bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 405: A new mechanism of drug resistance in cancer: extracellular ATP-induced resistance by macropinocytosis-mediated internalization and redox changes
Authors: Zhang Haiyun , Chen Xiaozhuo
Published: June 2022

Drug resistance are responsible for most relapses and up to 90% of cancer related death. The opportunistic uptake of extracellular molecules has been named as a key emerging hallmark of cancer metabolism. In tumor microenvironment, intratumoral extracellular ATP (eATP) levels are 1,000 times or more higher than those in corresponding normal tissues. Our previous studies have shown that eATP can be taken up by cancer cell via macropinocytosis, leading to substantial increase in intracellular ATP levels. We found that this high intracellular ATP levels contribute to drug resistance in several ways: first, it directly fueled and enhanced drug-pumping activity of major ATP-binding cassette (ABC) multidrug transporters, which are located in plasma membrane and can pump out a wide range of substrates including anticancer drugs, leading to reduced intracellular drug retention. Secondly, ATP treatment upregulated gene expression of the major ABC transporters, and this gene regulatory effect of ATP was comparable to TGF-beta, which is a well-established epithelial-mesenchymal transition (EMT) inducer, and EMT is known to induce ABC transporter expression and drug resistance. Moreover, eATP treatment led to an increase in intracellular glutathione (GSH) levels, probably by enhancing GSH synthesis. Increased GSH levels have been described to significantly contribute to drug resistance. We also found eATP altered cellular redox state, which potentially stimulates EMT. Furthermore, we performed RNA-sequencing and identified several genes that may serve as downstream factors of eATP in promoting EMT and drug resistance. We are currently investigating the roles of these genes by knocking down gene expression or knocking out these genes.

Citation Format: Haiyun Zhang, Xiaozhuo Chen. A new mechanism of drug resistance in cancer: extracellular ATP-induced resistance by macropinocytosis-mediated internalization and redox changes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 405.
Abstract 4068: The potent quadruplex-binding compound SOP1812 shows potent anti-proliferative activity in a prostate cancer cell panel and anti-tumor activity in an in vivo model of metastatic prostate cancer
Authors: Williams Nicole , Worthington Jenny , Neidle Stephen , Ahmed Ahmed
Published: June 2022

The compound SOP1812, a tetra-substituted naphthalene diimide (ND) derivative has been designed as a potent compound for targeting quadruplex sequences in cancer genes. It has been previously disclosed to have single-digit nM anti-proliferative activity in a panel of human cancer cell lines (Ahmed et al., ACS Med Chem Lett, 2020, 11, 1634-1644). It also has significant anti-tumor activity in several models for pancreatic cancer. We have also previously shown that two early-generation ND derivatives are active in both androgen-positive and negative prostate cancer cell lines (Mitchell et al, Biochemistry, 2013, 32, 1429-1436) and that these compounds down-regulate the transcription of quadruplex-containing genes such as c-MYC. We now report that this compound also shows significant anti-proliferative activity in several prostate cancer cell lines, notably with a GI50 value of 3 nM in the PC3 cell line. Abiraterone has a GI50 in this line of 4820 nM. By contrast SOP1812 has a GI50 of 247 nM in the LNCaP line, which is also derived from a patient with metastatic prostate cancer but is androgen positive. The PC3 line is derived from a metastatic carcinoma following androgen suppression therapy and is thus androgen independent and is a model for castration-resistant prostate cancer when hormone therapies are no longer effective. We have evaluated the activity of SOP1812 in the PC3 xenograft model using a twice-weekly 1 mg/kg dose regimen IV administered, against a saline control and abiraterone, at a daily dose of 200 mg/kg, administered by the PO route, both over a 28-day period. No weight loss was observed in treated animals with either drug. SOP1812 produced statistically significant tumor shrinkage (P value of 0.0008) relative to the controls, with a T/C value of 33.5% on day 28. Abiraterone treatment resulted in a T/C value of 61.6%, with a P value of 0.0382. SOP1812 is bio-available at therapeutic doses and is well tolerated at these levels in this animal model. It is currently being evaluated as a candidate for clinical development by Qualigen Therapeutics Inc.

Citation Format: Nicole Williams, Jenny Worthington, Stephen Neidle, Ahmed Ahmed. The potent quadruplex-binding compound SOP1812 shows potent anti-proliferative activity in a prostate cancer cell panel and anti-tumor activity in an in vivo model of metastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4068.
Abstract 4071: Utilizing colforsin as a novel therapeutic for high grade serous ovarian cancer treatment
Authors: Knarr Matthew , Reavis Hunter , Mitchell Marilyn , Drapkin Ronny
Published: June 2022

