bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4554: Novel combination therapy for treating proteasome inhibitor-resistant multiple myeloma
Authors: Kim Byung-Gyu , Choi Sung Hee , Nguyen Huong , Liang Fu-Sen , Kim Seong-Jin , Letterio John , Huang Alex
Published: March 2024

Multiple myeloma (MM) is an incurable plasma cell malignancy characterized by osteolytic bone disease and immunosuppression. Proteasome inhibitors (PIs) have remarkably improved the survival of MM patients, but dose-limiting toxicities and the development of drug resistance limit their long-term utility. Elevated TGF-β levels in MM patient sera correlate with drug resistance, disease progression, metastasis and poor prognosis. Therefore, we evaluated the anti-MM therapeutic potential of a TGF-β type I receptor kinase inhibitor, Vactosertib. In vitro treatment of Vactosertib synergistically inhibited the growth of bortezomib (BTZ)-resistant MM cells in combination with either BTZ or ixazomib (IXZ) by suppressing TGF-β activation of Smad2/3 and expression of PSMB5, which encodes the proteasome 5 catalytic subunit targeted by PIs. Oral administration of Vactosertib as a single agent decreased MM progression and mortality of the mice bearing BTZ-resistant MM. Vactosertib alone also attenuated PSMB5 expression and proteasome activity, reduced the expansion of CD11b+Gr-1+ myeloid derived suppressor cells (MDSCs) in bone marrow (BM) tumor microenvironment (TME), and diminished the population of Foxp3+ regulatory T cells (Treg) in the spleen. Combination therapy of Vactosertib plus PI (BTZ or IXZ) exhibited a synergistic anti-myeloma effect when compared to either Vactosertib or PI alone by greatly prolonged survival and significant a reduction in both MDSCs and Tregs. Furthermore, therapy of BCMA+ CAR T cells in combination with Vactosertib exhibited a synergistic anti-tumor effect, compared to either CAR T cells or Vactosertib. Taken together, our data provide the rationale for clinical evaluation of Vactosertib in MM and demonstrate proof-of-concept that combination of Vactosertib and either PI or cell therapy may overcome drug resistance and enhance durable patient responses.

Citation Format: Byung-Gyu Kim, Sung Hee Choi, Huong Nguyen, Fu-Sen Liang, Seong-Jin Kim, John Letterio, Alex Huang. Novel combination therapy for treating proteasome inhibitor-resistant multiple myeloma [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 4554.
Abstract 4588: Combination of MTA-cooperative PRMT5 inhibitor and direct mutant-selective KRAS inhibitors as a novel therapeutic approach for MTAP-deficient pancreatic cancer
Authors: Drizyte-Miller Kristina , Chang Wen-Hsuan , Waters Andrew M. , Stalnecker Clint A. , Wang Junning , Aguirre Andrew J. , Cox Adrienne D. , Der Channing J.
Published: March 2024

KRAS is mutationally activated in 95% of pancreatic ductal adenocarcinoma (PDAC) patients. Direct KRAS inhibitors are under intense preclinical and clinical development, with two KRASG12C mutant-selective inhibitors (G12Ci) now approved. However, treatment-associated resistance to KRAS inhibitors has been reported in the clinic highlighting an urgent need to identify both additional therapeutic targets and novel combination treatment strategies with KRAS inhibitors. To that end, we performed a CRISPR/Cas9 loss-of-function screen using a library targeting ~2,500 druggable genes in KRASG12C/D-mutant PDAC cell lines. We identified multiple genes that were essential for PDAC cell growth and selected PRMT5, a protein arginine methyltransferase, to assess as a novel therapeutic target for pancreatic cancer. We found that suppression of PRMT5 activity using two distinct first-generation clinical candidate small molecule inhibitors (JNJ-64619178 and GSK3326595) demonstrated single agent activity and reduced PDAC cell growth. We further assessed a mechanistically distinct MTA-cooperative clinical candidate PRMT5 inhibitor, MRTX1719, that is selective for MTAP-deleted tumors, which occur in ~25% of PDAC patients. We determined that MRTX1719 exhibited low nanomolar GI50 activities in MTAP-deficient but not MTAP wild-type KRAS-mutant cell lines. Unexpectedly, PDAC cells treated with MRTX1719 exhibited a paradoxical activation of ERK, suggesting that combined inhibition of PRMT5 and KRAS might be therapeutically advantageous. In support of our hypothesis, we demonstrated that combination treatment with MRTX1719 and mutant selective KRAS inhibitors (G12Ci/MRTX849 and G12Di/MRTX1133) further sensitized KRASG12C/D-mutant PDAC cells to KRAS inhibition in short- and long-term growth assays as well as in vivo xenograft studies. Our ongoing studies are evaluating the consequences of co-targeting PRMT5 and KRAS on gene expression changes using RNA-Seq and cancer cell signaling pathways using RPPA analyses. In summary, our data support concurrent inhibition of PRMT5 and KRAS as a promising therapeutic strategy for MTAP-deficient KRAS-mutant pancreatic cancer.

