bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1726: Structure-function analysis of retinoblastoma tumor suppressor protein in human cone precursors
Authors: Wang Sijia , Grubbs Brendan , Thornton Matthew , Cobrinik David 
Published: August 2019

Abstract
Background: The retinoblastoma protein, pRB, is a key cell cycle governor that is functionally impaired in most cancers, but its mechanism of suppressing tumorigenesis in a tumor cell-of-origin has not been characterized. This study aims to define pRB structural features and corresponding cellular functions that suppress cone precursor (CP) proliferation, likely the first step in retinoblastomagenesis.
Method: Intact human fetal retinae were co-transduced with lentiviruses to knockdown endogenous pRB and ectopically express wild type or structure-based substitution mutant pRBs. The ectopically expressed pRB mutants had selectively impaired interactions with E2F transactivation domains (ΔG), with the E2F1 “marked box” domain (ΔS), or with the LxCxE protein interaction motif (ΔL). At day 12-75 post-infection, transduced retinae were analyzed by quantitative immunofluorescence staining of Ki67/EdU, pRB and CP marker L/M-opsin.
Results: In intact retina, pRB knockdown induced cell cycle re-entry of L/M-opsin+ postmitotic cone precursors, whereas those reconstituted with wild type pRB did not express Ki67 indicative of a block to cell cycle entry. Unexpectedly, all three mutants (pRB-ΔG, -ΔL, and -ΔS) were able to block cell cycle re-entry when expressed at the high-normal range the of endogenous pRB. However, at the low-normal expression level, ectopic wild type but not mutant pRBs suppressed proliferation.
Conclusion: All three surface targeted mutants (pRB-ΔG, ΔL, and ΔS) retain partial ability to suppress cone precursor cell cycle entry. This may be attributed to the presence of multiple independent cell cycle inhibitory functions. These findings suggest that pRB-mediated regulation of E2F-responsive cell cycle genes, interactions with LxCxE motif-containing proteins, and EZH2 mediated repression of repetitive elements are individually dispensable for suppressing aberrant cone precursor proliferation.
Citation Format: Sijia Wang, Brendan Grubbs, Matthew Thornton, David Cobrinik. Structure-function analysis of retinoblastoma tumor suppressor protein in human cone precursors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1726.
Abstract 1740: Characterization of CDK9 role in the DNA damage response
Authors: Nepomuceno Thales C. , Suarez-Kurtz Guilherme , Monteiro Alvaro N. , Carvalho Marcelo A. 
Published: August 2019

Abstract
Introduction: The DNA damage response (DDR) is a well-coordinated pathway capable of sensing and repairing different types of DNA damage. Double-strand break (DSB) lesions activate the ATM-CHK2 axis, which is responsible for the cell cycle arrest, prompting cells for DNA repair. DSBs are primarily repaired through two distinct pathways: homology-directed recombination (HR) and non-homologous end-joining (NHEJ). BRCA1 and 53BP1 play an important role in DDR by orchestrating the decision between HR and NHEJ, but the precise mechanisms regarding both pathways are not entirely understood. Previously, our group identified the putative interaction of the cyclin-dependent kinase 9 (CDK9) with BRCA1 and BARD1 (BRCA1-associated RING domain 1). CDK9 is a component of the positive transcription elongation complex and has been implicated in genome integrity maintenance associated with the replication stress response. More recently, we characterized CDK9 as a DDR player by modulating BRCA1 recruitment to DNA damaged sites and consequently the HR pathway. We also showed that cells lacking CDK9 failure to form RAD51, but not 53BP1, ionizing radiation-induced foci (IRIF) and are characterized by an increased sensitivity to DSBs
Methods and Results: Here we show that the CDK9-BRCA1 interaction occurs through BRCA1 N-terminal region in a BRCA1-BARD1 heterodimer formation-dependent manner. We also identified a CDK9 mutant (E369A) that abrogates the CDK9-BRCA1 interaction (through BRCA1 C-terminal region). Moreover, we characterized CHK2 as a novel CDK9-interaction partner, through ectopic GST-pulldown and constitutive co-immunoprecipitation assays. Further, cells lacking CDK9 are deficient in promoting G2/M arrest after IR-induced DNA damage. We also identified new CDK9 interactions in a DDR-related context using a TAP-MS approach.
Conclusion: Collectively, our data suggest a role for CDK9 in the DDR through DNA damage repair and cell cycle checkpoint regulation
Citation Format: Thales C. Nepomuceno, Guilherme Suarez-Kurtz, Alvaro N. Monteiro, Marcelo A. Carvalho. Characterization of CDK9 role in the DNA damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1740.
Abstract 1743: Evaluating the effect of USP22 depletion on chromosome instability in colorectal cancer
Authors: Jeusset Lucile M. , McManus Kirk J. 
Published: August 2019

