Affinage

TM9SF2

Transmembrane 9 superfamily member 2 · UniProt Q99805

Round 2 corrected
Length
663 aa
Mass
75.8 kDa
Annotated
2026-04-28
44 papers in source corpus 9 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TM9SF2 is a lysosome-localized, nine-transmembrane (nonaspanin) glycoprotein that governs intracellular vesicle trafficking, membrane receptor dynamics, and innate immune signaling. It maintains Golgi integrity by controlling intracellular cholesterol distribution, with its depletion causing cholesterol accumulation in Golgi compartments and consequent Golgi fragmentation (PMID:40423301), and it orchestrates PD-L1 surface expression by recruiting PGK1 to promote PD-L1 recycling while suppressing HIP1R-mediated lysosomal degradation—a complex destabilized by the ceramide species Cer(d18:1/26:0) (PMID:41888515). TM9SF2 functions as a broadly required host factor for adeno-associated virus transduction across multiple serotypes (PMID:32280726), promotes Fcγ receptor-mediated phagocytosis upstream of PLCγ1 in macrophages (PMID:38218914), and suppresses type I interferon signaling by restraining IRF3 phosphorylation (PMID:40525335). In Drosophila, the ortholog physically associates with the innate immune receptor PGRP-LC and regulates actin cytoskeleton organization in haemocytes (PMID:25139117).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2007 High

    Establishing the basic identity of TM9SF2 as a mannose-6-phosphate-bearing lysosomal glycoprotein with six N-glycosylation sites resolved its subcellular address and post-translational processing, framing it as a potential regulator of endolysosomal trafficking.

    Evidence MPR overlay assay, PNGase F deglycosylation, immunofluorescence, and subcellular fractionation in mouse liver

    PMID:17105447

    Open questions at the time
    • No functional role or binding partners identified at this stage
    • Whether lysosomal localization is constitutive or regulated was not addressed
    • Mechanism of lysosomal targeting beyond Man6P modification unknown
  2. 2014 Medium

    Demonstrating that the Drosophila TM9SF2 ortholog physically associates with the innate immune receptor PGRP-LC and regulates actin organization in haemocytes established the first link between TM9SF family members and immune receptor trafficking and cytoskeletal control.

    Evidence Co-immunoprecipitation, RNAi knockdown, immunofluorescence co-localization, and actin assays in Drosophila S2 cells

    PMID:25139117

    Open questions at the time
    • Findings are in Drosophila; conservation of PGRP-LC-like interaction in mammals unconfirmed
    • Molecular mechanism linking TM9SF2 to actin remodeling not identified
    • Whether TM9SF2 directly controls receptor surface delivery versus retention was not resolved
  3. 2018 Medium

    CRISPR knockout revealing that TM9SF2 loss impairs colorectal cancer cell fitness in vitro and in xenografts connected TM9SF2 to cell proliferation, while transcriptome analysis implicated it in cell cycle, oxidative phosphorylation, and ceramide signaling pathways.

    Evidence CRISPR/Cas9 knockout, anchorage-independent growth assay, xenograft tumor model, and transcriptome profiling in CRC cells

    PMID:30333512

    Open questions at the time
    • Pathway involvement is transcriptome-inferred, not mechanistically validated
    • Whether growth defect is cell-autonomous or microenvironment-dependent was not dissected
    • Direct molecular targets mediating TM9SF2 pro-proliferative effect not identified
  4. 2020 High

    Genome-wide CRISPR screens identifying TM9SF2 as an essential host factor for AAV transduction across eight serotypes demonstrated a broad, serotype-independent role in viral entry or intracellular trafficking, distinct from the Golgi-localized factor GPR108.

    Evidence Genome-wide CRISPR pooled screen with multi-serotype AAV transduction validation by flow cytometry and imaging

    PMID:32280726

    Open questions at the time
    • Precise step in the AAV entry/trafficking pathway mediated by TM9SF2 remains undefined
    • Whether TM9SF2 acts at the endosomal escape or uncoating stage was not resolved
    • Structural basis for TM9SF2 requirement across diverse AAV capsids unknown
  5. 2024 Medium

    Showing that TM9SF2 knockdown impairs Fcγ receptor-mediated phagocytosis and attenuates PLCγ1 activation in macrophages placed TM9SF2 upstream of a defined signaling node in innate immune effector function.

