bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1413: Replication obstacles formed within common fragile sites under replication stress are targeted by the global genomic nucleotide excision repair pathway
Authors: Mistrik Martin , Beresova Lucie , Vesela Eva , Chamrad Ivo , Voller Jiri , Yamada Masayuki , Furst Tomas , Lenobel Rene , Chroma Katarina , Gursky Jan , Bartek Jiri
Published: July 2017

CFS’s are genomic loci present in higher vertebrates that are particularly sensitive to various forms of replication stress and suffer from increased breakage and rearrangements in tumors. They have rather enigmatic evolutionary role and employ various DNA repair and checkpoint mechanisms promoting their stability. We used an original approach for identification of CFS’s associated factors based on DNA probe designed to match the high flexibility island sequences typically present in some of the highly expressed CFS’s. This probe was used as affinity bait for fishing specifically enriched proteins which were further identified using SILAC and quantitative mass spectrometry. Among already known CFS’s stabilizers we identified also hits so far not implicated in CFS’s maintenance. Interestingly, most of these novel hits are components of the global genomic nucleotide excision repair pathway (GG-NER). Knock down-based functional experiments revealed that GG-NER works most likely as an important trigger turning the CFS’s-associated replication obstacles into DNA lesion further recognized by the ATR-promoted cellular checkpoint which function is to block an escape of DNA replication intermediates into mitosis and the next cell generation. Work was supported by the Grant Agency of the Czech Republic 13-17555S, Czech-BioImaging project (LM2015062 funded by MEYS, CR) and Ministry of Education of the Czech Republic (LO1304).

Citation Format: Martin Mistrik, Lucie Beresova, Eva Vesela, Ivo Chamrad, Jiri Voller, Masayuki Yamada, Tomas Furst, Rene Lenobel, Katarina Chroma, Jan Gursky, Jiri Bartek. Replication obstacles formed within common fragile sites under replication stress are targeted by the global genomic nucleotide excision repair pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1413. doi:10.1158/1538-7445.AM2017-1413
Abstract 1417: Expression of BARD1δ induces genetic instability and is associated with cervical carcinogenesis
Authors: Pilyugin Maxim , André Pierre-Alain , Concin Nicole , Hofstetter Gerda , Irminger-Finger Irmgard
Published: July 2017

Cervical cancer is always linked to infection with the human papilloma virus (HPV), which causes hyper-proliferation of cervical epithelial cells and neoplasia and cervical cancer. The viral oncoprotein interaction with host tumor suppressor proteins partially explains the uncontrolled proliferation, which ultimately progresses to cervical cancer. However, little is known about the specific factors that promote or inhibit the malignant transformation. Since a portion of HPV infections never evolves into cancer, the identification of discriminatory factors would be an important step towards the development of prognostic and therapeutic tools.

Based on this notion, we investigated whether an isoform of BARD1, BARD1δ, which we found frequently expressed in cancer cells, plays a role in the malignant transformation of cervical epithelial cells. Using immunohystochemistry staining on tissue sections and RT-PCR we found that BARD1δ is expressed in proliferating cervical cancer cells, while normal BARD1 is repressed. BARD1 might be a driver of carcinogenesis and might be a critical event in the progression from hyper-proliferating cervical epithelium after HPV infection to cervical cancer.

Together, our results show that an isoform of BARD1, BARD1δ, is increasingly expressed in precancerous stages of cervical cancer and the specific inhibition of BARD1δ may represent a novel approach for therapeutic interventions to prevent cervical carcinogenesis after HPV infection.

Citation Format: Maxim Pilyugin, Pierre-Alain André, Nicole Concin, Gerda Hofstetter, Irmgard Irminger-Finger. Expression of BARD1δ induces genetic instability and is associated with cervical carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1417. doi:10.1158/1538-7445.AM2017-1417
Abstract 1418: G9a methyltransferase plays a role in ATM-dependent DNA damage response
Authors: Rodriguez-Colon Lizahira , Ginjala Vasudeva , Kulkarni Atul , Ansari Safia , Ganesan Shridar
Published: July 2017

Induction of DNA damage leads to a choreographed set of local chromatin changes that ensures an efficient recruitment of DNA repair factors. One principal regulator of the DNA Damage Response (DDR) signaling pathway is ATM kinase, which phosphorylates key factors at early stages of the response. G9a protein methyltransferase has been identified as a novel substrate for ATM. We have found that G9a localizes to sites of DNA damage in an ATM-dependent fashion and that inhibition of its activity affects recruitment of multiple DNA repair factors. Moreover G9a catalytic inhibition using UNC0638 leads to hyperactivation of ATM induced by DNA breaks. This was associated with an increased ATM-dependent “spreading” of pH2AX and MDC1 signals seen at regions of localized DNA breaks induced by UV-laser scissors. These data suggest that G9a activity is required for regulating the extent of ATM activation as well as for efficient recruitment of downstream DNA repair factors. Biochemical data will be presented that explore potential mechanisms for these findings. Overall our data suggests that G9a plays a critical role in the regulation of ATM-dependent signaling during the DNA damage response, and raises the possibility of using G9a inhibitors to target cancers with certain DNA repair defects.

