MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery

MOTIVATION

Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due to the tremendous size of the chemical space, experimental bioactivity screening efforts require the aid of computational approaches. Although deep learning models have been successful in predicting bioactive compounds, effective and comprehensive featurization of proteins, to be given as input to deep neural networks, remains a challenge.

RESULTS

Here, we present a novel protein featurization approach to be used in deep learning-based compound-target protein binding affinity prediction. In the proposed method, multiple types of protein features such as sequence, structural, evolutionary and physicochemical properties are incorporated within multiple 2D vectors, which is then fed to state-of-the-art pairwise input hybrid deep neural networks to predict the real-valued compound-target protein interactions. The method adopts the proteochemometric approach, where both the compound and target protein features are used at the input level to model their interaction. The whole system is called MDeePred and it is a new method to be used for the purposes of computational drug discovery and repositioning. We evaluated MDeePred on well-known benchmark datasets and compared its performance with the state-of-the-art methods. We also performed in vitro comparative analysis of MDeePred predictions with selected kinase inhibitors' action on cancer cells. MDeePred is a scalable method with sufficiently high predictive performance. The featurization approach proposed here can also be utilized for other protein-related predictive tasks.

AVAILABILITY AND IMPLEMENTATION

The source code, datasets, additional information and user instructions of MDeePred are available at https://github.com/cansyl/MDeePred.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

d. Sous. Lopes SM. P–803 Novel culture conditions for the improvement of the in vitro expansion of human male fetal germ cells

Study question

Do different ECMs/substrates and growth media culture conditions improve in vitro male human primordial germ cell (hPGC) expansion?

Summary answer

We achieved in vitro expansion improvement of male hPGCs with specific growth factors such as LIF, EGF, FGF2 and GDNF on gelatin- and vitronectin-coating cultures.

What is known already

PGCs are the precursors of male and female gametes, which are specified during early mammalian post-implantation embryonic development. PGCs undergo sequential cell divisions to differentiate into pro-spermatogonia (pSPG). In vitro propagation of pSPG could be important to understand the transition to spermatogonial stem cells (SSCs), important for fertility preservation in patients with infertility. Here, we aimed at performing a comparative analysis on in vitro feeder-free culture systems, based on different extracellular matrix (ECM) and growth media culture conditions, to support the expansion of the male germline stem cell populations using second trimester human male gonads as primary material.

Study design, size, duration

We collected human 2nd trimester male fetal gonads from elective abortions. Male gonads were dissected in saline solution (0.9% NaCl) and were either fixed overnight in 4% paraformaldehyde (PFA) for immunohistochemistry or disaggregated by enzymatic digestion for in vitro culture.

Participants/materials, setting, methods

After differential plating, fetal cells were cultured for 6 days. Disaggregated gonads were cultured with two different growing media (Medium 1 supplemented with LIF, EGF, FGF–2 and GDNF and Medium 2 supplemented with RA, BMP 4 and Activin A) on gelatin, laminin, vitronectin or matrigel coated plates. Cultured cells were immunostained, quantified for the expression of DDX4 and POU5F1 after 3 days (D3) and 6 days (D6) of culture.

Main results and the role of chance

We pursued to evaluate whether germ cells dissociated from a pool of male fetal gonads could propagate in vitro when cultured for D6 in different conditions.

We observed that expansion of POU5F1-positive early PGCs and DDX4-positive late PGCs was only observed when cells were plated on gelatin or vitronectin and cultured with Medium 1, containing the growth factors LIF, EGF, FGF2 and GDNF. However, a reduced percentage of PGCs was observed in all four different coatings when grown with Medium 2, containing RA, BMP4 and Activin A.

We analyzed the relative expression of the PGC markers POU5F1, DDX4 and MAGEA4 in histological sections of gonads from embryos at 18.5 weeks of gestation. Two populations of hPGCs were observed: ∼10–30% of the gonadal cells expressed solely DDX4 (late PGCs), whereas less than 10% of gonadal cells expressed POU5F1 (early PGCs). SOX9 and STARD1 expression was evaluated, confirming the presence of Sertoli cells and Leydig cells, respectively.

Limitations, reasons for caution

Due to the limited and difficulty to obtain human fetal tissue, a limited number of samples were used.

Wider implications of the findings: We expanded human male fetal germ cells in vitro for D6 on gelatin and vitronectin coated plates with Medium 1, containing growth factors LIF, EGF, FGF2 and GDNF. Our findings provide a 2D culture system to expand hPGCs that could be useful to study propagation to pSPGs and eventually SSCs.

