Choosing Wisely audit: CT KUB ordering in emergency department renal colic presentations

OBJECTIVE

Our aim was to safely reduce unnecessary CT KUBs (kidneys, ureters, bladder) in patients with renal colic.

METHODS

This was a before and after intervention observational study of 74 patients in April 2023 and 57 patients in October 2023.

RESULTS

Seventy-five per cent of patients with suspected renal colic underwent a CT KUB in the pre-audit period. Following education, an update in the ED Renal Colic Policy, electronic medical record ordering and short stay pathway, a re-audit was undertaken in October 2023 resulting in an absolute reduction of 15% of CT KUBs ordered.

CONCLUSIONS

Audit interventions can reduce unnecessary CT KUBs in renal colic.

A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data

Spatial proteomics can reveal the spatial organization of immune cells in the tumor immune microenvironment. Relating measures of spatial clustering, such as Ripley's K or Besag's L, to patient outcomes may offer important clinical insights. However, these measures require pre-specifying a radius in which to quantify clustering, yet no consensus exists on the optimal radius which may be context-specific. We propose a SPatial Omnibus Test (SPOT) which conducts this analysis across a range of candidate radii. At each radius, SPOT evaluates the association between the spatial summary and outcome, adjusting for confounders. SPOT then aggregates results across radii using the Cauchy combination test, yielding an omnibus p-value characterizing the overall degree of association. Using simulations, we verify that the type I error rate is controlled and show SPOT can be more powerful than alternatives. We also apply SPOT to an ovarian cancer study. An R package and tutorial is provided at https://github.com/sarahsamorodnitsky/SPOT.

Human mesenchymal stromal cell adhesion and expansion on fluoropolymer surfaces modified with oxygen and nitrogen-rich plasma polymers

Fluorinated ethylene propylene (FEP) vessels are of significant interest for therapeutic cell biomanufacturing applications due to their chemical inertness, hydrophobic surface, and high oxygen permeability. However, these properties also limit the adhesion and survival of anchorage-dependent cells. Here, we develop novel plasma polymer coatings to modify FEP surfaces, enhancing the adhesion and expansion of human mesenchymal stromal cells (hMSCs). Similar to commercially available tissue culture polystyrene vessels, oxygen-rich or nitrogen-rich surface chemistries can be achieved using this approach. While steam sterilization increased the roughness of the coatings and altered the surface chemistry, the overall wettability and oxygen or nitrogen-rich nature of the coatings were maintained. In the absence of proteins during initial cell attachment, cells adhered to surfaces even in the presence of chelators, whereas adhesion was abrogated with chelator in a protein-containing medium, suggesting that integrin-mediated adhesion predominates over physicochemical tethering in normal protein-containing cell seeding conditions. Albumin adsorption was more elevated on nitrogen-rich coatings compared to the oxygen-rich coatings, which was correlated with a higher extent of hMSC expansion after 3 days. Both the oxygen and nitrogen-rich coatings significantly improved hMSC adhesion and expansion compared to untreated FEP. FEP surfaces with nitrogen-rich coatings were practically equivalent to commercially available standard tissue culture-treated polystyrene surfaces in terms of hMSC yields. Plasma polymer coatings show significant promise in expanding the potential usage of FEP-based culture vessels for cell therapy applications.

An NKG2A biased immune response confers protection for infection, autoimmune disease, and cancer

Infection, autoimmunity, and cancer are the principal human health challenges of the 21st century and major contributors to human death and disease. Often regarded as distinct ends of the immunological spectrum, recent studies have hinted there may be more overlap between these diseases than appears. For example, pathogenic inflammation has been demonstrated as conserved between infection and autoimmune settings. T resident memory (TRM) cells have been highlighted as beneficial for infection and cancer. However, these findings are limited by patient number and disease scope; exact immunological factors shared across disease remain elusive. Here, we integrate large-scale deeply clinically and biologically phenotyped human cohorts of 526 patients with infection, 162 with lupus, and 11,180 with cancer. We identify an NKG2A+ immune bias as associative with protection against disease severity, mortality, and autoimmune and post-acute chronic disease. We reveal that NKG2A+ CD8+ T cells correlate with reduced inflammation, increased humoral immunity, and resemble TRM cells. Our results suggest that an NKG2A+ bias is a pan-disease immunological factor of protection and thus supports recent suggestions that there is immunological overlap between infection, autoimmunity, and cancer. Our findings underscore the promotion of an NKG2A+ biased response as a putative therapeutic strategy.

Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing

The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.

Abstract 2325: IRF1 displays opposing tumor cell-intrinsic and -extrinsic roles in anti-tumor immunity

Interferons (IFNs), including IFN-α/β and IFN-γ, are multifaceted cytokines critical for antitumor immunity but contribute to T cell exhaustion through immune checkpoints. Recently, tumor cell expression of IRF1 was shown to enhance antitumor immunity, but a comprehensive evaluation of how IRF1 regulates IFN responses in the tumor and host has not been performed. Here, we show that Irf1-/- mice display enhanced tumor growth of WT and Irf1-/- tumors, as they fail to recruit sufficient NK cells and cytotoxic T cell (CTL). However, Irf1-/- tumors in wild-type mice displayed rapid immunogenic control, expansion of intratumoral lymphoid cells with enhanced effector programs and diminished exhaustion programs when compared to WT tumors. Mechanistically, IRF1 positively regulates the expression of distinct subsets of anti-tumor immunity suppression genes including the CD274/PD-L1, TRAIL, and IDO-1 checkpoints but not the IFN-inducible chemokines CXCL9-11. Surprisingly, control of Irf1-/- tumors required host IFN-α/β signaling but not IFN-γ signaling, while PD-L1 overexpression only weakly restored tumor growth. Thus, IRF1 selectively regulates the effects of IFNs on tumor cells and the tumor microenvironment and may be targeted to boost anti-tumor immunity.

