bims-bicyki 2023-01-01 papers

PLoS Genet. 2022 Dec 27. 18(12): e1010560

Tracking N- and C-termini of C. elegans polycystin-1 reveals their distinct targeting requirements and functions in cilia and extracellular vesicles.

Jonathon D Walsh, Juan Wang, Molly DeHart, Inna A Nikonorova, Jagan Srinivasan, Maureen M Barr.

The cilium acts as an antenna receiving and sending signals, the latter via extracellular vesicles (EVs). In C. elegans and mammals, the Autosomal Dominant Polycystic Kidney Disease (ADPKD) gene products polycystin-1 (PC1) and polycystin-2 (PC2) localize to both cilia and EVs, act in the same genetic pathway, and function in a sensory capacity, suggesting ancient conservation. However, the functions of the polycystins on cilia and EVs remain enigmatic. We used our C. elegans model and endogenously fluorescent-tagged LOV-1/polycystin-1 to study LOV-1 processing, trafficking, transport, EV biogenesis, and function in living animals. Super resolution, real time imaging reveals that LOV-1 is processed into N-terminal (NTM) and C-terminal (CTM) forms via a conserved GPCR proteolytic site (GPS). The LOV-1 NTM is secreted into the extracellular matrix and not localized to ciliary tip EVs. In contrast, LOV-1 CTM and PKD-2 are co-trafficked, co-transported, and co-localized in cilia and on environmentally released ciliary EVs. LOV-1 CTM requires PKD-2 for ciliary EV localization, while PKD-2 localizes to ciliary EVs independent of LOV-1. We find that LOV-1 but not PKD-2 is required for chemosensation of an ascaroside mating pheromone. These findings indicate that the polycystins LOV-1 and PKD-2 function together and independently and provide insight to how cargo is selected and packaged in ciliary EVs.

DOI: https://doi.org/10.1371/journal.pgen.1010560

CEN Case Rep. 2022 Dec 27.

Microbiome of infected cysts, feces and saliva in patients with autosomal dominant polycystic kidney disease.

Tatsuya Suwabe, Hidetoshi Morita, Anushka Khasnobish, Hideki Araoka, Junichi Hoshino.

Cyst infection is a frequent and serious complication of autosomal dominant polycystic kidney disease (ADPKD). Hematogenous spread via bacterial translocation in the intestine is considered to be the main cause, so intestinal flora may be involved. However, the exact role of the intestinal flora in cyst infection in ADPKD is unknown. We report a 66-year-old woman and a 56-year-old man with ADPKD who had severe hepatic cyst infection. We analyzed the microbiome of infected cyst content, feces, and saliva in these two patients. The microbiome of patient 1 showed various bacteria in an infected cyst, whereas that of patient 2 showed only one bacterium. In both patients, the composition of the microbiome of the cyst content was quite different from those of feces and saliva, and the main bacteria in the infected cyst content represented a small proportion of those in feces and saliva. Lactobacilli were not almost detected in the infected cyst content though some lactobacilli are endemic in the gastrointestinal tract and the saliva. The association between bacteria in cysts and those in feces or saliva remains uncertain, and further research on this topic is needed.

Keywords: ADPKD; Cyst infection; Infected cyst; Polycystic kidney disease

DOI: https://doi.org/10.1007/s13730-022-00767-2

JAMA. 2022 12 27. 328(24): 2412-2421

Exome Sequencing of a Clinical Population for Autosomal Dominant Polycystic Kidney Disease.

Alexander R Chang, Bryn S Moore, Jonathan Z Luo, Gino Sartori, Brian Fang, Steven Jacobs, Yoosif Abdalla, Mohammed Taher, David J Carey, William J Triffo, Gurmukteshwar Singh, Tooraj Mirshahi.

