bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1394: Bioorthogonal Profiling of Protein Methylation (BPPM) identified MCM5 as a new substrate for SETD8 in DNA replication
Authors: Silva Fabio Pittella , Blum Gil , Senevirathne Chamara , Minkui Luo 
Published: July 2017

Abstract
SETD8 is the only member of the SET domain containing methyltransferase family, which catalyzes mono-methylation of K20 on histone H4 (H4K20me1). Lysine residues of non-histone proteins such as p53 and proliferating cell nuclear antigen (PCNA) are also monomethylated, while lysine residues in Numb were found to be dimethylated. As a consequence, SETD8 methyltransferase activity is implicated in several fundamental cellular processes such as transcriptional regulation and heterochromatin formation as well as processes that ensures genomic stability including DNA replication and the DNA damage response. Although it has been suggested that SETD8 is involved in DNA replication as a positive regulator of origin licensing through H4K20 methyation and by supporting Okazaki fragment processing through PCNA methylation, to date, there is no evidence whether other key protein in the replication fork is directly modified by SETD8. To address this question, we used Bioorthogonal Profiling of Protein Methylation (BPPM) with engineered enzyme and synthetic SAM analogues to profile new substrates for SETD8. We genetically engineered SETD8 and identified mutants amenable to accommodate non-native SAM analogues containing a terminal alkyne moiety for click chemistry. The engineered SETD8 can transfer this distinct chemical moiety into target proteins for subsequent pulldown and identification of the modified substrates. Among the new substrates discovered, we identified MCM5, a subunit of the hexameric minichromosome maintenance (MCM) DNA helicase complex. MCM5 directly interacts with MCM2 and 3 to form the MCM2-7 hexamer which associates with the origins of DNA replication to form part of the pre-replicative complex (preRC), playing a key role during replication initiation and elongation. We found that SETD8 can mono-methylate MCM5 directly affecting its binding affinity to MCM2 and 3. In addition, MCM5 mutations at the methylated lysine further evidenced a stronger binding to its interacting partners contributing to the formation of the MCM hexamer. Taken together our results indicate that MCM5 methylation contributes to the assembly of the MCM complex suggesting an important role for SETD8 in replication initiation. Our findings may bring new perspectives on the biological importance of SETD8 during DNA replication.
Citation Format: Fabio Pittella Silva, Gil Blum, Chamara Senevirathne, Luo Minkui. Bioorthogonal Profiling of Protein Methylation (BPPM) identified MCM5 as a new substrate for SETD8 in DNA replication [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 1394. doi:10.1158/1538-7445.AM2017-1394
Abstract 1398: Loss of PIWIL4 and piRNAs attenuate somatic methylome and genome stability
Authors: Lin Syuan-Cih , Chiu Chia-Chen , Chen Shou-Tung , Chen Yao-Li , Lin Ping-Yi , Hsiao Shu-Huei , Leu Yu-Wei 
Published: July 2017

Abstract
Piwi-like RNA-mediated gene silencing 4 (PIWIL4) is expressed in somatic tissues and is proposed to silence the transposition of repetitive elements like long interspersed nuclear elements (LINEs) through DNA methylation and maintain the genome stability. Through the knockout of PIWIL4 gene by CRISPR/Cas9 system in mesenchymal stem cells (MSCs), MDA-MB-231 (breast cancer cell line), HT29 (colon cancer cell line) and AGS (gastric cancer cell line), the piRNA biogenesis was decreased and so was the methylation within LINE1 target loci and global methylation. The recruitment of SUV39H1, a histone H3 methyl-transferase, into nucleus was blocked, leading to the reduction of silencing tri-methylation of histone H3 at lysine 9. Concurrently, the active H3K4me3 mark increased after knockout. Also, global CTCF bindings were distorted after the knockout of PIWIL4 especially at the bindings franking the piRNA clusters. This distortion implied the disorganization of genomic conformation which was validated by karyotyping. Through chromosomal G-banding, aneuploidy was observed which indicated the loss of genomic stability. The knockout of PIWIL4 also results in disorganized cytoskeleton, therefore, changed cell stiffness as measured by atomic force microscopy. Neural and hepatic induction of MSCs were also blocked by the knockout of PIWIL4. In correlation, tissue arrays detected abnormal PIWIL4 expression in gastric (n=45), colon (n=30) and breast cancers (n=30). In conclusion, we found that PIWIL4-piRNA interaction helps to maintain somatic DNA methylome, genome stability and stiffness in somatic stem cells. The loss of PIWIL4 expression might then a candidate for cancer biomarker. (Supported by: MOST-105-2314-B-371 -008, MOST-105-2320-B-194 -004, MOST Taiwan)
Citation Format: Syuan-Cih Lin, Chia-Chen Chiu, Shou-Tung Chen, Yao-Li Chen, Ping-Yi Lin, Shu-Huei Hsiao, Yu-Wei Leu. Loss of PIWIL4 and piRNAs attenuate somatic methylome and genome stability [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 1398. doi:10.1158/1538-7445.AM2017-1398
Abstract 1399: In vitro characterization of several enzymes of the Fe(II)/2-oxoglutarate-dependent dioxygenase superfamily using a universal succinate detection assay
Authors: Alves Juliano , Goueli Said , Zegzouti Hicham 
Published: July 2017

