A common intronic single nucleotide variant modifies PKD1 expression level.

Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in PKD1 and PKD2 (PKD1/2), has unexplained phenotypic variability likely affected by environmental and other genetic factors. Approximately 10% of individuals with ADPKD phenotype have no causal mutation detected, possibly due to unrecognized risk variants of PKD1/2. This study was designed to identify risk variants of PKD genes through population genetic analyses. We used Wright's F-statistics (Fst) to evaluate common single nucleotide variants (SNVs) potentially favored by positive natural selection in PKD1 from 1000 Genomes Project (1KG) and genotyped 388 subjects from the Rogosin Institute ADPKD Data Repository. The variants with >90th percentile Fst scores underwent further investigation by in silico analysis and molecular genetics analyses. We identified a deep intronic SNV, rs3874648G> A, located in a conserved binding site of the splicing regulator Tra2-ß in PKD1 intron 30. Reverse-transcription PCR (RT-PCR) of peripheral blood leukocytes (PBL) from an ADPKD patient homozygous for rs3874648-A identified an atypical PKD1 splice form. Functional analyses demonstrated that rs3874648-A allele increased Tra2-ß binding affinity and activated a cryptic acceptor splice-site, causing a frameshift that introduced a premature stop codon in mRNA, thereby decreasing PKD1 full-length transcript level. PKD1 transcript levels were lower in PBL from rs3874648-G/A carriers than in rs3874648-G/G homozygotes in a small cohort of normal individuals and patients with PKD2 inactivating mutations. Our findings indicate that rs3874648G > A is a PKD1 expression modifier attenuating PKD1 expression through Tra2-ß, while the derived G allele advantageously maintains PKD1 expression and is predominant in all subpopulations.

Deployed Deep Learning Kidney Segmentation for Polycystic Kidney Disease MRI.

This study develops, validates, and deploys deep learning for automated total kidney volume (TKV) measurement (a marker of disease severity) on T2-weighted MRI studies of autosomal dominant polycystic kidney disease (ADPKD). The model was based on the U-Net architecture with an EfficientNet encoder, developed using 213 abdominal MRI studies in 129 patients with ADPKD. Patients were randomly divided into 70% training, 15% validation, and 15% test sets for model development. Model performance was assessed using Dice similarity coefficient (DSC) and Bland-Altman analysis. External validation in 20 patients from outside institutions demonstrated a DSC of 0.98 (IQR, 0.97-0.99) and a Bland-Altman difference of 2.6% (95% CI: 1.0%, 4.1%). Prospective validation in 53 patients demonstrated a DSC of 0.97 (IQR, 0.94-0.98) and a Bland-Altman difference of 3.6% (95% CI: 2.0%, 5.2%). Last, the efficiency of model-assisted annotation was evaluated on the first 50% of prospective cases (n = 28), with a 51% mean reduction in contouring time (P < .001), from 1724 seconds (95% CI: 1373, 2075) to 723 seconds (95% CI: 555, 892). In conclusion, our deployed artificial intelligence pipeline accurately performs automated segmentation for TKV estimation of polycystic kidneys and reduces expert contouring time. Keywords: Convolutional Neural Network (CNN), Segmentation, Kidney ClinicalTrials.gov identification no.: NCT00792155 Supplemental material is available for this article. © RSNA, 2022.

Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by the development of multiple cysts in the kidneys. It is often caused by pathogenic mutations in PKD1 and PKD2 genes that encode polycystin proteins. Although the molecular mechanisms for cystogenesis are not established, concurrent inactivating germline and somatic mutations in PKD1 and PKD2 have been previously observed in renal tubular epithelium (RTE). METHODS: To further investigate the cellular recessive mechanism of cystogenesis in RTE, we conducted whole-genome DNA sequencing analysis to identify germline variants and somatic alterations in RTE of 90 unique kidney cysts obtained during nephrectomy from 24 unrelated participants. RESULTS: Kidney cysts were overall genomically stable, with low burdens of somatic short mutations or large-scale structural alterations. Pathogenic somatic "second hit" alterations disrupting PKD1 or PKD2 were identified in 93% of the cysts. Of these, 77% of cysts acquired short mutations in PKD1 or PKD2 ; specifically, 60% resulted in protein truncations (nonsense, frameshift, or splice site) and 17% caused non-truncating mutations (missense, in-frame insertions, or deletions). Another 18% of cysts acquired somatic chromosomal loss of heterozygosity (LOH) events encompassing PKD1 or PKD2 ranging from 2.6 to 81.3 Mb. 14% of these cysts harbored copy number neutral LOH events, while the other 3% had hemizygous chromosomal deletions. LOH events frequently occurred at chromosomal fragile sites, or in regions comprising chromosome microdeletion diseases/syndromes. Almost all somatic "second hit" alterations occurred at the same germline mutated PKD1/2 gene. CONCLUSIONS: These findings further support a cellular recessive mechanism for cystogenesis in ADPKD primarily caused by inactivating germline and somatic variants of PKD1 or PKD2 genes in kidney cyst epithelium.

