bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2049: Cell-cycle dependent regulation of Sp1 at DSBs promotes repair via NHEJ and sensitizes cells to PARP inhibition
Authors: Swift Michelle , Azizkhan-Clifford Jane
Published: July 2021

DNA double-strand breaks (DSBs) are life-threatening lesions that must be repaired to preserve chromosomal integrity. These lesions are repaired by two primary pathways: homologous recombination (HR) and non-homologous end-joining (NHEJ). The factors that mediate pathway choice are critical to maintain genomic integrity. While many of these factors, epigenetic changes and cell cycle stages are known, with HR predominating in S and G2, the underlying mechanisms that determine pathway choice are not well understood. Previously, we found that the transcription factor Sp1 is rapidly recruited to DSBs and is necessary for repair. Here, we demonstrate that Sp1 integrates repair pathway choice with cell cycle by promoting NHEJ in G1. Sp1 localizes to DSBs in G1 to recruit the NHEJ repair factors 53BP1 and Ku70. Sp1 is phosphorylated by Cyclin A/cdk2 upon entry into S phase, evicting both Sp1 and 53BP1 from the break site, thereby permitting BRCA1 binding and HR. Mutation of this phosphorylation site (Sp1-S59A) results in persistence of Sp1 and 53BP1 at DSBs in S phase cells, precluding BRCA1 binding and HR. We also demonstrate that Sp1 is sumoylated in S phase in response to damage. This sumoylation in recognized by the E3-ubiquitin ligase, RNF4, and therefore polyubiquitylates Sp1 and targets it for proteasomal degradation. Expression of a sumoylation deficient Sp1 (Sp1-K16R) results in Sp1 and 53BP1 occupancy at DSBs in S phase, inhibiting BRCA1 binding to DSBs and HR. HR proteins are commonly mutated in cancers, resulting in cellular “addiction” to alternative repair pathways. Exploiting this addiction is the basis of synthetic lethality and is applicable to the treatment of many types of malignancies. Similar to BRCA1 deficiency, expression of Sp1-S59A or Sp1-K16R also increases cell sensitivity to PARP inhibition in BRCA1+/+ cells because of the inability to recruit BRCA1. Alternatively, synthetic lethality in BRCA1-/- cells requires 53BP1, whereas loss of 53BP1 confers PARPi resistance in a BRCA1 deficient cell. Consistent with this, depletion of Sp1 also results in PARPi resistance in BRCA1-/- cells. Interestingly, Sp1 is overexpressed in many tumors and is associated with poor prognosis. These data corroborate our finding that Sp1 is required for NHEJ and provide preliminary evidence that Sp1 may be a biomarker for PARPi sensitivity.

Citation Format: Michelle Swift, Jane Azizkhan-Clifford. Cell-cycle dependent regulation of Sp1 at DSBs promotes repair via NHEJ and sensitizes cells to PARP inhibition [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 2049.
Abstract 2052: TRIP13 amplification confers PARP inhibitor resistance and polymerase theta inhibitor sensitivity
Authors: Patterson-Fortin Jeffrey , Zhou Jia , D'Andrea Alan
Published: July 2021

Genome integrity is critical for cellular survival and is maintained by DNA repair pathways collectively known as the DNA damage response (DDR). Double-stranded breaks (DSBs) are the most deleterious form of DNA damage and can be repaired through homologous recombination (HR), non-homologous end-joining (NHEJ), and microhomology-mediated end-joining (MMEJ). The first step in both HR and MMEJ is resection of the DNA DSB termini to create single-stranded DNA 3' overhangs. In contrast, the 53BP1-Shieldin complex limits DNA end-resection and promotes NHEJ. Defects in HR repair can be present in cancer cells secondary to germline or somatic mutations in BRCA1, BRCA2, or other genes in the HR pathway, and such defects confer sensitivity to inhibitors of poly (ADP-ribose) polymerase (PARP). Resistance to PARP inhibitors can occur if there is loss of the 53BP1-Shieldin complex or amplification of TRIP13, a negative regulator of the 53BP1-Shieldin complex (Clairmont, et al. NCB 22:87, 2020). Here, we show that cells with TRIP13 amplification have increased DNA end-resection and increased expression of polymerase theta (POLQ), the critical enzyme for MMEJ. The resulting increase in POLQ activity limits DNA end-resection and increases MMEJ-mediated DSB repair. In these cells, inhibition of POLQ by a POLQ inhibitor, novobiocin (Zhou, et al. bioRxiv, 2020), resulted in excessive DNA end-resection, replication stress, activation of the ataxia-telangiectasia and Rad3 related (ATR) DNA damage response, and ultimately cell death. Conversely, knockdown of TRIP13 promotes PARP inhibitor sensitivity and POLQ inhibitor resistance. Thus, TRIP13 amplification may function as a biomarker for resistance to PARP inhibitors and sensitivity to a POLQ inhibitor. In summary, these results reveal a mechanism of PARP inhibitor resistance and POLQ inhibitor sensitivity in HR-deficient cells, provide a rationale for using TRIP13 as a biomarker for PARP inhibitor or POLQ inhibitor sensitivity, and may offer novel therapeutic strategies for PARP inhibitor resistant cancers.

