bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4123: Real-world data to identify the genomic association with response to CDK4/6i + Endocrine therapy in ER+ breast cancer patients
Authors: Yu Kun , Chen Tenghui , Korpal Manav , Zhu Ping , Zhang Zhaojie , Yu Lihua , Xiao Yonghong
Published: June 2022

Background Real-world data (RWD) has been increasingly used for drug development. RWD coupled with genomic data provides an opportunity to identify the association between certain genomic alterations and response to current standard of care (SOC). Such analyses may help identify predictive biomarkers to select patients who will benefit most from SOC, and/or potential therapeutic nodes that can be pharmacologically targeted to overcome resistance to SOC.

Methods We obtained Flatiron CGDB Breast Cancer (as of Q3 2020 release) data set. This data set includes clinical and genomic data from 6,918 breast cancer patients. Time to treatment discontinuation (TTD) was used as real world outcome. We performed two types of genomic-outcome association analysis: 1) Use Cox proportional hazards regression model to identify which baseline mutation (mutation occurred prior to the treatment) could predict the outcome; and 2) use Fisher exact test to identify which mutations are enriched in post-treatment tumors samples, compared to pre-treatment tumor samples.

Result We found TP53 mutation is associated with shorter TTD for Palbociclib + Aromatase inhibitor (AI); Palbociclib + Fulvestrant; and endocrine monotherapy. It is consistent with the reports that TP53 mutation is poor prognostic factor (ref). Interestingly, ESR1 mutation is associated with shorter TTD for Palbociclib + AI and AI monotherapy; but not associated with TTD for Palbociclib + Fulvestrant or Fulvestrant monotherapy. On the other hand, MYC amplification is associated shorter TTD for Palbociclib + Fulvestrant or Fulvestrant monotherapy. We found that genes associated with Palbociclib + Endocrine are by and large same as those associated with endocrine monotherapy; suggesting the association is largely driven by endocrine treatment. Comparison of post-treatment vs. pre-treatment analysis found that ESR1 mutation is enriched in post treatment of AI; but not Fulvestrant.

Conclusion We demonstrated that real-world clinicogenomic data could identify the biologically meaningful genomic biomarkers that are associated with real world response. This study warrants the further investigation of novel genomic biomarkers identified from the analysis.

Citation Format: Kun Yu, Tenghui Chen, Manav Korpal, Ping Zhu, Zhaojie Zhang, Lihua Yu, Yonghong Xiao. Real-world data to identify the genomic association with response to CDK4/6i + Endocrine therapy in ER+ breast cancer patients [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 4123.
Abstract 4144: An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens
Authors: Patel Bhavika , Allen Stephanie , Talwalkar Sameer , Mehra Navi , Thagaard Jeppe , Ramsing Thomas W. , Overgaard Agnete , Caldara Jenifer
Published: June 2022

Understanding the rate of tumor cell growth in breast cancer specimens may be indicative of disease aggressiveness, a tumor characteristic which can be used to make an informed treatment decision. The nuclear protein Ki-67 is increased in cells as they prepare to divide or proliferate and is therefore widely used as a proliferation marker for tumor progression. This degree of tumor cell proliferation, or the proliferative index, is commonly detailed in pathology reports shared with the patient care team. In this study, we utilized the Ki-67 [K2] immunohistochemistry (IHC) assay to stain 10 breast cancer specimens. Stained slides were imaged using the AT2 scanner (Leica Biosystems, Buffalo Grove, IL) and analyzed using the Visiopharm Image Analysis platform. Previous efforts to assess Ki-67 positivity utilizing image analysis have relied on the use of a secondary stain or manual effort by the pathologist to exclude non-invasive tumor regions. These antiquated methods are costly to the lab as they require additional materials or valuable pathologist time. Our novel image analysis approach utilizes artificial intelligence (AI) to automatically denote non-invasive verses invasive tumor regions, which can then be used to quantify the Ki-67 proliferative index. This valuable tool will allow for greater accuracy, cost-savings, and time efficiency when analyzing breast cancer samples compared to traditional methods.

Citation Format: Bhavika Patel, Stephanie Allen, Sameer Talwalkar, Navi Mehra, Jeppe Thagaard, Thomas W. Ramsing, Agnete Overgaard, Jenifer Caldara. An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens [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 4144.
Abstract 4148: Non-redundant upregulation of CD112R (PVRIG) and PD-1 on cytotoxic T-lymphocytes located in T-cell-nests of colorectal cancer
Authors: Lennartz Maximilian , Yang Cheng , Mandelkow Tim , Bady Elena , Simon Ronald , Hube-Magg Claudia , Sauter Guido , Blessin Niclas C.
Published: June 2022

