Affinage

NPNT

Nephronectin · UniProt Q6UXI9

Length
565 aa
Mass
61.9 kDa
Annotated
2026-06-10
35 papers in source corpus 12 papers cited in narrative 12 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NPNT (nephronectin/POEM) is a secreted extracellular matrix adhesion protein that engages cell-surface integrins to control cell adhesion, survival, and tissue homeostasis across kidney, bone, vasculature, and lung (PMID:11546798). It contains EGF-like domains, an RGD cell-binding motif, and a MAM domain; the RGD motif drives integrin-dependent cell spreading and survival while the MAM domain contributes to adhesion alone, and NPNT acts as a ligand for α8β1 integrin (PMID:11546798). NPNT signaling activates ERK1/2 to drive endothelial migration, tube formation, and angiogenesis (PMID:27782206), and in alveolar epithelium it interacts with integrin α3 (ITGA3) to suppress LATS1/MOB1 hyperactivation, promote YAP1 nuclear translocation, and block YAP1 ubiquitination, thereby protecting against cellular senescence and pulmonary fibrosis (PMID:40444575). Its expression is suppressed by TNF-α through NF-κB and by TGF-β through ERK1/2 and JNK, coupling inflammatory and growth-factor cues to NPNT-dependent osteoblast differentiation (PMID:17977532, PMID:21689636). NPNT is required for kidney development: a homozygous nonsense variant producing complete nonsense-mediated decay of the transcript causes autosomal recessive bilateral renal agenesis in humans (PMID:35246978), and NPNT supports glomerular filtration barrier integrity (PMID:28938947).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2001 High

    Established NPNT's foundational identity as an ECM adhesion molecule and defined which of its domains drive which activities, answering how a secreted protein supports cell adhesion, spreading, and survival.

    Evidence Bacterial recombinant protein, RGD→RGE mutagenesis, and adhesion/spreading assays on α8-integrin-expressing cell lines

    PMID:11546798

    Open questions at the time
    • Downstream intracellular signaling from the integrin not defined
    • Physiological tissue context not addressed in vitro
  2. 2007 Medium

    Placed NPNT under negative growth-factor control by showing TGF-β suppresses its expression, beginning to explain how NPNT levels are tuned in osteoblasts.

    Evidence TGF-β treatment with dose-response and TGF-βRI/ERK/JNK pathway inhibitors in MC3T3-E1 cells

    PMID:17977532

    Open questions at the time
    • Functional consequence of suppression not tested here
    • Single cell line
  3. 2011 Medium

    Connected NPNT to inflammatory signaling and bone biology, showing TNF-α/NF-κB suppresses NPNT and that NPNT positively regulates osteoblast differentiation.

    Evidence TNF-α treatment with NF-κB inhibition and NPNT overexpression rescue in MC3T3-E1 cells

    PMID:21689636

    Open questions at the time
    • Integrin/receptor mediating osteoblast effect not identified
    • In vivo bone phenotype not tested
  4. 2016 Medium

    Defined NPNT as a paracrine angiogenic factor and identified ERK1/2 as the required downstream signal, extending NPNT function from adhesion to vascular signaling.

    Evidence Recombinant NPNT in endothelial migration/tube-formation assays, ex vivo metatarsal angiogenesis, and ERK1/2 inhibitor rescue

    PMID:27782206

    Open questions at the time
    • Integrin receptor on endothelial cells not defined
    • Direct link to in vivo angiogenesis in disease not shown
  5. 2017 Medium

    Demonstrated tissue-specific NPNT roles: Wnt-regulated NPNT promotes aldosterone production in adrenal glomerulosa, and the miR-378a-3p/NPNT axis maintains glomerular filtration barrier integrity.

    Evidence IHC, NPNT overexpression/siRNA with aldosterone readout in adrenal cells; miR-378a-3p overexpression in zebrafish and mice with proteinuria readout

    PMID:28416583 PMID:28938947

    Open questions at the time
    • Integrin partner in adrenal/podocyte contexts not identified
    • Mechanism linking adhesion to aldosterone output unresolved
  6. 2022 Medium

    Established NPNT as causally required for human kidney development through loss-of-function genetics, and implicated NPNT in cancer metastasis via FAK/PI3K/AKT.

