bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6095: SMOC2 as a potential biomarker with diagnostic value in uterine leiomyosarcoma
Authors: Cai Chen , Falcao Raul , Kokaraki Georgia , Souza Jorge Estefano , de Souza Gustavo , Carlson Joseph Woodard , Petta Tirzah Braz
Published: June 2022

Uterine leiomyosarcoma (uLMS) is a rare and aggressive malignant tumor with poor prognosis. In contrast, uterine leiomyoma (uLM) is the most common benign tumor of the uterus found in women of reproductive age. Extracellular matrix (ECM) accumulation and remodeling are thought to be crucial for the development of these two tumors. To better understand the differences of ECM dynamics in these tumors, we have collected samples from 67 uLMS, 66 uLM and 68 normal myometrium (MM) which were analyzed by RNAseq (Illumina) and a high-resolution isoelectric focusing (HiRIEF) liquid chromatography-mass spectrometry (LC-MS)-based method (Dionex UltiMate™ 3000 RSLCnano System coupled to a Q-Exactive mass spectrometer, Thermo Scientific). After meta-analysis between uLM and uLMS groups using DESeq2 and edgeR, 112 genes were defined as common shared differentiatly expressed genes (DEG). Specific uLMS DEG were analyzed by gene ontology, KEGG pathway, and Reactome pathway. In the top 10 ranking of most affected biological processes/molecular functions/cellular components, we identified the gene SMOC2, a secreted calcium-binding protein of the BM-40/SPARC family which is present in the ECM and has been shown to be involved in fibrosis by modulating TGF-β1. SMOC2 is upregulated in uLM and is downregulated in both RNA and protein expression level in uLMS, compared to MM samples. We also observed that the TGFB1 pathway is downregulated in uLMS and upregulated in uLM, suggesting that this may induce high production of ECM which is related to fibrosis. In conclusion, this preliminary data shows SMOC2 as a potential biomarker to differentiate uLM and uLMS at the protein level and we plan to further study the role of SMOC2 in cell lines to improve our understanding on uLMS malignancy.

Citation Format: Chen Cai, Raul Falcao, Georgia Kokaraki, Jorge Estefano Souza, Gustavo de Souza, Joseph Woodard Carlson, Tirzah Braz Petta. SMOC2 as a potential biomarker with diagnostic value in uterine leiomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6095.
Abstract 6106: The effect of neoadjuvant chemotherapy on tumor immune microenvironment in ovarian cancer
Authors: Cao Guangming , Hua Dingchao , Cui Lina , Zhao Xiaochen , Wang Shuzhen , Zhu Lei
Published: June 2022

Background: Ovarian cancer (OC) is a highly lethal gynecologic malignancy, neoadjuvant chemotherapy (NACT) with interval de-bulking surgery (IDS) is an established strategy for woman with advanced epithelial ovarian cancer (EOC). Tumor infiltrating lymphocytes (TILs) play an important role in the pathogenesis of OC. However, the effect of NACT on tumor immune microenvironment (TIME) has not been evaluated.

Methods: All patients underwent NACT with IDS. Formalin-fixed paraffin-embedded tissue samples were collected from biopsy specimens and the corresponding post-NACT surgical specimens. The densities and percentage of specific TILs [CD8+, CD3+, CD4+, CD20+, tumor associated macrophages (TAMs), dim CD56+NK, bright CD56+NK, PD-1+ etc.] within the TIME were analyzed by multiplex immunohistochemistry (3DMedcines Inc.). Serum CA 125 was measured 3-weekly per protocol and evaluated the response to NACT using GCIG CA125 response criteria.

Results: A total of 28 patients were enrolled in this study with planned IDS after NACT. Of 25 patients evaluated by GCIG CA125 response criteria, 76% (19/25) had a CA125 response. In CA125 response patients, we observed significant recruitments of the densities and percentage of CD8+ in tumor, percentage of PD-1+ cell in tumor after-NACT vs before-NACT (34.85/mm3 vs 110.54/mm3, p=0.0258; 0.50% vs 1.73%, p=0.0132; 0.53% vs 2.66%, p=0.0576, respectively), while no significant change was found in TAMs, NK cells and CD20+ cells. However, in CA125 non-response patients, the TILs in tumor did not change significantly.

Conclusion: NACT could release the tumor associated antigen by killing tumor cells for uptake by tumor-infiltrating dendritic cells and promote the infiltration of CD8+ and PD-1+ T lymphocyte in CA125 response OC patients. Given the limited clinical prognostic information and the number of patients in this study, the results of this study will need confirmation in larger studies in the future.

Citation Format: Guangming Cao, Dingchao Hua, Lina Cui, Xiaochen Zhao, Shuzhen Wang, Lei Zhu. The effect of neoadjuvant chemotherapy on tumor immune microenvironment in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6106.
Abstract 613: AL009 is a multi-Siglec inhibitor engineered to bind myeloid cells that enhances innate and adaptive immunity to cancer
Authors: Nalle Sam , Lam Helen , Barner Cheryl , Long Hua , Liang Spencer , Rosenthal Arnon , Maslyar Daniel
Published: June 2022

Background - Inhibitory sialic acid-binding immunoglobulin-type lectins (Siglecs) are a subset of the Siglec family of cell surface receptors that potentiate immune tolerance. A multitude of inhibitory Siglecs on myeloid cells become engaged in sialic acid-rich tumor microenvironments, suggesting that disrupting Siglec-sialic acid signaling could confer therapeutic benefit in cancer. To accomplish this, we designed AL009, an engineered Siglec-9 extracellular domain-Fc fusion molecule that acts as a sialic acid trap and a multi-Siglec inhibitor, repolarizing suppressive myeloid cells and activating an anti-cancer response.

