bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2301: Atomic-level insights into PI3K activation
Authors: Zhang Mingzhen , Jang Hyunbum , Nussinov Ruth
Published: July 2021

PI3Kα (PIK3CA) is the second highly mutated oncogene in cancer. It is activated by the receptor tyrosine kinases (RTKs) and Ras on the membrane, regulating the PI3K/Akt/mTOR pathway for the cell growth and proliferation. PI3Kα is an obligate dimer with p110α catalytic subunit and p85α regulatory subunit. Their interactions stabilize and maintain PI3Kα in the inactive state. At the molecular level, the activation of PI3Kα requires two events, (i) the release of nSH2 by phosphorylated tyrosine (pY) motif in the RTK and (ii) the membrane localization facilitated by Ras. The mechanism of PI3Kα activation at the atomic level suggests that PI3Kα undergoes the significant conformational change upon nSH2 release. The iSH2 in p85α subunit moves, which facilitates the membrane interactions and catalysis. The activation loop (a-loop) in the kinase domain becomes more flexible, exposing the basic residues for the substrate binding. The activation mechanism expedites our understanding of the PI3K autoinhibition, activation, and catalysis. By collecting and analyzing the available PI3K structures, we have identified the structural features that distinguish the inactive and active class IA PI3Ks. The a-loop is “collapsed” with kα11 in the regulatory arch “IN” in the inactive PI3Ks. Upon activation, the a-loop becomes “extended” and kα11 moves “OUT”. These features provide the functional explanations for both hotspot and weak oncogenic mutations and indicate their additive effects. The mechanism reveals a principle for PI3K allosteric drug discovery. The inhibitors that may modulate the iSH2 dynamics can allosterically prevent PI3K activation in the signaling pathways. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261200800001E.

Citation Format: Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov. Atomic-level insights into PI3K activation [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 2301.
Abstract 2308: The protein interaction landscape of breast cancer
Authors: Kim Minkyu , Park Jisoo , Bouhaddou Mehdi , Kim Kyumin , Rojc Ajda , Modak Maya , Soucheray Margaret , O'Leary Patrick , Wolf Denise , Mitchell Dominique C. , Zheng Fan , Gordan John D. , Coppé Jean-Philippe , Swaney Danielle L. , van' t Veer Laura , Ashworth Alan , Ideker Trey , Krogan Nevan J.
Published: July 2021

Cancers have been associated with a diverse array of genomic alterations, many of which are rare with unknown significance. To understand the cellular mechanisms impacted by such alterations in breast invasive carcinoma, we have applied affinity-purification mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer proteins across three human breast cell lines, providing a novel resource of context-specific and shared protein-protein interaction networks in breast cancer cells. These networks interconnect and enrich for common and rare cancer mutations, and are substantially rewired by mutations. Our analysis identifies novel PIK3CA-interacting proteins which repress AKT signaling, and UBE2N emerges as a BRCA1 interactor predictive of clinical response to PARP inhibition. We also show that Spinophilin interacts with and dephosphorylates BRCA1 to promote DNA double-strand break repair. Thus, cancer protein interaction landscapes provide a framework for recognizing oncogenic drivers and drug vulnerabilities.

Citation Format: Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Patrick O'Leary, Denise Wolf, Dominique C. Mitchell, Fan Zheng, John D. Gordan, Jean-Philippe Coppé, Danielle L. Swaney, Laura van' t Veer, Alan Ashworth, Trey Ideker, Nevan J. Krogan. The protein interaction landscape of 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 2308.
Abstract 2313: The characteristics of ERBB2 exon 20 insertion in a large cohort of Chinese NSCLC patients
Authors: Wang Danhua , Yuan Hongling , Zhu Honglin
Published: July 2021

Background: ERBB2 mutations, especially exon 20 insertion (ERBB2ex20ins) had been extensively reported in NSCLC as classical driver factors. Previous researches indicate that NSCLC pts with ERBB2ex20ins are drug-resistant to afatinib, gefitinib and erlotinib. Up to now, approvals of targeted therapy of ERBB2ex20ins are still in process. Therefore, the objective of this study is to discover the features of ERBB2ex20ins in Chinese NSCLC patients, which could lead to more effective and personalized diagnosis and treatment.

Methods: 20656 Chinese NSCLC cases who had undergone molecular profiling at a Clinical Laboratory Improvement Amendments (CLIA) certified genomics laboratory in China between January 2017 to May 2020 were screened for our study. Some patients' clinical characteristics and treatment history were retrieved from the database for further evaluation.

Results: 11492 males and 9134 females were included in our cohort. ERBB2 gene mutation rate was 5.94% (1226/20656). Among them, 290 patients (1.4%), including 114 males and 176 females, harbored with ERBB2ex20ins, which include with p. Tyr772_Ala775dup (84.56%), p.Gly778_Pro780dup (10.74%), p.Ala775_Gly776insLeu(1.01%), p.Ala775_Gly776insVal(1.01%) and others(2.68%). Additionally, ERBB2ex20ins occurred more frequently in female patients (61% vs 39%, p<0.005, fisher exact test), and had a relatively young age (p<0.005, wilcoxon test) compared with others. Moreover co-variations of 290 pts are occurring with EGFR(4, 1.38%), KRAS(3, 1.03%), TP53(156, 53.79%), ERBB2 amp(21, 7.24%), MET amp (2, 0.69%), ALK amp (1, 0.34%) and RET fusion (1, 0.34%). Besides, a relatively lower TMB (p<0.005, wilcoxon test) is shown on the patients with ERBB2ex20ins. We followed up 5 patients with ERBB2ex20ins mutations, who were all insensitive to traditional radiotherapy and chemotherapy and had poor prognosis with short PFS (1.5-12.4 months) and short OS (3.9-13.7 months).

