Virus-specific T-cells (VST) from third-party donors mediate short- and long-term antiviral effects in allogeneic stem cell transplant (HSCT) recipients with relapsed or refractory viral infections. We investigated early administration of third-party VST together with antiviral therapy in patients requiring treatment for their first CMV or EBV infection. Thirty HSCT patients were treated with 1-4 VST infusions (2x107cells/m2; CMV=27, EBV=3) at a median of 4 days after initiation of antiviral treatment. The overall viral response rate was 100% with a complete response rate of 94%. Of the 28 patients who achieved a CR, 23 remained virus PCR negative (n=9) or below quantitation limit (n=14) for the duration of follow up. 4 patients had brief episodes of quantifiable reactivation not requiring additional therapy and one patient required a second infusion following initial CR, and remained PCR negative thereafter. All 3 patients treated for EBV PTLD achieved sustained CR. Rates of acute and chronic GVHD post-infusion were 13% (4/30) and 23% (7/30) respectively. There were no serious adverse events related to infusion. VST infusion was associated with rapid recovery of CD8+CD45RA-CD62L- and a slower recovery of CD4+CD45RA-CD62L- effector memory T-cells; CMV-specific T-cells comprised up to 13% of CD8+ cells. At 1 year post-transplant, non relapse mortality was 10%, cumulative incidence of relapse was 7%, overall survival was 88% and 25/27 patients had ECOG 0 or 1. Early administration of third-party VST in conjunction with antiviral treatment appears safe and leads to excellent viral control and clinical outcomes. Study ID ACTRN12618000343202.

Despite effective prevention programs targeting cardiovascular risk factors, coronary artery disease (CAD) remains the leading cause of death. Novel biomarkers are needed for improved risk stratification and primary prevention. To assess for independent associations between plasma metabolites and specific CAD plaque phenotypes we performed liquid chromatography mass-spectrometry on plasma from 1002 patients in the BioHEART-CT study. Four metabolites were examined as candidate biomarkers. Dimethylguanidino valerate (DMGV) was associated with presence and amount of CAD (OR) 1.41 (95% Confidence Interval [CI] 1.12–1.79, p = 0.004), calcified plaque, and obstructive CAD (p < 0.05 for both). The association with amount of plaque remained after adjustment for traditional risk factors, ß-coefficient 0.17 (95% CI 0.02–0.32, p = 0.026). Glutamate was associated with the presence of non-calcified plaque, OR 1.48 (95% CI 1.09–2.01, p = 0.011). Phenylalanine was associated with amount of CAD, ß-coefficient 0.33 (95% CI 0.04–0.62, p = 0.025), amount of calcified plaque, (ß-coefficient 0.88, 95% CI 0.23–1.53, p = 0.008), and obstructive CAD, OR 1.84 (95% CI 1.01–3.31, p = 0.046). Trimethylamine N-oxide was negatively associated non-calcified plaque OR 0.72 (95% CI 0.53–0.97, p = 0.029) and the association remained when adjusted for traditional risk factors. In targeted metabolomic analyses including 53 known metabolites and controlling for a 5% false discovery rate, DMGV was strongly associated with the presence of calcified plaque, OR 1.59 (95% CI 1.26–2.01, p = 0.006), obstructive CAD, OR 2.33 (95% CI 1.59–3.43, p = 0.0009), and amount of CAD, ß-coefficient 0.3 (95% CI 0.14–0.45, p = 0.014). In multivariate analyses the lipid and nucleotide metabolic pathways were both associated with the presence of CAD, after adjustment for traditional risk factors. We report novel associations between CAD plaque phenotypes and four metabolites previously associated with CAD. We also identified two metabolic pathways strongly associated with CAD, independent of traditional risk factors. These pathways warrant further investigation at both a biomarker and mechanistic level.

High-throughput single-cell technologies hold the promise of discovering novel cellular relationships with disease. However, analytical workflows constructed for these technologies to associate cell proportions with disease often employ unsupervised clustering techniques that overlook the valuable hierarchical structures that have been used to define cell types. We present treekoR, a framework that empirically recapitulates these structures, facilitating multiple quantifications and comparisons of cell type proportions. Our results from twelve case studies reinforce the importance of quantifying proportions relative to parent populations in the analyses of cytometry data — as failing to do so can lead to missing important biological insights.

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High-throughput single cell technologies hold the promise of discovering novel cellular relationships with disease and necessitate the use of effective analytical workflows. When manual gating is used to define cell types, the gating hierarchy can be used to identify cell types whose abundances change relative to a parent population. This strategy allows subtle changes to be observed that could be missed if small subsets were compared to all measured cells. However, typical analyses that employ unsupervised clustering overlook the valuable hierarchical structure present in cell type definitions by exclusively quantifying the proportions of cell type clusters relative to all cells. We present treekoR, a framework that facilitates multiple quantifications and comparisons of cell type proportions. Our results from twelve case studies reinforce the importance of quantifying proportions relative to parent populations in the analyses of cytometry data — as failing to do so can lead to missing important biological insights.

Disease relapse and infections cause significant morbidity and mortality post-allogeneic stem cell transplant (HSCT), which remains the only cure for many myeloid malignancies. We investigated a novel combination of donor-derived, tumour-associated, antigen-specific T-cells targeting Wilm’s tumour 1 (WT1) and preferentially expressed antigen in melanoma (PRAME), and multipathogen T-cells targeting CMV, EBV, Adenovirus and Aspergillus given prophylactically post-HSCT. Ten patients with acute myeloid leukaemia (n=6) or high risk myelodysplasia (n=4) who overexpressed WT1 and/or PRAME on diagnostic tumour samples received 1 infusion of multipathogen and 1-4 infusions of tumour-specific T-cells (all at 2x107cells/m2). There were no infusion-related severe adverse events. Low level viral reactivations occurred (CMV n=5, EBV n=7, Adenovirus n=1), however none required treatment. There were no cases of viral tissue disease or invasive fungal infections. At a median 2 years post-transplant, overall survival was 80%, all surviving patients were in complete remission and 6/8 patients had ECOG 0/1. Acute GVHD occurred in 2/10 patients, chronic GVHD in another 2/10. Infusion was associated with rapid, sustained reconstitution of pathogen- and tumour-specific immunity as measured by MHC tetramer for CMV and T-cell receptor based clone tracking. This novel combination of T-cell therapies was safe and associated with excellent clinical outcomes.

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