tbuckley/cabot-search huggingface dataset:
Abstract 578: Prediction of PD-1 treatment outcome in mismatch repair deficient metastatic colorectal cancer using a multi-omic approach
Authors: Bahar Saberzadeh-Ardestani, Oluwadunni E. Emiloju, Rondell P. Graham, Jason T. Lewis, Charles W. Abbott, Sean M. Boyle, Frank A. Sinicrope
Journal: Cancer Research (2024)

Abstract Background: Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of patients with deficient DNA mismatch repair (d-MMR) cancers, yet less than half of patients with metastatic colorectal cancer (mCRC) receive clinical benefit. We analyzed heterogeneity within d-MMR tumors using a multi-omics approach inclusive of percent unstable microsatellite loci (MS). Methods: We studied consecutive patients with d-MMR mCRC with available primary tumors (N=32) that were treated with an anti-PD-1 antibody at Mayo Clinic (2015-2022). Tumors were profiled using a whole exome and transcriptome platform (ImmunoID NeXT®). MSIsensor was used to calculate percent unstable microsatellite loci from whole exome sequencing data. CIBERSORT and ssGSEA were used to analyze immune gene expression in relationship to percent unstable microsatellite loci. An immune checkpoint gene expression signature was calculated as the mean expression of CD274, CTLA-4, HAVCR2, LAG-3, PDCD1, PDCD1LG2, TIGIT. Aforementioned variables were analyzed in relationship to objective tumor response (RECIST version 1.1). A Cox proportional hazards model was fit to predict progression-free survival (PFS). Results: Among 32 patients with d-MMR mCRC treated with PD-1 blockade, 16 (50%) received first-line anti-PD-1 therapy; others had &amp;gt; 1 prior chemotherapy regimen. Eighteen (56.3%) tumors harbored BRAFV600E, 4 (12.5%) had mutant KRAS, and median PFS was 24.6 months (95% CI: 8.4, NR) with 18 events. Neither tumor mutation burden (TMB) nor PD-L1 mRNA expression predicted PFS. Median percent unstable MS loci was 14.38 (IQR: 2.6-23.2). Patients whose tumors had higher percent unstable MS loci had significantly better PFS (Q2-4 vs Q1; HR: 0.22, 95%CI: 0.06, 0.62; P=0.003), and were associated with increased objective response (P=0.049). Tumors with higher unstable loci also had higher neoantigen clonality (R= 0.64; P= 0.0003) and increased M0 (resting) macrophages (P=0.02). Nonresponders (vs responders) to PD-1 blockade had an increased immune checkpoint expression signature (P= 0.005). Conclusion: A higher percentage of unstable microsatellite loci, associated with higher neoantigen clonality and resting macrophages, was predictive of anti-PD-1 efficacy. Furthermore, an immune checkpoint gene expression signature was associated with objective response. Citation Format: Bahar Saberzadeh-Ardestani, Oluwadunni E. Emiloju, Rondell P. Graham, Jason T. Lewis, Charles W. Abbott, Sean M. Boyle, Frank A. Sinicrope. Prediction of PD-1 treatment outcome in mismatch repair deficient metastatic colorectal cancer using a multi-omic approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 578.
