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Percentage of Patients With Head and Neck Squamous Cell Carcinoma Carrying Rare Variants and Rare Predicted Damaging Variants in Fanconi Anemia Genes Segregated by Age Group
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Background:
Patients with Fanconi anemia (FA) have an increased risk for head and neck squamous cell carcinoma (HNSCC). The authors sought to determine the prevalence of undiagnosed FA and FA carriers among patients with HNSCC as well as an age cutoff for FA genetic screening.
Methods:
Germline DNA samples from 417 patients with HNSCC aged <50 y...
Citations
... On the basis of its upregulation, FANCD2 has an unsatisfactory prognosis for other types of cancer, which may contribute to tumorigenesis. Such cancers are esophageal squamous cell carcinoma, head and neck carcinoma, nasopharyngeal carcinoma, and lung adenocarcinoma (Lei, 2020;Chandrasekharappa, 2017;Xu, 2019). ...
Chronic Myeloid Leukemia, resulting due to chromosomal aberration t(9;22) through formation of oncogenic BCR-ABL fusion oncogene. Modern BCR-ABL inhibitors, called TKIs, have revolutionized CML treatment. CML has three stages: chronic, accelerated, and blast crisis. TKIs work well in CP-CML, where patients survive as long as the normal population, but they don't work in AP- and BC-CML. Even with advances in treatment, BC-CML has an average overall survival of less than a year, giving oncologists little time to clinically intervene. Oncologists can delay or prevent CML advancement by detecting patients at risk of disease progression early and making timely treatment decisions, especially with third and fourth generation TKIs. However, no universal molecular biomarkers exist to diagnose CML patient groups at risk of disease progression. A recent study found that all BC-CML patients have mutant FANCD2. Our study was designed to detect mutant FANCD2 in AP-CML (early progression phase) to investigate its potential as a novel biomarker of early CML progression from chronic phase to accelerated phase due to the urgent need for such a biomarker. Our study comprised of 123 CP-CML (control group) and 60 AP-CML patients (as experimental group) from Hayatabad Medical Complex, Peshawar, Pakistan, from Jan 2020 to July 2023. DNA was extracted from the patients and FANCD2 gene was sequenced using Illumina next generation sequencer (NGS) Illumina MiSeq sequencer. NGS analysis revealed a unique splice site mutation in FANCD2 gene (c. 2022-5C>T). This mutation was detected in all CP-CML patients but in none of CP-CML. The mutation was confirmed by Sanger sequencing. FANCD2 is member of Fanconi anemia (FA-) pathway gene involved in DNA repair and genomic instability. Therefore, our studies show that FANCD2 (c. 2022-5C>T) mutation as a very specific molecular biomarker for early CML progression. We recommend to clinical validate this biomarker is prospective clinical trials.
... On the basis of its upregulation, FANCD2 has an unsatisfactory prognosis for other types of cancer, which may contribute to tumorigenesis. Such cancers are esophageal squamous cell carcinoma, head and neck carcinoma, nasopharyngeal carcinoma, and lung adenocarcinoma (Lei, 2020;Chandrasekharappa, 2017;Xu, 2019). ...
... Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 3 January 2024 doi:10.20944/preprints202108.0498.v210 ...
Background: Chronic Myeloid Leukemia (CML) is initiated in bone marrow due to chromosomal translocation t(22;9) leading to fusion oncogene BCR-ABL. Targeting BCR-ABL by tyrosine kinase inhibitors (TKI) have changed fatal CML into an almost curable disease. Despite that, TKIs lose their effectiveness due to disease progression. Unfortunately, mechanism of CML progression is poorly understood and common biomarkers for CML progression are unavailable. This study was conducted to find out novel biomarkers of CML progression by employing whole exome sequencing (WES).Materials and Methods: WES of accelerated phase (AP-) and blast crisis (BC-) CML patients was carried out, with chronic phase CML (CP-CML) patients as control. After DNA library preparation and exome enrichment, clustering and sequencing was carried out using Illumina platforms. Statistical analysis was carried out using [SAS/STAT] software version 9.4 and R package employed to find mutations shared exclusively by all AP-/BC-CML. Confirmation of mutations was carried out using Sanger sequencing and protein structure modelling using I-Tasser followed by mutant generation and visualization using PyMOL. Results: Three novel genes (ANKRD36, ANKRD36B and PRSS3) were mutated exclusively in all AP-/BC-CML patients. Only ANKRD36 gene mutations (c.1183_1184 delGC and c.1187_1185 dupTT) were confirmed by Sanger sequencing. Protein modelling studies showed that mutations induce structural changes in ANKRD36 protein. Conclusions: Our studies show that ANKRD36 is a potential common biomarker and drug target of early CML progression. ANKRD36 is yet uncharacterized in human. It has the highest expression in bone marrow, specifically myeloid cells. We recommend carrying out further studies to explore the role of ANKRD36 in biology and progression of CML.
