Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework

We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.

Abstract 6378: An in vitro human CD8 T cell exhaustion model for the functional screening of immune checkpoint inhibitors

T cell exhaustion is a state of dysfunction that frequently occurs during chronic infections and cancer due to persistent antigen stimulation and inflammation. It is defined by poor effector function, sustained expression of inhibitory receptors, and a transcriptional state distinct from that of functional effector or memory T cells. In this state, cells remain in the local environment but lack effector functions necessary to combat the tumor or infection. In the current study, we developed an in vitro human antigen-specific CD8 T cell exhaustion model to evaluate the ability of immune checkpoint inhibitors to restore functionality to exhausted T cells. Using the fully human, autologous MIMIC (Modular IMmune In vitro Construct) effector CD8 T cell assay as a framework, we assessed the effect of antigen dose, timing, and frequency of repeated antigen stimulation with antiviral HLA Class I-restricted peptides to drive the development of Ag-specific CD8 T cells toward an exhausted state. Epitope-specific CD8 T cell responses were monitored by HLA class I-restricted pentamers and establishment of an exhausted profile was evaluated by increased expression of inhibitory co-stimulatory receptors and decreased intracellular expression of antiviral effector cytokine via flow cytometry relative to functional Ag-specific CD8 T cells from the same donor. Repeated antigen exposure led to decreased production of IFN-γ and TNF-α and increased expression of inhibitory co-stimulation markers on antigen-specific CD8 T cells. After establishment of an exhausted phenotype, treatment with various immune checkpoint inhibitor molecules restored functionality to Ag-specific CD8 T cells upon an additional antigen re-stimulation. Moreover, here using this model we characterized distinct transcriptomic signatures of functional and exhausted MIMIC CD8 T cells. Development of an in vitro human viral antigen-specific CD8 T cell exhaustion model with characteristic features of dysfunctional CD8 T cells as observed in vivo and the ability to restore effector function by treatment with immune checkpoint inhibitors, provides a platform to assess the effectiveness of therapeutic mono-specific or bi-specific “checkpoint blockade” antibody candidates and, in general, the potential to evaluate a myriad of immunotherapeutic approaches for cancer treatment.

Citation Format: Roberto Carrio, Margot Cucchetti, Mikielia Devonish, Louis Poisson, Mihaela Babiceanu, Andrew Kettring, Yingchun Liu, Donald Jackson, Evan Gomes, Jeremy Baudhuin, Donald R. Drake, Valeria Fantin, Anthony Byers, Ingrid Sassoon. An in vitro human CD8 T cell exhaustion model for the functional screening of immune checkpoint inhibitors [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 6378.

353 Patients with N2 Non-Small Cell Primary Lung Cancer, Does Surgery Offer an Advantage?

Background

Non-small cell lung cancer (NSCLC) is one of two histological types of lung cancers. Evidence-based guidelines recommend radical resection in early-stage lung cancer, N2 disease is when there is moderately advanced lymph node spread of the cancer, recommendations for surgery at this stage are more contested.

Aim

This was a service evaluation of the management of patients with NSCLC N2 disease. We aimed to evaluate the management and outcomes of these patients to see whether surgery offers an advantage over other modalities.

Method

This was a retrospective cohort study reviewing patients treated at University Hospital Southampton (UHS) who were diagnosed with N2 NSCLC before the start of treatment from 2016–2018 and comparing survival of surgically managed patients with those treated in other ways.

Results

50 N2 patients were included, 32 had radical treatment and 11 of these underwent surgery. Kaplan-Meier survival analysis showed no significant statistical difference (Log rank = 2.342 p = 0.679) between surgery and other treatments, the survival plots showed a slightly better initial survival for chemoradiotherapy. Men were statistically more likely to have squamous cell carcinomas than women who had more adenocarcinomas. PS was shown to have significant effect on survival with higher PS having a worse survival.

Conclusions

We didn't find a statistically significant difference in the survival between patients managed surgically and other modalities. PS's effect on survival reiterates its importance when deciding on treatments to offer patients.

Abstract 5590: Inhibition of the autophagy protein Vps34 induces tumor cell secretion of proinflammatory chemokines

