bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1893: The dynamics of T cell clonal repertoire under targeted therapy vs. immunotherapy in melanoma
Authors: Ding Lizhong , Campbell Katie M. , Medina Egmidio , Chen Kevin , Hugo Willy
Published: July 2021

Introduction. The current standard of care for metastatic melanoma patients utilizes either MAPK pathway inhibitors (MAPKi)-based targeted therapies or immune checkpoint inhibitors (ICI)-based immunotherapies. Almost every melanoma patient treated with MAPKi will relapse in a median of one year, whereas a small subset of ICI-treated melanoma patients experienced prolonged tumor control. Multiple reports have shown that both MAPKi and ICI treatment will induce increased T cell infiltration into the tumor. However, the T-cell receptor (TCR) clonotype dynamics across different therapies (MAPKi vs. ICI) and/or clinical response (responding vs. resistant) is still unknown. This study aims to compare the TCR repertoire dynamics and their associated tumor microenvironment (TME) phenotypes in melanoma pre- vs. post-ICI or MAPKi to see if there are unique patterns associated with better tumor control.

Methods. Publicly available bulk RNA-seq data of 345 melanoma samples pre- and post- treatment were downloaded, including two MAPKi (n=116 tumors) and two ICI data sets (n = 229 tumors). All samples were classified into three groups: pre-treatment (PT), on-treatment responding (OT-R), and on-treatment non-responding (OT-NR). T cell clonotype and gene expression were quantified from the RNA-seq data using trust4 and HISAT2/htseq-count, respectively. Although the transcripts of T cells are mixed with tumor cells in the bulk RNA-seq data, the TCR clonotype abundance showed significant correlation with T cell marker expression, offering a measure of robustness in the identification of TCR from bulk tumor derived RNA-seq data.

Results. Both MAPKi and ICI therapies significantly increase the TCR count, abundance, diversity, and clonality in OT-R samples compared to PT and OT-NR samples. Intriguingly, we observed significantly higher clonal replacement of PT samples' T cell clonotypes with novel, OT-specific clonotypes under both therapies. Of note, in the tumor subset that responded to the ICI, the increase of these novel TCR were significantly associated with the enrichment of naïve/memory CD4 and CD8 T cell signatures.

Conclusions. In melanoma, intratumoral TCR dynamics patterns in response to MAPKi and ICI are mostly similar, except for the upregulation of naïve/memory T cell signatures in the subset of ICI-responder tumors. These insights may eventually lead to better markers for therapy-induced, productive anti-tumor immunity in melanoma.

Citation Format: Lizhong Ding, Katie M. Campbell, Egmidio Medina, Kevin Chen, Willy Hugo. The dynamics of T cell clonal repertoire under targeted therapy vs. immunotherapy in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1893.
Abstract 1895: caAtlas: An immunopeptidome atlas of human cancer
Authors: Yi Xinpei , Liao Yuxing , Wen Bo , Li Kai , Dou Yongchao , Savage Sara R. , Zhang Bing
Published: July 2021

At the core of immunotherapy is the T cell recognition of tumor antigens. Thus, comprehensive characterization of tumor antigens is essential for the design of effective and safe cancer immunotherapy strategies. Mass spectrometry (MS)-based immunopeptidomics allows high-throughput, direct identification of major histocompatibility complex (MHC)-bound peptides in vivo. Here, we collected 42 published human immunopeptidomic datasets, which include 327 cancer samples covering nine cancer types and 216 non-cancerous samples. A systematic, quality-controlled analysis of all 51.6 million MS/MS spectra using an open search algorithm identified 364,283 peptides, including 11,647 modified peptides associated with 80 types of modifications. Unmodified peptides showed high levels of predicted binding affinities by NetMHCpan; however, the predicted binding affinities for the modified peptides were much lower, suggesting a deficiency of existing computational tools in making predictions for modified peptides. Analysis of the 416 phosphorylated and 1,239 acetylated HLA class I peptides revealed distinct sequence motifs, and the pattern for the phosphopeptides was consistent with previous reports. Further interrogation of all identified peptides revealed evidence for tumor specific-presentation of hundreds of known and novel cancer-testis antigens as well as tumor associated antigens. We also found non-tumor-specific presentation of 44 previously annotated cancer-testis antigens. Applying NeoQuery, a newly developed computational pipeline, to our dataset identified immunopeptidomic evidence for more than 1,000 somatic mutation-derived neoantigens, and a subset of them were further validated through a traditional MS/MS peptide identification pipeline. We make all these data together with annotated MS/MS spectra supporting each individual antigen identification in a publicly accessible, easily browsable web portal named cancer antigen atlas (caAtlas, http://www.zhang-lab.org/caatlas/). caAtlas provides a fundamental resource for the selection and prioritization of MHC-bound peptides for immunogenicity testing and cancer immunotherapy development.

