DNA Repair Signaling Pathways Research Articles

Identification of Copy Number Variation-Driven Molecular Subtypes in Pancreatic Adenocarcinoma of Chinese Cohort

Pancreatic adenocarcinoma (PAAD) is one of the most lethal carcinomas all over the world. The current histopathological classifications for PAAD are of limited use to guide clinical decision-making, and there is an unmet need to identify new biomarkers for molecular subtyping. We profiled a comprehensive landscape of genomic alterations for 608 PAAD patients in a Chinese cohort, including somatic mutations, pathogenic germline variants and copy number variations (CNV). Our data provided no evidence of associations with prognosis based on the information of point mutations in either highly mutated genes (such as KRAS, TP53, CDKN2A and SMAD4) or homologous recombination repair genes. Instead, associated with worse prognosis were amplified genes involved in DNA repair and receptor tyrosine kinase related signaling pathways. Motivated by this observation, we categorized patients into four molecular subtypes (namely repair-deficient, proliferation-active, repair-proficient and repair-enhanced) that differed in prognosis. Together with the evidence from genomic footprint analysis, we suggested that repair-deficient and proliferation-active subtypes were better suited for DNA damage therapies, while immunotherapy was highly recommended for repair-proficient and repair-enhanced subtypes. Collectively, our findings represent a significant step in improving diagnosis and management for PAAD patients. Funding Statement: This work was supported by the National Natural Science Foundation of China (grant numbers 81470894, 81502695, 81672325, 81871906, 82073326) and the Shanghai Sailing Program (grant number 20YF1426900). Declaration of Interests: The authors declare no potential conflicts of interest. Ethics Approval Statement: The overall study protocol was approved by the Medical Ethical Committee of Ruijin Hospital and the research was conducted in accordance with relevant ethical guidelines.

Quantitative proteomic analysis of ahpC/F and katE and katG knockout Escherichia coli—a useful model to study endogenous oxidative stress

Alkyl hydroperoxide reductase (AhP), catalase G (KatG), and catalase E (KatE) are the main enzymes to scavenge the excessive hydrogen peroxide in E. coli. It was found the concentration of endogenous H2O2 was submicromolar in a mutant strain E. coli MG1655/ΔAhpΔKatEΔKatG, which was enough to cause damage to DNA and proteins as well as concomitant cell growth and metabolism. However, few studies explored how submicromolar intracellular hydrogen peroxide alters protein function and regulates the signaling pathways at the proteome level. In order to study the effect of endogenous oxidative stress caused by submicromolar hydrogen peroxide, this study first constructed a mutant strain E. coli MG1655/ΔAhpΔKatEΔKatG. Then, label-free quantitative proteomic analysis was used to quantify the differentially expressed proteins between the wild-type strain and the mutant strain. A total of 265 proteins were observed as differentially expressed proteins including 108 upregulated proteins and 157 downregulated proteins. Among them, three differentially expressed proteins were also validated by parallel reaction monitoring (PRM) methodology. The 265 differentially expressed proteins are not only involved with many metabolism pathways including the TCA cycle, the pentose phosphate pathway, and the glyoxylic acid cycle, but also activated the DNA repair and cellular antioxidant signaling pathway. These findings not only demonstrated that ahp, katE, and katG played the critical role in aerobic growth but also delineated proteins network and pathway regulated by submicromolar intracellular hydrogen peroxide, which allowed a deeper understanding of oxidative signaling in E. coli. The findings of this study also demonstrate that the mutant E. coli may serve as a cell model to investigate the effect of endogenous oxidative stress and downstream signaling pathways. KEY POINTS: • The mutant strain E. coli MG1655/ΔAhpΔKatEΔKatG was constructed to study the effect of endogenous oxidative stress in E. coli. • A total of 265 differentially expressed proteins were quantified and enriched in metabolic pathways and antioxidant systems by using label-free proteomics analysis. • The findings of this study demonstrate that the mutant E. coli may serve as an effective tool to investigate the endogenous oxidative stress.