Autophagy is the cellular process by which cytoplasmic contents are degraded and recycled through a lysosomal pathway. In cancer, autophagy can contribute to both tumor promotion and tumor suppression, and emerging evidence supports a role in resistance to immunotherapy. We investigated whether inhibition of autophagy with a small molecule inhibitor of the class III phosphoinositide 3-kinase Vps34 could stimulate anti-tumor immune responses and potentiate the efficacy of immune checkpoint blockade (ICB). Treatment with the Vps34 inhibitor (Vps34i) inhibited autophagy and was weakly cytotoxic to B16F10, MC38, EMT6 and CT26 mouse syngeneic tumor cell lines. In certain cancers, autophagy has been linked to lysosomal degradation of MHC I proteins, thereby downregulating expression and contributing to immune evasion. Notably, we observed minimal upregulation of MHC I surface expression on a subset of mouse and human cell lines. We further explored whether autophagy inhibition would result in release of any soluble immune stimulatory factors from mouse tumor cell lines. Inhibition of Vps34 markedly increased the secretion of several proinflammatory chemokines, including CCL5 and CXCL10. Increased chemokine secretion was also observed in a panel of human cancer cell lines, including NCI-H2009 lung cancer and PC-3 prostate cancer, confirming that the response is observed in human cancer cell lines derived from different tissue origins. As the chemokines CCL5 and CXCL10 are critical to the development of robust anti-tumor immunity, we next tested whether Vps34i treatment could potentiate the anti-tumor efficacy of ICB. We explored the activity of Vps34i as a single agent and in combination with anti-PD-1 antibody in three different syngeneic tumor models, including EMT6, CT26 and MC38. No single agent activity was observed in these models, however, combination of anti-PD-1 and Vps34i significantly inhibited the growth of CT26 tumors compared to control. Anti-tumor efficacy of combination treatment was not significantly different compared to single agents, and no complete tumor regressions were observed. No significant increases in CCL5 and CXCL10 were observed in the serum of combination treated mice, potentially explaining the lack of robust efficacy. Our results suggest that inhibition of autophagy promotes the secretion of proinflammatory cytokines from mouse and human cancer cells in vitro. As the autophagy pathway exhibits cross talk with other major cell signaling pathways, the tumor contexture may be a critical determinant of the role of autophagy in anti-tumor immune responses. Future experiments will explore which tumor contexts are sensitive to combination of autophagy inhibition and ICB.

Citation Format: Marie Bernardo, Yu-an Zhang, Martin Graf, Jane Cheng, Fangxian Sun, Virna Cortez-Retamozo, Sukhvinder Sidhu, Eladio Marquez, Donald Jackson, Jack Pollard, Timothy R. Wagenaar, Donald Shaffer. Inhibition of the autophagy protein Vps34 induces tumor cell secretion of proinflammatory chemokines [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 5590.

Evaluation of pharmacodynamic and patient enrichment biomarkers for SAR444881, a first-in-class anti-ILT2 monoclonal antibody for cancer immunotherapy

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Background: Leukocyte Ig-like receptor B1 [LILRB1; ILT2] is an inhibitory receptor expressed on various immune cells. ILT2 binds to classical and nonclassical MHC class I molecules, with highest affinity to HLA-G. ILT2-mediated inhibition leads to impairment of immune cell proliferation, differentiation, phagocytosis, cytotoxicity and cytokine secretion. Antagonism of ILT2 signaling may serve as a novel target for anti-cancer immunotherapy. SAR444881 (BND-22) is a novel humanized IgG4 monoclonal antagonist antibody which selectively binds to ILT2 and blocks its interaction with MHC I molecules. SAR444881 induces robust macrophage and lymphocyte-driven anti-tumor activity in in vitro and in vivo models. To overcome the limitation that LILRB proteins are not expressed in rodents, we conducted a series of in vivo studies using humanized mouse models, cancer patient biopsies and ex vivo co-culture systems to interrogate the pharmacodynamic (PD) response of ILT2 antagonism as well as inform the combinatorial and patient enrichment strategies for SAR444881. Methods: SAR444881-induced modulation of PD biomarkers was evaluated in humanized xenograft models. Ex vivo co-culture system has been established using patient tumor tissues and isolated PBMC or other immune cells. Biomarker expression on immune cells and secreted soluble proteins were monitored by flow cytometry and ELISA, respectively. Procured tumor samples of patients with various advanced solid tumors, including Head and neck squamous cell carcinoma (HNSCC), Gastric Cancer (GC), Non-Small Cell Lung Cancer (NSCLC) and Colorectal Cancer (CRC) were utilized to evaluate protein or gene expression levels of potential predictive biomarkers (ILT2, HLA = G, PD-L1) using immunohistochemistry (IHC) and whole transcriptomic analysis (RNAseq). Results: 1) PD biomarkers: in murine models, SAR444881 modulates intra-tumoral sub-populations of CD8+ T cells, NK cells and Macrophage polarization; 2) Combination strategy: functional study in an ex vivo system showed that addition of an anti-PD-1 antibody induced an increased production of pro-inflammatory cytokines, including IFNγ and TNFα, compared to SAR444881 or anti-PD-1 alone. Concomitantly, combining SAR444881 with cetuximab resulted in increased phagocytosis compared to isotype control. 3) Predictive biomarkers: protein and gene profiling results suggest enriched expression of ILT2 in majority of biopsies from several tumor types including NSCLC, HNSCC and CRC. Conclusions: These data inform the PD response biomarkers, combination, and patient enrichment strategies for the clinical development of SAR444881 to maximize its benefits for cancer patients. An ongoing phase 1/2 trial of SAR444881 mono- and combination therapy in patients with advanced solid tumors is testing these concepts in the clinic (NCT04717375).