Focal T-lymphocyte aggregates occur commonly in colorectal cancer, but their biological significance is unknown. To study focal aggregates of T-lymphocytes, a deep learning-based framework for automated identification of T-cell accumulations (T-cell-nests) was developed using CD8, PD-1, CD112R, and Ki67 multiplex fluorescence immunohistochemistry. To evaluate the clinical significance of these parameters, a cohort of 523 colorectal cancers with clinical-follow up data was analyzed. The spatial analysis of locally enriched CD8+ T-cell densities and cell-to-cell contacts identified T-cell-nests in the tumor microenvironment of colorectal cancer. CD112R and PD-1 expression on CD8+ T-cells located in T-cell-nests was found elevated as compared to CD8+ T-cells in all other tumor compartments (p<0.001 each). Although the highest mean CD112R expression on CD8+ T-cells was observed at the invasive margin, the PD-1 expression on CD8+ T-cells was elevated in the center of the tumor (p<0.001 each). Across all tissue compartments, proliferating CD8+ T-cells showed higher relative CD112R and PD-1 expression compared to non-proliferating CD8+ T-cells (p<0.001 each). Integration of all available spatial and immune checkpoint expression parameters (AUC: 0.65) revealed a superior predictive performance for overall survival compared to the commonly used CD8+ TILs density (AUC 0.57, p<0.001). Cytotoxic T-cells with elevated CD112R and PD-1 expression levels are orchestrated in T-cells-nests of colorectal cancer, predict favorable patient’s outcome and the spatial non-redundancy underlies fundamental differences of both inhibitory immune checkpoints that provide a rationale for dual anti-CD112R/PD-1 immune checkpoint therapy.

Citation Format: Maximilian Lennartz, Cheng Yang, Tim Mandelkow, Elena Bady, Ronald Simon, Claudia Hube-Magg, Guido Sauter, Niclas C. Blessin. Non-redundant upregulation of CD112R (PVRIG) and PD-1 on cytotoxic T-lymphocytes located in T-cell-nests of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4148.
Abstract 415: The characterization of in vitro models demonstrating a significant delay of acquired resistance to ulixertinib (ERK1/2)
Authors: Knoerzer Deborah , Reddy Anupama , Sorrell David , Emery Caroline M.
Published: June 2022

Ulixertinib (BVD-523) is a first-in-class small molecule inhibitor of ERK1/2 currently being investigated in several oncology clinical trials, both as a single agent and in combination with other anti-cancer therapeutics. Clinical acquired resistance has been described by others for numerous efficacious small molecule agents. Relevant to the MAPK pathway, emergence of resistance to BRAF and MEK inhibitors limits their clinical efficacy.

In vitro models of ulixertinib resistance were generated in an endeavor to characterize and predict potential clinical mechanisms of resistance and guide rational combination therapies. The BRAF-V600E mutant melanoma cell line, A375, was cultured in progressively increasing concentrations of ulixertinib or other MAPK pathway inhibitors (dabrafenib and/or trametinib). Drug-resistant A375 clones were readily obtained following growth in high concentrations of dabrafenib or trametinib. In contrast, developing resistance to ulixertinib proved challenging. Eventually, ulixertinib resistant clones emerged and demonstrated varying degrees of cross-resistance to other MAPK pathway inhibitors and displayed bell-shaped dose-response curves indicative of drug addiction for optimal proliferation. To elucidate potential mechanisms of resistance, Reverse Phase Protein Array profiling of 306 proteins was performed on parental A375 and ulixertinib-resistant clones following treatment with ulixertinib at varying concentrations and treatment times. Principal component analysis revealed clustering of resistant clones by ulixertinib treatment conditions (concentrations and duration). Differences between parental A375 and ulixertinib resistant clones were revealed, including components of MAPK, HER2, and autophagy markers.

This work begins to tease out potential mechanisms of resistance to ulixertinib and guide potential combination partners that could circumvent acquired resistance.

Citation Format: Deborah Knoerzer, Anupama Reddy, David Sorrell, Caroline M. Emery. The characterization of in vitro models demonstrating a significant delay of acquired resistance to ulixertinib (ERK1/2) [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 415.
Abstract 4153: First-in-class inhibitors of ERAP1 alter the HLA-I-restricted cancer immunopeptidome leading to the generation of novel peptides presented for immune recognition
Authors: Paes Wayne , Leishman Andrew , Anderton Kate , Liao Hanqing , Woodhouse Isaac , Parker Robert , Nicastri Annalisa , Joyce Peter , Ternette Nicola
Published: June 2022

The antigen processing machinery of a cell shapes the repertoire of peptides presented for immune recognition on the cell surface. Human leukocyte antigen class I (HLA-I) molecules present peptides that are recognised by both CD8+ T cells and NK cells, and these complexes play a vital role in the recognition and eradication of malignant cells. During direct presentation, the endoplasmic reticulum aminopeptidase 1 (ERAP1) enzyme processes a subset of HLA-I ligand precursors which are translocated into the endoplasmic reticulum (ER) following intracellular proteasomal degradation. Here, we show that inhibition of ERAP1 with highly potent and selective small molecule inhibitors drives significant qualitative and quantitative changes in the HLA-I-restricted immunopeptidome, resulting in the generation of altered and novel peptides from tumour-associated antigens that are then presented on HLA-I molecules. A major consequence of inhibiting the processing of precursor ligands by ERAP1 within the ER of cancer cells was not only the generation of unique peptides which were not detectable under baseline conditions, but a shift in the peptide length distribution towards longer HLA-I-restricted peptides. Importantly, we demonstrate that the degree of bias towards longer HLA-I-bound ligands uniquely presented following ERAP1 inhibition was governed by both ERAP1 and HLA-I haplotypes. Such dramatic changes in the peptide repertoire presented for immune recognition have the potential to enhance anti-tumoural immunogenicity through T cell recognition of a novel cancer immunopeptidome, and, in addition to global shifts in the peptide length distributions, unique peptides presented for immune recognition during ERAP1 inhibition may be used as biomarkers for monitoring activity of this novel therapeutic approach in the clinic.

