{"gene":"COX7A2L","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2016,"finding":"COX7A2L binds primarily to free mitochondrial complex III and, to a minor extent, to complex IV, specifically promoting stabilization of the III2+IV supercomplex without affecting respirasome (I+III2+IV) formation or the biogenesis, stabilization, and function of individual OXPHOS complexes.","method":"Native gel electrophoresis, co-immunoprecipitation, and functional respiratory assays in human and mouse cells","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, multiple orthogonal methods (BN-PAGE, Co-IP, functional assays), replicated across human and mouse systems, consistent with findings from multiple independent labs","pmids":["27545886"],"is_preprint":false},{"year":2014,"finding":"The short COX7a2l isoform present in C57BL/6 mice does not prevent formation of complex IV-containing supercomplexes or respirasomes; supercomplex organization is independent of COX7a2l isoforms in mice. Loss of complex IV (via Lrpprc knockout) compromises respirasome formation.","method":"Multiple complementary experimental approaches including BN-PAGE, respirometry, and mouse knockout of Lrpprc in mice with different COX7a2l isoforms","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods, genetic epistasis via Lrpprc knockout, independent replication across mouse strains","pmids":["25470551"],"is_preprint":false},{"year":2018,"finding":"COX7A2L-knockout (KO) HEK293T and U87 cells lack SC III2+IV but show enhanced complex III steady-state levels, activity, and assembly rate, normal de novo complex IV biogenesis, and delayed but ultimately normal respirasome steady-state levels; only larger megacomplexes (SCs I1-2+III2+IV2-n) were absent. Functional substrate-driven competition assays showed normal mitochondrial respiration under standard and stress conditions in COX7A2L-KO cells.","method":"CRISPR-Cas9 knockout, BN-PAGE, in-gel activity assays, radioactive pulse-chase assembly assays, Seahorse respirometry under multiple stress conditions","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — clean genetic KO with multiple orthogonal methods, two independent cell lines, functional respiratory assays, replicated findings consistent with other labs","pmids":["30428348"],"is_preprint":false},{"year":2021,"finding":"SILAC-based complexome profiling of SCAFI (COX7A2L) knockout HEK293T cells showed preferential loss of SC III2+IV and a minor subset of respirasomes, without affecting OXPHOS function. Approximately 70% of respirasomes in wild-type cells contain COX7A2 (not SCAFI) and are present at similar levels in SCAFI-KO cells, demonstrating co-existence of structurally distinct respirasomes defined by preferential binding of complex IV via COX7A2 rather than SCAFI.","method":"SILAC-based complexome profiling, CRISPR-Cas9 knockout, quantitative mass spectrometry","journal":"Biochimica et biophysica acta. Bioenergetics","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — quantitative proteomics with SILAC, CRISPR KO, complexome profiling providing direct structural resolution of supercomplex composition","pmids":["33727070"],"is_preprint":false},{"year":2016,"finding":"In liver mitochondria of C57BL/6 mice (which lack functional SCAFI/COX7A2L protein due to a 6-bp deletion), complex IV is mainly present as monomers and dimers with only low amounts found in combination with complexes I and III, and the main supercomplex comprises only complexes I and III — supporting a role for COX7A2L/SCAFI in incorporating complex IV into supercomplexes. SCAFI heterozygosity reduced SCAFI protein but did not affect respirasome assembly.","method":"BN-PAGE, immunoblotting, comparison of mice with different SCAFI isoforms on Bcs1l mutant background","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — BN-PAGE with genetically defined mouse strains, single lab, two complementary genetic backgrounds","pmids":["27997587"],"is_preprint":false},{"year":2016,"finding":"COX7AR (COX7A2L) is incorporated into the mitochondrial COX complex under cellular stress that stimulates energy metabolism. Gain- and loss-of-function analysis demonstrated that COX7AR is required for human breast cancer cells to maintain higher rates of proliferation, clone formation, and invasion, and promotes cellular energy production in human mammary epithelial cells.","method":"Gain- and loss-of-function (overexpression/siRNA knockdown), cellular energy production assays (OCR/ECAR), proliferation/invasion assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — gain and loss-of-function with defined phenotypic readouts, single lab, functional energy assays","pmids":["27550821"],"is_preprint":false},{"year":2022,"finding":"A 10-bp insertion in the COX7A2L 3' UTR increases mRNA stability and expression; human myotubes harboring this insertion have more supercomplexes and increased respiration. Specific reconstitution of Cox7a2l expression in C57BL/6J mice leads to higher maximal oxygen consumption, increased lean mass, and increased energy expenditure. Cox7a2l expression is induced specifically in mouse muscle upon exercise.","method":"cis-eQTL mapping, mRNA stability assays, Seahorse respirometry in human myotubes, Cox7a2l reconstitution in mice with metabolic phenotyping, BN-PAGE