Disentangling the riddle of systemic lupus erythematosus with antiphospholipid syndrome: blood transcriptome analysis reveals a less-pronounced IFN-signature and distinct molecular profiles in venous versus arterial events

INTRODUCTION

Systemic lupus erythematosus with antiphospholipid syndrome (SLE-APS) represents a challenging SLE endotype whose molecular basis remains unknown.

METHODS

We analysed whole-blood RNA-sequencing data from 299 patients with SLE (108 SLE-antiphospholipid antibodies (aPL)-positive, including 67 SLE-APS; 191 SLE-aPL-negative) and 72 matched healthy controls (HC). Pathway enrichment analysis, unsupervised weighted gene coexpression network analysis and machine learning were applied to distinguish disease endotypes.

RESULTS

Patients with SLE-APS demonstrated upregulated type I and II interferon (IFN) pathways compared with HC. Using a 100-gene random forests model, we achieved a cross-validated accuracy of 75.6% in distinguishing these two states. Additionally, the comparison between SLE-APS and SLE-aPL-negative revealed 227 differentially expressed genes, indicating downregulation of IFN-α and IFN-γ signatures, coupled with dysregulation of the complement cascade, B-cell activation and neutrophil degranulation. Unsupervised analysis of SLE transcriptome identified 21 gene modules, with SLE-APS strongly linked to upregulation of the 'neutrophilic/myeloid' module. Within SLE-APS, venous thromboses positively correlated with 'neutrophilic/myeloid' and 'B cell' modules, while arterial thromboses were associated with dysregulation of 'DNA damage response (DDR)' and 'metabolism' modules. Anticardiolipin and anti-β2GPI positivity-irrespective of APS status-were associated with the 'neutrophilic/myeloid' and 'protein-binding' module, respectively.

CONCLUSIONS

There is a hierarchical upregulation and-likely-dependence on IFN in SLE with the highest IFN signature observed in SLE-aPL-negative patients. Venous thrombotic events are associated with neutrophils and B cells while arterial events with DDR and impaired metabolism. This may account for their differential requirements for anticoagulation and provide rationale for the potential use of mTOR inhibitors such as sirolimus and the direct fIIa inhibitor dabigatran in SLE-APS.

Enhanced medullary and extramedullary granulopoiesis sustain the inflammatory response in lupus nephritis

OBJECTIVES

In SLE, deregulation of haematopoiesis is characterised by inflammatory priming and myeloid skewing of haematopoietic stem and progenitor cells (HSPCs). We sought to investigate the role of extramedullary haematopoiesis (EMH) as a key player for tissue injury in systemic autoimmune disorders.

METHODS

Transcriptomic analysis of bone marrow (BM)-derived HSPCs from patients with SLE and NZBW/F1 lupus-prone mice was performed in combination with DNA methylation profile. Trained immunity (TI) was induced through β-glucan administration to the NZBW/F1 lupus-prone model. Disease activity was assessed through lupus nephritis (LN) histological grading. Colony-forming unit assay and adoptive cell transfer were used to assess HSPCs functionalities.

RESULTS

Transcriptomic analysis shows that splenic HSPCs carry a higher inflammatory potential compared with their BM counterparts. Further induction of TI, through β-glucan administration, exacerbates splenic EMH, accentuates myeloid skewing and worsens LN. Methylomic analysis of BM-derived HSPCs demonstrates myeloid skewing which is in part driven by epigenetic tinkering. Importantly, transcriptomic analysis of human SLE BM-derived HSPCs demonstrates similar findings to those observed in diseased mice.

CONCLUSIONS

These data support a key role of granulocytes derived from primed HSPCs both at medullary and extramedullary sites in the pathogenesis of LN. EMH and TI contribute to SLE by sustaining the systemic inflammatory response and increasing the risk for flare.

The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease

Chronic inflammatory diseases (CIDs), including inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are thought to emerge from an impaired complex network of inter- and intracellular biochemical interactions among several proteins and small chemical compounds under strong influence of genetic and environmental factors. CIDs are characterised by shared and disease-specific processes, which is reflected by partially overlapping genetic risk maps and pathogenic cells (e.g., T cells). Their pathogenesis involves a plethora of intracellular pathways. The translation of the research findings on CIDs molecular mechanisms into effective treatments is challenging and may explain the low remission rates despite modern targeted therapies. Modelling CID-related causal interactions as networks allows us to tackle the complexity at a systems level and improve our understanding of the interplay of key pathways. Here we report the construction, description, and initial applications of the SYSCID map (https://syscid.elixir-luxembourg.org/), a mechanistic causal interaction network covering the molecular crosstalk between IBD, RA and SLE. We demonstrate that the map serves as an interactive, graphical review of IBD, RA and SLE molecular mechanisms, and helps to understand the complexity of omics data. Examples of such application are illustrated using transcriptome data from time-series gene expression profiles following anti-TNF treatment and data from genome-wide associations studies that enable us to suggest potential effects to altered pathways and propose possible mechanistic biomarkers of treatment response.

A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies

Objective

A blood-based biomarker is needed to assess lupus nephritis (LN) disease activity, minimizing the need for invasive kidney biopsies. Long non-coding RNAs (lncRNAs) are known to regulate gene expression, appear to be stable in human plasma, and can serve as non-invasive biomarkers.

Methods

Transcriptomic data of whole blood samples from 74 LN patients and 20 healthy subjects (HC) were analyzed to identify differentially expressed (DE) lncRNAs associated with quiescent disease and flares. Weighted gene co-expression network analysis (WGCNA) was performed to uncover lncRNAs with a central role (hub lncRNAs) in regulating key biological processes that drive LN disease activity. The association of hub lncRNAs with disease activity was validated using RT-qPCR on an independent cohort of 15 LN patients and 9 HC. cis- and trans-targets of validated lncRNAs were explored in silico to examine potential mechanisms of their action.

Results

There were 444 DE lncRNAs associated with quiescent disease and 6 DE lncRNAs associated with flares (FDR <0.05). WGCNA highlighted IFN signaling and B-cell activity/adaptive immunity as the most significant processes contributing to nephritis activity. Four disease-activity-associated lncRNAs, namely, NRIR, KLHDC7B-DT, MIR600HG, and FAM30A, were detected as hub genes and validated in an independent cohort. NRIR and KLHDC7B-DT emerged as potential key regulators of IFN-mediated processes. Network analysis suggests that FAM30A and MIR600HG are likely to play a central role in the regulation of B-cells in LN through cis-regulation effects and a competing endogenous RNA mechanism affecting immunoglobulin gene expression and the IFN-λ pathway.

Conclusions

The expression of lncRNAs NRIR, KLHDC7B-DT, FAM30A, and MIR600HG were associated with disease activity and could be further explored as blood-based biomarkers and potential liquid biopsy on LN.

The genomic landscape of ANCA-associated vasculitis: Distinct transcriptional signatures, molecular endotypes and comparison with systemic lupus erythematosus

Introduction

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAVs) present with a complex phenotype and are associated with high mortality and multi-organ involvement. We sought to define the transcriptional landscape and molecular endotypes of AAVs and compare it to systemic lupus erythematosus (SLE).

Methods

We performed whole blood mRNA sequencing from 30 patients with AAV (granulomatosis with polyangiitis/GPA and microscopic polyangiitis/MPA) combined with functional enrichment and network analysis for aberrant pathways. Key genes and pathways were validated in an independent cohort of 18 AAV patients. Co-expression network and hierarchical clustering analysis, identified molecular endotypes. Multi-level transcriptional overlap analysis to SLE was based on our published data from 142 patients.

Results

We report here that “Pan-vasculitis” signature contained 1,982 differentially expressed genes, enriched in leukocyte differentiation, cytokine signaling, type I and type II IFN signaling and aberrant B-T cell immunity. Active disease was characterized by signatures linked to cell cycle checkpoints and metabolism pathways, whereas ANCA-positive patients exhibited a humoral immunity transcriptional fingerprint. Differential expression analysis of GPA and MPA yielded an IFN-g pathway (in addition to a type I IFN) in the former and aberrant expression of genes related to autophagy and mRNA splicing in the latter. Unsupervised molecular taxonomy analysis revealed four endotypes with neutrophil degranulation, aberrant metabolism and B-cell responses as potential mechanistic drivers. Transcriptional perturbations and molecular heterogeneity were more pronounced in SLE. Molecular analysis and data-driven clustering of AAV uncovered distinct transcriptional pathways that could be exploited for targeted therapy.

Discussion

We conclude that transcriptomic analysis of AAV reveals distinct endotypes and molecular pathways that could be targeted for therapy. The AAV transcriptome is more homogenous and less fragmented compared to the SLE which may account for its superior rates of response to therapy.

Microglia activation in the presence of intact blood-brain barrier and disruption of hippocampal neurogenesis via IL-6 and IL-18 mediate early diffuse neuropsychiatric lupus

INTRODUCTION

Inflammatory mediators are detected in the cerebrospinal fluid of systemic lupus erythematosus patients with central nervous system involvement (NPSLE), yet the underlying cellular and molecular mechanisms leading to neuropsychiatric disease remain elusive.

METHODS

We performed a comprehensive phenotyping of NZB/W-F1 lupus-prone mice including tests for depression, anxiety and cognition. Immunofluorescence, flow cytometry, RNA-sequencing, qPCR, cytokine quantification and blood-brain barrier (BBB) permeability assays were applied in hippocampal tissue obtained in both prenephritic (3-month-old) and nephritic (6-month-old) lupus mice and matched control strains. Healthy adult hippocampal neural stem cells (hiNSCs) were exposed ex vivo to exogenous inflammatory cytokines to assess their effects on proliferation and apoptosis.

