bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 621: ZL-1211 exhibits robust anti-tumor activity by enhancing ADCC and activating innate and adaptive immunity in CLDN18.2-high and -low expressing gastric cancer models
Authors: Konno Hiroyasu , Lin Tracey , Sun Bee-Chun , Wu Renyi , Szeto Christopher , Bellovin David , Hsu Karl , Kabbarah Omar
Published: June 2022

CLDN18.2 (Claudin18.2)-targeting therapeutic antibodies have shown promising clinical efficacy in ~30% of gastric cancers expressing high levels of CLDN18.2 and less pronounced activity in the majority of low expressing malignancies. ZL-1211 is a monoclonal antibody targeting CLDN18.2 engineered to promote enhanced ADCC with the goal of achieving more potent activity in a wider spectrum of high- and low-CLDN18.2 expressing tumors than the leading clinical benchmark. To further assess the potency of ZL-1211, we utilized a panel of gastric tumor cell lines that endogenously express CLDN18.2 and more accurately reflect target levels in human gastric tumors than engineered overexpressing models. ZL-1211 demonstrated more robust in vitro ADCC activity than clinical benchmark not only in CLDN18.2-high but also -low expressing gastric cell lines. Greater anti-tumor efficacy was also observed in mouse xenograft models with CLDN18.2-high, -medium, and low-expressing gastric cell lines in response to treatment with ZL-1211 compared to the clinical benchmark. NK cell depletion abrogated ZL-1211-mediated ADCC activity in vitro. ZL-1211 efficacy in vivo was also dependent on the presence of an NK compartment, as CLDN18.2-expressing gastric tumors grown in Balb/c nude with an intact NK function were sensitive to ZL-1211 treatment, while NOD-SCID with partially competent NK activity exhibited minimal response, and NCG without NK cells did not display any evidence of in vivo efficacy. Strikingly, NK cells strongly induced an inflammatory response in response to ZL-1211 treatment, including increased IFNγ, TNFα, and IL-6 production. Interestingly, ZL-1211 treatment led to NK cell and monocyte stimulation and enhanced CD8+ T cell activation, suggesting a mechanism of action that not only involves innate but also adaptive immunity. Taken together, our data suggest that ZL-1211 more effectively targets CLDN18.2-high gastric cancers as well as -low expressing malignancies that are not eligible for treatment with the leading clinical benchmark by inducing a robust ADCC response and activating innate and adaptive immunity to enhance anti-tumor efficacy. Clinical activity of ZL-1211 is currently under evaluation in a Phase I clinical trial (NCT05065710).

Citation Format: Hiroyasu Konno, Tracey Lin, Bee-Chun Sun, Renyi Wu, Christopher Szeto, David Bellovin, Karl Hsu, Omar Kabbarah. ZL-1211 exhibits robust anti-tumor activity by enhancing ADCC and activating innate and adaptive immunity in CLDN18.2-high and -low expressing gastric cancer models [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 621.
Abstract 6223: PD3D®models: New age in cancer research and clinical diagnostics
Authors: Pflaume Alina , Exner Samantha , Herrera-Glomm Katja , Loskutov Jürgen , Pfohl Ulrike , Regenbrecht Manuela , Sankarasubramanian Sushmitha , Wedeken Lena , Finkler Sabine , Ruhe Larissa , Adelmann Quirin Graf , Reinhard Christoph , Stroebel Philipp , Regenbrecht Christian R.
Published: June 2022

Patient-derived 3D cell culture models (PD3D®) developed as a powerful tool for disease modelling, biomarker and drug discovery. Currently, they are gaining increasing significance in the field of personalized oncology, as they recapitulate the histopathology of the original tumor tissue and preserve its genetic markup. PD3D® can be used to model intratumoral heterogeneity and for medium and high throughput drug screens. Using a reverse clinical engineering approach, PD3D® models allow identification of chemoresistance/sensitivity signatures (i.e., biomarkers) and can be applied in personalized oncology to identify treatment for an individual patient. We successfully established PD3D® models from more than 300 tumor tissue samples, ranging from more prevalent cancers like colorectal, breast and pancreas carcinoma, to rare tumor entities including various sarcoma types and thymoma. PD3D® models from different tumor entities differ in morphology and culture media requirements. When treating PD3D® from the same tumor entity with standard of care drugs, we found that their response differed, as does clinical response of patients. Furthermore, we successfully used PD3D® models to identify a biomarker for predicting chemosensitivity towards a targeted drug. For application of PD3D® in truly personalized oncology, we developed a protocol that allows us to generate a PD3D® culture and perform a drug sensitivity assay for an individual patient within a therapy-relevant timeframe. Using this protocol, we identified a combination therapy for a pretreated, metastasized appendix carcinoma within 29 days, that resulted in stable disease of the patient. In conclusion, PD3D® models can be derived from various cancer entities and used to analyze drug response in cohorts of models for drug development or identification of signatures related to drug resistance or sensitivity. Furthermore, PD3D® models can be used to predict a patient tumor’s drug response in a personalized manner, supporting the oncologist to identify the best treatment option for the patient.

