A monodispersed metal-complexing peptide-based polymer for mass cytometry enabling spectral applications

We report the synthesis of a novel class of metal-complexing peptide-based polymers, which we name HyperMAPs (Hyper-loaded MetAl-complexed Polymers). The controlled solid-phase synthesis of HyperMAPs' scaffold peptide provides our polymer with a well-defined molecular structure that allows for an accurate on-design assembly of a wide variety of metals. The peptide-scaffold features a handle for direct conjugation to antibodies or any other biomolecules by means of a thiol-maleimide-click or aldehyde-oxime reaction, a fluorogenic moiety for biomolecule conjugation tracking, and a well-defined number of functional groups for direct incorporation of metal-chelator complexes. Since metal-chelator complexes are prepared in a separate reaction prior to incorporation to the peptide scaffold, polymers can be designed to contain specific ratios of metal isotopes, providing each polymer with a unique CyTOF spectral fingerprint. We demonstrate the complexing of 21 different metals using two different chelators and provide evidence of the application of HyperMAPs on a 13 parameter CyTOF panel and compare its performance to monoisotopic metal-conjugated antibodies.

In-depth immune profiling of peripheral blood mononuclear cells in patients with pancreatic ductal adenocarcinoma reveals discriminative immune subpopulations

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis with a 5-year survival of less than 10%. More knowledge of the immune response developed in patients with PDAC is pivotal to develop better combination immune therapies to improve clinical outcome. In this study, we used mass cytometry time-of-flight to undertake an in-depth characterization of PBMCs from patients with PDAC and examine the differences with healthy controls and patients with benign diseases of the biliary system or pancreas. Peripheral blood mononuclear cells from patients with PDAC or benign disease are characterized by the increase of pro-inflammatory cells, as CD86+ classical monocytes and memory T cells expressing CCR6+ and CXCR3+, associated with T helper 1 (Th1) and Th17 immune responses, respectively. However, PBMCs from patients with PDAC present also an increase of CD39+ regulatory T cells and CCR4+CCR6-CXCR3- memory T cells, suggesting Th2 and regulatory responses. Concluding, our results show PDAC develops a multifaceted immunity, where a proinflammatory component is accompanied by regulatory responses, which could inhibit potential antitumor mechanisms.

Adaptive immune changes associate with clinical progression of Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is the most frequent cause of dementia. Recent evidence suggests the involvement of peripheral immune cells in the disease, but the underlying mechanisms remain unclear.

METHODS

We comprehensively mapped peripheral immune changes in AD patients with mild cognitive impairment (MCI) or dementia compared to controls, using cytometry by time-of-flight (CyTOF).

RESULTS

We found an adaptive immune signature in AD, and specifically highlight the accumulation of PD1+ CD57+ CD8+ T effector memory cells re-expressing CD45RA in the MCI stage of AD. In addition, several innate and adaptive immune cell subsets correlated to cerebrospinal fluid (CSF) biomarkers of AD neuropathology and measures for cognitive decline. Intriguingly, subsets of memory T and B cells were negatively associated with CSF biomarkers for tau pathology, neurodegeneration and neuroinflammation in AD patients. Lastly, we established the influence of the APOE ε4 allele on peripheral immunity.

CONCLUSIONS

Our findings illustrate significant peripheral immune alterations associated with both early and late clinical stages of AD, emphasizing the necessity for further investigation into how these changes influence underlying brain pathology.

Lymphopenia is associated with broad host response aberrations in community-acquired pneumonia

OBJECTIVES

Lymphopenia at hospital admission occurs in over one-third of patients with community-acquired pneumonia (CAP), yet its clinical relevance and pathophysiological implications remain underexplored. We evaluated outcomes and immune features of patients with lymphopenic CAP (L-CAP), a previously described immunophenotype characterized by admission lymphocyte count <0.724 × 109 cells/L.

METHODS

Observational study in 149 patients admitted to a general ward for CAP. We measured 34 plasma biomarkers reflective of inflammation, endothelial cell responses, coagulation, and immune checkpoints. We characterized lymphocyte phenotypes in 29 patients using spectral flow cytometry.

