bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3967: CRISPR/Cas9 screening identified novel membrane targets sensitizing hepatocellular carcinoma cells to natural killer cell-mediated cytotoxicity
Authors: Li Shuo , Han Lin , Zhang Siyao , Geng Guangfeng , Huo Lei , Huang Dawei , He Zhaoren , Li Shuoran , Jiang Zhaoshi , Rong James X.
Published: April 2023

Natural killer cells (NK) play a central role in cancer immune surveillance by directly killing cancer cells and producing pro-inflammatory cytokines to stimulate and recruit other immune cells to elaborate long-lasting anti-tumor responses. However, little is known about the immune escape mechanisms and regulatory proteins, particularly those for NK, involved in hepatocellular carcinoma (HCC), one of the most common and lethal cancers. To identify the determinants of NK killing function, we performed an HCC cell line-based CRISPR/Cas9 loss-of-function genetic screen, using a human whole membrane protein library containing ~7000 genes curated from 3 public membrane protein datasets. The human SNU449 was chosen as a representative HCC cell line for CRISPR/Cas9 editing based on the genetic profile analysis, representing one HCC patient subpopulation (> 30%) in the TCGA cohort. The cell line was incubated with NK92 cells at ratios of 2:1, 1:1, and 0.5:1. Bioinformatics methods for prioritizing genes (e.g., MAGeCK) were applied on 3 tested groups with different ratios. Single guide RNAs targeting genes in the antigen presentation machinery were depleted, including HLA-C, B2M, and TAP1/2, whereas components of the tumor-immune synapse, such as NCR3LG1 and ICAM1, were enriched, confirming the validity of the screen. SLC33A1 (an endosomal acetylCoA transporter) and SLC31A1 (the major copper influx transporter) were also depleted, previously unknown as NK regulators. The effects of SLC33A1 and SLC31A1 were validated in individual gene knockout cells generated respectively by lentiviral sgRNA expression. Furthermore, knockout of either transporter in SNU449 cells increased IFNγ secretion, confirming NK92 activation. Our results revealed that CRISPR/Cas9-based functional genomics screens in HCC cell lines could identify novel targets modulating NK-mediated killing. Further analysis of mechanisms of action, and particularly functional validation in in vivo systems, will potentially provide novel targets for the treatment of HCC.

Citation Format: Shuo Li, Lin Han, Siyao Zhang, Guangfeng Geng, Lei Huo, Dawei Huang, Zhaoren He, Shuoran Li, Zhaoshi Jiang, James X. Rong. CRISPR/Cas9 screening identified novel membrane targets sensitizing hepatocellular carcinoma cells to natural killer cell-mediated cytotoxicity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3967.
Abstract 3971: Developing cancer cell based in vitro and in vivo models with CRISPR-mediated knock-in technology for anti-tumor drug discovery
Authors: Xu Nengwei , Wang Reifeng , Xiang Jian , Gu Qingyang , Qiang Xiangnan
Published: April 2023

Human cancer cell lines have long been applied for anti-tumor drug discovery considering their acquired genomic diversity of different carcinomas. Genetic engineering based on cancer cell lines is no doubt a useful and promising approach in induction of new therapeutic targets/elements while maintaining intrinsic characteristics of original cell in parallel. Recently, the emergence of CRISPR knock-in technology has accelerated precise editing across whole genome, from gene depletion, small fragment insertions to site-direct mutations, thereby prompting our understanding of the influence of a specific oncotarget in given tumor genetic background. Herein, by employing CRISPR/Cas9 system, two human cancer cell line-based, inheritable drug resistance models were established where the mutation site C481S of BTK in REC-1 conferred resistance to Ibrutinib and the mutation site R537S/D538G of ESR1 exerted resistance to Fulvestrant in MCF-7. In addition, the engineered cell models also enable the mechanism characterization and development of viable therapeutic agents targeting those oncogenic-driver mutations in a subtype of cancers. The murine colon cancer cell line CT26, which harbors KRASG12D mutation, was genetically modified to express KRASG12C protein to allow for an expandable pocket providing opportunities for compound recruitment. The resultant KRASG12C CT26 cell line showed pronounced inhibitory effect after treatment with AMG510. More interestingly, the therapeutic combination involving both AMG510 and anti-PD1 antibodies demonstrated more effective anti-tumor activities when compared to monotherapy. Moreover, CRIPSR-mediated engineered knock-in cells with a traceable tag linked to endogenous oncotarget also exhibit capability in new therapeutic modality discovery. Based on HiBiT protein tagging technology, we generated a series of HiBiT knock-in cell lines for real-time cell-based protein degradation analysis on various compelling targets, such as ESR1, KRAS, and BRD4, et al. Thereby, the construction of these in vitro and in vivo models with the ease of CRISPR KI technology is indispensable in new generation of therapeutic drug exploration.

