Fanconi Anemia Pathway Genes Research Articles

Clinical Validation of the Somatic FANCD2 Mutation (c.2022-5C>T) as a Novel Molecular Biomarker for Early Disease Progression in Chronic Myeloid Leukemia: A Case-Control Study.

Background: Chronic myeloid leukemia (CML) results from chromosomal translocation t(9;22) leading to the formation of the BCR-ABL fusion oncogene. CML has three stages: the chronic phase (CP), the accelerated phase (AP), and the blast crisis (BC). Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of CML. TKIs work well in CP-CML, and these patients have a survival rate similar to the normal population, but TKIs are less effective in advanced-phase CML. Even with current advances in treatment, BC-CML patients have an average overall survival of less than a year. Early recognition of CML patients at risk of disease progression can help in timely interventions with appropriate TKIs or other therapeutic modalities. Although some markers of disease progression like BCR-ABL kinase domain, ASXL1, and GATA2 mutations are available, no universal and exclusively specific molecular biomarkers exist to early diagnose CML patients at risk of CML progression for timely therapeutic interventions to delay or minimize blast crisis transformation in CML. A recent study found that all BC-CML patients harbored the FANCD2 (c.2022-5C>T) mutation. Therefore, the current study was designed to detect this FANCD2 mutant in AP-CML (early progression phase) and to clinically validate its potential as a novel molecular biomarker of early CML progression from CP to AP. Methods: Our study comprised 123 CP-CML (control group) and 60 AP-CML patients (experimental group) from 2 oncology centers, from January 2020 to July 2023. Mean hemoglobin level, WBC count, platelet count, treatment type, hepatomegaly, splenomegaly, and survival status of AP-CML patients were significantly different from those of CP-CML patients. However, as these clinical parameters cannot help in the early detection of patients at risk of CML progression, there was a need for a clinically validated biomarker of AP-CML. DNA was extracted from the patients' blood samples, and the FANCD2 gene was sequenced using an Illumina NextSeq500 next-generation sequencer (NGS). Results: The NGS analysis revealed a unique splice-site mutation in the FANCD2 gene (c.2022-5C>T). This mutation was detected in the majority (98.3%) of AP-CML patients but in none of the CP-CML patients or healthy control sequences from genomic databases. The mutation was confirmed by Sanger sequencing. FANCD2 is a member of the Fanconi anemia pathway genes involved in DNA repair and genomic stability, and aberrations of this gene are associated with many cancers. Conclusions: In conclusion, our study shows that the somatic FANCD2 (c.2022-5C>T) mutation is a new molecular biomarker for early CML progression. We recommend further clinical validation of this biomarker in prospective clinical trials.

Abstract A025: FANCI regulates Fanconi anemia pathway and counteracts the effects of DNA damaging chemotherapy in prostate cancer

Abstract Prostate cancer is one of the leading causes of death among men worldwide and thus research on the genetic factors enabling the formation of treatment resistant cancer cells is crucial for improving patient outcomes. Here, we report a cell-line specific dependence on FANCI and related signaling pathways to counteract effects of DNA damaging chemotherapy in prostate cancer. Our results reveal that FANCI depletion results in significant downregulation of Fanconi anemia (FA) pathway members in prostate cancer cells indicating that FANCI is an important regulator of FA pathway. Furthermore, we found that FANCI silencing reduces proliferation in p53-expressing prostate cancer cells. This extends the evidence that inactivation of FANCI may convert cancer cells from a resistant to an eradicable state under the stress of DNA-damaging chemotherapy. Our results also indicate that high expression of FA pathway genes correlates with poorer survival in prostate cancer patients. Moreover, genomic alterations of FA pathway members are prevalent in prostate adenocarcinoma patients; mutation and copy number information for the FA pathway genes in seven patient cohorts (N = 1732 total tumor samples) reveals that 1025 (59.2%) tumor samples have an alteration in at least one of the FA pathway genes, suggesting that genomic alteration of the pathway is a prominent feature in patients with the disease. Citation Format: Heidi Kaljunen, Sinja Taavitsainen, Roosa Kaarijärvi, Eerika Takala, Ville Paakinaho, Matti Nykter, G. Steven Bova, Kirsi Ketola. FANCI regulates Fanconi anemia pathway and counteracts the effects of DNA damaging chemotherapy in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A025.

Mutation spectrum, expression profiling, and prognosis evaluation of Fanconi anemia signaling pathway genes for 4259 patients with myelodysplastic syndromes or acute myeloid leukemia

BackgroundIndividuals diagnosed with Fanconi anemia (FA), an uncommon disorder characterized by chromosomal instability affecting the FA signaling pathway, exhibit heightened vulnerability to the onset of myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML).MethodsHerein, we employed diverse bioinformatics and statistical analyses to investigate the potential associations between the expression/mutation patterns of FA pathway genes and MDS/AML.ResultsThe study included 4295 samples, comprising 3235 AML and 1024 MDS from our and nine other online cohorts. We investigated the distinct proportion of race, age, French-American-British, and gender factors. Compared to the FA wild-type group, we observed a decrease in the expression of FNACD2, FANCI, and RAD51C in the FA mutation group. The FA mutation group exhibited a more favorable clinical overall survival prognosis. We developed a random forest classifier and a decision tree based on FA gene expression for cytogenetic risk assessment. Furthermore, we created an FA-related Nomogram to predict survival rates in AML patients.ConclusionsThis investigation facilitates a deeper understanding of the functional links between FA and MDS/AML.

