bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB063: Anti-tumor activity in preclinical models utilizing a conditional bispecific redirected activation molecule (COBRA) targeting Her2
Authors: Stringer Bradley , Chouitar Johara , Cerbone Jacqualine , Fortin Sarah , Ainbinder Alina , Kysilovsky Cassie , Scott Brittany , Banerjee Antara
Published: April 2024

Among strategies to recruit cytotoxic T-cells into the tumor micro-environment (TME) are the use of T-cell engager molecules. One such therapeutic modality are molecules that recognize specific tumor associated antigens (TAA) but are activated preferentially in the TME. Conditional Bispecific Redirected Activation molecules (COBRA) are designed to be administered as a prodrug, and cleaved via matrix metalloproteinase to engage with both a tumor TAA and CD3 (Panachi, et.al. MAbs 2020 12(1) 1792130). In this study, we sought to determine the preclinical efficacy of a COBRA molecule targeting the Her2 receptor. Sub-cutaneous xenograft models (SCID mice using adoptive T-cell transfer) were utilized representing various levels of the TAA (HT-55, SNU-16, JIMT-1, and HCC827) to measure both efficacy and mechanism of action (T-cell extravasation). The COBRA molecule was dosed at 0.03, 0.1, 0.3, and 1 mg/kg using a Q3dx7 schedule. A non-cleavable COBRA molecule with the Her2 TAA was included as a control at 1 mg/kg. Efficacy was determined by caliper measurements of sub-cutaneous tumor size twice per week after dosing, and T-cell extravasation into the TME was measured by immunohistochemistry (IHC) at days 10, 19, and termination. IHC data was quantified using HALO imaging software. In our study, we measured dose-dependent tumor regression and/or stasis in all models tested. No anti-tumor activity was measured after dosing with the non-cleavable COBRA molecule. T-cell extravasation as measured by IHC and Halo analysis followed a dose and time dependent course. Comparison of Day 19 T-cell extravasation (one day after the last dose) showed a linear relationship to TAA expression. Our data indicate that treatment with a COBRA molecule in preclinical models with a Her2 TAA results in anti-tumor activity as measured by tumor stasis/regression, and exhibit the expected mechanism of action as evaluated by T-cell extravasation into the TME.

Citation Format: Bradley Stringer, Johara Chouitar, Jacqualine Cerbone, Sarah Fortin, Alina Ainbinder, Cassie Kysilovsky, Brittany Scott, Antara Banerjee. Anti-tumor activity in preclinical models utilizing a conditional bispecific redirected activation molecule (COBRA) targeting Her2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB063.
Abstract LB091: A multigene signature for immunotherapy in patients with high risk non-muscle-invasive bladder cancer
Authors: Baek Seung-Woo , Kim Seon-Kyu , Leem Sun-Hee , Chu In-Sun
Published: April 2024

Introduction: Approximately 80% of bladder cancer patients are initially diagnosed with non-muscle invasive bladder cancer (NMIBC). However, most NMIBC patients have a high recurrence rates, and up to 45% progress to muscle-invasive bladder cancer (MIBC) and metastatic disease. Treatment for NMIBC includes transurethral resection and, depending on the risk of recurrence or progression, intravesical chemotherapy or immunotherapy, such as Bacillus Calmette-Guérin(BCG). Our aim is to use a multigene signature in patients with high-risk NMIBC to determine whether patients may benefit from improved ICIs compared to conventional PD-L1 expression and to evaluate the clinical utility.

Methods: A multi-gene signature obtained from the various NMIBC data was applied to stratify the UROMOL2021 cohort (n=535) using consensus clustering. Each subtype was distinguished by biological pathway analysis. Validation analysis was performed in three independent cohorts including the IMvigor210 (n=298), IMvigor010 (n=377) and ABACUS (n=148) clinical trials treated with PD-L1 inhibitors. The log-rank test, chi-square test, Fisher’s exact test, and cox regression analysis were used to evaluate clinical utility.

Results: Based on consensus cluster analysis, NMIBC patients in the UROMOL2021 cohort were classified into five subgroups exhibiting unique characteristics, including DNA damage repair (DDR). Cross-validation was performed using two independent NMIBC cohorts and one MIBC cohort. Survival analysis showed that the subgroup associated with DDR (DDR and DDR+Tcell) had the highest rates of relapse and disease progression (progression-free survival, p<0.001) and benefited from Immune checkpoint inhibitors (ICIs) (response, p=0.01; overall survival, p=0.004).

Conclusions: This study suggests that the multi-gene signature may play a role to enhance the responsiveness of ICIs for high-risk NMIBC. Additionally, it is important to help improve ICI treatment approaches that currently focus on PD-L1 expression on cancer cells, allowing more patients to receive priority consideration for ICI therapy.