Citation Format: Kristina Drizyte-Miller, Wen-Hsuan Chang, Andrew M. Waters, Clint A. Stalnecker, Junning Wang, Andrew J. Aguirre, Adrienne D. Cox, Channing J. Der. Combination of MTA-cooperative PRMT5 inhibitor and direct mutant-selective KRAS inhibitors as a novel therapeutic approach for MTAP-deficient pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4588.
Abstract 4611: The co-targeting of PLK1 and FoxM1 contributes to synergistic antitumor effects in PTC
Authors: Poyil Pratheeshkumar , Siraj Abdul K. , Padmaja Divya , Parvathareddy Sandeep Kumar , Thangavel Saravanan , Al-Sobhi Saif S. , Al-Dayel Fouad , Al-Kuraya Khawla S.
Published: March 2024

Polo-like Kinase 1 (PLK1) plays a key role in cell proliferation with vital regulatory functions in mitosis and cell survival. We investigated the expression of PLK1 protein in a large cohort of PTC patient’s samples and explored its functional role in PTC cell lines in vitro and in vivo. PLK1 overexpression was observed in 54% of all PTC and was significantly associated with aggressive clinico-pathological parameter and it was found to be independent prognostic marker for recurrence-free survival. PLK1 inhibition indeed inhibited cell proliferation and induced cell cycle arrest and apoptosis in PTC cell lines. Importantly, silencing of PLK1 decreases the self-renewal ability of spheroids generated from PTC cells. Immunoprecipitation analysis shows that PLK1 binds to FoxM1 and vice versa in vitro. Mechanistically, PLK1 knockdown suppresses FoxM1 expression, whereas inhibition of FoxM1 does not affect PLK1 expression, which suggests that PLK1 acts through the FoxM1 pathway. The combined inhibition of PLK1 with volasertib and FoxM1 with thiostrepton synergistically attenuated PTC cell growth in vitro and in vivo. Our findings suggest that co-targeting of PLK1 and FoxM1 could be a viable therapeutic strategy for treating patients with an aggressive subtype of PTC.

Citation Format: Pratheeshkumar Poyil, Abdul K. Siraj, Divya Padmaja, Sandeep Kumar Parvathareddy, Saravanan Thangavel, Saif S. Al-Sobhi, Fouad Al-Dayel, Khawla S. Al-Kuraya. The co-targeting of PLK1 and FoxM1 contributes to synergistic antitumor effects in PTC [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 4611.
Abstract 4650: RalBP1, a novel approach for ovarian cancer therapy
Authors: Singhal Sharad S. , Ramisetty Sravani , Mohanty Atish , Kulkarni Prakash , Horne David , Awasthi Sanjay , Salgia Ravi
Published: March 2024

Ovarian cancer (OC) is the most devastating gynecologic cancer. The ever-climbing incidence rate of OC makes it the most lethal female reproductive disorder. Triggering apoptosis is one of the potential strategies to overcome chemoresistance. Recent evidence suggests that the failure of drug-induced apoptosis may be an underlying cause of drug-resistance. Molecular mechanisms of failed apoptosis in chemoresistant OC cells include p53 mutations, abnormal expression of the Bcl2 family proteins, and upregulation of other inhibitors of apoptosis that block caspases and stabilize the mitochondrial permeability pore. RalBP1 (Ral-binding protein) is a required stress-defense protein for OC, and its specific depletion or inhibition will cause apoptosis in cancer cells expressing RalBP1. RalBP1 is a multifunctional 76 kDa protein encoded as a splice variant in the human RALBP1 gene (18p11.22). RalBP1 is an ATP dependent efflux transporter for glutathione (GSH) conjugates (GS-E) of products of oxidative stress, like 4HNE and GSH-conjugates of chemotherapy drugs. Our recent studies indicate that upon depletion/inhibition of RalBP1, malignant cells are significantly more sensitive to apoptosis than non-malignant cells, suggesting that the stress-protective, anti-apoptotic activity of RalBP1 is necessary for malignant cells. This differential sensitivity to RalBP1 translates into tumor regression, a lack of toxicity, and the prolonged survival of mice bearing subcutaneous OC cells in which RalBP1 is inhibited by anti-RalBP1 IgG or depleted using RalBP1 antisense oligonucleotides. These studies demonstrate that inhibition or depletion of RalBP1 exerts anti-neoplastic effects in OC and indicate that this GS-E and xenobiotic transporter occupies an important position in the hierarchy of stress defense mechanisms necessary for cancer cell survival. Overall, the present research focuses on hypothesis-driven studies to define novel relationships between RalBP1 and signaling pathways, and to determine the suitability of RalBP1 as an anticancer target for OC.

Citation Format: Sharad S. Singhal, Sravani Ramisetty, Atish Mohanty, Prakash Kulkarni, David Horne, Sanjay Awasthi, Ravi Salgia. RalBP1, a novel approach for ovarian cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4650.
Abstract 4660: Characterization of a nicotinamide-based kinase inhibitor HSN748 for inhibition of RET-driven tumors
Authors: Khatri Ujjwol , Dayal Neetu , Shen Tao , Hu Xueqing , Sintim Herman , Wu Jie
Published: March 2024

Rearranged during transfection (RET) is a protein tyrosine kinase that is aberrantly activated by gene fusions or mutations in many types of human cancer including thyroid cancer and non-small cell lung cancer (NSCLC). Selpercatinib (LOXO-292) and pralsetinib (BLU-667) are FDA approved RET-selective tyrosine kinase inhibitors (TKIs) being used to treat RET-altered cancer. However, these tumors develop selpercatinib/pralsetinib-resistance via acquisition of RET(G810C/R/S) mutations located at the solvent front of the ATP binding pocket. The overall goal of our research is to discover next-generation of RET kinase inhibitors to inhibit selpercatinib/pralsetinib-resistant RET solvent-front mutants. In this study, we characterized one of the nicotinamide-based RET kinase inhibitor, HSN748, in vitro and in vivo. HSN748 was able to inhibit selpercatinib/pralsetinib-resistant RET(G810C/R) solvent-front mutations. In BaF3/KIF5B-RET(G810C) tumor xenograft experiment, HSN748 treatment resulted in tumor regression. In immune competent transgenic mice, KIF5B-RET-induced lung tumors regressed after HSN748 treatment by oral gavage for one month (10-15 mg/kg, QD) without affecting body weight. These results identify HSN748 as an orally available RET inhibitor capable of inhibiting KIF5B-RET and its solvent-front mutant-driven tumors.