Semi-Automated 3D Volumetric Renal Measurements in Polycystic Kidney Disease Using b0-Images-A Feasibility Study.

Autosomal dominant polycystic kidney disease (ADPKD) eventually leads to end stage renal disease (ESRD) with an increase in size and number of cysts over time. Progression to ESRD has previously been shown to correlate with total kidney volume (TKV). An accurate and relatively simple method to perform measurement of TKV has been difficult to develop. We propose a semi-automated approach of calculating TKV inclusive of all cysts in ADPKD patients based on b0 images relatively quickly without requiring any calculations or additional MRI time. Our purpose is to evaluate the reliability and reproducibility of our method by raters of various training levels within the environment of an advanced 3D viewer. Thirty patients were retrospectively identified who had DWI performed as part of 1.5T MRI renal examination. Right and left TKVs were calculated by five radiologists of various training levels. Interrater reliability (IRR) was estimated by computing the intraclass correlation (ICC) for all raters. ICC values calculated for TKV measurements between the five raters were 0.989 (95% CI = (0.981, 0.994), p < 0.01) for the right and 0.961 (95% CI = (0.936, 0.979), p < 0.01) for the left. Our method shows excellent intraclass correlation between raters, allowing for excellent interrater reliability.

Prevalence of Inferior Vena Cava Compression in ADPKD.

INTRODUCTION: Kidney and liver cysts in autosomal dominant polycystic kidney disease (ADPKD) can compress the inferior vena cava (IVC), but IVC compression prevalence and its risk factors are unknown. METHODS: Patients who have ADPKD (n = 216) with abdominal magnetic resonance imaging (MRI) studies and age-/sex-matched controls (n = 216) were evaluated for IVC compression as well as azygous vein diameter (a marker of collateral blood flow) and IVC aspect ratio (left-to-right dimension divided by anterior-to-posterior dimension with a value of 1 corresponding to a circular (high pressure) IVC caudal to compression. RESULTS: Severe IVC compression (≥70%) was observed in 33 (15%) ADPKD subjects and mild compression (≥50% to <70%) was observed in 33 (15%) subjects; whereas controls had no IVC compression (P < 0.001). Severe IVC compression was associated with larger azygous vein (4.0 ± 1.3 mm versus 2.3 ± 0.8 mm without IVC compression; P < 0.001) and a more circular IVC cross-section upstream (mean IVC aspect ratio: 1.16 ± 0.27 vs. 1.69 ± 0.67, P < 0.001), suggesting higher pressure upstream from the compression. IVC compression was associated with older age, lower estimated glomerular filtration rate (eGFR), greater height-adjusted total kidney volumes, greater height-adjusted liver volume (ht-LV), and greater liver and renal cyst fractions (P < 0.001). No subject younger than 30 years had IVC compression, but ADPKD subjects ≥40 years old had 12-fold higher risk of IVC compression (95% confidence interval [CI]: 4.2-42.4), with highest predicted probability for Mayo Clinic classes 1D (59%; 95% CI: 39%-76%) and 1E (74%; 95% CI: 49%-90%) after adjustment (P < 0.001). Women with ht-LV ≥ 2000 ml/m had 83% (95% CI: 59%-95%) prevalence of IVC compression. Complications of IVC compression included deep vein thrombosis (DVT) and symptomatic hypotension. CONCLUSIONS: IVC compression is common in ADPKD patients >40 years old, with Mayo Clinic class 1D/E, and in females with ht-LV > 2000 ml/m.

Hemorrhagic Cysts and Other MR Biomarkers for Predicting Renal Dysfunction Progression in Autosomal Dominant Polycystic Kidney Disease.

