bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2443: Massively parallel single-cell RNA-Seq identifies diverse subpopulations displaying EMT and stem-like features
Authors: Lau Billy , Chen Jiamin , Ji Hanlee P. 
Published: July 2017

Abstract
Single-cell transcriptome analysis enables a new paradigm for studying complex systems in cancer. As opposed to bulk sequencing, which averages genomic signals across thousands or millions of cells and obscures the presence of rare subtypes, single cell sequencing enables the interrogation of individual cells. In cancer, intratumoral heterogeneity is observed at both genomic and epigenomic levels, and its analysis enables the discovery of new actionable targets and treatment modalities tailored to individual subpopulations. As an example, many cancer cell lines and those derived from patients contain subpopulations marked by distinct patterns of surface markers such as CD44, and are linked to drug resistant and tumor initiating phenotypes. A complete characterization of such cellular populations ideally requires marker-free sampling, followed by clustering into distinct subgroups. In this study, we demonstrate the significant advantages of such an approach; we utilize a high-throughput single-cell RNA-Seq method to characterize the transcriptomic profiles of cellular populations.
We performed single-cell RNA-Seq on thousands of cells in the matched SW480 (primary) and SW620 (metastatic) colorectal cell lines using a microfluidic droplet barcoding technology that enables the tracking of single cells during library preparation. By focusing on genes with high inter-cell variability, we discovered a small subpopulation of cells that displayed a distinct gene expression signature from the major subpopulation. Differential gene expression analysis of this subpopulation yielded genes virtually all enriched in the epithelial-to-mesenchymal transition (EMT) pathway. These cells showed significant increases in canonical mesenchymal marker genes such as VIM, CD44, and SOX9. Gene expression profiles of these subpopulations also correlated with established EMT signatures. Remarkably, this subpopulation did not display mutual exclusivity in gene expression with the epithelial marker EPCAM, which possibly indicates an intermediate mesenchymal phenotype. We also observed in the major population cluster a small subset of cells totaling less than 1% of the population that were significantly enriched for LGR5 expression, a common stem-like marker in colorectal cancer. Overall, we demonstrate the use of single-cell RNA-Seq to discover and characterize a diversity of cellular states that would otherwise be impossible from bulk analysis.
Citation Format: Billy Lau, Jiamin Chen, Hanlee P. Ji. Massively parallel single-cell RNA-Seq identifies diverse subpopulations displaying EMT and stem-like features [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 2443. doi:10.1158/1538-7445.AM2017-2443
Abstract 2462: Whole-exome sequencing reveals genetic variants in ERC1 and KCNG4 in complete hydatidiform moles from Chinese Han women
Authors: Yu Yan , Lu Bingjian , Lu Weiguo , Wang Xinyu , Liu Pengyuan , Lu Yan , Cheng Xiaodong , Xie Xing 
Published: July 2017

Abstract
Complete hydatidiform mole (CHM) is an uncommon pregnancy-related disease with an invasive potential. The genetic background of the sporadic CHM has not been addressed previously despite the possible mechanisms of maternal genetic variants to the development of this disease with biparental origin. We performed the whole-exome sequencing analysis on 51 CHM patients and 47 normal healthy women, then the second screening of the probable mutations by mass spectrometry in 199 CHM patients and 400 normal healthy women. Finally the candidate genetic polymorphisms were validated by direct Sanger sequencing in 247 cases and 599 controls with another 205 new controls. We eventually found that two SNPs c.G48C(p.Q16H) in ERC1 and c.G1114A(p.G372S) in KCNG4, were associated with an increased risk for CHM (p&lt;0.05). These genetic variants will facilitate our understanding on the pathogenesis of CHM and related tumors as well as the oogenesis and embryonic implantation. They will provide beneficial information for the pregnant women both in physiology and psychology. Further multiple-disciplinary collaborations should be encouraged to clarify the accurate pathogenesis of CHM.
Citation Format: Yan Yu, Bingjian Lu, Weiguo Lu, Xinyu Wang, Pengyuan Liu, Yan Lu, Xiaodong Cheng, Xing Xie. Whole-exome sequencing reveals genetic variants in ERC1 and KCNG4 in complete hydatidiform moles from Chinese Han women [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 2462. doi:10.1158/1538-7445.AM2017-2462
Abstract 2469: The B-cell lymphoma specific aptamer C10.36 binds a ribonucleoprotein complex on the cell surface of cancer cells
Authors: Tonapi Sonal S. , Duncan Janet E. , Rosenow Matthew , Richards Melissa , Tinder Teresa L. , O'Neill Heather A. , Miglarese Mark R. , Spetzler David , Famulok Michael , Mayer Günter 
Published: July 2017

