bims-bicyki 2023-05-28 papers

bims-bicyki

Biomed News

on Bicaudal-C1 and interactors in cystic kidney disease

Issue of 2023–05–28
twenty-one papers selected by
Céline Gagnieux, École Polytechnique Fédérale de Lausanne

Cystic Diseases of the Kidneys: From Bench to Bedside.
Modeling Pkd1 gene-targeted strategies for correction of polycystic kidney disease.
Urinary Biomarkers in Monitoring the Progression and Treatment of Autosomal Dominant Polycystic Kidney Disease-The Promised Land?
Osteoclastogenesis requires primary cilia disassembly and can be inhibited by promoting primary cilia formation pharmacologically.
Primary cilia TRP channel regulates hippocampal excitability.
Cerebrovascular Pulsatility Index is Reduced in Autosomal Dominant Polycystic Kidney Disease.
CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion.
Genomics in the kidney clinic.
Mutation Analysis of PKD1 and PKD2 Genes in a Large Italian Cohort Reveals Novel Pathogenic Variants Including A Novel Complex Rearrangement.
Reply to Comments on the SENefro Consensus Document on Autosomal Dominant Polycystic Kidney Disease.
Corrigendum to "Ttc21b deficiency attenuates autosomal dominant polycystic kidney disease in a kidney tubular- and maturation-dependent manner." Kidney Int. 2022;102:577-591.
Polygenic risk affects the penetrance of monogenic kidney disease.
Ciliary ARL13B inhibits developmental kidney cystogenesis in mouse.
Rab11a is essential for the development and integrity of the stereocilia and kinocilia in the mammalian organ of Corti.
TRiPPing the sensors: The osmosensing pathway of Polycystin 2.
Cilia-associated wound repair mediated by IFT88 in retinal pigment epithelium.
Novel insight into ferroptosis in kidney diseases.
Genetic and protein interaction studies between the ciliary dyslexia candidate genes DYX1C1 and DCDC2.
Esrrγa regulates nephron and ciliary development by controlling prostaglandin synthesis.
Loss of Primary Cilia Potentiates BRAF/MAPK Pathway Activation in Rhabdoid Colorectal Carcinoma: A Series of 21 Cases Showing Ciliary Rootlet CoiledCoil (CROCC) Alterations.

Indian J Nephrol. 2023 Mar-Apr;33(2):33(2): 83-92

Cystic Diseases of the Kidneys: From Bench to Bedside.

Rupesh Raina, Francis Lomanta, Siddhartha Singh, Alisha Anand, Riti Kalra, Vignasiddh Enukonda, Oren Barat, Davinder Pandher, Sidharth K Sethi.

  Exploration into the causes of hereditary renal cystic diseases demonstrates a deep-rooted connection with the proteomic components of the cellular organelle cilia. Cilia are essential to the signaling cascades, and their dysfunction has been tied to a range of renal cystic diseases initiating with studies on the oak ridge polycystic kidney (ORPK) mouse model. Here, we delve into renal cystic pathologies that have been tied with ciliary proteosome and highlight the genetics associated with each. The pathologies are grouped based on the mode of inheritance, where inherited causes that result in cystic kidney disease phenotypes include autosomal dominant and autosomal recessive polycystic kidney disease, nephronophthisis (Bardet-Biedl syndrome and Joubert Syndrome), and autosomal dominant tubulointerstitial kidney disease. Alternatively, phakomatoses-, also known as neurocutaneous syndromes, associated cystic kidney diseases include tuberous sclerosis (TS) and Von Hippel-Lindau (VHL) disease. Additionally, we group the pathologies by the mode of inheritance to discuss variations in recommendations for genetic testing for biological relatives of a diagnosed individual.

Keywords:  Bardet–Biedl syndrome; Joubert syndrome; Von Hippel–Lindau; Zellweger spectrum disorders; ciliopathy; genetic counseling; kidney disease; nephronophthisis; polycystic kidney disease; renal cystic disease; tuberous sclerosis

DOI:  https://doi.org/10.4103/ijn.ijn_318_21
Mol Ther Methods Clin Dev. 2023 Jun 08. 29 366-380

Modeling Pkd1 gene-targeted strategies for correction of polycystic kidney disease.

Almira Kurbegovic, Rey Christian Pacis, Marie Trudel.

