# The Role of Protein Post-Translational Modifications in the Pathogenesis of Nephrolithiasis: Mechanistic Insights and Translational Potential

**Authors:** Wenlong Wan, Baokang Wang, Junyi Yang, Yang Xun, Xiao Yu

PMC · DOI: 10.3390/cells15060554 · Cells · 2026-03-19

## TL;DR

Protein modifications play a key role in kidney stone formation and could lead to new treatments.

## Contribution

This paper reveals how post-translational modifications regulate kidney stone disease mechanisms and suggests targeting these modifications as a novel therapy.

## Key findings

- Protein post-translational modifications regulate crystal-cell adhesion and cell death pathways in kidney stones.
- The kidney stone environment shapes these modifications, influencing injury and repair processes.
- Targeting PTM-regulating enzymes offers a new strategy to prevent and manage kidney stones.

## Abstract

What are the main findings?
Protein post-translational modifications (PTMs) such as phosphorylation, acetylation, and ubiquitination act as central “molecular switches” that orchestrate crystal-cell adhesion, oxidative stress, inflammatory signaling, and diverse programmed cell death pathways (ferroptosis, pyroptosis, necroptosis) in nephrolithiasis.The kidney stone microenvironment (hyperoxaluria, oxidative stress, metabolic reprogramming) actively shapes the PTM landscape of key proteins, creating a complex regulatory network that determines the balance between renal injury and repair.

Protein post-translational modifications (PTMs) such as phosphorylation, acetylation, and ubiquitination act as central “molecular switches” that orchestrate crystal-cell adhesion, oxidative stress, inflammatory signaling, and diverse programmed cell death pathways (ferroptosis, pyroptosis, necroptosis) in nephrolithiasis.

The kidney stone microenvironment (hyperoxaluria, oxidative stress, metabolic reprogramming) actively shapes the PTM landscape of key proteins, creating a complex regulatory network that determines the balance between renal injury and repair.

What is the implication of the main finding?
Targeting specific PTM-regulating enzymes (e.g., Sirt1 activators, HDAC2 inhibitors, AMPK activators) represents a promising novel therapeutic strategy to interrupt stone formation and halt disease progression.Deciphering the “PTM code” that integrates microenvironmental signals to dictate cell fate decisions provides a new framework for understanding stone pathogenesis and developing precision intervention strategies.

Targeting specific PTM-regulating enzymes (e.g., Sirt1 activators, HDAC2 inhibitors, AMPK activators) represents a promising novel therapeutic strategy to interrupt stone formation and halt disease progression.

Deciphering the “PTM code” that integrates microenvironmental signals to dictate cell fate decisions provides a new framework for understanding stone pathogenesis and developing precision intervention strategies.

Nephrolithiasis is a prevalent urological disorder worldwide, whose pathogenesis involves a complex network of crystal formation, cellular injury, and microenvironmental dysregulation. As a critical mechanism for regulating cellular functions, protein post-translational modifications (PTMs) have been increasingly implicated in multiple facets of kidney stone formation, including crystal–cell interactions, oxidative stress responses, and inflammatory signaling pathways. This review systematically synthesizes the biochemical foundations of PTMs, the molecular microenvironment of nephrolithiasis, and the roles of key modifications such as phosphorylation and acetylation in the pathogenesis of calculi. It further explores the translational potential of PTM detection technologies in clinical practice. Current evidence indicates that PTMs influence the nucleation, growth, and aggregation of crystals by modulating the activity of pro-/anti-lithogenic proteins, the expression of cell adhesion molecules, and inflammatory pathways. Consequently, therapeutic strategies targeting PTMs may offer novel avenues for the prevention and management of kidney stones. Future research should focus on integrating multi-omics approaches with functional validation to elucidate the dynamic regulatory networks of PTMs within the stone microenvironment, thereby advancing the development of precision medicine.