Citation Format: Ujjwol Khatri, Neetu Dayal, Tao Shen, Xueqing Hu, Herman Sintim, Jie Wu. Characterization of a nicotinamide-based kinase inhibitor HSN748 for inhibition of RET-driven tumors [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 4660.
Abstract 4662: High-throughput screening identifies potential combinatorial therapies to overcome lenvatinib resistance in liver cancer
Authors: Chau Kevin , McDermott Martina S. , Gong KeWei , Slamon Dennis J.
Published: March 2024

Liver cancer has seen an increase in mortality rate over recent decades due to limited targeted therapies and growth in specific etiologies. Lenvatinib, a multi-TKI inhibitor, is used as a first-line therapy for liver cancer patients who cannot receive immunotherapy, which is a component of the current standard of care. Unfortunately, lenvatinib efficacy is short. Understanding why liver cancers become resistant and identifying interventions to restore sensitivity can help prolong the clinical efficacy of lenvatinib. A panel of 20 liver cancer lines was screened to identify four lenvatinib-sensitive lines. These lines were subsequently conditioned to grow under increasing lenvatinib concentrations to generate lenvatinib-resistant (LR) models. One such model, Hep3B LR, exhibited a stable resistance to lenvatinib for up to 12 weeks in culture. Hep3B LR showed cross-resistance to selective inhibitors of FGFR4 and FGFR1 but not of MAPK14 and PDGFR, suggesting that the resistance phenotype may result from FGFR dysfunction. Unlike parental Hep3B, Hep3B LR exhibited a 3.4X increase in migration. Western blot detected an increase in pAKT, a survival marker. Additionally, proteins associated with cancer drug resistance were higher in Hep3B LR cells: Notch receptors and ligands, pStat3, and Axl. To identify means of overcoming lenvatinib resistance in Hep3B LR, a Cell-Titer Glo high-throughput assay was developed to measure the growth inhibition of candidate drugs in the presence and absence of lenvatinib. Preliminary results from the first 24 drugs screened reproduced known drug sensitivities associated with lenvatinib resistance (i.e., MEK/ERK, EGFR, GPX4 inhibition) but also identified novel sensitivities to inhibition of PKMYT1 or γ-secretase, the latter a cleavage enzyme involved in Notch signaling activation. Validation of these candidate hits using a grid-based titration of both drugs showed additive growth inhibition of lenvatinib in combination with ERK, EGFR, or GPX4 inhibitors but not with PKMYT1 or γ-secretase inhibitors in resistant cells. Interestingly, EGFRi and lenvatinib were substantially synergistic in parental cells, suggesting that an upfront combination of these inhibitors could potentially be used before the emergence of lenvatinib resistance in liver cancer. We have established a lenvatinib-resistant liver cancer cell model and validated a drug screening assay to identify potential combinatorial therapies to overcome lenvatinib resistance in liver cancer.

Citation Format: Kevin Chau, Martina S. McDermott, KeWei Gong, Dennis J. Slamon. High-throughput screening identifies potential combinatorial therapies to overcome lenvatinib resistance in liver 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 4662.
Abstract 4667: HDAC9 as a potential regulator of lenvatinib resistance in hepatocellular carcinoma
Authors: Xie Yunong , Zhang Minghe , Liu Yan , Liu Linglin , Cheng Alfred Sze-Lok , Ma Stephanie , Tong Man
Published: March 2024

Lenvatinib is used as the first-line therapy for advanced hepatocellular carcinoma (HCC) patients. However, poor response and compromised therapeutic effect with prolonged treatment are frequently observed in HCC patients. To elucidate the underlying mechanisms, lenvatinib responsive and non-responsive stages were modeled in liver tumor-bearing immunocompetent mice which were divided into lenvatinib and vehicle control treatment groups. Tumor tissues after short and prolonged lenvatinib treatment were harvested for single-cell RNA sequencing. Results from single-cell RNA sequencing revealed heterogenous tumor cell sub-populations associated with tumor differentiation and identified an upregulated expression of class IIa histone acetylase HDAC9 in lenvatinib-treated tumor at the non-responsive stage. Upregulation of HDAC9 was similarly observed in lenvatinib-resistant human patient-derived xenograft (PDX). Functional studies suggested that suppressing HDAC9 could re-sensitize lenvatinib response in both in vitro and in vivo models. In sum, we identified a potential regulator of lenvatinib treatment response in HCC.

Citation Format: Yunong Xie, Minghe Zhang, Yan Liu, Linglin Liu, Alfred Sze-Lok Cheng, Stephanie Ma, Man Tong. HDAC9 as a potential regulator of lenvatinib resistance in hepatocellular carcinoma [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 4667.
Abstract 4671: Efficacy and mechanism of mebendazole for ovarian cancer therapy
Authors: Rai Rajani , Penta Dhanamjai , Dey Debasish , Benbrook Doris M , Wang Lin , Bieniasz Magdalena , Dockery Lauren E
Published: March 2024

Introduction: Ovarian cancer (OvCa) is the most lethal gynecological malignancy. Although most OvCa patients initially respond to frontline platinum-based therapies with approximately 80% of patients experiencing remission, approximately 75% of those women experience a recurrence with only approximately 50% of patients alive 5 years following diagnosis. There is a critical need to develop novel therapeutic agents or methods to overcome chemoresistance and toxicities experienced with conventional chemotherapy regimens used for OvCa patients. Repurposing drugs is a promising strategy to safely and more rapidly evaluate potentially effective treatment regimens. Over the past two decades, Mebendazole (MBZ), an anti-parasitic drug, has gained much attention in oncology due to its favorable biosafety profile and potent anti-cancerous activity seen in several human malignancies. Therefore, we examined the efficiency and mechanism of MBZ against OvCa.