RESULTS

At the prenephritic stage, BBB is intact yet mice exhibit hippocampus-related behavioural deficits recapitulating the human diffuse neuropsychiatric disease. This phenotype is accounted by disrupted hippocampal neurogenesis with hiNSCs exhibiting increased proliferation combined with decreased differentiation and increased apoptosis in combination with microglia activation and increased secretion of proinflammatory cytokines and chemokines. Among these cytokines, IL-6 and IL-18 directly induce apoptosis of adult hiNSCs ex vivo. During the nephritic stage, BBB becomes disrupted which facilitates immune components of peripheral blood, particularly B-cells, to penetrate into the hippocampus further augmenting inflammation with locally increased levels of IL-6, IL-12, IL-18 and IL-23. Of note, an interferon gene signature was observed only at nephritic-stage.

CONCLUSION

An intact BBB with microglial activation disrupting the formation of new neurons within the hippocampus represent early events in NPSLE. Disturbances of the BBB and interferon signature are evident later in the course of the disease.

ATR-mediated DNA damage responses underlie aberrant B cell activity in systemic lupus erythematosus

B cells orchestrate autoimmune responses in patients with systemic lupus erythematosus (SLE), but broad-based B cell-directed therapies show only modest efficacy while blunting humoral immune responses to vaccines and inducing immunosuppression. Development of more effective therapies targeting pathogenic clones is a currently unmet need. Here, we demonstrate enhanced activation of the ATR/Chk1 pathway of the DNA damage response (DDR) in B cells of patients with active SLE disease. Treatment of B cells with type I IFN, a key driver of immunity in SLE, induced expression of ATR via binding of interferon regulatory factor 1 to its gene promoter. Pharmacologic targeting of ATR in B cells, via a specific inhibitor (VE-822), attenuated their immunogenic profile, including proinflammatory cytokine secretion, plasmablast formation, and antibody production. Together, these findings identify the ATR-mediated DDR axis as the orchestrator of the type I IFN-mediated B cell responses in SLE and as a potential novel therapeutic target.

Combined – whole blood and skin fibroblasts- transcriptomic analysis in Psoriatic Arthritis reveals molecular signatures of activity, resistance and early response to treatment

Background

An interplay between immune cells and resident skin and joint stromal cells is implicated in psoriatic arthritis (PsA), yet the mechanisms remain elusive with a paucity of molecular biomarkers for activity and response. Combined transcriptomic and immunophenotypic analysis of whole blood and skin fibroblasts could provide further insights.

Methods

Whole blood RNA-seq was performed longitudinally in 30 subjects with PsA at the beginning, one and six months after treatment, with response defined at six months. As control groups, 10 healthy individuals and 10 subjects with rheumatoid arthritis (RA) were recruited combined with public datasets from patients with psoriasis (PsO) and systemic lupus erythematous (SLE). Differential expression analysis and weighted gene co-expression network analysis were performed to identify gene expression signatures, while deconvolution and flow cytometry to characterize the peripheral blood immune cell profile. In a subset of affected and healthy individuals, RNA-seq of skin fibroblasts was performed and subjected to CellChat analysis to identify the blood-skin fibroblast interaction network.

Results

PsA demonstrated a distinct “activity” gene signature in the peripheral blood dominated by TNF- and IFN-driven inflammation, deregulated cholesterol and fatty acid metabolism and expansion of pro-inflammatory non-classical monocytes. Comparison with the blood transcriptome of RA, PsO, and SLE revealed a “PsA-specific signature” enriched in extracellular matrix remodeling. This was further supported by the skin fibroblast gene expression profile, displaying an activated, proliferating phenotype, and by skin-blood interactome analysis revealing interactions with circulating immune cells through WNT, PDGF and immune-related semaphorins. Of note, resistance to treatment was associated with upregulation of genes involved in TGFβ signaling and angiogenesis and persistent increase of non-classical monocytes. Differentially expressed genes related to platelet activation and hippo signaling discriminated responders and non-responders as early as one month after treatment initiation.

Conclusion

Transcriptome analysis of peripheral blood and skin fibroblasts in PsA reveals a distinct disease activity signature and supports the involvement of skin fibroblasts through their activation and interaction with circulating immune cells. Aberrant TGFβ signaling and persistently increased non-classical monocytes characterize treatment-resistant PsA, with pro-inflammatory pathways related to platelet activation and Hippo signaling predicting early response to treatment.

Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis

Objectives

Patients with lupus nephritis (LN) are in urgent need for early diagnosis and therapeutic interventions targeting aberrant molecular pathways enriched in affected kidneys.

Methods

We used mRNA-sequencing in effector (spleen) and target (kidneys, brain) tissues from lupus and control mice at sequential time points, and in the blood from 367 individuals (261 systemic lupus erythematosus (SLE) patients and 106 healthy individuals). Comparative cross-tissue and cross-species analyses were performed. The human dataset was split into training and validation sets and machine learning was applied to build LN predictive models.

Results

In murine SLE, we defined a kidney-specific molecular signature, as well as a molecular signature that underlies transition from preclinical to overt disease and encompasses pathways linked to metabolism, innate immune system and neutrophil degranulation. The murine kidney transcriptome partially mirrors the blood transcriptome of patients with LN with 11 key transcription factors regulating the cross-species active LN molecular signature. Integrated protein-to-protein interaction and drug prediction analyses identified the kinases TRRAP, AKT2, CDK16 and SCYL1 as putative targets of these factors and capable of reversing the LN signature. Using murine kidney-specific genes as disease predictors and machine-learning training of the human RNA-sequencing dataset, we developed and validated a peripheral blood-based algorithm that discriminates LN patients from normal individuals (based on 18 genes) and non-LN SLE patients (based on 20 genes) with excellent sensitivity and specificity (area under the curve range from 0.80 to 0.99).

Conclusions

Machine-learning analysis of a large whole blood RNA-sequencing dataset of SLE patients using human orthologs of mouse kidney-specific genes can be used for early, non-invasive diagnosis and therapeutic targeting of LN. The kidney-specific gene predictors may facilitate prevention and early intervention trials.

POS0210 A PREDOMINANT NON-SPECIFIC INTERSTITIAL PNEUMONIA PATTERN AND ABERRANT TRANSCRIPTOMIC NEUTROPHIL-MEDIATED IMMUNITY CHARACTERIZE A CONTEMPORARY RA-ILD COHORT

Background

Lung involvement is the most common extra-articular manifestation. Rheumatoid arthritis related interstitial lung disease (RA-ILD) comprises a heterogeneous group of parenchymal lung disorders classified by distinct clinical, pathologic, and radiographic features. According to the current paradigm, circulating immune complexes and aberrant neutrophil extracellular trap formation (NETosis) contribute to disease pathogenesis.

Objectives

To characterize the pattern of lung disease in “Attikon” RA-ILD cohort and develop insights about the pathophysiologic mechanisms via whole blood RNA sequencing.

Methods

Retrospective and prospective study to identify clinical, laboratory and radiologic characteristics of patients with RA and pulmonary manifestations in the “Attikon” RA-ILD cohort. Changes in pulmonary function tests (PFTs), pattern of lung involvement (chest HRCT), disease activity (DAS28-ESR) and incidence of complications and comorbidities, were prospectively analyzed during the one-year follow-up period. Peripheral blood was collected in a subset of RA-ILD (n=11) and control RA patients (n=9) for RNA isolation and RNA sequencing. The gene expression profile of RA-ILD was inferred through differential gene expression analysis, followed by pathway and enrichment analyses.

Results

114 patients with RA-ILD were included [67% female, mean (SD) age at diagnosis 71.5 (9) years, 58% seropositive]. Non-specific interstitial pneumonia (NSIP) was the radiologic pattern most frequently observed (52%), followed by usual interstitial pneumonia (UIP) (24%). RA was diagnosed after ILD in 40% of patients. Mean (SD) FVC and DLCOsb at baseline was 80.5 (19.2) and 55.4 (19.5), respectively. Disease activity was lower in seropositive compared to seronegative both at baseline and at 1-year follow-up (p=0.025). PFTs at 12 months from baseline had been stabilized. Respiratory infections were observed in 17.6% of patients during the first year of follow-up, more common in the NSIP vs UIP group (p=0.01), possibly due to the higher doses of glucocorticoids in NSIP patients. RNA-sequencing analysis revealed a distinct gene expression profile in RA-ILD, characterized by the activation of type I interferon response, neutrophil activation and degranulation, and CCR1 chemokine interactions.

Conclusion

NSIP is the most frequent pattern of ILD in this RA-ILD cohort, carrying a higher risk for respiratory infections probably related to higher doses of glucocorticoid used. Myeloid cells’ migration via CCR1 and the formation of pro-inflammatory and pro-fibrotic NETs by activated neutrophils may contribute to RA-ILD pathogenesis.

References

[1]Y Dai et al, Rheumatoid arthritis–associated interstitial lung disease: an overview of epidemiology, pathogenesis and management Clin Rheumatol. 2021 Apr;40(4):1211-1220

[2]X Zulma Yunt et al, Lung Disease in Rheumatoid Arthritis Rheum Dis Clin North Am. 2015 May;41(2):225-36

Table 1.

Patients’ characteristics with RA-ILD in Attikon cohort

Patients CharacteristicsN=114Mean age71.5±9Female: Male76/38Smoking (current/ex)23/43Arterial hypertension71Diabetes mellitus32Dyslipidemia52COPD/BA17Thyroid disease30Latent TB17Seropositive66Diagnosis RA before ILD34Diagnosis RA after ILD45NSIP59UIP27Mixed NSIP-UIP5Organizing Pneumonia (OP)17Nodules21

Disclosure of Interests

None declared

POS0461 DISRUPTED HIPPOCAMPAL NEUROGENESIS MEDIATED BY IL-6 AND IL-18 INDUCE NEUROPSYCHIATRIC CHANGES IN MURINE LUPUS

Background

Systemic lupus erythematosus (SLE) frequently affects the nervous system (NPSLE), however, its pathogenesis is only partly understood. We have previously characterized the behavioral phenotype of the NZΒ/W-F1 lupus-prone mouse which recapitulates the NPSLE phenotype exhibiting hippocampal-linked behavior including depressive-like disorder, anxiety and cognitive impairment both at early and late stages of the disease characterized by a profound hippocampal inflammatory response1,2. Defective hippocampal neural stem cell (hNSC) response is associated with cognitive dysfunction, depression and anxiety, all of which represent common neuropsychiatric features of both human and murine SLE.