Citation Format: Seung-Woo Baek, Seon-Kyu Kim, Sun-Hee Leem, In-Sun Chu. A multigene signature for immunotherapy in patients with high risk non-muscle-invasive bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB091.
Abstract LB093: Low IGFBP7 expression identifies a subset of breast cancers with favorable prognosis and sensitivity to IGF-1 receptor targeting with ganitumab: Data from I-SPY2 and SCAN-B
Authors: Godina Christopher , Pollak Michael N. , Jernström Helena
Published: April 2024

Background and Hypothesis: To date, no IGF-1R targeting agent has shown clinical benefit in patients despite promising preclinical data. We hypothesized that Insulin-like growth factor binding protein-7 (IGFBP7) expression predicts response to Insulin-like growth factor-1 receptor (IGF-1R) targeting agents, for which there are no biomarkers predictive of efficacy. High IGFBP7 expression was previously associated with breast cancer progression.

Materials and Methods: The predictive value of IGFBP7 expression was interrogated in I-SPY2 (NCT01042379) for pathological complete response (pCR) to neoadjuvant treatment and in SCAN-B (NCT02306096) for clinical outcome. In I-SPY2, IGFBP7 expression was examined as a predictor of pCR to neoadjuvant chemotherapy alone and separately to the combination of chemotherapy plus ganitumab (anti-IGF-1R antibody) and metformin. Odds ratios (OR) and hazard ratios (HR) with 95% confidence interval (CI) were calculated with logistic and Cox regression, respectively.

Results: Higher IGFBP7 expression conferred lower odds of achieving pCR in the ganitumab/metformin plus chemotherapy arm, ORadj 0.38 (95% CI 0.17-0.80) but not in the chemotherapy-alone arm, adjusted OR 1.23 (95% CI 0.63-2.45; P interaction=0.016). In the ganitumab/metformin plus chemotherapy arm, 46.9% of patients with tumors in the lowest quartile of IGFBP7 expression achieved pCR compared to compared to only 5.6% in the highest quartile. In SCAN-B, higher IGFBP7 expression was associated with distant metastasis risk HRadj 1.41 (95% CI 1.16-1.73).

Conclusion: Low IGFBP7 gene expression identifies a subset of breast cancer patients for whom the addition of ganitumab and metformin to chemotherapy results in a significantly improved pCR rate compared to neoadjuvant chemotherapy alone. Furthermore, we add to prior evidence that high IGFBP7 expression is predictive of poor outcome.

Citation Format: Christopher Godina, Michael N. Pollak, Helena Jernström. Low IGFBP7 expression identifies a subset of breast cancers with favorable prognosis and sensitivity to IGF-1 receptor targeting with ganitumab: Data from I-SPY2 and SCAN-B [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB093.
Abstract LB096: Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma
Authors: Tomasova Kristyna , Seborova Karolina , Kroupa Michal , Horak Josef , Vodickova Ludmila , Rob Lukas , Hruda Martin , Mrhalova Marcela , Bartakova Alena , Bouda Jiri , Fleischer Thomas , Kristensen Vessela , Vodicka Pavel , Vaclavikova Radka
Published: April 2024

Impaired telomere length (TL) maintenance in ovarian tissue may play a pivotal role in epithelial ovarian carcinoma (OvC) onset. TL in either target or surrogate tissue (blood) is currently being investigated as a predictor in anti-OvC therapy or as a biomarker of the disease progression, respectively. There is presently an urgent need for an appropriate approach to chemotherapy response prediction. We performed a monochrome multiplex qPCR measurement of TL in peripheral blood and tumor tissues of 209 OvC patients. Methylation status and gene expression of shelterin complex and telomerase catalytic subunit (hTERT) were determined within tumor tissues by High-Throughput DNA methylation profiling and RNA sequencing (RNA-Seq) analysis, respectively. The patients sensitive to cancer treatment (n=46) had shorter telomeres in peripheral blood cells compared to those treatment-resistant (n=93; P=0.037). Cancer tissue TL lower than the median predisposed to better overall survival (P=0.002). Gene expression of TPP1, which recruits telomerase to telomeres, was positively associated with TL in tumor tissue (P=0.026). TL measured in peripheral blood cells could serve as a marker of platinum therapy response in OvC patients. Additionally, TL determined in tumor tissue provides information on OvC patients' overall survival. The study was financed by the project NPO (LX22NPO05102), the Czech Health Research Council (NU21-03-00145), and the Czech Science Foundation (21-27902S).

Citation Format: Kristyna Tomasova, Karolina Seborova, Michal Kroupa, Josef Horak, Ludmila Vodickova, Lukas Rob, Martin Hruda, Marcela Mrhalova, Alena Bartakova, Jiri Bouda, Thomas Fleischer, Vessela Kristensen, Pavel Vodicka, Radka Vaclavikova. Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB096.
Abstract LB108: Specific plasma DNA end-motifs distinguish patients with lung adenocarcinoma versus benign nodules
Authors: Hyun Jason C. , Yip Shun H. , Swarup Neeti , Ramamurthy Raghuraman , Cheng Jordan C. , Choi Irene , Wong Edmund , Arora Akanksha , Aberle Denise , Wong David T. , Tang Cheuk Y.
Published: April 2024

Background: Recent studies have identified blood plasma DNA as a rich source of biomarkers for non-invasive cancer detection. In particular, analysis of shorter DNA fragments or “fragmentomics” have shown promising results with numerous competing approaches such as those based on mutation calls, length distributions, or preferred fragmentation patterns. In this study, we assessed the potential of fragment end motif distributions in discriminating patients with lung adenocarcinoma versus benign tumors.

