Detection and Identification of Potential Biomarkers of Non-small Cell Lung Cancer

Lipoproteins and cancer: The role of HDL-C, LDL-C, and cholesterol-lowering drugs

Cholesterol is an amphipathic sterol molecule that is vital for maintaining normal physiological homeostasis. It is a relatively complicated molecule with 27 carbons whose synthesis starts with 2-carbon units. This in itself signifies the importance of this molecule. Cholesterol serves as a precursor for vitamin D, bile acids, and hormones, including estrogens, androgens, progestogens, and corticosteroids. Although essential, high cholesterol levels are associated with cardiovascular and kidney diseases and cancer initiation, progression, and metastasis. Although there are some contrary reports, current literature suggests a positive association between serum cholesterol levels and the risk and extent of cancer development. In this review, we first present a brief overview of cholesterol biosynthesis and its transport, then elucidate the role of cholesterol in the progression of some cancers. Suggested mechanisms for cholesterol-mediated cancer progression are plentiful and include the activation of oncogenic signaling pathways and the induction of oxidative stress, among others. The specific roles of the lipoprotein molecules, high-density lipoprotein (HDL) and low-density lipoprotein (LDL), in this pathogenesis, are also reviewed. Finally, we hone on the potential role of some cholesterol-lowering medications in cancer.

Apolipoprotein C1 stimulates the malignant process of renal cell carcinoma via the Wnt3a signaling

Background

Renal cell carcinoma (RCC) is a clinically common tumor in the urinary system, showing an upward trend of both incidence and mortality. Apolipoprotein C1 (APOC1) has been identified as a vital regulator in tumor progression. This study aims to uncover the biological function of APOC1 in RCC process and the underlying mechanism.

Methods

Differential levels of APOC1 in RCC samples and normal tissues in a downloaded TCGA profile and clinical samples collected in our center were detected by quantitative reverse transcription PCR (qRT-PCR). The prognostic value of APOC1 in RCC was assessed by depicting Kaplan–Meier survival curves. After intervening APOC1 level by transfection of sh-APOC1 or oe-APOC1, changes in phenotypes of RCC cells were examined through CCK-8, colony formation, Transwell assay and flow cytometry. Subsequently, protein levels of EMT-related genes influenced by APOC1 were determined by Western blot. The involvement of the Wnt3a signaling in APOC1-regulated malignant process of RCC was then examined through a series of rescue experiments. Finally, a RCC xenograft model was generated in nude mice, aiming to further clarify the in vivo function of APOC1 in RCC process.

Results

APOC1 was upregulated in RCC samples. Notably, its level was correlated to overall survival of RCC patients, displaying a certain prognostic value. APOC1 was able to stimulate proliferative, migratory and invasive abilities in RCC cells. The Wnt3a signaling was identified to be involved in APOC1-mediated RCC process. Notably, Wnt3a was able to reverse the regulatory effects of APOC1 on RCC cell phenotypes. In vivo knockdown of APOC1 in xenografted nude mice slowed down the growth of RCC.

Conclusions

APOC1 stimulates the malignant process of RCC via targeting the Wnt3a signaling.

A Validation Study of a Multiple Reaction Monitoring-Based Proteomic Assay to Diagnose Breast Cancer

Purpose

Currently, the standard screening tool for breast cancer is screening mammography. There have been many efforts to develop a blood-based diagnostic assay for breast cancer diagnosis; however, none have been approved for clinical use at this time. The purpose of this study was to determine the accuracy of a novel blood-based proteomic test for aiding breast cancer diagnosis in a relatively large cohort of cancer patients.

Methods

A blood-based test using multiple reaction monitoring (MRM) measured by mass spectrometry to quantify 3 peptides (apolipoprotein C-1, carbonic anhydrase 1, and neural cell adhesion molecule L1-like protein) present in human plasma was investigated. A total of 1,129 blood samples from 575 breast cancer patients, 454 healthy controls, and 100 patients with other malignancies were used to verify and optimize the assay.

