bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1022: Integration of cerebrospinal fluid methylome and proteome can obviate the need for biopsy in central nervous system lymphoma
Authors: Landry Alex P. , Zuccato Jeffrey A. , Patil Vikas , Voisin Mathew , Wang Justin Z. , Ellenbogen Yosef , Gui Chloe , Ajisebutu Andrew , Nassiri Farshad , Zadeh Gelareh
Published: March 2024

Background: The diagnosis of intra-axial brain tumors requires histopathological examination of tissue obtained by neurosurgery in current clinical practice, which comes with inherent risks. Some patients, particularly those with primary CNS lymphoma (PCNSL), only undergo surgery to obtain a diagnosis and do not derive any therapeutic benefit from surgical resection or debulking. Less-invasive techniques for diagnosis, such as liquid biopsy, therefore provides an opportunity to mitigate surgical risk in these patients.

Methods: Patients with histopathology confirmed glioblastoma (GBM, IDH wild type), brain metastases (BM), and PCNSL with accompanying cerebrospinal fluid (CSF) samples were included in our study. Cell-free DNA methylation profiling and shotgun proteomics were obtained for all patients and used to train classifiers to distinguish each tumour entity from others. Specifically, binomial elastic net regression models were built by combining both data modalities using established early and late integration paradigms and performance was compared to classifiers built from individual data types alone. Each model was repeated 100 fold and performance assessed on an untouched testing subset.

Results: Our cohort includes 20 patients with GBM, 17 with BM, and 14 with PCNSL, each with matching CSF cell-free DNA methylation and shotgun proteomic profiling. We show that these data can be integrated to fully discriminate PCNSL from its major diagnostic counterparts with a perfect median AUC of 1.00 (95% CI 1-1) and 100% specificity. Integrated "lymphoma vs other" models significantly outperform models trained on methylation or protein data alone, though the same dramatic improvement was not demonstrated in GBM or BM, suggesting synergistic biological information is specific to lymphoma.

Conclusions: There is a critical need to diagnose patients with intra-axial tumours, particularly PCNSL, without relying on invasive and costly surgery. We present the most specific and accurate CNS lymphoma classifier to date by integrating the methylome and proteome of CSF. This has the potential for immediate clinical utility, eliminating the need for biopsy in an important subset of these patients.

Citation Format: Alex P. Landry, Jeffrey A. Zuccato, Vikas Patil, Mathew Voisin, Justin Z. Wang, Yosef Ellenbogen, Chloe Gui, Andrew Ajisebutu, Farshad Nassiri, Gelareh Zadeh. Integration of cerebrospinal fluid methylome and proteome can obviate the need for biopsy in central nervous system lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1022.
Abstract 107: Application of MSD on the lung cancer associated idiopathic pulmonary fibrosis
Authors: Bao Wei , Li Ying-Ji , Gu Jin-Fan , Yang Cong-Lin , Wang Yi-Da , Bing Tie-Jun , Yu Wen-Jen
Published: March 2024

Idiopathic pulmonary fibrosis (IPF) is a progressive and irreversible chronic disease that kill ten thousand of people in China every year. The risk of IPF is highly correlated with smoke, air pollution, dust, virus infection and aging. Average survival period of patients diagnosed as IPF is around 2.8 years which is less than several types of cancers, therefore, IPF is also thought to be a lung cancer-like disease. In the past few decades, many animal models were created to mimic human IPF, however, induction materials, animal species and strain differences, sex, physiology structure and progress of disease make the choice of IPF animal models selection more difficult. In addition, lack of strong evidence of cytokines biomarker detection hampered the discovery of anti-IPF drugs. Meso Scale Discovery (MSD) instrument is an efficient tool to high throughput analyze the lowest level of several cytokines and other biomarkers in the same time and was used to detect the bleomycin (BLM) induced mouse lung fibrosis. Meanwhile, animal sex and dose effects of BLM were also tested to define the proper mouse model for anti-IPF drugs development. Our results indicated that 0.6-0.8 mg/kg of intratracheal injection of single dose BLM is sufficient to create the IPF model without sex differences by examining the lung weight, lung ratio, soluble hydroxyproline, HE staining and mason staining. However, male mice were more resistant to the lethal effect of BLM due to the larger size or bodyweight. Using MSD detection, several mouse cytokines were measured simultaneously and showed that IFN-γ, IL-5, TNF-α, and IL-10 were increased in the IPF mouse model and were recovered after pirfenidone treatment at day 14 which mimics the cytokines profile in IPF patients. In summary, the MSD detection and pathological evaluation prove that male mouse treated with 0.8 mg/kg BLM through intratracheal injection is a suitable mouse model for the development of anti-IPF dugs.