Objectives

To further investigate the hippocampal neurogenesis in lupus mice and determine its involvement in disease pathogenesis.

Methods

All experiments were performed in female NZW/NZB F1 and C57BL/6 (WT) mice at the age of 3 months (pre-nephritic) and 6 months (nephritic stage) (n=5-8/condition/experiment). Neurogenesis was assessed in sagittal sections of hippocampus by immunohistochemical staining (DCX, Sox2, GFAP, Iba1) and morphological criteria. RNA-sequencing was performed in hippocampal tissue followed by pathway and enrichment analysis. Apoptosis (cleaved-caspase 3) and immune cell infiltration (CD11b, CD45, Ly6G, Ly6C, MHC-II, CD4, CD8, B220, Iba1, CD80, CD86, Argianse-1, iNOS) were assessed by flow-cytometry. Cytokines levels were measured by Legendplex. Ex vivo assays were performed in adult hippocampal neural stem cells extracted by 2-month-old female WT mice.

Results

We identified a profound disruption (~2-fold) of hippocampal neurogenesis (decreased DCX+ cells) both at 3 ad 6 month-old lupus mice together with decreased differentiated cells in both time-points, suggesting that lupus mice exhibit impaired neuronal differentiation. Although the number of the neuronal precursors radial glial-like cells (RGLs) was normal at pre-nephritic stage, lupus mice express increased number of both activated RGLs (Sox2+/GFAP+) and proliferating neuronal progenitors (Sox2+ cells) indicating enhanced self-renewal ability of neural precursors and augmented proliferation. Levels of cleaved-caspase 3 were elevated in lupus hippocampus supporting increased hippocampal apoptosis. Transcriptomic analysis of hippocampal tissue revealed a profound inflammatory response in lupus mice. Flow-cytometry analyses showed a pronounced immune cell trafficking in lupus hippocampus with a myeloid predominant response –involving predominantly the microglia- both at early and late stages of the disease. Multiplex assays revealed elevated levels of IL-6 and IL-18 in lupus hippocampus. Ex vivo exposure of adult hNSCs to IL-6 or IL-18 promoted cell proliferation and induced apoptosis.

Conclusion

The NZB/W-F1 mouse model of SLE exhibits defective neurogenesis due to increased apoptosis, and decreased differentiation of neuronal progenitors. Inflammation in lupus hippocampus results in elevated levels of IL-6 and IL-18 with both cytokines negatively affecting the hNSCs response. IL-6 and IL-18 may induce behavioral changes in NZB/W-F1 lupus mediated by altered neurogenesis and may represent therapeutic targets in NPSLE.

References

[1]Nikolopoulos, D., et al. “THU0223 THE NEUROPSYCHIATRIC PHENOTYPE OF NZB/W LUPUS-PRONE MOUSE MODEL AT PRE-NEPHRITIC AND NEPHRITIC STAGES OF THE DISEASE: MURINE MODEL RECAPITULATES HUMAN DISEASE.” (2020): 334-335. http://dx.doi.org/10.1136/annrheumdis-2020-eular.1807

[2]Nikolopoulos D. et al. “OP0040 HIPPOCAMPAL IMMUNE CELL TRAFFICKING AND A MYELOID PREDOMINANT INFLAMMATORY RESPONSE WITH ENHANCED ANTIGEN PRESENTATION AND DECREASED LEVELS OF NEUROTRANSMITTERS UNDERLY THE NEUROPSYCHIATRIC PHENOTYPE OF THE NZW/NZB MURINE LUPUS MODEL.” (2021): 2021. http://dx.doi.org/10.1136/annrheumdis-2021-eular.3972

Acknowledgements

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742390)

Disclosure of Interests

None declared.

Molecular Taxonomy of Systemic Lupus Erythematosus Through Data-Driven Patient Stratification: Molecular Endotypes and Cluster-Tailored Drugs

Objectives

Treatment of Systemic Lupus Erythematosus (SLE) is characterized by a largely empirical approach and relative paucity of novel compound development. We sought to stratify SLE patients based on their molecular phenotype and identify putative therapeutic compounds for each molecular fingerprint.

Methods

By the use of whole blood RNA-seq data from 120 SLE patients, and in a data-driven, clinically unbiased manner, we established modules of commonly regulated genes (molecular endotypes) and re-stratified patients through hierarchical clustering. Disease activity and severity were assessed using SLEDAI-2K and Lupus Severity Index, respectively. Through an in silico drug prediction pipeline, we investigated drugs currently in use, tested in lupus clinical trials, and listed in the iLINCS prediction databases, for their ability to reverse the gene expression signatures in each molecular endotype. Drug repurposing analysis was also performed to identify perturbagens that counteract group-specific SLE signatures.

Results

Molecular taxonomy identified five lupus endotypes, each characterized by a unique gene module enrichment pattern. Neutrophilic signature group consisted primarily of patients with active lupus nephritis, while the B-cell expression group included patients with constitutional features. Patients with moderate severity and serologic activity exhibited a signature enriched for metabolic processes. Mild disease was distributed in two groups, exhibiting enhanced basic cellular functions, myelopoiesis, and autophagy. Bortezomib was predicted to reverse disturbances in the "neutrophilic" cluster, azathioprine and ixazomib in the "B-cell" cluster, and fostamatinib in the "metabolic" patient subgroup.

Conclusion

The clinical spectrum of SLE encompasses distinct molecular endotypes, each defined by unique pathophysiologic aberrancies potentially reversible by distinct compounds.

OP0019 DEFINING SYSTEMIC LUPUS ERYTHEMATOSUS MOLECULAR TAXONOMY THROUGH DATA-DRIVEN RESTRATIFICATION AND IDENTIFICATION OF CLUSTER-TAILORED DRUGS FOR A PERSONALIZED MEDICINE APPROACH

Background:

Systemic Lupus Erythematosus (SLE) is characterized by lack of treatment diversity, largely empirical treatment decisions, and paucity of novel compound development.

Objectives:

We sought to stratify SLE patients based on their molecular phenotype and predict personalized therapeutic compounds, tailored to the molecular fingerprint of each subgroup.

Methods:

We performed a co-expression analysis using our publicly available whole blood RNA-seq data of 120 SLE patients. Modules of commonly regulated genes were established and used to re-stratify patients through hierarchical clustering, in a data-driven, clinically independent, manner. Next, we established an in silico, subgroup signature-based, drug prediction pipeline. Investigated drugs included both those currently in practice and those who have been tested in SLE clinical trials and are listed in the iLINCS prediction databases. Finally, drug repurposing analysis was performed, to identify novel perturbagens that counteract group-specific SLE signatures.

Results:

Molecular taxonomy identified five distinct lupus molecular endotypes, each characterized by a unique gene module enrichment pattern. A group defined by strong neutrophilic signature encompassed almost exclusively patients with active nephritis, while a B-cell expression group included patients with severe lupus phenotype. Metabolic processes enrichment defined a group of patients with disease of moderate severity and serologic activity. Finally, patients with mild lupus features were distributed in two groups, which demonstrated enhanced basic cellular functions, myelopoiesis, and autophagy. The ability of different compounds to reverse the transcriptomic aberrancies observed in each patient group was examined. Bortezomib efficiently reversed disturbances in the “neutrophilic” cluster. Azathioprine and ixazomib might be a reasonable option for patients of the “B-cell” cluster, whereas fostamatinib appeared efficacious for the “Metabolism” patient subgroup.

Conclusion:

The clinical spectrum of SLE encompasses distinct molecular endotypes, each defined by unique pathophysiologic aberrancies, which can be utilized to guide personalized care and direct novel compound development.

Acknowledgements:

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742390).

Disclosure of Interests:

None declared

OP0040 HIPPOCAMPAL IMMUNE CELL TRAFFICKING AND A MYELOID PREDOMINANT INFLAMMATORY RESPONSE WITH ENHANCED ANTIGEN PRESENTATION AND DECREASED LEVELS OF NEUROTRANSMITTERS UNDERLY THE NEUROPSYCHIATRIC PHENOTYPE OF THE NZW/NZB MURINE LUPUS MODEL

Background:

Neuropsychiatric events are common in patients with systemic lupus erythematosus (SLE), yet the underlying pathogenesis remains ill-defined, as the access to brain tissue is limited. We have previously shown that NZW/NZB F1 murine lupus model recapitulates the neuropsychiatric lupus phenotype including depressive-like behavior, increased rates of anxiety, cognitive dysfunction and motor disturbances, both at pre-nephritic and nephritic stages of the disease.

Objectives:

To dissect specific regions in the brain, which account for this phenotype and elucidate inflammatory and non-inflammatory mechanisms involved.

Methods:

Four distinct brain regions (hippocampus, amygdala, striatum and pre-frontal cortex) were dissected from brains of female C57BL/6 (WT) and NZW/NZB F1 mice at the age of 3 months (pre-nephritic) and 6 months (nephritic stage) (n=5-8/condition/experiment). Since most of the behavioral phenotype corresponds to the hippocampus, we first examined in depth the hippocampal pathology by bulk RNA sequencing, measurements of neurotransmitters levels via high-performance liquid chromatography (HPLC) and by immunophenotyping via flow cytometry analyses. For comparisons, statistical significance was indicated as a two-sided P<0.05.

