OBJECTIVE

To investigate the abnormal change of immune function in patients with Pi-Qi deficiency Syndrome, and to explore the genomic mechanism of its genesis by cDNA chip techniques.

METHODS

The cross probe was made by extracting and microamplifying the total RNA and mRNA of peripheral white blood cells (WBC) in healthy subjects and patients with chronic gastritis and ulcerative colitis, which were labeled by Cy3 and Cy5 respectively. Then equal quantity of the two labeled probes were mixed and hybridized with cDNA chip, fluorescent signal of the chips were scanned with scanner. Data obtained were analyzed for comparing the difference of the expressive levels of immune associated genome in peripheral WBC in healthy subjects with those in patients.

RESULTS

Expressions of CD9, CD164, PF4 and RARB gene in WBC of patients, both gastritis and colitis, were down-regulated while those of IGKC, DEFA1 and GNLY were up-regulated.

CONCLUSIONS

The genesis of Pi-Qi deficiency syndrome has its immune associated genomic basis, and the immune functions are disordered in patients with that syndrome.

Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A, C, W and Y) are available as plain-polysaccharide and protein-polysaccharide conjugate vaccines. Here we apply contemporary methods to describe B-cell responses to meningococcal polysaccharide and conjugate vaccines.

Twenty adults were randomly assigned to receive either a meningococcal plain-polysaccharide or conjugate vaccine; one month later all received the conjugate vaccine. Blood samples were taken pre-vaccination and 7, 21 and 28 days after vaccination; B-cell responses were assessed by ELISpot, serum bactericidal assay, flow cytometry and gene expression microarray.

Seven days after an initial dose of either vaccine, a gene expression signature characteristic of plasmablasts was detectable. The frequency of newly generated plasma cells (CXCR3+HLA-DR+) and the expression of transcripts derived from IGKC and IGHG2 correlated with immunogenicity. Notably, using an independent dataset, the expression of glucosamine (N-acetyl)-6-sulfatase was found to reproducibly correlate with the magnitude of immune response. Transcriptomic and flow cytometric data revealed depletion of switched memory B cells following plain-polysaccharide vaccine.

These data describe distinct gene signatures associated with the production of high-avidity antibody and a plain-polysaccharide-specific signature, possibly linked to polysaccharide-induced hyporesponsiveness.

BACKGROUND

Hepatitis B virus (HBV) is a global health problem, and infected patients if left untreated may develop cirrhosis and eventually hepatocellular carcinoma. This study aims to enlighten pathways associated with HBV related liver fibrosis for delineation of potential new therapeutic targets and biomarkers.

METHODS

Tissue samples from 47 HBV infected patients with different fibrotic stages (F1 to F6) were enrolled for 2D-DIGE proteomic screening. Differentially expressed proteins were identified by mass spectrometry and verified by western blotting. Functional proteomic associations were analyzed by EnrichNet application.

RESULTS

Fibrotic stage variations were observed for apolipoprotein A1 (APOA1), pyruvate kinase PKM (KPYM), glyceraldehyde 3-phospahate dehydrogenase (GAPDH), glutamate dehydrogenase (DHE3), aldehyde dehydrogenase (ALDH2), alcohol dehydrogenase (ALDH1A1), transferrin (TRFE), peroxiredoxin 3 (PRDX3), phenazine biosynthesis-like domain-containing protein (PBLD), immuglobulin kappa chain C region (IGKC), annexin A4 (ANXA4), keratin 5 (KRT5). Enrichment analysis with Reactome and Kegg databases highlighted the possible involvement of platelet release, glycolysis and HDL mediated lipid transport pathways. Moreover, string analysis revealed that HIF-1α (Hypoxia-inducible factor 1-alpha), one of the interacting partners of HBx (Hepatitis B X protein), may play a role in the altered glycolytic response and oxidative stress observed in liver fibrosis.

CONCLUSIONS

To our knowledge, this is the first protomic research that studies HBV infected fibrotic human liver tissues to investigate alterations in protein levels and affected pathways among different fibrotic stages. Observed changes in the glycolytic pathway caused by HBx presence and therefore its interactions with HIF-1α can be a target pathway for novel therapeutic purposes.