Methods: Plasma samples from 37 patients (20 benign, 17 malignant) were subject to whole genome sequencing. For each sample, DNA fragments were grouped as short (30-99bp) and long (100-269bp) and end motif distributions were calculated by counting occurrences of 4-9bp sequences at either the 5’ or 3’ end of each fragment. A proprietary machine learning algorithm was employed to identify a minimal set of motifs capable of accurately distinguishing benign from malignant samples.

Results: Just two 5’ end motifs in long fragments, CCAT and GACA, were sufficient for distinguishing malignant from benign samples in a two-step decision tree (89% accuracy with all samples, 86% accuracy in leave-one-out cross validation). Accuracy was significantly higher when compared to random guessing by shuffling labels (p=1.6*10−6, FWER < 0.05, Bonferroni correction, 351 tests). CCAT motif frequency was also significantly associated with cancer stage (p=0.04, Kruskal-Wallis test) and specifically elevated in early stage samples (I, II).

Conclusions: These results suggest that plasma DNA end motif distributions are informative in discriminating patients with lung adenocarcinoma versus benign tumors. The two-motif model suggests that specific, rather than systemic changes in end motif distributions are more strongly associated with lung cancer patients and may point to specific mechanisms linked to cancer progression.

Citation Format: Jason C. Hyun, Shun H. Yip, Neeti Swarup, Raghuraman Ramamurthy, Jordan C. Cheng, Irene Choi, Edmund Wong, Akanksha Arora, Denise Aberle, David T. Wong, Cheuk Y. Tang. Specific plasma DNA end-motifs distinguish patients with lung adenocarcinoma versus benign nodules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB108.
Abstract LB109: Detection of high grade intraepithelial neoplasia in colorectal cancer using a new blood-based multiplex septin9 methylation assay
Authors: Wu Youming , Tong Yongqin Tong , Zhang Haitao , Li Yun , Li Ming , Qiu Lili , Liu Wenlan , Mei Siqing , Mao Yu , Cao Yanhua , Su Caiyan , Yu Wentao , Wang Junli , Wang Taizhong , Zhu Zhongyuan , Yu Dehua Derek
Published: April 2024

Colorectal cancer (CRC) is the third most common cancer worldwide, and regular screening is effective in reducing its mortality. Epi proColon was the first blood-based Septin9 gene methylation assay approved by the US FDA for CRC screening. However, the broader application of this assay has been hindered by its relatively lower sensitivity in detecting early-stage CRC and precancerous lesions. In this study, we developed a new multiplex Septin9 methylation assay, named ColonUSK, which simultaneously detects two CpG-rich subregions in the promoter of the Septin9 gene and an internal control in a single reaction. In comparison with the Sepin9 assay targeting only one CpG-rich subregion, this new assay demonstrated improved sensitivity, with a detection limit as low as 12pg of the positive DNA. To assess its value in CRC screening, we conducted an opportunistic screening study involving a total of 1366 subjects. Blind testing was performed to evaluate ColonUSK in comparison with clinical diagnosis using colonoscopy and pathological examination (the clinical gold standard). The clinical sensitivities of ColonUSK for detecting CRC and advanced adenoma were 77.34% (95% CI: 72.89%-81.26%) and 25.26% (95% CI: 17.16%-35.41%), respectively. The clinical specificity of the assay for non-CRC cases was 95.95% (95% CI: 94.36%-97.13%). Notably, ColonUSK was able to detect 54.29% of cases with high-grade intraepithelial neoplasia. The Kappa test value for this experiment was 0.76, indicating a high degree of consistency between ColonUSK and pathological diagnosis. Our results suggest that ColonUSK holds potential as a non-invasive screening tool for colorectal cancer.

Citation Format: Youming Wu, Yongqin Tong Tong, Haitao Zhang, Yun Li, Ming Li, Lili Qiu, Wenlan Liu, Siqing Mei, Yu Mao, Yanhua Cao, Caiyan Su, Wentao Yu, Junli Wang, Taizhong Wang, Zhongyuan Zhu, Dehua Derek Yu. Detection of high grade intraepithelial neoplasia in colorectal cancer using a new blood-based multiplex septin9 methylation assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB109.
Abstract LB110: Impact of circulating tumor cell-expressed prostate-specific membrane antigen and prostate-specific antigen transcripts in various stages of prostate cancer
Authors: Cho Hyungseok , Byun Seok-Soo , Son Nak-Hoon , Chung Jae Il , Seo Won Ik , Lee Chan Ho , Morgan Todd M , Han Ki-Ho , Chung Jae-Seung
Published: April 2024

PurposeProstate-specific membrane antigen (PSMA)-based images, which visually quantify PSMA expression, are used to determine prostate cancer (PCa) micrometastases. This study evaluated whether a circulating tumor cell (CTCs-based transcript platform, including PSMA mRNA, could help identify potential prognostic markers in PCa.

