Abstract The Fanconi anaemia (FA) DNA repair pathway is an emerging target for precision cancer therapy. Using a high-throughput FANCD2-monoubiquitination assay, we identified a class of small molecules, including MSG010, that inhibit the FA E3 ligase complex in vitro . Because these molecules, and the metabolite, palmitoyl-CoA, are known to engage allosteric drug and metabolite (ADaM) binding site in AMP-activated kinase (AMPK), we hypothesised that a similar pocket exists within the FA complex. Supporting this, long-chain, but not short-chain, fatty acyl-CoA molecules inhibited the FA E3 ligase complex activity, and sequence analysis revealed similarity between the AMPK ADaM site and a WD40 repeat in the FA subunit FANCX. Targeted mutagenesis of this FANCX region disrupted E3 ligase activity or abolished inhibition by MSG010, suggesting the presence of an ADaM-like site in FANCX. Moreover, MSG010 preferentially killed BRCA1 -deficient cells in vitro . These findings identify a putative small-molecule binding site in the FA pathway that may be developed further to test for exploitation as anticancer therapeutics.

Protein-protein interactions (PPIs) form complex cellular networks fundamental to many key biological processes, including signal transduction, cell proliferation and DNA repair. In consequence, their perturbation is often associated with many human diseases. Targeting PPIs offers a promising approach in drug discovery and ongoing advancements in this field hold the potential to provide highly specific therapies for a wide range of complex diseases. Despite the development of PPI modulators is challenging, advances in the genetic, proteomic and computational level have facilitated their discovery and optimization. Focusing on anticancer drugs, in the last years several PPI modulators have entered clinical trials and venetoclax, which targets Bcl-2 family proteins, has been approved for treating different types of leukemia. This review discusses the clinical development status of drugs modulating several PPIs, such as MDM2-4/p53, Hsp90/Hsp90, Hsp90/CDC37, c-Myc/Max, KRAS/SOS1, CCR5/CCL5, CCR2/CCL2 or Smac/XIAP, in cancer drug discovery.

Recessive Fanconi anemia (FA) phenotype is used in classification of BRCA1/FANCS, BRCA2/FANCD1 and PALB2/FANCN variants with respect to dominant hereditary breast-ovarian cancer syndrome. We assessed its utility by examining the spectrum of phenotypes observed in individuals biallelic for BRCA1, BRCA2 or PALB2 pathogenic variants, and exploring the relationship between cancer presentation and allele severity score based on variant molecular features. A data collection instrument comprising 158 Human Phenotype Ontology (HPO) terms was used to document clinical features for individuals with FA from published and/or prospectively collected (total n=172, 43 previously unpublished) phenotypic data. Unique FA-related variants (15 BRCA1, 123 BRCA2, 22 PALB2) were annotated for predicted molecular impact, location, observed splicing or functional impact, and potential in-frame splice rescue. Annotations were used to assign different permutations of allele severity scores, which were assessed for correlation with FA presentation features. The association of BRCA1 and BRCA2 allele severity score with magnitude of breast cancer risk in heterozygotes was evaluated using case-control analysis. Patient-detected features extended beyond the FA ORPHA:84 HPO list, including 84 terms related by hierarchy, and 94 novel terms. Genotype severity score was significantly associated with age at cancer diagnosis in BRCA2 FA individuals (p=1.8×10-8). A similar permutation approach revealed significant differences in magnitude of breast cancer risk according to BRCA1 and BRCA2 allele severity score in heterozygotes. Findings indicate potential to redefine the existing list of FA-related HPO terms, and to use an allele severity scoring approach to predict cancer risk in both FA patients and heterozygotes.