Abstract 3208: A nano sized system for the treatment of gastrointestinal cancers
Authors: Daniella Vaskovich, Rita Acúrcio, Ron Kleiner, Barbara Carreira, Ana Matos, Helena Florindo, Ronit Satchi-Fainaro
Journal: Cancer Research (2024)

Abstract Despite the recent progress in cancer immunotherapies, most patients do not benefit from the currently available immune checkpoint blockers, and many develop severe immune-related adverse events. Therefore, it is urgent to develop alternative, effective immunotherapeutic approaches. An example of non-responsive cancers are gastrointestinal (GI) cancers, which account for 26% of the global cancer incidence and 35% of all cancer-related deaths. In many GI cancers, the failure of immunotherapies to yield clinical response is partially attributed to the inefficient antigen presentation by DC, which results in insufficient T cell stimulation despite their expression of tumor-associated antigens (TAA). To overcome these hurdles, we designed novel polymeric-based nanoparticles (NP) to deliver a combination of GI cancers antigens of CEACAM5 protein and toll-like receptor ligands to DC. We chose to encapsulate CEACAM5 antigens because it is overexpressed in GI cancers, such as gastric cancer, colorectal cancer, and pancreatic cancer. With this approach, we aim to modulate the tumor milieu-immune cell interactions to an anti-cancer phenotype in order to control tumor growth and improve overall survival. Our NP present an average diameter below 200 nm, narrow polydispersity index, slightly negative surface charge, spherical morphology, and high antigens and immune potentiators loading. Cy5-labeled NPs were found to be extensively internalized by DC, which triggered their activation in vivo, shown by the increasing expression of DC-related co-stimulatory molecules such as CD80, CD86, and CD40. Furthermore, we assessed the immunotherapeutic effect of our NP on mouse models and on a human 3D multi-cellular spheroid ex-vivo model, composing the patient’s tumor cells and peripheral blood mononuclear cells (PBMC). We found that the NP successfully induced a potent immune-mediated anti-tumor response against CEACAM5-positive GI tumors, sensitizing the tumor microenvironment to other therapies and decreasing tumor volume, ultimately leading to prolonged survival. Taken together, the developed NP induced a strong antigen-specific immune response and overall sensitized CEACAM5-expressing GI cancers to the clinically relevant treatments in vivo, that so far have shown limited clinical outcomes in addition to a specific T cell anti-tumor activity that was shown on our patient-derived ex vivo model. Citation Format: Daniella Vaskovich, Rita Acúrcio, Ron Kleiner, Barbara Carreira, Ana Matos, Helena Florindo, Ronit Satchi-Fainaro. A nano sized system for the treatment of gastrointestinal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3208.
Abstract 3426: Real-world biomarker testing rates and trends among patients with advanced non-small cell lung cancer in the US
Authors: Yiyu Chen, Angeline Carlson
Journal: Cancer Research (2024)

Abstract Background: Broad biomarker profiling before treatment initiation for non-small cell lung cancer (NSCLC) is recommended. Patients may not receive or receive inadequate biomarker testing before treatment initiation. This study assesses rates and trends of biomarker testing in community and academic oncology practices in the US. Methods: A descriptive cohort study was conducted using electronic health records from an NSCLC registry. Patients who initiated NSCLC treatment following diagnosis of advanced NSCLC (stage IIIB/IIIC/IV) from 01/01/2015-12/31/2021 were identified. Patient demographics (age, gender, race, region) along with histology type (squamous/non-squamous) and hospital type (academic/community) were included. The percentage of patients receiving tests for any of the nine biomarkers before and during therapy was calculated and compared. Results: 8,769 patients were identified with advanced NSCLC; 65.9% having non-squamous cell carcinoma; 22.4% having squamous cell carcinoma; 11.7% unknown. 13.4% of patients were from academic centers, 78.7% from community hospitals, 8.0% unknown. The majority (59%) were 65+ years; 47.3% were female. Overall, 83.2% had biomarker testing at some point in treatment; only 66.3% before treatment initiation. Over time, biomarker testing rates prior to treatment initiation increased (46.9% in 2015 to 73.8% in 2021). The use of biomarker testing in non-squamous cell carcinoma was greater than in squamous cell carcinoma. The most frequent biomarker testing before treatment initiation were PD-L1 (52.2%), EGFR (51.6%), and ALK (50.7%), followed by ROS1 (46.9%), BRAF (39.5%), and KRAS (34.1%). Testing rates for the newest biomarkers NTRK, MET, and RET were 20.4%, 28.4%, and 28.0%, respectively. Testing rates were similar between academic centers and community-based hospitals, except for the newest biomarkers, where use in academic settings was greater. Biomarker testing rates were higher among female patients (χ2 P-value&amp;lt;0.001); rates by race were similar (χ2 P-value=0.83). Conclusion: While the use of biomarker testing in advanced NSCLC is growing, 26% of patients remained untested before treatment initiation. Biomarker testing in non-squamous cell carcinoma is higher than in squamous cell carcinoma, in keeping with the guideline emphasis on biomarker testing for that histology type. Results suggest that further dissemination of guideline recommendations to obtain biomarker test results prior to treatment initiation is important to optimize treatment decisions in the NSCLC landscape. Citation Format: Yiyu Chen, Angeline Carlson. Real-world biomarker testing rates and trends among patients with advanced non-small cell lung cancer in the US [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3426.