Citation Format: Lizahira Rodriguez-Colon, Vasudeva Ginjala, Atul Kulkarni, Safia Ansari, Shridar Ganesan. G9a methyltransferase plays a role in ATM-dependent DNA damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1418. doi:10.1158/1538-7445.AM2017-1418
Abstract 1420: The endonuclease Metnase promotes base excision repair of Clustered abasic DNA lesions
Authors: Jaiswal Aruna S. , Williamson Elizabeth A. , Patel Bhavita , Srinivasan Gayathri , Narayan Satya , Hromas Robert A.
Published: July 2017

Metnase, a human SET-transposase fusion protein contains two functional domains: a SET domain and transposase domain. Transposase domain exhibit strand transfer and end joining activity while set domain is responsible for histone lysine methyltransferase activity (KMT). Metnase also increases the efficiency of double strand break repair by non-homologous end joining (NHEJ); however, its role in the excision of clustered DNA damage remains to be investigated. We hypothesize that 5’-3’ endonuclease activity of metnase could possibly substitute for APE1 in BER and serve as an alternative initiator of BER in tumor cells lacking APE1. In the present study, we examined in vitro endonuclease activity of Metnase using abasic site containing artificial DNA, and describe its activity in BER. Its unique 5’ endonuclease activity was selective only for abasic lesions, but not other base modifications such as 8-oxoguanine, uracil, hypoxanthine or xanthenes. Metnase specifically initiates removal of reduced abasic lesions from DNA, and allows completion of short-patch or long-patch BER. APE1 has difficulty cleaving 5’ of clustered abasic lesions. This endonuclease that promotes BER in clustered oxidative DNA damage is not known. Metnase also cleaves multiple abasic lesions (clustered DNA damage) and facilitates the repair of DNA if the multiple DNA damages are 3 or more nucleotides apart on the opposing strands. However, repair of multiple DNA damages remains inefficient if these are in close proximity of each other (< 3nt apart on the opposing strands) and results in DNA double strand break (DSB). These results suggest that Metnase can promote BER of oxidative nucleotides, where APE1 is unable to function.

Citation Format: Aruna S. Jaiswal, Elizabeth A. Williamson, Bhavita Patel, Gayathri Srinivasan, Satya Narayan, Robert A. Hromas. The endonuclease Metnase promotes base excision repair of Clustered abasic DNA lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1420. doi:10.1158/1538-7445.AM2017-1420
Abstract 1421: Evaluation of DDR-targeting strategy using ATR inhibitor in biliary tract cancer
Authors: Nam Ah Rong , Park Ji Eun , Bang Ju Hee , Jin Mei Hua , Oh Do Youn , Bang Yung Jue
Published: July 2017

Background: The DNA damage response (DDR) is a multicomplex network of signaling pathways involved in DNA damage repair, cell cycle checkpoints and apoptosis. The ataxia telangiectasia and Rad3-related (ATR) protein kinase is a key enzyme in the DDR that activates checkpoint kinase 1 (Chk1), resulting in cell cycle arrest. Tumor types with loss of ATM function and/or high replication stress are expected to be more susceptible to DDR targeting. In biliary tract cancer (BTC), DNA repair pathway, which includes BAP1, MSH6, BRCA1, ATM, MLH1, MSH2, is altered in about 20 % of cases. TP53 module is observed in 33.9% of BTC cases (Nat Genet 2015). The purpose of this study is to test DDR targeting strategy using ATR inhibitor in biliary tract cancer.

Methods: Using 9 kinds of BTC cells, MTT assay and colony formation assay were done for determining growth inhibitory effect of AZD6738, an ATR inhibitor. Cell cycle analysis was done by FACS Calibur flow cytometer and the methods described by Chou and Talalay were used to determine whether a synergistic effect existed between AZD6738 and cytotoxic chemotherapeutic agents (cisplatin, 5-FU, gemcitabine). The alkaline comet assay was done to measure of DNA damage in individual cells. Tumor xenografts model was used for in vivo test of AZD6738.

Results: Among 9 BTC cells, SNU478 and SNU869 were most sensitive to AZD6738, which showed low expression of both ATM and p53. AZD6738 blocked ATR-mediated Chk1 phosphorylation and increased rH2AX, a marker of DNA damage, in sensitive cells. AZD6738 significantly increased apoptosis (cleavage of PARP and caspase-7) and G2/M arrest, increased level of p21, and decreased cdc2. In addition, combination of AZD6738 and cytotoxic chemotherapeutic agents demonstrated synergistic effects in colony formation assay, cell cycle analysis and comet assay. In xenograft model of SNU478, AZD6738 monotherapy decreased tumor growth. The combination of AZD6738 and cisplatin showed more potent growth inhibitory effects, decreased Ki67, increased Tunel than monotherapy of each drug.

Conclusion: In BTC, DDR targeting strategy using ATR inhibitor demonstrated promising antitumor activity alone or in combination with cytotoxic chemotherapeutic agents. This supports further clinical development of DDR targeting strategy in BTC.

Citation Format: Ah Rong Nam, Ji Eun Park, Ju Hee Bang, Mei Hua Jin, Do Youn Oh, Yung Jue Bang. Evaluation of DDR-targeting strategy using ATR inhibitor in biliary tract cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1421. doi:10.1158/1538-7445.AM2017-1421
Abstract 1426: Blinding the CYCLOPS - Cancer vulnerabilities unveiled by genomic loss
Authors: Torkov Alica , Henrich Kai-Oliver , Shao Chunxuan , Gartlgruber Moritz , Westermann Frank
Published: July 2017

Background:

Heterozygous deletions within distal 1p are observed in 30% of neuroblastomas. So far, several potential 1p tumor suppressor genes have been identified. However, in this study we are focussing on 1p genes whose inactivation is not necessarily linked to tumor development but which mediate cell-essential functions, rendering cells with copy number loss vulnerable to further impairment. These genes are candidate therapeutic targets according to the concept of CYCLOPS (copy number alterations yielding cancer liabilities owing to partial loss).

