The Fanconi Anemia Pathway in Cancer

Abstract

Fanconi anemia (FA) is a complex genetic disorder characterized by bone marrow failure (BMF), congenital defects, inability to repair DNA interstrand cross-links (ICLs), and cancer predisposition. FA presents two seemingly opposite characteristics: (a) massive cell death of the hematopoietic stem and progenitor cell (HSPC) compartment due to extensive genomic instability, leading to BMF, and (b) uncontrolled cell proliferation leading to FA-associated malignancies. The canonical function of the FA proteins is to collaborate with several other DNA repair proteins to eliminate clastogenic (chromosome-breaking) effects of DNA ICLs. Recent discoveries reveal that the FA pathway functions in a critical tumor-suppressor network to preserve genomic integrity by stabilizing replication forks, mitigating replication stress, and regulating cytokinesis. Homozygous germline mutations (biallelic) in 22 FANC genes cause FA, whereas heterozygous germline mutations in some of the FANC genes (monoallelic), such as BRCA1 and BRCA2, do not cause FA but significantly increase cancer susceptibility sporadically in the general population. In this review, we discuss our current understanding of the functions of the FA pathway in the maintenance of genomic stability, and we present an overview of the prevalence and clinical relevance of somatic mutations in FA genes.

Keywords: DNA interstrand cross-links; DNA repair; Fanconi anemia; genomic instability; somatic cancer.

Figure 1

Classification of Fanconi anemia genes and their molecular functions. Data from Frohnmayer et al. (2014). Abbreviations: FA, Fanconi anemia; FAAP, FA-associated proteins; HR, homologous recombination; ICL, interstrand cross-link; NER, nucleotide excision repair; PARPi, poly (ADP-ribose) polymerase inhibitor; TLS, translesion synthesis. ^a FAAPs are important for ICL repair, but to date no FA patient has been found harboring biallelic mutations of them.

Figure 2

Coordination of multiple DNA repair pathways in a common DNA ICL repair pathway. (a,b) Stalled replication forks at DNA ICLs are recognized by FANCM-FAAP24-MHF1-MFH2 (FAAPs) or UHRF1. Eviction of the replicative CMG helicase by BRCA1 allows one replication fork to approach the ICLs. (c) FANCM promotes the ATR kinase–dependent checkpoint response. (d) The FA core complex monoubiquitinates the FANCI-FANCD2 (ID2) complex. (e,f) FANCD2-Ub and SLX4/FANCP recruit SSEs to execute the unhooking step, generating DNA DSBs in the strand opposite to the strand on which the cross-linked nucleotide tethers. (g) DNA replication resumes by the bypass step, passing the tethered ICL by TLS polymerases, such as REV1 or Polζ. The USP1-UAF1 complex deubiquitinates the ID2 complex to efficiently execute the FA pathway. (h) The DSB ends are processed to generate single-strand DNA by the initial DSB resection machinery. The processed DSB ends can be repaired by alt-NHEJ. Alternatively, inhibition of end resection leads to direct ligation of the DNA ends by C-NHEJ. (i) Extensive DSB resection by EXO1 and the BLM-DNA2 complex generate longer stretches of RPA-coated ssDNA. (j) RPA is displaced by recombination mediators to load RAD51 to promote HR. (k,l) Alternatively, the repair is diverted to RAD52-mediated SSA. The different consequences of these DSB repair pathways are deletions, insertions, and LOH. The key players of each pathway are shown in the insets. Abbreviations: alt-NHEJ, alternative nonhomologous end joining; C-NHEJ, classical nonhomologous end joining; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; DSB, double-strand break; FA, Fanconi anemia; FAAPs, Fanconi anemia–associated proteins; HR, homologous recombination; ICL, interstrand cross-link; LOH, loss of heterozygosity; SSA, single-strand annealing; ssDNA, single-stranded DNA; SSE, structure-specific endonuclease; TLS, translesion synthesis.

Figure 3

Architecture of the Fanconi anemia (FA) core complex, with FAAPs (Fanconi anemia–associated proteins) indicated by numbers. The FAAP20-FANCG-FANCA subcomplex (red dotted line) is a link between the translesion synthesis (TLS) complex and the FA pathway through a direct interaction between FAAP20 and REV1, which interacts with REV3-REV7 (purple dotted line). FANCA gains its stability by binding to FAAP20, a small UBZ4-containing zinc finger protein that prevents its SUMOylation and RNF4-mediated degradation. The ternary complex FANCF-FANCC-FANCE (orange dotted line) bridges FANCD2, the substrate to the ICL-recognizing anchoring complex consisting of FANCM and FAAPs (gray solid line). Current understanding of mechanisms of FANCD2 monoubiquitination derived from biochemical and genetic approaches suggests that the FANCB-FANCL-FANC100-UBE2T complex (yellow dotted line) is a minimum module for FANCD2 and FANCI monoubiquitination.

Figure 4

Roles of FA proteins in replication stress. (a) The FANCI-FANCD2-Ub complex stabilizes the extracentromeric CFSs and mediates loading of the Bloom complex (BLM, RMI1, RMI2, and TOPOIII) on these under-replicated CFSs to ensure their protection, repair, and unperturbed mitosis. The endogenously produced R-loops (RNA-DNA hybrids) at some susceptible genetic loci are remodeled by the components of the FA pathway. (b) At low doses of replication stress, nonubiquitinated FANCD2 binds and inhibits the MCM2–7 helicase complex to restrain DNA synthesis. ATR stimulates binding of FANCD2 to MCM 2–7 to prevent p21-mediated cellular senescence by precluding the accumulation of ssDNA. FANCI also binds to MCM2–7 to fire dormant origins. The dormant origin firing by FANCI is inhibited by its phosphorylation by ATR kinase and the FANCD2-BLM complex. FANCM opposes fork movement, possibly by remodeling the stalled replication forks. (c) High doses of replication stress elicit the classical FA pathway. FANCA, FANCC, FANCJ, and FANCM, together with BOD1L, bind to nascent DNA strands to protect them from MRE11- or DNA2-mediated unwanted nucleolytic degradation. RAD51-ssDNA filaments on stalled replication forks are protected by BRCA1, BRCA2, and FANCD2-Ub by nucleases. Abbreviations: CFS, chromosomal fragile site; FA, Fanconi anemia; ssDNA, single-strand DNA; UFB, ultrafine bridge.

Figure 5

Genetic alterations of the Fanconi anemia (FA) genes (Figure 1) in somatic cancers. (a) Proportions of FA gene mutations and copy number variations in 3,407 cancers of nine common cancer types. (b) Proportions of FA genetic alterations by the FA pathway in 3,407 cancers. FA genes were divided into groups based on their functions listed in Figure 1. At least one FA gene alteration was detected in 40% of the cancers, FA/HR (homologous recombination) being the most commonly altered pathway. (c) Proportions of mutations, deletions, and amplifications in 1,363 FA-altered cancers. Data were generated by The Cancer Genome Atlas and were downloaded from cBioPortal on (a) March 28,2018 and (b,c) May3, 2018.