bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2219: Analysis of gene landscape of small cell lung cancer of Chinese through next-generation sequencing
Authors: Zhang Jing , Zhang Hushan , Ling Feng , Wang Yuanhan , Li Long , Yang Song
Published: July 2021

Background: As the more malignant subtype of lung cancer, small cell lung cancer (SCLC) displayed more aggressive and worse prognosis. Standard treatments have rarely changed in decades, therefore, in recent years, there have been attempts to explore targeted therapy and even immunotherapy. However, SCLC has more challenging targets. It was reported that almost 100% of SCLC has p53 and Rb mutations, and also has functional changes in Myc. Here we report some data about gene mutation of SCLC of Chinese patients.

Methods: Tumor samples of 410 SCLC patients were consecutively collected in China from July 2018 to May 2020, next generation sequencing (NGS) was performed to detect gene mutation, and tumor mutational burden (TMB) measured by a 733 gene panel. PD-L1 expression detected by using Dako PD-L1 IHC 22C3 pharmDx, Tumor Proportion Score (TPS) was used to determine expression of PD-L1. TPS was arranged into the following intervals: strong positive ≥50%, moderate positive ≥5% and <50%, weak positive ≥1% and <5%, and negative <1%. All these were performed by 3D Medicines, a laboratory accredited by College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA).

Results: NGS results showed that the top gene mutation in these 410 Chinese SCLC patients were TP53 (88.0%,361/410), RB1(63.9%,262/410), BRCA1/2(34.0%,139/410), LRP1B(28.3%,116/410), FAM135B(24.1%,99/410), PIK3CA(23.9%,98/410), CYP2D6(21.0%,86/410), POLA1(20.2%,83/410), NTRK1(19.5%,80/410), MSH2(19.3%,79/410), ATM(19.3%,79/410), AKT2(18.8%,77/410), VEGFA(18.8%,77/410). Furthermore, 159 samples available for TMB analysis, and results showed that the average TMB level was 11.7 mutants/Mb, and 49.7%(79/159) were higher than 10 mutants/Mb, and 50.3%(80/159) were under 10mutants/Mb. In addition, 167 samples available for PD-L1 analysis, and results showed that 86.8% (145/167) with PD-L1 negative, 7.8(13/167) moderate positive, none with PD-L1 strong positive.

Conclusion: Chinese patients with SCLC have rich spectrum of gene mutations, it suggests that targeted therapy should also have certain potential. In addition, about half of SCLCs have a TMB level above 10mutants/Mb, and immunotherapy should been considered more in the future treatment for Chinese SCLC patients.

Citation Format: Jing Zhang, Hushan Zhang, Feng Ling, Yuanhan Wang, Long Li, Song Yang. Analysis of gene landscape of small cell lung cancer of Chinese 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 2219.
Abstract 2254: Coding and noncoding RNA determinants of invasion and migration in papillary thyroid cancer
Authors: Carnazza Michelle , Dadafarin Sina , Moscatello Augustine , Tiwari Raj , Geliebter Jan
Published: July 2021

Papillary thyroid cancer (PTC) is now the 8th most common cancer in women in the United States and has been increasing in incidence over the last few decades. While it is often curable, aggressive forms of PTC that are not adequately treated by current therapeutic modalities invade into surrounding tissue, with a poor prognosis. Thus, the identification of genes involved in PTC migration and invasion is an unmet need. Differentially expressed (PTC vs. matched, normal) coding and noncoding genes from our own biobank were ranked, comparing invasive vs noninvasive, and lymph node positive vs lymph node negative samples. This analysis was supplemented with the interrogation s of The Cancer Genome Atlas (TCGA) PTC gene expression database for survival-associated genes (Kaplan Meier survival curves) utilizing the Xena Browser. This meta-analysis identified genes with a significant impact on survival, that correlated with lymph node metastasis and tumor invasion. SPOCK3, a Ca+2-binding proteoglycan protein with metalloendopeptidase activity, with a role in both extracellular matrix (ECM) degradation and ERK signaling, correlated with both invasiveness and lymph node spread. SLC30A3 (Solute Carrier Family 30 Member 3), involved in the accumulation of zinc in synaptic vesicles and the transport of sugars, bile salts, organic acids, metal ions and amine compounds, also correlated with both invasiveness and lymph node spread. COL26A1, was found to be correlated to tumor invasion and codes for collagen type XXVI α1 chain with known roles in degradation of the ECM and collagen chain trimerization. Long noncoding RNAs (lncRNAs) have vast implications in different cancer types with roles in gene expression via modulation of coding and noncoding RNAs, and are cell, tissue and stage-specific. lncRNAs were identified that correlated with differentiation, invasion and lymph node spread. CRISPR guides were designed and introduced into thyroid cancer cell lines and decreased the invasion and migration capacity of the thyroid cancer cells. This implies their potential use as prognostic markers and actionable therapeutic targets for small molecule inhibitors.