To investigate molecular mechanisms of peripheral nerve vasculitis, gene expression patterns in archived frozen sural nerve biopsies from patients with vasculitic neuropathy were compared to control nerves by DNA microarray technology. There was a striking upregulation of mRNA of genes involved in immune system processes. Of special interest was the activation of immunoglobulin genes, such as IGLJ3, IGHG3, IGKC, and IGL, and of several chemokines, such as CXCL9 or CCR2. Genes involved in vascular proliferation or remodelling such as CXC31 and AIF were also upregulated. Among the downregulated genes were the Krüppel-Like Transcription Factors KLF2, KLF4 and the nuclear orphan receptor NR4A1 genes known to be involved in endothelial cell activation. Thus, this gene expression profile analysis revealed that in peripheral nerve vasculitis a prominent activation of immune response related genes as well as genes involved in vascular proliferation is taken place, while genes inhibiting endothelial cell activation are down regulated. These data point to interesting mechanistic clues to the molecular pathogenesis of vasculitic neuropathies.

Translocations involving the immunoglobulin loci are recurring events of B cell oncogenesis. The majority of translocations involve the immunoglobulin heavy chain (IGH) locus, while a minor part involves the immunoglobulin light chain loci consisting of the kappa light chain (IGK) located at 2p11.2 and the lambda light chain (IGL) located at 22q11.2. We characterised BAC clones, spanning the IGK and IGL loci, for detection of illegitimate rearrangements by fluorescence in situ hybridisation (FISH). Within the IGL region we have identified six end sequenced probes (22M5, 1152K19, 2036J16, 3188M21, 3115E23 and 274M7) covering the variable (IGLV) cluster and two probes (165G5 and 31L9) covering the constant (IGLC) cluster. Within the IGK region four probes (969D7, 316G9, 122B6 and 2575M21) have been identified covering the variable (IGKV) cluster, and one probe (1021F11) covering the IGK constant (IGKC) cluster. A series of 24 cell lines of different origin have been analysed for the presence of translocations involving the immunoglobulin light chain loci by dual-colour FISH where the split of the variable cluster and the constant cluster indicated a translocation. Probes established in this study can be used for universal screening of illegitimate rearrangements within the immunoglobulin light chain loci in B cell malignancies.

Twenty-two B-cell chronic lymphocytic leukemia (CLL) patients were investigated to evaluate residual disease in clinico-hematological remission. Residual disease was determined by monotypy of surface light-chain expression and by dual-color staining with CD5 and CD19 markers. Samples were analyzed on flow cytometer. Total CD19+ cells above 25%, the CD5+CD19+/total CD19+ cells ratio above 0.25, clonal excess above 0.4 were considered positive for residual disease. According to these immunological criteria, only four cases achieved phenotypic remission. Our data confirm that dual marker analysis is more sensitive than clonal excess and may predict an early relapse. Ig gene rearrangements were studied by Southern blot analysis using IGHJ and IGKC probes in fifteen cases. All 12 cases that retained a detectable rearrangement displayed a phenotypic residual disease. Conversely, in two cases, DNA analysis failed to detect the residual disease characterized by flow cytometry. In conclusion, this study suggests that in B-CLL, dual marker analysis is sensitive in predicting an early relapse in sequential evaluations of residual disease, whereas rearranged bands are undetectable when the proportion of malignant cells is low.