Citation Format: Xinpei Yi, Yuxing Liao, Bo Wen, Kai Li, Yongchao Dou, Sara R. Savage, Bing Zhang. caAtlas: An immunopeptidome atlas of human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1895.
Abstract 1899: Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting
Authors: Bear Adham S. , Blanchard Tatiana , O'Hara Mark H. , Scholler John , Vonderheide Robert H. , Linette Gerald P. , Carreno Beatriz M.
Published: July 2021

Activating missense mutations within RAS oncogenes are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here, we employ multi-omic approaches to characterize optimal HLA class I-restricted mKRAS epitopes. Using in silico epitope prediction, we identify candidate mKRAS G12 epitopes with high predicted binding affinity to prevalent HLA class I alleles. We utilize biochemical approaches to identify mKRAS epitopes with high measured binding affinity and stability to HLA-A*03:01, -A*11:01 and -B*07:02. Furthermore, we provide proteomic validation of epitope processing and presentation by these alleles. We report mKRAS G12V and G12R epitopes are immunogenic as evidenced by the isolation of mKRAS G12V- and G12R-specific TCRαβ from healthy donors. The transfer of mKRAS-TCRs to primary CD8+ T cells serves as sensitive probes to validate mKRAS epitope processing and presentation by tumor cells and confers cytotoxicity against mKRAS human tumor cell lines of various histologies. The kinetics of lytic activity correlate with measured TCR avidity and mKRAS/HLA class I complex abundance expressed on the tumor cell surface. Finally, the adoptive transfer of mKRAS-TCR engineered primary CD8+ T cells to NOD scid gamma mice leads to tumor eradication in an orthotopic mKRAS lung cancer model. This study validates mKRAS as a bona fide tumor neoantigen and supports strategies to identify recurrent driver alterations for immunological targeting. Based on this work, clinical studies targeting mKRAS in cancer patients using vaccines and adoptive T cell therapy are under active investigation.

Citation Format: Adham S. Bear, Tatiana Blanchard, Mark H. O'Hara, John Scholler, Robert H. Vonderheide, Gerald P. Linette, Beatriz M. Carreno. Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1899.
Abstract 1907: Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity
Authors: Papp Benjamin Tamas , Manczinger Máté , Balogh Gergő , Koncz Balázs , Asztalos Leó , Kemény Lajos , Papp Balázs , Pál Csaba
Published: July 2021

The human leukocyte antigen class I (HLA-I) genes shape our immune response against pathogens and cancer. Certain HLA-I variants can bind a much wider range of peptides than others, a feature that could be favorable against a range of viral diseases. However, the implications of this phenomenon on cancer immune response is unknown. In this paper, we quantified peptide repertoire breadth (or promiscuity) of a representative set of HLA-I alleles, and found that cancer patients that carry HLA-I alleles with high peptide binding promiscuity are characterized by significantly worse prognosis after immune checkpoint inhibitor treatment. This trend can be explained by a reduced capacity of promiscuous HLA-I molecules to discriminate between human self and tumor peptides, yielding a shift in regulation of T-cells in the tumor microenvironment from activation to tolerance. In summary, HLA-I peptide binding specificity shapes neopeptide immunogenicity and the self-immunopeptidome repertoire in an antagonistic manner. It could also underlie a negative trade-off between antitumour immunity and the genetic susceptibility to viral infections.

Citation Format: Benjamin Tamas Papp, Máté Manczinger, Gergő Balogh, Balázs Koncz, Leó Asztalos, Lajos Kemény, Balázs Papp, Csaba Pál. Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1907.
Abstract 1930: 4-nitroquinoline-1-oxide enhances induction of apoptosis preferentially in HPV positive head and neck squamous cell carcinoma cells
Authors: Shishodia Gauri , Lee Alice , Toledo Rhodee Ric , Zimmerman Emily , Rong Xiaohua , Xiao Adam , Harrison Lynn , Nathan Cherie Ann
Published: July 2021

Background: Tobacco use and human papillomavirus (HPV) infection are both strong contributors to the oncogenesis of head and neck squamous cell carcinoma (HNSCC). Despite HPV's causative role in HNSCC, it confers no statistically significant difference in mutational profile between HPV-associated HNSCC smokers and non-smokers. Our earlier preliminary data suggested that HPV positive (+) HNSCC cells have better activation of DNA repair proteins compared to HPV negative (-) HNSCC cells when treated with 4NQO, a mutagen and carcinogen which serves as a surrogate for tobacco exposure. This may partially explain HPV+ HNSCC's higher mutational resistance. In addition to increased DNA repair, HPV+ cells may also eliminate mutations through higher rates of apoptosis compared to HPV- cells. Hence, we wanted to test this hypothesis by analyzing the effects of 4NQO on apoptosis in HPV+ and HPV- HNSCC cells.

Methods: NOK, NOK E6.E7, SCC40 (HPV-), SCC104 and UMSCC47 (HPV+) cells were treated with different concentrations of 4NQO (0, 0.1, and 0.2 ug/ml) for 24 and 48 hours. Untreated (control) and 4NQO treated cells were assessed for cell viability using MTT assay. Apoptotic cells were determined using Annexin-V FITC flow cytometry analysis, and Western blot was performed to check the apoptotic proteins for the afore-mentioned control and 4NQO treatments.

Results: MTT assay showed decreased cell viability of NOK E6.E7, SCC47 and SCC104 cells in response to 4NQO treatment compared to relatively higher cell viability of SCC40 cells. Flow cytometry confirmed that HPV+ HNSCC cells are relatively more apoptotic compared to HPV- cells following 4NQO treatment at 24 and 48 hours. This is further supported by activation of pro-apoptotic proteins including p53, cleaved caspase 3, cleaved PARP, cleaved caspase 9, and p21 to a greater extent in HPV+ cells at different time points of 4NQO treatment using Western blot analysis.

Conclusion: Our in-vitro data suggest HPV may stimulate a protective measure against smoking-induced mutations by increasing apoptosis before cells can contribute to the HNSCC mutational profile. Taken together, these data explain why HPV associated HNSCC have a better prognosis than HPV negative irrespective of smoking history.

