The Role of Genomics and Proteomics in Lung Cancer Early Detection and Treatment.

Lung cancer is the leading cause of cancer-related death worldwide, with non-small-cell lung cancer (NSCLC) being the primary type. Unfortunately, it is often diagnosed at advanced stages, when therapy leaves patients with a dismal prognosis. Despite the advances in genomics and proteomics in the past decade, leading to progress in developing tools for early diagnosis, targeted therapies have shown promising results; however, the 5-year survival of NSCLC patients is only about 15%. Low-dose computed tomography or chest X-ray are the main types of screening tools. Lung cancer patients without specific, actionable mutations are currently treated with conventional therapies, such as platinum-based chemotherapy; however, resistances and relapses often occur in these patients. More noninvasive, inexpensive, and safer diagnostic methods based on novel biomarkers for NSCLC are of paramount importance. In the current review, we summarize genomic and proteomic biomarkers utilized for the early detection and treatment of NSCLC. We further discuss future opportunities to improve biomarkers for early detection and the effective treatment of NSCLC.

A novel role for aspirin in enhancing the reprogramming function of miR-302/367 cluster and breast tumor suppression.

Recent studies have provided evidence for tumor suppressive function of the embryonic stem cell-specific miR-302/367 cluster through induction of a reprogramming process. Aspirin has been found to induce reprogramming factors of mesenchymal-to-epithelial transition in breast cancer cells. Therefore, we aimed to investigate whether overexpression of miR-302/367 cluster and aspirin treatment cooperate in the induction of reprogramming and tumor suppression in breast cancer cells. MDA-MB-231 and SK-BR-3 human breast cancer cell lines were transfected with a miR-302/367 expressing vector and treated with aspirin. The cells were evaluated for indices of apoptosis, proliferation, migration, and invasion. In both cell lines, treatment of miR-302/367-transfected cells with aspirin upregulated expression of some main pluripotency factors such as OCT4, SOX2, NANOG, and KLF4, and downregulated expression of some invasion and angiogenesis markers at gene and protein levels. Aspirin increased the apoptotic rate in both cell lines transfected with miR-302/367. Both miR-302/367 and aspirin upregulated the expression of FOXD3 protein which is a known inducer of OCT4 and NANOG. Our results demonstrate that aspirin can enhance miR-302/367-induced reprogramming of breast cancer cells possibly through upregulation of FOXD3 expression. This can further augment the reversal of epithelial-mesenchymal transition and inhibits migration, invasion, and angiogenic signaling in breast cancer cells reprogrammed by miR-302/367. Therefore, aspirin may serve as a useful adjuvant for reprogramming of cancer cells.

The Role of Dihydropyrimidine Dehydrogenase and Thymidylate Synthase Polymorphisms in Fluoropyrimidine-Based Cancer Chemotherapy in an Iranian Population.