Abstract
Aptamers have recently gained prominence for their diagnostic and therapeutic potential. The DNA aptamer C10.36 forms a G-quadruplex and has been shown to bind the Ramos Burkitt’s lymphoma cell line. However, its binding partner on the cell surface remains unknown. Here we report on the identification of the molecular target of C10.36, which suggests its application in the therapy of B-cell lymphoma and leukaemia. Aptamer-affinity purification, followed by LC-MS/MS revealed unique proteins pulled down with C10.36 associated with Ramos cells but not Jurkat, a T-cell lymphocyte cell line. The majority of the identified target molecules were found to be associated within ribonucleoprotein complexes, of which the abundant and consistent ones belong to the nucleolin complex including nucleolin (NCL) itself and its interacting partners, i.e. nucleophosmin (NPM1), heterogeneous nuclear ribonucleoprotein (HNRNP) family members such as HNRNP C1C2 and U, rRNA 2'-O-methyltransferase fibrillarin (FBL), actin (ACTB), nucleolar RNA helicase 2 (DDX21), and proline- and glutamine-rich splicing factors (SFPQ). All proteins identified in the above ribonucleoprotein complex are aberrantly expressed on the surface of several disparate cancer cell types and have been shown to play an oncogenic role in cancer. Another G-rich anti-NCL aptamer, AS1411, has been shown to induce cell death in &gt;100 cancer cell lines. Therefore, we tested the effect of C10.36 on viability of Ramos and other non-Hodgkin B-cell lymphoma (NHL) cancer cell lines. Our results indicate that C10.36 treatment causes specific cell death of certain lymphoma cell lines such as Ramos but not Jurkat cells. The present study identifies C10.36 as a novel anti-B cell lymphoma aptamer and underscores its potential for the development of a new targeted therapy to treat B-cell lymphomas.
Citation Format: Sonal S. Tonapi, Janet E. Duncan, Matthew Rosenow, Melissa Richards, Teresa L. Tinder, Heather A. O'Neill, Mark R. Miglarese, David Spetzler, Michael Famulok, Günter Mayer. The B-cell lymphoma specific aptamer C10.36 binds a ribonucleoprotein complex on the cell surface of cancer 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 2469. doi:10.1158/1538-7445.AM2017-2469
Abstract 2470: Compromised BRCA1-PALB2 interaction is associated with breast cancer risk
Authors: Foo Tzeh Keong , Tischkowitz Marc , Simhadri Srilatha , Boshari Talia , Burke Kathleen A. , Berman Samuel H. , Zayed Nadia , Ding Yuan Chun , Neuhausen Susan L. , Weigelt Britta , Reis-Filho Jorge S. , Foulkes William D. , Xia Bing 
Published: July 2017

