Gaining insights into cancer biology through exploration of the cancer secretome using proteomic and bioinformatic tools

Introduction: Tumor-associated proteins released by cancer cells and by tumor stroma cells, referred as ‘cancer secretome’, represent a valuable resource for discovery of potential cancer biomarkers. The last decade was marked by a great increase in number of studies focused on various aspects of cancer secretome including, composition and identification of components externalized by malignant cells and by the components of tumor microenvironment.

Areas covered: Here, we provide an overview of achievements in the proteomic analysis of the cancer secretome, elicited through the tumor-associated interstitial fluid recovered from malignant tissues ex vivo or the protein component of conditioned media obtained from cultured cancer cells in vitro. We summarize various bioinformatic tools and approaches and critically appraise their outcomes, focusing on problems and challenges that arise when applied for the analysis of cancer secretomic databases.

Expert commentary: Recent achievements in the omics- analysis of structural and metabolic aspects of altered cancer secretome contribute greatly to the various hallmarks of cancer including the identification of clinically significant biomarkers and potential targets for therapeutic intervention.     

Clinical applications of dendritic cell vaccination in the treatment of cancer

Dendritic cell (DC) immunotherapy has shown significant promise in animal studies as a potential treatment for cancer. Its application in the clinic depends on the results of human trials. Here, we review the published clinical trials of cancer immunotherapy using exogenously antigen-exposed DCs. We begin with a short review of general properties and considerations in the design of such vaccines. We then review trials by disease type. Despite great efforts on the part of individual investigative groups, most trials to date have not yielded data from which firm conclusions can be drawn. The reasons for this include nonstandard DC preparation and vaccination protocols, use of different antigen preparations, variable means of immune assessment, and nonrigorous criteria for defining clinical response. While extensive animal studies have been conducted using DCs, optimal parameters in humans remain to be established. Unanswered questions include optimal cell dose, use of mature versus immature DCs for vaccination, optimal antigen preparation, optimal route, and optimal means of assessing immune response. It is critical that these questions be answered, as DC therapy is labor- and resource-intensive. Cooperation is needed on the part of the many investigators in the field to address these issues. If such cooperation is not forthcoming, the critical studies that will be required to make DC therapy a clinically and commercially viable enterprise will not take place, and this therapy, so promising in preclinical studies, will not be able to compete with the many other new approaches to cancer therapy presently in development. Trials published in print through June 2003 are included. We exclude single case reports, except where relevant, and trials with so many variables as to prevent interpretation about DC therapy effects.     

Proteomic analysis of mitochondria: biological and clinical progresses in cancer

Introduction: Mitochondria play important roles in regulating multiple biological processes and signalling pathways in eukaryotic cells, and mitochondrial dysfunction may result in a wide range of serious diseases, including cancer. With improvements in the identification of mitochondrial proteins, mitochondrial proteomics has made great achievements. In particular, this approach has been widely used to compare tumour cells at different stages of malignancy. Therefore, there is an urgent need to identify and characterize the function of mitochondrial proteins in cancer progression and to determine the involved mechanisms.

Areas covered: We provide an overview of recent progress related to mitochondrial proteomics in cancer and the application of comparative mitochondrial proteomics in various biological processes, including apoptosis, necroptosis, autophagy and metastasis, as well as clinical progress in cancer. Proteomics-related reports were found using PubMed and Google Scholar databases.

Expert commentary: Understanding both post-translational modification and post-translational processing is important in the comprehensive characterization of protein function. The application of comparative mitochondrial proteomics to investigate clinical samples and cancer cells will contribute to our understanding of the molecular interplay of mitochondrial proteins in the development of cancer. This approach will mine more biomarkers for diagnosis and prognosis and improve therapeutic outcomes among cancer patients.     