Next-generation sequencing for identification of actionable gene mutations in intestinal-type sinonasal adenocarcinoma

Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumor carrying poor prognosis and needing new treatment options. The aim of this study was to identify actionable gene mutations that can guide new personalized target-specific therapies in ITAC patients. A series of 48 tumor and 27 corresponding germline DNA samples were analyzed by next generation sequencing using a panel of 120 genes. In total, 223 sequence variants were found in 70 genes. Matched tumor/germline comparison in 27 cases revealed that 57% were in fact germline variants. In 20 of these 27 cases, 58 somatic variants in 33 different genes were identified, the most frequent being PIK3CA (5 cases), APC and ATM (4 cases), and KRAS, NF1, LRP1B and BRCA1 (3 cases). Many of the somatic gene variants affected PI3K, MAPK/ERK, WNT and DNA repair signaling pathways, although not in a mutually exclusive manner. None of the alterations were related to histological ITAC subtype, tumor stage or survival. Our data showed that thorough interpretation of somatic mutations requires sequencing analysis of the corresponding germline DNA. Potentially actionable somatic mutations were found in 20 of 27 cases, 8 of which being biomarkers of FDA-approved targeted therapies. Our data implicate new possibilities for personalized treatment of ITAC patients.

Integrate analysis of the promote function of Cell division cycle-associated protein family to pancreatic adenocarcinoma.

Background: The cell division cycle-associated (CDCA) protein family plays a pivotal role in the regulation of the cell cycle during tumorigenesis and predicts the prognosis of tumors, but an analysis of these proteins in pancreatic adenocarcinoma (PAAD) is still lacking.Methods: Oncomine and GEPIA were used to observe the expression and prognostic value of eight CDCAs in pan-cancer. Univariate Cox analysis of single CDCAs and multivariate Cox analysis of all eight CDCAs were performed to evaluate the integrated prognostic value of CDCAs, and the results are displayed as hazard ratios (HRs) and 95% confidence intervals (95% CIs). K-M plots and receiver operating characteristics curves were used to display the predicted function and accuracy of CDCAs to determine the risk score. Annotation of CDCA-related genes, gene sets enrichment analysis (GSEA) and gene sets variation analysis (GSVA) were performed to reveal the CDCAs that impact biological processes.Results: CDCAs expression in most tumors is higher than that in normal tissues and is associated with a poor prognosis. Regarding PAAD, increased CDCA expression along with advanced PAAD tumor stage, NUF2, CDCA2, CDCA3, CDCA4 and CDCA5 expression are risk factors for poor prognosis, while CBX2 expression is a protective factor (P < 0.05). The integrated prognostic value of CDCAs in PAAD patients was validated by SurvExpress in the TCGA-PAAD cohort (P < 0.001, HR = 2.16, 95% CI = 1.41-3.3) and the ICGC-PACA cohort (P < 0.001, HR = 2.56, 95% CI = 1.73-3.79). Genetic alteration and DNA methylation of CDCAs might not affect the prognosis of PAAD patients. After comparing high- and low-risk groups separated by CDCA risk scores, the activated pathways were revealed and included the cell cycle, DNA repair, P53, MYC-targets, E2F-targets and PI3K pathways.Conclusion: CDCAs can predict the OS prognosis of PAAD patients. The cell cycle, DNA repair, E2F, P53 and PI3K signaling pathways, in which CDCAs are involved, impact the tumorigenesis of PAAD.

Identification and Characterization of Alcohol-related Hepatocellular Carcinoma Prognostic Subtypes based on an Integrative N6-methyladenosine methylation Model.

Background: Alcohol consumption increases the risk of hepatocellular carcinoma (HCC), and associated with a high mortality rate and poor prognosis. N6-methyladenosine (m6A) methylations play key roles in tumorigenesis and progression. However, our current knowledge about m6A in alcohol-related HCC (A-HCC) remains elucidated. Herein, the authors construct an integrative m6A model based on A-HCC subtyping and mechanism exploration workflow.Methods: Based on the m6A expressions of A-HCC and in vivo experiment, different prognosis risk A-HCC subtypes are identified. Meanwhile, multiple interdependent indicators of prognosis including patient survival rate, clinical pathological prognosis and immunotherapy sensitivity.Results: The m6A model includes LRPPRC, YTHDF2, KIAA14219, and RBM15B, classified A-HCC patients into high/low-risk subtypes. The high-risk subtype compared to the low-risk subtype showed phenotypic malignancy, poor prognosis, immunosuppression, and activation of tumorigenesis and proliferation-related pathways, including the E2F target, DNA repair, and mTORC1 signalling pathways. The expression of Immunosuppressive cytokines DNMT1/EZH2 was up-regulated in A-HCC patients, and teniposide may be a potential therapeutic drug for A-HCC.Conclusion: Our model redefined A-HCC prognosis risk, identified potential m6As linking tumour progress and immune regulations and selected possible therapy target, thus promoting understanding and clinical applications about A-HCC.