Citation Format: Wei Bao, Ying-Ji Li, Jin-Fan Gu, Cong-Lin Yang, Yi-Da Wang, Tie-Jun Bing, Wen-Jen Yu. Application of MSD on the lung cancer associated idiopathic pulmonary fibrosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 107.
Abstract 1074: Plasma EV profiling facilitates low abundance biomarker discovery in pancreatic cancer
Authors: Bansal Shivani , Wang Shu , Li Yaoxiang , Bansal Sunil , Smith Jill , Tyburski John B. , Unger Keith , Cheema Amrita
Published: March 2024

The lack of reliable biomarkers for early detection of pancreatic ductal adenocarcinoma (PDAC) results in poor prognosis due to advanced disease at diagnosis. Biopsies for pancreatic cancer are known to be particularly difficult to perform because of the location of the pancreas and low volume of primary tumors that metastasize aggressively. Currently, there is no blood test or other screening modality in use, for stratification of individuals with higher-than-average risk (5-8-fold) of developing PDAC in their lifetime. Given this existing void in the US and worldwide, an FDA-compliant, minimally invasive, quantitative biomarker test for the early detection of PDAC would be critical for screening subpopulations with, a) inherent genetic or familial predisposition; history of chronic pancreatitis; c) precursor lesions of pancreas; and d) older patients (>50 years) with new onset diabetes or sudden weight loss. Extracellular vesicles (EVs) are shed by normal and cancer cells and carry a rich molecular cargo that can be leveraged for biomarker discovery. Whereas molecular profiling of bio-fluids poses intrinsic limitations for detection of low abundant, disease-specific biomarkers due to matrix effects; EVs, on the other hand, offer promise as a robust and minimally invasive biomarker resource. Mass spectrometry data were developed in our laboratory, based on multi-omics (proteomics, lipidomics and metabolomics) analyses of plasma EVs derived from patients diagnosed with early-stage PC (N=60), pancreatitis (N=39), precursor lesions of pancreas (N=45) as well as normal controls (N=50). These clinically annotated samples were made available by the Georgetown University Medical Center (GUMC) repository. Feature selection using a training-validation design allowed the development of a multiplexed biomarker panel comprising of 12-analytes (5-lipids, 2-metabolites and 5-proteins) that can robustly stratify early-stage PC from normal controls with high accuracy (AUC>95%). Availability of a FDA compliant, multi-analyte-based classification algorithm that can stratify patients with precursor lesions of the pancreas that are at potential risk of progression to PC with > 90% specificity and sensitivity is a critical clinical need. Refinement of panel to improve positive predictive value as well as identification of markers predictive of progression of precursor lesions to malignant transformation is ongoing.

Citation Format: Shivani Bansal, Shu Wang, Yaoxiang Li, Sunil Bansal, Jill Smith, John B. Tyburski, Keith Unger, Amrita Cheema. Plasma EV profiling facilitates low abundance biomarker discovery in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1074.
Abstract 1093: Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma
Authors: Shaw Taryn , Nakazawa Kay , Tiwari Purushottam , Nelson Eryn , Formen Jeffrey , Wolf Christian , Toretsky Jeffrey , Üren Aykut
Published: March 2024

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. It is commonly divided into subtypes based on histopathological appearance. The oncogenic fusion proteins PAX3::FOXO1 or PAX7::FOXO1 are present in the alveolar subtype of RMS (ARMS). These chimeric proteins are formed by reciprocal chromosomal translocations and consist of an N-terminal portion of the PAX3 or PAX7 transcription factor fused to a C-terminal portion of the FOXO1 transcription factor. These fusion proteins have been shown to drive malignant transformation in ARMS, and patients with fusion-positive ARMS have a worse prognosis than patients with fusion-negative ARMS and embryonal RMS. We recently reported that piperacetazine, a phenothiazine derivative and first-generation antipsychotic, is capable of binding to and inhibiting the transcriptional activity of PAX3::FOXO1, reducing the expression of PAX3::FOXO1 target genes, and inhibiting the ability of fusion-positive RMS cells to grow in soft agar. We hypothesize that other phenothiazine derivatives may have stronger binding affinity for PAX3::FOXO1 and greater ability to reduce tumor growth in vivo. We employed a structure-activity relationship campaign to develop new phenothiazine derivatives that may be more potent inhibitors of PAX3::FOXO1 than piperacetazine. We synthesized and tested 10 new compounds, in addition to 9 existing FDA-approved phenothiazine derivatives, for their ability to bind to PAX3::FOXO1 and inhibit its transcriptional activity and target gene expression as well as inhibiting the growth of fusion-positive RMS cells in 3D culture. Seven derivatives inhibited PAX3::FOXO1 reporter activity better than piperacetazine, nine of them performed worse, and three of them showed comparable activity to piperacetazine. We demonstrated that piperacetazine does not alter PAX3::FOXO1 levels, subcellular localization, binding to a PAX3::FOXO1 target DNA sequence, or phosphorylation at Ser256 in the FOXO1 portion of the fusion protein. We therefore hypothesize that piperacetazine may be disrupting interactions between PAX3::FOXO1 and its partner proteins. We are employing a proximity-based biotinylation method to identify proteins that are competed away from PAX3::FOXO1 by piperacetazine. Our data suggest that it is possible to target PAX3::FOXO1 protein using small molecules that can directly bind to it and inhibit its activity in fusion-positive RMS cells.