Abstract 5831: The TLE1 transcriptional and epigenetic machinery contributes to EGFR targeted therapy resistance in human lung adenocarcinoma
Authors: Hector Ramos Biliran, Xin Yao, Nasir Roberts, Prince Iheukwumere, Renwei Chen, Ma. Carmela Dela Cruz
Journal: Cancer Research (2024)

Abstract In human lung adenocarcinoma that carry Epidermal Growth Factor Receptor (EGFR) sensitizing mutations, targeting the EGFR pathway with the use of EGFR tyrosine kinase inhibitors (EGFR-TKIs) has emerged as a promising therapeutic strategy providing initial clinical benefit to many patients. Unfortunately, resistance to EGFR-TKIs eventually develops leading to disease progression. In addition to genetic mutations, transcriptional and epigenetic mediated changes in gene expression remain an important mechanism contributing to EGFR-TKI resistance. Here, we report a novel function of the transcriptional corepressor Transducin-Like Enhancer of Split-1 (TLE1) in mediating EGFR-TKI resistance in EGFR mutant LUAD cells through its survival promoting gene transcriptional program. In EGFR mutant, EGFR TKI sensitive LUAD cells, sole activation of the TLE1 nuclear function attenuates EGFR TKI sensitivity with concomittant reduction of EGFR-TKI-mediated apoptosis. Conversely, downregulation of endogenous TLE1 expression via siRNAs/shRNAs and deletion of TLE1 gene via CRISPR-Cas9 in EGFR-mutant, EGFR-TKI resistant cells partially restore EGFR-TKI sensitivity via induction of EGFR-TKI apoptosis. Mechanistically, the anti-apoptosis promoting gene transcriptional program of TLE1 is dependent on its functional interaction with the transcriptional repressor HES-1, a downstream Notch target which has been associated with relapse in LUAD patients following EGFR-TKI treatment. Collectively, these studies indicate the TLE1 corepressor as a determinant of resistance to EGFR targeted therapy and raise the possibility that inhibiting TLE1 nuclear function may serve as an adjuct therapy to circumvent EGFR-TKI resistance. Citation Format: Hector Ramos Biliran, Xin Yao, Nasir Roberts, Prince Iheukwumere, Renwei Chen, Ma. Carmela Dela Cruz. The TLE1 transcriptional and epigenetic machinery contributes to EGFR targeted therapy resistance in human lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5831.
Abstract 4617: Fisetin, a multi-kinase inhibitor enhances chemotherapeutic sensitivity in head and neck cancer
Authors: Dhanir Tailor, Deepali Mishra, Sanjay V. Malhotra, Rana P. Singh
Journal: Cancer Research (2024)

Abstract Background: The limitations of chemotherapeutic applications are often imposed by dose-related toxicity and the emergence of therapeutic resistance. Fisetin, a naturally occurring flavonoid, has demonstrated anticancer properties in various cancer types. Despite its proven effectiveness against cancer, the molecular target of fisetin remains unknown. Methods: Our study focused on understanding how fisetin and chemotherapy work together to inhibit the growth and survival of human HNC. We conducted in silico, in vitro and in vivo investigations. We employed target prediction, kinase profiling, transcriptome analysis and tumor xenograft to identify the chemosensitivity efficacy and mechanism of fisetin. Results: In-silico target prediction suggested that fisetin might target multiple kinases. Based on this lead, we have screened fisetin for different kinase inhibition activities and found that it inhibits multiple CDKs including CDK1, 2, 4, 5 and 6 at nanomolar concentration. To test its cellular activity, we have selected the head and neck cancer (HNC) model and found that fisetin treatment strongly inhibited cell proliferation and arrested the HNC cells in G1 phase followed by apoptotic cell death. In tumor xenograft experiment, we found that oral fisetin treatment inhibited the FaDu and SAS tumor growth in the athymic mouse model. Transcriptome analysis on FaDu and SAS cell lines indicated that fisetin treatment significantly modulates pathways associated with cell cycle progression and regulation. These pathways include cellular assembly, DNA replication, cell death, and cell morphology. Pretreatment of HNC cells with fisetin improved the effectiveness of chemotherapy drugs including cisplatin, 5-fluorouracil, and docetaxel. Consistent with this, fisetin pre-treated cells showed elevated levels of cellular and mitochondrial ROS followed by the activation of caspases and apoptosis induction when compared with that in control cells after cisplatin, 5-FU, or docetaxel treatment. Conclusion: These results imply that fisetin has the potential to be utilized as a multi-kinase inhibitor in cancer cells. The study revealed that fisetin has a strong potential for increasing the sensitivity of cancer cells to chemotherapy. Citation Format: Dhanir Tailor, Deepali Mishra, Sanjay V. Malhotra, Rana P. Singh. Fisetin, a multi-kinase inhibitor enhances chemotherapeutic sensitivity in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4617.