Citation Format: Prabhat Kumar Purbey, Manash K. Paul, Keisuke S. Iwamoto, Allison Daly, Joowon Seo, Ameya S. Champhekar, Katie Campbell, Dorthe Schaue, William H. McBride, Steven M. Dubinett, Antoni Ribas, Stephen T. Smale, Philip O. Scumpia. IRF1 displays opposing tumor cell-intrinsic and -extrinsic roles in anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2325.

medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata

MOTIVATION

Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software.

RESULTS

We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019).

AVAILABILITY AND IMPLEMENTATION

The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Abstract 765: Hybridized-capture sequencing methods bias analysis of antigen presentation genes

Introduction: Tumor-immune dynamics are often interrogated using hybridized capture-based sequencing approaches which require the use of baits that target the protein-coding regions of the genome. However, the genes encoding the antigen presentation machinery, including human leukocyte antigen (HLA) proteins, are very polymorphic, resulting in thousands of unique genotypes across patient cohorts. Here, using whole exome sequencing (WES) and hybridized capture-based RNA sequencing (RNAseq) from melanoma patients, we show that these genes are not uniformly assessed by common sequencing methods, and require careful analysis for accurate detection of copy number and somatic alterations.

Methods: WES and RNAseq data was analyzed from 760 melanoma tumor biopsies, with WES derived from patient-matched normal blood samples. Coverage metrics for 26 antigen presentation genes, including classical and non-classical HLA genes, were evaluated, and the difference in coverage was calculated for heterozygous alleles. Each individual was assessed for heterozygous single nucleotide polymorphisms (SNPs) within each allele, and with respect to the haplotype of the human reference genome.

Results: Focusing on the 26 genes assessed, HLA-A, HLA-B, HLA-C, and HLA-DRB1 were the most diverse across our patient cohort; there was an average of 134 unique pairs of HLA alleles in these genes. We compared the SNP profiles of allele combinations to the haplotype of the human reference genome, and observed four patterns: heterozygous alleles are similar to each other and the reference haplotype, heterozygous alleles are different from each other and different to the reference, alleles are very similar to each other and greatly differ from the reference, or one allele is more similar to the reference haplotype. The fourth pattern showed the greatest bias in sequencing, where the allele more similar to the human reference genome had a median 4-fold increase in coverage in normal WES data.

Conclusions: Capture-based sequencing shows selection bias, as exome probes have been designed based upon the reported human reference genome, but results in selection bias in hybridized capture sequencing approaches. Alleles that have higher polymorphic differences with respect to the reference are not equally captured, resulting in nonuniform sequencing of heterozygous alleles.

Citation Format: Egmidio Medina, Katie Campbell, Antoni Ribas. Hybridized-capture sequencing methods bias analysis of antigen presentation genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 765.

Abstract 1213: Uncovering HLA loss of heterozygosity and allelic imbalance in cancer for the improvement of personalized neoTCR immunotherapy with PACT-ESCAPE

Introduction: PACT Pharma is a clinical-stage adoptive cell therapy company that develops personalized neoTCR-T cells using a state-of-the-art approach to discover and validate predicted neoepitopes and their cognate T cell receptors (clinical trial NCT03970382). An important mechanism of resistance to adoptive cell therapy targeting tumor-specific neoantigens is the genetic loss of human leukocyte antigen (HLA) alleles or alterations in HLA expression in tumor cells. Therapies targeting neoantigens presented by HLA alleles that have either been deleted, mutated or are strongly downregulated are likely to lack efficacy due to the absence or reduction of epitope presentation. Surveying neoepitope presentation escape mechanisms is key for personalized immunotherapy.

Methods: PACT Pharma has developed PACT-ESCAPE, a method that integrates DNA and RNA sequencing data to quantify allelic imbalance at HLA loci, including the most extreme case of loss of heterozygosity (LOH). Allelic imbalance is first determined at the DNA level by determining the patient’s maternal and paternal haplotypes across chromosome 6p to infer their copy number states. Twenty-six HLA Class I and II loci from chromosome 6 are then genotyped at high resolution, enabling accurate assignment of copy number states to the patient’s alleles, including any alleles that have been deleted in the tumor. Unlike other currently available methods, PACT-ESCAPE also measures the relative RNA expression of HLA alleles to provide an orthogonal estimate of allelic imbalance across chromosome 6 and support loss of heterozygosity calls made at the DNA level. Presentation machinery genes are also surveyed for loss of function mutations. To benchmark PACT-ESCAPE, we compared loss of heterozygosity calls at HLA-A, HLA-B, and HLA-C between our method and a previously published DNA-based HLA LOH classifier for 17 samples for which we had matched tumor/normal whole exome sequencing.

Results: We found 100% concordance between PACT-ESCAPE and the benchmark, with four samples showing LOH at HLA-A, HLA-B, and HLA-C at the DNA level. Next, we evaluated RNA sequencing from tumor samples and confirmed that the relative expression of the lost allele compared to the kept allele was lower when LOH was called. High levels of allelic imbalance in gene expression, however, were not unique to samples with LOH, suggesting that differential expression of HLA alleles might also be an important contributor to immune escape in cancer.

Conclusions: Evaluation of allelic imbalance in DNA copy number and RNA expression in PACT-ESCAPE provides new insights into immune escape in cancer. Adoptive cell therapy targeting neoantigens will benefit by enabling the accurate selection of targets most likely to be presented by the tumor.