BACKGROUND: The fluoropyrimidine drug 5-Fluorouracil (5-FU) and the prodrug capecitabine have been extensively used for treatment of many types of cancer including colorectal, gastric, head and neck. Approximately, 10 to 25% of patients suffer from severe fluoropyrimidine-induced toxicity. This may lead to dose reduction and treatment discontinuation. Pharmacogenetics research could be useful for the identification of predictive markers in chemotherapy treatment. The aim of the study was to investigate the role of five genetic polymorphisms within two genes (DPYD, TYMS) in toxicity and efficacy of fluoropyrimidine-based chemotherapy. METHODS: Total genomic DNA was extracted from 83 cancer patients treated with fluoropyrimidine-based chemotherapy. In this study, three polymorphisms were genotyped in dihydropyrimidine dehydrogenase gene c.1905+1 G>A (DPYD*2A; rs3918290), c.1679 T>G (I560S; DPYD*13; rs55886062), and c.2846A>T (D949V; rs67376798) and two polymorphisms, besides the Variable Number of Tandem Repeat (VNTR) polymorphism and 6-bp insertion/deletion polymorphism in thymidylate synthase gene. The analysis of polymorphisms for rs3918290, rs55886062, rs67376798 and 6-bp insertion/deletion in TYMS was done by Polymerase Chain Reaction-restriction Fragment Length Polymorphism (PCRRFLP) TYMS VNTR analysis. 5-FU-related toxicities such as anemia, febrile neutropenia, neurotoxicity, vomiting, nausea, and mucositis were evaluated according to NCI-CTC criteria version 4.0. T-test and chi-square were used and p-values less than 0.05 were considered statistically significant. RESULTS: DPYD gene polymorphisms were not observed in this study. The frequency of the TYMS +6 bp allele was 40.35% and the -6 bp allele was 59.65% in this study. The frequency of VNTR 2R allele was 48.75% and 3R allele was 51.15%. Toxicity grade II diarrhea, mucositis, nausea, vomiting, and neurotoxicity was 2.2, 24.1, 15.7, 6, and 51.8%, respectively. Thymidylate synthase ins/del polymorphisms were associated with increased grade III neurotoxicity (p=0.02). Furthermore, anemia grade III was significantly associated with 2R/2R genotype (0.009). CONCLUSION: Thymidylate synthase gene polymorphisms may play a key role in fluoropyrimidne -based chemotherapy. Although rare DPYD polymorphisms were not observed in our study, according to large population studies, DPYD gene polymorphisms could be used as a predictive biomarker for patient treatments.

The Frequency and Importance of Common α-globin Gene Deletions Among ß-Thalassemia Carriers in an Iranian Population.

[This retracts the article on p. 196 in vol. 9, PMID: 29090069.].

The Frequency and Importance of Common α-globin Gene Deletions Among ß-Thalassemia Carriers in an Iranian Population.

BACKGROUND: ß-thalassemia is the most common monogenic disorder in Iran, and one of the challenges in the screening of the carriers is the coinheritance of α-thalassemia mutations. In the view of high prevalence of α-thalassemia mutations in many parts of the country, the aim of this study was to determine the carrier frequency of common alpha deletions, as a secondary modifier in clinical manifestations of beta thalassemia, in known beta-thalassemia carriers and some hematology parameter changes. METHODS: The study included families referred from different primary health care centers with microcytic hypochromic anemia [MCV<80fl; MCH<27 pg] and A2>3.4%]. Genomic DNA was extracted from peripheral blood leukocytes by salting out method. For common ß-globin gene mutation analysis, amplification refractory mutation system- polymerase chain reaction (ARMS-PCR) and for rare ß-thal alleles, DNA sequencing were used. Also, for investigation of common α-globin gene cluster deletions (-α3.7, -α4.2, --MED and -α20.5), multiplex Gap-PCR was performed. RESULTS: Among 227 ß-thalassemia minor individuals studied, α-globin gene deletions were found in 43 cases: 37 heterozygote -α3.7 (16.3%), 5 homo -α3.7 (2.2%) and 1 --MED (0.44%). Also, the co-inheritance of α-globin gene deletion and triplication was not found in the studied individuals. CONCLUSION: Although it is highly recommended that physicians and genetic counselors involved in the screening program of beta-thal major in the country consider this phenomenon because of high prevalence of this coinheritance, hematologic indices changes are very slight.

Evaluation of interleukin 12 and CD56+ lymphocyte cells in pediatric hematopoietic stem cell transplantation for early diagnosis of acute graft versus host disease.