Abstract
The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are physically and functionally linked by a third tumor suppressor, PALB2 (partner and localizer of BRCA2), in the HR pathway. Heterozygous PALB2 mutation carriers have increased risk of breast, ovarian and pancreatic cancer. While truncating mutations in BRCA genes are generally pathogenic, interpretations of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to establish their pathogenicity in humans. Variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have not been reported. Here, we report on the identification of a novel PALB2 variant, c.104T&gt;C [p.L35P], that segregated in a family with a strong history of breast cancer. Functional analyses showed that L35P abrogates the PALB2-BRCA1 interaction, resulting in impaired HR and sensitivity to platinum salts and PARP inhibitors. Whole-exome sequencing of breast tumor from a c.104T&gt;C carrier revealed a somatic, truncating mutation in the second allele of PALB2, with the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects. Using a combination of traditional clinical genetics, tumor whole-exome sequencing and in-depth functional analyses, we have provided direct evidence to cement the pathogenicity of L35P. Parallel analyses of other germline variants in the PALB2 N-terminal BRCA1-binding domain also identified multiple variants that affect HR function to varying degrees, suggesting their possible contribution to cancer development. Our findings establish p.L35P as the first pathogenic missense mutation in PALB2 identified to date and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression.
Citation Format: Tzeh Keong Foo, Marc Tischkowitz, Srilatha Simhadri, Talia Boshari, Kathleen A. Burke, Samuel H. Berman, Nadia Zayed, Yuan Chun Ding, Susan L. Neuhausen, Britta Weigelt, Jorge S. Reis-Filho, William D. Foulkes, Bing Xia. Compromised BRCA1-PALB2 interaction is associated with breast cancer risk [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 2470. doi:10.1158/1538-7445.AM2017-2470
Abstract 2472: Defining the role of the XAB2 complex during homologous recombination
Authors: Onyango David O. , Stark Jeremy 
Published: July 2017

Abstract
Several factors associated with RNA processing are important for homologous recombination (HR), but the mechanistic links between these processes remain poorly understood. To this end, we have examined the function of the tetratricopeptide repeat factor XAB2 in HR, since this factor has a conserved function in RNA processing. We have found that XAB2 is important for chromosomal double strand break (DSB) repair via two pathways of HR that require end resection as an intermediate step, end resection of camptothecin (Cpt) induced DNA damage, and RAD51 recruitment to ionizing radiation induced foci (IRIF). Furthermore, XAB2 mediates CtIP hyperphosphorylation induced by Cpt and BRCA1 IRIF, as well as histone acetylation events linked to HR proficiency. The capacity for XAB2 to promote HR correlates with its ability to form a complex with ISY1 and PRP19, which show a similar influence as XAB2 on HR. Our recent efforts include examining other members of the XAB2 complex, as well as the transcription unit aberrations caused by loss of this complex, which may contribute to the defects in HR.
Citation Format: David O. Onyango, Jeremy Stark. Defining the role of the XAB2 complex during homologous recombination [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 2472. doi:10.1158/1538-7445.AM2017-2472
Abstract 2485: Development and validation of Predi-HRD liquid biopsy test for PARP inhibitor clinical trials
Authors: Zhao Zhixin , Wiegers Toni , Cheung Tak , Du Pan , Jia Shidong 
Published: July 2017

Abstract
Response to DNA-damaging agents, such as platinum and recently emerged PARP inhibitors, is associated with homologous recombination deficiency (HRD) pathway. In fact, as reported by multiple clinical trials, patients with advanced breast, prostate, and ovarian cancers who have harmful mutations in BRCA1 and BRCA2 have demonstrated a great benefit from treatment of PARP inhibitors including olaparib, niraparib, and talazoparib. Current companion diagnostic assays that mainly examine germline defects from blood or somatic alterations from tumor tissues have shown several practical challenges: germline test does not capture somatic alterations of a tumor, initial biopsies from a tumor may not reflect the current status of the tumor’s genetic profile over time, and tissue biopsy may be of insufficient quantity or unavailable/unobtainable for downstream molecular profiling.
Here we introduce the Predi-HRD blood test, a non-invasive, next-generation sequencing (NGS)-based multiplex assay that enables real-time monitoring of temporal change of tumor heterogeneity and highly sensitive detection of defects in HR genes including BRCA1, BRCA2, ATM, CHEK2, among others. Technical validation was performed to evaluate assay sensitivity, specificity and accuracy using reference samples with known genetic profiling and further validated on a variety of orthogonal platforms such as digital PCR, allele-specific PCR and Sanger sequencing. Mutation prevalence of HR genes was examined in clinical plasma samples from patients with advanced ovarian cancer after systemic chemotherapy. The successful development of Predi-HRD liquid biopsy test offers an efficient solution to stratify and monitor cancer patients who may benefit from HRD-targeted therapeutics such as PARP inhibitors.
Citation Format: Zhixin Zhao, Toni Wiegers, Tak Cheung, Pan Du, Shidong Jia. Development and validation of Predi-HRD liquid biopsy test for PARP inhibitor clinical trials [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 2485. doi:10.1158/1538-7445.AM2017-2485
Abstract 2486: Tumor hypoxia induces DNA repair vulnerabilities through contextual loss of heterozygosity
Authors: Mahamud Osman , Chua Melvin , Lo Winnie , Zafarana Gaetano , Bristow Robert 
Published: July 2017