With an objective to understand natural development of bovine neonatal immunity, we analyzed 18 RNA-seq libraries from peripheral blood lymphocytes of three neonatal calves pre- (day 0) and post-colostrum (7, 14 and 28) uptake as compared to their dams. A significant global shift in neonatal transcriptome occurs within first week post-birth, in contrast to dams, with an upregulation of 717 genes. Global pathway analysis of the transcriptome revealed 110 differentially expressed immune-related genes, such as, complement, MHCII, chemokine receptors, defensins and cytokines, at birth. The signaling molecules (LAX1, BLK) and transcription factors (GATA3, FOXP3) are expressed at high levels. High expression of GATA3 transcription factor at birth seems to skew the neonatal immune response towards TH2 type. The high levels of T-cell signaling molecules, CD3G and CD3D, at birth are important in neonatal T cell development. Unlike adults, IGKC expression is high in the neonates where IGKV12 is preferentially expressed at birth. But IGLC is predominant in both neonates and adult where IGLV3.4 is preferentially expressed in B cells at birth. Both IGHM and IGHD are expressed at birth and IGHM achieves adult levels by day 7. This is followed by IGHA and IGHG expression 14-28 days post-birth. Importantly, preferential expression of IGHV1S1(BF4E9) and longest IGHD2(DH2) genes that encode immunoglobulin with exceptionally long CDR3H at birth indicates their critical role, as B cell antigen receptor, in the B cell development via idiotype-anti-idiotype interactions. The transcriptome signatures described here permit assessment bovine neonatal immunocompetence. Bovine neonates acquire innate and IgM-mediated humoral immunocompetence within first week post-birth.

The initiation of spontaneous breast cancer (SBC) in Tientsin Albino 2 (TA2) mice is related to mouse mammary tumor virus (MMTV) infection, and MMTV amplification is hormonally regulated. To explore the insertion site of MMTVLTR in TA2 mouse genome, reverse PCR and nested PCR were used to amplify the unknown sequence on both sides of the MMTV-LTRSAG gene in SBC and normal breast tissue of TA2 mice. Furthermore, the clinicopathological significance of the insertion site was evaluated in 43 samples of normal breast tissue, 46 samples of breast cystic hyperplasia, 54 samples of ductal carcinoma in situ, 142 samples of primary breast cancer and 47 samples of lymph node metastatic breast cancer by RNA in situ hybridization. We confirmed that the insertion site of the MMTV-LTRSAG gene was located between Igκv2-112 and Igκv14-111 in chromosome 6 of TA2 mouse. IGκC was localized in the stromal cells of TA2 mouse with SBC and in human breast cancer tissues. Tumor cells were negative for IGκC in RNA in situ hybridization. The positive staining index of IGκC in stromal cells was the highest in lymph node metastatic breast cancer, followed by primary breast cancer, ductal carcinoma in situ, and breast cystic hyperplasia. Furthermore, the positive staining index of IGκC was related to the expression of ER, PR, HER2 and Ki-67. Our findings showed that stromal IGκC expression was associated with the initiation of SBC in TA2 mice. IGκC may be a high-risk factor for the initiation and progression of human breast cancer.

Calcific aortic valve disease (CAVD) is the most prevalent valvular heart disease in the developed world, yet no pharmacological therapy exists. Here, we hypothesize that the integration of multiple omic data represents an approach towards unveiling novel molecular networks in CAVD. Databases were searched for CAVD omic studies. Differentially expressed molecules from calcified and control samples were retrieved, identifying 32 micro RNAs (miRNA), 596 mRNAs and 80 proteins. Over-representation pathway analysis revealed platelet degranulation and complement/coagulation cascade as dysregulated pathways. Multi-omics integration of overlapping proteome/transcriptome molecules, with the miRNAs, identified a CAVD protein-protein interaction network containing seven seed genes (apolipoprotein A1 (APOA1), hemoglobin subunit β (HBB), transferrin (TF), α-2-macroglobulin (A2M), transforming growth factor β-induced protein (TGFBI), serpin family A member 1 (SERPINA1), lipopolysaccharide binding protein (LBP), inter-α-trypsin inhibitor heavy chain 3 (ITIH3) and immunoglobulin κ constant (IGKC)), four input miRNAs (miR-335-5p, miR-3663-3p, miR-21-5p, miR-93-5p) and two connector genes (amyloid beta precursor protein (APP) and transthyretin (TTR)). In a metabolite-gene-disease network, Alzheimer's disease exhibited the highest degree of betweenness. To further strengthen the associations based on the multi-omics approach, we validated the presence of APP and TTR in calcified valves from CAVD patients by immunohistochemistry. Our study suggests a novel molecular CAVD network potentially linked to the formation of amyloid-like structures. Further investigations on the associated mechanisms and therapeutic potential of targeting amyloid-like deposits in CAVD may offer significant health benefits.