  Autosomal dominant polycystic kidney disease (ADPKD) causes renal cysts and leads to end-stage renal disease in midlife due mainly to PKD1 gene mutations. Virtually no studies have explored gene therapeutic strategies for long-term effective treatment of PKD. Toward this aim, the severely cystic Pkd1-null mouse model was targeted with a series of transgene transfers using genomic Pkd1 under its regulatory elements (Pkd1wt), a kidney-targeted Pkd1 gene (SBPkd1), or Pkd1Minigene. The introduced Pkd1wt gene constructs with ∼8-fold overexpression display similar endogenous cellular profiles and full complementation of Pkd1-/- phenotype and establish the referral Pkd1 genomic length for proper regulation. SBPkd1 transgene transfer expressing 0.6- or 7-fold Pkd1 endogenous levels is sufficient to correct glomerular and proximal tubular cysts and to markedly postpone cysts in other tubular segments as well, showing that the small SB elements appreciably overlap with Pkd1 promoter/5' UTR regulation. Renal-targeted Pkd1Minigene at high copy numbers conveys an expression level similar to that of the endogenous Pkd1 gene, with widespread and homogeneous weak Pkd1 cellular signal, partially rescuing all cystic tubular segments. These transgene transfers determine that Pkd1 intragenic sequences regulate not only expression levels but also spatiotemporal patterns. Importantly, our study demonstrates that Pkd1 re-expression from hybrid therapeutic constructs can ameliorate, with considerably extended lifespan, or eliminate PKD.

Keywords:  PKD mouse models; PKD transcriptional regulation; Pc1; Pkd1 RNAscope; Pkd1 gene therapy; Pkd1 locus/minigene; polycystic kidney disease; polycystin; small SB renal cassette

DOI:  https://doi.org/10.1016/j.omtm.2023.03.016
Medicina (Kaunas). 2023 May 10. pii: 915. [Epub ahead of print]59(5):

Urinary Biomarkers in Monitoring the Progression and Treatment of Autosomal Dominant Polycystic Kidney Disease-The Promised Land?

Camelia Pana, Alina Mihaela Stanigut, Bogdan Cimpineanu, Andreea Alexandru, Camer Salim, Alina Doina Nicoara, Periha Resit, Liliana Ana Tuta.

  Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic kidney disease, and it leads to end-stage renal disease (ESRD). The clinical manifestations of ADPKD are variable, with extreme differences observable in its progression, even among members of the same family with the same genetic mutation. In an age of new therapeutic options, it is important to identify patients with rapidly progressive evolution and the risk factors involved in the disease's poor prognosis. As the pathophysiological mechanisms of the formation and growth of renal cysts have been clarified, new treatment options have been proposed to slow the progression to end-stage renal disease. Furthermore, in addition to the conventional factors (PKD1 mutation, hypertension, proteinuria, total kidney volume), increasing numbers of studies have recently identified new serum and urinary biomarkers of the disease's progression, which are cheaper and more easily to dosing from the early stages of the disease. The present review discusses the utility of new biomarkers in the monitoring of the progress of ADPKD and their roles in new therapeutic approaches.

Keywords:  ADPKD combined with one of the following: urinary biomarkers; TKV; diagnosis; disease severity; non-coding RNAs; progression; proteomics; risk stratification; specific biomarkers; treatment; urinary exosome

DOI:  https://doi.org/10.3390/medicina59050915
Cells Tissues Organs. 2023 May 22.

Osteoclastogenesis requires primary cilia disassembly and can be inhibited by promoting primary cilia formation pharmacologically.

Michael M Sutton, Michael P Duffy, Stefaan W Verbruggen, Christopher R Jacobs.

The primary cilium is a solitary, sensory organelle with many roles in bone development, maintenance, and function. In the osteogenic cell lineage, including skeletal stem cells, osteoblasts and osteocytes, the primary cilium plays a vital role in the regulation of bone formation and this has made it a promising pharmaceutical target to maintain bone health. While the role of the primary cilium in the osteogenic cell lineage has been increasingly characterized, little is known about the potential impact of targeting the cilium in relation to osteoclasts, a hematopoietic cell responsible for bone resorption. The objective of this study was to determine whether osteoclasts have a primary cilium and to investigate whether or not the primary cilium of macrophages, osteoclast precursors, serves a functional role in osteoclast formation. Using immunocytochemistry, we showed the macrophages have a primary cilium while osteoclasts lack this organelle. Furthermore, we increased macrophage primary cilia incidence and length using fenoldopam mesylate and found that cells undergoing such treatment showed a significant decrease in the expression of osteoclast markers tartrate-resistant acid phosphatase, cathepsin K, and c-Fos as well as decreased osteoclast formation. This work is the first to show that macrophage primary cilia resorption may be a necessary step for osteoclast differentiation. Since primary cilia and pre-osteoclasts are responsive to fluid flow, we applied fluid flow at magnitudes present in the bone marrow to differentiating cells and found that osteoclastic gene expression by macrophages was not affected by fluid-flow mechanical stimulation, suggesting that the role of the primary cilium in osteoclastogenesis is not a mechanosensory one. The primary cilium has been suggested to play a role in bone formation, and our findings indicate that it may also present a means to regulate bone resorption, presenting a dual benefit of developing ciliary-targeted pharmaceuticals for bone disease.

DOI: https://doi.org/10.1159/000531098
Proc Natl Acad Sci U S A. 2023 05 30. 120(22): e2219686120

Primary cilia TRP channel regulates hippocampal excitability.