Exploiting DNA repair pathways for tumor sensitization, mitigation of resistance, and normal tissue protection in radiotherapy.

More than half of cancer patients are treated with radiotherapy, which kills tumor cells by directly and indirectly inducing DNA damage, including cytotoxic DNA double-strand breaks (DSBs). Tumor cells respond to these threats by activating a complex signaling network termed the DNA damage response (DDR). The DDR arrests the cell cycle, upregulates DNA repair, and triggers apoptosis when damage is excessive. The DDR signaling and DNA repair pathways are fertile terrain for therapeutic intervention. This review highlights strategies to improve therapeutic gain by targeting DDR and DNA repair pathways to radiosensitize tumor cells, overcome intrinsic and acquired tumor radioresistance, and protect normal tissue. Many biological and environmental factors determine tumor and normal cell responses to ionizing radiation and genotoxic chemotherapeutics. These include cell type and cell cycle phase distribution; tissue/tumor microenvironment and oxygen levels; DNA damage load and quality; DNA repair capacity; and susceptibility to apoptosis or other active or passive cell death pathways. We provide an overview of radiobiological parameters associated with X-ray, proton, and carbon ion radiotherapy; DNA repair and DNA damage signaling pathways; and other factors that regulate tumor and normal cell responses to radiation. We then focus on recent studies exploiting DSB repair pathways to enhance radiotherapy therapeutic gain.

Abstract 1313: Genomic and transcriptomic profiles of primary prostate cancer identify unique targets for therapeutic intervention

Abstract The tumor microenvironment and genomic landscape of intermediate and high-risk primary localized prostate cancers are clinically heterogeneous and result in variable treatment response in individuals. Cancer-specific alterations at DNA and RNA level is a critical driver of intra-tumoral heterogeneity that significantly impacts the molecular processes which influence the path of disease progression and outcome. In this study, we have performed genomic and transcriptomic analysis of 267 primary prostate cancer. Our analysis revealed actionable alterations and gene signatures for risk stratification and decision support. Clinically significant variants were detected in DNA repair (HR and Mismatch pathway), PI3/AKT, and TP53 signaling pathways with a strong association with disease progression. Further, single-cell analysis (scRNA-seq) of prostate cancer that progressed to metastasis post-therapy identified the unique tumor and immune cell-clusters. Functional annotation of these clusters and drug repurposing studies revealed novel targets for therapeutic intervention that was validated using organoid cultures. Our studies show that an Integrated analysis using genomic, clinical, and pathological features has the potential to define prostate cancer subtypes or phenotypes associated with poor prognosis. Our approach can advance prostate cancer treatment in patients with adverse clinical features by providing treatment options beyond the standard of care (surgery or radiation) and with better therapeutic benefit. Citation Format: Dimple Chakravarty, Zichen Wang, Michael Rossi, Parita Ratnani, Boris Reva, Dmitry Rykunov, Kamala Bhatt, Vinayak Wagaskar, Rachel Weil, Kristin Beaumont, Michael Beaumont, Avi Maayan, Robert Sebra, Nina Bhardwaj, Sujit S. Nair, Ashutosh K. Tewari. Genomic and transcriptomic profiles of primary prostate cancer identify unique targets for therapeutic intervention [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1313.

Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma.