Methods - Cooperative binding of AL009 was analyzed by flow cytometry using cultured human tumor cell lines and myeloid-derived suppressor cells (MDSCs) differentiated from primary human monocytes. Monocytes, MDSCs, and macrophages differentiated from primary human monocytes were assessed for AL009 binding by flow cytometry. AL009m (AL009 with a mouse Fc) was fluorophore-labeled and intravenously injected into B6 mice to analyze biodistribution via ex vivo tissue imaging over time. Initial toxicology screening was conducted in cynomolgus monkeys in a non-terminal study.

Results - AL009 displays cooperative binding with sialic acid and Fc gamma receptors on myeloid cells. When comparing binding among myeloid cell subsets, AL009 preferentially binds MDSCs. Analysis of the biodistribution of labeled AL009m in mice showed the greatest accumulation in the spleen, consistent with immune cell targeting in vivo. Further, Fc engineering of AL009 improved the pharmacodynamic profile compared to a non-engineered Fc. In cynomolgus monkeys, single doses of 80 mg/kg appeared safe and without clinically significant findings.

Conclusions - The engineered structure of AL009 leads to preferential binding to an immunosuppressive subset of myeloid cells. This targeting leads to repolarization of myeloid cells and activates an innate and adaptive anti-cancer response. Pharmacologically relevant doses of AL009 appear well-tolerated in initial studies in non-human primates, supporting further development for entry into clinical studies.

Citation Format: Sam Nalle, Helen Lam, Cheryl Barner, Hua Long, Spencer Liang, Arnon Rosenthal, Daniel Maslyar. AL009 is a multi-Siglec inhibitor engineered to bind myeloid cells that enhances innate and adaptive immunity to cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 613.
Abstract 6183: A novel NQO1 bioactivatable drug induces mitochondrial dysfunction and G2/M phase cell cycle arrest to selectively kill pancreatic cancer cells
Authors: Huang Xiumei , Jiang Lingxiang , Boudreau Matthew W. , Hergenrother Paul J.
Published: June 2022

As a fatal disease with short overall survival, pancreatic cancer is among the top five leading cause of cancer-related deaths worldwide, current therapies against pancreatic cancer lack tumor specificity and generally cause toxic side effects on normal and healthy tissues. Thus, exploring and developing novel tumor-specific agents for treating pancreatic cancer is a critical need. NAD(P)H:quinone oxidoreductase 1 (NQO1) is elevated in the pancreatic cancers whereas it lacks in associated normal tissues. Therefore, NQO1 bioactivatable drugs are promising due to tumor-selective killing NQO1-positive cancer cells. Our previous studies have revealed that the novel NQO1 bioactivatable drug - deoxynyboquinone (DNQ) is ten-fold more potent than the prototypic NQO1 bioactivatable drug β-lapachone to efficiently kill NQO1-positive cancer cells. However, DNQ causes a severe side effect action - high-grade methemoglobinemia that limits its clinical usefulness. Here, we developed a novel DNQ derivative, isopentyl-deoxynboquinone (IP-DNQ), which selectively killed pancreatic ductal adenocarcinoma (PDA) cells in an NQO1-dependent way with an extremely low IC50 (0.1 µM). IP-DNQ evoked massive ROS production and oxidative DNA lesions, resulting in PARP1 hyperactivation and mitochondrial catastrophe. Furthermore, we also observed that IP-DNQ induced G2/M phase cell cycle arrest and promoted programmed necrosis and caspase-dependent apoptosis co-existing in IP-DNQ-treated NQO1-positive pancreatic cancer cells. In addition, IP-DNQ treatment caused extremely low side effect of methemoglobinemia, significantly suppressed tumor growth and extended mice lifespan in orthotopic pancreatic cancer xenograft model. In summary, our findings offer a novel potential therapy against NQO1-positive pancreatic cancers and enable mechanism-based synergy with other anticancer drugs.

Citation Format: Xiumei Huang, Lingxiang Jiang, Matthew W. Boudreau, Paul J. Hergenrother. A novel NQO1 bioactivatable drug induces mitochondrial dysfunction and G2/M phase cell cycle arrest to selectively kill pancreatic cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6183.
Abstract 6221: Tandem use of multi-omics and artificial intelligence identified novel prognostic and therapeutic biomarkers for head and neck squamous cell carcinoma
Authors: Bhat Ajaz A. , Masoodi Tariq , Mishra Deepika , Singh Mayank , Nisar Sabah , Hashem Sheema , Baba Sana K. , Bagga Puneet , Reddy Ravinder , Bedognetti Davide , Uddin Shahab , El-Rifai Wael , Macha Muzafar A. , Haris Mohammad
Published: June 2022

Introduction: Head and neck squamous cell carcinoma (HNSCC) is categorized into Human Papilloma Virus positive (HPV+ve) and negative (HPV-ve) tumors, with the latter being more aggressive and displaying poor overall survival (OS). There is a need to identify aggressive biomarkers for patient stratification and improved patient care.

