Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis

Relevance of proteomics and metabolomics approaches to overview the tumorigenesis and better management of cancer

Proteomics and metabolomics, integral combination of OMICs platform are gaining prominence in cancer research to enhance scientific knowledge of bio-molecular interactions occurs in the cellular processes during cancer progression. This approach designed to identify potential tools for addressing the complexities of this multifaceted disease. This analysis focussed on the intricate interplay between proteins and metabolites within cancer cells and their surrounding microenvironment. By reviewing current proteomics and metabolomics studies, we aim to gain invaluable insights into tumour biology, progression, and its implication in therapeutic responses. This study highlights the importance of proteomics and metabolomics in discovering therapeutic targets and diagnostic biomarkers for targeted cancer treatment. Proteomics facilitates the analysis of protein expression, modifications and interactions, exemplified by the identification of HER2 mutations leads to development of breast cancer hence targeted therapies like trastuzumab could be initiated. Metabolomics reveals metabolic alternations such as elevated 2-hydroxyglutarate levels in gliomas linked to cancer progression and treatment resistance. The integration of these approaches clarifies complex signalling network driving oncogenesis and paves the way for innovative cancer therapies, including immune cheque point inhibitors. Proteomics and metabolomics have revolutionised cancer biology by revealing intricate signalling networks, metabolic dysregulations, and unique molecular alterations. This information is crucial for early cancer identification and prognosis, and for designing personalized therapeutic strategies. Innovative technologies like artificial intelligence and high-throughput mass spectrometry further enhance the potential of these studies. Fostering multidisciplinary collaboration and data-sharing is essential for maximising the impact of these approaches to cure as well as better management of the cancer.

The paradoxical role of SERPINB5 in gastrointestinal cancers: oncogene or tumor suppressor?

BACKGROUND

SERPINB5, also known as Maspin, is a non-inhibitory member of the serine protease inhibitor superfamily. SERPINB5 exerts diverse effects on a variety of human cancers, including cell proliferation, angiogenesis, apoptosis, tumor invasion, and metastasis. SERPINB5 has traditionally been regarded as a tumor suppressor gene, but emerging evidences supports its oncogenic properties.

METHODS

We conducted a comprehensive review of the existing literature on SERPINB5 in gastrointestinal cancers, synthesizing data on its expression patterns, subcellular localization, epigenetic modifications, and clinical significance.

RESULTS

Depending on its subcellular localization and epigenetic modifications, SERPINB5 demonstrate either protumor or antitumor activity in different gastrointestinal cancers, such as colorectal cancer, gastric cancer, pancreatic cancer, gallbladder cancer and liver cancer. We elucidate its potential as a predictive and prognostic biomarker, with a focus on its implications for diagnosis, prognosis, and therapeutic intervention, emphasizing its utility in early lesion detection and treatment.

CONCLUSIONS

SERPINB5 plays a complex and context-dependent role in gastrointestinal cancers, highlighting further research to dissect the true significance of SERPINB5 expression and the molecular mechanisms underlying its divergent clinical behaviors in cancer.

A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants

The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.

Functional TET2 gene polymorphisms increase the risk of neuroblastoma in Chinese children

The 5-methylcytosine (m5C) is the key chemical modification in RNAs. As one of the demethylases in m5C, TET2 has been shown as a tumor suppressor. However, the impact of TET2 gene polymorphisms on neuroblastoma has not been elucidated. 402 neuroblastoma patients and 473 controls were genotyped for TET2 gene polymorphisms using the TaqMan method. The impact of TET2 gene polymorphisms on neuroblastoma susceptibility was determined using multivariate logistic regression analysis. We also adopted genotype-tissue expression database to explore the impact of TET2 gene polymorphisms on the expression of host and nearby genes. We used the R2 platform and Sangerbox tool to analyze the relationship between gene expression and neuroblastoma risk and prognosis through non-parametric testing and Kaplan-Meier analysis, respectively. We found the TET2 gene polymorphisms (rs10007915 G > C and rs7670522 A > C) and the combined 2-5 risk genotypes can significantly increase neuroblastoma risk. Stratification analysis showed that these significant associations were more prominent in certain subgroups. TET2 rs10007915 G > C and rs7670522 A > C are significantly associated with reduced expression of TET2 mRNA. Moreover, lower expression of TET2 gene is associated with high risk, MYCN amplification, and poor prognosis of neuroblastoma. The rs10007915 G > C and rs7670522 A > C are significantly related to the increased expression of inorganic pyrophosphatase 2 mRNA, and higher expression of PPA2 gene is associated with high risk, MYCN amplification, and poor prognosis of neuroblastomas. In summary, TET2 rs10007915 G > C and rs7670522 A > C significantly confer neuroblastoma susceptibility, and further research is needed to investigate the underlying mechanisms.

ANP32B promotes colorectal cancer cell progression and reduces cell sensitivity to PRAP1 inhibitor through up-regulating HPF1

ANP32B, a member of the acidic leucine-rich nuclear phosphoprotein 32 family member B, is aberrantly expressed in various cancers, including colorectal cancer. However, the function and mechanism of action of ANP32B in colorectal cancer remain unclear. The present study therefore analyzed the expression of ANP32B and its activity in colorectal cancer patient samples and colorectal cancer cell lines. ANP32B expression was found to be significantly upregulated in colorectal cancer patient samples and cell lines. Upregulation of ANP32B enhanced colorectal cancer cell proliferation and migration, whereas downregulation of ANP32B suppressed colorectal cancer cell proliferation. RNA sequencing analysis of differentially expressed genes in ANP32B silenced colorectal cancer cells showed that histone PARylation factor 1 (HPF1), which protects against DNA damage by interacting with the anti-tumor target PARP1, was significantly downregulated. Luciferase promoter assays testing the regulatory association between ANP32B and HPF1 showed that ANP32B interacted with the HPF1 promoter. Analysis of colorectal cancer samples from The Cancer Genome Atlas showed that ANP32B and HPF1 expression were positively correlated, and recovery assays showed that ANP32B promoted colorectal cancer progression by up-regulating HPF1. Overexpression of ANP32B also reduced the sensitivity of colorectal cancer cells to PARP1 inhibitor, consistent with the oncogenic role of ANP32B. ANP32B may alter the sensitivity of colorectal cancer cells to PARP1 inhibitor via a mechanism associated with the HPF1 gene. In summary, these findings showed that ANP32B acted as a tumor promoter, potentiating both colorectal cancer malignancy and drug resistance. Targeting the ANP32B/HPF1 axis may have benefit for patients with colorectal cancer.