Methods: The in vitro efficacy of MBZ was evaluated in cisplatin-resistant (CPR) and parent (WT/sensitive) OVCAR-8 cell lines as well as in ascites samples collected from chemo-resistant OvCa patients by using 2D and/or 3D cell viability assay and invasion assay. The in vivo efficacy of MBZ was assessed in orthotopic animal models, utilizing CPR-OVCAR8 spheroids, and patient-derived xenograft (PDX) animal models with specimens from chemo-resistant ovarian cancer patients. Molecular mechanisms were investigated through western blot and immunofluorescence analysis.

Result: Our results confirmed that MBZ efficiently decreased cell viability, spheroid size, and the invasion ability of OvCa cell lines and ascites samples. OvCa cells treated with MBZ demonstrated downregulation of proliferation markers and upregulation of apoptosis markers indicating inhibition of cell proliferation and induction of apoptosis. Mechanistically, MBZ inhibited the Wnt/β-catenin signaling pathway by downregulating the expression and nuclear localization of β-catenin and epithelial-mesenchymal transition (EMT) markers. Preclinical studies showed that MBZ at 50 mg/kg/day dose for 28 days significantly reduced tumor growth in PDXs and orthotopic tumor models without any evidence of toxicity.

Conclusion: Collectively, our study strongly supports the therapeutic potential of MBZ against OvCa particularly, which warrants further clinical studies.

Citation Format: Rajani Rai, Dhanamjai Penta, Debasish Dey, Doris M Benbrook, Lin Wang, Magdalena Bieniasz, Lauren E Dockery. Efficacy and mechanism of mebendazole for ovarian cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4671.
Abstract 4775: Unveiling caveolin-1's crucial role in breast cancer progression and metastasis: A molecular perspective
Authors: Begum Rizwana , Thota Shilpa , Singh Dhirendra Pratap , Chintala Naveen , Pandit Abhishek , Sapkota Biplov , Francis Joseph
Published: March 2024

Background: Breast cancer, particularly its metastatic form, constitutes a significant portion of oncological mortality. Caveolin-1 (Cav-1), a caveolae structural protein, has been implicated in cellular processes such as proliferation, apoptosis, autophagy, and cellular motility (aberrant in breast cancer). With its dual role as a tumor suppressor and promoter, Cav-1's function in breast cancer pathophysiology requires elucidation for potential therapeutic targeting.

Methods: We utilized a syngeneic mouse model to engineer Cav-1 deficient 4T1 murine mammary carcinoma cells which mirror the characteristics of stage IV breast cancer to investigate Cav-1's role in tumor growth and metastasis. We assessed cellular proliferation and lung metastasis, compared with wild-type controls, and performed molecular analyses to evaluate epithelial and mesenchymal marker expression, stemness-related markers, and autophagy-related gene expression.

Results: Cav-1 ablation corresponded with a marked decrease in tumor proliferation and lung metastasis, indicating a suppressive role in tumor progression. Molecular characterization revealed downregulated epithelial markers (E-cadherin, β-catenin), transcription factors (TWIST1/2), and stem cell markers (NANOG, OCT4, SOX2, c-MYC, SALL4), with concurrent upregulation of the mesenchymal marker vimentin. Enhanced expression of autophagy-related genes (Beclin-1, ATG5, ATG16) was also observed, suggesting a disruption in autophagic pathways.

Conclusion: Our findings underscore the critical role of Cav-1 in breast cancer progression, specifically its function in suppressing metastasis and modulating cellular phenotypes. Targeting Cav-1 could represent a novel therapeutic strategy to mitigate breast cancer growth and dissemination. Further research is warranted to explore the therapeutic potential of modulating Cav-1 in breast cancer treatment.

Citation Format: Rizwana Begum, Shilpa Thota, Dhirendra Pratap Singh, Naveen Chintala, Abhishek Pandit, Biplov Sapkota, Joseph Francis. Unveiling caveolin-1's crucial role in breast cancer progression and metastasis: A molecular perspective [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 4775.
Abstract 4788: Noninvasive longitudinal monitoring of residual disease in chemotherapy-treated colorectal cancer patients
Authors: Tang Alison D. , Gupte Rebecca , Cheung Victoria , Qing Tao , Cauwels Austin , Leff Emily , Walter Kimberly , Tabari Ehsan , Lovejoy Alex , Lin Jimmy C.
Published: March 2024

Noninvasive monitoring of cancer shows great promise in assessing therapy response and improving patient outcomes. Recently, various groups have developed methods that detect circulating tumor DNA (ctDNA) in the plasma to measure minimal or molecular residual disease (MRD). Aberrant DNA methylation patterns are a hallmark of cancers, and robust signals can be detected by sensitive ctDNA assays. Here, we present a methylation-based approach for longitudinal monitoring of tumor burden that is tumor-naive, i.e., with no reliance on prior characterization of tumor molecular characteristics. We assess the effectiveness of our approach in a cohort of colorectal cancer (CRC) patients receiving chemotherapy with or without additional targeted agents.

