. It can be hypothesized that a vast lymphatic drainage system carrying increased T-cells may play a role in creating dissimilarity. On the other hand, angiogenic factors and coagulation cascade rule left colon. This could be the reason for early metastatic potential in LCRCs. Our study unambiguously differentiates LCRC from RCRC by correlating anatomical, physiological, and multi-omic variables. Citation Format: Anu R I, Aastha Vatsyayan, Ambily Sivadas, Dileep Damodaran, Kurt van der Speeten. Multi-omic analysis classifies colorectal cancer into distinct angiogenic and immunogenic subtypes based on anatomical laterality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1154.

A pilot study on some critical immune elements in HBV infection: evidence of Alpha-1 Antitrypsin as an immunological biomarker.

This study is an attempt to screen the key immune elements that participate during HBV infection and the related pathways that are modulated. The pathogenesis of Hepatitis B virus and the corresponding clinical manifestations in the host are primarily immune-mediated. This study utilizes a PCR array to screen immune-related genes that are differentially expressed in the presence of the virus in HBV replicating HepG2.2.15 cells as compared to control HepG2 cells. The significantly up-regulated genes were subjected to bioinformatic analysis utilizing GSEA and STRING. Additionally, ELISA was used to corroborate the levels of Alpha 1 antitrypsin (AAT) from patients' sera. The expressions of 31% of the studied genes were significantly up-regulated (> 2-fold, p<0.05) in HepG2.2.15 cells compared to controls, and this included the SERPINA1, FN1, IL1R2, LBP, LY96, LYZ and PROC genes. When they were clustered based on biological processes, signaling pathways, and disease progression, the genes related to biotic stimulus, complement-coagulation cascades, and fibrosis, respectively, showed the highest (p<0.05) enrichment. Analysis of patients' sera by ELISA revealed that the serum AAT (SERPINA1) levels were significantly higher in asymptomatic carriers and in patients with chronic liver disease than in controls (p<0.05). Moreover, SERPINA1 levels were also positively correlated with the levels of serum ALT (r=0.4495, p<0.05) among HBV infected patients. The current study highlights the key immune elements and pathways that are modulated during HBV infection and proposes the possible use of AAT as a non-invasive immunological biomarker to follow the progression of liver disease.

Quantitative analysis of differential proteins in liver tissues of patients with non-alcoholic steatohepatitis using iTRAQ technology

To screen differentially expressed proteins (DSPs) in the liver tissues of patients with nonalcoholic steatohepatitis (NASH) using proteomic technologies to identify potential therapeutic targets of NASH. Liver tissue specimens were obtained from 3 patients with pathologically confirmed NASH and 3 normal control subjects. The total proteins were extracted from the specimens, and iTRAQ reagent was used to label the peptides for liquid chromatography tandem mass spectrometry (LC-MS/MS) detection. The DSPs were identified by comparing the data against UniProt protein database using Mascot2.3.02 software and were annotated and enriched using GO database; KEGG database was used for enrichment of the pathways involving these proteins. Real-time fluorescent quantitative PCR (qPCR) was performed to detect the mRNA expressions of the significant DSPs in NASH. By the criteria that a DSP has >1.2 or < 0.8 fold difference between NASH group and the control group and with P < 0.05 as the threshold, a total of 648 significant DSPs in NASH were identified, including 246 up-regulated and 402 down-regulated proteins. GO functional enrichment analysis showed that the DSPs were involved mainly in small molecule metabolism, organic acid metabolism, oxygen acid metabolism and other biological processes, and were enriched in KEGG pathways including the metabolic pathways, complement coagulation cascades, and ribosomes. Among the 25 DEPs with a fold difference >2.0 or < 0.5 (P < 0.05), 6 proteins showed consistent results between qPCR verification and proteomic analysis, including 5 down-regulated proteins: Jumonji protein (JARID2), Lebasillinlike protein (LCA5L), synaptophysin 1 (SYN1) and collagen α-1 (XIII) chain (COL13A1), FYVE, RhoGEF and PH domain protein 5 (FGD5), and 1 upregulated protein glutathione S-transferase Mu 4 (GSTM4). We identified 648 DEPs inthe liver tissue of patients NASH using iTRAQ technology and bioinformatics methods, and among them JARID2, SYN1, COL13A1, FGD5, and GSTM4 may serve as the key target proteins of NASH.

Identification of Candidate Biomarkers and Prognostic Analysis in Colorectal Cancer Liver Metastases.