Results

The diagnostic sensitivity, specificity, and accuracy of the MRM-based proteomic assay were 71.6%, 85.3%, and 77%, respectively; the area under the receiver operating characteristic curve was 0.8323. The proteomic assay did not demonstrate diagnostic accuracy in patients with other types of malignancies including thyroid, pancreatic, lung, and colon cancers. The diagnostic performance of the proteomic assay was not associated with the timing of blood sampling before or after anesthesia.

Conclusion

The data demonstrated that an MRM-based proteomic assay that measures plasma levels of three specific peptides can be a useful tool for breast cancer screening and its accuracy is cancer-type specific.

Apolipoproteins and cancer

The role of apolipoproteins in cardiovascular disease has been well investigated, but their participation in cancer has only been explored in a few published studies which showed a close link with certain kinds of cancer. In this review, we focused on the function of different kinds of apolipoproteins in cancers, autophagy, oxidative stress, and drug resistance. The potential application of apolipoproteins as biomarkers for cancer diagnosis and prognosis was highlighted, together with an investigation of their potential as drug targets for cancer treatment. Many important roles of apolipoproteins and their mechanisms in cancers were reviewed in detail and future perspectives of apolipoprotein research were discussed.

Apolipoprotein C1 promotes prostate cancer cell proliferation in vitro

Here, we aimed to investigate the carcinogenic effects of apolipoprotein C1 (APOC1) in prostate cancer (PCa). APOC1 expression was evaluated in PCa and normal prostate specimens, and lentivirus-mediated RNA interference was used to knockdown APOC1 in DU145 cells. The effects of APOC1 silencing on cell proliferation, cell cycle arrest, and apoptosis were assessed. APOC1 expression was much higher in PCa tissues than in normal tissues. Moreover, APOC1 silencing inhibited cell proliferation and colony formation, arrested cell cycle progression, and enhanced apoptosis in DU145 cells. Additionally, APOC1 silencing decreased survivin, phospho-Rb, and p21 levels and increased cleaved caspase-3 expression. These data supported the procarcinogenic effects of APOC1 in the pathogenesis of PCa and suggested that targeting APOC1 may have applications in the treatment of PCa.

Proteomics in pediatric cystic craniopharyngioma

Adamantinomatous craniopharyngioma (ACP) is still often burdened by a poor prognosis in children as far as the risk of recurrence and the quality of life are concerned. Therefore, many efforts are now dedicated to investigate the molecular characteristics of this tumor aiming at finding new therapeutic options. ACP is prevalently a cystic lesion so that an increasing number of researches are focused on the analysis of its cystic content. In the present article, the main results of the current proteomic analysis (PA) on the ACP fluid are summarized. Both "bottom-up" and "top-down" approaches have been utilized. In the bottom-up approach, proteins and peptides are enzymatically or chemically digested prior to liquid chromatography and mass spectrometry analyses. The bottom-up approach pointed out several proteins of the inflammation (namely, α2-HS-glycoprotein, α1-antichymotrypsin and apolipoproteins) as possibly involved in the genesis and growth of the cystic component of ACP. The top-down strategy analyzes proteins and peptides in the intact state, making it particularly suitable for the identification of peptides and low molecular weight proteins and for the characterization of their possible isoforms and post-translational modifications. The top-down approach disclosed the presence of the thymosin β family. Thymosin β4, in particular, which is involved in the cytoskeleton organization and migration of several tumors, could play a role in the progression of ACP. Finally, PA was utilized to investigate alterations in cyst fluid character after treatment with interferon-α. The analyzed samples showed a progressive reduction of the levels of α-defensins (proteins involved in the inflammatory-mediated response) after the intracystic injection of interferon-α, thus reinforcing the hypothesis that inflammation contributes to ACP cyst pathogenesis. Additional studies on the solid component of ACP are still necessary to further validate the previous results and to identify possible markers for targeted therapy.

Identification of Apolipoprotein C-I Peptides as a Potential Biomarker and its Biological Roles in Breast Cancer

Background

Breast cancer (BC) is one of the most common cancers and is among the main causes of death in females around the world. Although several serum biomarkers have been identified for breast cancer, due to lack of adequate sensitivity and specificity they do not adequately distinguish BC from confounding conditions. New approaches are urgently needed to improve BC detection and treatment.