Citation Format: Gauri Shishodia, Alice Lee, Rhodee Ric Toledo, Emily Zimmerman, Xiaohua Rong, Adam Xiao, Lynn Harrison, Cherie Ann Nathan. 4-nitroquinoline-1-oxide enhances induction of apoptosis preferentially in HPV positive head and neck squamous cell carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1930.
Abstract 1932: Talazoparib interacts with oncolytic reovirus to enhance death-inducing signaling complex (DISC)-mediated apoptosis and immune response
Authors: Kyula Joan N. , Roulstone Victoria , Elliott Richard , Whittock Harriet , Bozhanova Galabina , McLaughlin Martin , Pedersen Malin , Krastev Dragomir , Pettitt Stephen , Legrand Arnaud , Tenev Tencho , Wright James , Yu Lu , Choudhary Jyoti , Meier Pascal , Lord Christopher J. , Melcher Alan , Wilkinson Grey , Coffey Matt , Harrington Kevin J.
Published: July 2021

Reovirus (RT3D) is a naturally occurring double-stranded RNA oncolytic virus that has shown preclinical efficacy in a wide range of tumor types. Early phase clinical studies have shown that this agent has modest monotherapy efficacy and can safely be combined with cytotoxic chemotherapy regimens. In the current studies, we used a high-throughput drug screen approach of different targeted therapeutic agents with the aim of looking for potential viral sensitizers that could enhance RT3D tumor killing. BMN-673 (talazoparib), a clinically approved poly(ADP)-ribose polymerase 1 (PARP-1) inhibitor was identified as a top hit and found to sensitize profoundly to RT3D both in vitro and in vivo in human xenograft tumors in a nude mouse model. We found that RT3D activated cellular PARP1 and was associated with PARylation of cellular proteins, including components of the DISC-associated cell death machinery. Combined treatment with RT3D and talazoparib enhanced extrinsic apoptosis (amplified by autocrine/paracrine TNF-α and TRAIL signaling), NF-κB pathway activity and pro-inflammatory cytokine production (CCL5/RANTES, CXCL8/IL8, CXCL1/GRO and CXCL10/IP10). Signaling was shown to be dependent on nucleic acid sensing mechanisms mediated by RIG-I and TLR3. We also found anti-tumour efficacy in an immunocompetent mouse model and this correlated with an increase in an immune response following combination treatment of RT3D and talazoparib. Our data provide a strong rationale for the combination of oncolytic RT3D with PARP1 inhibitors to exploit immunogenic response in cancer treatment.

Citation Format: Joan N. Kyula, Victoria Roulstone, Richard Elliott, Harriet Whittock, Galabina Bozhanova, Martin McLaughlin, Malin Pedersen, Dragomir Krastev, Stephen Pettitt, Arnaud Legrand, Tencho Tenev, James Wright, Lu Yu, Jyoti Choudhary, Pascal Meier, Christopher J. Lord, Alan Melcher, Grey Wilkinson, Matt Coffey, Kevin J. Harrington. Talazoparib interacts with oncolytic reovirus to enhance death-inducing signaling complex (DISC)-mediated apoptosis and immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1932.
Abstract 1950: A ubiquitination cascade regulates the integrated stress response and epithelial cancer survival
Authors: Cervia Lisa D. , Shibue Tsukasa , Gaeta Benjamin , Borah Ashir , Leung Lisa , Li Naomi , Dumont Nancy , Gonzalez Alfredo , Bick Nolan , Kazachkova Mariya , Dempster Joshua , Krill-Burger John M. , Udeshi Namrata , Olive Meagan , Carr Steven A. , Root David E. , Piccioni Federica , McFarland James M. , Vazquez Francisca , Hahn William C.
Published: July 2021

Systematic identification of signaling pathways required for the viability of cancer cells will facilitate the development of novel cancer therapies. We used gene essentiality measurements in 726 cancer cell lines to identify selective co-essentiality modules and found a functional ubiquitination cascade containing UBA6, BIRC6, KCMF1 and UBR4, which encode an E1, E2, and two heterodimeric E3 subunits, respectively, as a vulnerability in a subset of epithelial tumors. Suppressing BIRC6 in cancer cell lines that are dependent on this ubiquitination cascade led to a strong reduction in cell fitness in vitro, and to potent tumor regression and metastasis suppression in vivo. Mechanistically, BIRC6 suppression resulted in selective and robust activation of the integrated stress response (ISR) signaling via upregulation of the heme-regulated inhibitor (HRI). Using proteomic profiling, we found that HRI itself is a key degradation target of the UBA6/BIRC6/KCMF1/UBR4 cascade. These observations demonstrate a protein ubiquitination cascade regulating ISR and highlight the potential of this cascade as a novel therapeutic target for a subset of epithelial cancers.

