Quantitative proteomics analysis of early recurrence/metastasis of huge hepatocellular carcinoma following radical resection

Metabolomic Analysis and Computational Biology Reveal the Potential Metabolic Pathways for Improvement of Fucoxanthin and Eicosapentaenoic Acid (EPA) Biosynthesis in Phaeodactylum tricornutum

This work aims to provide a basis for the enhancement of fucoxanthin (FCX) and eicosapentaenoic acid (EPA) biosynthesis in the microalga Phaeodactylum tricornutum using metabolomics and computational biology. To achieve this, both targeted (UHPLC and GC-FID) and untargeted (FTIR and NMR) analyses were conducted throughout various stages of cell cultivation. Targeted analyses revealed that EPA concentrations peaked at the end of the logarithmic growth phase, while fucoxanthin levels remained consistent from the onset of this phase through to the stationary phase. Untargeted analyses provided metabolic profiles by correlating FTIR absorbance bands with functional groups. When combined with cultivation strategies designed to improve EPA and FCX content, the optimal time for harvesting cells was identified as the end of the logarithmic phase. NMR further highlighted potentially key metabolic pathways for optimizing EPA and FCX production in Phaeodactylum tricornutum, particularly those involved in glyoxylate and dicarboxylate metabolism.

Artificial intelligence assists precision medicine in cancer treatment

Cancer is a major medical problem worldwide. Due to its high heterogeneity, the use of the same drugs or surgical methods in patients with the same tumor may have different curative effects, leading to the need for more accurate treatment methods for tumors and personalized treatments for patients. The precise treatment of tumors is essential, which renders obtaining an in-depth understanding of the changes that tumors undergo urgent, including changes in their genes, proteins and cancer cell phenotypes, in order to develop targeted treatment strategies for patients. Artificial intelligence (AI) based on big data can extract the hidden patterns, important information, and corresponding knowledge behind the enormous amount of data. For example, the ML and deep learning of subsets of AI can be used to mine the deep-level information in genomics, transcriptomics, proteomics, radiomics, digital pathological images, and other data, which can make clinicians synthetically and comprehensively understand tumors. In addition, AI can find new biomarkers from data to assist tumor screening, detection, diagnosis, treatment and prognosis prediction, so as to providing the best treatment for individual patients and improving their clinical outcomes.

Clinical significance of half-hepatic blood flow occlusion technology in patients with hepatocellular carcinoma with cirrhosis

BACKGROUND

Most patients with primary hepatocellular carcinoma (HCC) have a history of chronic hepatitis B and usually present with varying degrees of cirrhosis. Owing to the special nature of liver anatomy, the blood vessel wall in the liver parenchyma is thin and prone to bleeding. Heavy bleeding and blood transfusion during hepatectomy are independent risk factors for liver cancer recurrence and death. Various clinical methods have been used to reduce intraoperative bleeding, and the Pringle method is most widely used to prevent blood flow to the liver.

AIM

To investigate the effect of half-hepatic blood flow occlusion after patients with HCC and cirrhosis undergo hepatectomy.

METHODS

This retrospective study included 88 patients with HCC and liver cirrhosis who underwent hepatectomy in our hospital from January 2017 to September 2020. Patients were divided into two groups based on the following treatment methods: the research group (n = 44), treated with half-hepatic blood flow occlusion technology and the control group (n = 44), treated with total hepatic occlusion. Differences in operation procedure, blood transfusion, liver function, tumor markers, serum inflammatory response, and incidence of surgical complications were compared between the groups.

RESULTS

The operation lasted longer in the research group than in the control group (273.0 ± 24.8 min vs 256.3 ± 28.5 min, P < 0.05), and the postoperative anal exhaust time was shorter in the research group than in the control group (50.0 ± 9.7 min vs 55.1 ± 10.4 min, P < 0.05). There was no statistically significant difference in incision length, surgical bleeding, portal block time, drainage tube indwelling time, and hospital stay between the research and control groups (P > 0.05). Before surgery, there were no significant differences in serum alanine transaminase (ALT), aspartate aminotransferase (AST), total bilirubin, and prealbumin levels between the research and control groups (P > 0.05). Conversely, 24 and 72 h after the operation the respective serum ALT (378.61 ± 77.49 U/L and 246.13 ± 54.06 U/L) and AST (355.30 ± 69.50 U/L and 223.47 ± 48.64 U/L) levels in the research group were significantly lower (P < 0.05) than those in the control group (ALT, 430.58 ± 83.67 U/L and 281.35 ± 59.61 U/L; AST, 416.49 ± 73.03 U/L and 248.62 ± 50.10 U/L). The operation complication rate did not significantly differ between the research group (15.91%) and the control group (22.73%; P > 0.05).

CONCLUSION

Half-hepatic blood flow occlusion technology is more beneficial than total hepatic occlusion in reducing liver function injury in hepatectomy for patients with HCC and cirrhosis.