Individuals diagnosed with Fanconi anemia (FA) present an incidence of 500- to 700-fold higher to develop head and neck squamous carcinomas (HNSCCs) compared to the general population. Effective anticancer treatments for FA-HNSCCs are missing. Several studies demonstrated that FA-HNSCCs overexpress the epithelial growth factor receptor (EGFR) and their viability is highly dependent on this pathway, as FA-HNSCCs cells are highly sensitive to EGFR inhibitors such as afatinib in preclinical models, which led to an orphan drug designation by EMA in 2018. The AFAN trial is a phase Ib/II, single arm, non-randomized, open-label, multicenter study to determine whether afatinib is effective and safe in patients with FA and advanced / metastatic HNSCC. Patients could be treatment-naïve or progressed to a previous systemic treatment with immunotherapy, chemotherapy or cetuximab. Afatinib will be administered orally at a starting dose of 20 mg /day (weeks 1–2), escalating to 30 mg / day at weeks 3–4 and to 40 mg / day thereafter provided no adverse events occur. Treatment will be maintained until disease progression / secondary primary tumor, loss to follow-up, unacceptable toxicity, patient withdrawal or death. Dose reductions and delays will be allowed. All patients will undergo periodic tumor assessments by CT or MRI scan every 12 weeks (3 months) from the start of the study treatment until progression / SPT or patient withdrawal. The primary endpoint is objective response rate (ORR) after 9 months of study treatment initiation according to RECIST V1.1. Secondary endpoints include disease control rate, duration of response, disease-free survival, overall survival, safety, patient reported outcomes and ancillary studies. The expected sample size is 25 patients calculated using a Simon II stage design (α = 0.1; β = 80

Eltrombopag stimulates hematopoiesis in aplastic anemia, and preclinical studies suggest it promotes DNA repair in Fanconi Anemia (FA) hematopoietic stem cells. We conducted a clinical trial to explore its safety and efficacy in bone marrow failure due to FA. Eltrombopag was administered to 8 pediatric patients with one or more significant cytopenias. After 6 months, those who achieved at least a partial response in peripheral blood continued treatment for 6 additional months. Median age was 7 years (4-12), one patient had somatic mosaicism in bone marrow, and two had been treated by gene therapy (GT). At 6 months, three patients (37.5%) achieved a response, persisting in one at 12 months. The three patients with either somatic mosaicism or with GT-corrected cells showed an enhanced increase of corrected cells. One patient required dose modifications due to gastrointestinal intolerance and two because of hepatobiliary laboratory toxicity. No clonal evolution was observed by conventional cytogenetics, but a patient developed a transient somatic variant in RUNX1. In conclusion, eltrombopag did not mediate clinically relevant responses, although a possible impact of dose reductions and treatment duration must be considered. The increase of gene-corrected cells suggests it promoted a proliferative advantage over uncorrected ones. Www.clinicaltrials.gov #NCT06045052.

Fanconi Anemia (FA) is an inherited disorder associated with profound DNA repair defects, marked by failure to thrive, congenital malformations, progressive bone marrow failure (BMF), and an increased susceptibility to cancer. Clinical manifestations of FA vary widely, with BMF and clonal evolution predominantly affecting younger individuals, while adults are more frequently presenting with solid tumors. Individuals with FA are at a 500-fold increased risk of developing head and neck squamous cell carcinoma (HNSCC), which tends to appear at a median age of 30 years, often at advanced stages with only a 57 % two-year survival rate. The DNA repair deficiency prohibits the use of cisplatin and radiation therapy, limiting the treatment options for FA patients. Given the critical importance of early HNSCC detection in FA patients, innovative and less invasive diagnostic techniques are needed. This review discusses the role of brush biopsy-based cytology combined with molecular and morphometric analyses, as well as next-generation sequencing. Cytology alone demonstrated significant potential for detecting high-grade oral epithelial dysplasia and early-stage HNSCC, achieving sensitivities and specificities of 97.7 % and 84.5 %, respectively. Such techniques allow for stringent surveillance of the oral cavity in FA patients, essential given the aggressive nature of HNSCC in FA and the limited treatment options. In the absence of oral mucosal lesions, a six-month follow-up is recommended. For oral lesions persisting beyond three weeks, diagnostic evaluation is warranted, with clinical follow-up every three months for low-grade dysplasia and treatment of high-grade dysplasia. Integrating modern diagnostic tools within a comprehensive screening framework, alongside patient participation, is essential for personalized care, improved surveillance, and developing preventive measures to enhance FA patient care.