Conclusion: Our results showed that the ERBB2ex20ins mutation tended to occur in younger, female patients. Additionally, ERBB2ex20ins mutated samples exhibited lower levels of TMB compared to wildtype tumors, which may not benefit from anti-PD1 treatment. We also found patients with ERBB2ex20ins mutation have been associated with short PFS and short OS. The detail mechanism of resistance and appropriate therapeutic strategies remain to be further study.

Citation Format: Danhua Wang, Hongling Yuan, Honglin Zhu. The characteristics of ERBB2 exon 20 insertion in a large cohort of Chinese NSCLC 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 2313.
Abstract 2316: Analysis of APC-1B promoter region responsible for familial adenomatous polyposis
Authors: Nakagawa Saya , Yamaguchi Kiyoshi , Saito Kimiko , Takane Kiyoko , Ikenoue Tsuneo , Furukawa Yoichi
Published: July 2021

APC (APC regulator of WNT signaling pathway) is not only a gene responsible for familial adenomatous polyposis (FAP), a hereditary disease characterized by hundreds or thousands adenomatous polyps in the colon, but also plays a crucial role in sporadic human cancers. Although most of FAP cases are caused by germline mutations in the coding region of APC, deletions or point mutations in the promoter regions are involved in a limited number of cases. Previously, we reported an FAP case with a large deletion of approximately 10 kb encompassing APC promoter 1B and exon1B of the APC gene. Since precise regulatory mechanism(s) of the transcription of APC remains to be clarified, we searched in this study the regulatory domain(s) in the deleted region. First, we performed cap analysis of gene expression (CAGE) analysis, and compared the amount of APC-1A and APC-1B transcripts in the peripheral blood cells of the patient with that of healthy volunteers. As a result, we found that the deletion decreased the amount of APC-1B to 39% - 45% in the patient compared to the healthy controls, and that it did not change the amount of APC-1A in the patient. In addition, an allele-specific expression analysis by deep cDNA sequencing revealed that the amount of APC transcripts from the mutated APC allele is reduced to 11.2% by the deletion in the patient, suggesting that the deletion resulted in the marked decrease of the transcription of the affected allele and that the remaining expression of deleted allele may be driven by other regulatory region(s) such as promoter 1A. Consistently, CAGE analysis demonstrated that APC-1B transcripts are more abundantly expressed than APC-1A transcripts in all tissues tested except for the brain, suggesting that promoter 1B plays a crucial role in the expression of APC transcription. Analysis of promoter 1B by reporter assay identified a critical region for the transcriptional activation between -117 bp and -49 bp of promoter 1B. These data will contribute to the better understanding of regulatory mechanisms of APC transcription and the evaluation of genetic variants located in promoter 1B.

Citation Format: Saya Nakagawa, Kiyoshi Yamaguchi, Kimiko Saito, Kiyoko Takane, Tsuneo Ikenoue, Yoichi Furukawa. Analysis of APC-1B promoter region responsible for familial adenomatous polyposis [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 2316.
Abstract 232: The abscopal effect: modelling and predicting the effect of radiation therapy on non-irradiated tumour when combined with immune checkpoint blockers
Authors: Brightman Frances , Ortega Fernando , Orrell David , Chassagnole Christophe
Published: July 2021

We have developed preclinical and clinical ‘Virtual Tumour' (‘VT') models that can predict how a tumour will respond to drug exposure. This agent-based method is particularly suitable for modelling not only tumour cells, but also those involved in the immune response, and interactions between cells (1-3). The purpose of the study was to extend the VT platform to be able to model simultaneously i) the response of a tumour treated with radiation only or in combination with immune-checkpoint blockers, ii) the tumour response in areas where radiation has not been performed in the absence/presence of an immune-checkpoint blocker. Building on previous work, in which the VT platform was extended by the addition of a module that captures the synergistic of PD(L)-1 blockade with conventional anticancer therapies, we have further expanded the model to integrate the immune-checkpoint blocker module with other immune species activated by irradiation of the target tumour - in particular circulating CD8+ T cells - in order to be able to mimic the systemic abscopal effect. Ultimately, this expansion enables us to simulate the effect of tumour growth control on out-of-field tumour lesions when delivered in combination with an immune-checkpoint blocker. Through preclinical case studies derived from the literature (4) we demonstrate that the extended VT can be applied to simulate the efficacy of diverse radiation regimens in combination with immune-checkpoint blockers, and correctly describe the combination treatment effect on the progression of irradiated and non-irradiated tumours. Furthermore, we demonstrate that the model can be applied to optimize the timing of the combination in order to maximize the systemic efficacy of the treatment. Our enhanced VT capability represents a key step towards a strategic tool for optimizing dosing and scheduling of immune-checkpoint block and radiation combinations. [1] Brightman, FA et al., Abstract 680. Cancer Res 75, 4866-66 (2015). [2] Ortega, F et al., Abstract 4866. Cancer Res 79, (13 Suppl) (2019). [3] Orrell, DA et al., Abstract 4918. Cancer Res 71, (8 Suppl) (2011). [4] Dovedi, S et al., Clin Cancer Res 23(18); 5514-26 (2017).