Epithelial ovarian cancer (EOC) is currently the deadliest gynecological cancer with approximately 20,000 new cases and 15,000 deaths per year in the United States. Ovarian cancer can be stratified into distinct subtypes of which high-grade serous ovarian cancer (HGSOC) comprises 90% of all cases. The majority of HGSOC patients are diagnosed with late-stage disease and have a poor prognosis with a 5-year survival rate of less than 30%. Thus, there is a critical need to develop novel therapeutic strategies to improve patient treatment and survival outcomes. Our lab has recently discovered that the small molecule colforsin has potent anti-cancer properties when used to treat HGSOC in vitro and in vivo. Colforsin is a water-soluble derivative of forskolin, and acts as an activator of cAMP signaling via direct binding and activation of adenylyl cyclase. It is currently in clinical use for treatment of conditions such as glaucoma, diabetes, and liver fibrosis. This makes colforsin a prime candidate for drug repurposing to treat ovarian cancer. Our data show that colforsin can induce cell cycle arrest and cell death in established HGSOC cell line models in vitro. We have also found that colforsin can inhibit tumor growth and tumor burden in an intraperitoneal model of HGSOC using HEYA8 cells. In addition, we have also found that colforsin acts synergistically with cisplatin to cause HGSOC cell death. Taken together, our data show that colforsin has potential as a new therapeutic tool to aid in HGSOC treatment in combination with existing therapies.

Citation Format: Matthew Knarr, Hunter Reavis, Marilyn Mitchell, Ronny Drapkin. Utilizing colforsin as a novel therapeutic for high grade serous ovarian cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4071.
Abstract 4124: Clinical outcomes in women with metastatic HER2-Low breast cancer in the real world
Authors: Jiang Changchuan , Perimbeti Stuthi , Deng Lei , Shapiro Charles L. , Gandhi Shipra
Published: June 2022

Background: The development of novel anti-HER2 drugs opens new treatment options for patients with breast cancers, including women with lower expression of HER2. The aim of this study was to compare the clinical outcomes of HER2-low and HER2-zero metastatic breast cancer in the real world.

Methods: Female patients diagnosed with metastatic breast cancer and low HER2 expression or HER2-zero expression between 2010 and 2017, and who received systematic therapy, were identified from the National Cancer Database (NCDB). The National Cancer Data Base (NCDB) is a nationwide oncology outcomes database that collects information on approximately 70% of all new invasive cancer diagnoses in the United States.HER2-Low was defined as IHC1+ or 2+/ISH negative, whereas HER2-zero was defined as IHC0, based on the American Society of Clinical Oncology/College of American Pathologists guideline. The primary outcome was overall survival(OS). A multivariable Cox regression model was performed to estimate hazard ratios (HR), adjusting for age, race/ethnicity, education, comorbidities, grade, presence of visceral metastasis, and the type of cancer center where patients were treated. The analyses were stratified by hormone receptor status.

Results: A total of 22817 of 33417 (68%) were HER2-low and 10600 (32%) were HER2-zero. Hormone receptor-positivity was in 19988 (88%) with HER2-low tumors, whereas 8112 (77%) was in HER2-zero tumors. Women with HER2-low tumors had significantly longer overall survival (OS) than did with Her2-zero tumors in both hormone receptor-positive (median OS 39.0 months vs 37.1 months; adjusted HR: 0.93, 95%CI (0.90-0.96), p<0.001) and hormone receptor-negative groups (median OS 15.8 months vs 14.1 months; adjusted HR: 0.92 95%CI (0.86-0.98), p=0.005).

Conclusion: In the metastatic setting, HER2-low tumors have a better survival than HER2-zero tumors, irrespective of hormone receptor status. Specific therapies, such as trastuzmab deruxtecan, have activity in women with HER-low breast cancers and additional therapeutics for HER-2 low should be sought.

Citation Format: Changchuan Jiang, Stuthi Perimbeti, Lei Deng, Charles L. Shapiro, Shipra Gandhi. Clinical outcomes in women with metastatic HER2-Low breast cancer in the real world [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4124.
Abstract 4247: Development of NK humanized mice models for the in vivo evaluation of NK cell engagers
Authors: Rettman Pauline , Bourges Dorothée , Meyer Laure-Marie , Rangara Ravi , Ponchet-Lac Anna , Moindrot Nicolas , Sidhu Sukhvinder , Nicolazzi Céline
Published: June 2022

Novel immunotherapeutic strategies targeting Natural Killer (NK) cells using monoclonal or multi-specific antibodies and immune modulator molecules are under development and there is a pressing need to have suitable mouse models for the evaluation of these therapeutics. To date, there are no validated in vivo mouse models that support the development of fully functional human NK cells. In recent years, the adoptive transfer of human peripheral mononuclear blood cells or CD34+ stem cells into highly immunodeficient mouse strains mostly allowed the evaluation of T cell-based therapies. However, these humanized mouse models have limitations and do not show an optimal development of innate immune cells such as NK, dendritic or myeloid cells. This is mostly due to the poor interspecies cross-reactivity of key factors necessary for cell development and maturation, like cytokines and growth factors.Here, we report the development and characterization of robust in vivo models that allow the engraftment and maintenance of fully functional human NK (huNK) cells, using several strains of immunodeficient transgenic mice for human cytokines (IL-15). The optimal parameters (source of immune cells, pre-conditioning regimen, route of administration) were identified. These models were characterized and validated by flow cytometry, and in vivo efficacy studies using an anti-CD20 Ab.In summary, we developed several murine models that exhibit significant numbers of functional huNK cells maintained over time in vivo. Different sources of human immune cell (CD34+ HSC, huNK cells) were used to implant immunodeficient huIL15 transgenic mice. HuNK cells were monitored by flow cytometry in all tested models. We showed huNK engraftment in both irradiated and non-irradiated models and confirmed the maintenance of expression of important functional NK markers on these cells. Efficacy studies performed in disseminated models showed promising results as efficacy of an anti-CD20 Ab, rituximab, was improved in presence of huNK cells, thus confirming the engagement of huNK cells in vivo in these models. Overall, we have developed several models that can sustain fully functional huNK cells over a period of several weeks that can be proficiently recruited in vivo by various NK-based therapeutics.

