APAF1 (Apoptotic protease activating factor 1)

2004-09-01 Marco Corvaro , Francesco Cecconi Affiliation

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

Identity

HGNC

APAF1

LOCATION

12q23.1

LOCUSID

317

ALIAS

APAF-1,CED4

FUSION GENES

Show Gene Fusions

DNA/RNA

Description

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

Transcription

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

Proteins

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)

Description

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.

Expression

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

Localisation

cytosolic

Function

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.

Homology

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

Mutations

Germinal

not known in H. sapiens.

Somatic

not known in H. sapiens.

Implicated in

Entity name

Skin Cancers ( Melanoma, Basal Cell Carcinoma, Squamous Cell Carcinoma).

Cytogenetics

Frequent LOH in 12q22-23 locus (primary melanomas: 20-25% metastatic melanomas 35-40%).

Oncogenesis

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)

Cytogenetics

Frequent LOH in 12q22-23 locus in glioblastomas (40%)

Oncogenesis

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.

Oncogenesis

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).

Oncogenesis

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)

Cytogenetics

12q 1ocus deletions could be considered among the most frequent deletions in PDAC.

Oncogenesis

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

Oncogenesis

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

Oncogenesis

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)

Oncogenesis

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)

Cytogenetics

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%)

Oncogenesis

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)

Oncogenesis

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.

Oncogenesis

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)

Oncogenesis

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)

Oncogenesis

At present, there is no direct evidence of APAF1 involvement in the carcinogenesis of these neoplasms.