## Linked entities

- **Diseases:** nephrolithiasis (MONDO:0008171)

## Full-text entities

- **Genes:** Vdr (vitamin D receptor) [NCBI Gene 24873] {aka Nr1i1}, PRDM9 (PR/SET domain 9) [NCBI Gene 56979] {aka KMT8B, MEISETZ, MSBP3, PFM6, ZNF899}, USP11 (ubiquitin specific peptidase 11) [NCBI Gene 8237] {aka UHX1}, STAT1 (signal transducer and activator of transcription 1) [NCBI Gene 6772] {aka CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91}, PKM (pyruvate kinase M1/2) [NCBI Gene 5315] {aka CTHBP, HEL-S-30, OIP3, PK3, PKM2, TCB}, Sirt1 (sirtuin 1) [NCBI Gene 309757] {aka Sir2}, PEBP1 (phosphatidylethanolamine binding protein 1) [NCBI Gene 5037] {aka HCNP, HCNPpp, HEL-210, HEL-S-34, HEL-S-96, PBP}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, HDAC2 (histone deacetylase 2) [NCBI Gene 3066] {aka HD2, KDAC2, RPD3, YAF1}, Mtor (mechanistic target of rapamycin kinase) [NCBI Gene 56718] {aka Frap1, RAFT1}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, Hdac3 (histone deacetylase 3) [NCBI Gene 84578], VHL (von Hippel-Lindau tumor suppressor) [NCBI Gene 7428] {aka HRCA1, RCA1, VHL1, pVHL}, BICD2 (BICD cargo adaptor 2) [NCBI Gene 23299] {aka SMALED2, SMALED2A, SMALED2B, bA526D8.1}, RIPK3 (receptor interacting serine/threonine kinase 3) [NCBI Gene 11035] {aka RIP3}, CLDN14 (claudin 14) [NCBI Gene 23562] {aka DFNB29}, LGALS3 (galectin 3) [NCBI Gene 3958] {aka CBP35, GAL3, GALBP, GALIG, L31, LGALS2}, GSDMD (gasdermin D) [NCBI Gene 79792] {aka DF5L, DFNA5L, FKSG10, GSDMDC1}, Hmox1 (heme oxygenase 1) [NCBI Gene 24451] {aka HEOXG, Heox, Hmox, Ho-1, Ho1, hsp32}, SIRT6 (sirtuin 6) [NCBI Gene 51548] {aka SIR2L6, hSIRT6}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, UMOD (uromodulin) [NCBI Gene 7369] {aka ADMCKD2, ADTKD1, FJHN, HNFJ, HNFJ1, MCKD2}, Prkaa2 (protein kinase AMP-activated catalytic subunit alpha 2) [NCBI Gene 78975] {aka Ampk, Ampka2}, Akt1 (AKT serine/threonine kinase 1) [NCBI Gene 24185] {aka Akt}, MAPK8 (mitogen-activated protein kinase 8) [NCBI Gene 5599] {aka JNK, JNK-46, JNK1, JNK1A2, JNK21B1/2, PRKM8}, PPP3R1 (protein phosphatase 3 regulatory subunit B, alpha) [NCBI Gene 5534] {aka CALNB1, CNB, CNB1}, PRMT1 (protein arginine methyltransferase 1) [NCBI Gene 3276] {aka ANM1, HCP1, HRMT1L2, IR1B4}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, Osm (oncostatin M) [NCBI Gene 289747], EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, PRKN (parkin RBR E3 ubiquitin protein ligase) [NCBI Gene 5071] {aka AR-JP, LPRS2, PARK2, PDJ}, Slc5a2 (solute carrier family 5 member 2) [NCBI Gene 64522] {aka Sglt2}, CASR (calcium sensing receptor) [NCBI Gene 846] {aka CAR, EIG8, FHH, FIH, GPRC2A, HHC}, HSP90AA1 (heat shock protein 90 alpha family class A member 1) [NCBI Gene 3320] {aka EL52, HEL-S-65p, HSP86, HSP89A, HSP90A, HSP90N}, SPP1 (secreted phosphoprotein 1) [NCBI Gene 6696] {aka BNSP, BSPI, ETA-1, OPN}, KLF4 (KLF transcription factor 4) [NCBI Gene 9314] {aka EZF, GKLF}, CASP1 (caspase 1) [NCBI Gene 834] {aka ICE, IL1BC, P45}, GPX4 (glutathione peroxidase 4) [NCBI Gene 2879] {aka GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx}, PRKCZ (protein kinase C zeta) [NCBI Gene 5590] {aka PKC-ZETA, PKC2}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, PPARG (peroxisome proliferator activated receptor gamma) [NCBI Gene 5468] {aka CIMT1, FPLD3, GLM1, NR1C3, PPARG1, PPARG2}, UBE2M (ubiquitin