Trial registration number

Not applicable

P–563 Assessing ovarian age: Could we use leukocyte telomere length as a surrogate marker of cumulus cells telomere content?

Study question

Is leukocyte telomere length (LTL) correlated with cumulus cells telomere length (CCTL) in an age-heterogeneous women population?

Summary answer

LTL showed a positive correlation with CCTL in the studied population. Hence, its potential value as indicator of ovarian age would deserve further evaluation.

What is known already

Progressive telomere shortening has been related to ovarian aging and genomic instability during early development. A positive correlation between short telomere length of the first polar body and aneuploidy rate has been reported. CCTL has shown to be a biomarker of oocyte and embryo quality, but its assessment is impractical. LTL has been proposed as a surrogate of TL of follicular cells, but telomere lengthening through folliculogenesis could be controlled by different mechanisms. Thus, we aimed to determine if LTL in an age-heterogeneous population is correlated with CCTL and therefore considered an accurate surrogate for telomere length in the ovary.

Study design, size, duration

In this prospective non-interventional cohort study, 35 egg donors and 17 women undergoing Preimplantation Genetic Testing for Aneuploidy (PGT-A) treatment were included during sixteen months. Following controlled ovarian stimulation determined by treating physicians, oocyte retrieval was performed 36 hours after final maturation induction. Cumulus cells (CC) for telomere length (TL) measurement were obtained after the pick-up and oocyte stripping. A blood sample was collected through peripheral venous access for LTL measurement.

Participants/materials, setting, methods

Genomic DNA of CC and leukocytes from the 52 subjects was isolated. Average delta cycle threshold (ΔCt) was determined using a SYBR green quantitative real-time PCR protocol for relative TL. For normalization of measurements, a Taqman assay for the multicopy gene Alu was performed. ΔCtL and ΔCtCC were compared by a paired t-test analysis and the fold change was calculated. Additionally, the association between them and patient age was analyzed by a Pearson correlation test.

Main results and the role of chance

Mean participant’s age was 29.94 ± 7.55 years and mean values for ΔCtL and ΔCtCC were 7.99 ± 0.53 and 7.46 ± 0.75, respectively. A positive significant correlation was found between age and ΔCt (ΔCtL: R2=0.71, p-value=5.18e–09; ΔCtCC: R2=0.47, p-value=0.00049). Since ΔCt values are inversely proportional to the amount of nucleic acids amplified and, therefore, to the telomere length, this correlation means that TL in both cell types decreases as women age. Additionally, ΔCtL was significantly higher than ΔCtCC (ΔCt fold change: 0.93, p-value=9e–07), meaning that CC showed significantly longer telomeres than leukocytes, thus supporting our previous published results in young egg donors. When analyzing the ΔCtL and ΔCtCC in these age-heterogeneous sample, a positive moderate and significant correlation was observed (R2=0.42, p-value=0.002). Thus, LTL could be suggested as a potential indicator of CCTL and therefore as a candidate for a biological marker of ovarian aging.

Limitations, reasons for caution

The sample size of this study was moderate and perhaps increasing the number of subjects might give additional strength to our findings. In addition, although relative telomere length allowed for adequate comparison between subjects, this method did not allow for absolute TL measurement.

Wider implications of the findings: While reproductive implications of LTL measurement need to be further studied, our results support the potential usefulness of LTL measurement as an indicator of CCTL and ovarian aging when analyzing an age-heterogeneous population. Further, our findings suggest that CC could possess different mechanisms to cope against telomere length shortening.

Trial registration number

Not applicable

[Selective IgA deficiency]

Selective IgA deficiency (SIgAD) is defined by the European Society for Immunodeficiencies (ESID) as a serum IgA of less than 0.07g/L in patients greater than 4 years old with normal levels of IgG and IgM, normal vaccine responses, and with the exclusion of secondary causes of hypogammaglobulinemia. When serum IgA level is higher than 0.07g/L but two standard deviations below normal for age, the condition may be referred to as partial IgA deficiency, which is quite common. SIgAD is the most common primary immunodeficiency in Europe (1/600 in France) and most patients with SIgAD are asymptomatic (75-90%). The clinical complications associated with SIgAD include recurrent respiratory infections (in particular involving Haemophilus influenza and Streptococcus pneumoniae) and gastrointestinal (mainly due to Giardialamblia), autoimmune and allergic manifestations (anaphylaxis if blood products with IgA are administrated), inflammatory gastrointestinal disease. There is no specific treatment for SIgAD and each patient must be managed individually. While asymptomatic subjects do not need any treatment, it is still necessary for them to be up-to-date with vaccinations. If the patient experiences recurrent infections, prophylactic antibiotics may be beneficial. Immunoglobulin replacement therapy should be considered in patients with SIgAD and concomitant IgG subclass deficiency. Treatment for autoimmune and allergic manifestations is based on current standards of care for specific disease entities. To improve quality of life and reduce morbidity, an interdisciplinary team approach is essential.