Citation Format: Jeffrey Patterson-Fortin, Jia Zhou, Alan D'Andrea. TRIP13 amplification confers PARP inhibitor resistance and polymerase theta inhibitor sensitivity [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 2052.
Abstract 2069: Targeting the DNA damage response in combination with high Z metal nanoparticle radiosensitizers in glioblastoma
Authors: Kerr Brianna
Published: July 2021

Introduction: Glioblastoma (GBM) is a devastating disease with an extremely poor prognosis of approximately 11-15 months following standard-of-care treatments. There is a critical need for the development of clinical unmet need and a need for novel therapies in GBM. Combining novel drugs with radiotherapy has clear potential to considerably improve patient outcomes. Metal nanoparticles (NPs) and inhibitors of the DNA damage response (DDRIs) have been successfully translated to the clinical setting to benefit patients. In this study, we aimed to evaluate a novel multi-modal treatment in GBM by combining radiotherapy with metal NPs and DDRIs.

Materials and methods: GBM cell models (U87 & U251) were screened with different NP formulations and sizes, including gadolinium-, iron- and gold-based NPs, to determine the most effective NP. Cells were transiently exposed to NPs for 1 or 24 hr prior to irradiation by x-rays and cell survival determined. IC50 values were determined for various DDRIs which specifically target PARP, ATR, ATM and DNA-PKcs. Clonogenic cell survival assays were conducted and cells treated with NP and DDRI combinations either 1 or 24 hr prior to irradiation to define the optimum schedule for drugging.

Results and conclusions: We have demonstrated the radiosensitizing potential of Activation and Guidance of Irradiation by X-ray (AGuIX), a gadolinium-based NP, at low-moderate concentrations with the highest concentration tested (2mM) showing the greatest efficacy. A promising lack of cytotoxicity on both GBM cell models was observed. In contrast to AGuIX, U87 and U251 cell survival responses indicated a lack of dose dependency when exposed to varying concentrations of Superparamagnetic Iron Oxide Nanoparticles (SPIONs). Both cell models exhibited differential radiotherapy responses when exposed to ID10 and ID11, gold-based NPs with varying PEG chain lengths. Combination treatment with AGuIX and Olaparib resulted in differential efficacy between cell lines. A non-significant difference in cell survival was observed between differing treatment scheduling. Future work will explore several variations of NP and DDRI treatments in combination with irradiation by x-rays on GBM cell models. The future implications of this research are GBM patients would receive combination therapies tailored to the specific DNA mutations in their tumor.

Citation Format: Brianna Kerr. Targeting the DNA damage response in combination with high Z metal nanoparticle radiosensitizers in glioblastoma [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 2069.
Abstract 2076: Low OGG1 protects against the DNA damage induced by MTH1 inhibition
Authors: Lincheta Laura Misiara , Zhang Ling , Samaranayake Govindi , Sharma Nisha , Nguyen Dao , Tahara Yu-Ki , Kool Eric , Rai Priyamvada
Published: July 2021

Increased metabolic activity of cancer cells due to uncontrolled proliferation, often leads to the accumulation of reactive oxygen species (ROS). High ROS can produce tumor-suppressive oxidative DNA damage either directly in the genome or through oxidation of deoxynucleotides that can then be incorporated into DNA. The human 8-oxoguanine glycosylase 1 (OGG1), a base excision repair (BER) enzyme, protects cells from the former by excising genomic 8-oxodG; MutT Homolog 1 (MTH1), the mammalian 8-oxodGTPase, protects cells from the latter by degrading 8-oxo-dGTP. There has been much interest in increasing oxidative DNA damage in tumors as a therapeutic option. Accordingly, inhibitors are being developed that can target both MTH1 and 8-oxodG glycosylase 1 (OGG1) with the speculation that this co-targeting will significantly increase tumor suppression efficiency. Our lab has shown that MTH1 inhibition leads to DNA strand breaks and tumor-suppressive effects in cancers characterized by high MTH1enzymatic activity. Here we assessed whether co-inhibition of OGG1 would provide benefits in tumor-suppressive effects over MTH1 inhibition alone. We first compared OGG1 and MTH1 expression in paired normal versus tumor tissue from lung adenocarcinoma patients and found that, unlike MTH1, OGG1 tends to remain within normal range in cancerous tissue. Similarly, TCGA lung adenocarcinoma patients show minimal OGG1 elevations and a positive correlation between OGG1 and MTH1 mRNA levels even when both are low. This data suggests that tumors with low OGG1 and MTH1 are robustly represented in the tumor continuum. We then co-depleted OGG1/MTH1 in the A549 lung cancer cell line and found this co-depletion led to lower DNA strand breaks and decreased cell senescence over those caused by MTH1 depletion alone. The shMTH1-transduced cells were less sensitive to SU0268, a potent OGG1 inhibitor compared to shGFP-transduced counterparts. We also treated A549 cells with SU0383, a dual OGG1/MTH1 inhibitor. The dual-inhibitor did not consistently increase cytotoxicity either with duration or dose of treatment beyond single inhibitors or combined single MTH1 and OGG1 inhibitors. In conclusion, our findings suggest that the co-inhibition of OGG1 with MTH1 does not produce enhanced therapeutic benefit in tumor cells, and could instead diminish the tumor-inhibitory effects of MTH1 inhibition that arise from induction of DNA strand breaks and p53-induced senescence.