Results:

Transcriptomic analysis revealed aberrant immune mediated response in the hippocampus of 6 month-old lupus mice compared to WT. Specifically, inflammatory pathways including both innate and adaptive immune responses, increased cytokine production, increased antigen presentation and immune cell trafficking, along with increased apoptosis and decreased cell proliferation suggest that immune aberrancies may lead to neuronal damage. These aberrancies were present in mice at 3 month-old, yet were progressed with time being more prominent at 6 month of age in lupus hippocampus. The RNA sequencing date were validated by immunophenotyping on lupus hippocampus demonstrating increased reactive GFAP+ astrocytes both at 3 and 6-month old mice. Activated IBA1+ microglia and CD11b+CD45hi CNS myeloid cells were increased only at 6 months of age. Furthermore, increased immune cell infiltration from the periphery including lymphocytes (CD45+CD11b-) mainly T cells (CD4+/CD8+) and monocytes (CD45+CD11b+Ly6G-Ly6C+), was evident only in 6 month-old lupus hippocampus compared to WT. Importantly, microglia cells in lupus hippocampus at 6 but not at 3 month of age, exhibited increased expression of antigen presenting markers including CD80, CD86 and MHC-II indicating that microglia cells may carry out the antigen presentation process seen in transcriptomic data. Low levels of serotonin and noradrenaline were observed at both 3 and 6 months of age in lupus mice; these aberrancies were mainly attributed to decreased serotonin synthesis as evidenced by intact serotonin metabolism (no differences were observed at its metabolite: 5-hydroxyindoleacetic acid). Analysis of the remaining regions of the brain combined with studies of metabolic activities of various brain regions by PET-CT scanning is in progress.

Conclusion:

Immune cell trafficking from the periphery combined with marked inflammatory response in the hippocampus underlie the neuropsychiatric phenotype in NZW/B murine lupus. Our data indicate increased expression of activated myeloid cells -including microglia- in the hippocampus of lupus mice culminating in increased antigen presentation and decreased neurotransmitter levels.

References:

[1]Nikolopoulos, D., et al. “THU0223 THE NEUROPSYCHIATRIC PHENOTYPE OF NZB/W LUPUS-PRONE MOUSE MODEL AT PRE-NEPHRITIC AND NEPHRITIC STAGES OF THE DISEASE: MURINE MODEL RECAPITULATES HUMAN DISEASE.” (2020): 334-335.

Acknowledgements:

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742390)

Disclosure of Interests:

None declared

Mitophagy Balance in Various Cell Subsets in Patients with ANCA-Associated Vasculitis and Correlation with the Presence of Anti-Neutrophil Cytoplasmic Antibodies

ANCA-associated vasculitides (AAVs) are characterised by heterogeneous molecular and pathophysiological traits, causing ambiguous differential diagnosis and taxonomy. Response to therapy has proven far from successful, contributing to high mortality. Transcriptome analysis of different vasculitis subtypes adds new leads in elucidating mechanisms of disease and the role of specific cell subsets to them. Recent findings have shown that mitophagy is a procedure whose imbalance could lead to immune dysregulation with certain involvement to autoimmunity. Inflammatory response related mitophagy is yet to be described in AAVs. We here describe a research protocol to investigate mitophagy in monocytes, neutrophils, and T cells in AAV patients, and the relationship of disturbed mitophagy with ANCA seropositivity.

Are vaccine shortages a relevant public health issue in Europe?

Background

National immunisation programmes depend on an adequate supply of vaccines but shortages have become more frequent globally in recent years. Vaccine shortages can lead to missed opportunities for vaccination and a greater risk of occurrence of vaccine-preventable diseases (VPD).

Methods

The EU-Joint Action on Vaccination is a European Commission-funded project* which aims to strengthen cooperation between European countries against VPDs, including improvement of vaccine supply and preparedness. In this context, from February to May 2019, we conducted a survey amongst persons in charge of national immunisation programmes or of vaccine supply/procurement in EU/EEA, to collect information on vaccine shortages in the previous three years.

Results

Twenty-one of 28 invited countries responded, of which 19 reported at least one shortage, for a total of 115 shortage events. The median number of shortages per country was 5 (range 0-15). At the time of survey completion, there were ongoing shortages in six countries. DT/dt-containing combination vaccines, hepatitis A, hepatitis B and BCG vaccines were the most frequently involved vaccines. Supply and production issues, and global shortage, were the most frequent causes. Median duration of shortages was five months; 34% caused a disruption in immunization services. Procurement and purchase methods varied by country. Only half of countries have recommendations or procedures in place to address shortages.

Conclusions

Vaccine shortages are a serious public health issue in the EU. Causes are complex and multifaceted and more research is needed to understand the economic and market-related causes. Improved communication between public health authorities, manufacturers and regulatory agencies is essential. Procurement and tender mechanisms should be improved. In case of vaccine shortages, all countries should have procedures or recommendation in place regarding the use of alternative vaccines or vaccination schedules.

Key messages

Vaccine shortages are a relevant public health issue in the EU. More research is needed on the complex and multifaceted causes of vaccine shortages. Timely communication between supply and demand is needed and procurement and tender mechanisms should be improved.

Who is at risk for measles in Italy? Continued measles outbreaks in 2019 and barriers to elimination

Background

Measles is a highly contagious vaccine preventable disease that can lead to serious complications, including death. All five regions of the World Health Organization have set targets to eliminate measles. In Italy, measles vaccination was introduced in 1976, with sustained low uptake in the 1980s and 1990s. Uptake improved in subsequent years but never reached 95% coverage required for elimination. Two doses of measles-mumps-rubella (MMR) vaccine are recommended (at 12-15 months and 5-6 years respectively). Since July 2017, MMR vaccine has become mandatory for all children up to 16 years of age. Large outbreaks continue to occur, with over 8.000 cases reported in 2017-2018.

Methods

We analysed measles cases reported to the national integrated measles and rubella surveillance system during January 1 - December 31, 2019.

Results

From 1 January to 31 December 2019, 1,627 cases (87% laboratory-confirmed), were reported from all 21 administrative regions. National incidence was 27 cases/million. Overall, 86% of cases were unvaccinated. Median age was 30 years but the highest incidence was in infants below one year of age. Ninety-six cases were reported amongst healthcare workers and transmission in the healthcare setting was frequent. Overall, 31% of cases reported complications, including three cases of encephalitis (in two adults and one child) and one death in an adult patient. Complications were more frequent in cases ≥20 years of age compared to younger patients. Forty-six percent of cases were hospitalised.

Conclusions

The median age of cases has increased further in 2019 compared to 2017 (27 years) and 2018 (28 years). The proportions of complicated and hospitalised cases are high, this may be due to the high median age of cases but also to underreporting from general practitioners who are likely to see milder cases. Wide immunity gaps among adults (including healthcare workers) and nosocomial transmission are major challenges to measles elimination in Italy.

Key messages

Measles is still endemic in Italy and large outbreaks continue to occur, with a significant public health impact. Wide immunity gaps among adults (including healthcare workers) and nosocomial transmission are major challenges to measles elimination in Italy.

P0359CROSS-TISSUE AND MURINE-HUMAN COMPARATIVE TRANSCRIPTOME ANALYSES IDENTIFY TARGETABLE GENES FOR HUMAN SYSTEMIC LUPUS ERYTHEMATOUS AND LUPUS NEPHRITIS

Background and Aims

Systemic Lupus Erythematosus (SLE) is a complex disease associated with non-synchronous multi-tissue dysfunction of varying severity. Involvement of major organs, such as kidneys, contributes significantly to morbidity and mortality. We sought to unravel new pathways to be used as potential biomarkers and therapeutic targets. To this end, we compared the patterns of gene transcription -as determined by the use of RNA-sequencing- across tissues between healthy and lupus-prone mice at different stages of the disease, and explored their implications for human disease and prediction of kidney involvement, in our whole blood RNA sequencing dataset comprised of 120 SLE [55 lupus nephritis (LN), 65 non-LN] patients and 58 healthy individuals (HI).

Method

NZB/W-F1 lupus-prone mice were sacrificed at the pre-puberty, pre-autoimmunity and nephritic stage. Age-matched C57BL/6 mice were used as controls. An “effector” tissue (spleen) and major end-organ tissues (kidneys, brain) were collected. Total RNA was isolated, and mRNA-sequencing was performed. Differential expression and time-series analyses were performed using DESeq2. Differentially expressed genes (DEGs) were hierarchically clustered and functionally interpreted using gProfiler enrichment analysis. Human orthologous genes of mouse common DEGs in each tissue and across all disease stages, were compared to human DEGs. Using machine learning techniques, human orthologs identified in the common DEGs across all stages in the kidneys of lupus-prone vs healthy mice were used to predict kidney involvement in the human dataset, which was split in training and validation sets.

Results: Gene signatures: the common cross-tissue signature was identified by the comparison of DEGs between tissues of lupus-prone vs healthy mice at each stage of the disease. A total 134 genes (including C4A, LYRM7 and HDDC3) were found, suggesting their involvement in a common pathogenic mechanism across “effector” and end-organ tissues. Tissue-specific signatures showed enrichment of FCERI mediated NF-kB activation pathway in the spleen, steroid hormone biosynthesis pathway in the kidney and phosphatidylcholine metabolic process in the brain, suggesting distinct pathways implicated in end-organ injury.

Comparative murine-human transcriptome analysis: 76 human orthologs (including CCL5, IFIT and HLA genes) identified in the murine spleen signature were also differentially expressed in SLE patients vs HI, suggesting their involvement in systemic autoimmunity. A total of 68 human orthologs (including FCGR2A, C1R and JAK1) identified in the mouse kidney-signature and 25 human orthologs (including APOA2) identified in the mouse brain-signature, were differentially expressed in LN patients vs HI and neuropsychiatric SLE patients vs HI, respectively.

Kidney involvement prediction in human SLE: using a neural network model, 193 human orthologs predicted LN patients vs HI with high accuracy (accuracy=0.86, sensitivity=0.82, specificity=0.91 in the validation set). Using a support vector machine model, 30 human orthologs and age and gender were the best predictors of LN vs non-LN SLE patients (accuracy=0.71, sensitivity=0.73, specificity=0.69 in the validation set).

