Systematic Implementation of Effective Quality Assurance Processes for the Assessment of Radiation Target Volumes in Head and Neck Cancer

PURPOSE

Significant heterogeneity exists in clinical quality assurance (QA) practices within radiation oncology departments, with most chart rounds lacking prospective peer-reviewed contour evaluation. This has the potential to significantly affect patient outcomes, particularly for head and neck cancers (HNC) given the large variance in target volume delineation. With this understanding, we incorporated a prospective systematic peer contour-review process into our workflow for all patients with HNC. This study aims to assess the effectiveness of implementing prospective peer review into practice for our National Cancer Institute Designated Cancer Center and to report factors associated with contour modifications.

METHODS AND MATERIALS

Starting in November 2020, our department adopted a systematic QA process with real-time metrics, in which contours for all patients with HNC treated with radiation therapy were prospectively peer reviewed and graded. Contours were graded with green (unnecessary), yellow (minor), or red (major) colors based on the degree of peer-recommended modifications. Contours from November 2020 through September 2021 were included for analysis.

RESULTS

Three hundred sixty contours were included. Contour grades were made up of 89.7% green, 8.9% yellow, and 1.4% red grades. Physicians with >12 months of clinical experience were less likely to have contour changes requested than those with <12 months (8.3% vs 40.9%; P < .001). Contour grades were significantly associated with physician case load, with physicians presenting more than the median number of 50 cases having significantly less modifications requested than those presenting <50 (6.7% vs 13.3%; P = .013). Physicians working with a resident or fellow were less likely to have contour changes requested than those without a trainee (5.2% vs 12.6%; P = .039). Frequency of major modification requests significantly decreased over time after adoption of prospective peer contour review, with no red grades occurring >6 months after adoption.

CONCLUSIONS

This study highlights the importance of prospective peer contour-review implementation into systematic clinical QA processes for HNC. Physician experience proved to be the highest predictor of approved contours. A growth curve was demonstrated, with major modifications declining after prospective contour review implementation. Even within a high-volume academic practice with subspecialist attendings, >10% of patients had contour changes made as a direct result of prospective peer review.

Efficacy of incisional negative pressure therapy in preventing post-sternotomy wound complications

BACKGROUND

Sternal wound infections represent a source of significant morbidity and mortality following median sternotomy. The use of incisional negative pressure wound therapy in prevention has yet to be elucidated.

METHODS

A retrospective study was conducted before and after a universal wound care protocol was implemented including the prophylactic use of negative pressure wound therapy (NPWT). The primary endpoint was sternal infections within 90 days of the index operation.

RESULTS

In the control period, there was a 3.0% rate of sternal infection within 90 days compared to 0.8% in the intervention period (p < 0.001). An odds ratio of 0.25 (95% confidence interval 0.11, 0.57; p < 0.001) in the intervention period as compared to the control period was demonstrated.

CONCLUSIONS

The use of a standardized wound care protocol including the universal application of NPWT for patients undergoing cardiac surgery with median sternotomy was an independent predictor of decreased rates of sternal infection.

Volumetric Modulated Arc Therapy Craniospinal Irradiation Utilizing a Vertebral Body Sparing Approach: A Toxicity Analysis

PURPOSE/OBJECTIVE(S)

Craniospinal irradiation (CSI) is indicated for adult patients diagnosed with leptomeningeal disease (LMD). Proton-based vertebral-body-sparing (VBS) CSI has been explored with pediatric patients to minimize hematologic toxicity; however, utilization of VBS in an adult population is limited. A recent phase II trial (Yang et al, JCO 2022) has shown efficacy of proton-based CSI to treat non-small cell lung and breast cancer with LMD. We hypothesize that VBS-CSI utilizing volumetric modulated arc therapy (VMAT) could also effectively reduce dose to vertebral bodies and surrounding organs-at-risk (OARs), minimizing toxicity for adult patients with LMD and comparing favorably to proton-based CSI.

MATERIALS/METHODS

Consecutive patients with leptomeningeal disease received VMAT VBS-CSI, 30 Gy in 10 fractions, as a part of a prospective registry. Full VMAT arcs for the brain fields matched to two spine isocenters for the upper and lower spine were created utilizing limited posterior arcs. The PTV was created with margins of 3mm uniformly around the brain contour and 7mm around the spinal canal. To further decrease the vertebral body dose, an avoid entry and exit contour was created. This structure was a margin on the PTV anteriorly designed to carve dose out of the vertebral bodies while still maintaining coverage to the PTV. Acute toxicity data were collected using Common Terminology Criteria for Adverse Events (CTCAE) v5 and was defined as toxicity occurring within 30 days of treatment conclusion.

RESULTS

Ten adult patients were treated in this cohort. All patients completed radiation treatment. One patient experienced Grade 2 neutropenia with the remaining nine experiencing Grade 1 hematologic toxicity (three Grade 1 pancytopenia, six Grade 1 thrombocytopenia). Three patients experienced Grade 2 gastrointestinal toxicity (Grade 2 nausea, Grade 2 esophagitis, Grade 2 esophagitis/Grade 2 diverticulitis) with the remaining seven experiencing Grade 1 nausea. No patient experienced Grade 3+ toxicities in this cohort. One patient experienced a 5-day delay in systemic therapy initiation due to neutropenia; otherwise, all patients planned for systemic therapy started without delay.