Citation Format: Alina Pflaume, Samantha Exner, Katja Herrera-Glomm, Jürgen Loskutov, Ulrike Pfohl, Manuela Regenbrecht, Sushmitha Sankarasubramanian, Lena Wedeken, Sabine Finkler, Larissa Ruhe, Quirin Graf Adelmann, Christoph Reinhard, Philipp Stroebel, Christian R. Regenbrecht. PD3D®models: New age in cancer research and clinical diagnostics [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 6223.
Abstract 6227: An optimized preclinical antibody-drug conjugate against cancers with cKIT overexpression or activating mutations
Authors: Kim Jin-Ock , Ko Han-Jik , Kim Jae-Won , Park Sang Gyu
Published: June 2022

cKIT overexpression and activating mutations have been observed in many types of cancer, including small cell lung cancer (SCLC), gastrointestinal stromal tumor (GIST), and acute myeloid leukemia (AML), and are known to be predictive of poor prognosis. In previously reported work, NN2101-DM1, a fully human, anti-cKIT antibody-drug conjugate (ADC), was developed as a proof-of-concept (PoC) entity by conjugating the site-nonspecific and uncleavable linker SMCC with the microtubule inhibitory payload DM1. This linker-payload system is the same used in ado-trastuzumab emtansine, an approved ADC for HER2-positive breast cancer. NN2101-DM1 showed therapeutic efficacy against SCLC and GIST both in vitro and in xenograft models in vivo, demonstrating the feasibility of ADC development using NN2101. Despite the potent efficacy of NN2101-DM1, there are inherent limitations to SMCC linker and DM1 payload systems. The nonspecific attachment of the linker to the antibody produces highly heterogeneous drug-antibody ratios (DARs) with unpredictable attachment. Additionally, impaired lysosomal proteolytic activity has been shown to contribute to resistance to SMCC-DM1 cleavage. To optimize the ADC configuration for advancement to a clinical candidate, four types of ADC with different linker-payload combinations and DARs were designed, and their efficacy and safety were evaluated in vitro and in vivo. Among them, NN3201, a conjugation of the antimitotic payload MMAE to the cKIT-targeting antibody NN2101 via a site-specific, cleavable peptide linker, with a homogenous (>95%) DAR of 4 was selected as a lead candidate. This linker system utilizes a cysteine re-bridging technology to produce site-specific conjugation with high DAR homogeneity. NN3201 showed consistent sub-nanomolar IC50s in several in vitro cell lines and demonstrated complete remission as monotherapy in SCLC (H526), GIST (GIST-T1), AML (Kasumi-1), and mastocytoma (HMC 1.2) cell-derived xenograft models in doses ranging from 1.0-3.0 mg/kg. There were no significant toxicities detected at doses up to 60 mg/kg in normal mice, suggesting a therapeutic index greater than 20 times. In conclusion, NN3201 showed potent anti-tumor activity and was selected as preclinical candidate.

Citation Format: Jin-Ock Kim, Han-Jik Ko, Jae-Won Kim, Sang Gyu Park. An optimized preclinical antibody-drug conjugate against cancers with cKIT overexpression or activating mutations [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 6227.
Abstract 6253: RNA-seq based somatic variant calling and gene expression analysis reveals tumor heterogeneity and metastatic potential in colorectal cancers
Authors: Choi Ji Won , Ahn Kwangsung , Kim Sangsoo , Park Dong-Il , Park Soo-kyung
Published: June 2022

Colorectal cancer (CRC) is the third common malignant tumor and the second most responsible for worldwide cancer deaths. Also, RNAseq technology has been used for two purposes: to find exonic regions on the genome and quantify the expression level of the gene. We tried to validate the pipeline for identifying somatic variants from RNA-seq data, mainly following GATK4 somatic calling pipelines with some optimizing modifications. It is intended to examine whether somatic mutations driven from RNAseq data are associated with the biological behaviors of the individual colorectal cancer cells. We found that key genes (i.e., tumor suppressor genes such as APC and p53) are mostly mutated by T to C (in the non-coding region) or C to T (in the coding region) transitions, so that causes missense and nonsense mutations. However, highly mutated genes did not show significant expressional changes compared to the normal tissue. Otherwise, genes related to the metastatic potentials were observed to have highly increased expression. Our results can substantially verify the reliability of the somatic mutation calling approach using RNAseq data to call cancer-driving mutation and confirm an increase of extracellular matrix metabolism in the CRC.

Citation Format: Ji Won Choi, Kwangsung Ahn, Sangsoo Kim, Dong-Il Park, Soo-kyung Park. RNA-seq based somatic variant calling and gene expression analysis reveals tumor heterogeneity and metastatic potential in colorectal cancers [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 6253.
Abstract 6275: Evaluation of FRα/TRPV6 expression in gynecological cancer
Authors: Li Ning , Li Yifan , Tan Wei , Teng Yan , Huang Baohua , Wu Lingying
Published: June 2022

Purpose:Folate Receptor Alpha (FRα) is highly expressed in multiple malignancies, including ovarian, NSCLC and breast cancer. Transient Receptor Potential Vanilloid 6(TRPV6) is upregulated in breast, ovarian and prostate cancer. However, there is no report on expression and correlation between expression of the two markers. Since both markers are highly expressed in ovarian cancer, it is of great interest to evaluate expression of FRα and TRPV6 in a panel of gynecological cancer, including those major subtypes.