Citation Format: Nengwei Xu, Reifeng Wang, Jian Xiang, Qingyang Gu, Xiangnan Qiang. Developing cancer cell based in vitro and in vivo models with CRISPR-mediated knock-in technology for anti-tumor drug discovery. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3971.
Abstract 4023: Inhitibing GRP78 in non-small cell lung cancer with acquired resistance to EGFR-TKI
Authors: Park Jaewoo , Purushothaman Baskaran , Hong Sera , Choi Munkyung , Song Joon Myong , Kang Keon Wook
Published: April 2023

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have improved the survival of non small cell lung cancer (NSCLC) patients with active mutation of EGFR. However, some of the patients who received EGFR-TKIs showed the acquired resistance, and eventually relapsed within several months. In the TCGA data sets, gene expression of glucose-related protein 78 (GRP78), an ER chaperone, was upregulated in NSCLC tissues. We also confirmed that protein level of GRP78 was increased in HCC827-GR, H1993-GR and H1993-ER NSCLC cell lines with acquired resistance to EGFR-TKIs. Since GRP78 modulates ER stress level which induces ROS and apoptosis, Ru(II) complex 1 and HA15, both the known GRP78 inhibitors induced higher ER stress and ROS generation accompanying more remarkable anti-proliferative and apoptotic effects in EGFR-TKI-resistant NSCLC cell lines. GRP78 level was also found to be higher in H1975, EGFR-TKI-resistant T790M-mutant cell line than other NSCLC cell lines. Blockade of GRP78 also led to apoptosis in H1975, which is consistent with the results found in the acquired EGFR-TKI-resistant cell lines. In summary, we suggest GRP78 targeting as a potential therapeutic strategy for the acquired EGFR-TKI-resistant NSCLC patients.

Citation Format: Jaewoo Park, Baskaran Purushothaman, Sera Hong, Munkyung Choi, Joon Myong Song, Keon Wook Kang. Inhitibing GRP78 in non-small cell lung cancer with acquired resistance to EGFR-TKI. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4023.
Abstract 4024: Overcoming ALK resistance with covalent cysteine-reactive inhibitors in lung cancer
Authors: Yang Diane , Harry Stefan , Zhang Edwin , Oppong-Holmes Zavontae , Carlin Alexander Daniel , Yang Wenxin , Smith Abigail , Onozato Maristela , Bar-Peled Liron , Iafrate Anthony J.
Published: April 2023

The EML4-ALK fusion gene is the main oncogenic driver in 5% of non-small cell lung cancer and has been effectively targeted using ALK-specific tyrosine kinase inhibitors. While survival rates have improved steadily with each new generation of ALK TKI, resistance generally develops, including second site ALK kinase mutations as well as by-pass track activation. Since almost all anti-ALK approaches have focused on kinase domain inhibition, we sought to develop novel inhibitors with alternative mechanisms of action against ALK to overcome current drug resistance. Cysteine-reactive small molecule drugs may enable new mechanisms of target inhibition, and clinically successful examples of recent FDA-approved drugs in NSCLC include afatinib, osimertinib, sotorasib, and adagrasib.We aimed to explore and uncover novel cysteine-reactive covalent inhibitors of EML4-ALK. Using cysteine druggability mapping (CDM), a proteome-wide mass spectrometry target engagement assay, we first determined the landscape of reactive cysteines in ALK-positive cell lines and identified various targetable cysteines within the MAPK pathway and within the EML4-ALK fusion protein itself. To identify small molecules that modulate ALK activation, degradation, and downstream signaling, we conducted a high-content phosphorylated protein screen by testing 4,400 reactive cysteine compounds and found 20 potential hits that impacted ALK phosphorylation or expression. Using proteomic analysis, we have determined the comparative specificity of these compounds, and have ranked them based on p-ALK reduction efficiency and on their off-target binding patterns. We have initiated hit-to-lead development on a compound that binds to the EML4 portion of the fusion and we are performing a detailed analysis of its mechanism of action. To further optimize the potency of the compound, we designed, synthesized, and are testing several hundred analog compounds. By applying the hit compounds from the screen in ALK TKI-resistant models, we will be able to evaluate the ability of these compounds to overcome ALK resistance. To our knowledge, we have identified the first EML4-ALK covalent binder targeting the EML4 domain. Using the unique mechanism of action of the current ALK kinase inhibitor, we have uncovered a potential compound to overcome ALK resistance.

Citation Format: Diane Yang, Stefan Harry, Edwin Zhang, Zavontae Oppong-Holmes, Alexander Daniel Carlin, Wenxin Yang, Abigail Smith, Maristela Onozato, Liron Bar-Peled, Anthony J. Iafrate. Overcoming ALK resistance with covalent cysteine-reactive inhibitors in lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4024.
Abstract 4043: Stimulation of the mapk and pi3k/akt pathways in pancreatic cancer cells by polyisoprenylated cysteinyl amide inhibitors
Authors: Ofosu-Asante Kweku , Lazarte Jassy M. , Burra Amarendar G. , Lamango Nazarius S.
Published: April 2023