Comprehensive Analysis of the Prognosis and Correlations With Immune Infiltration of S100 Protein Family Members in Hepatocellular Carcinoma

S100 protein family members (S100s) are commonly dysregulated in various tumors including hepatocellular carcinoma (HCC). However, the diverse expression, mutation, prognosis and associations with immune infiltration of S100s in HCC have yet to be analyzed. Herein we investigated the roles of S100s in HCC from the Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal and TIMER databases. Compared with para-cancer tissues, the expression levels of S100A4/S100A6/S100A10/S100A11/S100A13/S100A14/S100P were higher in HCC tissues, while the expression levels of S100A8/S100A9/S100A12 were decreased in tumor tissues. The mRNA levels of S100A2/S100A7/S100A7A/S100A8/S100A9/S100A11 were correlated with advanced tumor stage. Besides, higher mRNA expressions of S100A6/S100A10/S100A11/S100A13/S100A14/S100P were shown to have shorter overall survival (OS), while higher expression of S100A12 was associated with favorable OS. Further, the mutation rate of S100s was investigated, and the high mutation rate (53%) was associated with shorter OS. Additionally, the expressions of S100s were found to be significantly associated with various immune infiltrating cells. Hence, our results showed that S100A6/S100A10/S100A11/S10012/S100A13/S100A14/S100P may be regarded as new prognostic or therapeutic markers and S100s inhibitors may be helpful in the combination of immunotherapies.

Proteomic Profiling and Artificial Intelligence for Hepatocellular Carcinoma Translational Medicine

Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver with high morbidity and mortality rates worldwide. Since 1963, when alpha-fetoprotein (AFP) was discovered as a first HCC serum biomarker, several other protein biomarkers have been identified and introduced into clinical practice. However, insufficient specificity and sensitivity of these biomarkers dictate the necessity of novel biomarker discovery. Remarkable advancements in integrated multiomics technologies for the identification of gene expression and protein or metabolite distribution patterns can facilitate rising to this challenge. Current multiomics technologies lead to the accumulation of a huge amount of data, which requires clustering and finding correlations between various datasets and developing predictive models for data filtering, pre-processing, and reducing dimensionality. Artificial intelligence (AI) technologies have an enormous potential to overcome accelerated data growth, complexity, and heterogeneity within and across data sources. Our review focuses on the recent progress in integrative proteomic profiling strategies and their usage in combination with machine learning and deep learning technologies for the discovery of novel biomarker candidates for HCC early diagnosis and prognosis. We discuss conventional and promising proteomic biomarkers of HCC such as AFP, lens culinaris agglutinin (LCA)-reactive L3 glycoform of AFP (AFP-L3), des-gamma-carboxyprothrombin (DCP), osteopontin (OPN), glypican-3 (GPC3), dickkopf-1 (DKK1), midkine (MDK), and squamous cell carcinoma antigen (SCCA) and highlight their functional significance including the involvement in cell signaling such as Wnt/β-catenin, PI3K/Akt, integrin αvβ3/NF-κB/HIF-1α, JAK/STAT3 and MAPK/ERK-mediated pathways dysregulated in HCC. We show that currently available computational platforms for big data analysis and AI technologies can both enhance proteomic profiling and improve imaging techniques to enhance the translational application of proteomics data into precision medicine.

VSP‑17 suppresses the migration and invasion of triple‑negative breast cancer cells through inhibition of the EMT process via the PPARγ/AMPK signaling pathway

VSP-17, a novel peroxisome proliferator-activated receptor γ (PPARγ) agonist, has been previously demonstrated to suppress the metastasis of triple-negative breast cancer (TNBC) by upregulating the expression levels of E-cadherin, which is a key marker of epithelial-mesenchymal transition (EMT). However, the mechanism of action of VSP-17, in particular whether it may be associated with the EMT process, remains unknown. The present study investigated the ability of VSP-17 to inhibit the invasiveness and migratory ability of TNBC cell lines (MDA-MB-231 and MDA-MB-453) performed in in vitro experiments. including cell migration assay, cell invasion assay, cell transfection, RT-qPCR, western blot (WB) analysis and immunofluorescence. The present study aimed to ascertain whether and how the PPARγ/AMP-activated protein kinase (AMPK) signaling pathway serves a role in the inhibitory effects of VSP-17 on cell migration and invasion. The results revealed that both treatment with compound C (an AMPK inhibitor) and transfection with small interfering RNA (si)AMPK notably diminished the inhibitory effect of VSP-17 treatment on the migration and invasion of MDA-MB-231 and MDA-MB-453 cells, indicating that VSP-17 may, at least partly, exert its effects via AMPK. Furthermore, both compound C and siAMPK markedly diminished the VSP-17-induced downregulation of vimentin expression levels and upregulation of E-cadherin expression levels, further indicating that the VSP-17-induced inhibition of the EMT process may be dependent on AMPK. The combination of GW9662 (a PPARγ antagonist) or siPPARγ diminished the inhibitory effect of VSP-17 treatment on the migration and invasion of the TNBC cells, indicating that PPARγ may serve an important role in the VSP-17-induced inhibition of the migration and invasion of TNBC cells. In addition, both GW9662 and siPPARγ significantly reversed the VSP-17-induced downregulation of vimentin expression levels and upregulation of E-cadherin expression levels, implying that the VSP-17-induced inhibition of the EMT process may be dependent on PPARγ. VSP-17 treatment also upregulated the expression levels of p-AMPK, which could be reversed by either GW9662 or siPPARγ, indicating that the VSP-17-induced activation of the AMPK signaling pathway was PPARγ-dependent. In conclusion, the findings of the present study indicated that VSP-17 treatment may inhibit the migration and invasion of TNBC cells by suppressing the EMT process via the PPARγ/AMPK signaling pathway.

