Fanconi anemia and the underlying causes of genomic instability

Abstract

Fanconi anemia (FA) is a rare genetic disorder, characterized by birth defects, progressive bone marrow failure, and a predisposition to cancer. This devastating disease is caused by germline mutations in any one of the 22 known FA genes, where the gene products are primarily responsible for the resolution of DNA interstrand cross-links (ICLs), a type of DNA damage generally formed by cytotoxic chemotherapeutic agents. However, the identity of endogenous mutagens that generate DNA ICLs remains largely elusive. In addition, whether DNA ICLs are indeed the primary cause behind FA phenotypes is still a matter of debate. Recent genetic studies suggest that naturally occurring reactive aldehydes are a primary source of DNA damage in hematopoietic stem cells, implicating that they could play a role in genome instability and FA. Emerging lines of evidence indicate that the FA pathway constitutes a general surveillance mechanism for the genome by protecting against a variety of DNA replication stresses. Therefore, understanding the DNA repair signaling that is regulated by the FA pathway, and the types of DNA lesions underlying the FA pathophysiology is crucial for the treatment of FA and FA-associated cancers. Here, we review recent advances in our understanding of the relationship between reactive aldehydes, bone marrow dysfunction, and FA biology in the context of signaling pathways triggered during FA-mediated DNA repair and maintenance of the genomic integrity. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.

Keywords: ALDH2; DNA-protein cross-link; Fanconi anemia; bone marrow failure; reactive aldehydes.

Figure 1.. The causes and effects of Fanconi anemia (FA)

FA is a rare genetic disorder with onset of symptoms at a young age, primarily affecting bone marrow function in conjunction with developmental abnormalities. It is caused by germ-line mutations in the FA genes, which lead to deficiencies in coping with DNA damage, especially damage from DNA ICLs. The FA gene products constitutes the FA DNA repair pathway that resolves DNA ICLs and other lesions generated by endogenous cross-linkers, exogenous genotoxins, and cytotoxic chemotherapeutic agents such as platinum and nitrogen mustards. Due to their reduced ability to counteract genome instability, affected children are highly susceptible to a variety of cancers.

Figure 2.. FA signaling in the DNA ICL repair pathway

(A) A DNA ICL is recognized by the FANCM-FAAP24-MHF1/2 (FAAP16/FAAP10) complex and UHRF1 at stalled replication forks. CMG unloading is required for the replication fork to approach the ICL and is mediated by TRAIP-dependent MCM7 polyubiquitination and extraction from DNA by the AAA+ ATPase p97/VCP. (B) FANCM at stalled forks promotes the ATR checkpoint and activates the FA core complex, targeting it to DNA ICLs. The FA core complex is composed of three central modules that are responsible for catalysis, structural integrity, and substrate targeting. (C) UBE2T ubiquitin E2 conjugating enzyme and the FA core ubiquitin E3 ligase complex monoubiquitinate FANCD2 to target the ID complex to ICLs. (D) FANCD2-Ub functions as a platform to recruit the SLX4/FANCP-XPF/FANCQ nuclease complex to incise and unhook the DNA ICL. The SNM1A exonuclease may process the unhooked intermediate to facilitate downstream lesion bypass. (E) The lesion bypass by the REV1-polζ TLS polymerase complex restores the nascent strand and resumes replication. (F) The DNA double-strand break (DSB) ends are processed and repaired by HR, which is mediated by the recombinase RAD51/FANCR and its associated HR factors. Regulated turnover of RAD51 (and RPA) by RFWD3/FANCW is required for completion of the HR step. (G) FANCD2-Ub activity is downregulated by the USP1-UAF1 deubiquitinase complex and p97-dependent extraction of the ID complex from DNA lesions.

Figure 3.. Mechanisms of reactive aldehyde detoxification cooperating to preserve HSC function

The elevated ALDH2 and ADH5 activities in HSCs alleviate the genotoxic effect of endogenous reactive aldehydes, such as acetaldehyde and formaldehyde. DNA damage caused by reactive aldehydes is resolved by the FA pathway, which would otherwise result in exhaustion of the HSC pool via activation of p53. In Aldh2^−/− Fancd2^−/− DKO mice, the burden of accumulated reactive aldehydes in the absence of the FA pathway leads to HSC dysfunction, spontaneous BMF, and cellular transformation.

Figure 4.. DNA protein cross-link (DPC) repair pathway

(A) DPCs are generated by physiological processes (e.g. formaldehyde from histone demethylation), nucleic acids metabolism (e.g. TOPcc intermediate), or experimentally in vitro (e.g. M. HpaII adduct introduced into a plasmid). In Xenopus egg extracts, when the CMG helicase collides a DPC lesion, the ubiquitin E3 ligase TRAIP stimulates DPC ubiquitination and proteasome targeting. (B) CMG bypasses an intact DPC, which is facilitated by the DNA helicase RTEL1. CMG bypass is required for efficient DPC proteolysis, which occurs either by ubiquitin-dependent proteasome activity or by the metalloprotease SPRTN with the help of the ATP-driven p97 segregase in a post-replicative manner. Unlike DNA ICL repair, this process does not involve CMG unloading or incision of a stalled fork. (C) Leading strand extension resumes via TLS, which is mediated by the REV1-Pol ζ (FANCV) TLS polymerase complex. The role of FANCD2-Ub in DPC repair is currently not clear, and whether the FA pathway directly regulates DPC repair has yet to be determined. The FA core complex may promote the recruitment of TLS polymerases independently of FANCD2-Ub.