bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6160: Targeting RNA N6-methyladenosine methyltransferase, METTL3 activates p53 and apoptosis pathways in osteosarcoma cells
Authors: Shin Seungjae , Oh Yumi , Yang Yoojin , Cho Sung-Yup
Published: April 2023

Osteosarcoma (OS) is a malignant tumor which is mesenchymal origin from bone stroma. The 5-year overall survival of localized OS is approximately 70%, however patients who have metastasis to other organs, mostly lung, have a poor 5-year survival rate, approximately 20%. Recently, oncogenic role of Methyltransferase-like 3 (METTL3), which is the only catalytic subunit of RNA N6-Methyladenosine methyltransferase complex, has been suggested, but its mechanism in OS is still unclear. To elucidate the roles of METTL3 in OS, we generated METTL3 knock-out U2OS osteosarcoma cell lines by CRISPR knock-out system. Knock-out of METTL3 decreased cell proliferation on U2OS cells, which was assessed by WST-1 assay and manual cell counting assay. Also, RNA-sequencing was conducted in METTL3 wild type and knock-out cell lines. Gene set enrichment analysis (GSEA) revealed that gene sets of ‘Programmed cell death’ in gene ontology (GO) category, ‘p53 pathway’ and ‘Apoptosis’ in HALLMARK gene sets, and ‘p53 signaling pathway’ and ‘Apoptosis’ in KEGG pathway were enriched in METTL3 knock-out cells. To validate the result of GSEA in our METTL3 knock-out cells, mRNA and protein levels of GADD45A and CDKN1A, which are downstream targets of p53, and BAX and BAK, which are apoptosis-related molecules induced by p53, were detected by real-time PCR and western blot, respectively, and these genes were upregulated in METTL3 knock out cell lines. Collectively, these results suggest that inhibition of METTL3 is potential therapeutic targets against OS by activating p53 and apoptosis pathways.

Citation Format: Seungjae Shin, Yumi Oh, Yoojin Yang, Sung-Yup Cho. Targeting RNA N6-methyladenosine methyltransferase, METTL3 activates p53 and apoptosis pathways in osteosarcoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6160.
Abstract 6174: ATX-101, a peptide drug targeting PCNA, enhances the effect of gemcitabine in liposarcoma and leiomyosarcoma
Authors: Musi Elgilda , Sheikh Tahir , Ingham Matthew , Bose Sminu , Schwartz Gary K.
Published: April 2023

Soft tissue sarcomas are heterogeneous mesenchymal neoplasms and account for 1% of all cancers in adults. Over 50 sarcomas subtypes have been classified and many have very limited treatment options which include surgery, chemotherapy and radiation. Two of the most common sarcomas are liposarcoma and leiomyosarcoma which are often treated with chemotherapies such as doxorubicin, dacarbazine and gemcitabine with low response rates. There is now more than ever an urgent need for new therapies for sarcoma. PCNA (Proliferating Cell Nuclear Antigen) is considered to be a key regulator of DNA and cell cycle control. In addition, it has been implicated to have roles in metabolism, cellular signaling and some immunological functions. PCNA forms complexes with proteins bearing a novel PCNA-interacting Peptide Motif called APIM (AlkB homolog 2 PCNA Interacting Motif). This binding usually occurs during stress responses such as those achieved during cancer therapy or cancer development. By preventing stress proteins from repairing or defending themselves, cancer therapies can be made more effective. We examined the in vitro effects of ATX-101, a PCNA-APIM protein interaction blocking peptide, on liposarcoma cell lines LS141, DDLS, SW872, 93T449 and 94T778 and leiomyosarcoma cell lines SK-LMS, SK-UT1 and SK-UT-1B. Cell survival, as measured by cell proliferation assays, indicated IC50s of 7.5-15µM with ATX-101. Enhanced combination effects with ATX-101 and chemotherapies such as doxorubicin, irinotecan and gemcitabine were also observed by proliferation assay. Synergism, with ATX-101 and gemcitabine, was indicated with SynergyFinder analysis. Cell cycle changes exhibited increases of S and G2 phases when treated with ATX-101 and gemcitabine. This correlated with increase of cell cycle proteins, cyclin B1 and cyclin A2. Western blot observations included increase of apoptotic marker, cleaved caspase 3, and DNA damage marker, pH2A.X. In addition, immunofluorescence assay showed increasing pH2A.X with ATX-101 and gemcitabine. In vivo studies revealed ATX-101 enhanced gemcitabine decrease of tumor volume in leiomyosarcoma cell line xenograft, SK-UT1. Tumor target inhibition by western blot showed increased pH2A.X and cleaved PARP along with decreased RAD51 API protein with combination treatment. Taken these observations and results, there is strong evidence of combining gemcitabine with ATX-101 in liposarcoma and leiomyosarcoma.