Materials and Methods: Using the multi-omics data, including somatic mutations, copy number alterations, RNA sequencing, miRNA sequencing, and methylation from 513 HNSCC patients, we performed an integrative clustering analysis to differentiate HPV+ve and HPV-ve tumors and identify novel prognostic biomarkers for survival and treatment response. Using artificial intelligence (AI) based machine learning approach by implementing scikit-learn, we developed a model to predict the patient's OS.

Results: Our clustering analysis robustly segregated HNSCC patients into HPV+ve and HPV-ve tumors. Artificial intelligence-based machine learning model identified a 30 gene signature panel specific to HPV-ve tumors precisely predicting poor OS with an accuracy of 90.5±0.8% (95% CI) and AUC of 80.2%. Furthermore, the multivariate Cox regression survival model identified 12 genes as independent prognostic biomarkers in HPV-ve tumors, including overexpression of novel genes NT5E and TRIML2. Interestingly, higher expression of NT5E and TRIML2 due to promoter hypomethylation predicted therapy resistance in 62.8% and 65.1% of HNSCC patients, respectively. The prognostic signature panel of 30 genes was further validated using three additional expression data sets (n = 450) of HNSCC.

Conclusion: Our multi-omics and AI analysis revealed a novel HPV-ve molecular cluster with implications for predicting disease aggressiveness, therapeutic response, and OS in HNSCC patients.

Citation Format: Ajaz A. Bhat, Tariq Masoodi, Deepika Mishra, Mayank Singh, Sabah Nisar, Sheema Hashem, Sana K. Baba, Puneet Bagga, Ravinder Reddy, Davide Bedognetti, Shahab Uddin, Wael El-Rifai, Muzafar A. Macha, Mohammad Haris. Tandem use of multi-omics and artificial intelligence identified novel prognostic and therapeutic biomarkers for head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6221.
Abstract 6278: Per- polyfluoroalkyl substance (PFAS) modulates steatosis and fibrogenic signaling in hepatocellular carcinoma cells
Authors: Qi Qi , Niture Suryakant , Gadi Sashi , Kumar Deepak
Published: June 2022

Perfluorooctanoic acid (PFOA), heptafluorobutyric acid (HFBA), and perfluorotetradecanoic acid (PFTA) are the per- and polyfluoroalkyl substances (PFAS) and organic pollutants that predominantly exist in the environment. Exposure to PFAS affects immune, thyroid and kidney function, lipid and insulin dysregulation, liver disease, and cancer. Mechanisms underlying the impact of low and physiologically relevant concentration of PFAS in liver diseases remain elusive. In the current study, we investigated the effect of PFOA, HFBA, and PFTA on cell proliferation, steatosis, and fibrogenic signaling in hepatocytes and liver cancer cell models. Exposure of PFOA and PFBA (10 to 1000 nM) specifically promoted cell proliferation in non-tumor derived HepaRG liver cells and in hepatocellular carcinoma HepG2 cells. PFASs increased the expression of TNFα and IL6 inflammatory markers and produced endogenous reactive oxygen species (ROS) production. Further, PFAS enhanced cell steatosis in liver (HepaRG and HepG2) cells which was accompanied by upregulation of steatotic, and fibrogenic markers as well as activated Unfolded Protein Response (UPR) signaling. RNA-seq data suggested that chronic exposures of PFOA modulated the expression of fatty acid/lipid metabolic gene expression that is involved in the development of fatty liver disease. Collectively our data suggests that chronic exposure to low concentration of PFAS may modulate cell steatosis and fibrogenic signaling in hepatocytes and HCC cells by activation of UPR signaling.

Citation Format: Qi Qi, Suryakant Niture, Sashi Gadi, Deepak Kumar. Per- polyfluoroalkyl substance (PFAS) modulates steatosis and fibrogenic signaling in hepatocellular carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6278.
Abstract 6309: Activated neutrophils inhibit chemotactic migration of activated T lymphocytes to CXCL11 by multiple mechanisms
Authors: Tamura Kohei , Kaneko Yuki , Futoh Yurie , Takahashi Kazuya , Kimura Yuki , Saito Akira , Tojo Mineyuki , Miyato Hideyo , Ohzawa Hideyuki , Saga Yasushi , Takei Yuji , Fujiwara Hiroyuki , Kitayama Joji
Published: June 2022