Article Bibliography

Pubmed ID	Last Year	Title	Authors
12473344	2002	Apoptosomes: engines for caspase activation.	Adams JM et al
11516099	2001	Proteasome 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
15009102	2004	Analysis of APAF-1 expression in human cutaneous melanoma progression.	Baldi A et al
10722681	2000	Expression 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
12670467	2003	Hairy-cell leukaemia as a model for drug development.	Carson DA et al
11875189	2002	Transcriptional and physiological responses of HepG2 cells exposed to diethyl maleate: time course analysis.	Casey W et al
10578178	1999	Apaf1 and the apoptotic machinery.	Cecconi F et al
11706994	2001	Apaf1 in developmental apoptosis and cancer: how many ways to die?	Cecconi F et al
11936259	2002	Apoptosis: molecular regulation of cell death and hematologic malignancies.	Chiarugi V et al
15305193	2004	Reduced Apaf-1 expression in human cutaneous melanomas.	Dai DL et al
12932638	2003	Molecular targeting of drug delivery systems to ovarian cancer by BH3 and LHRH peptides.	Dharap SS et al
11748635	2002	Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours.	Esteller M et al
15314285	2004	Modulation of pro- and anti-apoptotic factors in human melanoma cells exposed to histone deacetylase inhibitors.	Facchetti F et al
12767258	2003	Physiological and pathological roles of Apaf1 and the apoptosome.	Ferraro E et al
12545166	2003	Role of DNA methylation in the suppression of Apaf-1 protein in human leukaemia.	Fu WN et al
11264002	2001	Apaf-1XL is an inactive isoform compared with Apaf-1L.	Fu WN et al
15026369	2004	Allelic imbalance of 12q22-23 associated with APAF-1 locus correlates with poor disease outcome in cutaneous melanoma.	Fujimoto A et al
12149244	2002	Apaf-1 is a mediator of E2F-1-induced apoptosis.	Furukawa Y et al
15273730	2004	5-aza-2'-deoxycytidine upregulates caspase-9 expression cooperating with p53-induced apoptosis in human lung cancer cells.	Gomyo Y et al
14566819	2003	Autocrine motility factor signaling induces tumor apoptotic resistance by regulations Apaf-1 and Caspase-9 apoptosome expression.	Haga A et al
11429044	2001	Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.	Ikenoue T et al
14749477	2004	Resveratrol 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
12642862	2003	Role of Smac in human leukaemic cell apoptosis and proliferation.	Jia L et al
11435311	2001	Apaf-1 protein deficiency confers resistance to cytochrome c-dependent apoptosis in human leukemic cells.	Jia L et al
12761489	2003	Response of Ewing tumor cells to forced and activated p53 expression.	Kovar H et al
15101558	2004	Increased expression of Apaf-1 and procaspase-3 and the functionality of intrinsic apoptosis apparatus in non-small cell lung carcinoma.	Krepela E et al
12543167	2003	Inhibition of caspase-9 activity and Apaf-1 expression in cisplatin-resistant head and neck squamous cell carcinoma cells.	Kuwahara D et al
11830553	2002	Dysfunctional apoptosome activation in ovarian cancer: implications for chemoresistance.	Liu JR et al
10679386	2000	Tumor suppressor genes.	Macleod K et al
11295216	2001	Preliminary evaluation of caspases-dependent apoptosis signaling pathways of free and HPMA copolymer-bound doxorubicin in human ovarian carcinoma cells.	Minko T et al
12172980	2002	Enhancing the anticancer efficacy of camptothecin using biotinylated poly(ethylene glycol) conjugates in sensitive and multidrug-resistant human ovarian carcinoma cells.	Minko T et al
12569576	2003	Differential expression of genes induced by resveratrol in LNCaP cells: P53-mediated molecular targets.	Narayanan BA et al
12804598	2003	APAF-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
9788601	1998	Overexpression of Apaf-1 promotes apoptosis of untreated and paclitaxel- or etoposide-treated HL-60 cells.	Perkins C et al
10749135	2000	The role of Apaf-1, caspase-9, and bid proteins in etoposide- or paclitaxel-induced mitochondrial events during apoptosis.	Perkins CL et al
15077155	2004	Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks.	Pommier Y et al
12082529	2002	Regulation of apoptosis by p53 in UV-irradiated human epidermis, psoriatic plaques and senescent keratinocytes.	Qin JZ et al
15198948	2004	Promoter hypermethylation of cancer-related genes: a strong independent prognostic factor in acute lymphoblastic leukemia.	Roman-Gomez J et al
15210786	2004	Fas-mediated apoptosome formation is dependent on reactive oxygen species derived from mitochondrial permeability transition in Jurkat cells.	Sato T et al
11870542	2002	Co-transduction of Apaf-1 and caspase-9 highly enhances p53-mediated apoptosis in gliomas.	Shinoura N et al
12789290	2003	Apoptosis and melanoma chemoresistance.	Soengas MS et al
15031599	2004	Mechanisms of paclitaxel-induced apoptosis in an ovarian cancer cell line and its paclitaxel-resistant clone.	Sugimura M et al
11090079	2000	Evaluation of Apaf-1 and procaspases-2, -3, -7, -8, and -9 as potential prognostic markers in acute leukemia.	Svingen PA et al
11896617	2002	Caspase-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
15193036	2004	Frequent LOH at chromosome 12q22-23 and Apaf-1 inactivation in glioblastoma.	Umetani N et al
11119689	2000	A comparison of the expression and properties of Apaf-1 and Apaf-1L.	Walke DW et al
14655749	2003	Frequent LOH at chromosome 12q22-23 and Apaf-1 inactivation in glioblastoma.	Watanabe T et al
11429402	2001	Defective 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
10819600	2000	Frameshift mutations in Fas, Apaf-1, and Bcl-10 in gastro-intestinal cancer of the microsatellite mutator phenotype.	Yamamoto H et al
12591734	2003	Predominant 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
12433278	2002	Methylation 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

Variants:

dbSNP: 317
ClinVar: 317
TCGA: ENSG00000120868
COSMIC: APAF1

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000120868	ENST00000333991	O14727
ENSG00000120868	ENST00000357310	O14727
ENSG00000120868	ENST00000359972	O14727
ENSG00000120868	ENST00000547045	O14727
ENSG00000120868	ENST00000547743	F8VNZ0
ENSG00000120868	ENST00000549007	C9JLV4
ENSG00000120868	ENST00000550527	O14727
ENSG00000120868	ENST00000551964	O14727
ENSG00000120868	ENST00000552268	O14727

Expression (GTEx)