Citation Format: Laura Misiara Lincheta, Ling Zhang, Govindi Samaranayake, Nisha Sharma, Dao Nguyen, Yu-Ki Tahara, Eric Kool, Priyamvada Rai. Low OGG1 protects against the DNA damage induced by MTH1 inhibition [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 2076.
Abstract 2077: Activity of DHODH inhibitor BAY2402234 in subcutaneous and intracranial models of SCLC
Authors: Kaulfuss Stefan , Janzer Andreas , Siemeister Gerhard , Borowicz Renan , Jaensch Katrin , Gutberlet Katrin , Schlenz Ricarda , Triller Andrea , Eheim Ashley , Jeffers Michael , Christian Sven
Published: July 2021

Introduction: BAY2402234 is a potent and specific orally administered inhibitor of dihydroorotate dehydrogenase (DHODH) which showed anti-tumor activity in preclinical models of AML and is under clinical evaluation in myeloid malignancies (NCT03404726). Small cell lung cancer (SCLC) is a highly metastatic malignancy (the brain being a frequent metastatic site), which carries a dismal clinical prognosis. Previous preclinical research indicated that SCLC was particularly sensitive to DHODH inhibition, and in the current investigation the activity of BAY2402234 in this tumor indication was evaluated.

Experimental Procedures: A variety of in vivo models derived from human SCLC samples were evaluated: (1) cell-line derived xenograft (CDX) subcutaneous models; (2) a CDX intracranial model; and (3) patient-derived xenograft (PDX) subcutaneous models. As is typical for SCLC, most of these models harbored mutations in both p53 and Rb1. BAY2402234 was administered orally either once daily or on an intermittent schedule (4 days on/3 days off). Standard-of-care (SoC) therapies were included in some experiments. Tumor tissue and plasma were collected for pharmacodynamic analyses.

Results: In subcutaneous CDX models, BAY2402234 exhibited robust anti-tumor activity, including tumor regressions in some models. Strong anti-tumor activity was also observed in various subcutaneous PDX models, including activity in a model resistant to SoC therapy. In an intracranial tumor model, BAY2402234 significantly enhanced survival compared to the vehicle-treated cohort. Both dosing schedules tested were well-tolerated and highly active. Pharmacodynamic analyses to quantify the level of target inhibition observed in the various models are ongoing.

Conclusions: The results of this investigation confirm and extend previous preclinical results and indicate that BAY2402234 may represent a novel treatment for SCLC, including patients with brain metastases.

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Citation Format: Stefan Kaulfuss, Andreas Janzer, Gerhard Siemeister, Renan Borowicz, Katrin Jaensch, Katrin Gutberlet, Ricarda Schlenz, Andrea Triller, Ashley Eheim, Michael Jeffers, Sven Christian. Activity of DHODH inhibitor BAY2402234 in subcutaneous and intracranial models of SCLC [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 2077.
Abstract 2092: Effects of Yi Sui Granules, an herbal medicine, on MDS/AML: Similar to decitabine or other mechanisms
Authors: Wang Jing , Gao Chong , Gullen Elizabeth , Wu Jieya , Zhang Xiaoyuan , Chen Xinyi
Published: July 2021

Objective Yi Sui Granules (YSG) has been clinically used and proved efficacious in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) for 25 years, however, its mechanism remains unclear. This study is to evaluate the effects of YSG on DNA methylation of AML/MDS.

Methods and Results From cytotoxicity assays using CCK-8 method, we found out YSG inhibited SKM-1, HL-60, K-562 and CEM cells in a dose-dependent manner with an IC50 of 1.173±0.165 mg/ml, 1.70±0.2 mg/ml, 2.85±0.05 mg/ml, 1.70±0.2 mg/ml respectively. In vivo, decitabine inhibited tumor growth in terms of tumor volume and tumor weight but led to significant weight loss of SKM-1 xenographed BALB/c-nu mice. While YSG (50.69%) showed similar tumor weight inhibition rate to decitabine (56.64%) without side effects including body weight loss. To explore its mechanism, we discovered that DNA methyltransferase 1 (DNMT1) expression was significantly down-regulated(P<0.05) and SFRP5 gene was demethylated(P<0.01) after treated with either YSG or decitabine using RT-PCR, western blot and bisulfite amplicon sequencing methods. Furthermore, we found significant up-regulation of SFRP5 expression(P<0.05), down-regulation of Wnt3a protein(P<0.05) and β-catenin expression(P<0.05), as well as down-regulation of C-myc(P<0.05) and CyclinD1 expression(P<0.05) in decitabine group and YSG group. Equally interestingly, survival benefits were observed in YSG high-dose group but not in Decitabine group(P<0.05).

Conclusion Similar to decitabine, YSG's suppression of SKM1 tumor may be related to the inhibition of DNMT1 expression, de-methylation of SFRP5 and up-regulation of SFRP5 expression, preventing Wnt3a from binding to Frizzled receptors, therefore inhibiting the abnormal activation of Wnt signaling, and down-regulating its target gene expression including C-myc and CyclinD1. Unlike decitabine, YSG prolong overall survival though other mechanisms, which will be further investigated in our future research.

