bluuebunny/crossref_metadata_2025_split huggingface dataset:
#2263 Computational drug repurposing screen targeting PLA2R antibody binding
Authors: Lloyd Aled , Austin-Muttitt Karl , Mullins Jonathan 
Published: May 2024

Abstract

Background and Aims
Approximately 60% of patients with membranous nephropathy have antibodies against the phospholipase A2 receptor (PLA2R). The cysteine rich (CysR) epitope of PLA2R is a likely site of protein-antibody interaction. Current treatment regimens for membranous nephropathy involve maximal conservative management or systemic immunosuppression in severe cases. We have developed protocols and programs for an in silico high-throughput repurposing screen using structural modelling, docking, and molecular dynamics (MD). Uniquely, our approach uses a bespoke interface on Google Colab for graphic processing units to run the MD simulations. We describe their application to a repurposing screen aiming to identify larger licensed drug molecules capable of impeding antibody-protein interactions at the site of the CysR epitope.

Method
A complete model of PLA2R was obtained from I-TASSER using the canonical sequence on the UNIPROT database. This structure was equilibrated using a five nanosecond molecular dynamics (MD) simulation. The simulation was prepared using CHARMM-GUI and run on the GROMACS-ON-COLAB platform. The centroid of the MD system between three and five nanoseconds was used for docking experiments using PLANTS PLP with a study area that included the CysR epitope. A library of compounds listed in the British National Formulary was used for the docking studies. The results would be analysed by PLANTS energy and by key residue overlap score.

Results
Viable docking results were obtained for 891 of the 1510 compounds tested. 60 of these compounds were in contact with at least 10% of the residues in the CysR region. By restricting these results to compounds in the lowest 20% of the total sample for calculated binding energy, 22 compounds remained. 16 of these compounds have been assessed for their safety for oral or intravenous use. These sixteen compounds were then identified for further investigation by MD to assess the stability of the identified interactions. The sixteen compounds include Lymecycline, Trazodone, Mirabegron, Sulfasalazine, Methotrexate, Rosuvastatin and Montelukast.

Conclusion
Structural bioinformatics methods provide a relatively fast and economical option for identifying protein-drug interactions that could result in new treatment strategies. The compounds identified for investigation are used for an array of different health conditions. However, they all share the chemical properties of large molecular weight and have the potential to form multiple hydrogen bonds. If validated experimentally, these compounds could provide new treatment options for PLA2R antibody positive membranous nephropathy.
#2518 The decrease of the filtration slit density, not proteinuria, is the early indication of the filtration barrier dysfunction
Authors: Endlich Nicole , Chadjichristos Christos , Chatziantoniou Christos , Telli Nihal , Drenic Vedran , Endlich Tim 
Published: May 2024

Abstract

Background and Aims
Intact podocyte foot processes (FP) play a crucial role in ensuring proper selective filtration in the kidney. Changes in FP morphology are thought to be the initial trigger for proteinuria, but definitive proof is still missing. As FP structures are below the optical resolution of light microscopes, changes are investigated by electron microscopy (EM) on ultrathin sections. In this study, the correlation between morphology and proteinuria was investigated using the Podocyte Exact Morphology Measurement Procedure (PEMP), a 3D-SIM-based technique. Our investigation was focused on podocyte damage caused by treatment with nephrotoxic serum (NTS) as a model for focal segmental glomerulosclerosis.

Method
The mice were treated with nephrotoxic serum (NTS), and kidneys were taken at 24, 48, and 72 hours after injection. Kidney sections (3 µm thick) were prepared for 3D-SIM analysis after staining with podocin and integrin and then fixed in formalin and embedded in paraffin. Filtration slit density (FSD) was quantified using the Podocyte Exact Morphology Measurement Procedure (PEMP) as described earlier (Siegerist et al. 2017). In addition, EM was performed on glutaraldehyde-fixed tissue samples using standard protocols. The albumin to creatinine ratio was also determined.

Results
We observed that NTS-treated mice developed moderate proteinuria after 48 hours. Using the super-resolution microscopy-based 3D-SIM technique to quantify podocyte PF morphology by calculating the filtrations slit density (FSD) revealed a significant reduction of the FSD in NTS-treated mice already after 24 hours. This structural change was confirmed by transmission electron microscopy analysis, showing that the effacement of podocytes FPs is the first sign of a change in the filtration barrier function before proteinuria is measurable.