    Evidence siRNA knockdown in THP-1-derived M2 macrophages, phagocytosis assays with IgG-coated beads and apoptotic cells, Western blotting for PLCγ1 phosphorylation

    PMID:38218914

    Open questions at the time
    • Single-lab study; independent replication in primary macrophages not reported
    • Whether TM9SF2 acts on Fcγ receptor surface expression, clustering, or downstream adaptor recruitment is unknown
    • Relationship between lysosomal localization and phagocytic function not mechanistically explained
  6. 2025 Medium

    Discovering that TM9SF2 maintains Golgi integrity through cholesterol trafficking control—and that pharmacological restoration of cholesterol homeostasis rescues Golgi fragmentation in TM9SF2-depleted cells—provided the first mechanistic explanation for TM9SF2's broad influence on membrane trafficking.

    Evidence siRNA knockdown, filipin staining, cholesterol fractionation, Golgi morphology imaging, ricin cytotoxicity and retrograde transport assays, pharmacological rescue with A939572/avasimibe

    PMID:40423301

    Open questions at the time
    • Single-lab study; the cholesterol sensor or transporter that TM9SF2 directly regulates is unidentified
    • Whether Golgi fragmentation explains the AAV and phagocytosis phenotypes was not tested
    • Contribution of individual TM9SF2 transmembrane domains to cholesterol sensing unknown
  7. 2025 Medium

    Demonstrating that TM9SF2 knockdown enhances IRF3 phosphorylation and IFN-β induction upon poly(I:C) stimulation revealed TM9SF2 as a negative regulator of type I interferon signaling, linking its trafficking function to innate antiviral immunity.

    Evidence siRNA knockdown in A549 cells, VSV-GFP infection, plaque assay, RT-qPCR, Western blotting for phospho-IRF3

    PMID:40525335

    Open questions at the time
    • Single-lab study; mechanism by which TM9SF2 restrains IRF3 activation (e.g. receptor turnover, adaptor sequestration) not identified
    • Whether this reflects altered STING or RIG-I/MAVS pathway trafficking was not examined
    • In vivo relevance of immune suppression not tested
  8. 2025 High

    Mechanistic dissection of TM9SF2's role in PD-L1 trafficking—recruiting PGK1 for recycling while opposing HIP1R-mediated lysosomal degradation, with ceramide Cer(d18:1/26:0) as an endogenous disruptor of the TM9SF2-PGK1 complex—provided a unified model for how TM9SF2 coordinates receptor surface expression with therapeutic implications for antitumor immunity.

    Evidence CRISPR screen targeting glycosphingolipid metabolism, co-immunoprecipitation, PD-L1 trafficking assays, genetic and pharmacological disruption, ceramide treatment, antitumor immunity assays

    PMID:41888515

    Open questions at the time
    • Whether TM9SF2-PGK1 recycling applies to receptors beyond PD-L1 is untested
    • Structural basis of the TM9SF2-PGK1 interaction and ceramide-mediated disruption unresolved
    • In vivo pharmacological targeting of TM9SF2-PGK1 axis not yet evaluated in clinical models

Open questions

Synthesis pass · forward-looking unresolved questions
  • A unifying structural and mechanistic model explaining how TM9SF2 coordinates cholesterol trafficking, receptor recycling, Golgi maintenance, and innate immune regulation through its nine-transmembrane architecture remains to be established.
  • No crystal or cryo-EM structure of TM9SF2 exists
  • Whether cholesterol-binding is direct and mediates all downstream phenotypes is unknown
  • Relative importance of TM9SF2 in different tissue and immune cell contexts has not been systematically compared

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 2 GO:0060090 molecular adaptor activity 1
Localization
GO:0005764 lysosome 2 GO:0031410 cytoplasmic vesicle 2 GO:0005794 Golgi apparatus 1
Pathway
R-HSA-168256 Immune System 2 R-HSA-5653656 Vesicle-mediated transport 2
Partners
HIP1RPD-L1PGK1PGRP-LC