Citation Format: Frances Brightman, Fernando Ortega, David Orrell, Christophe Chassagnole. The abscopal effect: modelling and predicting the effect of radiation therapy on non-irradiated tumour when combined with immune checkpoint blockers [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 232.
Abstract 2321: Comprehensive metabolic profiling of high MYC medulloblastoma revealed key differences between in vitro and in vivo in glucose and glutamine usage
Authors: Pham Khoa Dang , Poore Bradley , Hanaford Allison , Maxwell Micah J. , Sweeney Heather , Parthasarathy Akhila , Alt Jesse , Rais Rana , Slusher Barbara S. , Eberhart Charles G. , Raabe Eric H.
Published: July 2021

Medulloblastoma is the most common malignant brain tumor of children. Genomic amplification of MYC is a hallmark of a subset of poor-prognosis medulloblastoma. In other cancers, high-level expression of MYC increase glutamine transport and fuels the TCA cycle, supporting cell growth and proliferation. However, the metabolism of high MYC amplified medulloblastoma subgroup remains underexplored. We performed comprehensive metabolic studies of xenografts of human MYC-amplified medulloblastoma tumors. We found that glucose was the main carbon source for TCA cycle. We also found that glutaminase ii pathway was the main pathway utilizing glutamine. In orthotopic xenografts, glutathione was the most abundant upregulated metabolite in tumor compared to normal brain. Glutamine derived glutathione was synthesized through glutamine transaminase K (GTK) enzyme in vivo, and it was significantly inhibited by glutamine analog 6-diazo-5-oxo-l-norleucine (DON). We engineered a DON prodrug with higher lipophilicity (JHU395) and found that JHU395 suppressed medulloblastoma growth in vitro and induced apoptosis. A single dose of JHU395 induced apoptosis in orthotopic D425 MED tumors but not in normal cerebellum or cortex. Twice weekly 15mg/kg dosing of JHU395 significantly extended the survival of the mice with D425 MED orthotopic xenografts (p<0.001 by log-rank test comparing treated vs vehicle control). Glutamine antagonists exploit MYC-amplified medulloblastoma's reliance on glutamine metabolism and may have therapeutic applications in human patients.

Citation Format: Khoa Dang Pham, Bradley Poore, Allison Hanaford, Micah J. Maxwell, Heather Sweeney, Akhila Parthasarathy, Jesse Alt, Rana Rais, Barbara S. Slusher, Charles G. Eberhart, Eric H. Raabe. Comprehensive metabolic profiling of high MYC medulloblastoma revealed key differences between in vitro and in vivo in glucose and glutamine usage [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 2321.
Abstract 2325: Hypoxia-mediated ATF4 induction promotes survival in detached conditions in metastatic murine mammary cancer cells
Authors: Kiesel Violet A. , Hursting Stephen D. , Teegarden Dorothy
Published: July 2021

Regions of hypoxia are common in solid tumors and drive changes in gene expression that increase risk of cancer metastasis. Tumor cells must respond to the stress of hypoxia by activating genes to modify cell metabolism and antioxidant response to improve survival. The goal of the current studies was to determine the effect of hypoxia on cell metabolism and markers of oxidative stress in non-metastatic M-Wnt compared to metastatic metM-Wntlung murine mammary cancer cell lines. We show that hypoxia increased expression of genes involved in antioxidant response in metastatic compared to non-metastatic cells, including glutamate cysteine ligase catalytic and modifier subunits and malic enzyme 1. Further, hypoxia induces a greater suppression of glutamine to glutamate conversion in metastatic cells (15% in metastatic cells compared to 9% in non-metastatic cells). Interestingly, hypoxia increased the mRNA level of the transaminase glutamic pyruvic transaminase 2 (Gpt2, 7.7-fold) only in metM-Wntlung cells. The change in Gpt2 expression was accompanied by transcriptional (4.2-fold) and translational (6.5-fold) induction of the integrated stress response effector protein activating transcription factor 4 (ATF4), which mediated survival of hypoxic metastatic cells in detached conditions, as shown by genetic ATF4 depletion. These data indicate that more aggressive, metastatic cancer cells rely on metabolic reprogramming and induction of antioxidant defense, including activation of ATF4, in hypoxia for survival in detached conditions.

Citation Format: Violet A. Kiesel, Stephen D. Hursting, Dorothy Teegarden. Hypoxia-mediated ATF4 induction promotes survival in detached conditions in metastatic murine mammary cancer 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 2325.
Abstract 2331: Metabolic evasion of mCRPC immunotherapy by ACOD1 production of itaconate
Authors: Schofield James H. , Hawk Mark A. , Rahmy Sharif , Sheldon Ryan D. , Leimbach Casey , Sun Seunghoon , Lu Xin , Jones Russell G. , Schafer Zachary T.
Published: July 2021

