bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3965: Histone H3 K27M mediated regulation of cancer cell stemness and differentiation in diffuse intrinsic pontine glioma (DIPG)
Authors: Sharma Monika , Magnuson Brian , Cruz Jeanette , Kauss McKenzie , Buschhaus Alexander , Ljungman Mats , Galban Stefanie
Published: June 2022

Diffuse Intrinsic Pontine Glioma (DIPG) is a rare pediatric brain tumor with a median survival of 10-15 months. Histone H3 is mutated in 80% of DIPGs, dictating tumor location, onset, and outcome of this devastating disease. Therapeutic resistance remains a major obstacle to preventing tumor recurrence and is in part driven by cancer stem cells (CSCs), which exhibit self-renewal properties and tumorigenic potential. In previous studies, we have identified these proliferative and tumorigenic features in aldehyde dehydrogenase positive (ALDH+) CSCs in H3K27M mutant DIPG. Among the 19 ALDH isoforms known in humans, aldehyde dehydrogenase family 1 member A3 (ALDH1A3) is most highly expressed in malignant cells when compared to immune cells or oligodendrocytes in H3K27M DIPG biopsies, indicating an important mechanistic role in regulating stemness in DIPG. We hypothesize that ALDH-mediated cancer stemness and resistance may in part be driven by H3K27M. Indeed, ALDH1A3 expression was dramatically reduced in CRISPR-edited DIPG cells where the H3K27M mutation had been removed (H3K27M-KO). Furthermore, these cells lost their neurosphere forming potential, began to express glial fibrillary acidic protein (GFAP) and attached to the plastic, changes indicative of differentiation. Transcriptomic and GSEA pathway analyses suggested Wnt-dependent regulation of ALDH1A3, with Wnt 7b and Wnt 11 demonstrating the largest difference in the isogenic DIPGs. In addition, DNA repair, along with PI3K/AKT and Wnt signaling, were found to be upregulated upon radiation of DIPG cells, indicating future therapeutic opportunities to prevent radio resistance. We have co-targeted these cell-intrinsic vulnerabilities to eradicate CSCs in DIPG and prevent tumor recurrence, using a combination of radiotherapy, the PI3K/mTOR inhibitor GDC-0084 and the ALDH inhibitor Disulfiram. This combination has produced an exquisite synergy in cells, which we will test in clinically-relevant DIPG models. Taken together, through these studies we have gained mechanistic insight into H3K27M mediated regulation of cancer cell stemness and differentiation in DIPG, which appears to be mediated by Wnt-dependent signaling of ALDH1A3 and provides rationale for exploring new therapeutic targets.

Citation Format: Monika Sharma, Brian Magnuson, Jeanette Cruz, McKenzie Kauss, Alexander Buschhaus, Mats Ljungman, Stefanie Galban. Histone H3 K27M mediated regulation of cancer cell stemness and differentiation in diffuse intrinsic pontine glioma (DIPG) [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 3965.
Abstract 3974: Investigating doxorubicin resistance in fibrosarcoma
Authors: Dorand Rodney Dixon , Dang Donna , Davis Elizabeth J. , Park Ben Ho
Published: June 2022

Cytotoxic chemotherapy has been the backbone of medical oncology for nearly a century for multiple cancer types. However, when treating advanced or metastatic disease toxicity, side effects, and acquired resistance often limit the duration of therapy. While randomized control trials have traditionally served as the proving ground for first and subsequent line therapies, rare tumor subtypes including soft tumor sarcoma (STS) provide unique challenges for developing robust treatment data. By developing human based in vitro models, we can investigate potential therapeutic mechanisms for STS. Fibrosarcoma is one distinct histologic STS subtype that relies heavily on anthracycline treatment in the first line setting, however, there are limited options once resistance develops. Anthracyclines, including doxorubicin, exert their effect through a variety of mechanisms including reactive oxygen species, DNA-adduct formation, and inhibiting topoisomerase II, histone eviction, calcium and iron homeostasis, and ceramide overproduction. However, there have also been multiple mechanisms of doxorubicin resistance including disruption of cell membrane, alteration of cell surface molecules, inactivation of drugs, gene amplification, activating alternative signaling pathways, and affecting cellular repair mechanisms. In order to investigate the role of anthracycline resistance in fibrosarcoma lines we acquired two human derived fibrosarcoma lines SW684 and HT-1080 from American Type Culture Collection (ATCC). Characterization of HT-1080 using publicly available datasets demonstrated that TP53, CDK2NA and NF1 serve as major driver mutations while SW684 relies on NRAS and IDH1 mutations. We further characterized these cell lines in vitro and noted that HT-1080 has a quick doubling time of 16 hours while SW684 has a doubling time of 91 hours. Additionally, after doxorubicin treatment, we found that HT-1080 is sensitive with an IC50 of 5.594 nanomolar while SW684 is relatively doxorubicin resistant with an IC50 of 28.915 micromolar. While proliferative rate may play a role in the sensitivities of these cell lines further characterization of the mechanism leading to doxorubicin resistance is needed. To that end, we are using a CRISPR-Cas9 approach for further genome wide screening of these fibrosarcoma lines in the presence of doxorubicin. Exploring the genetic mechanisms that result in development of doxorubicin resistance may reveal novel, targetable mechanisms expanding treatment durability in this rare STS.