Keywords: amyloid structures; calcific aortic valve disease; multi-omics integration; proteomics; transcriptomics.

The immune cells in the local environments surrounding non-small cell lung cancer (NSCLC) implicate the balance of pro- and antitumor immunity; however, their transcriptomic profiles remain poorly understood.

A transcriptomic microarray study of bronchoalveolar lavage (BAL) cells harvested from tumor-bearing lung segments was performed in a discovery group. The findings were validated (1) in published microarray datasets, (2) in an independent group by RT-qPCR, and (3) in non-diseased and tumor adjacent non-neoplastic lung tissue by immunohistochemistry and in BAL cell lysates by immunoblotting.

The differential expression of 129 genes was identified in the discovery group. These genes revealed functional enrichment in Fc gamma receptor-dependent phagocytosis and circulating immunoglobulin complex among others. Microarray datasets analysis (n = 607) showed that gene expression of BAL cells of tumor-bearing lung segment was also the unique transcriptomic profile of tumor adjacent non-neoplastic lung of early stage NSCLC and a significantly gradient increase of immunoglobulin genes' expression for non-diseased lungs, tumor adjacent non-neoplastic lungs, and tumors was identified (ANOVA, p < 2 × 10-16). A 53-gene signature was determined with significant correlation with inhibitory checkpoint PDCD1 (r = 0.59, p = 0.0078) among others, where the nine top genes including IGJ and IGKC were RT-qPCR validated with high diagnostic performance (AUC: 0.920, 95% CI: 0.831-0.985, p = 2.98 × 10-7). Increased staining and expression of IGKC revealed by immunohistochemistry and immunoblotting in tumor adjacent non-neoplastic lung tissues (Wilcoxon signed-rank test, p < 0.001) and in BAL cell lysates (p < 0.01) of NSCLC, respectively, were noted.

The BAL cells of tumor-bearing lung segments and tumor adjacent non-neoplastic lung tissues present a unique gene expression characterized by IGKC in relation to inhibitory checkpoints. Further study of humoral immune responses to NSCLC is warranted.

UNASSIGNED

Thyroid carcinomas have comprised the fastest rising incidence of cancer in the past decade. Currently, the diagnosis of thyroid tumors is performed by the fine-needle aspiration biopsy (FNAB) method, which still holds some challenges and limitations, mostly in discriminating malignant and benign lesions. Therefore, the development of molecular markers to distinguish between these lesion types are in progress.

UNASSIGNED

A 2D-PAGE separation of proteins was performed followed by tandem mass spectrometry with the aim of discovering potential serum protein markers for papillary thyroid carcinoma and multinodular goiter. Protein-protein interaction network analysis revealed the most important pathways involved in the progression of papillary thyroid cancer. The enzyme-linked immunosorbent assay method was used to confirm a part of the results.

UNASSIGNED

The significantly altered proteins included C3, C4A, GC, HP, TTR, APOA4, APOH, ORM2, KRT10, AHSG, IGKV3-20, and IGKC. We also confirmed that increased complement component 3 and decreased apolipoprotein A4 occurred in papillary thyroid cancer. Network investigations demonstrated that complement activation cascades and PPAR signaling might play a role in the pathogenesis of thyroid cancer.

UNASSIGNED

The results demonstrated that serum proteomics could serve as a viable method for proposing novel potential markers for thyroid tumors. Surely, further research must be performed in larger cohorts to validate the results.

Introduction: The pathophysiology and temporal dynamics of affected tissues in chronic rhinosinusitis (CRS) remain poorly understood. Here, we present a multiomics-based time-series assessment of nasal polyp biopsies from three patients with CRS, assessing natural variability over time and local response to systemic corticosteroid therapy.