Citation Format: Pauline Rettman, Dorothée Bourges, Laure-Marie Meyer, Ravi Rangara, Anna Ponchet-Lac, Nicolas Moindrot, Sukhvinder Sidhu, Céline Nicolazzi. Development of NK humanized mice models for the in vivo evaluation of NK cell engagers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4247.
Abstract 435: COVID-19 & cancer prevention in Texas: Reasons cited for HPV vaccination hesitancy and refusal during the pandemic
Authors: Chido-Amajuoyi Onyema , Pande Mala , Yu Robert , Shete Sanjay
Published: June 2022

Background: HPV vaccination is highly effective at preventing several squamous cell carcinomas. However, the uptake of this vaccine remains sub-optimal in the US, with further exacerbation of this poor uptake during the pandemic. This study aims to describe changes and barriers to HPV vaccination during the COVID-19 pandemic as observed by healthcare professionals (HCPs) in the state of Texas.

Methods: Data for this study were derived from a statewide cross-sectional survey of HCPs in the state of Texas (n=1283). Survey instruments were developed at MD Anderson Cancer Center, and reviewed by its IRB. Survey frequencies were used to estimate for the proportional distribution of changes as observed by HCPs regarding HPV vaccination i) uptake ii) hesitancy and iii) refusal during the COVID-19 pandemic. HCPs who observed increases in vaccination hesitancy or refusal, were then asked for the reasons cited by their patients. Survey frequencies were then used to determine the proportional distribution of the reasons cited for HPV vaccination hesitancy and refusal during the pandemic. All statistical analysis were conducted using R version 3.5.2.

Results: Overall, 730 HCPs responded to the study questions of interest. A predominant proportion of respondents were employed in group practice settings or university teaching/affiliated hospitals. About 20% of HCPs in Texas observed decreases in HPV vaccination uptake. Observed increments in HPV vaccination hesitancy and refusal were reported by 17.1% and 14.8% of HCPs, respectively. Among HCPs who observed increased hesitancy and refusal, difficulties in scheduling clinic visit during the pandemic and fear of contracting corona virus during the clinic visit were the most cited reasons.

Discussion: Findings of the index study suggest that the COVID-19 pandemic has had a negative impact on HPV vaccination in Texas. Results identify perceived barriers to HPV vaccination unique to the pandemic. With the pandemic still ongoing, amid the emergence of novel strains with heightened virulence, despite the presence of highly effective FDA-approved vaccines, findings of this study provides useful insight for public health interventions, as well as to guide physician-patient interactions around HPV vaccination.

Citation Format: Onyema Chido-Amajuoyi, Mala Pande, Robert Yu, Sanjay Shete. COVID-19 & cancer prevention in Texas: Reasons cited for HPV vaccination hesitancy and refusal during the pandemic [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 435.
Abstract 455: Automating integration of histomorphologic and immunohistochemistry data using computer vision tools
Authors: Lee Michael K. , Faust Kevin , Rabindranath Madhumitha , Diamandis Phedias
Published: June 2022

Background: Modern diagnostic pathology workflows involve the integration of histomorphologic, immunohistochemical (IHC), and molecular data to reach a final diagnosis. Recently, advances in deep learning have revolutionized pathology by providing the prospect for expert-level autonomous image analysis tools. Despite recent innovations in deep learning, integrating histomorphologic and molecular information found on respective H&E- and IHC-stained tissue sections still remains a challenge. Here, we aim to address this issue by incorporating computer vision tools, including deep learning and scale-invariant feature transform (SIFT), to align H&E-stained sections with accompanying IHC studies for automated subclassification of gliomas.

Methods: To test the workflow, we trained the publicly available VGG19 convolutional neural network (CNN) using patches of pathologist-annotated H&E-stained WSIs to recognize histological patterns of 16 common tissue and brain tumor classes, including diffuse glioma, meningioma, metastatic carcinoma, and schwannoma. To complement the histomorphologic analysis, we optimized several deep learning classifiers, including Mask R-CNN, to recognize various IHC markers, such as Ki-67, IDH1-R132H and ATRX, relevant for molecular subclassification of gliomas. For the integrated analysis, we employed SIFT to align lesional regions of H&E and IHC images.