Pancreatic cancer is the third deadliest cancer with a 5-year survival rate of less than 10%. Over 90% of reported cases are driven by KRAS mutations. KRAS signals through the MAPK and PI3K pathways. Targeting mutant KRAS has been a decades-long challenge until recently whereby drugs that react with specific mutant proteins have been developed. Polyisoprenylated cysteinyl amide inhibitors (PCAIs) are potential anticancer agents with an alternative design strategy targeting polyisoprenylation-dependent processes of hyperactive mutant or overexpressed G-proteins. The effect of PCAIs on the viability and downstream mediators of KRAS signaling was determined on PANC-1 and MIAPaCa-2 cells. Of the 16 different analogs tested, NSL-YHJ-2-45 and NSL-YHJ-2-27 were the most potent with EC50 values of 3.6 and 3.8 against PANC-1 cells, respectively. For MIAPaCa-2 cells, NSL-YHJ-2-27 was the most potent with an EC50 value of 2.2. Western blotting analysis of PCAIs-treated PANC-1 cells revealed that phosphorylated BRAF, MEK 1/2, ERK 1/2 and p90RSK increased by 64, 129, 152 and 79%, respectively, while phosphorylated CRAF levels decreased by 27%. Moreover, monomeric G-proteins, CDC42, RHOA and RAC 1/2/3 protein levels decreased by 20, 58 and 13%, respectively. NSL-YHJ-2-27 (5 µM) also increased the levels of pAKT (Ser 473) and pAKT (Thr 308) by 72 and 192%, respectively. When MIAPaCa-2 cells were treated with 0-5 µM NSL-YHJ-2-27, MEK 1/2, ERK 1/2 and p90RSK phosphorylation increased by 78, 270 and 260%, respectively. However, at 5 µM NSL-YHJ-2-27, there were no significant changes in protein levels of the monomeric G proteins RAC 1/2/3 and RHOA, but protein levels of CDC42 increased by 132%. NSL-YHJ-2-27 (5 µM) increased the levels of pAKT (Ser 473) and pAKT (Thr 308) of MIAPaCa-2 cells by 97 and 82%, respectively. The results indicate the effect of PCAIs on the phosphorylation of important kinases involved in MAPK and AKT pathways. These effects on these signaling pathways strongly indicate the potential of the PCAIs against RAS-driven cancers.

Citation Format: Kweku Ofosu-Asante, Jassy M. Lazarte, Amarendar G. Burra, Nazarius S. Lamango. Stimulation of the mapk and pi3k/akt pathways in pancreatic cancer cells by polyisoprenylated cysteinyl amide inhibitors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4043.
Abstract 4064: PD-1 blockade therapy enhances the antitumor effects of lymphodepletion and adoptive T cell transfer
Authors: Watanabe Satoshi , Takahashi Miho , Suzuki Ryo , Arita Masashi , Sato Ko , Fujisaki Toshiya , Ohtsubo Aya , Shoji Satoshi , Shono Kunihiro , Masuda Takaaki , Sekiya Tomoki , Nozaki Koichiro , Tanaka Tomohiro , Kondo Rie , Saida Yu , Hokari Satoshi , Koya Toshiyuki , Kikuchi Toshiaki
Published: April 2023

Background: Lymphodepleting cytotoxic regimens, such as chemotherapy and radiotherapy, have shown the ability to enhance antitumor immunity. Although the mechanisms of antitumor effects augmentation in tumor-bearing hosts after lymphodepletion and T cell transfer have been intensively investigated, the influence of lymphodepletion followed by T cell transfer on immune checkpoint molecules (ICMs) expressed on tumor cells and immune cells remains to be elucidated. In the current study, we evaluated the effects of lymphodepletion and adoptive T cell transfer on ICMs in the tumor microenvironment. In addition, we investigated whether lymphodepletion and adoptive transfer of T cells augments antitumor effects of anti-PD-1 blockade therapy.

Methods: B6 mice were inoculated subcutaneously with the MCA205 murine fibrosarcoma. On day 7, mice were lymphodepleted by sublethal irradiation with 500 cGy and were reconstituted intravenously with spleen cells from normal mice as a source of naïve T cells. These mice were injected intraperitoneally with anti-PD-1 mAb on days 7 and 14. On day 21, tumor tissues were harvested, and single cell suspensions were labeled with fluorophore-conjugated antibodies for FACS analyses.

Results: The expressions of ICMs, including PD-L1, PD-1, TIGIT, TIM-3 and LAG-3, were upregulated on recipient CD4+ and CD8+ T cells in the tumor microenvironment. In contrast, these ICMs were significantly reduced in transferred donor T cells. Administration of anti-PD-1 antibodies after lymphodepletion and adoptive transfer of T cells significantly inhibited tumor progression. Furthermore, transfer of both donor CD4+ and CD8+ T cells was responsible for this augmentation of antitumor effects.

Conclusions: Our observations suggest that a possible mechanism of the antitumor effect augmentation mediated by lymphodepletion followed by T cell transfer is the prevention of donor T cell exhaustion and dysfunction. Blockade of PD-1 significantly enhanced the antitumor effects of lymphodepletion and T cell transfer.