conjugating enzyme E2 M) [NCBI Gene 9040] {aka UBC-RS2, UBC12, hUbc12}, Spp1 (secreted phosphoprotein 1) [NCBI Gene 25353] {aka OSP}, Igf1r (insulin-like growth factor 1 receptor) [NCBI Gene 25718] {aka IGF-1 receptor, IGFIRC, Igfr1, JTK13}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, PINK1 (PTEN induced kinase 1) [NCBI Gene 65018] {aka BRPK, PARK6}, ANXA2 (annexin A2) [NCBI Gene 302] {aka ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2}, Nfe2l2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 83619], AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, TXNIP (thioredoxin interacting protein) [NCBI Gene 10628] {aka ARRDC6, EST01027, HHCPA78, THIF, VDUP1}, Hist1h3b (histone cluster 1, H3b) [NCBI Gene 680498], SMYD2 (SET and MYND domain containing 2) [NCBI Gene 56950] {aka HSKM-B, KMT3C, ZMYND14}, RIPK1 (receptor interacting serine/threonine kinase 1) [NCBI Gene 8737] {aka AIEFL, IMD57, RIP, RIP-1, RIP1}, FGFR4 (fibroblast growth factor receptor 4) [NCBI Gene 2264] {aka CD334, JTK2, TKF}, CASP3 (caspase 3) [NCBI Gene 836] {aka CPP32, CPP32B, SCA-1}, Pik3cb (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta) [NCBI Gene 85243], Hsp90aa1 (heat shock protein 90 alpha family class A member 1) [NCBI Gene 299331] {aka Hsp86, Hsp90, Hspca}, FOXO1 (forkhead box O1) [NCBI Gene 2308] {aka FKH1, FKHR, FOXO1A}, BRAF (B-Raf proto-oncogene, serine/threonine kinase) [NCBI Gene 673] {aka B-RAF1, B-raf, BRAF-1, BRAF1, NS7, RAFB1}, BMP7 (bone morphogenetic protein 7) [NCBI Gene 655] {aka OP-1}
- **Diseases:** Inflammation (MESH:D007249), CaOx stone formation (MESH:C563477), CKD (MESH:D051436), renal tubular injury (MESH:D015499), metabolic disturbances (MESH:D024821), urological disorder (MESH:D014570), Stone-Associated Renal Injury (MESH:D007669), hyperglycemia (MESH:D006943), renal lipid accumulation (MESH:D011017), cancers (MESH:D009369), fibrosis (MESH:D005355), Crystal injury (MESH:D000070657), Nephrolithiasis (MESH:D053040), hyperoxaluria (MESH:D006959), calculi (MESH:D002137), energy metabolism disorder (MESH:D008659), neurodegenerative disorders (MESH:D019636), mitochondrial dysfunction (MESH:D028361), stone formation (MESH:D058426), cardiovascular diseases (MESH:D002318), pain (MESH:D010146), Kidney Injury (MESH:D007674), renal tubular epithelial cell injury (MESH:C567703), hypercalciuria (MESH:D053565), hypercalciuric (MESH:C562793), injury to (MESH:D014947), Metabolic dysregulation (MESH:D021081), forming (MESH:C565541), tubular (MESH:D000230)
- **Chemicals:** Melatonin (MESH:D008550), itaconate (MESH:C005229), oxalate (MESH:D010070), short-chain fatty acids (MESH:D005232), amino acid (MESH:D000596), palmitic acid (MESH:D019308), ROS (MESH:D017382), lipid peroxides (MESH:D008054), lipid (MESH:D008055), succinyl-CoA (MESH:C012046), CaOx (MESH:D002129), hyperoside (MESH:C021304), iron (MESH:D007501), Lactate (MESH:D019344), Lysimachia christinae extract (-), 4-PBA (MESH:C121358), cadmium (MESH:D002104), DCA (MESH:D003840), calcium (MESH:D002118), H2S (MESH:D006862)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606]

## Full text

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## References

140 references — full list in the complete paper: https://tomesphere.com/paper/PMC13025954/full.md

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Source: https://tomesphere.com/paper/PMC13025954