Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells

Nucleotide excision repair (NER) acts repairing damages in DNA, such as lesions caused by cisplatin. Xeroderma Pigmentosum complementation group C (XPC) protein is involved in recognition of global genome DNA damages during NER (GG-NER) and it has been studied in different organisms due to its importance in other cellular processes. In this work, we studied NER proteins in Trypanosoma cruzi and Trypanosoma evansi, parasites of humans and animals respectively. We performed three-dimensional models of XPC proteins from T. cruzi and T. evansi and observed few structural differences between these proteins. In our tests, insertion of XPC gene from T. evansi (TevXPC) in T. cruzi resulted in slower cell growth under normal conditions. After cisplatin treatment, T. cruzi overexpressing its own XPC gene (TcXPC) was able to recover cell division rates faster than T. cruzi expressing TevXPC gene. Based on these tests, it is suggested that TevXPC (being an exogenous protein in T. cruzi) interferes negatively in cellular processes where TcXPC (the endogenous protein) is involved. This probably occurred due interaction of TevXPC with some endogenous molecules or proteins from T.cruzi but incapacity of interaction with others. This reinforces the importance of correctly XPC functioning within the cell.

Differential expression of Fanconi anemia complementation group I in triple negative breast cancer.

Women diagnosed with triple negative breast cancer are predicted to benefit neither from endocrine therapy nor from HER2-targeted therapies (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding Fanconi anemia complementation group I, FANCI, when comparing the tumor cells of patients with triple negative breast cancer to normal mammary ductal cells (2). FANCI was also differentially expressed in bulk tumor in human breast cancer (3). FANCI mRNA was present at significantly increased quantities in TNBC tumor cells relative to normal mammary ductal cells. Analysis of human survival data revealed that expression of FANCI in primary tumors of the breast was correlated with overall survival in patients with basal-like and luminal A type cancer, while within triple negative breast cancer, primary tumor expression of FANCI was correlated with overall survival in patients with immunomodulatory subtype disease. FANCI may be of relevance to initiation, maintenance or progression of triple negative breast cancers.

TGF-β2-induced NEAT1 regulates lens epithelial cell proliferation, migration and EMT by the miR-26a-5p/FANCE axis

AIM: To explore the regulatory mechanism of nuclear paraspeckle assembly transcript 1 (NEAT1) in the pathogenesis of posterior capsule opacification (PCO). METHODS: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was executed to analyze NEAT1 and microRNA (miR)-26a-5p expression in transforming growth factor-beta 2 (TGF-β2)-disposed lens epithelial cells (LECs). The proliferation, cell cycle progression, apoptosis, and migration of TGF-β2-disposed LECs were evaluated. The relationship between NEAT1 or fanconi anemia (FA) complementation group E (FANCE) and miR-26a-5p was verified by dual-luciferase reporter assay. RESULTS: TGF-β2 induced NEAT1 expression in LECs. NEAT1 inhibition accelerated apoptosis, cell cycle arrest, decreased proliferation, epithelial-mesenchymal transition (EMT), and migration of TGF-β2-disposed LECs. NEAT1 sponged miR-26a-5p to further regulate FANCE expression. Rescue experiments presented that miR-26a-5p downregulation overturned NEAT1 silencing-mediated impacts on TGF-β2-disposed LEC biological behaviors. Additionally, FANCE overexpression reversed miR-26a-5p mimic-mediated impacts on TGF-β2-disposed LEC biological behaviors. CONCLUSION: TGF-β2-induced NEAT1 facilitates LEC proliferation, migration, and EMT by upregulating FANCE via sequestering miR-26a-5p.