Abstract
Chromosome instability (CIN) is an aberrant phenotype defined as an increase in the rate at which whole chromosomes or large chromosomal fragments are gained or lost, and is observed in virtually all cancer types. Although CIN is associated with aggressive tumors, multi-drug resistance and poor patient prognosis, the genetic defects underlying CIN remain poorly understood. Preliminary data from our laboratory suggest that diminished USP22 (Ubiquitin-Specific Peptidase 22) expression induces CIN. Importantly, USP22 deletions and reduced USP22 expression are frequently observed in multiple cancer types, including colorectal cancer, suggesting diminished USP22 expression/function may be a pathogenic event underlying oncogenesis. Therefore, the present study seeks to evaluate the impact diminished USP22 expression has on CIN by determining whether karyotypically stable colorectal cancer (HCT116) and immortalized fibroblast (hTERT) cell lines can be converted into karyotypically unstable lines following the reduction of USP22 expression. Diminished USP22 expression was achieved by siRNA-based silencing or CRISPR-Cas9-mediated gene knockout (KO) and quantitative image-based single-cell analyses were employed to monitor changes in surrogate markers for CIN, including nuclear areas and chromosome numbers. USP22 silencing induced significant changes in nuclear area as well as increased frequencies of chromosomes gains and losses, which suggest USP22 is a CIN gene. Next, to assess the long-term impact diminished USP22 expression has on CIN, two HCT116 USP22-KO clones were monitored for 10 weeks and revealed dynamic changes in nuclear areas and chromosome numbers over time relative to controls. Collectively, these data identify USP22 as a novel CIN gene and indicate that USP22 deletions in cancer may have long-term impact on CIN and may thereby promote oncogenesis. Further analysis is ongoing to investigate the mechanism through which USP22 depletion induces CIN, and in particular its effect on H2B monoubiquitination. Characterizing the effect diminished USP22 expression has on CIN is the first step towards the development of therapeutic strategies targeting USP22-deficient cancers.
Citation Format: Lucile M. Jeusset, Kirk J. McManus. Evaluating the effect of USP22 depletion on chromosome instability in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1743.
Abstract 1744: SAMHD1 expression and impact on clinical outcome in diffuse large B-cell lymphoma: a potential therapeutic target
Authors: Daddacha Waaqo 
Published: August 2019

Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma. While standard treatment with rituximab, cyclophosphamide, doxorubicin, vincris- tine, and prednisone (R-CHOP) can cure DLBCL, failed patients have poor outcome. Thus, a search for stand-alone or adjuvant therapy to improve patient’s outcome is important. Sam and HD domain-containing protein 1 (SAMHD1) is a well-established deoxyribonucleotide triphosphate (dNTP) triphosphohydrolase. Its dNTPase activity has been associated with cellular defence mechanism against infection by depleting cellular dNTP pool bellow level required for viral replication. SAMHD1 mutations have been associated with Aicardi Goutières (AGS) and cancers such as chronic lymphocytic leukemia (CLL), demonstrating its relevance beyond viral infection. In addition, it has been shown that SAMHD1 expression in Recently, our lab has defined a novel role for SAMHD1 in DNA end resection to facilitate DNA double strand break (DSB) repair by homologous recombination (HR). SAMHD1 expression and its diagnostic or therapeutic relevance in DLBCL is not known. Thus, we analyzed SAMHD1 expression in patients with DLBCL and determined its correlation with clinical outcome. In addition, we studied the SAMHD1 expression in germinal center B cell (GCB) and activated B cell (ABC) DLBCL cells lines. Also, we examined the possibility of depleting SAMHD1 using a virus like particles (VLPs) containing viral protein x (Vpx) in DLBCL cell lines. Finally, we determined the effect on cells sensitivity to standard DLBCL therapy, R-CHOP, and other DNA damage inducing agents. Low SAMHD1 expression correlates with improved overall survival. SAMHD1 was downregulated in ABC as compared to GCB DLBCL cell lines and SAMHD1 depletion sensitizes DLBCL cell lines to R-CHOP and other DNA damage inducing agents. These findings suggest that SAMHD1 is a potential therapeutic target to improve the DLBCL patient’s clinical outcome.
Citation Format: Waaqo Daddacha. SAMHD1 expression and impact on clinical outcome in diffuse large B-cell lymphoma: a potential therapeutic target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1744.
Abstract 1745: Ku70 suppresses alternative end-joining in G1-arrested progenitor B cells
Authors: Frock Richard L. , Kumar Vipul , Liang Zhouyi , Zurita Jeff , Du Zhou , Lin Sherry G. , Boboila Cristian , Alt Frederick W. 
Published: August 2019

Abstract
Classical non-homologous end-joining (C-NHEJ) repairs DNA double-stranded breaks (DSBs) throughout interphase but is thought to predominate in G1-phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/Ligase4 core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While such factors are exclusively required for joining RAG-initiated DSBs during V(D)J recombination in G1-phase lymphocyte progenitors, cycling cells deficient for core C-NHEJ factors join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination to C-NHEJ has been attributed to RAG-mediated exclusion of A-EJ; however, it remains unclear whether A-EJ is similarly excluded from more general DSBs in G1. Here, we report that Ku actively and robustly suppresses A-EJ of both RAG- and Cas9-mediated DSBs in G1-arrested progenitor B cell lines. Thus, while Cas9/gRNA DSBs remain as free broken ends in Ligase4-deficient G1-arrested progenitor B cells, deletion of Ku70 in Ligase4-deficient cells restores DSB re-joining and translocation to levels observed in Ku70-deficient counterparts. Correspondingly, while V(D)J recombination is abrogated in Ligase4-deficient lines, V(D)J-like joining occurs in Ku70-deficient and Ku70/Ligase4-double-deficient lines through a translocation-based A-EJ mechanism. We conclude that in G1, Ligase4-deficient progenitor B cells are functionally end-joining deficient due to a complete Ku-dependent block in A-EJ. Thus, the differential impacts of Ku deficiency versus XRCC4/Ligase4 deficiency on V(D)J recombination, severity of neuronal apoptosis, and embryonic development, including ability of Ku-deficiency to rescue Ligase4-deficient embryonic lethality, may be explained by Ku-mediated inhibition of A-EJ in the G1 cell cycle phase.
Citation Format: Richard L. Frock, Vipul Kumar, Zhouyi Liang, Jeff Zurita, Zhou Du, Sherry G. Lin, Cristian Boboila, Frederick W. Alt. Ku70 suppresses alternative end-joining in G1-arrested progenitor B cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1745.
Abstract 1748: RAD51 has an anti-recombinase activity that is countered by BRCA2 - In vitro
Authors: Wang Charles , Jimenez-Sainz Judit , Jensen Ryan B. , Mazin Alexander A. 
Published: August 2019

Abstract
Homologous Recombination (HR) is a high-fidelity process with a range of biologic functions from generation of genetic diversity to repair of DNA double-strand breaks (DSBs). In mammalian cells, BRCA2 facilitates the polymerization of RAD51 onto ssDNA to form a presynaptic nucleoprotein filament. This filament can then strand invade a homologous dsDNA to form the displacement loop (D-loop) structure leading to the eventual DSB repair. This pro-recombinatory feature of RAD51-BRCA2 is well documented. Here, we present biochemical evidence that RAD51 can cause D-loop disassembly. Furthermore, we show that this RAD51 anti-recombinatory activity is countered by BRCA2. These results demonstrate that BRCA2 may have a previously unexpected role: regulation of HR at a post-synaptic stage by modulating RAD51-mediated D-loop dissociation. Our results provide a biochemical mechanistic understanding of homeostasis between RAD51 and BRCA2, which has been suggested to be an important factor of HR based on previously published cellular data.
Citation Format: Charles Wang, Judit Jimenez-Sainz, Ryan B. Jensen, Alexander A. Mazin. RAD51 has an anti-recombinase activity that is countered by BRCA2 - In vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1748.
Abstract 1750: USP22 directly interacts with PALB2 and is required for efficient homologous recombination of DNA double-strand breaks
Authors: Nardi Isaac K. , Stark Jeremy , Larsen Adrien , Raz Dan 
Published: August 2019