Methods:

To identify a subset of 1p genes for which heterozygous loss may be tolerated but further reduction leads to cell death, we performed siRNA screens mediating the systematic knock-down of distal 1p genes in five 1p-deleted versus five non-1p-deleted neuroblastoma cell lines. We used 3 different siRNAs per gene in a liquid forward approach. After 96h Hoechst stained nuclei were count. Among others, a neuron-related candidate gene has been identified as a potential CYCLOPS. The candidate gene was validated by viability assays, immunocytochemistry and cell cycle analysis via FACS.

Results:

We identified many potential CYCLOPS genes mapping on the distal end of chromosome arm 1p. One of these genes is involved in neuronal and embryonic development and has been further validated. Knock-down of the gene impaired cell viability in 1p-deleted cell lines but did not in 1p-non-deleted cells. G1/G0 phase arrest with corresponding S phase decrease was observed in both 1p-deleted and 1p-non-deleted cells. Additionally, neurite-like outgrowth could be observed in 1p-non-deleted cells indicating an induction of differentiation.

Conclusion:

This study identified a candidate CYCLOPS gene in neuroblastoma. Heterozygous deletions of chromosome arm 1p are also frequently observed in other cancers including melanoma, colorectal and breast cancer. We hypothesize that this proof-of-principle opens a new therapeutic window for tumors harbouring a heterozygous deletion of our candidate gene or other cell essential genes on chromosome arm 1p.

Citation Format: Alica Torkov, Kai-Oliver Henrich, Chunxuan Shao, Moritz Gartlgruber, Frank Westermann. Blinding the CYCLOPS - Cancer vulnerabilities unveiled by genomic loss [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1426. doi:10.1158/1538-7445.AM2017-1426
Abstract 1430: The spliceosome U2 snRNP factors promote genome stability through distinct mechanisms; transcription of repair factors and R-loop processing
Authors: Tanikawa Michihiro
Published: July 2017

(Objective)Recent whole-exome sequencing studies of malignancies have detected recurrent somatic mutations in U2 snRNP components of the spliceosome. These factors have also been listed as novel players of DNA damage response in several genome wide screens and proteome analysis for DDR genes. Although accumulating evidences have implied that the spliceosome plays an important role in genome stability and is an emerging hallmark of carcinogenic pathways, its precise role in genome stability still remains ambiguous. The aim of this study is to clarify the functions of U2 snRNP splicing factors, especially SNRPA1 (Small Nuclear Ribonucleoprotein Polypeptide A1) in DDR pathway.

(Methods)SNAPA1 and other U2 snRNP splicing factors were identified as HR repair genes by genome-wide screens based on homologous recombination and RAD51 immunofoci formation. Each splicing factor was depleted by siRNA knockdown in USOS cells. The functions of SNRPA1 in DNA repair were analyzed by HR assay (DR-GFP assay), immunofluorescence, real-time laser micro-irradiation and comet assay (single cell gel electrophoresis).

(Results)HR assay showed strong HR deficiencies in splicing factor's depleted cells. In these cells, accumulation of BRCA1 and Rad51, major HR factors, to DNA damage sites were severely impaired. Especially, live cell imaging showed recruitment of SNRPA1 to laser induced DNA damage sites and unveiled its direct involvement to DNA damage repair. Comet assay also showed that depletion of SNRPA1 markedly caused DNA damage with the tail of broken DNA fragments. This DNA damage was R-loop (DNA-RNA hybrid) mediated DNA damage and rescued by overexpression of RNAseH1.

(Conclusion) Here we unveiled two distinct pathways how spliceosome U2 snRNP factors contribute to genome stability. The main function is indirect, through transcription, to maintain the protein levels of essential repair factors and contribute to homologous recombination repair. Our data suggest that depletion of splicing factors can be one mechanism for HR deficiency (i.e. BRCAness). In addition real-time laser microirradiation analysis identified the rapid recruitment of SNRPA1 to DNA damage sites. Intensive functional analysis of SNRPA1 unveiled the other, more immediate and direct effect to process R-loop structure, deleterious transcriptional by-products for the genome, at sites of on-going transcription.