Initial Whole Exome Sequencing frequently fails to resolve rare disease cases. Bioinformatic reanalysis of existing genomic data utilizes advancing knowledge to enhance diagnosis without additional testing. This study investigated six patients with clinical features consistent with Fanconi Anemia but negative chromosomal breakage tests, whose initial genetic analyses were inconclusive. Whole Exome Sequencing data from these patients (collected 2005–2009) underwent comprehensive reanalysis, including single nucleotide variants, insertions/deletions, and copy number variants across genes beyond those typically associated with Fanconi Anemia. Telomere length was assessed via monochrome multiplex quantitative PCR. Reanalysis identified clinically significant variants in two patients (33.3

Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and atypical physical features whose genetic diagnosis was initially inconclusive. Over time, his bone marrow karyotype shifted from diploid (46,XY) to triploid (69,XXY). The triploid cells lacked the Fanconi anemia cellular phenotype, enabling sustained hematopoiesis and providing an unexpected route to phenotypic rescue. Genomic analysis indicated early post-zygotic incorporation of the second polar body as the triploid origin. These findings suggest that the selective advantage of restored DNA repair in hematopoietic stem cells, outweigh the potentially deleterious effects of triploidy. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement W.C. receives a fellowship related to this work from the Victorian Cancer Agency (MCRF21006) and funding from the National Health and Medical Research Council (GNT2030115). SVI receives Operational Infrastructure Support from the Victorian State Government. The funding bodies played no role in the research. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Human Research Ethics Committee of the Royal Childrens Hospital, Melbourne, Australia gave ethical approval for this work. Study participants provided written informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

The recessive Fanconi anemia (FA) phenotype is used to classify BRCA1 (FANCS), BRCA2 (FANCD1), and PALB2 (FANCN) variants with respect to dominant hereditary breast-ovarian cancer syndrome. We assessed its utility by examining the phenotypic spectrum observed in individuals with bi-allelic BRCA1, BRCA2, or PALB2 pathogenic variants and exploring the relationship between cancer presentation and allele severity score based on variant molecular features. A data collection instrument comprising 158 Human Phenotype Ontology (HPO) terms was used to document clinical features for individuals with FA from published and/or prospectively collected sources (total n = 172, 43 previously unpublished). Distinct FA-related variants (15 BRCA1, 123 BRCA2, and 22 PALB2) were annotated for predicted molecular impact, location, observed splicing or functional impact, and potential in-frame splicing rescue and used to assign different permutations of allele severity scores, which were assessed for correlation with FA presentation features. The association of BRCA1 and BRCA2 allele severity score with the magnitude of breast cancer risk in heterozygotes was evaluated using case-control analysis. Clinical features extended beyond the HPO list, including 84 terms related by hierarchy and 94 additional terms. The BRCA2 genotype severity score was associated with age at cancer diagnosis in individuals with FA (p = 1.8 × 10-8). A similar permutation approach revealed significant differences in the magnitude of breast cancer risk according to the BRCA1 and BRCA2 allele severity score in heterozygotes. Our findings indicate the potential to redefine FA ORPHA:84 HPO terms and to use an allele severity scoring approach to predict cancer risk in individuals with bi-allelic or heterozygous BRCA1 or BRCA2 variants.

Fanconi anemia (FA) is a rare genetic disease characterized by high phenotypic and genotypic heterogeneity, and extreme chromosome fragility. To better understand the natural history of FA, identify genetic risk and prognostic factors, and develop novel therapeutic strategies, the Spanish Registry of Patients with FA collects data on clinical features, chromosome fragility, genetic subtypes, and DNA sequencing with informed consent of participating individuals. In this article, we describe the clinical evolution of 227 patients followed up for up to 30 years, for whom our data indicate a cumulative cancer incidence of 86% by age 50. We found that patients with lower chromosome fragility had a milder malformation spectrum and better outcomes in terms of later-onset hematologic impairment, less severe bone marrow failure, and lower cancer risk. We also found that outcomes were better for patients with mutations leading to mutant FANCA protein expression (genetic hypomorphism) than for patients lacking this protein. Likewise, prognosis was consistently better for patients with biallelic mutations in FANCD2 (mainly hypomorphic mutations) than for patients with biallelic mutations in FANCA and FANCG , with the lack of the mutant protein in patients with biallelic mutations in FANCG contributing to their poorer outcomes. Our results regarding the clinical impact of chromosome fragility and genetic hypomorphism suggest that mutant FA proteins retain residual activity. This finding should encourage the development of novel therapeutic strategies aimed at partially or fully enhancing mutant FA function, thereby preventing or delaying bone marrow failure and cancer in patients with FA. Clinical Trial Registration number: NCT06490510.