... Also, intrinsic deactivation of the DDR by genetic defects, as in rare DNA repair deficiency syndromes like Fanconi anemia (FA) or BRCAness in hereditary breast and ovarian cancer, triggers cGAS/STING signaling and inflammatory processes through genomic instability [25,26]. Somatic mutations, hypermethylation, and copy number variations of FA/BRCA repair pathway genes have also been described in more than 30% of sporadic HPV-negative HNSCCs associated with early onset and poor prognosis [27][28][29][30][31][32]. On the other hand, a compromised FA/BRCA repair pathway fosters sensitization to DNAdamaging tumor therapies and a pro-inflammatory phenotype including upregulation of STING expression [27,33,34]. ...
Locally advanced head and neck squamous cell carcinomas (HNSCC) are often refractory to platinum-based radiochemotherapy and new immuno-oncological strategies. To stimulate immunogenic antitumor responses in HNSCC patients, we investigated the cGAS/STING/IFN-1 signaling pathway after genotoxic treatments and concomitant abrogation of the DNA damage response (DDR). For this purpose, FaDu and UM-SCC1 cells were exposed to X-rays or cisplatin and treated with an ATR or Chk1 inhibitor, or by Fanconi anemia gene A knockout (FANCA ko). We assessed clonogenic survival, cell cycle regulation, micronuclei, free cytosolic double-stranded DNA, and the protein expression and activity of the cGAS/STING/IFN-1 pathway and related players. Cell survival, regulation of G2/M arrest, and formation of rupture-prone cGAS-positive micronuclei after genotoxic treatments were most affected by ATR inhibition and FANCA ko. In UM-SCC-1 cells only, 8 Gy X-rays promoted IFN-1 expression unaltered by abrogation of the DDR or concomitant increased TREX1 expression. At a higher dose of 20 Gy, this effect was observed only for concurrent Chk1- or ATR-inhibition. FANCA ko or cisplatin treatment was ineffective in this regard. Our observations open new perspectives for the enhancement of cGAS/STING/IFN-1-mediated antitumor immune response in HNSCC by hypofractionated or stereotactic radiotherapy concepts in multimodal settings with immuno-oncological strategies.
... Most patients were male, smokers, and almost half were HPV positive. At least one GPV in DNA repair pathway genes was found in 67 % of cases, including GPVs in CDKN2A and RECQL4 in HPVne gative patients with oral cancer and in FANCG in HPV positive HNSCC patients (Chandrasekharappa et al., 2017). ...
Head and neck squamous cell carcinoma (HNSCC) presents a significant global health problem with variable geographic distribution and risk factors, including tobacco and alcohol abuse, human papillomavirus infections, and genetic predisposition. While the majority of cases are sporadic, several well-defined hereditary syndromes have been associated with a higher risk of developing HNSCC including Li-Fraumeni syndrome, Fanconi anaemia, Bloom syndrome, familial atypical multiple mole melanoma, and dyskeratosis congenita. There is also evidence of familial clusters of HNSCC, suggesting a genetic component in the development of the disease. Germline genetic testing in HNSCC using next-generation sequencing has revealed a wide range of germline variants, some of which were not anticipated based on standard guidelines. These variants may influence treatment decisions and have the potential to be targeted with precision medicine in the future. Despite these advances, routine germline genetic testing for HNSCC is not currently recommended and remains reserved for HNSCC cases with early onset or strong family cancer history. However, the increasing availability of germline genetic testing warrants development of more comprehensive and standardized testing protocols. Germline genetic testing also has the potential to influence precision-guided treatment in HNSCC patients carrying germline pathogenic variants.
... The molecular characterization of rare genetic diseases can identify predisposing genes, broadening knowledge about common diseases such as cancer. [3][4][5] Fanconi anemia (FA) is an inherited and progressive bone marrow failure syndrome characterized by congenital abnormalities, inability to repair DNA interstrand cross-links (ICLs), and cancer predisposition, especially in young adults. 2,6 FA can be caused by biallelic mutations in most of the genes, except for those rare cases with FANCB mutations located on X-chromosome and FANCR/RAD51 autosomal dominant mutations. ...
Introduction:
This study proposed to identify Fanconi anemia (FA) mutations in Brazilian patients and to investigate their impact on clinical manifestations and malignancies onset.
Methods:
A total of 116 patients were screened for nine mutations in FANCA, FANCC, FANCG. Those with no mutations were investigated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing for FANCA, FANCC, FANCE, FANCF, FANCG, FANCD1/BRCA2.