Citation Format: Michihiro Tanikawa. The spliceosome U2 snRNP factors promote genome stability through distinct mechanisms; transcription of repair factors and R-loop processing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1430. doi:10.1158/1538-7445.AM2017-1430
Abstract 1435: Immune/inflammatory polymorphisms predict lung cancer survival
Authors: Watza Donovan , Lusk Chrissy , Wenzlaff Angie , Neslund-Dudas Christine , Dyson Gregory , Soubani Ayman , Gadgeel Shirish , Schwartz Ann G.
Published: July 2017

Lung cancer is the leading cause of cancer related mortality in the United States, with a median five year survival of ~16%. Recent advancements in the treatment of lung cancer focus on modulating the immune system to improve patient outcomes with markedly reduced toxicity profiles. This study aims to investigate single nucleotide polymorphisms (SNPs) within functional units of the immune system genome to identify genetic markers indicative of overall survival in a cohort of metropolitan Detroit lung cancer patients. This cohort presents a unique population of lung cancer patients for analysis, consisting of 40% African Americans, whom are known to have worse outcomes than their Caucasian counterparts. To assess SNPs within functional units of the immune genome, a hierarchical immune system gene and pathway list was constructed, incorporating genes and pathway identifiers from the Reactome database as well as previous genetic and inflammatory specific cancer studies to generate a well curated gene and pathway dataset. Genomic locations for the genes, together with proximal regulatory regions, were obtained from the UCSC genome browser for cross-referencing with the Illumina MEGA SNP array to generate SNPs for inclusion. Preliminary analysis of 848 NSCLC patients in association with 29,126 immune specific SNPs identified six SNPs as significantly associated with survival (p-value <10-4) in this lung cancer cohort, implicating the following six genes, PXN, GFRA3, HLA-DQA1, KSR2, BTBD1, and ATF2; although further gene/pathway analysis is necessary to elucidate how these associations interact in the context of genes and pathways of the immune system. PXN over expression has been previously implicated in both high risk lung epithelial dysplasia as well as in the development of lung adenocarcinoma in prior clinical studies. Additionally, GFRA3 has been identified as an activator of the RET kinase and increased GFRA3 activity in context of the Artemin pathway is a known promoter of NSCLC progression. As well, select polymorphisms in the HLA-DQA1 gene are known clinical modifiers of lung squamous cell carcinoma risk. Finally, ATF2 is a broadly active transcription factor and ATF2 upregulation has been associated with tumorigenesis and metastasis in both cell models and patient tumor samples in multiple cancer studies. The previous association of these genes in lung cancer is promising and further immune system gene/pathway analysis is warranted.

Citation Format: Donovan Watza, Chrissy Lusk, Angie Wenzlaff, Christine Neslund-Dudas, Gregory Dyson, Ayman Soubani, Shirish Gadgeel, Ann G. Schwartz. Immune/inflammatory polymorphisms predict lung cancer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1435. doi:10.1158/1538-7445.AM2017-1435
Abstract 144: Src leads to a novel mechanism of resistance to PI3K inhibitors through regulation of PI3K/p85 activation
Authors: Kim Gui Chul , Nam Hae Yun , Lee Hyang Ju , Kim Min Kyung , Lee Geun Hee , Han Myung Woul , KIM Seong Who , Kim Sang Yoon
Published: July 2017

Activation of the PI3K pathway is commonly observed and is correlated with tumor development, progression, poor prognosis, and resistance to cancer therapies, such as radiotherapy, in most cancers. As a central node of this pathway, PI3K is an attractive target for PI3K-addicted cancer therapy and PI3K inhibitors may thus restore sensitivity to other treatments when administered as part of combination regimens. Here, we found that PI3K/p85 was expressed predominantly in the radioresistant head and neck cancer cell line (HN31 cell line). And then, we investigated whether PI3K modulation was crucial for the development of novel treatment strategies for radioresistant cancer cell line. Interestingly, we found that head and neck cancer cell lines with PI3K/p85 activation showed the resistance to PI3K inhibitors and the resistance mechanism was associated with Src activation which is a member of a superfamily of membrane-associated nonreceptor protein tyrosine kinases. Src inhibitor improves the efficacy of PI3K inhibitor treatment through suppression of Src and PI3K/p85 activation in HN31 cell line. Collectively, our study highlights the role of p85 and Src activation in the resistance for PI3K inhibition and the potential clinical application of combination regimens of Src and PI3K inhibitors in head and neck cancers. This is the first investigation to analyze the role of Src in resistance to the PI3K inhibitors of head and neck cancer. As a consequence, a greater understanding of resistance mechanisms through our results will enable the rational design of combination regimens and sequential treatment algorithms to improve clinical outcomes.

Citation Format: Gui Chul Kim, Hae Yun Nam, Hyang Ju Lee, Min Kyung Kim, Geun Hee Lee, Myung Woul Han, Seong Who KIM, Sang Yoon Kim. Src leads to a novel mechanism of resistance to PI3K inhibitors through regulation of PI3K/p85 activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 144. doi:10.1158/1538-7445.AM2017-144
Abstract 1446: Super-enhancer identification via Bru/BrUV-Seq and H3K27Ac ChIP-Seq
Authors: Tang Chunlao , Yadav Vipin , Qian Hui-Rong , Cunningham Jason B. , Gao Hong , Liu Yushi , Ting Jason C. , Bray Steven M. , Ebert Philip J. , Lin Yuhao , Aggarwal Amit , Calley John N. , Patel Bharvin K.
Published: July 2017