CONCLUSION

VMAT VBS-CSI is an effective technique to reduce dose to surrounding OARs and vertebral bodies. In this study, VMAT VBS-CSI led to acceptable toxicity compared to patients treated with proton CSI on a phase 2 clinical trial. An NRG phase 3 clinical trial may be developed to evaluate the efficacy of proton-based CSI for patients with LMD. However, these data show how VMAT VBS-CSI may be an acceptable alternative for centers without proton therapy capabilities. Given its promising early results, future prospective evaluation of the technique is warranted.

A feasibility study of perioperative vitamin D supplementation in patients undergoing colorectal cancer resection

Background

Vitamin D supplementation improves colorectal cancer (CRC) survival outcomes in randomized trials. The aim of this study was to test the feasibility, safety and efficacy of vitamin D supplementation in the pre- and perioperative period in patients undergoing CRC surgery.

Methods

Patients were given 3200IU oral cholecalciferol (D3) per day perioperatively. Serial serum 25-hydroxyvitamin (25OHD) was measured by liquid chromatography tandem mass spectrometry and compared to untreated CRC controls. 25OHD and C-reactive protein (CRP) levels were compared using adjusted generalized linear mixed-effects models.

Results

A total of 122 patients underwent serial perioperative sampling, including 41 patients given high-dose perioperative supplementation. Supplementation was well-tolerated with no adverse or serious adverse events related to supplementation reported. Pre-operative supplementation increased 25OHD levels on the day of surgery (103.9 vs. 42.5 nmol/l, P = 8.2E-12). Supplementation increased 25OHD levels at all post-operative timepoints (P < 0.001) and attenuated the post-operative drop in 25OHD (46 vs. 24% drop, P = 3.0E-4). Rate of vitamin D peri-operative insufficiency was significantly less in those on supplementation (e.g., day 3-5, 14 vs. 84%, P = 1.41E-08), with multivariate modeling across all timepoints indicating a ∼59 nmol/l higher 25OHD compared to control patients (P = 3.7E-21). Post-operative CRP was lower in patients taking supplementation (e.g., day 3-5 timepoint; 129 vs. 81 mg/l, P = 0.04).

Conclusion

High dose pre-operative vitamin D supplementation is associated with higher perioperative 25OHD levels, lower rates of vitamin D insufficiency and reduced early post-operative CRP. Alongside published evidence for a beneficial effect of vitamin D on CRC survival outcomes, these novel findings provide strong rationale for early initiation of vitamin D supplementation after a diagnosis of CRC.

290 ‘Save Blood' - Strategies to Reduce Inappropriate Routine Bloods Tests in a Surgical Department

Aim

To quantify the number of inappropriate blood tests in our 72-bed Surgical Department and identify strategies that reduce the number of unnecessary electronic blood test requests. This should reduce patient harm, demands on staff time, laboratory processing burden and financial expenditure.

Method

Each audit involved logging all blood tests for every surgical inpatient over two consecutive days. Upon reviewing the clinical records, it was decided whether tests were clinically indicated or ‘inappropriate’.

Following a baseline audit, three interventions were sequentially introduced over a one-year period, and the department re-audited after each: (1) educational sessions with junior medical staff and creation of ordering guidelines, (2) poster presentations, and (3) policing of requests by middle-grade doctors and removal of electronic blood test ordering bundles.

Results

Across the baseline audit to interventions 1–3, numbers of patients with at least one inappropriate test were recorded as 45/73 (62%), 51/63 (81%), 41/57 (72%), and 27/32 (84%), accruing totals of 363, 289, 303, and 149 inappropriate tests respectively. This gave an overall reduction in the rate of inappropriate blood tests per patient per day from a baseline of 0.9, to 0.9 then 0.8 to 0.5 with successive interventions.

Conclusions

Despite the innovation of electronic ordering systems enabling close audit of test schedules, inappropriate tests remain common. Educational sessions for junior doctors, written guidelines, and poster presentations had little influence on this.

However, rationalising electronic order bundles and involving senior doctors in decision-making, almost halved the rate of inappropriate tests. These more effective strategies will be disseminated throughout our hospital.

425 The Impact Of COVID-19 On Hernia Surgery in The Lothian Region Of Scotland

Aim

The COVID-19 pandemic resulted in a lockdown in South East Scotland on the 23 March 2020. This had an impact on the volume of benign elective surgery able to be undertaken. The degree to which this reduced hernia surgery was unknown.

The aim of this study was to review the hernia surgery workload in the Lothian region of Scotland and assess the impact of COVID-19 on hernia surgery.

Method

The Lothian Surgical Audit database was used to identify all elective and emergency hernia operations over a six-month period from 23 March 2020, and for the same time period in 2019. Data was collected on age, gender, location of the hernia, type of hernia repair and whether elective or emergency operation.