Results: The histomorphologic classifier excelled at classification with accuracies of 100% for glioma, meningioma and metastatic carcinoma, and 93% for schwannoma (n = 125). The Mask R-CNN was tested on 147 images generated from 34 brain tumor Ki-67 WSIs and showed a high concordance with aggregate pathologists’ estimates (n = 3 assessors; y = 0.9712x -1.945, r = 0.9750). Using the deep learning classifiers and SIFT, we were able to identify tumor regions from the H&E images and align them to their corresponding IHC images. This resulted in significant improvement of ATRX and IDH1-R132H quantification compared to unaligned WSIs. Finally, SIFT and partially sampling the lesional regions decreased computational time significantly without compromising accuracy.

Conclusion: SIFT can work in concert with deep learning tools to help examine the histomorphologic and molecular patterns of various brain tumors and provide a framework for integrating deep learning tools to provide automated diagnoses.

Citation Format: Michael K. Lee, Kevin Faust, Madhumitha Rabindranath, Phedias Diamandis. Automating integration of histomorphologic and immunohistochemistry data using computer vision tools [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 455.
Abstract 498: TARE and PVE as pre-operative strategies in highly selected patients with primary and metastatic hepatic malignancies
Authors: Freitas Julia Pedo , Podila Pradeep , Powell Daniel K. , Angel Wes , Deneve Jeremiah L. , Dickson Paxton V. , Glazer Evan S.
Published: June 2022

Background: The treatment of malignancies confined to the liver (hepatocellular carcinoma [HCC], intrahepatic cholangiocarcinoma [ICC], metastatic neuroendocrine tumors [NET] and colorectal hepatic metastases [CRHM]) is challenging. Liver resection leading to post-operative liver failure is a devastating complication that can be mitigated by pre-resection embolization techniques to increase the future liver remnant, such as portal vein embolization (PVE) and transarterial radioembolization (TARE). The purpose of this study was to understand the natural history of this treatment algorithm in disparate patient populations.

Methods: This was a retrospective case-control study from 2008 to 2018. The population consisted of non-transplant eligible patients that had various malignancies without extra-hepatic disease who underwent TARE, PVE, or resection at our institution; they were propensity matched based on co-morbidities, etiology of liver disease, Child-Pugh Score, and ECOG performance status. Statistical analyses were performed with chi-square.

Results: We identified 196 patients with an average age of 57.8±12.6 years and 119 patients were male (60.7%). There were 137 Caucasian patients (CC, 70%) and 59 African American patients (AA, 30%). The tumor histologies were 61 HCC, 31 ICC, 65 CRHM, 12 NET, and 28 other. 148 of these patients underwent liver resection. HCC patients were more likely to undergo TARE (36.4%) compared to ICC (20%), CRHM (23.6%), or NET (9.1%, P= 0.043). While AA patients were more likely to undergo any embolization procedure compared to CC patients (47% vs 31%, P=0.03), they were less likely to undergo PVE (P=0.018). 126 patients (64%) did not undergo any pre-resection embolization procedures. Of patients requiring pre-resection embolization, CRHM patients were more likely to undergo PVE (80%) than other patients (P=0.029). TARE was a bridge to resection for 9 patients.

Conclusions: AA patients underwent more embolization procedures compared to CC patients. It is not clear whether this was because that population required more interventions to optimize FLR or had limited access to care.

Citation Format: Julia Pedo Freitas, Pradeep Podila, Daniel K. Powell, Wes Angel, Jeremiah L. Deneve, Paxton V. Dickson, Evan S. Glazer. TARE and PVE as pre-operative strategies in highly selected patients with primary and metastatic hepatic malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 498.
Abstract 500: Neuropsychological symptoms in patients with head and neck cancer undergoing radiation therapy: A network analysis
Authors: Lin Yufen , Bruner Deborah W. , Paul Sudeshna , Miller Andrew H. , Saba Nabil F. , Higgins Kristin A. , Shin Dong M. , Zhang Wenhui , Miaskowski Christine , Xiao Canhua
Published: June 2022

Objectives: Patients with head and neck cancer experience neuropsychological symptoms (NPS) (i.e., depression, fatigue, sleep disturbance, pain, and cognitive dysfunction) during radiation therapy (RT) that decrease their functional status and quality of life. The purposes of this study were to examine and visualize the relationships among NPS within networks over time and evaluate demographic and clinical characteristics associated with symptom networks.

Methods: A total of 192 patients (mean age 59.5±10.1 years, 75% male, 81% White) completed symptom questionnaires four times, namely, before RT (T1), 1 month (T2), 3 months (T3), and 1 year (T4) after RT. Network analysis was used to explore relationships among the five common NPS. Centrality indices, including strength, closeness, and betweenness, were used to describe the degrees of symptom interconnection. The network comparison test was used to assess the differences between two symptom networks.

Results: Depression (reported by 13%-24% of patients) was associated with the other four symptoms, and fatigue (reported by 54%-77% of patients) was associated with the other three symptoms across four times. Based on centrality indices, depression (rstrength=1.1-1.4, rcloseness=0.07-0.08, rbetweeness=4-12) was the most central symptom in all four symptom networks, followed by fatigue (rstrength=0.8-1.0, rcloseness=0.05-0.06, rbetweeness=0-2). Higher levels of stress and no alcohol use were associated with stronger symptom networks in network global strength (low stress: 1.49 vs. moderate to high stress: 1.92; p=0.02; no alcohol use: 2.38 vs. alcohol use: 1.75; p=0.01), but not in network structure or edge strength prior to RT. No significant differences were found in other time points.

