Identification of serum protein markers for breast cancer relapse with SELDI-TOF MS

Differential levels of Alpha-1-inhibitor III, Immunoglobulin heavy chain variable region, and Hypertrophied skeletal muscle protein GTF3 in rat mammary tumorigenesis

Early detection of breast cancer can be best facilitated by the development of precancerous markers. Serum proteins being the sensitive signatures, can be the ideal choice. We previously demonstrated the reduced levels of two serum proteins at a very early stage of tumorigenesis in a breast cancer model, developed in Wistar rats by 7,12-dimethylbenz[a]anthracene (DMBA) administration. Here we report the dysregulation of three more proteins in the serum collected at another early stage (15 weeks) of tumorigenesis in the same model. The proteins were identified (as Alpha-1-inhibitor III (Mug1), Immunoglobulin heavy chain variable region (IGHV), and Hypertrophied skeletal muscle protein GTF3) by MALDI-TOF MS after the screening and fingerprinting of serum samples by one-dimensional (1D) and two-dimensional (2D) electrophoresis respectively. Relative expression analysis of corresponding genes was also carried out, and the results were found as supporting the proteomic findings. In addition, the candidate proteins of the study and their corresponding ribonucleic acids (RNAs) were subjected to homology modelling and docking (using softwares like MODELLER, 3dRNA, Autodock4.0, and GROMACS etc), which revealed the binding sites for carcinogen (DMBA) and its nature of interaction with proteins and RNAs. Moreover, the network analysis by GeneMANIA unraveled the protein/gene functional network in which Mug1, IGHV, and GTF3 are involved. Based on the significant protein and gene expression alterations in early tumorigenesis, these proteins may prove very effective in search for biomarkers for the early detection of mammary cancer. Further, these proteins can also be tried as targets for chemotherapy.

Reduced expression of SETD2 and SNX9 proteins in chemically induced mammary tumorigenesis in Wistar rats: a prognostic histological and proteomic study

Breast cancer is a major global health concern, appealing for precise prognostic approaches. Thus, the need is to have studies focusing on the identification and recognition of preliminary events leading to the disease. The present study reports the tracing of precancerous progression and serum proteomic analysis in a breast cancer model developed as a result of 7,12-dimethylbenz[a]anthracene (DMBA) administration. Mammary gland histological changes of prime importance were examined by histopathology, and immunohistochemical analysis with Ki-67 was performed to monitor enhanced cell proliferation, right from the onset of hyperplasia till neoplasia. Serum proteomics (one-dimensional (1D) and two-dimensional (2D) electrophoresis, followed by MALDI-TOF MS characterization) was performed to decipher the differentially expressed serum proteins in animals undergoing tumorigenesis vis-à-vis controls. The significance of our study lies in reporting the significantly reduced expression of two proteins: histone-lysine N-methyltransferase (SETD2) and sorting nexin-9 (SNX9) at very early stage (13 weeks) of tumorigenesis, while the full-fledged tumors developed after 6 months. The reduced expression of SETD2 and SNX9 was validated by western blotting and relative expression analysis using quantitative real-time PCR. These proteins may hence prove as potentially useful tools in search for prognostic markers for the early detection of mammary cancer.

Identification of biomarkers for radiation-induced acute intestinal symptoms (RIAISs) in cervical cancer patients by serum protein profiling

Radiation-induced acute intestinal symptoms (RIAISs) are the most frequent complication of radiotherapy that causes great pain and limits the treatment efficacy. The aim of this study was to identify serum biomarkers of RIAISs in cervical cancer patients by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Serum samples were collected from 66 cervical cancer patients prior to pelvic radiotherapy. In our study, RIAISs occurred in 11 patients. An additional 11 patients without RIAISs were selected as controls, whose age, stage, histological type and treatment methods were matched to RIAISs patients. The 22 sera were subsequently analyzed by SELDI-TOF MS, and the resulting protein profiles were evaluated to identify biomarkers using appropriate bioinformatics tools. Comparing the protein profiles of serum samples from the RIAIS group and the control group, it was found that 22 protein peaks were significantly different (P < 0.05), and six of these peaks with mass-to-charge (m/z) ratios of 7514.9, 4603.94, 6887.41, 2769.21, 3839.72 and 4215.7 were successfully identified. A decision tree model of biomarkers was constructed based on three biomarkers (m/z 1270.88, 1503.23 and 7514.90), which separated RIAIS-affected patients from the control group with an accuracy of 81%. This study suggests that serum proteomic analysis by SELDI-TOF MS can identify cervical cancer patients that are susceptible to RIAISs prior to pelvic radiotherapy.

