A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification, and prioritization of microbial proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant [to generate peptide-spectral matches (PSMs) and quantification], PepQuery2 (to verify the quality of PSMs), Unipept (for taxonomic and functional annotation), and MSstatsTMT (for statistical analysis). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies.

IMPORTANCE

Clinical metaproteomics has immense potential to offer functional insights into the microbiome and its contributions to human disease. However, there are numerous challenges in the metaproteomic analysis of clinical samples, including handling of very large protein sequence databases for sensitive and accurate peptide and protein identification from mass spectrometry data, as well as taxonomic and functional annotation of quantified peptides and proteins to enable interpretation of results. To address these challenges, we have developed a novel clinical metaproteomics workflow that provides customized bioinformatic identification, verification, quantification, and taxonomic and functional annotation. This bioinformatic workflow is implemented in the Galaxy ecosystem and has been used to characterize diverse clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness and availability for use by the research community via analysis of residual fluid from cervical swabs.

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.

Virtual urgent care is here to stay: driving toward safe, equitable, and sustainable integration within emergency medicine

BACKGROUND

Virtual care in Canada rapidly expanded during the COVID-19 pandemic in a low-rules environment in response to pressing needs for ongoing access to care amid public health restrictions. Emergency medicine specialists now face the challenge of advising on which virtual urgent care services ought to remain as part of comprehensive emergency care. Consideration must be given to safe, quality, and appropriate care as well as issues of equitable access, public demand, and sustainability (financial and otherwise). The aim of this project was to summarize current literature and expert opinion and formulate recommendations on the path forward for virtual care in emergency medicine.

METHODS

We formed a working group of emergency medicine physicians from across Canada working in a variety of practice settings. The virtual care working group conducted a scoping review of the literature and met monthly to discuss themes and develop recommendations. The final recommendations were circulated to stakeholders for input and subsequently presented at the 2023 Canadian Association of Emergency Physicians (CAEP) Academic Symposium for discussion, feedback, and refinement.

RESULTS

The working group developed and reached unanimity on nine recommendations addressing the themes of system design, equity and accessibility, quality and patient safety, education and curriculum, financial models, and sustainability of virtual urgent care services in Canada.

CONCLUSION

Virtual urgent care has become an established service in the Canadian health care system. Emergency medicine specialists are uniquely suited to provide leadership and guidance on the optimal delivery of these services to enhance and complement emergency care in Canada.

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant (to generate peptide-spectral matches (PSMs) and quantification), PepQuery2 (to verify the quality of PSMs), and Unipept and MSstatsTMT (for taxonomy and functional annotation). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies.

Gender equity of authorship in pulmonary medicine over the past decade

BACKGROUND

Gender disparity in authorship broadly persists in medical literature, little is known about female authorship within pulmonary medicine.

METHODS

A bibliometric analysis of publications from 2012 to 2021 in 12 journals with the highest impact in pulmonary medicine was conducted. Only original research and review articles were included. Names of the first and last authors were extracted and their genders were identified using the Gender-API web. Female authorship was described by overall distribution and distribution by country/region/continent and journal. We compared the article citations by gender combinations, evaluated the trend in female authorship, and forecasted when parity for first and last authorship would be reached. We also conducted a systematic review of female authorship in clinical medicine.

RESULTS

14,875 articles were included, and the overall percentage of female first authors was higher than last authors (37.0% vs 22.2%, p<0.001). Asia had the lowest percentage of female first (27.6%) and last (15.2%) authors. The percentages of female first and last authors increased slightly over time, except for a rapid increase in the COVID-19 pandemic periods. Parity was predicted in 2046 for the first authors and 2059 for the last authors. Articles with male authors were cited more than articles with female authors. However, male-male collaborations significantly decreased, whereas female-female collaborations significantly increased.

CONCLUSIONS

Despite the slow improvement in female authorship over the past decade, there is still a substantial gender disparity in female first and last authorship in high-impact medical journals in pulmonary medicine.

Radiation Therapy Knowledge and Health Literacy among Culturally Diverse Patients with Prostate Cancer Treated at a Safety-Net Hospital

PURPOSE/OBJECTIVE(S)

Shared decision making is integral to the physician-patient relationship for radiotherapy (RT) patients. It is implicit that patients both comprehend and retain information explained during consultation. However, quality and quantity of patient knowledge following this visit is unknown. The purpose of this study was to evaluate post-consultation RT knowledge and health literacy among a diverse group of patients.

MATERIALS/METHODS

Participants were patients ≥18 years old who received consultation for definitive or salvage RT to the prostate gland/fossa between April 2021 and January 2023 at an urban safety-net hospital. Following consultation, patients completed the Radiation Oncology Knowledge Assessment Survey (ROKAS), designed to measure patient understanding of proposed RT treatment (e.g., treatment frequency, length, safety) and possible short- and long-term side effects (SE). Additional measures included patients' health literacy, health numeracy (numerical medical concepts), acculturation (assimilation to the dominant culture), and socioeconomic factors. ROKAS was administered in both English and Spanish with Spanish-speaking patients offered medical translation if desired. Bivariate Pearson correlations were conducted to examine the relationships between independent variables and post-consultation RT knowledge. Two-sided t-tests were conducted to examine differences in patients' knowledge by language.

RESULTS

Overall, 39 ROKAS were completed by 24 English-speaking and 15 Spanish-speaking patients (mean age 64.4 [SD 6.8], range 52-79). The majority (93%) of patients 'agreed' or 'strongly agreed' that they understood all the RT information presented. However, only 70% of the RT questions were answered correctly with 26% of patients answering all RT questions correctly. Similarly, 95% of patients 'agreed' or 'strongly agreed' with knowing the side effects of their proposed treatment, but only 71% and 74% of short- and long-term SE questions, respectively, were answered correctly. Higher health literacy (p = 0.04) and health numeracy (p = 0.001) were significantly correlated with better understanding of short-term SE, but not with RT knowledge or long-term SE. Spanish-speaking patients had significantly lower scores of health literacy (p = 0.001) and understanding of long-term (p = 0.01), but not short-term SE.

CONCLUSION

There is a significant gap between perceived and measured knowledge of RT treatment and SE in patients who receive consultation for RT to the prostate gland/fossa. Health literacy was significantly associated with improved knowledge of RT and short-term SE. Spanish-speaking patients had poorer understanding of long-term SE than English-speaking patients. Efforts to identify gaps in patient health literacy are needed to target those at risk and ensure that culturally diverse patient populations can engage in shared decision making with their providers.

Contouring Analysis on Synthetic Contrast-Enhanced MR from GRMM-GAN and Implications on MR-Guide Radiation Therapy

PURPOSE/OBJECTIVE(S)

MR-guided linear accelerators have been commercialized making MR-only planning and adaptation an appealing alternative circumventing MR-CT registration. However, obtaining daily contrast-enhanced MR images can be prohibitive due to the increased risk of side effects from repeated contrast injections. In this work, we evaluate the quality of contrast-enhanced multi-modal MR image synthesis network GRMM-GAN (gradient regularized multi-modal multi-discrimination sparse-attention fusion generative adversarial network) for MR-guided radiation therapy.

MATERIALS/METHODS

With IRB approval, we trained the GRMM-GAN based on 165 abdominal MR studies from 65 patients. Each study included T2, T1 pre-contrast (T1pre), and T1 contrast enhanced (T1ce) images. The two pre-contrast MR modalities, T2 and T1pre images were adopted as inputs for GRMM-GAN, and the T1ce image at the portal venous phase was used as an output. Ten MR scans containing 21 liver tumors were selected for contouring analysis. A Turing test was first given to six radiation oncologists, in which 100 real T1ce and synthetic T1ce image slices are randomly given to the radiation oncologists to determine the authenticity of the synthesis. We then invited two radiation oncologists (RadOnc 1 and RadOnc2) to manually contour the 21 liver tumors independently on the real T1ce images. RadOnc2 then performed contouring on the respective synthetic T1ce MRs. DICE coefficient (defined as the intersection over the average of two volumes) and Hausdorff distance (HD, measuring how far two volumes are from each other) were used as analysis metrics. The DICE coefficients were calculated from the two radiation oncologists' contours on the real T1ce MR for each tumor. The DICE coefficients were also calculated from RadOnc 2's contours on real and synthetic MRs. Besides, tumor center shifts were extracted. The tumor center of mass coordinates was extracted from real and synthetic volumes. The difference in the coordinates indicated the shifts in the superior-inferior (SI), right-left (RL), and anterior-posterior (AP) directions between real and synthetic tumor volumes.