Thuy N Vien, My C Ta, Louise F Kimura, Tuncer Onay, Paul G DeCaen.

  Polycystins (PKD2, PKD2L1, and PKD2L2) are members of the transient receptor potential family, which form ciliary ion channels. Most notably, PKD2 dysregulation in the kidney nephron cilia is associated with polycystic kidney disease, but the function of PKD2L1 in neurons is undefined. In this report, we develop animal models to track the expression and subcellular localization of PKD2L1 in the brain. We discover that PKD2L1 localizes and functions as a Ca2+ channel in the primary cilia of hippocampal neurons that apically radiate from the soma. Loss of PKD2L1 expression ablates primary ciliary maturation and attenuates neuronal high-frequency excitability, which precipitates seizure susceptibility and autism spectrum disorder-like behavior in mice. The disproportionate impairment of interneuron excitability suggests that circuit disinhibition underlies the neurophenotypic features of these mice. Our results identify PKD2L1 channels as regulators of hippocampal excitability and the neuronal primary cilia as organelle mediators of brain electrical signaling.

Keywords:  TRP channels; channelopathy; ciliopathy; polycystins; primary cilia

DOI:  https://doi.org/10.1073/pnas.2219686120
Am J Nephrol. 2023 May 16. 1

Cerebrovascular Pulsatility Index is Reduced in Autosomal Dominant Polycystic Kidney Disease.

Cortney N Steele, Ester S Oh, Wei Wang, Heather Farmer-Bailey, Berenice Y Gitomer, Michel Chonchol, Kristen L Nowak.

INTRODUCTION: Cerebrovascular dysfunction, characterized by increased brain pulsatile flow, reduced cerebrovascular reactivity, and cerebral hypoperfusion precedes the onset of dementia and is linked to cognitive dysfunction. Autosomal dominant polycystic kidney disease (ADPKD) may increase the risk of dementia, and intracranial aneurysms are more prevalent in ADPKD patients. However, cerebrovascular function has not been previously characterized in patients with ADPKD.
METHODS: Using transcranial Doppler, we compared middle cerebral artery (MCA) pulsatility index (PI; cerebrovascular stiffness) and MCA blood velocity response to hypercapnia (normalized for blood pressure and end-tidal CO2; cerebrovascular reactivity) in patients with early-stage ADPKD vs. age-matched healthy controls. We also administered the NIH cognitive toolbox (cognitive function) and measured carotid-femoral pulse-wave velocity (PWV; aortic stiffness).
RESULTS: Fifteen participants with ADPKD (9F, 27±4 yrs, eGFR: 106±22 ml/min/1.73m2) were compared to 15 healthy controls (8F, 29±4 yrs, eGFR: 109±14 ml/min/1.73m2). MCA PI was unexpectedly lower in ADPKD (0.71±0.07) vs. controls (0.82±0.09 A.U.; p<0.001); however, normalized MCA blood velocity in response to hypercapnia did not differ between groups (2.0±1.2 vs. 2.1±0.8 %△/mmHg; p=0.85). Lower MCA PI was associated with a lower crystalized composite score (cognition), which persisted after adjustment for age, sex, eGFR, and education (β = 0.58, p=0.007). There was no association of MCA PI with carotid-femoral PWV (r=0.01, p=0.96), despite greater carotid-femoral PWV in ADPKD, suggesting MCA PI reflects vascular properties other than arterial stiffness (such as low wall shear stress) in ADPKD.
DISCUSSION/CONCLUSION: MCA PI is lower in patients with ADPKD. Follow-up research on this observation is merited, as low PI has been associated with intracranial aneurysm in other populations.

DOI: https://doi.org/10.1159/000530583
BMC Biol. 2023 05 24. 21(1): 124

CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.

Yujuan Wang, Yuan Zhang, Xinyu Guo, Yiqiang Zheng, Xinjie Zhang, Shanshan Feng, Hui-Yuan Wu.

