APAF1 (Apoptotic protease activating factor 1)

2004-09-01   Marco Corvaro , Francesco Cecconi 

Dulbecco Telethon Institute,Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy





The APAF1 gene is comprised of 27 exons, with the coding region spanning 26 exons (the ATG is in the second exon


Five isoforms of APAF1 cDNA have been identified in Homo sapiens
  • the original APAF1 (also called Apaf-1S) is 3585 bp long (it contains 12 WD40 repeats);
  • the APAF1-1M isoform (3618 bp) contains an insertion of 33 nt after position 295 of the first published sequence (11 aa insertion GKDSVSGITSY between aa 98 and 99; it also contains 12 WD40 repeats);
  • the APAF1XS isoform (3516 bp) contains the same insertion of Apaf-1M form, lacks the base pairs from 3171 to 3296 of the Apaf-1S form (the deletion is in WD40 domain) but has an insertion of 24 nt at position 1725
  • the APAF1L (3714 bp) contains an insertion of 129 nt at position 2466(contains 13 WD40 repeats);
  • the APAF1XL (3747 bp)isoform contains the same insertion of APAF1M form, plus and additional insertion of 129 bp (43 aa beetween aa 811-812; Apaf-1XL also contains 13 WD40 repeats);
  • Pseudogene

    not known


    Atlas Image
    Figure 1: The conformational changes in the APAF1 molecules lead to apoptosome formation and to the activation of apoptosis. However, the assembly and the functioning of the apoptosome is regulated by mithocondrial and cytosolic factors (modif. from E. Ferraro et al. 2004)


    the protein can be divided into three domains: the N-terminal is a CARD domain and is necessary for APAF1 function; alternatively, it can bind the WD40 domain or cytochrome C. The ced-4-like domain is responsible for APAF1 conformational changes. The C-terminal WD40 domain is a negative regulator element composed of 12 or 13 WD40 repeats: it can bind the CARD domain but it can probably interact with other apoptotic regulator proteins as well.


    APAF1 Promoter can interact with E2F1 (also E2F2-3) and p53 which can in turn regulate its expression.




    APAF1 is the structural core of the apoptosome. When the mitochondrial pathway of apoptosis is activated, cytochrome c is released from mitochondria to cytosol, and then binds to APAF1 CARD domain changing its conformation. A further binding of ATP molecules mediates a second conformational change which leads to open APAF1 conformation. By means of the CARD domain, seven APAF1 molecules bind to each other and to seven molecules of initiator Caspase-9 forming the apoptosome and causing the activation of effector caspases. The formation of apoptosome and the activation of caspases are regulated by numerous interacting proteins.


    CED-4 (C. elegans); DARK (D. melanogaster); CARD proteins.



    not known in H. sapiens.


    not known in H. sapiens.