Conclusion

Murine RNA-sequencing uncovered both shared cross-tissue and tissue-specific gene signatures that could be potentially targeted in SLE. Murine-human comparative transcriptome analysis revealed common gene signatures suggesting that similar biological processes and pathways are disturbed across species, with murine kidney lupus signature predicting kidney involvement in human SLE. Validation in other datasets is ongoing.

THU0014 COMPARATIVE TRANSCRIPTOME ANALYSES ACROSS TISSUES AND SPECIES IDENTIFY TARGETABLE GENES FOR HUMAN SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) AND LUPUS NEPHRITIS (LN)

Background:

Systemic Lupus Erythematosus (SLE) is a complex disease associated with the dysfunction of multiple tissues and cells. The causal tissue for each disease phenotype is not known a priori. Despite improvements in diagnosis and treatment, major organ involvement (such as the kidneys) contributes significantly to morbidity and mortality that still remain increased. There is an unmet need for timely targeted therapy.

Objectives:

RNA-sequencing was performed to investigate the patterns of transcription variation across tissues between healthy and lupus-prone mice at different stages of lupus, and how these patterns associate with human Systemic Lupus Erythematosus (SLE).

Methods:

NZB/W-F1 lupus prone mice were sacrificed at the pre-puberty, pre-autoimmunity and nephritic stage. Age-matched C57BL/6 were used as controls. An “effector” tissue (spleen) and “end-organs” (kidneys, brain) were collected. Total RNA was isolated, and mRNA-sequencing was performed. A time-series analysis was developed and differentially expressed genes (DEGs) were analyzed with DESeq. Hierarchical clustering and functional enrichment analysis were performed with gProfiler. Human orthologs of mouse tissue DEGs were identified in the whole-blood RNA-sequencing dataset comprised of 55 lupus-nephritis (LN), 65 non-LN SLE patients and 58 healthy individuals (HI). Human orthologs were compared to human DEGs. Using machine learning, human orthologs identified in the mouse dataset were used to predict kidney involvement in the human dataset, which was split in training and validation sets.

Results:

Lupus susceptibility and progression signatures at different tissues and different stages of the disease were identified. Tissue-specific signatures and a common cross-tissue signature were also described. Previously described and novel biological processes and pathways were revealed. The comparative murine-human transcriptome analysis identified human orthologs from the mouse spleen-signature (including CCL5, IFIT and HLA genes) that are involved in systemic autoimmunity. It also identified human orthologs from the kidney- and brain-signature (including FCGR2A, C1Q, JAK1 and APOA2) that are involved in major “end-organ” damage and response mechanisms. Using a neural network model, 193 human orthologs accurately predicted LN patients vs HI (accuracy=0.86, sensitivity=0.82, specificity=0.91 in the validation set). Using a support vector machine model, 30 human orthologs and age and gender were the best predictors of LN vs non-LN SLE patients (accuracy=0.71, sensitivity=0.73, specificity=0.69 in the validation set).

Conclusion:

Murine tissue gene signatures identified by RNA-sequencing analysis revealed biological processes and pathways that could be potentially used as biomarkers or therapeutic targets in human SLE. Comparison of the murine tissue-transcriptome with the whole-blood human-transcriptome revealed common gene signatures, demonstrating similar biological processes and pathways. Machine learning identified a murine kidney lupus signature that can accurately predict kidney involvement in human SLE. Validation in other datasets is ongoing.

References:

[1]Panousis NI, et al. Ann Rheum Dis 2019;78:1079

Acknowledgments:

This work was supported by FOREUM, SYSCID and ERC -Advanced Grant

Disclosure of Interests:

Eleni Frangou: None declared, Panayiotis Garantziotis: None declared, Maria Grigoriou: None declared, Aggelos Banos: None declared, Nikolaos Panousis: None declared, Emmanouil Dermitzakis: None declared, George Bertsias Grant/research support from: GSK, Consultant of: Novartis, Dimitrios Boumpas: None declared, Anastasia Filia: None declared

Transcriptomic Analysis Reveals Prognostic Molecular Signatures of Stage I Melanoma

PURPOSE

Previously identified transcriptomic signatures have been based on primary and metastatic melanomas with relatively few American Joint Committee on Cancer (AJCC) stage I tumors, given difficulties in sampling small tumors. The advent of adjuvant therapies has highlighted the need for better prognostic and predictive biomarkers, especially for AJCC stage I and stage II disease.

EXPERIMENTAL DESIGN

A total of 687 primary melanoma transcriptomes were generated from the Leeds Melanoma Cohort (LMC). The prognostic value of existing signatures across all the AJCC stages was tested. Unsupervised clustering was performed, and the prognostic value of the resultant signature was compared with that of sentinel node biopsy (SNB) and tested as a biomarker in three published immunotherapy datasets.

RESULTS

Previous Lund and The Cancer Genome Atlas signatures predicted outcome in the LMC dataset (P = 10-8 to 10-4) but showed a significant interaction with AJCC stage (P = 0.04) and did not predict outcome in stage I tumors (P = 0.3-0.7). Consensus-based classification of the LMC dataset identified six classes that predicted outcome, notably in stage I disease. LMC class was a similar indicator of prognosis when compared with SNB, and it added prognostic value to the genes reported by Gerami and colleagues. One particular LMC class consistently predicted poor outcome in patients receiving immunotherapy in two of three tested datasets. Biological characterization of this class revealed high JUN and AXL expression and evidence of epithelial-to-mesenchymal transition.

CONCLUSIONS

A transcriptomic signature of primary melanoma was identified with prognostic value, including in stage I melanoma and in patients undergoing immunotherapy.

Vitamin D-VDR Signaling Inhibits Wnt/β-Catenin-Mediated Melanoma Progression and Promotes Antitumor Immunity

1α,25-Dihydroxyvitamin D3 signals via the vitamin D receptor (VDR). Higher serum vitamin D is associated with thinner primary melanoma and better outcome, although a causal mechanism has not been established. As patients with melanoma commonly avoid sun exposure, and consequent vitamin D deficiency might worsen outcomes, we interrogated 703 primary melanoma transcriptomes to understand the role of vitamin D-VDR signaling and replicated the findings in The Cancer Genome Atlas metastases. VDR expression was independently protective for melanoma-related death in both primary and metastatic disease. High tumor VDR expression was associated with upregulation of pathways mediating antitumor immunity and corresponding with higher imputed immune cell scores and histologically detected tumor-infiltrating lymphocytes. High VDR-expressing tumors had downregulation of proliferative pathways, notably Wnt/β-catenin signaling. Deleterious low VDR levels resulted from promoter methylation and gene deletion in metastases. Vitamin D deficiency (<25 nmol/L ∼ 10 ng/mL) shortened survival in primary melanoma in a VDR-dependent manner. In vitro functional validation studies showed that elevated vitamin D-VDR signaling inhibited Wnt/β-catenin signaling genes. Murine melanoma cells overexpressing VDR produced fewer pulmonary metastases than controls in tail-vein metastasis assays. In summary, vitamin D-VDR signaling contributes to controlling pro-proliferative/immunosuppressive Wnt/β-catenin signaling in melanoma and this is associated with less metastatic disease and stronger host immune responses. This is evidence of a causal relationship between vitamin D-VDR signaling and melanoma survival, which should be explored as a therapeutic target in primary resistance to checkpoint blockade. SIGNIFICANCE: VDR expression could potentially be used as a biomarker to stratify patients with melanoma that may respond better to immunotherapy.

Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus

Objectives

Haematopoietic stem and progenitor cells (HSPCs) are multipotent cells giving rise to both myeloid and lymphoid cell lineages. We reasoned that the aberrancies of immune cells in systemic lupus erythematosus (SLE) could be traced back to HSPCs.

Methods

A global gene expression map of bone marrow (BM)-derived HSPCs was completed by RNA sequencing followed by pathway and enrichment analysis. The cell cycle status and apoptosis status of HSPCs were assessed by flow cytometry, while DNA damage was assessed via immunofluorescence.

Results

Transcriptomic analysis of Lin⁻Sca-1⁺c-Kit⁺ haematopoietic progenitors from diseased lupus mice demonstrated a strong myeloid signature with expanded frequencies of common myeloid progenitors (CMPs)—but not of common lymphoid progenitors—reminiscent of a ‘trained immunity’ signature. CMP profiling revealed an intense transcriptome reprogramming with suppression of granulocytic regulators indicative of a differentiation arrest with downregulation trend of major regulators such as Cebpe, Cebpd and Csf3r, and disturbed myelopoiesis. Despite the differentiation arrest, frequencies of BM neutrophils were markedly increased in diseased mice, suggesting an alternative granulopoiesis pathway. In patients with SLE with severe disease, haematopoietic progenitor cells (CD34⁺) demonstrated enhanced proliferation, cell differentiation and transcriptional activation of cytokines and chemokines that drive differentiation towards myelopoiesis, thus mirroring the murine data.

Conclusions

Aberrancies of immune cells in SLE can be traced back to the BM HSPCs. Priming of HSPCs and aberrant regulation of myelopoiesis may contribute to inflammation and risk of flare.

Trial registration number

4948/19-07-2016.

High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material

Systematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.

Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma

The immune response to melanoma improves the survival in untreated patients and predicts the response to immune checkpoint blockade. Here, we report genetic and environmental predictors of the immune response in a large primary cutaneous melanoma cohort. Bioinformatic analysis of 703 tumor transcriptomes was used to infer immune cell infiltration and to categorize tumors into immune subgroups, which were then investigated for association with biological pathways, clinicopathologic factors, and copy number alterations. Three subgroups, with "low", "intermediate", and "high" immune signals, were identified in primary tumors and replicated in metastatic tumors. Genes in the low subgroup were enriched for cell-cycle and metabolic pathways, whereas genes in the high subgroup were enriched for IFN and NF-κB signaling. We identified high MYC expression partially driven by amplification, HLA-B downregulation, and deletion of IFNγ and NF-κB pathway genes as the regulators of immune suppression. Furthermore, we showed that cigarette smoking, a globally detrimental environmental factor, modulates immunity, reducing the survival primarily in patients with a strong immune response. Together, these analyses identify a set of factors that can be easily assessed that may serve as predictors of response to immunotherapy in patients with melanoma. SIGNIFICANCE: These findings identify novel genetic and environmental modulators of the immune response against primary cutaneous melanoma and predict their impact on patient survival.See related commentary by Anichini, p. 2457.