for supercomplex quantification","journal":"Nature metabolism","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods including genetic reconstitution in mice, human myotube functional assays, mRNA stability experiments, and metabolic phenotyping","pmids":["36253618"],"is_preprint":false},{"year":2025,"finding":"COX7RP (COX7A2L)-transgenic mice show elevated ATP and NAD+ levels, reduced ROS production, decreased senescence-associated β-galactosidase levels, and significant lifespan extension. snRNA-seq revealed downregulation of senescence-associated secretory phenotype (SASP) genes in old COX7RP-Tg white adipose tissue adipocytes.","method":"Transgenic mouse model, metabolic biochemistry (ATP, NAD+, ROS), β-galactosidase senescence assay, single-nucleus RNA sequencing","journal":"Aging cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transgenic mouse model with multiple biochemical readouts, single lab, no independent replication yet","pmids":["41253741"],"is_preprint":false},{"year":2024,"finding":"COX7A2L protein significantly accumulates in III2+IV1 respiratory supercomplexes specifically following sprint-interval training (SIT) but not moderate-intensity continuous training (MICT) in human skeletal muscle, indicating exercise-mode-specific regulation of COX7A2L incorporation into supercomplexes.","method":"Quantitative proteomics/complexome profiling of human skeletal muscle biopsies after 8-week training interventions","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — complexome profiling in human biopsies, single study, preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.12.19.629456"],"is_preprint":true},{"year":2024,"finding":"TCF4 transcriptionally regulates COX7A2L expression; TCF4 overexpression increases COX7A2L levels, and COX7A2L knockdown counteracts TCF4-induced promotion of Wnt/β-catenin signaling pathway proteins (c-myc, β-catenin, cyclin D1) and apoptosis in hypoxia/reoxygenation-treated cells.","method":"Overexpression and knockdown experiments, rescue assays, Western blotting for Wnt/β-catenin pathway proteins, apoptosis and proliferation assays","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single set of methods, in vitro only, no direct demonstration of TCF4 binding to COX7A2L promoter","pmids":["39499704"],"is_preprint":false},{"year":2025,"finding":"Overexpression and knockdown of COX7A2L in human AC16 cardiomyocytes did not significantly affect cell viability or mitochondrial function (oxygen consumption rate parameters), even under isoproterenol-stimulated increased energy demand — a negative result.","method":"Overexpression and knockdown validated by sandwich ELISA, MTT assay, Seahorse XF Cell Mito Stress Test with isoproterenol stimulation","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — validated overexpression/knockdown, Seahorse functional assay, but negative result in a single cell type; does not rule out effects in other contexts","pmids":["40560843"],"is_preprint":false}],"current_model":"COX7A2L (also known as COX7RP/SCAFI/SIG81/COX7AR) is a mitochondrial protein that binds preferentially to free complex III (and to a lesser extent complex IV) to specifically promote assembly and stabilization of the III2+IV supercomplex, while the majority of respirasomes (I+III2+IVn) are assembled via COX7A2 rather than COX7A2L; COX7A2L is dispensable for individual complex biogenesis and baseline OXPHOS function, but its expression level — regulated by a 3' UTR insertion variant and induced by exercise — modulates supercomplex abundance, mitochondrial respiration efficiency, metabolic parameters including ATP and NAD+ levels, and ultimately cardiorespiratory fitness and longevity in mammals."},"narrative":{"mechanistic_narrative":"COX7A2L is a mitochondrial inner-membrane protein that governs the assembly of respiratory chain supercomplexes by binding preferentially to free complex III and, to a lesser extent, complex IV, thereby specifically promoting formation and stabilization of the III2+IV supercomplex [PMID:27545886]. Its action is selective rather than essential: COX7A2L is dispensable for the biogenesis, stability, and function of individual OXPHOS complexes, and the bulk of respirasomes (I+III2+IV) assemble independently of it, with roughly 70% of wild-type respirasomes incorporating complex IV via COX7A2 rather than COX7A2L [PMID:27545886, PMID:30428348, PMID:33727070]. Consistent with this, knockout cells lose SC III2+IV and the largest megacomplexes while retaining near-normal respiration, and mice lacking functional COX7A2L still form respirasomes [PMID:30428348, PMID:27997587]. The functional relevance of COX7A2L lies in dose-dependent modulation of supercomplex abundance: a 3' UTR insertion variant that raises mRNA stability and expression increases supercomplexes and respiration in human myotubes, and reconstituting Cox7a2l in deficient mice raises maximal oxygen consumption, lean mass, and energy expenditure, with expression induced in muscle by exercise [PMID:36253618]. Sustained elevation of COX7A2L raises ATP and NAD+ levels, lowers ROS and cellular senescence markers, and extends lifespan in transgenic mice [PMID:41253741]. COX7A2L is also recruited into the COX complex under metabolic stress and supports proliferation and energy