An active learning framework improves tumor variant interpretation

For precision medicine to reach its full potential for treatment of cancer and other diseases, protein variant effect prediction tools are needed that characterize variants of unknown significance (VUS) in a patient's genome with respect to their likelihood to influence treatment response and outcomes. However, the performance of most variant prediction tools is limited by the difficulty of acquiring sufficient training and validation data. To overcome these limitations, we applied an iterative active learning approach starting from available biochemical, evolutionary, and functional annotations. The potential of active learning to improve variant interpretation was first demonstrated by applying it to synthetic and deep mutational scanning (DMS) datasets for four cancer-relevant proteins. We then probed its utility to guide interpretation and functional validation of tumor VUS in a potential biomarker for cancer therapy sensitivity, the nucleotide excision repair (NER) protein Xeroderma Pigmentosum Complementation Group A (XPA). A quantitative high-throughput cell-based NER activity assay, fluorescence-based multiplex flow-cytometric host cell reactivation (FM-HCR), was used to validate XPA VUS selected by the active learning strategy. In all cases, selecting VUS for validation by active learning yielded an improvement in performance over traditional learning. These analyses suggest that active learning is well-suited to significantly improve interpretation of VUS and cancer patient genomes.

Fanconi Anemia Complementation Group E (FANCE), 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 two 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 (H2AFX and CHEK1) 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.

Severe cisplatin-induced renal toxicity in a patient with xeroderma pigmentosum

Introduction Xeroderma pigmentosum is a rare genetic disorder of DNA repair, defined by extreme sensitivity to sunlight, leading to sunburn, skin pigmentation and increased incidence of skin cancers. Cisplatin acts by interfering with DNA repair mechanisms to cause DNA damage and apoptosis. It has indications in many malignancies including bladder, head and neck and lung cancers. Acute kidney injury is a well-known complication of cisplatin. Case report We report a 42-year-old male with a long history of Xeroderma pigmentosum treated with adjuvant cisplatin (40 mg/m2) in combination with radiotherapy for cutaneous squamous cell carcinoma of the neck. He presented to clinic prior to his second weekly dose of cisplatin with a severe acute kidney injury and a creatine level of 813 mmol/L and eGFR of 7 mL/min. No myelosuppression was present. Management and outcome Treatment consisted of aggressive electrolyte and fluid management. Creatinine levels slowly improved with conservative management without the need for dialysis. Radiation was completed without further cisplatin. Discussion Three cases of severe adverse effects from cisplatin administration in patients with Xeroderma pigmentosum have been reported, with all fatal. Xeroderma pigmentosum complementation group C plays an important role in the DNA repair process with the recognition and repair of damage to normal cells following cisplatin. Patients with Xeroderma pigmentosum can be carriers of defective Xeroderma pigmentosum complementation group C and if the degree of Xeroderma pigmentosum complementation group C inactivity is significant, fatalities could occur. Physicians should be aware of this rare but potentially lethal toxicity when considering systemic therapy for squamous cell carcinoma in patients diagnosed with Xeroderma pigmentosum.

Increased H2O2 levels and p53 stabilization lead to mitochondrial dysfunction in XPC-deficient cells

XPC deficiency is associated with mitochondrial dysfunction, increased mitochondrial H2O2 production and sensitivity to the Complex III inhibitor antimycin A (AA), through a yet unclear mechanism. We found an imbalanced expression of several proteins that participate in important mitochondrial function and increased expression and phosphorylation of the tumor suppressor p53 in Xeroderma pigmentosum complementation group C (XP-C) (XPC-null) cells compared with an isogenic line corrected in locus with wild-type XPC (XPC-wt). Interestingly, inhibition of p53 nuclear import reversed the overexpression of mitochondrial proteins, whereas AA treatment increased p53 expression more strongly in the XP-C cells. However, inhibition of p53 substantially increased XP-C cellular sensitivity to AA treatment, suggesting that p53 is a critical factor mediating the cellular response to mitochondrial stress. On the other hand, treatment with the antioxidant N-acetylcysteine increased glutathione concentration and decreased basal H2O2 production, p53 levels and sensitivity to AA treatment in the XPC-null back to the levels found in XPC-wt cells. Thus, the results suggest a critical role for mitochondrially generated H2O2 in the regulation of p53 expression, which in turn modulates XP-C sensitivity to agents that cause mitochondrial stress.