Results

The number of hernia repairs reduced dramatically between 2019 and 2020 (570 versus 149). The majority of this can be explained by a reduction in elective operating (488 versus 87). There was, however, also a reduction in the numbers of hernias repaired as an emergency over the same study periods (82 to 62). Lockdown in 2020 had the biggest effect on elective incisional hernia repair (74 versus 2).

Conclusions

The COVID-19 pandemic has reduced both the number of elective and emergency hernia operations in 2020 compared to 2019. While the reduction in elective surgery has not resulted in an associated increase in emergency surgery over the study period, it is possible that if continuing reduced availability to elective hernia surgery continues in Lothian, the emergency hernia workload may increase.

Reported rationales for HPV vaccination vs. Non-vaccination among undergraduate and medical students in South Carolina

Objective: We sought to identify factors that influence Human Papillomavirus (HPV) vaccination rates in individuals at two higher education institutions in South Carolina (SC).Participants: We surveyed 1007 students with a mean age and standard deviation of 20.3 ± 3.3 from September 2018 to December 2018.Methods: Participants answered 13 questions, assessing HPV vaccination rates, demographics, and rationales for vaccination vs. non-vaccination.Results: Of 1007 respondents, 700 received HPV vaccination, 165 were unvaccinated, 75 received partial vaccination and 138 were uncertain. Commonalities in HPV vaccination existed between females (p = 0.037), individuals who received standard childhood vaccinations (p = 0.04), and those not native-born in SC (p < 0.001). Of non-vaccinated individuals, 37% "never thought about vaccination," 32% did not perceive a need for vaccination, and 31% reported vaccine safety as reasons for not receiving the vaccine.Conclusions: Promotion of HPV vaccination may benefit from targeting SC natives, males, and individuals who are under-vaccinated or unvaccinated.

Abstract 1207: Custom next-generation sequencing primer designs for targeted sequencing of multi strain viral targets

Viruses are infectious agents that can cause many diseases including cancers. A viral species is comprised of many strains each having a unique pathology. For example, over 170 types of HPV have been described, of which only 2 strains, HPV16 and HPV18, are implicated in 70% of cervical cancer cases. Accurate identification of viral strains is often critical and also facilitates research into their association with prognosis or response and personalized therapies. Currently, sequencing virus genes or genome requires complex procedures that involve purifying the virus particle and its genomes from the host genome. Whole genome sequencing is inefficient since viral genomes are orders of magnitude smaller than human genomes, and human DNA is orders of magnitude more abundant than viral DNA. In contrast, targeted next-generation sequencing allows focusing of sequencing and analysis to the region or species of interest using PCR based enrichment.

We developed a viral design pipeline that accepts a multiple sequence alignment of the viral genomes or genomic regions of interest to identify and design primer pairs in conserved regions flanking the variable regions. The presence/absence of a set of 1 or more amplicons is used to precisely differentiate the many strains of a viral species. For whole genome sequencing, the complete viral genomic sequence is used as target to design unique and highly specific amplicons covering the whole genome for enrichment of the entire virus. All primers pass through rigorous quality checks to meet our sensitivity, specificity, and primer quality standards.

We have successfully designed multi-strain Ion Ampliseq custom viral panels for HCV, HIV, CMV, Measles and Pestivirus. Some of these panels were designed with the objective of targeting a specific region on a virus genome; other panels were designed to enrich and sequence the whole virus genome. The panel primers were highly specific to the region of interest in the viral genomes and did not amplify the host genome.

In conclusion, our custom Ion AmpliSeq viral panels enable the enrichment and amplification of the unique regions of interest in the viral genomes or the whole virus genome, avoiding the massive excess of the host genome. These panels allow precise identification of the virus species and strains for many applications including research, phylogenomic classification and comparative genomics.

For Research Use Only. Not for use in diagnostic procedures

Citation Format: Ratnesh Singh, Na Li, Zunping Luo, Anna McGeachy, Antonio F. Martinez Alcantara, Aren Ewing, Fiona C. Hyland. Custom next-generation sequencing primer designs for targeted sequencing of multi strain viral targets [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1207.

Abstract 158: Custom primer design pipeline and analysis workflow for targeted methylation sequencing using NGS Ion AmpliSeq technology

Changes in DNA methylation, causing chromosome instability and altered gene expression, have been strongly associated with carcinogenesis. Due to the involvement of methylation in cancer, methylation profiles have been heralded as promising cancer biomarkers. Here, we present a primer design pipeline and an analysis workflow that we have developed to design and analyze custom methylation panels and detect methylation status.

An automated primer design pipeline for methylation sequencing has been developed, consisting of genome conversion, primer selection, amplicon tiling, and generation of optimal amplicons. Custom methylation panels can be designed using pre-converted genomes or reference genome sequences for any other organism which can then be converted. The pipeline has the capability to create custom targeted panels specific to any methylation sites of interest. The pipeline designs Ion AmpliSeq primers to enable high multiplexing and robust amplification of low abundance or degraded DNA.