Transcriptional super-enhancers (SEs) are large clusters of active enhancers that drive expression of genes critical to cell identity and function. In cancer and other human diseases, SEs can be acquired through somatic aberrations. Importantly, SEs and their target genes are particularly sensitive to perturbation, making this mechanism a promising target for both diagnosis and therapy. Histone modification H3K27Ac is a good single predicative marker of active enhancers, though additional marks would help. Accordingly, a common approach to SE identification is using H3K27Ac ChIP-Seq. The non-TSS (transcription start site) histone binding sites (e.g., principally excluding TSS±2.5kb regions) are mapped to genome and then subject to near-neighbor stitching (e.g., within 12.5kb). From the resulted relatively broad regions, SEs are identified by exceptional binding enrichment. Another potentially powerful approach is to use Bru/BrUV-Seq in combination. By directional sequencing of bromouridine(Bru)-labeled nascent RNAs, Bru-Seq has been developed to study nascent transcription. In the derivative BrUV-Seq, UV irradiation is additionally conducted to stabilize transcripts prior to labeling, thereby allowing more sensitive detection of TSSs and unstable transcripts, including enhancer RNAs (eRNAs). It has been shown that eRNAs indicate enhancer activity better than H3K27Ac binding. In this study, both approaches were used to identify SEs for three colon cancer cell lines, HCT-116, SW48, and SW620. We have demonstrated that Bru/BrUV-Seq has advantages in differentiating between mRNAs and eRNAs, and between overlapping transcripts; the reduced complexity helps prevent false identifications, which inflated our results obtained from ChIP-Seq.

Citation Format: Chunlao Tang, Vipin Yadav, Hui-Rong Qian, Jason B. Cunningham, Hong Gao, Yushi Liu, Jason C. Ting, Steven M. Bray, Philip J. Ebert, Yuhao Lin, Amit Aggarwal, John N. Calley, Bharvin K. Patel. Super-enhancer identification via Bru/BrUV-Seq and H3K27Ac ChIP-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1446. doi:10.1158/1538-7445.AM2017-1446
Abstract 1448: Unraveling the oncogenic pathway of serrated polyposis syndrome driven by RNF43 germline mutation
Authors: Yan Helen Hoi Ning , Lai Jeffrey C W , Ho Siu Lun , Chan Anthony K W , Tsui Wai Yin , Chan Annie S Y , Yuen Siu Tsan , Leung Suet Yi
Published: July 2017

Serrated polyps can arise in a sporadic or familial polyposis setting and predispose to colorectal cancer (CRC). Recently, we have identified RNF43 germline mutation in a family with Serrated Polyposis Syndrome (Yan et al, GUT 2016). The presence of second somatic hit in all serrated polyps examined from members of this family further confirmed the pathogenicity of RNF43 germline mutation. In an attempt to further delineate the global genomic alterations in these serrated polyps, so as to understand the RNF43 driven serrated neoplasia pathway for the development of colorectal cancer, we performed whole exome sequencing (WES) on two sessile serrated adenomas (SSAs) resected from an RNF43 germline mutation carrier, together with the paired blood DNA. Consistent with the results from our previous Sanger sequencing study, WES detected complete inactivation of RNF43 through a 2nd hit somatic mutation, c.461 C>T P154L, or loss of heterozygosity (LOH) in the two SSAs, respectively. We also identified 51 and 58 somatic mutations in the two SSAs, respectively. BRAFV600E mutation was the only shared mutation between the two polyps. Interestingly, each of the SSAs carried a truncating mutation in a histone-methyltransferase gene, either PRDM9 or SETD1B, respectively. Other truncating or deleterious mutations included chromatin modifiers (CHD2, CHD4, TSPYL2) or other genes with methyltransferase activity (TRMT2B, METTL12, METTL14, ECE2). In addition, we found few instances of chromosomal aberration or LOH, apart from a region of LOH at chromosome 17 encompassing RNF43 in one of the SSAs.

Overall, we have revealed the genomic landscape of two sessile serrated adenomas resected from a germline RNF43 mutation carrier. The results confirmed somatic RNF43 2nd hit and BRAFV600E mutation as the key events, along with putative roles for histone methyltransferase, as well as other chromatin modifiers. These findings highlight the potentially important role of an altered chromatin in the oncogenic pathway of serrated neoplasia.

Citation Format: Helen Hoi Ning Yan, Jeffrey C W Lai, Siu Lun Ho, Anthony K W Chan, Wai Yin Tsui, Annie S Y Chan, Siu Tsan Yuen, Suet Yi Leung. Unraveling the oncogenic pathway of serrated polyposis syndrome driven by RNF43 germline mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1448. doi:10.1158/1538-7445.AM2017-1448
Abstract 145: PIK3CB inhibitors selectively block the survival of glioblastoma cells
Authors: Le Lamvy , Sheng Zhi
Published: July 2017

Objective: To explore the divergent role of PI3K isoforms in glioblastoma

Background: Glioblastoma multiforme is the most malignant brain tumor in adults. Despite aggressive treatments, the median survival and five-year overall survival of glioblastoma patients remains low (14.6 months and 4.7%, respectively). Nearly 90% of patients experience recurrence within two years, leaving patients with few treatment options. Recently, PI3K pan inhibitors have been used to treat recurrent glioblastoma and achieved modest effect in the clinic. PI3K has four catalytic isoforms (PIK3CA, B, D, and G); hence, it is possible that these isoforms may have different roles in glioblastoma and need to be selectively targeted. This idea is further supported by our recent results, in which we have shown that elevated expression of PIK3CB, but not other PI3K isoforms, significantly correlated with higher rate, risk, and poor prognosis of recurrent glioblastomas. Hence, we hypothesize that PIK3CB-selective inhibitors are more effective for glioblastoma.

Design/Methods: We used a panel of glioblastoma cells with different levels of PIK3CB, treated them with PI3K-isoform-selective inhibitors, and compared them to pan PI3K inhibitors. We measured cell viability using the MTS cell viability assay. Normal human astrocytes were used as controls to determine toxicity.