A new tumor biomarker, serum protein peak at 3,144 m/z, in patients with node-positive breast cancer

Purpose

To explore the association between the 3,144 m/z protein peak and the clinicopathological features and prognosis in breast cancer.

Methods

Using SELDI–TOF MS, we analyzed serum protein peak at 3,144 m/z in 283 patients with node-positive breast cancer, its relationship with clinicopathological features and their prognosis evaluating value of survival.

Results

3,144 m/z positive rate was higher in elderly patients (42.8 % in ≥50-year-old vs. 31.2 % in <50, P = 0.04). However, no correlation was observed between 3,144 m/z and other clinicopathological features (body mass index, menstrual status, family history, TNM, molecular subtypes, vascular invasion, neural invasion, p53 and CA15-3). However, the positive rate of 3,144 m/z was higher than that of CA15-3 (35.5 vs. 11.4 %, McNemar χ² test, p < 0.001). 3,144 m/z-negative patients (n = 177) had a better 3-year overall survival (OS) than 3,144 m/z-positive patients (n = 106) (89.8 vs. 81.2 %, P = 0.045). Younger patients (P = 0.016), postmenopausal status (P = 0.019), small tumor (P < 0.001), less positive nodes (P < 0.001), early stage (P < 0.001), favorable molecular subtype (P = 0.007), normal CA15-3 (P = 0.003) and neoadjuvant chemotherapy (P = 0.001) predicted better survival. Cox analysis showed that T3–4 (95 % CI 1.419–8.057, P = 0.006), lymph node metastasis (95 % CI 1.242–3.632, P = 0.006) and p53 mutation (95 % CI 1.088–6.378, P = 0.032) were independent adverse prognostic factors. But childbirth ≥2 (95 % CI 0.163–0.986, P = 0.046), adjuvant chemotherapy (95 % CI 0.062–0.921, P = 0.038) and adjuvant radiotherapy (95 % CI 0.148–0.928, P = 0.034) were the independent factors in reducing risk of death in breast cancer patients. Combination testing of 3,144 m/z and CA15-3 will improve the prognosis value of 3-year survival (P = 0.011); patients with CA153−/3144− were characterized by the longest survival (89.8 %) and the CA153+/3144+ patients by the shortest.

Conclusions

Serum protein peak at 3,144 m/z is a new biomarker for breast cancer diagnosis and prognosis and showed a higher positive rate than serum CA15-3. Combining 3,144 m/z and CA15-3 testing may improve prognosis of longer survival in breast cancer patients.

Advances in Proteomic Technologies and Its Contribution to the Field of Cancer

Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.

Impact of tumor removal on the systemic oxidative profile of patients with breast cancer discloses lipid peroxidation at diagnosis as a putative marker of disease recurrence

BACKGROUND

Recent studies have suggested a regulatory role for some of the metabolites derived from oxidative stress in breast cancer. In this way, cancer-induced oxidative changes could modify the breast environment and potentially trigger systemic responses that may affect disease prognosis and recurrence. In this study, we investigated the systemic oxidative profile of women with early breast cancer bearing the primary tumor and after tumor withdrawal, and its long-term implications.

PATIENTS AND METHODS

Plasma samples were collected at diagnosis, and the systemic oxidative profile was determined by evaluating the lipid peroxidation, total antioxidant capacity of plasma (TRAP), malondialdehyde (MDA), protein carbonylation, and hydroperoxides. Nitric oxide, vascular endothelial growth factor (VEGF), and tumor necrosis factor alpha (TNF-α) levels were further measured. We also evaluated the impact of the oxidative profiling at diagnosis on disease recurrence in a 5-year follow-up.