Citation Format: Taryn Shaw, Kay Nakazawa, Purushottam Tiwari, Eryn Nelson, Jeffrey Formen, Christian Wolf, Jeffrey Toretsky, Aykut Üren. Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1093.
Abstract 1111: Poor radiation sensitivity and potential radiosensitizers for betel-nuts related head and neck squamous cell carcinoma in Taiwan
Authors: Chen Jo-Pai , Chang Jui-Ying , Hong Ruey-Long
Published: March 2024

Background: Betel nut chewing might contribute to strong invasion & treatment refractoriness in HNSCC from Taiwan. Betel-nuts exposed HNSCC cell line, TW2.6, had high PDL1, defective p53 mutation, p16 loss, & BCL2 overexpression. In our studies, PI3K/AKT/mTOR inhibitors, anti-angiogenesis therapies, CDK4/6 inhibitors, DDR interventions, epigenetic modifications, and immunotherapy-containing regimens will be future combination options. The genomic signature of TW2.6 has been figured out in our study(AACR2020 & 2023), too, mainly with PIK3CA H1047R mutation, high TMB(8.42 muts/Mb)/MSS, VEGF-A amplification, p53/MYC/HRAS/DDR2/PDGFRbeta/EPHB1/ATM mutations, FAT1 loss, amplification of TERT/FGF10/CCND3/SOX9/IL-7R/SDHA/RICTOR/FLCN, CDK12/PTPRD loss of function, CDK8 mutation, & deletions of STK11/ARID1B/MITF/TNFAIP3 and molecularly-guided novel interventions will be designed. Purpose & Methods: Polo-like kinase 1 inhibitor(volasertib), gluconate(blocking citrate transport & glucose metabolism), IAP inhibitor(Debio1143), glutaminase 1 inhibitor(CB839) were tested on TW2.6 to evaluate synergistic effects with radiation. Results: TW2.6 was resistant to volasertib, gluconate, or radiation alone; but sensitive to Debio1143 and CB839. Volasertib significantly enhanced radiation. The flow cytometry revealed volasertib and radiation resulted in a significant G2/M arrest. Western blotting showed volasertib and radiation increased p-histone3, p-CDK1, & cyclin B levels and induced apoptosis. Gluconate, CB839, or Debio1143 each had significant synergistic effects with radiation. The radiosensitization efficacy would be volasertib>gluconate>CB839>Debio1143. Conclusions: In Taiwan, patients with R/M HNSCC progressing within 3 months after CCRT could be rescued by early ICIs. Recently, sequential CCRT followed by ICI or Debio-1143 with CCRT showed potential survival benefits. In our studies, novel agents such as PLK inhibitor, gluconate, and CB839 had even better radiosensitization compared with Debio1143. Sequential CCRT with novel agents followed by ICI will be the future trend, esp. in biology-aggressive betel-nuts related locally advanced HNSCC in Taiwan.

Citation Format: Jo-Pai Chen, Jui-Ying Chang, Ruey-Long Hong. Poor radiation sensitivity and potential radiosensitizers for betel-nuts related head and neck squamous cell carcinoma in Taiwan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1111.
Abstract 112: The NSG-Flt3KO; Tg(hFLT3LG); hIL15 mouse strain improves engraftment of innate immune cells post-CD34+ humanization
Authors: Boreddy Srinivas Reddy , Hu Shuang , Soper Brian
Published: March 2024

Human immune system mouse models play critical roles in numerous preclinical drug development pipelines, including immunology, infectious diseases, and immuno-oncology. These models are constantly evolving, with addition of human cytokines to sustain engraftment of human immune cells. To date, most humanized models have primarily focused on T lymphocyte cell biology, leaving room for improvement in developing models that effectively represent NK cells and the myeloid lineage. Previously, we demonstrated that the introduction of human IL-15 (NSG-IL-15) or FLT3L (NSG-FLT3L) to NOD-scid IL2rγnull (NSG) mice enhanced engraftment of innate immune cells, including human CD56+ NK cells, CD141+ and CD1c+ DC subsets, CD123+ pDCs, and CD14+ monocytes. In this study, we describe a new NSG mouse variant (NSG-Flt3KO; Tg(hFLT3LG); hIL15) that expresses physiological levels of both human IL-15 and FLT3L and detail the immune cell diversity following HSC engraftment. NSG-Flt3KO; Tg(hFLT3LG); hIL15 mice, along with control strains NSG, NSG-IL15, and NSG-FLT3L, were engrafted with human umbilical cord blood derived CD34+ hematopoietic stem cells from three different donors, and blood samples were collected until Week 20 post-transplantation. Blood samples were analyzed via flow cytometry to assess the engraftment of innate and adaptive immune cells. Spleen and bone marrow samples were collected at Week 12 post-transplantation and analyzed for lymphoid and myeloid immune cell populations via flow cytometry. To compare the differences among the strains in terms of immune cell sub-populations across weeks, a Two-Way ANOVA (mixed-model) was conducted, with p<0.05 considered statistically significant. Overall, the results demonstrate that NSG-Flt3KO; Tg(hFLT3LG); hIL15 mice have enhanced CD56+/dim CD16+ NK cells compared to NSG-FTL3L strain (20.5±12.8% vs 7.0±3.5% at Week 12), but comparable to NSG-IL15. Furthermore, myeloid sub-lineage cells in NSG-IL15-FLT3L mice, such as monocytes, macrophages (M1), granulocytes, dendritic cells, and neutrophils, were greater than in NSG or NSG-IL15 strains, but comparable to NSG-FLT3L mice. Overall levels of hCD45+ and T cell sub-populations (CD3+ or CD4+ or CD8+) were comparable across all strains tested. In sum, our NSG-Flt3KO; Tg(hFLT3LG); hIL15 engraftment data suggest an improved model that supports drug development targeting human myeloid and NK cell populations.