Citation Format: Elgilda Musi, Tahir Sheikh, Matthew Ingham, Sminu Bose, Gary K. Schwartz. ATX-101, a peptide drug targeting PCNA, enhances the effect of gemcitabine in liposarcoma and leiomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6174.
Abstract 6216: Pre-ribosomal RNA mediates HR repair via the BRCA1/BARD1 complex
Authors: Wu Duo , Huang Huang , Chen Tenglong , Gai Xiaochen , Liu Song , He Hu , Shi Song , Yu Xiaochun
Published: April 2023

The BRCA1/BARD1 complex plays a key role in DNA double-stand break (DSB) repair in both somatic cells and germ cells. However, the underlying molecular mechanism by which this complex mediates DSB repair remains elusive. Here, we show that the recruitment of the BRCA1/BARD1 complex to the unsynapsed axis of the XY body in male germ cells is mediated by pre-rRNA. Similarly, the BRCA1/BARD1 complex associates with pre-rRNA in somatic cells, which targets the BRCA1/BARD1 complex to DSBs. The interactions between the BRCT domains of the BRCA1/BARD1 complex and pre-rRNA induces liquid-liquid phase separations, which may be the molecular basis of DSB-induced nuclear foci formation of the BRCA1/BARD1 complex. Pre-rRNA also mediates BRCA1-dependent homologous recombination (HR). Cancer-associated mutations in the BRCT domains of BRCA1 and BARD1 abolish the interaction with pre-rRNA. We developed novel RNA pol I inhibitors to suppress pre-rRNA biogenesis, which not only abolished HR repair but also sensitized tumor cells to PARP inhibitor treatment. Collectively, this study reveals that pre-rRNA is a functional partner of the BRCA1/BARD1 complex in the DSB repair. It is also a potential therapeutic target for cancer therapy.

Citation Format: Duo Wu, Huang Huang, Tenglong Chen, Xiaochen Gai, Song Liu, Hu He, Song Shi, Xiaochun Yu. Pre-ribosomal RNA mediates HR repair via the BRCA1/BARD1 complex. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6216.
Abstract 624: The role of draining lymph nodes in the post-transplant recurrence of liver cancer: Examining immune response using spatial proteomics
Authors: Hickman Peyton , Thompson Aubrey E. , Nguyen Justin
Published: April 2023

Hepatocellular Carcinoma (HCC) and Cholangiocarcinoma (CCA) are the predominant forms of liver cancer, with a devastating combined incidence of 40,000 cases per year in the United States. Despite many differences between the cancers, liver transplant has found great success in treating both over traditional methods. However, up to 35% of patients’ cancer still recur within five years. Given the risk and resource intensiveness of this treatment, it is critical to identify factors that influence recurrence in these cancers. Previous studies have found the micro-environments of HCC tumors tend to be immune-active while those of CCA tumors tend to be immunosuppressive. Increased immune activity at the tumor level is associated with better patient outcomes, but the role and impact of the regional immune response in liver cancer is not well understood. Liver draining lymph node tissue was collected from patients undergoing orthotopic liver transplant (OLT) for HCC, CCA, or other reasons (control). Nanostring GeoMx Digital Spatial Profiler (DSP) was used to measure immune marker levelsWe found increased immune activity in the LNs of patients with HCC compared to CCA, showing significantly higher levels of lymphocytes and immune activity markers, matching previous tumor microenvironment findings. Additionally, comparing recurrent and non-recurrent HCC or CCA samples, we see generally increased immune activity in non-recurrent lymph nodes, also identifying specific immune markers in both cancer types that correlate with cancer recurrence or non-recurrence. These also reveal patterns of activity specific to both cancer type and recurrence status. Overall, this study provides novel insights into the regional immune response in liver cancers and identifies candidate proteins to serve as predictors of recurrence in liver cancer. We suggest CD163, CD66b, CD8, and CD56 as markers to predict post-OLT HCC recurrence and CD163, CD66b, ID01, and OX40L as candidate markers to predict post-OLT CCA recurrence using LN samples. Further spatial analysis of this data may further characterize immune activity in these lymph nodes, and future studies focusing on identified differences in immune activity may reveal factors affecting liver cancer aggressiveness and recurrence.

Citation Format: Peyton Hickman, Aubrey E. Thompson, Justin Nguyen. The role of draining lymph nodes in the post-transplant recurrence of liver cancer: Examining immune response using spatial proteomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 624.
Abstract 6380: Ultrasensitive detection of circulating human PD-1 and PD-L1 using Single Molecule Counting (SMC) technology
Authors: Faramarzi Laila , Lie Wen-Rong , Wiese Rick , Fiske Jared
Published: April 2023

Immune checkpoint proteins are key regulators of the immune system and potential drug targets for cancer immunotherapy. Cancer immunotherapy targeting immune checkpoint, like programmed cell death protein-1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors has shown treatment efficacy for a broad spectrum of human cancers. Immune checkpoint molecules PD-1 and PD-L1 are expressed on the cell surface of immune cells and tumor cells. Recent studies have also reported these immune checkpoint proteins may undergo alternative splicing or proteolytic cleavage to produce soluble checkpoint proteins. Multiple molecular forms of soluble PD-1 (sPD-1) and PD-L1 (sPD-L1) are detectable in patient sera of multiple types of cancer, and these soluble checkpoint proteins have been reported as putative liquid biopsy biomarkers in the diagnosis and prognosis of oncological disease. Though the clinical significance of circulating soluble immune checkpoint protein profiles as predictive biomarkers has yet to be fully explored and validated, we have committed to develop better and more reliable bioassays to further this research. With that, we have developed 2 Luminex-based multiplex immunoassays for simultaneous quantitation of 48 immune checkpoint proteins, including PD-1 and PD-L1, for patient sera and tumor lysate samples. Here we report the development of 2 novel Single Molecule Counting (SMC) technology-based ultrasensitive single-plex immune checkpoint immunoassays for the detection of sPD-L1 and sPD-1 in human serum and plasma samples. Comparative studies demonstrate these SMC ultrasensitive assays possesses at least 10-100-fold higher sensitivity as compared with the Luminex-based immunoassays. Using these novel ultrasensitive assays, we have validated the detection of significant increases in sPD-L1 and sPD-1 in cancer serum samples as compared with the levels in healthy controls. We have also applied these high sensitivity assays to measure human PD-L1 and PD-1 biomarkers in other sample types including urine, tumor lysates and exosomes. In conclusion, we envision that these PD-1 and PD-L1 SMC assays may overcome a major limitation in biomarker utility and enable the ultrasensitive detection of sPD-1 and sPD-L1 in liquid biopsy and blood biomarker research.