Abstract
DNA damage by environmental stressors and agents is a huge problem for cells and must be repaired quickly for the cell to maintain its integrity. Cells employ several repair pathways and mechanisms to rectify damaged DNA. Homologous Recombination (HR) repair comprises a series of pathways in a cell that can function to repair DNA double-stranded breaks (DSBs) through template-dependent mechanisms to preserve genomic integrity. Failure to repair DSBs can result in chromosomal loss, carcinogenesis, and apoptosis. Deubiquitylases (DUBs) are a family of proteases that cleave ubiquitin from proteins and have been implicated in several biological processes including tumor development, cell growth, cell cycle regulation, and signal transduction. There is a growing catalog of studies showing the vital role of DUB’s in the DNA Damage Response (DDR). But, given that there are over 100 DUBs in the human genome their functions in DDR have still not been fully fleshed out. Along with its role in antibody class switch repair, USP22 is a DUB that has been implicated as a putative oncogene with over-expression observed in various cancer types and is associated with a poor patient prognosis. Furthermore, over-expression of USP22 leads to cisplatin resistance in lung cancer cells strongly suggesting it plays in a vital role in DDR and chemoresistance in recurrent cancers. In this study we show USP22 is necessary for HR, localizes to sites of DNA damage, and is necessary for recruitment of the PALB2-BRCA2-Rad51 complex through stabilizing PALB2 protein levels. Lastly, we show USP22 directly binds to the WD40 domain of PALB2 and this binding stimulates USP22 catalytic activity. Taken together, these findings show a new and novel role of USP22 in the HR pathway.
Note: This abstract was not presented at the meeting.
Citation Format: Isaac K. Nardi, Jeremy Stark, Adrien Larsen, Dan Raz. USP22 directly interacts with PALB2 and is required for efficient homologous recombination of DNA double-strand breaks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1750.
Abstract 1760: Plasma vitamin D levels and DNA repair capacity in four molecular subtypes of women with breast cancer
Authors: Ortiz Carmen , Encarnacion Jarline , Vergne Ralphdy , Padilla Luis , Matta Jaime 
Published: August 2019