When to stay out of the abdomen: Extending extraperitoneal approaches to complex ventral and incisional hernias-A video-based guide to the technique

BACKGROUND

Ventral and incisional hernias are common surgical pathologies managed by acute care surgeons and also an area of exploration in repair options and approaches. Several new minimally invasive techniques have been developed to better tailor the repair to the individual patient and minimize the risk of intra-abdominal complications, particularly in patients with significant adhesions from prior surgery or trauma. The extended totally extraperitoneal approach to incisional ventral hernias allows the repair of complex hernias while entirely avoiding entry into the peritoneal cavity.

METHODS

We present video clips demonstrating key steps to minimally invasive extended totally extraperitoneal Rives-Stoppa and transversus abdominis release procedures to complex incisional and ventral hernias.

CONCLUSION

The application of robotic-assisted laparoscopic surgery has enabled surgeons to expand the use of minimally invasive techniques for a variety of operations. Hernia repair in particular has seen the most rapid growth because of the enhanced ability to suture on the anterior abdominal wall. This video illustrates the key technical points to performing a safe and effective repair without the need for intraperitoneal access.

The Structural Biology of Eastern Equine Encephalitis Virus, an Emerging Viral Threat

Alphaviruses are arboviruses that cause arthritis and encephalitis in humans. Eastern Equine Encephalitis Virus (EEEV) is a mosquito-transmitted alphavirus that is implicated in severe encephalitis in humans with high mortality. However, limited insights are available into the fundamental biology of EEEV and residue-level details of its interactions with host proteins. In recent years, outbreaks of EEEV have been reported mainly in the United States, raising concerns about public safety. This review article summarizes recent advances in the structural biology of EEEV based mainly on single-particle cryogenic electron microscopy (cryoEM) structures. Together with functional analyses of EEEV and related alphaviruses, these structural investigations provide clues to how EEEV interacts with host proteins, which may open avenues for the development of therapeutics.

The Pivotal Player: Components of NF-κB Pathway as Promising Biomarkers in Colorectal Cancer

Over the last several decades, colorectal cancer (CRC) has been one of the most prevalent cancers. While significant progress has been made in both diagnostic screening and therapeutic approaches, a large knowledge gap still remains regarding the early identification and treatment of CRC. Specifically, identification of CRC biomarkers that can help with the creation of targeted therapies as well as increasing the ability for clinicians to predict the biological response of a patient to therapeutics, is of particular importance. This review provides an overview of CRC and its progression stages, as well as the basic types of CRC biomarkers. We then lay out the synopsis of signaling pathways related to CRC, and further highlight the pivotal and multifaceted role of nuclear factor (NF) κB signaling in CRC. Particularly, we bring forth knowledge regarding the tumor microenvironment (TME) in CRC, and its complex interaction with cancer cells. We also provide examples of NF-κB signaling-related CRC biomarkers, and ongoing efforts made at targeting NF-κB signaling in CRC treatment. We conclude and anticipate that with more emerging novel regulators of the NF-κB pathway being discovered, together with their in-depth characterization and the integration of large groups of genomic, transcriptomic and proteomic data, the day of successful development of more ideal NF-κB inhibitors is fast approaching.

Abstract 1020: Amplification of 22q11 is associated with hypersensitivity to AURKB inhibition in cell line models of resistance to EGFR TKIs

Background: Non-small cell lung cancer (NSCLC) tumors with mutations in the EGF receptor (EGFR) ultimately relapse to therapy with EGFR tyrosine kinase inhibitors (TKIs). Cell line models of resistance to EGFR TKIs have been described to be sensitive to AURKB inhibitors, such as AZD2811, but the mechanisms and markers of hypersensitivity remain to be elucidated.