9526 Background: Lung cancer remains the leading cause of death from cancer around the world. Several oncogenic drivers have been identified from large cancer genome projects focused mainly on profiling early-stage lung cancers. Targeted therapies have been developed for specific activated driver gene mutations and are used in advanced-stage patients. For instance, advanced EGFR mutant lung cancer is primarily treated with EGFR tyrosine receptor inhibitors (TKIs). However, resistance remains an obstacle to durable anti-tumor control. We hypothesize that concurrent genetic alterations co-exiting with EGFR driver mutations contribute to the failure of EGFR TKI therapy. Methods: To understand the complexity and diversity of genetic alterations present in EGFR mutant advanced lung cancers, we utilized 660 EGFR mutant advanced lung adenocarcinomas samples with targeted DNA sequencing from Foundation Medicine, 394 cases from MSK-IMPACT dataset, along with TCGA lung cancer data. We performed systematic co-mutation analysis, molecular simulation, functional annotation and pathway enrichment analysis. Results: We updated mutational profiling on EGFR gene with hotspots at exon 18, 19, 20 and 21. Among them, EGFR L858R, exon19 deletion, T790M and G719A are top ranking alleles among EGFR mutations. Interestingly, a subset (n = 26 cases) of EGFR T790M mutations parallel with other EGFR mutations, which could affect the TKI binding pocket as inferred by molecular simulations. Furthermore, in advanced lung cancer EGFR mutations co-occurred with known oncogenic mutations in KRAS, MET, NF-1, MAP2K1, ERBB2, and ALK/ROS-1/RET fusions. Functional annotation suggests that concurrent mutated genes and copy number alterations in advanced EGFR mutant lung cancer were enriched in signatures of epigenetic modifiers, genome instability, WNT signaling, and RNA splicing. Compared to early stage TCGA-lung adenocarcinomas, Cell cycle, DNA repair, WNT signaling and androgen receptor-mediated signaling pathways are predominantly altered in advanced EGFR mutant lung cancers. Conclusions: We characterized the genetic landscape of advanced EGFR-mutant lung adenocarcinomas and further dissected concurrent mutated genes with EGFR driver mutations. Our findings provide a rational for polytherapy roadmap for testing in advanced EGFR-mutant lung cancer.

Full-Process Radiosensitization Based on Nanoscale Metal-Organic Frameworks.

Full-process radiosensitization, that is, pre-increasing radiation sensitivity of cancer cells, magnifying •OH formation during ionizing irradiation, and intervention on the resultant DNA repair for final cells death, could enhance the overall radiotherapeutic effects, but has not yet been achieved. Herein, Hf-nMOFs with Fe3+ ions uniformly dispersed (Hf-BPY-Fe) were constructed to integratedly improve radiotherapeutic effects via a multifaceted mechanism. The in vitro experiments demonstrated that persistent reactive oxygen species stress from Hf-BPY-Fe-activated in situ Fenton reaction reassorted cell cycle distribution, consequently contributing to increased tumoral radiosensitivity to photon radiation. Upon irradiation during the course of radiation therapy, Hf4+ in Hf-BPY-Fe gave substantial amounts of high-energy electrons, which partially converted H2O to •OH and, meanwhile, relaxed to a low-energy state in nMOF pores, leading to an electron-rich environment. These aggregated electrons facilitated the reduction from Fe3+ to Fe2+ and further promoted the production of •OH in the Fenton process to attack DNA. The Hf-BPY-Fe postponed the DNA damage response process by interfering with certain proteins involved in the DNA repair signaling pathway. The in vivo experiments showed improved radiotherapeutic effects from integrated contributions from Fe3+-based Fenton reaction and Hf4+-induced X-ray energy conversion in tumors. This work provides a nMOFs-based full-process radiosensitizing approach for better radiotherapeutic efficacy.

The lipogenic LXR-SREBF1 signaling pathway controls cancer cell DNA repair and apoptosis and is a vulnerable point of malignant tumors for cancer therapy.

Cancer cells are defective in DNA repair, so they experience increased DNA strand breaks, genome instability, gene mutagenesis, and tumorigenicity; however, multiple classic DNA repair genes and pathways are strongly activated in malignant tumor cells to compensate for the DNA repair deficiency and gain an apoptosis resistance. The mechanisms underlying this phenomenon in cancer are unclear. We speculate that a key DNA repair gene or signaling pathway in cancer has not yet been recognized. Here, we show that the lipogenic liver X receptor (LXR)-sterol response element binding factor-1 (SREBF1) axis controls the transcription of a key DNA repair gene polynucleotide kinase/phosphatase (PNKP), thereby governing cancer cell DNA repair and apoptosis. Notably, the PNKP levels were significantly reduced in 95% of human pancreatic cancer (PC) patients, particularly deep reduction for sixfold in all of the advanced-stage PC cases. PNKP is also deficient in three other types of cancer that we examined. In addition, the expression of LXRs and SREBF1 was significantly reduced in the tumor tissues from human PC patients compared with the adjacent normal tissues. The newly identified LXR-SREBF1-PNKP signaling pathway is deficient in PC, and the defect in the pathway contributes to the DNA repair deficiency in the cancer. Strikingly, further diminution of the vulnerable LXR-SREBF1-PNKP signaling pathway using a small molecule triptonide, a new LXR antagonist identified in this investigation, at a concentration of 8 nM robustly activated tumor-suppressor p53 and readily elevated cancer cell DNA strand breaks over an apoptotic threshold, and selectively induced PC cell apoptosis, resulting in almost complete elimination of tumors in xenograft mice without obvious complications. Our findings provide new insight into DNA repair and apoptosis in cancer, and offer a new platform for developing novel anticancer therapeutics.