The present study tried to explain CD56+ lymphocyte cells activities and possible prognostic role of these cells in Graft-Versus-Host-Disease (GVHD). The role of IL-12 activation and function is of interest in this study. Peripheral blood samples of 51 Hematopoietic Stem Cell Transplantation (HSCT) recipients collected at before (day -8) and after (days 7 and 14). PBMC were collected by Ficoll separation and analyzed by Flow Cytometry using triple antibody (CD45-PerCP, CD56-FITC, and CD69-PE staining and control antibody. Levels of the cytokine IL-12 in the patient's serum were evaluated by ELISA. Percentage of CD56+ lymphocytes (CD56+bright) cells was significantly increased at day 14 in patients with acute GVHD and percentage of lymphocytes expressing CD69 was significantly increased at days 7 and 14 posts HSCT in patients with acute GVHD in comparison to those in non-GVHD patients. Baseline serum IL-12 levels (pre-HSCT, day -8) were significantly higher in those HSCT recipients who did not develop GVHD. This study showed that post-transplant CD56+ lymphocytes and pre-transplant serum levels of IL-12 play significant roles in the induction of and protection against GVHD, respectively. The increase in the percentage of CD69+ cells indicates the activation of lymphocyte in acute GVHD group.

Effect of Chronic Restraint Stress on HPA Axis Activity and Expression of BDNF and Trkb in the Hippocampus of Pregnant Rats: Possible Contribution in Depression during Pregnancy and Postpartum Period.

INTRODUCTION: Brain-Derived Neurotrophic Factor (BDNF) and its receptor, TrkB, in the hippocampus are targets for adverse effects of stress paradigms; in addition, BDNF and its receptor play key role in the pathology of brain diseases like depression. In the present study, we evaluated the possible role of hippocampal BDNF in depression during pregnancy. METHODS: To achieve the purpose, repeated restrain stress (1 or 3 hours daily for 7 days) during the last week of pregnancy was used and alteration in the gene expression of hippocampal BDNF and TrkB evaluated by semi-quantitative PCR. RESULTS: The results showed that in stress group the level of ACTH and Corticosterone is increased showing that our model was efficient in inducing psychological stress; we also found that BDNF and TrkB expression are decreased in 3 hours stress group but not in 1 hour stress compared to control group. DISCUSSION: Our results imply that decrease in BDNF and its receptor could contribute in some adverse effects of stress during pregnancy such as elevation of depressive like behavior.

Association study of the TNF-α -1031T/C and VEGF +450G/C polymorphisms with susceptibility to endometriosis.

Tumor necrosis factor-α (TNF-α), a multifunctional proinflammatory cytokine, and vascular endothelial growth factor (VEGF), a major mediator of angiogenesis and vascular permeability, have been investigated in endometriosis patients of different populations. This study was carried out to investigate whether the two polymorphisms, TNF-α -1031T/C and VEGF +450G/C are associated with susceptibility to endometriosis in an Iranian population. Totally, 135 women with diagnosis of endometriosis and 173 women with no evidence of the disease were included in this study. The -1031T/C and +450G/C polymorphisms were assessed by PCR-RFLP analysis, using the two restriction enzymes BbsI and BsmFI, respectively. The frequencies of the TNF-α -1031TC genotype (p = 0.038) and the -1031 C allele (p = 0.048) were significantly lower in patients than control group. In contrast, no significant differences in the genotype and allele frequencies of the VEGF +450G/C polymorphism were found between the case and control groups. Our results suggest that the TNF-α -1031T/C polymorphism was associated with susceptibility to endometriosis in Iranian population, and the -1301C allele may have a protective role in development of endometriosis; On the contrary, we find no association between the VEGF +450G/C polymorphism and risk of endometriosis.

Prostaglandin E2 induces growth inhibition, apoptosis and differentiation in T and B cell-derived acute lymphoblastic leukemia cell lines (CCRF-CEM and Nalm-6).

