Affinage

RAPH1

Ras-associated and pleckstrin homology domains-containing protein 1 · UniProt Q70E73

Length
1250 aa
Mass
135.3 kDa
Annotated
2026-06-10
27 papers in source corpus 10 papers cited in narrative 10 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RAPH1 (lamellipodin) is a PI(3,4)P2-binding effector that couples class I PI3K/SHIP-generated phosphoinositide signaling to actin-based cell migration (PMID:26022180). It localizes to lamellipodia and lamellipodia-like structures, where it functions as a component of Arp2/3-dependent actin remodeling that can proceed independently of the WAVE regulatory complex in a Rac/Cdc42-driven pathway (PMID:35971979); its peripheral distribution is dynamically controlled, as supervillin overexpression redistributes RAPH1 from the cell edge toward internal podosome/invadopodial sites (PMID:19109420). As a paralogue of RIAM, RAPH1 supports integrin activation and homing selectively in regulatory T cells, compensating for RIAM deficiency (PMID:33104169), and its expression is induced by ECM stiffness through an integrin-FAK-Cas-Rac module to drive cyclin expression and proliferation (PMID:34152388). RAPH1 is phosphorylated by NDR1/2 kinases to support endocytosis and membrane recycling in neurons (PMID:36446521). Independently of its actin-regulatory role, the proline-rich region encoded by the terminal RAPH1 exon assembles butyrylcholinesterase into 340 kDa tetramers via direct interaction with the BChE tetramerization domain, defining RAPH1 as the CHE2 locus underlying the BChE C5 variant (PMID:18076380, PMID:28661448, PMID:27346732). A nuclear isoform, RAPH1-i3, interacts with FOXQ1 to activate STAT3 signaling and confer proliferation, migration, and radioresistance in triple-negative breast cancer (PMID:38062011).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2008 High

    Established an unexpected non-cytoskeletal function for RAPH1: its proline-rich peptides organize the catalytic subunits of butyrylcholinesterase into tetramers, explaining how a secreted enzyme acquires its mature oligomeric state.

    Evidence HPLC/MS peptide sequencing and CHO cell reconstitution of BChE tetramer assembly with a 17-residue proline-rich peptide

    PMID:18076380

    Open questions at the time
    • Does not define the stoichiometry or affinity of the polyproline-tetramerization domain interaction in vivo
    • Does not connect this assembly function to RAPH1's actin-regulatory roles
  2. 2008 Medium

    Placed RAPH1 in the lamellipodial actin machinery and showed its localization is regulated, with supervillin redirecting it from the cell periphery to invadopodial sites.

    Evidence Fluorescence microscopy, immunolocalization of endogenous RAPH1, and RNAi in cultured cells overexpressing EGFP-supervillin

    PMID:19109420

    Open questions at the time
    • Mechanism by which supervillin redistributes RAPH1 is not defined
    • Functional consequence of relocalization for invadopodia is correlative
  3. 2015 Medium

    Defined the phosphoinositide specificity that places RAPH1 downstream of PI3K signaling, identifying it as a PI(3,4)P2-selective effector linking lipid signals to migration.

    Evidence Review summarizing PH-domain lipid-binding assays for PI(3,4)P2 selectivity downstream of class I PI3K and SHIP

    PMID:26022180

    Open questions at the time
    • Primary binding data are summarized rather than generated here
    • Does not establish in vivo membrane recruitment kinetics
  4. 2016 Medium

    Confirmed genetically that the RAPH1 gene is the CHE2 locus controlling the BChE C5 phenotype, linking specific haplotypes to C5 presence and BChE activity.

    Evidence SNP genotyping and haplotype association analysis in 126 individuals stratified by C5 phenotype

    PMID:27346732

    Open questions at the time
    • Association is correlative without functional dissection of individual SNPs
    • Does not explain how haplotype affects fragment processing
  5. 2017 Medium

    Identified the molecular basis of the BChE C5 variant as a noncovalently bound ~60 kDa fragment encoded by the terminal RAPH1 exon, and showed it is normally shortened during maturation.

    Evidence Western blot with C-terminus-specific anti-lamellipodin antibody, native PAGE, and MS of the C5 band

    PMID:28661448

    Open questions at the time
    • The 60 kDa fragment was not reconstituted or mutagenized
    • Mechanism and protease responsible for maturation shortening unknown
  6. 2021 High

    Demonstrated a cell-type-specific integrin-regulatory role: RAPH1 substitutes for its paralogue RIAM in regulatory T cells to activate integrins and drive gut homing.