RESULTS

L-CAP occurred in 45 patients (30.2%) and was associated with prolonged time-to-clinical-stability (median 5 versus 3 days), also when we accounted for competing events for reaching clinical stability and adjusted for baseline covariates (subdistribution hazard ratio 0.63; 95% confidence interval 0.45-0.88). L-CAP patients demonstrated a proportional depletion of CD4 T follicular helper cells, CD4 T effector memory cells, naïve CD8 T cells and IgG+ B cells. Plasma biomarker analyses indicated increased activation of the cytokine network and the vascular endothelium in L-CAP.

CONCLUSIONS

L-CAP patients have a protracted clinical recovery course and a more broadly dysregulated host response. These findings highlight the prognostic and pathophysiological relevance of admission lymphopenia in patients with CAP.

The immunological landscape of peripheral blood in glioblastoma patients and immunological consequences of age and dexamethasone treatment

Background

Glioblastomas manipulate the immune system both locally and systemically, yet, glioblastoma-associated changes in peripheral blood immune composition are poorly studied. Age and dexamethasone administration in glioblastoma patients have been hypothesized to limit the effectiveness of immunotherapy, but their effects remain unclear. We compared peripheral blood immune composition in patients with different types of brain tumor to determine the influence of age, dexamethasone treatment, and tumor volume.

Methods

High-dimensional mass cytometry was used to characterise peripheral blood mononuclear cells of 169 patients with glioblastoma, lower grade astrocytoma, metastases and meningioma. We used blood from medically-refractory epilepsy patients and healthy controls as control groups. Immune phenotyping was performed using FlowSOM and t-SNE analysis in R followed by supervised annotation of the resulting clusters. We conducted multiple linear regression analysis between intracranial pathology and cell type abundance, corrected for clinical variables. We tested correlations between cell type abundance and survival with Cox-regression analyses.

Results

Glioblastoma patients had significantly fewer naive CD4+ T cells, but higher percentages of mature NK cells than controls. Decreases of naive CD8+ T cells and alternative monocytes and an increase of memory B cells in glioblastoma patients were influenced by age and dexamethasone treatment, and only memory B cells by tumor volume. Progression free survival was associated with percentages of CD4+ regulatory T cells and double negative T cells.

Conclusion

High-dimensional mass cytometry of peripheral blood in patients with different types of intracranial tumor provides insight into the relation between intracranial pathology and peripheral immune status. Wide immunosuppression associated with age and pre-operative dexamethasone treatment provide further evidence for their deleterious effects on treatment with immunotherapy.

High-dimensional phenotyping of the peripheral immune response in community-acquired pneumonia

Background

Community-acquired pneumonia (CAP) represents a major health burden worldwide. Dysregulation of the immune response plays an important role in adverse outcomes in patients with CAP.

Methods

We analyzed peripheral blood mononuclear cells by 36-color spectral flow cytometry in adult patients hospitalized for CAP (n=40), matched control subjects (n=31), and patients hospitalized for COVID-19 (n=35).

Results

We identified 86 immune cell metaclusters, 19 of which (22.1%) were differentially abundant in patients with CAP versus matched controls. The most notable differences involved classical monocyte metaclusters, which were more abundant in CAP and displayed phenotypic alterations reminiscent of immunosuppression, increased susceptibility to apoptosis, and enhanced expression of chemokine receptors. Expression profiles on classical monocytes, driven by CCR7 and CXCR5, divided patients with CAP into two clusters with a distinct inflammatory response and disease course. The peripheral immune response in patients with CAP was highly similar to that in patients with COVID-19, but increased CCR7 expression on classical monocytes was only present in CAP.

Conclusion

CAP is associated with profound cellular changes in blood that mainly relate to classical monocytes and largely overlap with the immune response detected in COVID-19.

Investigating the Influence of Cardiac Substructure Dose on Survival of Lung Cancer Patients

PURPOSE/OBJECTIVE(S)

Since RTOG 0617, the relationship between cardiac dose and overall survival for lung cancer patients (pts) is increasingly scrutinized. However, clinical cardiac substructure (CS) contours are typically lacking. In this study, we use deep learning (DL) to create accurate CS contours for a large lung cohort, and then investigate the influence of CS dose and delineation-induced dose uncertainty on overall survival.