Fanconi anemia pathway regulation by FANCI in prostate cancer.

Prostate cancer is one of the leading causes of death among men worldwide, and thus, research on the genetic factors enabling the formation of treatment-resistant cancer cells is crucial for improving patient outcomes. Here, we report a cell line-specific dependence on FANCI and related signaling pathways to counteract the effects of DNA-damaging chemotherapy in prostate cancer. Our results reveal that FANCI depletion results in significant downregulation of Fanconi anemia (FA) pathway members in prostate cancer cells, indicating that FANCI is an important regulator of the FA pathway. Furthermore, we found that FANCI silencing reduces proliferation in p53-expressing prostate cancer cells. This extends the evidence that inactivation of FANCI may convert cancer cells from a resistant state to an eradicable state under the stress of DNA-damaging chemotherapy. Our results also indicate that high expression of FA pathway genes correlates with poorer survival in prostate cancer patients. Moreover, genomic alterations of FA pathway members are prevalent in prostate adenocarcinoma patients; mutation and copy number information for the FA pathway genes in seven patient cohorts (N = 1,732 total tumor samples) reveals that 1,025 (59.2%) tumor samples have an alteration in at least one of the FA pathway genes, suggesting that genomic alteration of the pathway is a prominent feature in patients with the disease.

Abstract 1371: Tumor treating fields exposure causes an imbalance of reactive oxygen homeostasis likely through the cytosolic function of the fanconi′s anemia genes

Abstract The use of Tumor Treating Fields (TTFields) has been shown to significantly benefit patients with non-resectable locally advanced or metastatic glioblastoma and malignant pleural mesothelioma. Although the disruption of mitosis that was initially attributed as the mechanism of tumor cell killing, in subsequent studies, it has been shown that TTFields inhibits DNA damage repair by downregulating DNA repair genes and proteins, including those associated with Fanconi's Anemia (FA). As a result, radiation-induced DNA damage repair is reduced and DNA replication fork protection is impaired, leading to replication stress and replication fork collapse. As the FA genes play a critical role in multiple repair pathways, TTFields is likely to increase susceptibility to other chemo agents besides radiation that cause DNA damage which is repaired by FA-dependent DNA repair and replication fork maintenance pathways in nuclei. In addition to their nuclear role, the FA proteins also regulate mitophagy in the cytosol. Using a panel of non-small cell lung cancer cell lines, it was found that TTFields exposure disrupted the clearance of damaged mitochondria despite the presence of a well-defined membrane markers for autophagosomal destruction of damaged mitochondria, that being PINK1 and parkin. Analysis of electron micrographs revealed disrupted mitochondrial cristae, while radical oxygen metabolism studies identified an imbalance leading to the production of reactive oxygen species (ROS) and ultimately, cell death. The downregulation of key mitochondrial genes including DAPIT, OSCP1, ATP5S, ATP5B and COXIV that are related to electron transport and mitochondrial integrity was confirmed by gene expression analysis. The small molecule dichloroacetate (DCA), an inhibitor of pyruvate dehydrogenase kinase, changes the metabolic state of cancer cells from cytoplasmic glycolysis to mitochondrial glucose oxidation, resulting in a decrease in mitochondrial membrane potential and an increase in ROS production in cancer cells. A combination of DCA with TTFields is therefore being investigated as a means of exploiting mitochondrial dysfunction caused by TTFields. The inhibition of mitophagy suggests a new mechanism of action for TTFields exposure tied to the downregulation of the FA pathway genes, the result being both nuclear and cytosolic perturbations in cell homeostasis. This study offers an evidence-based rationale for combining TTFields with various chemotherapy agents that may cause DNA damage, induce replication stress, and expose cells to radical oxygen byproducts of disrupting electron transport chains and the disruption of mitochondrial integrity. Citation Format: Narasimha Kumar Karanam, Michael Story. Tumor treating fields exposure causes an imbalance of reactive oxygen homeostasis likely through the cytosolic function of the fanconi′s anemia genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1371.

Long non-coding RNA TILR constitutively represses TP53 and apoptosis in lung cancer.