Glutaredoxins regulate maize inflorescence meristem development via redox control of TGA transcriptional activity

Glutaredoxins (GRXs) are small oxidoreductases that can modify target protein activities through control of the redox (reduction/oxidation) state by reducing or glutathionylating disulfide bridges. Although CC-type GRXs are plant specific and play important roles in many processes, the mechanisms by which they modulate the activity of target proteins in vivo are unknown. In this study, we show that a maize CC-type GRX, MALE STERILE CONVERTED ANTHER1 (MSCA1), acts redundantly with two paralogues, ZmGRX2 and ZmGRX5, to modify the redox state and the activity of its putative target, the TGA transcription factor FASCIATED EAR4 (FEA4) that acts as a negative regulator of inflorescence meristem development. We used CRISPR-Cas9 to create a GRX triple knockout, resulting in severe suppression of meristem, ear and tassel growth and reduced plant height. We further show that GRXs regulate the redox state, DNA accessibility and transcriptional activities of FEA4, which acts downstream of MSCA1 and its paralogues to control inflorescence development. Our findings reveal the function of GRXs in meristem development, and also provide direct evidence for GRX-mediated redox modification of target proteins in plants.

606 SAR444245 (THOR-707), an engineered non-alpha IL-2, enhances NK mediated antibody-dependent cellular cytotoxicity

Background

SAR444245 is a non-alpha IL-2 Synthorin TM molecule designed with a site-specific non-natural amino acid serving as a bioconjugation site for a single PEG. The non-natural amino acid is positioned to enable the PEG bioconjugation to obscure block binding to the IL-2 alpha receptor, while retaining near-native affinity with the intermediate affinity βγ IL-2 receptor. The non-alpha features of SAR444245 minimize activation of immune suppressive regulatory CD4+ T cells, while retaining activity on CD8+ T cells and NK cells expressing the IL-2 βγ receptors. NK cells exert anti-tumor activity through antibody dependent cellular cytotoxicity (ADCC) of IgG antibodies as well as antibody independent mechanisms.

Methods

Here, we utilized a panel of human primary PBMC based immunoassays and transcriptomic analysis to evaluate whether SAR444245 may improve ADCC function of IgG1 anti-tumor target antibodies.

Results

We characterized the ability of SAR444245 to enhance the cytolytic function of NK cells towards the prototypic NK target cell K562 as well as to modulate NK cell ADCC in combination with EGFR or CD20-targeting antibodies. In vitro assays demonstrated that SAR444245 can activate NK cells, promote NK cell proliferation and improve cytotoxicity of NK cells against K562 cells and across a panel of human EGFR and CD20 positive cell lines. In PBMC based ADCC assays with 1ug/ml of antibody, SAR444245 improved ADCC function maximally by 9-fold for an anti-EGFR antibody and at 5-fold for an anti-CD20 antibody. SAR444245 exhibited dose-dependent enhancement of NK cell ADCC function. Notably, this activity was observed in cell lines expressing varying levels of EGFR and CD20. SAR444245 treatment was associated with dose dependent increases in NK cell degranulation and IFN-γ production. Transcriptomic profiling revealed that SAR444245 had broad effects on NK cell biology leading to changes in inhibitory and activating receptors.

Conclusions

In summary, these results indicate that SAR444245 can enhance the cytolytic activity of NK cells and enhance the ADCC effect of tumor-directed antibodies by activating NK cells.

Abstract 2280: A comprehensive sample tracking and data processing workflow for next generation sequencing

The successful application of Next Generation Sequencing (NGS) to drug discovery requires systems to manage and document each step of the sequencing process from sample receipt through data generation and data processing. We combined BenchlingTM, a solution for tracking NGS lab processes, with FONDA (Framework Of Next generation sequencing Data Analysis) an internally developed data processing platform, to support multiple types of NGS data generation and processing. Benchling combines a digital notebook and a laboratory information management system (LIMS). The system documents and automates steps in the NGS process including: sample registration, nucleic acid extraction, library construction, flow cell construction, sequencer sample sheet generation and BCL2FASTQ conversion. This enables wet lab scientists to easily retrieve an appropriate protocol for each sample and sequencing library type. We connected our sequencers to Benchling in order to monitor each sequencing run and to keep track of the quality of NGS data. In addition, it generates “analysis ready sample sheet” (contains project and study information, location of FASTQ, sample species and library type) and uploads it into designated S3 buckets for data processing. Benchling dashboards provide overviews of NGS sample preparation, data generation and quality control. In summary, Benchling interconnects the original sample, the labels, the barcodes, the cDNA/DNA, the library, and all the QC results. We process NGS data using pipelines implemented in FONDA on a dockerized Amazon Web Services cloud platform. Analyses can be configured automatically from information exported by Benchling or launched manually. After data processing is completed, output files such as gene expression counts or variant calls are deposited into project-specific folders, ready for secondary analysis. In the current FONDA version (as of Nov 2020), we have developed pipelines for single cell multi-omics (CITE-seq and single-cell immune profiling) and bulk RNA-seq. The modular design of FONDA facilitates the development, the updating, and the extension of pipelines to new sequencing technologies. In summary, Benchling and FONDA enable high quality sample and NGS data flows from the lab for target identification, understanding mechanism of action, patient stratification and biomarker discovery. Availability and implementation: FONDA is implemented in Java and released under the Apache License 2.0. FONDA can be downloaded from GitHub at https://github.com/epam/fonda.