Importance: Most studies of autosomal dominant polycystic kidney disease (ADPKD) genetics have used kidney specialty cohorts, focusing on PKD1 and PKD2. These can lead to biased estimates of population prevalence of ADPKD-associated gene variants and their phenotypic expression.
Objective: To determine the prevalence of ADPKD and contributions of PKD1, PKD2, and other genes related to cystic kidney disease in a large, unselected cohort.
Design, Setting, and Participants: This retrospective observational study used an unselected health system-based cohort in central and northeast Pennsylvania with exome sequencing (enrolled from 2004 to 2020) and electronic health record data (up to October 2021). The genotype-first approach included the entire cohort and the phenotype-first approach focused on patients with ADPKD diagnosis codes, confirmed by chart and imaging review.
Exposures: Loss-of-function (LOF) variants in PKD1, PKD2, and other genes associated with cystic kidney disease (ie, ALG8, ALG9, DNAJB11, GANAB, HNF1B, IFT140, SEC61B, PKHD1, PRKCSH, SEC63); likely pathogenic missense variants in PKD1 and PKD2.
Main Outcomes and Measures: Genotype-first analysis: ADPKD diagnosis code (Q61.2, Q61.3, 753.13, 753.12); phenotype-first analysis: presence of a rare variant in PKD1, PKD2, or other genes associated with cystic kidney disease.
Results: Of 174 172 patients (median age, 60 years; 60.6% female; 93% of European ancestry), 303 patients had ADPKD diagnosis codes, including 235 with sufficient chart review data for confirmation. In addition to PKD1 and PKD2, LOF variants in IFT140, GANAB, and HNF1B were associated with ADPKD diagnosis after correction for multiple comparisons. Among patients with LOF variants in PKD1, 66 of 68 (97%) had ADPKD; 43 of 43 patients (100%) with LOF variants in PKD2 had ADPKD. In contrast, only 24 of 77 patients (31.2%) with a PKD1 missense variant previously classified as "likely pathogenic" had ADPKD, suggesting misclassification or variable penetrance. Among patients with ADPKD diagnosis confirmed by chart review, 180 of 235 (76.6%) had a potential genetic cause, with the majority being rare variants in PKD1 (127 patients) or PKD2 (34 patients); 19 of 235 (8.1%) had variants in other genes associated with cystic kidney disease. Of these 235 patients with confirmed ADPKD, 150 (63.8%) had a family history of ADPKD. The yield for a genetic determinant of ADPKD was higher for those with a family history of ADPKD compared with those without family history (91.3% [137/150] vs 50.6% [43/85]; difference, 40.7% [95% CI, 29.2%-52.3%]; P < .001). Previously unreported PKD1, PKD2, and GANAB variants were identified with pedigree data suggesting pathogenicity, and several PKD1 missense variants previously reported as likely pathogenic appeared to be benign.
Conclusions and Relevance: This study demonstrates substantial genetic and phenotypic variability in ADPKD among patients within a regional health system in the US.

DOI: https://doi.org/10.1001/jama.2022.22847

Cancer Genomics Proteomics. 2023 Jan-Feb;20(1):20(1): 40-50

Concurrent Reduced Expression of Contiguous PKD1, TSC2 and NTHL1 Leading to Kidney Diseases and Multiple Diverse Renal Cancers.

Satoru Meguro, Tomoyuki Koguchi, Yusuke Hakozaki, Akifumi Onagi, Kanako Matsuoka, Seiji Hoshi, Junya Hata, Yuichi Sato, Hidenori Akaihata, Masao Kataoka, Soichiro Ogawa, Yoshiyuki Kojima.

BACKGROUND/AIM: Several cases of concurrent reduction of expression of polycystin 1 (PKD1) and Tuberous Sclerosis Complex 2 (TSC2) that are contiguous in chromosome 16p13 have been previously reported. This study newly addresses the concurrent reduction of expression of PKD1, TSC2 and NTHL1, which is adjacent to TSC2 and is a tumor suppressor gene.
MATERIALS AND METHODS: We investigated the mRNA expression levels of PKD1, TSC2, PKD2, TSC1 and NTHL1 in blood and renal cell carcinoma (RCC) tissues in a proband with autosomal dominant polycystic kidney disease (ADPKD), tuberous sclerosis complex (TSC) and multiple pathologically diverse RCCs, including clear cell, papillary and chromophobe types. Additionally, we investigated germline variants in blood using whole exome sequencing (WES) in the proband and her four siblings.
RESULTS: mRNA expression levels of PKD1, TSC2 and NTHL1 were reduced in the proband's blood and RCCs, compared with control groups. WES identified one novel variant with amino acid changes in the PKD1 exon in the three subjects with ADPKD, including the proband. Moreover, two variants in the TSC2 intron specific to the proband were also identified.
CONCLUSION: In this study, we report a novel pathogenic variant in the PKD1 exon which likely led to ADPKD, and two variants in the TSC2 intron, which might have led to reduction in the expression of both TSC2 and NTHL1, consequently leading to TSC and multiple pathologically diverse RCCs.

Keywords: NTHL1; PKD1; TSC2; autosomal dominant polycystic kidney disease; renal cell carcinoma; tuberous sclerosis

DOI: https://doi.org/10.21873/cgp.20363

Front Cell Dev Biol. 2022 ;10 1082141

Neuronal cilia in energy homeostasis.

Kathryn M Brewer, Katlyn K Brewer, Nicholas C Richardson, Nicolas F Berbari.

A subset of genetic disorders termed ciliopathies are associated with obesity. The mechanisms behind cilia dysfunction and altered energy homeostasis in these syndromes are complex and likely involve deficits in both development and adult homeostasis. Interestingly, several cilia-associated gene mutations also lead to morbid obesity. While cilia have critical and diverse functions in energy homeostasis, including their roles in centrally mediated food intake and peripheral tissues, many questions remain. Here, we briefly discuss syndromic ciliopathies and monogenic cilia signaling mutations associated with obesity. We then focus on potential ways neuronal cilia regulate energy homeostasis. We discuss the literature around cilia and leptin-melanocortin signaling and changes in ciliary G protein-coupled receptor (GPCR) signaling. We also discuss the different brain regions where cilia are implicated in energy homeostasis and the potential for cilia dysfunction in neural development to contribute to obesity. We close with a short discussion on the challenges and opportunities associated with studies looking at neuronal cilia and energy homeostasis. This review highlights how neuronal cilia-mediated signaling is critical for proper energy homeostasis.

