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WilsonData-dependent acquisitionMass SpectrometryBottom-up proteomicsAutosomal Recessive Polycystic Kidney DiseaseNot availableArpkdCystin-1Myristoyl-electrostatic switchPpm1a-dephosphorylationPka-phosphorylationCystinhttps://www.ebi.ac.uk/pride/archive/projects/PXD048013KidneyTandem Affinity Purification (TAP) protocol: TAP was performed using the previously published protocol19 with minor modifications. Briefly, two 15 cm plates of N-SF-TAP stable cells were grown to 5 dpc and then lysed in the TAP lysis buffer [30 mM Tris-Cl (pH 7.4), 150 mM NaCl, 0.5% Nonidet P-40, 1x complete proteinase inhibitor cocktail (Millipore Sigma, Roche, # 11697498001)]. The lysate was then incubated 4°C overnight with the Strep-Tactin Superflow Resin (IBA Lifesciences, # 2-1206-002) using end-over-end rotation. The resin with bound proteins was then washed twice with TAP wash buffer [30 mM Tris-Cl (pH 7.4), 150 mM NaCl, 0.5 % NP-40] and the proteins were eluted from the resin using Buffer E (IBA Lifesciences, # 2-1000-025). The resulting eluate was then incubated for several hours at 4°C with the anti-FLAG-M2 affinity gel (Millipore Sigma, # A2220), followed by two more rounds of washes with TAP wash buffer at 4°C. Finally, the purified proteins were eluted from the anti-FLAG-M2 resin using a FLAG elution buffer [30 mM Tris-Cl (pH 7.4), 150 mM NaCl] and 200 µg/ml FLAG peptide (Millipore Sigma, # F3290) and the eluted proteins were resolved using SDS-PAGE electrophoresis. SDS-PAGE gels were stained with SYPRO Ruby Protein Gel Stain (Millipore Sigma, # S4942) and Pierce Silver Stain Kit (Thermo Fisher Scientific, # 24612) according to manufacturers’ protocols. In-gel digestion: SDS gel bands were excised, and the excess stain was removed by an overnight wash in a 1:1 mixture of 100 mM ammonium bicarbonate and 100% acetonitrile. After destaining, disulfide bonds were reduced by incubation in 25 mM dithiothreitol at 50°C for 30 min. Alkylation of the free thiol groups was carried out with 55 mM iodoacetamide for 30 min protected from light. The gel pieces were washed twice with 100 mM ammonium bicarbonate for 30 min each and dehydrated in a Savant SpeedVac before the addition of the enzyme. Twelve and a half ng/µl trypsin (Promega Gold Mass Spectrometry Grade, # V5280) was added to each gel sample and incubated overnight at 37°C. Peptides were extracted from the gel pieces by two incubations in a 1:1 mixture of 5% formic acid and 50% aqueous acetonitrile for 15 min each. The extracts were pooled, and the buffer evaporated away followed by resuspension in 20 µl of 0.1% formic acid and Mass Spectrometry analysis. Nano cHiPLC tandem Mass Spectrometry (MS): An aliquot (4 µl) of each digest was loaded onto a Nano cHiPLC 200µm x 0.5mm ChromXP C18-CL 3µm 120Å reverse-phase trap cartridge at 2 µl/min using an Eksigent autosampler. The cartridge was washed for 4 min with 0.1% formic acid in ddH20. The bound peptides were flushed onto a Nano cHiPLC column 75 µm x 15 cm ChromXP C18-CL 3 µm 120 Å with a 90 min linear acetonitrile gradient (5-50%) in 0.1% formic acid at a rate of 300 nl/min using an Eksigent Nano1D+LC. The column was washed with 90% acetonitrile + 0.1% formic acid for 10 min followed by 5% acetonitrile + 0.1% formic acid for 10 min. The HPLC system and components were purchased from Eksigent in Dublin, CA. The Applied Biosystems 5600 Triple-TOF mass spectrometer (AB-Sciex, Toronto, Canada) was used to analyze the protein digest. The IonSpray voltage was set to 2300 V and the declustering potential was at 80 V. The IonSpray and curtain gases were set at 10 psi and 25 psi, respectively. The interface heater temperature was 120°C. The eluted peptides were subjected to a time-of-flight survey scan from 400-1250 m/z to determine the top twenty most intense ions for