Conclusion
PEMP analysis of standard histological sections from NTS-injected and control mice demonstrated that the first event in the functional loss of the size selectivity of the filtration barrier is the effacement of FP morphology, followed by detectable proteinuria. Therefore, the assessment of the FSD is a promising strategy for early and accurate detection of the loss of filtration barrier integrity, providing opportunities for faster and more precise diagnostics.
#2922 The role of urinary extracellular-derived miRNAs dysregulation in IgA nephropathy
Authors: Ardalan Mohammadreza , Farzamikia Negin , Zununivahed Sepideh 
Published: May 2024

Abstract

Background and Aims
IgA nephropathy (IgAN) is one of the most common forms of glomerulonephritis and causes hematuria and proteinuria by damaging the mesangial and podocyte cells. Urinary extracellular vesicles (uEVs) derived from damaged podocytes may reflect podocyte damage in various glomerular diseases and are considered an early and noninvasive diagnostic method. This study aimed to extract urinary extracellular vesicles (EVs) and investigate the expression dysregulation and diagnostic value of miR-29c, miR-146a, miR-148b, miR-155, miR-200b, and miR-429 in urine samples from patients with IgAN.

Method
Urine samples were collected from 20 patients with IgAN, 30 patients with membranous nephropathy (MGN), and 16 healthy individuals to extract Urinary EVs by ultracentrifugation. The characterization of EVs was evaluated by the specific protein markers of the EVs, flotillin-1, ALiX, and CD-9, along with histone H1 and podocyte-specific marker podocalyxin via western blotting. SEM and DLS were used to investigate the size and morphology of EVs. The expression levels of the miRNAs were evaluated using Real-time PCR.

Results
Numerous extracellular vesicles &gt;100 nm in size were present in the urine sample which were considered as EVs based on references. There were higher levels of the specific markers flotillin-1, ALiX, and podococalyxin in the urine samples of IgAN patients than in the control samples (P &lt; 0.001 and P &lt; 0.001, respectively). There was a statistically significant difference among the expression level of miR-29c (P = 0.002 and P = 033) in the group of IgAN patients compared to MGN patients and the group of healthy people, based on Rock curve analysis this urinary marker could discriminate the IgAN patients from MGN group, the area under the curve AUC ≥ 0.73.

Conclusion
This study showed that the different levels of miRNAs studied in urinary EVs may indicate podocyte damage and have a direct relationship with the pathology of IgAN and MGN. Further studies are needed to confirm these results and determine the diagnostic value of these markers.
#2229 miR-186, a potential noninvasive diagnostic biomarker of Membranous nephropathy in urinary microparticles
Authors: Farzamikia Negin , Ardalan Mohammad Reza , Zununivahed Sepideh 
Published: May 2024

Abstract

Background and Aims
Membranous nephropathy (MN) is one of the most common causes of nephrotic syndrome, and is associated with podocyte damage and proteinuria. Invasive biopsy is the gold-standard diagnostic method for this disease. The use of specific biomarkers, such as microparticles (MPs) originating from damaged podocytes released in a patient's urine, has been proposed as an early, noninvasive, and repetitive diagnostic method. According to the previous studies, MPs derived from podocytes are present in the urine of patients with different glomerulonephritis, such as diabetic nephropathy, lupus nephritis, renal injury in preeclampsia, and renovascular hypertensive disorders. The analysis of urinary microparticle-derived miRNAs from patients with kidney diseases can help detect diagnostic biomarkers. This study aimed to analyze podocyte damage-related miRNAs in MN, miR-30c, miR-135, and miR-18 in the urinary MP of MN patients to identify appropriate candidate biomarkers for MN

Method
Urine samples from 30 patients with membranous nephropathy and 16 healthy individuals were collected to extract podocyte MPs using ultracentrifugation. Characterization of these particles was determined using the specific protein marker of MPs, TSG-101, and the podocyte-specific marker Nephrin, by western blotting, and SEM was used to check the size and morphology. The expression levels of microRNAs extracted from podocyte MPs, miR-30c, miR-135, and miR-186, were also evaluated by real-time PCR.

