{"gene":"SLC9A7","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":2005,"finding":"NHE7 (SLC9A7) resides chiefly in the trans-Golgi network (TGN) and post-Golgi vesicles, and its cytoplasmic C-terminus directly interacts with SCAMP2 (and also SCAMP1 and SCAMP5) via the TM2-TM3 cytoplasmic loop of SCAMP2. This interaction regulates NHE7 trafficking between the TGN and recycling vesicles; disruption of the binding interface (SCAMP2 deletion mutant lacking residues 184-208 or a GFP-TM2-TM3 construct) causes redistribution of NHE7 to scattered recycling vesicles without affecting other TGN/Golgi markers.","method":"Yeast two-hybrid screen, co-immunolocalization, co-immunoprecipitation, sucrose density gradient co-sedimentation, in vitro protein binding assays, dominant-negative/deletion mutant overexpression","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Y2H, co-IP, in vitro binding, fractionation, dominant-negative mutants) in a single study with strong mechanistic follow-up","pmids":["15840657"],"is_preprint":false},{"year":2006,"finding":"Caveolins directly bind to the C-terminal extension of NHE7 via an unconventional binding module. NHE7 associates with caveolae/lipid raft fractions dependent on this C-terminal extension and on cholesterol; a deletion mutant lacking the C-terminal extension is excluded from caveolae/lipid rafts. NHE7 endocytosis proceeds via clathrin-dependent (not caveolar) mechanisms, as pharmacological blockade of clathrin-dependent endocytosis inhibits NHE7 internalization while dominant-negative caveolin or methyl-β-cyclodextrin does not.","method":"Co-immunoprecipitation, lipid raft fractionation, dominant-negative caveolin mutants, cholesterol-depleting drugs, deletion mutagenesis, endocytosis inhibition assays","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (co-IP, fractionation, mutagenesis, pharmacological perturbation) with functional endocytosis readout","pmids":["17207967"],"is_preprint":false},{"year":2008,"finding":"Mass spectrometry-based interactome analysis of affinity-captured NHE7 identified cytoskeletal proteins, cell adhesion molecules, membrane transporters, and signaling molecules as binding partners. Among these: (1) calcium-calmodulin (but not apo-calmodulin) binds NHE7 and regulates its organellar transporter activity; (2) vimentin co-immunoprecipitates with endogenous NHE7 and colocalizes with NHE7 at focal complexes in migrating cells; (3) CD44 shows regulated interaction with NHE7 that is enhanced by phorbol ester treatment and dependent on lipid raft integrity.","method":"Affinity capture mass spectrometry, co-immunoprecipitation, co-immunolocalization, phorbol ester treatment, lipid raft disruption","journal":"Molecular membrane biology","confidence":"Medium","confidence_rationale":"Tier 2/3 — MS interactome plus co-IP validation for specific partners, but functional follow-up is partial","pmids":["18654930"],"is_preprint":false},{"year":2014,"finding":"NHE7 transports Li+ and Na+, but not K+, and functions as a proton-loading (acidifying) transporter rather than a proton leak/alkalinizer. It is constitutively activated by cytosolic H+ and is non-reversible under physiological conditions. NHE7-mediated vesicular acidification is additive to that of V-ATPases and accelerates endocytosis. These transport parameters were established by selecting a cell line expressing wild-type NHE7 at the plasma membrane via proton-killing techniques, enabling direct functional measurements.","method":"Proton-killing selection of plasma-membrane NHE7-expressing cells, ion transport assays with Li+/Na+/K+ substitution, pH measurements, endocytosis assays, pharmacological inhibition of V-ATPase","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — direct functional transport measurements with ion substitution and rigorous controls; mechanistically defines substrate specificity and transport direction","pmids":["24767989"],"is_preprint":false},{"year":2019,"finding":"A gain-of-function missense variant (Leu515Phe) in SLC9A7 causes alkalinization of TGN/post-Golgi compartments, which impairs N-linked oligosaccharide maturation of both NHE7 itself and a co-transfected secretory glycoprotein (VSVG), while membrane trafficking to the cell surface remains relatively unaffected. Patient serum shows abnormal N-glycosylation of transferrin by mass spectrometry, establishing SLC9A7/NHE7 as a regulator of TGN/post-Golgi pH homeostasis required for proper glycosylation of exported cargo.","method":"Transfection of CHO AP-1 cells with wild-type vs. Leu515Phe mutant NHE7, organellar pH measurement, N-glycosylation assays, VSVG trafficking assay, patient serum mass spectrometry","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 1-2 — functional mutagenesis combined with organellar pH measurement, glycosylation assays, and patient biomarker validation providing multiple orthogonal lines of evidence","pmids":["30335141"],"is_preprint":false},{"year":2020,"finding":"NHE7 acidifies the Golgi lumen, and NHE7 suppression causes alkalinization of the Golgi leading to a buildup of cytosolic acid. This disruption of cytosolic pH