Regenerating hair cells in vestibular sensory epithelia from humans

Human vestibular sensory epithelia in explant culture were incubated in gentamicin to ablate hair cells. Subsequent transduction of supporting cells with ATOH1 using an Ad-2 viral vector resulted in generation of highly significant numbers of cells expressing the hair cell marker protein myosin VIIa. Cells expressing myosin VIIa were also generated after blocking the Notch signalling pathway with TAPI-1 but less efficiently. Transcriptomic analysis following ATOH1 transduction confirmed up-regulation of 335 putative hair cell marker genes, including several downstream targets of ATOH1. Morphological analysis revealed numerous cells bearing dense clusters of microvilli at the apical surfaces which showed some hair cell-like characteristics confirming a degree of conversion of supporting cells. However, no cells bore organised hair bundles and several expected hair cell markers genes were not expressed suggesting incomplete differentiation. Nevertheless, the results show a potential to induce conversion of supporting cells in the vestibular sensory tissues of humans.

The inner ear contains our balance system (the vestibular system) and our hearing organ (the cochlea). Their sensing units, the hair cells, detect movement or sound waves. A loss of hair cells is a major cause of inner ear disorders, such as dizziness, imbalance and deafness.

When hair cells die, supporting cells that surround them close the ‘wound’ to repair the tissue. In fish, amphibians, reptiles and birds, the supporting cells can replace lost hair cells, but in mammals – including humans – hair cells are unable to regenerate in the cochlea, so hearing loss is permanent. However, previous research has shown that in certain mammals, spontaneous replacement of lost hair cells in the vestibular system can occur, but not enough to lead to a full recovery.

Scientists have been able to convert supporting cells in the vestibular system of mice into hair cells by using either certain chemicals, or by introducing a specific gene into the supporting cells. In the mouse embryo, this gene, called Atoh1, switches on a signalling pathway in the inner ear, through which a non-specialised precursor cell becomes a hair cell. Inducing hair cell regeneration could be a therapy for inner ear disorders. Therefore, Taylor et al. wanted to find out if such procedures would work in inner ear tissue from humans.

The researchers collected intact tissue samples from the vestibular system of patients who had undergone surgery to have a tumour removed, which would normally destroy the inner ear. All existing hair cells were removed so that mainly supporting cells remained. Then, the tissue was either treated with chemicals that increased the production of hair cells or received the gene ATOH1. The results showed that the cells containing the gene were able to develop many features characteristic of hair cells. And a smaller number of hair cells treated with the chemicals also started to develop hair cell-like features. A gene analysis after the ATOH1 transfer revealed a number of active genes known to be markers of hair cells, but also several inactive ones. This suggests that additional factors are necessary for generating fully functional hair cells.

Dizziness and balance disorders present a major health care burden, particularly in the elderly population. Yet, they are often disregarded and overlooked. This study suggests that hair cell regeneration could be a feasible therapy for some forms of balance disorders linked to loss of vestibular hair cells. More research is needed to identify the other factors at play to test if hair cell regeneration in the cochlea could be used to treat hearing impairment.

β-Catenin-mediated immune evasion pathway frequently operates in primary cutaneous melanomas

Immunotherapy prolongs survival in only a subset of melanoma patients, highlighting the need to better understand the driver tumor microenvironment. We conducted bioinformatic analyses of 703 transcriptomes to probe the immune landscape of primary cutaneous melanomas in a population-ascertained cohort. We identified and validated 6 immunologically distinct subgroups, with the largest having the lowest immune scores and the poorest survival. This poor-prognosis subgroup exhibited expression profiles consistent with β-catenin-mediated failure to recruit CD141+ DCs. A second subgroup displayed an equally bad prognosis when histopathological factors were adjusted for, while 4 others maintained comparable survival profiles. The 6 subgroups were replicated in The Cancer Genome Atlas (TCGA) melanomas, where β-catenin signaling was also associated with low immune scores predominantly related to hypomethylation. The survival benefit of high immune scores was strongest in patients with double-WT tumors for BRAF and NRAS, less strong in BRAF-V600 mutants, and absent in NRAS (codons 12, 13, 61) mutants. In summary, we report evidence for a β-catenin-mediated immune evasion in 42% of melanoma primaries overall and in 73% of those with the worst outcome. We further report evidence for an interaction between oncogenic mutations and host response to melanoma, suggesting that patient stratification will improve immunotherapeutic outcomes.

Abstract 3388: Copy number alteration in primary melanoma

The systematic analysis of the genomic characteristics of melanoma primaries has been infeasible given the limited size of these formalin-fixed paraffin embedded (FFPE) lesions. Further studying a clearly ascertained, deeply phenotyped patient population allows meaningful extrapolation of the prevalence of distinct genomic features and investigation of the association of these features with lifestyle exposures and germline profiles. For these reasons, we focused on a recently recruited patient cohort, the Leeds Melanoma Cohort (LMC) consisting of 2184 recruits from a distinct geographical region of Northern England; the only selection applied to recruitment was to only include those whose melanoma was less than 0.75 mm Breslow thickness in the early years of recruitment.

Tumor samples from 703 cases have been analyzed for genome-wide gene expression (Pozniak et al, this meeting). For this study, we wanted to explore the prevalence of copy number alterations (CNA) and the mutation profile of tumors (reflecting the association of C&gt;T mutations with UV exposure, the primary environmental risk factor) and so we have adopted a next-generation sequencing (NGS) approach. Tumor blocks were recovered from local pathology laboratories for those cases already deceased at the time that this CNA analysis was initiated plus those surviving more than 5 years post diagnosis at this same time. Blocks at risk of being compromised for clinical purposes by sampling for this research study were excluded from sampling; this amounted to almost 50% of identified samples.

A total of 333 NGS libraries were sequenced on an Illumina GAII or HiSeq sequencer to produce &gt;100bp paired-end reads (either 5 or 1 per lane). DNA reads were aligned and mapped achieving approximately 1.8x coverage (9.4x for those at 1 per lane); the number of reads falling within each 10kb window was adjusted for GC content and mappability and compared to a composite normal FFPE sample to determine local copy number.

We adopted various approaches to assess the informativeness of the methodology. (i) Replicate samples showed high reproducibility (all p &lt; 0.0001). (ii) Focused analysis of the CDKN2A region with segmentation analyses to determine CNA breakpoints yielded high quality, biologically plausible data revealing multiple copy number events. 67% of samples showed no CNA across the 4 Mb region covering CDKN2A while, as expected, only a small proportion of CNAs did not involve CDKN2A. Four common distinct patterns were observed. Copy number loss ranged from 20kb to &gt; 4 Mb. (iii) A germline CNA could reliably be identified from the tumor data. (iv) CDKN2A expression levels correlated with estimated copy number.

We have shown that small FFPE melanomas can be characterized for genomic alterations using NGS opening up the potential for studies associating epidemiological and germline profile with the resulting tumor.

1. Newton-Bishop, J.A., et al. (2009) J Clin Oncol, 27, 5439-5444.

Funded by Worldwide Cancer Research and Cancer Research UK.

Citation Format: D. Timothy Bishop, Anastasia Filia, Alastair Droop, Joey Diaz, Mark Harland, Jon Laye, Juliette Randerson-Moor, Julia A. Newton-Bishop. Copy number alteration in primary melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3388. doi:10.1158/1538-7445.AM2017-3388

Independent replication of a melanoma subtype gene signature and evaluation of its prognostic value and biological correlates in a population cohort

Development and validation of robust molecular biomarkers has so far been limited in melanoma research. In this paper we used a large population-based cohort to replicate two published gene signatures for melanoma classification. We assessed the signatures prognostic value and explored their biological significance by correlating them with factors known to be associated with survival (vitamin D) or etiological routes (nevi, sun sensitivity and telomere length). Genomewide microarray gene expressions were profiled in 300 archived tumors (224 primaries, 76 secondaries). The two gene signatures classified up to 96% of our samples and showed strong correlation with melanoma specific survival (P=3 x 10(-4)), Breslow thickness (P=5 x 10(-10)), ulceration (P=9.x10-8) and mitotic rate (P=3 x 10(-7)), adding prognostic value over AJCC stage (adjusted hazard ratio 1.79, 95%CI 1.13-2.83), as previously reported. Furthermore, molecular subtypes were associated with season-adjusted serum vitamin D at diagnosis (P=0.04) and genetically predicted telomere length (P=0.03). Specifically, molecular high-grade tumors were more frequent in patients with lower vitamin D levels whereas high immune tumors came from patients with predicted shorter telomeres. Our data confirm the utility of molecular biomarkers in melanoma prognostic estimation using tiny archived specimens and shed light on biological mechanisms likely to impact on cancer initiation and progression.

Congenital rubella still a public health problem in Italy: analysis of national surveillance data from 2005 to 2013

In accordance with the goal of the World Health Organization Regional Office for Europe, the Italian national measles and rubella elimination plan aims to reduce the incidence of congenital rubella cases to less than one case per 100,000 live births by the end of 2015. We report national surveillance data for congenital rubella and rubella in pregnancy from 2005 to 2013. A total of 75 congenital rubella infections were reported; the national annual mean incidence was 1.5/100,000 live births, including probable and confirmed cases according to European Union case definition. Two peaks occurred in 2008 and 2012 (5.0 and 3.6/100,000 respectively). Overall, 160 rubella infections in pregnancy were reported; 69/148 women were multiparous and 38/126 had had a rubella antibody test before pregnancy. Among reported cases, there were 62 infected newborns, 31 voluntary abortions, one stillbirth and one spontaneous abortion. A total of 24 newborns were unclassified and 14 women were lost to follow-up, so underestimation is likely. To improve follow-up of cases, systematic procedures for monitoring infected mothers and children were introduced in 2013. To prevent congenital rubella, antibody screening before pregnancy and vaccination of susceptible women, including post-partum and post-abortum vaccination, should be promoted. Population coverage of two doses of measles-mumps-rubella vaccination of ≥ 95% should be maintained and knowledge of health professionals improved.

