bims-bicyki 2022-02-27 papers

bims-bicyki

Biomed News

on Bicaudal-C1 and interactors in cystic kidney disease

Issue of 2022–02–27
seventeen papers selected by
Céline Gagnieux, École Polytechnique Fédérale de Lausanne

Detection of DZIP1L mutations by whole-exome sequencing in consanguineous families with polycystic kidney disease.
Pericardial Effusion on MRI in Autosomal Dominant Polycystic Kidney Disease.
IRIS-Intelligent Rapid Interactive Segmentation for Measuring Liver Cyst Volumes in Autosomal Dominant Polycystic Kidney Disease.
Establishing a core outcome measure for pain in patients with autosomal dominant polycystic kidney disease: a consensus workshop report.
Volume Progression and Imaging Classification of Polycystic Liver in Early Autosomal Dominant Polycystic Kidney Disease.
Association of autosomal dominant polycystic kidney disease with cardiovascular disease: a US-National Inpatient Perspective.
Stone Prevalence in Autosomal Dominant Polycystic Kidney Disease: A Systematic Review and Meta-Analysis.
Increased Body Fat and Organic Acid Anions Production Are Associated with Larger Kidney Size in ADPKD.
Cytoskeletal Protein 4.1G Is Essential for the Primary Ciliogenesis and Osteoblast Differentiation in Bone Formation.
A cell-based GEF assay reveals new substrates for DENN domains and a role for DENND2B in primary ciliogenesis.
A Brief Review on the Regulatory Roles of MicroRNAs in Cystic Diseases and Their Use as Potential Biomarkers.
Quantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease.
Ift88 regulates enamel formation via involving Shh signaling.
Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.
Patient-derived cellular models of primary ciliopathies.
The Dual Effect of Rho-Kinase Inhibition on Trabecular Meshwork Cells Cytoskeleton and Extracellular Matrix in an In Vitro Model of Glaucoma.
Limitations of Nasal Nitric Oxide Measurement for Diagnosis of Primary Ciliary Dyskinesia with Normal Ultrastructure.

Pediatr Nephrol. 2022 Feb 24.

Detection of DZIP1L mutations by whole-exome sequencing in consanguineous families with polycystic kidney disease.

Jens Michael Hertz, Per Svenningsen, Henrik Dimke, Morten Buch Engelund, Hanne Nørgaard, Anita Hansen, Niels Marcussen, Helle Charlotte Thiesson, Carsten Bergmann, Martin J Larsen.

   BACKGROUND: Autosomal recessive polycystic kidney disease is a cystic kidney disease with early onset and clinically characterized by enlarged echogenic kidneys, hypertension, varying degrees of kidney dysfunction, and liver fibrosis. It is most frequently caused by sequence variants in the PKHD1 gene, encoding fibrocystin. In more rare cases, sequence variants in DZIP1L are seen, encoding the basal body protein DAZ interacting protein 1-like protein (DZIP1L). So far, only four different DZIP1L variants have been reported.
METHODS: Four children from three consanguineous families presenting with polycystic kidney disease were selected for targeted or untargeted exome sequencing.
RESULTS: We identified two different, previously not reported homozygous DZIP1L sequence variants: c.193 T > C; p.(Cys65Arg), and c.216C > G; p.(Cys72Trp). Functional analyses of the c.216C > G; p.(Cys72Trp) variant indicated mislocalization of mutant DZIP1L.
CONCLUSIONS: In line with published data, our results suggest a critical role of the N-terminal domain for proper protein function. Although patients with PKHD1-associated autosomal recessive polycystic kidney disease often have liver abnormalities, none of the present four patients showed any clinically relevant liver involvement. Our data demonstrate the power and efficiency of next-generation sequencing-based approaches. While DZIP1L-related polycystic kidney disease certainly represents a rare form of the disease, our results emphasize the importance of including DZIP1L in multigene panels and in the data analysis of whole-exome sequencing for cystic kidney diseases. A higher resolution version of the Graphical abstract is available as Supplementary information.

Keywords:  ARPKD; DZIP1L; Polycystic kidney disease; Primary cilia; Whole-exome sequencing

DOI:  https://doi.org/10.1007/s00467-022-05441-4
J Clin Med. 2022 Feb 21. pii: 1127. [Epub ahead of print]11(4):

Pericardial Effusion on MRI in Autosomal Dominant Polycystic Kidney Disease.

Jin Liu, Kana Fujikura, Hreedi Dev, Sadjad Riyahi, Jon Blumenfeld, Jiwon Kim, Hanna Rennert, Martin R Prince.