    Evidence Linkage/exome sequencing with NMD confirmation for renal agenesis; siRNA knockdown with FAK/PI3K/AKT readout in HCC cells

    PMID:35246978 PMID:35304239

    Open questions at the time
    • Cell-autonomous developmental mechanism in kidney not dissected
    • HCC pathway placement based on knockdown without rescue
  7. 2022 Low

    Proposed a regulatory axis whereby miR-378 targets NPNT in alveolar epithelial cells, linking NPNT downregulation to COPD-relevant phenotypes.

    Evidence miR-378 overexpression in A549 cells with proliferation/migration/apoptosis assays and COPD expression-data analysis

    PMID:36128198

    Open questions at the time
    • Direct targeting not confirmed by luciferase reporter or binding assay
    • Single cell line; correlative COPD association
  8. 2025 Medium

    Resolved a mechanistic pathway for NPNT in lung aging/fibrosis, showing NPNT–ITGA3 interaction restrains LATS1/MOB1 and stabilizes nuclear YAP1 to prevent alveolar epithelial senescence.

    Evidence NPNT knockout/overexpression mouse models with bleomycin fibrosis, LATS1/MOB1/YAP1 western blots, ubiquitination assay, and Escin pharmacological rescue

    PMID:40444575

    Open questions at the time
    • Structural basis of NPNT–ITGA3 interaction not defined
    • How integrin engagement mechanistically suppresses Hippo kinases unresolved
  9. 2025 Medium

    Provided a molecular mechanism for the COPD risk allele by showing rs34712979 shifts NPNT splicing to include an exon that disrupts an EGF-like domain.

    Evidence Long-read RNA sequencing, sQTL and GWAS colocalization, and AlphaFold structural prediction

    PMID:39978861

    Open questions at the time
    • Domain disruption predicted in silico, not validated functionally
    • Effect on integrin binding/downstream signaling not measured

Open questions

Synthesis pass · forward-looking unresolved questions
  • How distinct integrin partners (α8β1, ITGA3) and downstream pathways (ERK1/2, FAK/PI3K/AKT, Hippo/YAP1) are selected in different tissues to produce NPNT's divergent outcomes remains unresolved.
  • No unified model of receptor/pathway selection across tissues
  • No structural model of the NPNT–integrin complex
  • Roles of individual EGF/MAM domains in signaling beyond adhesion undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0048018 receptor ligand activity 2 GO:0098631 cell adhesion mediator activity 2
Localization
GO:0005576 extracellular region 2 GO:0031012 extracellular matrix 2
Pathway
R-HSA-1266738 Developmental Biology 2 R-HSA-162582 Signal Transduction 2 R-HSA-1474244 Extracellular matrix organization 1
Partners