Results
The evaluation of the characteristics of MPs showed that there were many particles with a size of more than 100 nm in the urine sample, and there were higher levels of the specific markers TSG-101 and Nephrin in the urine samples of MGN patients than in the control samples (P &lt; 0.001). The expression level of miR-186 was compared between the three studied groups and based on the results of the expression of this miRNA in the group of membranous nephropathy patients compared to healthy people group, there was a significant increase in expression (P = 0.000)

Conclusion
This study showed that although the expression levels of miR-186 in podocyte MPs samples extracted from the urine of patients with MN were significantly changed compared to the studied controls, more studies should be performed to determine the diagnostic values.
#2088 Renal outcome, cardio-vascular events and infections in patients with lupus nephritis: MassiLUP cohort 2001-2022
Authors: Goupille Berangere , Resseguier Noemie , Torrents Julia , Bataille Stanislas , Bobot Mickaël , Brunet Philippe , Burtey Stephane , Corthier Alice , Faraut Julien , Sallee Marion , Daniel Laurent , Jourde-Chiche Noemie 
Published: May 2024

Abstract

Background and Aims
Most epidemiological studies in lupus nephritis (LN) report the risk of end-stage kidney disease (ESKD) (10-20% of patients at 10-15 years in developed countries), but less data is available on the long-term risk of chronic kidney disease (CKD), even though CKD is a major risk factor for morbidity and mortality. While immunosuppressive therapy for LN aims to reach and maintain remission in order to prevent CKD, it also exposes patients to cardiovascular, infectious and neoplastic adverse events. We conducted a retrospective cohort study to evaluate survival without CKD and adverse events in patients with LN.

Method
The MassiLUP cohort comprises all patients who underwent a kidney biopsy for a first flare of LN between 2001 and 2022 in the University Hospital of Marseille, France. We assessed patient survival, renal survival and survival without CKD (defined by an estimated glomerular filtration rate &lt; 60 mL/min/1.73 m2), without cardiovascular event, without severe infection (requiring hospitalization, or zoster), and without cancer.

Results
A total of 168 patients (82.7% female; mean age 33 years; mean serum creatinine 102 µmol/L at the time of the first kidney biopsy) were included, with a mean follow-up of 9.6 ± 5.7 years. One (0.6%) patient had class I LN (ISN/RPS 2003 classification), 17 (10.1%) class II LN, 45 (26.8%) had class III (± V) LN, 73 (43.5%) had class IV (± V) LN, 29 (17.3%) patients had pure class V LN; 3 biopsies could not be classified.
Four patients died during the follow-up (3 of severe infections and 1 of stroke); 41 (24.4%) patients developed CKD, among whom 19 (11.3%) patients reached ESKD; 34 (20.2%) patients presented a cardiovascular event, 59 (35.1%) a severe infection, and 12 (7.1%) a cancer.
Survival rates without CKD were 82.9%, 74.6% and 67.3% at 5, 10 and 15 years, respectively.
Survival rates without ESKD were 94.4%, 88.6% and 79.9% at 5, 10 and 15 years, respectively.
Survival rates without cardiovascular event were 85.7%, 77.3% and 75.5% at 5, 10 and 15 years, respectively.
Survival rates without severe infection were 76.3%, 63.8% and 51.8% at 5, 10 and 15 years, respectively.
Survival rates without cancer were 96.3%, 92.9% and 85.6% at 5, 10 and 15 years, respectively.

Conclusion
Despite free access to treatment and care in France, the long-term prognosis of patients with lupus nephritis remains burdened by both a risk of CKD and ESKD, and a significant risk of cardiovascular and infectious events. This calls for continued efforts to improve therapeutic strategies, both in terms of efficacy and toxicity, and to strengthen the therapeutic alliance in the care of patients with LN.
#464 Survey results on the utility of the Renal Risk Score and Histopathological Classification of ANCA-glomerulonephritis
Authors: Uzzo Martina , Berden Annalies , Emmi Giacomo , Floyd Lauren , Jennette Charles , Kronbichler Andreas , Neumann Irmi , Vaglio Augusto , Wiech Thorsten , Jayne David R W , Brix Silke , Bajema Ingeborg 
Published: May 2024

Abstract

Background and Aims
The importance of kidney biopsy in ANCA-associated glomerulonephritis (AAV) is widely recognized: both the Berden classification and the ANCA renal risk score (ARRS) are widely used and reliable predictors of prognosis. AAV phenotypes, outcomes and treatment have changed over the last decades: whether and how the existing classification and ARRS need to be updated is a matter of discussion. A survey to assess the current use of the classification and ARRS in clinical practice was conducted on behalf of the newly formed “Working Group on classifications and risk scores”.

Method
An online survey was sent to the active members of the European Vasculitis Society (EUVAS) between September 13th and September 27th, 2023. The survey used an internet platform, contained 12 multiple-choice and 2 open questions and results were analyzed anonymously.