Citation Format: Lisa D. Cervia, Tsukasa Shibue, Benjamin Gaeta, Ashir Borah, Lisa Leung, Naomi Li, Nancy Dumont, Alfredo Gonzalez, Nolan Bick, Mariya Kazachkova, Joshua Dempster, John M. Krill-Burger, Namrata Udeshi, Meagan Olive, Steven A. Carr, David E. Root, Federica Piccioni, James M. McFarland, Francisca Vazquez, William C. Hahn. A ubiquitination cascade regulates the integrated stress response and epithelial cancer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1950.
Abstract 1954: Identifying synthetic lethality with novel CDK2 small molecule inhibitors via integration of high-content microscopy and -omics level platforms
Authors: Wang Tim Sen , Almaden Jon , Shen Chen , Lapek John , Niessen Sherry , Miller Nichol , Dann Stephen , VanArsdale Todd
Published: July 2021

CDK4/6 small molecule inhibitors represent a milestone in treating hormone receptor-positive breast cancer. PALOMA (Palbociclib: Ongoing Trials in the Management of Breast Cancer) studies have confirmed prolonged progression-free survival after CDK4/6 inhibitor and anti-estrogen therapy. Notably, disease progression is observed in a subset of patients receiving Palbociclib-Fulvestrant treatment (Turner et al., NEJM 2018). Circulating tumor DNA from PALOMA-3 patients revealed genetic mutations correlating with patient response (O'Leary et al., Cancer Discov, 2018). Compensations in CDK4/6i resistance include circumvention of CDK4/6 substrate regulation, CCNE1/2 amplification (Herrera-Abreu et al., Cancer Res. 2016), and compensatory CDK2 activity. The importance of compensatory CDK2 cancer re-wiring is highlighted by recently reported, highly efficacious CDK2/4/6i (Freeman-Cook et al., in review). Thus, mechanistic understanding of cancer cell and compensatory CDK2 activity is imperative to improve patient outcome. Acute, temporal phenotypes in CDK2-signaling have been observed by live single-cell tracking microscopy in human breast epithelial and ER+ breast cancer cells (Arora & Moser et al., in review). In extending these studies, we utilize first-in-class small molecule inhibitors against CDK2 combined with high content imaging approaches to illuminate cancer cell CDK2 signaling and identify potential synthetic lethality. We report biomarkers parsed in cycling populations as quantifiable phenotypes and identify disengaged control of several processes including S- and G2/M licensing after CDK2i. Combined with internal -omics studies, CDK2i selective molecules support a positive regulatory role of CDK2 on CCNB1-PLK1 signaling before mitotic entry. We combine our high-content techniques with proximity labeling to quantify alternative CDK-Cyclin complex formation following pharmacologic perturbation. We hypothesize that dysregulated CDK-Cyclin complex formation elicits unintended CDK2 kinase activity, revealing potential synthetic lethality with inhibition of centrosome duplication pathways in ER+ breast cancers.

Citation Format: Tim Sen Wang, Jon Almaden, Chen Shen, John Lapek, Sherry Niessen, Nichol Miller, Stephen Dann, Todd VanArsdale. Identifying synthetic lethality with novel CDK2 small molecule inhibitors via integration of high-content microscopy and -omics level platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1954.
Abstract 1961: Cyclin-dependent kinase inhibition in mesothelioma
Authors: Kratzke Marian , Kren Betsy , Porter Stephen , Scaria George , Klein Mark A.
Published: July 2021

Background: Mesothelioma is a cancer that arises out of the pleura or the peritoneum and is considered incurable in the majority of patients afflicted. Abnormalities of the cell cycle pathway are among the most common molecular alterations in mesothelioma. Previously, we have demonstrated that inhibition of CDK4/6 by abemaciclib or palbociclib is effective against mesothelioma in vitro. Increased expression of Cyclin E has been demonstrated to be one mechanism of resistance to CDK4/6 inhibition in other cancers. We hypothesized that select cell cycle-related proteins may compensate for inhibition of one part of the cell cycle machinery and that the CDK2 inhibitor dinaciclib may act synergistically in combination with abemaciclib.

Methods: Dinaciclib was evaluated for activity against mesothelioma cells in vitro with regard to cell proliferation and colony formation. In addition, dinaciclib was evaluated in combination with abemaciclib at several concentration combinations in a cell proliferation assay to determine if the combination may be additive or synergistic. Combination indices (CI) were calculated via the Chou-Talalay method. Immunoblotting was used to evaluate for expression of key survival proteins after treatment with abemaciclib.

Results: The IC50 of dinaciclib was determined to be 18 nM, 23 nM, 32 nM, and 33 nM in mesothelioma cell lines H2373, H2052, H2452, and H2461, respectively. Colony formation was decreased significantly after 72 hours incubation with 50 nM or 100 nM dinaciclib in Bap1-expressing (35.1 ± 2%; 22.8 ± 2%) and Bap1-null cell lines (14.5 ± 3%; 8.1 ± 2%) versus untreated controls. CI < 1 (denoting synergism) was identified for several combinations of varied concentrations of abemaciclib and dinaciclib for both cell lines evaluated. Further, treatment with abemaciclib for 72 hrs in both Bap1-expressing and Bap 1-null cells at 1x the IC50 resulted in complete loss of FoxM1 expression and pro-survival survivin and significantly decreased the expression of Mcl-1 and XIAP.

Conclusions: Dinaciclib is a potent inhibitor of mesothelioma cell growth. The combination of abemaciclib and dinaciclib is synergistic across a spectrum of concentrations in vitro. Further experiments are currently underway to determine which CDKs and related proteins may be more effectively targeted in mesothelioma. As the cell cycle is altered in the vast majority of mesothelioma tumors, select combinations of CDK inhibition may be a feasible future therapeutic strategy against mesothelioma.