Longitudinal blood samples were collected from patients (n = 57) while on therapy, which averaged 4.9 months, for a total of 239 sample collection time points (median per patient = 5). Based on RECIST status, 16 patients were classified as complete responders (CR) at the end of treatment.

We generated plasma cell free DNA-derived libraries for methylation sequencing targeting regions relevant to CRC. Next, we computed a disease burden score for each sample and related these scores to clinical response (CR vs. non-CR). We trained a classifier on an independent cohort of CRC and healthy donor plasma cfDNA samples, and used this classifier to check for residual disease at the end of treatment for each of our 57 patients. The classifier detected residual disease in only 3/16 CRs (19%) but 35/41 non-CRs (85%).

Two of the non-CR patients were initially assessed as CRs at earlier time points. In both cases, our method successfully detected residual disease at or prior to the CR assessment and consistently showed residual disease in all follow up samples. This suggests improved sensitivity relative to RECIST and highlights the potential of using noninvasive blood tests for continuous monitoring of CRC patients receiving therapy.

Citation Format: Alison D. Tang, Rebecca Gupte, Victoria Cheung, Tao Qing, Austin Cauwels, Emily Leff, Kimberly Walter, Ehsan Tabari, Alex Lovejoy, Jimmy C. Lin. Noninvasive longitudinal monitoring of residual disease in chemotherapy-treated colorectal cancer patients [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 4788.
Abstract 4850: Sex differences in cancer incidence: Prospective analyses in the UK Biobank
Authors: Khan Maira , Papier Keren , Pirie Kirstin , Atkins Joshua , Key Tim , Travis Ruth
Published: March 2024

Background: Exploring the underlying sex differences in cancer incidence and the potential reasons for the differences may provide insights into cancer aetiology. We aimed to examine the differences in incidence of cancer between men and women in the UK Biobank and to assess the extent to which any disparities persisted after accounting of established risk factors for those cancers.

Methods: Prospective analyses were performed in the UK Biobank to examine associations between sex and risk of 15 cancers (and 13 subtypes) common to both sexes using minimal and multivariable-adjusted Cox proportional hazards regression models.

Results: Over an average of 10.5 (SD 2.2) years of follow-up, 46,081 incident cancers were identified in 470,771 individuals (aged 37 to 73 years at recruitment); 24,634 cancers (53.5%) diagnosed in women and 21,447 (46.5%) in men. While some differences in cancer risk between the sexes were attenuated in the comprehensively multivariable-adjusted models, men compared to women remained at greater risk of cancers at eight sites. Compared to women, men had higher risks of oesophageal adenocarcinoma (hazard ratio 5.45; 95% confidence interval, 4.17-7.12), gastric cardia (3.65; 2.48-5.38), bladder (3.47; 2.85-4.24), oral (2.06; 1.69-2.51), liver (1.91; 1.48-2.47), kidney (1.77; 1.51-2.09), rectum (1.7; 1.47-1.96), and leukaemia (1.43; 1.21-1.69); while women had higher risks of cancers of the breast, thyroid (0.36; 0.26-0.49), anus (0.41; 0.26-0.64), gallbladder (0.56; 0.31-0.99), and lung adenocarcinoma (0.72; 0.62-0.84).

Conclusion: Further studies of unexplained sex differences may provide insights into cancer aetiology.

Citation Format: Maira Khan, Keren Papier, Kirstin Pirie, Joshua Atkins, Tim Key, Ruth Travis. Sex differences in cancer incidence: Prospective analyses in the UK Biobank [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 4850.
Abstract 4878: Enhancing non-invasive detection of urothelial carcinoma through combined cytology and methylation profiling of urinary cell-free DNA
Authors: Zhao Huan , Dong Hang , Tang Haoran , Zhang Zhihui , Wei Na , Xu Jingjing , Du Pan , Jia Shidong , Xiao Ting , Guo Huiqin
Published: March 2024

Detection of urothelial carcinoma (UC) faces a significant challenge in sensitivity due to the limitations of existing methodologies such as cytology. Identifying tumors through epigenetics pattern presents a promising advancement in diagnostic precision. This study aims to explore a non-invasive and more sensitive strategy by analyzing urinary cell-free DNA (ucfDNA) methylation profiles in conjunction with traditional urine cytology. The cohort for this study were collected from 20 patients with UC and 17 patients with benign or non-tumor lesions which histopathologic and cytopathologic results were reviewed by pathologist. Additional 16 cancer samples and 40 healthy donor samples were collected from independent research centers. We employed PredicineEPIC, a comprehensive whole-genome methylation assay, to investigate the DNA methylation characteristics in urine samples. The dataset was splited into 1:2 proportions for modeling and validation. The methylation signals were fed to three machine learning algorithms for determining the most effective classification model. Differentiating cancer and benign samples through urinary cytology has high specificity (1.0) but low sensitivity (0.3). Then we examined differentially methylated regions and implemented four most abnormally methylated regions as classify features. We found that the Gradient Boosting Machine (GBM) model achieved optimal performance in the validation set, with an AUC of 0.93, sensitivity of 0.81 (21/26), and specificity of 1.0 (36/36). The combination of methylation- and urine cytology-based models raised 2% prediction accuracy without reducing precision, suggesting that this assay could be applied to augment the cytology testing for UC detection. This study proposes a new and promising approach, leveraging cytology combined with epigenetic profiles of urinary cell-free DNA, for the precise diagnosis of urothelial carcinoma.