Material/Methods

Eighty serum samples from 20 healthy individuals and 60 patients with BC (22 triple-negative breast cancer, TNBC; 38 non-triple-negative breast cancer, NTNBC) were included. Protein profiling of serum samples was analyzed using surface-enhanced laser desorption/ionization time-of-flight mass spectroscopy (SELDI-TOF-MS). Candidate biomarkers were purified by SDS-PAGE electrophoresis and identified by MALDI-TOF/TOF.

Results

The candidate biomarker positioned at 6447.9 m/z was significantly decreased in BC patients. Moreover, the expression intensity of the candidate biomarker was weaker in the TNBC and pre-surgery group compared with the NTNBC and post-surgery group. We ultimately identified the biomarker as apolipoprotein C-I (ApoC-I). Furthermore, we found that ApoC-I peptides inhibited proliferation of human breast cancer cells in vitro and suppressed tumor growth in vivo.

Conclusions

These results suggest that ApoC-I peptides may be a potential diagnostic biomarker and therapeutic approach for BC.

Identification of apolipoprotein C-I as a potential Wilms' tumor marker after excluding inflammatory factors

Wilms' tumor is one of the most common malignant tumors observed in children, and its early diagnosis is important for late-stage treatment and prognosis. We previously screened and identified protein markers for Wilms' tumor; however, these markers lacked specificity, and some were associated with inflammation. In the current study, serum samples from children with Wilms' tumors were compared with those of healthy controls and patients with systemic inflammatory response syndrome (SIRS). After exclusion of factors associated with inflammation, specific protein markers for Wilms' tumors were identified. After comparing the protein peak values obtained from all three groups, a protein with a m/z of 6438 Da was specified. Purification and identification of the target protein using high-pressure liquid chromatography (HPLC) and two-dimensional liquid chromatography-linearion trap mass spectrometry(2D-LC-LTQ-MS) mass spectrometry, respectively, revealed that it was apolipoprotein C-I (APO C-I). Thus, APO C-I is a specific protein marker for Wilms' tumor.

Proteomic characterization of pediatric craniopharyngioma intracystic fluid by LC-MS top-down/bottom-up integrated approaches

The combination of top-down and bottom-up platforms was utilized for the LC-MS proteomic characterization of the intracystic fluid of adamantinomatous craniopharyngioma pediatric brain tumor disease. Proteins and peptides characterization was achieved by high-resolution LC-ESI-LTQ-Orbitrap-MS analysis while low-resolution LC-ESI-IT-MS was applied for the complete screening of the samples and the evaluation of the protein distribution within patients. Top-down analyses were applied to liquid/liquid extracted samples while bottom-up analyses were performed after trypsin digestion of both untreated and pretreated samples. The two proteomic approaches were complementary for the characterization of the proteome of craniopharyngioma intracystic fluid. Proteins and peptides involved in inflammation, mineralization processes and lipid transport were identified, in agreement with the calcium flecks, cholesterol granules and bone residues characteristic of this fluid. Apolipoprotein A-I, A-II, C-I and J, hemoglobin fragments, ubiquitin, α-2-HS-glycoprotein or fetuin A, α-1-antichymotrypsin, vitamin D binding protein, and α-1-acid glycoprotein were characterized. These data could be relevant for the comprehension of the processes involved in the pathogenesis of the disease and the development of the cyst and could contribute to the individuation of therapeutic targets for the reduction of the cyst volume delaying and/or avoiding invasive surgical treatments.