Citation Format: Chandra Sekhar Pedamallu, Joon Sang Lee, Shu Yan, Adalis Maisonet, Aleksandr Sidoruk, Tengui Chen, Yulia Kamyshova, Mariia Zueva, Mark Magid, Quan Wan, Jeffrey Thompson, Valerie Zebrouck, Immanuel Gadaczek, Mikhail Alperovich, Brian McNatt, Alexei Protopopov, Donald Jackson, Jack Pollard. A comprehensive sample tracking and data processing workflow for next generation sequencing [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 2280.

Frequentist rules for regulatory approval of subgroups in phase III trials: A fresh look at an old problem

Background

The number of Phase III trials that include a biomarker in design and analysis has increased due to interest in personalised medicine. For genetic mutations and other predictive biomarkers, the trial sample comprises two subgroups, one of which, say B+ is known or suspected to achieve a larger treatment effect than the other B−. Despite treatment effect heterogeneity, trials often draw patients from both subgroups, since the lower responding B− subgroup may also gain benefit from the intervention. In this case, regulators/commissioners must decide what constitutes sufficient evidence to approve the drug in the B− population.

Methods and Results

Assuming trial analysis can be completed using generalised linear models, we define and evaluate three frequentist decision rules for approval. For rule one, the significance of the average treatment effect in B− should exceed a pre-defined minimum value, say ZB−>L. For rule two, the data from the low-responding group B− should increase statistical significance. For rule three, the subgroup-treatment interaction should be non-significant, using type I error chosen to ensure that estimated difference between the two subgroup effects is acceptable. Rules are evaluated based on conditional power, given that there is an overall significant treatment effect. We show how different rules perform according to the distribution of patients across the two subgroups and when analyses include additional (stratification) covariates in the analysis, thereby conferring correlation between subgroup effects.

Conclusions

When additional conditions are required for approval of a new treatment in a lower response subgroup, easily applied rules based on minimum effect sizes and relaxed interaction tests are available. Choice of rule is influenced by the proportion of patients sampled from the two subgroups but less so by the correlation between subgroup effects.

Pre-existing influenza-specific nasal IgA or nasal viral infection does not affect live attenuated influenza vaccine immunogenicity in children

The United Kingdom has a national immunization programme which includes annual influenza vaccination in school-aged children, using live attenuated influenza vaccine (LAIV). LAIV is given annually, and it is unclear whether repeat administration can affect immunogenicity. Because LAIV is delivered intranasally, pre-existing local antibody might be important. In this study, we analysed banked samples from a study performed during the 2017/18 influenza season to investigate the role of pre-existing influenza-specific nasal immunoglobulin (Ig)A in children aged 6-14 years. Nasopharyngeal swabs were collected prior to LAIV immunization to measure pre-existing IgA levels and test for concurrent upper respiratory tract viral infections (URTI). Oral fluid samples were taken at baseline and 21-28 days after LAIV to measure IgG as a surrogate of immunogenicity. Antibody levels at baseline were compared with a pre-existing data set of LAIV shedding from the same individuals, measured by reverse transcription-polymerase chain reaction. There was detectable nasal IgA specific to all four strains in the vaccine at baseline. However, baseline nasal IgA did not correlate with the fold change in IgG response to the vaccine. Baseline nasal IgA also did not have an impact upon whether vaccine virus RNA was detectable after immunization. There was no difference in fold change of antibody between individuals with and without an URTI at the time of immunization. Overall, we observed no effect of pre-existing influenza-specific nasal antibody levels on immunogenicity, supporting annual immunization with LAIV in children.

Abstract 3021: Integrated pharmacokinetic (PK)/pharmacodynamic (PD) modeling leveraging PK, biomarker, and safety data to support dose and schedule selection for the BET inhibitor BMS-986158

Background: BMS-986158 is a potent, selective, and orally bioavailable small-molecule inhibitor of the bromodomain and extraterminal (BET) family of transcription modulators being evaluated in patients with various tumors in a phase 1 clinical study (NCT02419417). An integrated PK/PD analysis leveraging PK, biomarker, and safety data from the phase 1 study was performed to support dose and schedule (Sch) selection further clinical studies with BMS-986158.

Methods: Five doses (0.75-4.5 mg) and 3 dosing regimens (Sch A: 5 days on, 2 days off over 21 days; Sch B: 14 days on, 7 days off; Sch C: 7 days on, 14 days off) were evaluated. Reversible thrombocytopenia (TTP) was the primary safety signal observed, and peripheral gene expression modulation was a PD biomarker indicative of drug target engagement. BMS-986158 serum PK was characterized with a 2-compartment population PK (PPK) model. A semimechanistic PK/PD model describing the platelet-reducing effect with BMS-986158 was developed to characterize platelet profiles for individual patients and to simulate and project the incidence of TTP at different doses and dosing regimens. The association of BMS-986158 exposure with expression modulation of select peripheral BET target genes, including HEXM1 and CCR2, was also examined.