Objective High density of tumor-infiltrating lymphocytes (TILs) in the tumor is associated with favorable prognosis of cancer patients, while that of tumor-associated neutrophils (TAN) shows inverse correlation with outcome. We examined the effects of activated neutrophils on chemotactic migration of activated T cells in vitro. Methods Neutrophils and mononuclear cells (PBMC) were collected from the blood of healthy donor. Neutrophils were stimulated with PMA (1uM) or LPS (10ug/ml) for 15 min, washed extensively, and incubated for another 4 hours. PBMC were cultured on anti-CD3 mAb-coated plate with recomnibant-IL-2 (10ng/ml) for 7-14days. The activated T cells were placed in culture inserts with 3μm pore and migration to CXCL-11 (1000ng/ml) placed in lower chamber with or without neutrophils was examined after 2 hours. Random migration of activated T cells on fibronectin coated plate was evaluated with timelapsed analysis using Biostudio system. Degradation of CXCL-11 was examined with western blotting. Results Neutrophils stimulated with PMA or LPS produced neutrophil extracellular traps (NETs). Migration of T cells to CXCL-11 was drastically inhibited in the presence of PMA-activated neutrophils. The inhibition was similarly detected when NETs was removed from PMA-activated neutrophils by ultracentrifugation. Timelapse analysis also showed the NET-depleted supernatant greatly inhibited random migration, which was totally canceled by the pretreatment with 800U/ml catalase. When neutrophils were activated by LPS, T cell migration was also significantly inhibited (p=0.02) but not by NET-depleted supernatant (p=0.99). In western blotting, CXCL11 was totally degraded by LPS-stimulated neutrophils, which was greatly reduced by the depletion of NET component. CXCL11 degraded by NETs was restored by protease inhibitor, 5mM phenylmethylsulfonyl fluoride (PMSF). The reduced migration induced by LPS-stimulated neutrophils was mostly restored with 2mM PMSF. Conclusion Activated neutrophils inhibit chemotactic migration of activated T cells through multiple mechanisms including ROS production and chemokine degradation. TAN may have suppressive effects on the accumulation of TILs.

Citation Format: Kohei Tamura, Yuki Kaneko, Yurie Futoh, Kazuya Takahashi, Yuki Kimura, Akira Saito, Mineyuki Tojo, Hideyo Miyato, Hideyuki Ohzawa, Yasushi Saga, Yuji Takei, Hiroyuki Fujiwara, Joji Kitayama. Activated neutrophils inhibit chemotactic migration of activated T lymphocytes to CXCL11 by multiple mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6309.
Abstract 6324: Development and characterization of Ewing Sarcoma lung metastasis model
Authors: Dasgupta Atreyi , Kurenbekova Lyazat , Patel Tajhal , Yustein Jason T.
Published: June 2022

Introduction: Ewing Sarcoma (EwS) is the second most common bone tumor in children. At diagnosis, approximately 20-25% of patients with EwS have metastatic disease. While systemic chemotherapy, along with surgery and/or radiotherapy, has significantly increased the survival rate of patients with localized disease, metastatic Ewing sarcoma (EwS) has an extremely poor overall survival with a 5-year survival rate of approximately 20-30%. This prognosis has not changed in the last several decades. Thus, there is an imperative need to focus particularly on mechanisms of metastatic growth and progression and to identify and target the underlying intrinsic and extrinsic molecular features. Unfortunately, presently there is no reliable engineered mouse model to functionally study EwS development and metastasis. Using two independent EwS cell lines, we have developed highly aggressive, lung-specific metastatic models that show mechanistic overlap with human patient tumor data and are valuable resources to further study and target metastatic EwS.

Approach: Using a serial transplantation approach, we generated lung specific metastatic lines by repeated intra-tibial injection of two commonly used EwS cell lines (A673 and TC71), allowing metastatic foci to form, followed by dissociation and subsequent re-injection into the tibia. We repeated this 5 times to generate highly aggressive lung-specific metastatic cell lines. As a proof of principle, when equal numbers of GFP+ parental cells and mCherry+ lung metastatic cells are injected into the tibia in NSG mice they form primary tumors with red and green cells, while the metastatic lesions in lungs are almost exclusively mCherry+. A multi-omics approach including glycoproteomics, secretome, and transcriptomic analysis were then used to characterize these cells and compare them with patient tumor samples.

Results: Integration of focused proteomics and glycoproteomics data revealed upregulation in AXL, MEK6, STAT1, and STAT3 proteins and phosphoproteins in metastatic lesions. Focused RNA profiling with Nanostring technologies using formalin-fixed paraffin-embedded (FFPE) slides of patient tumor samples revealed increased expression of several other upstream genes that signal through STAT1, including IL-6, IKK-β, TRAF-6, and Myd88. In addition, upregulation in factors involved in tumor invasive front such as Furin, TIMP-2, MMP-2, and MMP-14 were also noted. We are currently in the process of further validating some of the key regulators using larger set of patient derived tumors and by targeting them in orthotopic mouse models.

Citation Format: Atreyi Dasgupta, Lyazat Kurenbekova, Tajhal Patel, Jason T. Yustein. Development and characterization of Ewing Sarcoma lung metastasis model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6324.
Abstract 6334: In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors
Authors: Jackson Paul J. , Andriollo Paolo , Veillard Nicolas , Procopiou George , Thurston David E.
Published: June 2022