Following the creation of a custom panel, a complete 3-day workflow has been developed, comprising bisulfite conversion, library construction, template preparation, sequencing and data analysis. This 3-day protocol offers manual or automated library options, low input (10-20ng DNA) and a flexible multiplexed approach with quantitative information at single base pair resolution. Sequencing is performed on the Ion GeneStudio S5 system. The bioinformatics analysis has been streamlined into a downloadable plugin performing alignment and DNA methylation calling for amplicons on both the Watson and Crick strands.

To evaluate the in silico performance of the primer design pipeline for targeted bisulfite sequencing, a custom methylation panel was created using a set of 48 oncology markers from the BLUEPRINT consortium. These markers were also used for the Ion AmpliSeq Methylation Panel for Cancer Research, which was compared to the custom methylation panel to evaluate the performance of the pipeline. Key metrics from in silico design such as total number of degenerate oligos, mean amplicon length and average Tm spread for the custom methylation panel are equal to or better than Ion AmpliSeq Methylation Panel for Cancer Research.

To assess the sequencing performance of the panel, two control gDNA samples were used. The expected average methylation status across all CpGs were &gt;98% and &lt;5% for the first sample and the second sample, respectively. The evaluation was also carried out with an equal mixture of these two samples. The wet lab testing of the custom methylation panel generated comparable results to the Ion AmpliSeq Methylation Panel for Cancer Research.

The primer design pipeline and 3-day workflow provide custom design of targeted methylation panels along with quantitative analysis of relevant oncology markers from low DNA input.

Citation Format: Zunping Luo, Loni Pickle, Andrew Hatch, Aren Ewing, Fiona Hyland, David Berman, Palak Patel, Mark Andersen. Custom primer design pipeline and analysis workflow for targeted methylation sequencing using NGS Ion AmpliSeq technology [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 158.

Abstract 1164: Targeted next generation sequencing microbiome assay design

Background: Targeted Next Generation Sequencing may provide a lower cost approach for characterizing the Microbiome. Sequencing of 16S rRNA is one approach to characterize microbial diversity. However, 16S sequencing alone is often insufficient to gain species level information. Here we describe the design capabilities of targeted sequencing panels comprising both 16S and species-specific primers using Ion AmpliSeqTM technology. These types assay can be used to understand the composition and diversity of the microbiomes at the species level for human health and other applications.

Method:

Our assays include the capability to customize primers to multiple hypervariable regions of the 16S region. However, 16S alone can still be insufficient in distinguishing highly homologous organisms. To address this we can design species-specific primers that provide high strain coverage and high specificity performance. We have developed and tested example assays that include primers for a variety of species identification. With this approach, we can generate reads from sequencing to report taxonomic classifications and relative abundance for organisms in the sample with high specificity and sensitivity.

Results: We designed many a multiplexed Ion AmpliSeqTM assays including 16S targets and species-specific markers targeting important microbial species that can be adapted to new species of interest. This approach is proven as example of our fixed panels including Ion AmpliSeq Microbiome Health research Panel, Pan Bacterial and Anti-Microbial Resistance (AMR) community panels using the Ion Genestudio S5™ system. With the data generated from the species-specific primers, we identified all the targeted species in the ATCC samples at the Species level. We also created mixed population pools using DNA from clonal isolates of different bacterial strains. We are able to identify most microbes at Genus level with 100% sensitivity using 16S alone. We improved the detection resolution to the Species level through the application of our species-specific primers.

Conclusions: Using the Ion AmpliSeq™ technology, we can create highly sensitive and specific assays for robust characterization of microbiota customized to an individual labs needs. This highly multiplexed PCR approach enables an efficient and affordable means for conducting extensive analyses of the microbiomes having applications in the study of the etiology of phenotypic variability.

For research use only. Not for use in diagnostic procedures.

Citation Format: Aren Ewing. Targeted next generation sequencing microbiome assay design [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1164.

Abstract 5472: Development of customizable targeted RNA fusion panels using a novel automated high-multiplexing primer design strategy

Introduction

Gene fusions play an important role in oncogenesis and the progression of cancer. As important biomarkers, sensitive identification of gene fusions is critical to future oncology research. Next generation sequencing with Ion Ampliseq targeted enrichment enables simple, accurate and specific detection of relevant fusion isoforms. Here we introduce a novel automatic high-multiplexing primer design strategy that has the flexibility to develop customized Ampliseq fusion panels for any combination of fusion isoforms, scaling to panels that can detect thousands of isoforms in a single primer pool, which increases the sensitivity of fusion detection while decreasing the sample input required to as low as 10 ng.

Methods

The automated primer design pipeline takes a Gene-Transcript-Exon (GTE) file as input. Each record in the GTE file represents a unique RNA fusion isoform to establish an easy-parsing format for the pipeline. The pipeline locates the fusion breakpoint position, extracts gene sequences of every candidate fusion target and builds the fusion reference. Candidate amplicons are generated against the fusion reference. According to the design requirements of pool number and the conflicts among primer pairs, the pipeline performs pooling to minimize primer interactions. Finally, the pipeline generates an optimal set of amplicons strategically targeted for fusion junctions. The output files are used for downstream analysis with a fully automated analysis pipeline.