Expression signature and prognostic value of CREC gene family in human colorectal cancer

Colorectal cancer (CRC) is one of the malignant tumors with the highest morbidity and mortality and poor prognosis. The mammalian gene family of Cab45/reticulocalbin/ERC-45/calumenin (CREC) consists of RCN1, RCN2, RCN3, SDF4 and CALU. Although CREC family members have been associated with CRC, the expression pattern, prognostic value, and the role of CREC family in CRC remain unclear. In this study, the expression, survival and biological functions of CREC family in CRC were determined via bioinformatic datasets analysis and experimental verification on clinical CRC specimen. Bioinformatic analysis showed that the expression levels of most CREC family genes were higher in CRC tissues than in normal colorectal tissues. The qPCR and western blot results also revealed that the transcriptional and protein levels of CREC family were elevated in CRC tissues compared with adjacent tissues. Besides, CREC family was significantly correlated with advanced tumor stage and poor prognosis of CRC patients. The expression levels of CREC family had correlations with genomic mutation and methylation, and with the infiltration levels of CD4 + T cells, macrophages, neutrophils, and dendritic cells in the microenvironment of CRC. Functional networks enrichment analysis indicated that the genes of CREC family were essential factors for CRC metastasis. Collectively, these findings suggest that CREC family might be potential targets for the treatment of CRC and candidate prognostic markers for CRC patients.

ANP32B promotes lung cancer progression by regulating VDAC1

It has been reported before that acidic leucine-rich nuclear phosphoprotein 32 family member B (ANP32B) plays roles in many cancers, yet no report of its role in lung cancer exists. In this study, we documented an elevation of ANP32B within lung cancer tissues and cells. Knockdown of ANP32B hindered the proliferation as well as migration of lung cancer cells, whereas overexpression of ANP32B helps to promote the malignant progression of lung cancer. ANP32B also regulates lung cancer cells' apoptosis and cell cycling. In addition, voltage-dependent anion channel 1 (VDAC1) has been found to be a downstream targeted gene of ANP32B and is positively regulated by ANP32B in lung cancer cells. According to our research, the expression of VDAC1 was positively associated with ANP32B expression in lung adenocarcinoma (r = 0.61, P < 0.001) samples by Pearson's correlation coefficient analysis. Furthermore, rescue experiments demonstrated that VDAC1 could rescue the effect of ANP32B expression on lung cancer cell proliferation and migration. Our results suggest that ANP32B overexpression facilitates lung cancer progression by increasing the expression of VDAC1. As such, we have revealed a novel mechanism regulating the connection between ANP32B and VDAC1 and a potential role of ANP32B as an oncogene and a clinical therapeutic target in lung cancer.

Network module function enrichment analysis of lung squamous cell carcinoma and lung adenocarcinoma

BACKGROUND

Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the two major subtypes of non-small cell lung cancer that pose a serious threat to human health. However, both subtypes currently lack effective indicators for early diagnosis.

METHODS

To identify tumor-specific indicators and predict cancer-related signaling pathways, LUSC and LUAD gene weighted co-expression networks were constructed. Combined with clinical data, core genes in LUSC and LUAD modules were then screened using protein-protein interaction networks and their functions and pathways were analyzed. Finally, the effect of core genes on survival of LUSC and LUAD patients was evaluated.

RESULTS

We identified 12 network modules in LUSC and LUAD, respectively. LUSC modules "purple" and "green" and LUAD modules "brown" and "pink" are significantly associated with overall survival and clinical traits of tumor node metastasis, respectively. Eleven genes from LUSC and eight genes from LUAD were identified as candidate core genes, respectively. Survival analysis showed that high expression of SLIT3, ABI3BP, MYOCD, PGM5, TNXB, and DNAH9 are associated with decreased survival in LUSC patients. Furthermore, high expression of BUB1, BUB1B, TTK, and UBE2C are associated with lower patient survival.

CONCLUSIONS

We found biomarker genes and biological pathways for LUSC and LUAD. These network hub genes are associated with clinical characteristics and patient outcomes and they may play important roles in LUSC and LUAD.

RCN3: a Ca2+ homeostasis regulator that promotes esophageal squamous cell carcinoma progression and cisplatin resistant

Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent cancers worldwide. There is a critical need to identify new mechanisms that contribute to ESCC progression. Reticulocalbin3 (RCN3) is mainly located in the endoplasmic reticulum and Ca²⁺‐binding protein containing EF‐hands. The function of RCN3 in tumor progression has not been clarified. We observed that the expression level of RCN3 was higher in ESCC tissues than in paired normal tissues. Overexpression of RCN3 was positively associated with tumor size, lymph node metastasis, TNM stage, lymphatic vessel infiltration, and poor outcome in patients with ESCC. Increased malignant phenotypes were observed in RCN3 overexpressing ESCC cells, whereas the opposite effects were achieved in RCN3‐silenced cells. Reticulocalbin3 promoted the expression of MMP‐2 and MMP‐9 by regulating the inositol 1,4,5‐trisphosphate receptor 1 (IP3R1)–Ca²⁺–calcium/calmodulin‐dependent protein kinase II–c‐Jun signaling pathway. Reticulocalbin3 induced cisplatin resistance by regulating IP3R1/Ca²⁺ to maintain intracellular Ca²⁺ homeostasis and reduced reactive oxygen species in ESCC cells. Finally, the expression of RCN3 was regulated by hypoxia inducible factor‐1α. Collectively, these data strongly support that RCN3 regulates Ca²⁺ homeostasis by targeting IP3R1 to promote the progression and platinum resistance of ESCC. Our studies suggest that RCN3 could serve as predictive factor of poor prognosis and potential therapeutic target for ESCC patients.

Quantitative proteomics approach reveals novel biomarkers and pathological mechanism of keloid

BACKGROUND

Keloid is a pathological skin scar formation with complex and unclear molecular pathology mechanism. Novel biomarkers and associated mechanisms are needed to improve current therapies.

