Real-world use of long-acting cabotegravir and rilpivirine: 12-month results of the inJectable Antiretroviral therapy feasiBility Study (JABS)

OBJECTIVES

The inJectable Antiretroviral feasiBility Study (JABS) aimed to evaluate the implementation of long-acting regimens in a 'real world' Australian setting, with inclusion of participants with complex medical needs, social vulnerability and/or historical non-adherence.

METHODS

JABS was a 12-month, single-centre, single-arm, open-label phase IV study of long-acting cabotegravir 600 mg plus rilpivirine 900 mg administered intramuscularly every 2 months to adults with treated HIV-1 infection. The primary endpoint was the proportion of attendances and administration of injections within a 14-day dosing window over 12 months, out of the total prescribed doses. Secondary endpoints included proportions of missed appointments, use of oral bridging, discontinuations, virological failures, adverse events and participant-reported outcomes. A multidisciplinary adherence programme embedded in the clinical service known as REACH provided support to JABS participants.

RESULTS

Of 60 participants enrolled by May 2022, 60% had one or more complexity or vulnerability factors identified, including absence of social supports (50%), mental health issues, alcohol or drug use (30%) and financial hardship or instability (13%), among others. Twenty-seven per cent of participants had historical non-adherence to antiretroviral therapy. Out of 395 prescribed doses, 97.2% of injections were administered within correct dosing windows at clinic visits. Two courses of short-term oral bridging were required. The rate of injection site reactions was 29%, the majority being grade 1-2. There were no virological failures, no serious adverse events and only one injection-related study discontinuation. High baseline treatment satisfaction and acceptability of injections increased by month 12. Those with vulnerability factors had similar adherence to injections as those without such factors. Ninety-eight per cent of the participants who completed 12 months on the study have maintained long-acting therapy, virological suppression and retention in care.

CONCLUSIONS

Long-acting cabotegravir plus rilpivirine was associated with very high adherence, maintenance of virological suppression, safety and treatment satisfaction in a diverse Australian clinic population, comparable to results of phase III randomized clinical trials. Individuals with vulnerability factors can achieve adherence to injections with individualized support. Long-acting therapies in this group can increase the subsequent engagement in clinical care.

Automated Spatial Omics Landscape Analysis Approach Reveals Novel Tissue Architectures in Ulcerative Colitis

The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

Graph Fourier transform for spatial omics representation and analyses of complex organs

Spatial omics technologies are capable of deciphering detailed components of complex organs or tissue in cellular and subcellular resolution. A robust, interpretable, and unbiased representation method for spatial omics is necessary to illuminate novel investigations into biological functions, whereas a mathematical theory deficiency still exists. We present SpaGFT (Spatial Graph Fourier Transform), which provides a unique analytical feature representation of spatial omics data and elucidates molecular signatures linked to critical biological processes within tissues and cells. It outperformed existing tools in spatially variable gene prediction and gene expression imputation across human/mouse Visium data. Integrating SpaGFT representation into existing machine learning frameworks can enhance up to 40% accuracy of spatial domain identification, cell type annotation, cell-to-spot alignment, and subcellular hallmark inference. SpaGFT identified immunological regions for B cell maturation in human lymph node Visium data, characterized secondary follicle variations from in-house human tonsil CODEX data, and detected extremely rare subcellular organelles such as Cajal body and Set1/COMPASS. This new method lays the groundwork for a new theoretical model in explainable AI, advancing our understanding of tissue organization and function.

Longitudinal clinical phenotyping of post COVID condition in Mexican adults recovering from severe COVID-19: a prospective cohort study

Introduction

Few studies have evaluated the presence of Post COVID-19 conditions (PCC) in people from Latin America, a region that has been heavily afflicted by the COVID-19 pandemic. In this study, we describe the frequency, co-occurrence, predictors, and duration of 23 symptoms in a cohort of Mexican patients with PCC.

Methods

We prospectively enrolled and followed adult patients hospitalized for severe COVID-19 at a tertiary care centre in Mexico City. The incidence of PCC symptoms was determined using questionnaires. Unsupervised clustering of PCC symptom co-occurrence and Kaplan-Meier analyses of symptom persistence were performed. The effect of baseline clinical characteristics was evaluated using Cox regression models and reported with hazard ratios (HR).

Results

We found that amongst 192 patients with PCC, respiratory problems were the most prevalent and commonly co-occurred with functional activity impairment. 56% had ≥5 persistent symptoms. Symptom persistence probability at 360 days 0.78. Prior SARS-CoV-2 vaccination and infection during the Delta variant wave were associated with a shorter duration of PCC. Male sex was associated with a shorter duration of functional activity impairment and respiratory symptoms. Hypertension and diabetes were associated with a longer duration of functional impairment. Previous vaccination accelerated PCC recovery.

Discussion

In our cohort, PCC symptoms were frequent (particularly respiratory and neurocognitive ones) and persistent. Importantly, prior SARS-CoV-2 vaccination resulted in a shorter duration of PCC.

Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease

Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.

Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype

Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures postradiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from Aldh3a1 -/- mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels, depletes glutathione pool, and accumulates ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

Subcortical Brain Morphometry Differences between Adults with Autism Spectrum Disorder and Schizophrenia

Autism spectrum disorder (ASD) and schizophrenia (SZ) are neuropsychiatric disorders that overlap in symptoms associated with social-cognitive impairment. Subcortical structures play a significant role in cognitive and social-emotional behaviors and their abnormalities are associated with neuropsychiatric conditions. This exploratory study utilized ABIDE II/COBRE MRI and corresponding phenotypic datasets to compare subcortical volumes of adults with ASD (n = 29), SZ (n = 51) and age and gender matched neurotypicals (NT). We examined the association between subcortical volumes and select behavioral measures to determine whether core symptomatology of disorders could be explained by subcortical association patterns. We observed volume differences in ASD (viz., left pallidum, left thalamus, left accumbens, right amygdala) but not in SZ compared to their respective NT controls, reflecting morphometric changes specific to one of the disorder groups. However, left hippocampus and amygdala volumes were implicated in both disorders. A disorder-specific negative correlation (r = −0.39, p = 0.038) was found between left-amygdala and scores on the Social Responsiveness Scale (SRS) Social-Cognition in ASD, and a positive association (r = 0.29, p = 0.039) between full scale IQ (FIQ) and right caudate in SZ. Significant correlations between behavior measures and subcortical volumes were observed in NT groups (ASD-NT range; r = −0.53 to −0.52, p = 0.002 to 0.004, SZ-NT range; r = −0.41 to −0.32, p = 0.007 to 0.021) that were non-significant in the disorder groups. The overlap of subcortical volumes implicated in ASD and SZ may reflect common neurological mechanisms. Furthermore, the difference in correlation patterns between disorder and NT groups may suggest dysfunctional connectivity with cascading effects unique to each disorder and a potential role for IQ in mediating behavior and brain circuits.

MITI minimum information guidelines for highly multiplexed tissue images

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

229 A Systematic Review Protocol Examining the Role of Immobilisation in Hand Infections

Aim

Hand infections are common and varied, leading to long-term complications when managed poorly. Splinting of the hand in a position of safe immobilisation (POSI) is frequently used to avoid complications including pain and stiffness, however it is not a universally accepted technique because the effects of splinting in hand infections remain unestablished.

This systematic review will compare outcomes in adult hand infections between those treated using hand immobilisation and those not immobilised. The primary aim is to compare patient reported outcomes, for example pain, and the secondary aim is to compare functional active range of motion, complications, and resource use.

Method

A systematic review protocol has been developed. The search strategy was developed following background reading, expert opinion, and review by an academic librarian, and will be used to search MEDLINE, Embase, CINAHL, Web of Science and the Cochrane Central Register of Controlled Trials, to identify publications on management of hand infections including use of hand immobilisation. Title, and full-text screening will be carried out by two independent investigators to identify studies for inclusion. Editorials, letters, and literature reviews will be excluded.

Results

This systematic review has been successfully registered on the PROSPERO International prospective register of systematic reviews (CRD42021232880)

Conclusions

This systematic review will summarise the available evidence to establish the effect of hand immobilisation in hand infections, including whether hand immobilisation leads to improved outcomes in hand infections, which could guide health care professionals in their practice and influence future clinical guidelines.

180 T cell phenotype drives restructuring of tumor microenvironment to balance T cell longevity and tumor control: insights from multiplexed imaging and multi-scale agent based modeling

Background

Immune cell therapies continue to have success in treatment of cancers yet face challenges of complexity, cost, toxicity, and low solid-tumor efficacy. Much work has focused on the phenotype characterization and control of ex vivo expanded cells; however, little is known about its relationship to changes in the tumor microenvironment in vivo. Thus, we imaged tumors treated with different phenotype tumor-specific CD8+ T cells with CODEX multiplexed imaging1–4 that is able to visualize 42 antibodies at the same tissue in the tissue (figure 1A). To further probe this data in a systems immunology approach we created a multiscale agent-based model including critical circuits from the T cell-tumor microenvironment interactions (figure 1B).

Methods

We initialized our agent-based models various percentages of either PD1+, PD1-, PDL1+, or PDL1- phenotypes and ran simulations for 72 hours. We also treated PMEL CD8+ T cells with or without 2 hydroxycitrate as a metabolic inhibitor during activation to achieve different input phenotypes of CD8+ T cells for therapeutic adoptive transfer on day 10 following B16-F10 tumors had been established. We performed neighborhood analysis on CODEX multiplexed imaging data by clustering neighboring cell types using a sliding window for neighborhood analysis.

