WHOLE EXOME SEQUENCING TO EXPLAIN PAIN IN PATIENTS WITH LOIN PAIN HEMATURIA SYNDROME

Loin pain hematuria syndrome (LPHS) is a rare clinical condition that is not well understood, characterized by severe loin pain and hematuria without an identifiable urinary tract pathology. Although hematuria is thought to originate from the glomeruli, mainly due to variants of type IV collagen genes (COL4A3-5), the mechanism of pain generation remains unknown. The pathway of visceral pain transmission to the brain involves a complex set of genes linked to sensory transduction, axonal conduction, synaptic communication, and neural modulation. We hypothesized that LPHS patients have either gain-of-function variants in the pain pathways or loss-of-function variants in the pain-dampening pathways. Since the origin of pain in LPHS remains unclear, there is limited information regarding pain-related genetic variants. This study aimed to describe the genetic findings of whole exome sequencing (WES) in pain-related genes in LPHS and isolated painless hematuria. Our goal was to identify pathogenic variants that increase afferent or decrease efferent pain signalling pathways.

Whole-exome sequencing (WES) was performed on 29 consecutive singleton patients, including 17 with LPHS and 12 with persistent isolated painless hematuria, collected between January 2022 and January 2023. We employed a virtual gene panel approach, focusing on a preselected list of 599 genes linked to chronic pain. Bioinformatic analysis, annotation, and interpretation of the variants were performed using the hereditary pipeline of the QIAGEN Clinical Insight (QCI) Interpret Translational (QIAGEN) software and the Franklin platform according to the American College of Medical Genetics Association for Molecular Pathology (ACMG/AMP) guidelines. 

Nine LPHS patients had a history of kidney stones, but none showed obstructing stones on imaging at the time of sequencing. Eight LPHS patients had a family history of kidney stones, and 3 had a family history of hematuria; 2 had a family history of LPHS. A total of 20 variants of uncertain significance (VUS) were identified in 16 pain-related genes in patients with LPHS or isolated hematuria. Ten VUS (50%) in 9 genes were found in 8 of 17 (47%) LPHS patients. In contrast, 10 distinct VUS in 10 genes were observed in 6 of 12 (50%) patients with isolated painless hematuria. Seven VUS affecting genes directly involved in neuronal signalling and excitability, which may contribute to flank pain, were identified, including TRPA1, KCNT2, SCN11A, and SCN9A, found in patients with both LPHS [3 VUS (43%)] and isolated hematuria [4 VUS (57%)]. Notably, the VUS in shared genes were located in different regions within each gene. No pathogenic or likely pathogenic variants were detected among genes associated with chronic pain. Consequently, no patients with LPHS had a monogenic cause for their pain.

This is the first report of pain-genes analysis in patients with LPHS globally. Diverse underlying mechanisms might drive pain in LPHS. Neither the pain gene panel, the hematuria gene panel, nor exome sequencing identified a single gene responsible for pain or hematuria. VUS in ion channels (Nav1.7, Nav1.9, and potassium channels) involved in pain pathway regulation and sensory neuron excitability were found in patients with LPHS and patients with isolated painless hematuria.