bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDsrv: visual sharing and analysis of molecular dynamics simulations
Authors: Kampfrath Michelle , Staritzbichler René , Hernández Guillermo Pérez , Rose Alexander S , Tiemann Johanna K S , Scheuermann Gerik , Wiegreffe Daniel , Hildebrand Peter W 
Published: May 2022

Abstract
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, based on Mol*, MDsrv now provides faster and more efficient visualization of even large trajectories compared to its predecessor tool NGL.
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)
Authors: Karmakar Shilpita , Ramirez Oscar , Paul Kiran V , Gupta Abhishek K , Kumari Vandana , Botti Valentina , de los Mozos Igor Ruiz , Neuenkirchen Nils , Ross Robert J , Karanicolas John , Neugebauer Karla M , Pillai Manoj M 
Published: May 2022

Abstract
Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3′ untranslated regions (3′UTRs) of mRNA, but the identity of functional targets remains unknown. Here, we used individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of mRNAs largely in 3′UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more ‘UAG’ motifs compared to targets bound nonproductively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute loss. Using complementary approaches, we determined eukaryotic translation initiation factor 3A (EIF3A) to be an immediate, direct target. We propose that MSI2 downregulation of EIF3A amplifies these effects on translation. Our results also underscore the challenges in defining functional targets of RBPs since mere binding does not imply a discernible functional interaction.
MO009: Creatine-Kinase Elevation in Autosomal Dominant Polycystic Kidney Disease Patients on Tolvaptan Treatment
Authors: Rodríguez Espinosa Diana , Jesus Broseta Monzo Jose , Cuadrado Elena , Fernando Quintana Porras Luis , Poch Esteban , Piñeiro Gaston , Agraz Irene , Sánchez-Baya Maya , Furlano Monica , Ruiz César , Torra Roser , Blasco Miquel 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary cause of end-stage kidney disease. Currently, tolvaptan is the only treatment that has proven to delay disease progression. The most notable side-effect of this therapy is drug-induced liver injury; however, recently, there have been two reports of creatine kinase (CK) elevation in ADPKD patients on tolvaptan treatment. We set out to monitor and determine the actual incidence of CK elevation and evaluate its potential association with other clinical factors.

METHOD
This is an observational prospective multicenter study performed in rapidly progressive ADPKD patients on tolvaptan treatment from Barcelona, Spain. Laboratory tests, demographics, treatment dose and reported symptoms were collected from October 2018 to March 2021.

RESULTS
Ninety-five patients initiated tolvaptan treatment during follow-up. The medication had to be discontinued in 31 (32.6%) patients, primarily due to aquaretic effects (12.6%), elevated liver enzymes (8.4%) and symptomatic or persistently elevated CK levels (3.2%). Moreover, a total of 27 (28.4%) patients elevated CK levels, with most of them being either transient (12.6%), mild and asymptomatic (4.2%), or resolved after dose reduction (3.2%) or temporary discontinuation (2.1%).

CONCLUSION
We present the largest cohort that has monitored CK levels in a real-life setting, finding them elevated in 28.4% of patients. More research and monitoring will help us understand the clinical implications and the pathophysiological mechanism of CK elevation in this population.
MO044: Cellular mechanism of the exceptional dominant transmission in NPHS2-associated glomerulopathy
Authors: Seidl Dániel , Antal-Kónya Violetta , Schay Gusztáv , Bertholet-Thomas Aurélia , Török György , Mollet Geraldine , Kellermayer Miklós , Antignac Corinne , Tory Kálmán 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Mutations of NPHS2 cause autosomal recessive steroid-resistant nephrotic syndrome (SRNS). The encoded podocin, a key component of the slit diaphragm, homo-oligomerizes through two C-terminal oligomerization sites. We formerly found that specific podocin variants may exert a dominant negative effect against R229Q podocin variant secondary to an altered oligomerization [1, 2]. Recently, two families with autosomal dominant focal segmental glomerulosclerosis were found to carry a de novo heterozygous NPHS2 last-exon frameshift mutations affecting the second oligomerization site (either c.989_992delTGTC, p.L330Pfs*17 or c.988_989delCT, p.L330Vfs*15) [3]. We hypothesized that these podocin variants exert a dominant negative effect against wild type (WT) podocin.