Non-coding RNAs have an integral regulatory role in numerous functions related to lung cancer development. Here, we report identification of a novel lncRNA, termed TP53-inhibiting lncRNA (TILR), which was found to function as a constitutive negative regulator of p53 expression, including activation of downstream genes such as p21 and MDM2, and induction of apoptosis. A proteomic search for TILR-associated proteins revealed an association with PCBP2, while the mid-portion of TILR was found to be required for both PCBP2 and p53 mRNA binding. In addition, depletion of PCBP2 resulted in phenocopied effects of TILR silencing. TILR was also shown to suppress p53 expression in a post-transcriptional manner, as well as via a positive feedback loop involving p53 and Fanconi anemia pathway genes. Taken together, the present findings clearly demonstrate that TILR constitutively inhibits p53 expression in cooperation with PCBP2, thus maintaining p53 transcriptional activity at a level sufficiently low for avoidance of spurious apoptosis induction.

High-Throughput DNA Sequencing Identifies a Novel Splice-Site Mutation in Fanconi Anemia Pathway Gene FANCD2 As a Potential Biomarker of Early and Late Phases of Disease Progression in Chronic Myeloid Leukemia

OtherAuthors: Muhammad Absar4, Tanveer Akhtar4, Masood Shammas8, Salman Basit9, Aamer Aleem10, Amer Mahmood10 8Dana Farbar Cancer Institute, University of Harvard , Boston USA, 9Centre for Genetics and Inherited Diseases, Taibah University, Madinah 10College of Medicine, King Saud University, Riyadh, Saudi Arabia. Introduction: Chronic Myeloid Leukemia (CML) results due to t(22;9) that leads to formation of Philadelphia chromosome and subsequently BCR-ABL fusion transcript, the later leading to leukemogenesis(1). This led to identification of tyrosine kinase inhibitors (TKIs) as novel drugs that revolutionised CML treatment in 21st century by improving the survival of CML equal to general population at least in developed countries (2). Nevertheless TKIs lose their effectiveness if CML patients progress to blast crisis (BC-CML). Despite extensive research in CML field, mechanism of its progression is still poorly understood and universal molecular biomarkers of CML progression are unknown (2). There are different mechanisms associated with initiation and progression of various cancers. DNA repair defects mediated through biologically very important Fanconi anemia (FA) pathway genes are associated with many cancers (3). Nevertheless, FA pathway genes have not been reported in myeloid malignancies. In this study, in searching for mutated genes associated with many mechanism, we hereby report mutations in a very important FA-pathway gene associated exclusively with CML progression for the first time in literature. Materials and Methods: Patient selection: Whole-exome sequencing (WES) was employed to find out mutations in novel TF-genes associated with accelerated phase (AP-CML) and blast crisis phase CML (BC-CML) patients (Experimental groups 1 & 2, respectively). Chronic phase treatment-naïve CML patients (CP-CML) were used as control 1, CP-CML CML long-term TKI responders (at least 3 continuous years of MMR) as control group 2 and TK-resistant CML patients as control group 3, along with healthy controls. Sample collection: DNA extraction and Clinical follow-up: 10 ml peripheral blood was collected from all study subjects. DNA was extracted and patient follow-up was carried out during course of this study. All treatment criteria per ENL guidelines were adopted. Whole Exome Sequencing (WES): WES was carried out using Illumina NGS instrument (HiSeq). bcl files were converted to fastq files by using bcl2fastqtool (4). Raw reads were aligned to genome using BWA tools while whole exome variants were annotated using Illumina Variant Studio (4). R package was employed to align gene mutants to disease phenotypes (5). DNA repair genes mutated in all AP/BC-CML patients but not mutated in any of control groups were selected. Variants were confirmed using Sanger sequencing. Results: A novel splice-site substitution (C2022T) in FANCD2 gene (that is a very important member of FA-pathway genes) was detected in all AP/BC-CML but in none of the controls. It shows that mutated FANCD2 can serve as a novel biomarker exclusively for advanced phases of CML. Discussion: It is the first report that a member of FA-pathway genes (FANCD2) has been reported mutated in progression of myeloid malignancies (6). It shows that DNA repair defects and genomic instability mediated through FA-pathway could be one of the important mechanisms in CML progression. Mutations in FANCD2 and such other genes could be reason why CML blast crisis patients have poor outcome of stem cell transplantation. Moreover, anti-cancer drugs targeting DNA repair defects (PARP inhibitors) like Olaparib in combination with TKIs could be effective in patients with mutated FANCD-2 and other such genes. Conflict of interest: The authors declare that they have no conflict of interests.