  Autosomal dominant polycystic kidney disease (ADPKD) has been associated with cardiac abnormalities including mitral valve prolapse and aneurysmal dilatation of the aortic root. Herein, we investigated the potential association of pericardial effusion with ADPKD. Subjects with ADPKD (n = 117) and control subjects without ADPKD matched for age, gender and renal function (n = 117) undergoing MRI including ECG-gated cine MRI of the aorta and heart were evaluated for pericardial effusion independently by three observers measuring the maximum pericardial effusion thickness in diastole using electronic calipers. Pericardial effusion thickness was larger in ADPKD subjects compared to matched controls (Mann-Whitney p = 0.001) with pericardial effusion thickness >5 mm observed in 24 of 117 (21%) ADPKD subjects compared to 4 of 117 (3%) controls (p = 0.00006). Pericardial effusion thickness in ADPKD was associated with female gender patients (1.2 mm greater than in males, p = 0.03) and pleural effusion thickness (p < 0.001) in multivariate analyses. No subjects exhibited symptoms related to pericardial effusion or required pericardiocentesis. In conclusion, pericardial effusion appears to be more prevalent in ADPKD compared to controls. Although in this retrospective cross-sectional study we did not identify clinical significance, future investigations of pericardial effusion in ADPKD subjects may help to more fully understand its role in this disease.

Keywords:  ADPKD; MRI; echocardiography; pericardial effusion; pleural effusion

DOI:  https://doi.org/10.3390/jcm11041127
Tomography. 2022 Feb 09. 8(1): 447-456

IRIS-Intelligent Rapid Interactive Segmentation for Measuring Liver Cyst Volumes in Autosomal Dominant Polycystic Kidney Disease.

Collin Li, Dominick Romano, Sophie J Wang, Hang Zhang, Martin R Prince, Yi Wang.

   PURPOSE: To develop and integrate interactive features with automatic methods for accurate liver cyst segmentation in patients with autosomal dominant polycystic kidney and liver disease (ADPKD).
METHODS: SmartClick and antiSmartClick were developed using iterative region growth guided by spatial and intensity connections and were integrated with automated level set (LS) segmentation and graphical user interface, forming an intelligent rapid interactive segmentation (IRIS) tool. IRIS and LS segmentations of liver cysts on T2 weighted images of patients with ADPKD (n = 17) were compared with manual segmentation as ground truth (GT).
RESULTS: Compared to manual GT, IRIS reduced the segmentation time by more than 10-fold. Compared to automated LS, IRIS reduced the mean liver cyst volume error from 42.22% to 13.44% (p < 0.001). IRIS segmentation agreed well with manual GT (79% dice score and 99% intraclass correlation coefficient).
CONCLUSION: IRIS is feasible for fast, accurate liver cyst segmentation in patients with ADPKD.

Keywords:  intelligent rapid interactive segmentation; lesion segmentation; liver cyst

DOI:  https://doi.org/10.3390/tomography8010037
Clin Kidney J. 2022 Mar;15(3): 407-416

Establishing a core outcome measure for pain in patients with autosomal dominant polycystic kidney disease: a consensus workshop report.

Patrizia Natale, Ronald D Perrone, Allison Tong, Tess Harris, Elyssa Hannan, Angela Ju, Eva Burnette, Niek F Casteleijn, Arlene Chapman, Sarah Eastty, Ron T Gansevoort, Marie Hogan, Shigeo Horie, Bertrand Knebelmann, Richard Lee, Reem A Mustafa, Richard Sandford, Amanda Baumgart, Jonathan C Craig, Gopala K Rangan, Bénédicte Sautenet, Andrea K Viecelli, Noa Amir, Nicole Evangelidis, Chandana Guha, Charlotte Logeman, Karine Manera, Andrea Matus Gonzalez, Martin Howell, Giovanni F M Strippoli, Yeoungjee Cho.

   Background: Pain is the highest prioritized patient-reported outcome in people with autosomal dominant polycystic kidney disease (ADPKD) but remains infrequently and inconsistently measured in clinical trials and poorly managed in clinical settings. A recently completed systematic review of pain in ADPKD identified 26 different outcome measures. None of these measures were considered appropriate as a core outcome measure due to the lack of patient-important dimensions, inadequate content, relatively long duration of completion time and limited evidence to support psychometric robustness.
Methods: We convened an international Standardized Outcomes in Nephrology-Polycystic Kidney Disease consensus workshop involving 21 patients/caregivers and 40 health professionals (clinicians, nurses, researchers, policy makers and industry representatives) from 18 countries to discuss the identification or development of a core outcome measure for pain.
Results: Four themes were identified highlighting fundamental issues for the measurement of pain in ADPKD: distressing and disrupting life participation; variability and ambiguity in defining pain; stigma, frustration and adaptation to pain; and ensuring validity and feasibility of pain measures.
Conclusions: Existing measures were found to be insufficient in capturing pain as a core outcome and there was consensus on the need for a new validated measure that is simple, succinct and addresses the impact of pain on life participation. This measure will facilitate the appropriate prioritization of pain in all trials and guide clinical decision making in people with ADPKD.