Conclusions: Network analysis provided a novel approach to gain insights into the relationships of co-occurring NPS and identify central symptoms and associated characteristics. Clinicians can use this information to develop personalized symptom management interventions that target central symptoms and interactions within a network.

Citation Format: Yufen Lin, Deborah W. Bruner, Sudeshna Paul, Andrew H. Miller, Nabil F. Saba, Kristin A. Higgins, Dong M. Shin, Wenhui Zhang, Christine Miaskowski, Canhua Xiao. Neuropsychological symptoms in patients with head and neck cancer undergoing radiation therapy: A network analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 500.
Abstract 5013: Integrated analysis of intragastric microbiome and human gene expression uncovers genetic, microbial, and immunological associations in gastritis and gastric cancer
Authors: Park Chan Hyuk , Hong Changjin , Lee A-reum , Sung Jaeyun , Hwang Tae Hyun
Published: June 2022

Background: Gastric carcinogenesis has been found to be associated with intragastric microbiome, gastric mucosal gene expression, and immune cells comprising the tumor microenvironment separately in independent studies. However, to date, there has been no multi-omic investigations analyzing these biological traits simultaneously. Thus, there is a paucity in our understanding of the intricate relationship between intragastric microbes and the host in gastric disease. To address this gap, we aimed to comprehensively investigate the microbiome, host gene expression, and immune cells in the stomach across a range of different states along the gastric carcinogenesis pathway.

Methods: Gastric biopsy samples were obtained from healthy individuals or patients with gastritis or gastric cancer (biopsy cohort, n=30). Surgical samples (of cancer and adjacent severe gastritis tissues) were obtained from gastric cancer patients (surgery cohort, n=40). Using 16S rRNA gene sequencing, RNA-seq, and cell-type enrichment analysis of each participant’s biospecimens, we identified associations between the microbiome and host transcriptome or inferred immune cell types.

Results: Microbiome composition and gene expression patterns showed significant differences between disease states (healthy, gastritis, or cancer). Expression of ‘Cell cycle’ pathway genes was enriched in gastric cancer in both biopsy and surgery cohorts. In the biopsy cohort, Helicobacteraceae, which was abundant in gastritis, was highly correlated with FAM3D, which was previously found to be involved in gastrointestinal inflammation. In the surgery cohort, Lachnospiraceae, which was abundant in gastric cancer, was highly correlated with UBD, which is known to regulate mitosis and reduce cell cycle time. Cell-type enrichment analysis revealed lower B cell infiltration in gastric cancer than in gastritis (both cohorts). Tissue-infiltrating B cells were associated with Helicobacteraceae.

Conclusions: Associations between the intragastric microbiome, human gene expression, and tissue-infiltrating immune cells are unique to gastric disease state. The findings herein may aid the discovery of novel biomarkers or therapeutic targets of gastric cancer.

Citation Format: Chan Hyuk Park, Changjin Hong, A-reum Lee, Jaeyun Sung, Tae Hyun Hwang. Integrated analysis of intragastric microbiome and human gene expression uncovers genetic, microbial, and immunological associations in gastritis and gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5013.
Abstract 5027: PTMcosmos: A web portal of post-translational modifications and proteogenomic resources in cancer
Authors: Wang Liang-Bo , Govindan Akshay , Cao Song , Ding Li
Published: June 2022

PTMcosmos is a comprehensive database with an interactive web portal designed to catalog and visualize post-translational modifications (PTMs) in humans. It contains 469,183 experimentally-validated PTM sites and their supporting evidence from UniProt Knowledge Base, PhosphoSitePlus, and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). PTMcosmos summarizes the entire spectrum of CPTAC proteomics data on human cancer patients, including protein and PTM peptide abundance data from 10 different cancer types. Additionally, PTMcosmos contains cancer somatic mutations from The Cancer Genome Atlas (TCGA), thus allowing for the collective integration and analysis of different data types. In PTMcosmos, we have built an ensemble of interactive visualization tools that allow researchers to investigate altered PTM functions due to genetic alterations in close proximity. The database is live at https://ptmcosmos.wustl.edu. We used PTMcosmos to investigate PTM regulation across cancer types. First, we examined the differential abundance of the PTM sites of cancer driver genes, focusing primarily on phosphorylation of the tumor suppressor retinoblastoma protein (encoded by RB1) and acetylation of the histone acetyltransferase E1A Binding Protein P300 (EP300) across cancer types. We analyzed the association between these PTM events and downstream targets, as well as with tumor subtypes, significantly mutated gene (SMG) mutation status, and clinical features. Second, we investigated the association of the protein abundance of cancer driver genes with ubiquitylsites in lung squamous cell carcinoma (LSCC) to nominate potentially novel modes of regulation of these proteins’ activities. We further analyzed the tumor subtype specificity and tumor-normal abundance changes of these ubiquitylsites and their corresponding substrate proteins, identifying several EGFR ubiquitylsites which may regulate EGFR abundance in LSCC. Finally, we identified the linear and spatial clustering of mutations and PTM sites, identifying multiple mutation-PTM clusters in cancer related genes, including TP53, PIK3CA, CTNNB1, EGFR, and IDH1. We envision that PTMcosmos will serve both the CPTAC consortium and the wider research community to better understand the role of PTMs in cancer.