Citation Format: Rodney Dixon Dorand, Donna Dang, Elizabeth J. Davis, Ben Ho Park. Investigating doxorubicin resistance in fibrosarcoma [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 3974.
Abstract 4002: Identification of signal transduction pathway activity with potential clinical target in high-grade serous ovarian carcinoma
Authors: Van der Ploeg Phyllis , Wesseling-Rozendaal Yvonne J.W. , Biezen-Timmermans Eveline C. , Piek Jurgen M.J.
Published: June 2022

Background: High-grade serous carcinoma (HGSC) is the most common subtype of ovarian cancer. It has a high mortality rate, even after successful first-line treatment with debulking surgery and chemotherapy. Although therapeutic options for targeted therapy are rapidly expanding, identification of patients who respond to these therapies remains a challenge. In recognition of the importance of the functional phenotype of cancer cells, Verhaegh et al. (Cancer Res 2014) developed assays to measure functional activity of signal transduction pathways (STPs) based on mRNA expression levels of pathway-specific target genes. In this study, we aimed to identify HGSCs with STP activity with a potential clinical target by comparing their activity with STP activity in normal Fallopian tube epithelium (FTE), the tissue of origin of most HGSCs.

Methods: We included 50 primary tumor samples taken prior to start of chemotherapy of postmenopausal patients diagnosed with advanced stage HGSC and 9 morphologically normal FTE samples of healthy postmenopausal women. Using pathway assays, we assessed functional pathway activity of the androgen receptor (AR), estrogen receptor (ER), PI3K, MAPK, Hedgehog, TGFβ and Notch pathways. Differences in STP activity between groups were compared with Mann-Whitney U tests. Cut-off value for aberrant STP activity was defined as two standard deviations above the mean value of STP activity measured in FTE samples.

Results: In the HGSC group we observed lower median ER (p < 0.001) pathway activity and higher median PI3K (p < 0.001), Hedgehog (p < 0.001) and TGFβ pathway (p = 0.020) activity as compared to the FTE group. In individual HGSC samples, aberrant activity was identified for the MAPK (n = 10), PI3K (n = 22), Hedgehog (n = 28) and TGFβ (n = 21) pathways. Frequently observed combinations of aberrant STP activity were Hedgehog/TGFβ (n = 12) and Hedgehog/PI3K (n = 9). In total, we identified at least one STP with potential clinical target in 88% (44/50) of HGSC samples.

Conclusions: Our analysis enabled the identification of STP activity with a potential clinical target in 88% of the analyzed HGSC samples. Differentiation between normal and aberrant STP activity could have clinical utility in the selection of HGSC patients for targeted therapy. A prospective study (STAPOVER) has been designed to demonstrate clinical utility.

Citation Format: Phyllis Van der Ploeg, Yvonne J.W. Wesseling-Rozendaal, Eveline C. Biezen-Timmermans, Jurgen M.J. Piek. Identification of signal transduction pathway activity with potential clinical target in high-grade serous ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4002.
Abstract 4003: Identification of a targeted anti-mitotic agent that degrades Myc and specifically induces cancer cell death
Authors: McAnulty Jessica , Dziubinski Michele , Gandhi Agharnan , Farah Margaret , Lee Pil , White Andrew D. , DiFeo Analisa
Published: June 2022

For decades, chemotherapy has remained the standard of care for ovarian cancer patients. Although 70% of patients initially respond to platinum-based therapy, >90% succumb to chemoresistance. There is a need to uncover targeted drugs for ovarian cancer. A quicker, more cost-effective, and lower-risk route to identify new treatments is through repurposing FDA approved drugs. Using a computational drug repositioning platform, DrugPredict, we previously uncovered that the antiarrhythmic drug amiodarone potently decreases cell viability and triggers apoptosis in numerous patient-derived ovarian cancer cell lines through the degradation of c-Myc. However, given the dose-limiting toxicity of amiodarone, we applied structure-activity relationship to identify DL78, which lacks hERG activity but retains the anti-cancer properties and ability to regulate Myc. DL78 is significantly more potent and tumor specific than amiodarone. It rapidly induces G2/M arrest which ultimately leads to loss of Myc, mitotic catastrophe, and apoptosis in several types of cancer cells. Furthermore, pharmacokinetics studies show that the compound is retained in the tumor upon intraperitoneal injection and has reasonable solubility and permeability, yielding good absorption, distinct from amiodarone. Given its structural and molecular differences, we expect that DL78 works through a different mechanism that amiodarone and could represent an effective treatment for ovarian cancer and other MYC-driven tumors. Additional studies will establish the foundation for further development of this novel compound, as well as reveal targeted ovarian cancer vulnerabilities.