Experimental design We prospectively enrolled 21 healthy individuals and 247 patients with PCa (localized PCa [LPCa]: 94; metastatic hormone-sensitive PCa [mHSPC]: 44; and metastatic castration-resistant PCa [mCRPC]: 109). The mRNA expression of six transcripts (PSMA, prostate-specific antigen [PSA], AR, AR-V7, EpCAM, and KRT 19) from CTCs was measured, and their relationship with biochemical recurrence (BCR) in LPCa and mCRPC progression-free survival (PFS) rate in mHSPC was assessed. PSA-PFS and radiological-PFS were also calculated to identify potential biomarkers for predicting androgen receptor signaling inhibitor (ARSI) and taxane-based chemotherapy resistance in mCRPC.

Results CTC detection rates were 75.5%, 95.3%, and 98% for LPCa, mHSPC, and mCRPC, respectively. In LPCa, PSMA (hazard ratio [HR]: 3.35; P=0.028) and PSA mRNA (HR: 1.42; P=0.047) expression was associated with BCR. mHSPC patients with high PSMA (HR: 4.26; P=0.020) and PSA mRNA (HR: 3.52; P=0.042) expression showed significantly worse mCRPC-PFS rates than those with low expression. Increased PSA and PSMA mRNA expression was significantly associated with shorter PSA-PFS and radiological PFS in mCPRC, indicating an association with drug resistance.

Conclusion PSMA and PSA mRNA expression is associated with BCR in LPCa. In advanced PCa, PSMA and PSA mRNA can also predict rapid progression from mHSPC to mCRPC and ARSI or taxane-based chemotherapy resistance.

Citation Format: Hyungseok Cho, Seok-Soo Byun, Nak-Hoon Son, Jae Il Chung, Won Ik Seo, Chan Ho Lee, Todd M Morgan, Ki-Ho Han, Jae-Seung Chung. Impact of circulating tumor cell-expressed prostate-specific membrane antigen and prostate-specific antigen transcripts in various stages of prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB110.
Abstract LB115: Strong antitumor effect elicited by inhibition of AKT or FOXP3 in combination with anti-PD-L1 in Pten mutant lung squamous cell carcinoma
Authors: Houry Maeva , Redrado Miriam , Carnevalli Larissa , Barry Simon , Galan Nuria , Otegui Nerea , Leon Sergio , Montuenga Luis , Exposito Francisco , Calvo Alfonso
Published: April 2024

PTEN is mutated in ~10% lung squamous cell carcinoma (LUSC) patients, which results in hyperactivation of PI3K-AKT-mTOR signaling pathways. Mutations in the PI3K-AKT-mTOR pathway influence the configuration the tumor microenvironment (TME). We have recently reported that PTEN mutations in LUSC are associated with increased tumor infiltration of T regulatory immunosuppressive cells (Tregs) and fibrogenesis (PMID: 37311042). Moreover, we have demonstrated that PTEN mutations in LUSC induces resistance to anti-PD-1 therapy. Based on these findings, we have investigated whether blockade of AKT signaling with capivasertib (AZD5363) and/or inhibition of Treg-associated FOXP3 transcription factor, using the FOXP3 targeting antisense oligonucleotide (ASO) AZD8701 (FOXP3i), would cause tumor growth inhibition in the PTEN mutant context. In in vitro assays we found that Pten-null LUSC UN680 murine cells were highly sensitive to capivasertib, with inhibition of the AKT-mediated signaling cascade, reduction in cyclin D1 levels, cytoplasmic translocation of FOXO1 and increase in apoptosis and autophagy. In in vivo studies using Pten-null UN680 cells subcutaneously injected in AJ immunocompetent mice, treatment with either capivasertib or the FOXP3i induced >90% tumor regression and increased survival. Moreover, on average 3/8 (~37%) animals were cured in each treatment group. In a re-challenge experiment performed in animals cured by the FOXP3i, tumors were not developed upon injection of Pten-null UN680 cells, demonstrating immunological memory. Combination of capivasertib+FOXP3i at the same doses did not cause further tumor growth inhibition, but combination of capivasertib+anti-PD-L1 or FOXP3i+anti-PD-L1 increased antitumor benefit compared to monotherapy treatment, and further increased survival. In summary, we demonstrate that immunotherapy resistant tumors with hyperactivation of AKT due to Pten mutation are highly sensitive to AKT or FOXP3 inhibition and that combinatorial strategies using these targets and anti-PD-L1 can be appropriate strategies to treat these tumors.

Citation Format: Maeva Houry, Miriam Redrado, Larissa Carnevalli, Simon Barry, Nuria Galan, Nerea Otegui, Sergio Leon, Luis Montuenga, Francisco Exposito, Alfonso Calvo. Strong antitumor effect elicited by inhibition of AKT or FOXP3 in combination with anti-PD-L1 in Pten mutant lung squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB115.
Abstract LB159: Discovery of HP560, a novel BET inhibitor for the treatment of myelofibrosis
Authors: Li Jing , Fan Lei , Yuan Hongwei , Huo Yongxu , Yu Hua , Wang Fei , Li Xinghai
Published: April 2024