Citation Format: Laila Faramarzi, Wen-Rong Lie, Rick Wiese, Jared Fiske. Ultrasensitive detection of circulating human PD-1 and PD-L1 using Single Molecule Counting (SMC) technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6380.
Abstract 6389: Differential role of CD8 cells and CD4 cells in anti-tumor immunity triggered by tumor cell apoptosis using HSVtk/GCV system
Authors: Umegaki Sho , Shirota Hidekazu , Iwasaki Tomoyuki , Kasahara Yuki , Ishioka Chikashi
Published: April 2023

Immune cells can recognize tumor antigens and elicit an adaptive immune response, potentially resulting in tumor regression. Drug-induced dead tumor cells have been reported to enhance anti-tumor immunity, but results are conflicting, possibly due to the immunosuppressive effects of the cytotoxic drugs. To investigate whether apoptotic tumor cells trigger anti-tumor immunity independent of anti-cancer treatment, local immune responses were evaluated after direct induction of tumor cell apoptosis using a herpes simplex virus thymidine kinase (HSV-tk)/ganciclovir (GCV) system. The inflammatory cytokines IFNγ and IL-12β and anti-inflammatory factor PD-1 and TGFβ1 were upregulated at the tumor site after apoptosis induction. HSV-tk/GCV-induced tumor cell apoptosis resulted in suppression of tumor growth in vivo and promoted the infiltration of CD8 and CD4 T lymphocytes in tumor. To explore the role of T cells after induction of tumor cell death, GCV was administered together with anti-CD8 or anti-CD4 depleting antibodies to syngeneic HSV-tk transfected tumor-bearing mice. CD8 T cell depletion abrogated the anti-tumor efficacy of GCV, indicating that tumor regression was mainly dependent on CD8 T cells. This anti-tumor immunity was enhanced by anti-PD-1 antibody injection. On the contrary, CD4 T cell depletion further inhibited tumor growth than GCV alone, suggesting the potential role of CD4 T cells in suppressive tumor immunity. To elucidate this immunological mechanism, tumor tissues were evaluated after tumor cell apoptosis and CD4 T cell depletion. Foxp3, a regulatory T cell marker, was decreased after CD4 T cell depletion. In addition, Arg1, a marker of immunosuppressive myeloid cells, was significantly downregulated, which was expressed on tumor-associated macrophages (TAMs) and monocytic myeloid-derived suppressor cells (mMDSCs). Collectively, these findings indicate that tumor cell apoptosis accelerates CD8 T cell-dependent anti-tumor immunity and CD4 T cell-mediated Arg1 production from TAMs and mMDSCs.

Citation Format: Sho Umegaki, Hidekazu Shirota, Tomoyuki Iwasaki, Yuki Kasahara, Chikashi Ishioka. Differential role of CD8 cells and CD4 cells in anti-tumor immunity triggered by tumor cell apoptosis using HSVtk/GCV system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6389.
Abstract 6398: Targeting ENPP1 to boost anti-tumor immunity during PARP inhibition
Authors: Li Jie , Mason Charlotte , Hanggi Kay , Luca Vincent , Ruffell Brian
Published: April 2023

Homologous recombination (HR) deficiency confers sensitivity to poly (ADP-ribose) polymerase inhibitors (PARPi), which have been approved for use in ovarian and triple negative breast cancers (TNBC) carrying loss-of-function mutations in HR pathway genes, most commonly BRCA1/2. Preclinical studies in BRCA1-deficient tumor models have demonstrated that the immune compartment is required for PARPi efficacy through the ability of PARPi to cause micronuclei formation and activate cGAS in tumors cells. The production of the 2’3’-cGAMP secondary intermediate stimulates STING in neighboring tumor-infiltrating immune cells to promote an anti-tumor response. Despite this evidence of immune stimulation, PARPi does not extend overall survival in TNBC patients, suggesting that immune suppression remains a significant barrier for efficacy. Here we sought to evaluate the role of ectonucleotide pyrophosphatase/phosphodiesterase 1(ENPP1), a type II transmembrane glycoprotein that hydrolyzes extracellular 2’3’-cGAMP. We generated Brca1/Pten/Trp53-deficient TNBC cell lines from a genetically engineered mouse model and found that these expressed higher levels of ENPP1 than Brca1-proficient TNBC and non-TNBC cell lines. Knocking out Enpp1 via CRISPR/Cas9 increased 2’3’-cGAMP production during Niraparib treatment but did not affect cellular proliferation in vitro. Critically, knocking out Enpp1 significantly reduced the growth of orthotopic Brca1-deficient tumors, with no change in growth observed for orthotopic E0771 or PyMT models, suggesting an important role for ENPP1 in HR-deficient tumors. Therapeutic dosing of Niraparib further reduced the growth of Enpp1 knockout tumors in a manner that was dependent upon host STING and correlated with higher CD8+ T cell infiltration and effector function. These findings demonstrate that ENPP1 suppresses anti-tumor immunity in Brca1-deficient tumors, suggesting that blocking the enzymatic activity of ENPP1 may provide therapeutic benefits during PARPi treatment for TNBC patients.