Citation Format: Jessica McAnulty, Michele Dziubinski, Agharnan Gandhi, Margaret Farah, Pil Lee, Andrew D. White, Analisa DiFeo. Identification of a targeted anti-mitotic agent that degrades Myc and specifically induces cancer cell death [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 4003.
Abstract 4023: Low nutrient availability drives increased macropinocytosis and MEK inhibitor resistance in KRASG12R-mutant pancreatic ductal adenocarcinoma
Authors: Linke Amanda , Burge Rachel , Hobbs Aaron
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is the third most deadly human cancer with a dismal five-year survival rate of 10%. KRAS is mutated in over 95% of PDAC tumors and is a key driver of PDAC tumorigenesis. Mutant KRAS is constitutively active and drives proliferation through the upregulation of numerous signaling and metabolic pathways to support tumor proliferation. Despite the promise of targeted inhibitors of the RAF-MEK-ERK MAPK signaling pathway, arguably the most critical RAS-mediated proliferative signaling pathway, clinical trials targeting oncogenic MEK/ERK signaling as a single-agent therapy have been unsuccessful. The PDAC tumor microenvironment has been shown to be depleted of glutamine and free amino acids, suggesting that PDAC relies heavily on nontraditional metabolic processes for proliferation such as macropinocytosis, the nonselective uptake of proteins and molecules from extracellular spaces, and autophagy, a mode of cellular recycling. Macropinocytosis has been shown to be elevated in PDAC cell lines and human tumors. Despite recent findings describing the limited nutrient availability in the tumor microenvironment, cell culture studies supporting the use of MEK/ERK inhibitors are predominately performed in a high glutamine medium. By utilizing a minimal glutamine medium supplemented with bovine serum albumin, a large protein that is absorbed via macropinocytosis, we show that this growth medium drives resistance to MEK MAPK inhibition. To evaluate whether PDAC cells proliferating in a low glutamine medium can be sensitized to MEK inhibition, we have performed a CRISPR/Cas9 loss-of-function screen targeting the druggable genome to determine effective therapeutic combinations under these conditions. To follow up on our in vitro screen, we will evaluate the therapeutic efficacy of our findings with 2D and 3D PDAC proliferation assays. These studies will describe novel treatment strategies for PDAC patients with elevated macropinocytosis.

Citation Format: Amanda Linke, Rachel Burge, Aaron Hobbs. Low nutrient availability drives increased macropinocytosis and MEK inhibitor resistance in KRASG12R-mutant 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 4023.
Abstract 4052: Evaluation of anti-tumor activity of SB-216, a novel potent tubulin inhibitor, in pancreatic cancer
Authors: Wang Rui , Pochampally Satyanarayana , Hamilton David , Miller Duane D. , Li Wei
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with high mortality. It is the 4th leading cause of cancer-related death in the U.S. and has the lowest 5-year survival rate among all cancer types. One of the main hurdles for the treatment is limited effective chemotherapy and rapidly acquired resistance against it. Advanced PDAC research and various treatment options only showed minimal enhancement to the overall survival outcomes. Hence more effective drugs and therapies are in need for improving overall therapeutic outcomes for PDAC patients. Recently, we reported the discovery of a new generation of tubulin inhibitors (SB-216) that targets the colchicine binding site and serves as a potent anti-cancer agent for various cancer types. Here, we evaluated the in vitro effects of SB-216 on the PDAC cell lines in comparison with one of the first-line treatment paclitaxel. We also established luciferase labeled Mia PaCa-2 cell line, Mia PaCa-2-Luc, for live monitoring tumor progression and evaluating the anti-tumor effect in subcutaneous mouse models. The results showed that SB-216 effectively inhibited cell proliferation, colony formation, and cell migration dose-dependently at low nanomolar concentrations. Immunoblotting also confirmed SB-216 induced cell apoptosis in a dose-dependent manner. Cell cycle arrest assay confirmed that SB-216 can arrest cells in the G2/M phase. In vivo study suggested that SB-216 inhibited tumor growth significantly in Mia PaCa-2-Luc subcutaneous xenograft model with low toxicity. Our preclinical data demonstrated the potential of SB-216 to inhibit proliferation and induce apoptosis in PDAC cells, indicating a promising chemotherapy agent in treating PDAC. However, further evaluations are warranted in orthotopic and PDX tumor models for clinical significance.

Citation Format: Rui Wang, Satyanarayana Pochampally, David Hamilton, Duane D. Miller, Wei Li. Evaluation of anti-tumor activity of SB-216, a novel potent tubulin inhibitor, in pancreatic 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 4052.
Abstract 4056: ONC201 in combination with carboplatin and etoposide as a novel triple drug treatment for small cell lung cancer (SCLC)
Authors: Lee Young S. , Zhou Lanlan , Azzoli Christopher , El-Deiry Wafik S.
Published: June 2022

Lung cancer is the leading cause of cancer death in both men and women according to the American Cancer Society, with more deaths than colon, breast, and prostate cancer combined. Small cell lung cancer (SCLC) comprises about 10 to 15 percent of all lung cancer diagnoses. Frequent loss of RB1 and mutations in p53 in SCLC make it rather difficult to develop targeted therapies. Many current therapies rely on toxic chemotherapy or immunotherapy to combat the aggressive nature of SCLC; however, even with the advent of new therapies, the median survival rate has remained relatively low at 12 to 16 months. SCLC is also characterized by a high mutation rate, resulting in patients becoming increasingly resistant to treatments. This calls for a novel combination to extend patient life expectancy. ONC201 is an imipridone that is currently in clinical trials for its proapoptotic effects in several cancer types. We propose that combining ONC201 with standard first-line chemotherapeutic agents etoposide and carboplatin will result in a synergistic effect and serve as a novel treatment plan for SCLC patients. SCLC cell lines H1048 and H1105 were treated with the novel triple drug combination ONC201, etoposide, and carboplatin. Cell-Titer Glo cell viability assays were conducted for 72 hours to see the additive and/or synergistic effect of novel triple drug treatment. Western blots were also run to evaluate the expression of proapoptotic protein cleaved PARP or expression of cellular metabolic stress protein ATF4 to explore the synergistic effect of triple drug treatments in SCLC cell lines. Cell viability after the triple drug treatment in both cell lines H1048 and H1105 may indicate a potential synergistic effect. Preliminary western results indicate that the triple drug treatment results in an increase in cPARP or ATF4 expression relative to the vehicle, suggesting a synergistic effect of the triple drug treatment. We are currently exploring the novel combination and potential underlying mechanisms behind the synergistic effects of the triple drug treatment. Future studies will evaluate this triple drug combination treatment in mouse models of SCLC.