MATERIALS/METHODS

Retrospectively included are 2075 lung cancer pts (T stage 1-4 with median survival times of 49, 36, 19, and 16 months respectively, median [range] age 70 [36-95], 58% male), treated with radiotherapy (RT) between 2009 and 2019 in a single academic institution. Re-irradiated pts were excluded. Input for DL were 70 randomly selected pts, which had manual ground-truth CS contours created on their RT planning scan. The 70 pts were split between training, validation, and test set (50, 10, 10). The trained network was then used to create 13 CS contours for the remaining pts. The influence of delineation-induced dose uncertainty on survival was investigated, first, by dilating, and second, by eroding the DL-created contours using the mean surface distance (MSD) ± 2SD of MSD, as estimated from the test set. Significant variables from univariable cox regression (CR) were included in multivariable CR (MCR). Separate MCR's include dose to one CS or the whole heart and age, gender, and log(V95%) while stratifying for T-stage, and palliative treatment. V95% is the volume receiving 95% prescribed dose. Tumor laterality was insignificant in the univariable analysis.

RESULTS

DL test output was deemed sufficient (median dice score > 0.80 and/or MSD < 2mm) for all CS but the ascending aorta, aortic valve, coronary sinus, and pulmonary veins. Max and mean dose to inferior vena cava were not significant. Table 1 shows significant CS dose parameters in MCR's for 1465 pts with complete data. Hazard ratios (HR) for max and mean dose parameters (per Gy [EQD2]) are only shown when significant for all three contour variations. Confidence intervals (CI) are based on the interval over the three contour variations. *, **, *** indicating p-values <0.05, <0.01, <0.001 respectively.

CONCLUSION

Nearly all CS dose parameters were significantly associated with reduced overall survival in MCR even after accounting for delineation uncertainty. Additional analysis is required to find the most crucial CS by solving multicollinearity, whereafter dosimetric constraints can be investigated.

Characterization of myelodysplastic syndromes hematopoietic stem and progenitor cells using mass cytometry

BACKGROUND

Myelodysplastic syndromes (MDS) at risk of transformation to acute myeloid leukemia (AML) are difficult to identify. The bone marrows of MDS patients harbor specific hematopoietic stem and progenitor cell (HSPC) abnormalities that may be associated with sub-types and risk-groups. Leukemia-associated characteristics of such cells may identify MDS patients at risk of progression to AML and provide insight in the pathobiology of MDS.

METHODS

Bone marrow samples from healthy donors (n = 10), low risk (n = 12) and high risk (n = 13) MDS patients were collected, in addition, AML samples for 5 out of 6 MDS patients that progressed. Mass cytometry was applied to assess expression of stem cell subset and leukemia-associated immunophenotype markers.

RESULTS

We analyzed the data using FlowSOM to cluster cells with similar expression of 10 commonly used stem cell markers. Metaclusters (n = 20) of these clusters represented populations of cells with a related phenotype, largely resembling known stem cell subsets. Within specific subsets, intra-cellular expression levels of pCREB, IkBα, or pS6 differed significantly between healthy bone marrow (HBM) and MDS or consecutive secondary AML samples. CD34, CD44, and CD49f expression was significantly increased in high risk MDS and AML-associated metaclusters. We identified MDS/sAML cells with aberrant phenotypes when compared to HBM. Such cells were observed in clusters of both primary MDS and secondary AML samples.

CONCLUSIONS

High-dimensional mass cytometry and computational data analyses enabled characterization of HSPC subsets in MDS and identification of leukemia stem cell populations based on their immunophenotype. Stem cells in MDS that display leukemia-associated features may predict the risk of developing AML.