BACKGROUND: Screening for rapidly progressing autosomal dominant polycystic kidney disease (ADPKD) is necessary for assigning and monitoring therapies. Height-adjusted total kidney volume (ht-TKV) is an accepted biomarker for clinical prognostication, but represents only a small fraction of information on abdominal MRI. PURPOSE: To investigate the utility of other MR features of ADPKD to predict progression. STUDY TYPE: Single-center retrospective. POPULATION: Longitudinal data from 186 ADPKD subjects with baseline serum creatinine, PKD gene testing, abdominal MRI measurements, and ≥2 follow-up serum creatinine were reviewed. FIELD STRENGTH/SEQUENCE: 1.5T, T2 -weighted single-shot fast spin echo, T1 -weighted 3D spoiled gradient echo (liver accelerated volume acquisition) and 2D cine velocity encoded gradient echo (phase contrast MRA). ASSESSMENT: Ht-TKV, renal blood flow (RBF), number and fraction of renal and hepatic cysts, bright T1 hemorrhagic renal cysts, and liver and spleen volumes were independently assessed by three observers blinded to estimated glomerular filtration rate (eGFR) data. STATISTICAL TESTS: Linear mixed-effect models were applied to predict eGFR over time using MRI features at baseline adjusted for confounders. Validation was performed in 158 patients who had follow-up MRI using receiver operator characteristic, sensitivity, and specificity. RESULTS: Hemorrhagic cysts, fraction of renal and hepatic cysts, height-adjusted liver and spleen volumes were significant independent predictors of future eGFR (final prediction model R2 = 0.88 P < 0.05). The number of hemorrhagic cysts significantly improved the prediction compared to ht-TKV in predicting future eGFR (area under the curve [AUC] = 0.94, 95% confidence interval [CI]: 0.9-0.94 vs. R2 = 0.9, 95% CI: 0.85-0.9, P = 0.045). For baseline eGFR ≥60 ml/min/1.73m2 , sensitivity for predicting eGFR<45 ml/min/1.73m2 by ht-TKV alone was 29%. Sensitivity increased to 72% with all MRI variables in the model (P < 0.05 = 0.019), whereas specificity was unchanged, 100% vs. 99%. DATA CONCLUSION: Combining multiple MR features including hemorrhagic renal cysts, renal cyst fraction, liver and spleen volume, hepatic cyst fraction, and renal blood flow enhanced sensitivity for predicting eGFR decline in ADPKD compared to the standard model including only ht-TKV. Level of Evidence 2 Technical Efficacy Stage 2 J. MAGN. RESON. IMAGING 2021;53:564-576.

Bosutinib versus Placebo for Autosomal Dominant Polycystic Kidney Disease.

Overactivation of Src has been linked to the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD). This phase 2, multisite study assessed the efficacy and safety of bosutinib, an oral dual Src/Bcr-Abl tyrosine kinase inhibitor, in patients with ADPKD. Patients with ADPKD, eGFR≥60 ml/min per 1.73 m2, and total kidney volume ≥750 ml were randomized 1:1:1 to bosutinib 200 mg/d, bosutinib 400 mg/d, or placebo for ≤24 months. The primary endpoint was annualized rate of kidney enlargement in patients treated for ≥2 weeks who had at least one postbaseline magnetic resonance imaging scan that was preceded by a 30-day washout (modified intent-to-treat population). Of 172 enrolled patients, 169 received at least one study dose. Per protocol amendment, doses for 24 patients who initially received bosutinib at 400 mg/d were later reduced to 200 mg/d. The annual rate of kidney enlargement was reduced by 66% for bosutinib 200 mg/d versus placebo (1.63% versus 4.74%, respectively; P=0.01) and by 82% for pooled bosutinib versus placebo (0.84% versus 4.74%, respectively; P<0.001). Over the treatment period, patients receiving placebo or bosutinib had similar annualized eGFR decline. Gastrointestinal and liver-related adverse events were the most frequent toxicities. In conclusion, compared with placebo, bosutinib at 200 mg/d reduced kidney growth in patients with ADPKD. The overall gastrointestinal and liver toxicity profile was consistent with the profile in prior studies of bosutinib; no new toxicities were identified. (ClinicalTrials.gov: NCT01233869).

A randomized clinical trial in vitamin D-deficient adults comparing replenishment with oral vitamin D3 with narrow-band UV type B light: effects on cholesterol and the transcriptional profiles of skin and blood.