Abstract
Background: Vitamin D regulates estrogen synthesis among other mechanisms involved in breast cancer (BC) carcinogenesis. An important gap, to our knowledge, is whether blood levels of vitamin D are associated with DNA repair capacity in women with BC. Previously, we reported that a low DNA repair capacity (DRC) is a risk factor for BC and that DRC levels are associated with estrogen receptor (ER) positivity in women with BC. Moreover, we also reported that there is an intrinsic variability in DRC levels among the four principal BC subtypes. Therefore, our aim is to study the link between DRC and plasma vitamin D levels in BC and among BC subtypes.
Methods: Treatment-naïve BC cases and controls were selected from our cohort of Hispanic women (n=1,187). DRC was assessed in lymphocytes through the host-cell reactivation assay. Vitamin D was measured using LC/MS/MS.
Results: Women with BC (n=91) had higher (+6.6 ng/ml) vitamin D than controls (n=22) (p=0.007). There were significant differences in vitamin D levels (p&lt;0.05) between BC cases with high (≥3.8%) (n=17) and low (&lt;3.8%) (n=74) DRC levels. Vitamin D and DRC were negatively correlated in BC cases (r=-0.2296, p=0.03). When women with BC and low DRC levels (n=56) were stratified into: luminal A (n=17), luminal B (n=11), HER2+ (n=10), and triple-negative (n=18), women with HER2+ and TNBC showed the highest levels of vitamin D (p&lt;0.05). Women with ER- had higher levels (+7.6 ng/ml) of vitamin D than women with ER+ tumors (p=0.005). After finding that plasma vitamin D levels from women with BC and controls were significantly different when stratified by DRC levels and BC subtypes, ROC curves were constructed to examine whether these levels could allow us to discriminate between our four study groups. Significant differences (p=0.0126) were found for cases and controls with low DRC; AUC of 0.7178. When considering all women with BC independently of DRC levels, the AUC was 0.7353 (p=0.0300).
Conclusions: This study provides the first evidence of a link between vitamin D and DRC levels in women with BC. We also present data as to how vitamin D varies across four molecular subtypes of BC in Hispanic women.
Impact: Our results fills an important gap on the link between plasma vitamin D and DRC levels in women with BC.
Funding: This study was supported by grants #S06GM008239-20, 9SC1CA182846-04, and 5SC1CA157250-02, 5U54CA163071-04, 5R25GM096955-08.
Citation Format: Carmen Ortiz, Jarline Encarnacion, Ralphdy Vergne, Luis Padilla, Jaime Matta. Plasma vitamin D levels and DNA repair capacity in four molecular subtypes of women with breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1760.
Abstract 1762: The START domain of the DLC1 tumor suppressor binds phosphatidylserine and two proteins, PLCD1 and Caveolin-1
Authors: Sanchez-Solana Beatriz , Wang Dunrui , Qian Xiaolan , Papageorge Alex , Velayoudame Parthibane , Acharya Jairaj , Lowy Douglas R. 
Published: August 2019

Abstract
The tumor suppressor gene DLC1 encodes a multi-domain protein, which includes a Rho-GAP domain (Rho GTPase activating protein domain) that negatively regulates the activity of RhoA, B, and C, and has been hypothesized to be the basis of its tumor suppressor functions. DLC1 also contains a less well characterized START (StAR-related lipid transfer) domain in its C-terminus, whose overall contribution to DLC1 function remains incompletely understood. START domains in other proteins have been shown to bind lipids, but no lipid has yet been identified that binds the DLC1 START domain. In the present study, we attempted to gain further insight into the molecular function and lipid binding properties of the DLC1 START domain.
We previously determined that Caveolin-1, the main structural component and marker of caveolae, interacts with the DLC1 START domain, and this interaction contributes to the full tumor suppressor activity of DLC1. In unpublished studies, we additionally identified Phospholipase C delta 1 (PLCD1), which participates in intracellular Ca2+ mobilization, forming a complex with the DLC1 START domain and with Caveolin-1.
We have now developed evidence that, in addition to binding Caveolin-1 and PLCD1, the DLC1 START domain binds a lipid, phosphatidylserine (PS), and have identified a colon cancer-associated DLC1-START domain mutant (R947C) that results in a protein deficient in forming a complex with all three binding partners and displays reduced tumor suppressor activity but intact RhoGAP activity. The interaction between the DLC1-START domain and PS can occur independently of PLCD1 and/or Caveolin-1, but PS promotes complex formation between the DLC1 START domain and PLCD1 or Caveolin-1, without altering PLCD1 to Caveolin-1 binding. Biological assays with wild type DLC1 show cooperation between DLC1 and PLCD1 or Caveolin-1 to inhibit cell migration, but no cooperation is observed when all three genes are overexpressed, suggesting that Caveolin-1 and PLCD1 occupy the same migration signaling pathway. Thus, we have identified a biologically relevant complex between DLC1 and three macromolecules (PLCD1, PS and Caveolin-1) that contributes to the full tumor suppressor function of DLC1 independently of its RhoGAP activity, and are testing the hypothesis that PS serves as a linker between the DLC1 START domain and PLCD1 or Caveolin-1.
Citation Format: Beatriz Sanchez-Solana, Dunrui Wang, Xiaolan Qian, Alex Papageorge, Parthibane Velayoudame, Jairaj Acharya, Douglas R. Lowy. The START domain of the DLC1 tumor suppressor binds phosphatidylserine and two proteins, PLCD1 and Caveolin-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1762.