Myelofibrosis (MF) is a myeloproliferative neoplasm characterized by defective clonal hematopoiesis, bone marrow fibrosis, splenomegaly, severe anemia, and the propensity for transformation to acute myeloid leukemia (AML). Inhibitors targeting JAKs (Janus kinases) have revolutionized the treatment of MF, but are limited by modest efficacy or acquired resistance after prolonged treatment. Here, we report a novel inhibitor, HP560 that targets BET (bromodomain and extra-terminal) proteins and shows promising therapeutic activities against MF and AML. Through engaging the bromodomain pocket of BET proteins in a competitive manner with acetylated histones, HP560 causes the disruption of BET proteins from chromatin. HP560 has high binding affinities for all BET proteins and strong anti-proliferative activity as well as synergistic anti-proliferative effect in combination with ruxolitinib, a JAK1/2 inhibitor. In an MF cell line derived tumor xenograft (CDX) mouse model, HP560 prolongs survival and improves splenomegaly and anemia, and these effects are enhanced when combined with ruxolitinib. HP560 also significantly and dose-dependently inhibits tumor growth in an AML CDX mouse model. Together, HP560 is a potent pan-BET inhibitor and can be developed as a monotherapy or in combination with a JAK inhibitor for the treatment of MF. HP560 structure will not be disclosed.

Citation Format: Jing Li, Lei Fan, Hongwei Yuan, Yongxu Huo, Hua Yu, Fei Wang, Xinghai Li. Discovery of HP560, a novel BET inhibitor for the treatment of myelofibrosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB159.
Abstract LB169: Using a global reporter on transcript abundance to identify a selective inhibitor of Nrf2 signaling in KEAP1-mutant non small cell lung cancer
Authors: Read Timothy J. , Damon Leah , Yoo Reo , Grochala Carter , Liechty Cole , Rhine Christy , Rimel Jenna , Simpson David , Lundblad Riley , Pham Casey , Steel Richard , Azofeifa Joey
Published: April 2024

Loss-of-function mutations in Kelch-like ECH-associated protein 1 (KEAP1) are common in non-small cell lung cancer (NSLC) and result in particularly poor prognosis. Such mutations activate the transcription factor Nrf2, leading to aberrant expression of chemoprotective genes and rendering cells resistant to chemotherapy. We used our chemo-transcriptomic platform, termed GRETA, for Global Reporter on Transcript Abundance, to identify compounds that inhibit Nrf2 transcription factor activity in KEAP1-mutant NSCLC cell lines. After defining the transcriptomic signature imparted by constitutive activation of Nrf2 in a KEAP1 KO NCI-H1975 cell line, we generated over 10,000 transcriptomes to identify compounds that dampen the Nrf2-overactive transcriptional signature. One such compound, ARP-4316, displays selectivity for KEAP1-mutant cell lines, reduces nuclear Nrf2 protein levels, and reduces Nrf2 transcriptional activity in an ARE reporter assay. Furthermore, ARP-4316 synergizes with 5-fluorouracil in two KEAP1-mutant cell models, A549 and NCI-H2122, suggesting that ARP-4316 may sensitize KEAP1 mutant cell lines to chemotherapy by inhibiting Nrf2 transcriptional activity. Efforts to identify the cellular target and mechanism of action of ARP-4316 are underway.

Citation Format: Timothy J. Read, Leah Damon, Reo Yoo, Carter Grochala, Cole Liechty, Christy Rhine, Jenna Rimel, David Simpson, Riley Lundblad, Casey Pham, Richard Steel, Joey Azofeifa. Using a global reporter on transcript abundance to identify a selective inhibitor of Nrf2 signaling in KEAP1-mutant non small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB169.
Abstract LB177: Discovery of HC-4955, a novel AR-V7-targeting PROTAC for the treatment of mCRPC
Authors: Li Jing , Tu Zhilin , Du Wu , Xiang Xi , Wen Zeyu , You Yang , Zhao Lijuan , Chen Yin , Yang Chengcheng , Yuan Hongwei , Li Xinghai
Published: April 2024

Prostate cancer is the second most commonly diagnosed cancer and the second leading cause of cancer death among men worldwide. Androgens play an important role in the development and progression of prostate cancers and targeting androgen receptor (AR) signaling axis over decades has remained a mainstay of prostate cancer therapy. Next generation hormonal agents (NHAs) enzalutamide and abiraterone have brought clinical benefits for metastatic castrate-resistant prostate cancer (mCRPC) patients, AR axis-targeted therapy resistance is inevitable due to AR gene amplification or mutations. AR-V7 is the most clinically relevant AR splice variant associated with endocrine resistance and poor prognosis. AR-V7 constitutively activates AR signaling and lacks the ligand binding domain (LBD) where hormones and AR antagonists interact, resulting in resistance to AR signaling inhibitors (ARSi). Thus, AR-V7 is a promising therapeutic target to address ARSi resistance in mCRPC. We have discovered a highly potent AR-V7 proteolysis targeting chimera (PROTAC), HC-4955 that degrades both the wild-type AR (WT-AR) and AR-V7 mutant. HC-4955 degrades AR-V7 with DC50 < 5 nM. In silico molecular docking analysis predicts the binding of HC-4955 to the N-terminal domain of AR and then the essential amino acids contributed to HC-4955 binding are validated by mutational analysis studies. HC-4955 also potently degrades mutants of AR-LBD mutations including L702H and T878A and these mutations are also associated with ARSi resistance. HC-4955 strongly inhibits proliferation of ARSi-resistant prostate cancer cell lines with IC50 < 10 nM. HC-4955 shows a robust anti-tumor activity in the AR-V7-bearing 22Rv1 cell line derived tumor xenograft (CDX) and patient-derived xenograft (PDX) mouse models, with majority of the tumors completely regressed and > 90% AR-V7 expression decreased at 1-5 mg/kg (QD, PO) in these models. The pre-clinical results support the clinical development of HC-4955 for the treatment of mCRPC. Selected pre-clinical data along with the chemical structure of HC-4955 will be presented.