Citation Format: Michelle Carnazza, Sina Dadafarin, Augustine Moscatello, Raj Tiwari, Jan Geliebter. Coding and noncoding RNA determinants of invasion and migration in papillary thyroid 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 2254.
Abstract 2257: Effect ofALDH1L1folate enzyme on hepatocellular carcinoma inachemical carcinogenesismodel
Authors: Sharma Jaspreet , Krupenko Natalia I. , Pediaditakis Peter , Helke Kristi , Strickland Kyle C. , Krupenko Sergey A.
Published: July 2021

Background: ALDH1L1 (aldehyde dehydrogenase 1 family member L1, or cytosolic 10-formyltetrahydrofolate dehydrogenase) is an abundant enzyme in folate metabolism representing about 1% of total soluble protein in hepatocytes. Expression of this protein is strongly and ubiquitously downregulated in human cancers through the promoter methylation. Several studies indicate that patients with hepatocellular carcinoma who had low expression of ALDH1L1 had poorer prognosis than those with high expression.

Hypothesis: We propose that in the absence of ALDH1L1, liver tumors proliferate faster and grow to a larger size.

Methods: The effect of the Aldh1l1 knockout (Aldh1l1−/−) on hepatocellular carcinoma was investigated using DEN (diethyl nitrosamine) model of chemical carcinogenesis. Fifteen-days-old male Aldh1l1−/- mice and their wild-type littermate controls (Aldh1l1+/+) were injected intraperitoneally with DEN at the dose of 15 mg/kg body weight. Mice were sacrificed 10, 20, 28- and 36-weeks post-injection and livers were examined for for histopathology.

Results: Significant reduction in total body weight was observed in the DEN-injected knockout compared to wild type animals at 28 and 36 weeks. Immunohistochemical analysis reveals that tumor size was significantly bigger in Aldh1l1−/− compared to Aldh1l1+/+ mice and also indicated fibrosis in livers of knockout vs wild-type mice. Vascular involvement, highlighted by reticulin staining, was present in both Aldh1l1−/− and Aldh1l1+/+ mice as early as 20 weeks after the injection. Tumor multiplicity did not differ significantly between the Aldh1l1−/− and Aldh1l1+/+ animals.

Conclusion:. Aldh1l1 knockout promoted aggressiveness of liver tumors without affecting the tumor initiation.

Acknowledgement: These studies were supported by the National Institutes of Health grants DK54388 and CA095030 (S.A.K.).

Citation Format: Jaspreet Sharma, Natalia I. Krupenko, Peter Pediaditakis, Kristi Helke, Kyle C. Strickland, Sergey A. Krupenko. Effect ofALDH1L1folate enzyme on hepatocellular carcinoma inachemical carcinogenesismodel [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 2257.
Abstract 2282: Rapid and accurate variant calling of FFPE samples with the genexus system
Authors: Casuga Iris , Gioia Jason , Au-Young Janice , Chan Frances , Huynh Milton , Crowe Michael
Published: July 2021

Next Generation Sequencing technology has enhanced oncology research by enabling the detection of relevant variants for clinical and drug discovery programs. The Oncomine Comprehensive Assay v3, a pan-cancer panel, used with the Ion Torrent Genexus System allows for formalin-fixed paraffin embedded (FFPE) samples to be examined across 161 unique genes in an automated workflow from sample to result in 30hrs. This study demonstrates ≥ 90% accuracy for detecting SNV/Indel/CNV and Fusion variants.

The Genexus System consists of two software linked instruments, the Genexus Purification System and the Genexus Integrated Sequencer. The purification system is used first to extract and quantify 6 FFPE sections from human colon and lung tissue for matching DNA & RNA pairs. The nucleic acid output plate from the purification instrument is directly transferred to the sequencer for library preparation and sequencing using the Oncomine Comprehensive Assay v3. Variant calling analysis of 6 DNA & RNA pairs are completed the following day. Results show that the variants were detected with ≥ 90% Sensitivity when compared to the Ion Torrent GeneStudio S5 System as an orthogonal method. All variants report p-values ≤ 10^-5 signifying more confidence that the variant call is correct. The Genexus System is a seamless solution for sample to variant calling results.

Citation Format: Iris Casuga, Jason Gioia, Janice Au-Young, Frances Chan, Milton Huynh, Michael Crowe. Rapid and accurate variant calling of FFPE samples with the genexus system [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 2282.
Abstract 2302: The mechanism of activation of monomeric B-Raf V600E
Authors: Maloney Ryan C. , Zhang Mingzhen , Jang Hyunbum , Nussinov Ruth
Published: July 2021

B-Raf V600E mutations are frequent in cancer, including over 50% of all melanoma. B-Raf, like many other kinases, undergoes structural changes as it transitions between the inactive and active conformations. Key among these changes are the movement of αC helix from an inactive “OUT” conformation to an active “IN” conformation, and the movement of the activation loop from a closed inactive conformation to an open active conformation. Yet even with the knowledge of what the inactive and active conformations are, questions remain concerning how the V600E mutation activates B-Raf. In particular, we seek to understand why B-Raf V600E is constitutively active in its monomeric state while wild type B-Raf requires dimerization. Here, we investigate the differences between the wild type and mutant B-Raf monomers using molecular dynamics (MD) simulations. We included ATP in the nucleotide binding pocket to more fully explore how it is positioned within B-Raf. Our results show that the 1 µs simulations are too short to capture large conformational changes, however some of the simulations show a transient formation and breaking of the key salt-bridge between Lys483 and Glu501, which gives insight into the movement of the αC helix between the OUT and IN conformations. In addition, the dihedral angles around the DFG motif move towards a more active configuration for B-Raf V600E, while those of the wild type adopt a more inactive orientation. These simulations aid in our understanding of the dynamics of activation in B-Raf V600E.