OBJECTIVES

To identify novel biomarkers and underlying pathological mechanisms of keloids.

METHODS

Six pairs of keloid scar tissues and corresponding normal skin tissues were quantitatively analyzed by a high-resolution label-free mass spectrometry-based proteomics approach. Differential protein expression data was further analyzed by a comprehensive bioinformatics approach to identify novel biomarkers and mechanistic pathways for keloid formation. Candidate biomarkers were validated experimentally.

RESULTS

In total, 1359 proteins were identified by proteomic analysis. Of these, 206 proteins exhibited a significant difference in expression between keloid scar and normal skin tissues. RCN3 and CALU were significantly upregulated in keloids. RCN1 and PDGFRL were uniquely expressed in keloids. Pathway analysis suggested that the XBP1-mediated unfolded protein response (UPR) pathway was involved in keloid formation. Moreover, a PDGFRL centric gene coexpression network was constructed to illustrate its function in skin.

CONCLUSIONS AND CLINICAL RELEVANCE

Our study proposed four novel biomarkers and highlighted the role of XBP1-mediated UPR pathway in the pathology of keloids. It provided novel biological insights that contribute to develop novel therapeutic strategies for keloids.

A Three-Genes Signature Predicting Colorectal Cancer Relapse Reveals LEMD1 Promoting CRC Cells Migration by RhoA/ROCK1 Signaling Pathway

Objective

Colorectal cancer (CRC) patients that experience early relapse consistently exhibit poor survival. However, no effective approach has been developed for the diagnosis and prognosis prediction of postoperative relapsed CRC.

Methods

Multiple datasets from the GEO database and TCGA database were utilized for bioinformatics analysis. WGCNA analyses and RRA analysis were performed to identify key genes. The COX/Lasso regression model was used to construct the recurrence model. Subsequent in vitro experiments further validated the potential role of the hub genes in CRC.

Results

A comprehensive analysis was performed on multiple CRC datasets and a CRC recurrence model was constructed containing LEMD1, SERPINE1, and SIAE. After further validation in two independent databases, we selected LEMD1 for in vitro experiments and found that LEMD1 could regulate CRC cell proliferation, migration, invasion, and promote EMT transition. The Rho-GTPase pulldown experiments further indicated that LEMD1 could affect RhoA activity and regulate cytoskeletal dynamics. Finally, we demonstrated that LEMD1 promoted CRC cell migration through the RhoA/ROCK1 signaling pathway.

Conclusions

In this study, a CRC relapse model consisting of LEMD1, SERPINE1, and SIAE was constructed by comprehensive analysis of multiple CRC datasets. LEMD1 could promote CRC cell migration through the RhoA/ROCK signaling pathway.

Aldehyde Dehydrogenase 2 Family Member (ALDH2) Is a Therapeutic Index for Oxaliplatin Response on Colorectal Cancer Therapy with Dysfunction p53

Oxaliplatin resistance is a major issue in the treatment of p53 mutant colorectal cancer (CRC). Finding the specific biomarkers would improve therapeutic efficacy of patients with CRC. In order to figure out the biomarker for CRC patients with mutant p53 access oxaliplatin, a Gene Expression Omnibus dataset (GSE42387) was used to determine differentially expressed genes (DEGs). The Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software were used to predict protein-protein interactions. The Database for Annotation, Visualization, and Integrated Discovery online tool was used to group the DEGs into their common pathways. 138 DEGs were identified with 46 upregulated and 92 downregulated. In the PPI networks, 7 of the upregulated genes and 13 of the downregulated genes were identified as hub genes (high degrees). Four hub genes, aldehyde dehydrogenase 2 family member (ALDH2), aldo-keto reductase family 1 member B1 (AKR1B1), aldo-keto reductase family 1 member B10 (AKR1B10), and monoglyceride lipase (MGLL) were enriched in the most significant pathway, glycerolipid metabolism. Further, we found that low expression of ALDH2 is correlated with poor overall survival and oxaliplatin resistance. Finally, we found that combined treatment with ALDH2 inhibitor and oxaliplatin will reduce the sensitivity to oxaliplatin in p53 mutant HT29 cells. In conclusion, we demonstrate that ALDH2 may be a biomarker for oxaliplatin resistance status in CRC patients and bring new insight into treatment strategy for p53 mutant CRC patients.

AKR1B1 as a Prognostic Biomarker of High-Grade Serous Ovarian Cancer

Simple Summary

We evaluated the levels of AKR1B1 and AKR1B10 in 99 patients with high-grade serous ovarian cancer and their association with clinicopathological characteristics, survival, and response to chemotherapy. An immunohistochemical analysis showed that higher AKR1B1 levels correlated with a better disease-free survival of patients whereas we saw no differences for AKR1B10 levels. A multivariant Cox analysis identified high AKR1B1 levels as an important prognostic factor for both overall and disease-free survival. A further analysis revealed no association between AKR1B1 and AKR1B10 levels and response to chemotherapy.

Abstract

Although aldo-keto reductases (AKRs) have been widely studied in cancer, no study to date has examined the roles of AKR family 1 members B1 (AKR1B1) and B10 (AKR1B10) in a large group of ovarian cancer patients. AKR1B1 and AKR1B10 play a significant role in inflammation and the metabolism of different chemotherapeutics as well as cell differentiation, proliferation, and apoptosis. Due to these functions, we examined the potential of AKR1B1 and AKR1B10 as tissue biomarkers. We assessed the immunohistochemical levels of AKR1B1 and AKR1B10 in tissue paraffin sections from 99 patients with high-grade serous ovarian cancer (HGSC) and compared these levels with clinicopathological characteristics, survival, and response to chemotherapy. A higher immunohistochemical AKR1B1 expression correlated with a better overall and disease-free survival of HGSC patients whereas AKR1B10 expression did not show any significant differences. A multivariant Cox analysis demonstrated that a high AKR1B1 expression was an important prognostic factor for both overall and disease-free survival. However, AKR1B1 and AKR1B10 were not associated with different responses to chemotherapy. Our data suggest that AKR1B1 is involved in the pathogenesis of HGSC and is a potential prognostic biomarker for this cancer.

Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.