Citation Format: Chad C. Smith, Yan Ma, Katie Campbell, Zheng Pan, Eric Stawiski. Uncovering HLA loss of heterozygosity and allelic imbalance in cancer for the improvement of personalized neoTCR immunotherapy with PACT-ESCAPE [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1213.

Isolated IgG2 deficiency is an independent risk factor for exacerbations in bronchiectasis

BACKGROUND

Immunoglobulin G (IgG) subclass 2 deficiency is the most frequent IgG subclass deficiency identified in patients with bronchiectasis, but its clinical significance is not known.

AIM

To analyse if bronchiectasis patients with isolated IgG2 deficiency at risk of recurrent exacerbations and/or hospitalization? Do patients with IgG2 deficiency have worse disease progression?

DESIGN AND METHODS

This is a retrospective study (2015-20) exploring independent risk factors for recurrent exacerbations (3 or more per year) and/or hospitalization with bronchiectasis exacerbations using multivariable models using binary logistic regression. There was no patient with IgG deficiency, IgG 1, 3 or 4 deficiency, or IgA or IgM deficiency included. In this model, the authors included: serum IgG2 level; lung function; body mass index; MRC breathlessness scale; age; sex; number of bronchiectatic lobes; bacterial colonization; comorbidities; and the use of long-term immunosuppressant drugs or antibiotics for more than 28 days. Analysing 2-year longitudinal data, one-way ANOVA and Mann-Whitney U-test were used to compare bronchiectasis severity between patients with different IgG2 levels.

RESULTS

Serum IgG2 levels (<2.68 g/l, 2.68-3.53 g/l and 3.54-4.45 g/l); hospital admission in the preceding 2 years; bacterial colonization with potentially pathogenic organisms and asthma were independent predictors for three or more bronchiectasis exacerbations. Those with low IgG2 levels (<2.68 g/l and 2.68-3.53 g/l), had worsening progression of their bronchiectasis, using the Bronchiectasis Severity Index, over 1 year compared with those who were IgG2 replete (>4.45 g/l) (P = 0.003, 0.013).

CONCLUSION

Reduced IgG2 levels were an independent predictor for bronchiectasis exacerbations and have increased disease progression.

[D-CBP study: Evaluation of lung cancer management times]

INTRODUCTION

Lung cancer is the leading cause of cancer-related death. Delays may have an impact on patient survival. The objective of this study was to evaluate the diagnostic and therapeutic management times for patients admitted for lung cancer treatment in the Respiratory Department of CHU de Caen Normandie.

MATERIALS AND METHODS

This is a retrospective, single-center and observational study, conducted on all patients treated for lung cancer from June 2017 to January 2018 in our department of pneumology in the Caen Normandie CHU. The main median times were investigated were: Global Time (abnormal imaging-treatment), Diagnosis time (abnormal imaging-diagnosis) and Treatment Time (diagnosis-treatment).

RESULTS

One hundred and twenty-seven (127) patients were included. Median global time was 55.5 days [31,25; 393], median diagnosis time was 22 days [13; 49], and median treatment time was 24.5 days [12,25; 45].

DISCUSSION

Our treatment times are consistent with those previously published. Areas for improvement are being developed in accordance with the 2014-2019 cancer plan, in particularly the creation in our institution of a specific care pathway for patients with lung cancer.

Abstract CT032: CMP-001 demonstrates improved response in noninflamed anti-PD-1 refractory melanoma and response is associated with serum CXCL10

Background

In the treatment-naive setting, PD-1 blockade is associated with greater response in T cell-inflamed vs non-T cell-inflamed tumors. CMP-001 is a CpG-A oligonucleotide TLR9 agonist in a virus-like particle that is hypothesized to activate tumor-associated plasmacytoid dendritic cells (pDCs) to secrete type I interferons. Through this activity, CMP-001 may convert the tumor microenvironment to a Th1-like chemokine milieu (eg, increased CXCL10) and induce an antitumor CD8+ T-cell response. We have recently reported that intratumoral injection of CMP-001 + IV pembrolizumab (pembro) had an acceptable safety profile and can reverse PD-1 blockade resistance in patients (pts) with melanoma (Milhem et al, SITC 2019). Regression was observed in injected and uninjected lesions. Herein we report pharmacodynamic and translational data.

Methods

This 2-part, open-label, multicenter, phase 1b study (NCT02680184) enrolled pts with metastatic/unresectable melanoma and stable disease (SD) or progressive disease (PD) on/after anti−PD-1 therapy. In part 1 (3+3 dose-escalation and dose-expansion), pts received CMP-001 + pembro. In part 2, pts received CMP-001 monotherapy. Determination of safety and clinical activity were the study's main objectives. Prespecified pharmacodynamic and translational studies evaluated serum chemokines and evaluated tumor biopsies using RNA and/or whole exome sequencing and immunohistochemistry for PD-L1 (reported as H-score), CD8, and CD303 (pDC marker).

Results

As of September 30, 2020, 159 pts (part 1) and 40 pts (part 2) have been treated. A greater median fold increase of serum CXCL10 (a marker of innate immunity, n=40) was observed in responders (R) to CMP-001 + pembro (18.8x) vs nonresponders (NR) after treatment (9.9x in SD; 6.15x in PD; differences were not statistically significant). Preliminary analyses showed that interferon gene expression distinguished R vs NR. Tumor biopsy analyses (part 1, n=139; part 2, n=34) showed that pts with high PD-L1, high CD8+ T cells, or inflamed transcriptional signatures at baseline were less likely to respond to CMP-001 + pembro vs pts without inflammation markers at baseline. Baseline mean PD-L1 expression (H-score) was 8.1 in R (n=10) vs 21.8 in NR (n=49). Posttreatment biopsies generally showed increased PD-L1, CD8+ T cells, and inflamed transcriptional signatures in R vs NR. Neither tumor mutational burden nor baseline pDC density distinguished R vs NR.