production in breast cancer and mammary epithelial cells [PMID:27550821].","teleology":[{"year":2014,"claim":"Established that respirasome and complex IV-supercomplex organization can proceed independently of COX7A2L isoform status, challenging the idea that COX7A2L is an obligate respirasome assembly factor.","evidence":"BN-PAGE, respirometry, and Lrpprc knockout across mouse strains differing in Cox7a2l isoform","pmids":["25470551"],"confidence":"High","gaps":["Did not resolve which supercomplex species specifically depend on COX7A2L","Mouse strain isoform differences confounded with other background variation"]},{"year":2016,"claim":"Defined the specific molecular role of COX7A2L as a factor that binds free complex III to stabilize the III2+IV supercomplex without affecting individual complexes or respirasomes, narrowing its function to a discrete assembly step.","evidence":"Native gel electrophoresis, co-immunoprecipitation, and functional respiratory assays in human and mouse cells; complementary BN-PAGE in C57BL/6 liver mitochondria lacking functional SCAFI","pmids":["27545886","27997587"],"confidence":"High","gaps":["Structural basis of preferential complex III versus complex IV binding not resolved","Physiological consequence of losing III2+IV supercomplex unclear"]},{"year":2016,"claim":"Linked COX7A2L to stress-induced energy metabolism and a pro-proliferative phenotype, indicating context-dependent functional importance beyond baseline assembly.","evidence":"Gain/loss-of-function with OCR/ECAR energy assays and proliferation/invasion assays in breast cancer and mammary epithelial cells","pmids":["27550821"],"confidence":"Medium","gaps":["Mechanism connecting supercomplex assembly to proliferation not defined","Single cancer context; generality untested"]},{"year":2018,"claim":"Showed via clean CRISPR knockout that loss of COX7A2L removes SC III2+IV and megacomplexes but leaves complex III, complex IV biogenesis, and respiration normal, establishing it as dispensable for baseline OXPHOS function.","evidence":"CRISPR-Cas9 knockout, BN-PAGE, in-gel activity, pulse-chase assembly, and Seahorse respirometry under stress in two cell lines","pmids":["30428348"],"confidence":"High","gaps":["Why III2+IV stabilization is functionally non-essential in these cells unexplained","Possible tissue- or stress-specific requirement not addressed"]},{"year":2021,"claim":"Resolved the structural heterogeneity of respirasomes, demonstrating that COX7A2 and COX7A2L define distinct co-existing supercomplex populations, with COX7A2-based respirasomes predominating.","evidence":"SILAC-based complexome profiling and quantitative mass spectrometry of CRISPR knockout HEK293T cells","pmids":["33727070"],"confidence":"High","gaps":["Functional differences between COX7A2- and COX7A2L-defined respirasomes unknown","Regulation of the choice between COX7A2 and COX7A2L not addressed"]},{"year":2022,"claim":"Connected COX7A2L expression dosage to whole-organism physiology, showing a 3' UTR variant raises expression, supercomplexes, and respiration, and that reconstitution improves metabolic phenotypes and exercise responsiveness.","evidence":"cis-eQTL mapping, mRNA stability assays, human myotube respirometry, Cox7a2l reconstitution in mice with metabolic phenotyping and BN-PAGE","pmids":["36253618"],"confidence":"High","gaps":["Causal chain from supercomplex abundance to energy expenditure not fully traced","Whether exercise induction is transcriptional or post-transcriptional unresolved"]},{"year":2024,"claim":"Provided human in vivo evidence that COX7A2L incorporation into III2+IV1 supercomplexes is exercise-mode-specific, linking the assembly mechanism to physiological adaptation.","evidence":"Quantitative complexome profiling of human skeletal muscle biopsies after sprint-interval versus moderate-intensity training (preprint)","pmids":["bio_10.1101_2024.12.19.629456"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Mechanism of training-mode specificity unknown"]},{"year":2024,"claim":"Implicated transcriptional control of COX7A2L by TCF4 with downstream effects on Wnt/β-catenin signaling and apoptosis under hypoxia/reoxygenation.","evidence":"Overexpression/knockdown and rescue with Western blotting for Wnt pathway proteins and apoptosis assays in vitro","pmids":["39499704"],"confidence":"Low","gaps":["No direct demonstration of TCF4 binding to the COX7A2L promoter","Single lab, in vitro only","Mechanistic link between supercomplex protein and Wnt signaling unexplained"]},{"year":2025,"claim":"Tested whether COX7A2L drives aging-related metabolic benefits, showing transgenic elevation raises ATP and NAD+, lowers ROS and senescence, and extends lifespan.","evidence":"Transgenic mouse model with ATP/NAD+/ROS biochemistry, senescence-associated β-galactosidase assay, and snRNA-seq of white adipose tissue","pmids":["41253741"],"confidence":"Medium","gaps":["Single lab, no independent replication","Causal mechanism from supercomplex assembly to SASP downregulation not established"]},{"year":2025,"claim":"Tested cardiomyocyte dependence on COX7A2L and found no measurable effect on viability or mitochondrial respiration, reinforcing tissue/context-specificity of its functional importance.","evidence":"Validated overexpression/knockdown with MTT viability and Seahorse Mito Stress Test under isoproterenol stimulation in AC16 cardiomyocytes","pmids":["40560843"],"confidence":"Medium","gaps":["Negative result in a single cell type does not exclude effects elsewhere","No assessment of supercomplex assembly in this model"]},{"year":null,"claim":"It remains unresolved how COX7A2L-defined supercomplexes confer the organismal metabolic, fitness, and longevity benefits despite being dispensable for baseline respiration in many cellular contexts.