    Evidence Apbb1ip-/- (RIAM-null) mouse with Raph1 genetic comparison, integrin activation assays, and in vivo homing in a colitis model

    PMID:33104169

    Open questions at the time
    • Why Tregs but not conventional T cells rely on RAPH1 is unresolved
    • Direct interaction with integrin activation machinery not mapped
  7. 2021 Medium

    Connected mechanotransduction to RAPH1 expression, showing ECM stiffness induces RAPH1 via integrin-FAK-Cas-Rac to promote cyclin expression and proliferation.

    Evidence ECM stiffness manipulation with RAPH1 overexpression/siRNA, cyclin western blots, AFM stiffness measurement, and proliferation assays in MEFs

    PMID:34152388

    Open questions at the time
    • Transcriptional mechanism of stiffness-induced RAPH1 expression unknown
    • Single cell-type study
  8. 2022 Medium

    Identified RAPH1 as an NDR1/2 kinase substrate required for neuronal endocytosis and membrane recycling, extending its function to membrane trafficking.

    Evidence Phosphoproteomics of Ndr1/2 knockout mouse brain, biochemical substrate validation, and endocytosis/recycling assays in knockout neurons

    PMID:36446521

    Open questions at the time
    • Phosphosites and their functional impact on RAPH1 not fully mapped
    • Direct role of RAPH1 phosphorylation in the trafficking defect not isolated from NDR1/2 loss
  9. 2022 Medium

    Refined RAPH1's place in actin remodeling by showing it is recruited to lamellipodia-like structures that form without the WAVE regulatory complex, distinguishing it from Ena/VASP proteins.

    Evidence Nap1/Hem1 double-knockout B16-F1 cells with immunofluorescence localization of RAPH1 and GTPase/growth-factor stimulation

    PMID:35971979

    Open questions at the time
    • Recruitment mechanism to WRC-independent structures not defined
    • Functional requirement of RAPH1 for these structures not tested
  10. 2023 Medium

    Revealed a nuclear function for a RAPH1 isoform: RAPH1-i3 binds FOXQ1 to activate STAT3 and drive proliferation, migration, and radioresistance in breast cancer.

    Evidence Co-IP/MS identification of FOXQ1, RAPH1-i3 overexpression/depletion, downstream effector westerns, and in vitro/in vivo radioresistance assays

    PMID:38062011

    Open questions at the time
    • How a nuclear isoform arises and localizes is not defined
    • Mechanism by which the FOXQ1 complex activates STAT3 not resolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RAPH1's distinct activities — PI(3,4)P2-dependent lamellipodial actin regulation, integrin activation, membrane trafficking, BChE tetramerization, and the nuclear FOXQ1/STAT3 axis — are partitioned across isoforms and cell types remains unresolved.
  • No unified structural model relating domains to the separate functions
  • Isoform-specific functional assignment incomplete
  • No structural data on RAPH1 complexes

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 2 GO:0060090 molecular adaptor activity 2 GO:0008289 lipid binding 1
Localization
GO:0005856 cytoskeleton 2 GO:0005886 plasma membrane 2 GO:0005634 nucleus 1
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-168256 Immune System 1 R-HSA-8953897 Cellular responses to stimuli 1
Partners
BCHEFOXQ1STK38STK38LSVIL
Complex memberships
butyrylcholinesterase tetramer

