Gesualdo, Loreto

Artificial intelligence (AI)–based protein structure prediction has rapidly entered nephrology, providing plausible atomic models for channels, transporters, receptors and scaffolds that previously lacked structural information. AlphaFold and RoseTTAFold now underpin mechanistic interpretations of inherited kidney diseases, including autosomal-dominant polycystic kidney disease, cystinosis and Alport syndrome, and support experimental design in cryo-electron microscopy and cryo-electron tomography. For nephrologists, this means that renal proteins no longer need to be treated as black boxes: genetic, biochemical and physiological data can now be mapped onto concrete three-dimensional scaffolds. However, the apparent precision of AI models can be misleading. Renal proteins frequently fall within underrepresented classes, including multipass membrane proteins, intrinsically disordered scaffolds, and human-specific isoforms with shallow multiple sequence alignments, where confidence scores may not accurately reflect model reliability. Current predictors typically deliver static snapshots, whereas transporters, channels and slit-diaphragm complexes function as dynamic ensembles embedded in specific lipid and macromolecular environments. Attempts to use AlphaFold directly for variant classification or to estimate changes in thermodynamic stability or function show only modest agreement with mutagenesis data, particularly for gain-of-function and dominant-negative alleles that depend on subtle conformational and interaction changes. Common pitfalls include overinterpreting oligomeric stoichiometry inferred from AlphaFold Multimer, reading too much into domain orientations with high predicted aligned error, and dismissing low-confidence regions as modelling failures rather than recognising intrinsically disordered, potentially regulatory segments. Integrative approaches combining cryo-electron tomography, crosslinking mass spectrometry and molecular dynamics can mitigate these limitations but remain labour-intensive and low-throughput. An explainable, hypothesis-driven use of AI that treats predicted structures as working scaffolds to be cross-validated against imaging, biophysics and functional assays offers the most reliable path towards a genuinely mechanistic nephrology and responsible clinical translation of AI-based structural insights.

Abstract Background and Aims Malignancy is commonly seen in patients with membranous Nephropathy (MN) with a prevalence up to 22%. M-type phospholipase A2 receptor (PLA2R) antigen and its associated antibody account for up to 80% of the cases but its association with malignancy is less clear. To date, no study has specifically evaluated cancer incidence and risk factors in patients with PLA2R associated MN as most studies were conducted in an era before many MN antigens were identified. Here, we report cancer incidence, types of cancer, and effect of immunosuppressive therapy and clinical parameters in a cohort of patients with PLA2R-associated MN. Method A single center retrospective cohort study in adults with diagnosis of PLA2R associated MN from 1/1/1996 to 12/31/2021. Follow-up was defined as the time from MN diagnosis to the last follow-up or if the patient initiated dialysis or underwent transplantation. The primary outcome in this study was the incidence of cancer events reported as cancer incidence/1000 patients/year. The cancer events were compared to the age-adjusted United States (U.S.) general population using Centers for Disease Control (C.D.C) data. The standardized incidence ratio (SIR) was calculated by dividing the cancer rates in our cohort to the cancer rates in general population. Time-to-event analysis was conducted using the Kaplan-Meier method. The log-rank test compared age, sex, smoking habits, hypertension, diabetes, body mass index (BMI), previous immunosuppression (IS), remission of the MN, PLA2R titers at the time of diagnosis. Cox proportional hazards regression was used to evaluate the associations between baseline characteristics and cancer incidence. For the multivariate model of cancer incidence, we evaluated variables clinically relevant for the outcome. Results We identified 239 patients with PLA2R-associated MN, with mean (±SD) age of 52 (±13) years, with 72.8% male (n = 174), median [IQR] BMI of 29.8 [26.3, 33.6] kg/m2, median eGFR of 68 [45, 94] ml/min, median proteinuria of 8.2 [5.1, 11.2] g/24h, and median PLA2R titers of 38 [9, 122] RU/ml. Common comorbidities included hypertension (60.2%), and diabetes (17.1%). Majority of patients drank alcohol (90.7%) and 32.6% were smokers (active or former). Of 239 patients, 15 had a history of cancer before the MN diagnosis. But in all these patients, cancer had been treated and was considered to be in full remission. A diagnosis of cancer was made in 37 patients (15.4%) during a median follow-up of 60 [27.5, 145.5] months. Incidence of cancer in our cohort was 22.6 [95% CI, 15.9 to 31.1] per 1000 persons/year. In comparison, age adjusted U.S. general population has a lower cancer incidence of 15.9 [95% CI, 15.9 to 16.1] cases per 1000 person/year. The resulting SIR of cancer in our cohort was 1.42. This SIR is lower than the one reported by Bjørneklett and al. (2007) in a Norwegian cohort that included all patients with MN and was not limited to PLA2R-positive MN. The cumulative incidence of cancer diagnosis is shown in Fig. 1. Mean age at cancer diagnosis was 66 (±10.2) years old. Prostate cancer was the most common (n = 11) type of cancer, followed by skin cancer (n = 9), followed by cancer of the urinary tract (n = 5). In univariate and multivariate analysis (Table 1), only older age (>65 years) and tobacco use were associated with statistically significant increased risk of cancer. Other clinical parameters such as sex, eGFR, baseline proteinuria, BMI, hypertension, diabetes, alcohol use, anti-PLA2R antibody titer, type of immunosuppression, remission status (partial, complete, no response) were not associated with a significant increased risk of cancer. Conclusion Patients with PLA2R associated MN are at increased risk of developing cancer following diagnosis compared to general population and routine age-appropriate cancer screening in this population is essential. The increased incidence of cancer is independent of IS therapy, response to therapy or other comorbidities. These data suggests that there are likely mechanisms beyond the traditional risk factors at play that may be unique to the presence of PLA2R antibodies.