Effects of Catalpa Alcohol From Rehmannia glutinosa on Calcium-Binding Protein, Interleukin-1β, and Galectin-3 in Synovial Tissues of Rats With Knee Osteoarthritis

Objectives

We aimed to evaluate the effects of catalpa alcohol from Rehmannia glutinosa on the expressions of calcium-binding protein (S100A12), interleukin-1β (IL-1β), and galectin-3 in the synovium of rats with early knee osteoarthritis (KOA).

Methods

Fifty-two adult male Wistar rats aged 3 to 8 weeks were divided into normal control (n = 16), model (n = 12), low-dose (n = 12), and high-dose groups (n = 12). On the 10th day after modeling, 6 rats in normal control group and 6 in the other 3 groups were randomly selected. X-ray and 3-dimensional computed tomography (3D CT) images of the left knee joint were taken under live anesthesia. The joint cavity of sacrificed rats was opened to observe cartilage surface. After 28 consecutive days of administration, the synovial tissue of left knee joint was collected.

Results

The S100A12, IL-1β, and galectin-3 levels in synovial tissue were detected by immunohistochemistry and ELISA. There were articular cartilage defects in left knees. Radiologic examination showed significant joint space narrowing and hyperplasia, and 3D CT joint space value decreased (P &lt; 0.05). The Mankins and OARSI scores of synovial histopathology were significantly different (P &lt; 0.05). The S100A12, IL-1β, and galectin-3 levels in synovial tissue of the model group significantly exceeded those of the normal control group (P &lt; 0.01). Compared with the model group, such levels of low-dose (P &lt; 0.05) and high-dose groups (P &lt; 0.01) were significantly lower.

Conclusions

The S100A12, IL-1β and galectin-3 levels in synovium tissue decreased with rising concentration of catalpa alcohol from R. glutinosa. Therefore, this drug is potentially suitable for inhibiting an inflammatory response to delay the progression of KOA.

RCC2 contributes to tumor invasion and chemoresistance to cisplatin in hepatocellular carcinoma

Tumor metastasis and chemoresistance are the main causes of treatment failure and high mortality in hepatocellular carcinoma (HCC). Therefore, it is critical to clarify the biological action and potential mechanisms in HCC cells to develop novel therapeutics. The regulator of chromosome condensation 2 (RCC2), a component of the chromosomal passenger complex, was shown to have important roles in tumor development and radio-chemotherapy resistance. However, its role in the aggressive phenotypes and cisplatin (DDP)-resistance of HCC is not known. Therefore, this study aimed to investigate the role of RCC2 in HCC pathogenesis. Interestingly, we found that RCC2 was upregulated in HCC patient specimens and HCC cell lines and was correlated with the pathological grade of HCC. To evaluate the function of RCC2 in HCC cell, lentivirus vector-based shRNAs were transfected into HCC cells. Silencing RCC2 inhibited the HCC cell proliferation, migration, invasion, and increased the apoptosis rate upon DDP treatment. Further analysis showed that RCC2-mediated downregulation of the expression of survival proteins occurred via the AKT and Bcl2 pathways. Our results suggest that RCC2 might act as an oncogenic protein promoting metastatic behaviors and cisplatin resistance in HCC cells, and thereby could be a potential prognostic biomarker and therapeutic target for HCC.

Downregulation of S100 calcium binding protein A12 inhibits the growth of glioma cells

Background

S100 calcium binding protein A12 (S100A12) is a member of the S100 protein family and is widely expressed in neutrophil and low expressed in lymphocytes and monocyte. However, the role of S100A12 in glioma has not yet been identified.

Methods

In the present study, we carried out immunohistochemical investigation of S100A12 in 81 glioma tissues to determine the expression of S100A12 in glioma cells, and evaluate the clinical significance of S100A12 in glioma patients. Futher we knockdown the S100A12 by shRNA, and evaluated cell proliferation, cell migration and cell apoptosis by MTT, colony formation assay, transwell assay,flow cytometry assa and western blot.

Results

We found that S100A12 was upregulated in tissues of glioma patients and the expression was correlated to WHO stage and tumor size. Further, we found that knockdown S100A12 inhibits the proliferation, migration and invasion of glioma cells through regulating cell apoptosis and EMT.

Conclusion

S100A12 plays a vital role in glioma progression, and may be an important regulatory molecule for biological behaviors of glioma cell lines.

S100A12 is a promising biomarker in papillary thyroid cancer

S100A12 belongs to the S100 family and acts as a vital regulator in different types of tumors. However, the function of S100A12 in thyroid carcinoma has not yet been investigated. In this study, we analyzed the expression of S100A12 in human papillary thyroid cancer (PTC) samples and two PTC cell lines. In addition, we explored the effects of S100A12 on PTC cell progression in vitro and in vivo. Our results showed that S100A12 was significantly upregulated in PTC specimens. Moreover, silencing S100A12 markedly inhibited PTC cell proliferation, migration, invasion and cell cycle progression. In addition, knockdown of S100A12 significantly reduced the expression of CyclinD1, CDK4 and p-ERK in PTC cells. An in vivo study also showed that silencing S100A12 dramatically suppressed tumor cell growth and decreased Ki67 expression in a xenograft mouse model. This study provides novel evidence that S100A12 serves as an oncogene in PTC. Knockdown of S100A12 suppressed PTC cell proliferation, migration, and invasion and induced G0/G1 phase arrest via the inhibition of the ERK signaling pathway. Therefore, S100A12 may be a potent therapeutic target for PTC.