The value of surface enhanced laser desorption/ionization-time of flight mass spectrometry at the diagnosis of non-small cell lung cancer: a systematic review

Numbers of studies used surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS) to find novel serum biomarkers for non-small cell lung cancer (NSCLC). It is arguable whether the SELDI technique has its value of diagnostic accuracy for NSCLC. The purpose of our study is to determine the diagnostic accuracy of SELDI-TOF-MS for diagnosing NSCLC. The Cochrane Central Register of Controlled Trials, MEDLINE, Pub Med, EMBASE, the Chinese Biomedical Literature Database, the China Academic Journals Full-text Database, and the Chinese Scientific Journals Database were searched systematically for potential studies. Reference lists of included studies and review articles were also reviewed. All studies that reported data on patients with a confirmed diagnosis of NSCLC and that compared the measurement of SELDI-TOF-MS with pathology standard were considered for inclusion. 11 studies were included in the systematic review. The ranges of the diagnostic value of SELDI-TOF-MS for NSCLC were as follows: sensitivity (SEN) was 0.70~1.00; specificity (SPE) was 0.68~1.00; positive likelihood ratio (PLR) was 2.23~23.14; negative likelihood ratio (NLR) was 0.04~0.43; and diagnostic odds ratio (DOR) was 5.17~621.0, respectively. SELDI-TOF-MS showed high accuracy in identifying NSCLC, and could be a potential screening tool for diagnosing NSCLC patients.

Identification of novel low molecular weight serum peptidome biomarkers for non-small cell lung cancer (NSCLC)

AIM

To identify discriminating protein patterns in serum samples among non-small cell lung cancer (NSCLC), chronic obstructive pulmonary disease (COPD), pneumonia, and healthy controls. To discover specific low molecular weight (LMW) serum peptidome biomarkers and establish a diagnostic pattern for NSCLCby using proteomic technology.

METHODS

We used magnetic bead-based separation followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify patients with NSCLC, COPD, and pneumonia. A total of 154 serum samples were analyzed in this study, among which there were 60 serum samples from NSCLC patients, 30 from patients with other lung-related diseases (16 pneumonia patients and 14 patients with COPD) as disease controls, and 64 from healthy volunteers as healthy control. The mass spectra, analyzed using ClinProTools software, distinguished between cancer patients and healthy individuals based on GA algorithm model.

RESULTS

In this study, we generated numerous discriminating m/z peaks as well as disease-specific discrimination peaks. A set of five potential biomarkers (m/z: 7,763.24, 1,012.61, 4,153.16, 1,450.55, and 2,878.89) could be used as the diagnostic biomarkers to distinguish NSCLCpatients from healthy controls. In the training set, patients with NSCLC could be identified with sensitivity of 97.5% and specificity of 98.8%. Similar results were obtained in the testing set, showing 80.7% sensitivity and 91.2% specificity.

CONCLUSION

Our study demonstrated that a combined application of magnetic beads with MALDI-TOF MS technique was suitable for identification of serum biomarkers for NSCLC.

Correspondence between salivary proteomic pattern and clinical course in primary Sjögren syndrome and non-Hodgkin's lymphoma: a case report

Background

In the last years human proteomic has represented a promising tool to promote the communication between basic and clinical science.

Methods

To explore the correspondence between salivary proteomic profile and clinical response, herein, we used a proteomic approach to analyse the whole saliva of a patient with primary Sjögren's Syndrome (pSS) and non-Hodgkin's-MALT type parotid lymphoma before, during and after a standard treatment with cyclophosphamide (CTX) and rituximab (RTX). To identify any discriminatory therapeutic salivary biomarker patient's whole saliva was collected at the baseline, after the fourth infusion of rituximab, and on remission and analysed combining two-dimensional electrophoresis (2DE) and MALDI-TOF/TOF mass spectrometry.

Results

Proteomic results obtained from the comparison of salivary samples indicated several qualitative and quantitative modifications in the salivary expression of putative albumin, immunoglobulin J chain, Ig kappa chain C region, alpha-1-antitrypsin, haptoglobin and Ig alpha-1 chain C region.

Conclusion

This study suggests that clinical and functional changes of the salivary glands driven by autoimmune and lymphoproliferative processes might be reflected in patients' whole saliva proteins, shedding new light on the potential usefulness of salivary proteomic analysis in the identification of prognostic and therapeutic biomarkers for patients with pSS and non Hodgkin's lymphomas.