Citation Format: Liang-Bo Wang, Akshay Govindan, Song Cao, Li Ding. PTMcosmos: A web portal of post-translational modifications and proteogenomic resources in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5027.
Abstract 5048: Imaging based EGFR mutation subtype classification using EfficientNet
Authors: Franklin Daniel L. , Pattilachan Tara , Magliocco Anthony
Published: June 2022

This study aimed to determine whether EfficientNet-B0 was able to classify EGFR mutation subtypes with H&E stained whole slide images of lung and lymph node tissue.

Background: Non-small cell lung cancer (NSCLC) accounts for the majority of all lung adenocarcinomas, with estimates that up to a third of such cases have a mutation in their epidermal growth factor receptor (EGFR). EGFR mutations can occur in various subtypes, such as Exon19 deletion, and L858R substitution, which are important for early therapy decisions. Here, we propose a deep learning approach for detecting and classifying EGFR mutation subtypes, which will greatly reduce the cost of determining mutation status, allowing for testing in a low resource setting.

Methods: An EfficientNet-B0 model was trained with whole slide images of lung tissue or metastatic lymph nodes with known EGFR mutation subtype (wild type, exon19 deletion or L858R substitution). Regions of interest were tiled into 512x512 pixel images. The RGB .jpeg tiles are augmented by rotating 90°, 180°, 270°, and mirroring. The model was initialized with random parameters and trained with a batch size of 32, a learning rate of 0.0001 for 1 epoch before the validation loss increased for the next 5 epochs.

Results: The model achieved a slide AUC of 0.8333, and a tile AUC of 0.8010. Slide AUC is the result of averaging all tiles within a slide and measuring performance based on correctly predicted slides (n=18). Tile AUC is the result of measuring performance based on correctly predicted tiles (n=102,000).

Conclusion: Using EfficientNet-B0 architecture as the basis for our EGFR mutation classification system, we were able to create a top performing model and achieve a slide AUC of 0.833 and tile AUC of 0.801. Healthcare providers and researchers may utilize this AI model in clinical settings to allow for detection of EGFR mutation from routinely captured images and bypass expensive and time consuming sequencing methods.

Table 1. Number of image tiles used and the number of slides they were extracted from. Train Validation Test Exon19 tiles 187,384 47,904 33,096 L858R tiles 166,288 19,512 26,136 Wild type tiles 225,944 27,696 42,768 Exon19 slides 47 6 6 L858R slides 46 6 6 WIld type slides 43 6 6

Citation Format: Daniel L. Franklin, Tara Pattilachan, Anthony Magliocco. Imaging based EGFR mutation subtype classification using EfficientNet [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5048.
Abstract 5080: Age- and pregnancy-related impact on soluble immune checkpoint protein profiles in mice as analyzed by a novel multiplex immunoassay
Authors: Lie Wen-Rong , Kornmeier Christine , Zeng Ling , Hoberg James
Published: June 2022

Immune checkpoint proteins are key regulators of the immune system and drug targets of cancer immunotherapy. There is extensive literature on the use of various types of mouse models for biomarker discovery and drug testing. Only a few studies have examined the association between soluble immune checkpoint proteins and the immune status. Following the development of multiplex immunoassay panels for profiling human co-inhibitory and co-stimulatory immune checkpoint proteins, here we report the development of a novel magnetic bead-based Luminex multiplex assay for the quantitative detection of 28 mouse immune checkpoint proteins and immune regulators in 25 μL of sample (PD-1, PD-L1, PD-L2, CTLA-4/CD152, TIM-3, LAG-3, B7-H2/ICOSL, B7-H3/CD276, BTLA, GITR, HVEM, CD27, CD40, CD80/B7-1, CD226/DNAM-1, 4-1BBL/TNFSF9, CD137/4-1BB, 5’-NT/CD73, BCA-1/CXCL13, CD25/IL-2Rα, Granzyme B, E-cadherin, Galectin-1, Galectin-3, IFNγ, IL-10, TLR-2, and TNFα). Immune function declines with age, while the incidence of cancer rises. In this study, we examined age-related serum samples by quantitative profiling soluble checkpoint proteins from young (age of 8-month-old, n=8) and old-aged mice (48-month-old, n=8) of C57BL/6 strain. A significant age effect was observed on the levels of soluble checkpoint proteins in mouse serum samples tested. Comparing with the young mice, decreased levels of circulating HVEM, Granzyme B, LAG-3, PD-L1, CD73, B7-H2, CD25, and CD27; and increased levels of circulating TIM-3, PD-1, PD-L2, CD40, Galectin-3, IL-10, BCA-1, and TLR-2 were observed in aged C57BL/6 mice (Mann Whitney test, P value <0.05). The immune system also changes during pregnancy. We used the similar multiplex array approach to profile the soluble checkpoint proteins in non-pregnant (n=16) and pregnant CD-1 mice (n=9). Significant decreased levels of soluble LAG-3, B7-H2, B7-H3, CD25, CD27, and Galectin-1; and significant increase of soluble CD137, Galectin-3, and CD73 expression levels were detected in the serum samples of pregnant mice, as compared to the samples from the non-pregnant mice (Mann Whitney test, P value <0.05). Altogether, using bead-based quantitative multiplex analysis, our results demonstrate that the changes on circulating immune checkpoint protein profiles occur in the immunologic adaptations with age and during pregnancy in mice.