Citation Format: Wayne Paes, Andrew Leishman, Kate Anderton, Hanqing Liao, Isaac Woodhouse, Robert Parker, Annalisa Nicastri, Peter Joyce, Nicola Ternette. First-in-class inhibitors of ERAP1 alter the HLA-I-restricted cancer immunopeptidome leading to the generation of novel peptides presented for immune recognition [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 4153.
Abstract 416: A novel non-covalent and rapidly reversible proteasome inhibitor for multiple myeloma and various solid cancers
Authors: Ahn Won-Gyun , Jeon Yeejin , Yang Yeong-In , Kim Jaeseung , Lee Seung-Joo , Koch Uwe , Zischinsky Gunther , Choidas Axel , Pasha Ayesha , Klebl Bert , Huber Robert , Hamacher Michael , Nam Kiyean
Published: June 2022

The existing proteasome inhibitors, such as bortezomib and ixazomib, are effective in multiple myeloma, but have little activity against solid tumors. These are covalent boronic acid-based compounds and are associated with undesired side effects, mainly hematologic toxicity and peripheral neuropathy. A variety of improved covalent proteasome inhibitors have been developed, but lack of oral availability and low distribution in tumors make them ineffective in solid tumors. In addition, they still have a narrow therapeutic window due to unexpected adverse effects such as cardiac and pulmonary toxicity. We report a non-covalent and rapidly reversible proteasome inhibitor as a potential anti-cancer agent against solid tumors as well as multiple myeloma. These novel inhibitors, called QL compounds, are non-covalent chymotrypsin-like selective proteasome inhibitors that can be taken orally. They effectively inhibited tumor growth in multiple myeloma xenograft model without hematologic toxicity through improved PK properties, especially partition of compound between plasma and RBC. Moreover, this improved PK properties of the QL compounds allowed for sufficient distribution outside the blood compartment and induced tumor growth inhibition in some types of solid cancer xenograft models that were sensitive to proteasome inhibition. These results indicate that non-covalent and rapidly reversible proteasome inhibitors are an ideal strategy for multiple myeloma and potential agents for solid tumors.

Citation Format: Won-Gyun Ahn, Yeejin Jeon, Yeong-In Yang, Jaeseung Kim, Seung-Joo Lee, Uwe Koch, Gunther Zischinsky, Axel Choidas, Ayesha Pasha, Bert Klebl, Robert Huber, Michael Hamacher, Kiyean Nam. A novel non-covalent and rapidly reversible proteasome inhibitor for multiple myeloma and various solid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 416.
Abstract 4161: An in vivo screen to identify short peptide mimotopes with enhanced anti-tumor immunogenicity
Authors: He Xuedan
Published: June 2022

Tumor-associated self-antigens are cancer vaccines targets but suffer from limited immunogenicity. There have been examples of mutated, short self-peptides inducing epitope-specific CD8+ T cells more efficiently than the wild-type epitope, but current approaches cannot yet reliably generate such enhanced mimotopes (“e-mimotopes”). Here, we present a generalized strategy to develop e-mimotopes, using the tyrosinase-related protein 2 peptide Trp2180-188, a major histocompatibility complex (MHC)-I epitope, as a test case. Using a vaccine adjuvant that induces peptide particle formation and strong cellular responses with nanogram antigen doses, a two-step method systematically identified e-mimotope candidates with murine immunization. First, position-scanning peptide micro libraries were generated in which each position of the wild-type epitope sequence was randomized. Randomization of only one specific residue of the Trp2 epitope increased anti-tumor immunogenicity. Second, all 20 amino acids were individually substituted and tested at that position, enabling the identification of two e-mimotopes with single amino acid mutations. Despite similar MHC-I affinity compared to the wild-type epitope, e-mimotope immunization elicited improved Trp2-specific cytotoxic T cell phenotypes and improved T cell receptor affinity for both the e-mimotopes and the native epitope, resulting in better outcomes in multiple prophylactic and therapeutic tumor models. The screening method was also applied to other targets with different murine MHC-I restriction elements, including the gp70 AH1 epitope, to identify additional e-mimotopes with enhanced potency.

Citation Format: Xuedan He. An in vivo screen to identify short peptide mimotopes with enhanced anti-tumor immunogenicity [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 4161.
Abstract 417: Identification of next-generation EGFR degraders to treat non-small cell lung cancer (NSCLC) patients
Authors: Ki Dong Hyuk , Nam Joonwoo , Kim Eunjung , Choi Hunmi , Kim Chulwon , Kim Jiyeon , Jin Jimmy , Kang Sang-Uk , Han Wooseok
Published: June 2022

Although EGFR-targeted tyrosine kinase inhibitors (TKIs) developed over a couple of decades have made great progress in the treatment of EGFR-mutant driven NSCLC, patients are at great risk to their lives due to drug resistance caused by constantly emerging EGFR mutations. Targeted protein degraders (TPDs), also known as heterobifunctional protein degraders or PROteolysis TArgeting Chimeras (PROTACs), have drawn great attention as a new modality to overcome drug resistance by achieving selective degradation of disease-causing proteins, like an EGFR mutant protein, which are required for the survival and proliferation of various malignant tumor cells. Therefore, we have developed a series of EGFR mutant degraders using BBT-176, a 4th generation EGFR TKI developed by Bridge BioTherapeutics, and novel EGFR inhibitors as warheads which are expected not only to treat various EGFR mutated NSCLC including C797S but also to delay drug resistant-mechanisms by further mutations in the EGFR TKI target site.