4E-BP1Thr46 Phosphorylation Association with Poor Prognosis in Quantitative Phosphoproteomics of Portal Vein Tumor Thrombus Revealed that 4E-BP1Thr46 Phosphorylation is Associated with Poor Prognosis in HCC

Purpose

Early formation of portal vein tumor thrombosis (PVTT) is a key characteristic of hepatocellular carcinoma (HCC) metastasis, but to date, the aetiology of PVTT in HCC metastasis is largely unknown. We aim to find highly sensitive and specific biomarkers for the prediction of HCC prognosis.

Patients and methods

We used isobaric tags for relative and absolute quantitation (iTRAQ) based quantitative phosphoproteomics approach to investigate the molecular signatures of the HCC with PVTT in primary HCC tissues, surrounding non-cancerous tissues and PVTT tissues. The different proteome profiles in three groups were investigated and might reveal different underlying molecular mechanisms.

Results

In total, we identified 1745 phosphoproteins with 2724 phosphopeptides and 4594 phosphorylation sites in three groups. Among these phosphoproteins, 80 phosphoproteins were dysregulated in PVTT/Pan group, 51 phosphoproteins were dysregulated in HCC/Pan group, and 10 phosphoproteins were dysregulated in PVTT/HCC group. Furthermore, the phosphorylation of 4E-BP1 was elevated in HCC tissues and PVTT tissues in comparison with surrounding non-cancerous tissues,  and the elevated fold change of phosphorylation level was higher than that in expression level of 4E-BP1. The further IHC analysis in acohort of 20 HCC tissues showed that the phosphorylation of 4E-BP1 on Thr46 might be closely related to HCC prognosis.

Conclusion

The high phosphorylation level of 4E-BP1^Thr46 might serve as a biomarker for the diagnosis of early recurrence and metastasis of HCC.

Dataset for quantitative phospho-proteomics analysis of a serial hepatoma cell lines with increasing invasion and metastasis potential

Hepatoma is one of the most common malignant tumor, and most patients have very poor prognosis. Early prediction and intervention of the hepatoma recurrence/metastasis are the most effective way to improve the patients' clinical outcomes. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) based quantitative phospho-proteomics approach to identify biomarkers associated with hepatoma recurrence/metastasis in hepatoma cell lines with increasing metastasis ability. In total, 75 phosphorylated peptides corresponding to 60 phosphoproteins were significantly dysregulated. Bioinformatics analysis (GO, KEGG and IPA) allowed these data to be organized into distinct categories. These data represent the first in-depth proteomics analysis of a serial hepatoma cell lines with increasing invasion and metastasis potential. The data are related to (Xing et al., 2019).

ANXA2Tyr23 and FLNASer2152 phosphorylation associate with poor prognosis in hepatic carcinoma revealed by quantitative phosphoproteomics analysis

Hepatoma is one of the most common malignant tumors, and most patients have very poor prognosis. Early prediction and intervention of the hepatoma recurrence/metastasis are the most effective way to improve the patients' clinical outcomes. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) based quantitative phospho-proteomics approach to identify biomarkers associated with hepatoma recurrence/metastasis in hepatoma cell lines with increasing metastasis ability. In total, 75 phosphorylated peptides corresponding to 60 phosphoproteins were significantly dysregulated and the participated biological processes of these phosphoproteins were tightly associated with tumor metastasis. Further signaling pathway analysis revealed that key signaling pathways which play crucial roles in cancer metastasis have been significantly over activated in the highly metastatic cells. Furthermore, the phosphorylation of FLNASer2152 and ANXA2Tyr23 were validated to be significantly up regulated in the high-metastatic cells comparing with the low-metastatic cells. By further investigation the clinical significance of the phosphorylation of FLNASer2152 and ANXA2Tyr23 in large-scale clinical samples, revealed that the over phosphorylation of FLNASer2152 and ANXA2Tyr23 were associated with poor prognosis and might be potential prognostic biomarkers for the primary hepatoma. When FLNASer2152 combined with ANXA2Tyr23, it had a better prognostic value for both OS and TTR.

Comparative proteomics of side population cells derived from human hepatocellular carcinoma cell lines with varying metastatic potentials

Metastasis and recurrence following surgery are major reasons for the high mortality rate and poor prognosis associated with hepatocellular carcinoma (HCC). Cancer stem cells (CSCs) are thought to be able to cause cancer, and to be the primary cause of tumor recurrence and metastasis. The underlying mechanisms of the metastatic potential of CSCs is poorly understood. In the present study, side population (SP) cells were isolated from 4 HCC cell lines, and their self-renewal and migratory abilities were compared. The results demonstrate that SP cells from different cell lines exhibited similar self-renewal abilities but different metastatic potentials. Furthermore, the overall proteomes of the SP cells were systematically quantified. This revealed 11 and 19 differentially expressed proteins (DEPs), upregulated and downregulated, respectively, associated with increased metastatic potential. These proteins were involved in the 'regulation of mRNA processing' and 'cytoskeleton organization' biological processes. The majority of the proteins were involved in 'cell proliferation', 'migration' and 'invasion of cancer', and may promote HCC metastasis in a synergistic manner. The AKT and nuclear factor-κB signaling pathways may contribute to the regulation of HCC metastasis through regulating the DEPs in SP cells. To the best of our knowledge, the present study is the first to demonstrate the overall proteome difference among SP cells from the different HCC cell lines with different metastatic potentials. The present study provides novel information regarding the metastatic potential of CSCs, which will facilitate further investigation of the topic.