    Implicated in

    Entity name
    Skin Cancers ( Melanoma, Basal Cell Carcinoma, Squamous Cell Carcinoma).
    Frequent LOH in 12q22-23 locus (primary melanomas: 20-25% metastatic melanomas 35-40%).
    The silencing of Apaf1 expression is often found in Melanomas. Two main mechanisms have been posited for APAF1 dimininution, either the allelic LOH in 12q22-23 locus and/or a transcriptional silencing by promoter methylation. The inactivation was not found in Nevi but it increased significantly in the later stages of carcinogenesis, when primary melanomas are fully developed (1-3mm of diameter). Very often such inactivation was associated with metastatic melanomas. Moreover, the APAF1 level is correlated with chemosensivity to different agents; different studies demonstrate that overexpressing or restoring a normal APAF1 level could sensitize chemoresistant melanoma cell lines, in vitro. Recently, APAF1 LOH determination on blood serum DNA has been proposed as a marker for selecting appropriate chemotherapy in stage IV melanoma patients.
    Entity name
    Brain tumors (neural tumors, glial tumors)
    Frequent LOH in 12q22-23 locus in glioblastomas (40%)
    APAF1 seems to be downregulated or absent in Glioblastomas at mRNA and protein level. In addition, the co-overexpression of APAF1 and Caspase-9 sensitizes glioma cell lines (U-251 and U-373 MG) to p53-dependent apoptosis. Other modulations of the apoptosome-related apoptosis have been successfully conducted in order to induce apoptosis in glioma resistant lines. By contrast, APAF1 seems to be active in Neuroblastomas while there are no studies about a putative APAF1 role in other glial tumors (such as ependimoma, astrocytoma, ganglioglioma).
    Entity name
    Head and neck cancers and odontogenic tumors.
    There is no direct evidence of APAF1s role in the oncogenesis of these types of cancer even though Apaf1 loss has been correlated with gain of Cisplatin Chemoresistance in HSC-2CR cells (derived from HSC-2 head squamous carcinoma cells).
    Entity name
    Gastro-intestinal tract cancers ( oesophagus cancer, gastric cancer, gallbladder cancer, ampulla of vater cancer, peritoneum cancer, vermiform appendix cancer, colon cancer, rectal cancer, cancer of the anus).
    A low frequency of mutations (10-15 % of cases) is found in ColoRectal and Gastric Cancer. these mutations are due to the genetics of microsatellite instability and appear to be heterozygous. No evidences of APAF1 involvement have been found in the pathogenesis of the other tumors mentioned
    Entity name
    Exocrinus pancreas cancers (various stages of the pancreas ductal adenocarcinoma - PDAC)
    12q 1ocus deletions could be considered among the most frequent deletions in PDAC.
    There is no direct evidence of APAF1 mutations in the progression of the PDAC (some even deny its possible role completely). There are many studies, however, which point out the 12q22-23 locus LOH or mutation in PDAC. Most of the mutated genes involved (such as K-Ras, p53, p16INK4a, p19ARF) can control the APAF1 level directly or indirectly throught the action of p53 and E2F-1 which both have active binding boxes to the APAF1 promoter.
    Entity name
    Liver cancer and liver metastases
    Methylation is a common feature in hepatocellular carcinoma (HCC) regulation. While the analysis of promoters methylation in HCC samples showed that the APAF1 gene is not hypermethylated, the HepG2 cells exposed to a demethylating agent (DEM, diethyl maleate) showed an increased level of Apaf1 and of some caspases which lead to G2 phase arrest and apoptosis.
    Entity name