INFLECT: an R-package for cytometry cluster evaluation using marker modality

Background

Current methods of high-dimensional unsupervised clustering of mass cytometry data lack means to monitor and evaluate clustering results. Whether unsupervised clustering is correct is typically evaluated by agreement with dimensionality reduction techniques or based on benchmarking with manually classified cells. The ambiguity and lack of reproducibility of sequential gating has been replaced with ambiguity in interpretation of clustering results. On the other hand, spurious overclustering of data leads to loss of statistical power. We have developed INFLECT, an R-package designed to give insight in clustering results and provide an optimal number of clusters. In our approach, a mass cytometry dataset is overclustered intentionally to ensure the smallest phenotypically different subsets are captured using FlowSOM. A range of metacluster number endpoints are generated and evaluated using marker interquartile range and distribution unimodality checks. The fraction of marker distributions that pass these checks is taken as a measure of clustering success. The fraction of unimodal distributions within metaclusters is plotted against the number of generated metaclusters and reaches a plateau of diminishing returns. The inflection point at which this occurs gives an optimal point of capturing cellular heterogeneity versus statistical power.

Results

We applied INFLECT to four publically available mass cytometry datasets of different size and number of markers. The unimodality score consistently reached a plateau, with an inflection point dependent on dataset size and number of dimensions. We tested both ConsenusClusterPlus metaclustering and hierarchical clustering. While hierarchical clustering is less computationally expensive and thus faster, it achieved similar results to ConsensusClusterPlus. The four datasets consisted of labeled data and we compared INFLECT metaclustering to published results. INFLECT identified a higher optimal number of metaclusters for all datasets. We illustrated the underlying heterogeneity within labels, showing that these labels encompass distinct types of cells.

Conclusion

INFLECT addresses a knowledge gap in high-dimensional cytometry analysis, namely assessing clustering results. This is done through monitoring marker distributions for interquartile range and unimodality across a range of metacluster numbers. The inflection point is the optimal trade-off between cellular heterogeneity and statistical power, applied in this work for FlowSOM clustering on mass cytometry datasets.

A BET Protein Inhibitor Targeting Mononuclear Myeloid Cells Affects Specific Inflammatory Mediators and Pathways in Crohn’s Disease

Background: Myeloid cells are critical determinants of the sustained inflammation in Crohn’s Disease (CD). Targeting such cells may be an effective therapeutic approach for refractory CD patients. Bromodomain and extra-terminal domain protein inhibitors (iBET) are potent anti-inflammatory agents; however, they also possess wide-ranging toxicities. In the current study, we make use of a BET inhibitor containing an esterase sensitive motif (ESM-iBET), which is cleaved by carboxylesterase-1 (CES1), a highly expressed esterase in mononuclear myeloid cells. Methods: We profiled CES1 protein expression in the intestinal biopsies, peripheral blood, and CD fistula tract (fCD) cells of CD patients using mass cytometry. The anti-inflammatory effect of ESM-iBET or its control (iBET) were evaluated in healthy donor CD14+ monocytes and fCD cells, using cytometric beads assay or RNA-sequencing. Results: CES1 was specifically expressed in monocyte, macrophage, and dendritic cell populations in the intestinal tissue, peripheral blood, and fCD cells of CD patients. ESM-iBET inhibited IL1β, IL6, and TNFα secretion from healthy donor CD14+ monocytes and fCD immune cells, with 10- to 26-fold more potency over iBET in isolated CD14+ monocytes. Transcriptomic analysis revealed that ESM-iBET inhibited multiple inflammatory pathways, including TNF, JAK-STAT, NF-kB, NOD2, and AKT signaling, with superior potency over iBET. Conclusions: We demonstrate specific CES1 expression in mononuclear myeloid cell subsets in peripheral blood and inflamed tissues of CD patients. We report that low dose ESM-iBET accumulates in CES1-expressing cells and exerts robust anti-inflammatory effects, which could be beneficial in refractory CD patients.

Stereotactic arrhythmia radioablation in europe: treatment planning benchmark results of the STOPSTORM consortium

Funding Acknowledgements

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): EU

Background

In patients with refractory ventricular tachycardia (VT), STereotactic Arrhythmia Radioablation (STAR) showed promising results for otherwise untreatable patients [1]. The STOPSTORM.eu project coordinates European efforts to clinically validate STAR and to refine protocols and guidelines to ensure treatment harmonization.