METHODS
We coexpressed eGFP-tagged WT podocin with either hemagglutinin-tagged (HA) WT, p.L330Pfs*17 or p.L330Vfs*15 podocin variants in cultured podocytes. Plasma membrane was stained with CF405M-conjugated wheat germ agglutinin (WGA), and immunohistochemical staining was performed with primary anti-HA and secondary AlexaFluor568-conjugated antibodies. All analysis was done in a blinded fashion. The membrane-targeting of podocin was assessed by the ratio of the WGA-labeled perimembranous area that colocalized with podocin (Mander's overlap coefficients, MOC) and the colocalization of the coexpressed variants were estimated as Pearson correlation coefficients (PCC) by FiJi software on confocal microscopic images. MOC and PCC were compared by Holmes–Bonferroni adjusted Wilcoxon signed-rank test.

RESULTS
The frameshift podocin variants were not membranous in monoexpression [MOC: HA-p.L330Pfs*17 (n = 26): 0.08 (0.03–0.22) median (interquartile ranges); HA-p.L330Vfs*15 (n = 24): 0.07 (0.02–0.16)]. The GFP-tagged WT podocin strongly colocalized with the HA-tagged WT or frameshift podocin variants [PCC: WT-eGFP + HA-WT (n = 19): 0.64 (0.49–0.71); WT-eGFP + HA-L330Pfs*17 (n = 17): 0.54 (0.35–0.58); WT-eGFP + HA-L330Vfs*15 (n = 17): 0.44 (0.29–0.66)]. The GFP-WT podocin was retained in intracellular compartments in the presence of any of the two frameshift podocin variants [MOCWT(WT) = 0.58 (0.46–0.69)], MOCWT(L330Pfs*17) = 0.01 (0.002–0.029), P = 2x10-6 versus WT(WT); MOCWT(L330Vfs*15) = 0.003 (0.001–0.013), P = 2 x 10−6 versus WT(WT)].

CONCLUSIONS
The dominant podocin variants retain WT podocin in intracellular compartments explaining the exceptional dominant transmission of NPHS2-associated glomerulopathy. This is in accordance with our former results showing the primary role of C-terminal hetero-oligomerization in exerting interallelic interactions of NPHS2 alleles.

FUNDING
MTA-SE Lendulet Research Grant (LP2015-11/2015), OTKA KH125566 and K135798, and ÚNKP-20–3-I-SE-29 from the source of the National Research, Development and Innovation Fund.
MO047: Biallelic pathogenic variants in ROBO1 associate with syndromic CAKUT
Authors: Münch Johannes , Engesser Marie , Schönauer Ria , Hamm J Austin , Akay Gulsen , Tüysüz Beyhan , Shirakawa Toshihiko , Dateki Sumito , Claus Laura , van Eerde Albertien M , Wagner Timo , Bergmann Carsten , Buchan Jillian , Wegner Tara , Posey Jennifer , Lupski James R , Petit Florence , Mccarthy Andrew A , Pazour Gregory J , Lo Cecilia W , Popp Bernt , Halbritter Jan 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Congenital anomalies of the kidney and urinary tract (CAKUT) represent the most common cause of chronic kidney failure in children. Despite growing knowledge of the genetic causes of CAKUT, the majority of cases remain etiologically unsolved. Genetic alterations in roundabout guidance receptor 1 (ROBO1) have been associated with neuronal and cardiac developmental defects in living individuals. Although Slit-Robo signaling is pivotal for kidney development, diagnostic ROBO1 variants have not been reported in viable CAKUT to date.

METHOD
We collected phenotypic data of all participants. Genetic analysis was conducted by either exome or whole genome sequencing, respectively. We used Sanger sequencing for variant confirmation and segregation analysis and performed in-silico analysis of identified missense variants. In an ENU-induced mouse model, we examined mice with the mutation Robo1Ile270Thr/Ile270Thr.