Establishment of Immune-related Gene Pair Signature to Predict Lung Adenocarcinoma Prognosis

Tumor microenvironment (TME) has critical impacts on the pathogenesis of lung adenocarcinoma (LUAD). However, the molecular mechanism of TME effects on the prognosis of LUAD patients remains unclear. Our study aimed to establish an immune-related gene pair (IRGP) model for prognosis prediction and internal mechanism investigation. Based on 702 TME-related differentially expressed genes (DEGs) extracted from The Cancer Genome Atlas (TCGA) training cohort using the ESTIMATE algorithm, a 10-IRGP signature was established to predict LUAD patient prognosis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly associated with tumor immune response. In both TCGA training and Gene Expression Omnibus validation datasets, the risk score was an independent prognostic factor for LUAD patients using Lasso-Cox analysis, and patients in the high-risk group had poorer prognosis than those in the low-risk one. In the high-risk group, M2 macrophage and neutrophil infiltrations were higher, while the levels of T cell follicular helpers were significantly lower. The gene set enrichment analysis results showed that DNA repair signaling pathways were involved. In summary, we established an IRGP signature as a potential biomarker to predict the prognosis of LUAD patients.

FOXM1 functions collaboratively with PLAU to promote gastric cancer progression.

Background: Gastric cancer (GC) is one of the main mortality cause worldwide. Previously, we found Forkhead box protein (FOXM1) or Urokinase-type plasminogen activator (PLAU) are independent prognostic markers of GC. This study aims to explore the combining prognostic efficacy and the potential insights underlying additive effect of FOXM1 to PLAU in GC progression through in-silico analyses.Method: The expression of FOXM1 and PLAU were profiled in 33 cancer types using public data. A merged GC expression dataset containing 598 samples was used for evaluating prognostic significance of FOXM1/PLAU. Gene Set Enrichment Analysis (GSEA) was performed to elucidate the mechanisms underlying FOXM1/PLAU promoted GC progression. The Cancer Genome Atlas (TCGA) was used for analyzing the association between FOXM1/PLAU and tumor immune infiltration. Genomic and proteomic differences between FOXM1+PLAU+ and FOXM1-PLAU- groups were also computed using TCGA GC data. Drugs targeting FOXM1/PLAU associated gene expression pattern was analyzed using LINCs database.Results: FOXM1 and PLAU are overexpressed in 17/33 cancer types including GC. Kaplan-Meier analyses indicate that the FOXM1+PLAU+ subgroup have the worst prognosis, while FOXM1-PLAU- subgroup have the best survival. Bioinformatics analysis indicated that FOXM1+PLAU+ associated genes are enriched in TGF-beta, DNA repair and drug resistance signaling pathways; FOXM1 and PLAU expression are negatively correlated with tumor immune infiltration. Genomic and proteomic differences between FOXM1+PLAU+ and FOXM1-PLAU- groups were presented. Data mining from LINCs suggested several chemicals or drugs that could target the gene expression pattern of FOXM1+PLAU+ patients.Conclusion: FOXM1+PLAU+ can serve as effective prognostic biomarkers and potential therapeutic targets for GC. Due to the additive effect of these two genes, screening for drugs or chemicals that targeting the expression patterns PLAU+FOXM1+ subgroup may exert important clinical impact on GC management.

Tea Polyphenols Attenuate Methamphetamine-Induced Neuronal Damage in PC12 Cells by Alleviating Oxidative Stress and Promoting DNA Repair.