Citation Format: Jing Li, Zhilin Tu, Wu Du, Xi Xiang, Zeyu Wen, Yang You, Lijuan Zhao, Yin Chen, Chengcheng Yang, Hongwei Yuan, Xinghai Li. Discovery of HC-4955, a novel AR-V7-targeting PROTAC for the treatment of mCRPC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB177.
Abstract LB186: Rapid photoinhibition of the autophagy pathway
Authors: Mondal Payel , Cyril Amanda , Towers Christina
Published: April 2024

Autophagy is a highly regulated and conserved cellular recycling process that is activated under stress conditions. Although cancer cells are known to rely on autophagy for survival, recent studies indicate that when the nutrient recycling process is blocked, a few rare cancer cells still can circumvent autophagy inhibition and maintain their aggressive growth rate. To understand the autophagy inhibition adaptation mechanism, we have developed a novel optogenetic autophagy inhibition tool (ASAP) that can rapidly and reversibly block the autophagy pathway in response to blue light. Our preliminary data shows ASAP releases a mutant autophagy inhibitory protein from the plasma membrane within 5 minutes of blue light exposure, blocks autophagosome-lysosome fusion, and induces LC3-II protein accumulation. In comparison, bafilomycin, a known autophagosome-lysosome fusion inhibitor, takes 4-hours to reproduce similar inhibitory effects as ASAP. Additionally, unlike bafilomycin, ASAP-induced autophagy inhibition is reversible within 2-6 hours. As light-induced autophagy inhibition has not been previously tested, our system brings a novelty to the conventional genetic and pharmacological approaches of autophagy inhibition. We will utilize the novel ASAP tool to understand the rapid changes in cellular proteomics and signaling events that dictate autophagy inhibition adaptation in cancer cells. We will perform tandem mass tag (TMT) based total proteomics and phospho-proteomics screen to visualize the temporal kinetics of protein turnover rates and changes in cell-signaling pathways following rapid autophagy inhibition. Additionally, our optogenetic tool will be applied in vivo in C. elegans to rapidly block autophagy and answer key questions of the spatial and temporal roles of autophagy in aging.

Citation Format: Payel Mondal, Amanda Cyril, Christina Towers. Rapid photoinhibition of the autophagy pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB186.
Abstract LB204: EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression
Authors: Das Dipanwita , Bajaj Upasana , Yu Leung Jia , Rashi Nurul Fateha Binti Abdul , Tergaonkar Vinay , Taneja Reshma
Published: April 2024

Embryonal Rhabdomyosarcoma (ERMS) stands as the prevailing subtype of Rhabdomyosarcoma (RMS), the most prevalent pediatric soft tissue sarcoma. With a survival rate below 20% in the metastatic stage, RMS lacks targeted drug therapies, emphasizing the need for novel treatment avenues. Genomic analyses have unveiled a low incidence of somatic mutations in RMS, highlighting the substantial role of epigenetic modifiers in oncogenesis.This investigation focuses on EHMT1's involvement in ERMS oncogenesis. Our findings illuminate EHMT1 as a pivotal contributor to the migratory and invasive capabilities of ERMS cells, both in vitro and in vivo. Transcriptomic analysis following EHMT1 depletion unveils significant alterations in pathways crucial for cell migration and invasion. Specifically, the transcription factor SOX8, essential for cellular motility, experiences a substantial reduction upon EHMT1 loss. Notably, the phenotypic effects of EHMT1 loss are mirrored upon SOX8 depletion.Further RNA-Sequencing of SOX8-depleted cells exposes the downregulation of multiple integrin genes. Mechanistically, we delineate EHMT1's role in the upregulation of SOX8 through the regulation of BRD4 expression, influencing its occupancy at the promoter. This study unravels a novel EHMT1-SOX8 axis as a key driver of metastasis in ERMS, providing valuable insights for potential therapeutic interventions in this challenging clinical landscape.

Citation Format: Dipanwita Das, Upasana Bajaj, Jia Yu Leung, Nurul Fateha Binti Abdul Rashi, Vinay Tergaonkar, Reshma Taneja. EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB204.
Abstract LB223: The molecular landscape of injury-induced mammary epithelial cell fate switching
Authors: Martín Queralt Vallmajó , Lytle Nikki K. , Murali Divya , Srinivasan Sumana , Ma Zhibo , Mukund Kavitha , Dravis Christopher , Zamora Liliana , Peterson Ana , Khramtsova Galina , Olopade Funmi , Subramaniam Shankar , Wahl Geoffrey M.
Published: April 2024

The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression.