homeostasis acts primarily through dysregulation of actin, compromising pancreatic cancer cell fitness and abolishing tumor growth in vivo.","method":"NHE7 knockdown (siRNA/shRNA), organellar and cytosolic pH measurements (biosensors), actin cytoskeleton analysis, in vivo xenograft tumor growth assays","journal":"Cancer discovery","confidence":"High","confidence_rationale":"Tier 2 — clean KD with defined pH and actin phenotypes, replicated in vivo, multiple orthogonal methods","pmids":["32200349"],"is_preprint":false},{"year":2023,"finding":"NHE7 alkalized intracellular (cytosolic) pH and acidified endosomal pH, promoting maturation of macropinosomes and thereby enhancing uptake of small extracellular vesicles (sEVs) via macropinocytosis in hepatocellular carcinoma cells. Inducible NHE7 inhibition in established tumors delayed tumor development and suppressed lung metastasis.","method":"NHE7 knockdown and overexpression, pH biosensor measurement, dextran/sEV internalization assays, EIPA pharmacological inhibition, inducible in vivo silencing","journal":"Cancer communications","confidence":"Medium","confidence_rationale":"Tier 2 — KD/OE with defined pH and macropinocytosis phenotype and in vivo validation, single lab","pmids":["38152992"],"is_preprint":false},{"year":2025,"finding":"NHE7 binds to a cAMP-related transcription factor (CREB), increasing GRIN2B expression and thereby elevating intracellular Ca2+ influx, which delays cellular senescence and promotes endometrial cancer progression in vitro and in vivo.","method":"Co-immunoprecipitation/binding assays, RNA-seq, overexpression and knockdown functional assays, xenograft mouse model, Ca2+ measurement","journal":"Communications biology","confidence":"Low","confidence_rationale":"Tier 3 — single lab, binding to CREB supported by pulldown but mechanistic pathway is partially characterized","pmids":["40473875"],"is_preprint":false},{"year":2026,"finding":"In macrophages, lactate-induced lactylation of Histone 3 at the DNMT1 promoter activates DNMT1 transcription, which then silences NHE7 gene expression. NHE7 downregulation in macrophages drives M2 polarization and senescence through MAPK pathway activation, promoting endometrial cancer progression.","method":"ChIP for histone lactylation, RT-qPCR, western blotting, NHE7 overexpression in macrophages, xenograft tumor model","journal":"Cell death & disease","confidence":"Low","confidence_rationale":"Tier 3 — single lab, mechanistic pathway relies on correlative ChIP and KD/OE without full reconstitution","pmids":["41617670"],"is_preprint":false},{"year":2011,"finding":"NHE7 dynamically shuttles between the TGN, endosomes, and the plasma membrane, and regulates the luminal pH of these organelles. NHE7 overexpression in breast cancer MDA-MB-231 cells enhances cell-cell adhesion, invasion, anchorage-independent growth, and in vivo tumor formation, distinct from NHE1 overexpression effects.","method":"NHE7 overexpression, in vitro invasion and adhesion assays, anchorage-independent growth assay, in vivo xenograft tumor formation","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2/3 — gain-of-function with multiple functional cellular readouts; subcellular localization established by prior work cited in the paper","pmids":["22076128"],"is_preprint":false}],"current_model":"SLC9A7/NHE7 is a (Na+)/H+ exchanger (transporting Na+ and Li+, but not K+) that localizes primarily to the trans-Golgi network and post-Golgi vesicles, where it acidifies the lumen to regulate organellar and cytosolic pH homeostasis, proper N-linked glycosylation of secretory cargo, endocytic/macropinocytic vesicle maturation, and actin cytoskeleton integrity; its trafficking between the TGN and recycling vesicles is regulated by direct interactions with SCAMP family members (via their TM2-TM3 loop) and caveolins (via its C-terminal extension), while calmodulin (Ca2+-bound), vimentin, and CD44 modulate its activity and membrane domain association."},"narrative":{"teleology":[{"year":2005,"claim":"Establishing where NHE7 resides and how it is retained there resolved its organellar identity and revealed a SCAMP-dependent trafficking mechanism controlling TGN versus recycling-vesicle distribution.","evidence":"Yeast two-hybrid, co-IP, in vitro binding, and dominant-negative mutant overexpression in mammalian cells","pmids":["15840657"],"confidence":"High","gaps":["Signal or motif within NHE7 that mediates TGN retention was not mapped","Whether SCAMP interaction regulates NHE7 transport activity (not just localization) was untested","Physiological trigger for NHE7 redistribution to recycling vesicles was unknown"]},{"year":2006,"claim":"Defining how NHE7 associates with lipid raft/caveolar domains via its C-terminal extension, while undergoing clathrin-dependent (not caveolar) endocytosis, separated its membrane-domain partitioning from its internalization route.","evidence":"Co-IP with caveolins, lipid raft fractionation, deletion mutagenesis, clathrin and caveolin pathway inhibitors","pmids":["17207967"],"confidence":"High","gaps":["Functional consequence of caveolar association for NHE7 transport