   BACKGROUND: The axonemal microtubules of primary cilium undergo a conserved protein posttranslational modification (PTM) - polyglutamylation. This reversible procedure is processed by tubulin tyrosine ligase-like polyglutamylases to form secondary polyglutamate side chains, which are metabolized by the 6-member cytosolic carboxypeptidase (CCP) family. Although polyglutamylation modifying enzymes have been linked to ciliary architecture and motility, it was unknown whether they also play a role in ciliogenesis.
RESULTS: In this study, we found that CCP5 expression is transiently downregulated upon the initiation of ciliogenesis, but recovered after cilia are formed. Overexpression of CCP5 inhibited ciliogenesis, suggesting that a transient downregulation of CCP5 expression is required for ciliation initiation. Interestingly, the inhibitory effect of CCP5 on ciliogenesis does not rely on its enzyme activity. Among other 3 CCP members tested, only CCP6 can similarly suppress ciliogenesis. Using CoIP-MS analysis, we identified a protein that potentially interacts with CCP - CP110, a known negative regulator of ciliogenesis, whose degradation at the distal end of mother centriole permits cilia assembly. We found that both CCP5 and CCP6 can modulate CP110 level. Particularly, CCP5 interacts with CP110 through its N-terminus. Loss of CCP5 or CCP6 led to the disappearance of CP110 at the mother centriole and abnormally increased ciliation in cycling RPE-1 cells. Co-depletion of CCP5 and CCP6 synergized this abnormal ciliation, suggesting their partially overlapped function in suppressing cilia formation in cycling cells. In contrast, co-depletion of the two enzymes did not further increase the length of cilia, although CCP5 and CCP6 differentially regulate polyglutamate side-chain length of ciliary axoneme and both contribute to limiting cilia length, suggesting that they may share a common pathway in cilia length control. Through inducing the overexpression of CCP5 or CCP6 at different stages of ciliogenesis, we further demonstrated that CCP5 or CCP6 inhibited cilia formation before ciliogenesis, while shortened the length of cilia after cilia formation.
CONCLUSION: These findings reveal the dual role of CCP5 and CCP6. In addition to regulating cilia length, they also retain CP110 level to suppress cilia formation in cycling cells, pointing to a novel regulatory mechanism for ciliogenesis mediated by demodifying enzymes of a conserved ciliary PTM, polyglutamylation.

Keywords:  CCP5; CCP6; CP110; Ciliogenesis; Polyglutamylation

DOI:  https://doi.org/10.1186/s12915-023-01622-1
Mol Med. 2023 05 22. 29(1): 67

Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion.

Elizabeth J Wilk, Timothy C Howton, Jennifer L Fisher, Vishal H Oza, Ryan T Brownlee, Kasi C McPherson, Hannah L Cleary, Bradley K Yoder, James F George, Michal Mrug, Brittany N Lasseigne.

   BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is one of the most prevalent monogenic human diseases. It is mostly caused by pathogenic variants in PKD1 or PKD2 genes that encode interacting transmembrane proteins polycystin-1 (PC1) and polycystin-2 (PC2). Among many pathogenic processes described in ADPKD, those associated with cAMP signaling, inflammation, and metabolic reprogramming appear to regulate the disease manifestations. Tolvaptan, a vasopressin receptor-2 antagonist that regulates cAMP pathway, is the only FDA-approved ADPKD therapeutic. Tolvaptan reduces renal cyst growth and kidney function loss, but it is not tolerated by many patients and is associated with idiosyncratic liver toxicity. Therefore, additional therapeutic options for ADPKD treatment are needed.
METHODS: As drug repurposing of FDA-approved drug candidates can significantly decrease the time and cost associated with traditional drug discovery, we used the computational approach signature reversion to detect inversely related drug response gene expression signatures from the Library of Integrated Network-Based Cellular Signatures (LINCS) database and identified compounds predicted to reverse disease-associated transcriptomic signatures in three publicly available Pkd2 kidney transcriptomic data sets of mouse ADPKD models. We focused on a pre-cystic model for signature reversion, as it was less impacted by confounding secondary disease mechanisms in ADPKD, and then compared the resulting candidates' target differential expression in the two cystic mouse models. We further prioritized these drug candidates based on their known mechanism of action, FDA status, targets, and by functional enrichment analysis.
RESULTS: With this in-silico approach, we prioritized 29 unique drug targets differentially expressed in Pkd2 ADPKD cystic models and 16 prioritized drug repurposing candidates that target them, including bromocriptine and mirtazapine, which can be further tested in-vitro and in-vivo.
CONCLUSION: Collectively, these results indicate drug targets and repurposing candidates that may effectively treat pre-cystic as well as cystic ADPKD.

Keywords:  ADPKD; Drug prioritization; Drug repurposing; LINCS; PKD; Polycystic kidney disease; Signature reversion

DOI:  https://doi.org/10.1186/s10020-023-00664-z
Clin Med (Lond). 2023 May;23(3): 246-249

Genomics in the kidney clinic.

Gabriel T Doctor, Daniel P Gale, Melanie My Chan.

  Inherited diseases are a frequent cause of end-stage kidney disease and often seen in the kidney clinic. Clinical genomic testing is increasingly available in the UK and eligible patients in England can be referred through the NHS Genomic Medicine Service. Testing is useful for diagnosis, prognostication and management of conditions such as autosomal dominant polycystic kidney disease (ADPKD), Alport syndrome, autosomal dominant tubulointerstitial kidney disease (ADTKD) and focal segmental glomerulosclerosis (FSGS). As more patients undergo genomic testing and newer technologies such as whole genome sequencing are applied, we are developing a greater appreciation of the full phenotypic spectrum of inherited kidney diseases and the challenges associated with the interpretation of clinically significant variants.

Keywords:  ADPKD; ADTKD; Alport syndrome; FSGS; genomics

DOI:  https://doi.org/10.7861/clinmed.2023-RM2
Nephron. 2023 May 25.