Despite advances in the treatment of ALL, in most patients long-term survival rates remain unsatisfactory. The objective of the present study was to investigate the anti-cancer effects of Prostaglandin E2 (PGE2) in two different ALL cell lines (CCRF-CEM (T-ALL) and Nalm-6 (B-ALL)). The anti-leukemic effects of PGE2 were also compared with two epigenetic compounds (trichostatin A and 5-aza-2'-deoxycytidine). MTT assay was used to assess growth inhibition by anti-cancer drugs in these cells. All three compounds were shown to induce apoptosis in both ALL cell lines using flow cytometry and Western blotting. To evaluate the differentiation induction by these agents, the expressions of CD19 and CD38 markers on Nalm-6 cell line and CD7 marker on CCRF-CEM cell line were assayed. Surprisingly, the flow cytometric analysis showed a significant increase in CD markers expression in response to PGE2 treatments. We, for the first time, provide evidences that PGE2 has anti-leukemic effects and induces differentiation at micromolar ranges in both T- and B-cell derived ALL cell lines. Since T-ALL cells are insensitive to current chemotherapies, these findings may help the designing of new protocols for T-ALL differentiation therapy in the future.

Evaluation of the relationship between endometriosis and omega-3 and omega-6 polyunsaturated fatty acids.

BACKGROUND: Endometriosis is a common chronic inflammation causing major problems including infertility. The role of omega-3 and omega-6 fatty acids as their potential anti-inflammatory effects in endometriosis needs to be further explored. The objective of this study was to compare serum phospholipid fatty acid profile in endometriosis patients with controls, and to explore the correlation of this profile with the severity of the disease. METHODS: Sixty-four endometriosis patients and 74 control women, in reproductive age, participated in this study. Among the endometriosis patients, 19 cases were in stage I, 27 cases in stage II, 8 cases in stage III, and 10 cases in stage IV. Each patient underwent laparoscopy. Before surgery, 5 ml of blood was obtained. After extraction of the total lipids, serum total phospholipid fraction was isolated by thin layer chromatography. Fatty acid composition of the phospholipid fraction was determined by gas chromatography and the resulted profile was compared in endometriosis patients and controls. The profile was also compared in the endometriosis group based on the severity of disease. RESULTS: Stearic acid was significantly lower in the endometriosis group as compared to controls (P= 0.030). No other fatty acid compositions were significantly different between patients and controls. Serum ratio of eicosapentaenoic acid (EPA) to arachidonic acid (AA) was in reasonable correlation with the severity of endometriosis (r = 0.34, P = 0.006). CONCLUSION: According to these findings, levels of fatty acids in serum total phospholipids seem not to be a marker for endometriosis, but the EPA to AA ratio was a relevant factor indicating severity of illness.

Non-Invasive Detection of Esophageal Cancer using Genetic Changes in Circulating Cell-Free DNA.

Cell free DNA (cfDNA) is a genetic biomarker that is present in serum or plasma in high concentration in many types of cancer. Identification of circulating cancer related DNA molecules in serum or plasma is a non-invasive tool for early diagnosis and prognosis in many cancer patients. For this review, study selection and data extraction were performed by the authors. Detection of point mutations, microsatellite alterations, DNA hypermethylations and losses of heterozygosity in circulating cell free DNA have been characterized in esophagus cancer. Application of circulating cell free DNA as a biomarker, provide the best opportunity for constructing non-invasive tests for early detection, prognosis and management of cancer patients, after therapy in many types of cancer.

Stress-induced proteomic changes in the hippocampus of pregnant wistar rats.

Stress is a threatening factor that all living organisms encounter throughout life. Depending on the type of stress, there are several mechanisms for keeping body homeostasis to minimize stress effects. Brain is an organ which shows high sensitivity to stress conditions. Although many studies have shown induced-stress effects on rat embryos, little is known about the mechanisms involved in coping with stress by female rats during pregnancy. In the present study, restraint stress method was applied because this technique has been widely used in animal models to induce both psychological and physical stress. Restraint stress was applied in regular sessions (1 and 3 hrs) in two groups of 6 pregnant Wistar rats and similar number of animals was used as control group receiving no stress. ACTH and corticosterone levels in plasma samples were shown to increase in response to stress treatments. On the last day of pregnancy, rat hippocampus from the brain of each animal in all three groups was removed and analyzed using 2 Dimensional Gel Electrophoresis (2DE) technique. Using Image Master Software, approximately 2000 proteins were detected in the 2D gels analyzed, among which 34 proteins exhibited differential expression. These results indicate that the proteome patterns from the hippocampus of pregnant rats subjected to 1 and 3 hr of stress differs significantly from the control (unstressed) group. Future mass spectrometry identification of the 34 protein spots discovered in this study should allow a more precise understanding of molecules and cellular pathways involved in stress-induced responses during pregnancy.