    Lung cancer
    There is no direct evidence for abrogation of APAF1 function in lung cancer. However, the APAF1/Caspase-9 upregulation seem to be a protective mechanism in some NSCLC ( non small cell lung carcinoma) cell lines, while in other NSCLC lines (such as the NCI-H460) an indirect APAF1 loss of function is mediated by the upregulation of XIAP (an inhibitor of Apoptosome assembly). Furthermore, a driven expression of APAF1/ Caspase-9 (through the Inibition of XIAP in NCI-H460 cells or with low dose lung cancer cell lines) seems to augment sensitivity to death.
    Entity name
    Tumors of the female reproductive organs ( ovarian carcinoma, neoplasms of Fallopian tube, endometrium, cervix, vulva and vagina)
    In ovarian carcinoma, the APAF1 gene seems to be active. However, dysfunction in the apoptosome assembly process has been correlated with chemoresistance. In contrast, loss of heterozygosity was found in the apaf1 locus in malignant ovarian germ cell tumors. There is no information about the reproductive tract.
    Entity name
    Tumors of the male reproductive organs ( seminoma, nonseminomatous germ cell tumors, sex cord-stromal tumors , other testis cancers, neoplasms of prostate, tumor of the penis)
    Frequent deletions in Chromosome 12 long and short arm in germ line tumors; LOH in 12q22-23 is present in seminomas, non-seminomatous tumors and in mixed teratomas with various reported percentage (20-45%)
    In Germ line tumors the APAF1 locus is often deleted; however it seems that APAF1 level was normal in various analyzed lines. Interestingly, Cisplatin treatment of a embryonal carcinoma cell line, TTSC-3 lead to the differentiation of the carcinoma through the up-regulation of pro-differentiation and pro-apoptotic genes (such as APAF1, Caspase-8 and TNFR1). In Prostatic Tumor there is no evidence of APAF1 involvement; however some studies have been conducted demontrating an increase of Apaf1 at transcription level as a cellular response to chemotherapeutic agents.
    Entity name
    Urinary tract tumors ( renal cell carcinoma, neoplasms of the renal pelvis, ureter, bladder, urethra)
    The Apoptosome function seems to be active in primary samples and in a few cell lines of Renal Cell Carcinoma. There are no informations about the urinary tract.
    Entity name
    Hematopoietic system tumors.
    Its not clear if APAF1 gene is corrupted in Leukaemias and Lymphomas. However, while the methylation of the promoter was demonstrated in different kinds of leukaemia, the protein level does not correlate with the messenger level, suggesting a multistep regulation in APAF1 expression. Furthermore, it has been demonstrated that the APAF1 overexpression, conducted by in vitro transfection or by chemoadiuvants, could overcome the resistance to chemo-radiotherapeutic agents.
    Entity name
    Bone and soft tissue cancers (osteoma, sarcoma, fibroma, osteosarcoma)
    There is no direct evidence of APAF1 role in the oncogenesis of these types of cancer even though in Ewings sarcoma cell lines the Apaf1 low level found in two different lines (STA-ET-2.1 and STA-ET-2.2) was correlated with chemoresistance to p53-dependent death stimuli compared with lines with normal APAF1 level. APAF1 was also absent and correlated with chemoresistance in the HT-1080 fibrosacroma cell line.
    Entity name
    Various tumors ( eye tumor, heart and great vessels tumors, neoplasm of the endocrine glands and of the diffuse endocrine system, tumor of mesotheliums)
    At present, there is no direct evidence of APAF1 involvement in the carcinogenesis of these neoplasms.