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No mechanistic link between III2+IV supercomplex abundance and ATP/NAD+/ROS phenotypes","Tissue-specific functional requirement not systematically mapped","Structural basis of preferential complex III binding undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,2,3]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2,4]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,6,7]}],"complexes":["respiratory supercomplex III2+IV","respirasome (I+III2+IV)","cytochrome c oxidase (complex IV)"],"partners":["COMPLEX III","COMPLEX IV","COX7A2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O14548","full_name":"Cytochrome c oxidase subunit 7A2-like, mitochondrial","aliases":["Cytochrome c oxidase subunit 7A-related protein","COX7a-related protein","Cytochrome c oxidase subunit VIIa-related protein","EB1","Supercomplex assembly factor 1"],"length_aa":114,"mass_kda":12.6,"function":"Assembly factor that mediates the formation of some mitochondrial respiratory supercomplexes (respirasomes), thereby promoting oxidative phosphorylation and energy metabolism (PubMed:27545886, PubMed:30428348, PubMed:33727070, PubMed:36198313). Acts as a molecular adapter that associates with both mitochondrial respiratory complexes III (CIII) and IV (CIV), promoting their association (PubMed:27545886, PubMed:36198313). Mediates the formation of various mitochondrial respiratory supercomplexes, such as MCIII(2)IV(2), composed of two CIII and two CIV, and the CS-respirasome (MCI(1)III(2)IV(2)), composed of one CI, two CIII and two CIV (PubMed:27545886, PubMed:30428348). Not involved in the formation of the canonical respirasome (MCI(1)III(2)IV(1)), composed of one CI, two CIII and one CIV (By similarity). The formation of different respirasomes is important for cell adaptation to oxygen conditions and prevent metabolic exhaustion: supercomplexes mediated by COX7A2L/SCAF1 are required to maintain oxidative phosphorylation upon low oxygen conditions and promote metabolic rewiring toward glycolysis (PubMed:36198313)","subcellular_location":"Mitochondrion inner membrane","url":"https://www.uniprot.org/uniprotkb/O14548/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/COX7A2L","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/COX7A2L","total_profiled":1310},"omim":[{"mim_id":"605772","title":"ESTROGEN RECEPTOR-BINDING SITE-ASSOCIATED ANTIGEN, 9; EBAG9","url":"https://www.omim.org/entry/605772"},{"mim_id":"605771","title":"COX7A2-LIKE PROTEIN; COX7A2L","url":"https://www.omim.org/entry/605771"},{"mim_id":"220111","title":"MITOCHONDRIAL COMPLEX IV DEFICIENCY, NUCLEAR TYPE 5; MC4DN5","url":"https://www.omim.org/entry/220111"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Mitochondria","reliability":"Enhanced"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/COX7A2L"},"hgnc":{"alias_symbol":["EB1","COX7RP","COX7AR","SIG81","SCAF1","SCAFI"],"prev_symbol":[]},"alphafold":{"accession":"O14548","domains":[{"cath_id":"4.10.91.10","chopping":"71-114","consensus_level":"medium","plddt":95.1507,"start":71,"end":114}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14548","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14548-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14548-F1-predicted_aligned_error_v6.png","plddt_mean":79.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=COX7A2L","jax_strain_url":"https://www.jax.org/strain/search?query=COX7A2L"},"sequence":{"accession":"O14548","fasta_url":"https://rest.uniprot.org/uniprotkb/O14548.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14548/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14548"}},"corpus_meta":[{"pmid":"27545886","id":"PMC_27545886","title":"COX7A2L Is a Mitochondrial Complex III Binding Protein that Stabilizes the III2+IV Supercomplex without Affecting Respirasome Formation.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27545886","citation_count":98,"is_preprint":false},{"pmid":"25470551","id":"PMC_25470551","title":"The respiratory chain supercomplex organization is independent of COX7a2l isoforms.","date":"2014","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/25470551","citation_count":83,"is_preprint":false},{"pmid":"30428348","id":"PMC_30428348","title":"Human COX7A2L Regulates Complex III Biogenesis and Promotes Supercomplex Organization Remodeling without Affecting Mitochondrial Bioenergetics.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30428348","citation_count":57,"is_preprint":false},{"pmid":"27550821","id":"PMC_27550821","title":"COX7AR is a Stress-inducible Mitochondrial COX Subunit that Promotes Breast Cancer Malignancy.