Results

The pipeline has been used extensively to develop high performing multiplex RNA fusion panels. The pipeline generates 175-base amplicons for use on formalin-fixed, paraffin-embedded (FFPE) samples or 120-base amplicons for use on cfRNA from blood samples. A single panel can include thousands of known fusion variants. This pipeline has been used to design the fusion assays contained in Oncomine Focus and Comprehensive assays, Oncomine Precision Assay, and others. Oncomine Comprehensive Assay v3 fusion panel was tested using the Ion GeneStudio S5 Sequencer; for example, testing on SeraCare fusion control confirms that all 14 fusion isoforms were detected with 100% accuracy. Testing on FFPE samples with known positive fusions confirms that the expected fusions including NTRK1, ERG, ETV1 and MET driver genes were also detected with 100% accuracy.

Conclusions

In summary, we have developed an automatic pipeline that can generate robust, comprehensive customized multiplex RNA fusion assays for targeted next-generation sequencing.

For research use only. Not for use in diagnostic procedures.

Citation Format: NA LI, Antonio Martinez-Alcantara, Aren Ewing, Rajesh Gottimukkala, Fiona Hyland, Seth Sadis. Development of customizable targeted RNA fusion panels using a novel automated high-multiplexing primer design strategy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5472.

Abstract 179: Comprehensive genomic profiling of solid tumors for key targeted and immuno-oncology biomarkers using Ion Torrent NGS technology on the Oncomine Comprehensive Assay Plus (OCA Plus)

Comprehensive genomic profiling (CGP) of tumor samples by next-generation sequencing is used to support clinical and translational research into the genetic variants that serve as biomarkers for diagnosis, prognosis and potential therapeutic response. However, as these assays grow in size to meet the expanding demands of users, it is challenging to maintain performance in the face of limited sample input necessitated by small sample volumes and to provide a simple and fast sample to report workflow with limited hands-on time. We, therefore, developed OCA Plus to meet user needs for a large CGP assay with excellent performance.

Gene content was prioritized based on potential clinical relevance and variant prevalence in solid tumors. Over 500 genes were selected including genes in the indication statements of approved drug labels, clinical guidelines, and in the enrollment criteria of clinical trials. In addition, driver genes were selected in key pathways including DNA repair and immune checkpoint response. Amplicon design strategies were optimized accordingly for key hotspots, full coding sequences or copy number variation (CNV). The assay used Ion AmpliSeq™ technology with manual library preparation or automated templating on the Ion Chef™ System and sequencing on the Ion GeneStudio™ S5 platform. Twenty ng of purified DNA was routinely used as input. An automated tumor-only workflow for variant calling and sample quality reporting was provided within Ion Reporter™ Software. Streamlined access to reporting of variant relevance was enabled by Oncomine™ Reporter.

In development studies of cancer cell line and formaldehyde-fixed, paraffin-embedded (FFPE) tumor samples, the assay displayed excellent uniformity (98% and 94%, respectively). Detection of single nucleotide variants and indels in cell lines and FFPE samples showed &gt;95% sensitivity and PPV. Detection of CNV gain and loss in cell lines and FFPE samples showed &gt;95% sensitivity and PPV. Assessment of tumor mutational burden (TMB) using publicly available whole-exome cancer sequencing data as well as test cell lines and FFPE samples showed high concordance with whole exome sequencing (R2 &gt; 0.90). MSI sensitivity and specificity was &gt;95% as tested using a diverse set of tumor samples. Targeted fusions were reported with 100% sensitivity and specificity when tested with commercially available controls. Total time from purified DNA to end of sequencing was &lt; 2 days with &lt; 3 hours of hands-on time and the time from post-sequencing to report generation was &lt; 2 hours.

Oncomine Comprehensive Assay (OCA Plus) was developed to support CGP and routine clinical research in oncology. The assay design and informatics workflow were optimized to support low input and rapid sample-to-report turn-around time, which will accelerate clinical and translational research.

Citation Format: Vinay Mittal, Jennifer Kilzer, Dinesh Cyanam, Janice Au-Young, Santhoshi Bandla, Gary Bee, Sameh El-Difrawy, Aren Ewing, Rajesh Gottimukkala, Mohit Gupta, Nickolay Khazanov, Anelia Kraltcheva, Amir Marcovitz, Scott Myrand, Rose Putler, Yu-Ting Tseng, Warren Tom, Cristina Van Loy, James Veitch, Paul Williams, Elaine Wong-Ho, Huimin Xie, Chenchen Yang, Zheng Zang, Seth Sadis. Comprehensive genomic profiling of solid tumors for key targeted and immuno-oncology biomarkers using Ion Torrent NGS technology on the Oncomine Comprehensive Assay Plus (OCA Plus) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 179.