BackgroundColorectal cancer (CRC), one of the most common malignant tumors worldwide, has a high mortality rate, especially for patients with CRC liver metastasis (CLM). However, CLM pathogenesis remains unclear.MethodsWe integrated multiple cohort datasets and databases to clarify and verify potential key candidate biomarkers and signal transduction pathways in CLM. GEO2R, DAVID 6.8, ImageGP, STRING, UALCAN, ONCOMINE, THE HUMAN PROTEIN ATLAS, GEPIA 2.0, cBioPortal, TIMER 2.0, DRUGSURV, CRN, GSEA 4.0.3, FUNRICH 3.1.3 and R 4.0.3 were utilized in this study.ResultsSixty-three pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened from three gene expression profiles (GSE6988, GSE14297 and GSE81558). Thirty-one up-regulated genes and four down-regulated genes were identified from these three gene expression profiles and verified by another gene expression profiles (GSE 49355) and TCGA database. Two pathways (IGFBP-IGF signaling pathway and complement-coagulation cascade), eighteen key differentially expressed genes (DEGs), six hub genes (SPARCL1, CDH2, CP, HP, TF and SERPINA5) and two biomarkers (CDH2 and SPARCL1) with significantly prognostic values were screened by multi-omics data analysis and verified by Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) cohort.ConclusionsIn this study, we identified a robust set of potential candidate biomarkers in CLM, which would provide potential value for early diagnosis and prognosis, and would promote molecular targeting therapy for CRC and CLM.

"Complimenting the Complement": Mechanistic Insights and Opportunities for Therapeutics in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver and a leading cause of death in the US and worldwide. HCC remains a global health problem and is highly aggressive with unfavorable prognosis. Even with surgical interventions and newer medical treatment regimens, patients with HCC have poor survival rates. These limited therapeutic strategies and mechanistic understandings of HCC immunopathogenesis urgently warrant non-palliative treatment measures. Irrespective of the multitude etiologies, the liver microenvironment in HCC is intricately associated with chronic necroinflammation, progressive fibrosis, and cirrhosis as precedent events along with dysregulated innate and adaptive immune responses. Central to these immunological networks is the complement cascade (CC), a fundamental defense system inherent to the liver which tightly regulates humoral and cellular responses to noxious stimuli. Importantly, the liver is the primary source for biosynthesis of >80% of complement components and expresses a variety of complement receptors. Recent studies implicate the complement system in liver inflammation, abnormal regenerative responses, fibrosis, carcinogenesis, and development of HCC. Although complement activation differentially promotes immunosuppressive, stimulant, and angiogenic microenvironments conducive to HCC development, it remains under-investigated. Here, we review derangement of specific complement proteins in HCC in the context of altered complement regulatory factors, immune-activating components, and their implications in disease pathogenesis. We also summarize how complement molecules regulate cancer stem cells (CSCs), interact with complement-coagulation cascades, and provide therapeutic opportunities for targeted intervention in HCC.

Pancreatic Tissue Proteomics Unveils Key Proteins, Pathways, and Networks Associated with Type 1 Diabetes

Type 1 diabetes (T1D) is characterized by autoimmune mediated self-destruction of the pancreatic islet beta cells and the resultant insulin deficiency. However, little is known about the underlying molecular pathogenesis at the pancreatic tissue level given the limited availability of clinical specimens. Quantitative proteomic studies is performed on age-matched T1D and healthy cadaveric pancreatic tissues (n = 18 each) using TMT 10plex-based isobaric labeling and BoxCar-based label-free LC-MS/MS approaches. ELISA is used to validate the differentially expressed proteins (DEPs). Overall, the two quantitative proteomics approaches identified 8824 proteins, of which 261 are DEPs. KEGG pathway and functional network analyses of the DEPs reveal dysregulations to pancreatic exocrine function, complement coagulation cascades, and extracellular matrix receptor interaction pathways in T1D. A selected list of the DEPs associated with pathways, subnetworks, and plasma proteome of T1D are validated using ELISA. Integrating labeling and label-free approaches improve the confidence in quantitative profiling of pancreatic tissue proteome, which furthers the understanding of the dysregulated pathways and functional subnetworks associated with T1D pathogenesis and may aid to develop diagnostic and therapeutic strategies for T1D.

Serum sCD14, PGLYRP2 and FGA as potential biomarkers for multidrug-resistant tuberculosis based on data-independent acquisition and targeted proteomics.