DNA integrity plays a crucial role in cell survival. Methamphetamine (METH) is an illegal psychoactive substance that is abused worldwide, and repeated exposure to METH could form mass free radicals and induce neuronal apoptosis. It has been reported that free radicals generated by METH treatment can oxidize DNA and hence produce strand breaks, but whether oxidative DNA damage is involved in the neurotoxicity caused by METH remains unclear. Tea polyphenols exert bioactivities through antioxidant-related mechanisms. However, the potential neuroprotective effect of tea polyphenols on METH-induced nerve cell damage and the underlying mechanism remain to be clarified. In this study, oxidative stress, DNA damage, and cell apoptosis were increased after METH exposure, and the expressions of DNA repair-associated proteins, including the phosphorylation of ataxia telangiectasia mutant (p-ATM) and checkpoint kinase 2 (p-Chk2), significantly declined in PC12 cells after high-dose or long-time METH treatment. Additionally, tea polyphenols could protect PC12 cells against METH-induced cell viability loss, reactive oxide species and nitric oxide production, and mitochondrial dysfunction and suppress METH-induced apoptosis. Furthermore, tea polyphenols could increase the antioxidant capacities and expressions of p-ATM and p-Chk2 and then attenuate DNA damage via activating the DNA repair signaling pathway. These findings indicate that METH is likely to induce neurotoxicity by inducing DNA damage, which can be reversed by tea polyphenols. Supplementation with tea polyphenols could be an effective nutritional prevention strategy for METH-induced neurotoxicity and neurodegenerative disease.

Heat-shock proteins: chaperoning DNA repair.

Cells are repeatedly exposed to environmental or endogenous stresses that can alter normal cell behavior and increase cell vulnerability. In order to ensure tissue integrity and function, cells cope with cellular injuries by adapting their metabolism, protecting essential intracellular constituents, inhibiting cell death signaling pathways and activating those devoted to damage repair. The molecular chaperones of the heat-shock protein (HSP) family are critical effectors of this adaptive response. They protect intracellular proteins from misfolding or aggregation, inhibit cell death signaling cascades and preserve the intracellular signaling pathways that are essential for cell survival. Most HSPs are rapidly overexpressed in response to cellular injuries including genotoxic stress. DNA damage can dramatically alter cell behavior and contribute to a number of diseases including developmental defects, neurodegenerative disorders, and cancer. Thus, the ability of cells to repair DNA damage is essential for preserving cell integrity. DNA damage activates a coordinated response that includes detecting DNA lesions before their transmission to daughter cells, blocking cell cycle progression and DNA replication and repairing the damage. Although the role of HSPs in proteins homeostasis and cell death, especially apoptosis has been widely reported, much less is known about their function in DNA repair. This review aims to present the role of HSPs in DNA repair signaling pathways.

Sam68 is required for the growth and survival of nonmelanoma skin cancer.

Although targeting DNA repair signaling pathways has emerged as a promising therapeutic for skin cancer, the relevance of DNA damage responses (DDR) in the development and survival of nonmelanoma skin cancer (NMSC), the most common type of skin cancer, remains obscure. Here, we report that Src‐associated substrate during mitosis of 68 kDa (Sam68), an early signaling molecule in DDR, is elevated in skin tumor tissues derived from NMSC patients and skin lesions from Gli2‐transgenic mice. Downregulation of Sam68 impacts the growth and survival of human tumor keratinocytes and genetic ablation of Sam68 delays the onset of basal cell carcinomas (BCC) in Gli2‐transgenic mice. Moreover, Sam68 plays a critical role in DNA damage‐induced DNA repair and nuclear factor kappa B (NF‐κB) signaling pathways in keratinocytes, hence conferring keratinocyte sensitivity to DNA damaging agents. Together, our data reveal a novel function of Sam68 in regulating DDR in keratinocytes that is crucial for the growth and survival of NMSC.