Conclusions

In pts with anti-PD-1 refractory melanoma, intratumoral CMP-001 ± pembro appears to disproportionately induce antitumor responses in noninflamed tumors. Clinical response to CMP-001 ± pembro was associated with induction of markers of both innate and adaptive antitumor immunity.

Citation Format: Jason John Luke, Riyue Bao, John M. Kirkwood, Yousef Zakharia, Diwakar Davar, Elizabeth Buchbinder, Theresa Medina, Adil Daud, Antoni Ribas, Jiaxin Niu, Geoffrey Gibney, Kim Margolin, Anthony J. Olszanski, Inderjit Mehmi, Takami Sato, Montaser Shaheen, Aaron Morris, Dmitri Bobilev, Katie Campbell, George Weiner, James E. Wooldridge, Arthur M. Krieg, Mohammed Milhem. CMP-001 demonstrates improved response in noninflamed anti-PD-1 refractory melanoma and response is associated with serum CXCL10 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT032.

Basal-IQ technology in the real world: satisfaction and reduction of diabetes burden in individuals with type 1 diabetes

AIM

To describe person-reported outcomes of the Basal-IQ predictive low-glucose-suspend system (Tandem Diabetes Care, San Diego, CA, USA) in real-world use.

METHODS

Adults with type 1 diabetes/caregivers of minors with type 1 diabetes completed the Diabetes Impact and Device Satisfaction questionnaire (11 items scored on 10-point Likert scales) prior to Basal-IQ system initiation, and at 2, 4 and 6 months post-initiation. Analysis was stratified by previous insulin treatment method. Beta mixed models were used to measure change in device satisfaction (e.g. trust, ease of use) and diabetes impact (e.g. hypoglycaemia fear, poor sleep) scores between time points, adjusting for baseline covariates.

RESULTS

A total of 967 adults and caregivers [54% women, mean (sd) age 36 (17) years, 57% Tandem pump users, 27% non-Tandem pump users, 17% multiple daily injection users] completed surveys. Device satisfaction significantly increased from baseline to 2 months in all groups (P<0.001 multiple daily injection and non-Tandem pump users; P=0.048 Tandem pump users), and was sustained from 2 to 6 months in all groups. Diabetes impact decreased significantly from baseline to 2 months in all groups (P<0.001 for all), was sustained from 2 to 6 months in multiple daily injection and Tandem pump users, and increased slightly at 4 months/decreased at 6 months in non-Tandem users.

CONCLUSION

The Basal-IQ system increased device satisfaction and reduced diabetes impact in all users in the first 2 months of use, and satisfaction was sustained over 6 months, with small fluctuations.

Perspectives in immunotherapy: meeting report from the "Immunotherapy Bridge" (December 4th-5th, 2019, Naples, Italy)

Over the last few years, numerous clinical trials and real-world experience have provided a large amount of evidence demonstrating the potential for long-term survival with immunotherapy agents across various malignancies, beginning with melanoma and extending to other tumours. The clinical success of immune checkpoint blockade has encouraged increasing development of other immunotherapies. It has been estimated that there are over 3000 immuno-oncology trials ongoing, targeting hundreds of disease and immune pathways. Evolving topics on cancer immunotherapy, including the state of the art of immunotherapy across various malignancies, were the focus of discussions at the Immunotherapy Bridge meeting (4-5 December, 2019, Naples, Italy), and are summarised in this report.

Safeguards for Using Viral Vector Systems in Human Gene Therapy: A Resource for Biosafety Professionals Mitigating Risks in Health Care Settings

Introduction

Health care workers who work daily with human body fluids and hazardous drugs are among those at the highest risk of occupational exposure to these agents. The Occupational Safety and Health Administration's (OSHA) Bloodborne Pathogens Standard (29 CFR 1910.1030) prescribes safeguards to protect workers against health hazards related to bloodborne pathogens. Similarly, the United States Pharmacopeia General Chapter 800 (USP <800>), a standard first published in February 2016 and implementation required by December 2019, addresses the occupational exposure risks of health care workers at organizations working with hazardous drugs. With emerging technologies in the field of gene therapy, these occupational exposure risks to health care workers now extend beyond those associated with bloodborne pathogens and hazardous drugs and now include recombinant DNA. The fifth edition of the Biosafety in Microbiological and Biomedical Laboratories (BMBL) and the National Institutes of Health Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (NIH Guidelines) mostly govern work with biohazardous agents and recombinant DNA in a laboratory research setting. When gene therapy products are utilized in a hospital environment, health care workers have very few resources to identify and reduce the risks associated with product use during and after the administration of treatments.

Methods

At the Abigail Wexner Research Institute at Nationwide Children's Hospital, a comprehensive gap analysis was executed between the research and health care environment to develop a program for risk mitigation. The BMBL, NIH Guidelines, World Health Organization Biosafety Manual, OSHA Bloodborne Pathogens Standard, and USP <800> were used to develop a framework for the gap analysis process.

Results

The standards and guidelines for working with viral vector systems in a research laboratory environment were adapted to develop a program that will mitigate the risks to health care workers involved in the preparation, transportation, and administration of gene therapies as well as subsequent patient care activities. The gap analysis identified significant differences in technical language used in daily operations, work environment, training and education, disinfection practices, and policy development between research and health care settings. These differences informed decisions and helped the organization develop a collaborative framework for risk mitigation when a gene therapy product enters the health care setting.