Measles outbreak on a cruise ship in the western Mediterranean, February 2014, preliminary report

A measles outbreak occurred in February 2014 on a ship cruising the western Mediterranean Sea. Overall 27 cases were reported: 21 crew members, four passengers.For two cases the status crew or passenger was unknown. Genotype B3 was identified. Because of different nationalities of cases and persons on board,the event qualified as a cross-border health threat. The Italian Ministry of Health coordinated rapid response.Alerts were posted through the Early Warning and Response System.

[Update for the standard procedures of diagnosis and therapy in cases of congenital rubella]

Congenital Rubella is the dramatic consequence of rubella during gestation. A combined strategy of Measles and Rubella universal vaccination on children and selective vaccination of susceptible women has been shown effective in the elimination of congenital rubella requiring an incidence of < 1 case of CRS per 100,000 live births. Verification processes of rubella elimination require that physicians early and appropriately diagnose all cases of congenital rubella, including those unpatent at birth. The paper highlights clinical and laboratory aspects channeling diagnosis of congenital rubella infection or syndrome even after the first year of life, and the short- and long-term management criteria.

Analysis of national measles surveillance data in Italy from October 2010 to December 2011 and priorities for reaching the 2015 measles elimination goal

From 1 October 2010 to 31 December 2011, Italy experienced high measles burden with 5,568 measles cases (37.4% laboratory-confirmed) reported to the enhanced measles surveillance system (cumulative incidence in the 15-month reference period: 9.2/100,000 population). Adolescents and young adults were especially affected, and the median age of cases was 18 years. Most cases (95.8%) were either unvaccinated or incompletely vaccinated. Complications were reported for 20.3% of cases, including 135 cases of pneumonia, seven of encephalitis and one case of Guillain–Barré syndrome. One death occurred in an immunocompromised adult. Over 1,300 cases were hospitalised. Identified priorities for reaching the measles elimination goal include evidence-based interventions such as reminder/recall for both doses of measles vaccine, supplementary immunisation activities aimed at susceptible age cohorts, and vaccinating healthcare workers.

Analysis of national measles surveillance data in Italy from October 2010 to December 2011 and priorities for reaching the 2015 measles elimination goal

Binary file ES_Abstracts_Final_ECDC.txt matches

Prevalence of hospital-associated infections can be decreased effectively in developing countries

BACKGROUND

Hospital-acquired infections (HAI) are an important public health problem worldwide. Little information is available from African countries, but published data show that the burden of HAI is greater in Africa than in developed countries. In 2002, the World Health Organization (WHO) published guidelines for preventing HAI.

AIM

To evaluate the impact of a hospital infection control programme on the prevalence of HAI among patients in a large Ugandan hospital.

METHODS

A one-day cross-sectional prevalence survey and a ward procedure survey were performed in Lacor Hospital in March 2010 using standardized questionnaires. All patients admitted to hospital not less than two days before the survey were eligible to participate in the prevalence survey. Modified WHO criteria for HAI were used. The ward procedure survey examined the procedures to prevent HAI. Several hospital infection control measures were subsequently implemented, in accordance with WHO infection control guidelines, starting in October 2010. The prevalence survey and ward procedure survey were repeated in October 2011.

FINDINGS

The prevalence of HAI was 34% in 2010 and 17% in 2011. The prevalence of infected patients reduced from 28% to 14%. The prevalence of HAI was lower in all age groups and for all types of HAI except urinary tract infections following the implementation of infection control activities.

CONCLUSION

This study showed that HAI is an important problem in this large African hospital, and that the prevalence of HAI can be reduced effectively following the adoption of basic infection control procedures.

Abstract 3140: Using formalin-fixed paraffin-embedded melanoma tumors for the detection of copy number variation by next generation sequencing

DNA copy number variation (CNV) has been identified in many cancers. Recent studies have shown that CNV data, in combination with other high-throughput techniques, can provide novel biological insight to tumor biology. Although a number of CNV whole-genome studies have been performed on melanoma using cell lines and frozen tumors, very few have used formalin fixed paraffin embedded (FFPE)-derived material. Melanoma tumors are small and rarely frozen, which means that FFPE tumor blocks would be a very valuable source of genomic material to be used for CNV analysis if the methodologies were adequately developed. It has been shown that reliable next generation sequencing data can be produced from FFPE-derived DNA in lung cancers (Wood et al., 2010). Here, we report a study showing that DNA from FFPE melanoma tumor blocks can be used for CNV detection on a next generation sequencing platform. DNA from 20 FFPE melanoma samples was used to prepare genomic libraries, which were sequenced on the Illumina GAIIx instrument. Successful library preparation occurred at DNA levels of at least 30ng, while current protocols generally suggest 50ng with high quality material and 1μg generally. The use of SPRIworks (Beckman Coulter) and Bravo (Agilent) robots was compared with the manual method for library preparation with input DNA mass of 30-150ng. Libraries prepared manually were always of better quality and yield. We also investigated means of improving library preparation. Melanin co-purifies with DNA and inhibits downstream reactions, and indeed lower coverage was seen in our samples if they were heavily pigmented. To overcome the adverse effects of melanin, 10 DNA samples (5 pairs) were used for library preparation with and without bovine serum albumin (BSA). BSA has been shown to bind to melanin, and as a result the melanin does not inhibit the DNA polymerase reaction. All 5 libraries with BSA were of higher quality and yield when compared to those prepared without BSA. All comparisons were made after running the libraries on an Agilent DNA chip.

Currently available data from the GAIIx were used to develop the analysis pipeline. The first 10 samples were multiplexed together and run twice, while the remaining 10 were multiplexed at 5 samples per lane and run once. The average coverage obtained was 0.10x with a range of 0.03x-0.11x. We observed a strong effect on mapping quality based upon the end-cycle quality scores, leading us to adopt an aggressive data trimming procedure. More samples from the Leeds Melanoma Cohort will soon be prepared and sequenced on the Illumina HiSeq2000 instrument. We aim to identify if tumors with driver BRAF mutations have different genomic signatures when compared to those with NRAS mutations. Finally, genomic data will be combined with clinical data and we will check for the prognostic significance of CNV changes identified in our samples.

Citation Format: Anastasia Filia, Alastair Droop, Mark Harland, Tim Bishop, Julia Newton-Bishop. Using formalin-fixed paraffin-embedded melanoma tumors for the detection of copy number variation by next generation sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3140. doi:10.1158/1538-7445.AM2013-3140

Evaluation of human papilloma virus diagnostic testing in oropharyngeal squamous cell carcinoma: sensitivity, specificity, and prognostic discrimination

PURPOSE

Human papillomavirus-16 (HPV16) is the causative agent in a biologically distinct subset of oropharyngeal squamous cell carcinoma (OPSCC) with highly favorable prognosis. In clinical trials, HPV16 status is an essential inclusion or stratification parameter, highlighting the importance of accurate testing.

EXPERIMENTAL DESIGN

Fixed and fresh-frozen tissue from 108 OPSCC cases were subject to eight possible assay/assay combinations: p16 immunohistochemistry (p16 IHC); in situ hybridization for high-risk HPV (HR HPV ISH); quantitative PCR (qPCR) for both viral E6 RNA (RNA qPCR) and DNA (DNA qPCR); and combinations of the above.

RESULTS

HPV16-positive OPSCC presented in younger patients (mean 7.5 years younger, P = 0.003) who smoked less than HPV-negative patients (P = 0.007). The proportion of HPV16-positive cases increased from 15% to 57% (P = 0.001) between 1988 and 2009. A combination of p16 IHC/DNA qPCR showed acceptable sensitivity (97%) and specificity (94%) compared with the RNA qPCR "gold standard", as well as being the best discriminator of favorable outcome (overall survival P = 0.002). p16 IHC/HR HPV ISH also had acceptable specificity (90%) but the substantial reduction in its sensitivity (88%) impacted upon its prognostic value (P = 0.02). p16 IHC, HR HPV ISH, or DNA qPCR was not sufficiently specific to recommend in clinical trials when used in isolation.

CONCLUSIONS

Caution must be exercised in applying HPV16 diagnostic tests because of significant disparities in accuracy and prognostic value in previously published techniques.

Measles in Italy, July 2009 to September 2010

Outbreaks of measles continue to occur in Italy, as in other European countries. We present here details of cases reported through the Italian enhanced measles surveillance system from July 2009 to September 2010. In total, 2,151 cases were reported, 42% (n=895) of which were laboratory confirmed. The median age of cases was 18 years and 1,709 of 1,856 cases (92%) were unvaccinated. Many cases with complications were reported (n=305), including three with encephalitis. A total of 652 of 1,822 cases (36%) were hospitalised. Molecular characterisation revealed circulation of a limited number of measles virus genotypes (D4, D8 and B3), which is consistent with the current epidemiology of the disease in Italy. A national measles elimination plan was approved in 2003 with the aim of interrupting endemic measles transmission by 2007. Since elimination was not achieved, the target date was recently moved to 2015. The emphasis of the new elimination plan, approved in March 2011, is on strengthening surveillance, implementing evidence based-interventions to increase measles-mumps-rubella vaccine uptake in children, adolescents and young adults, and implementing communication activities related to the vaccine. The strategies proposed by the plan should be implemented fully and appropriately by all regions in order to meet the elimination goal by 2015.