Results: BMS-986158 exhibited linear PK with rapid oral absorption (Tmax ≈ 2-4 h) and a terminal half-life of ≈ 60 h over the dose range of 0.75-4.5 mg. PPK modeling and simulation suggested that at the same dose level, Sch A led to comparable Cmax, with a higher Ctrough and Cavg at steady state compared with Sch B and C across the dosing interval. The semimechanistic PK/PD model predicted a higher incidence rate of TTP with Sch A than Sch C at the same dose level, and the predictions agreed with observed primary safety data from the phase 1 study. The model predicted grade 4 TTP incidence rates of 24% (95% CI, 21%-26%) and 43% (95% CI, 38%-45%) at 4.5 and 6 mg, respectively, with Sch A. This suggests that 4.5 mg would be the maximum tolerated dose, given that a 6 mg dose was predicted to exceed the target dose-limiting toxicity (DLT) rate of grade 4 TTP at 27%. The exploratory analysis of BMS-986158 exposure and expression of selected peripheral genes associated with the BET pathway suggested a direct association between BMS-986158 exposure and the magnitude of peripheral gene expression modulation.

Conclusions: An integrated PK/PD analysis of BMS-986158 incorporating incidence of reversible TTP and modulation of peripheral BET target genes identified a maximum dose of 4.5 mg at Sch A for further clinical development. With the assumption that sustained gene expression modulation is desirable for BMS-986158 efficacy, Sch A, which provides sustained drug exposure, is recommended to enable continuous BET target gene expression modulation.

Citation Format: Xi (Cindy) Chen, Lora Hamuro, Shodeinde Coker, John Hilton, Jennifer R. Diamond, Capucine Baldini, Mark Voskoboynik, Mihaela Cristea, William Edenfield, Kezi Unsal-Kacmaz, Donald Jackson, Abraham Apfel, Ke Xu, Li Zhu, Amit Roy, Akintunde Bello, Ronald Fleming, Paul Statkevich. Integrated pharmacokinetic (PK)/pharmacodynamic (PD) modeling leveraging PK, biomarker, and safety data to support dose and schedule selection for the BET inhibitor BMS-986158 [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 3021.

Are Gypsy Roma Traveller communities indigenous and would identification as such better address their public health needs?

INTRODUCTION

Across Europe, large numbers of Gypsy Roma Traveller communities experience significant health inequities such as higher morbidity, mortality and infant mortality. This health inequity is perpetuated by wider determinants such as a lower social status, lower educational attainment and substandard accommodation. This is not dissimilar to other indigenous peoples, even though many Gypsy Roma Traveller communities are not identified as indigenous.

METHODS

This article presents contemporary literature and research alongside the internationally agreed principles of indigenous peoples, examining similarities between Gypsy Roma Traveller communities and other indigenous peoples.

RESULTS

We argue that Gypsy Roma Traveller communities could be recognised as indigenous in terms of the internationally agreed principles of indigeneity and shared experiences of health inequity, colonisation and cultural genocide. Doing so would enable a more robust public health strategy and development of public health guidelines that take into account their cultural views and practices.

CONCLUSION

Recognising Gypsy Roma Traveller communities in this way is important, especially concerning public health, as formal recognition of indigeneity provides certain rights and protection that can be used to develop appropriate public health strategies. Included within this are more nuanced approaches to promoting health, which focus on strengths and assets rather than deficit constructs that can perpetuate problematising of these communities.

Lung nodules are reliably detectable on ultra-low-dose CT utilising model-based iterative reconstruction with radiation equivalent to plain radiography

AIM

To determine if ultra-low-dose (ULD) computed tomography (CT) utilising model-based iterative reconstruction (MBIR) with radiation equivalent to plain radiography allows the detection of lung nodules.

MATERIALS AND METHODS

Ninety-nine individuals undergoing surveillance of solid pulmonary nodules undertook a low-dose (LD) and ULD CT during the same sitting. Image pairs were read blinded, in random order, and independently by two experienced thoracic radiologists. With LD-CT as the reference standard, the number, size, and location of nodules was compared, and inter-rater agreement was established.

RESULTS

There was very good inter-rater agreement with regards nodules ≥4mm for both the LD- (k=0.931) and ULD-CT (k=0.869). One hundred and ninety-nine nodules were reported on the LD-CT by both radiologists and 196 reported on the ULD-CT, with no nodules reported only on the ULD-CT. This gives a sensitivity of 98.5% and specificity of 100% for ULD-CT with MBIR. The effective dose of radiation was significantly different between the two scans (p<0.0001), 1.67 mSv for the LD-CT and 0.13 mSv for the ULD-CT.

CONCLUSION

ULD-CT utilising MBIR and delivering radiation equivalent to plain radiography, allows detection of lung nodules with high sensitivity. The attendant 10-fold reduction in radiation may allow for dramatic reductions in cumulative radiation exposure.

A Cross-Sectional Investigation of Cognition and Ultrasound-Based Vascular Strain Indices

OBJECTIVE

We examine the relationship between variability in the plaque strain distribution estimated using ultrasound with multiple cognitive domains including executive, language, visuospatial reasoning, and memory function.

METHOD

Asymptomatic (n = 42) and symptomatic (n = 34) patients with significant (>60%) carotid artery stenosis were studied for plaque instability using ultrasound strain imaging and multiple cognitive domains including executive, language, visuospatial reasoning, and memory function. Correlation and ROC analyses were performed between ultrasound strain indices and cognitive function. Strain indices and cognition scores were also compared between symptomatic and asymptomatic patients to determine whether there are significant group differences.