Discussion

With continuing advances in the field of gene therapy, the oversight structure needs to evolve for the health care setting. To deliver the best outcomes to the patients of these therapies, researchers, Institutional Biosafety Committees, and health care workers need to collaborate on training programs to safeguard the public trust in the use of this technology both in clinical trials and as FDA-approved therapeutics.

Temporally Distinct Roles for the Zinc Finger Transcription Factor Sp8 in the Generation and Migration of Dorsal Lateral Ganglionic Eminence (dLGE)-Derived Neuronal Subtypes in the Mouse

Progenitors in the dorsal lateral ganglionic eminence (dLGE) are known to give rise to olfactory bulb (OB) interneurons and intercalated cells (ITCs) of the amygdala. The dLGE enriched transcription factor Sp8 is required for the normal generation of ITCs as well as OB interneurons, particularly the calretinin (CR)-expressing subtype. In this study, we used a genetic gain-of-function approach in mice to examine the roles Sp8 plays in controlling the development of dLGE-derived neuronal subtypes. Misexpression of Sp8 throughout the ventral telencephalic subventricular zone (SVZ) from early embryonic stages, led to an increased generation of ITCs which was dependent on Tshz1 gene dosage. Additionally, Sp8 misexpression impaired rostral migration of OB interneurons with clusters of CR interneurons seen in the SVZ along with decreased differentiation of calbindin OB interneurons. Sp8 misexpression throughout the ventral telencephalon also reduced ventral LGE neuronal subtypes including striatal projection neurons. Delaying Sp8 misexpression until E14-15 rescued the striatal and amygdala phenotypes but only partially rescued OB interneuron reductions, consistent with an early window of striatal and amygdala neurogenesis and ongoing OB interneuron generation at this late stage. Our results demonstrate critical roles for the timing and neuronal cell-type specificity of Sp8 expression in mouse LGE neurogenesis.

CTIM-19. MOLECULAR AND GENETIC DETERMINANTS OF RESPONSE TO PD-1 BLOCKADE IN RECURRENT GLIOBLASTOMA PATIENTS

Despite immune checkpoint inhibitors having success in several other tumor types, many glioblastoma (GBM) patients fail to respond or maintain a sustained response. Work published by our group (Cloughesy et al, 2019) demonstrated that relative to adjuvant programmed cell death-1 (PD-1) blockade, neoadjuvant treatment doubled the median overall survival (OS) for recurrent GBM patients and resulted in an enhanced interferon-γ signature. This suggests that anti-PD-1 given in the neoadjuvant setting may improve outcomes for recurrent GBM patients. The challenge remains in identifying the molecular and genetic signatures associated with response to immune checkpoint blockade. To address this, we analyzed the tumor sample and clinical response data from the patients treated in this clinical trial (n=31). We stratified patients as stable disease (SD) versus progressive disease (PD) based on their response assessment in neuro-oncology criteria (RANO) scores from cycle 2 of treatment post-surgery. Among the SD patients, 77.8% received neoadjuvant treatment while 22.2% received adjuvant therapy. In this group, a median OS was not reached. Among the PD patients, 40.9% received neoadjuvant treatment and 59.1% received adjuvant therapy, with a median OS of 257 days. Next, we analyzed factors that impact response to immunotherapy, which includes somatic mutational burden and interferon-γ pathway induction. We calculated somatic mutational variants, copy number variants (CNVs), and differential gene expression from the bulk tumor exome and RNA-sequencing data. The total mutation counts were similar between groups and no association was identified with increased mutational burden. In addition, total CNV stability was similar between groups. However, when looking at genes involved in the JAK/STAT signaling pathway, there were notably more copy number losses of JAK2 in the PD group when compared to the SD group (85.0% versus 66.7%). These findings merit further exploration as the JAK/STAT pathway has been implicated in response to immune checkpoint blockade.

Disseminated Saksenaea infection in an immunocompromised host associated with a good clinical outcome: a case report and review of the literature

Background

Saksenaea species (spp.) are uncommon causes of mucormycosis but are emerging pathogens mostly associated with trauma and soil contamination often in immunocompetent hosts. Due to lack of sporulation in the laboratory, diagnosis and susceptibility testing is difficult so optimal treatment regimens are unknown.

Case presentation

A 67 year-old man from the Northern Territory in Australia, with a history of eosinophilic granulomatosis with polyangiitis, developed disseminated Saksenaea infection after initially presenting with symptoms consistent with bacterial pyelonephritis. Despite a delay in diagnosis; with aggressive surgical management and dual therapy with amphotericin B and posaconazole, he survived.

Conclusions

We describe an unusual case of disseminated infection with a favourable outcome to date.

Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma

We analyze the transcriptome of baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). We find that T cell infiltration and interferon-γ (IFN-γ) signaling signatures correspond most highly with clinical response to therapy, with a reciprocal decrease in cell-cycle and WNT signaling pathways in responding biopsies. We model the interaction in 58 human cell lines, where IFN-γ in vitro exposure leads to a conserved transcriptome response unless cells have IFN-γ receptor alterations. This conserved IFN-γ transcriptome response in melanoma cells serves to amplify the antitumor immune response. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream IFN-γ signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

Evaluation of Mass Sensitive Micro-Array biosensors for their feasibility in multiplex detection of low molecular weight toxins using mycotoxins as model compounds