Citation Format: Queralt Vallmajó Martín, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB223.
Abstract LB246: Deep learning framework for patient recurrence and genetic marker prediction in diffuse glioma
Authors: Lin Ko-Hong , Zhang Kai , Lee Dung-Fang , Jiang Xiaoqian
Published: April 2024

Investigation of important molecular features of glioma patients may reveal driving mechanisms of patient recurrence and treatment failures in glioma. Applying various deep learning techniques enables the integration and systematic comparison of multi-omics features, allowing robust marker prediction and patient stratification. We extracted mutation and copy number variation data from the Glioma Longitudinal Analysis (GLASS) Consortium, consisting of 628 primary or recurrent samples. To achieve the patient recurrence classification task, we designed a transformer-based model that learns the genomic profiles and predicts patient recurrence status. Our model outperforms traditional machine learning models, including support vector machine (SVM), logistic regression, and decision trees, for up to 34% and 40% improvement of AUROC and AUPRC, respectively. Including mutational features alone can achieve the best prediction performance, while copy number variations are less informative in predicting patient recurrence status. Our approach is an early attempt that employs deep learning for dissecting the contribution of diverse genomic profiles on glioma recurrence and might provide insights into developing novel therapies for treating glioma.

Citation Format: Ko-Hong Lin, Kai Zhang, Dung-Fang Lee, Xiaoqian Jiang. Deep learning framework for patient recurrence and genetic marker prediction in diffuse glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB246.
Abstract LB247: TCPAplus: An LLM-empowered chatbot for analyzing a large protein expression atlas of human cancers
Authors: Liu Wei , Liu Jun , Tang Yitao , Liu Chaozhong , Song Meiyi , Ju Zhenlin , Kumar Shweth V. , Lu Yiling , Akbani Rehan , Mills Gordon , Liang Han
Published: April 2024

We present a comprehensive functional proteomics resource comprising nearly 9,000 samples from The Cancer Genome Atlas and Cancer Cell Line Encyclopedia, using ~500 high-quality antibodies through reverse phase protein arrays. To enhance its utility, we have developed an analytical chatbot harnessing advanced large language models. This intuitive platform empowers researchers to effortlessly query protein-centered cancer omics data, conduct related analyses, and visualize results using natural language, significantly easing the translation from intricate proteogenomic data to valuable biological insights.

Citation Format: Wei Liu, Jun Liu, Yitao Tang, Chaozhong Liu, Meiyi Song, Zhenlin Ju, Shweth V. Kumar, Yiling Lu, Rehan Akbani, Gordon Mills, Han Liang. TCPAplus: An LLM-empowered chatbot for analyzing a large protein expression atlas of human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB247.
Abstract LB253: Crafted experiments to evaluate feature selection methods for single cell RNA-seq data
Authors: Liu Siyao , Corcoran David , Garcia-Recio Susana , Perou Charles , Marron J.S.
Published: April 2024

Single-cell RNA sequencing (scRNA-seq) technologies have revolutionized our understanding of cellular compositions and tumor behavior at the single-cell level, and have been widely used in many biomedical applications, such as identifying and characterizing novel cell types/states. While numerous computational methods have been developed for analyzing scRNA-seq data, benchmarking various analytical methods remains a key challenge for two reasons. First, there is a lack of ground truth datasets where unambiguous cell type identities are known using external information. Second, simulation of scRNA-seq data tends to be overly artificial and simplistic, which may not well mimic the underlying biological complexity as well as high level of technical variability. Here, we propose the use of crafted experiments, a new approach based upon perturbing signals in a real dataset for comparing different scRNA-seq analytical methodologies. We demonstrate the effectiveness of crafted experiments in the context of a novel univariate distribution-oriented suite of feature selection methods, called GOF (Goodness of Fit). We show that GOF more frequently selects features that robustly identify crafted artificial clusters in crafted experiments and achieves similar performance compared to the field standard method using real datasets. Importantly, we show the use of crafted experiments for identifying the contexts in which each method performs the best. Crafted experiments offer valuable comparisons of scRNA-seq analysis methods, and the crafted datasets generated from this study provide a useful resource for the single-cell community.

Citation Format: Siyao Liu, David Corcoran, Susana Garcia-Recio, Charles Perou, J.S. Marron. Crafted experiments to evaluate feature selection methods for single cell RNA-seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB253.
Abstract LB258: ZDHHC20 is a potential target for overcoming ABCB1-mediated multidrug resisance (MDR) in cancer
Authors: Ji Ning , Peng Xin , Liu Yi-nan , Yang Yuqi , Chen Zhe-Sheng , Kong Dexin , Li Yueguo
Published: April 2024