Results: We found that PIK3CB inhibitors TGX-221 and GSK2636771 significantly blocked the proliferation of PIK3CB-high U87MG and SF295 cells, while it had no effect on the viability of PIK3CB-low A172 and LN229 cells. In contrast, other PI3K inhibitors and pan inhibitors either non-selectively blocked or had no effect on these cells. Importantly, these compounds, but not PIK3CB inhibitors, blocked the growth of astrocytes.

Conclusions: Selective blockade of PIK3CB, but not other PI3K isoforms, is an effective therapy for glioblastoma with a low toxicity to normal tissues.

Citation Format: Lamvy Le, Zhi Sheng. PIK3CB inhibitors selectively block the survival of glioblastoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 145. doi:10.1158/1538-7445.AM2017-145
Abstract 1462: Exosome-derived miR-429 contributes to prostate cancer chemoresistance
Authors: Liu Yang , Xie Liye , Li Jing , Mizokami Atsushi , Keller Evan T. , Lu Yi , Zhang Jian
Published: July 2017

Prostate cancer (PCa) is the most common cancer in men and the 2nd leading cause of cancer-related death in the United States. Certain miRNAs, act as tumor promoting or inhibiting factors in tumor development, function primarily by targeting specific mRNAs for degradation or inhibition of translation of their targeted proteins. Emerging evidence indicates that exosomes play a key role in tumor-host crosstalk, and exosome secretion, composition, and functional capacity are altered as tumors progress to aggressive phenotypes. From our prior report, we have constructed a potential network of 29 deregulated miRNAs, including 19 up and 10 down, in exosome samples derived from two kinds of paclitaxel resistant PCa cells (PC3-TXR and DU145-TXR) compared with their parental cells (PC3 and DU145). In this study, to further determine the roles of certain miRNAs derived from exosomes in chemoresistant cells, we firstly confirmed the lower expression level of miR-429 miRNA in the exosomes derived from the paclitaxel resistant PCa cells compared to their parental cells. In addition, when the miR-429 was over-expressed in PC3-TXR and DU145-TXR cells by stable transfection, epithelial-to-mesenchymal transition (EMT) markers significantly altered together with morphological changes. Overexpression of miR-429 decreased the tumor cell migration and invasion that associated with inactivation of PI-3K/AKT and Notch signaling pathways since the pathway specific inhibitors significantly diminished the transfected tumor cell migration and invasion. Finally, we found that overexpression of miRNA-429 significantly enhanced chemo-sensitivity of the chemoresistant PCa cells. These data suggested that exosome-derived miR-429 contributes to PCa chemoresistance and miR-429 may become a potential therapeutic target for PCa patients. This work was supported by Natural Science Foundation of China (NSFC) Key Project (81130046); NSFC (81171993; 81272415); Guangxi Projects of China (2013GXNSFEA053004; 2012GXNSFCB053004; 2013GXNSFBA019177; 1355004-5; 201201ZD004; GZPT13-35; 14122008-22; 11-031-05-K2; KY2015YB057; 14-045-12-K2).

Note: This abstract was not presented at the meeting.

Citation Format: Yang Liu, Liye Xie, Jing Li, Atsushi Mizokami, Evan T. Keller, Yi Lu, Jian Zhang. Exosome-derived miR-429 contributes to prostate cancer chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1462. doi:10.1158/1538-7445.AM2017-1462
Abstract 1466: QKI, a miRNA-200 target gene, suppresses epithelial-to-mesenchymal transition in oral squamous cell carcinoma cells
Authors: Ko Yoon Ho , Kim Eun Ju , Sun Der Sheng , Won Hye Sung , Ahn Young-Ho
Published: July 2017

Objectives:

The microRNA (miR)-200 family plays a major role in specifying the epithelial phenotype by preventing expression of the transcription repressors, ZEB1 and ZEB2, which are well-known regulators of epithelial-to-mesenchymal transition (EMT) in epithelial tumors including oral squamous cell carcinoma (OSCC). Here, we elucidated whether the miR-200 family members control RNA-binding protein quaking (QKI) which is a newly identified tumor suppressor and is regulated during EMT.

Methods:

We predicted that miR-200a and miR-200b could recognize QKI 3’-UTR by analyzing TargetScan and TCGA head and neck SCC dataset. To further verify the role of miR-200 on QKI in HNSCC, we carried out the functional study in CAL27 and HSC3 cells.

Results:

Forced expression of miR-200b/a/429 inhibited the expression of ZEB1 and ZEB2, and decreased cell migration in CAL27 and HSC3 cells. QKI expression was also suppressed by miR-200 over-expression, and the 3’-UTR of QKI mRNA was directly targeted by miR-200 in luciferase reporter assays. Interestingly, shRNA-mediated knockdown of QKI led to pronounced EMT and pro-tumor effects in vitro and in vivo studies of OSCC.

Conclusion:

QKI increases during EMT and is targeted by miR-200; while, it suppresses EMT and tumorigenesis, contradictorily. We suggest that QKI and miR-200 could form a balancing feedback loop maintaining homeostatic responses to EMT-inducing signals.