The use of immune checkpoint blockade (ICB) therapies in the form of αPD-1 & αCTLA-4 monoclonal antibodies (mAb) have made great strides in the battle against melanoma, lung, and breast cancers. However, these strategies are not universally effective. Roadblocks occur as certain cancers cannot be targeted by these therapies or may develop resistance to ICB. How resistance to ICB therapy arises represents a crucial barrier to more effective use of these therapies. Recent studies have demonstrated that the metabolic milieu of the tumor microenvironment (TME) plays a role in regulating the anti-tumor immune response. However, the specific mechanisms by which cancer cell secreted metabolites in the TME impact the responsiveness of cancer cells to ICB remain poorly understood. In order to better understand the factors that influence the effectiveness of ICB, we utilized a mouse model (Smad4-/-/Pten-/-/Trp53-/-) of male castration resistant prostate cancer (mCRPC) that is responsive to αCTLA-4 and αPD-1 ICB. Using serial culture and injection of residual tumor cells that survive ICB, we generated cell lines that had developed resistance to ICB. Unbiased metabolomic screening of these cell lines revealed a stark increase in the production of the anti-inflammatory metabolite itaconate in the resistant cell lines. This observation was supported by the increased abundance of the enzyme responsible for itaconate production, aconitate decarboxylase 1 (ACOD1) among the resistant lines. Reduction of this enzyme through shRNA compromises the viability of ICB resistant cells but not sensitive cells. Interestingly, conditioned media from the resistant cell lines restricts the in vitro activation of naïve CD8+ T cells. Furthermore, the reduction of ACOD1 among the resistant population results in increased activation of CD8+ T cells when treated with conditioned media from these resistant cells. These observations also extend to other, more established cell lines like the Lewis lung carcinoma (LLC). Taken together, these results indicate that cancerous epithelial cell production of itaconate, through the activity of ACOD1, may represent a mechanism that antagonizes T cell activation and thus promotes ICB evasion.

Citation Format: James H. Schofield, Mark A. Hawk, Sharif Rahmy, Ryan D. Sheldon, Casey Leimbach, Seunghoon Sun, Xin Lu, Russell G. Jones, Zachary T. Schafer. Metabolic evasion of mCRPC immunotherapy by ACOD1 production of itaconate [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 2331.
Abstract 2339: Halting head & neck squamous cell carcinoma progression by broadly targeting glutamine metabolic pathways
Authors: Allevato Michael , Yokoyama Yumi , Wild Robert , Gutkind Silvio
Published: July 2021

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, resulting in over 14,600 deaths each year in the United States alone. HNSCC is associated with human papillomavirus (HPV) infection, and tobacco use and abusive alcohol intake. Recent revolutionary immunotherapy approaches have changed the landscape of treatment options in HNSCC. However, less than 20% of HNSCC patients respond to FDA-approved anti-PD1 immune checkpoint blockade (ICB) (pembrolizumab and nivolumab), often not leading to durable responses. This highlights the unmet need to identify novel therapeutic options and biomarkers predicting more favorable response to maximize the efficacy of immune-oncology (IO) strategies for HNSCC treatment. Glutamine is a conditionally essential amino acid for rapidly proliferating cancer cells making glutamine pathway inhibition an attractive approach for anti-cancer therapy. Treatment with the glutamine antagonist (DRP-104), which irreversibly inhibits all known enzymes involved in glutamine metabolism within the tumor, resulted in metabolically halted cell growth in vitro in a large panel of cell lines (n=8) representing the spectra of HPV- and HPV+ HNSCC, with an IC50 of 0.2-25uM, Interestingly, HNSCC cells bearing genetic alterations in PIK3CA/PTEN were significantly more sensitive to glutamine antagonism in comparison to unaltered HNSCC cells. The dependence of glutamine in HNSCC growth and the increased sensitivity of PIK3CA/PTEN aberrant cells was also observed in orosphere assays and 6 distinct HNSCC tumor xenografts in NOD SCID mice. We next investigated the efficacy of glutamine suppression in the context of an intact immune system, taking advantage of new syngeneic HNSCC model system, 4MOSC and MOC1. Specifically, we recently developed orthotopic syngeneic mouse models, 4MOSC, reflecting human tobacco-related HNSCC genomic alterations and mutational landscape (Wang et al., Nature Comm 2019), while MOC1 is a DMBA-induced mouse HNSCC cell line grown in the subcutaneous flank of mice (Judd et al. Cancer Res 2011). Monotherapy administration of DRP- 104 (1.4mg/kg) was potent as a monotherapy in all three syngeneic HNSCC models. We also observed a trend of increased sensitivity when DRP-104 was combined with anti-PD-1 therapy. Our data suggest that broad glutamine antagonism using DRP-104 has therapeutic potential in HNSCC by both dismantling cancer metabolism and enhancing the anti-tumor immune response of immune checkpoint blockade. Clinical trials of DRP-104 are currently ongoing.

Citation Format: Michael Allevato, Yumi Yokoyama, Robert Wild, Silvio Gutkind. Halting head & neck squamous cell carcinoma progression by broadly targeting glutamine metabolic 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 2339.
Abstract 234: Risk of sepsis among patients with prostate cancer: A network-based modeling approach
Authors: Jazayeri Ali , Jafari Niusha , Yang Christopher C. , Nikita Nikita , Yao Grace Lu
Published: July 2021

Background: Prostate cancer (PCa) is the most common cancer among men, and sepsis is a leading cause of death in PCa, yet their association has not been quantified. This study aims to quantify the association between sepsis severity (identified as sepsis, severe sepsis, and septic shock) and prostate complications among PCa subgroups.

Methods: We used the SEER-Medicare data to identify patients diagnosed with PCa in 2010 -2015. PCa patients were classified as: localized or regional (L/R) stage and distant (D) stage and further stratified as survivors and non-survivors. Patients with no history of PCa composed the control group. Our network-based modeling approach used sepsis and prostate complications (identified using ICD codes) as network nodes. The association between complication pairs, represented as edges, were weighted by the probability of complication pairs occurring concurrently. The network densities for each subgroup were computed at different thresholds based on the weights of the edges.

Results: We identified 27,166 patients with PCa and 22,223 as controls. Increase in threshold was associated with highest decline in network density among controls followed by L/R survivors (Table). Additionally, prostate and sepsis complications co-occur more frequently among stage D than stage L/R patients. Also, stage D patients experience prostate complications with more severe sepsis conditions (severe sepsis and septic shock) than other subpopulations. The variances and medians of edges' weights among all subgroups were statistically different (p<0.001).