Citation Format: Srinivas Reddy Boreddy, Shuang Hu, Brian Soper. The NSG-Flt3KO; Tg(hFLT3LG); hIL15 mouse strain improves engraftment of innate immune cells post-CD34+ humanization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 112.
Abstract 1121: Targeting the DNA damage response in high-risk medulloblastoma
Authors: DeCarlo Alexandria , da Silva Carolina Fernandes , Shen Lily , Ramaswamy Vijay , Tabori Uri
Published: March 2024

Medulloblastoma (MB) is the most common malignant pediatric brain tumour and is currently treated with surgery, external beam radiation and chemotherapy however, current treatments are woefully inadequate, with survival of only 50% but morbidity approaching 100%. A very-high risk group of SHH-activated MB harboring TP53 mutations (TP53mut-SHH) account for a substantial proportion of treatment failures after radiotherapy with a uniformly fatal outcome. Through optimizing radiation as a selection pressure and employing a functional genetic approach through whole-genome CrisprCas-9 dropout screening, the present study aims to identify drivers of radiation resistance and uncover unique vulnerabilities to sensitize these tumours to therapy. The dropout screen was conducted across a panel of established in vitro models of sporadic murine TP53mut-SHH, which resemble the human disease with profound radio-resistance. Initial results reveal that targeting the DNA damage response confer radiation sensitization. However, consistent hits across all models demonstrate non-homologous end-joining (NHEJ) as being synthetically lethal with radiation specifically in TP53mut-SHH. Genetic knockout experiments confirm genes encoding main proteins involved in NHEJ are synthetically lethal in combination with radiation. A small molecule drug screen targeting NHEJ revealed such vulnerabilities may be therapeutically exploited in TP53mut-SHH and are able sensitize these tumours to radiation. Using our unique approach of leveraging newly established models of TP53mut-SHH with a combination of functional genetic screening and small-molecule drug screening, this study highlights the genetic mechanisms of treatment resistance and reveals novel approaches for radiation sensitization. Here, we develop a novel approach to identify targets that are synthetically lethal with radiotherapy and identify multiple synthetically lethal targets at the genetic level which can be therapeutically targeted, allowing the development of new treatments to overcome current barriers.

Citation Format: Alexandria DeCarlo, Carolina Fernandes da Silva, Lily Shen, Vijay Ramaswamy, Uri Tabori. Targeting the DNA damage response in high-risk medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1121.
Abstract 1157: Molecular signatures associated with the progression from DCIS to IDC
Authors: Chen Siqi , Karpova Alla , Lal Preet , Storrs Erik , Jayasinghe Reyka , Iglesia Michael , Houston Andrew , Zhao Yanyan , Shinkle Andrew , Mo Chia-Kuei , Herndon John , Chen Feng , Gillanders William , Ding Li
Published: March 2024

Patients with ductal carcinoma in situ (DCIS) are frequently overtreated. Identifying markers that accurately predict which cases of ductal carcinoma in situ (DCIS) would progress to invasive ductal carcinoma (IDC) is crucial to personalized medicine but remains a challenge. Deciphering the process of DCIS progression at cellular, molecular and genetic levels helps identify biomarkers, allowing for better informed clinical decision-making. To study molecular signatures associated with the progression from DCIS to IDC, we collected samples from breast cancer patients with co-occurring DCIS and IDC, and performed Visium spatial transcriptomics (ST), single-nucleus RNA sequencing and multiplex imaging on these samples. We identified MGP, SLC39A6, PLAT, MLPH, AZGP1, TFF1 and TFF3 as showing significant differential expression levels in DCIS compared to IDC from ST analysis, which was confirmed with snRNA analysis. Notably, in multiplex imaging, MGP and PLAT showed consistently higher expression in DCIS compared to IDC at the protein level. Moreover, we evaluated these molecular signatures using MMTV-PyMT genetic mouse models at various breast cancer progression stages (3, 6, 12, 15, and 20 weeks) with snRNA-seq and multiplex imaging platforms. Collectively, our findings highlight the importance of identifying biomarkers at the molecular level, and provide potential predictive biomarkers for DCIS progression.

Citation Format: Siqi Chen, Alla Karpova, Preet Lal, Erik Storrs, Reyka Jayasinghe, Michael Iglesia, Andrew Houston, Yanyan Zhao, Andrew Shinkle, Chia-Kuei Mo, John Herndon, Feng Chen, William Gillanders, Li Ding. Molecular signatures associated with the progression from DCIS to IDC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1157.
Abstract 1190: NK cell subsets as potential correlates of antitumor immunity in HPV+ cancers
Authors: O'Hara Madison , Sastry Jagannadha
Published: March 2024