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 Lamellipodin (RAPH1) contains proline-rich peptides that organize the four subunits of butyrylcholinesterase (BChE) into a 340 kDa tetramer by interacting with the C-terminal BChE tetramerization domain. A 17-amino-acid proline-rich peptide derived from lamellipodin drove assembly of human BChE secreted from CHO cells into tetramers. HPLC purification, electrospray ionization tandem MS, Edman degradation, CHO cell expression assay with proline-rich peptide addition The Biochemical journal High 18076380
2017 The C5 variant of BChE includes a noncovalently bound ~60 kDa fragment encoded by the last exon of the RAPH1 gene (containing an N-terminal polyproline region). Western blot with an antibody to the C-terminus of lamellipodin confirmed its presence in C5 and cord BChE. In 90% of adults the 60 kDa fragment is shortened to 3 kDa during maturation, leaving only 10% with C5 BChE. Western blot with C-terminus-specific anti-lamellipodin antibody, native PAGE, MS analysis of C5 band Molecules (Basel, Switzerland) Medium 28661448
2016 Genetic haplotype analysis of RAPH1 SNPs (rs2246118, rs3814365, rs2465520) showed that specific RAPH1 haplotypes associate with the CHE2 C5+ phenotype (presence/absence and intensity of the BChE C5 complex), corroborating that the RAPH1 gene is the CHE2 locus. BChE activity was higher in individuals with the intense C5+ haplotype (TGC) than the faint C5+ haplotype (CAC). SNP genotyping, haplotype association analysis in 126 individuals stratified by CHE2 C5 phenotype Annals of human genetics Medium 27346732
2015 Lamellipodin/RAPH1 was characterized as a PI(3,4)P2-specific effector protein; it selectively binds PI(3,4)P2 (phosphatidylinositol 3,4-bisphosphate) generated downstream of class I PI3K and SHIP phosphatases, thereby linking this phosphoinositide to cell migration signaling. Review citing lipid-binding assays (PH domain binding to PI(3,4)P2 established in prior literature summarized in review) Cellular signalling Medium 26022180
2008 Supervillin overexpression redistributes lamellipodin/RAPH1 away from the cell periphery to internal sites, and lamellipodin/RAPH1 is a component of lamellipodial structures; its redistribution coincides with increased actin punctae at podosome/invadopodial sites. Fluorescence microscopy of EGFP-supervillin overexpression, immunolocalization of endogenous lamellipodin/RAPH1, RNAi knockdown Molecular biology of the cell Medium 19109420
2021 Lamellipodin (Raph1), a paralogue of RIAM, compensates for RIAM deficiency in regulatory T cells (Tregs) to support integrin activation (αLβ2, α4β1, α4β7) and Treg homing to gut-associated lymphoid tissue, whereas conventional T cells depend on RIAM and not lamellipodin for integrin activation. Apbb1ip-/- (RIAM-null) mouse model, Raph1 genetic comparison, integrin activation assays, in vivo homing experiments in IBD colitis model The Journal of experimental medicine High 33104169
2022 Lamellipodin (RAPH1) is present in lamellipodia-like structures (LLS) that form independently of WAVE regulatory complex (WRC), identifying RAPH1 as a lamellipodial component in a WRC-independent Rac/Cdc42-driven Arp2/3-dependent actin remodeling pathway. Unlike Ena/VASP proteins, RAPH1 was recruited to these LLS. Genome editing (Nap1/Hem1 double knockout) in B16-F1 melanoma cells, immunofluorescence localization of RAPH1 in LLS, growth factor and active GTPase stimulation Journal of cell science Medium 35971979
2022 Raph1 (lamellipodin) is a novel substrate of NDR1/2 kinases; NDR1/2 phosphorylate Raph1, and both NDR1/2 and Raph1 are critical for endocytosis and membrane recycling in neurons. Loss of NDR1/2 leads to mislocalization and dysfunction consistent with impaired Raph1-dependent endocytic trafficking. Phosphoproteomics of Ndr1/2 knockout mouse brain, biochemical validation of Raph1 as NDR substrate, endocytosis and membrane recycling assays in knockout neurons Life science alliance Medium 36446521
2021 Lamellipodin (RAPH1) expression is upregulated by increased extracellular matrix (ECM) stiffness via an integrin-dependent FAK-Cas-Rac signaling module. Lamellipodin overexpression increased stiffness-induced cyclin expression, cell proliferation, and intracellular stiffness, while lamellipodin knockdown reduced these responses in mouse embryonic fibroblasts. ECM stiffness manipulation, lamellipodin overexpression and siRNA knockdown, cyclin western blots, atomic force microscopy for intracellular stiffness, proliferation assays Journal of cell science Medium 34152388
2023 A nuclear isoform of RAPH1 (RAPH1-i3) interacts with the transcription factor FOXQ1, as identified by co-immunoprecipitation and mass spectrometry. Co-expression of RAPH1-i3 and FOXQ1 activated STAT3 signaling and increased expression of CCND1, MCL1, Bcl-XL, and MMP2, promoting cell proliferation, migration, and radioresistance in triple-negative breast cancer cells. Co-immunoprecipitation, mass spectrometry, RAPH1-i3 overexpression and depletion, in vitro and in vivo radioresistance assays, western blot for downstream effectors Cell death & disease Medium 38062011