Citation Format: Huan Zhao, Hang Dong, Haoran Tang, Zhihui Zhang, Na Wei, Jingjing Xu, Pan Du, Shidong Jia, Ting Xiao, Huiqin Guo. Enhancing non-invasive detection of urothelial carcinoma through combined cytology and methylation profiling of urinary cell-free DNA [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 4878.
Abstract 4943: Benchmarking unpaired single-cell RNA and single-cell ATAC integration
Authors: Chen Jiani , Xiao Wanzi , Zhang Eric , Chen Xiang
Published: March 2024

The integration of single-cell RNA-sequencing (scRNA-seq) and single-cell ATAC-sequencing (scATAC-seq) data offers a unique opportunity to gain a comprehensive view of cellular identity with defining features and to infer gene-regulatory relationships. Despite the emergence of technologies that simultaneously capture both the gene expression and chromatin accessibility of individual cells (paired data), the practical challenges of these approaches (e.g., the unavailability in previous samples and prohibitive cost) have led researchers to turn to the existing trove of single-modality data generated from independent biological samples (unpaired data). Various computational tools have been developed to integrate these unpaired single modality datasets. However, the comparative performance of these tools has not been comprehensively evaluated, and a standard benchmark pipeline is still lacking. To address these challenges, we used pseudo-unpaired scRNA-seq and scATAC-seq data derived from publicly available paired single-cell multi-omics datasets to benchmark 14 publicly available integration methods. The primary goal of unpaired single-cell multi-omics integration is to narrow the omics gap while preserving cell type diversity. We therefore focused on pair-wise cell distance and cluster performance in the joint latent space constructed by various integration tools in our benchmarking pipeline. To ensure the robustness of these computational approaches, we examined their stability across a variety of scenarios, including variations in cell number, cell types, and biological and technical batch effects. A number of the integration methods tested produced promising results. While the widely used Seurat package was recently reported to have the best performance (Lee et al., Genome Biology 2023), other computational tools such as scVI, Cobolt, scJoint, scglue and scBridge performed equally well or better in reducing omics differences and facilitating the identification of cell clusters. Notably, scglue and Cobolt demonstrated strong performance in aligning the same cell from different modalities, and discrete clusters emerged in the joint latent space using scJoint and scBridge. These findings suggest that it may not be strictly necessary to use paired multi-omics data to guide integration to achieve favorable results. Our freely available benchmarking pipeline will empower researchers to identify the optimal data integration methods for their specific data, facilitate the benchmarking of new methods, and contribute to future method development in the field.

Citation Format: Jiani Chen, Wanzi Xiao, Eric Zhang, Xiang Chen. Benchmarking unpaired single-cell RNA and single-cell ATAC integration [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 4943.
Abstract 4977: The prevalence of key oncogenic driver mutations in stage I-III non-small cell lung cancer: Results from the AACR GENIE BPC dataset
Authors: Zu Ke , Ma Jiemin , Chen Cai , Pierce Christine
Published: March 2024

Background: While there is growing interest in targeted therapy for non-small cell lung cancer (NSCLC) in perioperative settings, data on key oncogenic driver mutations is limited in early-stage NSCLC. This real-world database study aims to evaluate the prevalence of select genomic alterations in stage I-III NSCLC.

Methods: From the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) V2.1-consortium dataset, we included adult patients with a confirmed diagnosis of NSCLC who had genomic testing using stage I-III NSCLC tissue samples. Descriptive statistics were used to summarize baseline characteristics and the prevalence of select genomic alterations.

Results: A total of 465 patients were included in this study, of whom 61% were female, 85% were white, 19% were never smokers, and 77% had adenocarcinoma. Less than 2% of the study population had BRAF V600E, HER2 activating mutations, HER2 amplification, MET amplification, HER3 amplification, RET fusion, ALK fusion, or ROS1 fusion. Among genomic alterations with a prevalence of 2% or higher, such as EGFR sensitizing mutations, KRAS G12C, MET exon 14 skipping, STK11, KEAP1, and TP53, some variations in prevalence were observed across baseline patient and disease characteristics such as race, smoking status, and histology (Table 1).

Conclusion: The prevalence of key oncogenic drivers and its relationship to select baseline disease characteristics among patients with early-stage NSCLC are similar to those of advanced NSCLC observed in other real-world clinico-genomic databases.

Table 1. Prevalence of Select Genomic Alterations in Stage I-III NSCLC (N=465) Prevalence of Positive Biomarker Status (%) EGFR KRAS G12C MET Exon 14 Skipping STK11* KEAP1* TP53 Overall 17.6 12.7 4.5 16.0 11.0 52.7 Gender Male 7.1 9.3 5.5 18.5 18.5 59.6 Female 24.5 15.9 3.9 14.3 6.3 48.2 Race White 15.6 14.1 4.5 16.5 12.0 53.7 Black 15.0 5.0 5.0 22.2 11.1 60.0 Asian 44.0 4.0 8.0 8.3 4.2 44.0 Smoking Status Never smoker 41.4 1.2 6.9 4.7 1.2 36.8 Former smoker 13.7 16.0 4.6 17.4 12.9 52.4 Current smoker 5.7 12.9 1.4 23.9 15.4 72.9 Histology Adenocarcinoma 20.1 14.3 4.6 18.1 10.4 46.0 Squamous cell carcinoma 0 2.9 4.4 4.6 14.1 86.8 *The numbers of patients tested for STK11 and KEAP1 were 457 and 445, respectively.