We synthesized a set of heterobifunctional degraders applying Cyrus BiFx Degrader (CBD) library platform containing different types of linkers and E3 ligase binders. DC50 (half-maximal degradation concentrations) values of the EGFR degraders were obtained in multiple human EGFR mutant NSCLC cell lines, where C-2051, C-2482, and C-4383 showed excellent EGFR degradation potency (DC50 = 7-25 nM, Dmax at 100 nM = 80-97%) with high selectivity against WT EGFR. Among those compounds, C-4383 was potent in cell viability assays with EGFR mutant HCC827 (Del19) and NCI-H1975 (L858R, T790M) cell lines showing a range of GI50 values from 77 to 81 nM at 72 h of compound exposure. By contrast, the compound was much less potent in A549 cells harboring wild-type EGFR (GI50 value at 72 h of treatment, 4.2 μM). We also performed proteomic analysis of C-4383 in H1975 cells resulting that EGFR was the most degraded protein with no off-target events at 100 nM (Dmax dose). A PK study of C-4383 in rats showed good exposure with moderate CL when administered intravenously (CL = 8.51 mL/min/kg, AUC = 5911 ng•h/mL).

In summary, we identified heterobifunctional degraders using a 4th generation EGFR inhibitor, BBT-176, that are active in EGFR mutant NSCLC cells harboring single or C797S-containing multiple mutations. We are currently making our efforts on the improvement of physicochemical properties of EGFR mutant targeted heterobifunctional compounds.

Citation Format: Dong Hyuk Ki, Joonwoo Nam, Eunjung Kim, Hunmi Choi, Chulwon Kim, Jiyeon Kim, Jimmy Jin, Sang-Uk Kang, Wooseok Han. Identification of next-generation EGFR degraders to treat non-small cell lung cancer (NSCLC) patients [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 417.
Abstract 4172: rhIL-7-hyFc (efineptakin alpha; NT-I7) enhances the anti-tumor response when combined with anti-TIGIT or anti-VEGF
Authors: Baek Seungtae , Im Sun-Kyoung , Lee Minji , Ji Mankyu , Kim Miyoung , Lee Kwang-Hoon , Choi Yun Hee , Kim Won Tae , Choi Donghoon
Published: June 2022

rhIL-7-hyFc (efineptakin-alfa; NT-I7) is a potent T cell amplifier, with a homodimeric interleukin-7 (IL-7) fused to the hybridizing IgD/IgG4 immunoglobulin domain. Previous work has shown that in mice, NT-I7 dramatically increases tumor-infiltrating CD8+ T cells while reducing the frequency of PD-1+ CD8+ T cells in the tumor. There is also significant expansion of Central Memory (CM)-phenotype CD8+ T cells (CD62L+CD44+) in the tumor and tumor draining lymph node. Here, we investigated the anti-tumor effect of NT-I7 in combination with two different T cell suppressor blockades; anti-TIGIT (YH29143) and anti-VEGF (Aflibercept) in MC38 tumor-bearing mice. NT-I7 was administered by intramuscular injection with the first dose of either YH29143 or Aflibercept. YH29143 or Aflibercept was administered every 3 days for 3 total doses, via intraperitoneal or intravenous route, respectively. The combination of NT-I7 with either T cell suppressor blockade enhanced the anti-tumor response. Surprisingly, NT-I7 combined with YH29143 increased the frequency of PD-1+TCF-1+TOX-CD39- stem-like CD8+ T cells in the draining lymph node. The combination also dramatically increased the frequency of CD62L-CD44+ effector memory CD8+ T cells in the tumor. Surprisingly, NT-I7 combined with YH29143 increased the frequency of PD-1+TCF-1+TOX-CD39- stem-like CD8+ T cells in the draining lymph node. In addition, Aflibercept reduced the expression of TOX in PD-1+ CD8+ T cells in the tumor. Our data suggests that NT-I7 can be applied in combination with other immunotherapies such as anti-TIGIT or anti-VEGF to enhance the anti-tumor response.