KAT5 Negatively regulates the proliferation of prostate cancer LNCaP cells via the caspase 3-dependent apoptosis pathway

ABSTRACTProstate cancer is one of the most common cancers in men over the age of sixty. Lysine acetyltransferase 5 (KAT5) is a histone acetyltransferase involved in transcriptional regulation, DNA repair, and cell signaling pathways. Previous studies have shown that KAT5 expression is reduced in the cytoplasm of the prostate cancer cell line LNCaP when exposed to androgen. Moreover, KAT5 has been reported to have a role in the molecular pathway leading to androgen-independent prostate cancer after long-term androgen deprivation therapy. Here, we showed that KAT5 expression was significantly reduced in prostate cancer tissues and cell lines by using the public databases Oncomine and Human Protein Atlas. Reduced KAT5 expression was significantly associated with high mortality in prostate cancer patients. Furthermore, KAT5 overexpression increased the level of apoptotic markers, such as cleaved-caspase 3, in LNCaP cells, thus enhancing the apoptotic death of LNCaP cells. Taken together, KAT5 induced apoptosis in prostate cancer cells via the caspase-3 pathway, indicating that KAT5 could be a gene therapy target for prostate cancer.

Personalised medicine in urothelial bladder cancer

Available treatment options and outcomes for patients suffering from urothelial bladder cancer, especially in the metastatic stage, have hardly improved over decades. However, the increasing use of high-throughput analyses and the concept of immune surveillance against tumours have recently changed our understanding of tumour biology in terms of tumour development and progression. Our knowledge of genetic mutations and molecular subtypes provides the possibility of tailor-made therapeutic approaches for patients suffering from bladder cancer. For example, changes in DNA repair signalling pathways are possible predictors of chemotherapy response, and targeted therapies using FGFR or PARP inhibitors are currently being tested in clinical trials. The extent to which molecular subtypes will find their way into clinical practice depends on the prospective evaluation of their prognostic and predictive value. The introduction of immune checkpoint inhibitors is probably the most significant expansion of available treatment options in bladder cancer. Despite their promising results, however, a lot of questions remain to be answered, as only 25 % of patients respond. Again, this highlights the need for predictive biomarkers. The large inter- and intratumoural heterogeneity represents a particular challenge for the clinical implementation of personalised treatment options in bladder cancer. All in all, some important steps towards personalised medicine in urothelial bladder cancer have been taken in the past few years, but, for the most part, their prospective evaluation is still pending.

Targeting PARP1 As an Effective Treatment for Diffuse Large B-Cell Lymphoma with High Level of γH2AX

IntroductionDNA damage repair process has been reported to be the cause of malignant cells resistance to genomic DNA-targeted chemicals. Whether DNA damage repair mediates chemo-resistance in diffuse large B-cell lymphoma (DLBCL) remains elusive. H2AX phosphorylation (γH2AX) is an early event of double-strand DNA repair signaling, which can trigger homologous recombination (HR), classical non-homologous end joining (cNHEJ), or alternative non-homologous end joining (aNHEJ) in a context-dependent manner. The priority choice of PARP1 following H2AX phosphorylation promotes aNHEJ signaling, a well-known oncogenic DNA repair process. PARP inhibitor has increased the efficacy of some neoplasms with HR deficiency. The study addressed the association of γH2AX level with DNA repair signaling and its prognostic value in DLBCL. The role of PARP1 as a therapeutic target was also explored in the study.MethodsγH2AX protein was examined in new-diagnosed patients with DLBCL (n=90) using immunohistochemistry method. Its prognostic value was evaluated with multivariate analysis. Gene expression profiling was performed on 50 patients and DNA repair signaling was compared based on γH2AX expression. H2AX shRNA was used to downregulate the expression of H2AX and γH2AX through lentivirus in vitro on cell line to observe the effect on doxorubicin-induced apoptosis using flow cytometry. γH2AX and PARP1 were detected using Western blotting and immunoflurescent assay, while DNA repair signaling was detected using PCR array in vitro on cell lines. PARP inhibitor-induced apoptosis was also compared among cell lines using flow cytometry.ResultγH2AX level suggested a poor prognosis in new-diagnosed patients with diffuse large B-cell lymphomaγH2AX was detected in 43.34% (39/90) of new-diagnosed DLBCL patients (Figure 1A). Patients clinical features were listed in Table 1. The complete remission (CR) rate was lower in positive patients (31.37% vs 68.62%, p=0.009) after anthrocycline-based chemotherapy. Multivariate analysis showed γH2AX to have an independent inverse association with overall survival after adjusting age, ECOG score, IPI score and Ann Arbor stage in these patients [HR=2.202 (1.161-4.184), p=0.016] (Figure 1B).DNA repair signaling pathway was enriched in patients with γH2AX expressionGene expression profiling was performed in 50 new-diagnosed patients with DLBCL. Gene clusters were compared between patients with and without γH2AX expression. The result displayed that DNA repair signaling pathway was enriched in patients with γH2AX expression (NSE=1.901, FDR q-value=0.010) (Figure 1C).The linkage of γH2AX with DNA repair signaling was confirmed in vitro on cell linesThe expression of H2AX and γH2AX was tested in OCI-ly7, OCI-ly3 and OCI-ly8 cell lines. The highest level of H2AX and γH2AX was observed in OCI-ly7 cells, followed by OCI-ly8 and OCI-ly3 cells (Figure 2A). DNA repair genes were proven to be highly expressed in OCI-ly7 cell line using DNA repair signaling PCR array compared with the other two cell lines (Figure 2B).Downregulating γH2AX expression increased doxorubicin-induced apoptosis in vitroThe reduction of γH2AX level was demonstrated in H2AX shRNA-transduced OCI-ly7 cell line (Figure 2C). The proportion of doxorubicin-induced (50ng/ml) apoptosis was increased in these cells compared with control (5.87±2.37% vs 39.18±3.78%, p<0.05). (Figure 2D)PARP1 level presented a positive correlation with γH2AX expression and PARP inhibitor-induced apoptosis in vitroThe level of PARP1 expression was proportional to γH2AX expression in OCI-ly7, OCI-ly3 and OCI-ly8 cell lines (Figure 3A). The result indicates an abnormal aNHEJ oncogenic DNA repair to be superior in DLBCL cells with high γH2AX expression. FEN, another key component of aNHEJ signaling was also overexpressed in cell line and patients with high expression of γH2AX. PARP inhibitor (25μM) induced the highest proportion of apoptosis in OCI-ly7 cell line, compared with OCI-ly8 and OCI-ly3 cell lines (42.90±5.29% vs 29.52±3.95% vs 9.41±2.35%, p<0.05) (Figure 3B).ConclusionγH2AX as a biomarker for abnormally activated DNA repair signaling is associated with poor outcome in the setting of conventional chemotherapy in DLBCL. PARP1-mediated aNHEJ signaling performs critical functions in DLBCL with γH2AX expression. Here, we demonstrated that PARP inhibitor may be efficacious in these patients. DisclosuresNo relevant conflicts of interest to declare.