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 NPNT (POEM) was identified as a novel extracellular matrix adhesion molecule containing five EGF-like domains, an RGD cell-binding motif, and a MAM domain. Recombinant POEM protein promoted cell adhesion, spreading, and survival. Mutation of the RGD sequence to RGE significantly decreased cell spreading and survival activities, while the MAM domain contributed only to cell adhesion and not spreading/survival. NPNT was identified as a ligand for α8β1 integrin: KA8 cells (K562 stably expressing α8 integrin) showed strong binding and spreading on NPNT, whereas parental K562 cells (expressing α5β1) did not bind NPNT. Bacterial recombinant protein production, site-directed mutagenesis (RGD→RGE), cell adhesion/spreading assays, stable integrin-expressing cell lines (K562/KA8) The Journal of biological chemistry High 11546798
2007 TGF-β strongly inhibited NPNT (POEM) gene expression in mouse osteoblastic MC3T3-E1 cells in a time- and dose-dependent manner. This suppression was mediated through activation of TGF-β receptor I and the ERK1/2 and JNK (c-Jun N-terminal kinase) signaling pathways. Gene expression analysis in MC3T3-E1 osteoblastic cells with TGF-β treatment, pathway inhibitor experiments targeting TGF-β receptor I, ERK1/2, and JNK FEBS letters Medium 17977532
2011 TNF-α strongly inhibited NPNT (POEM) expression in MC3T3-E1 osteoblastic cells in a time- and dose-dependent manner through the NF-κB signaling pathway. Over-expression of NPNT rescued TNF-α-induced inhibition of osteoblast differentiation, establishing NPNT as a positive regulator of osteoblast differentiation downstream of TNF-α/NF-κB. Gene expression analysis in MC3T3-E1 cells with TNF-α treatment, NF-κB pathway inhibition, NPNT overexpression rescue experiment Biochemical and biophysical research communications Medium 21689636
2016 NPNT is expressed by osteoblasts and functions as a paracrine angiogenic factor. Exogenous recombinant NPNT stimulated endothelial cell migration and tube-like structure formation in vitro, and promoted angiogenesis in an ex vivo fetal mouse metatarsal assay. NPNT activated phosphorylation of ERK1/2 and p38 MAPK in endothelial cells; pharmacological inhibition of ERK1/2 blocked NPNT-induced endothelial migration, tube formation, and angiogenesis, placing ERK1/2 downstream of NPNT in angiogenic signaling. Recombinant protein treatment of endothelial cells, migration assay, tube formation assay, ex vivo metatarsal angiogenesis assay, kinase phosphorylation assays, ERK1/2 inhibitor rescue experiments Scientific reports Medium 27782206
2017 NPNT is identified as a secreted extracellular matrix protein expressed exclusively around aldosterone-producing glomeruli in normal adrenal zona glomerulosa (ZG) and in ZG-like aldosterone-producing adenomas (APAs). NPNT production is regulated by the canonical Wnt signaling pathway (highest expression in APAs with gain-of-function CTNNB1 mutations). NPNT overexpression increased aldosterone production while NPNT silencing reduced aldosterone, and NPNT exhibited pro-adhesive activity in primary adrenal and APA cells, with binding to cell-surface integrins proposed to stimulate cell-cell contact within glomeruli. Immunohistochemistry, NPNT overexpression and siRNA silencing in adrenal/APA cells with aldosterone readout, microarray gene expression analysis Hypertension (Dallas, Tex. : 1979) Medium 28416583