RESULTS

Association of high-strain distributions with dysexecutive function was observed in both asymptomatic and symptomatic patients. For memory, visuospatial, and language functions, the correlations between strain and cognition were weaker for the asymptomatic compared to symptomatic group.

CONCLUSIONS

Both asymptomatic and symptomatic patients demonstrate a relationship between vessel strain indices and executive function indicating that silent strokes and micro-emboli could initially contribute to a decline in executive function, whereas strokes and transient ischemic attacks may cause the further decline in other cognitive functions.

Leadership and the functioning of maternal health services in two rural district hospitals in South Africa

Maternal mortality remains high in Eastern Cape Province, South Africa, despite over 90% of pregnant women utilizing maternal health services. A recent survey showed wide variation in performance among districts in the province. Heterogeneity was also found at the district level, where maternal health outcomes varied considerably among district hospitals. In ongoing research, leadership emerged as one of the key health systems factors affecting the performance of maternal health services at facility level. This article reports on a subsequent case study undertaken to examine leadership practices and the functioning of maternal health services in two resource-limited hospitals with disparate maternal health outcomes. An exploratory mixed-methods case study was undertaken with the two rural district hospitals as the units of analysis. The hospitals were purposively selected based on their maternal health outcomes: one reported good maternal health outcomes (pseudonym: Chisomo) and the other had poor outcomes (pseudonym: Tinyade). Comparative data were collected through a facility survey, non-participant observation of management and perinatal meetings, record reviews and interviews with hospital leadership, staff and patients to elicit information about leadership practices including supervision, communication and teamwork. Descriptive and thematic data analysis was undertaken. The two hospitals had similar infrastructure and equipment. Hospital managers at Chisomo used their innovation and entrepreneurial skills to improve quality of care, and leadership style was described as supportive, friendly, approachable but 'firm'. They also undertook frequent and supportive supervisory meetings. Each department at Chisomo developed its own action plan and used data to monitor their actions. Good performers were acknowledged in group meetings. Staff in this facility were motivated and patients were happy about the quality of services. The situation was different at Tinyade hospital. Participants described the leadership style of their senior managers as authoritarian. Managers were rarely available in the office and did not hold regular meetings, leading to poor communication across teams and poor coordination to address resource constraints. This demotivated the staff. The differences in leadership style, structures, processes and work culture affected teamwork, managerial supervision and support. The study demonstrates how leadership styles and practices influence maternal health care services in resource limited hospitals. Supportive leadership manifested itself in the form of focused efforts to build teamwork, enhance entrepreneurship and in management systems that are geared to improving maternal care.

The drivers of sea lice management policies and how best to integrate them into a risk management strategy: An ecosystem approach to sea lice management

The control of sea lice infestations on cultivated Atlantic salmon is a major issue in many regions of the world. The numerous drivers which shape the priorities and objectives of the control strategies vary for different regions/jurisdictions. These range from the animal welfare and economic priorities of the producers, to the mitigation of any potential impacts on wild stocks. Veterinary ethics, environmental impacts of therapeutants, and impacts for organic certification of the produce are, amongst others, additional sets of factors which should be considered. Current best practice in both EU and international environmental law advocates a holistic ecosystem approach to assessment of impacts and risks. The issues of biosecurity and ethics, including the impacts on the stocks of species used as cleaner fish, are areas for inclusion in such a holistic ecosystem assessment. The Drivers, Pressures, State, Impacts, Responses (DPSIR) process is examined as a decision-making framework and potential applications to sea lice management are outlined. It is argued that this is required to underpin any integrated sea lice management (ISLM) strategy to balance pressures and outcomes and ensure a holistic approach to managing the issue of sea lice infestations on farmed stock on a medium to long-term basis.

Prolonged and large outbreak of invasive group A Streptococcus disease within a nursing home: repeated intrafacility transmission of a single strain

OBJECTIVES

Multiple invasive group A Streptococcus (GAS) infections were reported to public health by a skilled nursing facility (facility A) in Illinois between May 2014 and August 2016. Cases continued despite interventions including antibiotic prophylaxis for all residents and staff. Two other geographically close facilities reported contemporaneous outbreaks of GAS. We investigated potential reasons for ongoing transmission.

METHODS

We obtained epidemiologic data from chart review of cases and review of facility and public health records from previous investigations into the outbreak. Infection control practices at facility A were observed and evaluated. Whole genome sequencing followed by phylogenetic analysis was performed on available isolates from the three facilities.

RESULTS

From 2014 to 2016, 19 invasive and 60 noninvasive GAS infections were identified at facility A occurring in three clusters. Infection control evaluations during clusters 2 and 3 identified hand hygiene compliance rates of 14% to 25%, appropriate personal protective equipment use in only 33% of observed instances, and deficient wound-care practices. GAS isolates from residents and staff of all three facilities were subtype emm89.0; on phylogenetic analysis, facility A isolates were monophyletic and distinct.