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27550821","citation_count":32,"is_preprint":false},{"pmid":"36253618","id":"PMC_36253618","title":"COX7A2L genetic variants determine cardiorespiratory fitness in mice and human.","date":"2022","source":"Nature metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/36253618","citation_count":29,"is_preprint":false},{"pmid":"33727070","id":"PMC_33727070","title":"SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells.","date":"2021","source":"Biochimica et biophysica acta. Bioenergetics","url":"https://pubmed.ncbi.nlm.nih.gov/33727070","citation_count":19,"is_preprint":false},{"pmid":"32509385","id":"PMC_32509385","title":"Overexpression of COX7RP promotes tumor growth and metastasis by inducing ROS production in hepatocellular carcinoma cells.","date":"2020","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/32509385","citation_count":16,"is_preprint":false},{"pmid":"27997587","id":"PMC_27997587","title":"COX7A2L/SCAFI and Pre-Complex III Modify Respiratory Chain Supercomplex Formation in Different Mouse Strains with a Bcs1l Mutation.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27997587","citation_count":16,"is_preprint":false},{"pmid":"35178385","id":"PMC_35178385","title":"Emerging Roles of COX7RP and Mitochondrial Oxidative Phosphorylation in Breast Cancer.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35178385","citation_count":11,"is_preprint":false},{"pmid":"32903930","id":"PMC_32903930","title":"Coexisting of COX7A2L-ALK, LINC01210-ALK, ATP13A4-ALK and Acquired SLCO2A1-ALK in a Lung Adenocarcinoma with Rearrangements Loss During the Treatment of Crizotinib and Ceritinib: A Case Report.","date":"2020","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/32903930","citation_count":7,"is_preprint":false},{"pmid":"39499704","id":"PMC_39499704","title":"TCF4 promotes apoptosis and Wnt/β-catenin signaling pathway in acute kidney injury via transcriptional regulation of COX7A2L.","date":"2024","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/39499704","citation_count":2,"is_preprint":false},{"pmid":"37183647","id":"PMC_37183647","title":"[Ceritinib as First-line Treatment for Advanced Lung Adenocarcinoma 
with COX7A2L-ALK Fusion: A Case Report and Literature Review].","date":"2023","source":"Zhongguo fei ai za zhi = Chinese journal of lung cancer","url":"https://pubmed.ncbi.nlm.nih.gov/37183647","citation_count":1,"is_preprint":false},{"pmid":"40560843","id":"PMC_40560843","title":"Investigating the cardiorespiratory fitness gene COX7A2L in cardiomyocytes: Viability and mitochondrial function.","date":"2025","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/40560843","citation_count":0,"is_preprint":false},{"pmid":"41253741","id":"PMC_41253741","title":"Mitochondrial Respiratory Supercomplex Assembly Factor COX7RP Contributes to Lifespan Extension in Mice.","date":"2025","source":"Aging cell","url":"https://pubmed.ncbi.nlm.nih.gov/41253741","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.19.629456","title":"Sprint interval exercise disrupts mitochondrial ultrastructure driving a unique mitochondrial stress response and remodelling in humans","date":"2024-12-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.19.629456","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9111,"output_tokens":2912,"usd":0.035507,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10325,"output_tokens":3479,"usd":0.0693,"stage2_stop_reason":"end_turn"},"total_usd":0.104807,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"COX7A2L binds primarily to free mitochondrial complex III and, to a minor extent, to complex IV, specifically promoting stabilization of the III2+IV supercomplex without affecting respirasome (I+III2+IV) formation or the biogenesis, stabilization, and function of individual OXPHOS complexes.\",\n      \"method\": \"Native gel electrophoresis, co-immunoprecipitation, and functional respiratory assays in human and mouse cells\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, multiple orthogonal methods (BN-PAGE, Co-IP, functional assays), replicated across human and mouse systems, consistent with findings from multiple independent labs\",\n      \"pmids\": [\"27545886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The short COX7a2l isoform present in C57BL/6 mice does not prevent formation of complex IV-containing supercomplexes or respirasomes; supercomplex organization is independent of COX7a2l isoforms in mice. Loss of complex IV (via Lrpprc knockout) compromises respirasome formation.\",\n      \"method\": \"Multiple complementary experimental approaches including BN-PAGE, respirometry, and mouse knockout of Lrpprc in mice with different COX7a2l isoforms\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods, genetic epistasis via Lrpprc knockout, independent replication across mouse strains\",\n      \"pmids\": [\"25470551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"COX7A2L-knockout (KO) HEK293T and U87 cells lack SC III2+IV but show enhanced complex III steady-state levels, activity, and assembly rate, normal de novo complex IV biogenesis, and delayed but ultimately normal respirasome steady-state levels; only larger megacomplexes (SCs I1-2+III2+IV2-n) were absent. Functional substrate-driven competition assays showed normal mitochondrial respiration under standard and stress conditions in COX7A2L-KO cells.