Methods: A panel of 36 clones with acquired in vitro resistance to EGFR TKIs was used in the study. Some of them had been previously demonstrated to be exquisitely sensitive to AZD2811 and to show a phenotypic response switch from polyploidy and senescence to apoptosis. Whole exome sequencing were employed for genotyping, while FISH and Q-PCR were used to determine copy number gains in particular genes. mRNA expression was studied by whole transcriptome sequencing, nCounter and RT-Q-PCR; and protein expression by proteomics and Western blotting. The effects of several drugs were analyzed by MTT, flow cytometry and beta-galactosidase staining. Finally, CRISPR was used to silence specifics genes. In vivo experiments were performed by implanting heterogenous pools of resistant cells in athymic nude mice. Selection against Chr22q11 amplification was assessed by FISH copy number analysis and polysomy assessment.

Results: Transcriptomics, proteomics, RT-Q-PCR and Western blotting of the EGFR TKI resistant clones revealed that hypersensitivity to AZD2811 was consistently associated with up-regulation of > 40 genes in the q11.2 segment of chromosome 22; including MAPK1, CRKL, BID or BCL2L13. FISH using probes against HIRA, CRKL and MAPK1 demonstrated 7-10 fold 22q11 amplification in all AZD2811 hypersensitive clones, compared to lack of amplification in parental and resistant clones. Amplification of 22q11, confirmed by WES, was mutually exclusive with known mechanisms of resistance to EGFR-TKIs. Cell cycle and beta-galactosidase staining revealed G2/M arrest upon AZD2811 treatment followed by apoptosis in 22q11-amplified cells and senescence in non-amplified clones. Silencing of one 22q11 gene - BID - specifically abolished sensitivity to AZD2811 in 22q11 cells with little or no effect on the IC50s to other drugs. Silencing of CRKL only partially restored sensitivity to osimertinib in 22q11 amplified cells. Furthermore, clonal selection analysis in vivo demonstrated that a nanoparticle formulation of AZD2811(NP) in combination with osimertinib selectively eliminated 22q11 amplified cells and rendered the remaining non-amplified cells polyploid.

Conclusions: Amplification of 22q11, leading to BID overexpression, predicts sensitivity to AURKB inhibition in cell line models of resistance to osimertinib and other EGFR TKIs. These data are consistent with overdrive in 22q11 amplified cells of a recently reported mitotic checkpoint mediated by AURKB phosphorylation of CASP2, and suppression of BID cleavage.

Citation Format: Jordi Bertran-Alamillo, Jon Travers, Ana Giménez-Capitán, Nicolas Floch, Ruth Román, Aisha Swaih, Sonia Rodríguez, Matthew Martin, Erika Aldeguer, Ricardo Miragaia, Josep Castellví, Paul Smith, Alejandro Martínez-Bueno, Elizabeth Pease, Henrik Ditzel, Giulia Fabbri, Rafael Rosell, Urszula Polanska, Miguel A Molina-Vila, Jelena Urosevic. Amplification of 22q11 is associated with hypersensitivity to AURKB inhibition in cell line models of resistance to EGFR TKIs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1020.

Abstract 1100: Gain and loss of function genome-wide CRISPR screens identify Hippo signaling as an important driver of resistance in EGFR mutant lung cancer