activity was not determined","Identity of the clathrin adaptor(s) mediating NHE7 endocytosis was not identified"]},{"year":2008,"claim":"An interactome survey revealed that Ca²⁺-calmodulin regulates NHE7 activity and that vimentin and CD44 are context-dependent binding partners, broadening the regulatory network beyond SCAMPs and caveolins.","evidence":"Affinity-capture mass spectrometry with co-IP and co-localization validation","pmids":["18654930"],"confidence":"Medium","gaps":["Calmodulin-binding site on NHE7 was not mapped","Functional significance of vimentin and CD44 interactions for NHE7 transport or trafficking was not established","Interactome was from a single purification approach without reciprocal validation for most hits"]},{"year":2014,"claim":"Direct measurement of NHE7 ion selectivity and transport direction established it as a proton-loading (luminal-acidifying), Na⁺/Li⁺-selective, constitutively H⁺-activated exchanger that works additively with V-ATPases, settling prior ambiguity about whether organellar NHEs alkalinize or acidify.","evidence":"Proton-killing selection for plasma-membrane NHE7, ion substitution transport assays, organellar pH biosensors, V-ATPase inhibition","pmids":["24767989"],"confidence":"High","gaps":["Structural basis of Na⁺/Li⁺ selectivity and K⁺ exclusion was unknown","Relative contribution of NHE7 versus V-ATPase to steady-state TGN pH in native cells was not quantified"]},{"year":2019,"claim":"A patient-derived gain-of-function Leu515Phe variant demonstrated that NHE7-dependent TGN pH is essential for N-linked glycosylation of secretory cargo, directly linking NHE7 dysfunction to a congenital disorder of glycosylation.","evidence":"Mutant versus wild-type transfection in CHO cells, organellar pH measurement, glycosylation assays, patient serum transferrin mass spectrometry","pmids":["30335141"],"confidence":"High","gaps":["How Leu515Phe mechanistically alters transporter kinetics or gating was not resolved","Whether other TGN-resident glycosyltransferases are differentially affected was not tested","Number of patients studied was limited"]},{"year":2020,"claim":"NHE7 suppression revealed that its Golgi-acidifying activity is required to prevent cytosolic acid accumulation and actin dysregulation, establishing the first mechanistic link between NHE7 loss and cancer cell fitness.","evidence":"siRNA/shRNA knockdown, pH biosensors, actin cytoskeleton analysis, in vivo xenograft tumor growth in pancreatic cancer cells","pmids":["32200349"],"confidence":"High","gaps":["Molecular pathway connecting cytosolic acidification to actin disruption was not delineated","Whether NHE7 loss similarly affects non-transformed cells was not addressed"]},{"year":2023,"claim":"NHE7 was shown to acidify endosomal compartments and promote macropinosome maturation, providing a mechanism by which NHE7 enhances extracellular vesicle uptake and supports hepatocellular carcinoma metastasis.","evidence":"KD/OE with pH biosensors, dextran and sEV internalization assays, inducible in vivo silencing in hepatocellular carcinoma","pmids":["38152992"],"confidence":"Medium","gaps":["Whether NHE7 acts on macropinosomes directly or via general endosomal pH alteration was not distinguished","Contribution of NHE7 to macropinocytosis in non-cancer contexts was not tested"]},{"year":2025,"claim":"A reported interaction between NHE7 and the transcription factor CREB, leading to GRIN2B upregulation and Ca²⁺ influx that delays senescence, suggested a non-canonical role for NHE7 in transcriptional regulation in endometrial cancer.","evidence":"Co-IP/binding assays, RNA-seq, KD/OE, xenograft model, Ca²⁺ measurement in endometrial cancer cells","pmids":["40473875"],"confidence":"Low","gaps":["NHE7–CREB interaction lacks independent confirmation and the mechanism by which a membrane transporter engages a nuclear transcription factor is unexplained","Whether ion transport activity is required for this effect was not tested","Single-lab finding with no reciprocal validation"]},{"year":null,"claim":"Key unresolved questions include the structural basis of NHE7 ion selectivity and non-reversibility, the precise molecular link between Golgi pH perturbation and actin dysregulation, and whether the reported NHE7–CREB interaction represents a bona fide non-canonical function or an indirect effect.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of NHE7 is available","Mechanism coupling cytosolic acidification to actin remodeling upon NHE7 loss is undefined","Role of NHE7 in normal physiology beyond cancer contexts is poorly characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[3,4,5,6]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0,4,5]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,3,6]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[6,9]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1,3,9]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[3,4,5,6]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4]}],"complexes":[],"partners":["SCAMP2","SCAMP1","SCAMP5","CAV1","CALM1","VIM","CD44"],"other_free_text":[]},"mechanistic_narrative":"SLC9A7 (NHE7) is an organellar Na⁺(Li⁺)/H⁺ exchanger that acidifies the lumen of the trans-Golgi network and post-Golgi vesicles, functioning additively with V-ATPases to maintain compartmental and cytosolic pH homeostasis [PMID:24767989, PMID:32200349]. It transports Na⁺ and Li⁺ but not K⁺, is constitutively activated by cytosolic H⁺, and operates non-reversibly under physiological conditions; its luminal acidification is required for proper N-linked glycosylation of secretory cargo in the TGN, and a gain-of-function Leu515Phe variant causes TGN alkalinization and defective glycosylation in patients [PMID:24767989, PMID:30335141]. NHE7 trafficking between the TGN and recycling vesicles is governed by direct interaction of its cytoplasmic C-terminus with SCAMP family proteins and caveolins, while Ca²⁺-calmodulin regulates its transport activity [PMID:15840657, PMID:17207967, PMID:18654930]. Loss of NHE7-mediated Golgi acidification disrupts cytosolic pH and actin cytoskeleton integrity, and NHE7 promotes macropinosome maturation through endosomal acidification, linking its ion-transport function to vesicle trafficking, cell migration, and tumor growth [PMID:32200349, PMID:38152992]."},"prefetch_data":{"uniprot":{"accession":"Q96T83","full_name":"Sodium/hydrogen exchanger 7","aliases":["Na(+)/H(+) exchanger 7","NHE-7","Solute carrier family 9 member 7"],"length_aa":725,"mass_kda":80.1,"function":"Golgi Na(+), K(+)/(H+) antiporter. Mediates the electoneutral influx of Na(+) or K(+) in exchange for H(+). May contribute to the regulation of Golgi apparatus volume and pH","subcellular_location":"Golgi apparatus, trans-Golgi network membrane; Recycling endosome membrane; Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q96T83/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SLC9A7","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SLC9A7","total_profiled":1310},"omim":[{"mim_id":"614997","title":"GATA ZINC FINGER DOMAIN-CONTAINING PROTEIN 2A; GATAD2A","url":"https://www.omim.org/entry/614997"},{"mim_id":"608396","title":"SOLUTE CARRIER FAMILY 9 (SODIUM/HYDROGEN EXCHANGER), MEMBER 9; SLC9A9","url":"https://www.omim.org/entry/608396"},{"mim_id":"301024","title":"INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 108; XLID108","url":"https://www.omim.org/entry/301024"},{"mim_id":"300578","title":"CHROMOSOME Xp11.3 DELETION SYNDROME","url":"https://www.omim.org/entry/300578"},{"mim_id":"300368","title":"SOLUTE CARRIER FAMILY 9, MEMBER 7; SLC9A7","url":"https://www.omim.org/entry/300368"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":28.7}],"url":"https://www.proteinatlas.org/search/SLC9A7"},"hgnc":{"alias_symbol":["NHE7","NHE-7"],"prev_symbol":[]},"alphafold":{"accession":"Q96T83","domains":[{"cath_id":"1.20.1530.20","chopping":"179-534","consensus_level":"high","plddt":86.3454,"start":179,"end":534}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96T83","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96T83-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96T83-F1-predicted_aligned_error_v6.png","plddt_mean":67.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SLC9A7","jax_strain_url":"https://www.jax.org/strain/search?query=SLC9A7"},"sequence":{"accession":"Q96T83","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96T83.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96T83/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96T83"}},"corpus_meta":[{"pmid":"15840657","id":"PMC_15840657","title":"Secretory carrier membrane proteins interact and regulate trafficking of the organellar (Na+,K+)/H+ exchanger NHE7.","date":"2005","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/15840657","citation_count":56,"is_preprint":false},{"pmid":"32200349","id":"PMC_32200349","title":"Golgi Acidification by NHE7 Regulates Cytosolic pH Homeostasis in Pancreatic Cancer Cells.","date":"2020","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/32200349","citation_count":45,"is_preprint":false},{"pmid":"24767989","id":"PMC_24767989","title":"The intracellular Na(+)/H(+) exchanger NHE7 effects a Na(+)-coupled, but not K(+)-coupled proton-loading mechanism in endocytosis.","date":"2014","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/24767989","citation_count":36,"is_preprint":false},{"pmid":"22076128","id":"PMC_22076128","title":"Organellar (Na+, K+)/H+ exchanger NHE7 regulates cell adhesion, invasion and anchorage-independent growth of breast cancer MDA-MB-231 cells.","date":"2011","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/22076128","citation_count":27,"is_preprint":false},{"pmid":"30335141","id":"PMC_30335141","title":"A recurrent missense variant in SLC9A7 causes nonsyndromic X-linked intellectual disability with alteration of Golgi acidification and aberrant glycosylation.","date":"2019","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30335141","citation_count":27,"is_preprint":false},{"pmid":"18654930","id":"PMC_18654930","title":"Identification and biochemical characterization of the SLC9A7 interactome.","date":"2008","source":"Molecular membrane