Conclusions: This is the first population-based study using network-based modeling to quantify the association between varying degrees of sepsis severity and prostate complications among PCa subgroups. The differentiating complication pairs identified among subgroups can be used as features in machine-learning algorithms to predict the severity of patient outcomes and to improve patient prognosis.

Table: Network densities of sepsis and PCa complication pairs at different weight thresholds for each PCa subgroupsNetwork densities at various threshold weightsQuantiles of Weights in Network (Median (Q1,Q3))Threshold Levels0.0000.0100.0200.0300.040Control0.1930.0050.0030.0010.0010.005 (0.002, 0.016)Stage L\R survivors0.2410.0290.0110.0070.0050.007 (0.003, 0.021)Stage L\R non-survivors0.1580.0380.0140.0070.0040.012 (0.005, 0.029)Stage D survivors0.0840.0270.0060.0020.0010.013 (0.006, 0.032)Stage D non-survivors0.1300.0360.0170.0090.0040.012 (0.005, 0.029)

Citation Format: Ali Jazayeri, Niusha Jafari, Christopher C. Yang, Nikita Nikita, Grace Lu Yao. Risk of sepsis among patients with prostate cancer: A network-based modeling 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 234.
Abstract 2341: Metabolomic analysis reveals unique biochemical signatures associated with microbial dysbiosis, inflammation and energy metabolism in breast tissues of obese and nonobese black and white breast cancer patients
Authors: Starlard-Davenport Athena , Smith Alana , Tolley Elizabeth , Lu Lu
Published: July 2021

Black women are more likely to be diagnosed with late-stage breast cancer than white women and have the lowest probability of cause-specific survival. Obesity is associated with increased breast cancer risk and deaths in black women. Insulin-resistant obesity features chronic systemic and local inflammation of fat, which has been linked to breast cancer outcomes. The breast also consists of a mucosal immune system that provides a complex mechanical barrier and an inherent defense against pathogens. Growing evidence shows that an imbalance in the microbiome due to inflammation may give rise to cancer development. However, there is a lack of data on the role of the microbiome in breast tumors from black women. Using a global metabolomics approach, we investigated normal (n= 24) and breast cancer (n=27) tissue from black and white women to identify microbial metabolites and metabolomic signatures that differ by breast tumor subtype and obesity status. Principal component analysis and hierarchical clustering of the global metabolite profiling data revealed separation between the metabolic signatures of normal and breast tumor tissue. Random forest analysis also revealed a unique biochemical signature in normal versus breast tumors by obesity status and breast tumor subtype, including triple negative breast tumors. Our data show that obesity associates with a unique set of metabolic pathways that facilitate the handling of inflammation, protein catabolism and tissue remodeling, and energy metabolism, which may be regulated by microbial processing in breast tumor tissue.

Citation Format: Athena Starlard-Davenport, Alana Smith, Elizabeth Tolley, Lu Lu. Metabolomic analysis reveals unique biochemical signatures associated with microbial dysbiosis, inflammation and energy metabolism in breast tissues of obese and nonobese black and white breast cancer 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 2341.
Abstract 2353: Metabolic reprogramming by SLC1A5 downregulation in pancreatic cancer cells
Authors: Sharma Raj Kumar , Krishnamachary Balalji , Sivakumar Ishwarya , Mironchik Yelena , Bharti Santosh Kumar , Bhujwalla Zaver M.
Published: July 2021

Introduction: Pancreatic cancers exhibit limited response to chemo- and radiation therapy. Identifying novel targets for pancreatic cancer treatment is important for new treatment strategies. Because pancreatic cancer cells are ‘glutamine avid' [1], targeting glutamine metabolic pathways can provide novel options for treatment. The glutamine transporter, SLC1A5, is being actively investigated as a pharmacological target in cancer [2]. Here we have engineered human pancreatic cells expressing shRNA to downregulate the glutamine transporter SLC1A5. We performed high-resolution 1H magnetic resonance spectroscopy (MRS) to understand the metabolic reprograming that occurs with SLC1A5 downregulation in these two cell lines.

Method: Panc1 and Pa04C pancreatic cancer cell lines were genetically engineered to express shRNA against SLC1A5 using lentiviral transduction. Downregulation of SLC1A5 was verified with qRTPCR and immunoblotting. Control cells expressing an empty vector (EV) were also engineered. Dual phase extraction was performed as previously described [3]. High-resolution 1H MRS was performed on the aqueous phase extracts and recorded on a 750 MHz spectrometer. All data acquisition, processing and quantification was performed with TOPSPIN 3.5 software. Spectra were obtained from Panc1EV (n=4), Pa04CEV (n=4), Panc1_SLC1A5_shRNA (n=4) and Pa04C_SLC1A5_shRNA (n=4) cells.

Results and Discussion: SLC1A5 downregulation significantly decreased the glutamine/glutamate ratio in Pa04C_SLC1A5_shRNA cells but not in Panc1_SLC1A5_shRNA cells. Instead, in Panc1_SLC1A5_shRNA cells, a significant decrease of the amino acids leucine, isoleucine, valine, tyrosine, histidine, and phenylalanine was observed. Lactate and fumarate also significantly decreased in Panc1_SLC1A5_shRNA cells. Other than the significant decrease of glutamine/glutamate in the Pa04C_SLC1A5_shRNA cells, no other significant metabolic differences were observed in these cells. Our data expand the understanding of the diverse metabolic reprogramming that occurs following SLC1A5 downregulation in two human pancreatic cancer cell lines that may lead to the development of additional metabolic targets.