Antibody-Drug Conjugates (ADCs) are a growing class of therapeutic agents for the treatment of cancer, with thirteen approved and over 100 others in clinical development. The pyridinobenzodiazepine (PDD) platform is a toolbox of sequence-selective, DNA Guanine mono-alkylating ADC payloads with varying potencies and biophysical properties, enabling a payload-based approach to targeting solid tumours and haematological malignancies. We recently reported the development of a lower potency DNA mono-alkylator, FGX20-75, with substantially superior in vivo properties to other DNA alkylating agents and an efficacy/tolerability profile on-par with a topoisomerase inhibitor-based ADC. This molecule is active in the low nanomolar range (i.e., median potency of 6 nM across a 15 cell-line screen), but is sufficiently hydrophilic to allow efficient conjugation to IgG antibodies with Drug Antobody Ratios (DARs) of up to 7. A maleimide-linked analogue of FGX20-75 has been conjugated to a number of antibodies with a DAR of 4. The ADCs produced exhibit significant in vivo efficacy in human tumour xenograft models. For example, in one case, an ADC targeted to an undisclosed antigen produced complete tumour regressions at 10 mg/kg dosing (Q7dx2) in patient-derived xenograft model of osteosarcoma. A substantially increased tolerability profile compared to other DNA-interactive payloads has been observed (e.g., single dose MED of < 1 mg/kg and MTD in mice of up to 80 mg/kg for a DAR 4 construct). Furthermore, in cynomolgus toxicity studies, a HNSTD has yet to be established at 8 mg/kg. Thus, the increase in loading compared to other DNA-interactive payloads compensates for the drop in potency of FGX20-75, resulting in a potent ADC with substantially increased tolerability and potent efficacy in solid tumours. The favourable hydrophobicity profile of the low potency alkylator FGX20-75, and its ease of conjugation to antibodies, along with the significant in vivo efficacy and tolerability of the ADCs produced from it, suggest that this low potency DNA-alkylating payload represents a promising new approach in the treatment of solid tumours.

Citation Format: Paul J. Jackson, Paolo Andriollo, Nicolas Veillard, George Procopiou, David E. Thurston. In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6334.
Abstract 6338: Higher-resolution protein interaction networks for precision medicine: A case for drug repurposing in head and neck cancer
Authors: Shah Maryam , Riaz Arsalan , Khan Faisal
Published: June 2022

Protein-Protein Interaction (PPI) networks can be useful scaffolds for the integration of whole cell multi-omics datasets that can aid significantly in drug discovery research. This study aims to use domain-domain interaction (DDI) data to produce high resolution protein interaction networks with enhanced topological insights for head and neck squamous cell carcinoma as well as the more well studies, triple negative breast cancer (TNBC). An extensive literature review identified 65 driver genes for HNSCC and 19 genes for TNBC which collectively had 557 and 316 protein domains. Eventually, 343/557 and 191/316 domains had well-annotated somatic mutations reported in COSMIC. PPI networks were created using BioGrid and STRING data and the top two hubs in PPI networks were TP53 for HNSCC and EGFR for TNBC, while the top two hubs in DDI networks were PF12796 (NOTCH) and PF07714 (EGFR) for HNSCC and TNBC networks, respectively. The top nodes in the densest sub-clusters based on module analysis in PPI networks were ERBB4, MET and NOTCH1 for HNSCC, and FGFR1, AR, and EGFR for TNBC. For DDI networks, the top nodes in the densest subcluster for HNSCC were PF06816 (NOTCH1-3), while for TNBC PF07714 domains from FGFR1, ERBB2 and EGFR were the top nodes. Our preliminary results re-emphasize the significance of NOTCH, EGFR and TP53, and their domains, in cancer networks. Next, we attempted to decipher potential candidates for drug repurposing and were able to map 20 out of the 31 FDA approved cancer drugs against proteins within our HNSCC network. EGFR was revealed as a hub gene in both HNSCC and TNBC networks with most of the therapies designed against the PF07714 kinase domain of EGFR. PF07714 is also a common domain in ERBB4, EPHA2, MAP2K1 and MET, and was targeted by different drugs in other cancer types. Next, we attempt to undertake an in vitro drug screen of all candidates against HNSCC cell lines to validate our in silico findings.

Citation Format: Maryam Shah, Arsalan Riaz, Faisal Khan. Higher-resolution protein interaction networks for precision medicine: A case for drug repurposing in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6338.
Abstract 659: Mechanisms of resistance to SHP2 inhibition
Authors: Wei Wei , Geer Mitchell , Guo Xinyi , Sanjana Neville , Neel Benjamin G.
Published: June 2022