RESULTS

An average of 52.3% test score was achieved from the six radiation oncologists, which is close to random guessing. RadOnc 1 and RadOnc 2, who had participated in the contouring analysis, achieved an average DICE of 0.91±0.02 from tumor volumes drawn on the real T1ce MRs. This result sets the inter-operator uncertainty baseline in the real clinical setting. RadOnc 2 achieved an average DICE (real vs. synth) of 0.90±0.04 and HD of 4.76±1.82 mm. Only sub-millimeter (SI: 0.67 mm, RL: 0.41 mm, AP: 0.39 mm) tumor center shifts were observed in all three directions.

CONCLUSION

The GRMM-GAN method has the potential for MR-guided liver radiation when contrast agents cannot be administered daily and provide synthetic contrast-enhanced MR for better tumor targeting. The network can produce synthetic MR images with satisfactory contour agreement and geometric integrity.

A Combined Phase 0/2 "Trigger" Trial Evaluating Pamiparib or Olaparib with Concurrent Radiotherapy in Patients with Newly-Diagnosed or Recurrent Glioblastoma

PURPOSE/OBJECTIVE(S)

This study evaluates the pharmacokinetic (PK) and pharmacodynamic (PD) profiles and clinical efficacy of PARP1/2 selective inhibitors, pamiparib and olaparib, in newly-diagnosed or recurrent glioblastoma (GBM) patients in combination with radiotherapy (RT).

MATERIALS/METHODS

In this combined phase 0/2 trial presumed newly-diagnosed (Arm A) or recurrent (Arm B) GBM patients received 4 days of pamiparib (60 mg BID) prior to resection either 2-4 or 8-12 hours following the final dose. Arm C enrolled patients with recurrent GBM to 4 days of olaparib (200 mg BID) prior to resection. Enhancing and nonenhancing tumor tissue, cerebrospinal fluid (CSF) and plasma were collected. Total and unbound drug concentrations were measured using validated LC-MS/MS methods. A PK 'trigger', defined as unbound drug and gt; 5-fold biochemical IC 50 in nonenhancing tumor, determined eligibility for the therapeutic expansion phase 2. PARP inhibition was assessed via ex vivo radiation and quantification of PAR levels compared to non-radiated control. Newly-diagnosed MGMT unmethylated GBMs and recurrent GBMs exceeding the PK threshold were eligible for an expansion phase of pamiparib (Arms A and B) or olaparib (Arm C) with concurrent RT followed by maintenance pamiparib or olaparib. RT was 60 Gy in 30 fractions in newly-diagnosed patients and 40 Gy in 15 fractions in recurrent patients, delivered using volumetric-modulated arc therapy (VMAT).

RESULTS

A total of 38 patients (Arm A, n = 16; Arm B, n = 16; Arm C, n = 6) were enrolled in the initial phase 0 study. The mean unbound concentrations of pamiparib in nonenhancing tumor region for Arm A and Arm B were 167.3 nM and 109.4 nM respectively, and in Arm C the mean unbound concentration of olaparib was 5.2 nM. All patients in the pamiparib arms (n = 32/32) but only 1 of 6 patients in the olaparib Arm C exceeded the PK threshold. Radiation-induced PAR expression was 2.44-fold in untreated control vs 1.16 in Arm A (p<0.05), 0.85 in Arm B (p<0.01) and 1.11 in Arm C patients, respectively. In Arm A, 11 patients had unmethylated tumors, and of those, 7 patients enrolled in phase 2. In Arm B, 9 of the 16 clinically eligible patients with positive PK results were enrolled in phase 2. At a median follow-up of 8.4 months [range: 1.3-15.7 months], the median progression-free survival (PFS) was 5.4, 6.0, and 3.8 months for Arms A (n = 7), B (n = 9), and C (n = 1), respectively. Grade 3+ toxicities related to pamiparib occurred in 4 patients, with 2 adverse events resulting in treatment discontinuation. No grade 3+ toxicities were documented in the olaparib arm.

CONCLUSION

Pamiparib achieved pharmacologically-relevant concentrations in nonenhancing GBM tissue and suppressed induction of PAR levels ex vivo post-radiation. The majority of patients with MGMT-unmethylated GBM advanced to the phase 2 portion of the trial, and pamiparib was generally well-tolerated in these patients.

A Combined Phase 0/2 "Trigger" Trial of Niraparib in Combination with Radiation in Patients with Newly-Diagnosed Glioblastoma

PURPOSE/OBJECTIVE(S)

Poly ADP-ribose (PAR) polymerase (PARP) mediates DNA damage response. Niraparib is an investigational PARP1/2-selective inhibitor. We conducted a combined phase 0/2 study to evaluate niraparib pharmacokinetics (PK) and pharmacodynamics (PD) in patients with newly-diagnosed glioblastoma (GBM), graduating patients to a phase 2 study evaluating a therapeutic regimen of niraparib with concurrent conventionally-fractionated radiotherapy (RT) in O6-methylguanine methyltransferase (MGMT) unmethylated tumors exceeding a prespecified PK threshold in non-enhancing tumor.

MATERIALS/METHODS

Patients with presumed newly-diagnosed GBM were enrolled in a phase 0 study receiving 4 days of niraparib (300 or 200 mg QD) prior to planned resection 3-5 or 8-12 hours following the last dose. Tumor tissue (enhancing and non-enhancing regions), cerebrospinal fluid (CSF), and plasma were collected. Total and unbound niraparib concentrations were measured using validated LC-MS/MS methods. PARP inhibition was assessed by quantification of PAR induction after 10 Gy ex vivo irradiation in surgical tissue compared to non-irradiated control tissue. A PK 'trigger' determined eligibility for the therapeutic phase 2 expansion portion of the study. This was defined as unbound [niraparib] > 5-fold biochemical IC50 (i.e., 19 nM) in non-enhancing tumor. Patients with MGMT unmethylated tumors exceeding this PK threshold were eligible for expansion phase dosing of niraparib with concurrent RT followed by a maintenance phase of niraparib. Patients with MGMT methylated tumors were not eligible for the expansion phase and proceeded with temozolomide (TMZ) plus RT followed by maintenance TMZ. RT dose was 60 Gy in 30 fractions using volumetric-modulated arc therapy (VMAT).

RESULTS

All 29 patients enrolled in the phase 0 portion of the study met the PK threshold. In non-enhancing regions, the mean unbound concentration of niraparib was 258.2 nM. The suppression of PAR levels after ex vivo RT was observed in 79% of the patients (17/22). Sixteen patients had unmethylated tumors, and of those, 11 patients enrolled in phase 2. Five of the 6 initial patients enrolled in phase 2 experienced thrombocytopenia related to niraparib, and 3/5 cases were deemed serious and life-threatening. Consequently, starting dose in both phases was lowered to 200 mg, and no serious AEs were observed thereafter. At a median follow-up of 8.1 months [range: 6.0-12.9 months], 6-month PFS was 64% with 4 patients remaining on treatment and 5 patients ongoing survival follow-up.

CONCLUSION

Niraparib achieves pharmacologically-relevant concentrations in non-enhancing, newly-diagnosed GBM tissue in excess of any other studied PARP inhibitor. When delivered with concurrent RT, niraparib was well-tolerated, with low rates of grade 3+ toxicity. Initial clinical efficacy data are encouraging.

Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study

BACKGROUND

The dog is the most popular companion animal and is a valuable large animal model for several human diseases. Canine immune-mediated hematological diseases, including immune-mediated hemolytic anemia (IMHA) and immune thrombocytopenia (ITP), share many features in common with autoimmune hematological diseases of humans. The gut microbiome has been linked to systemic illness, but few studies have evaluated its association with immune-mediated hematological disease. To address this knowledge gap, 16S rRNA gene sequencing was used to profile the fecal microbiota of dogs with spontaneous IMHA and ITP at presentation and following successful treatment. In total, 21 affected and 13 healthy control dogs were included in the study.

RESULTS

IMHA/ITP is associated with remodeling of fecal microbiota, marked by decreased relative abundance of the spirochete Treponema spp., increased relative abundance of the pathobionts Clostridium septicum and Escherichia coli, and increased overall microbial diversity. Logistic regression analysis demonstrated that Treponema spp. were associated with decreased risk of IMHA/ITP (odds ratio [OR] 0.24-0.34), while Ruminococcaceae UCG-009 and Christensenellaceae R-7 group were associated with increased risk of disease (OR = 6.84 [95% CI 2-32.74] and 8.36 [95% CI 1.85-71.88] respectively).

CONCLUSIONS

This study demonstrates an association of immune-mediated hematological diseases in dogs with fecal dysbiosis, and points to specific bacterial genera as biomarkers of disease. Microbes identified as positive or negative risk factors for IMHA/ITP represent an area for future research as potential targets for new diagnostic assays and/or therapeutic applications.

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients

During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.

Integrative meta-omics in Galaxy and beyond

BACKGROUND

'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.

RESULTS

In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum, Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO.

CONCLUSION

Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of 'omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows.

A Galaxy of informatics resources for MS-based proteomics

INTRODUCTION

Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software.

AREAS COVERED

The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses.

EXPERT OPINION

The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.

Machine Learning Classification of Alzheimer's Disease Pathology Reveals Diffuse Amyloid as a Major Predictor of Cognitive Impairment in Human Hippocampal Subregions

Analyzing Alzheimer's disease (AD) pathology within anatomical subregions is a significant challenge, often carried out by pathologists using a standardized, semi-quantitative approach. To augment traditional methods, a high-throughput, high-resolution pipeline was created to classify the distribution of AD pathology within hippocampal subregions. USC ADRC post-mortem tissue sections from 51 patients were stained with 4G8 for amyloid, Gallyas for neurofibrillary tangles (NFTs) and Iba1 for microglia. Machine learning (ML) techniques were utilized to identify and classify amyloid pathology (dense, diffuse and APP (amyloid precursor protein)), NFTs, neuritic plaques and microglia. These classifications were overlaid within manually segmented regions (aligned with the Allen Human Brain Atlas) to create detailed pathology maps. Cases were separated into low, intermediate, or high AD stages. Further data extraction enabled quantification of plaque size and pathology density alongside ApoE genotype, sex, and cognitive status. Our findings revealed that the increase in pathology burden across AD stages was driven mainly by diffuse amyloid. The pre and para-subiculum had the highest levels of diffuse amyloid while NFTs were highest in the A36 region in high AD cases. Moreover, different pathology types had distinct trajectories across disease stages. In a subset of AD cases, microglia were elevated in intermediate and high compared to low AD. Microglia also correlated with amyloid pathology in the Dentate Gyrus. The size of dense plaques, which may represent microglial function, was lower in ApoE4 carriers. In addition, individuals with memory impairment had higher levels of both dense and diffuse amyloid. Taken together, our findings integrating ML classification approaches with anatomical segmentation maps provide new insights on the complexity of disease pathology in AD progression. Specifically, we identified diffuse amyloid pathology as being a major driver of AD in our cohort, regions of interest and microglial responses that might advance AD diagnosis and treatment.

An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples

BACKGROUND

Clinical bronchoalveolar lavage fluid (BALF) samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, mass spectrometry (MS)-based proteomic analysis of BALF is challenged by the dynamic range of protein abundance, and potential for interfering contaminants. A robust, MS-based proteomics compatible sample preparation workflow for BALF samples, including those of small and large volume, would be useful for many researchers.

RESULTS

We have developed a workflow that combines high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, that is compatible with either qualitative or quantitative MS-based proteomic analysis. The workflow includes a value-added collection of endogenous peptides for peptidomic analysis of BALF samples, if desired, as well as amenability to offline semi-preparative or microscale fractionation of complex peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We demonstrate the effectiveness of this workflow on BALF samples collected from COPD patients, including for smaller sample volumes of 1-5 mL that are commonly available from the clinic. We also demonstrate the repeatability of the workflow as an indicator of its utility for quantitative proteomic studies.

CONCLUSIONS

Overall, our described workflow consistently provided high quality proteins and tryptic peptides for MS analysis. It should enable researchers to apply MS-based proteomics to a wide-variety of studies focused on BALF clinical specimens.

Sustained intra-cartilage delivery of interleukin-1 receptor antagonist using cationic peptide and protein-based carriers

OBJECTIVE

Blocking the interleukin-1 (IL-1) catabolic cascade following joint trauma can be achieved using its receptor antagonist, IL-1Ra. However, its clinical translation for osteoarthritis therapy has been unsuccessful due to its rapid joint clearance and lack of targeting and penetration into deep cartilage layers at therapeutic concentrations. Here, we target the high negative charge of cartilage aggrecan-glycosaminoglycans (GAGs) by attaching cationic carriers to IL-1Ra. IL-1Ra was conjugated to the cartilage targeting glycoprotein, Avidin, and a short length optimally charged cationic peptide carrier (CPC+14). It is hypothesized that electro-diffusive transport and binding properties of IL-1Ra-Avidin and IL-1Ra-CPC+14 will create intra-cartilage depots of IL-1Ra, resulting in long-term suppression of IL-1 catabolism with only a single administration.

DESIGN

IL-1Ra was conjugated to Avidin or CPC+14 using site specific maleimide linkers, and confirmed using gel electrophoresis, high-performance liquid chromatography (HPLC), and mass spectrometry. Intra-cartilage transport and retention of conjugates was compared with native IL-1Ra. Attenuation of IL-1 catabolic signaling with one-time dose of IL-1Ra-CPC+14 and IL-1Ra-Avidin was assessed over 16 days using IL-1α challenged bovine cartilage and compared with unmodified IL-1Ra.

RESULTS

Positively charged IL-1Ra penetrated through the full-thickness of cartilage, creating a drug depot. A single dose of unmodified IL-1Ra was not sufficient to attenuate IL-1-induced cartilage deterioration over 16 days. However, when delivered using Avidin, and to a greater extent CPC+14, IL-1Ra significantly suppressed cytokine induced GAG loss and nitrite release while improving cell metabolism and viability.

CONCLUSION

Charge-based cartilage targeting drug delivery systems hold promise as they can enable long-term therapeutic benefit with only a single dose.

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in a major health crisis worldwide with its continuously emerging new strains, resulting in new viral variants that drive "waves" of infection. PCR or antigen detection assays have been routinely used to detect clinical infections; however, the emergence of these newer strains has presented challenges in detection. One of the alternatives has been to detect and characterize variant-specific peptide sequences from viral proteins using mass spectrometry (MS)-based methods. MS methods can potentially help in both diagnostics and vaccine development by understanding the dynamic changes in the viral proteome associated with specific strains and infection waves. In this study, we developed an accessible, flexible, and shareable bioinformatics workflow that was implemented in the Galaxy Platform to detect variant-specific peptide sequences from MS data derived from the clinical samples. We demonstrated the utility of the workflow by characterizing published clinical data from across the world during various pandemic waves. Our analysis identified six SARS-CoV-2 variant-specific peptides suitable for confident detection by MS in commonly collected clinical samples.

Artificial intelligence-guided, single-lead EKG may be a game-changer for symptom-to-balloon time reduction in ST-elevated myocardial infarction

Background

Over decades, efforts to shave off life-saving minutes from ST-Elevated Myocardial Infarction (STEMI) care centred on reducing door-to-needle and door-to-balloon times. We firmly believe that symptom-to-balloon time should prove a better focus to this end. Challenges come with this goal as it heavily relies on a patient's perception and initiative to seek care, which we deem intelligent and wearable Artificial Intelligence (AI)-driven Single Lead EKG technologies as an attractive solution in modern-day cardiology.