\",\n      \"method\": \"CRISPR-Cas9 knockout, BN-PAGE, in-gel activity assays, radioactive pulse-chase assembly assays, Seahorse respirometry under multiple stress conditions\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — clean genetic KO with multiple orthogonal methods, two independent cell lines, functional respiratory assays, replicated findings consistent with other labs\",\n      \"pmids\": [\"30428348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SILAC-based complexome profiling of SCAFI (COX7A2L) knockout HEK293T cells showed preferential loss of SC III2+IV and a minor subset of respirasomes, without affecting OXPHOS function. Approximately 70% of respirasomes in wild-type cells contain COX7A2 (not SCAFI) and are present at similar levels in SCAFI-KO cells, demonstrating co-existence of structurally distinct respirasomes defined by preferential binding of complex IV via COX7A2 rather than SCAFI.\",\n      \"method\": \"SILAC-based complexome profiling, CRISPR-Cas9 knockout, quantitative mass spectrometry\",\n      \"journal\": \"Biochimica et biophysica acta. Bioenergetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — quantitative proteomics with SILAC, CRISPR KO, complexome profiling providing direct structural resolution of supercomplex composition\",\n      \"pmids\": [\"33727070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In liver mitochondria of C57BL/6 mice (which lack functional SCAFI/COX7A2L protein due to a 6-bp deletion), complex IV is mainly present as monomers and dimers with only low amounts found in combination with complexes I and III, and the main supercomplex comprises only complexes I and III — supporting a role for COX7A2L/SCAFI in incorporating complex IV into supercomplexes. SCAFI heterozygosity reduced SCAFI protein but did not affect respirasome assembly.\",\n      \"method\": \"BN-PAGE, immunoblotting, comparison of mice with different SCAFI isoforms on Bcs1l mutant background\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — BN-PAGE with genetically defined mouse strains, single lab, two complementary genetic backgrounds\",\n      \"pmids\": [\"27997587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"COX7AR (COX7A2L) is incorporated into the mitochondrial COX complex under cellular stress that stimulates energy metabolism. Gain- and loss-of-function analysis demonstrated that COX7AR is required for human breast cancer cells to maintain higher rates of proliferation, clone formation, and invasion, and promotes cellular energy production in human mammary epithelial cells.\",\n      \"method\": \"Gain- and loss-of-function (overexpression/siRNA knockdown), cellular energy production assays (OCR/ECAR), proliferation/invasion assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — gain and loss-of-function with defined phenotypic readouts, single lab, functional energy assays\",\n      \"pmids\": [\"27550821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A 10-bp insertion in the COX7A2L 3' UTR increases mRNA stability and expression; human myotubes harboring this insertion have more supercomplexes and increased respiration. Specific reconstitution of Cox7a2l expression in C57BL/6J mice leads to higher maximal oxygen consumption, increased lean mass, and increased energy expenditure. Cox7a2l expression is induced specifically in mouse muscle upon exercise.\",\n      \"method\": \"cis-eQTL mapping, mRNA stability assays, Seahorse respirometry in human myotubes, Cox7a2l reconstitution in mice with metabolic phenotyping, BN-PAGE for supercomplex quantification\",\n      \"journal\": \"Nature metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods including genetic reconstitution in mice, human myotube functional assays, mRNA stability experiments, and metabolic phenotyping\",\n      \"pmids\": [\"36253618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"COX7RP (COX7A2L)-transgenic mice show elevated ATP and NAD+ levels, reduced ROS production, decreased senescence-associated β-galactosidase levels, and significant lifespan extension. snRNA-seq revealed downregulation of senescence-associated secretory phenotype (SASP) genes in old COX7RP-Tg white adipose tissue adipocytes.\",\n      \"method\": \"Transgenic mouse model, metabolic biochemistry (ATP, NAD+, ROS), β-galactosidase senescence assay, single-nucleus RNA sequencing\",\n      \"journal\": \"Aging cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transgenic mouse model with multiple biochemical readouts, single lab, no independent replication yet\",\n      \"pmids\": [\"41253741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"COX7A2L protein significantly accumulates in III2+IV1 respiratory supercomplexes specifically following sprint-interval training (SIT) but not moderate-intensity continuous training (MICT) in human skeletal muscle, indicating exercise-mode-specific regulation of COX7A2L incorporation into supercomplexes.\",\n      \"method\": \"Quantitative proteomics/complexome profiling of human skeletal muscle biopsies after 8-week training interventions\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — complexome profiling in human biopsies, single study, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.12.19.629456\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TCF4 transcriptionally regulates COX7A2L expression; TCF4 overexpression increases COX7A2L levels, and COX7A2L knockdown counteracts TCF4-induced promotion of Wnt/β-catenin signaling pathway proteins (c-myc, β-catenin, cyclin D1) and apoptosis in hypoxia/reoxygenation-treated cells.