Citation Format: Wen-Rong Lie, Christine Kornmeier, Ling Zeng, James Hoberg. Age- and pregnancy-related impact on soluble immune checkpoint protein profiles in mice as analyzed by a novel multiplex immunoassay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5080.
Abstract 5081: Proteomic analysis of ascites- and cancer cell-derived EVs for identifying ovarian cancer diagnostic biomarkers
Authors: Wang Wenyu , Han Dohyun , Song Yong Sang
Published: June 2022

Ovarian cancer is the most lethal gynecologic cancer in the world. Most patients are diagnosed at advanced stages with the formation of ascites. Extracellular vesicles (EVs) have been elucidated to play a pivotal role in cancer development and progression, also emerging as promising resources for clinical biomarkers in liquid biopsy. In this study, we aim to identify cancer-specific protein biomarkers in ascites-derived EVs for ovarian cancer diagnosis. Malignant ascites from high grade ovarian cancer patients (HGSOC) and benign peritoneal fluids from female patients with benign gynecologic diseases were collected with informed consent. EVs were isolated from these biofluids using the Exoquick kit. Meanwhile, HGSOC cell lines and normal cell lines were cultured in conditioned media supplemented with EVs-depleted FBS. EVs were isolated from the culture media. Proteins were extracted from EVs and fragmented into peptides. Tandem mass tag (TMT) hyper multiplex quantitation assay was carried out to detect the EV proteomic profiling. EVs isolated from biofluids and cell culture media were identified as double-membrane nanoparticles sizing ranging from 30nm to 200nm. Proteomic analysis of biofluids-derived EVs showed that malignant ascites-derived EVs displayed different proteomic profiling compared to benign peritoneal fluids-derived EVs. The differently expressed proteins between malignant ascites-derived EVs and benign peritoneal fluids-derived EVs were defined as candidate EV protein biomarkers. In addition, proteins that were expressed in at least one cancer cell line-derived EVs but not expressed in normal cell line-derived EVs were also identified as ovarian cancer-specific proteins. A diagnostic model constructed based on the integrative analysis of candidate EV protein biomarkers and ovarian cancer-specific proteins yielded a good discrimination ability between benign and cancer patients.In conclusion, this study demonstrates the distinct proteomic profiling in ascites- and cancer cell-derived EVs in ovarian cancer, which sheds new light on implementing EV proteins as a potential diagnostic strategy in clinical settings.

Citation Format: Wenyu Wang, Dohyun Han, Yong Sang Song. Proteomic analysis of ascites- and cancer cell-derived EVs for identifying ovarian cancer diagnostic biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5081.
Abstract 5091: The early change of serum interleukin 14α levels predicts the response to anti-PD-1 therapy in cancer
Authors: Wang Bu Hai , Chen Cai Yue , Zhang Xian , Huang Yu Xiang , Zeng Yi Chun , Li Lei , Wang Mao Qi , Guo Jing Liang , Li Qiu Xian , Shen Long , Gu Juan J. , Liang Yi Chen
Published: June 2022

Background: Targeting programmed cell death-1 (PD-1) or programmed cell death ligand-1 (PD-L1) has been shown improved clinical efficacy in a wide range of tumor types. We evaluated serum interleukin 14α (IL14α) as a biomarker to predict the response of anti- PD-1 therapy.

Patients and methods: Thirty advanced cancer patients treated with PD-1 inhibitor were enrolled in this study. Serum levels of IL-14α were tested at baseline and after 2 cycles of treatment.

Result: Among these 30 patients, the mean expression level of IL14α before treatment was 2.1±1.21, whereas the mean level of IL14α after 2 cycles was 1.99±0.82. There were no association between the expression levels of IL14α and clinical outcome. Early change of IL14α after 2-cycles of anti-PD-1 therapy was calculated as delta IL14α % change = (IL14α level after 2 cycles - IL14α level before treatment)/IL14α level before treatment*100%. Receiver operating characteristic (ROC) was analyzed to get a cutoff point of delta IL14α % change as 2.46% (Sensitivity 85.71%, Specificity 62.5%; AUC=0.7277, P=0.034). Using this cutoff to subgroup the patients, we found higher delta IL14α % change was significantly associated with superior overall response to anit-PD-1 therapy (p=0.0072) and had a better progression free survival (p=0.0039).

Conclusion: Early changes of serum IL14α level may be a useful predicting factor in advanced cancer patients with anti-PD-1 therapy.