High-risk type human papillomaviruses (HPV) are associated with genital and oral cancers, and the incidence of head and neck squamous cell cancers is fast increasing in the USA and worldwide. Survival rates for patients with locally advanced disease are poor and variable after standard of care (SOC) chemoradiation treatment (CRT). Identifying the antitumor host immune mediators important for treatment response and designing strategies to promote them are essential for improving clinical outcome. Antitumor immunity comprises of adaptive and innate immune effectors. The immediate innate immune response by natural killer (NK) cells is a critical component for antitumor efficacy. The effector function of NK cells is modulated by various receptors via a wide array of activation or inhibitory signals. Among these receptors is HLA-DR, a recognized activation marker on CD8 T and NK cells. Literature studies refer to HLA-DR+ NK cells as pre-mNK. Preclinical data demonstrated therapeutic vaccine mediated induction of pre-mNK equivalent to contribute to tumor-free long-term survival. In our studies with clinical samples from HPV+ cancer patients, we’ve observed a dysfunctional phenotype of circulating pre-mNK when compared to healthy donors, demonstrated by flow cytometry methods. The correlates for dysfunction include increased PD-1 expression, a known inhibitory receptor, and reduced CD16, an NK receptor for Antibody Dependent Cellular Cytotoxicity (ADCC). Further, we observed circulating pre-mNK cells in HPV+ head and neck patients gain functionality post-treatment, as shown by significant increases in granzyme B and CD16, both known contributors for NK cytotoxicity. In cervical cancer patients, we had the opportunity to analyze the tumor microenvironment (TME). Interestingly, we found a significant increased frequency of cytotoxic pre-mNK cells, shown by granzyme B, in the TME that was not present in circulation. Overall, pre-mNK represent a uniquely activated immune subset for antiviral and antitumor immunity.

Citation Format: Madison O'Hara, Jagannadha Sastry. NK cell subsets as potential correlates of antitumor immunity in HPV+ cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1190.
Abstract 1220: Deep mutational scanning of EGFR reveals potential domain-specific TKI sensitivities in lung cancer and glioblastoma
Authors: Hayes Tikvah , Aquilanti Elisa , Kim Erica , Persky Nicole , Brenan Lisa , Goodale Amy , Sharpe Ted , Alan Doug , Shue Robert , Golomb Lior , Silverman Brianna , Li Yvonne , Westlake Lindsay , Piccioni Federica , Cherniack Andrew , Yang Xiaoping Yang , Root David , Hicks J. Kevin , Chi Andrew , Dietrich Jorg , Cahill Daniel , Johannessen Cory , Batchelor Tracy , Meyerson Matthew
Published: March 2024

The epidermal growth factor receptor, EGFR, is frequently activated in lung cancer and glioblastoma by genomic alterations including missense mutations. The different mutation spectra in these diseases are reflected in divergent responses to EGFR inhibition: significant patient benefit in lung cancer, but limited in glioblastoma. Here, we report a comprehensive mutational analysis of EGFR function. We performed saturation mutagenesis of EGFR and assessed function of ~22,500 variants in a human EGFR-dependent lung cancer cell line. This approach revealed enrichment of erlotinib-insensitive variants of known and unknown significance in the dimerization, transmembrane, and kinase domains. Multiple EGFR extracellular domain variants, lacking approved targeted therapies, were sensitive to dacomitinib. Strikingly, at least two glioblastoma patients with G598V dimerization domain mutations showed responses to dacomitinib treatment together with subsequent off-target resistance in one case. In summary, this comprehensive screen reveals novel functional EGFR variants and suggests broader clinical investigation of EGFR inhibition for cancers harboring extracellular domain mutations.

Citation Format: Tikvah Hayes, Elisa Aquilanti, Erica Kim, Nicole Persky, Lisa Brenan, Amy Goodale, Ted Sharpe, Doug Alan, Robert Shue, Lior Golomb, Brianna Silverman, Yvonne Li, Lindsay Westlake, Federica Piccioni, Andrew Cherniack, Xiaoping Yang Yang, David Root, J. Kevin Hicks, Andrew Chi, Jorg Dietrich, Daniel Cahill, Cory Johannessen, Tracy Batchelor, Matthew Meyerson. Deep mutational scanning of EGFR reveals potential domain-specific TKI sensitivities in lung cancer and glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1220.
Abstract 124: Validation of humanized TL1A mice for advancing preclinical research
Authors: Li Chong , Zhang Shujin , Zhang Zhi , Feng Jia , Jin James , Du Yibo
Published: March 2024

TL1A, or Tumor Necrosis Factor-Like Ligand 1A, plays a pivotal role in regulating the immune system and has garnered considerable attention in the field of cancer research. Studies have shown that TL1A can impact the tumor microenvironment via inflammatory signaling, immunosuppression, and tumor growth and survival. Targeting TL1A or its downstream effects could offer new avenues for cancer treatment and immunotherapy. To this end, we generated a human TL1A knock-in (B-hTL1A) mouse model. Human TL1A gene expression in B-hTL1A mice was confirmed by RT-PCR. TL1A protein expression was not altered following TL1A humanization in B-hTL1A mice as shown by flow cytometry. Lastly, soluble human TL1A was detected in B-hTL1A mice by ELISA. Due to the purported role of TL1A in mucosal immunity, efforts to induce inflammatory bowel disease in this humanized model are currently underway. Taken together, we established a preclinical B-hTL1A mouse model for the evaluation of TL1A-targeted immunotherapy.