Abstract 3137: Development of AT2604, a highly efficacious ADC targeting alkaline phosphatases ALPP and ALPPL2​
Authors: Bryan K. Yeung, Xiao Hui Koh, Wei Li Ling, Weiqi Tan, You Xue Wu, Xi Yun Zhang, Hong Yee Tan, Shao Jun Liu, Chen Zhong, Bin Zou
Journal: Cancer Research (2024)

Abstract Placental alkaline phosphatases, ALPP and ALPPL2, are highly homologous, membrane-bound proteins involved in fetal development. Despite having limited expression in normal tissues, they are highly differentiated in tumor cells making them ideal targets for antibody drug conjugate (ADC) development. AT2604 is an ADC that consists of a humanized IgG1 anti-ALPP/ALPPL2 antibody that displays specificity over other human alkaline phosphatases and is cross reactive to NHP ALPPL2 but not to murine ALPPL2. The anti-ALPP/ALPPL2 antibody shows high target binding affinity and internalization into ALPP and ALPPL2 positive cells.​ AT2604 utilizes AxcynCYSTM technology for site-specific conjugation to achieve a highly homogeneous (&amp;gt;97%) DAR4 ADC product. The payload is the clinically validated microtubule disrupting agent monomethyl auristatin E (MMAE) conjugated to the antibody via a protease-cleavable peptide linker approved for ADC use. When evaluated in mouse xenograft models of gastric (NCI-N87) and pancreatic (HPAC) cancer, AT2604 displayed strong tumor growth inhibition (&amp;gt;90%) at 1 mg/kg (QW3 × 2 dosing) in both models. Furthermore, a pre-tox study in non-human primates concluded AT2604 has a HNSTD of 10 mg/kg (QW3 × 3 dosing) and did not exhibit any non-reversible adverse effects; implying that AT2604 possesses an improved safety profile over other vedotin-based ADCs. Taken together, the data supports the continued development of AT2604 towards evaluation in human trials.​ Citation Format: Bryan K. Yeung, Xiao Hui Koh, Wei Li Ling, Weiqi Tan, You Xue Wu, Xi Yun Zhang, Hong Yee Tan, Shao Jun Liu, Chen Zhong, Bin Zou. Development of AT2604, a highly efficacious ADC targeting alkaline phosphatases ALPP and ALPPL2​ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3137.