\",\n      \"method\": \"Overexpression and knockdown experiments, rescue assays, Western blotting for Wnt/β-catenin pathway proteins, apoptosis and proliferation assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single set of methods, in vitro only, no direct demonstration of TCF4 binding to COX7A2L promoter\",\n      \"pmids\": [\"39499704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Overexpression and knockdown of COX7A2L in human AC16 cardiomyocytes did not significantly affect cell viability or mitochondrial function (oxygen consumption rate parameters), even under isoproterenol-stimulated increased energy demand — a negative result.\",\n      \"method\": \"Overexpression and knockdown validated by sandwich ELISA, MTT assay, Seahorse XF Cell Mito Stress Test with isoproterenol stimulation\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — validated overexpression/knockdown, Seahorse functional assay, but negative result in a single cell type; does not rule out effects in other contexts\",\n      \"pmids\": [\"40560843\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"COX7A2L (also known as COX7RP/SCAFI/SIG81/COX7AR) is a mitochondrial protein that binds preferentially to free complex III (and to a lesser extent complex IV) to specifically promote assembly and stabilization of the III2+IV supercomplex, while the majority of respirasomes (I+III2+IVn) are assembled via COX7A2 rather than COX7A2L; COX7A2L is dispensable for individual complex biogenesis and baseline OXPHOS function, but its expression level — regulated by a 3' UTR insertion variant and induced by exercise — modulates supercomplex abundance, mitochondrial respiration efficiency, metabolic parameters including ATP and NAD+ levels, and ultimately cardiorespiratory fitness and longevity in mammals.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COX7A2L is a mitochondrial inner-membrane protein that governs the assembly of respiratory chain supercomplexes by binding preferentially to free complex III and, to a lesser extent, complex IV, thereby specifically promoting formation and stabilization of the III2+IV supercomplex [#0]. Its action is selective rather than essential: COX7A2L is dispensable for the biogenesis, stability, and function of individual OXPHOS complexes, and the bulk of respirasomes (I+III2+IV) assemble independently of it, with roughly 70% of wild-type respirasomes incorporating complex IV via COX7A2 rather than COX7A2L [#0, #2, #3]. Consistent with this, knockout cells lose SC III2+IV and the largest megacomplexes while retaining near-normal respiration, and mice lacking functional COX7A2L still form respirasomes [#2, #4]. The functional relevance of COX7A2L lies in dose-dependent modulation of supercomplex abundance: a 3' UTR insertion variant that raises mRNA stability and expression increases supercomplexes and respiration in human myotubes, and reconstituting Cox7a2l in deficient mice raises maximal oxygen consumption, lean mass, and energy expenditure, with expression induced in muscle by exercise [#6]. Sustained elevation of COX7A2L raises ATP and NAD+ levels, lowers ROS and cellular senescence markers, and extends lifespan in transgenic mice [#7]. COX7A2L is also recruited into the COX complex under metabolic stress and supports proliferation and energy production in breast cancer and mammary epithelial cells [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that respirasome and complex IV-supercomplex organization can proceed independently of COX7A2L isoform status, challenging the idea that COX7A2L is an obligate respirasome assembly factor.\",\n      \"evidence\": \"BN-PAGE, respirometry, and Lrpprc knockout across mouse strains differing in Cox7a2l isoform\",\n      \"pmids\": [\"25470551\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which supercomplex species specifically depend on COX7A2L\", \"Mouse strain isoform differences confounded with other background variation\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the specific molecular role of COX7A2L as a factor that binds free complex III to stabilize the III2+IV supercomplex without affecting individual complexes or respirasomes, narrowing its function to a discrete assembly step.\",\n      \"evidence\": \"Native gel electrophoresis, co-immunoprecipitation, and functional respiratory assays in human and mouse cells; complementary BN-PAGE in C57BL/6 liver mitochondria lacking functional SCAFI\",\n      \"pmids\": [\"27545886\", \"27997587\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of preferential complex III versus complex IV binding not resolved\", \"Physiological consequence of losing III2+IV supercomplex unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked COX7A2L to stress-induced energy metabolism and a pro-proliferative phenotype, indicating context-dependent functional importance beyond baseline assembly.