Citation Format: Jie Li, Charlotte Mason, Kay Hanggi, Vincent Luca, Brian Ruffell. Targeting ENPP1 to boost anti-tumor immunity during PARP inhibition. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6398.
Abstract 6404: Clinical scenario of immune checkpoint inhibitor treatment in metastatic nasopharyngeal carcinoma
Authors: Hsu Cheng-Lung , Kuo Yung-Chia
Published: April 2023

Advanced in local treatment technology and early detection methodology, distant metastasis became a critical issue in Nasopharyngeal carcinoma (NPC). Recently, cancer immunotherapy especially immune checkpoint inhibitors (ICIs) including anti-programmed death-1 (PD-1) and PD-1 ligand (PD-L1) monoclonal antibodies (Mabs) had a rapid progress in cancer patient management. We try to clarify the clinical scenario of immune-related parameters in metastatic NPC. We had check 81 metastatic tissue PD-L1 expression without ICI treatment from the tissue bank of CGMH, Linkou, during 2005~2019. Using anti-PD-L1 antibody, 22C3 Dako, tumor proportional score (TPS) was positive in 43.2% (35/81) checked tissue and combine positive score (CPS) was positive in 58.0% (47/81) tissue respectively. For overall survival (OS) combined with PD-L1 expression in metastatic tissue analysis, positive CPS but not TPS correlated with longer survival with statistical significance (TPS: >0% vs =0%, median survival, 24m vs 22.5m, p=0.615186; CPS: >0% vs =0%, median survival, 28m vs 16m, p=0.003709). Retrospectively analysis of metastatic NPC treatment of combination of chemotherapy, ICIs, and local treatment in our institute in the past 6 years, total 40 patients was enrolled with median overall survival of 34.1 months. Objective response rate by RECIST criteria for immunotherapy-based regimen was 75% (CR:40%; PR:35%) and disease control rate was 85%. According to response by RECIST criteria, median overall survival were 34.1 months vs. 16.7 months respectively for responders and non-responders. With pre-treated NLR as cutoff value of 1.6, difference of median overall survival between two groups (responder vs nonresponder) was statistically significant (p=0.021). We also found that lower median post-treatment NLR in responders than in non-responders (1.4 vs. 3.2, p=0.013). Using rapid lymphocyte amplification protocol via IL-2 stimulation, the PBMC from most of the patient received ICIs treatment can be amplified 1~10 folds and positively correlated with total lymphocyte count. Through flowcytometry analysis, we found these amplified PBMC was lymphocyte dominant and rich in CD8+. We also found these amplified PBMC can kill the NPC EBV-positive cell line and xenograft in vitro and in vivo. These results demonstrated that combination of chemotherapy, ICIs, and local treatment will benefit metastatic NPC patients.

Citation Format: Cheng-Lung Hsu, Yung-Chia Kuo. Clinical scenario of immune checkpoint inhibitor treatment in metastatic nasopharyngeal carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6404.
Abstract 6497: Availability of healthcare providers and its association with survival outcomes in non-Hodgkin lymphoma in the United States
Authors: Gaddam Shiva Jashwanth , Grewal Udhayvir Singh , Hassan Zara , Ramadas Poornima
Published: April 2023

Background: Survival outcome in Non-Hodgkin lymphoma (NHL) is significantly better in earlier stages, compared to advanced stages. Early identification of signs and symptoms, and prompt specialist availability and referral, are crucial for diagnosis and treatment at earlier stages. Mounting physician shortages are a growing concern, and we sought to analyze their effect on NHL mortality rates.

Methods: We extracted data on the age-adjusted mortality rate (AAMR) and crude incidence rate (CIR) of NHL for all U.S. states and the District of Columbia from the Center for Disease Control (CDC) Wide-ranging Online Data for Epidemiologic Research (WONDER) database (2017-2019). Nevada was excluded due to missing information. Data on the state-wise number of primary care physicians (PCPs) was obtained from the Association of American Medical Colleges (AAMC) state physician workforce data report (2020), and of Hematology/Oncology specialists (HOs) was gathered from the National Provider Identifier (NPI) registry (2020). The number of PCPs and HOs per each NHL incidence (PCP/CIR, HO/CIR respectively) was then calculated. Correlations were analyzed using Pearson’s coefficient. Statistical analysis was performed using VassarStats.

Results: Median AAMR for NHL in the US was 5.15 (IQR 4.35, 5.95) per 100, 000 population. The median number of PCP and HO per each case of NHL incidence was 4.32 (IQR 3.43, 5.21), and 0.28 (IQR 0.1, 0.37) respectively. States with fewer PCPs per each NHL incidence had higher AAMR (r=-0.37, p=0.007). States with a lower number of HOs per each NHL incidence had higher AAMR (r=-0.41, p=0.003)

Conclusions: Based on the analysis, the availability of a lower number of PCPs and HOs per each NHL incidence is associated with increased AAMR of the disease. This data may strengthen the need for intensification of focus on decreasing the soaring physician shortages in the states, in order to help decrease the overall mortality associated with NHL.