Low plasma vitamin D is associated with adverse colorectal cancer survival after surgical resection, independent of systemic inflammatory response

OBJECTIVE

We assessed the effect of surgical resection of colorectal cancer (CRC) on perioperative plasma vitamin D (25OHD) and C-reactive protein (CRP) level. We investigated the relationship between circulating vitamin D level and CRC survival.

DESIGN

We sequentially sampled 92 patients undergoing CRC resection, and measured plasma 25OHD and CRP. For survival analyses, we assayed 25OHD and CRP in two temporally distinct CRC patient cohorts (n=2006, n=2100) and investigated the association between survival outcome, circulating vitamin D and systemic inflammatory response.

RESULTS

Serial sampling revealed a postoperative fall (mean 17.3 nmol/L; p=3.6e-9) in plasma 25OHD (nadir days 1-2). CRP peaked 3-5 days postoperatively (143.1 mg/L; p=1.4e-12), yet the postoperative fall in 25OHD was independent of CRP. In cohort analyses, 25OHD was lower in the 12 months following operation (mean=48.8 nmol/L) than preoperatively (54.8 nmol/L; p=1.2e-5) recovering after 24 months (52.2 nmol/L; p=0.002). Survival analysis in American Joint Committee on Cancer stages I-III demonstrated associations between 25OHD tertile and CRC mortality (HR=0.69; 95% CI 0.46 to 0.91) and all-cause mortality (HR=0.68; 95% CI 0.50 to 0.85), and was independent of CRP. We observed interaction effects between plasma 25OHD and rs11568820 genotype (functional VDR polymorphism) with a strong protective effect of higher 25OHD only in patients with GG genotype (HR=0.51; 95% CI 0.21 to 0.81). We developed an online tool for predicted survival (https://apps.igmm.ed.ac.uk/mortalityCalculator/) that incorporates 25OHD with clinically useful predictive performance (area under the curve 0.77).

CONCLUSIONS

CRC surgery induces a fall in circulating 25OHD. Plasma 25OHD level is a prognostic biomarker with low 25OHD associated with poorer survival, particularly in those with rs11568820 GG genotype. A randomised trial of vitamin D supplementation after CRC surgery has compelling rationale.

Autologous breast reconstruction using the immediately lipofilled extended latissimus dorsi flap

BACKGROUND

The latissimus dorsi flap is a popular choice for autologous breast reconstruction. To dramatically improve volume, we report our experience of using the immediately lipofilled extended latissimus dorsi (ELD) flap and show it as a valid option for autologous breast reconstruction.

METHODS

Patients undergoing the procedure between December 2013 and June 2016 were included. Demographic, clinical and operative factors were analysed, together with in-hospital morbidity and duration of postoperative hospital stay.

RESULTS

A total of 71 ELD flaps with immediate lipofilling were performed. Forty-five reconstructions were immediate and the remaining 26 delayed. Median (range) volume of autologous fat injected immediately was 171 ml (40-630 ml). Contralateral reductions were performed in 25 patients with the median reduction volume 185 g (89-683 g). Median duration of admission was 6.5 (3-18) days and patients were followed up for 12 months (1-37). Three total flap failures occurred and had to be excised (4%). One haematoma occurred requiring drainage (1%). Signs of infection requiring intravenous antibiotics occurred in five patients (7%). In 5 patients wound dehiscence occurred, and only two of these required resuturing (3%). In total, 7 patients developed a seroma requiring repeated drainage (10%). Three reconstructions experienced mild mastectomy flap necrosis with no needing reoperation (4%).

CONCLUSIONS

Our experience represents the largest series to date and shows that in carefully selected patients the technique is safe, can avoid the requirement for implants, and has the potential to streamline the reconstructive journey.

16S and 23S plastid rDNA phylogenies of Prototheca species and their auxanographic phenotypes

Because algae have become more accepted as sources of human nutrition, phylogenetic analysis can help resolve the taxonomy of taxa that have not been well studied. This can help establish algal evolutionary relationships. Here, we compare Auxenochlorella protothecoides and 23 strains of Prototheca based on their complete 16S and partial 23S plastid rDNA sequences along with nutrient utilization (auxanographic) profiles. These data demonstrate that some of the species groupings are not in agreement with the molecular phylogenetic analyses and that auxanographic profiles are poor predictors of phylogenetic relationships.

