Treating the Untreatable

Introduction Genetic kidney diseases represent a heterogeneous group of disorders characterized by de novo, inherited, polygenic, and gene–environment abnormalities. These disorders encompass a spectrum of pathogenic mechanisms, including mutations in more than 600 single genes, often with complex gene–gene interactions. For some, the gene of interest acts in the kidney, and for others, the gene acts in other organs, where the kidney is affected secondarily. Current treatment options commonly target symptoms rather than underlying molecular defects driving disease progression. Emerging therapeutic strategies, such as antisense oligonucleotides (ASOs), are disease-modifying therapies that can change the disease natural history.1 By precisely targeting the disease-causing mutation, ASOs target gene expression to restore cellular function, stabilize physiology, and potentially improve the disease course. However, identifying specific genetic kidney conditions and targets that could benefit from ASO therapies remains a challenge. The nonprofit n-Lorem Foundation is committed to discovering, developing, manufacturing, and providing experimental, individualized ASO treatments to patients with nano-rare mutations (i.e., <30 patients worldwide). Drugs are provided for free, for life for conditions where commercialization is unrealistic, taking advantage of the new US Food and Drug Administration Draft Guidance of 2021 on Individualized ASO treatments (see weblinks below). Since 2020, n-Lorem has advanced ASO programs for more than 100 patients with nano-rare conditions, with more than ten patients currently being treated in the clinic and the rest scheduled for treatment soon.2 n-Lorem welcomes nominations from physicians of patients with rare genetic nephropathies to consider individualized treatment. Mechanisms of Action of ASOs ASOs are short (12–24 nucleotides) single-stranded oligonucleotides that bind to complementary RNA sequence by Watson–Crick base pairing in the nucleus and trigger posthybridization mechanisms to modulate gene expression. ASOs can modulate gene expression through various post–RNA-binding mechanisms, including occupancy-mediated RNA degradation and occupancy-only strategies (Figure 1A), mediating downregulation or upregulation of gene expression through inhibition of translation suppression elements, RNA activation, or splicing or microRNAs modulation.3 ASOs can be designed to target one gene copy (allele-specific ASOs), allowing us to selectively target the mutant allele without affecting the wild-type allele, or both copies. ASOs show favorable pharmacokinetics in the liver and kidney using subcutaneous administration (Figure 1B).Figure 1: Common post–RNA-binding mechanisms of action and distribution of ASOs in the kidney. (A) Downregulation of target transcripts by single-stranded ASOs. Commonly used antisense mechanisms to degrade target RNAs include (i) RNase H1-dependent cleavage of cytoplasmic or nuclear RNAs; (ii) AGO2-mediated RNA degradation of cytoplasmic RNAs (also known as single-stranded siRNAs); (iii) splicing modulation to induce NMD—reduction of target RNA levels by acting on pre-mRNA to alter splicing and generate mRNAs that contain premature termination codons subject to NMD; (iv and v) translation inhibition—(iv) acting on mRNA during translation initiation to trigger the NGD quality control mechanism and degrade target mRNA and (v) inhibition of ribosome scanning of mature mRNA leading to reduced translation initiation and reduction in protein production; and (vi) acting on pre-mRNA cleavage to alter polyadenylation site usage and modulate mRNA stability and levels. (B) Routes of administration of ASOs in commonly targeted organs. (C) Top: simplified anatomy of the nephron showing in green parts of the kidney with high distribution of ASO. Bottom: table showing average reduction in target RNA observed in various compartments of the kidney following ASO-mediated knockdown of the Malat-1 gene. ASO knockdown of Malat-1 results in a significant reduction in Malat-1 RNA expression in the glomerulus, cortex, and medulla, with the highest Malat-1 RNA reduction observed in the kidney cortex. ASO, antisense oligonucleotide; CNS, central nervous system; Malat-1, Metastasis Associated Lung Adenocarcinoma Transcript 1; NGD, no-go decay; NMD, nonsense-mediated mRNA decay; PNS, peripheral nervous system; siRNA, small interfering RNA.The efficacy, tolerability, and safety profile of ASOs in the context of kidney physiology have been extensively studied.4,5 ASOs exhibit good specificity, enabling selective targeting of disease-causing genes while minimizing off-target effects. Chemical modifications of ASOs can prevent degradation, allowing for monthly dosing. Furthermore, advancements in ASO chemistry have enhanced their pharmacokinetic properties, facilitating efficient tissue distribution and cellular uptake without significant adverse effects on kidney function.5 Evidence of ASO Preclinical Benefit in Kidney Disease Models The use of ASOs in hereditary kidney cystic diseases models have shown promising results. In mouse models of autosomal dominant polycystic kidney disease, ASOs targeting key regulators of cyst growth, such as polycystin-1 or polycystin-2, have reduced overall kidney size and cyst volume and improved kidney function.6 ASOs targeting proinflammatory cytokines or profibrotic mediators have delayed progression to kidney failure in a model of Alport syndrome.7 These findings highlight therapeutic utility. Gain-of-Function versus Loss-of-Function Mutations and Therapeutic Implications Gain of