Methods: Polyp tissue biopsies were collected at three time points over two consecutive weeks. Patients were prescribed prednisone (30 mg daily) for 1 week between Collections 2 and 3. Polyp transcriptome, proteome, and microbiota were assessed via RNAseq, SWATH mass spectrometry, and 16S ribosomal RNA and ITS2 amplicon sequencing. Baseline interpatient variability, natural intrapatient variability over time, and local response to systemic corticosteroids, were investigated.

Results: Overall, the highly abundant transcripts and proteins were associated with pathways involved in inflammation, FAS, cadherin, integrin, Wnt, apoptosis, and cytoskeletal signaling, as well as coagulation and B- and T-cell activation. Transcripts and proteins that naturally varied over time included those involved with inflammation- and epithelial-mesenchymal transition-related pathways, and a number of common candidate target biomarkers of CRS. Ten transcripts responded significantly to corticosteroid therapy, including downregulation of TNF, CCL20, and GSDMA, and upregulation of OVGP1, and PCDHGB1. Members of the bacterial genus Streptococcus positively correlated with immunoglobulin proteins IGKC and IGHG1.

Conclusions: Understanding natural dynamics of CRS-associated tissues is essential to provide baseline context for all studies on putative biomarkers, mechanisms, and subtypes of CRS. These data further our understanding of the natural dynamics within nasal polypoid tissue, as well as local changes in response to systemic corticosteroid therapy.

Keywords: chronic rhinosinusitis; corticosteroids; mucosa; multiomics; polyposis.

Background: Rheumatoid arthritis (RA) is an autoimmune disorder with systemic inflammation and may be induced by oxidative stress that affects an inflamed joint. Our objectives were to examine isotypes of autoantibodies against 4-hydroxy-2-nonenal (HNE) modifications in RA and associate them with increased levels of autoantibodies in RA patients.

Methods: Serum samples from 155 female patients [60 with RA, 35 with osteoarthritis (OA), and 60 healthy controls (HCs)] were obtained. Four novel differential HNE-modified peptide adducts, complement factor H (CFAH)^1211-1230, haptoglobin (HPT)^78-108, immunoglobulin (Ig) kappa chain C region (IGKC)^2-19, and prothrombin (THRB)^328-345, were re-analyzed using tandem mass spectrometric (MS/MS) spectra (ProteomeXchange: PXD004546) from RA patients vs. HCs. Further, we determined serum protein levels of CFAH, HPT, IGKC and THRB, HNE-protein adducts, and autoantibodies against unmodified and HNE-modified peptides. Significant correlations and odds ratios (ORs) were calculated.

Results: Levels of HPT in RA patients were greatly higher than the levels in HCs. Levels of HNE-protein adducts and autoantibodies in RA patients were significantly greater than those of HCs. IgM anti-HPT^78-108 HNE, IgM anti-IGKC^2-19, and IgM anti-IGKC^2-19 HNE may be considered as diagnostic biomarkers for RA. Importantly, elevated levels of IgM anti-HPT^78-108 HNE, IgM anti-IGKC^2-19, and IgG anti-THRB^328-345 were positively correlated with the disease activity score in 28 joints for C-reactive protein (DAS28-CRP). Further, the ORs of RA development through IgM anti-HPT^78-108 HNE (OR 5.235, p < 0.001), IgM anti-IGKC^2-19 (OR 12.655, p < 0.001), and IgG anti-THRB^328-345 (OR 5.761, p < 0.001) showed an increased risk. Lastly, we incorporated three machine learning models to differentiate RA from HC and OA, and performed feature selection to determine discriminative features. Experimental results showed that our proposed method achieved an area under the receiver operating characteristic curve of 0.92, which demonstrated that our selected autoantibodies combined with machine learning can efficiently detect RA.

Conclusions: This study discovered that some IgG- and IgM-NAAs and anti-HNE M-NAAs may be correlated with inflammation and disease activity in RA. Moreover, our findings suggested that IgM anti-HPT^78-108 HNE, IgM anti-IGKC^2-19, and IgG anti-THRB^328-345 may play heavy roles in RA development.

Keywords: 4-hydroxy-2-nonenal; Autoantibody isotype; Rheumatoid arthritis; Serum.