10-20% of lung adenocarcinoma patients harbour activating mutations in EGFR. Although treatment with the EGFR kinase inhibitor osimertinib has improved overall survival in such patients, almost all patients ultimately develop drug resistance. In many cases the molecular resistance mechanisms remain unknown. A systematic identification of the involved genes and pathways is critical to overcome osimertinib resistance. To define the resistance landscape of EGFR kinase inhibition we performed genome-wide gain and loss of function CRISPR screens in EGFR mutant lung cancer cell lines treated with osimertinib. Resistance hits were enriched for genes in previously identified resistance pathways including PI3K (PTEN, TSC2), MAPK (NF1, MET), cell death (BCL2L11, BAX), the mediator complex (MED24, MED19) and ubiquitination (KCTD5, LZTR1). A secondary screen of 63 resistance genes that combined high content microscopy with CRISPR gene knockouts demonstrated that 21% (13/63) of genes were associated with increased nuclear localisation of YAP1/WWTR1, indicating transcriptional activation of the Hippo pathway. According to our screening data, many resistance hits mapped onto the Hippo signaling axis - upstream regulators (NF2, AMOTL2), core signaling genes (LATS1, LATS2), main effectors (WWTR1, YAP1), transcriptional co-effectors (TEAD3, FOSL1, VGLL4) and the SWI/SNF complex (ARID2, SMARCA4, SMARCB1, PBRM1). Hippo signaling is mediated through YAP1 and WWTR1 which bind to TEAD transcription factors and activate transcriptional programs affecting cell proliferation and apoptosis. We confirmed using CRISPR that knockout (NF2) or overexpression (YAP1, WWTR1) of key Hippo genes in the EGFR mutant lung cancer cell lines PC-9, HCC827 and HCC4006 resulted in up to 60-fold increased resistance to osimertinib and elevated activity of a TEAD reporter system, indicating activation of Hippo transcriptional programs. To maintain osimertinib resistance, expression of both YAP1 and WWTR1 was necessary, suggesting non-redundant roles for both Hippo main effectors in mediating osimertinib resistance. The combination of osimertinib and a TEAD inhibitor (MYF-01-37) reversed the resistance phenotype in NF2 KO cell line models in long-term proliferation assays and also substantially repressed the emergence of drug-tolerant persister cells in PC-9, HCC827 and HCC4006 cell lines following osimertinib treatment. These cells exhibited an enhanced apoptotic response when treated with combination of osimertinib and TEAD inhibitor. Consequently, we propose Hippo signaling as an important target mechanism for the prevention of resistance to osimertinib.

Citation Format: Matthias Pfeifer, Jonathan S. Brammeld, Stacey Price, Matthew Martin, Hannah Thorpe, Aurelie Bornot, Erica Banks, Nin Guan, Shanade Dunn, Maria Luisa Guerriero, Daniel O'Neill, James Pilling, Davide Gianni, James Brownell, Paul Smith, Ultan McDermott. Gain and loss of function genome-wide CRISPR screens identify Hippo signaling as an important driver of resistance in EGFR mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1100.

POS0877 THE EFFECT OF PLATELET INHIBITORS ON DIGITAL ULCERS IN SYSTEMIC SCLEROSIS - A DERIVATION AND VALIDATION EUSTAR STUDY

Background:

Digital ulcers (DUs) affect half of the patients with systemic sclerosis (SSc) and can be complicated by gangrene and amputation. The direct involvement of platelets in the development of DUs has been suggested by in vitro studies, which encouraged physicians to consider platelet inhibitors as a therapeutic option in the management of DUs. However, until now, there is no clinical study to assess the efficacy of platelet inhibitors for DUs in SSc patients.

Objectives:

To demonstrate a possible relationship between treatment with platelet inhibitors and the occurrence of DUs at the next follow-up visit in patients with SSc.

Methods:

This study used prospectively collected data from the European Scleroderma Trials and Research group (EUSTAR) registry. Patients fulfilling the 2013 ACR/EULAR SSc classification criteria with complete longitudinal data on the presence of DUs and platelet inhibitors were included in the analysis. Multiple imputation using a random forest algorithm was implemented to handle missing values.

The dataset was split into a derivation and validation cohort. To investigate the response for the binary dependent variable of DUs, a generalized linear mixed model (GLMM) was developed in the derivation cohort and validated using ROC analysis and Brier scores to address discrimination and calibration, respectively.

Results:

Of 3,463 patients (2,961 in the derivation cohort, 722 in the validation cohort), 453 had current DUs at the baseline and 245 were exposed to platelet inhibitors (table 1).

Our GLMM revealed that the exposure to platelet inhibitors is associated with a reduced risk of DUs at the next follow up visit (OR = 0.33, 95% CI = [0.13 to 0.82]). Further factors associated with absence or presence of DUs at the next follow-up visit are shown in figure 1. This confirmed the previously identified risk factors for the presence of DUs, supporting the overall robustness and the validity of our model.

The performance was evaluated by ROC curve analysis and showed an AUC = 97.97% (95% CI = [96.93% to 97.67%]) for the derivation cohort and AUC = 77.3% (95% CI = [74.01% to 81.39%]) for the validation cohort, respectively, showing an acceptable discrimination. The Brier score was 0.05 in the derivation cohort and 0.07 in the validation cohort, suggesting a good calibration of the model.

Conclusion:

Our model, with acceptable discrimination and good calibration, suggests a positive treatment effect of platelet inhibitors on DUs in clinical practice.

Table 1.