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 TM9SF2 (then called 'p76'/LOC196463) is a mannose-6-phosphate (Man6P)-bearing glycoprotein with six N-glycosylation sites that localizes to lysosomes, as demonstrated by Man6P-dependent interaction with mannose-6-phosphate receptors (MPR overlay), progressive PNGase F deglycosylation, immunofluorescence, and subcellular fractionation of mouse liver homogenates. MPR overlay assay, PNGase F deglycosylation, immunofluorescence microscopy, subcellular fractionation The Biochemical Journal High 17105447
2014 Drosophila TM9SF2 (ortholog of human TM9SF2) co-immunoprecipitates with the peptidoglycan recognition receptor PGRP-LC and co-localizes with it in intracellular vesicles and at the plasma membrane; silencing TM9SF2 does not prevent plasma membrane localization of PGRP-LC (unlike TM9SF4 silencing), and both TM9 proteins control actin cytoskeleton organization in haemocytes, with evidence that TM9 proteins suppress inappropriate signaling from the unstimulated PGRP-LC receptor. Co-immunoprecipitation, RNAi knockdown, immunofluorescence co-localization, actin cytoskeleton assays in Drosophila S2 cells and fat body Journal of Innate Immunity Medium 25139117
2018 CRISPR/Cas9 knockout of TM9SF2 substantially diminishes colorectal cancer (CRC) cell fitness in vitro and in vivo (anchorage-independent growth, tumor growth), and transcriptome analysis of knockout cells reveals TM9SF2 involvement in cell cycle progression, oxidative phosphorylation, and ceramide signaling. CRISPR/Cas9 knockout, RNAi silencing, anchorage-independent growth assay, in vivo tumor xenograft, transcriptome analysis Scientific Reports Medium 30333512
2019 LINC01232 recruits the RNA-binding protein EIF4A3 to boost TM9SF2 mRNA stability, thereby upregulating TM9SF2 expression; additionally, the transcription factor SP1 mediates transcriptional activation of both LINC01232 and TM9SF2, placing TM9SF2 downstream of a SP1/LINC01232/EIF4A3 regulatory axis in pancreatic adenocarcinoma. RNA pulldown, RIP assay, siRNA knockdown, luciferase reporter assay, qRT-PCR, mRNA stability assay Cell Death & Disease Medium 31541081
2020 Genome-wide CRISPR pooled screens identified TM9SF2 as a host cell factor required for AAV2 transduction across eight different AAV serotypes (including AAV1–4, AAV6–9); validation in flow cytometry and imaging studies confirmed TM9SF2's role, distinct from and complementary to GPR108 (which localizes to Golgi and shows serotype selectivity). Genome-wide CRISPR pooled screen, flow cytometry, imaging validation, multi-serotype AAV transduction assays Molecular Therapy: Methods & Clinical Development High 32280726
2024 Silencing TM9SF2 in THP-1-derived M2 macrophages significantly reduces phagocytosis of IgG-coated beads and apoptotic Jurkat cells, and attenuates activation of PLC-γ1, placing TM9SF2 upstream of PLC-γ1 in the Fcγ receptor-mediated phagocytic signaling pathway. siRNA knockdown, phagocytosis assay (IgG-coated beads and apoptotic cell co-culture), Western blotting for PLC-γ1 phosphorylation Journal of Orthopaedic Surgery and Research Medium 38218914
2025 TM9SF2 maintains Golgi integrity by regulating intracellular cholesterol trafficking; genetic knockdown of TM9SF2 causes abnormal cholesterol accumulation in Golgi compartments, severe Golgi fragmentation, and impaired retrograde transport of ricin, thereby attenuating ricin-induced cytotoxicity. Pharmacological restoration of cholesterol homeostasis (using A939572 or avasimibe) rescues Golgi integrity and reverses the ricin-resistant phenotype of TM9SF2-knockdown cells. siRNA/genetic knockdown, cholesterol trafficking assays (filipin staining, cholesterol fractionation), Golgi morphology imaging, ricin cytotoxicity assays, pharmacological rescue with A939572/avasimibe Toxins Medium 40423301
2025 TM9SF2 knockdown in A549 cells inhibits vesicular stomatitis virus (VSV) replication and positively regulates the type I interferon signaling pathway; specifically, TM9SF2 knockdown upregulates IFN-β mRNA and increases IRF3 phosphorylation upon poly(I:C) stimulation, indicating TM9SF2 normally suppresses innate antiviral immunity. siRNA knockdown, VSV-GFP infection model, plaque assay, RT-qPCR, Western blotting for IRF3 phosphorylation, poly(I:C) stimulation Chinese Journal of Cellular and Molecular Immunology Medium 40525335
2026 TM9SF2 orchestrates PD-L1 trafficking by: (1) recruiting phosphoglycerate kinase 1 (PGK1) to promote PD-L1 recycling to the plasma membrane, and (2) dismantling the HIP1R-mediated lysosomal degradation pathway for PD-L1. Genetic or pharmacological disruption of the TM9SF2-PGK1 complex depletes surface PD-L1 and enhances antitumor immunity. The endogenous ceramide species Cer(d18:1/26:0) destabilizes the TM9SF2-PGK1 complex, triggering PD-L1 lysosomal degradation; this mechanism was identified via CRISPR screen targeting glycosphingolipid metabolism. CRISPR screen (glycosphingolipid metabolism library), co-immunoprecipitation, PD-L1 trafficking assays, genetic knockdown/knockout, pharmacological disruption, ceramide treatment, antitumor immunity assays Nature Communications High 41888515