Citation Format: Marian Kratzke, Betsy Kren, Stephen Porter, George Scaria, Mark A. Klein. Cyclin-dependent kinase inhibition in mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1961.
Abstract 1963: High expression of Cyclin D1 is an independent marker for favorable prognosis in Middle Eastern breast cancer
Authors: Al-Kuraya Khawla S. , Siraj Abdul K. , Parvathareddy Sandeep K. , Siraj Sarah , Azam Saud , Annaiyappanaidu Padmanaban , Sabido Maria Angelita , Diaz Mark Ranier
Published: July 2021

Cyclin D1 protein regulates cell cycle progression which is mediated by its interactions with cyclin-dependent kinases. Over-expression of Cyclin D1 has been observed in several human cancers. This study was conducted to evaluate Cyclin D1 expression in a large cohort of Middle Eastern breast cancers and determine its prognostic significance. Cyclin D1 expression was assessed immunohistochemically and its association with clinico-pathological parameters was analyzed. Cyclin D1 was over-expressed in 59.4% (596/1003) of cases and significantly associated with a subset of breast cancers having favorable prognostic features such as low grade (p < 0.0001), low stage (p = 0.0276), estrogen receptor positive (p < 0.0001) and progesterone receptor positive (p < 0.0001) tumors. An inverse association was found with triple negative breast cancers (p < 0.0001). More importantly, Cyclin D1 expression was an independent predictor of favorable overall survival in our cohort (Hazard ratio = 0.69; 955 confidence interval = 0.48 - 0.98; p = 0.0405). Also, tumors that highly expressed cyclin D1 had a longer recurrence free survival. However, recurrence free survival was only significant in univariate analysis. In conclusion, our results reinforced the role of cyclin D1 in breast cancer pathology and revealed its expression as a valuable independent prognostic indicator for breast cancer from Middle Eastern ethnicity.

Citation Format: Khawla S. Al-Kuraya, Abdul K. Siraj, Sandeep K. Parvathareddy, Sarah Siraj, Saud Azam, Padmanaban Annaiyappanaidu, Maria Angelita Sabido, Mark Ranier Diaz. High expression of Cyclin D1 is an independent marker for favorable prognosis in Middle Eastern breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1963.
Abstract 1969: PTEN plays a role in histone modifications during mitosis
Authors: Choi Byeong Hyeok , Colon Tania Marlyn , Lee Eunji , Kou Ziyue , Dai Wei
Published: July 2021

The tumor suppressor PTEN plays an important role in the regulation of cell survival, proliferation, and angiogenesis. Deregulated expression and/or activities of PTEN frequently result in tumor development. PTEN is a plasma-membrane lipid-phosphatase, functioning to antagonize the PI3K/AKT signaling pathway. It also has a role in the nucleus regulating mitotic progression and suppressing chromosomal instability during cell division. To date, the exact function of nuclear PTEN remains not entirely clear. Several recent studies have revealed that PTEN physically interacts with histones and regulates their post-translational modifications. We previously found that PTEN is heavily phosphorylated by Plk1, which regulates mototic progression and chromosomal instability through its physical interaction with mitotic checkpoint complex (MCC). Therefore, we asked whether PTEN directly interacted with epigenetic regulators and mediated histone modifications and whether PTEN-mediated histone modifications functioned as an important regulatory mechanism during the cell cycle. Here we demonstrated that PTEN was associated with Chromobox Homolog proteins (CBXs) which are part of PRC1 complex that mediates histone modifications. Among CBXs, CBX8 levels were high in mitosis, which were correlated with an increase in PTEN mono-ubiquitination, suggesting its potential involvement in mitotic progression. Supporting this notion, we showed that CBX8 was required for cell proliferation and mitotic progression. Moreover, CBX8 was associated with PTEN/MCC during mitosis and mediated histone H2AK119 mono-ubiquitination. Combined, these results strongly suggest that CBX8/PTEN/MCC plays a significant role in modifying histones and suppressing chromosomal instability during mitotic progression.

Citation Format: Byeong Hyeok Choi, Tania Marlyn Colon, Eunji Lee, Ziyue Kou, Wei Dai. PTEN plays a role in histone modifications during mitosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1969.
Abstract 1975: Tumor treating fields triggers OFD1 removal from primary cilia to promote glioma cell survival
Authors: Shi Ping , Tian Jia , Sarkisian Matthew R.
Published: July 2021

Tumor Treating Fields (TTFields) significantly prolongs the survival of patients with glioblastoma, but glioma cells can still escape this therapy creating significant problems. Recent studies suggest glioma cells resist TTFields exposure by triggering AMP activated protein kinase (AMPK)-dependent autophagy pathway activation. Our group has been studying primary cilia, microtubule-based ‘antenna' whose growth is stimulated by autophagy-activated removal of Oral-Facial-Digital Syndrome 1 protein (OFD1) from the cilia base. Here we asked whether TTFields affect glioma primary cilia and/or play any role in the prosurvival response to TTFields. Using a low grade (S7) glioma cell line, we found that 1 or 3 intermittent cycles of 72hr 200kHz TTFields treatment in vitro caused a significant lengthening of primary cilia after cells were allowed to recover 3-4 days after TTFields. At the cilia base, TTFields led to recruitment of microtubule-associated protein 1A/1B light chain 3B (LC3B) and phospho-AMPK, and removal of OFD1, changes associated with autophagy pathway activation. Acutely after TTFields, we observed fewer cilia and apparent ‘ciliophagy' because the cilia appeared to detach or ‘dissolve' from the basal body. In U87 cells, TTFields induced a significant reduction of extranuclear clusters of OFD1 while increasing a dramatic formation of nuclear islands of OFD1, two phenomena that were disrupted by addition of the autophagy inhibitor chloroquine (CQ). TTFields also stimulated surprising growth of primary cilia in U87 cells which normally rarely elaborate cilia. Further, we found that TTFields was less effective at killing cilia-depleted S7 cells. Finally, TTFields plus inhibition of autophagy using CQ or a histone deacetylase 6 (HDAC6) inhibitor led to dramatically fewer cells and cilia, thus promoting TTFields toxicity. Altogether, our results suggest that primary cilia are potential membrane ‘hotspots' triggered by TTFields to promote glioma cell survival via OFD1.