biology","url":"https://pubmed.ncbi.nlm.nih.gov/18654930","citation_count":22,"is_preprint":false},{"pmid":"17207967","id":"PMC_17207967","title":"Caveolins bind to (Na+, K+)/H+ exchanger NHE7 by a novel binding module.","date":"2006","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/17207967","citation_count":18,"is_preprint":false},{"pmid":"20696265","id":"PMC_20696265","title":"Ammonia uptake in Manduca sexta midgut is mediated by an amiloride sensitive cation/proton exchanger: Transport studies and mRNA expression analysis of NHE7, 9, NHE8, and V-ATPase (subunit D).","date":"2010","source":"Comparative biochemistry and physiology. Part A, Molecular & integrative physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20696265","citation_count":16,"is_preprint":false},{"pmid":"38152992","id":"PMC_38152992","title":"NHE7 upregulation potentiates the uptake of small extracellular vesicles by enhancing maturation of macropinosomes in hepatocellular carcinoma.","date":"2023","source":"Cancer communications (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/38152992","citation_count":10,"is_preprint":false},{"pmid":"37970357","id":"PMC_37970357","title":"Inhibition of Na+/H+ exchanger (NHE) 7 by 5-(N-ethyl-N-isopropyl)-Amiloride displays anti-cancer activity in non-small cell lung cancer by disrupting cancer stem cell activity and downregulating PD-L1 expression.","date":"2023","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/37970357","citation_count":10,"is_preprint":false},{"pmid":"40473875","id":"PMC_40473875","title":"NHE7 drives endometrial cancer progression by delaying senescence through cAMP/CREB/GRIN2B axis-mediated Ca²⁺ influx.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40473875","citation_count":4,"is_preprint":false},{"pmid":"41617670","id":"PMC_41617670","title":"Lactate transmission from hypoxic tumor cells promotes macrophage senescence and M2 polarization via the DNMT1-NHE7 axis to accelerate endometrial cancer progression.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/41617670","citation_count":0,"is_preprint":false},{"pmid":"41575611","id":"PMC_41575611","title":"Hypoxic glycolysis-driven histone lactylation activates NHE7 to promote endometrial cancer progression via COX6C-mediated endoplasmic reticulum stress.","date":"2026","source":"Apoptosis : an international journal on programmed cell death","url":"https://pubmed.ncbi.nlm.nih.gov/41575611","citation_count":0,"is_preprint":false},{"pmid":"41451488","id":"PMC_41451488","title":"[Pathogenicity analysis and genetic counseling for a hemizygous c.1042-10G>C variant of SLC9A7 gene].","date":"2025","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41451488","citation_count":0,"is_preprint":false},{"pmid":"38818559","id":"PMC_38818559","title":"[Clinical and genetic analysis of a child with X-linked mental retardation due to variant of SLC9A7 gene].","date":"2024","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38818559","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9429,"output_tokens":2961,"usd":0.036351},"stage2":{"model":"claude-opus-4-6","input_tokens":6273,"output_tokens":2657,"usd":0.146685},"total_usd":0.183036,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"NHE7 (SLC9A7) resides chiefly in the trans-Golgi network (TGN) and post-Golgi vesicles, and its cytoplasmic C-terminus directly interacts with SCAMP2 (and also SCAMP1 and SCAMP5) via the TM2-TM3 cytoplasmic loop of SCAMP2. This interaction regulates NHE7 trafficking between the TGN and recycling vesicles; disruption of the binding interface (SCAMP2 deletion mutant lacking residues 184-208 or a GFP-TM2-TM3 construct) causes redistribution of NHE7 to scattered recycling vesicles without affecting other TGN/Golgi markers.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunolocalization, co-immunoprecipitation, sucrose density gradient co-sedimentation, in vitro protein binding assays, dominant-negative/deletion mutant overexpression\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Y2H, co-IP, in vitro binding, fractionation, dominant-negative mutants) in a single study with strong mechanistic follow-up\",\n      \"pmids\": [\"15840657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Caveolins directly bind to the C-terminal extension of NHE7 via an unconventional binding module. NHE7 associates with caveolae/lipid raft fractions dependent on this C-terminal extension and on cholesterol; a deletion mutant lacking the C-terminal extension is excluded from caveolae/lipid rafts. NHE7 endocytosis proceeds via clathrin-dependent (not caveolar) mechanisms, as pharmacological blockade of clathrin-dependent endocytosis inhibits NHE7 internalization while dominant-negative caveolin or methyl-β-cyclodextrin does not.