Keywords:  ADPKD; measure; pain; patient-reported outcomes; workshop

DOI:  https://doi.org/10.1093/ckj/sfab110
Clin J Am Soc Nephrol. 2022 Feb 25. pii: CJN.08660621. [Epub ahead of print]

Volume Progression and Imaging Classification of Polycystic Liver in Early Autosomal Dominant Polycystic Kidney Disease.

CRISP and HALT PKD Consortium

   BACKGROUND AND OBJECTIVES: The progression of polycystic liver disease is not well understood. The purpose of the study is to evaluate the associations of polycystic liver progression with other disease progression variables and classify liver progression on the basis of patient's age, height-adjusted liver cystic volume, and height-adjusted liver volume.
DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Prospective longitudinal magnetic resonance images from 670 patients with early autosomal dominant polycystic kidney disease for up to 14 years of follow-up were evaluated to measure height-adjusted liver cystic volume and height-adjusted liver volume. Among them, 245 patients with liver cyst volume >50 ml at baseline were included in the longitudinal analysis. Linear mixed models on log-transformed height-adjusted liver cystic volume and height-adjusted liver volume were fitted to approximate mean annual rate of change for each outcome. The association of sex, body mass index, genotype, baseline height-adjusted total kidney volume, and Mayo imaging class was assessed. We calculated height-adjusted liver cystic volume ranges for each specific age and divided them into five classes on the basis of annual percentage increase in height-adjusted liver cystic volume.
RESULTS: The mean annual growth rate of height-adjusted liver cystic volume was 12% (95% confidence interval, 11.1% to 13.1%; P<0.001), whereas that for height-adjusted liver volume was 2% (95% confidence interval, 1.9% to 2.6%; P<0.001). Women had higher baseline height-adjusted liver cystic volume than men, but men had higher height-adjusted liver cystic volume growth rate than women by 2% (95% confidence interval, 0.4% to 4.5%; P=0.02). Whereas the height-adjusted liver cystic volume growth rate decreased in women after menopause, no decrease was observed in men at any age. Body mass index, genotype, and baseline height-adjusted total kidney volume were not associated with the growth rate of height-adjusted liver cystic volume or height-adjusted liver volume. According to the height-adjusted liver cystic volume growth rate, patients were classified into five classes (number of women, men in each class): A (24, six); B (44, 13); C (43, 48); D (28, 17); and E (13, nine).
CONCLUSIONS: Compared with height-adjusted liver volume, the use of height-adjusted liver cystic volume showed greater separations in volumetric progression of polycystic liver disease. Similar to the Mayo imaging classification for the kidney, the progression of polycystic liver disease may be categorized on the basis of patient's age and height-adjusted liver cystic volume.

Keywords:  ADPKD; diagnostic imaging; disease progression; genetic renal disease; kidney volume; liver; liver cysts; polycystic kidney disease

DOI:  https://doi.org/10.2215/CJN.08660621
Clin Exp Nephrol. 2022 Feb 25.

Association of autosomal dominant polycystic kidney disease with cardiovascular disease: a US-National Inpatient Perspective.

Nassib Abou Heidar, Omar Chehab, Rami Z Morsi, Joseph Elias, Christopher El Mouhayyar, Amjad Kanj, Mustafa Ajam, Abdallah Haykal, Mohit Pahuja, Habib Dakik, Diane Levine, Nashat Imran, Aiden Abidov.