Proteomic analysis of colorectal cancer: discovering novel biomarkers

Colorectal cancer is one of the most common cancers in the Western world. When detected at an early stage, the majority of cancers can be cured with current treatment modalities. However, most cancers present at an intermediate stage. The discovery of sensitive and specific biomarkers has the potential to improve preclinical diagnosis of primary and recurrent colorectal cancer, and holds the promise of prognostic and therapeutic application. Current biomarkers such as carcinoembryonic antigen lack sensitivity and specificity for general population screening. This review aims to highlight the role of current proteomic technologies in the discovery and validation of potential biomarkers with a view to translation to the clinic.     

Genetic characterization of breast cancer and implications for clinical management

Breast cancer is a genetic disease caused by the accumulation of mutations in neoplastic cells. In the last few years, high-throughput microarray-based molecular analysis has provided increasingly more coherent information about the genetic aberrations in breast cancer. New biomarkers and molecular techniques are slowly becoming part of the diagnostic and prognostic armamentarium available for pathologists and oncologists to tailor the therapy for breast cancer patients. In this review, we will focus on the contribution of breast cancer somatic genetics to our understanding of breast cancer biology and its impact on breast cancer patient management.     

MiR-491在非小细胞肺癌发生发展过程中的作用机制研究

人类miR-491 (has-miR-491)是一段长度为84 bp的微小RNA,可以通过与靶mRNA的3'端非翻译区(3'-untranslated region,3'-UTR)结合,降解靶mRNA或抑制其翻译,在转录后水平对肿瘤细胞基因表达进行调控,影响肿瘤发展进程.非小细胞肺癌(non-small lang ca...     

Proteomic analysis of cancer stem cells in human prostate cancer cells

Results from recent studies support the hypothesis that cancer stem cells (CSCs) are responsible for tumor initiation and formation. Here, we applied a proteome profiling approach to investigate the mechanisms of CSCs and to identify potential biomarkers in the prostate cancer cell line DU145. Using MACS, the DU145 prostate cancer cell line was isolated into CD44+ or CD44− cells. In sphere culture, CD44+ cells possessed stem cell characteristics and highly expressed genes known to be important in stem cell maintenance. In addition, they showed strong tumorigenic potential in the clonogenic assay and soft agar colony formation assay. We then analyzed and identified proteins that were differentially expressed between CD44+ and CD44− using two-dimensional gel electrophoresis and LC-MS/MS. Cofilin and Annexin A5, which are associated with proliferation or metastasis in cancer, were found to be positively correlated with CD44 expression. These results provide information that will be important to the development of new cancer diagnostic tools and understanding the mechanisms of CSCs although a more detailed study is necessary to investigate the roles of Cofilin and Annexin A5 in CSCs.     

Current status of publicly available sarcoma cell lines for use in proteomic studies

Cell lines are valuable resources for proteomic studies and can be used as tools to verify the significance of proteomic findings. Here, the authors overview the current status of the publicly available sarcoma cell lines. The authors surveyed seven major cell banks and found that the diversity observed in the sarcoma cell banks was largely insufficient; sarcoma cell lines are available for only a limited histological subtype. They also observed a number of issues with the pathological diagnosis of the cell lines, limitations in their behavioral diversity, and various unmet needs. Well characterized cell lines with accurate diagnosis based on modern diagnosis criteria should be available from public cell banks. The authors conclude that additional cell lines, along with detailed genetic and pathological analyses, should be prepared and deposited in order to promote sarcoma-specific proteomic research. The authors focused on sarcoma cell lines, but their discussion can be applied to the other cancers.     

Proteomic analysis of global alteration of protein expression in squamous cell carcinoma of the esophagus

Squamous cell carcinoma of the esophagus (ESCC), a major subtype of esophageal carcinoma, is one of the aggressive cancers with worst prognosis in the world. The dismal outcome of ESCC is attributed to multiple reasons including its aggressive nature, largely unknown molecular mechanism of its progression, and the lack of biomarkers for early detection and effective prediction of its clinical behavior. To identify proteins with prognostic and/or predictive value, we applied a proteomics strategy to quantify proteins differentially expressed in ESCC using matched samples of carcinoma and adjacent normal epithelial cells. The analysis led to identification of 28 proteins aberrantly expressed in cancer cells with changes of at least three-fold in ESCC relative to normal squamous epithelial cells. These changes represent functional alterations of essential proteins for normal cellular physiology, accounting for many cellular changes involved in development of ESCC, including cell transformation, loss of differentiation, tumor growth, apoptosis, tumor invasion, and cell metabolism. The differentially expressed proteins shed new insights on the mechanism of tumorigenesis and provide candidate biomarkers for early detection of ESCC.     