Purpose

To provide an accurate, accessible, and cost-effective AI-driven Single Lead STEMI detection algorithm that can be embedded into wearable devices and employed in a self-administered fashion.

Methods

Database: EKG records from Mexico, Colombia, Argentina, and Brazil from April 2014 to December 2019. Dataset: A total of 11,567 12-lead EKG records of 10[s] length with a sampling frequency of 500 Hz, including the following balanced classes: angiographically confirmed and unconfirmed STEMI, branch blocks, non-specific ST-T abnormalities, normal and abnormal (200+ CPT codes, excluding those mentioned above). Cardiologists manually checked the label of each record to ensure precision. Pre-processing: We discard the first and last 250 samples as they may contain a standardisation pulse. The study applied a digital low pass filter of order 5 with a frequency cut-off of 35 Hz. The mean was subtracted from each Lead. Classification: The determined classes were “STEMI” (Including STEMI in different locations of the myocardium – anterior, inferior, and lateral); and “Not-STEMI” (Combination of randomly sample, branch blocks, non-specific ST-T changes, and abnormal records – 25% of each). Training and Testing: A 1-D Convolutional Neural Network was trained and tested with a dataset proportion of 90/10, respectively. A different model was trained and tested for each Lead, using the central 4,500 samples of the records. The last dense layer outputs a probability for each report of being STEMI or Not-STEMI. Lead V2 showed the best overall results. The model was further tested through the same methodology using the best Lead with a subset of the previous data, excluding the unconfirmed STEMI EKG records (Total 7,230 12-lead EKG records for Confirmed Only STEMI dataset). Performance metrics were reported for each experiment and compared.

Results

Combined STEMI data: Accuracy: 91.2%; Sensitivity: 89.6%; Specificity: 92.9%. Confirmed STEMI Only dataset: Accuracy: 92.4%; Sensitivity: 93.4%; Specificity: 91.4% (Figure 1).

Conclusion

By assiduously improving the quality of the model's input, we continue to assess our algorithm's performance and reliability for future clinical validation as a potential remote monitoring and early STEMI detection device.

Funding Acknowledgement

Type of funding sources: None.

Digoxin improves systolic cardiac function in patients with AF and HFpEF: the RATE-AF randomised trial

Background

The RAte control Therapy Evaluation in permanent AF trial (RATE-AF; NCT02391337) was the first head-to-head controlled trial of beta-blockers versus digoxin in patients with permanent atrial fibrillation (AF) and symptoms of heart failure. Patients randomised to digoxin had similar physical-related quality of life and heart rate, with significantly improved functional class, reduced N-terminal pro-brain natriuretic peptide (NT-proBNP) and substantially less adverse events. The impact of rate control therapy on measures of cardiac function is not currently understood.

Purpose

To compare the effect of digoxin versus beta-blockers on systolic and diastolic cardiac function according to heart failure sub-type.

Methods

Blinded echocardiograms assessing systolic and diastolic function were performed at baseline and 12 month follow-up, using a robust method to account for rhythm irregularity (average of three index-beats acquired in appropriate cardiac cycles). Outcomes were the change in left-ventricular ejection fraction (LVEF), systolic tissue Doppler velocity (s'), stroke volume, global longitudinal strain (GLS), diastolic tissue Doppler (e'), mitral E wave deceleration time, E/e', pulmonary vein diastolic deceleration time, isovolumic relaxation time and left atrial ejection fraction. Analyses were stratified by baseline LVEF (≥50%, 40–50% and &lt;40%).

Results

160 patients were randomised, of which 145 patients survived to 12-month follow-up with median age 75 years (IQR 69–82) and 44% women. Median baseline heart rate was 96 beats/min (IQR 86–112), blood pressure 135/85 mmHg (IQR 124/77–146/91), NTproBNP 1049 pg/mL (744–1463) and mean NYHA class 2.4 (SD 0.6). In 119 patients with LVEF ≥50% at baseline, diastolic and systolic parameters improved over time with digoxin therapy. There was a significantly greater improvement in systolic function in 63 patients on digoxin compared to 67 with beta-blockers; Figure 1. Patients randomised to digoxin had a higher LVEF at follow-up (adjusted mean difference [AMD] 2.3%, 95% CI 0.3–4.2; p=0.021), higher s' (1.1cm/s, 1.0–1.2; p=0.003) and higher stroke volume (6.5mL, 0.4–12.6; p=0.037) compared to beta-blockers, without any difference in diastolic parameters (Figure 2). In 16 patients with LVEF 40–50% at baseline, s' significantly increased with digoxin compared to beta-blockers (AMD 1.5 cm/s, 1.2–1.7; p=0.001), with no difference for other systolic or diastolic parameters. 10 patients with LVEF &lt;40% at baseline showed no difference between digoxin and beta-blockers for any echocardiographic measures.

Conclusion

Patients randomised to digoxin with permanent AF, heart failure symptoms and preserved LVEF have significantly greater improvement in multiple parameters of systolic function compared to conventional treatment with beta-blockers.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): National Institute of Health Research

Performance metrics of AI-enhanced single lead EKG maintained after entry of organised clustered data

Background

Our experience in creating innovative Artificial Intelligence-guided single lead EKG methodologies for ST-Elevation Myocardial Infarction (STEMI) detection within complex EKG records has been previously validated.

Purpose

By expanding the intricate variables of our previously tested algorithm input, we seek to further improve our STEMI detecting tool.

Methods

11,567 12-lead EKG records (10-s length, 500 Hz sample frequency) derived from the Latin America Telemedicine Infarct Network database from April 2014 to December 2019. From these records, we included the following balanced classes: angiographically confirmed and unconfirmed STEMI (divided by wall affected), branch blocks, non-specific ST-T changes, normal, and abnormal (Remaining 200+ CPT codes). Cardiologist annotations ensured precision (Ground truth). Determined classes were “STEMI” and “Not-STEMI”. A 1-D Convolutional Neural Network model was trained and tested for each lead with dataset proportions of 90/10, respectively. The last dense layer outputs a probability for each record being STEMI/Not-STEMI. The analysis also included performance metrics and false-negative reports.

Results

Overall, the most promising Single lead for STEMI detection was V2 (91.2% Accuracy, 89.6% Sensitivity, and 92.9% Specificity). 55% of false negatives were inferior wall STEMI (Table 1).

Conclusion

Appreciable progress of our new methodology compared to our previous experiences in AI-guided Single Lead for STEMI detection, especially for lead V2. By performing a thorough analysis of false-negative reports, we aspire to identify potential areas of STEMI detection weakness which will become the focus of future ventures.

Funding Acknowledgement

Type of funding sources: None.

No need for a cardiologist for AMI diagnosis – progress of transforming a behemoth telemedicine program with artificial intelligence

Background

The Latin American Telemedicine Infarct Network (LATIN) Telemedicine is a mammoth hub and spoke model that provides an umbrella of AMI protection for 100 million patients. In the program, 826,043 patients had a telemedicine encounter; 7,400 with AMI were diagnosed; 4,332 of them managed with guidelines-based strategies. We have gradually begun implementing a system for using Artificial Intelligence (AI) algorithms embedded into EKGs for rapid and accurate STEMI detection and validated the results with a cardiologist's interpretations.

Purpose

To test whether an AI-driven EKG algorithm can effectively substitute a cardiologist for STEMI telemedicine protocols.

Methods

The AI algorithm construction was in the following fashion. Sample: a selection of 8,511 EKG and 90,592 classified heartbeats. Pre-processing: segmentation of each EKG into individual heartbeats. Training & testing: 90% and 10% of the total dataset, respectively. Classification: 1-D Convolutional Neural Network; the study constructed classes for each heartbeat. The algorithm was next deployed on a consecutive series of LATIN EKG records to diagnose STEMI. We afterwards compared the algorithm's results with eight expert cardiologists' interpretations of the same sample.