Targeting PLK1 As a Novel Strategy for Acute Myeloid Leukemias with Fanconi Anemia Pathway Mutations

The Fanconi anemia (FA) signaling network is critical to maintaining genomic integrity during interphase and mitosis. Biallelic germline mutation of any of the 22 genes that constitute this pathway (FANCA-FANCW) results in the disorder FA, which is characterized by congenital malformations, a predisposition to bone marrow failure, and pediatric acute myeloid leukemias (AMLs). Among the general population, acquired genetic disruptions of the FA pathway are present in 18% of sporadic pediatric AMLs, underscoring the importance of this pathway in the prevention of hematological malignancy. FANCA is the gene most commonly mutated in FA and is one of the most frequently disrupted FA pathway genes in sporadic AML. Therefore, the identification of precision therapies for FANCA-deficient AML is a high clinical priority. To identify synthetic lethal targets of FANCA, we previously identified mitotic phosphosignaling pathways required for the survival of FANCA-/- patient-derived fibroblasts through a kinome-wide shRNA screen. This screen identified the mitotic kinases CHEK1, PLK1, and BUB1 as hits. These findings corroborate work by others who have identified synthetic lethal interactions between PLK1 and the FA pathway components FANCG and BRCA1, suggesting inactivation of the FA pathway may sensitize cancers to PLK1 inhibition. The clinical success of PLK1 inhibitors, such as volasertib and onvansertib, has been limited by the absence of predictive biomarkers of response and adverse side effects. To test our hypothesis that FA gene mutations may predict sensitivity to PLK1 inhibition we generated an isogenic panel of human AML cells with a stable knockout of the FANCA gene. Utilizing in vitro cell viability assays, we have demonstrated the selective killing of FA-deficient AMLs by pharmacological PLK1 inhibition through low doses of volasertib and onvansertib. We also found that PLK1-inhibition impairs the hematopoietic potential of Fanca-/- murine hematopoietic stem and progenitor cells by performing in vitro bone marrow colony formation assays. Similarly, we demonstrated that primary human AMLs with multiple disruptions within the FA-pathway were hypersensitive to low doses of volasertib. To investigate the mechanism of synthetic lethality, we performed quantitative proteomic analysis of FANCA immunoprecipitates, which identified PLK1 as a novel FANCA-binding partner during mitosis. We validated this finding through high-resolution immunofluorescence microscopy and proximity ligation assays, which revealed a direct interaction between FANCA and PLK1 at kinetochores. Additionally, we demonstrated that volasertib treatment induces monoubiquitination of FANCD2 and colocalization of FANCA with FANCD2 at gamma-H2AX foci. Together, these findings indicate that PLK1 inhibition causes damage to mitotic chromosomes and subsequent activation of the FA pathway. Our work identifies a mitosis-specific vulnerability of FA-deficient cells and suggests that genetic disruptions of the FA pathway may be predictive of sensitivity to PLK1 inhibition, providing a preclinical rationale for the development of precision therapies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Prevalence of Fanconi anemia gene mutations among men undergoing multigene germline testing for prostate cancer: Interim results from the EMPOWeR study.

188 Background: Germline testing for prostate cancer (PCA) is now central to treatment, screening, and hereditary cancer management. The Fanconi anemia (FA) pathway is a key DNA repair pathway involved in PCA biology and treatment. Prevalence of FA genes BRCA2, PALB2, and BRIP1 is well-described; however, multiple other FA genes are not routinely tested, with limited prevalence data. Here we report mutation prevalence of a spectrum of FA genes among men undergoing PCA multigene testing on the Evaluation and Management for Prostate Oncology, Wellness, and Risk (EMPOWeR) study. Methods: Eligibility includes any male with PCA or at-risk for PCA. Multigene testing includes 51 genes; FA pathway genes include BRCA2, PALB2, BRIP1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, and FANCM. Multiple additional cancer risk genes were tested. Fisher’s exact tests were conducted to compare the prevalence of FA gene mutations between participants in the EMPOWeR study vs population prevalence reported in the literature. Statistical significance level of all tests was set a priori to 0.05. Results: The current cohort includes 235 participants. Characteristics are White (83.3%), Black (13.7%), PCA diagnosis (83.4%), mean age of PCA diagnosis 61.7 + 7.69 years, Gleason score >=7 (66.2%), and T3 or higher (29.4%). Genetic results were available for 179 participants. Overall, 11.1% of participants (n=20) had a pathogenic/likely pathogenic mutation identified. Among mutation carriers, 45% (n=9) had mutations in FA genes, including FANCA (n=3), BRCA2 (n=2), FANCM (n=1), FANCD2 (n=1), PALB2 (n=1), and BRIP1 (n=1). Table shows clinical characteristics of participants with mutations in FANCA, FANCM, and FANCD2. Further mutation spectrum included: CHEK2 (n=3), NBN (n=2), MUTYH (n=2), BRCA (n=1), ATM (n=1), HOXB13 (n=1), APC (n=1). Compared to population prevalence, FA mutation prevalence was significantly higher overall (5.0% vs. 0.6%, p = 0.010) and among mutation carriers (45% vs. 0.6%, p<0.001). Conclusions: While prevalence of FA genes BRCA2, PALB2, and BRIP1 is well-described, our study supports testing a broader range of FA genes given the prevalence rates, potential implications for clinical trials, targeted therapy, inherited syndromes, and reproductive implications.[Table: see text]

Fanconi Anemia Pathway Genes Advance Cervical Cancer via Immune Regulation and Cell Adhesion.