2020 A COPD-associated SNP (rs34712979) creates a cryptic splice acceptor site in NPNT, resulting in inclusion of a 3-nucleotide exon extension encoding a serine residue near the N-terminus of the protein. Long-read sequencing identified 13 NPNT isoforms, 6 predicted to be protein coding, with two full-length isoforms differing only in this serine-encoding extension. Colocalisation analysis showed this splicing variant underlies COPD risk, spirometric lung function measures, and NPNT splicing (posterior probability 94%). Splice quantitative trait locus (sQTL) analysis, short-read RNA sequencing, Oxford Nanopore Technologies long-read sequencing, colocalization analysis with GWAS, RT-PCR medRxiv (preprint)preprint Medium 33173926
2022 Down-regulation of NPNT via siRNA transfection in hepatocellular carcinoma (HCC) cells inhibited cell migration and invasion, and suppressed the FAK/PI3K/AKT signaling pathway, identifying NPNT as a regulator of HCC metastasis acting through this pathway. siRNA knockdown, wound healing assay, Matrigel Transwell invasion assay, western blot for FAK/PI3K/AKT pathway Gene Medium 35304239
2022 A homozygous null (nonsense) variant in NPNT causes autosomal recessive bilateral renal agenesis in humans, confirmed by detection of complete nonsense-mediated decay of the NPNT transcript, establishing that complete loss of NPNT function can cause failure of kidney development (renal agenesis). Genome-wide linkage analysis, exome sequencing, RT-PCR demonstrating nonsense-mediated mRNA decay, Sanger sequencing for segregation Clinical genetics Medium 35246978
2025 NPNT acts as an antiaging/antifibrotic molecule in the lung via interaction with integrin α3 (ITGA3). NPNT deficiency exacerbates bleomycin-induced senescence in alveolar epithelial cells and worsens fibrosis, while NPNT overexpression in alveolar epithelium improves lung function and resistance to aging and fibrosis. Mechanistically, NPNT inhibits hyperactivation of LATS1 and MOB1, facilitates YAP1 nuclear translocation, and suppresses YAP1 ubiquitination and degradation contingent on NPNT–ITGA3 interaction. Pharmacological elevation of NPNT protein levels with Escin alleviated pulmonary fibrosis in mice. NPNT knockout and overexpression mouse models, bleomycin-induced fibrosis assay, western blotting for LATS1/MOB1/YAP1 pathway, ubiquitination assay, pharmacological intervention (Escin) Advanced science (Weinheim, Baden-Wurttemberg, Germany) Medium 40444575
2025 The COPD-risk allele rs34712979-A causes a shift in NPNT isoform usage away from the dominant isoform B (excludes exon 3) to isoform A (includes exon 3). AlphaFold protein structural analysis reveals that inclusion of exon 3 disrupts an EGF-like functional domain in NPNT, providing a structural mechanism for how this splicing change impairs NPNT function and increases COPD risk. Long-read RNA sequencing, sQTL analysis, colocalization with COPD GWAS, AlphaFold in silico protein structural analysis The European respiratory journal Medium 39978861
2017 Suppression of nephronectin (NPNT) expression by microRNA-378a-3p in zebrafish and mice significantly induced proteinuria due to loss of integrity of the glomerular filtration barrier, demonstrating that the miR-378a-3p/nephronectin axis regulates podocyte–glomerular basement membrane interaction and glomerular filtration barrier integrity. microRNA overexpression in zebrafish and mice, proteinuria measurement, glomerular filtration barrier integrity assessment Kidney international Medium 28938947
2022 miR-378 directly targets NPNT in A549 human alveolar epithelial cells. miR-378 overexpression increased cell proliferation, migration, and suppressed apoptosis; miR-378 is upregulated while NPNT is downregulated in COPD lung tissues, suggesting a regulatory axis relevant to COPD pathogenesis. miR-378 overexpression in A549 cells, bioinformatics target prediction confirmed by cell functional assays (CCK-8, colony formation, Transwell, flow cytometry), analysis of public COPD expression data PeerJ Low 36128198