Purpose

The aim of this work is to present the current clinical STAR practise in Europe based on three examples as baseline for further optimization.

Methods

Target Volumes (TV) and Organs-at-Risk (OAR) were generated from previous consortium benchmarks and consensus definitions for three well-selected STAR cases [1]. Planning Target Volumes (PTV) were generated based on three different compensation strategies for cardiac and respiratory motion [2] and overlapped close OAR like coronary arteries or stomach in some areas. The STOPSTORM.eu members were asked to generate single fraction treatment plans with 25 Gy dose prescription based on ICRU report 91 for each case based on their clinical practise and preferences for STAR including multi-disciplinary discussion and plan approval. Resulting dose distributions were analysed independently using a customized platform for multi-center treatment planning studies [3].

Results

Twenty centers submitted 22, 23 and 22 treatment plans for case 1, 2 and 3, respectively, mostly (75% of all plans) using Intensity Modulated Arc Therapy (IMAT) with 6 MeV FFF beams (73% of the IMAT plans) among other commonly used techniques for stereotactic radiotherapy. At this current stage, used guidelines for STAR treatment planning and OAR dose limits vary greatly and are mostly based on the AAPM TG-101 report or the RAVENTA trial publication [4]. As a major finding, 73% of all plans submitted preferred close OAR sparing over achieving high PTV coverage arguing that lower doses down to 20 Gy may also result in clinical efficiency as recently suggested [5]. As a minor finding, 80% of the centers chose to override strong artifact regions originating from e.g. left ventricular assist devices.

Conclusion

From this first STOPSTORM.eu multi-center multi-platform treatment planning benchmark study we obtained important information concerning current clinical preference and practise from major European centers performing STereotactic Arrhythmia Radioablation for VT. Using the individual and strongly varying approaches of the centers, the key task for the STOPSTORM.eu project is now to find consensus in order to harmonize and optimize STAR practise in Europe.

STereotactic Arrhythmia Radioablation in Europe: critical structure contouring benchmark results of the STOPSTORM Consortium

Funding Acknowledgements

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): EU Horizon

Background/Introduction

In patients with refractory ventricular tachycardia (VT), STereotactic Arrhythmia Radioablation (STAR) showed promising results for otherwise untreatable patients [1]. The STOPSTORM.eu project coordinates European efforts to clinically validate STAR.

Purpose

The primary goal of the critical structures benchmark study was to harmonize contouring of organs at risk (OAR) for STAR within the STOPSTORM.eu consortium. The results enable to refine protocols and guidelines to ensure treatment harmonization.

Methods

Three well-selected STAR cases [2] were provided for this benchmark and sent to all radiation oncology centres within the consortium. Every case had a contrast-enhanced cardiac-CT which was already deformed to the primary planning-CT to contour the OAR in detail. Every centre was asked to contour 31 OAR’s according to literature-based guidelines. The resulting structure sets were evaluated within VelocityTM 4.1.

Results

Twenty centres participated in the critical structure contouring benchmark.

Contouring of the structures was performed with high accuracy according to the provided guidelines. The contours of common OAR’s in radiotherapy, such as the heart, lungs, stomach, oesophagus, bronchus, great vessels, and spinal canal were correctly contoured by all centres. In the substructures of the heart (chambers, valves, arteries, and nodes), deviations in the contours occurred more frequently, but no large systematic errors were found (see figure 1-2). The centres that already performed STAR treatments had markedly less difficulties with the contouring of the substructures. However, these structures do not have a consensus for treatment planning purposes and late toxicity but need to be contoured correctly for future analysis within the STOPSTORM project.

Conclusion

This large STOPSTORM.eu multi-centre critical structure benchmark study showed a high accuracy regarding standard critical structures. In the case of heart substructures some deviations occurred, which lead to new definitions for contouring these structures within the consortium. In addition, a close collaboration between radiation oncologist and cardiac electrophysiologist is recommended.