Introduction: Fanconi anemia (FA) is a genome instability condition that drives somatic mosaicism in up to 25% of all patients, a phenomenon now acknowledged as a good prognostic factor. Herein, we describe the case of P1, a FA proband carrying a splicing variant, molecularly compensated by a de novo insertion. Methods and Results: Targeted next-generation sequencing on P1's peripheral blood DNA detected the known FANCA c.2778 + 83C > G intronic mutation and suggested the presence of a large deletion on the other allele, which was then assessed by MLPA and RT-PCR. To determine the c.2778 + 83C > G splicing effect, we performed a RT-PCR on P1's lymphoblastoid cell line (LCL) and on the LCL of another patient (P2) carrying the same variant. Although we confirmed the expected alternative spliced form with a partial intronic retention in P2, we detected no aberrant products in P1's sample. Sequencing of P1's LCL DNA allowed identification of the de novo c.2778 + 86insT variant, predicted to compensate 2778 + 83C > G impact. Albeit not found in P1's bone marrow (BM) DNA, c.2778 + 86insT was detected in a second P1's LCL established afterward, suggesting its occurrence at a low level in vivo. Minigene assay recapitulated the c.2778 + 83C > G effect on splicing and the compensatory role of c.2778 + 86insT in re-establishing the physiological mechanism. Accordingly, P1's LCL under mitomycin C selection preserved the FA pathway activity in terms of FANCD2 monoubiquitination and cell survival. Discussion: Our findings prove the role of c.2778 + 86insT as a second-site variant capable of rescuing c.2778 + 83C > G pathogenicity in vitro, which might contribute to a slow hematopoietic deterioration and a mild hematologic evolution.

Antecedentes: la Anemia de Fanconi (AF) es una enfermedad heredada, que afecta la reparación del ADN. Clínicamente es heterogénea; mayoritariamente se presentan malformaciones congénitas, aplasia medular temprana y predisposición a cáncer. El defecto genético causa hipersensibilidad a genotóxicos e inestabilidad cromosómica. Esta característica se considera el mejor marcador diagnóstico; sin embargo, llegar a él puede convertirse en un desafío. Objetivo: caracterizar pacientes con AF mediante pruebas citogenéticas en individuos con rasgos clínicos sugestivos de la enfermedad. Métodos: se analizaron 157 individuos con sospecha clínica de AF, 19 con asociación VACTERL, 15 hermanos, y 34 individuos sanos. Se realizó registro de datos clínicos, y prueba citogenética con Diepoxibutano (DEB). Resultados: se identificaron 43 afectados por AF. La relación de índices en células tratadas con DEB del grupo AF vs. No-AF fue significativamente incrementada, 6.7 veces la proporción de células aberrantes, 48 veces el número de roturas por célula, y 6.3 veces el número de roturas por célula aberrante. En AF la edad media de muestreo fue 9.2 años, la proporción de sexos M:F 1.5:1, consanguinidad en 11 casos. Los sistemas hematológico, esquelético, tegumentario, y urinario estuvieron significativamente alterados. Conclusiones: La AF se identificó en 26 % del grupo de sospecha y en 13 % de hermanos sin sospecha previa. La enfermedad hematológica fue el síntoma más recurrente presente en 93 % de los casos, y fue principalmente la primera sospecha de AF y motivo de estudio genético.