\",\n      \"method\": \"Co-immunoprecipitation, lipid raft fractionation, dominant-negative caveolin mutants, cholesterol-depleting drugs, deletion mutagenesis, endocytosis inhibition assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (co-IP, fractionation, mutagenesis, pharmacological perturbation) with functional endocytosis readout\",\n      \"pmids\": [\"17207967\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Mass spectrometry-based interactome analysis of affinity-captured NHE7 identified cytoskeletal proteins, cell adhesion molecules, membrane transporters, and signaling molecules as binding partners. Among these: (1) calcium-calmodulin (but not apo-calmodulin) binds NHE7 and regulates its organellar transporter activity; (2) vimentin co-immunoprecipitates with endogenous NHE7 and colocalizes with NHE7 at focal complexes in migrating cells; (3) CD44 shows regulated interaction with NHE7 that is enhanced by phorbol ester treatment and dependent on lipid raft integrity.\",\n      \"method\": \"Affinity capture mass spectrometry, co-immunoprecipitation, co-immunolocalization, phorbol ester treatment, lipid raft disruption\",\n      \"journal\": \"Molecular membrane biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — MS interactome plus co-IP validation for specific partners, but functional follow-up is partial\",\n      \"pmids\": [\"18654930\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NHE7 transports Li+ and Na+, but not K+, and functions as a proton-loading (acidifying) transporter rather than a proton leak/alkalinizer. It is constitutively activated by cytosolic H+ and is non-reversible under physiological conditions. NHE7-mediated vesicular acidification is additive to that of V-ATPases and accelerates endocytosis. These transport parameters were established by selecting a cell line expressing wild-type NHE7 at the plasma membrane via proton-killing techniques, enabling direct functional measurements.\",\n      \"method\": \"Proton-killing selection of plasma-membrane NHE7-expressing cells, ion transport assays with Li+/Na+/K+ substitution, pH measurements, endocytosis assays, pharmacological inhibition of V-ATPase\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct functional transport measurements with ion substitution and rigorous controls; mechanistically defines substrate specificity and transport direction\",\n      \"pmids\": [\"24767989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A gain-of-function missense variant (Leu515Phe) in SLC9A7 causes alkalinization of TGN/post-Golgi compartments, which impairs N-linked oligosaccharide maturation of both NHE7 itself and a co-transfected secretory glycoprotein (VSVG), while membrane trafficking to the cell surface remains relatively unaffected. Patient serum shows abnormal N-glycosylation of transferrin by mass spectrometry, establishing SLC9A7/NHE7 as a regulator of TGN/post-Golgi pH homeostasis required for proper glycosylation of exported cargo.\",\n      \"method\": \"Transfection of CHO AP-1 cells with wild-type vs. Leu515Phe mutant NHE7, organellar pH measurement, N-glycosylation assays, VSVG trafficking assay, patient serum mass spectrometry\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — functional mutagenesis combined with organellar pH measurement, glycosylation assays, and patient biomarker validation providing multiple orthogonal lines of evidence\",\n      \"pmids\": [\"30335141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NHE7 acidifies the Golgi lumen, and NHE7 suppression causes alkalinization of the Golgi leading to a buildup of cytosolic acid. This disruption of cytosolic pH homeostasis acts primarily through dysregulation of actin, compromising pancreatic cancer cell fitness and abolishing tumor growth in vivo.\",\n      \"method\": \"NHE7 knockdown (siRNA/shRNA), organellar and cytosolic pH measurements (biosensors), actin cytoskeleton analysis, in vivo xenograft tumor growth assays\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KD with defined pH and actin phenotypes, replicated in vivo, multiple orthogonal methods\",\n      \"pmids\": [\"32200349\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NHE7 alkalized intracellular (cytosolic) pH and acidified endosomal pH, promoting maturation of macropinosomes and thereby enhancing uptake of small extracellular vesicles (sEVs) via macropinocytosis in hepatocellular carcinoma cells. Inducible NHE7 inhibition in established tumors delayed tumor development and suppressed lung metastasis.\",\n      \"method\": \"NHE7 knockdown and overexpression, pH biosensor measurement, dextran/sEV internalization assays, EIPA pharmacological inhibition, inducible in vivo silencing\",\n      \"journal\": \"Cancer communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD/OE with defined pH and macropinocytosis phenotype and in vivo validation, single lab\",\n      \"pmids\": [\"38152992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NHE7 binds to a cAMP-related transcription factor (CREB), increasing GRIN2B expression and thereby elevating intracellular Ca2+ influx, which delays cellular senescence and promotes endometrial cancer progression in vitro and in vivo.\",\n      \"method\": \"Co-immunoprecipitation/binding assays, RNA-seq, overexpression and knockdown functional assays, xenograft mouse model, Ca2+ measurement\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, binding to CREB supported by pulldown but mechanistic pathway is partially characterized\",\n      \"pmids\": [\"40473875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In macrophages, lactate-induced lactylation of Histone 3 at the DNMT1 promoter activates DNMT1 transcription, which then silences NHE7 gene expression. NHE7 downregulation in macrophages drives M2 polarization and senescence through MAPK pathway activation, promoting endometrial cancer progression.