Fanconi anemia (FA) pathway is a typical and multienzyme-regulated DNA damage repairer that influences the occurrence and development of disease including cancers. Few comprehensive analyses were reported about the role of FA-related genes (FARGs) and their prognostic values in cancers. In this study, a comprehensive pan-cancer analysis on 79 FARGs was performed. According to the correlation analyses between HPV integration sites and FARGs, we found that FARGs played specific and critical roles in HPV-related cancers, especially in cervical cancer (CC). Based on this, a FARGs-associated prognostic risk score (FPS) model was constructed, and subsequently a nomogram model containing the FPS was developed with a good accuracy for CC overall survival (OS) and recurrence-free survival (RFS) outcome prediction. We also used the similar expression pattern of FARGs by consensus clustering analysis to separate the patients into three subgroups that exhibited significant differential OS but not RFS. Moreover, differential expressed genes (DEGs) between the two risk groups or three clusters were identified and immune pathways as well as cell adhesion processes were determined by functional enrichment analysis. Results indicated that FARGs might promote occurrence and development of CC by regulating the immune cells’ infiltration and cell adhesion. In addition, through the machine learning models containing decision tree, random forest, naïve bayes, and support vector machine models, screening of important variables on CC prognosis, we finally determined that ZBTB32 and CENPS were the main elements affecting CC OS, while PALB2 and BRCA2 were for RFS. Kaplan-Meier analysis revealed that bivariate prediction of CC outcome was reliable. Our study systematically analyzed the prognostic prediction values of FARGs and demonstrated their potential mechanism in CC aggressiveness. Results provided perspective in FA pathway-associated modification and theoretical basis for CC clinical treatments.

Fanconi Anemia Complementation Group E, a DNA Repair-Related Gene, Is a Potential Marker of Poor Prognosis in Hepatocellular Carcinoma

Introduction: Fanconi anemia complementation group E (FANCE) is a Fanconi anemia (FA) pathway gene that regulates DNA repair. We evaluated the clinical relevance of FANCE expression in hepatocellular carcinoma (HCC). Methods: First, the associations between the expression of FA pathway genes including FANCE and clinical outcomes in HCC patients were analyzed in 2 independent cohorts: The Cancer Genome Atlas (TCGA, n = 373) and our patient cohort (n = 53). Localization of FANCE expression in HCC tissues was observed by immunohistochemical staining. Gene set enrichment analysis (GSEA) and gene network analysis (SiGN_BN) were conducted using the TCGA dataset. Next, an in vitro proliferation assay was performed using FANCE-knockdown HCC cell lines (HuH7 and HepG2). The association between mRNA expression of FANCE and that of DNA damage response genes in HCC was analyzed using TCGA and Cancer Cell Line Encyclopedia datasets. Finally, the association between FANCE mRNA expression and overall survival (OS) in various digestive carcinomas was analyzed using TCGA data. Results: FANCE was highly expressed in HCC cells. Multivariate analysis indicated that high FANCE mRNA expression was an independent factor predicting poor OS. GSEA revealed a positive relationship between enhanced FANCE expression and E2F and MYC target gene expression in HCC tissues. FANCE knockdown attenuated the proliferation of HCC cells, as well as reduced cdc25A expression and elevated histone H3 pSer10 expression. SiGN_BN revealed that FANCE mRNA expression was positively correlated with DNA damage response genes (H2A histone family member X and checkpoint kinase 1) in HCC tissues. Significant effects of high FANCE expression on OS were observed in hepatobiliary pancreatic carcinomas, including HCC. Conclusions: FANCE may provide a potential therapeutic target and biomarker of poor prognosis in HCC, possibly by facilitating tumor proliferation, which is mediated partly by cell cycle signaling activation.

DNA Repair Gene Polymorphisms and Chromosomal Aberrations in Exposed Populations.

DNA damage and unrepaired or insufficiently repaired DNA double-strand breaks as well as telomere shortening contribute to the formation of structural chromosomal aberrations (CAs). Non-specific CAs have been used in the monitoring of individuals exposed to potential carcinogenic chemicals and radiation. The frequency of CAs in peripheral blood lymphocytes (PBLs) has been associated with cancer risk and the association has also been found in incident cancer patients. CAs include chromosome-type aberrations (CSAs) and chromatid-type aberrations (CTAs) and their sum CAtot. In the present study, we used data from our published genome-wide association studies (GWASs) and extracted the results for 153 DNA repair genes for 607 persons who had occupational exposure to diverse harmful substances/radiation and/or personal exposure to tobacco smoking. The analyses were conducted using linear and logistic regression models to study the association of DNA repair gene polymorphisms with CAs. Considering an arbitrary cutoff level of 5 × 10–3, 14 loci passed the threshold, and included 7 repair pathways for CTA, 4 for CSA, and 3 for CAtot; 10 SNPs were eQTLs influencing the expression of the target repair gene. For the base excision repair pathway, the implicated genes PARP1 and PARP2 encode poly(ADP-ribosyl) transferases with multiple regulatory functions. PARP1 and PARP2 have an important role in maintaining genome stability through diverse mechanisms. Other candidate genes with known roles for CSAs included GTF2H (general transcription factor IIH subunits 4 and 5), Fanconi anemia pathway genes, and PMS2, a mismatch repair gene. The present results suggest pathways with mechanistic rationale for the formation of CAs and emphasize the need to further develop techniques for measuring individual sensitivity to genotoxic exposure.

