# Uremic Toxin-Driven Vascular Calcification in Chronic Kidney Disease: Molecular Pathways and Integrated Phenotypes

**Authors:** Rodolfo Fernando Rivera, Maria Teresa Sciarrone Alibrandi, Nadia Edvige Foligno, Lorenza Magagnoli, Paola Ciceri, Mario Cozzolino

PMC · DOI: 10.3390/toxins18020112 · Toxins · 2026-02-21

## TL;DR

This paper explores how toxins in chronic kidney disease cause blood vessel calcification and proposes new ways to classify and treat this condition.

## Contribution

The paper introduces five new mechanistic-clinical phenotypes for vascular calcification linked to uremic toxins.

## Key findings

- Five distinct biological pathways of vascular injury are identified based on toxin-driven mechanisms.
- A biomarker panel is proposed for patient classification and monitoring treatment response.
- Emerging therapies are matched to specific phenotypes for targeted treatment.

## Abstract

Background: Vascular calcification (VC) affects up to 90% of patients with end-stage renal disease and increases cardiovascular mortality 3- to 5-fold. Once considered passive mineral deposition, VC is now recognized as an active, toxin-driven process orchestrating vascular smooth muscle cell transdifferentiation, endothelial dysfunction, and matrix remodeling. However, current uremic toxin classifications remain biochemically oriented, providing limited clinical guidance for risk stratification and therapeutic selection. Methods: This comprehensive review reframes uremic toxin-driven VC through an integrated phenotypic lens, synthesizing molecular mechanisms, clinical biomarkers, and therapeutic targets into a unified translational framework. Results: We propose five mechanistic-clinical phenotypes representing distinct biological trajectories of vascular injury. These include (1) inflammatory-oxidative (dominated by indoxyl sulfate, p-cresyl sulfate, NLRP3 inflammasome activation), (2) mineral-metabolic (hyperphosphatemia, FGF23 excess, Klotho deficiency), (3) epigenetic-senescent (histone modifications, microRNA dysregulation, cellular senescence), (4) endocrine cross-talk (vitamin D, PTH, gut-derived metabolites), and (5) integrated toxic continuum (convergence of multiple pathways in advanced disease). A comprehensive biomarker panel spanning inflammatory markers, mineral metabolism parameters, epigenetic indicators, and endocrine-gut metabolites enables phenotypic stratification and therapeutic monitoring. Emerging therapies—including tissue-nonspecific alkaline phosphatase inhibition, ectonucleotide pyrophosphatase/phosphodiesterase 1 enzyme replacement, vitamin K2 activation, senolytic agents, and SNF472 crystal-growth blockade—are mapped to their optimal phenotypic contexts. Conclusions: This phenotype-oriented paradigm transforms VC from an inevitable complication into a targetable and potentially reversible manifestation of uremic toxicity, establishing a translational foundation for precision-based vascular medicine in chronic kidney disease. The framework enables biomarker-guided patient stratification, rational therapeutic selection, and phenotype-enriched clinical trial design.

## Linked entities

- **Proteins:** NLRP3 (NLR family pyrin domain containing 3), FGF23 (fibroblast growth factor 23), CG9701 (uncharacterized protein)
- **Chemicals:** indoxyl sulfate (PubChem CID 10258), p-cresyl sulfate (PubChem CID 4615423), vitamin K2 (PubChem CID 4056), SNF472 (PubChem CID 91667962)
- **Diseases:** chronic kidney disease (MONDO:0005300)