Mutation Analysis of PKD1 and PKD2 Genes in a Large Italian Cohort Reveals Novel Pathogenic Variants Including A Novel Complex Rearrangement.

Silvia Orisio, Marina Noris, Miriam Rigoldi, Elena Bresin, Norberto Perico, Matias Trillini, Roberta Donadelli, Annalisa Perna, Ariela Benigni, Giuseppe Remuzzi.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited disease of the kidney. It occurs in adulthood but is also rarely diagnosed in early childhood. The majority of the disease-causing variants observed in ADPKD patients are in two genes: PKD1 and PKD2.
METHODS: 237 patients from 198 families with a clinical diagnosis of ADPKD were screened for PKD1 and PKD2 genetic variants using Sanger sequencing and Multiple Ligation-dependent Probe Amplification (MLPA) analysis.
RESULTS: Disease-causing (diagnostic) variants were identified in 173 families (211 patients), 156 on PKD1 and 17 on PKD2. Variants of unknown significance (VUS) were detected in 6 additional families, while no mutations were found in the remaining 19 families. Among the diagnostic variants detected, 51 were novel. In ten families, seven large rearrangements were found and the molecular breakpoints of 3 rearrangements were identified. Renal survival was significantly worse for PKD1 mutated patients, particularly those carrying truncating mutations. In patients with PKD1 truncating ( PKD1-T) mutations, disease onset was significantly earlier than in patients with PKD1 non-truncating (PKD1-NT) variants or PKD2 mutated patients.
CONCLUSIONS: Comprehensive genetic testing confirms its utility in diagnosing patients with ADPKD and contributes to explaining the clinical heterogeneity observed in this disease. Moreover, the genotype-phenotype correlation can allow a more accurate disease prognosis.

DOI: https://doi.org/10.1159/000530657
Nefrologia (Engl Ed). 2023 May 20. pii: S2013-2514(23)00089-5. [Epub ahead of print]

Reply to Comments on the SENefro Consensus Document on Autosomal Dominant Polycystic Kidney Disease.

Alberto Ortiz, Elisabet Ars, Carmen Bernis, Gloria Fraga, Mónica Furlano, Víctor Martínez, Judith Martins, Maria Vanessa Pérez-Gómez, José Carlos Rodríguez-Pérez, Laia Sans, Roser Torra.

DOI: https://doi.org/10.1016/j.nefroe.2022.07.009
Kidney Int. 2023 Jun;pii: S0085-2538(23)00250-8. [Epub ahead of print]103(6): 1202

Corrigendum to "Ttc21b deficiency attenuates autosomal dominant polycystic kidney disease in a kidney tubular- and maturation-dependent manner." Kidney Int. 2022;102:577-591.

Wei Wang, Luciane M Silva, Henry H Wang, Matthew A Kavanaugh, Tana S Pottorf, Bailey A Allard, Damon T Jacobs, Ruochen Dong, Joseph T Cornelius, Aakriti Chaturvedi, Katherine I Swenson-Fields, Timothy A Fields, Michele T Pritchard, Madhulika Sharma, Chad Slawson, Darren P Wallace, James P Calvet, Pamela V Tran.

DOI: https://doi.org/10.1016/j.kint.2023.04.001
medRxiv. 2023 May 10. pii: 2023.05.07.23289614. [Epub ahead of print]

Polygenic risk affects the penetrance of monogenic kidney disease.

Atlas Khan, Ning Shang, Jordan G Nestor, Chunhua Weng, George Hripcsak, Peter C Harris, Ali G Gharavi, Krzysztof Kiryluk.

Background: Chronic kidney disease (CKD) is a genetically complex disease determined by an interplay of monogenic, polygenic, and environmental risks. Most forms of monogenic kidney diseases have incomplete penetrance and variable expressivity. It is presently unknown if some of the variability in penetrance can be attributed to polygenic factors.
Methods: Using the UK Biobank (N=469,835 participants) and the All of Us (N=98,622 participants) datasets, we examined two most common forms of monogenic kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious variants in the PKD1 or PKD2 genes, and COL4A-associated nephropathy (COL4A-AN caused by deleterious variants in COL4A3 , COL4A4 , or COL4A5 genes). We used the eMERGE-III electronic CKD phenotype to define cases (estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 or kidney failure) and controls (eGFR >90 mL/min/1.73m2 in the absence of kidney disease diagnoses). The effects of the genome-wide polygenic score (GPS) for CKD were tested in monogenic variant carriers and non-carriers using logistic regression controlling for age, sex, diabetes, and genetic ancestry.
Results: As expected, the carriers of known pathogenic and rare predicted loss-of-function variants in PKD1 or PKD2 had a high risk of CKD (OR meta= 17.1, 95% CI: 11.1-26.4, P=1.8E-37). The GPS was comparably predictive of CKD in both ADPKD variant carriers (OR meta= 2.28 per SD, 95%CI: 1.55-3.37, P=2.6E-05) and non-carriers (OR meta= 1.72 per SD, 95% CI=1.69-1.76, P< E-300) independent of age, sex, diabetes, and genetic ancestry. Compared to the middle tertile of the GPS distribution for non-carriers, ADPKD variant carriers in the top tertile had a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile had only a 3-fold increased risk of CKD. Similarly, the GPS was predictive of CKD in both COL4-AN variant carriers (OR meta= 1.78, 95% CI=1.22-2.58, P=2.38E-03) and non-carriers (OR =1.70, 95%CI: 1.68-1.73 P<E-300). The carriers in the top tertile of the GPS had a 2.5-fold higher risk of CKD while the risk for carriers in the bottom tertile was similar to the middle tertile of non-carriers.
Conclusions: Variable penetrance of kidney disease in ADPKD and COL4-AN is partially explained by differences in polygenic risk profiles. Accounting for polygenic factors has the potential to improve risk stratification in monogenic kidney disease and may have implications for genetic counseling.