Citation Format: Ke Zu, Jiemin Ma, Cai Chen, Christine Pierce. The prevalence of key oncogenic driver mutations in stage I-III non-small cell lung cancer: Results from the AACR GENIE BPC dataset [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 4977.
Abstract 4979: Genomic profiling of early-onset metastatic colorectal cancer based on tumor sample location
Authors: Ozer Muhammet , Goksu Suleyman Y. , Goksu Busra Bacik , Sanford Nina N. , Jones Amy , Verma Nilesh , Kazmi Syed
Published: March 2024

Background: Here, we describe analyses towards identifying and comparing genetic variations between the primary and metastatic sites in early-onset metastatic colorectal cancer patients.

Methods: We selected patients with early-onset metastatic colorectal cancer (under 50 years old) using data from the American Association for Cancer Research Project GENIE (version 14.1). We used the Fisher exact test to compare genetic mutations between the primary tumor and metastatic sites, complemented by the Benjamini-Hochberg adjustment method.

Results: In a total of 1,791 patients with early-onset metastatic colorectal cancer, 27.1% had tumor samples from metastatic sites, while the majority, 72.9%, were from the primary tumor location. The most common mutations found were in the TP53 gene (77.6%), followed by APC (76.0%), KRAS (42.4%), and PIK3CA (19.0%). Notably, the metastatic samples had a significantly higher occurrence of SMAD4 mutations compared to their primary site counterparts (20.8% vs. 14.0%, p<0.001, q<0.001). Conversely, the primary tumor samples exhibited higher frequencies of TCF7L2 and ARID1A mutations (16.9% vs. 10.6%, p<0.001, q<0.001, and 13.0% vs. 6.4%, p<0.001, q<0.001, respectively).

Conclusion: Determining the specific genes responsible for the formation of metastatic tumors is crucial for a deeper understanding of the disease's underlying biology in early-onset metastatic colorectal cancer. Such genomic details are crucial to pave the way to the discovery of potential biomarkers for diagnosis and the development of new cancer therapeutics.

Citation Format: Muhammet Ozer, Suleyman Y. Goksu, Busra Bacik Goksu, Nina N. Sanford, Amy Jones, Nilesh Verma, Syed Kazmi. Genomic profiling of early-onset metastatic colorectal cancer based on tumor sample location [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 4979.
Abstract 5000: Low dose ionizing radiation elicits the extrusion of neutrophil extracellular traps
Authors: Teijeira Alvaro , Martinez-Riaño Ana , Pinci Beatrice , Manzanal Almudena , Molero Paula , Ruiz Maria E. Rodriguez- , Melero Ignacio
Published: March 2024

The majority of cancer patients undergo radiotherapy interventions at some point in their clinical management with unintended irradiation of blood vessels. We show that very low γ-irradiation doses (0.5-1 Gy) of human and mouse neutrophils elicit neutrophil extracellular trap (NET) formation in a manner dependent on oxidative stress, NADPH oxidase activity and autocrine interleukin-8. Radiation-induced NETs interfere with NK- and T-cell cytotoxicity-repelling effector lymphocytes away from tumor cells. As a consequence, pre-injection of irradiation-induced NETs increases the number of successful metastases in mouse tumor models. Increases in circulating NETs are readily detected in series of patients following radiotherapy interventions. Our results reveal new mechanisms whose knowledge may help to improve the efficacy and safety of radiotherapy, especially when used in combination with immunotherapy approaches.

Citation Format: Alvaro Teijeira, Ana Martinez-Riaño, Beatrice Pinci, Almudena Manzanal, Paula Molero, Maria E. Rodriguez- Ruiz, Ignacio Melero. Low dose ionizing radiation elicits the extrusion of neutrophil extracellular traps [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 5000.
Abstract 5029: VAF in ctDNA correlated with advanced breast cancer tumor burden and prognosis
Authors: Zhong Jianxin , Li Huiping , Shao Bin , Jiang Hanfang , Liu Xiaoran , Tang Haoran , Jia Shidong
Published: March 2024

Purpose: In patients with first-line advanced breast cancer (ABC), the correlation between ctDNA variant allele frequency (VAF) and tumor disease burden, and its prognostic value remains poorly investigated.

Methods: This study included patients with ABC diagnosed at Peking University Cancer Hospital who performed ctDNA test before receiving first-line treatment. Baseline plasma samples were collected for assessing ctDNA alterations and VAF with next-generation sequencing. The sum of tumor target lesion diameters (SLD) was measured with imaging methods according to RECIST 1.1 criteria.

Results: The final cohort included 184 patients. The median age of the cohort was 49.4 (IQR: 42.3-56.8) years. The median VAF was 15.6% (IQR: 5.4%-33.7%). VAF showed positive correlation with SLD in patients with relatively large tumor lesions (r = 0.314, p = 0.003), but not in patients with small tumor lesion (p = 0.226). VAF was associated with multiple metastasis sites (p = 0.001). Multivariate Cox regression analysis showed that high VAF was associated with shorter overall survival (OS) (HR: 3.519, 95% confidence interval (CI): 2.149-5.761), and first-line progression-free survival (PFS) (HR: 2.352, 95%CI: 1.462-3.782).

Conclusion: ctDNA VAF associated with tumor disease burden, and was a prognostic factor for patients with ABC. A combination of ctDNA test and radiographic imaging might enhance tumor burden evaluation, and improve prognosis stratification in patients with ABC.