Abstract 3842: Neuroendocrine differentiation and treatment of human SCLC: NRF2 has a role
Authors: Samera Hamad, Hansa Joshi, Yahui Li, Helen Toma, Nasrine Bendjilali, Stuart Jefferys, David Corcoran, Weam Elbezanti, Ben Major, Weissman Bernard, Francis Spitz
Journal: Cancer Research (2024)

Abstract SCLC is a lethal form of lung cancer and highly metastatic disease with limited therapeutic options. Four main neuro and non-neuroendocrine SCLC molecular subtypes have been identified which further complicate the efforts of finding targeted therapies. NRF2 is a transcription factor that is known to protect cells from oxidative damage by regulating more than 500 cytoprotective genes. NRF2 is frequently mutated in non-small cell lung cancer (NSCLC), however, whether alterations occur in small cell lung cancer (SCLC) is not clear due to limited sequencing data. Recently, our group has discovered a previously unrecognized role of NRF2 signaling pathway in the development of SCLC using a novel genetically engineered mouse model (GEMM). In this study, we have investigated the role of NRF2 in the progression and regression of human SCLC. Human SCLC cell lines were generated with NRF2E79Q/+ mutation (one of the most common mutations found in human tumors) to allow the constitutive activation of NRF2 in these cells. Results from hSCLC cell lines showed that NRF2 activation in NRF2-negative SCLCs can significantly inhibit their growth. Further, human SCLC gene expression data showed reduced levels of a NRF2 signature as hSCLC neuroendocrine SCLC transforms to non-neuroendocrine subtypes. As an anti-inflammatory pathway, NRF2 is known to inhibit immune cell gene signature. Our in vivo and invitro studies showed that NRF2 inhibits immune cell infiltration in SCLC; and increases PDL1 protein expression. Currently, we are investigating the effect of NRF2 activation in hSCLC growth, neuroendocrine differentiation and immune gene activation in vitro and in vivo. We are also using immune checkpoint inhibitors to determine the best therapeutic options for each SCLC subtype. Citation Format: Samera Hamad, Hansa Joshi, Yahui Li, Helen Toma, Nasrine Bendjilali, Stuart Jefferys, David Corcoran, Weam Elbezanti, Ben Major, Weissman Bernard, Francis Spitz. Neuroendocrine differentiation and treatment of human SCLC: NRF2 has a role [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3842.
Abstract 3213: A novel CDH17/PD-1 bispecific antibody for treatment of advanced gastrointestinal cancers
Authors: Kwan Wa Wong, Po Yee Wong, Kronos Chow, Chui Yee O, Dennis Wong, John Moon Luk, Kwong Fai Wong
Journal: Cancer Research (2024)

Abstract Targeting immune checkpoints like programmed death receptor 1 (PD-1) with monoclonal antibodies has achieved durable responses in a range of cancers, however, immune-related adverse events may occur in a subset of patients. As such, we developed a bispecific antibody targeting cadherin-17 (CDH17) and PD-1 with a hope to rejuvenate specifically the exhausted T cells within tumor microenvironment. In healthy individuals, CDH17 is expressed at a restricted level in intestinal epithelial junction that is not accessible to biologics, however, in gastrointestinal cancers, CDH17 is overexpressed and can be targeted by antibodies. Our new CDH17/PD-1 bispecific antibody would reactivate anti-tumor immunity with reduced risk of on-target off-tumor toxicity. Different bispecific antibody formats were designed, cloned, and expressed. Strong binders were first identified using CDH17 and PD-1 ELISA. The binding affinities to CDH17 and PD-1 of the selected candidate were examined using biolayer interferometry. The effect of these bispecific antibodies on blocking PD-1/PD-L1 axis in T cells was demonstrated in a cell-based reporter assay. T-cell mediated killing on CDH17-positive GI cancer cells and induction of T cell activation markers upon antibody treatment were also studied. A total of 7 CDH17/PD-1 bispecific antibodies of different formats were screened. Of these candidates, one, named ARB204, was selected because of its potent binding to both antigens in ELISA (i.e., EC50 values: CDH17, 1.6nM; PD-1, 0.4nM) and biolayer interferometry (i.e., KD values: CDH17, 2.4E-09M; PD-1, 6.02E-11M). ARB204 blocked PD-1/PD-L1 axis in the reporter assay with EC50 value 4.4nM. Notably, ARB204 redirected T cells to eradicate CDH17-positive pancreatic AsPC1 cells with an EC50 value of 3.5nM. No cytotoxicity against CDH17-negative cancer cells were seen. ARB204 effectively bound CDH17 on GI cancer cells and PD-1 on T cells. This bispecific design allowed selective T-cell mediated killing on cancer cells expressing CDH17, mitigating the risk of off-tumor toxicity. ARB204 warrants further studies on its immune checkpoint inhibition in animal models. Citation Format: Kwan Wa Wong, Po Yee Wong, Kronos Chow, Chui Yee O, Dennis Wong, John Moon Luk, Kwong Fai Wong. A novel CDH17/PD-1 bispecific antibody for treatment of advanced gastrointestinal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3213.