Fanconi anemia (FA) is the most prevalent inherited bone marrow failure (BMF) syndrome. Nevertheless, the pathophysiological mechanisms of BMF in FA have not been fully elucidated. Since FA cells are defective in DNA repair, we hypothesized that FA hematopoietic stem and progenitor cells (HSPCs) might express DNA damage-associated stress molecules such as natural killer group 2 member D ligands (NKG2D-Ls). These ligands could then interact with the activating NKG2D receptor expressed in cytotoxic NK or CD8(+) T cells, which may result in progressive HSPC depletion. Our results indeed demonstrated upregulated levels of NKG2D-Ls in cultured FA fibroblasts and T cells, and these levels were further exacerbated by mitomycin C or formaldehyde. Notably, a high proportion of BM CD34(+) HSPCs from patients with FA also expressed increased levels of NKG2D-Ls, which correlated inversely with the percentage of CD34(+) cells in BM. Remarkably, the reduced clonogenic potential characteristic of FA HSPCs was improved by blocking NKG2D-NKG2D-L interactions. Moreover, the in vivo blockage of these interactions in a BMF FA mouse model ameliorated the anemia in these animals. Our study demonstrates the involvement of NKG2D-NKG2D-L interactions in FA HSPC functionality, suggesting an unexpected role of the immune system in the progressive BMF that is characteristic of FA.

Fanconi anemia (FA) patients frequently develop oral squamous cell carcinoma (OSCC). This cancer in FA patients is diagnosed within the first 3-4 decades of life, very often preceded by lesions that suffer a malignant transformation. In addition, they respond poorly to current treatments due to toxicity or multiple recurrences. Translational research on new chemopreventive agents and therapeutic strategies has been unsuccessful partly due to scarcity of disease models or failure to fully reproduce the disease. Here we report that Fanca gene knockout mice (Fanca-/-) frequently display pre-malignant lesions in the oral cavity. Moreover, when these animals were crossed with animals having conditional deletion of Trp53 gene in oral mucosa (K14cre;Trp53F2-10/F2-10), they spontaneously developed OSCC with high penetrance and a median latency of less than ten months. Tumors were well differentiated and expressed markers of squamous differentiation, such as keratins K5 and K10. In conclusion, Fanca and Trp53 genes cooperate to suppress oral cancer in mice, and Fanca-/-;K14cre;Trp53F2-10/F2-10 mice constitute the first animal model of spontaneous OSCC in FA.

BRCA2 is essential for homologous recombination DNA repair. BRCA2 mutations lead to genome instability and increased risk of breast and ovarian cancer. Similarly, mutations in BRCA2-interacting proteins are also known to modulate sensitivity to DNA damage agents and are established cancer risk factors. Here we identify the tumor suppressor CDK5RAP3 as a novel BRCA2 helical domain-interacting protein. CDK5RAP3 depletion induced DNA damage resistance, homologous recombination and single-strand annealing upregulation, and reduced spontaneous and DNA damage-induced genomic instability, suggesting that CDK5RAP3 negatively regulates double-strand break repair in the S-phase. Consistent with this cellular phenotype, analysis of transcriptomic data revealed an association between low CDK5RAP3 tumor expression and poor survival of breast cancer patients. Finally, we identified common genetic variations in the CDK5RAP3 locus as potentially associated with breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. Our results uncover CDK5RAP3 as a critical player in DNA repair and breast cancer outcomes.

Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage1-3. The FA repair pathway protects against endogenous and exogenous carcinogenic aldehydes4-7. Individuals with FA are hundreds to thousands fold more likely to develop head and neck (HNSCC), oesophageal and anogenital squamous cell carcinomas8 (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or infection with human papillomavirus9 (HPV). Here, by sequencing genomes and exomes of FA SCCs, we demonstrate that the primary genomic signature of FA repair deficiency is the presence of high numbers of structural variants. Structural variants are enriched for small deletions, unbalanced translocations and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not in the context of HPV infection, and lead to somatic copy-number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte-intrinsic inflammatory signalling, which would contribute to the aggressive nature of FA SCCs. We propose that the genomic instability in sporadic HPV-negative HNSCC may arise as a result of the FA repair pathway being overwhelmed by DNA interstrand crosslink damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA-crosslinking damage.