SHP2 (PTPN11) is required for RAS activation, acting upstream of SOS1/2. Allosteric SHP2 inhibitors (SHP2is) stabilize auto-inhibition mediated by N-SH2/PTP interactions and prevent its activation by upstream stimuli. SHP2is impair the proliferation of oncogenic RTK- or cycling RAS mutant-expressing tumor cells and can overcome adaptive resistance to single agents targeting the RAS-MAPK-ERK pathway (e.g., EGFR, KRASG12C, BRAFV600E, MEK inhibitors). Multiple SHP2is are in clinical trials as single agents or in various combinations. As resistance to targeted therapy is universal, we sought to prospectively identify potential SHP2-extrinsic resistance mechanisms by performing genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive human FLT3-ITD driven AML cell lines, MOLM13 and MV4:11. We identified several expected “hits” based on known signaling pathways, including tumor suppressor (NF1, PTEN,CDKN1B) and “RASopathy” (LZTR1, RASA2) genes, as well as novel targets including INPPL1,MAP4K5, and some epigenetic modifiers. To test the generality of these findings, we built a“mini-CRISPR library of ~30 hits common to MOLM13 and MV4:11 cells and screened 15 SHP2i-sensitive lines. LZTR1 deletion conferred resistance in 14/15, followed by MAP4K5 (9/15),SPRED2 (6/15), STK40 (6/15), INPPL1 (5/15), NCOA6 (4/15), NCOR1 (4/15), and ELAVL1 (4/15). LZTR1 has been reported to regulate RIT or RAS stability. Notably, LZTR1 knockout universally increased RIT1, but in some lines, also increased RAS. INPPL1 encodes SHIP2, a 5’-inositide phosphatase that negatively regulates AKT activation in insulin signaling. However, INPPL1 deletion also increased RAS and ERK activity and activated ERK-dependent genes in FLT3-ITD AML lines. Experiments with INPPL1 mutant showed that SHC binding and an N-terminal region, but not the SH2 domain or phosphatase activity, is required for negative regulation of RAS. Interestingly, INPPL1 deletion also promoted resistance to SHP2 inhibition in several EGFR mutant cell lines. MAP4K5 deletion also increased ERK-dependent gene expression. Kinase activity, but not JNK activation, was required for MAP4K5 action. Our results predict multiple mechanisms of SHP2i resistance, emphasizing the need for detailed understanding of the resistance landscape to arrive a combinations that provide long term disease control.

Citation Format: Wei Wei, Mitchell Geer, Xinyi Guo, Neville Sanjana, Benjamin G. Neel. Mechanisms of resistance to SHP2 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 659.
Abstract 689: A randomized phase III study assessing the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors
Authors: Raoof Sana
Published: June 2022

We designed a 6,000-patient prospective, multi-institutional randomized clinical trial to assess the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors. To ensure over 25% of participants are of disadvantaged or minority status, we have recruited multiple community hospitals (Jamaica, Flushing, Wyckoff, and Staten Island/Bronx satellites of Northwell hospitals) to the study in partnership with Memorial Sloan Kettering Cancer Center. Patients included in this study are survivors of non-metastatic non-small cell lung cancer, status-post definitive treatment (surgery or radiation) with no evidence of disease for at least one year. These patients may be on maintenance therapy for their prior lung cancer but may not have any other active malignancy at the time of enrollment. Participants will be randomized 1:1 to standard surveillance at the discretion of the treating physician or standard surveillance plus six-monthly methylation-based liquid biopsy tests over a two-year study period, and strict guidelines on follow-up of positive liquid biopsy testing will be provided to reduce harms from false positives or overdiagnosis.

The primary endpoint of this study is the incidence of late stage cancer (distant recurrence or new primary cancer of stage III/IV). Secondary endpoints include incidence of early cancers (locoregional recurrence or new primary cancer of stage I/II), metastasis-free survival, and utilization of liquid biopsy versus standard of care scans. We will stratify our results by minority and socioeconomic status to specifically ascertain the effect of this intervention on populations of need. This is the first randomized controlled trial of liquid biopsy in a survivor population and the first trial utilizing liquid biopsy in a large minority population. We will have preliminary experiences to report in April 2022.

Citation Format: Sana Raoof. A randomized phase III study assessing the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 689.
Abstract 727: Detection of early-stage lung cancer using a liquid biopsy test based on extracellular vesicle proteins
Authors: Hinestrosa Juan P. , Lewis Jean M. , Schroder Gregor , Balcer Heath I. , Kurzrock Razelle , Krishnan Rajaram
Published: June 2022

We have recently conducted a study to evaluate the use of proteins associated with extracellular vesicles (EVs) isolated using an alternating current electrokinetic (ACE) system for the detection of early stage (I & II) non-small cell lung cancer (NSCLC). Most lung cancers are diagnosed at advanced stages when treatments are less effective, pointing to the need for developing non-invasive screening strategies such as liquid biopsies. We tested the feasibility of detecting the presence of early stage (I-II) lung cancer using protein biomarkers carried by EVs in patient blood. Using an ACE microelectrode array, EVs were purified from NSCLC patient (N = 62; Stage I = 39, Stage II = 23) or control plasma (N = 390) and tested for the presence of cancer biomarker proteins with bead-based multiplex immunoassay kits. A machine learning algorithm based on recursive feature elimination with cross-validation was developed to identify the most important features for differentiation between cases and controls. The algorithm identified 10 protein biomarkers that were able to distinguish between the NSCLC and control patient samples with a receiver-operator characteristic (AUC) of 0.986 (95% CI: 0.976 - 0.996). Sensitivity was 66.1% at 99.2% specificity, rising to 79.0% and 93.6% sensitivity at 98.2% and 95.1% specificity, respectively. When further stratified, Stage I sensitivity was 53.8% and stage II sensitivity was 86.7% at the 99.2% specificity level. These results suggest that it is possible to detect early-stage NSCLC when treatments may be more effective, that EVs may carry the earliest signals of cancer development, and that a test based on blood-based EV-protein biomarkers can yield high sensitivity and specificity. Our results warrant investigation in larger datasets to validate the current observations with the potential application of this methodology for routine screening of at-risk populations.