Citation Format: Chong Li, Shujin Zhang, Zhi Zhang, Jia Feng, James Jin, Yibo Du. Validation of humanized TL1A mice for advancing preclinical research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 124.
Abstract 1303: Harness the power of data to improve cancer care - Understanding the complex landscape of health policies and regulations
Authors: Huang Ying , Basehore Heather , Boja Emily S. , Auvil Jaime M. Guidry
Published: March 2024

In the era of big data and artificial intelligence, biomedical research and healthcare have been presented with unprecedented opportunities for improving the understanding of cancer biology. In addition, the Open Science Initiative aims to shift the current paradigm of research practice towards broad sharing and public access to research findings as the norm. Big data in oncology usually includes a combination of genomic sequencing, proteomics, medical imaging, electronic health records, payor records, and other data sources from pharmaceutical research, wearables, and medical devices. While combining, linking, and analyzing data from different sources across research and healthcare enterprises is key to realizing the promise of big data and a health learning system, it poses tremendous challenges for researchers and implementers to understand the nuances of relevant policies, laws, and regulations while striving for broad, equitable, timely and responsible data sharing, as well as tackling issues in data quality, harmonization, interoperability, and security. Herein, we aim to shine a light on the ever-evolving landscape of data privacy regulations, laws, and policies that govern different touch points of a patient's journey where data are collected for research and healthcare purposes throughout the lifecycle that would impact data-sharing outcomes. We hope the illumination of a complex landscape of data governance framework to consider for many data sources will facilitate broad community engagement including data scientists and technologists, patients and advocacy groups, and policymakers to maximize open data and science while protecting patient privacy and confidentiality.

Citation Format: Ying Huang, Heather Basehore, Emily S. Boja, Jaime M. Guidry Auvil. Harness the power of data to improve cancer care - Understanding the complex landscape of health policies and regulations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1303.
Abstract 1397: Metabolic CRISPR-Cas9 screening identifies loss of mitochondriaGene Min triple-negative breast cancer to promote lung metastasis via immune modulation
Authors: Chou Shu-Ting , Wang Xiaoyong , Edwards Deanna N. , Chen Jin
Published: March 2024

Triple-negative breast cancer (TNBC) is a heterogenous breast cancer characterized by an aggressive phenotype and high risk of metastatic occurrence. Metastasis is a multifaceted process that involves metabolic reprogramming, selection, and adaptation. Although studies have shown that alterations of metabolic processes can influence TNBC phenotype and sensitivity to treatments, less is known about how changes in metabolic enzymes in the tumor cells affect crosstalk between tumor and immune cells during metastasis. Here, we performed a high-throughput CRISPR-Cas9 screening of metabolic genes in an orthotopic basal-like mammary carcinoma 4T1 mouse model to identify key metabolic enzymes in the tumor cells that are associated with TNBC lung metastasis by affecting the tumor microenvironment (TME). The CRISPR-Cas9 screening showed an enrichment of sgRNA for mitochondria Gene M in the metastasized lungs of wild-type mice but not Rag1−/− mice, indicating that loss of Gene M could modulate adaptive immune cells in the TME or distant organs to promote 4T1 lung metastasis. Further pilot experiments revealed that loss of Gene M in 4T1 cells increased murine basal-like carcinoma lung metastasis in vivo and decreased population of B cells, CD4+ T cells, M2 macrophages, monocytes, and CXCR2+ neutrophils in the metastasized lungs without affecting the growth rate of the primary tumors. Overall, our preliminary results demonstrated that Gene M deficiency in 4T1 cells affects immune cell profile and drives lung metastasis of murine basal-like carcinoma cells, but the molecular and cellular mechanisms by which loss of Gene M grant tumor cells with metastatic advantage requires further investigation.

Citation Format: Shu-Ting Chou, Xiaoyong Wang, Deanna N. Edwards, Jin Chen. Metabolic CRISPR-Cas9 screening identifies loss of mitochondriaGene Min triple-negative breast cancer to promote lung metastasis via immune modulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1397.
Abstract 14: Identification of tumor-reactive T cell receptors through functional single cell interaction analyses for personalized T cell therapy
Authors: Wagner Tim Robin , Kehl Niklas , Steiger Simon , Kilian Michael , Schönfelder Bruno , Boschert Tamara , Lindner Katharina , Schmidt Patrick , Rippe Karsten , Goldschmidt Hartmut , Raab Marc-Steffen , Platten Michael , Friedrich Mirco , Eichmüller Stefan B.
Published: March 2024

Innovative immunotherapy approaches such as adoptive transfer of chimeric antigen receptor (CAR) T cells or tumor infiltrating lymphocytes (TILs) have shown great success in the treatment of solid tumors and hematological malignancies. Although treatment of multiple myeloma with CAR T cells can induce deep responses, relapses frequently occur due to antigen escape and limited CAR T cell persistence. TCR-engineered T cells may show prolonged persistence in vivo and could mediate sustained antitumor effects. A further benefit of TCR transgenic T cells is the ability to target intracellular antigens that are inaccessible to CAR T cells, expanding the range of potential targets for immunotherapy. In our project, we propose to identify T cell receptors (TCRs) specifically targeting autologous myeloma cells. Tumor-reactive T cells were identified using the Bruker Cellular Analysis Lightning® platform, allowing simultaneous functional analysis of up to 1500 individual T cell/target cell interactions on a chip. Reactive T cells were identified upon detection of secreted cytokines (IFNγ, TNFα, IL2) and measurement of 4-1BB (CD137) surface expression. Tumor-reactive T cells showing various cytokine secretion patterns and 4-1BB expression profiles were detected in each myeloma patient (on average 11.9 T cells out of 1243 cells tested per assay run). Individual tumor-reactive T cells have been isolated and their TCRs were sequenced. TCR sequences of tumor-reactive T cells were mapped to single-cell RNA sequencing data of T cells from the same patiens to reveal a gene expression signature of myeloma-reactive T cells. TCR genes of reactive T cells were cloned and overexpressed in autologous T cells for functional validation and analysis of tumor derived neoepitope specificity. In summary, we present a pipeline allowing identification of myeloma-recognizing T cells and recovery of bona fide tumor-reactive TCRs eligible for patient-individualized T cell therapy.