Method:We have collected 200+ FFPE samples achieved in pathology core at National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, including high grade and low grade serous ovarian cancer and clear cell ovarian cancer et al. Using validated IHC assays, expression of both FRα and TRPV6 are evaluated.

Result:Various levels of FRα and TRPV6 express in different histological subtypes of ovarian cancer. High grade serous ovarian cancer expresses the highest levels of FOLR1, which is about 2.8 and 2 folds over that of low-grade ovarian cancer and that of clear cancer ovarian cancer, respectively. The highest levels of TRPV6 expression are observed in clear cell ovarian cancer, which is 2.6 and 1.6 folds over that observed in low grade ovarian cancer and that observed in high grade ovarian cancer, respectively. The two biomarker expression is overlapped in about 45% of all samples analyzed. A comparison of samples from patients with or without good response to neoadjuvant therapy reveals samples with poor responses tend to express higher levels of FRα than those with good responses do. Addition evaluation and analysis are still on-going.

Conclusion: FRα and TRPV6 are highly express in gynecological cancer. Evaluation of their expression is of great value for molecularly-targeted therapies for those two targets and provide a precision medicine option for the clinical development for such drugs.

Citation Format: Ning Li, Yifan Li, Wei Tan, Yan Teng, Baohua Huang, Lingying Wu. Evaluation of FRα/TRPV6 expression in gynecological 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 6275.
Abstract 6308: Antitumor effects of RBPJ Inhibitor-1 on osteosarcoma cells
Authors: Callahan Dakota , Hinojosa Leetoria , Torres Haydee M. , Tao Jianning
Published: June 2022

Osteosarcoma (OS) is the most common primary malignancy of the bone in adolescents and children with limited treatment options. Drug resistance to current therapy together with severe side effects urgently calls for alternative treatment strategies targeting critical cancer signaling pathways. Recently, our and other studies suggest that hyperactivation of Notch signaling contributes to the pathogenesis of human and murine OS, and its inhibition may be a therapeutic approach for the treatment of OS. Notch pathophysiological activity involves activated Notch (i.e. NICD, the notch intracellular domain) forming a nuclear complex with DNA-binding factors and coactivators such as recombination signal binding protein for immunoglobulin kappa J region (RBPJ). This evolutionary conserved mechanism is involved in the maintenance and survival of cancer stem cells, which can govern various cell activities like metastasis and chemoresistance. This study aims to examine the in vitro effects of targeting the NICD-RBPJ interaction using a small molecular inhibitor of the RBPJ (RIN1) on osteosarcoma cell lines. We found that treatment of 10 µM RIN1 on SJSA-1 (ATCC, CRL-2098), a human osteosarcoma cell line with a high Notch activity, can significantly decrease cell proliferation at 48 and 72 hours (h). We also found that at 10 µM of RIN1 affects SJSA-1 migration using a Boyden chamber-based cell system at 24 h, a time point where we find minimal contribution from an effect on cell proliferation. Treatment with RIN1 can block SJSA-1 clonogenicity, but we showed that it has limited ability to block SJSA-1 cell invasion. Treatment with RIN1 does not initiate or enhance the osteoblast-like differentiation of SJSA-1. Notch target genes HEY1 and CyclinD1 was significantly modulated in SJSA-1 cells upon treatment in a Notch-independent manner. Interestingly, treatment with RIN1 on SJSA-1 decreases SOX2 protein expression, a well-known cancer stem cell marker, and upregulates tumor suppressor RB1 protein expression. Ongoing studies include additional cellular function assays and RNA-seq transcriptomic analysis of RIN1’s effect on two Notch-dependent cancer cell lines including MB 157 (ATCC, CRL-7721) and T29 in its activating context. In summary, RIN1 has been shown to have a significant effect on the different cell behaviors of human osteosarcoma, which may eventually facilitate with the treatment of patients that have metastatic disease.

Citation Format: Dakota Callahan, Leetoria Hinojosa, Haydee M. Torres, Jianning Tao. Antitumor effects of RBPJ Inhibitor-1 on osteosarcoma 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 6308.
Abstract 6315: Are a subset of patients at higher risk for mortality in stage III colon cancer: An analysis of the SEER database
Authors: Hajirawala Luv N. , Yi Yong , Bergeron Michelle A. , Dooley Danielle A. , Orangio Guy R. , Bevier-Rawls Elyse R. , Davis Kurt G. , Barton Jeffrey S.
Published: June 2022

Background: High-risk features (HRF) increase mortality for Stage II colon cancer (CC). These HRF include pathologic T4 disease, perineural invasion (PNI), lymphovascular invasion (LVI), an inadequate lymphadenectomy (less than 12 lymph nodes harvested) and poorly differentiated tumors. The presence of two or more HRF has an additive impact on survival for patients with Stage II CC. While T4 and disease greater than N1a raise the risk of mortality in Stage III CC, the effect of the other accepted HRF in patients with Stage III CC has not been studied.