Enriched sera protein profiling for detection of non-small cell lung cancer biomarkers

Background

Non Small Cell Lung Cancer (NSCLC) is the major cause of cancer related-death. Many patients receive diagnosis at advanced stage leading to a poor prognosis. At present, no satisfactory screening tests are available in clinical practice and the discovery and validation of new biomarkers is mandatory. Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-ToF-MS) is a recent high-throughput technique used to detect new tumour markers. In this study we performed SELDI-ToF-MS analysis on serum samples treated with the ProteoMiner™ kit, a combinatorial library of hexapeptide ligands coupled to beads, to reduce the wide dynamic range of protein concentration in the sample. Serum from 44 NSCLC patients and 19 healthy controls were analyzed with IMAC30-Cu and H50 ProteinChip Arrays.

Results

Comparing SELDI-ToF-MS protein profiles of NSCLC patients and healthy controls, 28 protein peaks were found significantly different (p < 0.05), and were used as predictors to build decision classification trees. This statistical analysis selected 10 protein peaks in the low-mass range (2-24 kDa) and 6 in the high-mass range (40-80 kDa). The classification models for the low-mass range had a sensitivity and specificity of 70.45% (31/44) and 68.42% (13/19) for IMAC30-Cu, and 72.73% (32/44) and 73.68% (14/19) for H50 ProteinChip Arrays.

Conclusions

These preliminary results suggest that SELDI-ToF-MS protein profiling of serum samples pretreated with ProteoMiner™ can improve the discovery of protein peaks differentially expressed between NSCLC patients and healthy subjects, useful to build classification algorithms with high sensitivity and specificity. However, identification of the significantly different protein peaks needs further study in order to provide a better understanding of the biological nature of these potential biomarkers and their role in the underlying disease process.

Profiling for novel proteomics biomarkers in neurodevelopmental disorders

Protein biomarker discovery from biological fluids, such as serum, has been widely applied to disorders such as cancer and has more recently also been utilized in neuro-psychiatric disorders with relatively clear biological causes, such as Alzheimer's disease and schizophrenia. The application of the associated technologies for the identification of protein biomarker signatures in neurodevelopmental disorders, such as autism spectrum disorder and attention deficit hyperactivity disorder, is comparatively less well established. The aim of this article is to provide an overview of the various protocols available for such analysis, discuss reports in which these techniques have been previously applied in biomarker discovery/validation in neurodevelopmental disorders, and consider the future development of this area of research.

Strategy for purification and mass spectrometry identification of SELDI peaks corresponding to low-abundance plasma and serum proteins

Analysis by SELDI-TOF-MS of low abundance proteins makes it possible to select peaks as candidate biomarkers. Our aim was to define a purification strategy to optimise identification by MS of peaks detected by SELDI-TOF-MS from plasma or serum, regardless of any treatment by a combinatorial peptide ligand library (CPLL). We describe 2 principal steps in purification. First, choosing the appropriate sample containing the selected peak requires setting up a databank that records all the m/z peaks detected from samples in different conditions. Second, the specific purification process must be chosen: separation was achieved with either chromatographic columns or liquid-phase isoelectric focusing, both combined when appropriate with reverse-phase chromatography. After purification, peaks were separated by gel electrophoresis and the candidate proteins were analyzed by nano-liquid-chromatography-MS/MS. We chose 4m/z peaks (9400, 13,571, 13,800 and 15,557) selected for their differential expression between two conditions, as examples to explain the different strategies of purification, and we successfully identified 3 of them. Despite some limitations, our strategy to purify and identify peaks selected from SELDI-TOF-MS analysis was effective.

An up to date look at lung cancer screening

Lung cancer is the leading cause of cancer-related death worldwide. At the time of initial presentation, most patients are at an advance stage of disease and have a poor associated prognosis. Those diagnosed and treated at earlier stages have a significantly better outcome with 5-year survival for stage I disease approaching 75%. Ideally a screening strategy for lung cancer would detect disease at an earlier stage and allow for potential surgical cure. The purpose of this review is to examine past and current evidence as it relates to lung cancer screening.