   PURPOSE: Data on the epidemiology of cardiovascular diseases (CVD) in patients with autosomal dominant polycystic kidney disease (ADPKD) are limited. In this study, we assess the prevalence of CVD in patients with ADPKD and evaluate associations between these two entities.
METHODS: Using the National Inpatient Sample database, we identified 71,531 hospitalizations among adults aged ≥ 18 years with ADPKD, from 2006 to 2014 and collected relevant clinical data.
RESULTS: The prevalence of CVD in the study population was 42.6%. The most common CVD were ischemic heart diseases (19.3%), arrhythmias (14.2%), and heart failure (13.1%). The prevalence of CVD increased with the severity of renal dysfunction (RD). We found an increase in hospitalizations of patients with ADPKD and CVD over the years (ptrend < 0.01), irrespective of the degree of RD. CVD was the greatest independent predictor of mortality in these patients (OR: 3.23; 95% CI 2.38-4.38 [p < 0.001]). In a propensity matched model of hospitalizations of patients with CKD with and without ADPKD, there was a significant increase in the prevalence of atrial fibrillation/flutter (AF), pulmonary hypertension (PHN), non-ischemic cardiomyopathy (NICM), and hemorrhagic stroke among patients with ADPKD when compared to patients with similar degree of RD without ADPKD.
CONCLUSIONS: The prevalence of CVD is high among patients with ADPKD, and the most important risk factor associated with CVD is severity of RD. We found an increase in the trend of hospitalizations of patients with ADPKD associated with increased risk of AF, PHN, NICM, and hemorrhagic stroke. History of CVD is the strongest predictor of mortality among patients with ADPKD.

Keywords:  Autosomal dominant polycystic kidney disease; Cardiovascular disease; Chronic kidney disease; Mortality

DOI:  https://doi.org/10.1007/s10157-022-02200-5
Can J Kidney Health Dis. 2020 ;7 2054358120934628

Stone Prevalence in Autosomal Dominant Polycystic Kidney Disease: A Systematic Review and Meta-Analysis.

Vinusha Kalatharan, Gary Grewal, Danielle M Nash, Blayne Welk, Sisira Sarma, York Pei, Amit X Garg.

   Background: It is uncertain how often patients with autosomal dominant polycystic kidney disease (ADPKD) develop kidney stones.
Objective: To review English-language studies reporting the incidence and prevalence of stones and stone interventions in adults with ADPKD.
Design: Systematic review and meta-analysis.
Setting: Any country of origin.
Patients: Adult patients with ADPKD.
Measurements: Incidence or prevalence of kidney stones and stone interventions.
Methods: We reviewed 1812 citations from bibliographic databases, abstracted data from 49 eligible studies, and assessed methodological quality in duplicate. In some studies, the proportion of adults with ADPKD with the outcome were compared to adults without ADPKD; for these studies, prevalence risk ratios were calculated and pooled using a random effects model.
Results: We identified 49 articles that met our review criteria. The methodological quality of many studies was limited (scores ranging from 2 to 14 out of 22, with a higher score indicating higher quality). No study clearly reported stone incidence, and in the cross-sectional studies, the definition of stones was often unclear. The prevalence of stones ranged from 3% to 59%, and a prevalence of stone interventions ranged from 1% to 8%; the average patient age at the time of assessment ranged from 26 to 61 years across the studies. Two studies reported a nonstatistically significant higher stone prevalence in patients with ADPKD compared to unaffected family members. Compared to unaffected family members, patients with ADPKD had a higher prevalence of kidney stones (6 cross-sectional studies; unadjusted prevalence ratio: 1.8; 95% confidence interval: 1.3 to 2.6; P = .0007; test for heterogeneity: I 2 = 0%, P = .8).
Limitations: Studies were limited to articles published in English.
Conclusions: The prevalence of kidney stones and stone interventions in adults with ADPKD remains uncertain. Future studies of higher methodological quality are needed to better characterize the incidence and prevalence of kidney stones in patients with ADPKD.
Trial registration: We did not register the protocol for this systematic review.

Keywords:  epidemiology; kidney stones; observational study; polycystic kidney disease; prevalence; stone intervention; systematic review

DOI:  https://doi.org/10.1177/2054358120934628
Medicina (Kaunas). 2022 Jan 19. pii: 152. [Epub ahead of print]58(2):

Increased Body Fat and Organic Acid Anions Production Are Associated with Larger Kidney Size in ADPKD.

Adriana Dos Santos Dutra, Fernanda Guedes Rodrigues, Daniel Ribeiro da Rocha, Larissa Collis Vendramini, Ana Cristina Carvalho de Matos, Ita Pfeferman Heilberg.