\",\n      \"method\": \"ChIP for histone lactylation, RT-qPCR, western blotting, NHE7 overexpression in macrophages, xenograft tumor model\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, mechanistic pathway relies on correlative ChIP and KD/OE without full reconstitution\",\n      \"pmids\": [\"41617670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NHE7 dynamically shuttles between the TGN, endosomes, and the plasma membrane, and regulates the luminal pH of these organelles. NHE7 overexpression in breast cancer MDA-MB-231 cells enhances cell-cell adhesion, invasion, anchorage-independent growth, and in vivo tumor formation, distinct from NHE1 overexpression effects.\",\n      \"method\": \"NHE7 overexpression, in vitro invasion and adhesion assays, anchorage-independent growth assay, in vivo xenograft tumor formation\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — gain-of-function with multiple functional cellular readouts; subcellular localization established by prior work cited in the paper\",\n      \"pmids\": [\"22076128\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SLC9A7/NHE7 is a (Na+)/H+ exchanger (transporting Na+ and Li+, but not K+) that localizes primarily to the trans-Golgi network and post-Golgi vesicles, where it acidifies the lumen to regulate organellar and cytosolic pH homeostasis, proper N-linked glycosylation of secretory cargo, endocytic/macropinocytic vesicle maturation, and actin cytoskeleton integrity; its trafficking between the TGN and recycling vesicles is regulated by direct interactions with SCAMP family members (via their TM2-TM3 loop) and caveolins (via its C-terminal extension), while calmodulin (Ca2+-bound), vimentin, and CD44 modulate its activity and membrane domain association.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SLC9A7 (NHE7) is an organellar Na⁺(Li⁺)/H⁺ exchanger that acidifies the lumen of the trans-Golgi network and post-Golgi vesicles, functioning additively with V-ATPases to maintain compartmental and cytosolic pH homeostasis [PMID:24767989, PMID:32200349]. It transports Na⁺ and Li⁺ but not K⁺, is constitutively activated by cytosolic H⁺, and operates non-reversibly under physiological conditions; its luminal acidification is required for proper N-linked glycosylation of secretory cargo in the TGN, and a gain-of-function Leu515Phe variant causes TGN alkalinization and defective glycosylation in patients [PMID:24767989, PMID:30335141]. NHE7 trafficking between the TGN and recycling vesicles is governed by direct interaction of its cytoplasmic C-terminus with SCAMP family proteins and caveolins, while Ca²⁺-calmodulin regulates its transport activity [PMID:15840657, PMID:17207967, PMID:18654930]. Loss of NHE7-mediated Golgi acidification disrupts cytosolic pH and actin cytoskeleton integrity, and NHE7 promotes macropinosome maturation through endosomal acidification, linking its ion-transport function to vesicle trafficking, cell migration, and tumor growth [PMID:32200349, PMID:38152992].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing where NHE7 resides and how it is retained there resolved its organellar identity and revealed a SCAMP-dependent trafficking mechanism controlling TGN versus recycling-vesicle distribution.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, in vitro binding, and dominant-negative mutant overexpression in mammalian cells\",\n      \"pmids\": [\"15840657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Signal or motif within NHE7 that mediates TGN retention was not mapped\",\n        \"Whether SCAMP interaction regulates NHE7 transport activity (not just localization) was untested\",\n        \"Physiological trigger for NHE7 redistribution to recycling vesicles was unknown\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defining how NHE7 associates with lipid raft/caveolar domains via its C-terminal extension, while undergoing clathrin-dependent (not caveolar) endocytosis, separated its membrane-domain partitioning from its internalization route.\",\n      \"evidence\": \"Co-IP with caveolins, lipid raft fractionation, deletion mutagenesis, clathrin and caveolin pathway inhibitors\",\n      \"pmids\": [\"17207967\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of caveolar association for NHE7 transport activity was not determined\",\n        \"Identity of the clathrin adaptor(s) mediating NHE7 endocytosis was not identified\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"An interactome survey revealed that Ca²⁺-calmodulin regulates NHE7 activity and that vimentin and CD44 are context-dependent binding partners, broadening the regulatory network beyond SCAMPs and caveolins.