XRCC1 and XPD polymorphisms and their relation to the clinical course in hepatocarcinoma patients

In this study genotyping of hepatocellular carcinoma (HCC) patients was conducted to detect polymorphisms on the X-ray repair cross-complementing 1 (XRCC1) and xeroderma pigmentosum complementary group D (XPD) genes and analyze the relationship of their presence with the clinical features of the cancer. A total of 172 patients with HCC were selected in Qilu Hospital, Shandong University, from January 2010 to September 2011. All patients underwent resection of HCC and no tumor metastases were found. Peripheral venous blood samples (3–5 ml) were collected from the patients to extract genomic DNA. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and gene sequencing. During the five-year follow-up, the survival of patients with various genotypes of XRCC1 and XPD genes were observed and compared. Logistic regression analysis was used to analyze the association between single nucleotide polymorphisms of XRCC1 and XPD genes and the prognosis of patients with HCC. χ² tests showed that XRCC1-194, XRCC1-280 and XPD-312 gene polymorphisms were significantly correlated with the number, location and diameter of the tumors (p<0.05). No significant difference was found in the survival curve of patients presenting different genotypes of the XRCC1-194 locus (p>0.05). Nevertheless, a significant difference was found in the survival curve of patients with AA and GG genotypes of the XRCC1-280 locus and in the patients with AA, GA and GG genotypes of the XPD-312 locus (p<0.05). Logistic regression analysis showed that the XRCC1-194 genotype was not an independent risk factor for HCC mortality risk (p>0.05), but XRCC1-280 (OR=1.815, p<0.01) and XPD-312 (OR=1.815, p<0.01) genotypes were independent risk factors for a poor prognosis. Taken together our results point to polymorphisms in XRCC1 and XPD genes as being related to the clinical characteristics of HCC, making them suitable prognostic markers of HCC.

Reveal the molecular signatures of hepatocellular carcinoma with different sizes by iTRAQ based quantitative proteomics

Tumor size of hepatocellular carcinoma (HCC) is a key parameter for predicting prognosis of HCC patients. The biological behaviors of HCC, such as tumor growth, recurrence and metastasis are significantly associated with tumor size. However, the underlying molecular mechanisms remain unclear. Here, we applied iTRAQ-based proteomic strategy to analyze the proteome differences among small, media, large and huge primary HCC tissues. In brief,88 proteins in small HCC, 69 proteins in media HCC, 118 proteins in large HCC and 215 proteins in huge HCC, were identified by comparing the proteome of cancerous tissues with its corresponding non-cancerous tissues. Further analysis of dysregulated proteins involved in signaling revealed that alteration of ERK1/2 and AKT signaling played important roles in the tumorigenesis or tumor growth in all subtypes. Interestingly, alteration of specific signaling was discovered in small and huge HCC, which might reflect specific molecular mechanisms of tumor growth. Furthermore, the dysregulation degree of a group of proteins has been confirmed to be significantly correlated with the tumor size; these proteins might be potential targets for studying tumor growth of HCC. Overall, we have revealed the molecular signatures of HCC with different tumor sizes, and provided fundamental information for further in-depth study.

BIOLOGICAL SIGNIFICANCE

In this study, we compared the protein expression profiles among different HCC subtypes, including small HCC, media HCC, large HCC and huge HCC for the first time. The results clearly proved that different molecular alterations and specific signaling pathways were indeed involved in different HCC subtypes, which might explain the different malignancy biological behaviors. In addition, the dysregulation degree of a group of proteins has been confirmed to be significantly correlated with the tumor size. We believe that these findings would help us better understand the underlying molecular mechanisms of the tumorigenesis and development of HCC.

Increased expression of PDIA3 and its association with cancer cell proliferation and poor prognosis in hepatocellular carcinoma

The prognosis of hepatocellular carcinoma (HCC) is unfavorable following complete tumor resection. The aim of the present study was to identify a molecule able to predict HCC prognosis through comprehensive protein profiling and to elucidate its clinicopathological significance. Comprehensive protein profiling of HCC was performed by liquid chromatography-tandem mass spectrometry. Through the bioinformatic analysis of proteins expressed differentially in HCC and non-HCC tissues, protein disulfide-isomerase A3 (PDIA3) was identified as a candidate for the prediction of prognosis. PDIA3 expression was subsequently examined in 86 cases of HCC by immunostaining and associations between PDIA3 expression levels and clinicopathological characteristics were evaluated. The Ki-67 index and apoptotic cell death of carcinoma cells were examined by immunostaining and terminal deoxynucleotidyl transferase dUTP nick-end labeling assay in 24 cases. The results demonstrated that PDIA3 was expressed in all 86 HCC cases; 56 HCC cases (65%) exhibited high expression of PDIA3 and 30 (35%) exhibited low expression. The disease-free and overall survival times of HCC patients with high PDIA3 expression were significantly shorter than in HCC patients with low expression. Furthermore, increased expression of PDIA3 was associated with an elevated Ki-67 index, indicating increased cancer cell proliferation and a reduction in apoptotic cell death. Taken together, these results suggest that PDIA3 expression is associated with tumor proliferation and decreased apoptosis in HCC, and that increased expression of PDIA3 predicts poor prognosis. PDIA3 may therefore be a key molecule in the development of novel targeting therapies for patients with HCC.