DOI: https://doi.org/10.1101/2023.05.07.23289614
Dev Biol. 2023 May 18. pii: S0012-1606(23)00080-5. [Epub ahead of print]

Ciliary ARL13B inhibits developmental kidney cystogenesis in mouse.

Robert E Van Sciver, Alyssa B Long, Harrison G Katz, Eduardo D Gigante, Tamara Caspary.

  ARL13B is a small GTPase enriched in cilia. Deletion of Arl13b in mouse kidney results in renal cysts and an associated absence of primary cilia. Similarly, ablation of cilia leads to kidney cysts. To investigate whether ARL13B functions from within cilia to direct kidney development, we examined kidneys of mice expressing an engineered cilia-excluded ARL13B variant, ARL13BV358A. These mice retained renal cilia and developed cystic kidneys. Because ARL13B functions as a guanine nucleotide exchange factor (GEF) for ARL3, we examined kidneys of mice expressing an ARL13B variant that lacks ARL3 GEF activity, ARL13BR79Q. We found normal kidney development with no evidence of cysts in these mice. Taken together, our results show that ARL13B functions within cilia to inhibit renal cystogenesis during mouse development, and that this function does not depend on its role as a GEF for ARL3.

Keywords:  ARL13B; ARL3; Cilia; GEF; Renal cysts

DOI:  https://doi.org/10.1016/j.ydbio.2023.05.004
eNeuro. 2023 May 23. pii: ENEURO.0420-22.2023. [Epub ahead of print]

Rab11a is essential for the development and integrity of the stereocilia and kinocilia in the mammalian organ of Corti.

Lindsey Knapp, Haojie Sun, Yan-Mei Wang, Bin-Jun Chen, Xi Lin, Nan Gao, Ping Chen, Dongdong Ren.

  The cochlea hair cells transform mechanic sounds to neural signals with a remarkable sensitivity and resolution. This is achieved via the precisely sculpted mechanotransduction apparatus of the hair cells and the supporting structure of the cochlea. The shaping of the mechanotransduction apparatus, the staircased stereocilia bundles on the apical surface of the hair cells, requires an intricate regulatory network including planar cell polarity and primary cilia genes in orienting stereocilia bundles and the building molecular machinery of the apical protrusions. The mechanism linking these regulatory components is unknown. Here we show that a small GTPase known for its role in protein trafficking, Rab11a, is required for ciliogenesis in hair cells during development in mice. In addition, in the absence of Rab11a, stereocilia bundles lost their cohesion and integrity, and mice are deaf. These data indicate an essential role of protein trafficking in the formation of hair cell mechanotransduction apparatus, implicating a role of Rab11a or protein trafficking in linking the cilia and polarity regulatory components with the molecular machinery in building the cohesive and precisely shaped stereocilia bundles.Significance StatementOur research discovered for the first time that the small GTPase Rab11a is required for ciliogenesis, and for the precise patterning and cohesion of the stereocilia bundles in cochlear hair cells.

Keywords:  Intraflagellar Transport; Planar cell polarity; Primary cilia; Stereocilia; Tip Link; apcial-basal protein targeting

DOI:  https://doi.org/10.1523/ENEURO.0420-22.2023
bioRxiv. 2023 May 12. pii: 2023.05.09.540007. [Epub ahead of print]

TRiPPing the sensors: The osmosensing pathway of Polycystin 2.

K M Márquez-Nogueras, R M Knutila, V Vuchkosvka, I Y Kuo.