Corresponding Author: Jing Wang and Xinyi Chen, Address: No.5 Haiyuncang, Dongcheng District, Beijing, 100700, China; Email: Jing.Wang@bucm.edu.cn and chenxinyi0729@126.comAcknowledgement: This work was supported by the Young Scientist Fund (81503575) and Key Program (81630080) of National Natural Science Foundation of China, the Golden Bridge Project of Beijing Association for Science and Technology(ZZ20059) and the Elite Program of Dongcheng district of Beijing (2020-dchrcpyzz-38).

Citation Format: Jing Wang, Chong Gao, Elizabeth Gullen, Jieya Wu, Xiaoyuan Zhang, Xinyi Chen. Effects of Yi Sui Granules, an herbal medicine, on MDS/AML: Similar to decitabine or other mechanisms [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 2092.
Abstract 2096: Genome wide remodeling of DNA methylation and CpG hypermethylation is tightly linked to acquired resistance in testicular cancer
Authors: Fazal Zeeshan , Singh Ratnakar , Tomlin Megan , Shokry Doha , Hattab Aleyah , Spinella Sarah , Spinella Michael
Published: July 2021

Acquired resistance to chemotherapy is perhaps the major barrier to cure of advanced cancers. Testicular germ cell tumors (TGCTs) are the most common cancers of young males. TGCTs are one of the few solid tumors that are cured at a high rate with standard cisplatin-based chemotherapy. However, TGCTs become resistance to cisplatin resulting in poor outcomes. While the mechanisms accounting for cisplatin hypersensitivity in TGCT remain elusive, it has been suggested that DNA hypermethylation may play a role. However, there is little direct experimental evidence to support this claim. In the present study, we have leveraged unique isogenic cell models to provide strong evidence for net DNA hypermethylation as a key mechanism leading to acquired cisplatin resistance in TGCT cells. Genome-wide DNA methylation analysis revealed that hypomethylated CpG loci were enriched for SUZ12 and EZH2 binding and H3K27me3 sites. In contrast hypermethylated CpG loci were significantly enriched for CTCF and RAD21 domains as well as repressive DNA segments indicating the global remodeling of nuclear chromatin structure in resistant cells. Integrative computational analysis of RNA-seq and EPIC DNA methylation array data revealed a strong inverse correlation between gene expression and CpG gene promoter methylation. This analysis also revealed a strong bidirectional shift between gene promoter and gene body DNA methylation that correlated closely with upregulated expression of PRC2 target genes and down regulation of tumor suppression genes in resistant cells. Hence the data further suggests a functional interplay between DNA methylation and the PRC2 pathway that modulates cisplatin sensitivity of TGCTs. Further studies including H3K27me3 ChIP-seq are ongoing to further elucidate this relationship. In conclusion, our finding supports the hypothesis that genome wide remodeling of DNA methylation is associated with cisplatin hypersensitivity and resistance of TGCTs and further supports the use of hypomethylation therapy for relapsed TGCT patients.

Citation Format: Zeeshan Fazal, Ratnakar Singh, Megan Tomlin, Doha Shokry, Aleyah Hattab, Sarah Spinella, Michael Spinella. Genome wide remodeling of DNA methylation and CpG hypermethylation is tightly linked to acquired resistance in testicular 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 2096.
Abstract 2133: Systematic mapping of genetic interactions in human cancer cells reveals context dependent cancer signaling pathways
Authors: Fong Samson H. , Kuenzi Brent M. , Lee John , Sanchez Kyle , Bojorquez-Gomez Ana , Ford Kyle , Munson Brenton P. , Licon Katherine , Hager Jeff , Shen John Paul , Kreisberg Jason F. , Mali Prashant , Ideker Trey
Published: July 2021

Genetic interaction screens have long been used to map gene functions and cellular pathways in model organisms and more recently in human cells. However, due to the technical challenges of these maps, most studies in human cells have focused on a single cell line, limiting the ability to determine how different genetic and cellular contexts influence genetic interactions. Here, we engineered a 110,728-element combinatorial CRISPR-Cas9 library to systematically map 12,282 genetic interactions among tumor suppressor genes and druggable targets. We mapped the landscape of genetic interactions in cell lines from breast cancer, head and neck squamous carcinoma, and non-small cell lung cancer as well as in non-cancerous, epithelial cells. The resulting genetic interaction maps emphasize the context dependency of these interactions. Of the interactions that are conserved across multiple cell lines, many include frequently essential genes, suggesting that these interactions may be critical for fundamental cellular functions. We found that genetic interaction maps from cancer cell lines are more similar to one another than non-cancer interaction maps, even between cancer and normal cells from the same tissue. Subsequent targeted chemogenetic screens confirmed interaction hubs across multiple cell lines while highlighting the robustness of some of the strongest interactions. Many of the identified genetic interactions suggest therapeutic interventions, such as the combination of CDK4 and MAPK inhibitors. Using the tissue-specific genetic interaction networks, we also built a deep learning model that accurately predicts patient outcomes, outperforming models that use accepted biomarkers such as MammaPrint. In summary, these genetic interaction maps provide a broad resource to investigate context dependency in cancer signaling pathways and in cancer drug response.