Source papers

Stage 0 corpus · 35 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 Peroral endoscopic myotomy (POEM) for esophageal achalasia. Endoscopy 1316 20354937
2001 Molecular cloning of POEM: a novel adhesion molecule that interacts with alpha8beta1 integrin. The Journal of biological chemistry 59 11546798
2016 NPNT is Expressed by Osteoblasts and Mediates Angiogenesis via the Activation of Extracellular Signal-regulated Kinase. Scientific reports 30 27782206
2017 The emerging role of NPNT in tissue injury repair and bone homeostasis. Journal of cellular physiology 26 28513838
2013 Improvement of endocytoscopic findings after per oral endoscopic myotomy (POEM) in esophageal achalasia; does POEM reduce the risk of developing esophageal carcinoma? Per oral endoscopic myotomy, endocytoscopy and carcinogenesis. BMC gastroenterology 25 23363448
2011 Expression of POEM, a positive regulator of osteoblast differentiation, is suppressed by TNF-α. Biochemical and biophysical research communications 22 21689636
2018 NPNT promotes early-stage bone metastases in breast cancer by regulation of the osteogenic niche. Journal of bone oncology 19 30591862
2007 TGF-beta suppresses POEM expression through ERK1/2 and JNK in osteoblasts. FEBS letters 19 17977532
2017 Physiological and Pathological Roles in Human Adrenal of the Glomeruli-Defining Matrix Protein NPNT (Nephronectin). Hypertension (Dallas, Tex. : 1979) 17 28416583
2020 Factors associated with admission after implementation of a same-day discharge pathway in patients undergoing peroral endoscopic myotomy (POEM). Surgical endoscopy 15 32780244
2005 POEM: Parameter Optimization using Ensemble Methods: application to target specific scoring functions. Journal of chemical information and modeling 15 16180906
2021 Long-term (17 years) subjective and objective evaluation of the durability of laparoscopic Heller esophagomyotomy in patients with achalasia of the esophagus (90% of follow-up): a real challenge to POEM. Surgical endoscopy 13 33471177
2023 LncRNA ADAMTS9-AS1 inhibits the stemness of lung adenocarcinoma cells by regulating miR-5009-3p/NPNT axis. Genomics 12 36870548
2020 Characterization of a COPD-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing. medRxiv : the preprint server for health sciences 11 33173926
2012 STEPS to POEM: introduction of a new technique at the IRCAD. Surgical innovation 11 22977085
2004 Recalculation of cardiovascular risk score as a surrogate marker of change in clinical care of diabetes patients: the Alphabet POEM project (Practice Of Evidence-based Medicine). Current medical research and opinion 10 15140344
2025 Characterisation of a COPD-associated nephronectin (NPNT) functional splicing genetic variant in human lung tissue via long-read sequencing. The European respiratory journal 9 39978861
2022 Integrated analysis identified NPNT as a potential key regulator in tumor metastasis of hepatocellular carcinoma. Gene 9 35304239
2018 Nephronectin (NPNT) and the prediction of nephrotic syndrome response to steroid treatment. European journal of human genetics : EJHG 9 29891875
2022 A null founder variant in NPNT, encoding nephronectin, causes autosomal recessive renal agenesis. Clinical genetics 7 35246978
2022 miR-378 associated with proliferation, migration and apoptosis properties in A549 cells and targeted NPNT in COPD. PeerJ 7 36128198
2017 Foreseeing the future of glomerular disease through slits: miR-NPNT axis. Kidney international 6 28938947
2022 Missense Variants in GFRA1 and NPNT Are Associated with Congenital Anomalies of the Kidney and Urinary Tract. Genes 4 36292572
2021 Eyebrows, Facial Expression, and "Poem to the Eyebrow (Blason du Sourcil)". The Journal of craniofacial surgery 4 34727455
2025 Nephronectin (NPNT) is a Crucial Determinant of Idiopathic Pulmonary Fibrosis: Modulating Cellular Senescence via the ITGA3/YAP1 Signaling Axis. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 3 40444575
2020 "The power of the poem": using poetic inquiry to explore trans-identities in Namibia. Arts & health 2 32762622
2016 POEM: Identifying Joint Additive Effects on Regulatory Circuits. Frontiers in genetics 2 27148351
2025 Saudi Gastroenterology Association (SGA) clinical care pathway and standards of care for peroral endoscopic myotomy (POEM) in achalasia. Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association 1 41498779
2023 Pulmonary manifestations of POEM syndrome: a retrospective analysis of 282 cases. BMC pulmonary medicine 1 37993859
2008 POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons. BMC genomics 1 18803852
1993 Alternating chemotherapy of CHOP-Bleo and POEM-Bleo for diffuse large-cell lymphoma: a single-institutional study with a long-term follow-up. International journal of hematology 1 7693030
2025 Skeletogenic Expression of Integrin Alpha, Talin and Npnt Genes and Npnt Role in Sea Urchin Skeletogenesis. Journal of experimental zoology. Part B, Molecular and developmental evolution 0 40855725
2021 Synthesis, Characterization, and CO2/N2 Separation Performance of POEM-g-PAcAm Comb Copolymer Membranes. Polymers 0 33419151
2005 Poem: A is for alanine. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology 0 21638613
1999 [POEM syndrome]. Polskie Archiwum Medycyny Wewnetrznej 0 11072537

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