Baseline characteristics of patients before imputation

CharacteristicsOverallDerivation setValidation setn3,4632,691772Age (median [IQR])56.00 [47.00, 66.00]56.00 [47.00, 65.00] 57.00 [48.00, 67.00]Disease duration (median [IQR]) 9.00 [4.00, 16.00] 9.00 [4.00, 16.00] 8.00 [4.00, 15.00]Disease subset = Limited cutaneous SSc (%) 1562 (65.2) 1164 (64.6) 398 (66.9)DUs (%): Current 453 (13.1) 378 (14.0) 75 (9.7)DUs (%): Never 1783 (51.5) 1326 (49.3) 457 (59.2)DUs (%): Previously 1227 (35.4) 987 (36.7) 240 (31.1)mRSS (median [IQR]) 5.00 [2.00, 11.00] 6.00 [2.00, 12.00] 4.00 [1.00, 11.00]Joint Contractures = Yes (%) 881 (26.8) 770 (29.4) 111 (16.5)LVEF (median [IQR])62.00 [60.00, 65.00]60.00 [60.00, 65.00] 65.00 [60.00, 67.00]Dyspnea NYHA III and IV (%)300 (9.5)214 (8.6)86 (12.7)Pulmonary hypertension = Yes (%) 244 (10.7) 200 (11.3) 44 (8.4)Lung fibrosis on HRCT = Yes (%) 685 (46.6) 600 (47.7) 85 (39.7)FVC % predicted (median [IQR])97.00 [82.00, 111.00]95.00 [81.00, 110.00]101.00 [85.00, 115.00]Serum creatinine mg/dl (median [IQR]) 0.70 [0.60, 0.90] 0.70 [0.60, 0.90] 0.70 [0.70, 0.90]Anti-Scl-70 positive = Yes (%) 1147 (33.1) 958 (35.6) 189 (24.5)CRP elevation = Yes (%) 639 (21.1) 490 (20.8) 149 (22.1)Platelet inhibitors therapy = Yes (%) 245 (7.1) 206 (7.7) 39 (5.1)Oral anti-coagulants therapy = Yes (%) 53 (1.5) 50 (1.9) 3 (0.4)

Disclosure of Interests:

None declared

BED domain-containing NLR from wild barley confers resistance to leaf rust

Leaf rust, caused by Puccinia hordei, is a devastating fungal disease affecting barley (Hordeum vulgare subsp. vulgare) production globally. Despite the effectiveness of genetic resistance, the deployment of single genes often compromises durability due to the emergence of virulent P. hordei races, prompting the search for new sources of resistance. Here we report on the cloning of Rph15, a resistance gene derived from barley's wild progenitor H. vulgare subsp. spontaneum. We demonstrate using introgression mapping, mutation and complementation that the Rph15 gene from the near-isogenic line (NIL) Bowman + Rph15 (referred to as BW719) encodes a coiled-coil nucleotide-binding leucine-rich repeat (NLR) protein with an integrated Zinc finger BED (ZF-BED) domain. A predicted KASP marker was developed and validated across a collection of Australian cultivars and a series of introgression lines in the Bowman background known to carry the Rph15 resistance. Rph16 from HS-680, another wild barley derived leaf rust resistance gene, was previously mapped to the same genomic region on chromosome 2H and was assumed to be allelic with Rph15 based on genetic studies. Both sequence analysis, race specificity and the identification of a knockout mutant in the HS-680 background suggest that Rph15- and Rph16-mediated resistances are in fact the same and not allelic as previously thought. The cloning of Rph15 now permits efficient gene deployment and the production of resistance gene cassettes for sustained leaf rust control.

AB0058 ASSOCIATION BETWEEN HLA-DRB1*04:01, RHEUMATOID NODULES AND PARTICULAR EPITOPES OF CITRULLINATED FIBRIN IN PATIENTS WITH RHEUMATOID ARTHRITIS

Background:

Rheumatoid arthritis (RA) is associated with HLA-DRB1 genes encoding the shared epitope (SE), a 5 amino acid motive. RA is usually preceded by the emergence of anti-citrullinated protein antibodies (ACPAs) detected by anti-CCP2 tests. Citrullin is a neutral amino acid resulting from post translational modification of arginin by Peptidyl Arginyl Deiminases (PADs). ACPAs recognize epitopes from citrullinated human fibrinogen (Fib-cit) and can be specifically detected by the AhFibA assay. Five peptides derived from Fib-cit together represent almost all of the epitopes recognized by patients with ACPA-positive RA: β60–74cit, α36–50cit, α621–635cit, α501–515cit and α171–185cit. As RA is a pleiomorphic disease, whose evolution is difficult to predict, the use of antibody fine specificity as a marker of clinical phenotypes has become a major challenge.