Citation Format: Samson H. Fong, Brent M. Kuenzi, John Lee, Kyle Sanchez, Ana Bojorquez-Gomez, Kyle Ford, Brenton P. Munson, Katherine Licon, Jeff Hager, John Paul Shen, Jason F. Kreisberg, Prashant Mali, Trey Ideker. Systematic mapping of genetic interactions in human cancer cells reveals context dependent cancer signaling pathways [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 2133.
Abstract 216: Functional annotations of membrane transport genes using genetic perturbation screens
Authors: Sailem Heba
Published: July 2021

Dysregulation of membrane transport and ion channels genes have been associated with through their role in cellular communication, regulation of cell size through osmoregulation and inflammation. However, a systematic profiling of the biological functions that are affected downstream of ion channels is not well studied due to challenges in monitoring their activity. Depleting known ligand-gated and voltage-gated ion channels has been shown to have a distinct phenotypic signature in HCT116 colorectal cells which is associated with their size and collective arrangement. These results were based on data from a genome-wide image-based siRNA screen where more than 500 million cells were segmented, and their shape and organisation were quantified. Single cells data were aggregated for each gene to capture cell heterogeneity and partial penetrance effects resulting in more than 1700 features per gene. Predictions of multiple functions for each gene were generated using KCML, a machine learning platform that automatically links gene perturbation phenotypes to molecular and biological function.

Here we analysed the predicted functions for known ligand-gated and voltage-gated ion channel genes using KCML. Top predicted functions included ubiquitin protein ligase activity, phosphatase activity, stress-activated protein kinase signalling cascade, positive regulation of inflammatory response and cellular response to starvation. To validate these predictions, we applied KCML to independent genome-wide CRISPR screens measuring cell viability in 60 cancer cell lines from different tissue types. We focused on the functional association between ion channels and inflammatory response which is well recognised. We confirmed the prediction of 62/86 ion channel genes role in positive regulation of inflammatory response based on viability phenotypes. Many of these genes are documented to play a role in inflammation but has not annotated with inflammatory function in the gene ontology including GAS1, CHRNA2, and TMEM37. Pathway analysis revealed that seven of these genes are associated with gastric acid secretion (p-value =3.4E-5) including KCNQ1 gene that its loss that has been linked to the expression of inflammatory genes in colon cancer and worse patient outcomes. These results show that a comprehensive analysis of gene perturbation screens utilising siRNA or CRISPR technologies allows functional annotation of different roles for known ion channel genes. In particular, we identify 62 ion channel genes to be associated with inflammation and therefore would be promising therapeutic targets in colorectal cancer.

Citation Format: Heba Sailem. Functional annotations of membrane transport genes using genetic perturbation screens [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 216.
Abstract 2160: Tumor suppressor p53 down-regulates programmed cell death protein 4 (PDCD4) expression
Authors: Yang Wei-Hsiung , George Andrew P. , Yang William H. , Wang Chiung-Min , Yang Richard H.
Published: July 2021

Programmed Cell Death Protein 4 (PDCD4), a well-known tumor suppressor, acts to inhibit translation initiation and cap-dependent translation by inhibiting the helicase activity of EIF4A. EIF4A tends to target mRNAs with structured 5'-UTR. PDCD4 can also prevent tumorigenesis by inhibiting tumor promoter-induced neoplastic transformation, and studies indicate that PDCD4 may inhibit translation of certain mRNAs via directly binding. A previous study has demonstrated that PDCD4 inhibits translation of p53 mRNA and treatment with DNA-damaging agents down-regulates PDCD4 expression but activates p53 expression. The study further demonstrated that treatment with DNA-damaging agents resulted in down-regulation of PDCD4 expression and an increase in p53 expression, suggesting a potential mechanism in which p53 regulates expression of Pdcd4. However, whether p53 directly regulates PDCD4 remains unknown. Herein, we demonstrate for the first time that p53 regulates PDCD4 expression. First, we found that overexpression of p53 in p53-null cells (H1299 and Saos2 cells) decreased PDCD4 protein level. Secondly, p53 dose-dependently decreased PDCD4 promoter activity in gene reporter assays. Moreover, we demonstrated that mutations on p53 (R273H: contact mutant, hotspot and R175H: conformational mutant, hotspot) abolished p53-mediated PDCD4 repression. Furthermore, using Tet-on expression system, PDCD4 protein level was decreased when WT p53, but not hotspot mutants of p53, was expressed in H1299 cells. Finally, mutations on DNA-binding domain, but not C-terminal regulatory domain, of p53 disrupted p53-mediated PDCD4 repression. Taken together, our results suggest that p53 functions as a novel regulator of PDCD4 and the relationship between of p53 and PDCD4 may be involved in tumor development and progression.

Citation Format: Wei-Hsiung Yang, Andrew P. George, William H. Yang, Chiung-Min Wang, Richard H. Yang. Tumor suppressor p53 down-regulates programmed cell death protein 4 (PDCD4) expression [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 2160.
Abstract 2166: The prevalence and molecular characteristics of EGFRlarge fragment deletion in Asian cancer population by comprehensive genome profiling
Authors: Yu Ruoying , Ou Qiuxiang , Bao Hua , Wu Xue , Shao Yang
Published: July 2021

Background: Large fragment deletion(LFD) of EGFR was associated with carcinogenesis in many types of cancers, especially in glioblastoma. Overall, there are five major types of EGFR large fragment deletion across EGFR extracellular region and carboxyl terminal domain which were originally discovered in gliomas. The prevalence and molecular feature of EGFR-LFD have not been studied in Asian Cancer population.