Downregulation of PPA2 expression correlates with poor prognosis of kidney renal clear cell carcinoma

Background

Kidney renal clear cell carcinoma (KIRC) is the most common subtype of kidney cancer. Inorganic pyrophosphatase (PPA2) is an enzyme that catalyzes the hydrolysis of pyrophosphate to inorganic phosphate; few studies have reported its significance in cancers. Therefore, we aimed to explore the prognostic value of PPA2 in KIRC.

Methods

PPA2 expression was detected via immunohistochemistry in a tissue chip containing specimens from 150 patients with KIRC. We evaluated the correlation between PPA2 expression, clinicopathological characteristics, and survival. Data from online databases and another cohort (paraffin-embedded specimens from 10 patients with KIRC) were used for external validation.

Results

PPA2 expression was significantly lower in KIRC tissues than in normal renal tissues (p < 0.0001). Low expression of PPA2 was significantly associated with a high histologic grade and poor prognosis. The differential expression of PPA2 was validated at the gene and protein levels. Multivariate Cox regression analysis showed that PPA2 expression was an independent prognostic factor in patients with KIRC. Gene set enrichment analysis suggested that decreased expression of PPA2 might be related to the epithelial-mesenchymal transition in KIRC.

Conclusions

Our study demonstrated that PPA2 is an important energy metabolism-associated biomarker correlated with a favorable prognosis in KIRC.

Excavating the pathogenic gene of breast cancer based on high throughput data of tumor and somatic reprogramming

Breast cancer (BC) is one of the most common malignancies in female, and has a high mortality rate. The mechanisms of tumorigenesis and reprogramming of somatic cells have a certain degree of similarity. Here, we focus on the relationship between gene expression, signaling pathways and functions in BC compared to induced pluripotent stem cells (iPSCs). We first identified differentially expressed genes (DEGs) common to BC and iPSCs in datasets from GEO and TCGA. We found 22 DEGs that were significantly associated with clinicopathological features and prognosis by performing Kaplan-Meier survival analysis and one-way ANOVA. The results of protein mass spectrometry of tumor stem cells (Mcfips) demonstrated that the proteins encoded by 8 of these DEGs were also differentially expressed. The functional enrichment analysis showed that most of the 30 DEGs were related to collagen and chromatin functions. Our results might offer targets for future studies into the mechanisms underlying tumor occurrence and progression, and our studies could provide valuable data for both basic research and clinical applications of BC.

AKR1B1 and AKR1B10 as Prognostic Biomarkers of Endometrioid Endometrial Carcinomas

Simple Summary

We evaluated the potential of AKR1B1 and AKR1B10 as tissue biomarkers of endometrial cancer by assessing the immunohistochemical levels of AKR1B1 and AKR1B10 in tissue paraffin sections from 101 well-characterized patients with endometrioid endometrial cancer and 12 patients with serous endometrial cancer. Significantly higher immunohistochemical levels of AKR1B1 and AKR1B10 were found in adjacent non-neoplastic endometrial tissue compared to endometrioid endometrial cancer. The group of patients with both AKR1B1 and AKR1B10 staining above the median values showed significantly better overall and disease-free survival compared to all other patients. Multivariant Cox analysis recognized a strong AKR1B1 and AKR1B10 staining as a statistically important survival prediction factor in patients with endometrioid endometrial cancer. In contrast, we observed no significant differences in AKR1B1 and AKR1B10 staining in patients with serous endometrial cancer. Our results suggest that AKR1B1 and AKR1B10 have protective roles in endometrioid endometrial cancer and represent prognostic biomarker candidates.

Abstract

The roles of aldo-keto reductase family 1 member B1 (AKR1B1) and B10 (AKR1B10) in the pathogenesis of many cancers have been widely reported but only briefly studied in endometrial cancer. To clarify the potential of AKR1B1 and AKR1B10 as tissue biomarkers of endometrial cancer, we evaluated the immunohistochemical levels of AKR1B1 and AKR1B10 in tissue paraffin sections from 101 well-characterized patients with endometrioid endometrial cancer and 12 patients with serous endometrial cancer and compared them with the clinicopathological data. Significantly higher immunohistochemical levels of AKR1B1 and AKR1B10 were found in adjacent non-neoplastic endometrial tissue compared to endometrioid endometrial cancer. A trend for better survival was observed in patients with higher immunohistochemical AKR1B1 and AKR1B10 levels. However, no statistically significant differences in overall survival or disease-free survival were observed when AKR1B1 or AKR1B10 were examined individually in endometrioid endometrial cancer. However, analysis of AKR1B1 and AKR1B10 together revealed significantly better overall and disease-free survival in patients with both AKR1B1 and AKR1B10 staining above the median values compared to all other patients. Multivariant Cox analysis identified strong AKR1B1 and AKR1B10 staining as a statistically important survival prediction factor. Conversely, no significant differences were found in serous endometrial cancer. Our results suggest that AKR1B1 and AKR1B10 play protective roles in endometrioid endometrial cancer and show potential as prognostic biomarkers.

Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics

Purpose

In most cases, the carcinogenesis of colorectal cancer (CRC) follows the normal-adenoma-carcinoma (N-A-C) sequence. In this study, we aimed to identify the key proteins in the N-A-C sequence.

Methods

Differentially expressed proteins (DEPs) in normal, adenoma, and carcinoma tissues were identified using the Tandem Mass Tag- (TMT-) based quantitative proteomics approach. The landscape of proteomic variation in the N-A-C sequence was explored using gene set enrichment analysis (GSEA) and Proteomaps. Key proteins in the N-A-C sequence were identified, verified, and validated based on our proteomic data, external proteomic data, and external transcriptomic data in the ProteomeXchange, CPTAC, GEO, and TCGA databases. The prognostic value of the key proteins in our database was evaluated by univariate and multivariate Cox regression analysis. The effects of the key proteins on adenoma organoids and colorectal cancer cells were explored in functional studies.