Survey results of the STOPSTORM consortium about stereotactic arrhythmia radioablation in Europe

Funding Acknowledgements

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): Horizon 2020 research and innovation programme

Background/Introduction

In patients with structural heart disease (SHD), ventricular tachycardia (VT) plays a decisive role in sudden cardiac death. VT patients are often treated with antiarrhythmic medication and catheter ablation. For refractory VTs, STereotactic Arrhythmia Radioablation (STAR) delivered to the underlying VT substrate has recently been introduced and showed promising results for otherwise untreatable patients. [1]

Purpose

The purpose of the STOPSTORM consortium is to harmonize and optimize STAR across Europe. It consists of 31 members including 24 electrophysiology and 22 radiation oncology departments performing or participating in STAR throughout eight European countries. To obtain initial overview of organization, equipment, procedures, experiences, and quality levels for STAR, a detailed survey was circulated among STOPSTORM members.

Methods

The survey included questions for electrophysiology (18 questions), radiation oncology (24 questions) and medical physics (23 questions). The survey was the first step for accreditation of the centres and therefore mandatory for all consortium members.

Results

All centres participating in STOPSTORM completed the survey. 16 centres performed a total of 84 STAR treatments until May 2021 and 11 centres already participate in clinical trials for STAR.

Annual number of VT ablations in SHD: less than 20 (17%), 20-50 (50%), 50-100 (21%), more than 100 (12%) and epicardial: less than 20 (71%), 20-50 (17%), n/s (12%). An overview of the availability of a clinical program for catheter ablation of ventricular arrhythmia with certification of the respective national cardiology society and the practice of general quality audits for ablation is given in figure 1. Participation in multicentre clinical trials in cardiology/EP were indicated by 19 departments (79%).

Target volume definition is based on invasive electroanatomical mapping during VT (96%), pace mapping (75%), reduced voltage areas (63%) and/or late ventricular potentials (75%). Half of the centres includes the clinical VT substrate, while the other half includes the whole arrhythmogenic substrate. Non-invasive surface ECG mapping has so far found little application: used clinically (13%), research purposes (8%) and evaluation (4%).

Stereotactic Body Radiotherapy experience (&gt; 10 years: 82%, &gt; 200 p.a.: 59%) is high. In all but one clinic, a dose of 25 Gy in a single fraction is applied. The prescription method, planning technique and inhomogeneity in the target volume, however, varies greatly. All departments perform patient-specific plan verifications for STAR, but with various evaluation criteria.

Conclusion

Experience in STAR within the STOPSTORM consortium is adequate, while the survey shows areas of harmonization and optimization need for substrate mapping, target delineation, dosimetry and quality assurance which will be addressed in the STOPSTORM project work-packages.

Carboxylesterase-1 Assisted Targeting of HDAC Inhibitors to Mononuclear Myeloid Cells in Inflammatory Bowel Disease

BACKGROUND AND AIMS

Histone deacetylase inhibitors [HDACi] exert potent anti-inflammatory effects. Because of the ubiquitous expression of HDACs, clinical utility of HDACi is limited by off-target effects. Esterase-sensitive motif [ESM] technology aims to deliver ESM-conjugated compounds to human mononuclear myeloid cells, based on their expression of carboxylesterase 1 [CES1]. This study aims to investigate utility of an ESM-tagged HDACi in inflammatory bowel disease [IBD].

METHODS

CES1 expression was assessed in human blood, in vitro differentiated macrophage and dendritic cells, and Crohn's disease [CD] colon mucosa, by mass cytometry, quantitative polymerase chain reaction [PCR], and immunofluorescence staining, respectively. ESM-HDAC528 intracellular retention was evaluated by mass spectrometry. Clinical efficacy of ESM-HDAC528 was tested in dextran sulphate sodium [DSS]-induced colitis and T cell transfer colitis models using transgenic mice expressing human CES1 under the CD68 promoter.