Citation Format: Tim Robin Wagner, Niklas Kehl, Simon Steiger, Michael Kilian, Bruno Schönfelder, Tamara Boschert, Katharina Lindner, Patrick Schmidt, Karsten Rippe, Hartmut Goldschmidt, Marc-Steffen Raab, Michael Platten, Mirco Friedrich, Stefan B. Eichmüller. Identification of tumor-reactive T cell receptors through functional single cell interaction analyses for personalized T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 14.
Abstract 1466: Tobacco carcinogen impacts redox pathway to facilitate pancreatic ductal adenocarcinoma (PDAC) initiation and progression
Authors: Lin Xiaoxue , Stamp McKenna , Fowler Alexandra , Bottomley Chelsea , Okhovat Shira , Peck Kristina , Engle Dannielle
Published: March 2024

The 5-year survival rate for pancreatic ductal adenocarcinoma (PDAC) is only 10%. PDAC is projected to soon become the second leading cause of cancer death. Tobacco is one of the main risk factors for PDAC. Incidence of PDAC increases 2-fold among tobacco users, and 20-35% of PDAC cases are attributed to smoking. However, the specific pathways activated by tobacco carcinogens remain elusive.This research project addresses the impact of carcinogens in pancreatic cancer etiology. We hypothesize that carcinogens in tobacco increase reactive oxygen species (ROS), which elevates the Nrf2 redox pathway to facilitate PDAC initiation and progression. Specifically, we focus on two major subclasses of carcinogens: the heavy metal cadmium (Cd) and the polycyclic aromatic hydrocarbon (PAH) benzo(a)pyrene (BaP). Using mouse pancreatic ductal organoid cultures, we found that acute carcinogen exposure increases Nrf2 activity, which is sustained after "intermediate" exposure (5 passages). Intriguingly, chronic exposure (10 passages) downregulates Nrf2 activity, which has been shown to be associated with acquired metastatic potential. Furthermore, we found an upregulation in NFkB and EGFR signaling after intermediate exposure, which are involved in microenvironment remodeling and increased proliferative potential. Overall, we demonstrate that acute carcinogen exposure elevates ROS levels and activates the Nrf2 pathway, whereas prolonged exposure upregulates NFkB and EGFR pathways. Furthermore, we have established a novel carcinogenesis model using 3D organoid culture to recapitulate each step in pancreatic tumorigenesis. Collectively, this project contributes to our understanding of tobacco-related PDAC pathogenesis.

Citation Format: Xiaoxue Lin, McKenna Stamp, Alexandra Fowler, Chelsea Bottomley, Shira Okhovat, Kristina Peck, Dannielle Engle. Tobacco carcinogen impacts redox pathway to facilitate pancreatic ductal adenocarcinoma (PDAC) initiation and progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1466.
Abstract 1474: Interleukin-8 and NF-κB mediated signaling axis: A potential driver for cadmium-induced prostate carcinogenesis
Authors: Gupta Kunj Bihari , Singh Rajendra K. , Seremak Juliette R. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: March 2024

Cadmium (Cd) is a toxic heavy metal, ubiquitous in nature, and an industrial pollutant. Cadmium exposure can cause irreversible damage to lungs, liver and kidney including cancers. Alarmingly, abnormally high levels of cadmium are found in human prostate tissues. Studies on rodents have shown cadmium exposure causes liver, lung, and prostate cancers. The mechanism of carcinogenesis caused by Cd is multifactorial and specific organ carcinogenesis remains unclear. We and others have reported that the CXC-chemokine IL-8 drives cancer progression in prostate cancer (PCa). We tested a hypothesis that chronic cadmium-exposure induces upregulation of proinflammatory cytokines, such as IL-1β, IL-6, and IL-8, which individually or combined promote carcinogenesis and progression. The study used two non-transformed prostate epithelial cell lines (RWPE-1 and NHPrE1) to test whether continuous exposure to Cadmium chloride (CdCl2) perturbs cytokine expression pattern and selective silencing of elevated cytokines delays carcinogenesis and invasive potential. The CdCl2 exposed cells and culture conditioned media were analyzed regularly for changes in inflammatory milieu and for hallmarks of carcinogenesis. These studies measured changes in cell proliferation, production of cytokines (IL-8, IL-1β, IL-6, IFN-γ, TGF-β, and others), activation of Nuclear Factor-kB (NF-κB), and pro-tumorigenic factors, e.g., vascular endothelial growth factors (VEGF-A and B), cellular motility, and invasive potential, etc. Cells exposed to CdCl2 showed increased cell proliferation and clonogenic potential and specifically, increased expression of IL-8, it’s receptors (CXCR1 and CXCR2), IL-1β, and other cytokines & related genes. While un-exposed RWPE-1 cells did not express IL-8, it was the first cytokine to increase when exposed to CdCl2, followed by activation of NF-κB (p65-rel), VEGF-A, & B, CXCR1 and other markers. Gene silencing of IL-8 suppressed motility, invasion, and survival activity. These data supported that immediate-early IL-8 expression probably upregulates NF-κB mediated inflammatory signaling axis which is critical for Cd-induced carcinogenesis and may expose targets for countermeasures to prevent metal-induced toxicity & carcinogenesis.