Supported by NIH R01CA193365 and R35CA209960.1. Son J et al., Nature. 2013; 2. Bhutia YD et al., Biochim Biophys Acta. 2016; 3. Winnard PT Jr. et al., J Cachexia Sarcopenia Muscle. 2020.

Citation Format: Raj Kumar Sharma, Balalji Krishnamachary, Ishwarya Sivakumar, Yelena Mironchik, Santosh Kumar Bharti, Zaver M. Bhujwalla. Metabolic reprogramming by SLC1A5 downregulation in pancreatic cancer 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 2353.
Abstract 2361: The functional roles of miRNA-193a-3p in colorectal cancer
Authors: Hiraide Sakura , Takahashi Masanobu , Yoshida Yuya , Komine Keigo , Ishioka Chikashi
Published: July 2021

Background: Patients with BRAF-mutated colorectal cancer (CRC) have a poor prognosis despite recent therapeutic advances such as combination therapy with BRAF, MEK, and EGFR inhibitors.

Aim: Our aim was to clarify the functions of the microRNAs (miRNAs) involved in oncogenesis and sensitivity to BRAF inhibitors and MEK inhibitors in BRAF-mutated CRC.

Methods and Results: To identify miRNAs that sensitize a BRAF inhibitor dabrafenib (DAB) and a MEK inhibitor trametinib (TRA), we screened 240 miRNAs in BRAF-mutated CRC cell line RKO. Among the screened miRNAs, we tried to elucidate the novel functional roles of miR-193a-3p in CRC cell lines. We found that miR-193a-3p overexpression inhibited cell proliferation in CRC cell lines. The protein array analysis revealed that protein phosphorylation levels were altered by miR-193a-3p overexpression in various pathways such as cell-cycle-related pathways and PI3K-AKT pathways. The enhanced cytotoxicity by miR-193a-3p in addition to DAB and TRA was validated in multiple BRAF-mutated cell lines. Furthermore, the enhanced cytotoxicity by miR-193a-3p in addition to DAB and TRA was shown to be through inhibiting reactivation of MAPK signaling. This enhanced cytotoxicity by miR-193a-3p was even observed under treatment of DAB, TRA, and an anti-EGFR antibody.

Conclusions: Our study shows that miR-193a-3p regulates multiple proteins involved in oncogenesis, and proposes that the combination therapy of miR-193a-3p and BRAF/MEK inhibitors could be a promising treatment strategy in BRAF-mutated CRC.

Citation Format: Sakura Hiraide, Masanobu Takahashi, Yuya Yoshida, Keigo Komine, Chikashi Ishioka. The functional roles of miRNA-193a-3p in colorectal 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 2361.
Abstract 2366: Malignant ascites-derived extracellular vesicles promote metastasis of ovarian cancer by transferring miR-1246 and miR-1290
Authors: Wang Wenyu , Jo HyunA , Song Yong Sang
Published: July 2021

Background and purpose: Ovarian cancer is the most lethal gynecologic cancer in females worldwide. The high mortality rate is due primarily to the lack of early diagnosis strategies and the high rate of recurrence. Ascites is detected in over one-third of ovarian cancer patients at initial diagnosis and present in almost all the patients with recurrence. Extracellular vesicles (EVs) are double-membrane particles secreted by cells into extracellular space. EV-mediated intercellular communication in the tumor microenvironment is crucial in cancer progression. Additionally, EVs are present in various body fluids, serving as fine analytes for liquid biopsy. Our research is aimed to explore the role of malignant ascites-derived EVs in ovarian cancer metastasis and the underlying mechanisms focusing on the miRNA cargos.

Methods: Patient-derived samples were collected from Seoul National University Hospital with the approval of the Institutional Review Board. EVs were isolated from ascites using the commercial kit and identified through transmission electron microscopy, nanoparticle tracking analysis and western blotting. Transwell assay was performed to investigate the effects of ascites-derived EVs on ovarian cancer cells. MiRNA sequencing was carried out in EVs derived from malignant ascites(n=10) and benign peritoneal fluids(n=9).

Results: Malignant ascites-derived EVs were characterized as double-membrane particles sizing ranging from 30nm to 150nm with the expression of CD63 and CD81. Those EVs significantly promoted the invasion and migration ability of ovarian cancer cells. MiRNA sequencing data showed that 118 miRNAs were upregulated and 44 miRNAs were downregulated in the ascites-derived EVs compared with benign peritoneal fluid-derived EVs. Among those, miR-1246 and miR-1290 were the top two upregulated miRNAs, which were negatively associated with the overall survival of ovarian cancer patients. Moreover, miR-1246 and miR-1290 could enhance the invasion and migration ability through activating Wnt/β-catenin signaling pathway via binding to RAR-related orphan receptor alpha (RORα).

Conclusion: Malignant ascites-derived EVs could facilitate the metastatic potential of ovarian cancer cells through transferring miR-1246 and miR-1290. Targeting miR-1246 and miR-1290 might be a promising therapeutic strategy in ovarian cancer treatment.