Background: Renal cell carcinoma (RCC) is a common urologic malignancy. Although the relationship between clear cell RCC (ccRCC) and obesity has been well-established by several large-scale retrospective studies, the molecular mechanisms and genetic characteristics behind this correlation remains unclear. In the current study, several bioinformatics tools were used to identify the key genes in ccRCC related to obesity.

Methods: Microarray data comparing ccRCC with normal renal tissues in patients with and without obesity were downloaded from the GEO database for screening of differentially expressed genes (DEGs). The DEGs were verified with expression level and survival analysis using several online bioinformatics tools.

Results: In the current study, the differential expression of five genes correlated with both ccRCC and obesity; IGHA1 and IGKC as oncogenes, and MAOA, MUC20 and TRPM3 as tumor suppressor genes. These genes were verified by comparing the relationship between the expression levels and survival outcomes from open-source data in The Cancer Genome Atlas (TCGA) dataset.

Conclusions: In conclusion, the five genes differentially expressed in ccRCC and obesity are related to disease progression and prognosis, and therefore could provide prognostic value for patients with ccRCC.

Keywords: Clear cell renal cell carcinoma (ccRCC); biomarker; obesity; prognosis.

We studied the prognostic impact of tumor immunoglobulin kappa C (IGKC) mRNA expression as a marker of the humoral immune system in the FinHer trial patient population, where 1010 patients with early breast cancer were randomly allocated to either docetaxel-containing or vinorelbine-containing adjuvant chemotherapy. HER2-positive patients were additionally allocated to either trastuzumab or no trastuzumab. Hormone receptor-positive patients received tamoxifen. IGKC was evaluated in 909 tumors using quantitative real-time polymerase chain reaction, and the influence on distant disease-free survival (DDFS) was examined using univariable and multivariable Cox regression and Kaplan-Meier estimates. Interactions were analyzed using Cox regression. IGKC expression, included as continuous variable, was independently associated with DDFS in a multivariable analysis also including age, molecular subtype, grade, and pT and pN stage (HR 0.930, 95% CI 0.870-0.995, p = 0.034). An independent association with DDFS was also found in a subset analysis of triple-negative breast cancers (TNBC) (HR 0.843, 95% CI 0.724-0.983, p = 0.029), but not in luminal (HR 0.957, 95% CI 0.867-1.056, p = 0.383) or HER2-positive (HR 0.933, 95% CI 0.826-1.055, p = 0.271) cancers. No significant interaction between IGKC and chemotherapy or trastuzumab administration was detected (P_interaction = 0.855 and 0.684, respectively). These results show that humoral immunity beneficially influences the DDFS of patients with early TNBC.

Keywords: immune system; immunoglobulin kappa C; prognosis; triple-negative breast cancer.

BACKGROUND

Graves' ophthalmopathy/orbitopathy (GO) patients often suffer ocular surface damages and tear fluid proteins play a significant role in maintaining healthy ocular surfaces, while changes in tear protein components reflect the changes ocular surface abnormalities. In this study proteomics techniques were used to investigate tear protein compositions in GO patients.

METHODS

We carried out a case-control study by comparing tear fluid contents of GO patients with that of healthy subjects. In the first step the tears were subjected to SDS-PAGE electrophoresis and then single protein bands were analyzed by to in-gel trypsin digestion and nano-flow liquid mass spectrometry (LC-MS/MS) using a MS software.

RESULTS

In tear samples of GO subjects, the protein fractions of inflammation-related protein immunoglobulin kappa chain C region (IgKC) and serum albumin were essentially reduced, whereas a novel isoform of complement component 3 (C3), which we detected in control subjects, was completely absent in the GO patients' tears.

CONCLUSIONS

Reduced protein concentrations of particularly IgKC and complement C3 as well as albumin in the tears of GO patients may contribute to changes in their ocular surfaces via diminished reactive oxygen species (ROS) depletion and adaptive immune responses. The completely absent of C3 in the GO patients' tears, may imply that an important inflammatory signaling pathway is affected, which needs further investigation.