Source papers

Stage 0 corpus · 27 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 Phosphatidylinositol (3,4) bisphosphate-specific phosphatases and effector proteins: A distinct branch of PI3K signaling. Cellular signalling 96 26022180
2012 MicroRNA-203 contributes to skin re-epithelialization. Cell death & disease 86 23190607
2008 Lamellipodin proline rich peptides associated with native plasma butyrylcholinesterase tetramers. The Biochemical journal 74 18076380
2014 Blood transcriptomic biomarkers in adult primary care patients with major depressive disorder undergoing cognitive behavioral therapy. Translational psychiatry 68 25226551
2008 Supervillin reorganizes the actin cytoskeleton and increases invadopodial efficiency. Molecular biology of the cell 61 19109420
2011 GWAS of butyrylcholinesterase activity identifies four novel loci, independent effects within BCHE and secondary associations with metabolic risk factors. Human molecular genetics 46 21862451
2021 Distinct integrin activation pathways for effector and regulatory T cell trafficking and function. The Journal of experimental medicine 34 33104169
2022 Lamellipodia-like actin networks in cells lacking WAVE regulatory complex. Journal of cell science 30 35971979
2021 Pilot validation of blood-based biomarkers during pregnancy and postpartum in women with prior or current depression. Translational psychiatry 19 33479202
2021 Mechanosensitive expression of lamellipodin promotes intracellular stiffness, cyclin expression and cell proliferation. Journal of cell science 15 34152388
2017 The C5 Variant of the Butyrylcholinesterase Tetramer Includes a Noncovalently Bound 60 kDa Lamellipodin Fragment. Molecules (Basel, Switzerland) 15 28661448
2022 Loss of NDR1/2 kinases impairs endomembrane trafficking and autophagy leading to neurodegeneration. Life science alliance 13 36446521
2021 Adiposity associated DNA methylation signatures in adolescents are related to leptin and perinatal factors. Epigenetics 13 33550919
2008 Two MER2-negative individuals with the same novel CD151 mutation and evidence for clinical significance of anti-MER2. Transfusion 9 18522704
2023 Joint analysis of WES and RNA-Seq identify signature genes related to metastasis in prostate cancer. Journal of cellular and molecular medicine 8 37378426
2023 Quantitative phosphoproteomics reveals molecular pathway network alterations in human early-stage primary hepatic carcinomas: potential for 3P medical approach. The EPMA journal 7 37605650
2023 miR-3200 accelerates the growth of liver cancer cells by enhancing Rab7A. Non-coding RNA research 7 37860266
2023 Nuclear isoform of RAPH1 interacts with FOXQ1 to promote aggressiveness and radioresistance in breast cancer. Cell death & disease 7 38062011
2022 Circulating circular RNA profiles associated with celiac disease seropositivity in children with type 1 diabetes. Frontiers in pediatrics 4 36210930
2013 Amplification and deletion of the RAPH1 gene in breast cancer patients. Molecular biology reports 4 24057252
2023 Co-Expression Analysis of Airway Epithelial Transcriptome in Asthma Patients with Eosinophilic vs. Non-Eosinophilic Airway Infiltration. International journal of molecular sciences 3 36835202
2024 Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis). Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 2 38218377
2016 Association between RAPH1 Gene Haplotypes and CHE2 Locus Phenotypes. Annals of human genetics 2 27346732
2025 Clinicopathologic and proteomic characteristics of low-grade undifferentiated spindle cell sarcoma. Frontiers in molecular biosciences 1 40666499
2026 Discovery of Seven ROS-Sensitive Immune Checkpoints and 46 Ligands Mediating Immune Suppression Through T cell-APC Networks. Journal of Cancer 0 41584046
2025 SHMT2 modulates the transcriptome and metabolism profiles to promote the tumor phenotypes of bladder cancer HT-1376 cells. Frontiers in genetics 0 41347062
2024 Bayesian colocalization of GWAS and eQTL signals reveals cell type-specific genes and regulatory variants for susceptibility to subtypes of ischemic stroke. Computational biology and chemistry 0 38744227

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