Citation Format: Young S. Lee, Lanlan Zhou, Christopher Azzoli, Wafik S. El-Deiry. ONC201 in combination with carboplatin and etoposide as a novel triple drug treatment for small cell lung cancer (SCLC) [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 4056.
Abstract 4093: COSMIC Actionability: Supporting precision oncology through Identification of actionable mutations from clinical trials databases and publications
Authors: Jupe Steven C. , Bindal Nidhi , Sondka Zbyslaw , Wang Shicai , Nair Sumodh , Ponting Laura , Sondheimer Doron , Hathaway Charlie , Forbes Simon A.
Published: June 2022

The availability of drugs that are effective in cancer patients with specific somatic mutations is rapidly evolving. Finding the most recent information is not straightforward; clinical progress and drug approvals are recorded in clinical trial repositories, files from drug regulatory agencies, publications and conference abstracts. Often there is a delay between trials reaching their outcomes, publication and deposition of results in clinical trial databases. COSMIC Actionability is a new addition to COSMIC’s (Catalogue Of Somatic Mutations In Cancer) portfolio of navigational databases for precision oncology. It indicates the availability of drugs that target mutations and tracks the progress of novel drugs through clinical development. All stages of drug development are represented, through safety and clinical efficacy to market approval, with additional data from case studies expanding mutation coverage. For each mutation-cancer type combination, a simple tiered system indicates whether marketed drugs are available and if not, indicates the progress of drug development efforts. Trial records available in databases such as Clinical Trials.gov and EudraCT are supplemented with trials identified in publications. Trial progression and outcomes are recorded; details are sourced from clinical trial databases, publications, conference abstracts, corporate announcements and regulatory authorities such as the FDA. Curation identifies results for approximately 40% more trials than are available in clinical trial databases alone.

Like other COSMIC resources, Actionability is manually curated by Ph.D. level experts. The current version of COSMIC Actionability (October 2021) has 49 fully curated genes with a further 237 having some clinical information. Details of 6244 drug-cancer type combinations are available, of which 2224 have clinical results. 963 drugs are represented, in 2224 treatment combinations. 149 point mutations and 520 further mutations or fusions are represented. This dataset will be made freely available in 2022 then released quarterly, with extended gene coverage and updates of previous content.

Citation Format: Steven C. Jupe, Nidhi Bindal, Zbyslaw Sondka, Shicai Wang, Sumodh Nair, Laura Ponting, Doron Sondheimer, Charlie Hathaway, Simon A. Forbes. COSMIC Actionability: Supporting precision oncology through Identification of actionable mutations from clinical trials databases and publications [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 4093.
Abstract 4097: Clinicopathologic descriptors of subcutaneous panniculitis-like T-cell lymphoma (SPTCL): Analysis of a pooled database of a rare entity
Authors: Haddad Philip A. , Ganey Nowell
Published: June 2022

Introduction: SPTCL is a rare primary cutaneous T-cell lymphoma. SPTCL was initially described as an aggressive cutaneous T-cell lymphoma frequently associated with hemophagocytic syndrome (HPS) and requiring aggressive multiagent chemotherapy. In 2005, this entity was restricted to SPTCL with αβ phenotype, a less aggressive entity compared to its γδ counterpart, currently known as primary cutaneous γδ T-cell lymphoma. We conducted this analysis to explore the clinicopathologic characteristics of this little-known primary cutaneous T-cell entity.

Methods: In order to study the demographic characteristics, molecular and immunohistochemical signatures, therapeutic interventions, survival, and prognostic factors, we compiled a pooled database of 214 cases. Descriptive statistics were calculated. Cox proportional-hazards model and Log-rank tests were used to assess the influence of demographic and clinicopathologic factors on overall survival (OS).

Results: A total of 214 patients with confirmed SPTCL diagnosis were identified. The median age was 34 years with a peak incidence between ages 13 and 26. There was a female predominance with F:M ratio of 1.7. Upon presentation, 12% had lymphadenopathy, 12% had hepatosplenomegaly, and 27% had bone marrow involvement. No extra-nodal or extra-cutaneous involvement were reported. Cases expressed CD2 (8%), CD3 (85%), CD4(10%), CD5(10%), CD7 (9%), CD8 (77%), CD56 (6%), Granzyme-B (33%), and TIA-1 (34%). None of the cases expressed CD30. The most common clinical presentations were nodular skin changes (87%) followed by constitutional symptoms (57%). Fifteen and ten percent of SPTCL patients had history of immune-deregulatory disorders and immunosuppressive therapies, respectively. HPS occurred in 24% of the cases. Karyorrhexis, fat necrosis, and dermal involvement were noted in 15%, 9%, and 17%. The median duration of symptoms prior to diagnosis was 4 months. Median OS of the whole group was not reached while the mean OS was 73 months. OS was not impacted by sex, constitutional symptoms, immunocompromising factors, presence of lymphadenopathy, hepatosplenomegaly, or bone marrow involvement. OS was not impacted by histological or immunohistochemical features either. While older age and the occurrence of HPS negatively impacted OS, attaining complete remission positively impacted OS.