## Full-text entities

- **Genes:** TAGLN (transgelin) [NCBI Gene 6876] {aka SM22, SM22-alpha, SMCC, TAGLN1, TGLN, WS3-10}, CAT (catalase) [NCBI Gene 847], TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, KL (klotho) [NCBI Gene 9365] {aka HFTC3, KLA}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, ABCC6 (ATP binding cassette subfamily C member 6) [NCBI Gene 368] {aka ABC34, ARA, EST349056, GACI2, MLP1, MOAT-E}, TNFSF11 (TNF superfamily member 11) [NCBI Gene 8600] {aka CD254, ODF, OPGL, OPTB2, RANKL, TNLG6B}, PRKAA1 (protein kinase AMP-activated catalytic subunit alpha 1) [NCBI Gene 5562] {aka AMPK, AMPK alpha 1, AMPKa1}, SOD1 (superoxide dismutase 1) [NCBI Gene 6647] {aka ALS, ALS1, HEL-S-44, IPOA, SOD, STAHP}, PRRT2 (proline rich transmembrane protein 2) [NCBI Gene 112476] {aka BFIC2, BFIS2, DSPB3, DYT10, EKD1, FICCA}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, CTSC (cathepsin C) [NCBI Gene 1075] {aka CPPI, DPP-I, DPP1, DPPI, HMS, JP}, ELN (elastin) [NCBI Gene 2006] {aka ADCL1, SVAS, WBS, WS}, MYH11 (myosin heavy chain 11) [NCBI Gene 4629] {aka AAT4, FAA4, SMHC, SMMHC, SMMS-1, VSCM2}, SENCR (smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA) [NCBI Gene 100507392] {aka FLI1-AS1, lncRNA9}, NFE2L2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 4780] {aka IMDDHH, NRF2, Nrf-2}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, FGFR1 (fibroblast growth factor receptor 1) [NCBI Gene 2260] {aka BFGFR, CD331, CEK, ECCL, FGFBR, FGFR-1}, CRP (C-reactive protein) [NCBI Gene 1401] {aka PTX1}, IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, ATF4 (activating transcription factor 4) [NCBI Gene 468] {aka CREB-2, CREB2, TAXREB67, TXREB}, Alpl (alkaline phosphatase, liver/bone/kidney) [NCBI Gene 11647] {aka ALP, APTNAP, Akp-2, Akp2, TNAP, TNSALP}, GLB1 (galactosidase beta 1) [NCBI Gene 2720] {aka EBP, ELNR1, MPS4B}, TXN (thioredoxin) [NCBI Gene 7295] {aka TRDX, TRX, TRX1, TXN1, Trx80}, SLC20A2 (solute carrier family 20 member 2) [NCBI Gene 6575] {aka GLVR-2, GLVR2, IBGC1, IBGC2, IBGC3, MLVAR}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, SLC5A2 (solute carrier family 5 member 2) [NCBI Gene 6524] {aka SGLT2}, BCL2 (BCL2 apoptosis regulator) [NCBI Gene 596] {aka Bcl-2, PPP1R50}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, HAMP (hepcidin antimicrobial peptide) [NCBI Gene 57817] {aka HEPC, HFE2B, LEAP1, PLTR}, HIF1A (hypoxia inducible factor 1 subunit alpha) [NCBI Gene 3091] {aka HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1}, EPO (erythropoietin) [NCBI Gene 2056] {aka DBAL, ECYT5, EP, MVCD2}, GGCX (gamma-glutamyl carboxylase) [NCBI Gene 2677] {aka VKCFD1, VKGC}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}, ANKH (ANKH inorganic pyrophosphate transport regulator) [NCBI Gene 56172] {aka ANK, CCAL2, CMDJ, CPPDD, HANK, MANK}, NOS3 (nitric oxide synthase 3) [NCBI Gene 4846] {aka EC-NOS, ECNOS, MYMY8, NOSIII, cNOS, eNOS}, MIR30C1 (microRNA 30c-1) [NCBI Gene 407031] {aka MIRN30C1, mir-30c-1}, H3P16 (H3 histone pseudogene 16) [NCBI Gene 644914] {aka H3.6, H3F3AP6, p21}, PTK2B (protein tyrosine kinase 2 beta) [NCBI Gene 2185] {aka CADTK, CAKB, FADK2, FAK2, PKB, PTK}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, BECN1 (beclin 1) [NCBI Gene 8678] {aka ATG6, VPS30, beclin1}, SIRT3 (sirtuin 3) [NCBI Gene 23410] {aka SIR2L3}, EIF2A (eukaryotic translation initiation factor 2A) [NCBI Gene 83939] {aka CDA02, EIF-2A, MST089, MSTP004, MSTP089}, ATG5 (autophagy related 5) [NCBI Gene 9474] {aka APG5, APG5-LIKE, APG5L, ASP, SCAR25, hAPG5}, ANCR (Angelman syndrome chromosome region) [NCBI Gene 282], MSX2 (msh homeobox 2) [NCBI Gene 4488] {aka CRS2, FPP, HOX8, MSH, PFM, PFM1}, BMP1 (bone morphogenetic protein 1) [NCBI Gene 649] {aka OI13, PCOLC, PCP, TLD}, ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) [NCBI Gene 5167] {aka ARHR2, COLED, M6S1, NPP1, NPPS, PC-1}, VDR (vitamin D receptor) [NCBI Gene 7421] {aka NR1I1, PPP1R163}, CASR (calcium sensing receptor) [NCBI Gene 846] {aka CAR, EIG8, FHH, FIH, GPRC2A, HHC}, UCMA (upper zone of growth plate and cartilage matrix associated) [NCBI Gene 221044] {aka C10orf49, GRP, GRP/UCMA}, SPP1 (secreted phosphoprotein 1) [NCBI Gene 6696] {aka BNSP, BSPI, ETA-1, OPN}, AHR (aryl hydrocarbon receptor) [NCBI Gene 196] {aka FVH3, RP85, bHLHe76}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, ATG7 (autophagy related 7) [NCBI Gene 10533] {aka APG7-LIKE, APG7L, GSA7, SCAR31}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, EIF2AK3 (eukaryotic translation initiation factor 2 alpha kinase 3) [NCBI Gene 9451] {aka PEK, PERK, WRS}, H19 (H19 imprinted maternally expressed transcript) [NCBI Gene 283120] {aka ASM, ASM1, BWS, D11S813E, GMRSP, LINC00008}, GLA (galactosidase alpha) [NCBI Gene 2717] {aka GALA}, POU1F1 (POU class 1 homeobox 1) [NCBI Gene 5449] {aka CPHD1, GHF-1, PIT1, POU1F1a, Pit-1}