Method: We retrospectively reviewed records of 66,500 Asian cancer patients who underwent genetic testing using capture-based targeted NGS between January 2014 to May 2020 at hospitals across China. Five to ten mL peripheral blood was collected from each patient in EDTA-coated tubes. Plasma was extracted within 2 hours of blood collection and shipped to the central testing laboratory. Formalin-fixed paraffin-embedded (FFPE) tumor tissue blocks/sections or fresh tumor tissues were obtained from the hospitals, with confirmation by the pathologists for diagnosis and tumor purity. Mean sequencing depths of tumor tissue and plasma were 500X and 3000X respectively.

Result: Our finding showed that EGFR-LFD was detected at a frequency of 0.03%, of which the most frequent was EGFRvIII in glioblastoma. In this EGFR-LFD cohort, there were 9 males(53%), 7 females(41%) and one unknown sex type with a median age of 54 years old, ranging from 42 to 85 years old. Interestingly, novel EGFR-LFDs spanning exon2-7 were identified in unreported cancer type including deletions of EGFR exon2-11(1case, lung cancer), exon2-15(1case, lung cancer), exon2-17(2 cases, lung cancer and colorectal cancer), exon2-28(1 case, cholangiocarcinoma). TERT promoter(TERTp) variants(60%) showed highest frequency in EGFR-LFD carriers, consisting of 6 cases of −124C>T and 2cases of −146C>T in glioblastoma(7) and melanoma(1). Concurrent EGFR amplification was identified in 67% of EGF-LFD cohort including glioblastoma(6), colorectal cancer(3), unknown(1). Over half of EGFR-LFD carriers harbored deletion on both arms of chromosome 10.

Conclusion: Our study provided valuable insights into the distribution and molecular characteristics of EGFR-LFD by employing a large Asian Cancer cohort, hoping to shed lights on the treatment management for Asian EGFR-LFD carriers.

Citation Format: Ruoying Yu, Qiuxiang Ou, Hua Bao, Xue Wu, Yang Shao. The prevalence and molecular characteristics of EGFRlarge fragment deletion in Asian cancer population by comprehensive genome profiling [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 2166.
Abstract 217: Mutations in iron-sulfur cluster proteins are associated with decreased bladder cancer cell senescence and improved survival outcomes
Authors: Patel Devin , Zheng Fan , Chen Michael , Kreisberg Jason , Silva Erica , Ideker Trey , Licon Kate
Published: July 2021

Recent tumor genome analyses have cataloged hundreds of mutated genes, including a large population of rarely mutated genes with ill-defined roles in cancer. Here we find that, when considering the 10 genes of the iron-sulfur (Fe-S) pathway as an integrated whole, somatic mutations occur with a higher than expected frequency in 21.3% of bladder tumors. Mutations in these genes are associated with increased survival and mutational burden. Analysis of tumor gene expression highlights a relationship between these Fe-S mutations and signalling regulating proliferation and quiescence, with mutations promoting proliferative programs and abolishing maintenance of quiescence. In bladder tumor cells, we show that replication of this proliferative program, using an DYRK1A kinase inhibitor, promotes sensitivity to genotoxic agents. Furthermore, disruption of Fe-S genes ERCC2, MMS19, CIOA1, BRIP1 or POLD1 promotes cell proliferation and concomitant sensitivity to genotoxic agents. These results suggest a model in which Fe-S pathway mutations are selected due to their ability to bypass DNA damage checkpoints and drive proliferation, an aspect which simultaneously creates vulnerability to chemotherapy and resultant improvements in survival.

Citation Format: Devin Patel, Fan Zheng, Michael Chen, Jason Kreisberg, Erica Silva, Trey Ideker, Kate Licon. Mutations in iron-sulfur cluster proteins are associated with decreased bladder cancer cell senescence and improved survival 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 217.
Abstract 2184: Gene characteristics of Chinese patients with small bowel cancer
Authors: Zhao Quan , Zhang Hushan , Lei Zhuyun , Sheng Jianing , Xiong Dun
Published: July 2021

Background: Small bowel cancer is a rare malignancy which account for only 1-3% of all malignant gastrointestinal tumors. Herein, we aim to provide an overview of gene characteristics of Chinese patients with small bowel cancer based on the location of the tumor in the small bowel.

Methods: Tumor samples of 324 Chinese patients with small bowel cancer were consecutively collected in China from February 2018 to May 2020, among them, 289 patients with cancer located in duodenum (group 1), 35 patients with cancer located in the other region of small bowel (group 2). Next generation sequencing (NGS) was performed to detect gene mutation, microsatellite instability (MSI), and tumor mutational burden (TMB) measured by a 733 gene panel by 3D Medicines, a laboratory accredited by College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA).