Conclusions: This study presents a comprehensive clinicopathologic data from a pooled cohort of patients with SPTCL. It describes the clinicopathologic features of SPTCL and identifies major determinants of OS in this rare disease.

Citation Format: Philip A. Haddad, Nowell Ganey. Clinicopathologic descriptors of subcutaneous panniculitis-like T-cell lymphoma (SPTCL): Analysis of a pooled database of a rare entity [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 4097.
Abstract 4100: Developmental deconvolution for classification of cancer origin
Authors: Moiso Enrico , Farahani Alexander , Marble Hetal , Hendricks Austin , Mildrum Samuel , Levine Stuart , Lennerz Jochen , Garg Salil
Published: June 2022

Cancer is a disease manifesting in abrogation of developmental programs, and malignancies are namedbased on their cell or tissue of origin. However, a systematic atlas of tumor origins is lacking. Here we map the single cell organogenesis of 56 developmental trajectories to the transcriptomes of over 10,000 tumors across 33 cancer types. We use this map to deconvolute individual tumors into their constituent developmental components. Based on these deconvoluted developmental programs, we construct a Developmental Machine Learning Perceptron (D-MLP) classifier that outputs cancer origin. The D-MLP classifier (ROC-AUC: 0.974 for top prediction) outperforms classification based on expression of either oncogenes or highly variable genes. We analyze tumors from patients with cancer of unknown primary (CUP), selecting the most difficult cases where extensive multimodal workup yielded no definitive tumor type. D-MLP revealed insights into developmental origins and diagnosis for most patient tumors. Our results provide a map of tumor developmental origins, provide a tool for diagnostic pathology, and suggest developmental classification may be a useful approach for otherwise unclassified patient tumors.

Citation Format: Enrico Moiso, Alexander Farahani, Hetal Marble, Austin Hendricks, Samuel Mildrum, Stuart Levine, Jochen Lennerz, Salil Garg. Developmental deconvolution for classification of cancer origin [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 4100.
Abstract 4147: CCX559, an orally administered small molecule PD-L1 inhibitor for the treatment of solid tumors
Authors: Sullivan Kathleen M. , Miao Shichang , Yue Huibin , Zhao Niky , Li Chris , Tai Ezra , Ebsworth Karen , Rico Gonzalo Tapia , De Souza Paul , Schall Tom , Zhang Penglie
Published: June 2022

Background: The small molecule CCX559 is a novel, highly potent inhibitor of human PD-L1 being developed as an oral treatment for cancer patients. We have previously demonstrated that CCX559 has nanomolar potency and high selectivity for PD-L1; that it enhances primary T cell activation and has anti-tumor efficacy, including the ability to induce complete responses, using in vivo models1.

Results: Safety pharmacology studies in preclinical animal species demonstrated pharmacokinetics and an acceptable safety profile for CCX559, which supported the initiation of human trials in patients with advanced tumors. Prior findings from toxicology studies were consistent with immune modulation, including consumptive coagulopathy, increased white blood cell counts, and changes in IL-6 plasma levels. A Phase 1, first in patient, multicenter, open-label, dose-escalation study was initiated, with a starting dose of once-daily (QD) oral dosing at 30 mg. The primary objectives are safety/tolerability, as well pharmacokinetic (PK) assessments aimed at determining a future phase 2 dose. Secondary objectives include pharmacodynamic (PD) assessments of immune cell activation in patient peripheral blood samples, as well as anti-tumor effects. For PK, intensive blood sampling is done on day 1 and day 21 of the first cycle of dosing; additional samples are collected on select days throughout the 21-day treatment cycles. PD analyses are done on selected blood draws as well. The first patient dosed (30 mg QD) showed that the drug was well tolerated with no adverse events reported. Preliminary PK results from this patient revealed CCX559 exposure levels consistent with preclinical predictions. Moreover, PD samples showed elevations in T cell proliferation and activation within the first 15 days, when compared to the predose sample. In conclusion, the preclinical data support clinical development of CCX559. CCX559 shows encouraging initial PK and PD results, and patient enrollment is ongoing in the trial (ACTRN12621001342808).

References: 1Chris Li, et al. CCX559 is a potent orally-administered small molecule PD-L1 inhibitor that induces anti-tumor immunity. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1274.