Population Frequency of Fanconi Pathway Gene Variants and Their Association with Survival After Hematopoietic Cell Transplantation for Severe Aplastic Anemia.

Severe aplastic anemia (SAA) is most frequently immune-mediated; however, rare inherited bone marrow failure syndromes, such as Fanconi anemia (FA), may be causal and can present as aplastic anemia (AA). FA is primarily an autosomal recessive disorder caused by the presence of 2 pathogenic variants in a single FA/BRCA DNA repair pathway gene. Patients with SAA often undergo genetic testing during clinical evaluation that may identify single deleterious alleles in FA pathway genes. We quantified the rate of germline single deleterious alleles in 22 FA genes using both a general population database (3234 variants, 125,748 exomes) and in a cohort of patients with SAA undergoing hematopoietic cell transplantation (HCT) (21 variants in 730 patients). The variants were classified as deleterious using in silico tools (REVEL, MetaSVM, VEP) and database resources (ClinVar, LOVD-FA). We found similar rates of single deleterious alleles in FA genes in both groups (2.6% and 2.9%). The presence of a single deleterious variant in a gene for FA in SAA HCT recipients did not affect the overall survival after HCT (hazard ratio, 0.85; 95% CI, 0.37 to 1.95; P =0.71), or post-HCT cancer risk (P = 0.52). Our results demonstrate that the identification of a germline monoallelic deleterious variant in an FA gene in patients with idiopathic SAA does not influence the outcome of HCT. Our findings suggest that there is no need for special treatment considerations for patients with SAA and a single deleterious FA allele identified on genetic testing.

Tumor treating fields cause replication stress and interfere with DNA replication fork maintenance: Implications for cancer therapy

Tumor treating fields (TTFields) is a noninvasive physical modality of cancer therapy that applies low-intensity, intermediate frequency, and alternating electric fields to a tumor. Interference with mitosis was the first mechanism describing the effects of TTFields on cancer cells; however, TTFields was shown to not only reduce the rejoining of radiation-induced DNA double-strand breaks (DSBs), but to also induce DNA DSBs. The mechanism(s) by which TTFields generates DNA DSBs is related to the generation of replication stress including reduced expression of the DNA replication complex genes MCM6 and MCM10 and the Fanconi's Anemia pathway genes. When markers of DNA replication stress as a result of TTFields exposure were examined, newly replicated DNA length was reduced with TTFields exposure time and there was increased R-loop formation. Furthermore, as cells were exposed to TTFields a conditional vulnerability environment developed which rendered cells more susceptible to DNA damaging agents or agents that interfere with DNA repair or replication fork maintenance. The effect of TTFields exposure with concomitant exposure to cisplatin or PARP inhibition, the combination of TTFields plus concomitant PARP inhibition followed by radiation, or radiation alone at the end of a TTFields exposure were all synergistic. Finally, gene expression analysis of 47 key mitosis regulator genes suggested that TTFields-induced mitotic aberrations and DNA damage/replication stress events, although intimately linked to one another, are likely initiated independently of one another. This suggests that enhanced replication stress and reduced DNA repair capacity are also major mechanisms of TTFields effects, effects for which there are therapeutic implications.

Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility.

Fanconi Anemia (FA) is a genomic instability syndrome resulting in aplastic anemia, developmental abnormalities, and predisposition to hematological and other solid organ malignancies. Mutations in genes that encode proteins of the FA pathway fail to orchestrate the repair of DNA damage caused by DNA interstrand crosslinks. Zebrafish harbor homologs for nearly all known FA genes. We used multiplexed CRISPR/Cas9-mediated mutagenesis to generate loss-of-function mutants for 17 FA genes: fanca, fancb, fancc, fancd1/brca2, fancd2, fance, fancf, fancg, fanci, fancj/brip1, fancl, fancm, fancn/palb2, fanco/rad51c, fancp/slx4, fancq/ercc4, fanct/ube2t, and two genes encoding FA-associated proteins: faap100 and faap24. We selected two indel mutations predicted to cause premature truncations for all but two of the genes, and a total of 36 mutant lines were generated for 19 genes. Generating two independent mutant lines for each gene was important to validate their phenotypic consequences. RT-PCR from homozygous mutant fish confirmed the presence of transcripts with indels in all genes. Interestingly, 4 of the indel mutations led to aberrant splicing, which may produce a different protein than predicted from the genomic sequence. Analysis of RNA is thus critical in proper evaluation of the consequences of the mutations introduced in zebrafish genome. We used fluorescent reporter assay, and western blots to confirm loss-of-function for several mutants. Additionally, we developed a DEB treatment assay by evaluating morphological changes in embryos and confirmed that homozygous mutants from all the FA genes that could be tested (11/17), displayed hypersensitivity and thus were indeed null alleles. Our multiplexing strategy helped us to evaluate 11 multiple gene knockout combinations without additional breeding. Homozygous zebrafish for all 19 single and 11 multi-gene knockouts were adult viable, indicating FA genes in zebrafish are generally not essential for early development. None of the mutant fish displayed gross developmental abnormalities except for fancp-/- fish, which were significantly smaller in length than their wildtype clutch mates. Complete female-to-male sex reversal was observed in knockouts for 12/17 FA genes, while partial sex reversal was seen for the other five gene knockouts. All adult females were fertile, and among the adult males, all were fertile except for the fancd1 mutants and one of the fancj mutants. We report here generation and characterization of zebrafish knockout mutants for 17 FA disease-causing genes, providing an integral resource for understanding the pathophysiology associated with the disrupted FA pathway.