RESULTS
By next-generation-sequencing methods, we identified six unrelated individuals and two non-viable fetuses from Germany, France, Turkey, Japan and the USA with biallelic truncating or combined missense and truncating variants in ROBO1. Renal and genitourinary manifestation included unilateral or bilateral renal agenesis, vesicoureteral junction obstruction, vesicoureteral reflux, posterior urethral valve, genital malformation and increased renal echogenicity. Further clinical characteristics were remarkably heterogeneous, including neurodevelopmental defects, intellectual impairment, cerebral malformations, eye anomalies, and cardiac defects (Figure 1).
By in-silico analysis, we determined the functional significance of identified missense variants and observed absence of renal ROBO1 expression in both human and murine mutant tissues (Figure 2).

CONCLUSION
This study describes six live-born and two non-viable individuals with syndromic CAKUT due to probably deleterious ROBO1 variants. While its expression in multiple tissues may explain heterogeneous organ involvement, variability of kidney disease suggests gene dosage effects due to a combination of null alleles with mild hypomorphic alleles. In conclusion, comprehensive genetic analysis in CAKUT should include ROBO1 as a new cause of recessively inherited disease. Conversely, in patients with already established ROBO1-associated cardiac or neuronal disorders, screening for renal involvement is indicated.
MO059: Trajectory Analysis of the Kidney Organoid Proteome Extends its Modelling Potential of Disease
Authors: Lassé Moritz , Bonin Léna L , El Saghir Jamal , Eddy Sean F , Hutzfeldt Arvid , Hoxha Elion , Dumoulin Bernhard , Lindenmeyer Maja , Schlüter Hartmut , Beck Bodo B , Brandts Paul , Kretzler Matthias , Demir Fatih , Harder Jennifer L , Rinschen Markus 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. It is unclear how their proteome changes during differentiation, and if more complex disease processes such as inflammatory tissue responses could be modelled with this approach.

METHOD
Here, we used proteomics to compare organoids with existing model systems such as native glomeruli and cultured cells. We characterize the trajectory of organoid differentiation and delineate innate immune responses in organoids to expand its scope as a model system in nephrology. We also compared our proteomics with bulk and single cell transcriptomic data.

RESULTS
Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. A novel signaling system discovered was the TNFα system, a system also available in podocytes. Incubation of organoids with high concentrations of TNFα led to an activation of NF-kB signaling, and secretion of cytokines and complement components, alongside with extracellular matrix components.

CONCLUSION
Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement, and production of extracellular matrix. Thus, we provide a repository of human kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases.
MO079: Treatment with Nebivolol Ameliorates Renovascular Alterations and Oxidative Stress in Tenofovir-Induced Nephrotoxicity in Rats
Authors: Moura Nascimento Mariana , Bernardo Desiree , Carolina de Braganca Ana , Heloisa Massola Shimizu Maria , Carlos Seguro Antonio , Aparecido Volpini Rildo , Canale Daniele 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Human immunodeficiency virus (HIV) continues to be a major global public health issue, having claimed millions of lives so far. Tenofovir disoproxil fumarate (TDF), a widely prescribed component in antiretroviral regimens for HIV treatment, has been associated with nephrotoxicity. Nebivolol (NBV) is a third generation selective β-1 adrenergic receptor blocker currently used in the treatment of hypertension and cardiovascular diseases. The potential mechanisms by which NBV may protect renal structure and function include suppression of oxidative stress and enhancement of nitric oxide synthesis. The aim of this study was to investigate whether NBV could be an effective therapeutic option to mitigate TDF-induced nephrotoxicity.

METHOD
We divided Wistar rats into four groups: control (C, n = 8), received a standard diet for 30 days; TDF (n = 9), received a standard diet with the addition of TDF (300 mg/kg food) for 30 days; NBV (n = 8), received a standard diet for 30 days with the addition of NBV (100 mg/kg food) in the last 15 days; and TDF + NBV (n = 9), received a standard diet with the addition of TDF for 30 days and NBV in the last 15 days. We evaluated inulin clearance (GFR); tubular injury; mean arterial pressure (MAP); renal blood flow (RBF) and calculated renal vascular resistance (RVR); plasma and tissue angiotensin II (AIIp and AIIt, respectively); plasma aldosterone; plasma asymmetric dimethylarginine (ADMA); plasma and urinary thiobarbituric acid reactive substances (TBARSp and TBARSu, respectively); and whole blood glutathione (GSH). In renal tissue, we immunoblotted for endothelial nitric oxide synthase (eNOS), p47phox and p67phox. Data are expressed as mean ± SEM.