CONCLUSIONS

Inadequate infection control and improper wound-care practices likely led to this 28-month-long outbreak of severe infections in a skilled nursing facility. Whole genome sequencing and phylogenetic analysis suggested that intrafacility transmission of a single highly transmissible GAS strain was responsible for the outbreak in facility A. Integration of genomic epidemiology tools with traditional epidemiology and infection control assessments was helpful in investigation of a facility-wide outbreak.

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

Association of distinct baseline tissue biomarkers with response to nivolumab (NIVO) and ipilimumab (IPI) in melanoma: CheckMate 064

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Background: CheckMate 064 (open label, phase 2) randomized advanced melanoma pts to NIVO 3 mg/kg Q2W for 6 doses then IPI 3 mg/kg Q3W for 4 doses (n = 70; cohort A), or the reverse (IPI then NIVO; n = 70; cohort B). More cohort A than cohort B pts had complete or partial response (54% and 31%, respectively). We sought to determine whether common or distinct baseline biomarkers were associated with response for each cohort. Methods: Protein expression of biomarkers identifying a broad array of cell lineages and immunoregulatory factors was determined by IHC and evaluated by 2 pathologists, with concordance. Global transcript expression was determined by RNAseq from frozen tissue. An elastic net predictor was trained on cohort A (α = 0.1, λ = 0.05) using leave-one-out cross-validation. RECIST v1.1 was used to assess tumor response. Results: Patients with tumors showing a pro-inflammatory transcriptional signature at baseline had superior overall response in cohort A, but not cohort B. Consistent with this observation, a parsimonious classifier of 10 immune/IFNγ-related genes predicted BOR (AUC 0.87) and OS (CPH log-likelihood P= 0.0003) for patients in cohort A, but not cohort B. In contrast, low baseline expression of MHC class I protein by malignant cells ( < 50% positive) was associated with disease progression (MHCI < 50% vs ≥50%: 12/13 vs 16/28 progressed) and inferior OS for patients in cohort B (MHCI < 50%: 6.42 mo [2.20, 9.66]; MHCI ≥50%: mOS 18.02 mo [7.98, not reached]: P= 0.0021, log-rank test), but not cohort A. Conclusions: Different pre-treatment biological characteristics of melanoma are associated with clinical response to NIVO followed by a planned switch to IPI (cohort A) and clinical response to IPI followed by NIVO (cohort B). Improved outcome with initial NIVO is strongly associated with a pro-inflammatory signature enriched for IFNγ targets. Inferior outcome with initial IPI is associated with reduction/loss of MHC I antigen presentation machinery. These data imply that NIVO broadly activates innate and adaptive immunity, whereas IPI is reliant upon CD8/MHC class I mediated adaptive immunity to effect clinical response. Clinical trial information: NCT01783938.

Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses

Deletion or truncation of NS1, the principal IFN antagonist of influenza viruses, leads to increased IFN induction during influenza virus infection. We have studied activation of the IFN induction cascade by both wild-type and NS1-defective viruses at the single-cell level using a cell line expressing GFP under the control of the IFN-β promoter and by examining MxA expression. The IFN-β promoter was not activated in all infected cells even during NS1-defective virus infections. Loss of NS1 expression is therefore insufficient per se to induce IFN in an infected cell, and factors besides NS1 expression status must dictate whether the IFN response is activated. The IFN response was efficiently stimulated in these cells following infection with other viruses; the differential IFN response we observe with influenza viruses is therefore not cell specific but is likely due to differences in the nature of the infecting virus particles and their subsequent replication.

A study of wrist-worn activity measurement as a potential real-world biomarker for late-life depression

BACKGROUND

Late-life depression (LLD) is associated with a decline in physical activity. Typically this is assessed by self-report questionnaires and, more recently, with actigraphy. We sought to explore the utility of a bespoke activity monitor to characterize activity profiles in LLD more precisely.

METHOD

The activity monitor was worn for 7 days by 29 adults with LLD and 30 healthy controls. Subjects underwent neuropsychological assessment and quality of life (QoL) (36-item Short-Form Health Survey) and activities of daily living (ADL) scales (Instrumental Activities of Daily Living Scale) were administered.

RESULTS

Physical activity was significantly reduced in LLD compared with controls (t = 3.63, p < 0.001), primarily in the morning. LLD subjects showed slower fine motor movements (t = 3.49, p < 0.001). In LLD patients, activity reductions were related to reduced ADL (r = 0.61, p < 0.001), lower QoL (r = 0.65, p < 0.001), associative learning (r = 0.40, p = 0.036), and higher Montgomery-Åsberg Depression Rating Scale score (r = -0.37, p < 0.05).

CONCLUSIONS

Patients with LLD had a significant reduction in general physical activity compared with healthy controls. Assessment of specific activity parameters further revealed the correlates of impairments associated with LLD. Our study suggests that novel wearable technology has the potential to provide an objective way of monitoring real-world function.

Sudden cardiac death in adults with congenitally corrected transposition of the great arteries

Background

Congenitally corrected transposition of the great arteries (ccTGA) is a rare congenital heart disease. There have been only few reports of sudden cardiac death (SCD) in patients with ccTGA and reasonable ventricular function.