Materials and Methods: Surveillance, Epidemiology and End Results (SEER) (2010 - 2017) was used to identify patients with Stage III and IV CC. Patients with Stage III CC were then further classified by the presence of zero, 1, or 2 or more of the following HRF: pathologic T4, PNI, inadequate lymphadenectomy, or poor differentiation. Overall (OS) and cause-specific (CS) survival were calculated.

Results: 57,640 patients with Stage III or IV CC were identified. 35,760 (62%) patients had Stage III disease and 21,880 (38%) had Stage IV disease. Among patients with Stage III disease, 16,733 (46.8%) had no HRF, 12,703 (35.5%) had 1 HRF and 6,324 (17.7%) had 2 or more HRF. For patients with 1 HRF, 4,610 (36.3%) had poor differentiation, 2,339 (18.4%) had PNI, 3,673 (28.9%) had T4 disease, and 2,078 (16.4%) had an inadequate nodal harvest. Patients with Stage III CC without HRF had the best OS (73.3%) and CS (81.4%,). This was followed by Stage III with 1 HRF (OS 63.7%, CS 71.6%) and Stage III with 2 or more HRF (OS 44%, CS 51%). Patients with Stage IV disease had the worst OS (18.1%) and CS (20.4%) (p<0.05). For patients with 1 HRF, pathologic T4 conferred worse OS (57.2%) and CS (63.2%), compared to PNI (OS 66.4%, CS 73.7%), inadequate lymphadenectomy (OS 64.6%, CS 74.9%) and poor differentiation (OS 66.6%, CS 75.4%) (p<0.01).

Conclusion: HRF have a cumulative influence on OS and CS in patients with Stage III CC. The presence of multiple HRF should be considered higher risk for patients with Stage III disease.

Citation Format: Luv N. Hajirawala, Yong Yi, Michelle A. Bergeron, Danielle A. Dooley, Guy R. Orangio, Elyse R. Bevier-Rawls, Kurt G. Davis, Jeffrey S. Barton. Are a subset of patients at higher risk for mortality in stage III colon cancer: An analysis of the SEER database [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 6315.
Abstract 6337: Assessing genomic literacy among medical trainees and practitioners in Pakistan
Authors: Barakzai Madina , Rehmat Shagufta , Khan Faisal F.
Published: June 2022

Genomic literacy has a significant impact on the successful application and deployment of new practices such as precision medicine. It can be described as the ability to achieve, process, understand, and apply genomic knowledge to health-related decision-making. The aim of this study is to assess the level of genomic literacy, including the knowledge of genetic testing, its outcomes, and its significance among medical trainees and practitioners in Pakistan. This study also offers recommendations for improving genomic literacy within the medical community in Pakistan. A cross-sectional study for which an online questionnaire was designed in the English language using Google Forms. The questionnaire was distributed among trainees and practitioners across Pakistan through online social media platforms. The survey comprised of 36 questions categorized into three sections namely demographics, quantitative questions, and knowledge section. A total of 219 medical professionals (56% trained in medicine while 44% in Dentistry) responded to the survey. Medical practitioners from 27 different cities across Pakistan participated in the survey but with a clear bias towards the city of Peshawar (90%). The majority of the participants (57.5%) were trainee medical officers. Most of the participants in this cohort were aware of genetics, the genome, and PCR technology but 74.9% were not familiar with genetic tests in their specialty. The mean total score for the multiple-choice questions among the participants was 62.5% graduates of medicine (65%) outperforming those in dentistry (59%). Participants were asked about their interest in further learning opportunities about genomics, for which 71% answered in affirmation, however, the remaining were not overly interested. Genomic literacy level can be considered satisfactory at the level of classical genetics, yet there is a clear need for training in molecular biology concepts such as protein synthesis, gene expression, and genome structure within the medical community. With a limited sample size and diversity of respondents, the subject warrants a broader survey to assess genomic literacy which can help in better planning for wider adoption of genomic testing in the medical community. Findings of this survey also highlight the need for assessing medical communities in other low-resource and underprivileged settings to help enhance our understanding and avoid a looming ‘genomics divide’.

Citation Format: Madina Barakzai, Shagufta Rehmat, Faisal F. Khan. Assessing genomic literacy among medical trainees and practitioners in Pakistan [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 6337.
Abstract 6340: Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale
Authors: Donovan Margaret , Huang Henry , Blume John , Ko Marwin , Benz Ryan , Platt Theodore , Cuevas Juan , Batzoglou Serafim , Siddiqui Asim , Farokhzad Omid
Published: June 2022

Introduction: Comprehensive assessment of the proteome remains elusive because of proteoforms arising from alternative splicing, allelic variation, and protein modifications. Characterization of the variable protein forms, or proteoforms will expand our understanding of the molecular mechanisms underlying diseases, however requires unbiased protein coverage at sufficient scale. Scalable, deep and unbiased proteomics studies have been impractical due to cumbersome and lengthy workflows required for complex samples, like blood plasma. Here, we demonstrate the power of Proteograph in a proof-of-concept proteogenomic analysis of 80 healthy controls and 61 early-stage non-small-cell lung cancer (NSCLC) samples to dissect differences between protein isoforms arising from alternative gene splicing, as well as the identification of novel peptides arising from allelic variation.