Measles in Italy, July 2009 to September 2010

Outbreaks of measles continue to occur in Italy, as in other European countries. We present here details of cases reported through the Italian enhanced measles surveillance system from July 2009 to September 2010. In total, 2,151 cases were reported, 42% (n=895) of which were laboratory confirmed. The median age of cases was 18 years and 1,709 of 1,856 cases (92%) were unvaccinated. Many cases with complications were reported (n=305), including three with encephalitis. A total of 652 of 1,822 cases (36%) were hospitalised. Molecular characterisation revealed circulation of a limited number of measles virus genotypes (D4, D8 and B3), which is consistent with the current epidemiology of the disease in Italy. A national measles elimination plan was approved in 2003 with the aim of interrupting endemic measles transmission by 2007. Since elimination was not achieved, the target date was recently moved to 2015. The emphasis of the new elimination plan, approved in March 2011, is on strengthening surveillance, implementing evidence based-interventions to increase measles-mumps-rubella vaccine uptake in children, adolescents and young adults, and implementing communication activities related to the vaccine. The strategies proposed by the plan should be implemented fully and appropriately by all regions in order to meet the elimination goal by 2015.

UHRF1-mediated tumor suppressor gene inactivation in nonsmall cell lung cancer

BACKGROUND

The UHRF1 gene possesses an essential role in DNA methylation maintenance, but its contribution to tumor suppressor gene hypermethylation in primary human cancers currently remains unclear.

METHODS

mRNA expression levels of UHRF1, DNMT1, DNMT3A, DNMT3B, and E2F1 were evaluated in 105 primary nonsmall cell lung carcinomas by quantitative polymerase chain reaction. The methylation status of CDKN2A and RASSF1 promoters was examined by pyrosequencing. UHRF1 was knocked down by short hairpin RNA in A549 lung adenocarcinoma cells.

RESULTS

All 4 genes were overexpressed in a coordinated manner in the lung tumor tissues, and their expression correlated with that of E2F1. Higher UHRF1 expression in tumor tissues correlated with the hypermethylation of CDKN2A (P = .005) and RASSF1 promoters (P = .034), and the relationship with a combined epigenotype was even stronger (P = 2.3 × 10(-4) ). When UHRF1 was knocked down in A549 lung adenocarcinoma cells, lower methylation levels of RASSF1, CYGB, and CDH13 promoters were observed. Also, UHRF1 knockdown clones demonstrated reduced proliferation and decreased cell migration properties.

CONCLUSIONS

Our data demonstrate that UHRF1 is a key epigenetic switch, which controls cell cycle in nonsmall cell lung carcinoma through its ability to sustain the transcriptional silencing of tumor suppressor genes by maintaining their promoters in a hypermethylated status. Thus, UHRF1 should be considered, along with DNMTs, among the potential targets for cancer treatment and/or therapeutic stratification.

Abstract 163: DTMETH: A novel method for increased length quantitative CpG methylation analysis

DNA methylation analysis has been blooming in the last decade as there is increasing evidence for epigenetic control of new pathways involved in normal cell function as well as the pathogenesis of human disease. A large number of methods have been devised to address the needs of DNA methylation detection in clinical samples. A DNA methylation detection method of preference should be able to interrogate multiple CpGs over long stretches of DNA, quantify DNA methylation, include multiple bisulphite conversion controls, provide increased sensitivity and low background. Here we present DTMETH, a novel method for DNA methylation analysis that bears the above characteristics. In principle, the desired locus is amplified from bisulphite treated-DNA using primers at CpG-free areas. Primers bear short 5’ tails which contain two cytosines (forward) or guanines (reverse) that will serve as normalisation tools. After a spin-column cleanup process, the PCR product is subjected to DTMETH. This is a thermostable reaction utilising FS Taq and labelled ddC (Applied Biosystems). The latter will be only incorporated at methylated cytosines, as post-bisulphite unmethylated cytosines are converted to uracils. The DTMETH products are cleaned by ethanol precipitation and subjected to analysis on a capillary sequencer. ddC peak areas corresponding to methylated Cs are normalised by the peak areas of the control Cs on the primer tail. As proof of principle we present DNA methylation analysis for the p16 gene. We amplified a 269 bp region of the gene's 5’UTR containing 28 CpGs. The assays provide excellent linearity and reproducibility. We used it to screen 90 non-small cell lung carcinomas for p16 methylation in comparison to an established pyrosequencing assay. p16 hypermethylation was detected in 23 samples with both methods, 3 samples with DTMETH only, while 64 samples were negative. DTMETH combines the read lengths of dideoxy terminator sequencing, and enables quantitation without the need of cloning. It is highly versatile, offering easy assay design and due to its thermostable nature can easily overcome secondary structure issues arising from the low complexity bisulphite DNA sequence composition.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 163.

Measles resurges in Italy: preliminary data from September 2007 to May 2008

Following an incidence rate of 1/100,000 inhabitants in 2006 [1], Italy has been facing an upsurge of measles cases since September 2007, with outbreaks being reported in various regions. In Italy, measles vaccination is currently offered free of charge as combined measles-mumps-rubella (MMR) vaccine. The current national vaccination schedule recommends two doses of MMR vaccine, given respectively at 11-12 months and 5-6 years of age. Although childhood vaccination coverage has increased in recent years, reaching the national average of 88% in 2006 (source: Ministry of Health), with some regional variability (Figure 1), it is still below the target of 95% set by the National Measles Elimination Plan (MEP) launched in 2003 [2], and outbreaks continue to occur.

A cluster of measles cases in northern Italy: a preliminary report

From 19 September to 19 November 2007, 46 measles cases related to a single outbreak were reported in the Piemonte region of northern Italy.

[Rubella epidemiology in Italy in years 1998-2004]

In November 2003 the National Plan for the elimination of measles and congenital rubella was approved, with the aim of reducing and maintaining the incidence of congenital rubella syndrome (CRS) at less than 1 case per 100,000 live births by 2007. In order to describe the epidemiology of rubella in Italy, we conducted a serosurvey and evaluated incidence and vaccination coverage data available for the period 1998-2004. In the years considered, national mean coverage of measles-mumps-rubella vaccination within the second year of life, even though still below the 95% threshold, has progressively increased reaching 87%. In addition, previously existing differences in coverage among regions have diminished. In the same period the incidence of rubella has decreased, with a historic minimum of 461 cases notified in 2004. The cyclic pattern typical of rubella persists, but with a prolongation of the interepidemic period and an increased mean age of acquisition of the infection. Although the proportion of immune individuals has increased, the percentage of women of childbearing age susceptible to rubella remains high (11% in the 15-19 year age group and 8% in the 20-39 year age group) and CRS cases continue to occur. Despite the clear results achieved through the implementation of vaccination strategies in children within the second year of life, a continued strong public health commitment is required to increase the proportion of vaccinated individuals and absolute priority must be given to immunising women of childbearing age.

Capture-recapture estimation of underreporting of legionellosis cases to the National Legionellosis Register: Italy 2002

The objective of this study was to evaluate the degree of underreporting to the Italian National Legionellosis Register (NLR). For the year 2002, all cases of Legionellosis notified to the NLR were compared with cases recorded in the hospital discharge record (HDR) database. The number of unreported cases and the total number of cases in the population were estimated using the capture-recapture method with two independent data sources. Seventeen out of 21 Italian regions participated in the study. Overall, underreporting was estimated to be 21.4% and was found to be significantly greater in the Centre-South (28.2%) than in the North (20.0%). However, even after taking into account the higher degree of underreporting, a significantly lower incidence of the disease is registered in central-southern Italy. The hypothesis, which needs to be verified, is that, in addition to underreporting, under-diagnosis of legionellosis is more widespread in this geographical area.

Rubella seroprofile of the Italian population: an 8-year comparison

The objective of this study is to evaluate how increasing MMR infant vaccination coverage in recent years has modified the epidemiology of rubella in Italy. A cross-sectional population-based seroprevalence study of rubella antibodies was conducted on 3094 sera, in 2004, and results were compared with data obtained by the same method in 1996. The overall proportion of rubella-seropositive individuals was found to be significantly higher in 2004 with respect to 1996 (84.6% vs. 77.4%). However, an increase in seropositivity was observed only in the 1-19 years age groups. Recent increases in childhood MMR vaccination coverage, therefore, have not had an impact on seroprevalence in women of childbearing age, over 5% of whom remain susceptible to rubella. Preconception screening and postpartum vaccination of susceptible women are fundamental if the WHO target of less than one case of congenital rubella syndrome per 100,000 live births is to be attained.

Cluster of measles cases in the Roma/Sinti population, Italy, June-September 2006

Three clusters of measles cases occurred between June and September 2006, in the Roma/Sinti populations in three different Italian regions: the Bolzano-South Tyrol in northern Italy; Lazio in central Italy; and the island of Sardinia in the southwest.

First cases of rubella infection during pregnancy detected by new reporting system in Italy

On 1 January 2005, rubella infection during pregnancy and congenital rubella syndrome/infection were made statutorily notifiable in Italy, as recommended by the national plan for the elimination of measles and congenital rubella

Rubella control in Italy

In Italy, rubella vaccination has been recommended since 1972 for pre-adolescent girls, and since the early 1990s for all children in the second year of life. Nevertheless, coverage in children from 12 to 24 months of age is suboptimal (i.e., 56% in 1998, 78% in 2003), with wide variations among regions. As a result, rubella is still circulating in Italy, and in 1996 the percentage of women susceptible to rubella between 15 and 39 years of age was &gt;5%. Congenital rubella syndrome (CRS) was a notifiable disease between 1987 and 1991, with a range of 8-76 cases reported annually. Since 1992, national incidence data are no longer available, but local reports show that CRS cases are still occurring. Nationwide, coordinated and uniform actions are needed to control CRS effectively. For this reason, the National Plan for the Elimination of Measles and of Congenital Rubella has recently been launched. This plan includes strategies aimed at increasing MMR vaccination coverage in children and specific control measures for congenital rubella control, i.e., improving the vaccination of susceptible women of childbearing age, and reintroducing national surveillance of CRS.