Results:
Genetic subtype was identified in 107/116 (78 FA-A, 8 FA-C, 13 FA-G, 8 FA-E), with only one mutation in 1/116, and no mutations in 9/116 patients. Before hematopoietic cell transplantation (HCT), malignancies were detected in 16/116 patients (14/78 FA-A, 01/08 FA-C, 01/08 FA-E), and 12 of them were hematological. Observed to expected ratio (O/E) of hematologic malignancy was 303.7 (95% CI = 148.6-458.7).
Conclusion:
This study allowed the identification of biallelic mutations in 91.4% of patients. FANCG and FANCC mutations had significantly earlier bone marrow failure onset, and FANCG severe cytopenia at diagnosis. Despite the inherent limitations of the small number of malignancy events in each genetic subtype, the hematologic malignancies O/E ratio was very high. Cumulative incidence of malignancy before HCT was higher in the third and fourth decades of life, considering HCT and death as competing risks. The cumulative incidence of HCT increased during the first decade, competing with malignancy development.
... 38,39 Significant PARP inhibitor sensitivity was also noted for this variant. 39 Previously, this variant was reported as in silico predicted likely pathogenic variant in a breast cancer patient from USA/Denmark, 40 a breast-pancreatic cancer patient from Spain, 41 and a head and neck squamous cell carcinoma patient from USA. 42 Recently, it was described as a VUS in a colorectal cancer patient from the USA 43 and the ClinVar database. In our study, the co-segregation of this variant with breast cancer could not be tested as the paternal aunt of the index patient was deceased. ...
Background
Partner and localizer of BRCA2 (PALB2) is a pancreatic cancer (PC) susceptibility gene reported in Caucasians. However, limited data are available among Asians. We investigated the contribution of PALB2 germline variants to Pakistani PC patients.
Methods
150 unselected and prospectively enrolled PC patients were comprehensively screened for PALB2 variants, using denaturing high-performance liquid chromatography and DNA sequencing. Novel variants were investigated for their pathogenic effect using in-silico tools. Potentially functional variants were further screened in 200 controls.
Results
Twenty-two different PALB2 variants were identified. A missense variant (p.Arg37His) was identified in a 48-years-old male patient with a family history of breast cancer. Another missense variant (p.Trp898Arg) was identified in a 48-years-old male patient with a family history of esophageal cancer. A novel 3’ downstream variant (c.*480A>G) was detected in a 34-years-old female patient with family history of lung cancer. Another novel 3’ downstream variant (c.*417A>C) was identified in a 41-years-old male patient. All these variants were absent in 200 controls. p.Arg37His and p.Trp898Arg were predicted as likely pathogenic. c.*417A>C and c.*480A>G were classified as variants of uncertain significance.
Conclusion
This is the first study that suggests a minimal contribution of PALB2 variants to PC risk in Pakistani population.
... The F o F 1 ATP-synthase (ATP Synthase) activity was evaluated incubating 2 × 10 5 cells at 25 • C for 10 min in a medium containing: 50 mM Tris-HCl (pH 7.4), 50 mM KCl, 1 mM EGTA, 2 mM MgCl 2 , 0.6 mM ouabain, 0.25 mM di(adenosine)-5-Penta-phosphate (an adenylate kinase inhibitor), and 25 µg/mL ampicillin (0.1 mL final volume); then, 10 mM pyruvate plus 5 mM malate or 20 mM succinate were employed to stimulate complexes I, III, and IV or complexes II, III, and IV pathways, respectively [17]. As for OCR evaluation, 3 µM BPTES, 4 µM Etomoxir, and 2 µM UK5099 were used for the cellular energy substrate affinity evaluation. ...
Fanconi Anaemia (FA) is a rare recessive genetic disorder characterized by a defective DNA repair mechanism. Although aplastic anaemia is the principal clinical sign in FA, patients develop a head and neck squamous cell carcinoma (HNSCC) with a frequency 500–700 folds higher than the general population, which appears more aggressive, with survival of under two years. Since FA gene mutations are also associated with a defect in the aerobic metabolism and an increased oxidative stress accumulation, this work aims to evaluate the effect of FANCA mutation on the energy metabolism and the relative mitochondrial quality control pathways in an HNSCC cellular model. Energy metabolism and cellular antioxidant capacities were evaluated by oximetric, luminometric, and spectrophotometric assays. The dynamics of the mitochondrial network, the quality of mitophagy and autophagy, and DNA double-strand damage were analysed by Western blot analysis. Data show that the HNSCC cellular model carrying the FANCA gene mutation displays an altered electron transport between respiratory Complexes I and III that does not depend on the OxPhos protein expression. Moreover, FANCA HNSCC cells show an imbalance between fusion and fission processes and alterations in autophagy and mitophagy pathways. Together, all these alterations associated with the FANCA gene mutation cause cellular energy depletion and a metabolic switch to glycolysis, exacerbating the Warburg effect in HNSCC cells and increasing the growth rate. In addition, the altered DNA repair due to the FANCA mutation causes a higher accumulation of DNA damage in the HNSCC cellular model. In conclusion, changes in energy metabolism and mitochondrial dynamics could explain the strict correlation between HNSCC and FA genes, helping to identify new therapeutic targets.