Materials, Methods and Results: Processing the 141 plasma samples with Proteograph yielded 21,959 peptides corresponding to 2,499 protein groups. Using peptides with significant abundance differences (p < 0.05; Benjamini-Hochberg corrected), we extracted proteins comprised of peptides where at least one peptide had significantly higher plasma abundance, and another significantly lower plasma abundance in controls vs. cancer, resulting in a set of putative proteoforms. For three of these proteins, the abundance variation is possibly explained by underlying protein isoforms. To identify protein variants, we performed exome sequencing on 29 individuals from the NSCLC study, created personalized mass spectrometry search libraries for each individual, and identified 464 protein variants.

Conclusions: Proteograph can generate unbiased and deep plasma proteome profiles that enable identification of protein variants and peptides present in plasma, at a scale sufficient to enable population-scale proteomic studies.

Citation Format: Margaret Donovan, Henry Huang, John Blume, Marwin Ko, Ryan Benz, Theodore Platt, Juan Cuevas, Serafim Batzoglou, Asim Siddiqui, Omid Farokhzad. Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale [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 6340.
Abstract 636: Prediction of therapeutic response via data-driven maps of tumor cell architecture
Authors: Silva Erica N. , Singhal Akshat , Park Sungjoon , Kreisberg Jason , Ideker Trey
Published: June 2022

Machine learning is revolutionizing the analysis of biological and biomedical data. One continued challenge is to build models that are not only predictive but also provide mechanistic explanations. Directly incorporating explainability into the model’s design has emerged as a possible solution. Recently, we reported several “visible” machine learning systems - DCell and DrugCell - which predict cellular growth based on genetic perturbations. In these visible models, the structure of the underlying neural network mirrors known aspects of cell biology. Here we designed a cancer-specific model of therapeutic response. First, we selected NeST (Nested Systems in Tumors; Zheng et al., Science 2021), a data-driven hierarchy of tumor cell systems under selection in cancer, as the structure for our visible neural network. Second, we restricted input features to genes currently assayed on clinical cancer gene panels. We considered training schemes that assess the model’s ability to generalize to novel genotypes. Most importantly, we assessed performance on patient data from the AACR Project GENIE clinical trial where we discriminated between patients who are likely to respond to selected drug treatments. Finally, we examined model explanations within the visible NeST architecture to highlight cellular mechanisms of response to drug therapy. Overall, we found that by considering a tumor cell architecture optimized for clinical application, we can design an interpretable deep learning model that both accurately stratifies patient responses and explains the drug mechanism in cancer cells.

Citation Format: Erica N. Silva, Akshat Singhal, Sungjoon Park, Jason Kreisberg, Trey Ideker. Prediction of therapeutic response via data-driven maps of tumor cell architecture [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 636.
Abstract 6386: Phosphomimetic Dicer rewires glutamine metabolism and gemcitabine resistance in pancreatic ductal adenocarcinoma
Authors: Chiu Ching-Feng , Park Ji Min , Shen Yu-Shiuan , Lin Chia-Ying , Hsu Tung-Wei , Su Yen-Hao , Chen Hsin-An
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is a common malignancy that shows high cancer-mortality and poor prognosis, in the absence of obvious symptoms and biomarkers for early diagnosis. Gemcitabine is a type of chemotherapy drug which commonly used to treat PDAC, however, the rapid acquisition of resistance to gemcitabine treatment has been observed in many of PDAC patients. The miRNA-producing enzymes Dicer is crucial for the maturation of miRNAs, and we found previously that ERK/Sp1 signaling transactivate both gene and protein expressions of Dicer, leading an acquisition of gemcitabine resistance in pancreatic cancer cells both in vitro and in vivo. In this study, we further identified that phosphomimetic S1016E of Dicer may regulate miRNAs maturation, resulting an imbalance of glutaminase (GLS) and glutamine synthetase (GS/GLUL). Metabolism analysis revealed that gemcitabine-resistant PANC-1 (PANC-1/GEM) cells have high glutamine dependence and GLS/GLUL ratio. Our study suggests that phosphomimetic Dicer S1016E plays a critical role in glutamine metabolism reprogramming and gemcitabine resistance of pancreatic cancer.

Citation Format: Ching-Feng Chiu, Ji Min Park, Yu-Shiuan Shen, Chia-Ying Lin, Tung-Wei Hsu, Yen-Hao Su, Hsin-An Chen. Phosphomimetic Dicer rewires glutamine metabolism and gemcitabine resistance in pancreatic ductal adenocarcinoma [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 6386.
Abstract 643: Non-classical sources of tumour specific antigen in checkpoint inhibitor response
Authors: Thakkar Krupa , Qian Danwen , Cha Hongui , Watkins Thomas B. , Swanton Charles , Litchfield Kevin
Published: June 2022

A large-scale meta-analysis of over 1000 CPI (immune checkpoint blockade) treated patients across multiple cancer types broadly categorised biomarkers into four categories: sources of antigen leading to T-cell responses, host-derived factors, immune evasion and infiltration mechanisms. Our analyses established tumour mutation burden (TMB) as the strongest predictor of CPI response, alongside clonal TMB and CXCL9 expression. However, over half of the patients in our cohort who responded to CPI treatment did not have high-TMB and showed no evidence of oncogenic viral infections, hence suggesting alternative sources of antigen could be driving the immune response. As well as this, data from the CPI1000 cohort suggested that the biomarkers identified in an extensive systematic review only accounted for ~60% of the variance in CPI response, promoting the search for non-classical sources of antigen.