Citation Format: Ryan C. Maloney, Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov. The mechanism of activation of monomeric B-Raf V600E [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 2302.
Abstract 2304: Regulation of the oncogenic tyrosine kinase ACK1 through ubiquitin-dependent mechanism
Authors: Balasooriyage Eranga Roshan Balasooriya Loku , Owen Jacob , Gashler Jack , Muir Colin , Pennington Katie , Moody James , Andersen Joshua L.
Published: July 2021

ACK1 is an oncogene in the ACK family of non-receptor tyrosine kinases (NRTK). In humans, ACK1 is located on chromosome 3q29, a region that is frequently amplified in a variety of cancers including prostate, lung and breast. The ACK kinase family has a unique domain arrangement with, most notably, a putative ubiquitin association (UBA) domain at their C-termini. In the present study, we focus on understanding the ubiquitin-binding nature of the ACK1 UBA and its role in kinase regulation. Structural modeling and sequence analysis suggest that the ACK1 UBA diverges from many other UBAs but shares similarities with the ACK family kinase, TNK1. We found that the ACK family UBA has a remarkably high affinity for diverse poly-ubiquitin linkages with dissociation constants in the low nanomolar range. Our preliminary data suggest that a non-covalent interaction between the UBA and ubiquitin is necessary for ACK kinase activation in cell culture systems. Furthermore, our preliminary data suggest this interaction is sufficient to induce ACK1 activation in vitro. In support of the idea that the UBA is important for ACK1 activation, we identified a variety of cancer patient mutations that disrupt the ACK1 UBA, which we are currently testing for oncogenic activity. Lastly, we have identified small molecule inhibitors of ACK with low nanomolar IC50 values in ACK1-driven cells. Altogether, our data suggest a model of ACK1 activation that involves direct, non-covalent interaction with ubiquitin and potential therapeutic approaches to inhibit ACK1 in cancer.

Citation Format: Eranga Roshan Balasooriya Loku Balasooriyage, Jacob Owen, Jack Gashler, Colin Muir, Katie Pennington, James Moody, Joshua L. Andersen. Regulation of the oncogenic tyrosine kinase ACK1 through ubiquitin-dependent mechanism [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 2304.
Abstract 2328: Interrogating the anti-cancer effects of co-enzyme Q10 (CoQ10) identifies metabolic and mitochondrial apoptotic responses as primary mechanisms in squamous cell carcinoma model
Authors: Narain Niven R. , Kazerounian Shiva , Khatu Shivani , Diers Anne R. , McCook John , Gesta Stephane , Kirsner Robert S. , Berman Brian , Sarangarajan Rangaprasad
Published: July 2021

Targeting mitochondrial function as a therapeutic modality in cancer has been extensively investigated. BPM 31510 is a proprietary drug-lipid nanoconjugate formulation enabling delivery of supra-physiological concentrations of oxidized CoQ10 specifically into mitochondria. In this study, the anti-cancer properties of CoQ10 in squamous cell carcinoma (SCC) and its mechanism of action were investigated in in vivo xenograft and in vitro model systems. Nude mice were inoculated with a squamous carcinoma cell line isolated from tongue, SCC-25, and treated with a topical formulation containing 1.5% or 5% CoQ10. Treatment was associated with a dose-dependent delay in the detection of palatable tumors (14 ± 3 days vehicle control, 27 ± 7 days 1.5% cream, 39 ± 9 days 5% cream), (p<0.05). Histology and immunostaining analysis demonstrated a decrease in expression of VEGF in the treatment groups (p<0.05). The anti-cancer mechanism of action of CoQ10 was further investigated by interrogating the influence of CoQ10 exposure on molecular profiles using SCC-25 cells in vitro. Cell based assays, mRNA-based RT-PCR assays, and protein-based antibody chip microarrays confirmed an apoptotic response as a major anti-cancer effect in SCC-25 cells in response to CoQ10 exposure. The change in anti- and pro-apoptotic markers (Bcl-2 and caspase families) was independently confirmed by western blotting. In addition, global proteomic analysis revealed alterations in key metabolic proteins in the Pentose Phosphate Pathway (PPP). For example, expression of Transaldolase 1, an enzyme involved in the cellular protection against oxidative stress, resistance/susceptibility to apoptosis, and SCC tumor development and progression, was reduced 1.5 fold at both 6 and 24 hour time point in response to CoQ10 treatment. Together, the data suggests that CoQ10 influences cancer metabolism and redox pathway in activating apoptosis in SCC cancer model.