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Pathways

Pathway	Source	External ID
p53 signaling pathway	KEGG	ko04115
Apoptosis	KEGG	ko04210
Alzheimer's disease	KEGG	ko05010
Amyotrophic lateral sclerosis (ALS)	KEGG	ko05014
Huntington's disease	KEGG	ko05016
Small cell lung cancer	KEGG	ko05222
p53 signaling pathway	KEGG	hsa04115
Apoptosis	KEGG	hsa04210
Alzheimer's disease	KEGG	hsa05010
Parkinson's disease	KEGG	hsa05012
Amyotrophic lateral sclerosis (ALS)	KEGG	hsa05014
Huntington's disease	KEGG	hsa05016
Small cell lung cancer	KEGG	hsa05222
Tuberculosis	KEGG	ko05152
Tuberculosis	KEGG	hsa05152
Legionellosis	KEGG	ko05134
Legionellosis	KEGG	hsa05134
Hepatitis B	KEGG	hsa05161
Apoptotic machinery	KEGG	hsa_M00685
Apoptotic machinery	KEGG	M00685
Immune System	REACTOME	R-HSA-168256
Innate Immune System	REACTOME	R-HSA-168249
Gene Expression	REACTOME	R-HSA-74160
Generic Transcription Pathway	REACTOME	R-HSA-212436
Transcriptional Regulation by TP53	REACTOME	R-HSA-3700989
Programmed Cell Death	REACTOME	R-HSA-5357801
Apoptosis	REACTOME	R-HSA-109581
Intrinsic Pathway for Apoptosis	REACTOME	R-HSA-109606
Apoptotic factor-mediated response	REACTOME	R-HSA-111471
Cytochrome c-mediated apoptotic response	REACTOME	R-HSA-111461
Formation of apoptosome	REACTOME	R-HSA-111458
Activation of caspases through apoptosome-mediated cleavage	REACTOME	R-HSA-111459
TP53 Regulates Transcription of Cell Death Genes	REACTOME	R-HSA-5633008
TP53 Regulates Transcription of Caspase Activators and Caspases	REACTOME	R-HSA-6803207
Apoptosis - multiple species	KEGG	ko04215
Apoptosis - multiple species	KEGG	hsa04215
Platinum drug resistance	KEGG	ko01524
Platinum drug resistance	KEGG	hsa01524
Neutrophil degranulation	REACTOME	R-HSA-6798695

Protein levels (Protein atlas)

Not detected

Low

Medium

High

References

Pubmed ID	Year	Title	Citations
38348717	2024	Exosomal circ_0037104 derived from Hu-MSCs inhibits cholangiocarcinoma progression by sponging miR-620 and targeting AFAP1.	0
38348717	2024	Exosomal circ_0037104 derived from Hu-MSCs inhibits cholangiocarcinoma progression by sponging miR-620 and targeting AFAP1.	0
37108258	2023	Upregulation of APAF1 and CSF1R in Peripheral Blood Mononuclear Cells of Parkinson's Disease.	0
37108258	2023	Upregulation of APAF1 and CSF1R in Peripheral Blood Mononuclear Cells of Parkinson's Disease.	0
34898374	2022	Exosomal microRNA⁃93⁃3p secreted by bone marrow mesenchymal stem cells downregulates apoptotic peptidase activating factor 1 to promote wound healing.	15
35030371	2022	Apoptotic protease activating factor-1 gene and MicroRNA-484: A possible interplay in relapsing remitting multiple sclerosis.	3
35975461	2022	APAF1-Binding Long Noncoding RNA Promotes Tumor Growth and Multidrug Resistance in Gastric Cancer by Blocking Apoptosome Assembly.	20
34898374	2022	Exosomal microRNA⁃93⁃3p secreted by bone marrow mesenchymal stem cells downregulates apoptotic peptidase activating factor 1 to promote wound healing.	15
35030371	2022	Apoptotic protease activating factor-1 gene and MicroRNA-484: A possible interplay in relapsing remitting multiple sclerosis.	3
35975461	2022	APAF1-Binding Long Noncoding RNA Promotes Tumor Growth and Multidrug Resistance in Gastric Cancer by Blocking Apoptosome Assembly.	20
33132160	2021	Loss of WD2 subdomain of Apaf-1 forms an apoptosome structure which blocks activation of caspase-3 and caspase-9.	8
33308446	2021	Apaf-1 Pyroptosome Senses Mitochondrial Permeability Transition.	51
33386492	2021	Intracellular leucine-rich alpha-2-glycoprotein-1 competes with Apaf-1 for binding cytochrome c in protecting MCF-7 breast cancer cells from apoptosis.	16
34298080	2021	Contribution of Apaf-1 to the pathogenesis of cancer and neurodegenerative diseases.	8
34507064	2021	Apaf1 nanoLuc biosensors identified lentinan as a potent synergizer of cisplatin in targeting hepatocellular carcinoma cells.	4

Citation

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)