Citation Format: Yoon Ho Ko, Eun Ju Kim, Der Sheng Sun, Hye Sung Won, Young-Ho Ahn. QKI, a miRNA-200 target gene, suppresses epithelial-to-mesenchymal transition in oral squamous cell carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1466. doi:10.1158/1538-7445.AM2017-1466
Abstract 1481: Determination of microRNA profile in lung cancer cell line treated with chemotherapy cisplatin (C), pemetrexed (P) or PC with bevacizumab (B) and its implication in resistance
Authors: Huang Chao H. , Motes Hannah C. , Sharma Siddarth , Kevern Jared , Borrego-Diaz Emma , Sharma Mukut
Published: July 2017

Background: Cellular microRNAs (miRNAs) regulate gene expression through modulation of messenger RNA transcription and are involved in epigenetic regulation, metastasis and cancer immunity. They have prognostic and therapeutic significance. The miRNAs associated with resistance in lung cancer without EGFR mutation are not yet known. We sought to determine the profile of miRNA of lung cancer cell lines without EGFR mutation treated with chemotherapy.

Methods: lung cancer cell lines HTB177 were treated with PC or PCB (0.05mg/mL Cisplatin, 0.05 mg/mL pemetrexed, 6.25 mg/mL Bevacizumab) for 24, 48, 72 and 144 hours. We obtained baseline miRNA prior to therapy and after treatment to determine the changes in miRNA profile using RT PCR technique. After 144 hours, we obtained miRNA profile of the cells that survived treatment to assess change in the miRNA profile. We chose miRNA that has been reported to influence on the outcome of lung cancer: Let 7 modulates RAS, miRNA 27 is involved as tumor suppressor gene, mir212 negatively regulates antiapoptotic protein PED, miR 375 down regulates ASH1 a transcription factor. Mir21 targets anti-apoptotic genes including PDCD4 and PTEN.

Results: We observed down regulation of these miRNA after 24h of treatment with PC and these miRNA then became upregulated after 48 hours, especially let 7f. In contrast, the treatment of PC with B caused upregulation of these miRNA, especially miR 27b and let 7f at 24 h and then decreased levels of upregulation at 48hours. These miRNA were not upregulated at 72h for both groups. The expression of miRNA 21 is upregulated 50 times in cells that survived treatment with PC or PCB at 144h.

Conclusions: The treatment using PC and PC with B in lung cancer cell lines regulates change in the profile of miRNA at different time points. There is a difference of the miRNA profile in these 2 treatment groups. miRNA 21 is upregulated in cells resistant to therapy. miRNA could be involved in the activity of chemotherapy and development of resistance.

Citation Format: Chao H. Huang, Hannah C. Motes, Siddarth Sharma, Jared Kevern, Emma Borrego-Diaz, Mukut Sharma. Determination of microRNA profile in lung cancer cell line treated with chemotherapy cisplatin (C), pemetrexed (P) or PC with bevacizumab (B) and its implication in resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1481. doi:10.1158/1538-7445.AM2017-1481
Abstract 1498: Melatonin inhibits mitochondrial transcription factor A expression in glioblastoma U87MG cell culture inducing an anti-tumorigenic effect
Authors: Franco Daiane G. , Moretti Isabele F. , Marie Suely K.
Published: July 2017

Melatonin, the major hormone of pineal gland, has been described to induce intrinsic apoptosis in tumor cell, while it is inhibited in non-tumor cell. In tumor cell, melatonin stimulates intracellular production of reactive oxygen species (ROS) by a mechanism not completely understood. Here we propose that melatonin inhibits the expression of the mitochondrial transcription factor A (TFAM) in culture of glioblastoma (GBM) cell lineage, leading to an increase of the production of ROS. TFAM is an important mitochondrial protein that maintains the mitochondrial DNA (mtDNA) integrity and consequently the oxidative phosphorylation. Human U87MG GBM cell lineage was treated with melatonin (1 mM) for 72 h to evaluate the expression of TFAM and the mtDNA copy number through Real Time PCR. Proliferation, apoptosis, cell cycle and ROS production were also evaluated by cytometry (Muse - Millipore Corporation) and the results were normalized to control (vehicle: ethanol 0.3 %). Melatonin reduced the expression of TFAM in 17.5 % compared to the control group, but had no effect on the mtDNA copy number. Moreover, the incubation of U87MG with melatonin induced a reduction in cell proliferation in 14.24 % ± 4.3 compared to control, with an arrest of cell cycle in G0/G1 phase, which increased from 67.4 ± 3.71 % to 72.78 ± 3.18 % in the group treated with melatonin compared to the control. Production of ROS presented an increase of 7.1 %, with no significant effect on apoptosis. These results suggest that TFAM maybe a target for the melatonin function for an anti-tumorigenic effect through an increase of ROS production, inducing a delay in the cell cycle and a reduction of cell proliferation. The melatonin effect onTFAM maybe a novel signaling pathway that could be explored for the control of GBM progression.