RESULTS
TDF + NBV rats showed an improvement in renal function, a normalization of MAP and attenuation in renal vasoconstriction, evidenced by increased RBF and diminished RVR. Administration of NBV also reduced AII and aldosterone levels in TDF-treated animals. Furthermore, the TDF + NBV group showed a lower plasma ADMA concentration and a higher protein expression of eNOS. Treatment with NBV was responsible for the maintenance of an adequate balance of TBARS and GSH levels, and it was associated with reductions in renal p47phox and p67phox. All results are described in Table 1.

CONCLUSION
Our data demonstrated the protective role of NBV in TDF-induced nephrotoxicity. The beneficial effects of NBV include a reduction in oxidative stress and RAAS activation, as well as a decrease in endothelial dysfunction, observed by an upregulation on the NO cascade. Therefore, NBV may be an effective therapeutic strategy in the treatment of patients with TDF-induced nephrotoxicity. Financial support: CAPES and FAPESP (2019/20840–0, 2018/12297–1, 2018/04930–6).
MO096: Chronic Liver Disease and Hepatic Calcium-Oxalate Deposition in Patients with Primary Hyperoxaluria Type I
Authors: Recker Pia , Beck Bodo B , Sikora Przemyslaw , Göbel Heike , Kemper Markus , Nazco Angel , Martin Higueras Cristina , Hoppe Bernd 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Patients with primary hyperoxaluria type I (PH I) are prone to develop early end-stage kidney failure (ESKF). Systemic deposition of calcium-oxalate (CaOx) crystals starts when renal function declines and plasma oxalate (Pox) increases &gt;30 µmol/L. It is anticipated that all parenchymal organs, but also bone (marrow), retina and the central nervous system can be involved. However, liver involvement, either as CaOx deposition or as chronic hepatitis/fibrosis, was never reported.

METHOD
We now examined liver involvement in 19 patients with PH I aged 1.5–52 years. Liver specimen was obtained by biopsy for diagnostic purposes (1), at autopsy (1) or at the time of combined or sequential liver kidney transplantation (17).

RESULTS
With polarization microscopy, crystals with the typical star-like appearance of CaOx were found in 3/19 patients. The crystals were located in small arteries but not within hepatocytes. Cirrhosis was seen in one patient. Fibrosis was seen in 10/19 patients, with porto-portal and nodular fibrosis (n = 1), and a limitation of fibrosis to the portal field in eight and/or to central areas in five patients. Unspecific hepatitis features were observed in seven patients. Fiber proliferations were detectable in 10 cases, and in one sample, transformed Ito-cells (myofibroblasts) were found. Iron deposition but also megakaryocytes as a sign of extramedullary erythropoiesis were found in nine and three patients, respectively.

CONCLUSION
Overall, liver involvement in patients with PH I was more pronounced, as previously described. However, compared with CaOx deposition in other organs/tissue, such crystal accumulations were only minimal in the liver, although the oxalate concentration must be the highest.
MO101: Atypical Haemolytic Uremic Syndrome Associated with COVID-19: Case Report
Authors: Gjyzari (Velaj) Albana , Muco Ermira , Como Najada 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Renal manifestations are common in hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report here the case of a patient with confirmed SARS-CoV-2 infection with the clinical picture of atypical haemolytic uremic syndrome (aHUS).