The application of proteomics in different aspects of hepatocellular carcinoma research

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, which is causing the second leading cancer-related death worldwide. With the significant advances of high-throughput protein analysis techniques, the proteomics offered an extremely useful and versatile analytical platform for biomedical researches. In recent years, different proteomic strategies have been widely applied in the various aspects of HCC studies, ranging from screening the early diagnostic and prognostic biomarkers to in-depth investigating the underlying molecular mechanisms. In this review, we would like to systematically summarize the current applications of proteomics in hepatocellular carcinoma study, and discuss the challenges of applying proteomics in study clinical samples, as well as discuss the possible application of proteomics in precision medicine.

BIOLOGICAL SIGNIFICANCE

In this review, we have systematically summarized the current applications of proteomics in hepatocellular carcinoma study, ranging from screening biomarkers to in-depth investigating the underlying molecular mechanisms. In addition, we have discussed the challenges of applying proteomics in study clinical samples, as well as the possible applications of proteomics in precision medicine. We believe that this review would help readers to be better familiar with the recent progresses of clinical proteomics, especially in the field of hepatocellular carcinoma research.

Overexpression of annexin A4 indicates poor prognosis and promotes tumor metastasis of hepatocellular carcinoma

The prognosis of hepatocellular carcinoma (HCC) after surgical resection remains unsatisfactory for the majority of HCC patients who developed early recurrence or metastasis. There is still a lack of reliable biomarkers that can be used to predict the possibility of recurrence/metastasis in HCC patients after operation. In the current study, annexin A4, a calcium-dependent phospholipid-binding protein, has been found to be significantly elevated in HCC patients with early recurrence/metastasis, and had a strong correlation with portal vein tumor thrombosis (p = 0.03) and advanced BCLC stage (p = 0.002). Cox proportional hazards regression analysis revealed that annexin A4 was an independent prognostic predictor for both early recurrence/metastasis (HR = 1.519, p = 0.032) and overall survival (HR = 1.827, p = 0.009) after surgical resection. Meanwhile, Kaplan-Meier analysis showed that Patients with high-expression levels of annexin A4 had higher recurrence rate and shorter overall survival than those with low expression (log-rank test, p < 0.001). Furthermore, in vitro studies have demonstrated that overexpression of annexin A4 facilitated HCC cell migration and invasion via regulating epithelial-mesenchymal transition (EMT). In conclusion, annexin A4 has played important roles in the progression of HCC, and might act as a potential prognostic biomarker for HCC.

Serum C-reactive protein and S100A12 concentrations in dogs with hepatic disease

OBJECTIVES

To describe serum C-reactive protein and S100A12 concentrations in dogs with hepatic disease and to determine whether there is a relationship between the concentration of either and the severity of hepatic necroinflammation.

METHODS

Serum C-reactive protein and S100A12 concentrations were measured in 46 dogs undergoing hepatic biopsy. Dogs were divided into three groups: congenital portosystemic shunts, chronic hepatitis and hepatic neoplasia. The histological severity of hepatic necroinflammation was scored.

RESULTS

C-reactive protein and S100A12 concentrations were greater than the upper limit of the reference intervals in 39 and 26% of dogs, respectively. There was no association of disease group with C-reactive protein (P=0·1733) or S100A12 (P=0·1513) concentrations. There was a positive correlation between serum C-reactive protein concentration and hepatic necroinflammatory activity (rs =0·428, P=0·006).

CLINICAL SIGNIFICANCE

Increased serum C-reactive protein and S100A12 concentrations were observed in a subpopulation of dogs with various types of hepatic diseases, suggesting acute-phase inflammation and activation of phagocytic cells, respectively. Dogs with higher hepatic necroinflammatory activity scores tended to have higher serum C-reactive protein concentrations. Further studies are needed to confirm this finding in a larger group of dogs.

Quantitative Proteomics Analysis of Tissue Interstitial Fluid for Identification of Novel Serum Candidate Diagnostic Marker for Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the fifth most common malignant cancer in the world. The sensitivity of alpha-fetoprotein (AFP) is still inadequate for HCC diagnosis. Tissue interstitial fluid (TIF), as the liquid microenvironment of cancer cells, was used for biomarker discovery in this study. Paired tumor and nontumor TIF samples from 6 HBV-HCC patients were analyzed by a proteomic technique named iTRAQ (isobaric tag for relative and absolute quantitation). Totally, 241 up-regulated proteins (ratio ≥ 1.3, p < 0.05) and 288 down-regulated proteins (ratio ≤ -1.3, p < 0.05) in tumor TIF were identified. Interestingly, proteins in S100 family were found remarkably up-regulated in tumor TIF. One dramatically up-regulated protein S100A9 (ratio = 19) was further validated by ELISA in sera from liver cirrhosis (LC, HCC high risk population) and HCC patients (n = 47 for each group). The level of this protein was significantly elevated in HCC sera compared with LC (p < 0.0001). The area under the curve of this protein to distinguish HCC from LC was 0.83, with sensitivity of 91% (higher than AFP) and specificity of 66%. This result demonstrated the potential of S100A9 as a candidate HCC diagnostic biomarker. And TIF was a kind of promising material to identify candidate tumor biomarkers that could be detected in serum.

Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics

Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study.