Objectives:

Our objective was to study whether clinical characteristics and HLA-DRB1 genetic background were associated with a specific reactivity against these epitopes.

Methods:

184 ACPA positive RA patients fulfilling the 2010 ACR/EULAR criteria were studied. Patients characteristics, including HLA-DRB1 genotype, were collected from their medical files. Anti-CCP2, AhFibA, Rheumatoid Factors (RF), and antibodies against the five major Fib-cit peptides were analyzed using ELISA assays.

Results:

Anti-CCP2 and AhFibA titres were strongly correlated (rs: 0.7037; p = 5.69x10-29, Pearson’s). Anti-α505-515cit antibodies were associated with HLA-DRB1*04:01 (OR = 5.52 [2.00 – 13.64]; p = 0.0003). High level anti-α505-515cit antibodies were significantly associated with rheumatoid nodules (OR = 2.71 [1.00 – 7.16], p= 0.044). Anti α501–515cit antibodies were associated with RF (OR=2.31 [1.10 – 4.78], p= 0.026).

Conclusion:

Immune complexes containing anti-α501–515cit antibodies and rheumatoid factors might be involved in the development of rheumatoid nodules on the HLA-DRB1*04:01 background. These findings highlight the role played by the HLA-DRB1*04:01 molecule and its rapid intracellular route into the lysosomes, enabling original antigen processing. Finally, purifying these epitope specific antibodies might be a new therapeutic opportunity for rheumatoid nodules.

Disclosure of Interests:

None declared

[Heredity and cancer]

A personal or family history of cancer has now become the primary cause of genetic consultations. In recent years, various genes have been identified that are associated with a more or less marked genetic predisposition to the development of cancers. The syndrome associated with the hereditary risk of breast and ovarian cancer and the Lynch syndrome are the most frequent ones, but there are many other, much less common, situations associated with familial cancer risk. In most cases, there are clear recommendations regarding the indications for genetic testing and the follow-up of patients identified as having a predisposition to cancer. At the CHU of Liège, we currently perform more than 1.400 oncogenetic consultations per year and we maintain a positivity rate of genetic tests performed in this indication higher than 10%. In this way, we allow a multidisciplinary care of patients with a high oncological risk and participate in a prevention and surveillance activity. We also pay increasing attention to the hereditary risk associated with pediatric cancers and to patients with multiple cancers, especially when these develop at an early age. Finally, the oncogenetic consultation must consider the psychological, ethical and legal aspects of a diagnosis that involves the patient and his or her future, but also the whole family.

[EBV and immunodeficiency]

Epstein-Barr virus (EBV), discovered in 1964, is a double-stranded DNA virus belonging to the Herpesviridae family. EBV has a lymphoid tropism with transforming capacities using different oncogenic viral proteins. This virus has two replication cycles: a lytic cycle mainly occuring during primary infection and a latent cycle allowing viral persistence into host memory B cells. More than 90% of adults are seropositive for EBV worldwide, with a past history of asymptomatic or mild primary infection. EBV infection can sometimes cause life-threatening complications such as hemophagocytic lymphohistiocytosis, and lead to the development of lymphoproliferative disorders or cancers. Risk factors associated with these phenotypes have been recently described through the study of monogenic primary immune deficiencies with EBV susceptibility. We here review the virological and immunological aspects of EBV infection and EBV-related complications with an overview of current available treatments.

Laparoscopic splenectomy as a definitive management option for high-grade traumatic splenic injury when non operative management is not feasible or failed: a 5-year experience from a level one trauma center with minimally invasive surgery expertise