Citation Format: Seungtae Baek, Sun-Kyoung Im, Minji Lee, Mankyu Ji, Miyoung Kim, Kwang-Hoon Lee, Yun Hee Choi, Won Tae Kim, Donghoon Choi. rhIL-7-hyFc (efineptakin alpha; NT-I7) enhances the anti-tumor response when combined with anti-TIGIT or anti-VEGF [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 4172.
Abstract 4175: Combining a novel MEK inhibitor with immunomodulation to promote an anti-tumor response
Authors: Dong Lauren , Choi Hyejin , Budhu Sadna , Schulze Isabell , Verma Svena , Mehanna Nezar , Rosen Neal , Merghoub Taha , Wolchok Jedd
Published: June 2022

To enhance the therapeutic scope of MEK inhibitors (MEKis), we aim to develop new strategies to extend their usage to MEKi resistant RAS mutant cancers, which represent an unmet clinical need. CH5126766 (CKI27) binds the allosteric site of MEK to inhibit its kinase activity but is novel due to its interaction with MEK S218 and 228, which blocks their phosphorylation by RAF. CKI27 bound MEK binds to RAF and cannot be released by phosphorylation, thus becoming a dominant negative inhibitor of RAF activation. This prevents the induction of MEK phosphorylation observed with other MEKis. Although this results in more potent tumor control, CKI27 is also capable of inhibiting T cell function because the MAPK/ERK pathway is activated downstream of T cell receptor signaling. We aim to balance the positive and negative immunomodulatory effects of MEKis for optimal combination with immunotherapy. We observed that CKI27 increased MHC expression on tumor cells and improved T cell mediated killing. Yet, CKI27 also decreased T cell proliferation, activation, and cytolytic activity. Intermittent administration of CKI27 allowed T cells to recover and partially relieved these inhibitory effects. Further combination with agonist antibodies anti-OX40 and GITR completely alleviated T cell inhibition and increased combination efficacy with immune checkpoint blockade antibody anti-CTLA-4. We also observed an increase in proliferation and T cell activation markers in LLC tumor bearing mice treated with the combination of CKI27, anti-GITR, and anti-CTLA-4. Understanding the immunomodulatory effects of combining CKI27 with immunotherapy will elucidate the mechanism behind this increased efficacy. This will allow us to make more informed decisions in dosing regimens, overcoming resistance, and generating long-term immune responses in future clinical trials treating patients with RAS mutant cancers.

Citation Format: Lauren Dong, Hyejin Choi, Sadna Budhu, Isabell Schulze, Svena Verma, Nezar Mehanna, Neal Rosen, Taha Merghoub, Jedd Wolchok. Combining a novel MEK inhibitor with immunomodulation to promote an anti-tumor response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4175.
Abstract 4231: Hypoxia reduction in tandem with anti-angiogenic therapy remodels the pancreatic tumor microenvironment
Authors: Liu Arthur J. , Curran Michael A.
Published: June 2022

Pancreatic cancer patients remain largely unresponsive to single agent immune checkpoint blockade (ICB) therapy. This refractory state originates from PDAC’s unique immunosuppressive microenvironment that is densely populated by suppressive myeloid cells, exhibits poor vascularity, and is highly hypoxic. We previously showed that the hypoxia-activated prodrug TH-302 (Evofosfamide) reduces intratumoral hypoxia through a tissue remodeling process, initiates tumor vasculature reorganization, and sensitizes aggressive, spontaneous murine models of prostate cancer to ICB. In a clinical trial testing the combination of Evofosfamide with cytotoxic T-lymphocyte-associated protein (CTLA-4) blockade (NCT03098160) a subset of metastatic, immune checkpoint blockade refractory patients showed prolonged progression free survival. While these studies highlight hypoxia reduction as therapeutically tractable, we lack complete understanding of the contribution of the tumor vasculature to hypoxia reduction therapy, as well as the downstream consequences of hypoxia reduction on the cellular composition of the tumor microenvironment and the responsiveness to immunotherapy.

We used a transplantable, orthotopic pancreatic tumor model derived from Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre mice and a syngeneic prostate tumor model to study tumor responses to hypoxia-reduction, anti-angiogenic therapy, and combination immunotherapy.

We find that Evofosfamide with anti-VEGFR-2 (DC101) significantly extends mouse survival. Combination therapy reduces intratumoral hypoxia, improves vessel integrity, and increases intratumoral DNA damage. In response to the improved metabolic microenvironment, CD8 T cells gain enhanced effector function and lose expression of exhaustion-associated features. Like other anti-angiogenic regimens, combination Evofosfamide and DC101 leads to an increased frequency of PD-L1 expressing cells within the tumor, however blockade of PD-1 failed to prolong survival. Bulk-tumor RNA sequencing and tumor infiltrating lymphocyte analysis implicates immature myeloid cells as mediators of resistance. Re-education of the infiltrating myeloid stroma with CD40 agonist could improve responses to hypoxia-reducing, anti-angiogenic therapy. Put together, these data indicate that targeted hypoxic reduction with anti-angiogenic therapy remodels the pancreatic tumor microenvironment. In this setting, CD40 agonist over PD-1 blockade provides an additive benefit in prolonging mouse survival.