Citation Format: Niven R. Narain, Shiva Kazerounian, Shivani Khatu, Anne R. Diers, John McCook, Stephane Gesta, Robert S. Kirsner, Brian Berman, Rangaprasad Sarangarajan. Interrogating the anti-cancer effects of co-enzyme Q10 (CoQ10) identifies metabolic and mitochondrial apoptotic responses as primary mechanisms in squamous cell carcinoma model [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 2328.
Abstract 2329: ONC212-induced impairment of oxidative phosphorylation is synergistic with glycolysis inhibition in treatment of pancreatic cancer in vitro and in vivo
Authors: Louie Anna Donovan , Ferrarini Isacco , Zhou Lanlan , El-Deiry Wafik S.
Published: July 2021

ONC212 is a fluorinated imipridone shown to have preclinical efficacy against multiple cancers, including pancreatic cancer. One of the binding targets of ONC212 is the mitochondrial peptidase, ClpP, but its role in the anticancer activity of ONC212 is incompletely understood. Understanding the effects of ONC212 on the bioenergetics of pancreatic cancer could facilitate understanding and amplification of its anti-tumor effects. On extracellular flux analysis, ONC212 impairs mitochondrial ATP production and oxidative phosphorylation in multiple pancreatic cancer lines. However, pancreatic adenocarcinoma uses both glycolysis and mitochondrial function to meet its energy demands. Some pancreatic cancer cell lines are resistant to ONC212 inhibition of oxidative phosphorylation alone, but co-treatment with glycolytic inhibitor 2-deoxy-D-glucose (2-DG) synergizes with ONC212 and increases tumor cell death in vitro. Suppression of ClpX, the regulatory binding protein of ClpP, occurs with ONC212 treatment and was used as a biomarker of ONC212 activity. This suppression was demonstrated in multiple pancreatic cancer lines in vitro and in vivo. In a xenograft mouse tumor model of pancreatic cancer using both the ONC212 resistant Bxpc3 pancreatic cancer cell line and the more sensitive HPAF-II cell line, the combination of ONC212 and 2-DG treatment significantly decreased tumor growth and reduced the intertumoral variability. Immunohistochemistry also revealed increased apoptotic markers in these tumors. There was no significant toxicity from dual treatment in mice, which suggests that tumor energy deprivation from dual inhibition of oxidative phosphorylation and glycolysis via ONC212 and 2-DG has a therapeutic window and should be explored further as a potential combination therapy. In addition, if this effect holds true across other models and cancer types, baseline mitoATP percentage could be used as a functional biomarker of sensitivity to ONC212.

Citation Format: Anna Donovan Louie, Isacco Ferrarini, Lanlan Zhou, Wafik S. El-Deiry. ONC212-induced impairment of oxidative phosphorylation is synergistic with glycolysis inhibition in treatment of pancreatic cancer in vitro and in vivo [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 2329.
Abstract 2334: Discovery of selective inhibitors of carbamoyl phosphate synthetase I (CPS1) to modulate cancer relevant metabolic pathways
Authors: Yao Shihua , Nguyen Tuong-Vi , Rolfe Alan , Agrawal Anant A. , Ke Jiyuan , Peng Shouyong , Colombo Federico , Yu Sean , Bouchard Patricia , Wu Jiayi , Huang Kuan-Chun , Bao Xingfeng , Omoto Kiyoyuki , Selvaraj Anand , Yu Lihua , Ioannidis Stephanos , Vaillancourt Frédéric H. , Zhu Ping , Larsen Nicholas A. , Bolduc David M.
Published: July 2021

Carbamoyl Phosphate Synthetase 1 (CPS1) catalyzes the first and rate-limiting step in ammonia detoxification through the urea cycle, generating carbamoyl phosphate from ammonia, bicarbonate and ATP. CPS1 is overexpressed in several cancers, including LKB1-deficient non-small cell lung carcinoma (NSCLC), where its activity has been proposed to support tumor growth by generating carbamoyl phosphate for use in pyrimidine synthesis. In other cancers, CPS1 has been reported to remove toxic ammonia from growing tumors to allow for sustained growth. Currently, no small molecule inhibitors of CPS1 have been identified, limiting researcher's ability to dissect the involvement of CPS1 function in cancer biology.

We describe here the discovery of the first known small molecule inhibitors of CPS1. From a high throughput screen, we identify two chemical series, which achieve inhibition of CPS1 by blocking bicarbonate phosphorylation in the first step of carbamoyl phosphate synthesis. Biochemical experiments reveal inhibition of bicarbonate phosphorylation occurs through competition between inhibitor and ATP. High-resolution co-crystal structures demonstrate that these novel inhibitors bind to a previously unidentified allosteric pocket located between the integrating domain and carbamate synthetase domain of CPS1. This allosteric mechanism of action allows for highly selective CPS1 inhibition, with no inhibition of CPS2 observed. Analogs with increased potency were developed, which are able to inhibit CPS1 cellular activity, blocking both urea production and the CPS1-mediated pyrimidine biosynthetic pathway in cultured cells. These novel CPS1 inhibitors are valuable, first-in-class tools for probing CPS1 biology. We will also discuss the opportunity to utilize these novel inhibitors of CPS1, along with genetic approaches, to probe the functional roles of CPS1 in LKB1-deficient NSCLC.