KIF20B promotes the progression of clear cell renal cell carcinoma by stimulating cell proliferation

Renal cell carcinoma (RCC) is a common urinary system cancer with high morbidity and mortality rate. Clear cell renal cell carcinoma (ccRCC) is a highly aggressive and common type of RCC. More and effective therapeutic targets are badly needed for the treatment of ccRCC. Kinesin family protein (KIF)20B, also named M-phase phosphoprotein 1, was reported as a microtubule-associated, plus-end-directed kinesin. KIF20B was involved in multiple cellular processes such as cytokinesis. Multiple studies indicated the oncogenic role for KIF20B in several types of tumors, including breast cancer and bladder cancer. However, the possible role of KIF20B in the progression of renal carcinoma is still unknown. Herein, our study demonstrated that KIF20B was relatively highly expressed in ccRCC tissues. In addition, KIF20B was inversely related to the clinical features including tumor size and T stage. We further found that inhibition of the KIF20B expression by a specific short hairpin RNA obviously reduces proliferation of ccRCC cells both in vitro and in vivo. Our study reveals the involvement of KIF20B in ccRCC progression. Generally, KIF20B is a promising novel therapeutic for the treatment of clear cell RCC.     

High FOXA1 levels induce ER transcriptional reprogramming,a pro-metastatic secretome,and metastasis in endocrine-resistant breast cancer

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Impact of low oxygen on the secretome of human adipose-derived stromal/stem cell primary cultures

Tissue fibrosis can lead to organ dysfunction, patient morbidity, and mortality. Adipose-derived Stromal/stem Cells (ASCs) represent a potential therapeutic. Immediately following grafting, ASCs would reside in a lower O₂ environment. ASC secretome was examined under 5% O₂ (“low O₂”) and 21% O₂ (“ambient O₂”) culture conditions. ASCs from five female donors were cultured in low or ambient O₂ conditions for 3 days and pooled conditioned medium was compared by two-dimensional liquid chromatography and tandem mass spectrometry (2D-LC–MS/MS). Of 71 proteins identified, five proteins involved in extracellular matrix (ECM) remodeling exhibited ≥2-fold decrease under low O₂ culture and were confirmed by Western immunoblot and qRT-PCR: fibronectin 1, TGF-β1-induced protein (βig-h3), osteonectin, and collagens type 1α₁ and α₂. ELISAs performed using 10 donors also confirmed significant decreases during low O₂ culture in 4–6 ASC donors. For low abundant proteins, a 36 cytokine/chemokine array was performed. Fifteen cytokines/chemokines including Type 2 cytokines IL-13, MCP-1, and CD40 ligand were detected in ambient O₂ ASC medium. IL-6 was detected in low O₂ but not ambient O₂ ASC medium. These findings demonstrate that low O₂ ASC exposure resulted in reduced ECM protein and Type 2 cytokine secretions that are significant with regard to inflammation in fibrosis.     

The emerging function and clinical significance of circRNAs in Thyroid Cancer and Autoimmune Thyroid Diseases

Thyroid cancer (TC) is one of the most common malignant tumors, with high morbidity and mortality rates worldwide. The incidence of TC, especially that of papillary thyroid carcinoma (PTC); has increased rapidly in recent decades. Autoimmune thyroid disease (AITD) is closely related to TC and has an estimated prevalence of 5%. Thus, it is becoming increasingly important to identify potential diagnostic biomarkers and therapeutic targets for TC and AITD. Circular RNAs (circRNAs) are a class of non-coding RNAs with covalently bonded circular structures that lack 5''-3'' polarity and polyadenylated tails. Several circRNAs play crucial roles in the development of various diseases, including TC and AITD, and could be important new biomarkers and/or targets for the diagnosis and therapy of such disorders. Although there are four subtypes of TC, research on circRNA has largely focused on its connection to PTC. Therefore, this review mainly summarizes the relationships between circRNAs and PTC and AITD, including the molecular mechanisms underlying these relationships. In particular, the functions of “miRNA sponges” and their interactions with proteins and RNA are discussed. The possible targeting of circRNAs for the prevention, diagnosis, and treatment of TC and AITD is also described. CircRNAs could be potential biomarkers of TC and AITD, although validation will be required before they can be implemented in clinical practice.     