Diagnostic importance of S100A9 and S100A12 in breast cancer

BACKGROUND

The most frequent cause of cancer deaths throughout the world is breast cancer (BC). Therefore, preventing, diagnosing and treating BC has gained importance. S100 protein probably plays an important role in carcinogenesis, cancer development, and metastasis. In this study, we aimed at diagnostic and clinic-pathological importance of serum levels of S100A9 and S100A12 with known cytokine-like pro-inflammatory effects in BC.

MATERIAL AND METHOD

Serum samples were collected with BC and the control group consisting of healthy individuals. All the samples were analyzed with enzyme-linked immunosorbent assay for serum S100A9 and S100A12 levels before starting the systemic chemotherapy. Clinicopathological characteristics of BC and other blood parameters were compared in relation with serum S100A9 and S100A12 levels.

RESULTS

While the serum S100A9 levels were found significantly higher as compared to healthy individuals (190.85±32.29 and 92.72±54, respectively) (p=0.001), it was observed that there were no differences in S100A12 (120.50±15.78 and 112.21±10.46, respectively) (p=0.056) levels. As regards the subgroup analysis in BC patients, no statistically significant results were found in body mass index (BMI), smoking, menopause status, histopathologic type, grade, and biological subtype of BC, tumor size, presence of lymph node metastases, lymphovascular invasion (LVI), perineural invasion (PNI) and stage. As regards the blood parameters and serum S100 A9, while only statistically significant results were found with anemia (209.05±33.12 and 181.75±28.21, respectively) (p=0.005), no statistically significant results were found with leukocytosis, thrombocytosis and tumor markers.

CONCLUSION

In this study, while we found the level of S100A9, which has a potential cytokine-like function in inflammation, significantly higher, we could not find any increase in S100A12 level. Therefore, it is possible that S100A9 can play a key role in inflammation-related BC. Despite of there are no significance relationship between S100A9 and S100A12 clinicopathological features of BC, the determination of S100A9 levels contributes to diagnosis the of BC patients. In future, we suggest that serum S100A9 is investigated as a diagnostic tool even the target marker in BC to suppress inflammation in treatment.

Comparative analysis of primary hepatocellular carcinoma with single and multiple lesions by iTRAQ-based quantitative proteomics

In clinical practices, the therapeutic outcomes and prognosis of hepatocellular carcinoma (HCC) patients with different tumor numbers after surgery are very different; however, the underlying mechanisms of the tumorigenesis and development of HCC with different tumor numbers are still not well understood. Here, we systematically compared the overall proteome profiles between the primary HCC with single and multiple lesions using iTRAQ-based quantitative proteomics approach. We identified that 107 and 330 proteins were dysregulated in HCC tissue with multiple lesions (MC group) and HCC tissue with a single lesion (SC group), compared with their non-cancerous tissue (MN and SN groups) respectively. The dysregulated proteins in MC group are concentrated in UBC signaling pathway and NFκB signaling pathway, but the dysregulated proteins in SC group are more concentrated in ERK signaling pathway and the NFκB signaling pathway. These information revealed that there might be different molecular mechanisms of the tumorigenesis and development of the HCC with single and multiple lesions. Furthermore, HSD17B13 were only down-regulated in MC group while HK2 were only up-regulated in SC group among these dysregulated proteins. Therefore, the protein HSD17B13 and HK2 might be potential biomarkers for the primary HCC with single and multiple lesions.

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.)

Rice hull, the outer cover of the rice grain, determines grain shape and size. Changes in the rice hull proteome in different growth stages may reflect the underlying mechanisms involved in grain development. To better understand these changes, isobaric tags for relative and absolute quantitative (iTRAQ) MS/MS was used to detect statistically significant changes in the rice hull proteome in the booting, flowering, and milk-ripe growth stages. Differentially expressed proteins were analyzed to predict their potential functions during development. Gene ontology (GO) terms and pathways were used to evaluate the biological mechanisms involved in rice hull at the three growth stages. In total, 5,268 proteins were detected and characterized, of which 563 were differentially expressed across the development stages. The results showed that the flowering and milk-ripe stage proteomes were more similar to each other (r=0.61) than either was to the booting stage proteome. A GO enrichment analysis of the differentially expressed proteins was used to predict their roles during rice hull development. The potential functions of 25 significantly differentially expressed proteins were used to evaluate their possible roles at various growth stages. Among these proteins, an unannotated protein (Q7X8A1) was found to be overexpressed especially in the flowering stage, while a putative uncharacterized protein (B8BF94) and an aldehyde dehydrogenase (Q9FPK6) were overexpressed only in the milk-ripe stage. Pathways regulated by differentially expressed proteins were also analyzed. Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), and two magnesium-chelatase subunits, ChlD (Q6ATS0), and ChlI (Q53RM0), were associated with chlorophyll biosynthesis at different developmental stages. The expression of Q9SDJ2 in the flowering and milk-ripe stages was validated by qRT-PCR. The 25 candidate proteins may be pivotal markers for controlling rice hull development at various growth stages and chlorophyll biosynthesis pathway related proteins, especially magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), may provide new insights into the molecular mechanisms of rice hull development and chlorophyll associated regulation.