    Pubmed IDLast YearTitleAuthors
    124733442002Apoptosomes: engines for caspase activation.Adams JM et al
    115160992001Proteasome inhibitor-induced apoptosis of B-chronic lymphocytic leukaemia cells involves cytochrome c release and caspase activation, accompanied by formation of an approximately 700 kDa Apaf-1 containing apoptosome complex.Almond JB et al
    150091022004Analysis of APAF-1 expression in human cutaneous melanoma progression.Baldi A et al
    107226812000Expression and functional analysis of Apaf-1 isoforms. Extra Wd-40 repeat is required for cytochrome c binding and regulated activation of procaspase-9.Benedict MA et al
    126704672003Hairy-cell leukaemia as a model for drug development.Carson DA et al
    118751892002Transcriptional and physiological responses of HepG2 cells exposed to diethyl maleate: time course analysis.Casey W et al
    105781781999Apaf1 and the apoptotic machinery.Cecconi F et al
    117069942001Apaf1 in developmental apoptosis and cancer: how many ways to die?Cecconi F et al
    119362592002Apoptosis: molecular regulation of cell death and hematologic malignancies.Chiarugi V et al
    153051932004Reduced Apaf-1 expression in human cutaneous melanomas.Dai DL et al
    129326382003Molecular targeting of drug delivery systems to ovarian cancer by BH3 and LHRH peptides.Dharap SS et al
    117486352002Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours.Esteller M et al
    153142852004Modulation of pro- and anti-apoptotic factors in human melanoma cells exposed to histone deacetylase inhibitors.Facchetti F et al
    127672582003Physiological and pathological roles of Apaf1 and the apoptosome.Ferraro E et al
    125451662003Role of DNA methylation in the suppression of Apaf-1 protein in human leukaemia.Fu WN et al
    112640022001Apaf-1XL is an inactive isoform compared with Apaf-1L.Fu WN et al
    150263692004Allelic imbalance of 12q22-23 associated with APAF-1 locus correlates with poor disease outcome in cutaneous melanoma.Fujimoto A et al
    121492442002Apaf-1 is a mediator of E2F-1-induced apoptosis.Furukawa Y et al
    1527373020045-aza-2'-deoxycytidine upregulates caspase-9 expression cooperating with p53-induced apoptosis in human lung cancer cells.Gomyo Y et al
    145668192003Autocrine motility factor signaling induces tumor apoptotic resistance by regulations Apaf-1 and Caspase-9 apoptosome expression.Haga A et al
    114290442001Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.Ikenoue T et al
    147494772004Resveratrol modifies the expression of apoptotic regulatory proteins and sensitizes non-Hodgkin's lymphoma and multiple myeloma cell lines to paclitaxel-induced apoptosis.Jazirehi AR et al
    126428622003Role of Smac in human leukaemic cell apoptosis and proliferation.Jia L et al
    114353112001Apaf-1 protein deficiency confers resistance to cytochrome c-dependent apoptosis in human leukemic cells.Jia L et al
    127614892003Response of Ewing tumor cells to forced and activated p53 expression.Kovar H et al
    151015582004Increased expression of Apaf-1 and procaspase-3 and the functionality of intrinsic apoptosis apparatus in non-small cell lung carcinoma.Krepela E et al
    125431672003Inhibition of caspase-9 activity and Apaf-1 expression in cisplatin-resistant head and neck squamous cell carcinoma cells.Kuwahara D et al
    118305532002Dysfunctional apoptosome activation in ovarian cancer: implications for chemoresistance.Liu JR et al
    106793862000Tumor suppressor genes.Macleod K et al
    112952162001Preliminary evaluation of caspases-dependent apoptosis signaling pathways of free and HPMA copolymer-bound doxorubicin in human ovarian carcinoma cells.Minko T et al
    121729802002Enhancing the anticancer efficacy of camptothecin using biotinylated poly(ethylene glycol) conjugates in sensitive and multidrug-resistant human ovarian carcinoma cells.Minko T et al
    125695762003Differential expression of genes induced by resveratrol in LNCaP cells: P53-mediated molecular targets.Narayanan BA et al
    128045982003APAF-1-ALT, a novel alternative splicing form of APAF-1, potentially causes impeded ability of undergoing DNA damage-induced apoptosis in the LNCaP human prostate cancer cell line.Ogawa T et al
    97886011998Overexpression of Apaf-1 promotes apoptosis of untreated and paclitaxel- or etoposide-treated HL-60 cells.Perkins C et al
    107491352000The role of Apaf-1, caspase-9, and bid proteins in etoposide- or paclitaxel-induced mitochondrial events during apoptosis.Perkins CL et al
    150771552004Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks.Pommier Y et al
    120825292002Regulation of apoptosis by p53 in UV-irradiated human epidermis, psoriatic plaques and senescent keratinocytes.Qin JZ et al
    151989482004Promoter hypermethylation of cancer-related genes: a strong independent prognostic factor in acute lymphoblastic leukemia.Roman-Gomez J et al
    152107862004Fas-mediated apoptosome formation is dependent on reactive oxygen species derived from mitochondrial permeability transition in Jurkat cells.Sato T et al
    118705422002Co-transduction of Apaf-1 and caspase-9 highly enhances p53-mediated apoptosis in gliomas.Shinoura N et al
    127892902003Apoptosis and melanoma chemoresistance.Soengas MS et al
    150315992004Mechanisms of paclitaxel-induced apoptosis in an ovarian cancer cell line and its paclitaxel-resistant clone.Sugimura M et al
    110900792000Evaluation of Apaf-1 and procaspases-2, -3, -7, -8, and -9 as potential prognostic markers in acute leukemia.Svingen PA et al
    118966172002Caspase-9 and Apaf-1 are expressed and functionally active in human neuroblastoma tumor cell lines with 1p36 LOH and amplified MYCN.Teitz T et al
    151930362004Frequent LOH at chromosome 12q22-23 and Apaf-1 inactivation in glioblastoma.Umetani N et al
    111196892000A comparison of the expression and properties of Apaf-1 and Apaf-1L.Walke DW et al
    146557492003Frequent LOH at chromosome 12q22-23 and Apaf-1 inactivation in glioblastoma.Watanabe T et al
    114294022001Defective cytochrome c-dependent caspase activation in ovarian cancer cell lines due to diminished or absent apoptotic protease activating factor-1 activity.Wolf BB et al
    108196002000Frameshift mutations in Fas, Apaf-1, and Bcl-10 in gastro-intestinal cancer of the microsatellite mutator phenotype.Yamamoto H et al
    125917342003Predominant suppression of apoptosome by inhibitor of apoptosis protein in non-small cell lung cancer H460 cells: therapeutic effect of a novel polyarginine-conjugated Smac peptide.Yang L et al
    124332782002Methylation profiling of twenty promoter-CpG islands of genes which may contribute to hepatocellular carcinogenesis.Yu J et al