BACKGROUND

Periodontitis is one of the most common oral diseases associated with the host's immune response against periodontopathogenic infection. Failure to accurately diagnose the stage of periodontitis has limited the ability to predict disease status. Therefore, we aimed to look for reliable diagnostic markers for detection or differentiation of early stage periodontitis using the immunoprotemic approach.

METHODS

In the present study, patient serum samples from four distinct stages of periodontitis (i.e., mild chronic, moderate chronic, severe chronic, and aggressive) and healthy controls were subjected to two-dimensional gel electrophoresis (2-DE), followed by silver staining. Notably, we consistently identified 14 protein clusters in the sera of patients and normal controls.

RESULTS

Overall, we found that protein levels were comparable between patients and controls, with the exception of the clusters corresponding to A1AT, HP, IGKC and KNG1 (p < 0.05). In addition, the immunogenicity of these proteins was analysed via immunoblotting, which revealed differential profiles for periodontal disease and controls. For this reason, IgM obtained from severe chronic periodontitis (CP) sera could be employed as a suitable autoantibody for the detection of periodontitis.

CONCLUSIONS

Taken together, the present study suggests that differentially expressed host immune response proteins could be used as potential biomarkers for screening periodontitis. Future studies exploring the diagnostic potential of such factors are warranted.

Tx gene is the DNA sequence with transforming activity which was cloned from the epithelial cell line (CNE2) of human nasopharyngeal carcinoma (NPC). In order to understand the role of Tx in carcinogenesis of NPC, the promoter function of potential promoter region in Tx2. 8 was detected using CAT reporter assay. The results showed that the region has no promoter function. It suggested that Tx2. 8 kb fragment homogenous to IGKC might be regulated by the specific mechanism of immunoglobulin gene.

Machine learning (ML) algorithms have been applied to predicting coronary artery disease (CAD). Our purpose was to utilize autoantibody isotypes against four different unmodified and malondialdehyde (MDA)-modified peptides among Taiwanese with CAD and healthy controls (HCs) for CAD prediction. In this study, levels of MDA, MDA-modified protein (MDA-protein) adducts, and autoantibody isotypes against unmodified peptides and MDA-modified peptides were measured with enzyme-linked immunosorbent assay (ELISA). To improve the performance of ML, we used decision tree (DT), random forest (RF), and support vector machine (SVM) coupled with five-fold cross validation and parameters optimization. Levels of plasma MDA and MDA-protein adducts were higher in CAD patients than in HCs. IgM anti-IGKC^76-99 MDA and IgM anti-A1AT^284-298 MDA decreased the most in patients with CAD compared to HCs. In the experimental results of CAD prediction, the decision tree classifier achieved an area under the curve (AUC) of 0.81; the random forest classifier achieved an AUC of 0.94; the support vector machine achieved an AUC of 0.65 for differentiating between CAD patients with stenosis rates of 70% and HCs. In this study, we demonstrated that autoantibody isotypes imported into machine learning algorithms can lead to accurate models for clinical use.

Keywords: autoantibody isotype; cardiovascular disease; malondialdehyde; plasma.

Background: Gastric cancer (GC) remains a major global health problem due to a poor understanding of its progression at the molecular level and a lack of early detection or diagnosis. Early detection is highly crucial for improving prognosis. The incidence of GC is very high in countries like India due to the limitations among the established biomarkers for GC owing to poor sensitivity and specificity.

Objective: To identify the novel biomarkers from serum samples obtained from GC patients when compared with healthy subjects.

Methods: Serum samples from GC patients were analyzed by two-dimensional gel electrophoresis (2DGE) coupled with tandem mass spectrometry (MS), including both matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF) and liquid chromatography-MS (LC-MS/MS) analysis. Identified proteins were further analyzed by gene ontology and protein interaction studies.

Results: A total of 73 protein spots were detected in 2DGE image analysis. Among them, seven differentially-expressed proteins were identified using MS analyses, which included serotransferrin/transferrin, albumin, ceruloplasmin, C-reactive protein (CRP), fibrinogen γ-chain (FGG), and two unreported novel proteins, immunoglobulin kappa constant (IgκC) region and Homo sapiens zinc finger protein 28 (ZNF28) homolog. Among these proteins, serotransferrin, albumin, ceruloplasmin, FGG, and ZNF28 were down-regulated in GC samples (p < 0.05), while IgκC region and CRP were up-regulated significantly.