Citation Format: Satoshi Watanabe, Miho Takahashi, Ryo Suzuki, Masashi Arita, Ko Sato, Toshiya Fujisaki, Aya Ohtsubo, Satoshi Shoji, Kunihiro Shono, Takaaki Masuda, Tomoki Sekiya, Koichiro Nozaki, Tomohiro Tanaka, Rie Kondo, Yu Saida, Satoshi Hokari, Toshiyuki Koya, Toshiaki Kikuchi. PD-1 blockade therapy enhances the antitumor effects of lymphodepletion and adoptive T cell transfer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4064.
Abstract 4133: OncoTAM, a comprehensive preclinical platform to explore macrophages as key drivers of cancer progression and develop new therapies against tumor-associated-macrophages
Authors: Mignard Caroline , France Damien , Bichat Francis , Legrand Nicolas , Duchamp Olivier
Published: April 2023

Tumor-Associated Macrophages (TAMs) play an important role in the development of tumors, modulation of neoangiogenesis, immune suppression, and metastasis. A high infiltration of macrophages in the tumor is also correlated with a poor prognosis in several cancer types. Therefore, they became an attractive target for cancer immunotherapies. Several macrophage-targeting approaches in anticancer therapy are under development, including TAM depletion, inhibition of new TAM differentiation, or re-education of TAM activation for cancer cell phagocytosis. In this presentation, we will share different examples of in vitro assays and in vivo models we are implementing to support preclinical development of novel TAM-targeting strategies. Antibody-dependent cellular phagocytosis (ADCP) has been used to demonstrate one crucial mechanism of action of different antibody (Ab) therapies targeting macrophages. Some of these Ab (including anti-CSF1) have then been tested in syngeneic in vivo tumor models. To reach this goal, we demonstrated that the tumor implantation site in mice (subcutaneous vs orthotopic) could impact the polarization of macrophages (M1 vs M2). Differences in the ratio of M1 and M2 subtypes infiltrating the PAN-02 pancreatic murine tumors were observed, and anti-CSF1 antibodies increased the survival of mice bearing orthotopic Renca murine kidney tumor by eliminating TAMs. Additionally, in xenograft models of human breast tumors in NOD-SCID mice, the eradication of TAMs by anti-CSF1R clearly demonstrated the importance of macrophages in the tumor progression and in the anti-tumor efficacy of Abs mediated by macrophages. By using an orthotopic Hepa1-6 murine liver cancer model, we showed high antitumor efficacy of compounds targeting the STAT6 pathway by reprogramming immunosuppressive TAMs into an M1 phenotype that promotes the induction of a cytotoxic immune response. For compounds displaying no cross-reactivity with murine target, we developed models and characterized the TAMs in breast, colon, melanoma and head & neck PDX and CDX tumors in different huCD34-engrafted mouse models. Altogether, the panel of in vitro assays and in vivo tumor models in OncoTAM should be useful to provide insights on the mechanism of action and antitumor efficacy of novel immune-oncology strategies targeting macrophages.

Citation Format: Caroline Mignard, Damien France, Francis Bichat, Nicolas Legrand, Olivier Duchamp. OncoTAM, a comprehensive preclinical platform to explore macrophages as key drivers of cancer progression and develop new therapies against tumor-associated-macrophages. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4133.
Abstract 4175: Development of breast cancer risk assessment tool: The Korean decision aid for cancer screening (K-DACS) study
Authors: Jung Wonyoung , Mark Park Yong-Moon , Park Sang Hyun , Han Kyungdo , Park Junhee , Yeo Yohwan , Lee Jung Kwon , Sandler Dale P. , Shin Dong Wook
Published: April 2023

Purpose: Widely used breast cancer risk prediction tools are based on data from Western countries, but risk factors may differ for Asian women. Hence, we aimed to develop a risk assessment tool for breast cancer in Asian women, using a nationwide, population-based cohort in Korea. Methods: Women aged ≥ 40 years who participated in both breast cancer screening and general health examination in 2009 were eligible for this study. Age, body mass index (BMI), breast density, lifestyle and reproductive factors, and comorbidities were used to develop 5-year breast cancer risk prediction models in premenopausal (n=771,856) and postmenopausal (n=1,108,047) women at baseline. Backward stepwise selection in the Cox proportional hazards model was used to construct the best-fit risk prediction model, which was then converted into a risk score nomogram, representing an individual probability estimate of incident breast cancer. Model performance was evaluated by discrimination and calibration. Results: Among premenopausal women, high BMI, low parity, short breastfeeding period, early age at menarche, high breast density, history of benign breast mass, and family history of breast cancer contributed to breast cancer risk prediction. The appropriate predictors in postmenopausal women additionally included age, type 2 diabetes, dyslipidemia, late age at menopause, hormone replacement therapy use, except for number of parities. The concordant statistic of risk prediction model was 0.58 (95% confidence interval [CI] 0.57-0.59) for premenopausal women, and 0.64 (95% CI 0.63-0.65) for postmenopausal women. Our model correlated well in the calibration plot in both premenopausal and postmenopausal women.Conclusions: Our breast cancer risk prediction model showed good performance for postmenopausal women, providing the background for risk-based screening recommendations in Asian women.