Abstract
Introduction: Intratumoural hypoxia leads to decreased expression in DNA damage response (DDR) and repair pathways. Given the ‘two-hit’ model for loss of gene function, we hypothesize that hypoxia-mediated down-regulation of gene expression and function, coupled with an already inactive allele contributes to an exploitable contextual ‘loss-of- heterozygosity’ phenotype.
Method: To interrogate this relationship, isogenic DLD-1 cells heterozygous and homozygous null for BRCA2, were placed under normoxic (21%) or hypoxic (0.2%) conditions for 72 hours. Hypoxia-mediated changes in DDR response and DNA repair were evaluated by cell proliferation, cell cycle analysis, western blots, qPCR, immunofluorescence, clonogenic assays and functional repair assays.
Results: No differences in proliferation and cell survival were observed between oxic and hypoxic cells (72 hours - 0.2% O2). Under chronic hypoxic conditions, confirmed by the up-regulation of VEGF and HIF1a, mRNA and protein expression of key homologous recombination (HR) genes (BRCA1, BRCA2, RAD51) were down-regulated. Functionally, BRCA2-/- null cells proved unable to recruit Rad51 foci and were profoundly sensitivity to PARP inhibition. Conversely, heterozygote BRCA2+/- cells retained the ability to recruit Rad51 foci under both oxic and hypoxic conditions. However, exposure to chronic hypoxia resulted in a reduction of foci formation. Chronically hypoxic BRCA2+/- cells exhibited a 30-40% increase in sensitivity to PARP inhibition compared to their oxic counterparts. Preliminary data shows a similar synthetically lethal relationship in genetic (BRCA2-/- ) and tumor microenvironment induced (BRCA2+/-) HR deficient cells, when challenged with DNA damage response (DDR) kinase inhibitors ATRi and DNAPKi.
Conclusions: Herein, we demonstrate a novel mechanism of contextual ‘loss-of heterozygosity’, which marries the tumour microenvironment and innate genetic alterations. The resultant increased sensitivity to DDR kinase inhibitors and PARPi highlights the therapeutic significance of this phenomenon.
Citation Format: Osman Mahamud, Melvin Chua, Winnie Lo, Gaetano Zafarana, Robert Bristow. Tumor hypoxia induces DNA repair vulnerabilities through contextual loss of heterozygosity [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 2486. doi:10.1158/1538-7445.AM2017-2486
Abstract 2489: Mre11-CDK2 interaction during the DNA double-strand break response
Authors: Morgan Mary J. , Festerling Todd A. , Buis Jeffrey , Ferguson David O. 
Published: July 2017