Citation Format: Kathleen M. Sullivan, Shichang Miao, Huibin Yue, Niky Zhao, Chris Li, Ezra Tai, Karen Ebsworth, Gonzalo Tapia Rico, Paul De Souza, Tom Schall, Penglie Zhang. CCX559, an orally administered small molecule PD-L1 inhibitor for the treatment of solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4147.
Abstract 4149: Knock-down of Neuropilin-1 by locked nucleic acid antisense oligonucleotides facilitates cancer immune control
Authors: Maaske Andre , Kirchhammer Nicole , Festag Julia , Rodriguez Laura Fernandez , Buchi Mélanie , Schell Monika , Raith Stefanie , Michel Sven , Klar Richard , Zippelius Alfred , Jaschinski Frank
Published: June 2022

Immune checkpoint inhibitors have become an important tool for the treatment of cancer. However, the majority of patients does not respond to the currently employed antibody-based treatments, indicating a need for additional targets and new treatment modalities. The invention of 3rd generation chemistries like locked nucleic acids (LNAs) has allowed the development of highly specific and efficacious antisense oligonucleotides (ASOs) that allow target knockdown in vivo without the need for complex delivery formulations.

The membrane-bound protein neuropilin-1 (NRP1) was initially identified as a factor involved in cell migration, -survival, and neoangiogenesis making it an attractive target for cancer therapy. It was subsequently shown that it has additional immune-mediated pro-tumorigenic roles. It can suppress anti-tumor immune activity via regulation of trafficking of tumor-associated macrophages, phenotypic stability of Tregs, and exhaustion of effector T cells. Considering that these effects are mediated by multiple domains of NRP1, there is a conceptual advantage to down-regulate the expression of the whole protein over the functional or steric blockade of individual domains.

We used our in-house Oligofyer™ bioinformatics system to design both human NRP1 specific LNAplus™ ASOs, as well as murine surrogates, which both achieved target knock-down of more than 85% in vitro. Furthermore, the murine surrogate down regulated NRP1 in tumor mouse models. Systemic application of mouse-specific ASOs without additional carriers or adjuvants has led to a strong delay of tumor growth or complete eradication in syngeneic mouse models. This effect was almost completely abrogated in immune-compromised NSG mice. Furthermore, re-challenge of immune-competent mice after tumor eradication did not result in new tumor growth, suggesting induction of a long-lasting immunity by LNAplus™ ASO-mediated knockdown of NRP1. Taken together, these encouraging results indicate that the ASO-mediated down-regulation of NRP1 has the potential to become a promising treatment option for patients in need. We are currently performing further experiments to fully elucidate the mechanisms that underlie the observed anti-tumor efficacy.

Citation Format: Andre Maaske, Nicole Kirchhammer, Julia Festag, Laura Fernandez Rodriguez, Mélanie Buchi, Monika Schell, Stefanie Raith, Sven Michel, Richard Klar, Alfred Zippelius, Frank Jaschinski. Knock-down of Neuropilin-1 by locked nucleic acid antisense oligonucleotides facilitates cancer immune control [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 4149.
Abstract 4181: CDK4/6 inhibition with Abemaciclib improves intracranial and extracranial response to checkpoint blockade in pre-clinical models of brain metastasis
Authors: Nayyar Naema , Singh Mohini , de Sauvage Magali , Ijad Nazanin , Dahal Ashish , Chuprin Jane , Brehm Michael , Brastianos Priscilla
Published: June 2022

While immune checkpoint inhibitors (ICI) have revolutionized treatment of advanced cancers, few of the 30% of cancer patients who develop brain metastases benefit from immunotherapy. Inhibition of CDK4/6 pathway - altered in >50% of brain metastatic patients - can reportedly increase tumor inflammation and sensitize extracranial tumors to ICI. To determine whether intracranial tumors can be similarly sensitized, we studied efficacy of combination CDK4/6 inhibitor Abemaciclib and ICI in immunocompetent mouse models of brain metastasis bearing concurrent intracranial and extracranial murine tumors that are ICI-resistant. 8-week-old female C57BL/6 mice received subcutaneous injections of 2x105 YUMM1.7 or B16-F10 melanoma cells 3 days prior to intracranial injections of 1x104 YUMM1.7-FmC (firefly luciferase-tagged) cells or 5x103 B16-F10 cells respectively. 8-week-old female BALB/C mice similarly received 2x105 4T1 mammary carcinoma cells in mammary fat pad 3 days prior to intracranial injections with 2x104 4T1-FmC cells. Mice were randomized into 4 treatment groups (n=5-7/group): Abemaciclib monotherapy (administered daily), anti-PD-1 monotherapy (every 3 days), Abemaciclib and anti-PD-1 (combination therapy), and treatment with vehicle and isotype-matched antibody as control. In all 3 tumor models, extracranial tumor growth was significantly reduced compared to control mice following combination therapy (P<0.05 for all), while Abemaciclib monotherapy only reduced growth of subcutaneous YUMM1.7 tumors (P<0.05). Intracranial tumor growth, calculated using bioluminescence imaging early-in-treatment and post-treatment, was significantly reduced compared to control-treated tumors following combination therapy in both YUMM1.7-FmC and 4T1-FmC models (P<0.05 for both). In mice bearing B16-F10 tumors, where overall survival was used as an indirect measure of intracranial tumor growth, combination therapy improved survival (p<0.05) compared to both control and Abemaciclib monotherapy arms. These results indicate CDK4/6 inhibition with Abemaciclib can improve both extracranial and intracranial responses to ICI and sensitize brain metastases to immunotherapy. Our pre-clinical findings warrant further investigation to determine whether this combination approach can improve patient outcomes.