Results

Interestingly, the agent-based modeling indicated that the tumor phenotype switch to decrease proliferation was more effective than direct T cell killing. We observed spatially restricted inflammatory immune fronts when simulating with different initial percentages of PD1+ T cells and also from our CODEX multiplexed imaging. Quantitatively we observe that there is a drastic increase in the PDL1+, MHCI+, Ki67- tumor phenotype that increases with metabolically inhibited T cells. Neighborhood analysis indicated that metabolically treated T cells were able to create distinct immune cell environments that supported productive T cell-tumor interactions and also helped maintain T cell phenotype.

Conclusions

This indicates there is a balance for therapeutic T cell to mitigate chronic tumor exposure while controlling tumor growth through killing and by changing tumor phenotype. We observe T cells create distinct tumor microenvironments that differs significantly based on the starting T cell phenotype. Controlling T cell phenotype to promote productive immune-tumor structures will be critical to maintain T cell functionality and efficacy. In the future we will investigate T cell recruitment of immune structures by similar systems biology technologies.

Acknowledgements

J.W.H. is funded by an ACS Postdoctoral Fellowship (PF-20-032-01-CSM).

References

Goltsev Y, Samusik N, Kennedy-Darling J, Bhate S, Hale M, Vazquez G, Black S and Nolan GP, Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell, 174(4):968–981.

Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR and Samusik N. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182(5):1341–1359.

Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM. and Nolan GP. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nature Protocols 1–36.

Kennedy-Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM and Nolan GP. Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. European Journal of Immunology 51(5):1262–1277.

Ethics Approval

All studies involving mice were approved under Stanford’s APLAC protocol 33502.

1350 Wide-Awake Local Anaesthetic No Tourniquet (WALANT) Vs General/Regional Anaesthetic for Flexor Tendon Injuries: A Single-Centre, Retrospective Cohort Study

Aim

Flexor tendon repairs are commonly performed under general/regional anaesthesia. Wide-awake local anaesthetic no tourniquet (WALANT) has potential advantages including the ability to test the repair intra-operatively; removal of the risks of general anaesthesia; no aerosol generation, thus reducing COVID-19 transmission risk. An ongoing systematic review identified no comparative studies. This study aimed to compare the functional outcomes and complications of flexor tendon repairs under WALANT and general/regional anaesthetic.

Method

A single-centre, retrospective cohort study was undertaken (July 2019-August 2020). Consecutive adult patients undergoing flexor tendon repair were included. Exclusion criteria were ≥ 3 injured fingers; concurrent hand fracture; revascularisation; replantation. Data were collected on demographics, injuries, operative technique, and outcomes.

Results

Overall, 139 patients with 165 injured digits were included. Most (60%) were repaired under general anaesthesia. Local anaesthetic (was used for 46 patients (21 with tourniquet, 25 WALANT). Only 30% (42/139) patients had range of motion data at 6-weeks, dropping to 19% (26/139) at 12-weeks. WALANT patients had fewer ruptures (8% vs 14%), fewer adhesions requiring tenolysis (0% vs 4%) and less complications overall than the general/regional anaesthesia group. The results were not found to be statistically significant.

Conclusions

The lack of data due to patients not attending follow-up, makes meaningful research on flexor tendon injuries very challenging. This study suggests WALANT may reduce complications but is limited by the inherent bias of a retrospective, non-randomised study, and small numbers. Adequately designed and powered studies are recommended in future to further investigate the potential benefits of wide-awake surgery.

968 Delivering Human Factors and Non-Technical Skills Training Using Interactive Online Platforms in the COVID Era

Aim

To evaluate the impact and effectiveness of an interactive online human factors (HF) and non-technical skills (NTS) course delivered to Core Surgical Trainees during the COVID-19 pandemic

Method

A 1-day HF and NTS course was conducted online, using the Zoom platform, to Core Surgical Trainees in the North West. The course consisted of interactive lectures, small group teaching sessions, and self-directed learning with written reflections. Pre- and post-course surveys were administered, evaluating the participants’ awareness, knowledge and skills using a 5-part Likert scale, along with a multiple-choice assessment of knowledge. Statistical analysis was undertaken with significance considered at p < 0.05

Results

The course was attended by 63 CT1/2 participants, representing all surgical specialties. In the post-course evaluation, participants’ self-rating of awareness and knowledge for both HF and patient safety increased by between 10-20%. There was a significant increase in the mean post-course test score from 7.54 (SD ± 1.7) to 8.65 (SD ± 1.2) out of 10 (p < 0.0001). The course overall was rated relevant and useful (weighted averages 4.4 and 4.5 respectively)

Conclusions

To our knowledge, this is the first time a video conferencing platform has been used to deliver a live HF/NTS course. This study provides evidence supporting the use of such interactive online platforms in postgraduate surgical education. Training and professional development must continue, despite the evolving pressures from COVID-19. Embracing new methods of education delivery is required, with ongoing reporting and evaluation of education practice, sharing lessons learned and informing the evidence base in postgraduate surgical training during this time