Extending the cohort to encompass 2500+ patients, using available genomic and transcriptomic data from checkpoint inhibitor trials and industry partners, the previously published multivariate predictor will be further validated in a larger patient cohort inclusive of more cancer types. The CPI1000 cohort utilised primarily whole exome-sequencing therefore, had limited ability to discern non-coding sources of tumour antigen and cell-type specific predictors of response. The CPI2500+ cohort will incorporate several additional cohorts as well as single-cell and T-cell reactivity data. The raw data will be harmonised across studies and processed using a robust bioinformatics pipeline. As well as this, alternative (non-classical) sources of tumour specific antigen will be studied. Alternative sources of antigen can originate from a diverse range of biological processes including retained introns, stop codon loss mutations and cancer associated bacterial/viral epitopes. Data from this exploratory analysis will be coupled with peptide reactivity assays from local UCL patient TIL (tumour infiltrating lymphocyte) and PMBC (peripheral blood mononuclear cells) samples to validate immunogenicity.

Current analysis has identified a novel subgroup of CPI-responders with low-TMB who have significantly higher rates of microbial diversity, consistent with a diverse tumour microbiome providing a source of immunogenic antigens in the absence of high-TMB. Here we will present insights from CPI2500+ and highlight the importance of emerging non-classical sources of tumour specific antigen.

Citation Format: Krupa Thakkar, Danwen Qian, Hongui Cha, Thomas B. Watkins, Charles Swanton, Kevin Litchfield. Non-classical sources of tumour specific antigen in checkpoint inhibitor response [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 643.
Abstract 707: Mahanine, a carbazole alkaloid attenuates lung cancer progression
Authors: Kandimalla Raghuram , Aqil Farrukh , Moholkar Disha N. , Samanta Suman K. , Gupta Ramesh C.
Published: June 2022

Lung cancer continues to be a major cause of cancer mortality. Emerging evidence suggests that cancer likely involves multiple mutations. Therefore, compounds targeting multiple signal transduction pathways would be ideal for the prevention and treatment of cancer. Mahanine, a carbazole alkaloid isolated from an Indian folklore medicinal plant Murraya koenigii (known as Curry Patta), widely consumed in traditional dishes, have been shown to possess anticancer activities and confound many oncogenic signaling events in breast, colon, and prostate cancers. In the current study, we determined the anticancer potential of mahanine against drug-sensitive and drug-resistant lung cancer cells and postulate the possible mechanism of action. Mahanine was isolated from the dried leaves of Murraya koenigii by hydro alcoholic extraction and fractionation with ethyl acetate, followed by preparative UPLC to isolate pure (>95%) compound and its identity was confirmed by LC-MS/MS and NMR spectroscopy. Antiproliferative activity of mahanine was determined against drug- sensitive (A549 and H1299) and taxol-resistant (A549-TR) human lung cancer cells. Mahanine showed a dose- and time-dependent inhibition of both drug-sensitive and drug-resistant lung cancer cell growth. Interestingly, the IC50 values of mahanine were essentially the same for drug sensitive (A549) (12.5 µM) and drug- resistant (12.5 µM) lung cancer cells; the IC50 value was somewhat lower (10 µM) against highly metastatic H1299 lung cancer cells. Mahanine attenuated the colony formation and reduced the wound healing of lung cancer cells. Mechanistically, mahanine dose dependently impeded the oncogenic markers such as KRAS, MET, AKT, mTOR and cMYC. Together, mahanine demonstrate ability to inhibit both drug- sensitive and drug-resistant lung cancer cells and modulate distinct oncogenic molecular targets providing potential to be developed for the treatment of drug-resistant and metastatic NSCLC (Supported from Duggan Endowment funds).

Keywords: Mahanine, Lung cancer, Oncogenes, Plant therapeutics.

Citation Format: Raghuram Kandimalla, Farrukh Aqil, Disha N. Moholkar, Suman K. Samanta, Ramesh C. Gupta. Mahanine, a carbazole alkaloid attenuates lung cancer progression [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 707.
Abstract 709: Metabolomic differences between pulmonary metastasis of Lewis lung carcinoma and normal lungs from C57BL/6 mice fed an obesogenic high-fat diet
Authors: Yan Lin , Sundaram Sneha , Rust Bret M. , Picklo Matthew J. , Bukowski Michael R.
Published: June 2022