The Human Antimicrobial Protein Calgranulin C Participates in Control of Helicobacter pylori Growth and Regulation of Virulence

During infectious processes, antimicrobial proteins are produced by both epithelial cells and innate immune cells. Some of these antimicrobial molecules function by targeting transition metals and sequestering these metals in a process referred to as "nutritional immunity." This chelation strategy ultimately starves invading pathogens, limiting their growth within the vertebrate host. Recent evidence suggests that these metal-binding antimicrobial molecules have the capacity to affect bacterial virulence, including toxin secretion systems. Our previous work showed that the S100A8/S100A9 heterodimer (calprotectin, or calgranulin A/B) binds zinc and represses the elaboration of the H. pylori cag type IV secretion system (T4SS). However, there are several other S100 proteins that are produced in response to infection. We hypothesized that the zinc-binding protein S100A12 (calgranulin C) is induced in response to H. pylori infection and also plays a role in controlling H. pylori growth and virulence. To test this, we analyzed gastric biopsy specimens from H. pylori-positive and -negative patients for S100A12 expression. These assays showed that S100A12 is induced in response to H. pylori infection and inhibits bacterial growth and viability in vitro by binding nutrient zinc. Furthermore, the data establish that the zinc-binding activity of the S100A12 protein represses the activity of the cag T4SS, as evidenced by the gastric cell "hummingbird" phenotype, interleukin 8 (IL-8) secretion, and CagA translocation assays. In addition, high-resolution field emission gun scanning electron microscopy (FEG-SEM) was used to demonstrate that S100A12 represses biogenesis of the cag T4SS. Together with our previous work, these data reveal that multiple S100 proteins can repress the elaboration of an oncogenic bacterial surface organelle.

Hepatocellular carcinoma with bile duct tumor thrombus: a clinicopathological analysis of factors predictive of recurrence and outcome after surgery

Although hepatocellular carcinoma (HCC) with bile duct tumor thrombus (BDTT) is a rare entity, most patients experience tumor recurrence even after curative resection and the prognosis remains dismal. This study aimed to analyze the clinicopathological risk factors for recurrence and poor outcome after surgical treatment of HCC with BDTT.Clinicopathological data of 37 patients with HCC and BDTT who underwent surgical treatment from July 2005 to June 2012 at the authors' hospital were reviewed retrospectively. Prognostic factors and potential risk factors for recurrence were assessed by Cox proportional hazard model and binary logistic regression model, respectively.Among the 37 patients, anatomical and nonanatomical liver resection was performed in 26 and 11 patients, respectively. The resection was considered curative in 19 patients and palliative in 18 patients. Also, 21 cases had tumor recurrence after operation and 7 cases of them were reoperated. Multivariate binary logistic regression model revealed that surgical curability was the only independent risk factor associated with postoperative tumor recurrence (P = 0.034). In addition, postoperative overall survival rates at 1, 2, and 3 years were 64.2%, 38.9%, and 24.3%, respectively. Cox multivariate analysis indicated that surgical curability and tumor recurrence were independent prognostic factors for both overall survival and recurrence-free survival (P < 0.05).Although patients with HCC and BDTT had a relatively high rate of early recurrence after surgery, relatively favorable long-term outcome after curative hepatic resection could be achieved. Therefore, extensive and curative surgical treatment should be recommended when complete resection can be achieved and liver functional reserve is satisfactory.

Galectin-4 serves as a prognostic biomarker for the early recurrence / metastasis of hepatocellular carcinoma

Galectin-4 is a multifunctional lectin found at both intracellular and extracellular sites. It could serve as a tumor suppressor intracellularly and promote tumor metastases extracellularly during colorectal cancer development. However, galectin-4 expression and its prognostic value for patients with hepatocellular carcinoma (HCC) have not been well investigated. Here we report that galectin-4 was significantly downregulated in early recurrent/metastatic HCC patients, when compared to non-recurrent/metastatic HCC patients. Low expression of gelectin-4 was well associated with larger tumor size, microvascular invasion, malignant differentiation, more advanced TNM stage, and poor prognosis. Cancer cell migration and invasion could be significantly reduced through overexpression of galectin-4, but upregulated by knocking down of galectin-4 in vitro. Moreover, the serum galectin-4 level could be significantly elevated solely by hepatitis B virus infection. Combined with clinicopathological features, the higher serologic level of galectin-4 was well associated with more aggressive characteristics of HCC. Taken together, galectin-4 expression closely associates with HCC progression and might have potential use as a prognostic biomarker for HCC patients.

α-Methylacyl-CoA racemase (AMACR) serves as a prognostic biomarker for the early recurrence/metastasis of HCC

AIMS

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and it is still lacking effective prognostic biomarkers so far. Previous results of the iTRAQ-based quantitative proteomics study (iTRAQ-2DLC-MS/MS) have shown that α-methylacyl-CoA racemase (AMACR) might be a promising prognostic biomarker for the early recurrence/metastasis of hepatocellular carcinoma (HCC). Here a large-scale cohort clinical study was performed to evaluate its prognostic potential.

METHODS

HCC samples from patients (n=158) were used for the construction of tissue microarray. The expression level of AMACR was determined by immunohistochemical staining. A large-scale cohort clinical study between the expression of AMACR and some major clinical parameter has been performed to assess the prognostic potential of AMACR for the early recurrence/metastasis of HCC.

RESULTS

Some important clinical parameters such as α-fetoprotein, tumour numbers, dissemination to regional lymph nodes, tumour capsule and portal vein tumour thrombosis are significantly associated with the low expression of AMACR. The expression of AMACR was an independent factor for the survival of patients with HCC. The median survival time was 17 months in the low-expression group compared with 45 months in the high-expression group.

CONCLUSIONS

This study reveals that the AMACR might be a potential prognostic marker for predicting early recurrence/metastasis of HCC after hepatectomy.