Results

This study achieved a concordance of 91% between the AI algorithm and cardiologist interpretation (Figure 1).

Conclusions

The initial results with AI algorithms for STEMI diagnosis are encouraging and may provide the base work for new tools for cardiologists to improve their efficiency. Moreover, implementing this innovative tool may overcome current limitations associated with the telemedical management of this disease.

Funding Acknowledgement

Type of funding sources: None.

Effect of aspirin discontinuation according to individualised patient bleeding and ischemic risks after PCI: a TWILIGHT trial sub-analysis

Background

The TWILIGHT trial demonstrated a reduction in BARC 2, 3 or 5 (BARC-235) bleeding without an increase in ischemic events at 1-year in high-risk PCI patients randomized to placebo or aspirin (ASA) on a background of ticagrelor 3-months after PCI. However, the effect of ASA discontinuation according to baseline risk of bleeding and ischemic events remain unclear.

Purpose

To a) develop separate models to predict the risk of bleeding and ischemic events, and b) to assess treatment effect of ASA discontinuation across the risk strata.

Methods

Using the TWILIGHT patient database (N=7,119), two multivariable models, one for BARC-235 bleeding and one for CV death, nonfatal MI or nonfatal ischemic stroke (ischemic endpoint) were developed, and their predictive capacity was assessed. The effect of randomized treatment on bleeding and ischemic events across different patient risk-group categories as determined by the risk scores was investigated.

Results

At 1-year, 350 (5.4%) patients experienced a BARC-235 bleeding event and 258 (3.6%) experienced an ischemic event. Independent predictors of BARC-235 included haemoglobin levels at index PCI, proton-pump inhibitor non-use at discharge, age, liver disease and active smoking (c-statistic 0.64). Independent predictors of the ischemic outcome included a positive troponin ACS, prior CABG, diabetes, age, peripheral artery disease, prior PCI, a history of congestive heart failure, active smoking, the level of index PCI complexity, and prior MI (c-statistic 0.71). The risk of a BARC-235 almost doubled between patients in lower versus higher bleeding risk categories (4.3% versus 7.9%) and ischemic risk more than tripled between patients in lower versus higher ischemic risk categories (2.0% versus 7.0%) (see Figure 1). There was no evidence of a differential treatment effect for dual antiplatelet therapy versus ticagrelor monotherapy across the different risk categories of bleeding (interaction P=0.54) and ischemic risk (interaction P=0.95) (Table 1).

Conclusion

Individual patient bleeding and ischemic risks after PCI can both be readily characterised with good discrimination. The effect of ASA discontinuation in preventing bleeding in ticagrelor-treated patients was consistent regardless of baseline bleeding risk. There was no evidence for increased ischemic events with ASA discontinuation according to baseline ischemic risk.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): AstraZenecaIcahn School of Medicine at Mount Sinai

P11.45.B Improved overall survival following Stereotactic Radiosurgery for brain metastases - a single institution experience

Background

Brain metastases are increasingly common due to longer survival associated with advancements in treatment. Approximately 40% of cancer patients are diagnosed with brain metastases at some point during their disease. Stereotactic radiosurgery (SRS) avoids the neuro-cognitive toxicity associated with whole brain radiotherapy and has been increasingly offered as a treatment alternative for brain metastases. Combined with developments in systemic treatments, this approach has resulted in improved overall survival (OS). This study reviewed patients treated with single fraction SRS at our institution with a primary endpoint of overall survival.

Material and Methods

A retrospective review determined overall survival for 237 patients who received single fraction SRS for 451 brain metastases from solid tumours between 1st January 2017 and 31st December 2021. Primary tumour sites were classified as breast, kidney, colorectal, melanoma, lung or other. SPSS v.27 was used for Kaplan Meier OS determination. The median follow up was 10.3 months. Cox regression analysis assessed the association between Gross Tumour Volume (GTV) and OS.

Results

In this patient cohort, 60% (N=142) were female and 40% (N=95) were male, with a median age of 63 [32-85]. 63.7% (N = 151) had a solitary metastasis. Patients received a single fraction of 15, 17.5 or 20 Gy (prescribed to 80% isodose) dependent on the planning target volume (PTV) size and whether it was initial treatment or re-treatment. 71% of all patients were alive at 6 months with median OS of 12.0 months [10.6-13.4]. Primary tumour site significantly affected OS (Log rank, Chi squared 15.656, p0.008) with breast cancer patients (N=58) surviving longest with a median OS 16.0 months [13.6-18.4] followed by melanoma median OS 15.0 months [7.6-22.4], kidney cancer patients (N = 24) median OS 12.0 months [8.3-15.7] and lung patients (N=87) median OS 10.0 months [8.9-11.3]. The lowest median OS was for colorectal patients at 7.0 months [1.4-12.6]. However, considering the small sample size, N = 15, more data is needed to confirm the significance. The larger the GTV volume the lower the survival time (Chi squared 8.692, p 0.003).

Conclusion

71% of patients had an OS of 6.0 months or more with a median of 12.0 months. As expected, primary tumour site has a significant impact on OS, with breast cancer patients living longest. In addition, increasing GTV size is associated with significantly worse survival. Given the improved survival for these patients, the avoidance of neuro cognitive decline remains of paramount importance and outcomes for these patients need to be reported in future work.

The influence of anastomotic techniques on postoperative anastomotic complications: Results of the Oesophago-Gastric Anastomosis Audit

BACKGROUND

The optimal anastomotic techniques in esophagectomy to minimize rates of anastomotic leakage and conduit necrosis are not known. The aim of this study was to assess whether the anastomotic technique was associated with anastomotic failure after esophagectomy in the international Oesophago-Gastric Anastomosis Audit cohort.

METHODS

This prospective observational multicenter cohort study included patients undergoing esophagectomy for esophageal cancer over 9 months during 2018. The primary exposure was the anastomotic technique, classified as handsewn, linear stapled, or circular stapled. The primary outcome was anastomotic failure, namely a composite of anastomotic leakage and conduit necrosis, as defined by the Esophageal Complications Consensus Group. Multivariable logistic regression modeling was used to identify the association between anastomotic techniques and anastomotic failure, after adjustment for confounders.

RESULTS

Of the 2238 esophagectomies, the anastomosis was handsewn in 27.1%, linear stapled in 21.0%, and circular stapled in 51.9%. Anastomotic techniques differed significantly by the anastomosis sites (P < .001), with the majority of neck anastomoses being handsewn (69.9%), whereas most chest anastomoses were stapled (66.3% circular stapled and 19.3% linear stapled). Rates of anastomotic failure differed significantly among the anastomotic techniques (P < .001), from 19.3% in handsewn anastomoses, to 14.0% in linear stapled anastomoses, and 12.1% in circular stapled anastomoses. This effect remained significant after adjustment for confounding factors on multivariable analysis, with an odds ratio of 0.63 (95% CI, 0.46-0.86; P = .004) for circular stapled versus handsewn anastomosis. However, subgroup analysis by anastomosis site suggested that this effect was predominantly present in neck anastomoses, with anastomotic failure rates of 23.2% versus 14.6% versus 5.9% for handsewn versus linear stapled anastomoses versus circular stapled neck anastomoses, compared with 13.7% versus 13.8% versus 12.2% for chest anastomoses.

CONCLUSIONS

Handsewn anastomoses appear to be independently associated with higher rates of anastomotic failure compared with stapled anastomoses. However, this effect seems to be largely confined to neck anastomoses, with minimal differences between techniques observed for chest anastomoses. Further research into standardization of anastomotic approach and techniques may further improve outcomes.