Keywords: GPCR signaling; Leptin-melanocortin signaling; Neuronal cilia; energy homeostasis; obesity

DOI: https://doi.org/10.3389/fcell.2022.1082141

Kidney Int. 2022 Dec 24. pii: S0085-2538(22)01089-4. [Epub ahead of print]

Individuals heterozygous for ALG8 protein-truncating variants are at increased risk of a mild cystic kidney disease.

Benjamin Apple, Gino Sartori, Bryn Moore, Kiran Chintam, Gurmukteshwar Singh, Prince Mohan Anand, Natasha Strande, Tooraj Mirshahi, William Triffo, Alexander R Chang.

ALG8 protein-truncating variants (PTVs) have previously been described in patients with polycystic liver disease and in some cases cystic kidney disease. Given a lack of well-controlled studies, we determined whether individuals heterozygous for ALG8 PTVs are at increased risk of cystic kidney disease in a large, unselected health system-based observational cohort linked to electronic health records in Pennsylvania (Geisinger-Regeneron DiscovEHR MyCode study). Out of 174,172 patients, 236 were identified with ALG8 PTVs. Using ICD-based outcomes, patients with these variants were significantly at increased risk of having any kidney/liver cyst diagnosis (Odds Ratio 2.42, 95% confidence interval: 1.53-3.85), cystic kidney disease (3.03, 1.26-7.31), and nephrolithiasis (1.89, 1.96-2.97). To confirm this finding, blinded radiology review of computed tomography and magnetic resonance imaging studies was completed in a matched cohort of 52 thirty-plus year old ALG8 PTV heterozygotes and related non-heterozygotes. ALG8 PTV heterozygotes were significantly more likely to have cystic kidney disease, defined as four or more kidney cysts (57.7% vs. 7.7%), or bilateral kidney cysts (69.2% vs. 15.4%), but not one or more liver cyst (11.5% vs. 7.7%). In publicly-available UK Biobank data, ALG8 PTV heterozygotes were at significantly increased risk of ICD code N28 (other disorders of kidney/ureter) (3.85% vs. 1.33%). ALG8 PTVs were not associated with chronic kidney disease or kidney failure in the MyCode study or the UK Biobank data. Thus, PTVs in ALG8 result in increased risk of a mild cystic kidney disease phenotype.

Keywords: autosomal dominant polycystic kidney disease (ADPKD); chronic kidney disease (CKD); genetics; genotype-first; polycystic liver disease; renal cyst

DOI: https://doi.org/10.1016/j.kint.2022.11.025

Respir Med. 2022 Dec 23. pii: S0954-6111(22)00360-2. [Epub ahead of print] 107095

Comparison of mental health in individuals with primary ciliary dyskinesia, cystic fibrosis, and parent caregivers.

Sonia Graziano, Nicola Ullmann, Raffaela Rusciano, Annalisa Allegorico, Francesca Boldrini, Lorenza Rosito, Alexandra L Quittner, Renato Cutrera, Paola Tabarini.

INTRODUCTION: Individuals with chronic respiratory diseases and caregivers are at higher risk for depression and anxiety. Primary ciliary dyskinesia (PCD) and cystic fibrosis (CF) are both rare genetic diseases, characterized by recurrent respiratory infections. This study compared depression and anxiety in people with PCD (pwPCD) and CF (pwCF), and caregivers, using the screening tools recommended in the CF guidelines.
METHODS: Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder (GAD-7) were administered to a PCD and CF sample. Given that PCD is extremely rare, they were matched on age and sex to pwCF at a 1:2 ratio. Similar procedures were performed with parents.
RESULTS: A total of 63 patients and 129 caregivers participated: 21 pwPCD and 42 pwCF (ages 12-34 years) plus 43 caregivers of pwPCD and 86 caregivers of pwCF. A high percentage of patients scored above the cut-off for depression (PCD: 33%; CF: 43%) and anxiety (PCD and CF both: 43%), mostly mild. Similarly, a high percentage of caregivers scored above the cut-off for depression (PCD: 42-54%; CF: 45-46%) and anxiety (PCD: 47-54%; CF: 39-56%). Suicidal ideation was endorsed by 9.5% of pwPCD, 20% of mothers and 10% of fathers and 5% of pwCF, 3% of mothers, but no fathers.
CONCLUSION: A large percentage of patients and caregivers reported elevated psychological distress and suicidal ideation. Addressing psychological symptoms is critical given they are associated with poor adherence, missed clinic visits, increased inflammation and worse quality of life. Mental health screening and treatment should be integrated into PCD care.

Keywords: Cystic fibrosis; Mental health; Primary ciliary dyskinesia; Screening

DOI: https://doi.org/10.1016/j.rmed.2022.107095