Results

Based on our proteomic profiles, we identified 1,294 DEPs between the carcinoma (CG) and normal (NG) groups, 919 DEPs between the adenoma group (AG) and NG, and 1,030 DEPs between the CG and AG. Ribosome- and spliceosome-related pathways were mainly enriched in the N-A process. Extracellular matrix- and epithelial-mesenchymal transition- (EMT-) related pathways were mainly enriched in the A-C process. RRP12 and SERPINH1 were identified, verified, and validated as candidate key proteins in the N-A and A-C processes, respectively. Furthermore, RRP12 and SERPINH1 knockdown impeded the viability and proliferation of adenoma organoids. SERPINH1 was validated as a risk factor for disease-free survival (DFS) based on the TCGA and our database, whereas RRP12 did not show prognostic value. SERPINH1 knockdown was accompanied by EMT-related protein variation, increased apoptosis, and reduced proliferation, invasion, and migration of CRC cells in vitro.

Conclusions

RRP12 and SERPINH1 may play an important role in the N-A and A-C processes, respectively. Furthermore, SERPINH1 showed favorable prognostic value for DFS in CRC patients. We speculate that SERPINH1 might promote not only the A-C process but also the development of CRC.

The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis

Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.

Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding

Phosphoglucomutase 5 (PGM5) in humans is known as a structural muscle protein without enzymatic activity, but detailed understanding of its function is lacking. PGM5 belongs to the alpha-D-phosphohexomutase family and is closely related to the enzymatically active metabolic enzyme PGM1. In the Atlantic herring, Clupea harengus, PGM5 is one of the genes strongly associated with ecological adaptation to the brackish Baltic Sea. We here present the first crystal structures of PGM5, from the Atlantic and Baltic herring, differing by a single substitution Ala330Val. The structure of PGM5 is overall highly similar to structures of PGM1. The structure of the Baltic herring PGM5 in complex with the substrate glucose-1-phosphate shows conserved substrate binding and active site compared to human PGM1, but both PGM5 variants lack phosphoglucomutase activity under the tested conditions. Structure comparison and sequence analysis of PGM5 and PGM1 from fish and mammals suggest that the lacking enzymatic activity of PGM5 is related to differences in active-site loops that are important for flipping of the reaction intermediate. The Ala330Val substitution does not alter structure or biophysical properties of PGM5 but, due to its surface-exposed location, could affect interactions with protein-binding partners.

Role of aldo-keto reductase family 1 member B1 (AKR1B1) in the cancer process and its therapeutic potential

The role of aldo‐keto reductase family 1 member B1 (AKR1B1) in cancer is not totally clear but growing evidence is suggesting to have a great impact on cancer progression. AKR1B1 could participate in a complicated network of signalling pathways, proteins and miRNAs such as mir‐21 mediating mechanisms like inflammatory responses, cell cycle, epithelial to mesenchymal transition, cell survival and apoptosis. AKR1B1 has been shown to be mostly overexpressed in cancer. This overexpression has been associated with inflammatory mediators including nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NFκB), cell cycle mediators such as cyclins and cyclin‐dependent kinases (CDKs), survival proteins and pathways like mammalian target of rapamycin (mTOR) and protein kinase B (PKB) or AKT, and other regulatory factors in response to reactive oxygen species (ROS) and prostaglandin synthesis. In addition, inhibition of AKR1B1 has been shown to mostly have anti‐cancer effects. Several studies have also suggested that AKR1B1 inhibition as an adjuvant therapy could render tumour cells more sensitive to anti‐cancer therapy or alleviate the adverse effects of therapy. AKR1B1 could also be considered as a potential cancer diagnostic biomarker since its promoter has shown high levels of methylation. Although pre‐clinical investigations on the role of AKR1B1 in cancer and the application of its inhibitors have shown promising results, the lack of clinical studies on AKR1B1 inhibitors has hampered the use of these drugs to treat cancer. Thus, there is a need to conduct more clinical studies on the application of AKR1B1 inhibitors as adjuvant therapy on different cancers.

Genome-Scale Metabolic Modeling with Protein Expressions of Normal and Cancerous Colorectal Tissues for Oncogene Inference

Although cancer has historically been regarded as a cell proliferation disorder, it has recently been considered a metabolic disease. The first discovery of metabolic alterations in cancer cells refers to Otto Warburg’s observations. Cancer metabolism results in alterations in metabolic fluxes that are evident in cancer cells compared with most normal tissue cells. This study applied protein expressions of normal and cancer cells to reconstruct two tissue-specific genome-scale metabolic models. Both models were employed in a tri-level optimization framework to infer oncogenes. Moreover, this study also introduced enzyme pseudo-coding numbers in the gene association expression to avoid performing posterior decision-making that is necessary for the reaction-based method. Colorectal cancer (CRC) was the topic of this case study, and 20 top-ranked oncogenes were determined. Notably, these dysregulated genes were involved in various metabolic subsystems and compartments. We found that the average similarity ratio for each dysregulation is higher than 98%, and the extent of similarity for flux changes is higher than 93%. On the basis of surveys of PubMed and GeneCards, these oncogenes were also investigated in various carcinomas and diseases. Most dysregulated genes connect to catalase that acts as a hub and connects protein signaling pathways, such as those involving TP53, mTOR, AKT1, MAPK1, EGFR, MYC, CDK8, and RAS family.

Comprehensive analysis of the long noncoding RNA expression profile and construction of the lncRNA-mRNA co-expression network in colorectal cancer

Long noncoding RNAs (lncRNAs) have been shown to play important roles in various tumors including colorectal cancer (CRC). Here, we obtained data from RNA-sequencing analysis using 3 paired of CRC tissues and corresponding normal tissues. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, the biological functions of these dysregulated genes were identified. Moreover, we analyzed the expression levels of lncRNA PGM5-AS1 and B3GALT5-AS1 by quantitative real-time PCR (qRT-PCR) assay. To evaluate the accuracy of the lncRNA-mRNA co-expression network we built, we also detected PGM5 expression and analyzed the relationship between PGM5-AS1 and PGM5 in CRC. In addition, we explored the potential function of PGM5-AS1 in vitro and in vivo. In conclusion, we identified dysregulated lncRNAs and constructed the lncRNA-mRNA co-expression network in CRC. Then, we showed that the expression levels of PGM5-AS1, B3GALT5-AS1 and PGM5 were significantly downregulated in CRC tissues compared with corresponding normal tissues. Besides, PGM5-AS1 expression was positively associated with PGM5 expression. These findings were consistent with our RNA-sequencing data. Functionally, overexpression of PGM5-AS1 could induce cell apoptosis and cell cycle arrest in CRC. Animal study indicated that PGM5-AS1 overexpression inhibited CRC growth in vivo. This work provides dysregulated lncRNAs as candidates for further study in CRC. The lncRNA-mRNA co-expression network brings novel insights into further function research. More importantly, PGM5-AS1 is a critical tumor suppressor in CRC.