Citation Format: Ping Shi, Jia Tian, Matthew R. Sarkisian. Tumor treating fields triggers OFD1 removal from primary cilia to promote glioma cell survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1975.
Abstract 1976: Ras-Raf-MEK-ERK signaling pathway: a novel target of ERRα and tamoxifen in TNBC cells
Authors: Musheyev David , Ronen Adi , Lattin Miriam T. , Alayev Anya
Published: July 2021

TNBC, or triple-negative breast cancer, is an aggressive type of breast cancer that is associated with a worse prognosis, higher rates of metastases, and a poorer outcome. Historically, TNBC has been proven challenging to treat, due to disease heterogeneity and the fact that the breast cancer tests negative for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) protein, and thus does not respond to traditional therapies. As such, treatment options for TNBC patients are extremely limited and there is a tremendous need to identify molecular targets and biomarkers that can offer novel targeted approaches. Additionally, due to disease heterogeneity in TNBC, it is important to subclassify TNBC based on prognostic markers and create tailored targeted therapies. ERRα, an orphan nuclear receptor, is an example of a prognostic marker that is correlated with a more aggressive disease progression and a worse outcome. However, ERRα is also a predictive marker for patient response to tamoxifen treatment of ER-negative and TNBC patients, indicating that there may be an alternative use for the selective estrogen modulator (SERM) tamoxifen in the context of TNBC. This led us to investigate whether there is a common pathway that is regulated by both ERRα and tamoxifen that would explain tamoxifen response in the context of TNBC cells. We performed a phosphoproteomic analysis of MDA-MB-231 cells, treated with either tamoxifen or XCT-790, an inverse agonist of ERRα, to identify common downstream targets of both ERRα and tamoxifen. Our findings indicate that the Ras-Raf-MEK-ERK signaling pathway is a common target of both XCT-790 and tamoxifen. This provides a novel treatment strategy that should be investigated for the treatment of TNBC patients, opens the door for investigation of novel targeted therapies, and highlights the need for the use of prognostic markers to identify sub-populations that benefit from individualized treatment strategies.

Citation Format: David Musheyev, Adi Ronen, Miriam T. Lattin, Anya Alayev. Ras-Raf-MEK-ERK signaling pathway: a novel target of ERRα and tamoxifen in TNBC cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1976.
Abstract 2015: Interplay of the pH regulator, carbonic anhydrase IX and the glutamine transporter, ASCT2 in hypoxic tumor microenvironment
Authors: Venkateswaran Geetha , Chafe Shawn , Awrey Shannon , Nemirovsky Oksana , Dedhar Shoukat
Published: July 2021

Solid tumors are characterized by poor vasculature, thereby causing insufficient oxygen and nutrient supply within the tumor. To thrive in such conditions, hypoxic tumor cells stimulate the expression of nutrient transporters to support cell metabolism and pH regulators to buffer the intracellular pH changes caused by metabolic by-products. Carbonic Anhydrase IX (CAIX) is a membrane-bound enzyme that plays a vital role in the pH regulation of hypoxic tumor cells. CAIX is highly expressed in several solid tumors, and is an indicator of poor prognosis and response to therapy. Although the importance of CAIX's role in mediating tumor progression is well-known, the underlying mechanism remains unclear. To identify the interactors of CAIX in the hypoxic tumor microenvironment, we performed a proteomic analysis using proximity dependent biotin identification (BioID) and found the Alanaine, Serine, Cysteine transporter (ASCT2) to be a high confidence interactor of CAIX from this analysis. ASCT2, which predominantly acts as a glutamine transporter is upregulated in several cancers and is shown to support tumor growth by facilitating increased glutamine uptake. In this study, using a panel of solid tumor cell lines, we validate the interaction of CAIX with ASCT2 in the hypoxic microenvironment. Functionally, loss of CAIX causes an increased glutamine uptake via ASCT2 and an increased capacity of cells to utilize glutamine for mitochondrial respiration. Concomitantly, ROS and glutathione (GSH) levels also increase upon CAIX inhibition. Cytotoxicity studies show a robust cell death in the absence of glutamine, following treatment with the CAIX/XII small molecule inhibitor SLC-0111. A similar effect on cell death is observed by blocking glutamine metabolism using inhibitors such as V-9302 (ASCT2 inhibitor) or CB-839 (Glutaminase-1 inhibitor) with SLC-0111. Furthermore, blocking GSH synthesis using BSO (Glutamylcysteine synthatase inhibitor) with SLC-0111 causes significant cell death. These results suggest that CAIX depletion causes increased cellular stress and to overcome this, cells increase glutamine uptake in part for GSH synthesis. In summary, we show that CAIX and ASCT2 coordinate their functions in hypoxic cancer cells to support tumor growth, and co-targeting them could be beneficial in treating solid tumors.