Citation Format: Arthur J. Liu, Michael A. Curran. Hypoxia reduction in tandem with anti-angiogenic therapy remodels the pancreatic tumor microenvironment [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 4231.
Abstract 4245: QL301, a PD-L1 dependent 4-1BB agonist with enhanced preclinical anti-tumor efficacy and minimal liver toxicity
Authors: Gu Shenda , Tang Irene , Mihardja Shirley , Prior Wei Wei , Tran Hieu V. , Chan Allan , McClain Anna , Kurtzman Aaron , Chen Shihao , Luo Youguang , Kang Xiaoyan , Wu Xiaoran , Zheng Qingmei , Jia Guodong
Published: June 2022

4-1BB (CD137, TNFRSF9) is a potent co-stimulatory receptor found on T and NK cells. Activation of 4-1BB requires receptor clustering, which is naturally mediated by the endogenous trimeric 4-1BB ligand. Cross-linking via agnostic monoclonal antibodies can also activate 4-1BB but has generally resulted in unwanted side effects, mainly liver toxicity. To address the shortcomings of 4-1BB agonists, we have developed QL301, a PD-L1 x 4-1BB bispecific antibody that conditionally activates 4-1BB only when concurrently engaged to PD-L1, an immune checkpoint mediator elevated in the immuno-suppressive tumor microenvironment. The IgG1 backbone of QL301 was mutated to eliminate Fc gamma receptor-dependent functions such as antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC), thereby preventing depletion of effector immune cells and non-specific activation of 4-1BB through Fc gamma receptor binding. In addition, QL301 blocks the suppressive interaction of PD-1 with PD-L1. Therefore, through a combination of 4-1BB agonism and PD-L1 blockade, QL301 provides both a co-stimulatory signal and the release of a suppressive signal to reinvigorate anti-tumor immune response. In vitro, QL301 induced robust cytokine release and expansion of CD8+ T cells conditional on the presence of tumor or antigen presenting cells expressing PD-L1. In xenograft and transgenic mice models, QL301 had potent anti-tumor effect that was superior to PD-L1 monoclonal antibodies. Tumor regression correlated with the expansion of CD8+ T cells. In addition, QL301 potentiated tumor cell killing mediated by an EGFR targeted CD3 bispecific antibody, providing a basis for combination therapy. In non-human primates, QL301 was well tolerated up to 30 mg/kg. There was no chronic elevation of serum AST and ALT levels, and histopathology analysis showed minimal inflammation of liver tissue. A phase 1 clinical trial to evaluate the safety, tolerability, and early efficacy of QL301 is currently ongoing.

Citation Format: Shenda Gu, Irene Tang, Shirley Mihardja, Wei Wei Prior, Hieu V. Tran, Allan Chan, Anna McClain, Aaron Kurtzman, Shihao Chen, Youguang Luo, Xiaoyan Kang, Xiaoran Wu, Qingmei Zheng, Guodong Jia. QL301, a PD-L1 dependent 4-1BB agonist with enhanced preclinical anti-tumor efficacy and minimal liver toxicity [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 4245.
Abstract 4256: YH012, a novel bispecific anti-HER2 and TROP2 antibody-drug conjugate, exhibits potent antitumor efficacy
Authors: Shang Chengzhang , Yang Liu , Zhang Jiyong , Han Yanfei , Li Zhuolin , Han Zhenyan , Li Jun , Meng Ying , An Gao , Yang Hao , An Wenqian , Chen Lei , Charpentier John
Published: June 2022

Bispecific antibodies (BsAbs) and antibody-drug conjugates (ADCs) are among the most promising and fastest growing classes of next-generation antibody therapeutics for cancer therapy. The strategy of targeting dual tumor-associated antigens (TAAs) with a BsAb offers several advantages, such as improved efficacy due to synergistic effects, increased target cross-linking and internalization, increased tumor cell specificity and reduced side effects in normal tissues. HER2 is an established therapeutic target for approximately 20% of breast cancers, and its overexpression has been observed in a variety of other solid tumors. Trop-2 is another ideal tumor-associated target overexpressed on a wide variety of solid tumors. Co-expression of HER2 and TROP2 has been found in a number of tumors including gastric, colorectal, bladder and breast cancers. Therefore, co-targeting these TAAs using bispecific antibodies has clinical potential. YH012 is a novel first-in-class bispecific antibody-drug conjugate targeting HER2-TROP2 (HER2-TROP2-ADC), which contains a novel fully human bispecific anti-HER2/TROP2 antibody conjugated with Monomethyl auristatin E (MMAE) via a protease-cleavable linker. The anti-HER2/TROP2 BsAb showed increased endocytosis activity compared with its parental mAbs in tumor cells co-expressing HER2/TROP2, whereas the monovalent HER2 or TROP2 antibodies showed reduced internalization. As expected, YH012 showed increased in vitro potency of cell killing compared to the monovalent HER2/TROP2-ADC. These results suggest that YH012 increases the selectivity of payload delivery demonstrating the beneficial effects of targeting dual TAAs using BsAb-ADC. Moreover, YH012 showed robust anti-tumor efficacy in multiple cell line-derived none-small cell lung cancer (NSCLC) and gastric xenografts. Treatment with YH012 showed sustained tumor growth inhibition, which is more pronounced than the effects of the parental mAb-ADCs and monovalent ADCs. These preclinical data suggest that YH012 could potentially benefit patients with tumors co-expressing HER2 and TROP2 through improved drug selectivity and efficacy. Further investigations on the antitumor activity and safety profile of YH012 are ongoing in dogs.