  Background and Objectives: A high body mass index (BMI) is associated with the progression of autosomal dominant polycystic kidney disease (ADPKD). However, body fat (BF), which is another adiposity marker, has not yet been studied. Excessive weight may promote elevation in the endogenous synthesis of organic acid (OA) anions. Accordingly, we aimed to investigate the possible association of the aforementioned markers with kidney volume and renal function in patients with ADPKD. Materials and Methods: We conducted a retrospective cohort study of adult ADPKD outpatients involving clinical, serum, and urinary laboratorial data and body composition assessments retrieved from their medical records. BF was estimated by skinfold thickness (mm) on the non-dominant arm and was considered as normal or high for each sex. Total kidney volume (TKV) and height-adjusted volume (htTKV) were measured by magnetic resonance imaging. The annual estimated glomerular filtration rate (eGFR) slope was analyzed during a median follow-up time of 6 (5.0-7.0) years to calculate rapid progression (decline in renal function ≥2.5 mL/min/year over 5 years). Results: A total of 104 patients were included (41.9 ± 11.9 years old, 38.5% men), with 62.5% of the patients classified as high BF. The High BF group presented higher levels of OA, glycosylated hemoglobin (HbA1c), C-reactive protein (CRP), 24 h urinary sodium (UNa), and htTKV, and lower eGFR than those with a normal BF. In the multivariate linear regression, the associated variables with TKV were high BF, OA and BMI (std. β 0.47, p < 0.05; std. β 0.36, p = 0.001; std. β 0.25, p = 0.01, respectively). In the binary logistic regression, when adjusted for potential confounders, UNa was the only parameter associated with an increased risk of eGFR decline ≥2.5 mL/min/year (OR 1.02, 95% CI 1.01-1.03, p = 0.02). Conclusions: Increased body fat and endogenous production of organic acid anions are associated with larger kidney size in ADPKD but not with a decline in renal function.

Keywords:  ADPKD; adiposity markers; body fat; obesity; organic acid anion; renal function decline; total kidney volume

DOI:  https://doi.org/10.3390/medicina58020152
Int J Mol Sci. 2022 Feb 14. pii: 2094. [Epub ahead of print]23(4):

Cytoskeletal Protein 4.1G Is Essential for the Primary Ciliogenesis and Osteoblast Differentiation in Bone Formation.

Masaki Saito, Marina Hirano, Tomohiro Izumi, Yu Mori, Kentaro Ito, Yurika Saitoh, Nobuo Terada, Takeya Sato, Jun Sukegawa.

  The primary cilium is a hair-like immotile organelle with specific membrane receptors, including the receptor of Hedgehog signaling, smoothened. The cilium organized in preosteoblasts promotes differentiation of the cells into osteoblasts (osteoblast differentiation) by mediating Hedgehog signaling to achieve bone formation. Notably, 4.1G is a plasma membrane-associated cytoskeletal protein that plays essential roles in various tissues, including the peripheral nervous system, testis, and retina. However, its function in the bone remains unexplored. In this study, we identified 4.1G expression in the bone. We found that, in the 4.1G-knockout mice, calcium deposits and primary cilium formation were suppressed in the trabecular bone, which is preosteoblast-rich region of the newborn tibia, indicating that 4.1G is a prerequisite for osteoblast differentiation by organizing the primary cilia in preosteoblasts. Next, we found that the primary cilium was elongated in the differentiating mouse preosteoblast cell line MC3T3-E1, whereas the knockdown of 4.1G suppressed its elongation. Moreover, 4.1G-knockdown suppressed the induction of the cilia-mediated Hedgehog signaling and subsequent osteoblast differentiation. These results demonstrate a new regulatory mechanism of 4.1G in bone formation that promotes the primary ciliogenesis in the differentiating preosteoblasts and induction of cilia-mediated osteoblast differentiation, resulting in bone formation at the newborn stage.

Keywords:  bone formation; cytoskeletal protein 4.1G; preosteoblasts; primary cilium

DOI:  https://doi.org/10.3390/ijms23042094
Sci Adv. 2022 Feb 25. 8(8): eabk3088

A cell-based GEF assay reveals new substrates for DENN domains and a role for DENND2B in primary ciliogenesis.

Rahul Kumar, Vincent Francis, Gopinath Kulasekaran, Maleeha Khan, Gary A B Armstrong, Peter S McPherson.

Primary cilia are sensory antennae crucial for cell and organism development, and defects in their biogenesis cause ciliopathies. Ciliogenesis involves membrane trafficking mediated by small guanosine triphosphatases (GTPases) including Rabs, molecular switches activated by guanine nucleotide exchange factors (GEFs). The largest family of Rab GEFs is the DENN domain-bearing proteins. Here, we screen all 60 Rabs against two major DENN domain families using a cellular GEF assay, uncovering 19 novel DENN/Rab pairs. The screen reveals Rab10 as a substrate for DENND2B, a protein previously implicated in cancer and severe mental retardation. Through activation of Rab10, DENND2B represses the formation of primary cilia. Through a second pathway, DENND2B functions as a GEF for RhoA to control the length of primary cilia. This work thus identifies an unexpected diversity in DENN domain-mediated activation of Rabs, a previously unidentified non-Rab substrate for a DENN domain, and a new regulatory protein in primary ciliogenesis.