Citation Format: Wonyoung Jung, Yong-Moon Mark Park, Sang Hyun Park, Kyungdo Han, Junhee Park, Yohwan Yeo, Jung Kwon Lee, Dale P. Sandler, Dong Wook Shin. Development of breast cancer risk assessment tool: The Korean decision aid for cancer screening (K-DACS) study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4175.
Abstract 4191: Assessing performance of biomarker extraction from electronic health records: Data augmentation methods for a hierarchical self-attention network (HiSAN)
Authors: Priya Shalini , Peluso Alina , Shekhar Mayanka Chandra , Danciu Ioana , Miller Jordan , Hanson Heidi A.
Published: April 2023

Background: Extraction of HER2 status from electronic health records (EHR) may expedite clinical trials matching and be used for survivorship research. Deep learning (DL) algorithms have potential to extract this data; however, inherent class imbalance leads to reduced model performance. We compare state of the art strategies to handle class imbalance in models trained to extract HER2 status. This comparative analysis may be used as a guideline for HER2 extraction.

Methods: 680,117 pathology reports collected from 2017-2021 by the National Cancer Institutes’ Surveillance, Epidemiology, and End-Results (SEER) program were used for this study. Pathology reports are manually labelled by cancer registrars as HER2 -, HER2+, or Unknown (class ratio 65%, 11%, 24% respectively). We compare six data augmentation (DA) methods: balanced frequency weighting, ROS while up-sampling HER2+ by 595%, RUS while down-sampling HER2- by 83%, SMOTE, ADASYN, and SMOTE-Tomek. As a comparison we consider the HiSAN model i.e., a DL architecture currently used by SEER for automatic classification of reports.

Result: Applying DA strategies did not improve the performance of the HiSAN model (Table 1). Frequency based class-weighting (Acc=0.78), ROS (Acc=0.81), and RUS (Acc=0.80) perform worse than the baseline model, suggesting simple data augmentation methods do not boost performance for this task. Advanced oversampling with SMOTE (Acc=0.88) and ADASYN (Acc=0.88) perform better than simple approaches, but do not improve the predictive accuracy of the baseline HiSAN.

Conclusion: Common DA methods do not improve the performance of the HiSAN biomaker method. While the overall accuracy of the baseline HiSAN model is quite high, other methods for improved accuracy should be explored.

Table 1. Method Accuracy (Acc) Sensitivity Specificity Precision HiSAN (Baseline) 0.8898 0.7583 0.8944 0.8507 Frequency class weighting 0.7826 0.8033 0.8932 0.7040 Random Over Sampling (ROS) 0.8057 0.7672 0.8883 0.7130 Random Under Sampling (RUS) 0.8042 0.7883 0.8930 0.6902 Synthetic Minority Oversampling Technique (SMOTE) 0.8796 0.7341 0.8827 0.8340 Adaptive Synthetic Sampling (ADASYN) 0.8764 0.7467 0.8863 0.8142 SMOTE-Tomek 0.8823 0.7620 0.8956 0.8200

Citation Format: Shalini Priya, Alina Peluso, Mayanka Chandra Shekhar, Ioana Danciu, Jordan Miller, Heidi A. Hanson. Assessing performance of biomarker extraction from electronic health records: Data augmentation methods for a hierarchical self-attention network (HiSAN). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4191.
Abstract 4222: Glyphosate and AMPA exposure: Associations with dietary intake and other factors
Authors: Lucia Rachel McFarland , Liao Xiyue , Huang Wei-Lin , Forman Danielle , Kim Alexis , Ziogas Argyrios , Norden-Krichmar Trina M. , Goodman Deborah , Alvarez Andrea , Masunaka Irene , Pathak Khyatiben , McGilvrey Marissa , David-Dirgo Victoria , Hegde Apurva , Pirrotte Patrick , Park Hannah Lui
Published: April 2023

Background: Animal and epidemiologic studies suggest that exposure to the weed killer, glyphosate, and its primary metabolite aminomethylphosphonic acid (AMPA), is associated with increased risk for cancer, including breast cancer and non-Hodgkin's lymphoma. The International Agency for Research on Cancer (IARC) has categorized glyphosate as a “probable carcinogen,” yet glyphosate is the most highly used pesticide in the world. Biomonitoring studies assessing levels of human glyphosate and AMPA exposure in the United States have been limited. Thus, we examined urinary levels of these chemicals in a cohort of postmenopausal women residing in Southern California and evaluated associations with demographics, dietary intake, and other behavioral factors.

Methods: 338 postmenopausal women provided two first-morning urine samples and at least one paired 24-hour dietary recall. Participants also reported on demographic and other factors. Urinary glyphosate and AMPA were measured using LC-MS/MS.

Results: Glyphosate was detected in nearly 90% of urine samples and AMPA in 67.2%. Urinary glyphosate and AMPA levels were lower in women who reported high levels of organic eating (p=0.04 and p=0.01, respectively). Urinary glyphosate was lower in women who reported higher levels of physical activity (p=0.03). Multivariate analysis showed that grain consumption, particularly refined grains, was significantly associated with higher urinary glyphosate levels (adjusted p=0.004). Alcohol consumption (adjusted p=0.001) and frequency of eating fast-food (adjusted p=0.006) were associated with higher urinary AMPA levels, while fruit (adjusted p=0.03) and corn (adjusted p=0.008) consumption were associated with lower AMPA.