PGM5 is a promising biomarker and may predict the prognosis of colorectal cancer patients

Background

Phosphoglucomutase (PGM), a key enzyme in the metabolism of glucose-1-phosphate and glucose-6-phosphate, has been found to be associated with proliferation, invasion, and metastasis of cancer. However, the expression and function of PGM5 in colorectal cancer (CRC) remains unknown.

Methods

We tested PGM5 mRNA and protein expression levels in 79 CRC tissue and their matched adjacent tissue samples by qRT-PCR and immunohistochemistry, respectively. Overall survival (OS) was estimated with the Kaplan-Meier method and compared between groups with the log-rank test. We performed multivariable Cox regression analyses to identify factors associated with CRC risk. The cell proliferation, migration and invasion abilities of CRC cells were detected by using CCK-8, Transwell migration and invasion assays, respectively.

Results

The PGM5 protein levels expression in CRC tissues were significantly lower than those in the adjacent tissues (t = 5.035, P < 0.001), and Kaplan-Meier analysis indicated that low PGM5 expression were significantly associated with poor overall survival (P = 0.0069). Univariate and multivariate analyses demonstrated that PGM5 was an independent risk factor for overall survival (hazard ratio = 0.3951, P = 0.014). PGM5 overexpression significantly inhibited the proliferation, invasion and migration abilities of CRC cells. On the contrary, knockdown of PGM5 promotes the invasion and migration of CRC cells.

Conclusions

PMG5 regulates proliferation, invasion, and migration in the CRC and decreased PGM5 is associated with poor prognosis. Therefore, PGM5 is a promising biomarker in CRC and decreased PGM5 may predict poor overall survival in patients with CRC.

Co-expression Network Analysis Identified Key Proteins in Association With Hepatic Metastatic Colorectal Cancer

PURPOSE

Intense efforts have been made in colorectal cancer (CRC) treatment in recent decades. However, the mechanism of development and metastasis of CRC has not been fully cleared. This study is designed to identify key proteins involved in stage III and hepatic metastatic CRC.

EXPERIMENT DESIGN

Protein expression profiles of paired tumor and benign tissue samples from stage III and hepatic metastatic CRC patients are characterized by using a label-free proteomics approach. Key proteins relevant to hepatic metastatic CRC are revealed by weighted gene correlation network analysis (WGCNA) and other bioinformatics tools.

RESULTS

WGCNA reveals three hub modules: CRC without specific stage (turquoise), stage III CRC (blue), and hepatic metastatic CRC (green). Nine key proteins (heat shock protein family D member 1 (HSPD1), eukaryotic translation elongation factor 1 gamma, heterogeneous nuclear ribonucleoprotein A2/B1, fibrinogen beta chain (FGB), Talin 1, adaptor related protein complex 2 subunit alpha 2, serrate RNA effector molecule homolog, apolipoprotein C3, phosphoglucomutase 5) are identified. Moreover, upregulation of HSPD1 is validated in CRC tissue by the immunohistochemistry. Upregulation of fibrinogen is validated in metastatic CRC by plasma fibrinogen assay.

CONCLUSION AND CLINICAL RELEVANCE

This study provides the proteomic analysis of stage III and hepatic metastatic CRC to identify key proteins of CRC. FGB plays a key role to serve as diagnostic and therapeutic biomarkers for hepatic metastatic CRC.

Olfactomedin 4 downregulation is associated with tumor initiation, growth and progression in human prostate cancer

The olfactomedin 4 (OLFM4) gene has been analyzed as a tumor‐suppressor gene and a putative biomarker in many cancers. In our study, we analyzed the relationship of OLFM4 expression with clinicopathological features and with CpG site methylation in the OLFM4 gene promoter region in human primary prostate adenocarcinoma. OLFM4 protein expression was significantly reduced in prostate cancer tissue compared to adjacent normal tissue and was further significantly reduced in more advanced cancers. Bioinformatic studies with clinical datasets revealed that primary prostate adenocarcinoma patients with reduced OLFM4 mRNA expression exhibited higher Gleason scores and higher preoperative serum prostate‐specific antigen levels, as well as lower recurrence‐free survival. Three of the eight CpG sites in the OLFM4 gene promoter region were hypermethylated in cancerous prostate cells compared to adjacent normal cells, and reduced methylation of eight CpG sites was associated with increased OLFM4 mRNA expression in RWPE1 and PC‐3 cells. Furthermore, knockdown of OLFM4 gene expression was associated with enhanced epithelial–mesenchymal transition (EMT)‐marker expression in RWPE immortalized normal prostate cells. In contrast, restoration of OLFM4 expression in PC‐3 and DU145 prostate cancer cells lacking OLFM4 significantly inhibited both EMT‐marker expression and tumor cell growth in in vitro and in vivo models, indicating that OLFM4 may play a tumor‐suppressor role in inhibiting the EMT program, as well as tumor initiation and growth, in prostate cells. Taken together, these findings suggest that OLFM4 plays an important tumor‐suppressor role in prostate cancer progression and might be useful as a novel candidate biomarker for prostate cancer.

What's new?

Altered expression of the OLFM4 gene appears to be involved in many cancers. In this study of prostate cancers, the authors found that OLFM4 can suppress tumor initiation, growth and progression. Downregulation of OLFM4 was associated with higher serum PSA levels, higher Gleason scores, and lower recurrence‐free survival in prostate cancer patients. These results indicate that OLFM4 may play an important tumor‐suppressor role in the progression of prostate cancer, and may provide a novel prognostic biomarker for prostate cancer treatment.

PGM5: a novel diagnostic and prognostic biomarker for liver cancer

BACKGROUND

Liver cancer is a common malignancy and a significant public health problem worldwide, but diagnosis and prognostic evaluation remain challenging for clinicians. Metabolic reprogramming is a hallmark of cancer, and we therefore examined the diagnostic and prognostic value of a metabolic enzyme, phosphoglucomutase-like protein 5 (PGM5), in liver cancer.

