Set-up of a Platform for Personalized Diagnosis of Rare Kidney Diseases (NIKE)

Chronic Kidney Diseases Clinical Trial

Official title:

Set-up of a Platform for Personalized Diagnosis of Rare Kidney Diseases (NIKE)

Clinical Trial Details — Status: Active, not recruiting

Administrative data

• NCT number: NCT06325072
• Other study ID #: NIKE
• Status: Active, not recruiting
• Phase: N/A
• Start date: July 9, 2021
• Est. completion date: June 30, 2024

Study information

• Verified date: March 2024
• Source: Meyer Children's Hospital IRCCS
• Contact: n/a
• Is FDA regulated: No
• Study type: Interventional

Clinical Trial Summary

Chronic kidney disease (CKD) is a major health problem, with steadily increasing incidence and prevalence and the threat of a true "epidemic". Converging evidence suggests a high prevalence of genetic etiology in rare kidney diseases and the list of new disease-causing genes is constantly updated. Recent advances in next-generation sequencing (NGS) technologies have prompted a significant improvement in the diagnosis of rare kidney diseases. Notwithstanding this, NGS generates high numbers of information that need to be properly analysed by the joint efforts of geneticists, nephrologists and bioinformatics in order to integrate clinical and genetic information in a personalized manner. In addition, in selected cases, the contribution of researchers proves essential for the development of experimental models of the disease to study and understand the pathogenic features and propose a personalized therapeutic approach. Such an innovative, integrated diagnostic paradigm is currently available in few centers all over the world and cannot be easily translated in daily clinical practice. The aim of the study is to set-up an integrated diagnostic algorithm to extend the newest personalized diagnostic and treatment strategies for rare kidney diseases to all patients in the Tuscany region, under 40 years of age with kidney disease. This algorithm will be based on a constant cross-talk between participating centers and a dedicated multidisciplinary team. Diagnostic and therapeutic performances will be validated at European level.

Recruitment information / eligibility

• Status: Active, not recruiting
• Enrollment: 160
• Est. completion date: June 30, 2024
• Est. primary completion date: June 27, 2023
• Accepts healthy volunteers: No
• Gender: All
• Age group: N/A to 40 Years

Eligibility

Inclusion Criteria:

• family history of kidney disease and/or parental consanguinity;
• extra-renal involvement (e.g., sensorineural hearing loss);
• resistance to treatment (e.g., immunosuppressive);
• metabolic acidosis or metabolic alkalosis in the absence of renal failure;
• ultrasound detection of of at least 2 cystic lesions in each kidney or nephrocalcinosis;
• ultrasound detection of congenital abnormalities of the kidney and urinary tract (CAKUT) and CKD stage = 2 according to KDIGO definition
• informed consent form.

Exclusion Criteria:

• age > 40
• refuse to participate to the study

Related Conditions & MeSH terms

• Chronic Kidney Diseases
• Kidney Diseases
• Renal Insufficiency, Chronic

Intervention

Diagnostic Test:
• Conclusive genetic testing
Patients will be referred for genetic counseling at the study coordinating center. This will lead to a conclusive genetic diagnosis.
• Genotype-phenotype correlation for personalized diagnosis
Patients and their family members will undergo a thorough clinical reassessment at the study coordinating center to identify diagnostic handles of the suspected disease based on the genetic test result (reverse phenotyping). The clinical reassessment could include the performance of additional clinical and instrumental tests, as well as other specialized consultations. This will lead to a conclusive genetic diagnosis in a substantial proportion of cases, cases, who will then be provided with genetic counselling.
• Personalized study of variants of uncertain clinical significance (VUS) through functional studies on 3D organ-on-a-chip
The investigators will perform functional assessment trough urine derived Renal Progenitor Cells (u-RPC) to establish the role of variants in determining the clinical phenotype.

Locations

Country	Name	City	State
Italy	Azienda Ospedaliero Universitaria Careggi	Firenze
Italy	Meyer Children's Hospital IRCCS	Firenze
Italy	USL Toscana Centro	Firenze
Italy	Azienda Ospedaliero Universitaria Pisana	Pisa

Sponsors (1)

Lead Sponsor	Collaborator
Meyer Children's Hospital IRCCS

Country where clinical trial is conducted

Italy, 

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	Validation of genetic diagnosis	The investigators will assess the role of potentially pathogenic variants and variants of uncertain clinical significance (VUS) in determining a conclusive genetic diagnosis by patient reassessment (reverse phenotyping) or in vitro functional studies.; In detail, after the results of ES, a multidisciplinary team will evaluate the results of sequencing and will eventually request additional investigations (e.g., laboratory or imaging tests, specific consultations, etc) to the patient and/or family member in order to look for previously undetected/overlooked signs of the genetic diseases suggested by ES (reverse phenotyping).; In vitro functional studies on u-RPC will be requested in a subset of patients. The number of patients with a conclusive diagnosis obtained trough these strategies will contribute to the overall diagnostic rate of the workflow (number of conclusive genetic diagnosis/number of patients enrolled in the study).	From enrollment (genetic testing) until the date of returning of genetic testing results (up to 6 months)
Secondary	Identification of molecular pathways	The investigators aim to o identify molecular pathways that could represent potential therapeutic targets in a selection of patients carrying potentially pathogenic variants.; To this goal, the investigators will perform single-cell RNA sequencing on kidney biopsy fragments of patients who have undergone a diagnostic kidney biopsy. After obtaining intracellular transcriptome of individual cells carrying the potentially pathogenic variants, the investigators will compare their RNA expression profile to the same type of cells obtained from non-mutated patients.	From enrollment (genetic testing) until the last patient last visit, estimated up to 12 months
Secondary	Explore the applicability of gene editing in rare kidney diseases	The investigators will explore the applicability of CRISPR/Cas9 gene editing in rare kidney diseases through u-RPCs obtained from patients carrying pathogenic mutations.; In order to achieve the rescue of disease causative variants, the investigators will perform a stable correction of genetic variants identified through CRISPR/Cas9 gene editing approach, in u-RPC isolated from patients carrying pathogenic variants.	From enrollment (genetic testing) until the last patient last visit, estimated up to 12 months