“Learning from the experts” – a novel advanced cadaveric course for Gynaecological Oncology (GO) Cytoreductive Surgery

Background: Ovarian cancer cytoreductive surgery necessitates the use of advanced Simulation-Based Learning (SBL) to optimise skill-based teaching and achieve technical proficiency. Objective: We describe and appraise the role of a novel postgraduate cadaveric course for cytoreductive surgery for advanced ovarian/fallopian tube or primary peritoneal cancer. Materials and Methods: Several consultant-level surgeons with expertise in upper gastrointestinal, colorectal, hepatobiliary and urological surgery, were invited to teach their counterpart GO surgeons. The 2-day course curriculum involved advanced dissections on thiel-embalmed cadavers. All dissections included applicable steps required during GO cytoreductive surgeries. Outcome measures: We used a feedback questionnaire and structured interviews to capture trainers and delegates views respectively. Results: All delegates reported a positive educational experience and improvement of knowledge in all course components. There was no difference in the perception of feedback across junior versus senior consultants. Trainers perceived this opportunity as a “2-way learning” whether they got to explore in depth the GO perspective in how and which of their skills are applicable during cytoreductive surgery. Conclusions: Collaborating with other surgical specialities promotes a “learning from the experts” concept and has potential to meet the rapidly increased demand for multi-viscera surgical excellence in GO surgery. What’s new? The concept of involving experts from other surgical disciplines in advanced cadaveric courses for cytoreductive surgery in ovarian cancer, will solidify the effort to achieve excellence in the GO training. Such courses can be essential educational adjunct for most GO fellowships.

Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome

Intestinal proteases mediate digestion and immune signaling, while increased gut proteolytic activity disrupts the intestinal barrier and generates visceral hypersensitivity, which in common in irritable bowel syndrome (IBS). However, the mechanisms controlling protease function are unclear. Here we show that members of the gut microbiota suppress intestinal proteolytic activity through production of unconjugated bilirubin. This occurs via microbial β-glucuronidase-mediated conversion of bilirubin conjugates. Metagenomic analysis of fecal samples from patients with post-infection IBS (n=52) revealed an altered gut microbiota composition, in particular a reduction in Alistipes taxa, and high gut proteolytic activity driven by specific host serine proteases compared to controls. Germ-free mice showed 10-fold higher proteolytic activity compared with conventional mice. Colonization with microbiota from high proteolytic activity IBS patients failed to suppress proteolytic activity in germ-free mice, but suppression of proteolytic activity was achieved with colonization using microbiota from healthy donors. High proteolytic activity mice had higher intestinal permeability, a higher relative abundance of Bacteroides and a reduction in Alistipes taxa compared with low proteolytic activity mice. High proteolytic activity IBS patients had lower fecal β-glucuronidase activity and end-products of bilirubin deconjugation. Mice treated with unconjugated bilirubin and β-glucuronidase overexpressing E. coli, which significantly reduced proteolytic activity, while inhibitors of microbial β-glucuronidases increased proteolytic activity. Together, these data define a disease-relevant mechanism of host-microbial interaction that maintains protease homeostasis in the gut.

Textbook outcome following oesophagectomy for cancer: international cohort study

Background

Textbook outcome has been proposed as a tool for the assessment of oncological surgical care. However, an international assessment in patients undergoing oesophagectomy for oesophageal cancer has not been reported. This study aimed to assess textbook outcome in an international setting.

Methods

Patients undergoing curative resection for oesophageal cancer were identified from the international Oesophagogastric Anastomosis Audit (OGAA) from April 2018 to December 2018. Textbook outcome was defined as the percentage of patients who underwent a complete tumour resection with at least 15 lymph nodes in the resected specimen and an uneventful postoperative course, without hospital readmission. A multivariable binary logistic regression model was used to identify factors independently associated with textbook outcome, and results are presented as odds ratio (OR) and 95 per cent confidence intervals (95 per cent c.i.).

Results

Of 2159 patients with oesophageal cancer, 39.7 per cent achieved a textbook outcome. The outcome parameter ‘no major postoperative complication’ had the greatest negative impact on a textbook outcome for patients with oesophageal cancer, compared to other textbook outcome parameters. Multivariable analysis identified male gender and increasing Charlson comorbidity index with a significantly lower likelihood of textbook outcome. Presence of 24-hour on-call rota for oesophageal surgeons (OR 2.05, 95 per cent c.i. 1.30 to 3.22; P = 0.002) and radiology (OR 1.54, 95 per cent c.i. 1.05 to 2.24; P = 0.027), total minimally invasive oesophagectomies (OR 1.63, 95 per cent c.i. 1.27 to 2.08; P &lt; 0.001), and chest anastomosis above azygous (OR 2.17, 95 per cent c.i. 1.58 to 2.98; P &lt; 0.001) were independently associated with a significantly increased likelihood of textbook outcome.

Conclusion

Textbook outcome is achieved in less than 40 per cent of patients having oesophagectomy for cancer. Improvements in centralization, hospital resources, access to minimal access surgery, and adoption of newer techniques for improving lymph node yield could improve textbook outcome.

Textbook outcome following oesophagectomy for cancer: international cohort study

BACKGROUND

Textbook outcome has been proposed as a tool for the assessment of oncological surgical care. However, an international assessment in patients undergoing oesophagectomy for oesophageal cancer has not been reported. This study aimed to assess textbook outcome in an international setting.

METHODS

Patients undergoing curative resection for oesophageal cancer were identified from the international Oesophagogastric Anastomosis Audit (OGAA) from April 2018 to December 2018. Textbook outcome was defined as the percentage of patients who underwent a complete tumour resection with at least 15 lymph nodes in the resected specimen and an uneventful postoperative course, without hospital readmission. A multivariable binary logistic regression model was used to identify factors independently associated with textbook outcome, and results are presented as odds ratio (OR) and 95 per cent confidence intervals (95 per cent c.i.).

RESULTS

Of 2159 patients with oesophageal cancer, 39.7 per cent achieved a textbook outcome. The outcome parameter 'no major postoperative complication' had the greatest negative impact on a textbook outcome for patients with oesophageal cancer, compared to other textbook outcome parameters. Multivariable analysis identified male gender and increasing Charlson comorbidity index with a significantly lower likelihood of textbook outcome. Presence of 24-hour on-call rota for oesophageal surgeons (OR 2.05, 95 per cent c.i. 1.30 to 3.22; P = 0.002) and radiology (OR 1.54, 95 per cent c.i. 1.05 to 2.24; P = 0.027), total minimally invasive oesophagectomies (OR 1.63, 95 per cent c.i. 1.27 to 2.08; P < 0.001), and chest anastomosis above azygous (OR 2.17, 95 per cent c.i. 1.58 to 2.98; P < 0.001) were independently associated with a significantly increased likelihood of textbook outcome.

CONCLUSION

Textbook outcome is achieved in less than 40 per cent of patients having oesophagectomy for cancer. Improvements in centralization, hospital resources, access to minimal access surgery, and adoption of newer techniques for improving lymph node yield could improve textbook outcome.

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow

Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, Rag2^−/−Il10^−/− mice were infected with Helicobacter hepaticus to induce chronic inflammation of the cecum and the colon. Transcriptomic data from harvested proximal colon samples were used to generate a customized FASTA database containing non-canonical protein sequences. Using a proteogenomic approach, mass spectrometry data for proximal colon proteins were searched against this custom FASTA database using the Galaxy for Proteomics (Galaxy-P) platform. In addition to the increased abundance in inflammatory response proteins, we also discovered several non-canonical peptide sequences derived from unique proteoforms. We confirmed the veracity of these novel sequences using an automated bioinformatics verification workflow with targeted MS-based assays for peptide validation. Our bioinformatics discovery workflow identified 235 putative non-canonical peptide sequences, of which 58 were verified with high confidence and 39 were validated in targeted proteomics assays. This study provides insights into challenges faced when identifying non-canonical peptides using a proteogenomics approach and demonstrates an integrated workflow addressing these challenges. Our bioinformatic discovery and verification workflow is publicly available and accessible via the Galaxy platform and should be valuable in non-canonical peptide identification using proteogenomics.