Conclusions: In the largest study to date examining paired dietary recall data and measurements of urinary glyphosate and AMPA, the vast majority of women sampled had detectable levels. Consumption of certain foods, including grains and alcoholic beverages, were associated with higher urinary levels of glyphosate and AMPA.

Citation Format: Rachel McFarland Lucia, Xiyue Liao, Wei-Lin Huang, Danielle Forman, Alexis Kim, Argyrios Ziogas, Trina M. Norden-Krichmar, Deborah Goodman, Andrea Alvarez, Irene Masunaka, Khyatiben Pathak, Marissa McGilvrey, Victoria David-Dirgo, Apurva Hegde, Patrick Pirrotte, Hannah Lui Park. Glyphosate and AMPA exposure: Associations with dietary intake and other factors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4222.
Abstract 4286: A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data
Authors: Xiao Feifei , Qin Fei , Cai Guoshuai
Published: April 2023

The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect from mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data since cells comprising a subpopulation are found to share genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified CNAs) in the procedure of CNA detection, hence diminishing the accuracy of subclones identification from a large complex cell population. In this study, we developed a CNA detection method based on a fused lasso model, referred to as FLCNA, which can simultaneously identify subclones in single cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA benchmarking to existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. FLCNA was also applied to a real scDNA-seq dataset with breast cancer and clusters identified using FLCNA showed clearly different genomic variation patterns. In conclusion, FLCNA provided superior performance in subclone identification and CNA detection with scDNA-seq data.

Citation Format: Feifei Xiao, Fei Qin, Guoshuai Cai. A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4286.
Abstract 4308: Cancer as a disease of information
Authors: Goldstein Adam Julian
Published: April 2023

The causes and symptoms of cancer are often described in physical terms, for example as DNA mutations leading to increased cell proliferation. These understandings have been immensely informative, but physical changes are only one of several ways to understand what cancer is and why it behaves the way it does. An alternative perspective builds upon Claude Shannon's work in information theory, and sees cancer as a result of missing, noisy, and/or distorted information. In this talk I summarize existing research and discuss the implications for understanding cancer as a disease of information. I then explain how detecting and treating cancer look different when viewed through this lens. In particular, I discuss how this approach offers the hope for rehabilitating cancer cells by restoring expected information flows, in contrast to some current treatments which exacerbate information disruptions.

Citation Format: Adam Julian Goldstein. Cancer as a disease of information. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4308.
Abstract 4311: Using multiomics analysis to identify dysregulated transcription factors in non-small cell lung cancer (NSCLC) to drive the expression of a cancer-activated synthetic biomarker
Authors: Zhang Yue Wendy , Rudina Shireen , Wodziak Dariusz , Xia Chloe , Louie Maggie , Park Albert , Suhy David
Published: April 2023

Early detection of cancer is an important driver of increased survival, quality of life and reduced healthcare costs. Earli is developing a highly sensitive, orthogonal approach that uses a genetic construct that usurps dysregulated pathways and actively forces cancer cells to drive the expression of a detectable ‘synthetic’ biomarker. Identification of abnormally elevated transcription factors (TF) in cancer is crucial when developing a cancer-activated expression platform. Evaluating TF function in a genome wide fashion is a challenge, especially since TF activity is not solely reflected by just its RNA expression or even by protein abundance, but also its post-translational modification including phosphorylation. In this study, we use the publicly available multiomics dataset from Clinical Proteomic Tumor Analysis Consortium (CPTAC) which includes RNA-seq based transcriptional profiling, MS based protein abundance and phosphorylation from 211 paired tumor and normal adjacent samples derived from NSCLC patients. Performing Multiomics Factor Analysis (MOFA) analysis, we identified a short list of 34 dysregulated TFs in NSCLC that displayed high expression levels in at least two of the three omics platforms relative to normal tissues, six of which scored highly across all three. A subset of candidate TF binding sequences were subcloned as multimers into expression constructs with a basal promoter and empirically evaluated in multiple cancer cell lines, including patient-derived xenograft (PDX) cell lines and normal cell lines.Transfection experiments demonstrated that these novel chimeric synthetic promoters could produce robust levels of expression in PDX-derived cell lines that was 10-20x higher than expression mediated by known cancer-activated promoters such as the endogenous survivin (BIRC5) promoter. Furthermore, levels achieved were only 3-4 fold lower than a control EF-1a promoter, one of the strongest promoters, typically used to drive constitutive expression in mammalian cells. Currently, a small subset of these chimeric constructs is being tested in murine tumor models and in large animal cancer models such as oncopigs. These experiments will further drive the development of this approach for use in early cancer detection.

