Donovan, F. X. | Search bioRxiv

bioRxiv2022

ALDH9A1 Deficiency as a Source of Endogenous DNA Damage that Requires Repair by the Fanconi Anemia Pathway

Fanconi anemia (FA) pathway is required for the repair of DNA interstrand crosslinks (ICL). ICLs are caused by genotoxins, such as chemotherapeutic agents or reactive aldehydes. Inappropriately repaired ICLs contribute to hematopoietic stem cell (HSC) failure and tumorigenesis. While endogenous acetaldehyde and formaldehyde are known to induce HSC failure and leukemia in humans with FA, the effects of other toxic metabolites in FA pathogenesis have not been systematically investigated. Using a metabolism-focused CRISPR screen, we found that ALDH9A1 deficiency causes synthetic lethality in FA pathway-deficient cells. Combined deficiency of ALDH9A1 and FANCD2 causes genomic instability, apoptosis, and decreased hematopoietic colony formation. Fanca-/-Aldh9a1-/- mice exhibited an increased incidence of ovarian tumors. A suppressor CRISPR screen revealed that the loss of ATP13A3, a polyamine transporter, resulted in improved survival of FANCD2-/-ALDH9A1-/- cells. These findings implicate high intracellular polyamines and the resulting 3-aminopropanal or acrolein in the pathogenesis of FA. In addition, we find that ALDH9A1 variants may be modifying disease onset in FA patients. Statement of SignificanceALDH9A1 deficiency is a previously unrecognized source of endogenous DNA damage. If not repaired by the Fanconi anemia pathway, such damage leads to increased genomic instability and tumorigenesis. Limiting substrates that accumulate when ALDH9A1 is absent can reduce aldehyde production and rescue synthetic lethality in the combined deficiency of ALDH9A1/FANCD2.

genetics↗

bioRxiv2021

Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas

Fanconi anemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink (ICL) repair resulting in chromosome breakage1-3. The FA repair pathway comprises at least 22 FANC proteins including BRCA1 and BRCA24-6, and protects against carcinogenic endogenous and exogenous aldehydes7-10. Individuals with FA are hundreds to thousands-fold more likely to develop head and neck (HNSCC), esophageal and anogenital squamous cell carcinomas (SCCs) with a median onset age of 31 years11. The aggressive nature of these tumors and poor patient tolerance of platinum and radiation-based therapy have been associated with short survival in FA11-16. Molecular studies of SCCs from individuals with FA (FA SCCs) have been limited, and it is unclear how they relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or human papillomavirus (HPV) infection17. Here, by sequencing FA SCCs, we demonstrate that the primary genomic signature of FA-deficiency is the presence of a high number of structural variants (SVs). SVs are enriched for small deletions, unbalanced translocations, and fold-back inversions that arise in the context of TP53 loss. The SV breakpoints preferentially localize to early replicating regions, common fragile sites, tandem repeats, and SINE elements. SVs are often connected forming complex rearrangements. Resultant genomic instability underlies elevated copy number alteration (CNA) rates of key HNSCC-associated genes, including PIK3CA, MYC, CSMD1, PTPRD, YAP1, MXD4, and EGFR. In contrast to sporadic HNSCC, we find no evidence of HPV infection in FA HNSCC, although positive cases were identified in gynecologic tumors. A murine allograft model of FA pathway-deficient SCC was enriched in SVs, exhibited dramatic tumor growth advantage, more rapid epithelial-to-mesenchymal transition (EMT), and enhanced autonomous inflammatory signaling when compared to an FA pathway-proficient model. In light of the protective role of the FA pathway against SV formation uncovered here, and recent findings of FA pathway insufficiency in the setting of increased formaldehyde load resulting in hematopoietic stem cell failure and carcinogenesis18-20, we propose that high copy-number instability in sporadic HNSCC may result from functional overload of the FA pathway by endogenous and exogenous DNA crosslinking agents. Our work lays the foundation for improved FA patient treatment and demonstrates that FA SCC is a powerful model to study tumorigenesis resulting from DNA crosslinking damage.

cancer biology↗