ABCB1-mediated multidrug resistance (MDR) in cancer cells is an increasingly important cause of anticancer drug treatment failure. The occurrence of MDR in cancer reduces the effectiveness of antitumor drugs, which results in poor quality of life and increased mortality of patients, and creates a heavy burden for the patient's family and society. Hence, the reversal of ABCB1-mediated MDR in cancer is a highly urgent clinical need. Although reversal agents targeting ABCB1 have been developed and partially tested in clinical trials, their main mechanism limits to inhibit the function of ABCB1 efflux pumps, which lacks tumor tissue specificity and has poor clinical effects, and the development of ABCB1-based resistance reversal strategies has entered a bottleneck. ABCB1 mediates tumor MDR through drug efflux and lysosomal segregation, and intervention in the plasma membrane/lysosomal membrane localization of ABCB1 is a potential strategy to reverse drug resistance. Palmitoylation, as a post-translational lipid modification, plays an important role in protein anchoring, transport, and functional regulation, and is highly relevant to human tumors. In the present study, palmitoylation modification was first identified as a key post-translational lipid modification of ABCB1. ABCB1 is palmitoylated in its cytoplasmic domain, which is further stabilized by blocking its ubiquitination, consequently suppressing ABCB1 degradation by lysosomes. We identified palmitoyltransferase ZDHHC20 (DHHC20) as the main acetyltransferase required for the palmitoylation of ABCB1, and show that the inhibition of ABCB1 palmitoylation via 2-bromopalmitate (2-BP), or the silencing of DHHC20, decreases ABCB1 expression and overcomes MDR in vitro as well as in mice bearing SW620/Ad300 resistance cells. Moreover, Cysteine residues C787 was identified as the main palmitoylation cite in human ABCB1. Database and RNAseq analyses revealed that ZDHHC20 is highly expressed in tumor tissues and tumor MDR cells, which makes it a potential tumor tissue-specific target for overcoming ABCB1-mediated MDR in cancer. Our results firstly identified the novel post-translational modification (palmitoylation) of ABCB1 and provide a new research direction and theoretical basis for breaking through the bottleneck of the development of reversal agents for ABCB1-mediated MDR in cancer.

Citation Format: Ning Ji, Xin Peng, Yi-nan Liu, Yuqi Yang, Zhe-Sheng Chen, Dexin Kong, Yueguo Li. ZDHHC20 is a potential target for overcoming ABCB1-mediated multidrug resisance (MDR) in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB258.
Abstract LB275: Reactivation of mitotic arrest upon targeting TACC3 restores immunogenic cell death and T-DM1 response in HER2-positive breast cancer
Authors: Saatci Ozge , Gedik Mustafa Emre , Oberholtzer Nathaniel , Uner Meral , Akbulut Ozge , Cetin Metin , Aras Mertkaya , Ibis Kubra , Caliskan Burcu , Banoglu Erden , Wiemann Stefan , Uner Aysegul , Aksoy Sercan , Mehrotra Shikhar , Sahin Ozgur
Published: April 2024

Immunogenic cell death (ICD) is a specific form of cell death that is characterized by the release of danger-associated molecular patterns (DAMPs), such as cell surface exposure of calreticulin, ATP and HMGB1 release, and can be induced by several different anti-cancer therapies. This, in turn, evokes a strong anti-tumor immune response, leading to reduced tumor growth. Despite being the first and one of the most successful antibody-drug conjugates (ADCs) approved for refractory HER2-positive breast cancer, little is known if response and resistance to trastuzumab emtansine (T-DM1) involves ICD modulation that can be leveraged to enhance T-DM1 response. Here we report that T-DM1 induces spindle assembly checkpoint (SAC)-dependent ICD in sensitive cells, mediated by its payload by inducing eIF2α phosphorylation, surface exposure of calreticulin, ATP and HMGB1 release, and secretion of ICD-related cytokines, all of which are lost in resistance. Accordingly, ICD-related gene signatures correlate with clinical response to T-DM1-containing therapy in pre-treatment samples, and increased infiltration of anti-tumor CD8+ T cells is correlated with better T-DM1 response in post-treatment samples. We found that transforming acidic coiled-coil containing 3 (TACC3) is overexpressed in T-DM1 resistant cells, and that T-DM1 responsive patients have reduced TACC3 protein while the non-responders exhibited increased TACC3 expression during T-DM1 treatment. Notably, genetic or pharmacological inhibition of TACC3 revives T-DM1-induced SAC activation and induction of ICD markers in vitro. TACC3 inhibition elicits ICD in vivo as shown by vaccination assay. It also potentiates T-DM1 in the human HER2-overexpressing MMTV-huHER2#5 (Fo5) transgenic model by activating ICD markers, release of cytokines and inducing dendritic cell (DC) maturation and enhancing infiltration of cytotoxic T cells. Together, our results show that ICD is a key mechanism of action of T-DM1 which is lost in resistance, and that targeting TACC3 restores T-DM1-mediated ICD and overcomes resistance.

Citation Format: Ozge Saatci, Mustafa Emre Gedik, Nathaniel Oberholtzer, Meral Uner, Ozge Akbulut, Metin Cetin, Mertkaya Aras, Kubra Ibis, Burcu Caliskan, Erden Banoglu, Stefan Wiemann, Aysegul Uner, Sercan Aksoy, Shikhar Mehrotra, Ozgur Sahin. Reactivation of mitotic arrest upon targeting TACC3 restores immunogenic cell death and T-DM1 response in HER2-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB275.