Mycotoxins produced by Fusarium species including trichothecenes, zearalenone and fumonisins, can co-contaminate food and feed throughout the supply chain, including cereal grains and animal feeds. There is an increasing demand to enhance global food security by improving the monitoring of mycotoxins throughout our food supply chain. For time and cost-efficient analysis, rapid tests capable of detecting multiple toxins from a single sample are ideal. Considering these current trends in mycotoxin testing, this project examined the feasibility of using both a portable and non-portable mass-based biosensor for multiplex mycotoxin detection. The biosensor was a mass sensitive microarray (MSMA) which consisted of 4 × 16 miniaturized mass sensitive transducer pixels based on solidly mounted resonator (SMR) technology. Functionalisation of individual pixels on the sensor surface using nano-spotting technology for the simultaneous and semi-quantitative detection of three regulated mycotoxins: T2-toxin (T2) zearalenone (ZEN), and fumonisin B1 (FumB1) was examined. With the integration of portable and non-portable microfluidic devices for antibody and standard sample injections, competitive inhibition assays were developed followed by singleplex and multiplex calibration curves. The characteristics and performance of the MSMA were evaluated including sensitivity which was determined as the concentration causing 50% inhibition. Sensitivity of singleplex assays using the portable microfluidic device (PMD) were 1.3 ng/ml, 2.0 ng/ml and 6.8 ng/ml for T2, FumB1 and ZEN, respectively. Sensitivity of the multiplex assay again using the PMD was 6.1 ng/ml, 3.6 ng/ml and 2.4 ng/ml for T2, FumB1 and ZEN, respectively. The PMD was an easy to use and highly sensitive screening tool which has been demonstrated for the multiplex detection of three regulated mycotoxins. Analysis was in real time and results were fully digital. Since detection of analytes was by mass it was both a label-free and cost-efficient method proposed method of analysis for mycotoxins.

Abstract 6590: Epigenetic suppression of transgenic T-cell receptor (TCR) expression in adoptive cell transfer (ACT) therapy

Background: ACT of TCR transgenic T cells recognizing shared tumor antigens is associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated most frequently using a murine stem cell virus (MSCV) gamma retroviral vector.

Patients and Methods: Between 2009 and 2016, 24 patients were treated at UCLA using transgenic TCR ACT directed against the tumor antigens MART-1 or NY-ESO-1 for the treatment of melanoma or sarcoma, respectively. We analyzed 16 of these patients' cell therapy products for in vivo persistence and expression of the transgenic TCR at baseline and over time. Transgenic TCR DNA, RNA, and surface protein expression were assessed over time via TCR sequencing, qRT-PCR, and MHC dextramer analysis via FACS, respectively. DNA methylation status of the MSCV 5'LTR promoter region was determined via targeted bisulfite sequencing. Custom biotinylated RNA probes that target the entire MSCV vector were utilized to assess whole vector methylation over time, as well as integration sites within the host genome.

Results: Despite overall strong persistence of the transgenic TCR at the DNA level in all patients over time, its expression was profoundly decreased over time at the RNA and protein levels. In a subset of these patients (N=6), the degree of TCR surface expression at day +70 was &lt;0.5%, and was significantly lower than the other patients (p&lt;0.0001). These patients displayed significant increases in DNA methylation over time within the MSCV 5'LTR promoter region, as determined via targeted bisulfite sequencing. These increases in MSCV promoter methylation were inversely correlated with the degree of transgenic TCR RNA and protein expression, and the patients with increases in the MSCV 5'LTR promoter region displayed significantly lower expression of the transgenic TCR at the protein and RNA levels (p&lt;0.001 and p&lt;0.01, respectively). Analysis of the entire MSCV vector revealed progressive increases in DNA methylation within the entire MSCV vector over time, which recapitulated the significantly higher degree of vector methylation in patients with the most profound decreases in transgenic TCR expression (p&lt;0.0001). These increases in vector methylation occurred independently of its integration site within the host genome.

Conclusions: Progressive acquisition of DNA methylation within the MSCV retroviral vector is associated with suppression of expression of the encoded transgenic TCR. These results have significant implications for the design of future transgenic cell therapies and their associated viral vectors.

Citation Format: Theodore S. Nowicki, Colin Farrell, Marco Morselli, Liudmilla Rubbi, Katie Campbell, Beata Berent-Maoz, Begonya Comin-Anduix, Matteo Pellegrini, Antoni Ribas. Epigenetic suppression of transgenic T-cell receptor (TCR) expression in adoptive cell transfer (ACT) therapy [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 6590.

Standardizing the classification of skin tears: validity and reliability testing of the International Skin Tear Advisory Panel Classification System in 44 countries

BACKGROUND

Skin tears are acute wounds that are frequently misdiagnosed and under-reported. A standardized and globally adopted skin tear classification system with supporting evidence for diagnostic validity and reliability is required to allow assessment and reporting in a consistent way.

OBJECTIVES

To measure the validity and reliability of the International Skin Tear Advisory Panel (ISTAP) Classification System internationally.

METHODS

A multicountry study was set up to validate the content of the ISTAP Classification System through expert consultation in a two-round Delphi procedure involving 17 experts from 11 countries. An online survey including 24 skin tear photographs was conducted in a convenience sample of 1601 healthcare professionals from 44 countries to measure diagnostic accuracy, agreement, inter-rater reliability and intrarater reliability of the instrument.

RESULTS

A definition for the concept of a 'skin flap' in the area of skin tears was developed and added to the initial ISTAP Classification System consisting of three skin tear types. The overall agreement with the reference standard was 0·79 [95% confidence interval (CI) 0·79-0·80] and sensitivity ranged from 0·74 (95% CI 0·73-0·75) to 0·88 (95% CI 0·87-0·88). The inter-rater reliability was 0·57 (95% CI 0·57-0·57). The Cohen's Kappa measuring intrarater reliability was 0·74 (95% CI 0·73-0·75).