Citation Format: Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, David M. Bolduc. Discovery of selective inhibitors of carbamoyl phosphate synthetase I (CPS1) to modulate cancer relevant 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 2334.
Abstract 2346: Prostate cancer castrate resistant progression usage of non-canonical androgen receptor signaling and ketone body fuel
Authors: Labanca Estefania , Bizzotto Juan , Yang Jun , Sanchis Pablo , Shepherd Peter , Paez Alejandra , Antico-Arciuch Valeria , Anselmino Nicolas , Lage-Vickers Sofia , Hoang Anh , Tituts Mark , Efstathiou Eleni , Cotignola Javier , Logothetis Christopher , Vazquez Elba , Navone Nora , Gueron Geraldine
Published: July 2021

Prostate cancer (PCa) that progresses after androgen deprivation therapy (ADT) remains incurable. The intricacy of metabolic pathways associated with PCa progression spurred us to develop a metabolism-centric analysis. Using PCa patient-derived xenografts (PDXs) we assessed the metabolic changes after castration of tumor-bearing mice. We found that relapsed tumors had a significant increase in fatty acids and ketone body content compared with baseline. We confirmed that critical ketogenic/ketolytic enzymes (ACAT1, OXCT1, BDH1) were significantly augmented after castrate-resistant progression. Further, these enzymes are increased in the human donor tissue after progressing to ADT. Increased ACAT1 and OXCT1 was also observed for a subset of PCa patients that relapsed with low AR and ERG expression. These factors were associated with decreased biochemical relapse and progression free survival. In summary, our studies reveal the key metabolites fueling castration resistant progression in the context of a partial or complete loss of AR dependence.

Citation Format: Estefania Labanca, Juan Bizzotto, Jun Yang, Pablo Sanchis, Peter Shepherd, Alejandra Paez, Valeria Antico-Arciuch, Nicolas Anselmino, Sofia Lage-Vickers, Anh Hoang, Mark Tituts, Eleni Efstathiou, Javier Cotignola, Christopher Logothetis, Elba Vazquez, Nora Navone, Geraldine Gueron. Prostate cancer castrate resistant progression usage of non-canonical androgen receptor signaling and ketone body fuel [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 2346.
Abstract 235: Identifying potential drug targets using patient-derived, tissue specific, gene regulatory networks
Authors: Forbes Andre Neil , Xu Duo , Khurana Ekta
Published: July 2021

Recent developments in sequencing have allowed consortiums like ENCODE and ROADMAP to probe the epigenome of normal and cancer cell lines. Applying these approaches in a broad fashion to patient data has been difficult but a pioneering TCGA study using ATAC-Seq, an assay for probing open chromatin and thus regulatory regions, provides an opportunity to analyze cancer patient epigenomes for key regulators and potential drug targets.

Utilizing this TCGA dataset, we identify the regulatory targets of open chromatin regions as assayed by ATAC-Seq and RNA-Seq across 371 patients on a patient-specific basis. We subsequently utilize transcription factor (TF) footprinting to identify regions bound by 850 TF &TF-families in each patient. The final output of this approach identifies which TF regulates individual genes for every patient. Using a combination of network metrics and TF abundance, we can identify known and rare subtypes of multiple cancers with similar underlying networks. We next identify a set of TFs with greater importance and predicted activity within each cluster of samples relative to others. To expand the set of potentially druggable genes, we use data from the Achilles/DepMap project to identify a set of genes whose essentiality is most highly correlated with the set of critical TFs for each cluster, i.e. “coessential genes”. We next combine our list with two datasets, the list of known druggable genes and the Drug Interaction Database to identify compounds that target this gene set. We prioritize genes highly correlated with our key TFs' essentiality, are not pan-cancer essential genes or targeted by drugs with high inferred toxicity. We identify a set of neuroendocrine-like cancers in lung and stomach adenocarcinoma, rare disease subtypes in their representative cancers. Further investigation finds these samples expressing high levels of known neuroendocrine markers synaptophysin and PCSK1. Within well-studied cancers like breast and colon adenocarcinoma we identify separate ER+ and ER- sample clusters as well as MSI-H samples as separate and featuring different key TFs than MSI-L and MSS clusters. Our drug candidate pipeline identified known targeted drugs in breast cancer such as Tamoxifen and Fulvestrant, non-specific chemotherapies like doxorubicin in addition to the novel candidates Nelfinavir and Indinavir as potential therapeutic agents. In summary we identify key TFs in multiple cancers and novel drugs for targeting those TFs or downstream effectors.

Citation Format: Andre Neil Forbes, Duo Xu, Ekta Khurana. Identifying potential drug targets using patient-derived, tissue specific, gene regulatory networks [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 235.
Abstract 2351: Multiomics integration elucidates onco-metabolic modulators of drug resistance in lymphoma
Authors: Singh Satishkumar , Choueiry Fouad , Hart Amber , Sircar Anuvrat , Zhu Jiangjiang , Sehgal Lalit
Published: July 2021

Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL). B-cell NHLs rely on Bruton's tyrosine kinase (BTK) mediated B-cell receptor signaling for survival and disease progression. However, they are often resistant to BTK inhibitors or soon acquire resistance after drug exposure. Upon reaching drug tolerance, B-cell NHL cells proliferate faster, which suggests increased metabolic activity. In this study, we explored the onco-metabolic regulators of ibrutinib -resistant activated B-cell (ABC) DLBCL using a ‘multi-omics' analysis that integrated metabolomics (using high-resolution mass spectrometry) and transcriptomics (gene expression analysis). We performed unbiased statistical analyses to uncover dysregulated metabolic pathways among the proteomic and transcriptomic datasets. Overlay of the analyses identified two significantly altered metabolic pathways at both the metabolic and transcript level. Gene-metabolite integration revealed interleukin 4 induced 1 (IL4I1) at the crosstalk of two significantly altered metabolic pathways involved in the production of various amino acids. We showed for the first time that a metabolic shift from glycolysis towards oxidative phosphorylation in these lymphomas is activated via the BTK-PI3K-AKT-IL4I1 axis and can be targeted therapeutically. These findings from our unbiased analyses highlight the role of metabolic dysregulation during drug resistance development. Furthermore, our work demonstrates that a multi-omics approach can be a powerful and unbiased strategy to uncover genes and pathways that drive metabolic dysregulation in cancer cells.