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2008 Identification of host proteins required for HIV infection through a functional genomic screen. Science (New York, N.Y.) 1165 18187620
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2015 Gene essentiality and synthetic lethality in haploid human cells. Science (New York, N.Y.) 657 26472760
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2020 Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.) 564 33060197
2021 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 532 33845483
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2015 A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell 433 26638075
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2012 Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 319 22810586
2012 Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PloS one 312 23251661
2011 Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. Immunity 286 21903422
2004 Functional proteomics mapping of a human signaling pathway. Genome research 247 15231748
2009 Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). Journal of proteome research 237 19199708
2016 An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature communications 211 27173435
2015 ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature 209 26618866
2014 Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Molecular cell 173 25544563
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2020 Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation. Cells 146 32344865
1997 A novel Rab9 effector required for endosome-to-TGN transport. The Journal of cell biology 119 9230071
2010 Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Molecular medicine (Cambridge, Mass.) 108 20379614
2021 Systematically defining selective autophagy receptor-specific cargo using autophagosome content profiling. Molecular cell 105 33545068
2000 p76(MDM2) inhibits the ability of p90(MDM2) to destabilize p53. The Journal of biological chemistry 64 10681559
2019 LINC01232 exerts oncogenic activities in pancreatic adenocarcinoma via regulation of TM9SF2. Cell death & disease 50 31541081
2020 Pooled Screens Identify GPR108 and TM9SF2 as Host Cell Factors Critical for AAV Transduction. Molecular therapy. Methods & clinical development 45 32280726
2018 Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene. Scientific reports 24 30333512
2014 The nonaspanins TM9SF2 and TM9SF4 regulate the plasma membrane localization and signalling activity of the peptidoglycan recognition protein PGRP-LC in Drosophila. Journal of innate immunity 19 25139117
2007 Biochemical characterization and lysosomal localization of the mannose-6-phosphate protein p76 (hypothetical protein LOC196463). The Biochemical journal 19 17105447
2010 Regulation of MDM4 (MDMX) function by p76(MDM2): a new facet in the control of p53 activity. Oncogene 14 20697359
2005 Caspase-9 can antagonize p53-induced apoptosis by generating a p76(Rb) truncated form of Rb. Oncogene 14 15735701
2024 Identification of sulfur metabolism-related gene signature in osteoarthritis and TM9SF2's sustenance effect on M2 macrophages' phagocytic activity. Journal of orthopaedic surgery and research 6 38218914
2010 The p76(Rb) and p100(Rb) truncated forms of the Rb protein exert antagonistic roles on cell death regulation in human cell lines. Biochemical and biophysical research communications 3 20638363
1983 A human B lymphocyte antigen (P-76) shared by B-cell chronic lymphocytic leukemia cells and hairy cell leukemia cells. Blut 1 6340759
2026 Ceramide disrupts TM9SF2-PGK1 axis to redirect PD-L1 trafficking and enhance antitumor immunity. Nature communications 0 41888515
2025 TM9SF2 Maintains Golgi Integrity and Regulates Ricin-Induced Cytotoxicity. Toxins 0 40423301
2025 [Preliminary study on the role of TM9SF2 knockdown in promoting the activity of the type I interferon signaling pathway to inhibit vesicular stomatitis virus replication]. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology 0 40525335