Metastasis, the spread of malignant cells from a primary tumor to distant organs, is the most devastating aspect of cancer. To understand the metabolism of metastases, we compared the metabolomes of pulmonary metastases of Lewis lung carcinoma (LLC) with that of normal lung tissues from mice fed an obesogenic high-fat diet. In a 2x2 design, male C57BL/6 mice, with or without a subcutaneous LLC inoculation, were fed the standard AIN93G diet or a high-fat diet (HFD), which provided 16% or 45% of energy from soybean oil, for 12 weeks. At the end of the study, lung metastases from injected mice and the lungs from non-injected mice were harvested for untargeted metabolomic analysis of primary metabolism by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). We identified 91 metabolites, 70 of which differed among the four groups. Pathway and network analyses along with the discriminant analysis showed that amino acid and carbohydrate metabolism were altered the most in metastases compared to the normal lung tissue (e.g., aminoacyl-tRNA biosynthesis pathways and the citric cycle). A 60% decrease in glutamine and a 25-fold elevation in sorbitol were observed in metastases. Cholesterol and its metabolite dihydrocholesterol were 50% lower in metastases than in the lungs. The HFD elevated arachidonic acid and its precursor linoleic acid in the lungs from non-LLC-bearing mice, which reflected dietary fatty acid composition of the HFD. However, such elevation did not occur in metastases from HFD-fed LLC-bearing mice, suggesting alterations in fatty acid metabolism during LLC metastatic progression. Differences in metabolomes between LLC pulmonary metastases and the normal healthy lungs identified in the present study can be useful in designing targeted studies for prevention and treatment of metastasis using this spontaneous metastasis model.

Citation Format: Lin Yan, Sneha Sundaram, Bret M. Rust, Matthew J. Picklo, Michael R. Bukowski. Metabolomic differences between pulmonary metastasis of Lewis lung carcinoma and normal lungs from C57BL/6 mice fed an obesogenic high-fat diet [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 709.
Abstract 713: Monoclonal antibodies for the detection of the uropathogenic specific protein (USP): A bacterial genotoxin linked to colorectal cancer
Authors: Martínez-Ramírez Rachell , Toro-Díaz Valeria Toro-Díaz , Akamine Pearl , Ruiz-Rosado Kimberly , Pino Ignacio , Baerga-Ortiz Abel
Published: June 2022

The Uropathogenic Specific Protein (USP) is an E. coli genotoxin nuclease primarily associated with urinary tract infections. Previous efforts in our laboratory found the USP gene in stool samples; more frequently found in stool samples from adenoma and CRC patients than in samples from healthy individuals. New efforts in our laboratory aim to find the USP protein in the same population of patient samples and this may require anti-USP antibodies, which at present are not commercially available. In this work, we report the first anti-USP monoclonal antibodies (mAbs) for the detection of USP in human samples. A total of 38 hybridoma supernatants containing mAbs were assayed by immunoblotting and biolayer light interferometry (BLI) for their ability to recognize purified USP(∆HNH). Results from BLI showed that the pair AB-A10 and AB-D5 presented the highest affinity with slow dissociation, moving forward for the development of a sandwich ELISA. Using AB-A10 as the capture antibody, and AB-D5 as the top antibody, results from the ELISA showed signals that were concentration-dependent above 6 ug/mL of USP. We also used the AB-D5 and AB-D10 in immunoblots for the detection of USP in proteins extracted from stool samples of patients with adenoma and CRC. The immunoblots reveal the detection of a 25 kDa protein that remains unidentified but is present only in some of the samples. This could be the first detection of USP protein directly in a biological sample. Efforts are underway to identify this protein band and confirm its identity as USP. Additional efforts are aimed at increasing the number of stool samples analyzed to establish whether USP protein is a risk factor for CRC or adenoma.

Citation Format: Rachell Martínez-Ramírez, Valeria Toro-Díaz Toro-Díaz, Pearl Akamine, Kimberly Ruiz-Rosado, Ignacio Pino, Abel Baerga-Ortiz. Monoclonal antibodies for the detection of the uropathogenic specific protein (USP): A bacterial genotoxin linked to colorectal 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 713.
Abstract 724: Examining the effects of obesity and weight loss on mammary tumor inflammation and fibrosis
Authors: Kuziel Genevra M. , Arendt Lisa M.
Published: June 2022

Obesity significantly increases risk of breast cancer development, and following diagnosis, obese breast cancer patients have an overall worsened prognosis. The complex relationship of obesity to breast cancer growth and aggressiveness must continue to be examined. Within breast adipose tissue, obesity causes a state of chronic, macrophage-driven inflammation. Chronic inflammation is associated with increased extracellular matrix (ECM) deposition. Increased collagen within the mammary microenvironment is a risk factor for tumor formation, as well as more aggressive tumors, in mouse models. In breast tumors from obese patients, tumor desmoplasia is also found to be increased. To better understand how obesity affects mammary tumor growth, inflammation, and fibrosis, we used a diet-induced obesity mouse model paired with the estrogen receptor alpha (ERα)+ TC2 mammary tumor cell line in female FVB mice. We observed that TC2 mammary tumors grew significantly faster in obese mice compared to lean mice and had significantly more macrophage infiltration. TC2 tumors from obese mice also had significantly more collagen deposition than TC2 tumors from lean mice, indicating that obesity leads to more fibrotic tumors. To identify how weight loss alters the mammary gland and mammary tumor microenvironments, obese mice were switched from a high-fat diet to a low-fat diet for six weeks, to induce weight loss. In non-tumor-bearing mammary glands, weight loss led to a significantly decreased number of crown-like structures, a marker of adipose tissue inflammation, similar to observations in human adipose tissue. TC2 mammary tumors grew at an intermediate rate between tumors from lean and obese mice, indicating that weight loss may be a viable option to reduce tumor aggressiveness, particularly for obese patients with other breast cancer risk factors. Understanding these weight-related changes in the mammary gland and mammary tumor microenvironments will provide greater insight into possible interventions for obese breast cancer patients.