Citation Format: Satishkumar Singh, Fouad Choueiry, Amber Hart, Anuvrat Sircar, Jiangjiang Zhu, Lalit Sehgal. Multiomics integration elucidates onco-metabolic modulators of drug resistance in lymphoma [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 2351.
Abstract 2370: Tumor suppression potential of tRNA modification enzyme TruBs via let-7
Authors: Kurimoto Ryota , Tsutsumi Hiroki , Ikeuchi Saki , Asahara Hiroshi
Published: July 2021

MicroRNA (miRNAs) let-7 is firstly discovered and widely involved in various tumors. Let-7 suppresses mRNAs of many oncogenes, such as KRAS and MYC. This, let-7 is strongly and selectively regulated by Lin28A/B. The let-7-Lin28A/B relationship could explain the pathogenesis of many tumors. However, the control mechanism of let-7, which cannot be explained by Lin28A/B alone, is reported. Furthermore, the regulatory mechanism of microRNAs by RNA-binding proteins such as Lin28 remains unclear. We have reported that TruB1, one of the tRNA modifying enzymes, specifically regulates let-7 by whole RNA binding protein screen (Kurimoto et al., EMBO J (2020)39:e104708). In this study, we evaluated in detail the effect of this TruB1-let-7 axis on the tumor phenotype. In addition to TruB1, another tRNA modifying enzyme TruB2 and other candidate RNA binding proteins were evaluated for its let-7 regulatory mechanism and tumor suppressive potential. We evaluated the effects of these candidates on cell proliferation and stemness in MTT assay, sphere formation assay and Xenograft model with knock down (KD) or over expression (in A549, HeLa or THP-1 cells). To elucidate that the phenotype was associated with let-7, we also use RNAi for let-7 families. We also checked the let-7-candidate proteins binding by RIP and eCLIP (enhanced version of the crosslinking and immunoprecipitation) analysis. Clinical effectiveness was assessed by public database (GEO and TCGA). In results, overexpression of TruB1 and other several genes suppressed the tumor growth and sphere formation ability in vitro with let-7 elevation. Interestingly, these suppressions were also seen in TruB enzymatic null mutants in TruBs (as we have reported in recently (Kurimoto et al., EMBO J (2020)39:e104708)). However, only TruB1 KD and one other candidate (gene A) KD showed the tendency to increase the tumor growth in vitro or in Xenograft model. The eCLIP and RIP analysis showed direct binding of TruB1 and gene A to let-7, but not TruB2 and others. In public database, only TruB1 and gene A strongly inversely correlated with several tumors. There was no relationship in TruB2 and tumor. These data introduced the novel players TruB1 and gene A to regulate the specific miRNA biogenesis and its impact on tumor phenotypes. Our data highlighted the potential of RNA binding protein independing on its known activity.

Citation Format: Ryota Kurimoto, Hiroki Tsutsumi, Saki Ikeuchi, Hiroshi Asahara. Tumor suppression potential of tRNA modification enzyme TruBs via let-7 [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 2370.
Abstract 2371: MicroRNA-99b-5p targets the mTOR/AR axis and induced autophagic cell death in prostate cancer cells
Authors: Niture Suryakant , Tricoli Lucas , Hayes Kala , Kumar Deepak
Published: July 2021

MicroRNAs are the small non-coding regulatory RNA molecules involved in a wide array of cellular and molecular processes. MicroRNAs negatively regulate gene expression via base-pairing with complementary sequences within mRNA molecules. In cancer, the dysregulation of miRNAs expression is associated with cancer development or suppression through the regulation of key gene expression followed by modulation of multiple cell signaling pathways. In the present study, we investigated the role of microRNA-99b-5p (miR-99b) on prostate cancer (PCa) cell survival, cell migration, and apoptosis. Overexpression of miR-99b in PCa cells inhibited cell proliferation, cell colony-forming capability, spheroid formation, and induced cell apoptosis. On the contrary, inactivation of miR-99b by miR-99b inhibitor promotes PCa cell proliferation, cell colony-forming capability, and cell migration. Mechanistically, miR-99b binds with the 3'UTR region of the mammalian target of the rapamycin (mTOR) gene and controls the expression of mTOR. Our preliminary data also suggest that miR-99b also inhibits androgen receptor (AR) activity in LNCaP cells and induced cell apoptosis. Further by inhibition of mTOR, miR-99b induced autophagy in PCa cells and autophagic cell death. Expression of miR-99b and inactivation of mTOR by rapamycin increased the sensitivity of PCa cells to anti-PCa drug docetaxel (DTX). Collectively the data suggest that miR-99b functions as a tumor suppressor in PCa cells, and therefore, miR-99b may be considered as novel biomarkers and therapeutic targets for PCa management in PCa patients.