MSMS analysis. Product ion time-of-flight scans at 50 msec were carried out to obtain the tandem mass spectra of the selected parent ions over a range from m/z 400-2000. Spectra were centroided and de-isotoped by Analyst software, version TF (Applied Biosystems). A β-galactosidase trypsin digest was used to calibrate the analysis.PrideNot availableIn-house ProteinPilot 5.02 software (AB-Sciex, Toronto, Canada) was utilized for database searches against the Mus musculus UniProt database for protein identifications using a trypsin digestion motif. Proteins with at least one peptide sequenced with a Confidence Scoreof >95% were included in the list of identified proteins.ProteomicsLisa Guay-WoodfordPARTIALCenter for Translational Research, Children’s National Research Institute, Children’s National Hospital, Washington,DC, United States & Children’s Hospital of Philadelphia, Philadelphia, PA, United StatesMus Musculus (mouse)41720266 Yang C, Harafuji N, Watts JA, Tao B, Moran C, Clements J, Price K, Laucevicius A, Burrill N, Gebb J, Soni S, Oliver E, Savla JJ, Christ L, Moldenhauer J, Hartung EA, Didier R, Santani A, Sandford RN, Selkirk L, Radley JA, Mann K, Simonicova I, Karl R, Kariat Ashraf AP, Wachten D, Wilson L, Bebok Z, Caldovic L, Guay-Woodford LM. Disruption of the human cystin-1 myristoyl-electrostatic switch causes polycystic kidney disease that phenocopies autosomal recessive polycystic kidney disease. Kidney Int. 2026:S0085-2538(26)00131-6 10.1016/j.kint.2026.01.023empy1977@uab.eduUniversity of Alabama at BirminghamUnited States<h4>Introduction</h4>Autosomal recessive polycystic kidney disease (ARPKD) is caused primarily by pathogenic variants in PKHD1, encoding fibrocystin/polyductin. In Cys1^cpk/cpk (cpk) mice, the kidney and liver lesions closely phenocopy ARPKD. Cys1 encodes cystin, a myristoylated protein that traffics to the primary cilium and nucleus. We recently reported the first patient with ARPKD due to a homozygous CYS1 splicing variant.<h4>Methods</h4>To study this, we utilized high-resolution ultrasound, array Comparative Genomic Hybridization and exon sequencing to identify an ARPKD-like kidney lesion and CYS1 defects in two families. Bioinformatic analyses compared cystin sequence conservation across mammals. Immunofluorescence, optogenetic studies, and 3D culture comparatively evaluated subcellular localization, ciliary trafficking, and cyst formation under cAMP stimulation of wild-type and mutant cystin. Tandem affinity purification/mass spectrometry identified cystin-binding partners. Serine-17 phosphorylation was evaluated functionally.<h4>Results</h4>The Family 1 proband carried a homozygous deletion about 24-kb in size encompassing the CYS1 regulatory region and exon 1. In Family 2, two affected siblings had a homozygous CYS1 c.4G>A (p.Gly2Ser) variant affecting Gly2 within the N-terminal myristoylation motif. This region, together with an adjacent arginine-rich stretch flanked by serines-8 (S8) and -17 (S17) residues, comprises a conserved myristoyl-electrostatic switch that can regulate reversible protein-membrane binding. S17 phosphorylation modulates cystin membrane association and intracellular trafficking. In 3D culture, CRISPR/Cas9-generated cystin-null cells or null cells expressing cystin-1_G2S showed enhanced cyst formation versus their respective controls. cAMP activation by cilia-specific optogenetic stimulation in cultured cells or pharmacologic treatment of ex vivo embryonic kidneys reduced cystin ciliary localization in a protein kinase A-dependent manner. Mass spectrometry identified the phosphatase PPM1A as a cystin-interacting partner, and pharmacologic inhibition reduced cystin S17 dephosphorylation.