Results: NGS results revealed that the main mutated genes were different between two groups, in detail, the top ten gene mutation in group 1 were TP53 (51.4%,18/35), KRAS (45.7%, 16/35), APC (34.3%, 12/35), POLE (20.0%,7/35), PIK3CA/POLD1/MSH2 (17.1%,6/35), mTOR/PRSS1/LPR1B/BRCA1/SMAD4 (14.3%,5/35). While top ten gene mutation in group 2 were TP53 (66.4%,192/289), KRAS (49.8%, 144/289), ERCC1 (38.8%, 112/289), UGT1A1 (31.5%, 91/289), APC (29.4%, 85/289), BRCA1 (28.7%,83/289), AKT2 (27.3%, 79/289).In addition, TMB level and percentage of MSI-H were also compared between the two groups. 12 patients were available for TMB analysis in group 1, 59 for group 2, the average TMB level in two groups were 23.84 mutants/Mb and 7.8 mutants/Mb, respectively. 50%(6/12) and 11.8%(7/59) were under 10 mutants/Mb in two groups. What's more, the percentage of MSI-H in two groups were 16.7% (5/30) and 3.2% (8/243).

Conclusion: Patients with cancer located in duodenum patients with cancer located in the other region of small bowel displayed obvious difference in gene landscape, this imply that these patients should be treated differently.

Citation Format: Quan Zhao, Hushan Zhang, Zhuyun Lei, Jianing Sheng, Dun Xiong. Gene characteristics of Chinese patients with small bowel 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 2184.
Abstract 2192: Transcriptomic classification of renal cancer: a machine learning approach
Authors: Satter Khaled Bin , Tran Paul MH , Purohit Sharad B. , She Jin-Xiong
Published: July 2021

Introduction: Accurate diagnosis is essential for cancer treatment. Sometimes, it is difficult to confirm histological diagnosis due to inadequate tissue sample or preparation. Using molecular markers for classification would be ideal in such cases. For renal cell carcinoma(RCC), we developed a molecular classification based on transcriptomics to address these issues and aid current diagnostic workflow.

Method: We obtained transcriptomic and phenotype data of renal cell carcinoma from The cancer genome atlas (TCGA) data repository. We developed an unsupervised algorithm, Density-based UMAP, based on two clustering methods, UMAP (Uniform manifold approximation and projection) and DBScan (Density-based spatial clustering of applications with noise). We iterated this algorithm 1000 times with random 1000 genes each time and classified each sample in each iteration. We used plurality voting of at least 70% of the iterations for consensus groups. The algorithm was able to identify all the major histological subtypes. We ran a differential expression analysis for each group. Finally, we developed a classification gene signature and a supervised algorithm to classify subtypes with fewer genes and implement this signature in an RCC metanalysis.

Results: Density-based UMAP Algorithm classified the samples with 91.4% concordance with WHO 2016 classification. Among the discrepant cases, 4.4 % cases (46) were not diagnosed the same as their histological classification. 4.2 % (44) cases were shown a mixed expression profile. These cases are of further interest as they might respond better with a different treatment. Based on molecular characteristics they share with major subtypes, they are named ClCh, Clear 2, and Clear 3. ClCh and Clear 2 have shown to be indolent and, Clear 3 has shown to be very aggressive. We manually curated 328 genes for supervised learning from differential expression analysis between the groups and able to identify the groups in a metanalysis.

Conclusion: Transcriptomic profiling is fast, robust and, simple. It can help in diagnosing histologically discrepant cases. This classifier would be a good edition in renal cancer diagnostic workflow and can complement current diagnostic guidelines for renal cancer.

Citation Format: Khaled Bin Satter, Paul MH Tran, Sharad B. Purohit, Jin-Xiong She. Transcriptomic classification of renal cancer: a machine learning approach [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 2192.
Abstract 2194: Comparison of molecular profiling between Chinese cholangiocarcinoma and gallbladder cancer through next-generation sequencing
Authors: Yu Chao , Zhang Hushan , Luo Jun , Zhao Songling
Published: July 2021

Background: Recently, some researchers proposed that molecular targeted therapies is ready for “prime time” in biliary tract cancer. However, few large-scale research data specifically analyze and compare the molecular characteristics of biliary tumors in the Chinese population. Here, we aim to report difference of molecular profiling of biliary tract cancers between Chinese cholangiocarcinoma (CCA) and gallbladder cancer (GCC) through next-generation sequencing, and summarize percentage of main targetable genetic alterations for CCA and GBC.

Methods: Totally 1439 tumor sample of Chinese patient with biliary tract cancer were consecutively collected in China from January 2018 to July 2020, 907 patients were CCA, 532 were GCC. Gene mutation, microsatellite instability (MSI) were detected through next generation sequencing (NGS) by 3D Medicines, a laboratory accredited by College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA).

Results: The main mutational gene between CCA and GCC were compared, and results showed that the top ten gene mutation in CCA patients were TP53 (57.6%,522/907), KRAS (35.2%, 320/907), XRCC5 (27.7%, 251/907), CYP2D6 (26.8%,243/907), MDM2 (26.0%,236/907), MSH2 (25.7%,233/907), BLM/VEGFA (24.9%,226/907), POLD (24.7%,224/907), PRSS1 (23.6%,214/907), ATM (23.3%, 212/907). While top ten gene mutation in GCC group were TP53 (76.3%,406/532), MSH2 (43.0%,229/532), CYP2D6 (30.4%, 162/532), MDM2 (28.8%,153/532), VEGFA (27.6%,147/532), POLD1 (27.4%, 146/532), BLM (27.4%,146/532), ATM (25.6%,136/532), PRSS1 (25.2%,134/532), PRKDC (24.8%,132/532). In addition, percentage of the main targetable genetic alterations were also compared between CCA and GCC, such as IDH (5.7% vs 0.9%), FGFR (10.2% vs 10.7%), BRAF (5.1% vs 4.3%), PIK3CA (9.9% vs 14.8%), NTRK (7.4% vs 8.3%), ERBB2/3 (11.8% vs 24.8%), CDKN2A/2B(18.5% vs 23.9%), ARID1A(17.3% vs 17.7&), PTEN (10.3% vs 13.9%), MET (6.3% vs 7.3%), SMAD4 (14.6% vs 14.5%).