RESULTS

Enhanced oxidative stress was detected in patients bearing the primary tumors, characterized by high lipid peroxidation, TRAP consumption, high carbonyl content, and elevated VEGF and TNF-α levels. After tumor removal, the systemic oxidative status presented attenuation in lipid peroxidation, MDA, VEGF, and TNF-α. The 5-year recurrence analysis indicated that all patients who recidivated presented high levels of lipid peroxidation measured by chemiluminescence at diagnosis.

CONCLUSIONS

Our data suggest that the presence of the primary tumor is indicative of the systemic pro-oxidant status of breast cancer and demonstrates a role for lipid peroxidation in disease recurrence, highlighting the need for a metabolic follow-up of patients with cancer at diagnosis before tumor removal.

BRCA1 germ-line mutations and tumor characteristics in eastern Chinese women with familial breast cancer

Although several studies detected the BRCA1 germ-line mutations in Chinese women with familial breast cancer, most of them did not employ conventional full gene sequencing, especially in eastern China. In addition, the clinicopathological features of BRCA1-associated breast cancer in Chinese women were not well investigated. In this study, we screened the complete coding regions and exon-intron boundaries of BRCA1 by polymerase chain reaction (PCR)-sequencing assay. Immunohistochemistry analyses were performed on tumor samples to detect the expression of estrogen receptor (ER), progesterone receptor (PR), P53, and human epidermal growth factor receptor-2 (HER-2). Breast cancer patients having one or more affected relatives referred from the Zhejiang Cancer Hospital, eastern China during 2008-2011 were selected for the study. A total of 62 familial breast cancer patients received the BRCA1 germ-line mutation screening. Five deleterious mutations were detected in this cohort. The mutation rate was 11.3% (7/62). We found two novel mutations (3414delC and 5,280 C > T) and two recurrent mutations (5,273 G > A and 5589del8). BRCA1 mutation tumors tended to be negative for ER, PR, and HER-2, and exhibited high histological grade compared with tumors without BRCA1 mutations. Our study suggests that recurrent mutations may exist in eastern Chinese women with familial breast cancer and PCR-sequencing assay is a useful tool to screen these mutations. It also suggests that BRCA1-associated breast cancers in Chinese women exhibit an aggressive phenotype.

Screening and identification of serum proteomic biomarkers for gastric adenocarcinoma

The aim of the present study was to screen for possible serum biomarkers for gastric adenocarcinoma. Surface-enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS) was used to screen serum samples from 109 cases of gastric adenocarcinoma and 106 control subjects (60 healthy subjects, 30 patients with chronic superficial gastritis and 16 cases of chronic atrophic gastritis). The differentially expressed protein peaks were selected and isolated using high performance liquid chromatography (HPLC) and processed with enzyme prior to liquid chromatography-mass spectrometry tandem mass spectrometry (LC-MS/MS) analysis and data mining with software XCalibur program components BioWorks 3.2. Among the gastric cancer cases, three differentially expressed protein peaks were selected as potential serum biomarkers: the m/z peaks at 5,906.5 showed increased expression (8.53±4.33 in the cancer group, and 0.88±0.31 in the control group); the m/z peaks at 6,635.7 and 8,716.3 showed decreased expression (6.54±2.44 and 0.93±0.29, respectively, in the cancer group and 17.56±4.43 and 2.16±0.98, respectively, in the control group) (P<0.01). The m/z peaks at 5,906.5, 6,635.7 and 8,716.3, were identified as fibrinogen α-chain, apolipo-protein A-II and apolipoprotein C-I. The combined use of the three biomarkers distinguished the cancer group patients from the control group samples at a sensitivity of 93.85% (61/65) and a specificity of 94.34% (50/53). In conclusion, fibrinogen α-chain, apolipoprotein A-II and apolipoprotein C-I were identified as potential markers for gastric cancer and appear to have diagnostic value for clinical applications.