Abstract
The MRN (Mre11/Rad50/NBS1) complex is a group of highly conserved proteins central to the detection and repair of DNA double-strand breaks (DSBs). Inherited deficiencies in DNA DSB signaling result in a spectrum of disorders featuring cancer predisposition, neurodegeneration, and immunodeficiency. MRN directly binds DNA DSB ends and facilitates activation of ataxia-telangiectasia mutated (ATM) kinase, which initiates cellular responses including DNA repair, cell cycle checkpoints, and in some circumstances, apoptosis. Cellular responses to DNA DSBs require rapid communication between DNA repair complexes and the cell cycle machinery, but much about this relationship remains unclear. Our lab recently discovered an interaction between Mre11 and Cyclin-dependent kinase 2 (CDK2), a key component of the cell cycle machinery (Buis et al., NSMB, 2012). CDK2, when bound to its regulatory partner Cyclin A, promotes cell cycle progression through S phase. We demonstrated that the Mre11-CDK2/Cyclin A interaction is important in regulating the capacity for DNA repair by homologous recombination in normally dividing cells. Current work is focused on understanding the role of this interaction during DNA damage responses. We hypothesize that Mre11 interaction with CDK2 is a component of a molecular switch between the normal cell cycle and the DNA damage response. To test our hypothesis, we take advantage of murine alleles of Mre11 previously generated in the lab. We performed immunoprecipitation studies to investigate the protein-protein interaction in the presence of DNA damage. We also utilized kinase inhibitors to investigate the role of apical kinases in regulating the interaction. Finally, we are currently optimizing in vitro kinase assays to further understand a relationship between Mre11 and CDK2 enzymatic activity.Unpublished findings reveal that the Mre11-CDK2/Cyclin A interaction is altered upon DNA damage, a process which appears to be important for cell cycle checkpoint regulation. In conclusion, we demonstrate that the Mre11-CDK2 interaction plays important roles both in normally dividing cells and in the DNA damage response. Taken together, our data suggests that Mre11 may act to bridge the gap between DNA repair complexes and the cell cycle machinery.
Citation Format: Mary J. Morgan, Todd A. Festerling, Jeffrey Buis, David O. Ferguson. Mre11-CDK2 interaction during the DNA double-strand break 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 2489. doi:10.1158/1538-7445.AM2017-2489
Abstract 2492: DNA polymerase beta participates in DNA end-joining
Authors: Ray Sreerupa , DeVeaux Michelle , Breuer Gregory , Bindra Ranjit , Zelterman Daniel , Sweasy Joann 
Published: July 2017

Abstract
DNA double strand breaks (DSBs) are one of the most deleterious lesions. If left unrepaired, DSBs lead to genomic instability and carcinogenesis. The cells combat DSBs by two classical pathways that include homologous recombination (HR) which requires the sister chromatid for sequence homology, and non-homologous end-joining (NHEJ), wherein the two DNA ends are re-joined. Recently a back-up NHEJ pathway has been reported and is referred non-canonical NHEJ which has been given many names, such as alternative NHEJ or microhomology-mediated end joining (MMEJ). The enzymatic mechanisms of non-canonical NHEJ are not well defined. NHEJ requires processing enzymes including nucleases and polymerases, although the roles of these enzymes in the pathway are poorly understood. Recent studies have implicated a role for DNA polymerase theta (Pol θ), an A-family polymerase is essential for non-canonical NHEJ pathway. Emerging evidence indicates X-family polymerases, mammalian DNA polymerases lambda (λ) and mu (μ) and yeast Pol 4 promote DNA end-joining. Our laboratory has recently provided evidence for a role for DNA polymerase beta (Pol β), another X-family polymerase, in V(D)J recombination, a process that requires end-joining. Here, using a recently developed fluorescence based assay that monitors non-canonical NHEJ and HR, we provide evidence that Pol β plays a role in the non-canonical NHEJ process. DNA sequencing at the break point junctions revealed Pol β-depleted cells have fewer small deletions than control cells, but significantly greater numbers of insertions and large deletions. We further demonstrate that Pol β-depleted cells have increased sensitivity to DNA damaging agents that induce double-strand breaks and that there is persistent accumulation of DSBs in these cells. In combination, our results suggest that Pol β is critical for double-strand break repair.
Citation Format: Sreerupa Ray, Michelle DeVeaux, Gregory Breuer, Ranjit Bindra, Daniel Zelterman, Joann Sweasy. DNA polymerase beta participates in DNA end-joining [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 2492. doi:10.1158/1538-7445.AM2017-2492