Citation Format: Suryakant Niture, Lucas Tricoli, Kala Hayes, Deepak Kumar. MicroRNA-99b-5p targets the mTOR/AR axis and induced autophagic cell death in prostate 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 2371.
Abstract 2373: Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy
Authors: Hahne Jens C. , Lampis Andrea , Ghidini Michele , Ratti Margherita , Senti Chiara , Passalacqua Rodolfo , Cascione Luciano , Braconi Chiara , Sansom Owen , Fassan Matteo , Valeri Nicola
Published: July 2021

Introduction: Monoclonal antibodies against the Epidermal Growth Factor Receptor (EGFR) such as cetuximab or panitumumab are used for the treatment of metastatic colorectal cancer (mCRC) patients. Unfortunately, most patients develop resistance against these therapies within months. Several studies have shown that aberrations in the RAS pathway are responsible for resistance. However, even in metastases that are refractory to anti-EGFR treatment a significant fraction of RAS wild-type (wt) cells remain. These findings suggest a cross-talk between RAS mutant and wt cells in mediating resistance in the wt compartment.

Methods: Mouse and patient-derived organoids from mCRC as well as CRC cell lines were used to test the contribution of extracellular vesicles in mediating resistance in RAS wt cells. Using conditioned media, transfection experiments and liquid biopsies (plasma and urine) from patients differential expression of the let-7g microRNA was demonstrated in microvesicles from cetuximab sensitive and resistant cells. Changes in expression of let-7g were further analyzed by in-situ hybridization in tissues.

Results: Conditioned media from RAS mutant organoids rendered RAS wt organoids resistant against cetuximab treatment. Basal let-7g expression from pre-treatment plasma and urine samples of RAS wt patients correlated with clinical outcome and changes in let-7g circulating levels mirrored clinical behavior. In-situ hybridization in tissues confirmed changes in expression of the let-7g microRNA observed in plasma and urine samples.

Conclusions: Our data suggest that let-7g microRNA might function as a paracrine mediator of anti-EGFR resistance and might be exploited as a non-invasive biomarker of resistance to cetuximab treatment. Further work is ongoing to characterize the molecular mechanisms underpinning let-7g mediated effect on anti-EGFR sensitivity in RAS wt CRC cells.

Citation Format: Jens C. Hahne, Andrea Lampis, Michele Ghidini, Margherita Ratti, Chiara Senti, Rodolfo Passalacqua, Luciano Cascione, Chiara Braconi, Owen Sansom, Matteo Fassan, Nicola Valeri. Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy [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 2373.
Abstract 2378: Circulating microRNAs and cytokines as prognostic biomarkers for doxorubicin-induced cardiac injury and for evaluating the beneficial effects of exercise
Authors: Jeyabal Prince , Kleinerman Eugenie S.
Published: July 2021

Introduction: Cardiotoxicity and late cardiomyopathies compromise survival in >50% of childhood cancer survivors treated doxorubicin (Dox). Early intervention is important for initiating therapy to preserve heart function. There are no accepted biomarkers identifying which patients are at risk for developing cardiac problems and no interventions to inhibit the cardiac damage. Troponin has not proved useful for predicting Dox-induced cardiotoxicity and patient outcome. We developed a pediatric mouse cardiotoxicity model to define early biomarkers of Dox-induced cardiac injury, investigate the efficacy of an exercise intervention, and whether these biomarkers can be used as a non-invasive method to monitor exercise effectiveness.

Hypothesis: Circulating micro-RNAs are increased during Dox but not Dox + exercise therapy which correlate with cardiac damage. These can be used to monitor intervention effectiveness.

Methods: Mice were treat with Dox (2.5mg/kg 2x/wk for 2 wks), Dox + exercise (walking 45 min/day at 12 meter/min) or PBS. Cardiac function was evaluated by echocardiography 24 hrs after therapy. Blood was collect before and 6 and 24 hrs after therapy. Plasma cytokine levels, troponin and miRNAs (miRNA 1, 29b, 499) were quantified. We also obtained plasma samples from Dox-treated osteosarcoma patients.

Results: Decreased ejection fraction and fractional shortening were seen in Dox but not Dox + exercise-treated mice. There was an increase in miR-1 and miR-499 and the pro-inflammatory cytokines IL-1α, IL-1β and IL-6, in Dox-treated but not Dox + exercise-treated mice compared with PBS controls. Troponin levels were not elevated until 24 hrs following therapy. Increased miRNAs and cytokines in the Dox-treated patient plasma samples 24 hrs after therapy mimicked the results observed in mice.

Conclusion: These data indicate that miRNA499, miRNA1, IL-1α, IL-1β and IL-6 are early biomarkers of Dox-induced cardiac injury which predict cardiac functional changes and can be used to evaluate intervention efficacy during combined therapy. Following these biomarkers may also assist in identifying patients at risk for cardiac late effects and also enable intervention modification as needed.