Statistical properties of the traditional algorithm-based designs for phase I cancer clinical trials

Although there are several new designs for phase I cancer clinical trials including the continual reassessment method and accelerated titration design, the traditional algorithm-based designs, like the '3 + 3' design, are still widely used because of their practical simplicity. In this paper, we study some key statistical properties of the traditional algorithm-based designs in a general framework and derive the exact formulae for the corresponding statistical quantities. These quantities are important for the investigator to gain insights regarding the design of the trial, and are (i) the probability of a dose being chosen as the maximum tolerated dose (MTD); (ii) the expected number of patients treated at each dose level; (iii) target toxicity level (i.e. the expected dose-limiting toxicity (DLT) incidences at the MTD); (iv) expected DLT incidences at each dose level and (v) expected overall DLT incidences in the trial. Real examples of clinical trials are given, and a computer program to do the calculation can be found at the authors' website approximately linyo" locator-type="url">http://www2.umdnj.edu/ approximately linyo.     

Treatment of patients with advanced cancer with the natural killer cell line NK-92

Background aimsNatural killer (NK) cells, either naive or genetically engineered, are increasingly considered for cellular therapy of patients with malignancies. When using NK cells from peripheral blood, the number of expanded NK cells can be highly variable and the need for NK cell enrichment can make the process expensive. The NK-92 cell line (CD56+/CD3?) that was isolated from a patient with lymphoma has predictable high cytotoxic activity and can be expanded under good manufacturing practice conditions in recombinant interleukin-2.MethodsFifteen patients (age, 9–71 years) with advanced, treatment-resistant malignancies, either solid tumors/sarcomas (n = 13) or leukemia/lymphoma (n = 2), received two infusions of NK-92 cells, given 48 h apart. Three cohorts of patients were treated with escalating doses of NK-92 cells (n = 7 at 1 × 10⁹, n = 6 at 3 × 10⁹ and n = 2 at 1 × 10¹⁰ cells/m²).ResultsNo infusion-related or long-term side effects were observed. The dose of 10¹⁰ cells/m² was considered the maximum expandable cell dose with the use of an established culture bag system. Three fourths of patients with lung cancer had some anti-tumor response. Only one patient of seven had development of human leukocyte antigen antibodies. The persistence of NK-92 cells (male origin) in the circulation was confirmed by Y chromosome–specific polymerase chain reaction in two female patients.ConclusionsInfusions of NK-92 cells up to 10¹⁰ cells/m² were well tolerated. Despite the allogeneic nature of NK-92, development of human leukocyte antigen antibodies in these patients with cancer appears to be rare. The cells can persist in the recipient's circulation for at least 48 h. Some encouraging responses were seen in patients with advanced lung cancer.     

Proteome profiling for the identification of lung cancer signatures

Evaluation of: Taguchi A, Politi K, Pitteri SJ et al. Lung cancer signatures in plasma based on proteome profiling of mouse tumor models. Cancer Cell 20(3), 289–299 (2011).

Comprehensive and in-depth discovery of the disease proteome is an important issue in recent proteomics developments. Previous studies have shown a number of biomarkers discovered in various diseases, including lung cancer. Some of them are potentially useful in lung cancer diagnostics and prognostics. However, few of them can act as organ-specific biomarkers to extensively compare multiple cancer models. This article evaluates a recently published study employing comparative proteomics on multiple genetically engineered mouse models and sheds light on the usefulness and application of the discovered marker panel for human lung cancer diagnostics.