DOI: https://doi.org/10.1126/sciadv.abk3088
Genes (Basel). 2022 Jan 22. pii: 191. [Epub ahead of print]13(2):

A Brief Review on the Regulatory Roles of MicroRNAs in Cystic Diseases and Their Use as Potential Biomarkers.

Luis M Ruiz-Manriquez, Schoenstatt Janin Ledesma Pacheco, Daniel Medina-Gomez, Andrea G Uriostegui-Pena, Carolina Estrada-Meza, Anindya Bandyopadhyay, Surajit Pathak, Antara Banerjee, Samik Chakraborty, Aashish Srivastava, Sujay Paul.

  miRNAs are small endogenous conserved non-coding RNA molecules that regulate post-transcriptional gene expression through mRNA degradation or translational inhibition, modulating nearly 60% of human genes. Cystic diseases are characterized by the presence of abnormal fluid-filled sacs in the body, and though most cysts are benign, they can grow inside tumors and turn malignant. Recent evidence has revealed that the aberrant expression of a number of miRNAs present in extracellular fluids, including plasma or serum, urine, saliva, follicular fluid, and semen, contribute to different cystic pathologies. This review aims to describe the role of different miRNAs in three worldwide relevant cystic diseases: polycystic ovarian syndrome (PCOS), polycystic kidney disease (PKD), and pancreatic cyst tumors (PCTs), as well as their potential use as novel biomarkers.

Keywords:  biomarkers; cystic diseases; microRNAs; pancreatic cyst tumors; polycystic kidney disease; polycystic ovarian syndrome

DOI:  https://doi.org/10.3390/genes13020191
Biomedicines. 2022 Jan 27. pii: 290. [Epub ahead of print]10(2):

Quantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease.

Adrian Cordido, Marta Vizoso-Gonzalez, Laura Nuñez-Gonzalez, Alberto Molares-Vila, Maria Del Pilar Chantada-Vazquez, Susana B Bravo, Miguel A Garcia-Gonzalez.

  (1) Background: Polycystic liver disease (PLD) is a heterogeneous group of congenital disorders characterized by bile duct dilatation and cyst development derived from cholangiocytes. Nevertheless, the cystogenesis mechanism is currently unknown and the PLD treatment is limited to liver transplantation. Novel and efficient therapeutic approaches are th6us needed. In this context, the present work has a principal aim to find novel molecular pathways, as well as new therapeutic targets, involved in the hepatic cystogenesis process. (2) Methods: Quantitative proteomics based on SWATH-MS technology were performed comparing hepatic proteomes of Wild Type and mutant/polycystic livers in a polycystic kidney disease (PKD) murine model (Pkd1cond/cond;Tam-Cre-/+). (3) Results: We identified several proteins altered in abundance, with two-fold cut-off up-regulation or down-regulation and an adjusted p-value significantly related to hepatic cystogenesis. Then, we performed enrichment and a protein-protein analysis identifying a cluster focused on hepatic fibrinogens. Finally, we validated a selection of targets by RT-qPCR, Western blotting and immunohistochemistry, finding a high correlation with quantitative proteomics data and validating the fibrinogen complex. (4) Conclusions: This work identified a novel molecular pathway in cystic liver disease, highlighting the fibrinogen complex as a possible new therapeutic target for PLD.

Keywords:  PLD; SWATH; quantitative proteomics; therapeutic targets

DOI:  https://doi.org/10.3390/biomedicines10020290
Oral Dis. 2022 Feb 21.

Ift88 regulates enamel formation via involving Shh signaling.

Takehisa Kudo, Maiko Kawasaki, Kataushige Kawasaki, Fumiya Meguro, Jun Nihara, Izumi Honda, Madoka Kitamura, Akira Fujita, Kazuaki Osawa, Kaya Ichikawa, Takahiro Nagai, Yoko Ishida, Paul T Sharpe, Takeyasu Maeda, Isao Saito, Atsushi Ohazama.

   OBJECTIVES: The ciliopathies are a wide spectrum of human diseases, which are caused by perturbations in the function of primary cilia. Tooth enamel anomalies are often seen in ciliopathy patients; however, the role of primary cilia in enamel formation remains unclear.
MATERIALS AND METHODS: We examined mice with epithelial conditional deletion of the ciliary protein, Ift88, (Ift88fl/fl ;K14Cre).
RESULTS: Ift88fl/fl ;K14Cre mice showed premature abrasion in molars. A pattern of enamel rods which is determined at secretory stage, was disorganized in Ift88 mutant molars. Many amelogenesis-related molecules expressing at the secretory stage, including amelogenin and ameloblastin, enamelin, showed significant downregulation in Ift88 mutant molar tooth germs. Shh signaling is essential for amelogenesis, which was found to be downregulated in Ift88 mutant molar at the secretory stage. Application of Shh signaling agonist at the secretory stage partially rescued enamel anomalies in Ift88 mutant mice.
CONCLUSION: Findings in the present study indicate that the function of the primary cilia via Ift88 is critical for the secretory stage of amelogenesis through involving Shh signaling.