- **Diseases:** endocrine disruption (MESH:D004700), stage 5 or 5D (OMIM:615065), ESRD (MESH:D007676), infection (MESH:D007239), cardiovascular calcification (MESH:D002318), idiopathic pulmonary fibrosis (MESH:D054990), CKD-MBD (MESH:D012080), Uremic Toxin (MESH:D006463), myocardial infarction (MESH:D009203), calciphylaxis (MESH:D002115), osteomalacia (MESH:D010018), CPP (MESH:D020288), Type II CPPs (MESH:D006938), myocardial toxicity (MESH:D064420), vitamin K deficiency (MESH:D014813), hypercalcemia (MESH:D006934), uremic vascular injury (MESH:D057772), adynamic bone disease (MESH:D001847), hypocalcemia (MESH:D006996), thrombotic complications (MESH:D013927), autophagy impairment (MESH:C564093), cardio-renal (MESH:D059347), anemia (MESH:D000740), VC (MESH:D061205), atherosclerosis (MESH:D050197), cardiac death (MESH:D003643), Klotho deficiency (MESH:D007153), malnutrition (MESH:D044342), hypertension (MESH:D006973), left ventricular hypertrophy (MESH:D017379), malabsorption (MESH:D008286), arterial stiffness (MESH:C566112), hyperphosphatemia (MESH:D054559), ENPP1 deficiency (MESH:C538557), coronary and valvular calcifications (MESH:D003323), atherosclerotic plaque calcification (MESH:D058226), immune dysregulation (OMIM:614878), diabetic kidney disease (MESH:D003928), chronic (MESH:D002908), medial calcification (MESH:D050380), cognitive decline (MESH:D003072), calcium (MESH:D002128), heart failure (MESH:D006333), Calcific degeneration (MESH:D009410), mineral (MESH:C537337), pyrophosphate deficiency (MESH:C563162), coronary artery calcification (MESH:D003324), vascular steal (MESH:D013349), EPO resistance (MESH:D060467), calcification (MESH:D002114), IS (MESH:C563094), diabetes (MESH:D003920), Endothelial Dysfunction (MESH:D014652), valvular calcification (MESH:D006349), dysbiosis (MESH:D064806), kidney failure (MESH:D051437), Secondary hyperparathyroidism (MESH:D006962), CKD (MESH:D051436), mineral metabolism disturbances (MESH:D024821), vascular toxicity (MESH:D016491)
- **Chemicals:** Vitamin D3 (MESH:D002762), SNF472 (MESH:C000633406), NADPH (MESH:D009249), PAGln (MESH:C003089), Dasatinib (MESH:D000069439), butyrate (MESH:D002087), vitamin K (MESH:D014812), urolithin A (MESH:C026423), nicotinamide mononucleotide (MESH:D009537), magnesium carbonate (MESH:C005479), hydroxyapatite (MESH:D017886), bile acid (MESH:D001647), curcumin (MESH:D003474), CPP (-), calcifediol (MESH:D002112), magnesium hydroxide (MESH:D008276), IS (MESH:D007200), 25-hydroxyvitamin D (MESH:C104450), SBI-425 (MESH:C000625880), N-acetylcysteine (MESH:D000111), indole-3-acetic acid (MESH:C030737), tryptophan (MESH:D014364), etelcalcetide (MESH:C583569), Spermidine (MESH:D013095), NAD+ (MESH:D009243), sevelamer (MESH:D000069603), calcitriol (MESH:D002117), Ca (MESH:D002118), ROS (MESH:D017382), 1,25-dihydroxyvitamin D (MESH:C097949), SCFA (MESH:D005232), indole (MESH:C030374), Magnesium (MESH:D008274), bisphosphonates (MESH:D004164), nicotinamide riboside (MESH:C018613), lanthanum carbonate (MESH:C119467), Paricalcitol (MESH:C084656), prebiotics (MESH:D056692), Citrate (MESH:D019343), ATP (MESH:D000255), lipid (MESH:D008055), Pyrophosphate (MESH:C107241), resistant starch (MESH:D000084922), quercetin (MESH:D011794), p-Cresyl sulfate (MESH:C408690), omega-3 fatty acids (MESH:D015525), carbon (MESH:D002244), menaquinone-7 (MESH:C062629), aldosterone (MESH:D000450), Vitamin K2 (MESH:D024482), Vitamin D (MESH:D014807), doxercalciferol (MESH:C042533), phytate (MESH:D010833), Cinacalcet (MESH:D000069449), TMAO (MESH:C005855), Phosphate (MESH:D010710), Pi (MESH:D010716), sucroferric oxyhydroxide (MESH:C000599459), inulin (MESH:D007444), kynurenine (MESH:D007737)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606], Bifidobacterium (genus) [taxon 1678], gut metagenome (species) [taxon 749906], Mus musculus (house mouse, species) [taxon 10090], Lactobacillus (genus) [taxon 1578]
- **Cell lines:** VSMC — Homo sapiens (Human), Finite cell line (CVCL_4009)

## Full text

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## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12944978/full.md

## References

100 references — full list in the complete paper: https://tomesphere.com/paper/PMC12944978/full.md

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Source: https://tomesphere.com/paper/PMC12944978