<h4>Conclusions</h4>Cystin-1 intracellular trafficking and function are regulated by a myristoyl-electrostatic switch mechanism. Cystic kidneys in three individuals with homozygous CYS1 pathogenic variants provide further support that cystin-1 deficiency causes polycystic kidney disease that phenocopies ARPKD.Disruption of the human cystin-1 myristoyl-electrostatic switch causes polycystic kidney disease that phenocopies autosomal recessive polycystic kidney disease.Yang Chaozhe C, Harafuji Naoe N, Watts Jacob A JA, Tao Binli B, Moran Claire C, Clements Jenna J, Price Kalyn K, Laucevicius Anthony A, Burrill Natalie N, Gebb Juliana J, Soni Shelly S, Oliver Edward E, Savla Jill J JJ, Christ Lori L, Moldenhauer Julie J, Hartung Erum A EA, Didier Ryne R, Santani Avni A, Sandford Richard N RN, Selkirk Lisa L, Radley Jessica A JA, Mann Kathy K, Simonicova Ingrid I, Karl Rudolfo R, Kariat Ashraf Arsila Palliyulla AP, Wachten Dagmar D, Wilson Landon L, Bebok Zsuzsanna Z, Caldovic Ljubica L, Guay-Woodford Lisa M LMfalseDisruption of the human Cystin-1 myristoyl-electrostatic switch causes autosomal recessive polycystic kidney disease (ARPKD)Autosomal recessive polycystic kidney disease (ARPKD; MIM#263200) is primarily caused by pathogenic variants in PKHD1, which encodes fibrocystin/polyductin (FPC). The Cys1cpk/cpk (cpk) mouse expresses a renal lesion that closely phenocopies ARPKD. Cys1-encoded cystin is a myristoylated protein that traffics to the primary cilium and the nucleus, where it regulates gene expression. We recently described the first human patient with ARPKD due to a homozygous CYS1 splicing variant. Here we present two siblings with ARPKD and homozygosity for a CYS1 c.4G>A (p.G2S) variant, which disrupts the G2 myristoylation site within the predicted N-terminal myristylation motif, MGxxxSx. Alignment of 97 vertebrate cystin protein sequences showed high conservation of a putative myristoyl-electrostatic switch that can regulate reversible protein binding to membranes. The conserved region includes the N-myristylation site and an adjacent arginine-rich stretch flanked by serine-8 (S8) and -17 (S17) residues. Using immunofluorescence and site-directed mutagenesis, we confirmed that S17 phosphorylation modulates cystin membrane association and intracellular trafficking. In turn, optogenetic activation of ciliary cAMP signaling reduced the cystin ciliary localization in a PKA-dependent manner. Tandem affinity purification (TAP) and mass spectroscopy identified the protein phosphatase PPM1A as a cystin-interacting partner. Inhibition of PPM1A with sanguinarine impeded cystin S17 de-phosphorylation confirming functional interaction. Our study demonstrates that cystin intracellular trafficking and nuclear function are regulated by a myristoyl-electrostatic switch mechanism, and further supports CYS1 as a disease-causing gene for human ARPKD, providing the first mechanistic insight for disease pathogenesis.2026-04-132023-12-20PXD048013NEWT:1773NEWT:3555NEWT:1182590NEWT:10090NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:347515NEWT:1216979NEWT:307972NEWT:92867NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:257309NEWT:284812NEWT:115104NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:544404NEWT:3702NEWT:8839NEWT:4232NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:885318NEWT:4081NEWT:876138NEWT:554NEWT:5691NEWT:260710NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:8030NEWT:380394NEWT:272563NEWT:507601NEWT:1639NEWT:188229NEWT:4909NCBITaxon:79857NEWT:746360NEWT:6239NEWT:135588NEWT:135622NEWT:6915NEWT:9986NEWT:101510NEWT:95486NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:146479NEWT:1000589NEWT:145943NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:235443NEWT:985076NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:243230NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10116NEWT:1280NEWT:1836NEWT:29760NEWT:260705NEWT:80863NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:709141720266