Technique, indications and outcomes of laparoscopic splenectomy in stable trauma patients have not been well described yet. All hemodynamically non-compromised abdominal trauma patients who underwent splenectomy from 1/2013 to 12/2017 at our Level 1 trauma center were included. Demographic and clinical data were collected and analysed with per-protocol and an intention-to-treat comparison between open vs laparoscopic groups. 49 splenectomies were performed (16 laparoscopic, 33 open). Among the laparoscopic group, 81% were successfully completed laparoscopically. Laparoscopy was associated with a higher incidence of concomitant surgical procedures (p 0.016), longer operative times, but a significantly faster return of bowel function and oral diet without reoperations. No significant differences were demonstrated in morbidity, mortality, length of stay, or long-term complications, although laparoscopic had lower surgical site infection (0 vs 21%).The isolated splenic injury sub-analysis included 25 splenectomies,76% (19) open and 24% (6) laparoscopic and confirmed reduction in post-operative morbidity (40 vs 57%), blood transfusion (0 vs 48%), ICU admission (20 vs 57%) and overall LOS (7 vs 9 days) in the laparoscopic group. Laparoscopic splenectomy is a safe and effective technique for hemodynamically stable patients with splenic trauma and may represent an advantageous alternative to open splenectomy in terms of post-operative recovery and morbidity.

Seasonal variations in the optical characteristics of dissolved organic matter in glacial pond water

Large amounts of dissolved organic matter (DOM) are stored in mountain glaciers. However, few researches have analysed the optical characteristics of DOM in surface waters fed by mountain glaciers and their seasonal variations. In a pond fed by a glacier we observed simultaneous decreases in the dissolved organic carbon, and increases in both absorbance at 254 nm and specific absorption coefficient (SUVA₂₅₄) during the ice-free season 2015. This behaviour differs from the typical behaviour of lake/pond water in summer, and from the trends observed in a nearby pond not fed by a glacier. The trends of DOM properties, main ions and water stable isotopes at the glacier-fed pond could be attributed to transient modifications of the subglacial hydrological system. Flushing of previously isolated pools of subglacially stored water, containing terrestrial DOM derived from glacially-overridden soil and vegetation, would be driven by intense rainfall events during the melting season. These findings suggest that heavy rainfall events during the melting season have the capability to transiently modify the characteristics of DOM in a glacial pond. These events may be further exacerbated in the future, as summer rainfall events in the Alps are predicted to increase due to global warming.

A173 INNOVATIVE CARE FOR INFLAMMATORY BOWEL DISEASE PATIENTS DURING THE COVID-19 PANDEMIC: USE OF BEDSIDE INTESTINAL ULTRASOUND TO OPTIMIZE MANAGEMENT

Background

The COVID-19 pandemic has led to significant alterations in the ability to deliver outpatient care to patients with inflammatory bowel disease (IBD) including endoscopic evaluation. This has highlighted the need for alternative, accurate, non-invasive strategies to safely assess disease activity.

Aims

The aim of this study is to describe the impact of point of care intestinal ultrasound (IUS) in a university-based tertiary care IBD urgent access clinic.

Methods

We prospectively evaluated a comprehensive care pathway which incorporated outpatient sigmoidoscopy and intestinal ultrasound with the purpose of directing further ambulatory clinical care and avoiding hospitalization or hospital-based investigations including endoscopy during the COVID pandemic for patients with established IBD with symptoms suggestive of a disease flare, or those at high risk of a new diagnosis of IBD. Non-invasive markers C Reactive Protein (CRP) and fecal calprotectin (fCal) were collected where available. Patients were pre-screened for influenza-like illness, as COVID-19 testing was not available for this population during the study period. Substantial management changes were defined as addition of any medications, biologic switch/ optimization, and or referral for surgical consultation.

Results

Between March 15^th and June 30^th 2020, a total of 72 patients were seen in the urgent access clinic. All patients were seen within 7 days of referral. The majority were female 57% (41/72) and/ or had Crohn’s disease 65.5% (47/72) (Table 1). Of these, 84.7% (61/72) underwent a substantial management change based on features of active inflammation detected by either IUS alone (53% 38/72) sigmoidoscopy alone (12.5% 9/72) or combination IUS with in-clinic sigmoidoscopy (32% 23/72) in addition to CRP and fCal. Three new diagnoses of IBD were made: one colonic Crohn’s and 2 with ulcerative colitis. One pregnant patient avoided all acute care utilization. Five patients were referred to colorectal surgery for urgent resection including two patients admitted directly for emergent operations. No patients required visits to the emergency department. Furthermore, there have been no unscheduled hospitalizations occurred in this cohort since inception March 23, 2020 til November 15^th 2020.

Conclusions

The implementation of IUS in a centralized, urgent access clinic pathway resulted in efficient and meaningful changes in IBD management while sparing the need for acute care services including ER visits, need for in-hospital endoscopy, and hospitalization. The pandemic highlights the utility of this patient-center tool and supports expansion of wider IUS adoption.

Funding Agencies

None