... Mutations in these FA genes may also contribute to the development of HNSCC in general [18]. Several studies have investigated the role of sporadic genetic variants of FA in the development of HNSCC in non-Fanconi patients, i.e., downregulation [19], loss of heterozygosity [18] and increased mutational loads [20] of multiple FA genes. Increased mutation of FANCD2, FANCE, and lower expression of Glutathione S-Transferase P1 (GSTP1), FANCA and FANCG proteins has been reported to be particularly common among younger patients [20,21]. ...
... Several studies have investigated the role of sporadic genetic variants of FA in the development of HNSCC in non-Fanconi patients, i.e., downregulation [19], loss of heterozygosity [18] and increased mutational loads [20] of multiple FA genes. Increased mutation of FANCD2, FANCE, and lower expression of Glutathione S-Transferase P1 (GSTP1), FANCA and FANCG proteins has been reported to be particularly common among younger patients [20,21]. ...
Background
In recent clinical practice, an increasing number of elderly patients suffering from head and neck squamous cell carcinoma (HNSCC) of unknown pathophysiology is observed. The majority of HNSCC patients can roughly be divided into three subcategories. First, a small group of young patients who present with variants of genomic aberrations and inheritable diseases like Fanconi anaemia. Second, an increasing population of HPV-related HNSCCs that are regarded as genomic stable tumours with a more favourable prognosis. Though HPV-related tumours used to be more common among younger males, a notable rise in the elderly population is observed. The third subcategory, that of HPV-negative tumours, has been shown to be more heterogeneous with involvement of a variety of oncogenic pathways related to lifestyle factors like smoking and alcohol consumption, often seen in middle-aged males. Some of these pathways could be related to age, such as TP53 alterations, EGFR activation, apoptotic pathway alterations and field cancerization.Conclusions
In this narrative review, we provide an overview of established and newly discovered age-specific pathophysiological mechanisms underlying HNSCC. We propose a fourth subcategory of patients with a suspected different pathophysiology: elderly (HPV-negative) HNSCC patients without a history of tobacco and alcohol consumption. In this subcategory, carcinogenesis seems to be a multi-step process based on genomic instability, immunosenescence, cell cycle disruption and telomere shortening. To conclude, we discuss suggestions for future research to fill the knowledge gap about age-dependent HNSCC carcinogenesis.
... 34 Increased mutational burden in three key genes -FANCL, FANCE and FANCD2 genes in the FANC pathway have also been identified among 417 head and neck cancer patients. 35 Polymorphisms in the gene RAD51 and XRCC3 have also been reported to increase the risk of HNC by a 2.5 and 16fold respectively. 36 In the North Eastern India, Choudhury et al. had reported polymorphisms in XRCC1 and XRCC2 and their interactions with tobacco consumption might exert an influence on the susceptibility of HNSCC. ...
Background
Head and Neck Squamous Cell Carcinoma (HNSCC) is commonly associated with tobacco and alcohol consumption. The aim of this study is to find the association between the risk factors with HNSCC in a small tribal population of Mizoram, North-East India.
Methods
Data were obtained through consented questionnaires and Logistic Regression was used to calculate the Odds Ratio (OR) between the parameters and HNSCC.
Result
Significant association was observed for smoking and alcohol with an OR of 6.703 and 4.527, respectively. The OR was found to increase with increase in smoking and alcohol consumption. Majority of the patients consumed local made alcohol and smoked the local made cigarettes known as Zozial. Moreover, the First-Degree Family History of Cancer showed a significant OR of 1.921 (95% CI: 1.040–3.547).
Conclusion
Regardless of the duration of smoking or alcohol consumption, Family History of Cancer might influence the risk of HNSCC. Further screening is essential to evaluate the potential role of germline mutational effect on development of HNSCC in the population.
... These FANCI variants were reported in Finnish [125] (4/1524, 0.3%), Chinese [124] (1/99, 1%), and two Spanish [122,126] (1/154, 0.6% and 1/94, 1.1%) studies. The role of FANCI in other cancer types remains to be determined, though there have been reports of FANCI variant carriers in a variety of cancer types such as prostate cancer [125,128,129], sarcoma [130], malignant pleural mesothelioma [131], acute myeloid leukaemia [132], head and neck carcinoma [133], and colorectal cancer [134] (see Additional file 1: Table S17 and Additional file 3: Fig. S7). ...
Background
Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes.
Methods
Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively.
Results
In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases ( P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2 , including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC ( P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples.
Conclusions
This is the first study to describe candidate OC variants in FANCI , a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families.