Abstract
The covalent modification of histone proteins, DNA and RNA by Fe(II)/2-oxoglutarate-dependent dioxygenases are key to the modulation of biological processes such as epigenetics, hypoxic signaling and DNA/RNA repair. Of these, JumonjiC domain-containing histone lysine demethylases (JMJCs), the ten-eleven-translocation (TET) DNA dioxygenases, the ALKB DNA/RNA hydroxylases and the prolyl hydroxylases EGLN1-3 have generated increased interest as potential drug targets for the treatment of a number of pathological conditions, including cancer. Since succinate is a common product to all Fe(II)/2-oxoglutarate-dependent dioxygenases, we determined the substrate specificities, the apparent kinetic constants for several JMJCs and members of the dioxygenase superfamily (i.e.: TET1, EGLN1, ALKBH3 and FTO), as well as inhibition profiles of reported inhibitors using a novel bioluminescent and homogenous succinate detection assay. Our results demonstrate that succinate detection is a useful strategy for the characterization of multiple Fe(II)/2-oxoglutarate-dependent dioxygenases with distinct substrate requirements, enabling the investigation of a large number of enzymes that cannot be evaluated in a miniaturized or high-throughput manner with the methods currently available.
Citation Format: Juliano Alves, Said Goueli, Hicham Zegzouti. In vitro characterization of several enzymes of the Fe(II)/2-oxoglutarate-dependent dioxygenase superfamily using a universal succinate detection assay [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 1399. doi:10.1158/1538-7445.AM2017-1399
Abstract 1400: Using tumor spheroids to evaluate the efficacy of EZH2 inhibitors in clear cell renal cell carcinoma (ccRCC)
Authors: Wei Darmood , Yang Youfeng , Ricketts Christopher J. , Sourbier Carole , Schmidt Laura S. , Linehan William M. 
Published: July 2017

Abstract
Enhancer of zeste homolog 2 (EZH2) is a key component of the polycomb repressive complex 2 (PRC2). EZH2 is frequently overexpressed in a wide variety of human malignancies including non-Hodgkin lymphoma, gastric cancer, pancreatic cancer, and lung cancer. Thus it has potential to become a therapeutic target. Characterization of EZH2 as a therapeutic target in clear cell renal cell carcinoma (ccRCC) has not been fully explored. ccRCC have been defined by mutation of the von Hippel-Lindau (VHL) tumor suppressor gene in combination with chromosome 3p loss. Recent sequencing efforts have revealed that several chromatin remodeling genes encoded on chromosome 3p are often mutated, of which PBRM1 is the most frequent (41%). The PBRM1 gene codes for the BAF180 protein, a SWI/SNF chromatin remodeling complex subunit. Loss of BAF180 in ccRCC may disrupt the PBAF variant of the SWI/SNF complex. The SWI/SNF complex remodels the chromatin landscape by either sliding or evicting the nucleosomes from the chromatin. This chromatin remodeling modulates the accessibility to promoter regions by transcriptional machinery. It is through this mechanism that the SWI/SNF complex can regulate a range of cellular processes. It has been demonstrated that the SWI/SNF complex can act antagonistically to the PRC2 complex by evicting PRC2 complex from the promoters of tumor suppressors. Disruption of the SWI/SNF complex would impede the eviction of the PRC2 complex, similarly observed in SNF5-deficient malignant rhabdoid tumors. Therefore, we hypothesize that PBRM1 inactivation disrupts specific SWI/SNF complexes allowing EZH2 to bind and repress target tumor suppressor genes. Thus inhibition of EZH2 in ccRCC may present as a targeted therapeutic option in tumors with PBRM1 mutations. We have investigated EZH2 in ccRCC cell lines with PBRM1 mutations and observed that these cells lines have overexpression of EZH2 in comparison to RPTEC (renal cortex proximal tubule epithelium cell line). We examined the effects of two EZH2 inhibitors (GSK126 and EPZ6438) on ccRCC tumor spheroids. Our preliminary data suggests EZH2 inhibition results in reduced growth of PBRM1 mutant cell lines grown as tumor spheroids.
Citation Format: Darmood Wei, Youfeng Yang, Christopher J. Ricketts, Carole Sourbier, Laura S. Schmidt, William M. Linehan. Using tumor spheroids to evaluate the efficacy of EZH2 inhibitors in clear cell renal cell carcinoma (ccRCC) [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 1400. doi:10.1158/1538-7445.AM2017-1400
Abstract 1402: NME3 links mitochondrial fusion to DNA repair in nuclear genome
Authors: Chang Zee-Fen 
Published: July 2017