function and loss of function represent two distinct mutational mechanisms by which mutations impair cellular homeostasis and contribute to disease pathogenesis. Although gain-of-function mutations enhance protein function, often leading to aberrant cellular signaling or toxic effects, loss-of-function mutations reduce protein function, compromising cellular processes critical for kidney homeostasis. Gain-of-function mutations present opportunities for targeted pharmacological inhibition, modulation of aberrant signaling pathways, or targeted degradation using ASOs, whereas loss-of-function mutations require restoration of protein function or compensation of the underlying molecular defect. ASOs can modulate gene expression in both gain-of-function and loss-of-function scenarios.3 For instance, in hereditary transthyretin (TTR) amyloidosis, gain-of-function mutations in TTR destabilize the TTR tetramer, leading to production of misfolded proamyloidogenic monomers and deposit as amyloid fibrils in extracellular spaces. ASO-mediated knockdown of liver TTR mRNA achieves a sustained reduction in circulating TTR levels.8 Conversely, in autosomal recessive polycystic kidney disease, loss-of-function mutations in PKHD1 cause collecting duct elongation and microcysts. ASOs targeting eligible splicing mutations could potentially restore protein production and preserve kidney function.9 However, poor ASO distribution to the collecting ducts and distal tubules may be a limitation. Individualized Therapy Trials: A Unique Design for Nano-Rare Genetic Diseases Patients with nano-rare genetic mutations affecting kidney function may be amenable to individualized ASO treatment if a validated genetic test and laboratory assessments have established the causality between the gene mutation, molecular mechanism, and disease phenotype. At n-Lorem, the benefit–risk ratio is determined on an individual basis, and if an ASO strategy is amenable, a development program is initiated. Outcomes assessment, specific to each patient, track disease progression before and after treatment, and quantitative measures track treatment response. To date, the US Food and Drug Administration has been favorable of research Investigational New Drug applications for individual or small groups of patients. Learnings from individualized ASO trials may expedite translation of underlying biological pathophysiology of specific nano-rare monogenic mutations to the larger and more complex causes of disease. Kidney Diseases Potentially Amenable to ASOs The versatility of ASOs enables personalized treatment regimens, optimizing therapeutic outcomes and minimizing adverse events. In addition, unconjugated ASOs distribute widely throughout the kidney after subcutaneous administration, including in the glomerulus (specifically in podocytes), cortex, and medulla (Figure 1C), with the highest uptake occurring in the proximal convoluted tubule epithelial cells because of their high endocytic activity.5N-acetylgalactosamine-conjugated ASOs are highly potent in the liver and are available for diseases that secondarily affect the kidney, including TTR mutations (Inotersen, approved 2018; Eplontersen, approved 2023).8,10 Other conditions potentially amenable for individualized ASOs include nephrogenic diabetes due to dominant AQP2 mutations; tubulointerstitial kidney disease due to gain-of-function UMOD mutations; or FSGS due to toxic gain-of-function TRPC6, INF2, ACTN4, or TRIM8 mutations. However, genetic kidney diseases are often diagnosed at late stages, thus challenging reversibility of damage. A shift in management strategies with earlier genetic testing could help leverage ASO therapy. Clinical Trials and Translational Perspectives There are several ongoing ASO trials for kidney diseases. Two phase 2/3 trials are evaluating ASOs for complement factor B in primary IgA nephropathy (NCT04014335; NCT05797610). A phase 2 trial assessing the efficacy of apo(a)-targeting ASO in individuals with hyperlipoproteinemia(a) and cardiovascular disease has shown promise (NCT03070782), suggesting potential therapeutic application in kidney diseases where lipoprotein(a) levels play a role. An ASO targeting renal antisense sodium-glucose cotransporter 2 to lower serum glucose levels is being assessed in patients with type 2 diabetes mellitus (NCT00836225). A phase 1b study assessing ASO targeting microRNA miR-17 is being evaluated in autosomal dominant polycystic kidney disease (NCT05521191). If promising, other conditions could be approached through ASOs. Challenges and Future Directions Despite the remarkable success of ASO therapies in central nervous system disorders, their use in nano-rare monogenic kidney diseases is still nascent. ASO distribution to the kidney after subcutaneous administration is generally quite high, except for areas such as distal convoluted tubules and collecting ducts, which remains a challenge.5 At present, n-Lorem is treating one patient with advanced kidney amyloidosis secondary to a mutation in hepatic SAA gene. This ASO has been well tolerated with promising clinical results, including reduction in SAA protein levels and stabilization of disease; however, longer treatment will provide the full clinical picture. Limitations of treating monogenic kidney diseases with individualized ASO at present hang less on the technology than on the identification of patients with amenable genotypes for such medicines. ASOs can be used to treat primary and secondary kidney diseases, as is exemplified with available commercial drugs. Nephrologist physician/scientists may consider ASOs for ultra-rare kidney diseases as well.