Keywords:  Ift88; Shh signaling; enamel formation; primary cilia

DOI:  https://doi.org/10.1111/odi.14162
Mol Biol Cell. 2022 Feb 23. mbcE21100509T

Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.

Skylar I Dewees, Romana Vargová, Katherine R Hardin, Rachel E Turn, Saroja Devi, Joshua Linnert, Uwe Wolfrum, Tamara Caspary, Marek Eliáš, Richard A Kahn.

The ARF family of regulatory GTPases is ancient, with 16 members predicted to have been present in the last eukaryotic common ancestor. Our phylogenetic profiling of paralogs in diverse species identified four family members whose presence correlates with that of a cilium/flagellum: ARL3, ARL6, ARL13, and ARL16. No prior evidence links ARL16 to cilia or other cell functions, despite its presence throughout eukaryotes. Deletion of ARL16 in MEFs results in decreased ciliogenesis yet increased ciliary length. We also found Arl16 KO in MEFs to alter ciliary protein content, including loss of ARL13B, ARL3, INPP5E, and the IFT-A core component IFT140. Instead, both INPP5E and IFT140 accumulate at the Golgi in Arl16 KO lines, while other IFT proteins do not, suggesting a specific defect in traffic from Golgi to cilia. We propose that ARL16 regulates a Golgi-cilia traffic pathway and is required specifically in the export of IFT140 and INPP5E from the Golgi.

DOI: https://doi.org/10.1091/mbc.E21-10-0509-T
J Med Genet. 2022 Feb 19. pii: jmedgenet-2021-108315. [Epub ahead of print]

Patient-derived cellular models of primary ciliopathies.

Lidia Pollara, Virginie Sottile, Enza Maria Valente.

  Primary ciliopathies are rare inherited disorders caused by structural or functional defects in the primary cilium, a subcellular organelle present on the surface of most cells. Primary ciliopathies show considerable clinical and genetic heterogeneity, with disruption of over 100 genes causing the variable involvement of several organs, including the central nervous system, kidneys, retina, skeleton and liver. Pathogenic variants in one and the same gene may associate with a wide range of ciliopathy phenotypes, supporting the hypothesis that the individual genetic background, with potential additional variants in other ciliary genes, may contribute to a mutational load eventually determining the phenotypic manifestations of each patient. Functional studies in animal models have uncovered some of the pathophysiological mechanisms linking ciliary gene mutations to the observed phenotypes; yet, the lack of reliable human cell models has previously limited preclinical research and the development of new therapeutic strategies for primary ciliopathies. Recent technical advances in the generation of patient-derived two-dimensional (2D) and three-dimensional (3D) cellular models give a new spur to this research, allowing the study of pathomechanisms while maintaining the complexity of the genetic background of each patient, and enabling the development of innovative treatments to target specific pathways. This review provides an overview of available models for primary ciliopathies, from existing in vivo models to more recent patient-derived 2D and 3D in vitro models. We highlight the advantages of each model in understanding the functional basis of primary ciliopathies and facilitating novel regenerative medicine, gene therapy and drug testing strategies for these disorders.

Keywords:  genetic research; genetics; medical

DOI:  https://doi.org/10.1136/jmedgenet-2021-108315
J Clin Med. 2022 Feb 15. pii: 1001. [Epub ahead of print]11(4):

The Dual Effect of Rho-Kinase Inhibition on Trabecular Meshwork Cells Cytoskeleton and Extracellular Matrix in an In Vitro Model of Glaucoma.

Juliette Buffault, Françoise Brignole-Baudouin, Élodie Reboussin, Karima Kessal, Antoine Labbé, Stéphane Mélik Parsadaniantz, Christophe Baudouin.