Results
76 of 295 EUVAS members replied to the questionnaire: 40 (52.6%) were nephrologists, 25 (32.9%) rheumatologists, 4 (5.3%) pathologists and 7 (9.3%) “others”. Their level of expertise was high, with 61 (80.3%) physicians encountering more than 10 new-diagnosed AAV patients per year. A total of 64 (84.2%) responders usually performed a kidney biopsy in suspected AAV patients, considering the pathological examination a useful tool for prognosis (89.5%), diagnosis (85.5%) and treatment (81.6%). More than 90% of responders indicated they discuss kidney biopsy results in a multidisciplinary meeting involving both clinicians and pathologists. Both the Berden classification and the ARRS are known by around 70% of experts in the field; the first being commonly used by clinicians in everyday practice (70.1% vs 52.5%, p = 0.08). Both systems were considered useful on a scale from 0 to 10, with a median grade of 7 [(IQR 5-8) vs (IQR 6-8), p = 0.21].
Suggested improvements were further standardizations and simplicity. New parameters (e.g., extraglomerular involvement, laboratory and clinical features) and biomarkers should be considered for future inclusion.

Conclusion
A survey assessing the current use of the Berden classification and ARRS in clinical practice showed that both systems are widely used among vasculitis clinicians and that the ideal system should be able to guide treatment decisions. The validation of pathological systems for targeted treatment decisions is an unmet need.
#1356 Kidney phenotype in interstitial lung disease associated with ANCA-vasculitis: European Multicentre Study
Authors: Chalkia Aglaia , Jones Rachel B , Kamath Ajay , Mohammad Aladdin , Monti Sara , Mukhtyar Chetan , Petrakis Ioannis , Petras Dimitrios , Smith Rona M , Stylianou Kostas , Vassilopoulos Dimitrios , Jayne David R W 
Published: May 2024

Abstract

Background and Aims
Interstitial lung disease (ILD) in ANCA-associated vasculitis (AAV) has the appearance of a progressive fibrotic disease on imaging and primarily affects the interstitial lung compartment and is usually associated with MPO-ANCA. Whether patients with AAV-ILD display a similar fibrotic pattern in their kidneys is unclear.

Method
A European multicentre retrospective study included patients with AAV-ILD. The diagnosis of ILD was confirmed by a CT chest pattern of usual interstitial pneumonia (UIP), non-specific interstitial pneumonia (NSIP), organising pneumonia or chronic hypersensitivity pneumonia. We aimed to determine if kidney involvement in AAV-ILD exhibited a more fibrotic pattern compared to AAV-related nephritis without ILD, using data from the Cambridge AAV cohort.

Results
135 patients with AAV-ILD were included; 94 (70%) had also kidney involvement, in whom the mean age was 71 ± 11 years and 87% MPO-ANCA positive. The ILD diagnosis preceded AAV in 17%, 64% presented concurrently with kidney involvement, 20% with pulmonary haemorrhage. The most common lung radiological pattern was UIP (67%).
At presentation, the median glomerular filtration rate (GFR) was 27 ml/min per 1.73 m2 (interquartile range 12-50), with a median albumin-to creatinine ratio 23 mg/mmol (IQR 10-97). Among 72 patients with available kidney biopsy, the most prevalent Berden class was focal in 45%, followed by mixed in 33%, crescentic in 18% and sclerotic in 4%. Although, the prevalence of Berden classes did not significantly differ between ILD-nephritis and no ILD-nephritis groups, the former group had a higher baseline GFR (p = 0.05), lower albuminuria level (p = 0.002), higher percentage of normal glomeruli (p = 0.027), lower glomerular necrosis percentage (p = 0.002) and higher interstitial fibrosis score (p = 0.049). Within five years, the ILD-nephritis group demonstrated renal recovery, as indicated by an adjusted mean delta GFR of 13.4 ml/min per 1.73 m2, without a significant difference compared to the no ILD-nephritis group. Over a median follow-up of 4.9 years (IQR 2-9), the progression to end-stage kidney disease (ESKD) was comparable between the groups. However, notably, the ILD-nephritis group experienced significantly poorer survival rates (mean 10.9 years vs 17.9 years, log-rank p &lt; 0.001).

Conclusion
In AAV-ILD, kidney involvement is often characterized by fewer inflammatory and a higher prevalence of fibrotic lesions than on non-ILD-AAV. Despite initial differences in renal pathology and kidney function between these groups, both demonstrated similar risks of progressing to ESKD. Nevertheless, it's crucial to underscore the significant influence of ILD on the overall outcomes of AAV patients with kidney involvement.
#71 Dysregulation of ITGAM and ITGB2 in the pathogenesis of diabetic kidney disease—results from bioinformatics analysis and in vitro studies
Authors: Yap Desmond , Xie Ruiyan , Jason Sher Ka Ho , Tang Sin Yu Cindy , Wu Qiongli 
Published: May 2024

Abstract

Background and Aims
Activated neutrophils can release web-like chromatin structures known as neutrophil extracellular traps (NETs), but their roles in the immunopathogenesis of diabetic kidney disease (DKD) remains elusive.