Citation Format: Shiva Jashwanth Gaddam, Udhayvir Singh Grewal, Zara Hassan, Poornima Ramadas. Availability of healthcare providers and its association with survival outcomes in non-Hodgkin lymphoma in the United States [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6497.
Abstract 6531: Point of care test for cervical cancer screening
Authors: Habbani Samrin Farouk Idris , Dowlatshahi Sayeh Jalali , Elumalai Monisha , Bolton Scott Charles , Tecle Lucy Teberh , Thakkar Pankti Rajesh , Linnes Jacqueline C , Mohammed Sulma I
Published: April 2023

Cervical cancer is a lethal gynecological malignancy and the fourth most common cancer among women. Most high-grade cervical pre-cancers and cancer cases are linked to infection with high-risk human papillomaviruses (HPV). There is an inequity between high-income countries (HICs) and low- and middle-income countries (LMICs) in cervical cancer burden; according to the World Health Organization, the estimated mortality rate of cervical cancer is 342,000 women worldwide in 2020, and 90% of these women reside in low- and middle-income nations where the human papillomavirus vaccine is unavailable and access to early detection testing are either unavailable or too expensive. This study aims to develop a simple and affordable point-of-care test based on four critical biomarkers for screening high-risk pre-cancer and invasive cervical cancer in collaboration with the biomedical engineering department. A cervical cancer swab will be used in the test. The swab will be placed on a paper-based device that looks for four protein biomarkers critical for the progression of noninvasive cervical cancer into invasive cervical cancer by combining two approaches using proteomics and lateral flow immunochromatography technology. We have validated the markers' expression in cervical cancer and precancerous tissues. The four markers were expressed in squamous cell carcinoma, glassy cell carcinoma, adenocarcinoma, clear cell carcinoma cancer tissues, and the high-grade cervical intraepithelial neoplasia. This point-of-care test will be affordable and implementable, especially in low and middle-income countries.

Citation Format: Samrin Farouk Idris Habbani, Sayeh Jalali Dowlatshahi, Monisha Elumalai, Scott Charles Bolton, Lucy Teberh Tecle, Pankti Rajesh Thakkar, Jacqueline C Linnes, Sulma I Mohammed. Point of care test for cervical cancer screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6531.
Abstract 6539: Application of optical genome mapping to identify samples with homologous recombination deficiency
Authors: Pang Andy Wing Chun , Chang Kelsea , Sahajpal Nikhil , Saul Daniel , Kolhe Ravindra , Chaubey Alka , Hastie Alex
Published: April 2023

Certain cancer treatments, such as the poly (ADP-ribos) polymerase (PARP) inhibitors, have been shown to be effective in killing cancer cells exhibiting genome instability signatures indicative of homologous recombination deficiency (HRD). Hence, these signatures are used as biomarkers to inform treatment decisions and prognosis. There are three measurements of HRD signatures commonly employed: loss of heterozygosity (HRD-LOH), telomeric allelic imbalance (TAI) and large-scale state transition (LST). It has been shown that combining all three scores can better determine the HRD phenotype, leading to a higher clinical impact. Yet current HRD signature tests, used to estimate HRD, have low negative predictive value, and one possible reason is that current genomic technologies lack sensitivity to capture the full extent of somatic genomic rearrangements. Here, optical genome mapping (OGM) was used to detect large structural variants (SVs) and calculate a HRD score. OGM captures high molecular weight DNA to call SVs by aligning these molecules to the public reference genome. OGM can comprehensively detect insertions and deletions >5kbp, inversions, interchromosomal translocations, plus large interstitial copy number variation (CNV) and aneusomies. Subsequently, an automated script was developed to compute the HRD score, which is the summation of the three HRD signatures: HRD-LOH, the number of regions with a loss >15 Mbp but shorter than the whole chromosome; TAI, the number of regions of gain and loss >10Mbp that extend to a subtelomere but do not cross the centromere; and LST, the number of chromosomal breakpoints whose SV size >10Mb but not the whole chromosome. We applied this script on 20 samples of solid tumors and myeloid neoplasms, and the automated scores are concordant with expertly curated scores, confirming the validity of the calculation. We believe that OGM data combined with this automated analysis of HRD signatures is much more sensitive and accurate for detection of HRD signatures and that this will enable more precise prediction of drug response for multiple tumor types.

Citation Format: Andy Wing Chun Pang, Kelsea Chang, Nikhil Sahajpal, Daniel Saul, Ravindra Kolhe, Alka Chaubey, Alex Hastie. Application of optical genome mapping to identify samples with homologous recombination deficiency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6539.
Abstract 6575: LinkedOmicsKB: A web portal to explore pan-cancer molecular and phenotype associations
Authors: Savage Sara R. , Liao Yuxing , Dou Yongchao , Shi Zhiao , Yi Xinpei , Jiang Wen , Lei Jonathan T. , Zhang Bing
Published: April 2023