\",\n      \"evidence\": \"Affinity-capture mass spectrometry with co-IP and co-localization validation\",\n      \"pmids\": [\"18654930\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Calmodulin-binding site on NHE7 was not mapped\",\n        \"Functional significance of vimentin and CD44 interactions for NHE7 transport or trafficking was not established\",\n        \"Interactome was from a single purification approach without reciprocal validation for most hits\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Direct measurement of NHE7 ion selectivity and transport direction established it as a proton-loading (luminal-acidifying), Na⁺/Li⁺-selective, constitutively H⁺-activated exchanger that works additively with V-ATPases, settling prior ambiguity about whether organellar NHEs alkalinize or acidify.\",\n      \"evidence\": \"Proton-killing selection for plasma-membrane NHE7, ion substitution transport assays, organellar pH biosensors, V-ATPase inhibition\",\n      \"pmids\": [\"24767989\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of Na⁺/Li⁺ selectivity and K⁺ exclusion was unknown\",\n        \"Relative contribution of NHE7 versus V-ATPase to steady-state TGN pH in native cells was not quantified\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"A patient-derived gain-of-function Leu515Phe variant demonstrated that NHE7-dependent TGN pH is essential for N-linked glycosylation of secretory cargo, directly linking NHE7 dysfunction to a congenital disorder of glycosylation.\",\n      \"evidence\": \"Mutant versus wild-type transfection in CHO cells, organellar pH measurement, glycosylation assays, patient serum transferrin mass spectrometry\",\n      \"pmids\": [\"30335141\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How Leu515Phe mechanistically alters transporter kinetics or gating was not resolved\",\n        \"Whether other TGN-resident glycosyltransferases are differentially affected was not tested\",\n        \"Number of patients studied was limited\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"NHE7 suppression revealed that its Golgi-acidifying activity is required to prevent cytosolic acid accumulation and actin dysregulation, establishing the first mechanistic link between NHE7 loss and cancer cell fitness.\",\n      \"evidence\": \"siRNA/shRNA knockdown, pH biosensors, actin cytoskeleton analysis, in vivo xenograft tumor growth in pancreatic cancer cells\",\n      \"pmids\": [\"32200349\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular pathway connecting cytosolic acidification to actin disruption was not delineated\",\n        \"Whether NHE7 loss similarly affects non-transformed cells was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"NHE7 was shown to acidify endosomal compartments and promote macropinosome maturation, providing a mechanism by which NHE7 enhances extracellular vesicle uptake and supports hepatocellular carcinoma metastasis.\",\n      \"evidence\": \"KD/OE with pH biosensors, dextran and sEV internalization assays, inducible in vivo silencing in hepatocellular carcinoma\",\n      \"pmids\": [\"38152992\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether NHE7 acts on macropinosomes directly or via general endosomal pH alteration was not distinguished\",\n        \"Contribution of NHE7 to macropinocytosis in non-cancer contexts was not tested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A reported interaction between NHE7 and the transcription factor CREB, leading to GRIN2B upregulation and Ca²⁺ influx that delays senescence, suggested a non-canonical role for NHE7 in transcriptional regulation in endometrial cancer.\",\n      \"evidence\": \"Co-IP/binding assays, RNA-seq, KD/OE, xenograft model, Ca²⁺ measurement in endometrial cancer cells\",\n      \"pmids\": [\"40473875\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"NHE7–CREB interaction lacks independent confirmation and the mechanism by which a membrane transporter engages a nuclear transcription factor is unexplained\",\n        \"Whether ion transport activity is required for this effect was not tested\",\n        \"Single-lab finding with no reciprocal validation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of NHE7 ion selectivity and non-reversibility, the precise molecular link between Golgi pH perturbation and actin dysregulation, and whether the reported NHE7–CREB interaction represents a bona fide non-canonical function or an indirect effect.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of NHE7 is available\",\n        \"Mechanism coupling cytosolic acidification to actin remodeling upon NHE7 loss is undefined\",\n        \"Role of NHE7 in normal physiology beyond cancer contexts is poorly characterized\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [3, 4, 5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 4, 5]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 3, 6]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1, 3, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [3, 4, 5, 6]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SCAMP2\",\n      \"SCAMP1\",\n      \"SCAMP5\",\n      \"CAV1\",\n      \"CALM1\",\n      \"VIM\",\n      \"CD44\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}