METHOD
Case report

RESULTS
Our case is a 31-year-old man with a nasopharyngeal swab with real-time reverse-transcriptase polymerase chain reaction (RT-PCR) for SARS-CoV-2 positive, who was hospitalized in the Clinic of Infectious Diseases. His medical history had a respiratory illness of 7-day evolution characterized by cough, fever, dyspnoea, muscle pain, nausea, vomiting and non-bloody diarrhoea, and decreased urine output with dark colour urine. The chest computed tomography (CT) scan showed few rounded ground-glass opacities.
Laboratory tests at admission revealed the following: (i) acute kidney injury stage 3 with a serum creatinine of 3.85 mg/dL (basal value 0.9 mg/dL); serum urea 221 mg/dL. His urinary volume in the first 24 h of hospitalization was 800 mL. (ii) Severe haemolytic anaemia with haemoglobin (Hgb) level of 3.7 g/dL, and peripheral smear showing large number of schistocytes, haptoglobin &lt;10 mg/dL and indirect bilirubin 9.7 mg/dL, direct coombs testing was negative; reticulocyte count 8.9%. (iii) Severe thrombocytopaenia with platelet count of 25 000/µL, prothrombin time 45%, international normalized ratio 1.7, D-dimer 1082 ng/dL and fibrinogen 880 mg/dL.
Increased blood levels of enzymes and inflammatory markers were present: lactate dehydrogenase 1867 U/L and protein C reactive 9.1 mg/dL. Electrolyte disturbances characterized by hyperkalaemia, hyperphosphatemia, hypocalcaemia and severe metabolic acidosis. Dynamic changes of laboratory data are presented in Table 1.
The usual liver panel tests, alkaline phosphatase, γ-glutamyl transferase and albuminemia were normal. Toxic hepatitis was excluded. Hepatobiliary and spleen imaging (ultrasonography) was normal.
ELISA serologic tests for HIV, hepatitis B, hepatitis C virus and cytomegalovirus were negative. Serological and virological tests for hepatitis A, B, C, HIV and CMV were negative. Stool was negative for Shiga toxin-producing Escherichia coli (STEC).
The results of antinuclear antibodies and anti-smooth-muscle antibodies were negative, C3 serum level was mildly depressed (82 mg/dL; normal range 88–201 mg/dL) and C4 serum level was normal (20 mg/dL; normal range 10–44 mg/dL). ADAMTS13 activity was 90% on day 10.
He was treated with broad spectrum antibiotics, intravenous dexamethasone and supportive therapy. One week from admission, renal function recovered, and 1 week after intravascular haemolysis and thrombocytopaenia recovered. The patient was hospitalized for 21 days.

CONCLUSION
Close monitoring and early intervention can help for a better outcome of SARS-CoV-2 patients complicated with aHUS.
MO102: Lean Tissue, as Assessed by Bioimpedance Spectroscopy, Is Dependent on Renal Function in Patients with HFREF
Authors: Popa Raluca , Sascau Radu , Statescu Cristian , Siriopol Ianis , Vasiliu Vlad , Neamtu Andreea , Bucur Andreea , Kanbay Mehmet , Siriopol Dimitrie 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Despite impressive improvements in treatment strategies, heart failure (HF) morbidity and mortality remain substantially high worldwide. Muscle wasting is common and is associated with increased morbidity and mortality in patients with HF. The aim of the study was to determine muscle mass, by bioimpedance spectroscopy (BIS), and to identify factors associated with decreased muscle mass in this population.

METHOD
This was a prospective observational study of outpatient adults referred for clinically indicated transthoracic echocardiograms at an academic hospital between 2016 and 2018. A left ventricular ejection fraction below 45% was required for inclusion (HFrEF).
Muscle mass was assessed using BIS (with the body composition monitor—BCM® device).

RESULTS
Our study included 151 patients. The mean age and eGFR values of the population at baseline were 67.1 years and 66.5 mL/min/1.73 m2. The median levels for lean tissue index (LTI, lean tissue mass/height2) were 11.3 (IQR 9.4–12.9) kg/m2.
LTI was positively associated with eGFR and negatively associated with uric acid, ST-2 and galectin-3 levels. Including all these variables in a stepwise multivariable regression only eGFR and ST-2 remained independently associated with LTI (see Table 1).
Based on the LTI median value, we also divided the patients into two groups—group 1 (LTI ≤ 11.3 kg/m2) and group 2 (LTI &gt; 11.3 kg/m2). In the univariable logistic regression age, using the haemoglobin, eGFR and ST-2 levels predicted the group appurtenance. Including all these variables in a stepwise multivariable logistic regression, only eGFR and eGFR remained independently associated with LTI groups (see Table 2).

CONCLUSION
A better understanding of the factors associated with decreased muscle mass is needed to develop preventive strategies for muscle wasting in patients with HF. Muscle mass, as measured by the BCM and expressed as the LTI, is strongly associated with eGFR.