Multidrug‐resistant tuberculosis (MDR‐TB), defined as tuberculosis (TB) resistant to at least isoniazid and rifampicin, is a major concern of TB control worldwide. However, the diagnosis of MDR‐TB remains a huge challenge to its prevention and control. To identify new diagnostic methods for MDR‐TB, a mass spectrometry strategy of data‐independent acquisition and parallel reaction monitoring was used to detect and validate differential serum proteins. The bioinformatic analysis showed that the functions of differential serum proteins between the MDR‐TB group and the drug‐sensitive tuberculosis group were significantly correlated to the complement coagulation cascade, surface adhesion and extracellular matrix receptor interaction, suggesting a disorder of coagulation in TB. Here, we identified three potential candidate biomarkers such as sCD14, PGLYRP2 and FGA, and established a diagnostic model using these three candidate biomarkers with a sensitivity of 81.2%, a specificity of 90% and the area under the curve value of 0.934 in receiver operation characteristics curve to diagnose MDR‐TB. Our study has paved the way for a novel method to diagnose MDR‐TB and may contribute to elucidate the mechanisms underlying MDR‐TB.

Proteomic Profiling of Plasma and Brain Tissue from Alzheimer's Disease Patients Reveals Candidate Network of Plasma Biomarkers.

Alzheimer's disease (AD) is the most prevalent form of dementia with two pathological hallmarks of tau-containing neurofibrillary tangles and amyloid-β protein (Aβ)-containing neuritic plaques. Although Aβ and tau have been explored as potential biomarkers, levels of these pathological proteins in blood fail to distinguish AD from healthy control subjects. We aim to discover potential plasma proteins associated with AD pathology by performing tandem mass tag (TMT)-based quantitative proteomic analysis of proteins from peripheral and central nervous system compartments. We performed comparative proteomic analyses of plasma collected from AD patients and cognitively normal subjects. In addition, proteomic profiles from the inferior frontal cortex, superior frontal cortex, and cerebellum of postmortem brain tissue from five AD patients and five non-AD controls were compared with plasma proteomic profiles to search for common biomarkers. Liquid chromatography-mass spectrometry was used to analyze plasma and brain tissue labeled with isobaric TMT for relative protein quantification. Our results showed that the proteins in complement coagulation cascade and interleukin-6 signaling were significantly altered in both plasma and brains of AD patients. Our results demonstrate the relevance in immune responses between the peripheral and central nervous systems. Those differentially regulated plasma proteins are explored as candidate biomarker profiles that illustrate chronic neuroinflammation in brains of AD patients.

ITRAQ-Based Quantitative Proteomics Analysis of HeLa Cells Infected With Chlamydia muridarum TC0668 Mutant and Wild-Type Strains.

Chlamydia muridarum, an obligate intracellular pathogen, was used to establish a murine model of female upper genital tract infection by Chlamydia trachomatis. TC0668 in C. muridarum is a hypothetical chromosomal virulence protein that is involved in upper genital tract pathogenesis. The infection of mice with the C. muridarum TC0668-mutant (G216*) strain results in less pathological damage in the upper genital tract. In this study, an isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics analysis was performed to identify differentially expressed proteins between TC0668 wild-type (TC0668wt) and TC0668 mutant (TC0668mut) strains at 6, 12, 18, and 24 h post-infection (p.i.). Of the 550 proteins differentially expressed at 18 h p.i., 222 and 328 were up-regulated and down-regulated, respectively, inTC0668mut-infected cells. The expression of seven up-regulated proteins (encoded by SRPRB, JAK1, PMM1, HLA-DQB1, THBS1, ITPR1, and BCAP31) and three down-regulated proteins (encoded by MAPKAPK2, TRAFD1, and IFI16) from the iTRAQ analysis were validated using quantitative real-time (qRT)-PCR. The qRT-PCR results were consistent with those of iTRAQ. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the differentially expressed proteins primarily participated in inflammatory responses, fibrosis, metabolic processes, and complement coagulation cascades, and were mainly enriched in the phosphatidylinositol 3′-kinase (PI3K)/Akt, nuclear factor kappa-B (NF-κB), and other signaling pathways. Using western-blotting and immunofluorescence detection, significant differences in activation of the PI3K/Akt and NF-κB signaling pathways were observed between the TC0668wt- and TC0668mut-infected cells. Differentially expressed proteins linked with inflammation and fibrosis were used in a protein-protein interaction network analysis. The results suggest that TC0668 may play a pivotal role in C. muridarum-induced genital pathology by inducing inflammatory responses and fibrosis, which may involve the activation of the PI3K/Akt and NF-κB signaling pathways.