Citation Format: Chengzhang Shang, Liu Yang, Jiyong Zhang, Yanfei Han, Zhuolin Li, Zhenyan Han, Jun Li, Ying Meng, Gao An, Hao Yang, Wenqian An, Lei Chen, John Charpentier. YH012, a novel bispecific anti-HER2 and TROP2 antibody-drug conjugate, exhibits potent antitumor efficacy [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 4256.
Abstract 461: Mixed supervision to improve the classification and localization: Coherence of tumors in histological slides
Authors: Tourniaire Paul , Ilie Marius , Hofman Paul , Ayache Nicholas , Delingette Hervé
Published: June 2022

With the growing standardization of Whole Slide Images (WSIs), deep learning algorithms have shown promising results for the automated classification and localization of tumors. Yet, it is often difficult to train such algorithms, as they usually require careful detailed annotations from expert pathologists, which are tedious to produce. This is why in general only slide-level labels are accessible while annotations of small regions (or tiles) are limited. With only slide-level information, it is difficult to obtain accurate predictions of the localization of pathological tissues inside a slide, despite reaching good slide-level classification. Besides, existing algorithms show limited consistency between slide- and tile-level predictions, leading to difficult interpretation in case of healthy tissue. Using the attention-based multiple instance learning framework, we propose to combine slide-level labels on all slides with tile-level labels on a small fraction (e.g. 20%) of slides within a histology dataset to improve both classification and localization performances. With this mixed supervision of slides, we aim to enforce a better consistency between slide- and tile-level labels. To this end, we introduce an attention-based loss function to further guide the model’s attention on discriminative regions inside tumorous slides, and display an equal attention among all tiles of normal slides. On the Camelyon16 dataset, we reached precision and recall scores as high as 0.99 and 0.85 respectively with an AUC of 0.93 on the competition test set, using only 50% of the slides with tile-level annotations in the training set. Experiments using various proportions of fully annotated slides in the training set show promising results for an improved localization of tumors and classification of slides. In this work, we showed that using a limited amount of fully annotated slides we can improve both the classification and localization performances of an attention-based deep learning model. This increased consistency and performances should help pathologists to better interpret the algorithm output and to focus on suspicious regions in probable tumorous slides.

Citation Format: Paul Tourniaire, Marius Ilie, Paul Hofman, Nicholas Ayache, Hervé Delingette. Mixed supervision to improve the classification and localization: Coherence of tumors in histological slides [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 461.
Abstract 479: The role of diffusion in molecular networks: Diffusion coefficients in describing the development of cancer
Authors: Garimella Narayana
Published: June 2022

To study and forecast the developments of cancers, the molecular networks, compositional fluctuations, diffusion in networks and altogether the biological processes resulting at cellular and intracellular levels, are highly important. Focusing on diffusion coefficients as the translational biomarkers to quantify the nucleation and growth of tumors and cancers has potential advantages. Because, diffusion coefficients act as guiding tools in preventing or treating the cancers and associated adversities. Collectively the biological, pharmacological and toxicological indicators during and prior to the course of cancer are taken as measures for the data over specific distances of the molecules to determine diffusion coefficients. Because, multiple mechanisms are simultaneously responsible in altering the compositions. In this work, the mass transportation in both healthy individuals and cancer patients are taken into account to compare and contrast the initiation and spread of cancers in the light of immunology and immunotherapy. Measurements through incoherent motion diffusion-weighted imaging (IVIM-DWI) and echo planar magnetic resonance (MR) imaging are applied in determining the diffusion parameters. Diffusion coefficients were within the ranges of 0.1 to 5 X 10-3 mm2/sec. Perfusion played important role in quantifications. Magnitudes of diffusion coefficients are used to forecast biological prevalence and to develop prevention and treatment therapeutics.

Citation Format: Narayana Garimella. The role of diffusion in molecular networks: Diffusion coefficients in describing the development of 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 479.
Abstract 490: De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
Authors: Weiskittel Taylor , Correia Cristina , Ung Choong , Zhang Cheng , Li Hu
Published: June 2022

Current understandings of individual disease etiology and therapeutics are limited despite great need. To fill the gap, we propose a novel computational pipeline which collects potent disease gene cooperative pathways to envision individualized disease etiology and therapies. Our algorithm constructs individualized disease modules de novo which enable us to elucidate the importance of mutated genes in specific patients and to understand the synthetic penetrance of these genes across patients. We reveal that importance of notorious cancer drivers TP53 and PIK3CA fluctuate widely across breast cancers and peak in tumors with distinct numbers of mutations, and that rarely mutated genes such as XPO1 and PLEKHA1 have high disease module importance in specific individuals. Furthermore, individualized module disruption enables us to devise customized singular and combinatorial target therapies which were highly varied across patients demonstrating the need for precision therapeutics pipelines. As the first analysis of de novo individualized disease modules, we illustrate the power of individualized disease modules for precision medicine by providing deep novel insights on the activity of diseased genes in individuals.

