Incorporating gene co-expression network in identification of cancer prognosis markers

<p>Abstract</p> <p>Background</p> <p>Extensive biomedical studies have shown that clinical and environmental risk factors may not have sufficient predictive power for cancer prognosis. The development of high-throughput profiling technologies makes it possible to survey the whole genome and search for genomic markers with predictive power. Many existing studies assume the interchangeability of gene effects and ignore the coordination among them.</p> <p>Results</p> <p>We adopt the weighted co-expression network to describe the interplay among genes. Although there are several different ways of defining gene networks, the weighted co-expression network may be preferred because of its computational simplicity, satisfactory empirical performance, and because it does not demand additional biological experiments. For cancer prognosis studies with gene expression measurements, we propose a new marker selection method that can properly incorporate the network connectivity of genes. We analyze six prognosis studies on breast cancer and lymphoma. We find that the proposed approach can identify genes that are significantly different from those using alternatives. We search published literature and find that genes identified using the proposed approach are biologically meaningful. In addition, they have better prediction performance and reproducibility than genes identified using alternatives.</p> <p>Conclusions</p> <p>The network contains important information on the functionality of genes. Incorporating the network structure can improve cancer marker identification.</p

Adjuvant Chemotherapy Versus Adjuvant Concurrent Chemoradiotherapy After Radical Surgery for Early-Stage Cervical Cancer: A Randomized, Non-Inferiority, Multicenter Trial

We conducted a prospective study to assess the non-inferiority of adjuvant chemotherapy alone versus adjuvant concurrent chemoradiotherapy (CCRT) as an alternative strategy for patients with early-stage (FIGO 2009 stage IB-IIA) cervical cancer having risk factors after surgery. The condition was assessed in terms of prognosis, adverse effects, and quality of life. This randomized trial involved nine centers across China. Eligible patients were randomized to receive adjuvant chemotherapy or CCRT after surgery. The primary end-point was progression-free survival (PFS). From December 2012 to December 2014, 337 patients were subjected to randomization. Final analysis included 329 patients, including 165 in the adjuvant chemotherapy group and 164 in the adjuvant CCRT group. The median follow-up was 72.1 months. The three-year PFS rates were both 91.9%, and the five-year OS was 90.6% versus 90.0% in adjuvant chemotherapy and CCRT groups, respectively. No significant differences were observed in the PFS or OS between groups. The adjusted HR for PFS was 0.854 (95% confidence interval 0.415-1.757; P = 0.667) favoring adjuvant chemotherapy, excluding the predefined non-inferiority boundary of 1.9. The chemotherapy group showed a tendency toward good quality of life. In comparison with post-operative adjuvant CCRT, adjuvant chemotherapy treatment showed non-inferior efficacy in patients with early-stage cervical cancer having pathological risk factors. Adjuvant chemotherapy alone is a favorable alternative post-operative treatment

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

A new combination in Pseudolappula (Boraginaceae, Rochelieae) based on morphological, molecular and palynological evidence

Lappula sinaica was recently transferred to the monotypic genus Pseudolappula based on phylogenetic studies, while the related species, L. occultata, has remained in the genus Lappula. In this study, morphological, molecular, and palynological evidence supports that L. occultata should be transferred to the genus Pseudolappula. Both L. occultata and P. sinaica share a combination of nutlets features that distinguish them from Lappula: a longer adaxial keel and a linear attachment scar. Phylogenetic analysis based on ITS and trnL-F strongly supports L. occultata as the sister taxon of P. sinaica. In addition, pollen grains of these two species are 3-syncolporate with 3 alternating pseudocolpi, which is significantly different from the grains of Lappula taxa. Based on the above evidence, the new combination Pseudolappula occultata is proposed

Insights into the Volatile Flavor Profiles of Two Types of Beef Tallow via Electronic Nose and Gas Chromatography–Ion Mobility Spectrometry Analysis

In the current study, an electronic nose (E-nose) and gas chromatography–ion mobility spectrometry (GC-IMS) were employed to investigate the volatile flavor compounds (VFCs) of intense flavor beef tallow (L) and ordinary beef tallow (P). The study results indicate that an E-nose combined with an LDA and GC-IMS combined with an OPLS-DA can effectively distinguish between the two types of beef tallow. Compared with ordinary beef tallow, the E-nose sensors of intense flavor beef tallow have stronger response signals to sulfides, terpenes, and nitrogen oxides. A total of 22 compounds contribute to making the flavor of intense flavor beef tallow more typical and richer; in contrast, ethyl acetate was the main aroma-active compound found in the ordinary beef tallow. Sulfur-containing compounds and terpenoids might be the key substances that cause sensory flavor differences between the two types of beef tallow. In conclusion, the results of this study clarify the characteristics and differences of the two types of beef tallow and provide an enhanced understanding of the differences in the flavors of the two types of beef tallow

Differences exist across insurance schemes in China post-consolidation.

In China, the basic insurance system consists of three schemes: the UEBMI (Urban Employee Basic Medical Insurance), URBMI (Urban Resident Basic Medical Insurance), and NCMS (New Cooperative Medical Scheme), across which significant differences have been observed. Since 2009, the central government has been experimenting with consolidating these schemes in selected areas. This study examines whether differences still exist across schemes after the consolidation.A survey was conducted in the city of Suzhou, collecting data on subjects 45 years old and above with at least one inpatient or outpatient treatment during a period of twelve months. Analysis on 583 subjects was performed comparing subjects' characteristics across insurance schemes. A resampling-based method was applied to compute the predicted gross medical cost, OOP (out-of-pocket) cost, and insurance reimbursement rate.Subjects under different insurance schemes differ in multiple aspects. For inpatient treatments, subjects under the URBMI have the highest observed and predicted gross and OOP costs, while those under the UEBMI have the lowest. For outpatient treatments, subjects under the UEBMI and URBMI have comparable costs, while those under the NCMS have much lower costs. Subjects under the NCMS also have a much lower reimbursement rate.Differences still exist across schemes in medical costs and insurance reimbursement rate post-consolidation. Further investigations are needed to identify the causes, and interventions are needed to eliminate such differences

Characteristics of subjects with outpatient treatments.

<p>Characteristics of subjects with outpatient treatments.</p

Density of predicted reimbursement rate.

<p>Left: Inpatient. Right: Outpatient.</p

Reasons for not using insurance for outpatient treatment.

<p>Reasons for not using insurance for outpatient treatment.</p