Citation Format: Jianxin Zhong, Huiping Li, Bin Shao, Hanfang Jiang, Xiaoran Liu, Haoran Tang, Shidong Jia. VAF in ctDNA correlated with advanced breast cancer tumor burden and prognosis [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 5029.
Abstract 5047: Identifying genomic features associated with pathologic lymph node metastasis in lung adenocarcinoma patients
Authors: Wang Shijie , Zhou Zhiwei , Wang Song , Guo Rongyun , Ma Zeming , Zhao Dachuan , Wang Liang , Liu Yinan , Ma Yuanyuan , Zhang Jianzhi , Wang Sha , Chen Yedan , Tang Haimeng , Ou Qiuxiang , Chen Jinfeng
Published: March 2024

Introduction: Lymph node metastasis evaluation in solid tumors is mainly complicated by the diagnostic yield of standard imaging modalities and tumor size contradictions. Exploring clinical/molecular features that complement the use of radiologic and bronchoscopy findings may provide significant values for a more accurate pathologic determination of nodal metastasis.

Methods: We analyzed surgery-resected tumor samples from 72 treatment-naïve lung adenocarcinoma (LUAD) patients via whole-exome sequencing (WES). Mutational profiles of patients categorized based on their pathologic lymph node metastasis (pN) status were assessed, and the association between metastatic-driving features and overall survival (OS) was then explored in both the study cohort and the Cancer Genome Atlas Program (TCGA) external cohort.

Results: Among all 72 patients, 41 (56.9%) were pathologically confirmed as positive for lymph node metastasis (pN-positive), while 31 (43.1%) were categorized as pN-negative. The most frequently mutated gene was TP53 in both subgroups (54.8% and 53.7%, respectively), and the aberrant KEAP1-NRF2 signaling pathway was found significantly more enriched in pN-negative patients. Copy-number variant analysis showed that chromosome 7p amplifications (X7p_amp) at the arm level and EGFR amplifications at the focal gene level were more frequently identified in pN-positive patients (P=0.008 and P=0.004, respectively). Importantly, these amplifications were associated with worse OS in both the study cohort and the TCGA external dataset. Consistent with the unfavorable prognosis, pN-positive patients demonstrated a higher chromosome instability score (CIS) (median: 0.32 vs. 0.14, P=0.14) and a lower tumor mutation burden (TMB) (median: 1.83 vs. 3.85 muts/Mb, P=0.048) compared to pN-negative patients.

Conclusion: Our findings suggest that X7p_amp, particularly EGFR amplification, might be associated with pathologic involvement of lymph nodes and an unfavorable prognosis in LUAD patients. Our study highlights the importance of integrating clinical and genomic data into conventional radiologic modalities for a more accurate determination of pathologic nodal involvement.

Citation Format: Shijie Wang, Zhiwei Zhou, Song Wang, Rongyun Guo, Zeming Ma, Dachuan Zhao, Liang Wang, Yinan Liu, Yuanyuan Ma, Jianzhi Zhang, Sha Wang, Yedan Chen, Haimeng Tang, Qiuxiang Ou, Jinfeng Chen. Identifying genomic features associated with pathologic lymph node metastasis in lung adenocarcinoma patients [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 5047.
Abstract 5079: Comparative studies of chemotherapy and immuno-oncology combinations in multiple mouse syngeneic tumor models
Authors: Park Eunsil , Hinton Marlene , Cai Mingmei , Gil Malgorzata A. , Hebert Gustave , Cui Long , Linn Doug , Long Brian J. , Barry Evan R.
Published: March 2024

The development of immune checkpoint inhibitors (ICIs) and combinations of immuno-oncology therapies with standard-of-care (SoC) chemotherapeutic agents has shifted therapeutic paradigms for patients with multiple cancer indications. For many patients, these combinations have shown a beneficial effect on clinical outcomes and disease management. However, additional combination therapies are still needed. Preclinically, a comparison of responses from SoC chemotherapies and ICI combinations in multiple disease models may be helpful in identifying optimal treatment combinations in the clinic. Here we report the results of multiple SoC/ICI in vivo combination efficacy studies in a large panel of mouse syngeneic models spanning seven tissue origins: 1) Colon: CT26, MC38; 2) Breast: EMT6, 4T1; 3) Kidney: Renca; 4) Bladder: MB49, MBT2; 5) Skin: B16F10, CM3; 6) Lung: TC1, LL/2, M109; 7) Brain: GL261. The advantage of using syngeneic models is not limited to the rapid and reproducible tumor growth, but importantly that the animals also have an intact immune system and clinically relevant tumor microenvironment, which are required for ICI combination studies. We tested > 10 chemo SoC combinations with a murinized anti-PD-1 antibody (DX400) in 14 syngeneic mouse models. We found that multiple SoC regimens combined well with DX400 treatment, including FOLFIRI, FOLFOX (colon), Carboplatin/Paclitaxel, Carboplatin/Pemetrexed (lung), Capecitabine/Docetaxel, Cisplatin/Gemcitabine (bladder), Cisplatin/5-FU/or capecitabine, and Oxaliplatin/5-FU/or capecitabine (gastric). Specifically, we observed that the SOC/ICI combinations resulted in enhanced antitumor activities compared to single-agent treatments in many of the models. These data, particularly specific SoC combination regimens that combine well with ICIs in each disease, are useful for optimizing promising combination approaches for clinical development and will be presented here.

Citation Format: Eunsil Park, Marlene Hinton, Mingmei Cai, Malgorzata A. Gil, Gustave Hebert, Long Cui, Doug Linn, Brian J. Long, Evan R. Barry. Comparative studies of chemotherapy and immuno-oncology combinations in multiple mouse syngeneic tumor models [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 5079.