    Other Information

    Locus ID:

    NCBI: 317
    MIM: 602233
    HGNC: 576
    Ensembl: ENSG00000120868


    dbSNP: 317
    ClinVar: 317
    TCGA: ENSG00000120868


    Gene IDTranscript IDUniprot

    Expression (GTEx)



    PathwaySourceExternal ID
    p53 signaling pathwayKEGGko04115
    Alzheimer's diseaseKEGGko05010
    Amyotrophic lateral sclerosis (ALS)KEGGko05014
    Huntington's diseaseKEGGko05016
    Small cell lung cancerKEGGko05222
    p53 signaling pathwayKEGGhsa04115
    Alzheimer's diseaseKEGGhsa05010
    Parkinson's diseaseKEGGhsa05012
    Amyotrophic lateral sclerosis (ALS)KEGGhsa05014
    Huntington's diseaseKEGGhsa05016
    Small cell lung cancerKEGGhsa05222
    Hepatitis BKEGGhsa05161
    Apoptotic machineryKEGGhsa_M00685
    Apoptotic machineryKEGGM00685
    Immune SystemREACTOMER-HSA-168256
    Innate Immune SystemREACTOMER-HSA-168249
    Gene ExpressionREACTOMER-HSA-74160
    Generic Transcription PathwayREACTOMER-HSA-212436
    Transcriptional Regulation by TP53REACTOMER-HSA-3700989
    Programmed Cell DeathREACTOMER-HSA-5357801
    Intrinsic Pathway for ApoptosisREACTOMER-HSA-109606
    Apoptotic factor-mediated responseREACTOMER-HSA-111471
    Cytochrome c-mediated apoptotic responseREACTOMER-HSA-111461
    Formation of apoptosomeREACTOMER-HSA-111458
    Activation of caspases through apoptosome-mediated cleavageREACTOMER-HSA-111459
    TP53 Regulates Transcription of Cell Death GenesREACTOMER-HSA-5633008
    TP53 Regulates Transcription of Caspase Activators and CaspasesREACTOMER-HSA-6803207
    Apoptosis - multiple speciesKEGGko04215
    Apoptosis - multiple speciesKEGGhsa04215
    Platinum drug resistanceKEGGko01524
    Platinum drug resistanceKEGGhsa01524
    Neutrophil degranulationREACTOMER-HSA-6798695

    Protein levels (Protein atlas)

    Not detected


    Pubmed IDYearTitleCitations
    118646142002Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation.165
    270214362016Exosomal transfer of stroma-derived miR21 confers paclitaxel resistance in ovarian cancer cells through targeting APAF1.162
    199131212009Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.85
    203796142010Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.62
    180424572007Nonapoptotic role for Apaf-1 in the DNA damage checkpoint.48
    184399022008PHAPI, CAS, and Hsp70 promote apoptosome formation by preventing Apaf-1 aggregation and enhancing nucleotide exchange on Apaf-1.44
    223351962012Simultaneous modulation of COX-2, p300, Akt, and Apaf-1 signaling by melatonin to inhibit proliferation and induce apoptosis in breast cancer cells.40
    229967412012MiR-155 inhibits the sensitivity of lung cancer cells to cisplatin via negative regulation of Apaf-1 expression.36
    121492442002Apaf-1 is a mediator of E2F-1-induced apoptosis.34
    216595562011Triggering of a novel intrinsic apoptosis pathway by the kinase inhibitor staurosporine: activation of caspase-9 in the absence of Apaf-1.34


    Marco Corvaro ; Francesco Cecconi

    APAF1 (Apoptotic protease activating factor 1)

    Atlas Genet Cytogenet Oncol Haematol. 2004-09-01

    Online version: http://atlasgeneticsoncology.org/gene/422/apaf1-(apoptotic-protease-activating-factor-1)