Citation Format: Juan P. Hinestrosa, Jean M. Lewis, Gregor Schroder, Heath I. Balcer, Razelle Kurzrock, Rajaram Krishnan. Detection of early-stage lung cancer using a liquid biopsy test based on extracellular vesicle proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 727.
Abstract 747: Deciphering tumor ecosystems at super-resolution from spatial transcriptomics
Authors: Hu Jian , Coleman Kyle , Lee Edward B. , Kadara Humam , Wang Linghua , Li Mingyao
Published: June 2022

The tumor microenvironment (TME) contains networks of cells and structures that surround tumor cells. Cell populations in the TME, including their abundance, composition, and spatial location are critical determinants of the occurrence, growth, and metastasis of a tumor. A comprehensive analysis of the multiple exchanges between tumor cells and their TME is essential for understanding the underlying mechanisms of tumor growth and response to anti-cancer therapies. Recent advances in spatially resolved transcriptomics (SRT) techniques have enabled gene expression profiling while preserving location information in tissues, which innovates a promising avenue to study the TME in a spatial context. With the power of SRT, we aim to provide a detailed annotation of tumor structure and different lymphocytes by integrating gene expression information and cell morphology features in the complemented high-resolution histology image obtained from the same tissue section.

A major challenge that hinders gene expression and histology integration in SRT data is the relatively low resolution of gene expression data compared to pixel-resolution histology images. As gene expression is only measured in discrete spots that are separated by tissue gaps, a large proportion of the tissue area remains unmeasured (e.g., >50% in 10x Visium). The incomplete coverage of gene expression in ST has prevented the deciphering of detailed TME structures such as the tertiary lymphoid structure (TLS).To overcome this challenge, we present TESLA (Tumor Edge Structure and Lymphocyte multi-level Annotation), a machine learning framework that integrates gene expression and histology image in SRT to investigate the detailed strictures in TME. TESLA first fills in the gene expression for unmeasured areas and generates gene expression images in the same resolution as the histology image. Next, TESLA integrates the gene images with the histology image to annotate different tumor/TME cell types at pixel resolution. Some specific tumor-infiltrating lymphocytes structures, such as TLSs, can also be detected by colocalization analysis of different lymphocytes. TESLA is also able to characterize high-resolution cellular and molecular spatial structures of tumor by separating tumor into different subtype regions and elucidating differential transcriptome programs. The detailed multi-level annotations performed by TESLA provide a comprehensive understanding of the spatial context and the nature of cellular heterogeneity of the TME.

Citation Format: Jian Hu, Kyle Coleman, Edward B. Lee, Humam Kadara, Linghua Wang, Mingyao Li. Deciphering tumor ecosystems at super-resolution from spatial transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 747.
Abstract 763: Linking Down syndrome, clonal hematopoiesis, and autophagy
Authors: Evans Edward James , Granrath Ross , Smith Keith , Espinosa Joaquin , Thorburn Andrew , DeGregori James
Published: June 2022

Down syndrome (DS) is the result of trisomy in chromosome 21 (T21) and is associated with an increased risk of diseases, particularly acute myeloid leukemia (AML). However, people with DS have variable disease risks and severities that have yet to be explained. We hypothesize that differing characteristics of clonal hematopoiesis (CH) may coincide with and/or contribute to poor health outcomes seen in people with DS and can help explain differences in disease outcome. To characterize CH, we use a rare-mutation detection technique called Duplex Seq, only requiring a blood draw to obtain the DNA from leukocytes. This targeted-sequencing tool uses a double-stranded tag to incorporate mutational data from both strands of DNA, enabling high sensitivity through the elimination of DNA processing errors. Using bioinformatics and COSMIC’s Cancer Gene Census, we have established differences in mutational patterns that enable us to distinguish people with DS from people without DS and characterize the variability among people with DS. Notably, protein-altering mutations in genes responsible for the differentiation of hematopoietic stem and progenitor cells are more prevalent among people with T21 than their counterparts who are disomic in chromosome 21 (D21). Coupling our genomic findings with other -omics approaches, we have drawn associations between the observed mutations and phenotypes of these individuals. Using mouse models of DS (Dp16, Dp17, and Dp10), we plan to investigate the susceptibility of CH and leukemogenesis with the use of a Moloney Murine Leukemia virus, expecting the mice modeling DS to have more prevalent CH and more leukemias. Furthermore, based on our analyses of leukocytic gene expression differences between people with DS with or without CH, we believe that people with DS have a varying reduction in autophagy that enables the presence of harmful CH and increased disease risk in some individuals. Using a GFP-LC3-RFP construct, we plan to quantify and compare basal autophagic flux between the mouse models of DS and their control littermates. This will enable us to draw the links between DS, CH, and autophagy. Future work will be centered around manipulating autophagy using transgenic mice and non-invasive interventions to see if deleterious phenotypes and risks to AML can be reversed. Overall, these studies offer a means by which disease risk in people with DS can be monitored through CH and a potential mechanism that can be altered by non-intrusive means to improve longevity and quality of life.