Quantitative proteomic reveals the differences of peripheral blood mononuclear cells in the host immune response to sepsis

Objective To investigate the feasibility of differential expression proteins identification in peripheral blood mononuclear cells (PBMCs) of sepsis patients using Data Independent Acquisition liquid chromatography-mass spectrometry (DIA LC-MS). Methods Prospective studies were employed and targeted at 10 sepsis patients admitted to the Intensive Care Unit (ICU) of Shanghai Fifth People's Hospital Affiliated to Fudan University from April 2016 to July 2016. And 10 patients admitted to the ICU with similar age and sex that were not complicated with sepsis were served as the control group. The proteins from peripheral blood mononuclear cells in 10 sepsis patients and 10 control persons were analyzed using the latest DIA LC-MS technology and the skyline data extraction software; the model of data obtained from the above analysis was further discriminatorily analyzed with principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA); then the differential proteins of peripheral blood mononuclear cells were analyzed by Pathway analysis and GO analysis. The possible markers were identified by preliminary screening according to variable importance in the projection (VIP). The top 3 proteins (VIP > 1, P< 0.05) were verified by ELISA and their ROC curves were analyzed. Results Totally 1 062 fragment ions were identified and 119 proteins were obtained. Among them, 31 proteins were up-regulated and 88 proteins down-regulated. Pathway analysis showed that carbon metabolism, platelet activation, bacterial invasion of epithelium, and complement coagulation cascade activation were participated in the development of sepsis. ELISA showed that significant difference of HMGB-1, MMP-8, and LCN2 in the expression of peripheral blood mononuclear cells in the sepsis and control people (P<0.01). The area under the ROC curve is greater than 0.85, which has good sensitivity and specificity. Conclusions DIA-MS is a compelling way for detecting differential expression proteins. PCA, PLSDA and OPLSDA are suitable for pattern recognition. The high expression of HMGB-1, NGAL and MMP-8 in immune cells may be the potential biomarker of the disease, which lays the foundation for research of early diagnosis and treatment of sepsis. Key words: Sepsis; Peripheral blood mononuclear cells; Data independent acquisition; Proteomics; Inflammatory immunity

Network spatio-temporal analysis predicts disease stage-related genes and pathways in renal cell carcinoma.

The purpose of this study was to screen the key genes and pathways of renal cell carcinoma (RCC) and lay the foundation for its diagnosis and therapy. Microarray data of normal subjects and RCC patients at different stages of disease were used to screen differentially expressed genes (DEGs). Based on the DEGs in the four disease stages, four co-expression networks were constructed using the Empirical Bayes method and hub genes were obtained by centrality analysis. The enriched pathways of the DEGs and the mutual hub genes in the cluster of each disease stage were investigated. The mutual hub genes of the four disease stages in RCC tissue were validated using reverse transcription-polymerase chain reaction (RT-PCR) and western blot analysis. A total of 432 DEGs were screened, including 233 upregulated and 199 downregulated genes, by statistical analysis. Centrality analysis of co-expression networks in different disease stages suggested that PLXDC1, IKZF1, RUNX2, and RNF125 were mutual hub genes. Pathway analysis showed that the DEGs were significantly enriched in seven terms. The hub modules in stage I disease were significantly enriched in the complement coagulation cascade pathway and the hub modules of the other three disease stages were enriched in natural killer cell-mediated cytotoxicity. The expression levels of PLXDC1, IKZF1, RUNX2, and RNF125 were significantly different between normal subjects and RCC patients by RT-PCR and western blot. Our study revealed four hub genes (PLXDC1, IKZF1, RUNX2, and RNF125) and two biological pathways that might be underlying biomarkers involved in RCC.

Effects of PAMAM dendrimers in the mouse brain after a single intranasal instillation

Dendrimers are highly branched spherical nanomaterials produced for use in diagnostic and therapeutic applications such as a drug delivery system. The toxicological profiles of dendrimers are largely unknown. We investigated the in vivo effects of nasal exposure to polyamidoamine (PAMAM) dendrimers on their effects on neurological biomarkers in the mouse brain. A single dose of PAMAM dendrimers (3 or 15μg/mouse) was intranasally administered to 8-week old male BALB/c mice. Twenty-four hours after administration, the olfactory bulb, hippocampus, and cerebral cortex were collected and potential biomarkers in the blood and brain were examined using blood marker, microarray and real-time RT-PCR analyses. No remarkable changes in standard serum biochemical markers were observed in the blood. A microarray analysis showed the alterations of the genes expression level related to pluripotent network, serotonin-anxiety pathway, TGF-beta receptor signaling, prostaglandin synthesis-regulation, complement-coagulation cascades, and chemokine-signaling pathway and non-odorant GPCR signaling pathways in brain tissues. Brain derived-neurotrophic factor mRNA was up-regulated in the hippocampus and cerebral cortex in mice treated with a high dose of dendrimers. These findings suggest that PAMAM dendrimers may reach the brain via the systemic circulation or an olfactory nerve route after intranasal instillation, and indicate that a single intranasal administration of PAMAM dendrimers may potentially lead to neuronal effects by modulating the gene expression of brain-derived neurotrophic factor signaling pathway.