Frontiers in cancer immunotherapy-a symposium report

Cancer immunotherapy has dramatically changed the approach to cancer treatment. The aim of targeting the immune system to recognize and destroy cancer cells has afforded many patients the prospect of achieving deep, long-term remission and potential cures. However, many challenges remain for achieving the goal of effective immunotherapy for all cancer patients. Checkpoint inhibitors have been able to achieve long-term responses in a minority of patients, yet improving response rates with combination therapies increases the possibility of toxicity. Chimeric antigen receptor T cells have demonstrated high response rates in hematological cancers, although most patients experience relapse. In addition, some cancers are notoriously immunologically "cold" and typically are not effective targets for immunotherapy. Overcoming these obstacles will require new strategies to improve upon the efficacy of current agents, identify biomarkers to select appropriate therapies, and discover new modalities to expand the accessibility of immunotherapy to additional tumor types and patient populations.

Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity

The transcription factor JUN is highly expressed in pulmonary fibrosis. Its induction in mice drives lung fibrosis, which is abrogated by administration of anti-CD47. Here, we use high-dimensional mass cytometry to profile protein expression and secretome of cells from patients with pulmonary fibrosis. We show that JUN is activated in fibrotic fibroblasts that expressed increased CD47 and PD-L1. Using ATAC-seq and ChIP-seq, we found that activation of JUN rendered promoters and enhancers of CD47 and PD-L1 accessible. We further detect increased IL-6 that amplified JUN-mediated CD47 enhancer activity and protein expression. Using an in vivo mouse model of fibrosis, we found two distinct mechanisms by which blocking IL-6, CD47 and PD-L1 reversed fibrosis, by increasing phagocytosis of profibrotic fibroblasts and by eliminating suppressive effects on adaptive immunity. Our results identify specific immune mechanisms that promote fibrosis and suggest a therapeutic approach that could be used alongside conventional anti-fibrotics for pulmonary fibrosis.

Fibroblast contributions to lung fibrosis and in particular their crosstalk with immune cells in the lung are incompletely understood. Here, the authors show an overall immune suppressive environment transcriptionally controlled and maintained by fibroblasts in lung fibrosis with possible therapeutic implications.

Immunologic timeline of Ebola virus disease and recovery in humans

A complete understanding of human immune responses to Ebola virus infection is limited by the availability of specimens and the requirement for biosafety level 4 (BSL-4) containment. In an effort to bridge this gap, we evaluated cryopreserved PBMCs from 4 patients who survived Ebola virus disease (EVD) using an established mass cytometry antibody panel to characterize various cell populations during both the acute and convalescent phases. Acute loss of nonclassical monocytes and myeloid DCs, especially CD1c+ DCs, was noted. Classical monocyte proliferation and CD38 upregulation on plasmacytoid DCs coincided with declining viral load. Unsupervised analysis of cell abundance demonstrated acute declines in monocytic, NK, and T cell populations, but some populations, many of myeloid origin, increased in abundance during the acute phase, suggesting emergency hematopoiesis. Despite cell losses during the acute phase, upregulation of Ki-67 correlated with recovery of cell populations over time. These data provide insights into the human immune response during EVD.

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

Understanding tissue structure and function requires tools that quantify the expression of multiple proteins while preserving spatial information. Here, we describe MIBI-TOF (multiplexed ion beam imaging by time of flight), an instrument that uses bright ion sources and orthogonal time-of-flight mass spectrometry to image metal-tagged antibodies at subcellular resolution in clinical tissue sections. We demonstrate quantitative, full periodic table coverage across a five-log dynamic range, imaging 36 labeled antibodies simultaneously with histochemical stains and endogenous elements. We image fields of view up to 800 μm × 800 μm at resolutions down to 260 nm with sensitivities approaching single-molecule detection. We leverage these properties to interrogate intrapatient heterogeneity in tumor organization in triple-negative breast cancer, revealing regional variability in tumor cell phenotypes in contrast to a structured immune response. Given its versatility and sample back-compatibility, MIBI-TOF is positioned to leverage existing annotated, archival tissue cohorts to explore emerging questions in cancer, immunology, and neurobiology.

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions.

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

Motivation

Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.

Results

We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.

Availability and implementation

Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Abstract 2275: Individualized drug combination based on single-cell drug perturbations

