Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

BACKGROUND: Long-read sequencing is increasingly used to uncover structural variants in the human genome, both functionally neutral and deleterious. Structural variants occur more frequently in regions with a high homology or repetitive segments, and one rearrangement may predispose to additional events. Bartter syndrome type 3 (BS 3) is a monogenic tubulopathy caused by deleterious variants in the chloride channel gene CLCNKB, a high proportion of these being large gene deletions. Multiplex ligation-dependent probe amplification, the current diagnostic gold standard for this type of mutation, will indicate a simple homozygous gene deletion in biallelic deletion carriers. However, since the phenotypic spectrum of BS 3 is broad even among biallelic deletion carriers, we undertook a more detailed analysis of precise breakpoint regions and genomic structure. METHODS: Structural variants in 32 BS 3 patients from 29 families and one BS4b patient with CLCNKB deletions were investigated using long-read and synthetic long-read sequencing, as well as targeted long-read sequencing approaches. RESULTS: We report a ~3 kb duplication of 3'-UTR CLCNKB material transposed to the corresponding locus of the neighbouring CLCNKA gene, also found on ~50 % of alleles in healthy control individuals. This previously unknown common haplotype is significantly enriched in our cohort of patients with CLCNKB deletions (45 of 51 alleles with haplotype information, 2.2 kb and 3.0 kb transposition taken together, p=9.16×10-9). Breakpoint coordinates for the CLCNKB deletion were identifiable in 28 patients, with three being compound heterozygous. In total, eight different alleles were found, one of them a complex rearrangement with three breakpoint regions. Two patients had different CLCNKA/CLCNKB hybrid genes encoding a predicted CLCNKA/CLCNKB hybrid protein with likely residual function. CONCLUSIONS: The presence of multiple different deletion alleles in our cohort suggests that large CLCNKB gene deletions originated from many independently recurring genomic events clustered in a few hot spots. The uncovered associated sequence transposition haplotype apparently predisposes to these additional events. The spectrum of CLCNKB deletion alleles is broader than expected and likely still incomplete, but represents an obvious candidate for future genotype/phenotype association studies. We suggest a sensitive and cost-efficient approach, consisting of indirect sequence capture and long-read sequencing, to analyse disease-relevant structural variant hotspots in general

NPHP4, a cilia-associated protein, negatively regulates the Hippo pathway

The cilia-associated protein NPHP4 is a negative regulator of Hippo signaling that modulates cell proliferation in mammals

Angina Pectoris in a Young Woman with Lupus Erythematosus

History and clinical findings We present a 31-year old woman with a 6-year history of cutaneous lupus erythematosus (CLE) who presented to the emergency room with typical chest pain. ECG and transthoracic echocardiography were normal. Her working diagnosis of pericarditis was made due to systemic progression of her lupus erythematosus (LE). Treatment with NSAIDs was initiated and her immunosuppressive regimen intensified. The patient was discharged after resolution of her symptoms. A week later, the patient was seen at the rheumatology clinic with recurrence and aggravation of her symptoms. She was found to have elevated troponin and cardiac enzymes and therefore underwent cardiac catheterization, revealing three vessel coronary artery disease. Therapy and course The patient underwent urgent open surgical myocardial revascularization. Despite the immunosuppressive therapy the postoperative course was uneventful. Conclusions The risk for coronary artery disease in LE patients is very high. Particularly in young women presenting with chest pain, regardless of typical cardiopulmonary manifestations of LE such as pericarditis and pleurisy, acute coronary syndrome should always be considered

Quantification of molecular heterogeneity in kidney tissue by targeted proteomics

Renal diseases are driven by alterations in the entity of proteins within the kidney, at the level of single cells, nephron subunits (such as glomerulus and tubule), tissues and body fluids. Histologically, kidney diseases are extremely heterogeneous. Mass-spectrometry based proteomics provides a unique opportunity to interrogate heterogeneity and dynamics of various proteome layers within the kidney to better understand physiology and pathophysiology, and to translate signaling networks into therapies. Yet, the success of this endeavor will largely depend on improving proteomic data acquisition methods toward increased reproducibility. Here, we provide an overview of targeted proteomics studies in renal tissue and their insights into major renal diseases such as diabetic nephropathy, acute kidney injury and chronic kidney disease. The technical approaches currently include antibody-based and mass spectrometry based approaches, range from single-cells to single-nephrons to bulk tissue proteomic acquisitions, and are applied to physiological studies and translational approaches in biomarker discovery. Within this context, we identify key challenges in proteomics of kidney biopsies. We also suggest that novel models of translational nephrology have increased need for targeted acquisition of proteomics data with focus on primary urinary cells, organoids and induced renal epithelial cells (IRECs). In conclusion, targeted proteomics will be very beneficial to identify heterogenic disease mechanisms that drive renal disease and further emerge as an important tool in translational kidney research. Significance: Improved targeted proteomics technologies will be an important cornerstone of renal systems medicine in order to identify and tackle the heterogenic disease mechanisms driving renal disease