CONCLUSIONS

The ISTAP Classification System is supported by evidence for validity and reliability. The ISTAP Classification System should be used for systematic assessment and reporting of skin tears in clinical practice and research globally. What's already known about this topic? Skin tears are common acute wounds that are misdiagnosed and under-reported too often. A skin tear classification system is needed to standardize documentation and description for clinical practice, audit and research. What does this study add? The International Skin Tear Advisory Panel Classification System was psychometrically tested in 1601 healthcare professionals from 44 countries. Diagnostic accuracy was high when differentiating between type 1, 2 and 3 skin tears using a set of validated photographs.

O85 Durable responses in anti-PD-1 refractory melanoma following intratumoral injection of a toll-like receptor 9 (TLR9) agonist, CMP-001, in combination with pembrolizumab

Background

Intratumoral (IT) injection of CMP-001, a CpG-A TLR9 agonist packaged within a virus-like particle, is designed to activate tumor-associated plasmacytoid dendritic cells, inducing an interferon-rich tumor microenvironment and anti-tumor CD8+ T cell responses.

Methods

CMP-001-001 is an ongoing Phase 1b trial evaluating the safety and efficacy of CMP-001 in combination with pembrolizumab (Part 1; N = 144) or alone (Part 2; N = 23) in patients with advanced melanoma resistant to prior anti-PD-1 therapy (Tables 1). CMP-001 is administered IT into accessible lesion(s) either with, or without on-site saline dilution (table 1), and response assessed by RECIST v1.1. Monotherapy patients who progress can be rolled over onto combination therapy and continue on study. Baseline and on-therapy serum is analyzed for cytokines, and immunohistochemistry and RNA-Seq are performed on available tumor biopsies.

Abstract O85 Table 1

Advanced anti-PD-1 Refractory melanoma patient population by treatment allocation

Results

Adverse events (AEs) attributed to CMP-001 in combination with pembrolizumab or as monotherapy consisted predominately of transient low-Grade flu-like symptoms and injection site reactions: Grade 3+ related AEs were reported in 33% of patients treated with combination therapy and 22% of patients with monotherapy.

The Objective Response Rate (ORR) with undiluted CMP-001 in combination with pembrolizumab was 24% (18/75; 95% confidence interval: 15%-35% (table 1); on-site dilution of CMP-001 was associated with a substantial decrease in ORR to 12% (7/61; 95% confidence interval: 5%-22% (table 1). Three additional patients had a delayed partial response after an initial period of disease progression. Anti-tumor response was comparable between injected and uninjected lesions. The median duration of response to combination therapy has not been reached. The ORR to CMP-001 monotherapy was 22% (5/23; 95% confidence interval: 7%-44% (table 1); time from last anti-PD-1 therapy before CMP-001 was 1.5 to >20 months in responders; 3 of the patients responding to CMP-001 monotherapy achieved PR at the first evaluation, but progressed by the second evaluation.

Serum and tumor biopsy translational studies in the patients receiving combination therapy supported the proposed mechanism of TLR9 activation and identified a possible association between induction of serum CXCL10 and response.

Conclusions

IT CMP-001 alone and in combination with pembrolizumab appears well tolerated, can reverse resistance to anti-PD-1 therapy, and can produce deep and durable clinical responses in patients with advanced melanoma.

Ethics Approval

CMP-001-001 was centrally approved by the WCG-WIRB, WIRB approval tracking number 20152597.

Viral Vector Systems for Gene Therapy: A Comprehensive Literature Review of Progress and Biosafety Challenges

INTRODUCTION

National Institutes of Health (NIH) defines gene therapy as an experimental technique that uses genes to treat or prevent disease. Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types of cancer, and certain viral infections), the technique remains risky and is still under study to make sure that it will be effective and safe.

METHODS

Applications of viral vectors and nonviral gene delivery systems have found an encouraging new beginning in gene therapy in recent years. Although several viral vectors and nonviral gene delivery systems have been developed in the past 3 decades, no one delivery system can be applied in gene therapy to all cell types in vitro and in vivo. Furthermore, the use of viral vector systems (both in vitro and in vivo) present unique occupational health and safety challenges. In this review article, we discuss the biosafety challenges and the current framework of risk assessment for working with the viral vector systems.

DISCUSSION

The recent advances in the field of gene therapy is exciting, but it is important for scientists, institutional biosafety committees, and biosafety officers to safeguard public trust in the use of this technology in clinical trials and make conscious efforts to engage the public through ongoing forums and discussions.

Modulation of the bacterial population in commercial cucumber fermentations by brining salt type

AIMS

Differences in the bacterial population of cucumber fermentations brined with no salt, 100 mmol l^-1 (1·1%) calcium chloride (CaCl₂ ) or 1·03 mol l^-1 (6%) sodium chloride (NaCl) were studied.

METHODS AND RESULTS

Changes in the microbiology and chemistry of commercial and laboratory scale cucumber fermentations occurring as a function of time were monitored using colony counts and metagenetic analysis, and a pH probe and high-performance liquid chromatography analysis respectively. Dissolved oxygen and carbon dioxide content were monitored in commercial fermentations. Fermentations brined with calcium chloride (CaCl₂ ) or no salt sustained faster microbial growth and reduction in pH than those brined with 1·03 mol l^-1 NaCl. Leuconostoc, Lactococcus and Weissella dominated in fermentations brined with no salt or 100 mmol l^-1 CaCl₂ on day 1 as compared to Weissella and enterobacteria in fermentations containing 1·03 mol l^-1 NaCl. Lactobacilli dominated all fermentations by the third day, regardless of salt type, and was followed, in relative abundance by Pediococcus, Leuconostoc, Lactococcus and Weissella. From 84 to 96% of the population was composed of Lactobacillus by day 7 of the fermentations, except in the no salt fermentations in which a mixed population of LAB remained. The population of LAB found in commercial cucumber fermentations brined with 100 mmol l^-1 CaCl₂ (n = 18) or 1·03 mol l^-1 NaCl (n = 9) mimicked that of laboratory fermentations. A declining population of aerobes was detected in commercial fermentations brined with CaCl₂ on day 1.