Method
The characteristic NETs associated targets of differentially expressed genes (DEGs) from human kidney biopsy datasets of patients with DKD (GSE30528 and GSE30529) were identified by machine learning method (LASSO and SVM-RFE). The genes expression was further validated using kidney biopsy dataset of GSE142025. The most abundant single cell of the targets in DKD was further selected by single-nucleus RNA sequencing datasets (GSE131882). Predictive pathway network of targeted genes was constructed using GENEMANIA database. The expressions and potential signaling pathway of these candidate genes were validated using flow cytometry and ELISA.

Results
Three predicting NETs related genes (ITGAM, ITGB2 and TLR7), identified by machine learning algorithms, which all showed significant upregulation in both glomerular and tubulointerstitial compartments in human DKD kidney samples. Single-cell analysis suggested that ITGAM, ITGB2 and TLR7 were most enriched in leucocytes. DKD patients (n = 18) showed significantly higher activated neutrophils as well as increased expression of ITGAM and ITGB2 compared to healthy controls (HCs, n = 9). DKD patients also exhibited higher serum levels of IL6 but lower IL-10 than HCs (all p &lt; 0.01). The significant network of IL10, IL6, ITGAM and ITGB2 was generated. This network might be associated with leukocyte activation, macrophage activation, JAK-STAT pathway, acute inflammatory response and lymphocyte immune response (all p &lt; 0.05).

Conclusion
Aberrant ITGAM and ITGB2 expressions in activated neutrophils contribute to DKD pathogenesis and may serve as novel therapeutic targets for DKD.
#314 Systemic lupus erythematous (SLE) and isolated multiple sclerosis: analysis of BAFF—VAR variant on gene TNSF13B
Authors: Orfeo Chiara Alessia , Vezzani Valeria , Capone Martina , Bonomini Mario 
Published: May 2024

Abstract

Background and Aims
We report a case of young a woman (33 years old) affected by SLE since 2007. In this year, a renal biopsy showed class IV lupus nephritis and the patient received corticosteroids and immunosuppressant for 3 years. The patient remained thereafter in disease remission with normal renal function, no proteinuria and normal complement levels.
In 2013 the patient performed brain MRI for sudden hearing loss. The MRI showed a pattern compatible with isolated multiple sclerosis (RIS), confirmed on subsequent radiographic checks. In 2023, due to the initial onset of renal failure, a new re-staging biopsy showed microscopic aspects compatible with class I/II lupus nephritis (INS/RPS Classification 2004, 2018); the activity index calculated with SLEDAI—2K was +4.
A new brain MRI carried out without onset of new symptoms showed a new hyperintense region at the level of the head of the right caudate nucleus and enlargement of the intrasellar CSF content as per the condition of a “partially empty” sella.
A genetic variant of the TNFSF13B gene was therefore suspected, since it is involved in encoding the cytochine and drug target B-cell activating factor (BAFF), associated with multiple sclerosis as well as SLE.
We searched for the genetic variant in order to undertake target therapy early in our patient.

Method
We performed PCR amplification and direct sequencing of all coding exons plus all the intron-exon junctions of the analyzed gene, by automatic sequencer with SeqStudio Genetic Analyzer (analytical sensitivity and specificity &gt;99%).

Results
We found the heterozygous presence of the BAFF-var variant in the 3' UTR region of the TNFSF13B gene (Heterozygous genotype for BAFF-var). This variant involves an insertion/deletion (GCTGT&gt;A) at the level of the 3' UTR region with consequent production of an alternative polyadenylation site (APA). This APA leads to the formation of a shorter transcript (BAFF-var mRNA) which causes greater production of the encoded protein compared to the wild-type transcript (BAFF-WT mRNA).

Conclusion
The molecular analysis conducted highlighted the presence of the BAFF-var variant in heterozygosis which leads to increased levels of soluble BAFF in the serum, with consequent up-regulation of humoral immunity. It is reported in the literature1 that this variant is associated with both Multiple Sclerosis and SLE and may represent a valid therapeutic target being treatable with the monoclonal antibody Belimumab.