An International Registry of Peritoneal Carcinomatosis from Appendiceal Goblet Cell Carcinoma Treated with Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy

PURPOSE

Peritoneal carcinomatosis from appendiceal goblet cell carcinoma (A-GCC) is a rare and aggressive form of appendiceal tumor. Cytoreductive surgery (CRS) and hyperthermic intra peritoneal chemotherapy (HIPEC) was reported as an interesting alternative regarding survival compared to surgery without HIPEC and/or systemic chemotherapy. Our aim was to evaluate the impact of CRS and HIPEC for patients presenting A-GCC through an international registry.

METHODS

A prospective multicenter international database was retrospectively searched to identify all patients with A-GCC tumor and peritoneal metastases who underwent CRS and HIPEC through the Peritoneal Surface Oncology Group International (PSOGI). The post-operative complications, long-term results, and principal prognostic factors were analyzed.

RESULTS

The analysis included 83 patients. After a median follow-up of 47 months, the median overall survival (OS) was 34.6 months. The 3- and 5-year OS was 48.5% and 35.7%, respectively. Patients who underwent complete macroscopic CRS had a significantly better survival than those treated with incomplete CRS. The 5-year OS was 44% and 0% for patients who underwent complete, and incomplete CRS, respectively (HR 9.65, p < 0.001). Lymph node involvement and preoperative chemotherapy were also predictive of a worse prognosis. There were 3 postoperative deaths, and 30% of the patients had major complications.

CONCLUSION

CRS and HIPEC may increase long-term survival in selected patients with peritoneal metastases of A-GCC origin, especially when complete CRS is achieved. Ideally, randomized control trials or more retrospective data are needed to confirm CRS and HIPEC as the gold standard in this pathology.

Postoperative outcomes in oesophagectomy with trainee involvement

BACKGROUND

The complexity of oesophageal surgery and the significant risk of morbidity necessitates that oesophagectomy is predominantly performed by a consultant surgeon, or a senior trainee under their supervision. The aim of this study was to determine the impact of trainee involvement in oesophagectomy on postoperative outcomes in an international multicentre setting.

METHODS

Data from the multicentre Oesophago-Gastric Anastomosis Study Group (OGAA) cohort study were analysed, which comprised prospectively collected data from patients undergoing oesophagectomy for oesophageal cancer between April 2018 and December 2018. Procedures were grouped by the level of trainee involvement, and univariable and multivariable analyses were performed to compare patient outcomes across groups.

RESULTS

Of 2232 oesophagectomies from 137 centres in 41 countries, trainees were involved in 29.1 per cent of them (n = 650), performing only the abdominal phase in 230, only the chest and/or neck phases in 130, and all phases in 315 procedures. For procedures with a chest anastomosis, those with trainee involvement had similar 90-day mortality, complication and reoperation rates to consultant-performed oesophagectomies (P = 0.451, P = 0.318, and P = 0.382, respectively), while anastomotic leak rates were significantly lower in the trainee groups (P = 0.030). Procedures with a neck anastomosis had equivalent complication, anastomotic leak, and reoperation rates (P = 0.150, P = 0.430, and P = 0.632, respectively) in trainee-involved versus consultant-performed oesophagectomies, with significantly lower 90-day mortality in the trainee groups (P = 0.005).

CONCLUSION

Trainee involvement was not found to be associated with significantly inferior postoperative outcomes for selected patients undergoing oesophagectomy. The results support continued supervised trainee involvement in oesophageal cancer surgery.

Individual and poly-substance use and condomless sex among HIV-uninfected adults reporting heterosexual sex in a multi-site cohort

BACKGROUND

We analyzed the association between substance use (SU) and condomless sex (CS) among HIV-negative adults reporting heterosexual sex in the Seek, Test, Treat, and Retain (STTR) consortium. We describe the impact of SU as well as person/partner and context-related factors on CS, identifying combinations of factors that indicate the highest likelihood of CS.

METHODS

We analyzed data from four US-based STTR studies to examine the effect of SU on CS using two SU exposures: 1) recent SU (within 3 months) and 2) SU before/during sex. Behavioral data were collected via 1:1 or self-administered computerized interviews. Adjusted individual-study, multivariable relative risk regression was used to examine the relationship between CS and SU. We also examined interactions with type of sex and partner HIV status. Pooled effect estimates were calculated using traditional fixed-effects meta-analysis. We analyzed data for recent SU (n = 6781; 82% men, median age = 33 years) and SU before/during sex (n = 2915; 69% men, median age = 40 years).

RESULTS

For both exposure classifications, any SU other than cannabis increased the likelihood of CS relative to non-SU (8-16%, p-values< 0.001). In the recent SU group, however, polysubstance use did not increase the likelihood of CS compared to single-substance use. Cannabis use did not increase the likelihood of CS, regardless of frequency of use. Type of sex was associated with CS; those reporting vaginal and anal sex had a higher likelihood of CS compared to vaginal sex only for both exposure classifications (18-21%, p < 0.001). Recent SU increased likelihood of CS among those reporting vaginal sex only (9-10%, p < 0.001); results were similar for those reporting vaginal and anal sex (5-8%, p < 0.01). SU before/during sex increased the likelihood of CS among those reporting vaginal sex only (20%; p < 0.001) and among those reporting vaginal and anal sex (7%; p = 0.002). Single- and poly-SU before/during sex increased the likelihood of CS for those with exclusively HIV-negative partners (7-8%, p ≤ 0.02), and for those reporting HIV-negative and HIV-status unknown partners (9-13%, p ≤ 0.03).

CONCLUSION

Except for cannabis, any SU increased the likelihood of CS. CS was associated with having perceived HIV-negative partners and with having had both anal/vaginal sex.

A phased city air quality management approach for faster clean air progress

Clean air is a basic human right, yet over 90% of people are exposed to unhealthy levels of pollution, resulting in over 5 million deaths each year. The burden of air pollution is the greatest in densely populated cities; and will continue to grow without rapid and aggressive action to reduce pollution emissions. Air pollution is associated with chronic illnesses, including diabetes and heart and lung diseases, which can make people more susceptible to COVID-19. Local governments must prioritise feasible and scalable proven solutions and innovations in their jurisdictions to control local emissions in the near term while engaging advocacy and cooperation for regional and national actions to improve air quality over the long term. Vital Strategies' Accelerating City Progress on Clean Air: Innovation and Action Guide (the Guide) is an evidence-based, pragmatic playbook for helping city governments develop comprehensive air quality management systems to rapidly promote clean air for health. This talk will summarise the pragmatic step-by-step approach laid out in the Guide, and describe progress underway in Jakarta, Indonesia, where this guidance is being implemented to strengthen the city's clean air plan. Strategies to be discussed will include: innovations to improve data on air pollution levels and sources, health impact analyses using local data and policy implications; improved data transparency and communication on air quality issues; and the intersectoral approach and coordination being undertaken to accelerate and sustain clean air action.

A comparative study on the influence of third point of reference on condylar guidance settings in a semi-adjustable articulator with lateral cephalographs: An in-vivo study

Aim

The study aimed to evaluate the effect on condylar guidance values with casts mounted by facebow transfer (Guichet's point as the third point of reference), Bonwill's, and radiographic method.

Materials and Methods

The dentulous subject's casts were mounted to a semi-adjustable articulator (Artex Type AR) after facebow transfer with Guichet's point as the third point of reference and also by Bonwill's method. Protrusive records made earlier were utilized to program the right and left side condylar guidance value. Two digital lateral cephalograms were made, one in centric relation, and one in protrusion and the condyles were traced and overlapped. The condylar guidance readings obtained by Bonwill's method, facebow transfer, and lateral cephalometric tracings were compared in this study using the SPSS (Version 17.0 Illinois, Chicago, USA) software.

Results

The condylar guidance values obtained from Bonwill's and the facebow transfer method (p < 0.001) was lesser than the radiographic method. The values obtained by casts mounted to the Bonwill's method differed significantly (p < 0.001) from the other two methods.

Conclusion

The values obtained by facebow transfer were closer to the radiographic values whereas the values obtained by Bonwill's method mounting differed markedly.