Background: Vitamin D deficiency, defined as a serum 25-hydroxyvitamin D [25(OH)D] concentration <20 ng/mL, is correlated with a more atherogenic lipid profile. However, oral vitamin D supplementation does not lower LDL-cholesterol concentrations or raise HDL-cholesterol concentrations. This uncoupling between association and causation may result from a failure of oral vitamin D to mimic the effect of dermally synthesized vitamin D in response to ultraviolet type B (UVB) light.Objective: We tested the hypothesis that, in vitamin D-deficient adults, the replenishment of vitamin D with UVB exposure would lower LDL-cholesterol concentrations compared with the effect of oral vitamin D3 supplementation.Design: We performed a randomized clinical trial in vitamin D-deficient adults and compared vitamin D replenishment between subjects who received oral vitamin D3 (n = 60) and those who received narrow-band UVB exposure (n = 58) ≤6 mo.Results: There was no difference in the change from baseline LDL-cholesterol concentrations between oral vitamin D3 and UVB groups (difference in median of oral vitamin D3 minus that of UVB: 1.5 mg/dL; 95% CI: -5.0, 7.0 mg/dL). There were also no differences within groups or between groups for changes in total or HDL cholesterol or triglycerides. Transcriptional profiling of skin and blood, however, revealed significant upregulation of immune pathway signaling with oral vitamin D3 but significant downregulation with UVB.Conclusions: Correcting vitamin D deficiency with either oral vitamin D3 or UVB does not improve the lipid profile. Beyond cholesterol, these 2 modalities of raising 25(OH)D have disparate effects on gene transcription. This trial was registered at clinicaltrials.gov as NCT01688102.

Intraobserver and interobserver variability of renal volume measurements in polycystic kidney disease using a semiautomated MR segmentation algorithm.

OBJECTIVE: Total renal volume and changes in kidney volume are markers of disease progression in autosomal-dominant polycystic kidney disease (ADPKD) but are not used in clinical practice in part because of the complexity of manual measurements. This study aims to assess the intra- and interobserver reproducibility of a semiautomated renal volumetric algorithm using fluid-sensitive MRI pulse sequences. SUBJECTS AND METHODS: Renal volumes of 17 patients with ADPKD were segmented from high-resolution coronal HASTE and true fast imaging with steady-state precession (FISP) MR acquisitions. Measurements performed independently by four readers were repeated, typically after 7 days. Intraobserver agreement indexes were calculated for total kidney volume for each patient. Interobserver agreement indexes were obtained for the six paired combinations of readers as well as for two readers after rigorous formalized training. Pearson and concordance correlation coefficients, coefficients of variation (CVs), and 95% limits of agreement were determined. RESULTS: The HASTE and true FISP sequences performed similarly with a median intraobserver agreement of greater than 98.1% and a CV of less than 2.4% across all readers. The median interobserver agreement was greater than 95.2% and the CV was less than 7.1%, across all reader pairs. Reader training further lowered interobserver CV. The mean total kidney volume was 1420 mL (range, 331-3782 mL) for HASTE imaging and 1445 mL (range, 301-3714 mL) for true FISP imaging, with mean image processing times per patient of 43 and 28 minutes, respectively. CONCLUSION: This semiautomated MR volumetric algorithm provided excellent intraobserver and very good interobserver reproducibility using fluid-sensitive pulse sequences that emphasize cyst conspicuity.

Is renal thrombotic angiopathy an emerging problem in the treatment of ovarian cancer recurrences?

BACKGROUND AND OBJECTIVE: Ovarian cancer is usually diagnosed at an advanced stage, with most patients undergoing surgery followed by platinum- and taxane-based chemotherapy. After initial clinical remission, the majority recur, leading to additional treatments, including not only platinums and taxanes but also pegylated liposomal doxorubicin (PLD), gemcitabine, topotecan, and, more recently, bevacizumab, which may extend survival times. PLD, in particular, has been extensively studied by our group, with encouraging therapeutic results. We, however, observed instances of chronic kidney disease (CKD) developing among patients who received long-term treatment for recurrent ovarian cancer. To document the frequency and contributing factors to the emergence of CKD, we initiated a retrospective review at two institutions. PATIENTS AND METHODS: Fifty-six consecutive patients with recurrent ovarian cancer receiving treatment at New York University Cancer Institute were reviewed for the presence of renal disease in 1997-2010. At Shaare Zedek Medical Center, 73 consecutive patients with ovarian cancer were reviewed in 2002-2010. Patients were diagnosed with CKD if they had an estimated GFR <60 mL/minute per 1.73 m2 for >3 months and were staged according to the National Kidney Foundation guidelines. RESULTS: Thirteen patients (23%) developed stage ≥3 CKD. Three patients had renal biopsies performed that showed thrombotic microangiopathy. CONCLUSIONS: CKD is emerging as a potential long-term consequence of current chemotherapy for recurrent ovarian cancer.