Citation Format: Yue Wendy Zhang, Shireen Rudina, Dariusz Wodziak, Chloe Xia, Maggie Louie, Albert Park, David Suhy. Using multiomics analysis to identify dysregulated transcription factors in non-small cell lung cancer (NSCLC) to drive the expression of a cancer-activated synthetic biomarker. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4311.
Abstract 4318: Cancer cell communication with macrophages prevents T cell activation during emergence of cell cycle therapy resistance
Authors: Griffiths Jason I. , Cosgrove Patrick A. , Castaneda Eric Medina , Nath Aritro , Chen Jinfeng , Adler Frederick R. , Chang Jeffrey T. , Khan Qamar J. , Bild Andrea H.
Published: April 2023

By corrupting signals for growth and survival, evolving cancer cells can engineer the tumor microenvironment (TME) to promote treatment resistance. However, the specific interactions between malignant and non-malignant cells that predispose drug resistance and their changes during treatment remain widely unknown. Here we examine the composition, communication, and phenotypic diversity of tumor-associated cell populations in serial biopsies from early-stage ER+ breast cancers. We used single-cell RNA sequencing to profile over 400 thousand malignant and non-malignant cells from patient tumor samples obtained before, during and after treatment. The patients received either endocrine therapy (letrozole) alone or in combination with a CDK4/6 cell cycle inhibitor (ribociclib). Our analyses reveal that cancer cells from ribociclib-resistant tumors stimulate macrophage differentiation towards an immune-suppressive phenotype through upregulation of a diversity of cytokines and growth factors. The macrophage phenotype shift leads to reduced crosstalk with cytotoxic T-cells via IL-2/15/18 receptors, diminishing T-cell activation and recruitment. These results indicate that cancer communications promoting an immune-cold TME predispose tumors to develop CDK4/6 cell cycle inhibitor resistance, and that the beneficial effects of blocking cancer cell proliferation must be balanced against their inhibitory effect on immune cell division and activation. An optimal treatment strategy will require coupling the prevention of cancer division with activation of an effective cytotoxic T-cell response.

Citation Format: Jason I. Griffiths, Patrick A. Cosgrove, Eric Medina Castaneda, Aritro Nath, Jinfeng Chen, Frederick R. Adler, Jeffrey T. Chang, Qamar J. Khan, Andrea H. Bild. Cancer cell communication with macrophages prevents T cell activation during emergence of cell cycle therapy resistance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4318.
Abstract 4322: AI assisted detection and characterization of tertiary lymphoid structures in patients with colorectal cancer
Authors: Burg Samantha , Hart Nathaniel , Powers Astin , Zhang Wenjun
Published: April 2023

Tertiary Lymphoid Structures (TLSs) are ectopic immune cell aggregates that form in response to abnormal physiology and inflammation. TLS presence in the tumor environment has been associated with positive clinical outcomes and response to immune checkpoint inhibition therapy. Using a fluorescent multiplex panel consisting of Pan-cytokeratin (PanCK), Programmed Death Ligand-1 (PD-L1), cluster of differentiation (CD) 8, CD3, and CD68 we developed a HALO-based artificial intelligence (AI) classifier to detect TLSs in colorectal cancer (CRC) tissue. In conjunction with cell-type and spatial analyses, we used the AI TLS classifier to characterize several features of the TLS and peri-TLS environment. We trained the AI classifier using 51 examples of TLSs from 8 patients, and applied it to images of 21 CRC patient tissues. TLSs were detected in 9/21 patient samples. We then used cellular detection and spatial analysis to characterize features of the TLS, including the germinal center (GC), T cell zone and peri-TLS area. We detected a higher cell density (Mean=12250 ±2039 SD; cells/mm2) within the interior of AI-detected GCs relative to the 1st 200 μm outside of the AI-defined GC border (8005±1870). In addition, we examined the spatial distribution of CD3+ and CD8+ T cells relative to the TLS GC. We found elevated CD3+ cell density in the interior of the GC (5784±1649) and within 200 μm of the GC border (5126±2239) which decreased at distances >200 μm from the GC border. We found CD8+ density to be elevated within the 1st 200 μm of the GC border (1903±1182) and declined 400 μm away from the GC border (963±828). The spatial distribution of T cells surrounding an area of high cell density is indicative of a T cell zone surrounding germinal center. Further analysis of the AI-detected TLS GCs indicated that PD-L1+ cell density was highest within the germinal center (355± 534;9) relative to the exterior of the germinal center (1st 150μm outside germinal center:276± 441). We created an AI classifier that can detect TLS(s) within patient tissue in the absence of a B-cell marker and confirmed that our AI classifier was detecting TLSs by characterizing canonical features of TLSs. Further exploration of the TLS and peri-TLS area may offer insights into immune-tumor interaction within the tumor microenvironment, and paired detection of TLSs in a clinical cohort with outcome data may predict patient response to immune checkpoint inhibitor therapy.