Citation Format: Naema Nayyar, Mohini Singh, Magali de Sauvage, Nazanin Ijad, Ashish Dahal, Jane Chuprin, Michael Brehm, Priscilla Brastianos. CDK4/6 inhibition with Abemaciclib improves intracranial and extracranial response to checkpoint blockade in pre-clinical models of brain metastasis [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 4181.
Abstract 4215: Combination of STING and TLR 7/8 agonists as vaccine adjuvants for cancer immunotherapy
Authors: Bhatnagar Shubhmita , Revuri Vishnu , Shah Manan , Larson Peter , Ferguson David , Panyam Jayanth
Published: June 2022

Various classes of molecules including toll-like receptor (TLR) agonists, exosomes, and metallo compounds have been evaluated as adjuvants for cancer vaccines. However, their wide-spread clinical use has been limited by transient immune responses and serious side-effects. Here, we propose the use of a multi-adjuvant approach that combines two different classes of adjuvants, STING and TLR 7/8 agonists, based on their distinct immune cell targets, signalling pathways, and significant roles in the activation and maintenance of immune responses. We evaluated the potential of combining 522, a novel TLR 7/8 agonist, and DMXAA, a STING agonist, for stronger DC activation and greater CD8 T cell responses. Mouse bearing B16F10-OVA (murine melanoma cell line which expresses ovalbumin) tumors were immunized with OVA mixed with 522 or DMXAA or a combination of 522 and DMXAA daily for 5 days. Immunization with OVA+DMXAA+522 resulted in significant tumor growth inhibition (p < 0.05) and improved survival (p<0.05) compared to other controls. Using flow cytometry, the costimulatory molecule expression and immune cell infiltration in mouse lymph node, spleen and tumor were evaluated. Immunization with OVA+DMXAA+522 resulted in the activation of antigen presenting cells (APCs) in lymph nodes, spleen and tumor (additive or equivalent to single treated groups). The combination also elicited stronger antigen specific CD8 T cell and natural killer (NK) cell responses than control or individual treatment groups. OVA + DMXAA+ 522 immunization increased the number of OVA-specific CD44high CD8 T cells by over 4-fold compared to other treatment groups and control mice in spleen and lymph nodes. A reduction in the frequency of M2 macrophages was observed with OVA+DMXAA+522 treatment. Cytokine analysis demonstrated higher levels of pro-inflammatory cytokines like IFNγ and lower levels of pro-tumorigenic cytokines in the serum of OVA+DMXAA+522 immunized mice compared to that in untreated or OVA-only treated mice. Taken together, these results suggest that combination of TLR7/8 and STING agonists is a promising multi-adjuvant approach for cancer vaccination

Citation Format: Shubhmita Bhatnagar, Vishnu Revuri, Manan Shah, Peter Larson, David Ferguson, Jayanth Panyam. Combination of STING and TLR 7/8 agonists as vaccine adjuvants for cancer immunotherapy [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 4215.
Abstract 4248: HFB200603, a novel anti-BTLA monoclonal antibody that provides therapeutic potential for immune escape and synergizes with anti-PD-1 treatment
Authors: Li Juying , Zhang Qian , Shen Bingqing , Shah Manan , Chen Mingjie , Li Sharon , Dong Ling , Adrian Francisco , Schweizer Liang
Published: June 2022

BTLA is a co-inhibitory immune checkpoint molecule sharing sequence and structural homology with PD-1 and CTLA4. Ligation of HVEM with BTLA induces recruitment of SHP1 and SHP2, and triggers inhibition of T cell proliferation and cytokine production. In melanoma, HVEM is described to have a broader expression than PD-L1 and constituted a negative prognostic marker; in PD-L1 negative NSCLC, the expression of HVEM has been shown to contribute to immune escape. Therefore BTLA-HVEM axis could play an important role in the immune escape, thus BTLA blockade in combination with PD-1/PD-L1 blockade could represent an effective therapeutic option. Using our proprietary microfluidic-based single cell platform CelliGO™, we identified a series of anti-human BTLA antibodies that were characterized for their binding affinity, cross-reactivity, selectivity and functional activity. Amongst them, HFB200603 was identified as a single-digit nanomolar binder to human and cynomolgus BTLA, capable of reversing HVEM-mediated immune suppression in a BTLA-HVEM reporter system and in a primary CD4+ T cell proliferation assay. HFB200603 showed synergistic effect with anti-PD-1 to enhance IFN-γ production in an MLR assay, and demonstrated favorable developability and pharmacokinetic profiles. Profiling of tumor infiltrating lymphocytes demonstrated that BTLA+PD-1+ T cells are present in melanoma, NSCLC, and HCC. Blockade of the BTLA-HVEM interaction with HFB200603 alone or in combination with anti-PD-1 led to increases in IFN-γ, CXCL9, IP-10 and other proinflammatory cytokines in primary dissociated tumor cultures. Based on its favorable pharmacological activity and excellent developability, HFB200603 is currently being developed as a potential novel immunotherapy coupled with a patient biomarker strategy derived from HiFiBiO’s Drug Intelligent Science (DIS™) single-cell immune profiling platform.