A pilot clinical study to evaluate changes in urine osmolality and urine cAMP in response to acute and chronic water loading in autosomal dominant polycystic kidney disease.

BACKGROUND AND OBJECTIVES: Autosomal dominant polycystic kidney disease (ADPKD) leads to kidney failure in half of those affected. Increased levels of adenosine 3':5'-cyclic monophosphate (cAMP) play a critical role in disease progression in animal models. Water loading, by suppressing arginine vasopressin (AVP)-stimulated cAMP production, is a proposed therapy for ADPKD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: The effects of acute and sustained water loading on levels of urine osmolality (Uosm) and cAMP in 13 subjects with ADPKD and 10 healthy controls were studied. Uosm and cAMP concentrations were measured before and after water loading. RESULTS: Urine [cAMP] indexed to Uosm significantly decreased with acute water loading in both groups (58% in controls and 35% in ADPKD). Chronic water loading resulted in a nonsignificant 13% decrease in 24-hour urine cAMP excretion in ADPKD participants, despite an increase in 24-hour urine volume by 64% to 3.14 +/- 0.32 L and decrease in mean Uosm by 46%, to below that of plasma (270 +/- 21 mOsm/L). CONCLUSIONS: Increased water intake of 3 L per day decreased Uosm in most ADPKD subjects. While urine [cAMP] accurately reflects changes in Uosm during acute water loading in ADPKD subjects, chronic water loading did not lower 24-hour urine cAMP excretion, although subjects with higher baseline [cAMP] (>2 nmol/mg Cr) responded best. Decreases in urine [cAMP] and osmolality are consistent with decreased AVP activity. These results support the need for a larger study to evaluate the effect of chronic water loading on ADPKD progression.

Moderate kidney disease inhibits atherosclerosis regression.

UNLABELLED: Chronic kidney disease (CKD) accelerates cardiovascular disease. The mechanisms that explain this independent, excess risk associated with CKD have not been fully elucidated. OBJECTIVES: We propose that impaired regression of atherosclerosis in renal disease represents a novel risk factor for the heightened morbidity and mortality and resistance to treatment observed in patients with CKD. METHODS AND RESULTS: Using a transplant model to study atherosclerosis regression, we transplanted atheromatous aortic segments generated in Apolipoprotein E knock-out (ApoE(-/-)) mice, into either control or moderately uremic, normolipidemic, wild-type mice. In non-uremic mice, lesions regressed 55%, whereas lesions in uremic mice increased in size by 17% (p<0.01 for control vs. uremic). The lesions in uremic mice were also characterized by a greater presence of macrophages (36,300 microm(2) vs. 12,600 microm(2), p<0.01). This finding was despite upregulation of chemokine receptor 7 (CCR7), normally a migration factor, in uremic lesion macrophages. Gene expression analysis of lesion macrophages showed relative down-regulation of serum response factor (SRF) target genes in the uremic group, consistent with impaired CCR7 signaling. CONCLUSION: Moderate kidney disease inhibits regression of atherosclerosis in a mouse transplant model. This inhibition may be a result of impaired CCR7 signaling.

Lipid metabolism in dialysis patients-the story gets more complicated.

Cardiovascular disease continues to be the foremost cause of morbidity and mortality in dialysis patients. Compared with the general population, dialysis patients suffer from an accelerated disease course that is, at least in part, resistant to conventional therapy. While there are a myriad of potential explanations for this resistance, derangements in lipid metabolism probably play an important role. Here, we discuss the significance of altered lipid metabolism in uremia, such as oxidative lipoprotein modification and the pathophysiology of adipose tissue; limitations of conventional approaches to dyslipidemia such as statin therapy and traditional lipid profiles; and areas of investigation with potential for new therapy, such as reverse cholesterol transport.

Chronic kidney disease in HIV infection: an urban epidemic.

Kidney disease is an important complication of HIV, particularly in minority populations. We describe the burden of chronic kidney disease among 1239 adults followed at an urban AIDS center, with an estimated prevalence of 15.5% (n = 192). Independent predictors of kidney disease included older age, black race, hepatitis C virus exposure, and lower CD4 cell count. These data suggest that chronic kidney disease remains a common complication of HIV infection in the era of antiretroviral therapy.