Citation Format: Geetha Venkateswaran, Shawn Chafe, Shannon Awrey, Oksana Nemirovsky, Shoukat Dedhar. Interplay of the pH regulator, carbonic anhydrase IX and the glutamine transporter, ASCT2 in hypoxic tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2015.
Abstract 2051: Inhibiting CDC7 kinase for the treatment of Ewing sarcoma
Authors: Martin Jeffrey C.
Published: July 2021

Ewing Sarcoma is a malignant tumor of the bone and soft tissue that is primarily driven by the fusion protein EWS-FLI1. With no current targeted therapy, treatment options remain limited and toxic. Recent reports have shown that Ewing tumors harbor large amounts of transcription-associated replication stress and that this offers an attractive therapeutic intervention point. Our group has shown that inhibition of the kinase complex DDK (CDC7-DBF4) results in apoptosis and a significant reduction in cell viability in EWS-FLI1-harboring Ewing's sarcoma cell lines. Also, low dose DDK inhibition in Ewing's sarcoma cells caused an S/G2 cell cycle accumulation at 24 hours, followed by re-entry into G1 and appearance of sub-G1 DNA. This suggests a failure to properly progress through S-phase followed by premature mitotic entry and mitotic catastrophe resulting in cell death. To this end, there was a significant increase in the formation of micronuclei and other aberrant mitotic structures upon DDK inhibition in Ewing's cells. Interestingly, there was minimal signs of mitotic accumulation, despite clear evidence of mitotic stress, indicating a failure to properly enforce a G2-M checkpoint. Importantly, these phenotypes were not mimicked with the use of the CDK2 inhibitor Roscotivine, suggesting an origin firing-independent basis for the sensitivity to DDK inhibition. Furthermore, we show that DDK inhibition synergizes with the TOP1 inhibitor Camptothecin and with the PARP1 inhibitor Talazoparib to kill Ewing Sarcoma cells in vitro. We have hypothesized this to be due to DDK's potential role in replication fork instability/restart. Together, these results suggest that Ewing sarcoma cells rely on the activity of DDK to maintain cell viability independently from its role in the regulation of replication origin initiation and suggest that DDK inhibition may prove to be a viable treatment option for patients with Ewing's sarcoma.

Citation Format: Jeffrey C. Martin. Inhibiting CDC7 kinase for the treatment of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2051.
Abstract 2054: Characterization of TQB3823, a differentiated PARP inhibitor with anti-tumor activity in BRCA-deficiency cancer models
Authors: Yanbin Hu , Xiquan Zhang , Ling Yang , Xin Tian , Gang Li , Lihong Hu , Ding Charles Z. , Yuanfeng Xia , Wei Li , Shanshan Yin , Ying Chen , Songliang Wu , Shuhui Chen
Published: July 2021

Objective: Homology-directed repair (HDR) pathway is the major DNA double-strand break repair pathway. BRCA-deficiency impairs this pathway, and combination with Poly(ADP-ribose) polymerase (PARP) inhibition results in cell death. This process is known as “synthetic lethality”. A proportion of breast cancer, ovarian cancer and other solid tumor patients carrying BRCA-mutated gene receive benefits from PARP inhibitors. In this study, we present in vitro activity and in vivo efficacy data of a novel small molecule PARP inhibitor, TQB3823 to support it as our clinical candidate.

Method: Enzyme inhibition activities of TQB3823 were determined in PARP1/PARP2/Tankyrase 1 assays. Cellular anti-proliferative activity and selectivity were evaluated in MDA-MB-436 cell line with BRCA1 mutation and BRCA wild type MDA-MB-231 cell line. Antitumor efficacy of TQB3823 was investigated in BRCA1 mutated MDA-MB-436 breast cancer CDX model.

Result: TQB3823 showed high potency and selectivity at both enzymatic and cellular level. IC50 of TQB3823 in PARP1/PARP2/Tankyrase 1 assays are 2.8/0.9/629.3 nM, respectively. It inhibited proliferation of BRCA1 mutant MDA-MB-436 cell with IC50 of 9.6 nM. In contrast, TQB3823 showed little anti-proliferative activity in BRCA-wild type MDA-MB-231 cell with IC50 >10 μM. TQB3823 demonstrated antitumor efficacy in dose dependent fashions with tumor regression was observed at 25 mg/kg in MDA-MB-436 CDX model. The level of antitumor effects was superior to niraparib at the same dose in the same study. DNA trapping experiments revealed similar potency to olaparib indicative of low toxicity.

Conclusion: We have identified a novel, potent and selective PARP inhibitor TQB3823, which inhibits the proliferation of BRCA mutant cells but spares the wild type cells. In vivo study in a BRCA-deficiency tumor model confirms the high in vivo efficacy of this molecule. In conclusion, TQB3823 represents a promising differentiated clinical candidate for treating solid cancers with homology directed repair.

Citation Format: Hu Yanbin, Zhang Xiquan, Yang Ling, Tian Xin, Li Gang, Hu Lihong, Charles Z. Ding, Xia Yuanfeng, Li Wei, Yin Shanshan, Chen Ying, Wu Songliang, Chen Shuhui. Characterization of TQB3823, a differentiated PARP inhibitor with anti-tumor activity in BRCA-deficiency cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2054.
Abstract 2064: Homologous recombination repair somatic/germline mutation detection in plasma by next-generation sequencing in Chinese solid tumor patients
Authors: Zhu Wei , Chen Hui , Zhang Bei , Zhao Xiaochen , Bai Yuezong
Published: July 2021

Purpose: PARP inhibitors (PARPis) have been approved for germline and/or somatic BRCA-mutated ovarian cancer, breast cancer, pancreatic cancer and homologous recombination repair gene (HRR)-mutated prostate cancer. Emerging evidence has shown that antitumor activity of PARPis could expand to other HRR-mutated solid tumors. Therefore, efficient and timely methods to detect both somatic and germline HRR mutations using tissue or blood are urgently needed. Here, we first specially reported the prevalence of HRR mutation in plasma samples using Next-generation sequencing (NGS).