Citation Format: Taylor Weiskittel, Cristina Correia, Choong Ung, Cheng Zhang, Hu Li. De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens [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 490.
Abstract 5008: The potential role of hsa-miR-3157-3p in prostate cancer pathogenesis
Authors: Wali Akhil , Koul Hari
Published: June 2022

Prostate cancer remains a major area of concern as it is the second leading cause of cancer mortalities amongst American men. Our study aimed to find the role of differentially expressed microRNAs that play a role in prostate cancer etiopathology. With the use of the National Center for Biotechnology Information (NCBI), we narrowed down a desired dataset (GSE138740). While analyzing the dataset, we found the expression pattern of hsa-miR-3157-3p (adjusted p-value 0.04797) to be significantly upregulated in low grade tumor samples (Gleason Score 6 and n=88) compared to high grade tumor samples (Gleason Score 8,9 and n=13). Furthermore, the role of hsa-miR-3157-3p in prostate cancer remains a novel finding. We have identified target genes such as E2F3, UBE2M, ABCF1, PKN3 and VANGL1 using the RNA Central website portal. Further studies are underway to elucidate the expression pattern of this miRNA and it’s target genes that would correlate with the disease progression observed among tumor samples in The Cancer Genome Atlas (TCGA) database. The Ingenuity Pathway Analysis (IPA) software generated report will be presented at the meeting to describe gene networks and pathways implicated in Prostate Cancer. Overall, these studies are designed to further validate whether this miRNA and its target genes can serve as potential biomarkers to predict the onset and progression from low to high grade prostate cancer.

Citation Format: Akhil Wali, Hari Koul. The potential role of hsa-miR-3157-3p in prostate cancer pathogenesis [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 5008.
Abstract 5019: Eliminating copy number alteration effects in the gene essentiality data from the Cancer Dependency Map project
Authors: Bhattacharya Arkajyoti , Urzúa-Traslaviña Carlos G. , van Vugt Marcel A. T. M. , Fehrmann Rudolf S. N.
Published: June 2022

The Cancer Dependency Map project (DepMap) aims to identify cancer vulnerabilities through the in vitro study of genetic dependencies in cancer cell lines using CRISPR/Cas9 loss-of-function screens. Cas9-mediated DNA break formation induces toxic effects that are proportional with the number of cuts. Consequently, the DepMap data displays a ‘copy number alteration effect’ (CNA effect), in which sgRNAs targeting highly amplified regions of the genome produce depletion effects. Indeed, when sgRNAs target intergenic regions of amplified regions, the observed effects are comparable to the targeting of essential genes. Hence, correcting the CNA effect is crucial to reduce false positive (and increase true negative) co-dependencies between genes. Currently, the CERES methodology is used to correct for CNA effects. By applying a consensus-independent component analysis-based (consensus ICA) algorithm on gene essentiality data after CERES correction, we observed that many CNA effects are still present in the CERES-corrected data. Subsequently, we developed a methodology that outperforms CERES in removing the CNA effect. For example, we identified a set of genes mapping to chromosome 8q of sample ACH-000542 (ovarian adenocarcinoma cell line HEYA8 having amplification at chromosome 8q) having significantly lower essentiality levels compared to the rest of the genome. Whereas the CERES algorithm did not correct this effect of the chromosome 8q amplification, it was captured by consensus ICA in a consensus estimated source and was corrected by our novel methodology. After removing all CNA effects from gene essentiality data, we observed that 12.07% of co-dependency scores reported by CERES-corrected data decreased by 0.2 (on a range of -1 to 1), and 11.34% co-dependency scores increased by 0.2. In conclusion, consensus ICA-based methodology improves the correction of the CNA effect on gene essentiality data. Application of our improved method of CNA effect correction could reduce the number of false positive targets in validating biological hypotheses leading to novel therapeutic strategies in cancer.

Citation Format: Arkajyoti Bhattacharya, Carlos G. Urzúa-Traslaviña, Marcel A. T. M. van Vugt, Rudolf S. N. Fehrmann. Eliminating copy number alteration effects in the gene essentiality data from the Cancer Dependency Map project [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 5019.
Abstract 5032: Data driven refinement of gene signatures for enrichment analysis and cell state characterization
Authors: Wenzel Alexander T. , Tamayo Pablo , Mesirov Jill P.
Published: June 2022

In the study of human disease, the use of gene expression data has been crucial to the functional characterization of changes in molecular pathway activity and for identifying targets for novel treatments. However, the interpretation of this data is often complicated by its high dimensionality and the difficulty of identifying biological signals within a list of differentially expressed genes. Gene Set Enrichment Analysis (GSEA) is a community standard method for identifying pathway enrichment in gene expression data by testing whether a set of genes whose expression would indicate the activity of a specific process or phenotype are coordinately up- or downregulated more than would be expected by chance. As GSEA relies on high quality gene sets with coordinately regulated member genes, we maintain the Molecular Signatures Database (MSigDB) which contains 9 collections of curated, annotated gene sets representing different biological pathways and processes. Over time, we have observed that some of the MSigDB gene sets, especially those that are manually curated or defined in a very specific biological context, may not provide a sensitive and specific enough co-regulation signature for their corresponding phenotype. In response, we have created a data-driven, matrix-factorization-based refinement method to build more sensitive and specific gene sets. This method incorporates large-scale datasets from multiple sources including compendia such as the Cancer Dependency Map as well as curated protein-protein interaction networks. We will present the initial results of this refinement method as well as our ongoing work which will yield a new collection of refined gene sets that will be made freely available in MSigDB for use with GSEA and many other applications.

Citation Format: Alexander T. Wenzel, Pablo Tamayo, Jill P. Mesirov. Data driven refinement of gene signatures for enrichment analysis and cell state characterization [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 5032.