Identification of a comprehensive spectrum of genetic factors for hereditary breast cancer in a Chinese population by next-generation sequencing.

The genetic etiology of hereditary breast cancer has not been fully elucidated. Although germline mutations of high-penetrance genes such as BRCA1/2 are implicated in development of hereditary breast cancers, at least half of all breast cancer families are not linked to these genes. To identify a comprehensive spectrum of genetic factors for hereditary breast cancer in a Chinese population, we performed an analysis of germline mutations in 2,165 coding exons of 152 genes associated with hereditary cancer using next-generation sequencing (NGS) in 99 breast cancer patients from families of cancer patients regardless of cancer types. Forty-two deleterious germline mutations were identified in 21 genes of 34 patients, including 18 (18.2%) BRCA1 or BRCA2 mutations, 3 (3%) TP53 mutations, 5 (5.1%) DNA mismatch repair gene mutations, 1 (1%) CDH1 mutation, 6 (6.1%) Fanconi anemia pathway gene mutations, and 9 (9.1%) mutations in other genes. Of seven patients who carried mutations in more than one gene, 4 were BRCA1/2 mutation carriers, and their average onset age was much younger than patients with only BRCA1/2 mutations. Almost all identified high-penetrance gene mutations in those families fulfill the typical phenotypes of hereditary cancer syndromes listed in the National Comprehensive Cancer Network (NCCN) guidelines, except two TP53 and three mismatch repair gene mutations. Furthermore, functional studies of MSH3 germline mutations confirmed the association between MSH3 mutation and tumorigenesis, and segregation analysis suggested antagonism between BRCA1 and MSH3. We also identified a lot of low-penetrance gene mutations. Although the clinical significance of those newly identified low-penetrance gene mutations has not been fully appreciated yet, these new findings do provide valuable epidemiological information for the future studies. Together, these findings highlight the importance of genetic testing based on NCCN guidelines and a multi-gene analysis using NGS may be a supplement to traditional genetic counseling.

The role of the Fanconi anemia pathway in the pathophysiology of ovarian cancer

We reviewed the literature on the relationship between the Fanconi anemia pathway (FA) and response to chemotherapy in patients with ovarian cancer. Despite continuous developments in medicine, ovarian cancer remains a challenge for both, physicians and researchers seeking ways to achieve better results of chemotherapy combined with other targeted therapies. Clinically relevant resistance to chemotherapy is a major problem in treating ovarian cancer. Researchers continue to investigate mechanisms responsible for drug resistance in order to develop better therapeutic methods against ovarian cancer. Among the resistance mechanisms, defects in DNA repair, including the FA pathway may be important in increasing the sensitivity of ovarian cancer cells to chemotherapy agents at the clinical level. A growing number of data has shown that disruption of the FA genes may be a useful predictor of OC sensitivity to chemotherapy agents whose activity is based on DNA crosslinking mechanisms.

The application of radiotherapy to the pediatric preclinical testing program: Results of a pilot study.