Bryostatin-1, Fenretinide and 1α,25 (OH)(2)D(3) Induce Growth Inhibition, Apoptosis and Differentiation in T and B Cell-Derived Acute Lymphoblastic Leukemia Cell Lines (CCRF-CEM and Nalm-6).

In many acute leukemias, normal differentiation does not occur. However, in many cell lines derived from hematologic malignancies, differentiation or apoptosis can be induced by variety of agents. Despite advances in the treatment of Acute Lymphoblastic Leukemia (ALL), in most patients long-term survival rates remain unsatisfactory, especially in T-cell derived ALL. Thus we studied the anti-cancer effects of fenretinide, 1α,25(OH)(2)D(3), and bryostatin-1 in CCRF-CEM (T-cell derived) and Nalm-6 (B-cell derived) ALL cell lines. Using MTT assays, both cell lines were shown to exhibit increased inhibition of proliferation at micro (fenretinide) and nanomolar (1α,25(OH)(2)D(3), bryostatin-1) concentrations. These anti-cancer agents were shown to induce apoptosis and activate caspase-3 pathway in both ALL cell lines. Furthermore, for the first time we are reporting consistent anti-proliferative and apoptotic effects of Bryostatin-1 in ALL T-cell derived cell line with the lowest ED(50) (ranging 4.6-7.4 nM). To evaluate the differentiation induction by fenretinide, 1α,25(OH)(2)D(3), and bryostatin-1 in ALL cell lines, we assayed for the expressions of CD19, CD38 markers on Nalm-6 and CD7 marker on CCRF-CEM cell line. The flow cytometric analysis showed a significant increase in expression of CD markers in response to anti-cancer drug treatments. To assay the effects of anti-cancer drugs on cell cycle distribution, cell cycle analysis using flow cytometry was employed. These anti-cancer drugs appear to affect the CCRF-CEM and Nalm-6 cell cycles differently (G0/G1 and G2/M arrest, respectively). Overall results demonstrate that the anti-cancer agents used in this study are strong inhibitors of ALL cell proliferation and inducers of apoptosis and differentiation in vitro. These findings may be quite helpful if these drugs are to be used for differentiation therapy of ALL patients in clinics in the future. Further studies are warranted to establish the in vivo effect of these drugs particularly in patients with T-cell derived ALL.

Genetically modified foods and social concerns.

Biotechnology is providing us with a wide range of options for how we can use agricultural and commercial forestry lands. The cultivation of genetically modified (GM) crops on millions of hectares of lands and their injection into our food chain is a huge global genetic experiment involving all living beings. Considering the fast pace of new advances in production of genetically modified crops, consumers, farmers and policymakers worldwide are challenged to reach a consensus on a clear vision for the future of world food supply. The current food biotechnology debate illustrates the serious conflict between two groups: 1) Agri-biotech investors and their affiliated scientists who consider agricultural biotechnology as a solution to food shortage, the scarcity of environmental resources and weeds and pests infestations; and 2) independent scientists, environmentalists, farmers and consumers who warn that genetically modified food introduces new risks to food security, the environment and human health such as loss of biodiversity; the emergence of superweeds and superpests; the increase of antibiotic resistance, food allergies and other unintended effects. This article reviews major viewpoints which are currently debated in the food biotechnology sector in the world. It also lays the ground-work for deep debate on benefits and risks of Biotech-crops for human health, ecosystems and biodiversity. In this context, although some regulations exist, there is a need for continuous vigilance for all countries involved in producing genetically engineered food to follow the international scientific bio-safety testing guidelines containing reliable pre-release experiments and post-release track of transgenic plants to protect public health and avoid future environmental harm.