Mice lacking microRNAs in Pax8-expressing cells develop hypothyroidism and end-stage renal failure

Background: Non-coding RNAs have gained increasing attention during the last decade. The first large group of non-coding RNAs to be characterized systematically starting at the beginning of the 21st century were small oligonucleotides-the so-called microRNAs (miRNAs). By now we have learnt that microRNAs are indispensable for most biological processes including organogenesis and maintenance of organ structure and function. The role of microRNAs has been studied extensively in the development of a number of organs, so far most studies focussed on e.g. the heart or the brain whilst the role of microRNAs in the development and maintenance of complex epithelial organs is less well understood. Furthermore most analyses regarding microRNA function in epithelial organs employed conditional knockout mouse models of the RNAse III Dicer to abrogate microRNA biogenesis. However, there is increasing evidence for Dicer to have multiple functions independent from microRNA maturation. Therefore Dicer independent models are needed to gain further insight into the complex biology of miRNA dependent processes. Results: Here we analyze the contribution of microRNA-dependent transcriptional control in Pax8-expressing epithelial cells. Pax8 is a transcription factor that is crucial to the development of epithelial organs. The miRNA machinery was disrupted by crossing conditional DiGeorge syndrome critical region 8 (Dgcr8) fl/fl mice to Pax8Cre mice. The Dgcr8/Drosha complex processes pri-miRNAs in the nucleus before they are exported as pre-miRNAs for further maturation by Dicer in the cytoplasm. Dgcr8 fl/fl; Pax8Cre+ knockout mice died prematurely, developed massive hypothyroidism and end stage renal disease due to a loss of miRNAs in Pax8 expressing tissue. Conclusion: Pax8Cre-mediated conditional loss of DiGeorge syndrome critical region 8 (Dgcr8), an essential component of the nuclear machinery that is required for microRNA biogenesis, resulted in severe hypothyroidism, massively reduced body weight and ultimately led to renal failure and death of the animals. These data provide further insight into the importance of miRNAs in organ homeostasis using a Dicer independent model

A Tailored Discharge Program Improves Frailty and Mood in Patients Undergoing Usual Rehabilitative Care: A Randomized Controlled Trial

Objective: To investigate whether a tailored intersectoral discharge program (TIDP) impacts on multidimensional frailty, rehospitalization days, and patient-related outcome measures in older in-patients undergoing acute care and usual rehabilitative care. Design: Randomized controlled trial of TIDP vs usual rehabilitative care with a 6-month follow-up, 2019 e2020, and historical control with a 6-month follow-up, 2016-2019. Setting and Participants: Geriatric co-managed internal medicine ward of a metropolitan university hospital. One hundred-twelve multimorbid patients older than age 60 years were consecutively assessed for eligibility and inclusion (age >= 60 years, multimorbidity, admitted for treatment of acute disease, at least 2 geriatric syndromes requiring usual rehabilitative care, and able to consent) and signed informed consent, with 110 recruited and randomized to either TIDP or usual rehabilitative care. At discharge, 104 patients were alive in the intention-to-treat group, the 6-month follow-up was completed for 91 patients. A historical control group of 468 patients was included for comparison. Methods: Fifty-four patients underwent TIDP, 53 patients underwent usual rehabilitative care only. Rehospitalization days at follow-up as primary endpoint; multidimensional frailty and prognosis (Multidimensional Prognostic Index, Geriatric Depression Scale, Rosenberg Self-Esteem Scale, quality of life, falls, mortality, home care service need, and need of long-term care at 1-, 3- and 6-month follow-up as secondary endpoints.Intervention: TIDP as intervention included contact with treating general practitioner to discuss the further treatment plan, a structured medical and lifestyle counseling to patients and caregivers at admission as well as a discharge program with internist, geriatrician, and general practitioner in shared decision making with patients. Results: TIDP (median age 76.0 years, 56% female) showed significantly improved Multidimensional Prognostic Index scores at discharge compared with usual rehabilitative care (median age 78.5 years, 58% female) (0.43 vs 0.49, P =.011). Compared with usual rehabilitative care, TIDP improved self-confidence (Rosenberg Self-Esteem Scale 13.9 vs 12.4, P =.009) and mood (Geriatric Depression Scale 4 vs 5, P =.027) at follow-up. Compared with historical control (median age 77.0 years, 39 % female), usual rehabilitative care patients showed significantly lower rehospitalization rates (53% vs 70%, P =.002) and lower mortality rates (13% vs 32%, P <.001). Conclusions and Implications: A feasible TIDP improves frailty and mood in advanced age. In older patients undergoing potentially disabling acute treatments, usual rehabilitative care significantly reduces rehospitalization rates. Therefore, implementing geriatric treatment in general is useful to improve outcomes in older in-patients and a tailored discharge program can further increase the benefit for this frail population. (c) 2022 AMDA e The Society for Post-Acute and Long-Term Care Medicine