METHODS

All data were from The Cancer Genome Atlas database. R and related statistical packages were used for data analysis. Hepatic PGM5 expression was determined in different groups, and the chi-squared test and Fisher's exact test were used to determine the significance of differences. The pROC package was used to determine receiver operating characteristic (ROC) curves, the survival package was used to for survival analysis and development of a Cox multivariable model, and the ggplot2 package was used for data visualization.

RESULTS

PGM5 expression was significantly lower in cancerous than adjacent normal liver tissues, and had modest diagnostic value based on ROC analysis and calculations of area under the curve (AUC). Hepatic PGM5 expression had positive associations with male sex and survival, but negative associations with advanced histologic type, advanced histologic grade, advanced stage, and advanced T classification. Patents with low PGM5 levels had poorer overall survival and relapse-free survival. PGM5 was independently associated with patient prognosis.

CONCLUSION

PGM5 has potential use as a diagnostic and prognostic biomarker for liver cancer.

Elevated urine histone 4 levels in women with ovarian endometriosis revealed by discovery and parallel reaction monitoring proteomics

Endometriosis is a common gynecologic disorder and due to a lack of non-invasive detection methods, it can take up to 12 years before an affected woman obtains a diagnosis and receives appropriate treatment. Therefore, the identification of a specific biomarker that can be detected quickly and non-invasively is urgently needed. In this study, the urine proteome, a potentially rich source of biomarkers, is examined in patients with or without endometriosis in an attempt to identify novel protein biomarkers that can be used to diagnose endometriosis. This study is the first to combine tandem mass tags and parallel reaction monitoring approaches to aid in identifying and validating urine biomarkers for endometriosis. The findings presented herein support previous conclusions that endometriosis is a chronic inflammatory disease. Additionally, Histone 4 was identified as a potential biomarker and/or therapeutic target for endometriosis. At a cutoff of 14.2, the area under the curve for H4 was 0.848, with a sensitivity of 70% and specificity of 80%. Moreover, to our knowledge, this is the first study to observe an elevated histone level in body fluids obtained from endometriosis patients. While this study provides a good foundation, further studies are required to further validate the results presented. SIGNIFICANCE: Endometriosis is a common gynecologic disorder and due to a lack of non-invasive detection methods, it can take up to 12 years before an affected woman obtains a diagnosis and receives appropriate treatment. Therefore, the identification of a specific biomarker that can be detected quickly and non-invasively is urgently needed. We believe our results have an important impact on detection and treatment of endometriosis. Firstly, this study is the first to combine tandem mass tags and parallel reaction monitoring approaches to aid in identifying and validating urine biomarkers for endometriosis, which has established the methodology required for subsequent studies. Secondly, this is also the first study to observe an elevated histone level in body fluids obtained from endometriosis patients. Compared with other urine biomarkers reported in literature, histone 4 has a potential to serve as a biomarker of endometriosis and a therapeutic target. Thirdly, our study supports previous conclusions that endometriosis is a chronic inflammatory disease. These findings can warrant further investigation of the pathophysiology of endometriosis.

Subcellular expression of maspin – from normal tissue to tumor cells

Maspin or SerpinB5, a member of the serine protease inhibitor family, was shown to function as a tumor suppressor, especially in carcinomas. It seems to inhibit invasion, tumor cells motility and angiogenesis, and promotes apoptosis. Maspin can also induce epigenetic changes such as cytosine methylation, de-acetylation, chromatin condensation, and histone modulation. In this review, a comprehensive synthesis of the literature was done to present maspin function from normal tissues to pathologic conditions. Data was sourced from MEDLINE and PubMed. Study eligibility criteria included: Published in English, between 1994 and 2019, specific to humans, and with full-text availability. Most of the 118 studies included in the present review focused on maspin immunostaining and mRNA levels. It was shown that maspin function is organ-related and depends on its subcellular localization. In malignant tumors, it might be downregulated or negative (e.g., carcinoma of prostate, stomach, and breast) or upregulated (e.g., colorectal and pancreatic tumors). Its subcellular localization (nuclear vs cytoplasm), which can be proved using immunohistochemical methods, was shown to influence both tumor behavior and response to chemotherapy. Although the number of maspin-related papers increased, the exact role of this protein remains unknown, and its interpretation should be done with extremely high caution.

Identification of Novel Regulatory Genes in APAP Induced Hepatocyte Toxicity by a Genome-Wide CRISPR-Cas9 Screen

Acetaminophen (APAP) is a commonly used analgesic responsible for more than half of acute liver failure cases. Identification of previously unknown genetic risk factors would provide mechanistic insights and novel therapeutic targets for APAP-induced liver injury. This study used a genome-wide CRISPR-Cas9 screen to evaluate genes that are protective against, or cause susceptibility to, APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR-Cas9 gene knockouts were treated with 15 mM APAP for 30 minutes to 4 days. A gene expression profile was developed based on the 1) top screening hits, 2) overlap of expression data from APAP overdose studies, and 3) predicted affected biological pathways. We further demonstrated the implementation of intermediate time points for the identification of early and late response genes. This study illustrated the power of a genome-wide CRISPR-Cas9 screen to systematically identify novel genes involved in APAP-induced hepatotoxicity and to provide potential targets to develop novel therapeutic modalities.

Histone-lysine N-methyltransferase SETD7 is a potential serum biomarker for colorectal cancer patients

Background

There is an urgent need for the identification of new, clinically useful biomarkers of CRC to enhance diagnostic and prognostic capabilities.

Methods

We performed proteomic profiling on serum samples from paired pre- and post-operative CRC patients, colorectal polyps patients and healthy controls using an approach combining magnetic bead-based weak cation exchange and matrix-assisted laser desorption ionization-time of flight mass spectrometry. We next performed liquid chromatography-electrospray ionization-tandem mass spectrometry to identify the proteins and selected potential biomarker based on bioinformatics analysis of the TCGA and GEO dataset. We examined SETD7 expression in serum and tissue samples by ELISA and immunohistochemistry respectively and explored the biological function of SETD7 in vitro.