Currently, cancer drug combinations primarily focus on mutational heterogeneity of the primary tumor and do not account for single-cell variations that can give rise to drug resistance. Moreover, even with the increasing number of potential FDA-approved targeted drugs including immunotherapies, methods are needed to identify better combination therapy that leverages intratumor heterogeneity, thereby potentially mitigating the need for trials with large numbers of patients. Despite advances in single-cell technologies that capture intratumor heterogeneity, there are no drug combination strategies that utilize single-cell platforms. One idea that has been proposed is to use Mass Cytometry Time-of-Flight (CyTOF) for drug screening by producing drug perturbation effects at the level of the single cell, but the required analytics for the resulting complex data were not addressed. To address this unmet need, we have developed a novel algorithm to optimize combination therapy for an individual patient by analyzing distinct single-cell drug perturbation responses on a tumor sample. This model framework, called “DRUGNEM,” can be applied to CyTOF data, single-cell RNA-seq, or any single-cell imaging data currently available. DRUGNEM is composed of three steps: (1) identify the subpopulations that make up the tumor and may respond differently to treatment; (2) reconstruct a drug-nested-effects model that integrates the drug effects across all subpopulations to capture sub-setting relationships among individual drug effects; and (3) systematically score potential drug combinations to identify or prioritize strategies that will be clinically (and economically) sustainable. Currently, DRUGNEM is optimized to select the minimum number of drugs that produces the maximal desired intracellular effect, predicated on the premise that fewer drugs lower treatment-related toxicities and costs, but the final selection criterion can be easily modified. As proof of concept, we applied the DRUGNEM framework to individualize drug combinations based on CyTOF data generated on de-identified malignant research samples from 30 ALL pediatric patients before and after exposure to 3 targeted FDA -pproved single drugs (dasatinib, tofacitinib and BEZ235). We found that the most common combination treatment strategy (dasatinib and BEZ235) might not be optimal for all 30 ALL patients, with 2 of the 30 likely responding best to tofacitinib alone. Using in vitro survival assays, we validated the DRUGNEM prediction of BEZ235 and dasatinib as a potential synergistic combination on ALL cell lines. In summary, DRUGNEM is a novel framework using single-cell technologies to guide drug-combination strategies and can be adapted to incorporate complementary molecular data and computational methods to ultimately achieve more effective therapy for the individual cancer patient.

Citation Format: Benedict Anchang, Kara Davis, Harris Fienberg, Sean Bendall, Loukia Karacosta, Garry Nolan, Sylvia K. Plevritis. Individualized drug combination based on single-cell drug perturbations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2275.

Practice Guidelines for Standards of Adult Sleep Medicine Services

Sleep disorders, i.e. diseases that affect, disrupt or involve sleep, represent major challenges for physicians and healthcare systems worldwide. The high prevalence, the complexity and the health burden of sleep disorders demand the establishment of specific clinical sleep centres where adequate and efficient diagnosis and management of patients with such diseases can be provided. This document describes practice guidelines for standards of adult sleep medicine centres in Ireland. These guidelines are the result of a consensus procedure in which all committee members of the Irish Sleep Society (ISS) were involved. The scope of these guidelines is to define the requirements of sleep medicine services, in terms of personnel, facilities, equipment and procedures.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

Regulation of IL-12p40 by HIF controls Th1/Th17 responses to prevent mucosal inflammation

Intestinal inflammatory lesions are inherently hypoxic, due to increased metabolic demands created by cellular infiltration and proliferation, and reduced oxygen supply due to vascular damage. Hypoxia stabilizes the transcription factor hypoxia-inducible factor-1α (HIF) leading to a coordinated induction of endogenously protective pathways. We identified IL12B as a HIF-regulated gene and aimed to define how the HIF-IL-12p40 axis influenced intestinal inflammation. Intestinal lamina propria lymphocytes (LPL) were characterized in wild-type and IL-12p40^-/- murine colitis treated with vehicle or HIF-stabilizing prolyl-hydroxylase inhibitors (PHDi). IL12B promoter analysis was performed to examine hypoxia-responsive elements. Immunoblot analysis of murine and human LPL supernatants was performed to characterize the HIF/IL-12p40 signaling axis. We observed selective induction of IL-12p40 following PHDi-treatment, concurrent with suppression of Th1 and Th17 responses in murine colitis models. In the absence of IL-12p40, PHDi-treatment was ineffective. Analysis of the IL12B promoter identified canonical HIF-binding sites. HIF stabilization in LPLs resulted in production of IL-12p40 homodimer which was protective against colitis. The selective induction of IL-12p40 by HIF-1α leads to a suppression of mucosal Th1 and Th17 responses. This HIF-IL12p40 axis may represent an endogenously protective mechanism to limit the progression of chronic inflammation, shifting from pro-inflammatory IL-12p70 to an antagonistic IL-12p40 homodimer.

Abstract 2083: Development of novel targeted adjuvant therapy for triple negative breast cancer

