In a study of genetic alterations, the Multiplex Ligation-dependent Probe Amplification (MLPA) assay was used to measure gain or loss of 113 gene-probes in tumor and non-tumor tissue samples collected from each of the 220 patients with squamous head and neck cancer (HNSCC). Conditional and marginal models were available; both models account for correlated data but have different aspects. The conditional logistic regression model was proposed to estimate the subject-specific risk of tumor based on the paired tumor and non-tumor data collection, which was in contrast with the marginal model to estimate population-average risk.
The modeling process included rigorous variable selection, an initial multivariable model, a final model selection, and model validation. Genes with individual effect (p<0.01) were considered as candidates for the initial multivariable model for tumor. The final model included gene-probes with p<0.01 and estimations of odds ratios (OR) 95% Confidence Intervals (CIs) and the model’s predictive ability, measured by the receiver operating characteristic curve (ROC). A 10-fold cross-validation was performed to validate the model. Of 113 gene-probes, using the conditional approach, 16 genes in 7 chromosomes, remained in the final multivariable model with p<0.01 and an ROC score of 0.94. The cross-validation showed ROC mean (SD) score of 0.96(0.04). The marginal model, in contrast, ended with 8 gene-probes and had an observed ROC of 0.81.
Conclusion: The conditional approach appears to be the model of choice when assessing gene-probe risks of subjects with paired data collection and fewer missing covariates, compared to the marginal approach. This multiple gene model demonstrated excellent ability to discriminate tumor from non-tumor, and supports its contribution to the pathogenesis of HNSCC as well as their potential utility for further markers of early tumor detection.
The radio-sensitizing effects of several chemotherapeutic agents and hyperthermia have been investigated in several animal and human cell culture systems. Cells are first treated with Cisplatin, Gemcitabine, Halogenated pyrimidines or hyperthermia and thereafter irradiated with different dose of radiation up to 8 Gy. After treatment the clonogenic survival was determined and from the survival curves the values of the linear and quadratic parameters were determined using the formula S(D)/S(O)= exp-(αD+βD2).
An increase in the value of the linear parameter, α, was observed in most cases, which corresponds to an enhanced (potentially) direct lethal damage (PLD) at low doses. The quadratic parameter β, which is assumed to depend on the interaction of sublethal lesions (SLD), was rarely affected. Furthermore, it appeared that more radioresistant cell lines were more sensitised than the radiosensitive lines. Furthermore it can be concluded that radiosensitization is also dependent on cell cycle stage like plateau or exponentially growing phase or post treatment plating conditions.
Androgen deprivation therapy (ADT) in the form of medical or surgical castration has been used as the standard therapy for localized and advanced prostate cancer (PCa). Although ADT leads to the initial regression of tumors, the recurrence of more aggressive PCa, also termed as castration-resistant PCa (CRPC) is inevitable. Androgen receptor (AR) and its associated network have been proposed to play central role in the progression of CRPC. Given that CRPC exhibits the nature of heterogeneity and complexity, multiple cellular pathways may cooperatively promote progression of CRPC and render the tumors insensitive to therapy. In this article, we will review some of the recent findings and clinical interventions to identify the novel targets and alternative signaling pathways associated with AR that may allow the aggressive forms of PCa to recur and become resistance to therapy. We will discuss about the role of the cyclic adenosine monophosphate (cAMP) activated protein kinase A (PKA) pathway in the progression of CRPC. The emerging evidence suggests that several key factors in PKA signalings may play important roles in the recurrence and treatment response of CRPC, and that PKA pathways may serve as potential diagnostic and predictive biomarkers for CRPC. We will also update with the information on the novel therapeutic strategies that have been designed and tested in laboratories to inhibit PCa growth by targeting both AR and PKA pathways. Understanding of the molecular mechanisms underlying the progression of CRPC and treatment resistance will provide novel insight for effective treatment of CRPC.
Mohammed M. Milhem, Tina Knutson, Shujie Yang, Danlin Zhu, Xinjun Wang, Kimberly K. Leslie and Xiangbing Meng
Ary Serpa Neto, Marcelo Langer Wroclavski, Jorge Luiz Freire Pinto, Sarah Rodrigues Marsicano, Pamela Oliveira Delgado, Patricia Granja Coelho, Ricardo Moreno, Viviane Aparecida Vilas Boas, Ligia Ajaime Azzalis, Virginia Berlanga Campos Junqueira, Auro Del Giglio and Fernando Luiz Affonso Fonseca
Background: Biological materials such as cells, DNA, RNA, and proteins can be recovered from blood, urine, feces, pancreatic juice and sputum of patients. Here, we described a method for free plasma DNA extraction used in our laboratory, compared it to one of the most reproduced in the literature, and also verified the effects of short time storage of plasma on DNA quantification.
Methods: We assessed DNA concentrations in four samples of peripheral blood one hour, one day and three days after plasma separation (part A). EDTA blood (10 mL) was collected from each individual (10) and the specimen was centrifuged at 1,300 g for 10 min. The supernatant was transferred into polypropylene tubes, with particular attention not to disturb the buffy coat layer and the plasma was microcentrifuged at 2,400 g. DNA extracted from plasma was quantified (part B).
Results: Mean DNA concentration after our extraction process was similar to those methods found in literature. Moreover, we found a consistently negative correlation between time after plasma collection and DNA concentrations (r = -0.568; p = 0.022).
Conclusion: We showed a new method for DNA extraction. Also, we verified that fast processing after plasma collection was necessary to produce realistic results of plasma DNA.
DNA damage and repair represent important biological processes that are targets of various chemotherapies against cancer. In many ways, chemotherapeutic agents can induce DNA damage in cancerous as well as normal cells. However, DNA damage induced by chemotherapeutic agents can be intrinsically repaired by normal physiologic responses, which hampers inhibition of tumor growth and cause drug-resistance. Base excision repair (BER) is one such physiologic process that is important in the cellular response to many chemotherapeutic agents, specifically those agents that target DNAs. Once the BER pathway is triggered, damaged DNA bases undergo a series of chemical modifications resulting in the formation of abasic or apurinic/apyrimidinic (AP) site, which serves as key intermediates in the excision of damaged DNA bases and restoration of regular bases. To monitor BER- conferred intrinsic drug-resistance to chemotherapeutic agents such as DNA-alternating temozolomide (TMZ), pemetrexed (Alimta ® ), and fludarabine, we have developed a F-18 labeled fluoroethoxyamine ([ 11 C]FEX) as an imaging agent for positron emission tomography (PET) imaging of DNA damage and repair in vivo . In this work, we report the synthesis, radiolabeling, and evaluation of [ 18 F]FEX in vivo in mice. We have shown that [ 18 F]FEX- PET can be used to monitor DNA damage and repair in tumor xenograft mouse models including an uracil DNA glycosylase (UDG)-knockout tumor mouse model of non-small cell lung cancer (NSCLC).