9544 Background: The Pediatric Preclinical Testing Program (PPTP) has been successfully utilized to determine the efficacy of novel agents by testing via its mouse-flank in vivo model. We report on the feasibility and biologic outcomes of a pilot study using rhabdomyosarcoma (RMS) xenograft lines treated with radiotherapy (RT) alone and concurrently with the mTOR tyrosine kinase inhibitor, AZD8055, using the PPTP model. Methods: We developed a mouse flank irradiation device for daily delivery of RT in clinically relevant doses (2 Gy per fraction up to 40 Gy).Two RMS xenograft lines of the PPTP, Rh30 (alveolar) and Rh18 (embryonal), were implanted into SCID mice, grown to appropriate volumes and were subjected to fractionated RT. In a second study, daily co-administration of AZD8055 (5-20 mg/Kg, gavage) with RT was performed. Cure rates (durable complete response >12 weeks post-treatment) and RT dose densities (given dose / initial xenograft volume, Gy/cc) were compared between groups. Results: With RT alone at mean dose-densities of 59-60 Gy/cc, cure was achieved in only 4/18 (22%) of the Rh30-bearing mice and 9/12 (75%) of the Rh18-bearing mice (p=0.006). Profiling data revealed higher levels of Fanconi anemia pathway gene expression in Rh30 compared to the more sensitive Rh18. Since recent data showed conditional knockout of mTOR resulted in the loss of FANCD2 gene expression, we postulated that blockade of TORC1/TORC2 with AZD8055 would reduce FANCD2 and increase the RT-sensitivity of Rh30. The addition of AZD8055 to RT resulted in a selective sensitization of the Rh30 line. With a mean RT dose-density of 27 Gy/cc, the cure rate in Rh30-bearing mice improved to 11/15 (73%). For the Rh18 group, the cure rate was 7/15 (46%) at a mean dose density of 44 Gy/cc. Western blot analysis showed the co-administration of AZD8055 abrogated the brisk increase in mTOR signaling and FANCD2 expression after the first several 2 Gy fractions of RT; most strikingly in Rh30. Conclusions: This study demonstrates the feasibility of applying RT to the PPTP model. It recapitulated the expected clinical radiobiology and demonstrated its utility in preclinical testing and the discovery of novel mechanisms of RT resistance in pediatric tumors.

Abstract 2116: CHEK2 (Chk2) endogenous activation is associated with p53 deficiency and downregulation of BRCA2 and Fanconi Anemia pathway gene members in the National Cancer Institute Anticancer Tumor Cell Line Panel (NCI-60)

Abstract CHEK2 codes for a serine/threonine kinase (Chk2) activated by ATM in response to DNA double-strand breaks (DSB). CHEK2 has been described as a tumor suppressor with pro-apoptotic, cell cycle checkpoint and mitotic functions. However, Chk2 is also commonly activated (phosphorylated at T68) in cancers and precancerous lesions. In the present report, we characterized CHEK2 across the panel of 60 established cancer cell lines from the NCI Anticancer Tumor Cell Line panel (the NCI-60) using genomic and proteomic analyses including exon-specific mRNA expression, DNA copy number variation (CNV) by aCGH, exome sequencing, as well as Western blotting analyses for total and activated (pT68-Chk2) Chk2. We demonstrate that the high heterogeneity of Chk2 levels in the NCI-60 is primarily due to its inactivation (owing to low gene expression, alternative splicing, point mutations, copy number alterations and premature truncation) or reduction of protein levels. Notably, we also found that a significant percentage of cancer cells (12% of the NCI-60 and the HeLa cervix cell line) display high endogenous Chk2 activation, always associated with p53 loss of function. Notably, all the 12 cancer cell lines characterized as being p53 wild-type showed almost undetectable levels of pT68-Chk2. The potential impact of endogenous Chk2 activation was analyzed by transcriptome profiling of the five highest pT68-Chk2 cell lines, comparing them with five, tissue-matched low pT68-Chk2 and p53-matched deficient cell lines. Two-sided t tests revealed 176 genes differentially expressed with statistical significance (P < 0.01, uncorrected) in the two groups (high vs. low pT68-Chk2). Among the downregulated expressed genes, a significant number codes for proteins involved in DNA recombination, replication and repair (FANCA, FANCG, FANCL, BRCA2, RAD51C, EME1, and RECQL5 being the most relevant), and centromere organization. Several of these downregulated genes were parts of the Fanconi Anemia pathway or related to homologous recombination (HR, P < 0.05 for statistically significant enrichment using Ingenuity Pathway Analysis®). In conclusion, the biology of Chk2 remains complex, multifaceted and fast evolving. Our study provides information on the relationship between different genomic and proteomic parameters related to Chk2 in cancer, and suggests a possible role for activated Chk2 in p53-deficient or HR/Fanconi Anemia-deficient cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2116. doi:1538-7445.AM2012-2116

Fanca-/- hematopoietic stem cells demonstrate a mobilization defect which can be overcome by administration of the Rac inhibitor NSC23766

Fanconi anemia is a severe bone marrow failure syndrome resulting from inactivating mutations of Fanconi anemia pathway genes. Gene and cell therapy trials using hematopoietic stem cells and progenitors have been hampered by poor mobilization of HSC to peripheral blood in response to G-CSF. Using a murine model of Fanconi anemia (Fanca(-/-) mice), we found that the Fanca deficiency was associated with a profound defect in hematopoietic stem cells and progenitors mobilization in response to G-CSF in absence of bone marrow failure, which correlates with the findings of clinical trials in Fanconi anemia patients. This mobilization defect was overcome by co-administration of the Rac inhibitor NSC23766, suggesting that Rac signaling is implicated in the retention of Fanca(-/-) hematopoietic stem cells and progenitors in the bone marrow. In view of these data, we propose that targeting Rac signaling may enhance G-CSF-induced HSC mobilization in Fanconi anemia.