There is an unmet clinical need for targeted adjuvant therapy in Triple Negative Breast Cancer (TNBC) to overcome its poor prognosis, short disease-free interval and metastatic dissemination. We previously reported that blocking interactions between the PAH2 domain of chromatin regulator Sin3 and Sin3 interaction domain (SID) containing proteins like PF1 and TGIF1 by SID decoys (peptides and small molecule, C16) decreased the cancer stem cell population, invasion, EMT, and metastases. This, programmed upregulation of retinoid signaling that sensitized TNBC cells to AM80, a novel clinically available RARα-specific agonist. Here we report preclinical investigations on effects of SID decoys and AM80 treatments on cellular heterogeneity, primary tumors, metastatic dissemination, minimum residual disease (MRD) and host microenvironment. Using CyTOF2, we made single cell measurements of markers of differentiation, proliferation and stemness in CSC-enriched 4T1 tumorspheres. Treatment with SID peptide decreased cell populations expressing nanog, sox2, vimentin and β-catenin with increase in γH2AX. Addition of AM80 in combination with C16, resulted in populations with increased expression of differentiation marker CD24 with decrease in vimentin, β-catenin and Ki-67. To interrogate the neo-adjuvant effects of C16-AM80 treatments, primary 4T1 tumors in Balb/c mice were treated with C16 and AM80 alone or in combination. Compared to DMSO, ~40 % decrease in tumor weight, 60% decrease in ALDH activity and 60% decrease in lung metastasis was seen in mice treated with C16-AM80 combination. In post-surgical adjuvant settings, in both 4T1 and MMTV-myc xenografts, we observed 100% disease-free survival and absence of macrometastasis in mice receiving minimally toxic adjuvant therapy with the C16-AM80 combination for 90 days. However, MRD was found consisting of a small number of single CK8+ cells which failed to form colonies when recovered from the bone marrow and selectively cultured in vitro. Upon stopping the treatments, 20-40% animals developed macrometastases within the first three months. To test the influence of C16-AM80 to condition the host microenvironment to prevent macrometastases mice received only pretreatment with C16 and AM80 followed by 4T1 cells injected in the tail vein. The percentage of parenchyma occupied by metastatic nodules were: DMSO = 50%; AM80 = 25%; C16 >10% and C16-AM = <<10%; the mitotic features were greatly reduce from 0-5 in DMSO to 0-1 per 400x/field in the C16-AM80 combination. The predominant effects were observed with C16 treatment, which was enhanced to a small degree in combination with AM80. These results suggest that C16 can potentially induce changes in the host microenvironment to prevent the colonization and metastatic growth of cancer cells in TNBC. Altogether, our preclinical studies merit expansion of a pre-clinical program for development of C16-AM80 combination as a targeted adjuvant therapy to treat TNBC.

Citation Format: Nidhi Bansal, Eduardo Farias, Veronica Gonzalez, Garry Nolan, Samuel Waxman. Development of novel targeted adjuvant therapy for triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2083. doi:10.1158/1538-7445.AM2017-2083

An anatomical study of the intersigmoid fossa and applications for internal hernia surgery

PURPOSE

To improve the knowledge of the morphometry and the surrounding anatomical structures of the intersigmoid fossa and to determine possible surgical applications.

METHOD

Forty eight adult cadavers (29 female and 19 male; mean age 83 years) underwent dissection in the Laboratoire d'Anatomie des Alpes Francaises. Two injections in the right carotid resulted in a total body concentration of formalin of 1.3 %. The study parameters were the dimensions of the intersigmoid fossa orifice and the fossa's relationship to surrounding structures. Data were recorded and analyzed using Microsoft Office Excel (MS Cerp). A Pearson coefficient r was used to examine the correlation between the length of colon and the ISF volume.

RESULTS

The intersigmoid fossa was present in 75 % of cases (n = 36). The average dimensions for the transverse diameter, longitudinal diameter, and the depth were, respectively, 20.5 ± 0.2, 20.3 ± 0.13, and 26.8 ± 0.2 mm. The primary and secondary roots bordering this fossa measured on average 59.1 ± 0.1 and 48.3 ± 0.13 mm. In 13.9 % of cases (n = 5), the maximum depth was >40 mm and in 16.7 % of cases (n = 6), one of the diameters of the orifice entry of the fossa was >40 mm. The ureter and external iliac artery were the most frequently encountered structures during the dissection of the fundus of the intersigmoid fossa.

CONCLUSION

The intersigmoid fossa remains present in most of the reported dissections of cadavers. It constitutes an essential landmark in the surgery of the sigmoid colon due to its deep structural relationship with the left ureter and external iliac artery.

A Framework for Meta-Analysis of Cytometry Data

Flow cytometry has been used to analyze cell populations with a certain condition, but because of the limitations of a single flow cytometry experiment, results only present a small portion of cell populations. Meta-analysis has been used to compare and contrast multiple datasets in hopes of discovering new insights. Scientists can then identify more cell populations linked to the condition. Therefore, we are developing a method to standardize and analyze multiple flow cytometry datasets.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes

The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of computational methods for identifying cell populations in multidimensional flow cytometry data. Here we report the results of FlowCAP-IV where algorithms from seven different research groups predicted the time to progression to AIDS among a cohort of 384 HIV+ subjects, using antigen-stimulated peripheral blood mononuclear cell (PBMC) samples analyzed with a 14-color staining panel. Two approaches (FlowReMi.1 and flowDensity-flowType-RchyOptimyx) provided statistically significant predictive value in the blinded test set. Manual validation of submitted results indicated that unbiased analysis of single cell phenotypes could reveal unexpected cell types that correlated with outcomes of interest in high dimensional flow cytometry datasets.

mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function

Understanding the consequences of tuning TCR signaling on selection, peripheral T cell function, and tolerance in the context of native TCR repertoires may provide insight into the physiological control of tolerance. In this study, we show that genetic ablation of a natural tuner of TCR signaling, mir-181a-1/b-1, in double-positive thymocytes dampened TCR and Erk signaling and increased the threshold of positive selection. Whereas mir-181a-1/b-1 deletion in mice resulted in an increase in the intrinsic reactivity of naive T cells to self-antigens, it did not cause spontaneous autoimmunity. Loss of mir-181a-1/b-1 dampened the induction of experimental autoimmune encephalomyelitis and reduced basal TCR signaling in peripheral T cells and their migration from lymph nodes to pathogenic sites. Taken together, these results demonstrate that tolerance can be modulated by microRNA gene products through the control of opposing activities in T cell selection and peripheral T cell function.

Pre-operative immune signatures correlate with recovery from surgical trauma (HUM1P.267)

Traumatic injury produces a profound immune response that mobilizes both innate and adaptive branches of the immune system. Patient recovery after a major trauma is highly variable. Protracted recovery after surgery -a major trauma- causes significant societal and economic costs. However, the mechanistic underpinning of recovery after surgery remains poorly understood. We recently applied high-parameter mass cytometry at the bedside for the deep immune profiling of patients undergoing orthopedic surgery1. The data revealed patient-specific immune responses in monocyte subsets that contained strong correlates of clinical recovery. In this study, we asked whether differences in patients’ pre-surgical immune states determined recovery. Activation of canonical signaling pathways was elicited in vitro, in pre-surgical patient samples. Single-cell evoked immune responses were analyzed in cell subsets spanning the entire immune system using mass cytometry. Surprisingly, the magnitude of these responses varied significantly across patients, thereby defining patient-specific “immune states”. Among these responses, signaling downstream of the TLR4 receptor in CD14+ monocytes strongly correlated with surgical recovery (R=0.64-0.69). The findings highlight a fundamental role for monocytes in the recovery process and provide the mechanistic basis for a pre-operative diagnostic test to predict the course of surgical recovery. 1.Gaudilliere et al., Sci Transl Med. 2014

Disordered breathing during sleep and exercise in idiopathic pulmonary fibrosis and the role of biomarkers

BACKGROUND AND OBJECTIVE

Idiopathic pulmonary fibrosis (IPF) patients report fatigue, possibly reflecting sleep disturbance, but little is known about sleep-related changes. We compared ventilation and gas exchange during sleep and exercise in a cohort of IPF patients, and evaluated associations with selected biological markers.

METHODS

Twenty stable IPF patients (aged 67.9 ± 12.3 [SD]) underwent overnight polysomnography following an acclimatization night. Cardiopulmonary exercise testing was performed and inflammatory markers measured including TNF-α, IL-6, CXCL8, C-C motif ligand 18 (CCL-18) and C-reactive protein (CRP) RESULTS: Nine patients had sleep-disordered breathing (SDB) with an apnea-hypopnea frequency (AHI) ≥ 5/h, but only two had Epworth sleepiness score ≥ 10, thus having an obstructive sleep apnea syndrome. Sleep quality was poor. Transcutaneous carbon dioxide tension (PtcCO2) rose by 2.56 ± 1.59 kPa overnight (P = 0.001), suggesting hypoventilation. Oxygen saturation (SaO2) was lower during sleep than exercise (P < 0.01), and exercise variables correlated with resting pulmonary function. CCL-18 and CRP levels were elevated and correlated with PtcCO2 rise during sleep (P < 0.05). CCL-18 negatively correlated with diffusion capacity of carbon monoxide (DLCO), arterial oxygen (PaO2) and mean arterial carbon dioxide (PaCO2) (P < 0.05) and CRP negatively correlated with DLCO, PaO2, sleep SaO2 and oxygen uptake (VO2) during exercise (P < 0.05).

CONCLUSIONS

IPF patients desaturate more during sleep than exercise; thus, nocturnal pulse oxymetry could be included in clinical assessment. CCL-18 and CRP levels correlate with physiological markers of fibrosis.

The systemic immune state of super-shedder mice is characterized by a unique neutrophil-dependent blunting of TH1 responses