Conclusion: Accurately understand the gene mutation characteristics of biliary tract tumors is required to make “Precision Medicine” a reality for the “majority” of patients diagnosed with biliary tract cancer. Chinese patients with CCA and GCC have different gene mutations, especially the proportion of mutant genes that are currently targetable. Therefore, different strategy should be performed for CCA and GCC patients.

Citation Format: Chao Yu, Hushan Zhang, Jun Luo, Songling Zhao. Comparison of molecular profiling between Chinese cholangiocarcinoma and gallbladder cancer through next-generation sequencing [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 2194.
Abstract 2202: Genetic characterization of metastasis and prognosis in high-grade serous ovarian cancer
Authors: Kotnik Emilee N. , Spies Nicholas C. , Li Tiandao , Inkman Matthew , Zhang Jin , Martins-Rodrigues Fernanda , Hagemann Ian S. , McCourt Carolyn K. , Thaker Premal H. , Hagemann Andrea R. , Powell Matthew A. , Mutch David G. , Maher Christopher A. , Miller Christopher A. , Fuh Katherine C.
Published: July 2021

High-grade serous ovarian cancer (HGSC) is the most lethal histotype of ovarian cancer and is highly prone to metastasis, with the majority of patients presenting at advanced stages of disease. There are few targeted treatment options for HGSC patients, especially for women with high metastatic tumor burdens. In order to identify potential genetic targets in metastatic disease, we characterized the genomic and transcriptomic alterations of metastatic tumors in HGSC patients. In this study, matched normal tissue, primary, and metastatic tumors from 23 HGSC short-term (ST) survivors (overall survival [OS] <3.5 years) and 14 long-term (LT) survivors (OS >5 years) underwent whole exome and RNA sequencing. We compared somatic mutations, copy number alternations, mutational burdens, differential expression, immune cell fractions, and gene fusion predictions between the primary and metastatic tumors of the ST and LT survival groups.

We confirmed that tumors of LT survivors were more likely to have BRCA1 alterations and more copy-altered segments when compared to tumors of ST survivors. There was a higher percentage of shared variants between the primary and metastatic tumors for ST survivors compared to LT survivors. ST survivors also had a greater mutational burden and more predicted gene fusions than LT. We observed few differentially expressed genes between primary and metastatic tumors, but we did observe significant differences between the transcriptomes of LT and ST survivors' tumors. Overall, we observed that HGSC primary and metastatic tumors had similar genomic and transcriptomic landscapes, but we identified genetic characteristics specific to metastatic tumors that correlate with survival.

Citation Format: Emilee N. Kotnik, Nicholas C. Spies, Tiandao Li, Matthew Inkman, Jin Zhang, Fernanda Martins-Rodrigues, Ian S. Hagemann, Carolyn K. McCourt, Premal H. Thaker, Andrea R. Hagemann, Matthew A. Powell, David G. Mutch, Christopher A. Maher, Christopher A. Miller, Katherine C. Fuh. Genetic characterization of metastasis and prognosis in high-grade serous ovarian 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 2202.
Abstract 2207: Genomic associations of biological sex and survival in head and neck squamous cell carcinoma
Authors: Yao Alexandria G. , Mezghani Nadia , Taylor Alison M. , Momen-Heravi Fatemeh
Published: July 2021

Approximately half of all head and neck squamous cell carcinoma patients die within five years of diagnosis despite treatment. Recent studies revealed that females have a worse overall prognosis; however, the genetic and molecular underpinnings have not yet been identified. We investigated the genetic characteristics of head and neck squamous cell carcinomas stratified by HPV status and biological sex. Within the HPV-negative cohort, female patients have worse survival outcomes compared to male patients, although tumors in female patients show lower levels of aneuploidy alterations and copy number changes. Specifically, chromosomes 4, 5, 6, and 20 were amplified at higher frequency in the tumors of male patients compared to female patients. Analysis of mRNA expression found that genes most highly expressed in females compared to males included sex-chromosome genes XIST and TISX. Interestingly, along with y chromosome gene PRKY, Notch signaling gene HES7 was also up-regulated in the tumors of male patients. In addition, tumors of female patients showed higher expression of immune pathway genes, even when potential confounding factors of age and tumor location are considered. This study provides new insight into possible gene expression biomarkers for HNSCC in female patients. Future research will incorporate these findings to better assess therapeutic response in women with HNSCC.

Citation Format: Alexandria G. Yao, Nadia Mezghani, Alison M. Taylor, Fatemeh Momen-Heravi. Genomic associations of biological sex and survival in head and neck squamous cell carcinoma [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 2207.