Pan-cancer multi-omics data produced from integrated genomic, epigenomic, transcriptomic, proteomic, and post-translational modification (PTM) profiling of a wide variety of cancer types holds great potential for understanding cancer biology and generating therapeutic hypotheses. To realize this potential and make analysis and visualization of these complex and interconnected data easily accessible to cancer biologists and clinicians, we have developed a web portal, LinkedOmicsKB. The web portal provides access to a harmonized proteogenomic dataset of over 1000 patient samples covering 10 cancer cohorts from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). We calculated associations between methylation, copy number variation (CNV), RNA, protein, and phosphosite data for each gene and further correlated the proteogenomics data with clinical and computed molecular phenotypes. All results are stored in a MongoDB database and visualizations are provided for exploring pan-cancer multi-omics relationships as well as individual statistics. We demonstrate the utility of LinkedOmicsKB to provide insights into clinical phenotypes, somatic mutations, and understudied genes. In the pan-cancer CPTAC data, overall survival was correlated with proteins involved in protein hydroxylation, including PLOD1 and PLOD2. Additionally, two phosphorylation sites on the tumor suppressor MIG-6 were associated with worse survival. These sites were also associated with hypoxia, MAPK, and EGFR pathway activity scores, suggesting a relationship between the signaling in these pathways and cancer prognosis. STK17B is an understudied kinase that regulates apoptosis. We found STK17B was upregulated in 6 cancer types at the protein level but only two at the RNA level. The protein abundance of STK17B was highly associated with immune scores and JAK/STAT signaling, supporting a role for STK17B in the immune response. We identified 3 phosphorylation sites on STK17B, which were associated with EGF pathway activity scores and immune-related scores. LinkedOmicsKB is a valuable tool that can be used to generate biological and clinical insights into any gene, phosphosite, mutation, or phenotype.

Citation Format: Sara R. Savage, Yuxing Liao, Yongchao Dou, Zhiao Shi, Xinpei Yi, Wen Jiang, Jonathan T. Lei, Bing Zhang. LinkedOmicsKB: A web portal to explore pan-cancer molecular and phenotype associations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6575.
Abstract 6588: Systems biology-based drug repositioning and biomarker discovery for Thai liver fluke-associated cholangiocarcinoma
Authors: Jamnongsong Supawan , Kueanjinda Patipark , Tawornparcha Piyathida , Vaeteewoottacharn Kulthida , Okada Seiji , Jirawatnotai Siwanon , Pongpaibul Ananya , Korphaisarn Krittiya , Sampattavanich Somponnat
Published: April 2023

Our group has recently reported the successful use of comprehensive drug response and pan-omic profiling for identifying repurposable drug shortlists in Asian cholangiocarcinoma. We also developed the CCA45 gene-expression signature that could accurately predict the prognosis of CCA patients, especially those with Asian ethnic backgrounds. To further explore therapeutic candidates and potential resistance mechanisms, we have established CCA1 cell lines resistant to their subgroup-specific drug candidates: MEK and SRC inhibitors. Reverse-phase protein arrays (RPPA)-based proteomic profiling revealed upregulation of cell cycle, apoptosis, MAPK, and mTOR-related proteins in both MEKi- and SRCi-resistant cells. Src pathway activity was found to be more significantly reduced in SRCi-resistant cells. We identified CDK4/6 inhibitors as the second-line therapeutic candidates for MEK inhibitor-resistant cells by systematic drug screening. SRCi-resistant cells unexpectedly developed cross-resistance to MEK inhibitors and showed sensitivity to only a few CDK4/6 inhibitors. These data are beneficial for the clinical translation of our proposed drug candidates for Asian CCA, preparing the alternate regimens after drug resistance. We also adopted the DSP-based spatial transcriptomic platform to compare the tumor microenvironment between chemotherapy-sensitive and chemotherapy-resistant CCA patients. While the CTA panel showed consistent patterns of normalized gene expression to those of the WTA panel, the CTA panel can only measure 17 of the 45 genes required for our CCA45 signature. Out of these 17 genes, ITGB4, FGFR3, VEGFC, NOTCH1, and RRAD showed significant gene expression changes with reducing tumor percentage. The microenvironment of gemcitabine/cisplatin responder (R) non-responder (NR) exhibited negative regulation of ERK1/2 and MAPK, high WNT pathway activity, and high tumor-infiltrating lymphocyte (TIL). In contrast, the microenvironment of the non-responder (NR) subgroup showed high neutrophil-related activity, high NFκB, high Treg, and the exhausted immune phenotype. Overall, our study contributes toward realizing the precision medicine concept for CCA patients.

Citation Format: Supawan Jamnongsong, Patipark Kueanjinda, Piyathida Tawornparcha, Kulthida Vaeteewoottacharn, Seiji Okada, Siwanon Jirawatnotai, Ananya Pongpaibul, Krittiya Korphaisarn, Somponnat Sampattavanich. Systems biology-based drug repositioning and biomarker discovery for Thai liver fluke-associated cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6588.
Abstract 6596: Genomic and proteome analysis using preoperative cell free DNA and extracellular vesicles of lung cancer patients
Authors: Koba Hayato , Kimura Hideharu , Yano Seiji
Published: April 2023

Background: The detection of circulating cell free DNA (cfDNA) has been examined as a predictor of postoperative recurrence and survival in lung cancer patients. Extracellular vesicles (EVs) have potent for searching a new target to cancers.

Objective: To analyze the association between cfDNA/EVs and prognosis after lung cancer surgery.

Methods: We retrospectively examined patient background, disease-free survival, overall survival, and preoperative cfDNA in lung cancer patients who underwent surgery at Kanazawa University Hospital between January 2017 and May 2020, in whom preoperative chemotherapy was not administered. We extracted cfDNA from 4 ml plasma within 7 days before surgery and measured its concentration. EVs were extracted from 500 μl serum via Tim4 protein. Proteins included in EVs were analyzed by mass spectrometry.