Host-to-host transmission of a pathogen ensures its successful propagation and maintenance within a host population. A striking feature of disease transmission is the heterogeneity in host infectiousness. It has been proposed that within a host population, 20% of the infected hosts, termed super-shedders, are responsible for 80% of disease transmission. However, very little is known about the immune state of these super-shedders. In this study, we used the model organism Salmonella enterica serovar Typhimurium, an important cause of disease in humans and animal hosts, to study the immune state of super-shedders. Compared to moderate shedders, super-shedder mice had an active inflammatory response in both the gastrointestinal tract and the spleen but a dampened T_H1 response specific to the secondary lymphoid organs. Spleens from super-shedder mice had higher numbers of neutrophils, and a dampened T cell response, characterized by higher levels of regulatory T cells (T_regs), fewer T-bet⁺ (T_H1) T cells as well as blunted cytokine responsiveness. Administration of the cytokine granulocyte colony stimulating factor (G-CSF) and subsequent neutrophilia was sufficient to induce the super-shedder immune phenotype in moderate-shedder mice. Similar to super-shedders, these G-CSF-treated moderate-shedders had a dampened T_H1 response with fewer T-bet⁺ T cells and a loss of cytokine responsiveness. Additionally, G-CSF treatment inhibited IL-2-mediated T_H1 expansion. Finally, depletion of neutrophils led to an increase in the number of T-bet⁺ T_H1 cells and restored their ability to respond to IL-2. Taken together, we demonstrate a novel role for neutrophils in blunting IL-2-mediated proliferation of the T_H1 immune response in the spleens of mice that are colonized by high levels of S. Typhimurium in the gastrointestinal tract.

Bacteria belonging to the genus Salmonella are capable of causing long-term chronic systemic infections in specific hosts where they are shed in the feces. These persistently infected individuals include typhoid carriers and they serve as a reservoir for disease transmission. Despite the importance of Salmonella as a human pathogen, relatively little is known about the host immune response to persistent bacterial infections in the context of transmission. We had shown previously in a mouse model of Salmonella infection that mice shedding high levels of Salmonella (>10⁸ bacteria per gram of feces), known as super-shedders, transmit disease to naïve mice. We show here that these super-shedder mice have a unique immune state compared to mice that have lower levels of Salmonella in their gut. The super-shedder immune state is characterized by an active inflammatory immune response with elevated serum IL-6 and high levels of neutrophils in both the gastrointestinal tract and the systemic sites but a dampened adaptive CD4 T helper type1 (T_H1) cell response specific to the spleen. Importantly, we show that the blunted adaptive response, as characterized by reduced T_H1 cell frequencies and ability to respond to IL-2 and IL-6, is intimately linked to the levels of neutrophils present in the spleen. We go on to show the functional consequences of dampened cytokine responsiveness, as T_H1 cells from moderate-shedders are unable to undergo IL-2-mediated expansion when neutrophilia is induced. Additionally, we show that neutrophil control of IL-2 mediated expansion of T_H1 cells is independent of infection. In summary, we describe an immune phenotype associated with transmission of a pathogen and a single immune cell type, neutrophils, which control specific aspects of the super-shedder immune state.

Single cell mass cytometry of human peripheral blood reveals an endogenous immune response to surgical trauma (P1144)

An integral component of understanding immune function is measuring how the system responds to perturbation. We hypothesized that studying the immune response to the physiological stress of surgical trauma in vivo would uncover endogenous immune signaling networks critical for the function of the human immune system. Mass cytometry enables the measurement of 45 parameters on single immune cells with antibodies to both surface antigens and intracellular signaling proteins. Upon analyzing peripheral blood from patients at several time points pre- and post-surgery, we discovered that surgical trauma produces distinct population size changes, phenotypic changes, and intracellular signaling responses. Single cell analysis of immune signaling networks identified serial waves of six signaling proteins (STAT1, STAT3, STAT5, P38, S6 and CREB) that coordinated the functional response of the innate and adaptive immune systems. In addition, a subset of myeloid cells expands from 1% to 8% of hematopoietic cells in the 24 hours following surgery in all patients. These cells signal through STAT3, STAT1, CREB, and p38, and are phenotypically similar to previously described myeloid-derived suppressor cells. This systems-level single cell analysis generates a personalized surgical immune response profile of unprecedented resolution. In future work we plan to determine the relationship between these profiles and differences in clinical outcomes.

A robust and sensitive flow cytometric method for multiplex RNA in-situ hybridization analysis of blood cells using oligo probes and branched DNA based signal amplification (P3356)

We present here a novel method for in-situ hybridization (ISH) detection of multiple RNA targets in single cells using standard flow cytometer. This method is based on the use of oligo pairs as probes and bDNA signal amplification for highly sensitive and specific ISH detection of RNA. The oligo pairs are designed to hybridize to specific target sequences and can be readily synthesized. The oligo probes/RNA target complex is detected after signal is generated by bDNA signal amplification. The method is compatible with immunostaining, so simultaneous staining of protein and RNA in single cells is feasible. We demonstrated the co-staining of RNA and surface marker proteins in PBMC, B cells, T cells and leukemic cell lines of U937, K562, Jurkat and M1. In addition, the flow cytometric analysis of cytokine gene induction by lipopolysaccharides/R848 in PBMC was shown by staining with antibody for CD14 protein and probes for RNAs encoding interleukin-1 beta, -6, -8 and tumor necrosis factor-alpha. Taken together, this novel RNA ISH flow cytometry assay offers an invaluable tool for studying immune response, stem cell biology and infectious diseases.