Methods: A total of 1601 paired plasma-white blood cell samples and 3404 paired tumor-white blood from Chinese solid tumor patients were collected between October 2019 and October 2020. The samples were assessed with targeted NGS of circulating tumor DNA (ctDNA) or tumor tissue DNA (ttDNA) to detect deleterious somatic and germline mutations in 16 core HR genes in a CLIA-certified laboratory.

Results: Overall, 165/1601 (10.3%) patients had at least one somatic or germline HRR gene mutations by ctDNA-based NGS analysis. The most commonly mutated tumor types were endometrium (42.9%, n=7), ovary (38.5%, n=13), prostate (27.8%, n=108), neuroendocrine (20%, n=5), breast (19%, n=42), melanoma (16.7%, n=6), stomach (15.8%, n=101), biliary tract (15.6%, n=64), cervix (12.5%, n=8), pancreas (11.4%, n=70), colorectum (9.8%, n=174) and bladder urinary tract (9.5%, n=21). Except for the four tumor types (endometrium, neuroendocrine, melanoma and cervix) with less than ten samples, the prevalence of HRR mutation was comparable with the ttDNA-based NGS data. Among HRR mutations, BRCA2 was the most commonly mutated gene (3.2%), followed by ATM (2.4%), BRCA1 (1.4%), CHEK2 (1.2%), BARD1 (0.7%), PALB2 (0.7%), CDK12 (0.7%) and FANCA (0.5%). Most of these data was similar to the results of ttDNA-based NGS. Moreover, slightly higher prevalence was found in BRCA2 (3.2% vs 2.5%) and CHEK2 (1.2% vs 0.7%), and slightly lower prevalence was found in ATM (2.4% vs 3.2%) and CDK12 (0.7% vs 1.4%).

Conclusion: We first described the prevalence of somatic and/or germline HRR mutations detected by ctDNA-based NGS in a Chinese solid tumor cohort. Further prospective study is needed to compare the impact of the HRR status identified by ctDNA and ttDNA NGS on PARPis efficacy.

Citation Format: Wei Zhu, Hui Chen, Bei Zhang, Xiaochen Zhao, Yuezong Bai. Homologous recombination repair somatic/germline mutation detection in plasma by next-generation sequencing in Chinese solid tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2064.
Abstract 2068: Radiotherapy is associated with a deletion signature that contributes to poor cancer patient outcomes
Authors: Kocakavuk Emre , Anderson Kevin J. , Johnson Kevin C. , Varn Frederick S. , Amin Samirkumar B. , Sulman Erik P. , Barthel Floris P. , Verhaak Roel G.
Published: July 2021

Diffuse gliomas are highly aggressive brain tumors that invariably relapse despite treatment with chemo- and radiotherapy. Treatment with alkylating chemotherapy can drive tumors to develop a hypermutator phenotype. In contrast, the genomic effects of radiation therapy (RT) remain unknown.

We analyzed the mutational spectra following treatment with ionizing radiation in sequencing data from 190 paired primary-recurrent gliomas from the Glioma Longitudinal Analysis (GLASS) dataset and 2116 post-treatment metastatic tumors from the Hartwig Medical Foundation.

We identified a significant increase in the burden of small deletions following radiation therapy that was independent of other factors and was significantly associated with the clinically applied RT-dosage in Gy (P = 1e-02, multivariable log-linear regression). These novel deletions demonstrated distinct characteristics when compared to pre-existing deletions present prior to RT-treatment and deletions in RT-untreated tumors. Radiation therapy-acquired deletions were characterized by a larger deletion size (GLASS and metastatic cohort, P = 1.2e-02 and P = 8e-11, respectively; Mann-Whitney U test), an increased distance to repetitive DNA elements (P < 2.2e-16, Kolmogorov-Smirnov test) and a reduction in microhomology at breakpoints (P = 3.2e-02, paired Wilcoxon signed-rank test). These observations suggested that canonical non-homologous end joining (c-NHEJ) was the preferred pathway for DNA double strand break repair of RT-induced DNA damage. Furthermore, radiotherapy resulted in frequent chromosomal deletions and significantly increased frequencies of CDKN2A homozygous deletions. Finally, a high burden of RT-associated deletions was associated with worse clinical outcomes (GLASS and metastatic cohort, P < 1e-04 and P = 2.6e-02, respectively; Wald test).

Our results collectively suggest that effective repair of RT-induced DNA damage is detrimental to patient survival and that inhibiting c-NHEJ may be a viable strategy for improving the cancer-killing effect of radiotherapy. Taken together, the identified genomic scars as a result of radiation therapy reflect a more aggressive tumor with increased levels of resistance to follow up treatments.

Citation Format: Emre Kocakavuk, Kevin J. Anderson, Kevin C. Johnson, Frederick S. Varn, Samirkumar B. Amin, Erik P. Sulman, Floris P. Barthel, Roel G. Verhaak. Radiotherapy is associated with a deletion signature that contributes to poor cancer patient outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2068.