Citation Format: Edward James Evans, Ross Granrath, Keith Smith, Joaquin Espinosa, Andrew Thorburn, James DeGregori. Linking Down syndrome, clonal hematopoiesis, and autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 763.
Abstract 776: Expression of SOX15 and Wnt pathway genes in papillary thyroid carcinoma
Authors: Buyru Ayse Nur , Soysal Ayşegul , Ozaydın Ahmet , Seyhan Betul , Arıkan Soykan , Dalay Nejat
Published: June 2022

Although thyroid cancer (TC) is a rare cancer with a rate of 2.1%, it is the most common cancer type among endocrine tumors. The molecular mechanisms of thyroid cancer, which develops as a result of environmental and genetic factors, are still unclear. SOX family genes are transcription factors that are expressed in a tissue-specific manner and play a role in the developmental processes. SRY-box transcription factor 15 (SOX15) is an important member of the SOX family and is involved in carcinogenesis. Its downregulation has been associated with the development and progression of different human malignancies. Some SOX family members have been reported to control cell proliferation by acting as negative regulators of the Wnt/β-catenin signaling pathway. MYC, CCND1 and CTNNB1 genes are important components of the Wnt signaling pathway. Recently, we have shown that epigenetic silencing of the SOX15 gene is associated with the pathogenesis of papillary thyroid carcinoma,In the present study, to further the understanding of the molecular mechanisms of SOX15 in papillary thyroid carcinoma (PTC) we investigated SOX15 expression in association with the transcriptional targets of the Wnt/β-catenin pathway.Primary thyroid tumors and adjacent nonmalignant tissue samples were collected from 52 patients, prior to any treatment. Total RNA was isolated from tissue samples and reverse transcription was performed. Expression levels of the SOX15, CTNNB1, c-MYC and CCND1 genes were analyzed by qRT-PCR using the SYBR green and Light-Cycler 480 system (Roche Diagnostics, Germany). β2M was used as the reference to normalize the mRNA levels. Statistical analysis was performed using the SPSS 21.0 (IBM® SPSS® Statistics, IBM Corporation Somers, NY, USA) program.SOX15 gene expression was significantly downregulated in 64.6% of PTC tissues compared to their normal counterparts. In contrast, CCND1, CTNNB1 and c-MYC gene expressions were significantly upregulated in 70.2%, 60% and 57.8% of the patients. Among the group of patients with downregulated SOX15 expression CCND1, CTNNB1 and c-MYC expression were upregulated in 46.8%, 40% and 40% of the subjects, respectively. Our data suggest that SOX15 downregulation may contribute to activation of Wnt signaling and provides further evidence indicating involvement of SOX15 in modulating the Wnt/β-catenin pathway in thyroid carcinogenesis.

Citation Format: Ayse Nur Buyru, Ayşegul Soysal, Ahmet Ozaydın, Betul Seyhan, Soykan Arıkan, Nejat Dalay. Expression of SOX15 and Wnt pathway genes in papillary thyroid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 776.
Abstract 808: In vivo targeting of replication protein A for cancer therapy
Authors: VanderVere-Carozza Pamela , Gavande Navnath , Jalal Shadia , Pollok Karen , Ekinci Elmira , Heyza Joshua , Patrick Steve , Masters Andi , Turchi John , Pawelczak Katherine
Published: June 2022

Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination and the DNA-damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second generation RPA inhibitors (RPAi’s) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first generation RPAi’s, second generation molecules with increased cellular permeability, induce cell death via apoptosis. Second gen RPAi’s elicit single agent in vitro anticancer activity across a broad spectrum of cancers and the cellular response supports a threshold exists before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors as well as traditional DNA damaging cancer therapeutics. Consistent with the chemical RPA exhaustion model, we demonstrate that the effects of RPAi on replication fork dynamics. An optimized formulation was developed that resulted in single agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAi’s eliciting a state of chemical RPA exhaustion can provide an effective therapeutic option for difficult to treat lung cancers.

Citation Format: Pamela VanderVere-Carozza, Navnath Gavande, Shadia Jalal, Karen Pollok, Elmira Ekinci, Joshua Heyza, Steve Patrick, Andi Masters, John Turchi, Katherine Pawelczak. In vivo targeting of replication protein A for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 808.
Abstract 824: Loss of Parkin's inactivation by autoubiquitination induces prostate cancer tumorigenesis
Authors: Lee SeungBaek
Published: June 2022

Mutations in the E3 ubiquitin ligase Parkin have been linked to familial Parkinson’s disease as well as various human cancers. Although the activation of Parkin's E3 ligase is well characterized, the mechanism that tunes down tumorigenesis by phosphorylation-mediated auto-ubiquitination is largely unknown. Here we found that Parkin S378 is phosphorylated in mitosis while Parkin S131 is phosphorylated in late G1-S. Parkin protein levels were significantly lower in interphase compared to mitosis. Also, we checked that parkin itself degraded the protein by autoubiquitination in the cells overexpressing Parkin S131. Parkin S131D mutant significantly increased the rate of tumorigenesis compared to the control in in vitro and mouse models. Furthermore, Parkin S131 mutation was found in several patients with prostate cancer. These results suggest that the inactivation of Parkin by auto-ubiquitination impairs its ubiquitination activity and abolishes its tumor-suppressive effect in prostate cancer.

Citation Format: SeungBaek Lee. Loss of Parkin's inactivation by autoubiquitination induces prostate cancer tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 824.