Findings

85 differentially expressed peptides were identified. Five peptides showing the most significant changes in abundance across paired pre- and post-operation CRC patients, colorectal polyps patients and healthy controls were identified as peptide regions of FGA, MUC5AC and SETD7. Bioinformatics analysis suggested that the up-regulation of SETD7 in CRC is relatively specific. Validation studies showed that SETD7 expression increased from healthy controls to those with colorectal polyps and finally CRC patients, and decreased after surgery. The sensitivity and specificity of SETD7 were 92.17% and 81.08%, with a high diagnostic value (AUC = 0.9477). In addition, SETD7 expression was significantly correlated with tumor stage and microsatellite instability. Knockdown of SETD7 inhibited cancer cell proliferation, induced G1/S cell cycle arrest and increased apoptosis.

Interpretation

Our data indicate that SETD7 could serve as a potential diagnostic and prognostic biomarker for CRC.

Label-free tissue proteomics can classify oral squamous cell carcinoma from healthy tissue in a stage-specific manner

OBJECTIVES

No prognostic or predictive biomarkers for oral squamous cell carcinoma (OSCC) exist. We aimed to discover novel proteins, altered in OSCC, to be further investigated as potential biomarkers, and to improve understanding about pathways involved in OSCC.

MATERIALS AND METHODS

Proteomic signatures of seven paired healthy and OSCC tissue samples were identified using ultra-definition quantitative mass spectrometry, then analysed and compared using Anova, principal component analysis, hierarchical clustering and OPLS-DA modelling. A selection of significant proteins that were also altered in the serum from a previous study (PMID: 28632724) were validated immunohistochemically on an independent cohort (n = 66) to confirm immunopositivity and location within tumour tissue. Ingenuity Pathways Analysis was employed to identify altered pathways.

RESULTS

Of 829 proteins quantified, 257 were significant and 72 were able to classify healthy vs OSCC using OPLS-DA modelling. We identified 19 proteins not previously known to be upregulated in OSCC, including prosaposin and alpha-taxilin. KIAA1217 and NDRG1 were upregulated in stage IVa compared with stage I tumours. Altered pathways included calcium signalling, cellular movement, haematological system development and function, and immune cell trafficking, and involved NF-kB and MAPK networks.

CONCLUSIONS

We found a set of proteins reliably separating OSCC tumour from healthy tissue, and multiple proteins differing between stage I and stage IVa OSCC. These potential biomarkers can be studied and validated in larger cohorts.

Probing the colorectal cancer proteome for biomarkers: Current status and perspectives

Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.

ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments

PURPOSE

Targeted proteomics using MRM with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept. Internal NAT-addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time.

EXPERIMENTAL DESIGN

To compare the following three methods, an MRM assay for 34 high-to-moderate abundance human plasma proteins is used: classical internal SIS-addition, internal NAT-addition, and external NAT-addition-generated in buffer using NAT and SIS peptides. Using endogenous-free chicken plasma, the accuracy is also evaluated.

RESULTS

The internal NAT-addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT-addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values.

CONCLUSIONS AND CLINICAL RELEVANCE

While the internal NAT-addition method may be "ideal", this new external NAT-addition can be used to determine the concentration of high-to-moderate abundance endogenous plasma proteins, providing a robust and cost-effective alternative for clinical analyses or other high-throughput applications.

The potential value of CDV3 in the prognosis evaluation in Hepatocellular carcinoma

CDV3 is correlated with tumorigenesis and may affect some biological process in cancer. In this study, we explore the role of CDV3 in HCC. According to the TCGA data base, CDV3 is over-expressed in HCC tissues. Up-regulation of CDV3 is correlated with lower over-all survival rate in HCC patients. In HCC samples from our hospital, CDV3 is also enriched in cancer tissues and CDV3 expression associated with HCC pathological T stage. What is more, higher CDV3 expression could forecast poor survival rate in HCC patients. In conclusion, CDV3 is a biomarker of HCC and could be a potential therapeutic target.

Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma

We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.

Identification of key lncRNAs in colorectal cancer progression based on associated protein-protein interaction analysis

BACKGROUND

Colorectal cancer (CRC) was one of the most commonly diagnosed malignancies. The molecular mechanisms involved in the progression of CRC remain unclear. Accumulating evidences showed that long noncoding RNAs (lncRNAs) played key roles in tumorigenesis, cancer progression, and metastasis. Therefore, we aimed to explore the roles of lncRNAs in the progression of CRC.

METHODS

In this study, we aimed to identify differentially expressed lncRNAs and messenger RNAs (mRNAs) in CRC by analyzing a cohort of previously published datasets: GSE64857. GO and KEGG pathway analyses were applied to give us insight in the functions of those lncRNAs and mRNAs in CRC.

RESULTS

Totally, 46 lncRNAs were identified as differentially expressed between stage II and stage III CRC for the first time screening by microarray. GO and KEGG pathway analyses showed that differentially expressed lncRNAs were involved in regulating signal transduction, cell adhesion, cell differentiation, focal adhesion, and cell adhesion molecules.

CONCLUSIONS

We found three lncRNAs (LOC100129973, PGM5-AS1, and TTTY10) widely co-expressed with differentially expressed mRNAs. We also constructed lncRNA-associated PPI in CRC and found that these lncRNAs may be associated with CRC progression. Moreover, we found that high PGM5-AS1 expression levels were associated with worse overall survival in CRC cancer. We believe that this study would provide novel potential therapeutic and prognostic targets for CRC.

Roles of Arf6 in cancer cell invasion, metastasis and proliferation

ADP-ribosylation factor 6 (Arf6), a member of small GTPases ADP-ribosylation factor (Arf) family, expresses widely in mammalian cells and mainly regulates the functions of membrane traffic and actin remodeling. Current studies indicated that the activation and high expression of Arf6 protein may be significantly correlated with the invasion and metastasis of several tumors, such as breast cancer, pancreatic cancer, lung cancer, etc. Meanwhile, the ability of tumor invasion and metastasis can be suppressed when Arf6 activity is blocked by the inhibitors or small-interfering RNAs of Arf6. To explore the precisely potential mechanisms between Arf6 and the process of tumor invasion, metastasis and proliferation, we concludes the functions and potential signaling pathways of Arf6 in tumor cells and provides an overview about clinical prospects of Arf6 in the screening, diagnosis, treatment and evaluation of prognosis of neoplasms.