Case report: a peculiar glomerulopathy in a patient suffering from nephrotic syndrome

Background Podocyte infolding glomerulopathy (PIG) is a rare histopathologic finding with global infolding of the podocytes into the glomerular basement membrane (GBM), accompanied by microstructures underneath. Described in 2002 for the first time, PIG was proposed as a new pathological entity in 2008 based on the largest case series so far. Yet all of the described cases derive from Asian countries. We report a case from Germany fulfilling the diagnostic criteria of PIG. Considering the scarcity of data on this entity especially in Western countries, collecting cases like ours and multicentric meta-analyses will be crucial to obtain a better understanding of PIG, its causes, clinical course and potential treatment options. Case presentation A 56-year-old Caucasian woman with a history of rheumatoid arthritis (RA), no other comorbidities and no known renal disease was admitted to the hospital with acute kidney injury (AKI) and nephrotic syndrome. Physical examination was unremarkable except for anasarca. Renal ultrasound revealed no abnormalities. Laboratory and urine analyses were consistent with the nephrotic syndrome and renal failure. Serological studies regarding ANA, ANCA, anti-PLA2R autoantibodies, complement, virus infections, immunofixation and quantitative light chain analysis were unremarkable. A renal biopsy was performed. Light microscopic examination showed flattened tubular epithelium consistent with acute tubular damage, no infiltrates and unremarkable glomeruli except diffuse and global holes in the GBM (Fig. 1a) and negative staining for immunoglobulin heavy-chains, light-chains and complement split products. Electron microscopy revealed a rare correlate for these holes: global peculiar infolding of podocyte cytoplasm into the GBM. Most of these infoldings were accompanied by condensation of the GBM underneath. No such condensation or electron dense deposits were found without these infoldings or outside the GBM. Conclusion Here we report the first case of PIG outside of Asia. Since there are only few reports about this specific finding, we feel there is a need to share information in an attempt to accumulate knowledge about this possible new entity and potential treatment options

Effectiveness and safety of immunoadsorption as a rescue treatment of inflammatory myopathies: report of three cases and literature review

Idiopathic inflammatory myopathy (IIM) summarizes rare, systemic autoimmune conditions primarily characterized by inflammatory damage to the skeletal muscle. Although primary damage occurs to the muscle, these IIM-related conditions involve other organs, including the skin, lungs, upper gastrointestinal tract, joints, and heart. While many patients have an adequate response to immunosuppressive treatment, some patients develop rapidly progressive and treatment-resistant life-threatening courses. Treatment-resistant IIM is challenging for the treating physician and requires interdisciplinary and individualized treatment approaches. Extracorporeal therapy is one option for rescue therapy, with immunoadsorption (IA) having proven more effective than plasma exchange regarding the removal of circulating antibodies. Despite its efficacy and desirable safety profile, the clinical value of IA use in IIM is understudied with no controlled trials reported. Here, we present a review of the current knowledge regarding the management of treatment-resistant IIM and the cases of three patients with treatment-resistant IIM (two with dermatomyositis and one with immune-mediated necrotizing myopathy) who have successfully been treated with IA. All patients responded well to the therapy and experienced no IA-related complications. Taken together, we found IA to be a safe and effective treatment option in treatment-resistant IIM

Label-free quantitative proteomic analysis of the YAP/TAZ interactome

The function of an individual protein is typically defined by protein-protein interactions orchestrating the formation of large complexes critical for a wide variety of biological processes. Over the last decade the analysis of purified protein complexes by mass spectrometry became a key technique to identify protein-protein interactions. We present a fast and straightforward approach for analyses of interacting proteins combining a Flp-in single-copy cellular integration system and single-step affinity purification with single-shot mass spectrometry analysis. We applied this protocol to the analysis of the YAP and TAZ interactome. YAP and TAZ are the downstream effectors of the mammalian Hippo tumor suppressor pathway. Our study provides comprehensive interactomes for both YAP and TAZ and does not only confirm the majority of previously described interactors but, strikingly, revealed uncharacterized interaction partners that affect YAP/TAZ TEAD-dependent transcription. Among these newly identified candidates are Rassf8, thymopoetin, and the transcription factors CCAAT/enhancer-binding protein (C/EBP)beta/delta and core-binding factor subunit beta (Cbfb). In addition, our data allowed insights into complex stoichiometry and uncovered discrepancies between the YAP and TAZ interactomes. Taken together, the stringent approach presented here could help to significantly sharpen the understanding of protein-protein networks