Citation Format: Wenyu Wang, HyunA Jo, Yong Sang Song. Malignant ascites-derived extracellular vesicles promote metastasis of ovarian cancer by transferring miR-1246 and miR-1290 [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 2366.
Abstract 2375: Comprehensive analysis of immunotherapy-related biomarkers in Chinese patients with gastric adenocarcinoma
Authors: Zhao Qun , Guo Yuntong , Cui XiaoLong , Peng LiangBiao , Li Junying , Wang Fei , Zhang Lin
Published: July 2021

Background: Gastric adenocarcinoma (GAC) is a deadly disease in need for new therapies. Recently, the most exciting developments in oncology are immune checkpoint inhibitors (ICIs) such as inhibitors of programmed cell death protein 1 (PD-1) which has shown response rates of 11-16% in unselected GAC patients. This study aimed to characterize the distributions of immunotherapy-related biomarkers in Chinese patients with gastric adenocarcinoma.

Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor samples and matched peripheral blood samples of 497 Chinese gastric adenocarcinoma patients were collected for YuansuTM NGS-panel assay (OrigiMed, Shanghai). Genomic alterations (GAs) including single nucleotide variations, short and long insertions/deletions, copy number variations, and gene rearrangements were assessed. Microsatellite instability (MSI), PD-L1 expression and tumor mutational burden (TMB) were assessed in 467(94%), 208(42%) and 467(94%) patients, respectively.

Results: There were 334 males (67.2%) and 163 females (32.8%) with a median age of 60 (range 23-87) years in this cohort, including 440 primary tumors and 57 metastases. MSI-H was detected in 39 samples (7.8%). The rate of MSI-H in the ACVR2A mutation group was significantly higher than that in the ACVR2A wild-type group (82.1% vs 17.9%, p<0.001). In addition, we found that patients with mutations of K437Rfs*5 (54.1%) or D96Tfs*54 (11.4%) of ACVR2A were all MSI-H. The frequency of ERBB2 amplification was 7.5%, which was mutually exclusive to MSI-H. PD-L1 expression levels by CPS of negative, 1-9 and ≥10 were 54%, 33% and 13%, respectively. The median value of TMB was 6.2 (0-99.3) muts/Mb and TMB ≥10 muts/Mb was seen in 27.4% tumors. The patients with ACVR2A mutations had a significantly higher TMB (ACVR2A: 5.7 vs 2.6 muts/Mb, respectively, p < 0.01). In addition, the biomarkers associated with hyperprogression (HP) to immune checkpoint inhibitors (ICIs) included 11q13 amp, MDM2/MDM4 amp, and CDKN2A/B gene loss, which were identified in 4%, 2% and 2% of patients, respectively.

Conclusions: We analyzed the distribution of microsatellite status, PD-L1 expression and TMB in Chinese patients with GAC. Interestingly, our data showed that mutated ACVR2A was significantly associated with MSI-H and TMB-H. In addition, approximately 8% of patients were identified harboring hyperprogression-related gene alterations. Therefore, the application of comprehensive genomic profiling might be necessary in guiding ICI treatments in GAC.

Citation Format: Qun Zhao, Yuntong Guo, XiaoLong Cui, LiangBiao Peng, Junying Li, Fei Wang, Lin Zhang. Comprehensive analysis of immunotherapy-related biomarkers in Chinese patients with gastric adenocarcinoma [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 2375.
Abstract 2377: microRNA expression profile in urinary exosomes is dependent on non-invasive lymphoma induction in mice
Authors: Wilson Brittany , Betar Rebekah , Martin Alexander , Niazi Zackaria , Boyer Michael , Winter Lori , Babich Victor , Sole Francesca Di , Ananieva Elitsa
Published: July 2021

Lymphoma accounts for approximately 4% of cancers in the United States, with an estimated 20,910 number of deaths per year. The standard method of diagnosis and staging of lymphoma involves surgical biopsy of the tumor - a procedure that has many negative associated risks. Exosomes are extracellular vesicles secreted in biological fluids that can serve as “liquid biomarkers”. Identification of unique cancer-related biomarkers in urinary exosomes may provide a novel non-invasive and cost-effective tool for lymphoma diagnosis. Analyses of biomarkers obtained from urinary exosomes have been used to evaluate urological cancers, however, these methods have not yet been translated to non-urological pathologies, such as lymphomas. The objective for this study was to determine the profile of microRNAs (miRNAs) expressed in urinary exosomes of mice challenged with lymphoma and compare it to miRNAs identified in urinary exosomes of control mice. Male and female C57BL/6 mice, (tumor (+), n=12), were injected with either 2.5x105 mouse EL-4 lymphoma cells or phosphate-buffered saline (tumor (-), n=12). Tumor growth was monitored for 20 days. Urine was collected for 48 hours starting on day 17 and serum, tumor tissues, and organs were collected on day 20. Extraction of urinary exosomes was followed by total RNA isolation and RT-qPCR for which a set of PCR arrays consisting of 709 mouse-specific miRNA primers was used. Fold changes in miRNA expression were quantified using the ΔΔCt method. Mice developed tumors by day 13 with initial tumor appearance around day seven. There were no statistically significant differences between final tumor mass, body weight, or food and water intake in tumor (+) versus tumor (-) mice. RT-qPCR arrays of miRNAs extracted from urinary exosomes revealed 464 miRNAs that were differentially expressed between tumor (+) and tumor (-). 215 miRNAs were up-regulated, while 249 miRNAs were down-regulated in tumor (+) mice. These results will be compared to miRNAs from serum and tumor tissues to identify tumor-specific miRNAs that can be used for potential application in the clinical setting.