CONCLUSION

A reduced NaCl content in cucumber fermentation enhances microbial diversity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study fills a knowledge gap and aids in the design of improved reduced NaCl cucumber fermentations.

Abstract P5-15-06: Potential Medicare beneficiary out-of-pocket cost reductions through use of biosimilar filgrastim-sndz over reference filgrastim among breast cancer patients: A simulation model analysis

Rationale & Objective: Granulocyte colony-stimulating factors (G-CSFs) are utilized to decrease the incidence of febrile neutropenia (FN) in patients with cancers undergoing chemotherapy treatments. In 2015 biosimilar filgrastim-sndz was the first biosimilar to be approved and launched in the US market. Limited data exists in ascertaining the impact of biosimilars on patient out-of-pocket (OOP) expenditures. The objective of this simulation model was to estimate potential OOP cost savings through use of filgrastim-sndz over reference filgrastim from a Medicare breast cancer patient perspective.

Methods: An Excel simulation analysis was conducted among breast cancer patients treated with biosimilar filgrastim-sndz or the branded reference filgrastim (identified through HCPCS codes). Data from the 2016 Medicare Limited Data Set (5% sample of the carrier file) was used to populate the model. The payment calculation worksheet within the Medicare carrier file was used to calculate the average Medicare payment to the provider and the average beneficiary OOP responsibility per claim of either filgrastim-sndz or reference filgrastim. The average OOP reduction per claim for a filgrastim-sndz beneficiary relative to a reference filgrastim beneficiary was multiplied to a hypothetical FN prevalent population of 100,000 beneficiaries (average of 10 claims per beneficiary) to estimate the potential OOP savings.

Results: Data for 616 filgrastim-sndz and 1,064 reference filgrastim claims were used to populate the model. The average Medicare allowed charge amount per claim for a filgrastim-sndz beneficiary was $362.8 versus $406.9 for a reference filgrastim beneficiary, while corresponding average Medicare payments to the provider were $284.1 and $316.9, respectively. On an average, OOP responsibility for a filgrastim-sndz beneficiary was lower compared to a reference filgrastim beneficiary ($72.9 versus $82.5) leading to a cost saving per claim of $9.60. When extrapolated to 100,000 beneficiaries (1,000,000 claims), the overall cost saving was projected to be around $9.6 million.

Conclusions: Our simulation model estimated a potential OOP Medicare breast cancer beneficiary saving of around $9.6 million, based on a hypothetical population of 100,000 FN beneficiaries, with the use of biosimilar filgrastim-sndz over reference filgrastim. Further real-world analyses are required to evaluate the true cost saving potential from a breast cancer patient perspective with the use of biosimilars over reference biologics.

Citation Format: Puckrein G, Xu L, Ryan A, Campbell K, Balu S. Potential Medicare beneficiary out-of-pocket cost reductions through use of biosimilar filgrastim-sndz over reference filgrastim among breast cancer patients: A simulation model analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-15-06.

The end user sensor tree: An end-user friendly sensor database

Detailed knowledge regarding sensor based technologies for the detection of food contamination often remains concealed within scientific journals or divided between numerous commercial kits which prevents optimal connectivity between companies and end-users. To overcome this barrier The End user Sensor Tree (TEST) has been developed. TEST is a comprehensive, interactive platform including over 900 sensor based methods, retrieved from the scientific literature and commercial market, for aquatic-toxins, mycotoxins, pesticides and microorganism detection. Key analytical parameters are recorded in excel files while a novel classification system is used which provides, tailor-made, experts' feedback using an online decision tree and database introduced here. Additionally, a critical comparison of reviewed sensors is presented alongside a global perspective on research pioneers and commercially available products. The lack of commercial uptake of the academically popular electrochemical and nanomaterial based sensors, as well as multiplexing platforms became very apparent and reasons for this anomaly are discussed.

Utility of Probiotics for Maintenance or Improvement of Health Status in Older People - A Scoping Review

OBJECTIVE

To evaluate the available evidence on probiotic use in older adults from human studies.

DESIGN

systematic review.

METHODS

The databases Embase, CINAHL and Medline were searched in December of 2017 for studies in humans where probiotics were used to modify a health outcome in older people. The quality of studies was evaluated using the Critical Appraisal Skills Program (CASP) assessment tool and the Cochrane Risk of Bias Assessment tool.

PARTICIPANTS

Subjects aged over sixty years either through specified selection criteria or where the mean participant age was greater than sixty.

INTERVENTIONS

Probiotic supplements.

MEASUREMENTS

Pre-specified clinically measurable health outcomes in age related conditions.

RESULTS

1210 articles were identified. After quality assessment and selection criteria were applied, 33 articles were identified to be included for review. As these studies cover a variety of applications and used customised protocols accordingly, meta-analysis was not possible and synthesis is in narrative form.

CONCLUSIONS

A growing body of research has applied commercially available probiotic preparations across care settings for age related conditions including gut dysmotility, osteoporosis, common infectious diseases and cognitive impairment. Although methodologies vary, randomised controlled trials have reproduced results in these areas, and so warrant consideration of probiotics as a low risk adjuvant treatment for specific indications in the elderly.