Mutations to polycystin-2 (PC2), a non-selective cation permeant transient receptor potential channel, results in polycystic kidney disease (PKD). Despite the disease relevance of PC2, the physiological agonist that activates PC2 has remained elusive. As one of the earliest symptoms in PKD is a urine concentrating deficiency, we hypothesized that shifts in osmolarity experienced by the collecting duct cells would activate PC2 and loss of PC2 would prevent osmosensing. We found that mice with inducible PC2 knocked out (KO) in renal tubules had dilute urine. Hyperosmotic stimuli induced a rise in endoplasmic reticulum (ER)-mediated cytosolic calcium which was absent in PC2 KO mice and PC2 KO cells. A pathologic point mutation that prevents ion flux through PC2 inhibited the calcium rise, pointing to the centrality of PC2 in the osmotic response. To understand how an extracellular stimulus activated ER-localized PC2, we examined microtubule-ER dynamics, and found that the osmotically induced calcium increase was preceded by microtubule destabilization. This was due to a novel interaction between PC2 and the microtubule binding protein MAP4 that tethers the microtubules to the ER. Finally, disruption of the MAP4-PC2 interaction prevented incorporation of the water channel aquaporin 2 following a hyperosmotic challenge, in part explaining the dilute urine. Our results demonstrate that MAP4-dependent microtubule stabilization of ER-resident PC2 is required for PC2 to participate in the osmosensing pathway. Moreover, osmolarity represents a bona fide physiological stimulus for ER-localized PC2 and loss of PC2 in renal epithelial cells impairs osmosensing ability and urine concentrating capacity.

DOI: https://doi.org/10.1101/2023.05.09.540007
Sci Rep. 2023 May 21. 13(1): 8205

Cilia-associated wound repair mediated by IFT88 in retinal pigment epithelium.

Ke Ning, Mohajeet B Bhuckory, Chien-Hui Lo, Brent E Sendayen, Tia J Kowal, Ming Chen, Ruchi Bansal, Kun-Che Chang, Douglas Vollrath, Nicolas F Berbari, Vinit B Mahajan, Yang Hu, Yang Sun.

Primary cilia are conserved organelles that integrate extracellular cues into intracellular signals and are critical for diverse processes, including cellular development and repair responses. Deficits in ciliary function cause multisystemic human diseases known as ciliopathies. In the eye, atrophy of the retinal pigment epithelium (RPE) is a common feature of many ciliopathies. However, the roles of RPE cilia in vivo remain poorly understood. In this study, we first found that mouse RPE cells only transiently form primary cilia. We then examined the RPE in the mouse model of Bardet-Biedl Syndrome 4 (BBS4), a ciliopathy associated with retinal degeneration in humans, and found that ciliation in BBS4 mutant RPE cells is disrupted early during development. Next, using a laser-induced injury model in vivo, we found that primary cilia in RPE reassemble in response to laser injury during RPE wound healing and then rapidly disassemble after the repair is completed. Finally, we demonstrated that RPE-specific depletion of primary cilia in a conditional mouse model of cilia loss promoted wound healing and enhanced cell proliferation. In summary, our data suggest that RPE cilia contribute to both retinal development and repair and provide insights into potential therapeutic targets for more common RPE degenerative diseases.

DOI: https://doi.org/10.1038/s41598-023-35099-3
Am J Nephrol. 2023 May 05. 1

Novel insight into ferroptosis in kidney diseases.

Liu Yang, Yong Liu, Sijie Zhou, Qi Feng, Yanfang Lu, Dongwei Liu, Zhangsuo Liu.

Kidney diseases involving renal cell injury, such as acute kidney injury (AKI), chronic kidney disease (CKD), polycystic kidney disease (PKD), renal cancer, and kidney stones, remain a global burden. Several pathways that affect cell sensitivity to ferroptosis have been identified within the last decade, and multiple studies have shown a close association between ferroptosis and renal cell injury. Ferroptosis is a type of nonapoptotic iron-dependent cell death caused by an excess of iron-dependent lipid peroxides. The differences between ferroptosis and other types of cell death, such as apoptosis, necroptosis, pyroptosis, cuprotosis, pathophysiological features of the kidney, and ferroptosis-induced kidney injury, are discussed in this review. We also provide an overview of the molecular mechanisms involved in ferroptosis. Furthermore, we summarize the progress of ferroptosis in drug treatment among various kidney diseases. The current research suggests that future therapeutic efforts to treat kidney ailments would benefit from a focus on ferroptosis.

DOI: https://doi.org/10.1159/000530882
BMC Mol Cell Biol. 2023 May 26. 24(1): 20

Genetic and protein interaction studies between the ciliary dyslexia candidate genes DYX1C1 and DCDC2.

Andrea Bieder, Gayathri Chandrasekar, Arpit Wason, Steffen Erkelenz, Jay Gopalakrishnan, Juha Kere, Isabel Tapia-Páez.