Citation Format: Brittany Wilson, Rebekah Betar, Alexander Martin, Zackaria Niazi, Michael Boyer, Lori Winter, Victor Babich, Francesca Di Sole, Elitsa Ananieva. microRNA expression profile in urinary exosomes is dependent on non-invasive lymphoma induction in mice [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 2377.
Abstract 2379: microRNA-7 replacement therapy: a promising approach for hepatocellular carcinoma
Authors: Beveridge Dianne J. , Kabir Tasnuva , Woo Andrew J. , Richardson Kirsty L. , Stuart Lisa M. , Leedman Peter J.
Published: July 2021

Hepatocellular carcinoma (HCC) is increasing in incidence, has a very poor prognosis and presents massive global unmet clinical need. Current treatment of advanced HCC with sorafenib and other targeted therapies offers short-term relief with little significant clinical advantage. New approaches to the treatment of HCC are urgently needed. Non-coding RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are gaining prominence in clinical medicine as potential diagnostics and therapeutics. The introduction of 2nd generation synthetic chemistry has led to dramatic stabilization of siRNAs and miRNAs producing prolonged effects on target gene expression. This has led the FDA to approve multiple RNA-mediated drugs starting in 2018, the first being a siRNA drug, Patisiran. A second major advance in the RNA-therapeutics field is the specific targeting of the liver by conjugating a galactose moiety (GalNAc) to the passenger RNA strand. This enables the dsRNA to be selectively and efficiently taken up by the asialoglycoprotein receptor (ASGPR) on the hepatocyte. The recent FDA approval of Givosiran, based on its clinical success in patients with porphyria using an ALAS-1 siRNA-GalNAc, illustrates the clinical utility of this system. We have shown that miRNA-7 (miR-7), a tumor suppressor miRNA, is a powerful inhibitor of HCC cell viability, via marked inhibition of EGFR, TYRO3, P-Akt and caveolin-1 signaling pathways. In vivo, miR-7 is a potent inhibitor of HCC tumor growth. In addition, miR-7 readily overcomes sorafenib resistance in multiple HCC cell lines. We utilized 2nd generation synthetic chemistry to develop a novel mimic of miR-7, mRx-7, for the treatment of HCC. mRx-7 is a significant inhibitor of HCC in vitro and is also substantially more stable than commercially available miR-7. In addition, we have engineered a liver-specific version of mRx-7 (mRx-7-GalNAc), which is a conjugate of mRx-7 plus GalNAc, and is a potent inhibitor of multiple signaling pathways, including P-Akt. Taken together, these data suggest that mRx-7 and mRx-7-GalNAc hold promise as novel HCC therapeutics.

Citation Format: Dianne J. Beveridge, Tasnuva Kabir, Andrew J. Woo, Kirsty L. Richardson, Lisa M. Stuart, Peter J. Leedman. microRNA-7 replacement therapy: a promising approach for hepatocellular 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 2379.
Abstract 2388: p73 - lncRNA Fer1l4 axis plays a critical role in suppression of cancer cell migration, invasion and metastasis in a p73-dependent manner via inhibition of miR-1273g-3p
Authors: Uboveja Apoorva , Satija Yatendra Kumar , Siraj Fouzia , Bareja Chanchal , Saluja Daman
Published: July 2021

p73 is a member of the p53 tumor suppressor family and exerts its tumor suppressor functions by suppressing metastasis. It is increasingly evident that long noncoding RNAs (lncRNAs) play a significant role in tumor suppression. The present study is aimed to identify novel lncRNAs that play a role in p73-mediated suppression of metastasis in colorectal cancer cells. Transcriptome analysis was performed to detect the differentially expressed lncRNAs in presence and absence of p73. Out of these, FER1L4 lncRNA was found to be significantly induced in a p73-dependent manner. p73 binding to FER1L4 promoter was confirmed through bioinformatic analysis, luciferase reporter, ChIP and site-directed mutagenesis assays. Knockdown of FER1L4 and p73 significantly increased the invasion and migration rate of colorectal cancer cells as confirmed by wound-healing assay. Knockdown of FER1L4 decreased the expression of E-cadherin and increased the expression of prominent EMT markers such as N-cadherin, Snail, Vimentin and Fibronectin. FER1L4 causes a G2/M cell cycle arrest in a p73-dependent manner in HCT116p53-/-p73+/+ cells and upon FER1L4kd, normal cell cycle progression was observed. Annexin V/PI and TUNEL apoptosis assays revealed that FER1L4 induced apoptosis in HCT116p53-/-p73+/+ cells with increase in time-dependent treatment of etoposide and FER1L4kd inhibited apoptosis even in the presence of p73. The protein expression level of pro-apoptotic genes such as Bad, Bax, Bik, Bim, BID, Bak and PUMA decreased upon FER1L4kd and p73kd, confirming that FER1L4 plays a role in p73 mediated apoptosis and cell cycle arrest. FER1L4 also sponges the expression of miR-1273g-3p, thus inhibiting its oncogenic role. RNA-In situ hybridization (RNA-ISH) confirmed the decreased expression of p73 and FER1L4 mRNA in 30 human metastatic CRC tissues as compared to 30 human non-metastatic CRC tissues. Taken together, we provide conclusive proof that p73 exerts its anti-metastatic function by inducing the expression of lncRNA FER1L4 in response to genotoxic stress.

Citation Format: Apoorva Uboveja, Yatendra Kumar Satija, Fouzia Siraj, Chanchal Bareja, Daman Saluja. p73 - lncRNA Fer1l4 axis plays a critical role in suppression of cancer cell migration, invasion and metastasis in a p73-dependent manner via inhibition of miR-1273g-3p [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 2388.