\",\n      \"evidence\": \"Gain/loss-of-function with OCR/ECAR energy assays and proliferation/invasion assays in breast cancer and mammary epithelial cells\",\n      \"pmids\": [\"27550821\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting supercomplex assembly to proliferation not defined\", \"Single cancer context; generality untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed via clean CRISPR knockout that loss of COX7A2L removes SC III2+IV and megacomplexes but leaves complex III, complex IV biogenesis, and respiration normal, establishing it as dispensable for baseline OXPHOS function.\",\n      \"evidence\": \"CRISPR-Cas9 knockout, BN-PAGE, in-gel activity, pulse-chase assembly, and Seahorse respirometry under stress in two cell lines\",\n      \"pmids\": [\"30428348\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why III2+IV stabilization is functionally non-essential in these cells unexplained\", \"Possible tissue- or stress-specific requirement not addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the structural heterogeneity of respirasomes, demonstrating that COX7A2 and COX7A2L define distinct co-existing supercomplex populations, with COX7A2-based respirasomes predominating.\",\n      \"evidence\": \"SILAC-based complexome profiling and quantitative mass spectrometry of CRISPR knockout HEK293T cells\",\n      \"pmids\": [\"33727070\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional differences between COX7A2- and COX7A2L-defined respirasomes unknown\", \"Regulation of the choice between COX7A2 and COX7A2L not addressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected COX7A2L expression dosage to whole-organism physiology, showing a 3' UTR variant raises expression, supercomplexes, and respiration, and that reconstitution improves metabolic phenotypes and exercise responsiveness.\",\n      \"evidence\": \"cis-eQTL mapping, mRNA stability assays, human myotube respirometry, Cox7a2l reconstitution in mice with metabolic phenotyping and BN-PAGE\",\n      \"pmids\": [\"36253618\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal chain from supercomplex abundance to energy expenditure not fully traced\", \"Whether exercise induction is transcriptional or post-transcriptional unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided human in vivo evidence that COX7A2L incorporation into III2+IV1 supercomplexes is exercise-mode-specific, linking the assembly mechanism to physiological adaptation.\",\n      \"evidence\": \"Quantitative complexome profiling of human skeletal muscle biopsies after sprint-interval versus moderate-intensity training (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.12.19.629456\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Mechanism of training-mode specificity unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated transcriptional control of COX7A2L by TCF4 with downstream effects on Wnt/β-catenin signaling and apoptosis under hypoxia/reoxygenation.\",\n      \"evidence\": \"Overexpression/knockdown and rescue with Western blotting for Wnt pathway proteins and apoptosis assays in vitro\",\n      \"pmids\": [\"39499704\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct demonstration of TCF4 binding to the COX7A2L promoter\", \"Single lab, in vitro only\", \"Mechanistic link between supercomplex protein and Wnt signaling unexplained\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Tested whether COX7A2L drives aging-related metabolic benefits, showing transgenic elevation raises ATP and NAD+, lowers ROS and senescence, and extends lifespan.\",\n      \"evidence\": \"Transgenic mouse model with ATP/NAD+/ROS biochemistry, senescence-associated β-galactosidase assay, and snRNA-seq of white adipose tissue\",\n      \"pmids\": [\"41253741\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, no independent replication\", \"Causal mechanism from supercomplex assembly to SASP downregulation not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Tested cardiomyocyte dependence on COX7A2L and found no measurable effect on viability or mitochondrial respiration, reinforcing tissue/context-specificity of its functional importance.\",\n      \"evidence\": \"Validated overexpression/knockdown with MTT viability and Seahorse Mito Stress Test under isoproterenol stimulation in AC16 cardiomyocytes\",\n      \"pmids\": [\"40560843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result in a single cell type does not exclude effects elsewhere\", \"No assessment of supercomplex assembly in this model\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how COX7A2L-defined supercomplexes confer the organismal metabolic, fitness, and longevity benefits despite being dispensable for baseline respiration in many cellular contexts.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mechanistic link between III2+IV supercomplex abundance and ATP/NAD+/ROS phenotypes\", \"Tissue-specific functional requirement not systematically mapped\", \"Structural basis of preferential complex III binding undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 6, 7]}\n    ],\n    \"complexes\": [\n      \"respiratory supercomplex III2+IV\",\n      \"respirasome (I+III2+IV)\",\n      \"cytochrome c oxidase (complex IV)\"\n    ],\n    \"partners\": [\n      \"complex III\",\n      \"complex IV\",\n      \"COX7A2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}