RESULTS

CES1 mRNA was highly expressed in human blood CD14+ monocytes, in vitro differentiated and lipopolysaccharide [LPS]-stimulated macrophages, and dendritic cells. Specific hydrolysis and intracellular retention of ESM-HDAC528 in CES1+ cells was demonstrated. ESM-HDAC528 inhibited LPS-stimulated IL-6 and TNF-α production 1000 times more potently than its control, HDAC800, in CES1high monocytes. In healthy donor peripheral blood, CES1 expression was significantly higher in CD14++CD16- monocytes compared with CD14+CD16++ monocytes. In CD-inflamed colon, a higher number of mucosal CD68+ macrophages expressed CES1 compared with non-inflamed mucosa. In vivo, ESM-HDAC528 reduced monocyte differentiation in the colon and significantly improved colitis in a T cell transfer model, while having limited potential in ameliorating DSS-induced colitis.

CONCLUSIONS

We demonstrate that monocytes and inflammatory macrophages specifically express CES1, and can be preferentially targeted by ESM-HDAC528 to achieve therapeutic benefit in IBD.

Epigenetic Signatures Discriminate Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis From Patients With Ulcerative Colitis

Background

Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease affecting the intra- and extrahepatic bile ducts, and is strongly associated with ulcerative colitis (UC). In this study, we explored the peripheral blood DNA methylome and its immune cell composition in patients with PSC-UC, UC, and healthy controls (HC) with the aim to develop a predictive assay in distinguishing patients with PSC-UC from those with UC alone.

Methods

The peripheral blood DNA methylome of male patients with PSC and concomitant UC, UC and HCs was profiled using the Illumina HumanMethylation Infinium EPIC BeadChip (850K) array. Differentially methylated CpG position (DMP) and region (DMR) analyses were performed alongside gradient boosting classification analyses to discern PSC-UC from UC patients. As observed differences in the DNA methylome could be the result of differences in cellular populations, we additionally employed mass cytometry (CyTOF) to characterize the immune cell compositions.

Results

Genome wide methylation analysis did not reveal large differences between PSC-UC and UC patients nor HCs. Nonetheless, using gradient boosting we were capable of discerning PSC-UC from UC with an area under the receiver operator curve (AUROC) of 0.80. Four CpG sites annotated to the NINJ2 gene were found to strongly contribute to the predictive performance. While CyTOF analyses corroborated the largely similar blood cell composition among patients with PSC-UC, UC and HC, a higher abundance of myeloid cells was observed in UC compared to PSC-UC patients.

Conclusion

DNA methylation enables discerning PSC-UC from UC patients, with a potential for biomarker development.

OS03.4.A Irradiation of the subventricular and subgranular zone and overall survival in high-grade glioma patients

BACKGROUND

Previous research has shown that neural stem cells (NSCs) in the subventricular zone (SVZ) may support the growth of glioma by recruiting new cells to the tumor. NSCs are located in the SVZ as well as in the subgranular zone (SGZ) of the hippocampus, the two neurogenic niches of the brain. This might indicate that irradiation of the SVZ and SGZ, and thereby damaging NSCs, reduces tumor growth and improves overall survival (OS). However, irradiation may also inhibit the repair capacity of healthy brain tissue by these neurogenic niches. Therefore, we investigated the effects of SVZ and SGZ irradiation dose on OS, in a cohort of high-grade glioma patients.

MATERIAL AND METHODS

We have retrospectively selected 221 patients (2014–2020) with WHO grade III and IV gliomas that underwent radiotherapy. Next to clinical baseline characteristics, T1 weighted MRI- and CT-images were collected. The SVZ and SGZ regions on the individual T1 images were delineated via non-linear registration of brain atlases. SVZ labels were created in 0.5mm isotropic MNI T1 and T2 templates, while SGZ atlas labels were available via the Hippocampus and Subfields CoBrA atlas. Next, the mean dose from the acquired SVZ and SGZ labels were extracted. The relationship between SVZ doses, SGZ doses and OS were examined using the Cox proportional hazards model and the Kaplan-Meier method (using the Log Rank test for significance).