Citation Format: Samantha Burg, Nathaniel Hart, Astin Powers, Wenjun Zhang. AI assisted detection and characterization of tertiary lymphoid structures in patients with colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4322.
Abstract 4340: HLA-B44 motif neoepitope is associated with a favorable tumor immune microenvironment and predicts ICB response in NSCLC
Authors: Li Rui , Fares Charlene M. , Grogan Tristan R. , Zhang Tianhao , Li Debory , Theisen Matthew , Velez Maria A. , Brodrick Paige M. , Lind-Lebuffe Jackson P. , Radwan Yazeed , Ayzenberg Gregory A. , Elashoff David , Liu Bin , Lisberg Aaron E. , Cumming Amy L. , Garon Edward B.
Published: April 2023

Immune check point blockade (ICB) has recently transformed the treatment of non-small cell lung (NSCLC). However, the majority of patients do not respond to ICB. For ICB to be effective, tumor neoantigens need to be presented in a human leukocyte antigen (HLA) class I-restricted manner. Recent studies by our group and others have shown that HLA-B44 supertype is associated with extended survival in patients treated with ICB. Herein, we hypothesize that HLA-B44-specific motif neoepitopes generate an active tumor immune microenvironment and a favorable ICB response in NSCLC. Utilizing the TCGA database, we found that nearly half of the NSCLC patients have at least one HLA-B44 allele, of whom 36.8% and 37.3% of patients harbor at least one B44 motif neoepitope in lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC), respectively. In a pooled analysis of patients with LUAD and LUSC, gene expression of PD-L1, CTLA-4, LAG-3, CXCL9, CXCL10, CXCL13, CD8A and cytolytic gene signature (includes GZMA and PRF1) is elevated in patients with B44 motif neoepitopes compared to those without motif neoepitopes. Immune cell component analysis showed increased infiltration of Th1, Th2 and CD8 T cells in LUAD and regulatory and CD8 T cells in LUSC. Although a linear regression model revealed a positive correlation between tumor mutational burden (TMB) and number of B44 motif neoepitopes, pooled analysis of LUAD and LUSC with similar TMB showed significant elevation of CTLA-4, LAG3, CXCL10 and a trend of increased expression of CXCL9 in motif patients. Upon investigation of possible immune editing, we found a significantly higher proportion of genes containing B44 neoepitope downregulated at the RNA level both in LUAD and LUSC. Lastly, we showed that combining B44 motif with either PD-L1 or TMB improved prediction of progression-free survival in NSCLC patients treated with ICB. In summary, we demonstrate that HLA-B44 motif neoepitopes are associated with a favorable tumor immune microenvironment and can serve as a potential biomarker for ICB benefit in NSCLC patients.

Citation Format: Rui Li, Charlene M. Fares, Tristan R. Grogan, Tianhao Zhang, Debory Li, Matthew Theisen, Maria A. Velez, Paige M. Brodrick, Jackson P. Lind-Lebuffe, Yazeed Radwan, Gregory A. Ayzenberg, David Elashoff, Bin Liu, Aaron E. Lisberg, Amy L. Cumming, Edward B. Garon. HLA-B44 motif neoepitope is associated with a favorable tumor immune microenvironment and predicts ICB response in NSCLC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4340.
Abstract 4375: A bootstrapping method to optimize go/no-go decisions from single-arm, signal-finding studies in oncology
Authors: Mohan Aparna , Dutta Raunak , Buros-Novik Jacqueline , Akala Omobolaji , Topp Brian Gregory
Published: April 2023

Background: Phase Ib, single-arm trials are common in oncology development. Since these trials are not powered for statistical significance, Go/No-Go decisions are largely driven by observed trends in ORR relative to historic control. Here we develop a bootstrapping method to systematically compare secondary endponts, such as the waterfall plot, to historic control data. In addition, we identify an actionable Go threshold and estimate the expected false positive and false negative rates associated with that threshold.

Method: A proprietary mathematical model was used to simulate thousands of single-arm trials (n = 30) with a combination of pembrolizumab and a novel agent with miserable (Rx0), modest (Rx1), moderate (Rx2) or magnificent (Rx3) efficacy. A bootstrapping method was used to compare waterfall plots from these trials to a simulated Phase III pembrolizumab monotherapy control arm (n = 511).

Results: The bootstrapping method provides a visualization of the observed waterfall plot for the single-arm combination trial relative to the range of possible outcomes from historic control data (5th, median, 95th percentile). The method also provides a score reflecting the probability that the observed data is different from the historic control. An ROC analysis showed a strong ability to separate drugs with modest (AUROC = 83%), moderate (AUROC = 96%) and magnificent combination efficacy (AUROC = 99%) from drugs with miserable efficacy. The method was shown to effectively move drugs with a range of efficacy through an in-silico pipeline while rejecting drugs without combination efficacy.

Conclusion: This bootstrapping method allows comparisons of secondary endpoints from early clinical trials to historic control data. The visualization is intuitive, and the quantification provides an actionable Go-threshold. The method also provides an estimate of the risk associated with that recommendation. We suggest incorporation of this as a component of Go/No-Go decision making in early oncology trials.

Citation Format: Aparna Mohan, Raunak Dutta, Jacqueline Buros-Novik, Omobolaji Akala, Brian Gregory Topp. A bootstrapping method to optimize go/no-go decisions from single-arm, signal-finding studies in oncology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4375.