Conclusion: Most of the differentially expressed proteins were involved in angiogenesis, plasminogen-activating cascade, and blood coagulation pathways which are known to play a critical role in gastric tumorigenesis. Our current results provide a panel of candidate biomarkers for GC with novel biomarkers which were not reported earlier.

Keywords: Gastric cancer; Gene ontology; LC-MS/MS analysis; MALDI-ToF; Proteomic analysis; Serum biomarkers.

A comparative transcription analysis of Ig κ-light chains (IGK) of the cattle breeds Holstein Friesian (HF), German Black Pied (GBP), German Simmental (GS) and Aubrac (A) revealed three alleles coding for two putative allotypic variants of IGKC. The amino acid residues p.Asp100Asn and p.Thr116Ala were located at the outer edge of the constant domain as demonstrated by homology-based modelling. Alleles were distributed in unequal frequencies within the breeds examined. While cattle breeds HF, GS, and A possessed all alleles and allotypic variants, GBP exhibited alleles encoding allotypic variant IGKC(a) . All three IGKJ segments were detected in 320 sequences analysed. IGKJ1 was combined predominantly with IGKC. The ORF2 of IGKJ2 was detected for the first time on transcriptional level.

Treatment of light chain (LC) deposition diseases both nonfibrillar and fibrillar is aimed at eliminating LC production but success is limited. We report on the testing of an small interfering RNA pool targeting the κ LC constant region mRNA (si[IGKC]) designed for use against all κ plasma cell clones. To test for changes in κ LC message and protein production we used real-time PCR, immunoblot, intracellular mean fluorescence intensity and κ LC secretion by enzyme-linked immunosorbent assay. In vitro we employed 4 human cell lines that make κ LCs and 20 specimens of CD138-selected marrow plasma cells from patients with κ plasma cell diseases. In vivo, we used a murine flank plasmacytoma xenograft model. In vitro and in vivo, there were significant reductions in message and protein production by all modalities in all cell types despite diversity in variable region sequence. In addition, in clones producing intact immunoglobulin, caspase 3/7 activity with si[IGKC] was significantly increased compared with clones producing κ LC only, consistent with the triggering of a terminal unfolded protein response by excess unpaired heavy chains. In conclusion, si[IGKC] can significantly reduce κ LC production by κ plasma cells. Further preclinical development is needed to optimize delivery.

Aim: We aimed to carry out proteomic assessment of long-term effects of hepatitis C on liver.

Background: Cirrhosis is a condition where liver is damaged and loses its efficiency, and has the high rate of mortality in the world. Proteome profiling may help to identify important proteins and find the pathogenesis Cirrhosis is a condition where liver is damaged and loses its efficiency, and has the high rate of mortality in the world. Proteome profiling may help to identify important proteins and find the pathogenesis.

Methods: Here, by the application of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), combined with (MALDI-TOF-TOF MS), proteome profile of decompensated HCV cirrhosis is determined compared to healthy matched controls. Furthermore, Cytoscape has used network analysis. The proteome comparison between two groups identified proteins with significant expression changes (p<0.05 and fold change ≥ 1.5).

Results: We found upregulation of IGHA1, C3, A1BG, IGKC and one isoform of HP. Also, lower expression of APOA4 and the other spot of HP in advanced cirrhosis patients were revealed based on HCV compared to matched controls. According to network analysis, ALB has been introduced as a key protein, which may play an important role in pathogenesis.

Conclusion: Integration of the proteomics with protein interaction data led to the identification of several novel key proteins related to the immune system that may reflect the long-term effects of hepatitis C virus on the liver, and can introduce as therapeutic targets for advanced HCV- cirrhosis.

Keywords: Protein –protein interaction; Proteomic; Two-dimensional gel electrophoresis (2DE); hepatitis C; liver cirrhosis.