Pja2 Inhibits Wnt/β-catenin Signaling by Reducing the Level of TCF/LEF1.

Ubiquitination of proteins plays an essential role in various cellular processes, including protein degradation, DNA repair, and cell signaling pathways. Previous studies have shown that protein ubiquitination is implicated in regulating pluripotency as well as fate determination of stem cells. To identify how protein ubiquitination affects differentiation of embryonic stem cells, we analyzed microarray data, which are available in the public domain, of E3 ligases and deubiquitinases whose levels changed during stem cell differentiation. Expression of pja2, a member of the RING-type E3 ligase family, was up-regulated during differentiation of stem cells. Wnt/β-catenin signaling is one of the most important signaling pathways for regulation of the self-renewal and differentiation of embryonic stem cells. Pja2 was shown to bind to TCF/LEF1, which are transcriptional factors for Wnt/β-catenin signaling, and regulate protein levels by ubiquitination, leading to down-regulation of Wnt signaling activity. Based on these results, we suggest that E3 ligase Pja2 regulates stem cell differentiation by controlling the level of TCF/LEF1 by ubiquitination.

Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer

Subclonal architecture and genomic evolution of small-cell lung cancer (SCLC) under treatment has not been well studied primarily due to lack of tumor specimens, particularly longitudinal samples acquired during treatment. SCLC is characterized by early hematogenous spread, which makes circulating cell-free tumor DNA (ctDNA) sequencing a promising modality for genomic profiling. Here, we perform targeted deep sequencing of 430 cancer genes on pre-treatment tumor biopsies, as well as on plasma samples collected prior to and during treatment from 22 SCLC patients. Similar subclonal architecture is observed between pre-treatment ctDNA and paired tumor DNA. Mean variant allele frequency of clonal mutations from pre-treatment ctDNA is associated with progression-free survival and overall survival. Pre- and post-treatment ctDNA mutational analysis demonstrate that mutations of DNA repair and NOTCH signaling pathways are enriched in post-treatment samples. These data suggest that ctDNA sequencing is promising to delineate genomic landscape, subclonal architecture, and genomic evolution of SCLC.