Citation Format: Daiane G. Franco, Isabele F. Moretti, Suely K. Marie. Melatonin inhibits mitochondrial transcription factor A expression in glioblastoma U87MG cell culture inducing an anti-tumorigenic effect [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1498. doi:10.1158/1538-7445.AM2017-1498
Abstract 15: Suppression of adaptive responses to targeted therapies by transcriptional inhibition
Authors: Rusan Maria , Li Kapsok , Li Yvonne , Christensen Camilla L. , Abraham Brian J. , Kwiatkowski Nicholas , Buczkowski Kevin , Bockorny Bruno , Chen Ting , Li Shuai , Zhang Haikuo , Terai Hideko , Tavares Tiffany , Zhang Tinghu , Kim Tae Jung , Silkes Michael , Mudianto Tenny , Tan Li , Shimamura Takeshi , Meyerson Matthew , Watanabe Hideo , Gray Nathanael S. , Young Richard A. , Wong Kwok-Kin , Hammerman Peter S.
Published: July 2017

Tumor cells become dependent on the expression of key genes that drive hallmark tumor traits, but these “addictions” also represent potential vulnerabilities for therapeutic intervention. Treating tumor cells with a small molecule inhibitor of the transcriptional kinase CDK7 selectively suppresses expression of key dependency genes in multiple cancers. Our previous work showed responses to the CDK7 inhibitor THZ1 were especially noteworthy in T cell leukemias, small cell lung cancers, and triple-negative breast cancers—tumor types where the prognoses are especially unfavorable. The genes whose expression is most sensitive to CDK7 inhibition and whose expression is essential for tumor cell survival are often associated with super-enhancers—clusters of constituent enhancers that are bound by unusually large amounts of transcription apparatus including CDK7 itself. This “Achilles’ cluster” of super-enhancer-associated genes thus represents the set of addictions of tumor cells whose expression is important for tumor cell survival. Transcriptional inhibition synergizes with targeted therapies in models of multiple tumor types. Treating tumors with therapies that target kinase proteins such as EGFR, FGFR, and KRAS leads to resistance, which is concurrent with changes in the activities of enhancers and super-enhancers and gene expression programs of resistant cells. Treating cells with a transcriptional inhibitor in addition to targeted therapies prevents “rewiring” of the gene expression program and increases cell death in tumor models. Thus transcriptional inhibition represents a promising avenue in both monotherapy and combination settings where drug resistance is acquired.

Citation Format: Maria Rusan, Kapsok Li, Yvonne Li, Camilla L. Christensen, Brian J. Abraham, Nicholas Kwiatkowski, Kevin Buczkowski, Bruno Bockorny, Ting Chen, Shuai Li, Haikuo Zhang, Hideko Terai, Tiffany Tavares, Tinghu Zhang, Tae Jung Kim, Michael Silkes, Tenny Mudianto, Li Tan, Takeshi Shimamura, Matthew Meyerson, Hideo Watanabe, Nathanael S. Gray, Richard A. Young, Kwok-Kin Wong, Peter S. Hammerman. Suppression of adaptive responses to targeted therapies by transcriptional inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 15. doi:10.1158/1538-7445.AM2017-15
Abstract 1501: Sideroflexin4: A novel regulator of iron metabolism in ovarian cancer
Authors: Paul Bibbin , Lynch Miranda , Torti Frank , Torti Suzy
Published: July 2017

The five year survival rate for women with ovarian cancer is 9-34%. This high mortality is due to late stage diagnosis, marginally effective treatment and frequent disease recurrence. Alterations in metabolism have been widely recognized as an important hallmark of cancer. Metabolism of the micronutrient iron is significantly altered in many cancers, including ovarian cancers. The expression of genes governing iron transport (TFR1 and FPN), iron storage (FTL and FTH) and iron regulation (IRP1 and IRP2) are significantly altered in ovarian cancer compared to normal ovarian epithelial cells, resulting in higher intratumoral iron retention. However, specific pathways of intracellular iron utilization that are altered in cancer cells, and the functional consequences of disrupting these pathways, remain poorly understood.

To identify pathways of iron utilization that are perturbed in ovarian cancer, we analyzed the expression of genes involved in iron metabolism using a publicly available microarray database of ovarian cancer and normal oviduct (GSE69428). We observed that sideroflexin4 (SFXN4), an inner mitochondrial membrane protein that is essential for mitochondrial respiratory homeostasis, was significantly upregulated (p= 0.002) in ovarian cancer patient samples. We screened several ovarian cancer cell lines and observed that SFXN4 was similarly up-regulated both at the mRNA and protein level when compared to normal human ovarian surface epithelial cells.

To test the role of SFXN4 in ovarian cancer cells we performed knockdown and overexpression studies. Knockdown of SFXN4 induced S and G2-phase cell cycle arrest and reduced the ability of MDAH2774 and SKOV3 ovarian cancer cells to form colonies. Further investigation revealed that modulation of SFXN4 alters mitochondrial respiration by affecting iron-sulfur cluster biogenesis. Thus, knock-out cells exhibited impaired respiratory activity and a phenotype similar to cells with defects in iron-sulfur cluster biogenesis, including increased IRP-IRE binding and a decrease in IRP1/ACO1 aconitase activity. Furthermore, SFXN4 knock-out decreased the activity of iron-sulfur cluster-containing enzymes such as mitochondrial aconitase and succinate dehydrogenase.

Based on these observations, we postulate that SFXN4 acts as a molecular mediator that channels the excess iron present in ovarian cancer cells to iron-sulfur cluster-dependent metabolic pathways that favor growth and metastasis. SFXN4 may be a potential druggable target in ovarian cancer.

Citation Format: Bibbin Paul, Miranda Lynch, Frank Torti, Suzy Torti. Sideroflexin4: A novel regulator of iron metabolism in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1501. doi:10.1158/1538-7445.AM2017-1501