Abstract
In mammals, there are 10 isoforms of NME (NDP Kinase), which catalyze the reversible reaction of NTPs formation from NDP and ATP. By RNA interference, NME3 was found critical for DNA repair. Data from analysis of the steady-state levels of rNTPs and dNTPs suggest that NME3 does not play a critical role in determining the total pools of these nucleotides. However, its mitochondrial localization and catalytic function are necessary for its function in DNA repair. Super-resolution microscopy analysis indicates the localization of NME3 at mitochondrial outer membrane. We further used APEX-mediated biotinylation to identify proteins interacting with NME3. Among them, Mfn1 is validated to associate with mitochondrial NME3 in vitro and in vivo. We provide evidence that NME3 is required for DNA damage-induced mitochondria fusion via GTP-mediated fueling of Mfn1. The lack of this process increased nucleotide oxidation and sustained DNA damage in nuclear genome. These data highlight the function of NME3 in mitochondrial fusion, which is required for the maintenance of genome integrity.
Citation Format: Zee-Fen Chang. NME3 links mitochondrial fusion to DNA repair in nuclear genome [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 1402. doi:10.1158/1538-7445.AM2017-1402
Abstract 1410: Proliferation during epithelial-to-mesenchymal transition induces genomic instability
Authors: Comaills Valentine , Kabeche Lilian , Morris Robert , Yu Min , Madden Marissa Wells , LiCausi Joseph A. , Aceto Nicola , Zheng Yu , Miyamoto David T. , Ramaswamy Sridhar , Zou Lee , Haber Daniel A. , Maheswaran Shyamala 
Published: July 2017

Abstract
Epithelial to mesenchymal transition (EMT), a morphogenetic process required for proper embryonic development, is adopted by cancer cells during tumor progression. We show that induction of EMT by TGFß or other EMT-inducers such as Snail leads to genomic instability, associated with failed cytokinesis and chromosome missegregation resulting in aneuploidy and polyploidy. These defects are dependent on persistent proliferation of cells undergoing EMT and are absent in normal cells that growth arrest during EMT. While EMT and the associated mitotic abnormalities are reversible upon removal of the EMT-inducer, the resulting chromosomal abnormalities are inherited. TGFß-induced genomic instability is associated with the acquisition of tumorigenic phenotypes and the resulting tumors are enriched for a genomically-altered tumor cell population, which exhibits differential drug sensitivity. In breast and prostate cancer cells circulating in the blood, TGFß and EMT gene signatures are significantly correlated with aneuploid gene signatures. Analysis of single circulating tumor cells (CTC) from women with metastatic breast cancer reveals increased in genomic instability in mesenchymal CTCs. Together, these findings identify a novel mechanism whereby tumor microenvironment-derived signals impact heritable genetic changes within cancer cells.
Citation Format: Valentine Comaills, Lilian Kabeche, Robert Morris, Min Yu, Marissa Wells Madden, Joseph A. LiCausi, Nicola Aceto, Yu Zheng, David T. Miyamoto, Sridhar Ramaswamy, Lee Zou, Daniel A. Haber, Shyamala Maheswaran. Proliferation during epithelial-to-mesenchymal transition induces genomic instability [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 1410. doi:10.1158/1538-7445.AM2017-1410
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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 (&lt; 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