  The trabecular meshwork (TM) is the main site of drainage of the aqueous humor, and its dysfunction leads to intraocular pressure elevation, which is one of the main risk factors of glaucoma. We aimed to compare the effects on cytoskeleton organization and extracellular matrix (ECM) of latanoprost (LT) and a Rho-kinase inhibitor (ROCKi) on a transforming growth factor beta2 (TGF-β2)-induced glaucoma-like model developed from primary culture of human TM cells (pHTMC). The TGF-β2 stimulated pHTMC were grown and incubated with LT or a ROCKi (Y-27632) for 24 h. The expression of alpha-smooth muscle actin (αSMA) and fibronectin (FN), and phosphorylation of the myosin light chain (MLC-P) and Cofilin (Cofilin-P) were evaluated using immunofluorescence and Western blot. The architectural modifications were studied in a MatrigelTM 3D culture. TGF-β2 increased the expression of αSMA and FN in pHTMC and modified the cytoskeleton with cross-linked actin network formation. LT did not alter the expression of αSMA but decreased FN deposition. The ROCKi decreased TGF-β2-induced αSMA and FN expression, as well as MLC-P and Cofilin-P, and stimulated the cells to recover a basal cytoskeletal arrangement. In the preliminary 3D study, pHTMC organized in a mesh conformation showed the widening of the TM under the effect of Y-27632. By simultaneously modifying the organization of the cytoskeleton and the ECM, with fibronectin deposition and overexpression, TGF-β2 reproduced the trabecular degeneration described in glaucoma. The ROCKi was able to reverse the TGF-β2-induced cytoskeletal and ECM rearrangements. LT loosened the extracellular matrix but had no action on the stress fibers.

Keywords:  3D culture; Matrigel; cytoskeleton; glaucoma; intraocular pressure; outflow; prostaglandin analog; rho-kinase inhibitor; trabecular meshwork

DOI:  https://doi.org/10.3390/jcm11041001
Ann Am Thorac Soc. 2022 Feb 24.

Limitations of Nasal Nitric Oxide Measurement for Diagnosis of Primary Ciliary Dyskinesia with Normal Ultrastructure.

Johanna Raidt, Henrike Krenz, Johannes Tebbe, Jörg Große-Onnebrink, Heike Olbrich, Niki Tomas Loges, Luisa Biebach, Christian Schmalstieg, Christina Keßler, Julia Wallmeier, Bernd Dworniczak, Petra Pennekamp, Martin Dugas, Claudius Werner, Heymut Omran.

Rationale Primary ciliary dyskinesia (PCD) is a heterogeneous, multisystem disorder characterized by defective ciliary beating. Diagnostic guidelines of the American Thoracic Society (ATS) and European Respiratory Society (ERS) recommend measurement of nasal nitric oxide (nNO) for PCD diagnosis. Several studies demonstrated low nNO-production rates in PCD individuals but underlying causes remain elusive. Objective To determine nNO-production rates in a well-characterized PCD cohort including subgroup analyses with regard to ultrastructural and ciliary beating phenotypes. Methods This study included 301 individuals assessed according to ERS guidelines. Diagnostic cutoffs for nNO-production rates for this study cohort and subgroups with normal and abnormal ultrastructure were determined. Diagnostic accuracy was also tested for the widely used 77 nl/min-cutoff in this study cohort. The relationship between nNO-production rates and ciliary beat frequencies (CBFs) was evaluated. Results The study cohort comprised 180 individuals with definite PCD diagnosis including 160 individuals with genetic diagnosis, 16 individuals with probable PCD diagnosis and 105 disease controls. The 77 nl/min nNO-cutoff showed a test sensitivity of 0.92 and specificity of 0.86. Test sensitivity was lower (0.85) in the subgroup of 47 PCD individuals with normal ultrastructure compared to 133 PCD individuals with abnormal ultrastructure (0.95). The optimal diagnostic cutoff for the nNO-production rate for the whole study cohort was 69.8 nl/min (sensitivity 0.92, specificity 0.89), however it was 107.8 nl/min (sensitivity 0.89, specificity 0.78) for the subgroup of PCD with normal ultrastructure. PCD individuals with normal ultrastructure compared to abnormal ultrastructure showed higher ciliary motility. Consistently, PCD individuals with higher CBFs showed higher nNO-production rates. In addition, laterality defects occurred less frequently in PCD with normal ultrastructure. Conclusion Measurements of nNO below the widely used 77 nL/min cutoff are less sensitive in detecting PCD individuals with normal ultrastructure. Our findings indicate, that higher nNO-production in this subgroup with a higher cutoff for the nNO-production rate (107.8 nl/min) and higher residual ciliary motility are dependent on the underlying molecular PCD defect. Higher nNO-production rates, higher residual CBFs and the lower prevalence of laterality defects hamper diagnosis of PCD with normal ultrastructure. Adjusting the cutoff of nNO-production rate to 107.8 nl/min might promote diagnosing PCD with normal ultrastructure.

DOI: https://doi.org/10.1513/AnnalsATS.202106-728OC