Methods

A retrospective review of the medical records of all patients attending our adult congenital heart centre, with known ccTGA.

Results

From a database of over 3500 adult patients with congenital heart disease, we identified 39 (∼1%) with ccTGA and ‘two-ventricle’ circulations. 65% were male. The mean age at diagnosis was 12.4±11.4 years and the mean age at last time of review was 34.3±11.3 years. 24 patients (56%) had a history of surgical intervention. 8 (19%) had had pacemaker implantation and 2 had had a defibrillator implanted for non-sustained ventricular tachycardia (NSVT). In 544 years of patient follow-up, there had been five cases of SCD in our population; 1 death per 109 patient-years. Two of these patients had had previously documented supraventricular or NSVT. However, they were all classified as New York Heart Association (NYHA) class I or II, and systemic (right) ventricular function had been recorded as normal, mildly or mildly–moderately impaired, at most recent follow-up.

Conclusions

Our experience suggests the need for improved risk stratification and/or surveillance for malignant arrhythmia in adults with ccTGA, even in those with reasonable functional class on ventricular function.

The Clinical and Bacteriological Assessment of a Twice Daily Formulation of Erythromycin Stearate: A General Practice Study

This report presents the clinical and bacteriological assessment of a twice daily formulation of erythromycin stearate. The activity of this twice daily formulation was compared with erythromycin stearate 250 mg 6 hourly, and the assessment carried out in a number of general practices, both urban and rural, distributed widely throughout the United Kingdom. The twice daily dosage regime of ‘Erythrocin 500’ was seen to be an effective therapy, to compare favourably with the smaller dose given 6 hourly and with minimal side-effects. Antibiotic sensitivity tests included penicillin and tetracycline as well as erythromycin, and the negligible incidence of resistance demonstrated for erythromycin contrasted with that of the two other commonly used antibiotics.

Systematic review and meta-analysis of the association between frailty and outcome in surgical patients

INTRODUCTION

Frailty is becoming increasingly prevalent in the elderly population although a lack of consensus regarding a clinical definition hampers comparison of clinical studies. More elderly patients are being assessed for surgical intervention but the effect of frailty on surgical related outcomes is still not clear.

METHODS

A systematic literature search for studies prospectively reporting frailty and postoperative outcomes in patients undergoing surgical intervention was performed with data collated from a total of 12 studies. Random effects meta-analysis modelling was undertaken to estimate the association between frailty and mortality rates (in-hospital and one-year), length of hospital stay and the need for step-down care for further rehabilitation/nursing home placement.

RESULTS

Frailty was associated with a higher in-hospital mortality rate (pooled odds ratio [OR]: 2.77, 95% confidence interval [CI]: 1.62-4.73), a higher one-year mortality rate (pooled OR: 1.99, 95% CI: 1.49-2.66), a longer hospital stay (pooled mean difference: 1.05 days, 95% CI: 0.02-2.07 days) and a higher discharge rate to further rehabilitation/step-down care (pooled OR: 5.71, 95% CI: 3.41-9.55).

CONCLUSIONS

The presence of frailty in patients undergoing surgical intervention is associated with poorer outcomes with regard to mortality and return to independence. Further in-depth studies are required to identify factors that can be optimised to reduce the burden of frailty in surgical patients.

Strain features and distributions in pneumococci from children with invasive disease before and after 13-valent conjugate vaccine implementation in the USA

The effect of second-generation pneumococcal conjugate vaccines on invasive pneumococcal disease (IPD) strain distributions have not yet been well described. We analysed IPD isolates recovered from children aged <5 years through Active Bacterial Core surveillance before (2008–2009; n = 828) and after (2011–2013; n = 600) 13-valent pneumococcal conjugate vaccine (PCV13) implementation. We employed conventional testing, PCR/electrospray ionization mass spectrometry and whole genome sequence (WGS) analysis to identify serotypes, resistance features, genotypes, and pilus types. PCV13, licensed in February 2010, effectively targeted all major 19A and 7F genotypes, and decreased antimicrobial resistance, primarily owing to removal of the 19A/ST320 complex. The strain complex contributing most to the remaining β-lactam resistance during 2011–2013 was 35B/ST558. Significant emergence of non-vaccine clonal complexes was not evident. Because of the removal of vaccine serotype strains, positivity for one or both pilus types (PI-1 and PI-2) decreased in the post-PCV13 years 2011–2013 relative to 2008–2009 (decreases of 32–55% for PI-1, and >95% for PI-2 and combined PI-1 + PI-2). β-Lactam susceptibility phenotypes correlated consistently with transpeptidase region sequence combinations of the three major penicillin-binding proteins (PBPs) determined through WGS analysis. Other major resistance features were predictable by DNA signatures from WGS analysis. Multilocus sequence data combined with PBP combinations identified progeny, serotype donors and recipient strains in serotype switch events. PCV13 decreased the frequency of all PCV13 serotype clones and concurrently decreased the frequency of strain subsets with resistance and/or adherence features conducive to successful carriage. Our results serve as a reference describing key features of current paediatric IPD strains in the USA after PCV13 implementation.