Citation Format: Prince Jeyabal, Eugenie S. Kleinerman. Circulating microRNAs and cytokines as prognostic biomarkers for doxorubicin-induced cardiac injury and for evaluating the beneficial effects of exercise [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 2378.
Abstract 2380: MiR29b may suppress peritoneal metastasis via the effects on peritoneal mesothelial cells
Authors: Kimura Yuki , Ohzawa Hideyuki , Kaneko Yuki , Futoh Yurie , Tamura Kohei , Takahashi Kazuya , Saito Akira , Tojo Mineyuki , Kumagai Yuko , Miyato Hideyo , Sata Naohiro , Kitayama Joji
Published: July 2021

Background: Mesothelial cells play tumor-promoting roles in the development of peritoneal metastasis (PM) through mesothelial-mesenchymal transition (MMT). MiR-29 family is well known as tumor suppressor.

Methods: MiR-29b mimics and negative control miRNA were transfected by lipofection method. Proliferation and migration of human gastric cancer cell lines, MKN45 and NUGC-4, were examined with MTT assay and transwell assay, respectively. MMT of human peritoneal mesothelial cells (HPMCs) was induced 10 ng/ml of TGF-β. Proliferation and migration of HPMCs were examined with the same methods, and MMT was evaluated with immunofluorescence staining for epithelial, mesothelial and mesenchymal markers. To evaluate the effect of miR-29b in vivo, we developed a highly metastatic subclone YTN16P2 from a murine gastric cancer cell line, YTN16, with in vivo selection, and inoculated the YTN16P2 in peritoneal cavity of syngenic C57BL/6 mice. MiR-29b mimics or negative control miRNA with atelocollagen were intraperitoneally (ip) injected every 3 days from tumor implantation. The mice were sacrificed at 14 days after tumor implantation, and formation of peritoneal metastasis were evaluated.

Results: Transfection of miR-29b mimics significantly decreased the proliferation of MKN45 and NUGC-4 by 20-60% (p<0.01) as compared with negative control miRNA. Migration was inhibited more strongly by 90% (p<0.001). After 48 hr-culture with TGF-β, HPMCs apparently changed the morphology from round to spindle shape. The expression level of E-cadherin and Calretinin in HPMCs was decreased while vimentin tended to be upregulated by TGF-β. However, transfection of miR-29b mimics significantly suppressed the morphological changes and reduced the expression levels of vimentin with restored expression of E-cadherin and Calretinin, suggesting the inhibition of MMT in HPMCs. MiR-29b also decreased the proliferation and migration of HPMCs by 20% (p<0.05) and 90% (p<0.001) as compared with negative control miRNA. Finally, mice treated with miR-29b developed less PM nodules than those treaded with negative control miRNA and only atelocollagen.

Conclusion: MiR-29b efficiently suppresses MMT. Replacement of the miR-29b in peritoneal cavity might be used for the treatment of PM partially via the effects on mesothelial cell.

Citation Format: Yuki Kimura, Hideyuki Ohzawa, Yuki Kaneko, Yurie Futoh, Kohei Tamura, Kazuya Takahashi, Akira Saito, Mineyuki Tojo, Yuko Kumagai, Hideyo Miyato, Naohiro Sata, Joji Kitayama. MiR29b may suppress peritoneal metastasis via the effects on peritoneal mesothelial 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 2380.
Abstract 2398: Disruption of mitochondrial metabolism by ClpP activation in triple negative breast cancer
Authors: Fennell Emily M. , Aponte-Collazo Lucas J. , Rushing Blake R. , Li Yuan-Yuan , Pathmasiri Wimal , Wynn Joshua D. , Graves Paul R. , Holmuhamedov Ekhson L. , Herring Laura E. , Iwanowicz Edwin J. , Graves Lee M.
Published: July 2021

ONC201 is a novel anticancer compound currently in over 20 clinical trials for multiple different cancers, including triple negative breast cancer (TNBC). We recently demonstrated that ONC201 and the more potent TR compounds selectively activate the mitochondrial protease ClpP. While previous studies demonstrated substantial effects on mitochondrial metabolism, the consequences of ClpP activation on cancer cell metabolism are yet to be defined. To investigate this, we performed an unbiased metabolomics and proteomics analysis comparing the effects of ONC201 and TR-57 on the TNBC metabolome and proteome. Consistent with these compounds targeting the mitochondria, our studies identified multiple mitochondrial metabolites and enzymes that were impacted by ClpP activation, such as TCA cycle intermediates and enzymes, heat shock proteins and mitochondrial ribosomal proteins. In addition to previously reported elements of the integrated stress response (ATF4, CHOP), we identified several proteins that were upregulated as part of the mitochondrial-nuclear signaling process. qRT-PCR was used to determine the impact of ONC201 or TR-57 treatment on transcript levels of proteomic hits. Importantly, the effects of ONC201 and the TR compounds on these proteins and cell growth were abolished in ClpP null cells. In summary, our studies further demonstrate that loss of metabolic function in mitochondria contributes to the anticancer activity of these ClpP activator compounds.

Citation Format: Emily M. Fennell, Lucas J. Aponte-Collazo, Blake R. Rushing, Yuan-Yuan Li, Wimal Pathmasiri, Joshua D. Wynn, Paul R. Graves, Ekhson L. Holmuhamedov, Laura E. Herring, Edwin J. Iwanowicz, Lee M. Graves. Disruption of mitochondrial metabolism by ClpP activation in triple negative 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 2398.