In vivo evaluation of safety of nanoporous silicon carriers following single and multiple dose intravenous administrations in mice

Porous silicon (pSi) is being extensively studied as an emerging material for use in biomedical applications, including drug delivery, based on the biodegradability and versatile chemical and biophysical properties. We have recently introduced multistage nanoporous silicon microparticles (S1MP) designed as a cargo for nanocarrier drug delivery to enable the loaded therapeutics and diagnostics to sequentially overcome the biological barriers in order to reach their target. In this first report on biocompatibility of intravenously administered pSi structures, we examined the tolerability of negatively (-32.5±3.1mV) and positively (8.7±2.5mV) charged S1MP in acute single dose (10(7), 10(8), 5×10(8) S1MP/animal) and subchronic multiple dose (10(8) S1MP/animal/week for 4 weeks) administration schedules. Our data demonstrate that S1MP did not change plasma levels of renal (BUN and creatinine) and hepatic (LDH) biomarkers as well as 23 plasma cytokines. LDH plasma levels of 145.2±23.6, 115.4±29.1 vs. 127.0±10.4; and 155.8±38.4, 135.5±52.3 vs. 178.4±74.6 were detected in mice treated with 10(8) negatively charged S1MP, 10(8) positively charged S1MP vs. saline control in single and multiple dose schedules, respectively. The S1MPs did not alter LDH levels in liver and spleen, nor lead to infiltration of leukocytes into the liver, spleen, kidney, lung, brain, heart, and thyroid. Collectively, these data provide evidence of a safe intravenous administration of S1MPs as a drug delivery carrier.

RG7128 alone or in combination with pegylated interferon-α2a and ribavirin prevents hepatitis C virus (HCV) Replication and selection of resistant variants in HCV-infected patients

INTRODUCTION

RG7128 (prodrug of PSI-6130) shows potent antiviral efficacy in patients infected with hepatitis C virus (HCV) genotypes 1, 2, or 3, with mean viral load decreases of 2.7 and 5 log(10) IU/mL, respectively, associated with 1500-mg doses twice daily after monotherapy for 2 weeks and with 1000-mg and 1500-mg doses twice daily after treatment in combination with the standard of care (SOC) for 4 weeks.

RESULTS

From 32 patients treated with RG7128 monotherapy for 2 weeks, marginal viral load rebound was observed in 3 HCV genotype 1-infected patients, whereas partial response was observed in 2 genotype 1-infected patients. From 85 patients receiving RG7128 in combination with SOC, 1 HCV genotype 1-infected patient experienced a viral rebound, and 2 genotype 3-infected patients experienced a transient rebound. Five genotype 1-infected patients had an HCV load of >1000 IU/mL at the end of 4-week treatment. No viral resistance was observed, per NS5B sequencing and phenotypic studies. PSI-6130 resistance substitution S282T needs to be present at levels of ≥90% within a patient's quasispecies to confer low-level resistance. No evidence of S282T was found by population or clonal sequence analyses.

CONCLUSIONS

The requirement for a predominant S282T mutant quasispecies, its low replication capacity, and the low-level resistance it confers probably contribute to the lack of RG7128 resistance observed in HCV-infected patients.

Measurements of catecholamine-mediated apoptosis of immunocompetent cells by capillary electrophoresis

Single cell analysis with capillary electrophoresis, a technique capable of detecting zeptomole quantities (10(-21) mole) of neurochemical species, has been used to demonstrate that lymphocytes are capable of active synthesis of dopamine and norepinephrine. Exposure of lymphocytes to catecholamines at concentrations as low as 10 nM leads to decreased proliferation and differentiation, e.g. interferon-gamma (IFN-gamma), interleukin-4 (IL-4) and immunoglobulin (Ig). In addition, both inhibition of dopamine uptake with nomifensine and inhibition of packing of catecholamines into vesicles with tetrabenazine, results in significantly lower levels of dopamine and norepinephrine (p < 0.01 and p < 0.05, respectively). The catecholamine-dependent inhibition of T- and B-lymphocyte activity is mediated via an induction of a Bcl-2/Bax and Fas/FasL involved apoptosis. These findings indicate a novel mechanism for regulation of lymphocyte activity in the central nervous system, whereby elevated regional levels of catecholamines might lead to the immunoprivilege of the brain.

Amphetamine redistributes dopamine from synaptic vesicles to the cytosol and promotes reverse transport

Whether amphetamine acts principally at the plasma membrane or at synaptic vesicles is controversial. We find that d-amphetamine injection into the Planorbis giant dopamine neuron causes robust dopamine release, demonstrating that specific amphetamine uptake is not required. Arguing for action at vesicles, whole-cell capillary electrophoresis of single Planorbis dopamine neurons shows that amphetamine reduces vesicular dopamine, while amphetamine reduces quantal dopamine release from PC12 cells by > 50% per vesicle. Intracellular injection of dopamine into the Planorbis dopamine neuron produces rapid nomifensine-sensitive release, showing that an increased substrate concentration gradient is sufficient to induce release. These experiments indicate that amphetamine acts at the vesicular level where it redistributes dopamine to the cytosol, promoting reverse transport, and dopamine release.

Discovery of endogenous catecholamines in lymphocytes and evidence for catecholamine regulation of lymphocyte function via an autocrine loop

Evidence has been obtained that catecholamines and their metabolites are present in single lymphocytes and extracts of T- and B-cell clones by use of capillary electrophoresis with electrochemical detection. Pharmacological inhibition of tyrosine hydroxylase reduces observed catecholamine levels, suggesting catecholamine synthesis by lymphocytes. Intracellular dopamine levels are shown to be increased by extra-cellular dopamine, suggesting a cellular-uptake mechanism. Furthermore, incubation with either dopamine or L-dihydroxyphenylalanine, a precursor of dopamine, results in a dose-dependent inhibition of lymphocyte proliferation and differentiation. Together, these results suggest the presence of an autocrine loop whereby lymphocytes down-regulate their own activity.