Keywords: IL14α, serum biomarker, anti-PD-1 therapy response, cancer

Citation Format: Bu Hai Wang, Cai Yue Chen, Xian Zhang, Yu Xiang Huang, Yi Chun Zeng, Lei Li, Mao Qi Wang, Jing Liang Guo, Qiu Xian Li, Long Shen, Juan J. Gu, Yi Chen Liang. The early change of serum interleukin 14α levels predicts the response to anti-PD-1 therapy in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5091.
Abstract 5100: Analysis of genetic alterations related to hyper-progressive disease after immunotherapy in patients with non-small cell lung cancer
Authors: Xiang Xudong , Zhang Hushan , Wang Deguang , Li Heng , Lei Qing , Ma Qianli
Published: June 2022

Background Hyper-progressive disease (HPD) is an unexpected response pattern observed in immune checkpoint therapy, such patients experience a very rapid disease progression (usually progressed seriously in three months). Predictors of HPD are one of the keys to the management of patients receiving immune checkpoint inhibitors. Some factors, such as MDM2/4 amplification, EGFR mutations and old age may be risk factors for HPD, but the results of different studies are inconsistent. Herein, we evaluated the characteristics of MDM2/4 alterations in Chinese patients with NSCLC.

Methods The formalin-fixed paraffin-embedded specimens of cancer patients who have underwent next-generation sequencing (NGS) in 3D Medicines, a laboratory accredited by CAP and Clinical Laboratory Improvement Amendments (CLIA) from May 2017 to May 2020, were included in this study. NGS was performed to detect gene mutation, and tumor mutational burden (TMB) measured by a 733 gene panel. PD-L1 expression detected by using Dako PD-L1 IHC 22C3 pharmDx.

Results The proportion of MDM2/4 amplification in Chinese NSCLC patients is 0.86%, the proportion of MDM2 and MDM4 amplification in Chinese NSCLC patients were 0.74% and 0.12%. respectively. Further analysis found lower TMB level in patients with MDM2/4 amplification than patients without MDM2/4 amplification (p<0.001). The median TMB level was also found lower in patients with MDM2/4 amplification than without, and higher ratio of patients with TMB-high (defined as TMB≥10mutant/Mb) was displayed in group with MDM2/4 amplification. Conversely, patients with TMB-high showed lower copy number gain in MDM2/4. However, no difference was found in level of PD-L1 expression between patients with and without MDM2/4 amplification.

Conclusion HPD happened during ICI treatment in solid tumor with MDM2/4 amplification may associated with lower TMB level, and PD-L1 expression level has limit effect on MDM2/4 alteration related HPD.

Citation Format: Xudong Xiang, Hushan Zhang, Deguang Wang, Heng Li, Qing Lei, Qianli Ma. Analysis of genetic alterations related to hyper-progressive disease after immunotherapy in patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5100.
Abstract 5126: PIANOS: A platform independent and normalization free single-sample classifier for colorectal cancer
Authors: Cai Du , Qi Haoning , Wang Wei , Zhong Min-Er , Fan Dejun , Li Cheng-Hang , Wu Xiaojian , Gao Feng
Published: June 2022

Objective: Identifying robust prognostic biomarkers of colorectal cancer (CRC) will significantly improve patients’ outcomes. However, due to the difference in detection methods, sequencing platforms and cohort populations, most of the previous molecular biomarkers were unable to cope with batch effects and rely on normalization algorithms, which might result in “test set bias”. This study aims to develop and validate a platform-independent single-sample prognostic model for colorectal cancer without the need for normalization.

Methods: A total of 2510 colorectal cancer patients from 13 microarray or sequencing cohorts with complete follow-up data were included in this study. The resampling algorithm and gene pair method were combined to improve the stability of the model. After 1000 times of resampling in the training cohort, an ensemble model was constructed by selecting the k-TSP (k-Top Scoring Pairs) classifiers with high balanced accuracy. The Decision-making process in each level was generated by voting, without the need for any cutoff value. C index and D index were used to evaluate the performance of the model.

Results: We constructed an ensemble model called “PIANOS”, which could significantly predict the prognosis of CRC in all 13 cohorts. The meta-estimated C index and D index of the PIANOS model were 0.74 (95%CI: 0.71-0.78, P < 0.001) and 2.77 (95%CI: 2.37-3.18, P < 0.001), respectively. After adjusting for clinicopathological factors, PIANOS was still independently associated with the prognosis of CRC. PIANOS also showed superior prognostic value when compared with previously published gene signatures or consensus molecular subtypes (CMS). GSEA analysis found that the high-risk group was enriched in angiogenesis, TGF-β and epithelial-mesenchymal transition (EMT) pathway, which was consistent with the characteristics of the CMS4 subtype in colorectal cancer.

Conclusion: The PIANOS could robustly predict the prognosis of colorectal cancer across different cohorts and platforms, without the need for any normalization, which is promising for refining treatment decisions in clinical practice.

Citation Format: Du Cai, Haoning Qi, Wei Wang, Min-Er Zhong, Dejun Fan, Cheng-Hang Li, Xiaojian Wu, Feng Gao. PIANOS: A platform independent and normalization free single-sample classifier for colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5126.