Citation Format: Genevra M. Kuziel, Lisa M. Arendt. Examining the effects of obesity and weight loss on mammary tumor inflammation and fibrosis [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 724.
Abstract 832: Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive function
Authors: Aylon Yael , Furth Noa , Mallel Giuseppe , Nataraj Nishanth , Friedlander Gilgi , Hassan Ori , Zoabi Rawan , Cohen Benjamin , Salame Tomer , Mukherjee Saptaparna , Johnson Randy , Shema Efrat , Oren Moshe
Published: June 2022

Purpose of study: Understanding the epigenetic mechanism underlying luminal-to-basal plasticity of breast cancer subtypes

Experimental procedures: Epigenetic focused CyTOF, ATAC-seq, RNA-seq, FACS-sorting, Proximity Ligation Assay, orthotopic syngeneic injections of tumor cells to mouse mammary gland, and others.

Summary: Breast cancer is the most frequent cancer in women. It is defined by specific types of tumors that are classified into distinct histological and molecular subtypes. However, lately, with the advent of single-cell technologies, the extent of cellular and functional intratumoral heterogeneity within breast cancer subtypes is being appreciated. Much of this heterogeneity, including transitions of luminal-to-basal cell identity, can be attributed to alterations in the activity of chromatin remodelers. The transcriptional corepressor, NCOR1, and the tumor suppressor, LATS1, are downregulated in luminal breast cancer tumors with poor prognosis. Here, we show that LATS1 impedes the emergence of an epigenetically distinct basal-like population in luminal B tumors by augmenting NCOR1 repressive activity and facilitating deacetylation of H3K27ac.

Conclusion: Rigorous repression of ERα-repressed genes facilitated by LATS1-NCOR1 maintains luminal cell identity and restricts progression of luminal breast cancer.

Citation Format: Yael Aylon, Noa Furth, Giuseppe Mallel, Nishanth Nataraj, Gilgi Friedlander, Ori Hassan, Rawan Zoabi, Benjamin Cohen, Tomer Salame, Saptaparna Mukherjee, Randy Johnson, Efrat Shema, Moshe Oren. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive function [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 832.
Abstract 84: Sensitive and unbiased detection of clinically actionable gene fusions from FFPE tumor biopsies using the Arima-HiC platform
Authors: Hermel David Jacob , Sikkink Kristin , Reid Derek , Schmitt Anthony , Sigal Darren S.
Published: June 2022

Accurate and sensitive identification of gene fusions is critical to understanding disease mechanisms and the development and selection of optimal treatment regimens for cancer patients. Typically, these fusions are detected using low-resolution karyotyping, low throughput and biased FISH assays, or RNA sequencing approaches; however, the accuracy and sensitivity of gene fusion detection can be limited by factors such as low transcript abundance, transcript length, RNA degradation from formalin fixed paraffin embedded (FFPE) tissues, or the limited availability of fresh biopsy samples for RNA extraction. To address these limitations, we developed a novel approach to identifying gene fusions from FFPE samples using the Arima-HiC platform and short-read sequencing. We performed pan-cancer analysis on 12 FFPE adult tumor biopsies, each with gene fusions known to be clinically actionable. With this newly developed Hi-C workflow we identified all the known gene fusions with 100% sensitivity in the samples including those involving ALK, NTRK3, ROS1, FGFR2, and SS18 genes. This approach also revealed that the NTRK3 gene fusion was the result of a more complex rearrangement within chr12, within chr15, and between chr12 and chr15. Additionally, we detected the presence of numerous structural variants per sample in addition to the known gene fusion in each sample. For example in a bile duct tumor, Arima-HiC detected an FGFR2-EEA1 gene fusion, as well as 25 other structural variants genome-wide including in a CPD-LASP1 gene fusion This gene fusion has not been reported to our knowledge, however, LASP1 is a reported 3’ fusion partner with MLL in leukemia. While these findings are not clinically actionable today, the unbiased, accurate, and sensitive detection of structural variants from frozen and FFPE solid tumor biopsies may facilitate further research into their relationship between disease mechanisms and clinical outcomes. Taken together, these findings demonstrate the analytical utility of Arima Hi-C sequencing technology to provide both chromosome-scale and gene-level resolution for the detection of structural variants in tumor biopsies samples. This workflow can provide improved access to critical genomic information from FFPE blocks for the identification of pathognomonic and druggable gene fusion events and other structural variants across tumor types.

Citation Format: David Jacob Hermel, Kristin Sikkink, Derek Reid, Anthony Schmitt, Darren S. Sigal. Sensitive and unbiased detection of clinically actionable gene fusions from FFPE tumor biopsies using the Arima-HiC platform [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 84.