Results: 285 patients were included, 179 males and 106 females, median age 71(36-88) years, and 8 patients had SCLC. EGFRm- positive lung cancer was included in 93 cases (32.6%). The pStage0/l/ll/lll/lV of NSCLC was 7/187/42/36/6 respectively, and the pStagel/ll/lll of SCLC was 4/1/3 respectively. The mDFS of NSCLC was 14.6 (7.8-29.7)/21.5 (8.5-NA) months in pStage lll/lV, respectively. mOS was 53.3 (28.7-NA) months in pStage lll and was not achieved in other stages. The mDFS of SCLC was 19.8 (1.9-NA)/NA/5.7 (1.9-NA) months in pStage l/ll/lll, respectively. mOS was NA/NA/9.3 (9.3-NA) months, respectively. cfDNA was detected in 283 (99.2%) patients, with a concentration of 4.7 (0-60.0) ng/μl. The correlation coefficient between cfDNA concentration and DFS/OS in NSCLC was -0.023 (P=0.70)/-0.014 (P=0.81). The correlation coefficient between cfDNA concentration and DFS/OS for SCLC was -0.86 (P=0.024)/-0.89 (P=0.012). No recurrence was observed in patients in whom cfDNA was not detected.EVs were detectable from pre-operative serum samples, and the proteins included in these were different, whether disease was recurrent or not.

Conclusion: The cfDNA concentration did not correlate with DFS/OS in post-operative NSCLC, whereas it correlated negatively with DFS/OS in SCLC. In the presentation, we will further discuss about the concrete genetic alterations and protein expression, based on the cfDNA sequencing and proteomics analysis.

Citation Format: Hayato Koba, Hideharu Kimura, Seiji Yano. Genomic and proteome analysis using preoperative cell free DNA and extracellular vesicles of lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6596.
Abstract 6599: Neomer and fragmentation profiles of cell-free DNA with low-pass whole genome sequencing to predict prostate cancer biopsy outcomes
Authors: Liu Fei , Peng Kaoqing , Chen Rui , Li Mingzhao , Zeng Tao , Zhao Yan , Wang Ming , Liu Hongxing , Wu Jianhao , Wu Min , Tang Haimeng , Bao Hua , Wu Xue , Shao Yang , Gu Di , Ren Shancheng
Published: April 2023

Prostate cancer is one of the most common types of cancer in men. Current prostate-specific antigen (PSA)-based diagnostic strategy for prostate cancer may frequently cause overdiagnosis. In this study, we prospectively recruited 380 individuals, including 167 with pathologically confirmed prostate cancer, 127 with negative prostate biopsy results, and 86 assessed healthy cohort with no need for biopsy. We collected a plasma sample from each participant, performed whole-genome sequencing, and profiled cell-free DNA (cfDNA) neomer and fragmentation characteristics. We then developed a machine learning model using these cfDNA profiles to predict prostate cancer biopsy outcomes. Our results showed that this assay could achieve high accuracy (Accuracy: 85.3%, AUROC: 0.919, 95% CI: 0.892 - 0.946) in repeated 5-fold cross validations. Patients with negative biopsy results had higher prediction scores than healthy individuals (P < 2.2X10-16), making them less distinguishable from prostate cancer patients (AUROC: 0.878, 95% CI: 0.837 - 0.918 vs. AUROC: 0.980, 95% CI: 0.963 - 0.997). We further combined this cfDNA-based assay with the PSA testing and constructed an ensemble model. The classification performance was further improved in the ensemble model, showing AUROC metrics of 0.951 (95% CI: 0.932 - 0.969) between cancer and non-cancer, 0.919 (95% CI: 0.889 - 0.949) between cancer and negative biopsy, and 0.998 (95% CI: 0.994 - 1.000) between cancer and healthy individuals. At a sensitivity of 90.4%, the ensemble assay accurately identified 85.4% of non-cancerous conditions, including 76.4% of negative biopsy patients and 98.8% of healthy individuals. We concluded that our cfDNA fragmentation and neomer-based assay could be incorporated into the PSA-based predicting system for prostate cancer to increase the accuracy and reduce the overdiagnosis.

Citation Format: Fei Liu, Kaoqing Peng, Rui Chen, Mingzhao Li, Tao Zeng, Yan Zhao, Ming Wang, Hongxing Liu, Jianhao Wu, Min Wu, Haimeng Tang, Hua Bao, Xue Wu, Yang Shao, Di Gu, Shancheng Ren. Neomer and fragmentation profiles of cell-free DNA with low-pass whole genome sequencing to predict prostate cancer biopsy outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6599.
Abstract 6652: Overcoming immune resistance in DNA mismatch repair deficient tumors
Authors: Mestrallet Guillaume
Published: April 2023