Hordenine: pharmacology, pharmacokinetics and behavioural effects in the horse

Hordenine is an alkaloid occurring naturally in grains, sprouting barley, and certain grasses. It is occasionally found in post race urine samples, and therefore we investigated its pharmacological actions in the horse. Hordenine (2.0 mg/kg bodyweight [bwt]) was administered by rapid intravenous (iv) injection to 10 horses. Typically, dosed horses showed a flehmen response and defecated within 60 secs. All horses showed substantial respiratory distress. Respiratory rates increased about 250 per cent and heart rates were approximately double that of resting values. All animals broke out in a sweat shortly after iv injection, but basal body temperature was not affected. These effects were transient, and the animals appeared normal within 30 mins of dosing. Treated horses were tested in a variable interval responding apparatus 30 mins after dosing and no residual stimulation or depressant effects of hordenine were apparent. Animals dosed orally with 2.0 mg/kg bwt of hordenine showed no changes in heart rate, respiratory rate, basal body temperature or behaviour. After iv injection of hordenine, (2.0 mg/kg bwt) plasma reached a maximum value of about 1.0 micrograms/ml, and declined thereafter in a biexponential fashion. Kinetics of plasma concentration satisfied the concept of a two compartment open system, with an alpha-phase half-life of about 3 mins, and a beta-phase half-life of about 35 mins. Total urinary concentrations of hordenine (free and conjugated) peaked at about 400 micrograms/ml, and then declined exponentially to background levels by 24 h after dosing.(ABSTRACT TRUNCATED AT 250 WORDS)

Infant mortality increase despite high access to tertiary care: an evolving relationship among infant mortality, health care, and socioeconomic change

In this study, the determinants of an apparent increase in the infant mortality rate of an urban population with high access to tertiary neonatal care are reviewed. For a 4-year period (1980 to 1983), all infant deaths (n = 422) of the 32,329 births to residents of the City of Boston were analyzed through linked vital statistics data and a review of medical records. A significant increase in the infant mortality rate occurred in 1982 due to increases in three components of the infant mortality rate: the birth rate of very low birth weight infants (less than 1,500 g), the neonatal mortality rate of normal birth weight infants (greater than or equal to 2,500 g), and the mortality rate of infants dying during the postneonatal period (28 to 365 days). These increases were associated with inadequate levels of prenatal care. Although transient, the impact of the observed alterations in these infant mortality rate components was enhanced by a more long-standing phenomenon: the stabilization of mortality rates for low birth weight infants. This stabilization allowed the increases in other component rates to be expressed more fully than in previous years. In this report a mechanism is shown whereby fully regionalized neonatal care ultimately may confer to the infant mortality rate a heightened sensitivity to socioeconomic conditions and levels of adequate prenatal care.

Interactions of asbestos-activated macrophages with an experimental fibrosarcoma

Supernatants from in vivo asbestos-activated macrophages failed to show any cytostatic activity against a syngeneic fibrosarcoma cell line in vitro. UICC chrysotile-induced peritoneal exudate cells also failed to demonstrate any growth inhibitory effect on the same cells in Winn assays of tumor growth. Mixing UICC crocidolite with inoculated tumor cells resulted in a dose-dependent inhibition of tumor growth; this could, however, be explained by a direct cytostatic effect on the tumor cells of high doses of crocidolite, which was observed in vitro.

Neuronal Mechanisms Underlying Control of Sound Production in a Cricket: Acheta Domesticus

1. The singing of the cricket Acheta domesticus has been studied with a view to examining the neuronal control mechanisms underlying the sound production.

2. Electrical activity was recorded from the muscles responsible for wing opening and closing during singing in intact, freely-moving crickets.

3. Three kinds of song which are both structurally distinct and clearly different in behavioural context were studied in detail: calling, aggression and courtship.

4. Each song is composed of a group of pulses of sound and each pulse corresponds to a single wing-closing movement. The songs differ only in regard to either the number of pulses in a group, or the loudness of the pulses.

5. The opening is caused by the tergosternal muscles receiving a brief burst of excitatory nerve impulses. Extra impulses, leading to extra wide opening, occur before loud sounds.

6. The closing movement is initiated by the first and second basalar and subalar muscles acting synergistically. The force, but not the velocity, of the closing stroke is increased by a late burst of activity in the indirectly acting dorsal longitudinal muscles, leading to louder sound.

7. Weak pulses are the result of (probably) only S axons firing. When F axons fire in addition loud sounds result.

8. During courtship songs the sound pulses are mainly weak and a large number of pulses occur consecutively.

9. The kind of neuronal machinery required to produce the observed output is considered theoretically, and a tentative simple scheme proposed.

10. It is not necessary to postulate separate neuronal centres for each sound, and a small number of neurons could, in principle, provide the underlying control of the different kinds of cricket song.