Transcatheter aortic valve implantation outcomes compared between bicuspid aortic and tricuspid aortic valve stenosis: an updated systematic review and meta-analysis

Background

TAVI has emerged as an attractive treatment modality based on promising recent trial data. Patients with BAV, a commonly encountered clinical condition have largely been excluded from a majority of trials.

Purpose

Elderly patients with BAV and severe AS are increasingly encountered in clinical practice. This meta-analysis compares clinical outcomes between bicuspid and tricuspid AV patients to address the current knowledge-gap and identify optimal management strategies of these patients.

Methods

A comprehensive literature search was performed in PubMed, Embase, and Cochrane to identify the available observational studies comparing outcomes of TAVI in BAV and TAV patients. Summary effects were calculated using a DerSimonian and Laird random-effects model as odds ratio with 95% confidence intervals for all the clinical endpoints.

Results

16 Observational studies met inclusion criteria, comprising 10,053 patients with BAV and 173,307 patients with TAV that underwent TAVI. No significant differences in 30-day and long-term mortality rates were observed. Patients with BAV had an increased risk of stroke (OR 1.23; 95% CI [1.06–1.44], p=0.007), re-intervention (OR 1.90; 95% CI [1.15–3.15], p=0.01), paravalvular leak (OR 1.42; 95% CI [1.25–1.61], p&lt;0.ehab724.22251), conversion to open surgery (OR 1.93; 95% CI [1.21–3.07], p=0.006), and new pacemaker implantation (1.57; 95% CI (1.06 - 2.33, p=0.02). Adverse event rates are lower with the use of newer generation of valves. No significant difference in major vascular complications, major bleeding, or incidence of AKI was noted.

Conclusions

Complication rates for BAV TAVI are higher, but mortality is similar to TAV TAVI indicating TAVI is an appropriate alternative for intermediate-high risk patients with BAV. A better understanding of valve anatomy, physician expertise, the use of newer-generation valves can help reduce these complications.

Funding Acknowledgement

Type of funding sources: None.

Ticagrelor monotherapy after percutaneous coronary intervention in patients with concomitant diabetes mellitus and chronic kidney disease: a TWILIGHT substudy

Background

Diabetes mellitus (DM) and chronic kidney disease (CKD) are established risk factors for cardiovascular events, with patients presenting both conditions being at extremely high risk. P2Y12 inhibitor monotherapy with ticagrelor after a short course of dual antiplatelet therapy has emerged as a bleeding avoidance strategy for high-risk patients undergoing percutaneous coronary intervention (PCI).

Purpose

To investigate ischemic and bleeding outcomes associated with ticagrelor monotherapy versus ticagrelor plus aspirin according to the presence or absence of CKD and DM.

Methods

The TWILIGHT trial enrolled patients undergoing PCI with a drug-eluting stent who fulfilled at least one clinical and one angiographic high-risk criterion. Both DM and CKD (estimated glomerular filtration rate &lt;60 mL/min/1.73m2) were clinical study entry criteria. Following 3 months of ticagrelor plus aspirin, patients who had been adherent to treatment and free from major adverse events were randomly assigned to either aspirin or placebo in addition to ticagrelor for 1 year. The primary endpoint was Bleeding Academic Research Consortium (BARC) type 2, 3 or 5 bleeding. The key secondary endpoint was the composite of all-cause death, myocardial infarction, or stroke. Net adverse clinical events (NACE) were defined as BARC type 3 or 5 bleeding, all-cause death, myocardial infarction, or stroke.

Results

Of the 6273 patients included in the analysis, 8.0% had both CKD and DM (DM+/CKD+), 8.9% had CKD only (DM-/CKD+), 29.0% had DM only (DM+/CKD-), and 52.1% had neither CKD nor DM (DM-/CKD-). At 1-year follow-up, there was a progressive increase in the rates of bleeding and ischemic events according to DM and CKD status (Figure 1). Ticagrelor plus placebo reduced the primary bleeding endpoint as compared with ticagrelor plus aspirin across all study groups, including DM+/CKD+ patients (4.7% vs. 8.7%; HR 0.52, 95% CI 0.25–1.07), with no evidence of heterogeneity (p-interaction=0.68). Similar treatment effects of ticagrelor monotherapy were observed for major BARC type 3 or 5 bleeding (p-interaction=0.17), with DM+/CKD+ patients showing the greatest absolute risk reduction (0.9% vs. 5.1%; HR 0.16, 95% CI 0.04–0.72). The key secondary endpoint was not significantly different between treatment arms across study groups, with the exception of a reduced risk in DM+/CKD- patients receiving ticagrelor monotherapy (p-interaction=0.033). A similar pattern in the DM+/CKD- group was observed for NACE (p-interaction=0.030) (Figure 2).

Conclusions

Among high-risk patients undergoing PCI, ticagrelor monotherapy reduced the risk of clinically relevant and major bleeding without a significant increase in ischemic events as compared with ticagrelor plus aspirin, irrespective of the presence of DM and CKD. Furthermore, ticagrelor monotherapy seemed to be associated with a more favourable net benefit in patients with DM without CKD.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Investigator-initiated grant from AstraZeneca Figure 1. Event rates according to DM/CKD statusFigure 2. Effects of ticagrelor monotherapy

Outcomes of permanent pacemaker insertion after TAVR: a systematic review and meta-analysis

Background/Introduction

Conduction abnormalities are frequently encountered after transcatheter aortic valve replacement (TAVR) performed for severe aortic stenosis, leading to post-procedure permanent pacemaker (PPM) insertion. Although the predictors of- and factors leading to post-TAVR PPM have been studied extensively, its short-term and long-term outcomes have not been established.

Purpose

PPM placement can lead to significant changes in outcomes in post-TAVR patients, which remain unclear. With this analysis, we aim to evaluate the differences between outcomes of patients requiring PPM and those not requiring PPM post-TAVR.

Methods

A comprehensive literature search was performed in PubMed, EMBASE, and Cochrane to identify relevant trials. Outcomes were compared between the two groups of patients- those requiring post-TAVR PPM and those not requiring post-TAVR PPM. Summary effects were calculated using a DerSimonian and Laird random-effects model as odds ratio (OD) with 95% confidence intervals (CI) for all the clinical endpoints.

Results

34 studies, including observational and prospective studies, met our inclusion criteria, with a total of 76,402 patients undergoing TAVR and 10,381 requiring post-TAVR PPM. There were no significant differences between 30-days (OR 1.04; 95% CI 0.96–1.13) and 1-year (OR 1.09; 95% CI 0.72–1.03) all-cause mortality rates, and 30-days (OR 0.86; 95% CI 0.72–1.03) and 1-year (OR 0.85; 95% CI 0.70–1.04) cardiovascular deaths among the two groups. Incidence of heart failure was higher in the post-TAVR PPM group at 30 days (OR 1.26; 95% CI 1.05–1.51) but not at 1 year (OR 1.21; 95% CI 0.93–1.57). No significant difference was noted between the two groups in 30-days or 1-year stroke, 30-days or 1-year myocardial infarction, 30-days or 1-year atrial fibrillation, 30-days or 1-year major bleeding, or 30-days and 1-year readmission rate. Other outcomes, including post-procedure aortic regurgitation, major vascular complications, minor bleeding, valve migration, and device success, also did not have any statistically significant difference in the two patient groups (Figure 1). Of all the patients who received post-TAVR PPM, an average of 46.4% and 58.5% patients had &gt;40% ventricular pacing, and 48.9% and 41.4% had &lt;40% ventricular pacing at 1-month, and 1-year follow up respectively.

Conclusions

Although there were no differences in the outcomes between the two groups at 30-days and 1-year follow-ups (except the higher incidence of heart failure at 30 days in the post-TAVR PPM group), long-term follow-up studies would be needed to identify any possible adverse events after one year. Also, a significant number of patients requiring post-TAVR PPM had &lt;40% ventricular pacing at 1-month and even at 1-year intervals, which might suggest adopting an alternate approach of closely monitoring any conduction disturbances and avoiding early PPM implantation in post-TAVR patients, if possible.

Funding Acknowledgement

Type of funding sources: None. Forest plot of differences in outcomes