   BACKGROUND: DYX1C1 (DNAAF4) and DCDC2 are two of the most replicated dyslexia candidate genes in genetic studies. They both have demonstrated roles in neuronal migration, in cilia growth and function and they both are cytoskeletal interactors. In addition, they both have been characterized as ciliopathy genes. However, their exact molecular functions are still incompletely described. Based on these known roles, we asked whether DYX1C1 and DCDC2 interact on the genetic and the protein level.
RESULTS: Here, we report the physical protein-protein interaction of DYX1C1 and DCDC2 as well as their respective interactions with the centrosomal protein CPAP (CENPJ) on exogenous and endogenous levels in different cell models including brain organoids. In addition, we show a synergistic genetic interaction between dyx1c1 and dcdc2b in zebrafish exacerbating the ciliary phenotype. Finally, we show a mutual effect on transcriptional regulation among DYX1C1 and DCDC2 in a cellular model.
CONCLUSIONS: In summary, we describe the physical and functional interaction between the two genes DYX1C1 and DCDC2. These results contribute to the growing understanding of the molecular roles of DYX1C1 and DCDC2 and set the stage for future functional studies.

Keywords:  Centrosome; Cilia; Dyslexia; Genetic interaction; Zebrafish

DOI:  https://doi.org/10.1186/s12860-023-00483-4
Development. 2023 May 15. pii: dev201411. [Epub ahead of print]150(10):

Esrrγa regulates nephron and ciliary development by controlling prostaglandin synthesis.

Hannah M Wesselman, Ana L Flores-Mireles, Aidan Bauer, Liming Pei, Rebecca A Wingert.

  Cilia are essential for the ontogeny and function of many tissues, including the kidney. Here, we report that transcription factor ERRγ ortholog estrogen related receptor gamma a (Esrrγa) is essential for renal cell fate choice and ciliogenesis in zebrafish. esrrγa deficiency altered proximodistal nephron patterning, decreased the multiciliated cell populace and disrupted ciliogenesis in the nephron, Kupffer's vesicle and otic vesicle. These phenotypes were consistent with interruptions in prostaglandin signaling, and we found that ciliogenesis was rescued by PGE2 or the cyclooxygenase enzyme Ptgs1. Genetic interaction revealed that peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (Ppargc1a), which acts upstream of Ptgs1-mediated prostaglandin synthesis, has a synergistic relationship with Esrrγa in the ciliogenic pathway. These ciliopathic phenotypes were also observed in mice lacking renal epithelial cell (REC) ERRγ, where significantly shorter cilia formed on proximal and distal tubule cells. Decreased cilia length preceded cyst formation in REC-ERRγ knockout mice, suggesting that ciliary changes occur early during pathogenesis. These data position Esrrγa as a novel link between ciliogenesis and nephrogenesis through regulation of prostaglandin signaling and cooperation with Ppargc1a.

Keywords:   esrrγa ; ptgs1 ; Cilia; Differentiation; Kidney; Multiciliated cell; Nephron; Prostaglandin; Zebrafish

DOI:  https://doi.org/10.1242/dev.201411
Genes (Basel). 2023 Apr 27. pii: 984. [Epub ahead of print]14(5):

Loss of Primary Cilia Potentiates BRAF/MAPK Pathway Activation in Rhabdoid Colorectal Carcinoma: A Series of 21 Cases Showing Ciliary Rootlet CoiledCoil (CROCC) Alterations.

Andrea Remo, Federica Grillo, Luca Mastracci, Michele Simbolo, Matteo Fassan, Maria Paola Cecchini, Giuseppe Miscio, Antonio Sassano, Paola Parente, Alessandro Vanoli, Giovanna Sabella, Guido Giordano, Emanuele Damiano Urso, Luigi Cerulo, Aldo Scarpa, Francesco Fiorica, Massimo Pancione.

  A rhabdoid colorectal tumor (RCT) is a rare cancer with aggressive clinical behavior. Recently, it has been recognized as a distinct disease entity, characterized by genetic alterations in the SMARCB1 and Ciliary Rootlet Coiled-Coil (CROCC). We here investigate the genetic and immunophenotypic profiling of 21 RCTs using immunohistochemistry and next-generation sequencing. Mismatch repair-deficient phenotypes were identified in 60% of RCTs. Similarly, a large proportion of cancers exhibited the combined marker phenotype (CK7-/CK20-/CDX2-) not common to classical adenocarcinoma variants. More than 70% of cases displayed aberrant activation of the mitogen-activated protein kinase (MAPK) pathway with mutations prevalently in BRAF V600E. SMARCB1/INI1 expression was normal in a large majority of lesions. In contrast, ciliogenic markers including CROCC and γ-tubulin were globally altered in tumors. Notably, CROCC and γ-tubulin were observed to colocalize in large cilia found on cancer tissues but not in normal controls. Taken together, our findings indicate that primary ciliogenesis and MAPK pathway activation contribute to the aggressiveness of RCTs and, therefore, may constitute a novel therapeutic target.

Keywords:  Ciliary Rootlet Coiled-Coil (CROCC); SMARCB1; rare cancers; rhabdoid colorectal tumors

DOI:  https://doi.org/10.3390/genes14050984