Application of single molecule technology to rapidly map long DNA and study the conformation of stretched DNA

Herein we describe the first application of direct linear analysis (DLA) to the mapping of a bacterial artificial chromosome (BAC), specifically the 185.1 kb-long BAC 12M9. DLA is a single molecule mapping technology, based on microfluidic elongation and interrogation of individual DNA molecules, sequence-specifically tagged with bisPNAs. A DNA map with S/N ratio sufficiently high to detect all major binding sites was obtained using only 200 molecule traces. A new method was developed to extract an oriented map from an averaged map that included a mixture of head-first and tail-first DNA traces. In addition, we applied DLA to study the conformation and tagging of highly stretched DNA. Optimal conditions for promoting sequence-specific binding of bisPNA to an 8 bp target site were elucidated using DLA, which proved superior to electromobility shift assays. DLA was highly reproducible with a hybridized tag position localized with an accuracy of ±0.7 µm or ±2.1 kb demonstrating its utility for rapid mapping of large DNA at the single molecule level. Within this accuracy, DNA molecules, stretched to at least 85% of their contour length, were stretched uniformly, so that the map expressed in relative coordinates, was the same regardless of the molecule extension

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

The Design of a Multi-component Intervention to Promote Screening Mammography in an American Indian Community: The Native Women’s Health Project

Background: Breast cancer is an important public health issue among American Indian/Alaska Native (AI/AN) women in the US. This article describes the design and implementation of a culturally sensitive intervention to promote breast health among AI/AN women through a hybrid model that incorporates clinical and community-based approaches. This is one of the first studies using this model addressing breast cancer disparities among AI/AN populations in the US. Methods: The Theory of Planned Behavior was used as the guiding framework of the intervention and Community Based Participatory Research was the primary vehicle for the intervention planning and implementation. Three preliminary studies took place that aimed to identify qualitatively and quantitatively what deterred or encouraged AI women to get past or future mammograms. The research results were shared with community members who, through a prioritization process, identified the theoretical focus of the intervention and its corresponding activities. The priority population consisted of AI women ages 40–74, with no recent mammogram, and no breast cancer history. Results: The intervention centered on the promotion of social modeling and physician recommendation. The main corresponding activities included enhancing patient-physician communication about screening mammography through a structured dialogue, receipt of a breast cancer brochure, participation in an inter-generational discussion group, and a congratulatory bracelet upon receipt of a mammogram. Environmental and policy related changes also were developed. Conclusion: Creating a theory-based, culturally-sensitive intervention through tribal participatory research is a challenging approach towards eliminating breast cancer disparities among hard-to-reach populations

Understanding the Bariatric Patient Perspective in the National Patient-Centered Clinical Research Network (PCORnet) Bariatric Study

BACKGROUND: In 2016, the Patient-Centered Outcomes Research Institute funded the National Patient Centered Clinical Research Network (PCORnet) Bariatric Study (PBS). Understanding the experience of postoperative patients was a key component of this study. METHODS: Nine focus groups were conducted in Southern California, Louisiana, Pennsylvania, and Ohio and in a national advocacy conference for patients with obesity. Participants were identified and recruited in both clinical and community settings. Focus group transcripts were analyzed using an iterative inductive-deductive approach to identify global overarching themes. RESULTS: There were 76 focus group participants. Participants were mostly women (81.4%), had primarily undergone gastric sleeve (47.0%), were non-Hispanic white (51.4%), had some college education (44.3%), and made $100,000 annual income or less (65.7%). Qualitative findings included negative reactions patients received from friends, family, and co-workers once they disclosed that they had bariatric surgery to lose weight; and barriers to follow-up care included insurance coverage, emotional and situational challenges, and physical pain limiting mobility. CONCLUSIONS: These findings confirm the other qualitative findings in this area. The approach to bariatric surgery should be expanded to provide long-term comprehensive care that includes in-depth postoperative lifetime monitoring of emotional and physical health