Citation Format: Juying Li, Qian Zhang, Bingqing Shen, Manan Shah, Mingjie Chen, Sharon Li, Ling Dong, Francisco Adrian, Liang Schweizer. HFB200603, a novel anti-BTLA monoclonal antibody that provides therapeutic potential for immune escape and synergizes with anti-PD-1 treatment [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 4248.
Abstract 44: Evolution of large copy number variants in breast cancer through genetic network rewiring
Authors: Kuzmin Elena , Monlong Jean , Bourgey Mathieu , Barber Jarry , Lesluyes Tom , Baker Toby , Morin Genevieve , Zou Dongmei , Schwartz Michael , Yang Yang , Pacis Alain , Martinez Constanza , Kuasne Hellen , Fortier Anne-Marie , Li Rui , Kleinman Claudia , Huang Sidong , van Loo Peter , Morris Quaid , Ragoussis Jiannis , Bourque Guillaume , Park Morag
Published: June 2022

Large chromosomal alterations are common in cancer and often show preferential gain or loss across many cancer types indicating their selective advantage. Triple negative breast cancer (TNBC) exhibits complex mutational spectrum without common oncogenic drivers yet displays consistent loss of large chromosomal regions. Here, we characterize selection pressures that maintain a recurrently deleted region of chromosome 4p in TNBC. We used single cell and bulk WGS phylogenetic analysis of TNCB PT/PDX panel to show that chr4p deletion is an early event in tumor evolution. We used scRNAseq gene expression and inferred copy number analysis to show that chr4p loss is associated with a proliferative state. This finding was confirmed by a combination of RNA in situ hybridization and immunofluorescence. We then tested the dosage sensitivity of genes residing within this region by individual and dual overexpression in TNBC PDX-derived cell lines and control normal cell line by assessing their effect on cell proliferation. The overexpression of genes within chr4p elicited a strong cell proliferation defect in cancer but not normal cell line models. We also characterized an unknown gene within chr4p region as a novel member of the STRIPAK complex. Genome-wide pooled ORFeome library screens identified a global pattern of background-specific dosage sensitive regions. Our study shows that large chromosomal deletions are maintained due to evolutionary early genetic network rewiring rendering multiple genes within such regions to be dosage sensitive. Ultimately, this work enhances our understanding of genetic events that modulate TNBC.

Citation Format: Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Jarry Barber, Tom Lesluyes, Toby Baker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Quaid Morris, Jiannis Ragoussis, Guillaume Bourque, Morag Park. Evolution of large copy number variants in breast cancer through genetic network rewiring [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 44.
Abstract 459: Identification of the PDAC immunogenic subtype using deep learning with multi-scaled digital H&E images
Authors: Si Han , Xu Steven , Muthuswamy Anantharaman , Liang Ryan , Sasser Kate , Hamadeh Hisham K. , Couto Suzana , Higgs Brandon
Published: June 2022

Background: Pancreatic ductal adenocarcinoma (PDAC) has proven a difficult cancer to treat. To improve treatment strategies, molecular subtypes have been identified, one being immunogenic with significant immune infiltrate and better prognosis. These subtypes have been determined by RNA profiling, which often exhibits technical challenges in a clinical setting. Here we present a deep learning-based method to identify PDAC immunogenic patients using H&E images. This method is robust to RNA quality issues and can elucidate unique morphological features not obtainable with RNA profiling to refine the selection of patients with this phenotype.

Methods: Patients (n=265) were primarily stage II or IV, treated previously with gemcitabine+nab-paclitaxel or FOLFIRINOX. Ground truth for immunogenic subtype (n=105) was defined with RNASeq. Whole slide images were subdivided into non-overlapping, fixed-size tiles at 4 magnifications: 2.5x, 5x, 10x, 20x, followed by feature extraction using a ResNet50 convolutional neural network. Principal component (PC) analysis reduced dimensionality of extracted features in each tile. The dataset was split into 80% training, 20% testing. Posterior probabilities from a linear model were inputs to a support vector machine to predict outcome (2-step model). Progression- free survival (PFS) was evaluated using the Kaplan Meier method.

Results: ImageNet-trained ResNet50 model extracted 2048 features from each tile and the first 75 PCs, explaining 87% variance, were input into the 2-step model; average AUC=0.77 (95% CI=0.70,0.83) across the 4 magnification datasets. A multi-scale ensemble approach combining these 4 magnifications improved the AUC to 0.80 (95% CI=0.66,0.93). Accuracy, sensitivity, and specificity were 0.79, 0.76, and 0.81, respectively. The predicted immunogenic subtype showed significantly improved PFS compared to the other 3 subtypes (HR 95%CI = 0.54 (0.36,0.81), p=0.003), while the RNASeq-derived immunogenic subtype had less differentiation (HR 95%CI = 0.64 (0.42,0.98), p=0.04).

Conclusions: This study presents a deep learning 2-step model approach using tumor H&E images to identify PDAC immunogenic subtype, with improved prognostic potential to that identified by RNA profiling, suggesting possible application in clinical settings for patient stratification. Future work will expand the model to larger independent cohorts.

Citation Format: Han Si, Steven Xu, Anantharaman Muthuswamy, Ryan Liang, Kate Sasser, Hisham K. Hamadeh, Suzana Couto, Brandon Higgs. Identification of the PDAC immunogenic subtype using deep learning with multi-scaled digital H&E images [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 459.