Patients with Lynch Syndrome, an inherited mismatch repair deficiency, have an increased risk for developing microsatellite unstable (MSI-H) cancers. Our team recently identified shared immunogenic frameshift peptides in patient tumors that can be targets of T cell surveillance and preventative MSI-H cancer vaccines. We hypothesize that in Lynch Syndrome some premalignant lesions are capable of evading immune surveillance from cytotoxic T lymphocytes due to immune checkpoint expression and immunosuppression from tumor, myeloid and stromal cell populations. Immune checkpoint blockade (ICB) showed promising results in the treatment of MSI-H tumors and are being evaluated in the adjuvant setting of patients with Lynch syndrome post surgical resection. However, a significant percentage of advanced MSI-H tumors resist ICB suggesting evolving mechanisms of immune resistance. We will use a MSI-H in vivo mouse model and additionally develop 3D spheroids cocultured with immune cells to characterize the underlying immune resistance mechanisms. The MSI-H mouse model will first be applied to identify shared frameshifts in MSI-H tumors by WES to develop vaccination approaches preventing tumor growth. Then, we will quantify MSI-H tumor growth and immune infiltration in the MSI-H mouse model, with or without ICB. We will analyze the presence of immunosuppressive pathways and myeloid subsets in high growth resisting tumors by immunohistochemistry, scRNAseq, spatial transcriptomics and flow cytometry. In addition, we will perform short-term in vitro spheroid-splenic cell co-cultures to better characterize the early immune resistance mechanisms. We will also perform these spheroid-immune cell co-cultures using the immune cells taken from mice after vaccination or ICB to identify the early myeloid immune resistance mechanisms. Overall, the identification of shared immune frameshifts in MSI-H tumors will allow developing peptide vaccination approaches to prevent tumor growth. Further, the identification of myeloid resistance pathways will guide therapeutic strategies against tumor resisting to ICB and/or vaccination.

Citation Format: Guillaume Mestrallet. Overcoming immune resistance in DNA mismatch repair deficient tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6652.
Abstract 6692: Identification of circulating tumor cells based on machine learning
Authors: Lee Jae Hyuk , Park Sung Ho , Kang Jihoon , Lee Jihyun , Kim Soee , Kim Jungwon , Sohn Young Woong , Lee Jong Kil
Published: April 2023

Circulating tumor cells (CTC) are tumor cells that have shed into the bloodstream from primary tumor and circulate in the blood. CTC could provide better understanding of tumor metastasis and show the possibility as promising biomarker for early detection of cancer, cancer prognosis, noninvasive monitoring of treatment response, and personalized medicine. However, the isolation and characterization has been a major technological challenge due to their rareness among the massive blood cells. CytoGen’s Smart BiopsyTM CTC platform comprised of CTC isolator, IF (Immunofluorescence) Stainer, and Cell Image Analyzer is a unique and competitive technology platform for the isolation and analysis of CTC from blood. Intact live CTC could be isolated gravity-based filtration via high-density micro-porous (HDM) chip with minimized cellular damage and high retrieval rate. For the more accurate and quick analysis of CTC after isolation with Smart BiopsyTM CTC platform, we are developing the analysis method of CTC identification using machine learning technologies. Preliminary results of machine learning showed the accurate separation of CTC and PBMC (peripheral blood mononuclear cells) based on the specific markers of them. CTC identification based on machine learning technologies might be reliable analysis method and give secure information of CTC.

Citation Format: Jae Hyuk Lee, Sung Ho Park, Jihoon Kang, Jihyun Lee, Soee Kim, Jungwon Kim, Young Woong Sohn, Jong Kil Lee. Identification of circulating tumor cells based on machine learning. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6692.
Abstract 812: Treatment of metastatic cancers using immunotherapeutic cowpea mosaic virus nanoparticles
Authors: Chung Young Hun , Volckaert Britney A. , Steinmetz Nicole F.
Published: April 2023

This study investigates the use of an immunotherapeutic plant virus, namely the cowpea mosaic virus (CPMV), that when used prophylactically and therapeutically can protect against metastatic cancer in multiple tumor mouse models. Metastatic cancer continues to be the main cause of death of most cancer patients, and new treatment modalities must be engineered to protect patients from metastatic disease. For instance, peritoneal metastases (PMs) are oftentimes fatal, and patients survive for a median 6 months following diagnosis. PMs are common for colon, ovarian, gastric, appendiceal, and pancreatic cancers. Previously, it was demonstrated that CPMV is a potent in situ vaccine causing tumor shrinkage with abscopal effect and long-term protection observed in tumor mouse models and canine cancer patients. CPMV functions as a toll like receptor (TLR) agonist and acts on innate immune cells to induce tumor cell killing and antigen processing to eventually prime adaptative and tumor-specific immunity. However, metastatic cancers such as PMs are not easily and directly injectable and therefore, we have expanded the ability of CPMV to protect against PMs by engineering targeted CPMV nanoparticles. Data indicates that CPMV can improve survival and slow tumor growth in a murine colon PM model compared to controls and that long-term survivors are further protected from re-challenge indicating tumor specificity. Analysis from current and past studies indicate that CPMV injection into the intraperitoneal space leads to distinct upregulation of immunostimulatory cytokines and recruitment of innate immune cell populations. PMs lead to extreme declines in quality of life of patients, and current treatments can be ineffective in slowing down or reducing tumor development and death - in tackling this problem, the data clearly points to the strong potential for CPMV-mediated therapeutics in the treatment and prophylaxis of PMs.

Dr. Steinmetz is a co-founder of and has a financial interest in Mosaic ImmunoEngineering Inc. The other authors have no conflict of interest to declare.

Acknowledgments: This work is supported in part through NIH grants R01 CA274640, R01 CA224605, R01 CA253615, CDMRP W81XWH2010742, and the Shaughnessy Family Fund for Nano-ImmunoEngineering (nanoIE at UC San Diego).

Citation Format: Young Hun Chung, Britney A. Volckaert, Nicole F. Steinmetz. Treatment of metastatic cancers using immunotherapeutic cowpea mosaic virus nanoparticles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 812.