RESULTS

For the mean dose in the SVZ, the hazard ratio (HR) was 1.024 per Gy (P = 0.002, [95% confidence interval, 1.009–1.040]) and the mean SGZ dose had a HR of 1.021 per Gy (P&lt; 0.001, [95% confidence interval, 1.012–1.031]). These results were then corrected for the following covariates: sex, age, total intracranial volume and extent of surgery. This resulted in a HR of 1.031 per Gy (P = 0,001, [95% confidence interval, 1.014–1.050]) for the mean SVZ dose, and a HR of 1.025 per Gy (P&lt; 0.001, [95% confidence interval, 1.015–1.036]) for the mean SGZ dose. Patients whose SVZ received greater than the median SVZ dose (= 31.3 Gy) showed a significant decrease in OS compared to patients who received less than the median dose (10.7 months vs 13.5 months median OS, P = 0.001). Patients whose SGZ received greater than the median SGZ dose (= 31.9) showed a significant decrease in OS compared to patients who received less than the median dose (10.7 months vs 15.1 months median OS, P&lt; 0.001).

CONCLUSION

Here, we present a large cohort of high-grade glioma patients, in which we show a statistically significant decrease in overall survival with increasing radiation dose on the SGZ and SVZ. This correlation suggests that both neurogenic niches might need to be spared during radiotherapy treatment to improve overall survival even in high-grade glioma patients. Modern radiotherapy planning and delivery options are available to implement this.

Adenovirus Armed With TNFa and IL2 Added to aPD-1 Regimen Mediates Antitumor Efficacy in Tumors Refractory to aPD-1

Immune checkpoint inhibitors such as anti-PD-1 have revolutionized the field of oncology over the past decade. Nevertheless, the majority of patients do not benefit from them. Virotherapy is a flexible tool that can be used to stimulate and/or recruit different immune populations. T-cell enabling virotherapy could enhance the efficacy of immune checkpoint inhibitors, even in tumors resistant to these inhibitors. The T-cell potentiating virotherapy used here consisted of adenoviruses engineered to express tumor necrosis factor alpha and interleukin-2 in the tumor microenvironment. To study virus efficacy in checkpoint-inhibitor resistant tumors, we developed an anti-PD-1 resistant melanoma model in vivo. In resistant tumors, adding virotherapy to an anti-PD-1 regimen resulted in increased survival (p=0.0009), when compared to anti-PD-1 monotherapy. Some of the animals receiving virotherapy displayed complete responses, which did not occur in the immune checkpoint-inhibitor monotherapy group. When adenoviruses were delivered into resistant tumors, there were signs of increased CD8 T-cell infiltration and activation, which - together with a reduced presence of M2 macrophages and myeloid-derived suppressor cells - could explain those results. T-cell enabling virotherapy appeared as a valuable tool to counter resistance to immune checkpoint inhibitors. The clinical translation of this approach could increase the number of cancer patients benefiting from immunotherapies.

Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID-19

Background

Knowledge of the pathophysiology of COVID-19 is almost exclusively derived from studies that examined the immune response in blood. We here aimed to analyse the pulmonary immune response during severe COVID-19 and to compare this with blood responses.

Methods

This was an observational study in patients with COVID-19 admitted to the intensive care unit (ICU). Mononuclear cells were purified from bronchoalveolar lavage fluid (BALF) and blood, and analysed by spectral flow cytometry; inflammatory mediators were measured in BALF and plasma.

Findings

Paired blood and BALF samples were obtained from 17 patients, four of whom died in the ICU. Macrophages and T cells were the most abundant cells in BALF, with a high percentage of T cells expressing the ƴδ T cell receptor. In the lungs, both CD4 and CD8 T cells were predominantly effector memory cells (87·3% and 83·8%, respectively), and these cells expressed higher levels of the exhaustion marker programmad death-1 than in peripheral blood. Prolonged ICU stay (>14 days) was associated with a reduced proportion of activated T cells in peripheral blood and even more so in BALF. T cell activation in blood, but not in BALF, was higher in fatal COVID-19 cases. Increased levels of inflammatory mediators were more pronounced in BALF than in plasma.

Interpretation

The bronchoalveolar immune response in COVID-19 has a unique local profile that strongly differs from the immune profile in peripheral blood. Fully elucidating COVID-19 pathophysiology will require investigation of the pulmonary immune response.