Citation Format: Kunj Bihari Gupta, Rajendra K. Singh, Juliette R. Seremak, Vinata B. Lokeshwar, Bal L. Lokeshwar. Interleukin-8 and NF-κB mediated signaling axis: A potential driver for cadmium-induced prostate carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1474.
Abstract 1478: Chronic perfluorooctanesulfonic acid exposure promotes proliferation of colorectal cancer cells
Authors: Durham Jerika , Tessmann Josiane Weber , Hennig Bernhard , Zaytseva Yekaterina
Published: March 2024

Background: Chronic exposure to long-term exposures to per- and polyfluoroalkyl substances (PFAS), widely known as “forever chemicals”, has been associated with multiple negative health outcomes including increased risk of cancer. Perfluorooctanesulfonic acid (PFOS), a “long-chain” subtype of PFAS, has high bioaccumulation potential with a long elimination half-life. PFOS is frequently detected in drinking water leading to its high absorption through the gastrointestinal tract. Recent studies demonstrate that PFAS exposures promote intestinal inflammation and gut barrier dysfunction. However, how a long-term PFOS exposure affects colorectal cancer (CRC) progression is not known. Therefore, the purpose of this study is to delineate the effect of PFOS exposure on CRC cell proliferation and test the potential mitigation strategy for the harmful effects of PFOS.

Methods: SW480 and HCT116 cells have been treated with 1 ug/mL PFOS and proliferation was measured at 1, 2, and 3 months using the Presto Blue Cell Viability Reagent fluorescence assay. Proliferation markers were assessed by qPCR and Western blot. Control and PFOS exposed cells were treated with sulforaphane, a nuclear factor erythroid 2-related factor 2 (Nrf-2) inducer, at concentration 5, 10 and 20 uM for 72 hours.

Results: We show that chronic, low-dose PFOS exposure promotes proliferation of SW480 and HCT116 cell lines starting at 3 months since the first exposure. The increase in proliferation is associated with upregulation of Cyclin D, pAkt and FASN. We also show that sulforaphane significantly decreases proliferation of HCT116 and SW480 cells, and its efficacy is significantly higher in PFOS exposed CRC cells. The current studies show no effect on sulforaphane on normal colon epithelium cells.

Conclusion: Our studies suggest that chronic PFOS exposure promotes proliferation of CRC cells by increasing pro-carcinogenic gene expression and signaling. Furthermore, our findings suggest that supplementation of diet sulforaphane can potentially mitigate the harmful effects from PFOS exposure. Our studies warrant further investigation of the mechanisms behind the effect of PFOS exposure on cancer progression that would guide development of effective intervention strategies to mitigate the harmful effects of the exposure to “forever chemicals”.

Citation Format: Jerika Durham, Josiane Weber Tessmann, Bernhard Hennig, Yekaterina Zaytseva. Chronic perfluorooctanesulfonic acid exposure promotes proliferation of colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1478.
Abstract 1528: Flowcytometric based approach to investigate prostate tumor microenvironment
Authors: sajnani karishma , Eerola Sini , Kukkonen Konsta , Rauhala Hanna , Visakorpi Tapio , Urbanucci Alfonso
Published: March 2024

Prostate cancer (PC) and its tumor microenvironment (TME) are heterogenous and evolving along with the treatment patients are exposed to. Modelling of the TME represents an attractive approach to understand how PC evolves and spreads. Flow cytometry is a technique for quantitative measurement of single cell profiling based on the cell surface as well as intracellular markers. We designed a flowcytometric based approach to investigate the interplay between the PC cells and immune cells in a direct coculture. Cells are fluorescently tagged with a cell tracer and the analysis is performed separately on the adherent and non-adherent cells. To optimize the readout method, we investigate the interplay between Jurkat cells and PC cells (LNCaP) as well as immortalized prostate epithelial cell models modified to mimic early events in prostate carcinogenesis (RWPE-1 cells overexpressing androgen receptor, RWPE-1-AR, and having PTEN deletion, RWPE-1-AR-PTENdel).Jurkat (suspension culture) cocultured with LNCaP (adherent culture) exhibited 40% decrease in viability but only 30% of LNCaP dying cell in the floating population compared to LNcaP only which is 60%. When Jurkat were activated using Phorbol 12-myristate 13-acetate (PMA), we observed an increase in LNCaP cell death. Jurkat viability was not impacted in presence of RWPE-1 neither when exposed to RWPE1-AR-PTENdel. In summary our Flowcytometric-based approach will help to understand the interplay between immune cells and prostate cancer cells.

Citation Format: karishma sajnani, Sini Eerola, Konsta Kukkonen, Hanna Rauhala, Tapio Visakorpi, Alfonso Urbanucci. Flowcytometric based approach to investigate prostate tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1528.