bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Current Status and Challenges of Vaccination Therapy for Glioblastoma
Authors: Hosseinalizadeh Hamed , Rahmati Mohammad , Ebrahimi Ammar , O'Connor Roddy S.
Published: April 2023

Abstract
Glioblastoma (GBM), also known as grade IV astrocytoma, is the most common and deadly type of central nervous system malignancy in adults. Despite significant breakthroughs in current GBM treatments such as surgery, radiotherapy, and chemotherapy, the prognosis for late-stage glioblastoma remains bleak due to tumor recurrence following surgical resection. The poor prognosis highlights the evident and pressing need for more efficient and targeted treatment. Vaccination has successfully treated patients with advanced colorectal and lung cancer. Therefore, the potential value of using tumor vaccines in treating glioblastoma is increasingly discussed as a monotherapy or in combination with other cellular immunotherapies. Cancer vaccination includes both passive administration of monoclonal antibodies and active vaccination procedures to activate, boost, or bias antitumor immunity against cancer cells. This article focuses on active immunotherapy with peptide, genetic (DNA, mRNA), and cell-based vaccines in treating GBM and reviews the various treatment approaches currently being tested. Although the ease of synthesis, relative safety, and ability to elicit tumor-specific immune responses have made these vaccines an invaluable tool for cancer treatment, more extensive cohort studies and better guidelines are needed to improve the efficacy of these vaccines in anti-GBM therapy.
Abstract 123: Molecular mechanisms of RNA and DNA editing in leukemic transformation of hemopoietic stem and progenitor cells
Authors: Isquith Jane Marie , Pham Jessica , Whisenant Thomas , Balaian Larisa , Jamieson Catriona
Published: April 2023

Dysregulation of inflammatory cytokine responsive APOBEC3 cytosine deaminases has been shown to be a contributing factor in cancer evolution, presenting as gene expression changes and inclusion of distinct C-to-T mutation patterns. However, the context specificity and mechanisms by which APOBEC3 enzymes promote cancer initiation and progression require further elucidation. Lentiviral overexpression of APOBEC3C and an editase deficient APOBEC3C mutant in healthy cord blood, bone marrow and MPN patient hematopoietic stem/progenitor cells (HSPCs) allows us to study the effects of innate immune deaminase dysregulation in the hematopoietic niche. We are focusing on the upregulation of APOBEC3C and adenosine deaminase acting on RNA1 (ADAR1), as we have previously shown them to be contemporaneously upregulated in the high-risk myelofibrosis (MF) stem cell population compared to normal aged bone marrow. We can compare these novel differential gene expression changes, RNA hyper-editing sites, and DNA mutation signatures induced by APOBEC3 mutagenesis to abnormalities seen in both hematopoietic malignancies and solid tumor cancers. Gene set enrichment analysis (GSEA) performed on this dataset has exposed numerous deregulated pathways brought on by exaggerated levels of APOBEC3, including changes in splicing pathways. To further investigate the complex relationship between splicing and deaminase deregulation, we treated myeloproliferative neoplasm patient samples and normal HPSCs with Rebecsinib (also known as 17S-FD-895), a pharmacologically stable, potent, and selective small molecule splicing modulator, which interestingly caused significant downregulation of APOBEC3C. We will continue to investigate these findings as a potential target to correct the dysregulation seen in MPN progression. Consequently, we aim to use these findings to identify predictive biomarkers and druggable targets of leukemic initiation progression.

Citation Format: Jane Marie Isquith, Jessica Pham, Thomas Whisenant, Larisa Balaian, Catriona Jamieson. Molecular mechanisms of RNA and DNA editing in leukemic transformation of hemopoietic stem and progenitor 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 123.
Abstract 1269: Evaluating the effect of metformin on components of extracellular matrix in colorectal cancer
Authors: Kaur Amar Preet , Bhattacharya Aditi , Bhat Muzaffer Ahmed , Bansal Aakriti , Sen Sudip
Published: April 2023

Introduction: Colorectal cancer (CRC) is the third most common cancer worldwide, and is associated with high morbidity and mortality. Approximately 50% of all CRC patients develop metastases. Tumor microenvironment (TME), including extracellular matrix (ECM), plays an important role in tumor progression and metastasis in CRC, indicating an important role of agents targeting ECM in the treatment of CRC. ECM acts as niche to support cancer cells. In this study, the role of metformin as a therapeutic agent in modulating ECM components of CRC has been studied.

Methods: HCT116 (aggressive, poorly differentiated) and HT 29 (less aggressive, moderately differentiated), human CRC cell lines were treated with different doses of metformin (0.1, 2.5 and 5 mM) for 14 days in vitro and subsequently microarray analysis was done to identify differentially expressed genes. To observe the role of metformin in modulating the ECM, ECM-receptor interaction pathway was given primary focus among the list of pathways identified by DAVID (Database for Annotation, Visualization and Integrated Discovery) bioinformatics resources. The seven differentially expressed genes of ECM-receptor interaction pathway (elucidated by microarray) were -COL3A1, COL4A2, COL5A2, VTN, ITGA6, TNXB and LAMC3. These genes were validated using RT-qPCR in both the cell lines. Protein expression was analyzed by Western blotting. Immunohistochemistry (IHC) was done in different histopathological grades of CRC samples to evaluate the expression and localization of ECM proteins.

Results: The gene expression of COL4A2, COL5A2, ITGA6, VTN and TNXB by RT-qPCR was decreased with metformin treatment and these results were consistent with microarray data. However, discrepancy was observed in the gene expression of COL3A1 and LAMC3 between microarray and RT-qPCR. Expression of COL3A1, VTN was found to be increased whereas a decrease in expression of ITGA6 was observed in different histopathological grades of CRC samples with IHC. The expression of PI3K and AKT proteins were decreased in HCT116 cells with metformin treatment justifying its anticancer properties.

Conclusions: Anticancer role of metformin via mTOR and PI3K-AKT signaling has been studied before, but this study identifies the novel ECM proteins in CRC that can be modulated by metformin. The results from this study indicates the promising role of metformin in CRC as it is associated with very less side effects and can influence various aspects of cancer biology.

Citation Format: Amar Preet Kaur, Aditi Bhattacharya, Muzaffer Ahmed Bhat, Aakriti Bansal, Sudip Sen. Evaluating the effect of metformin on components of extracellular matrix in colorectal cancer [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 1269.
Abstract 1357: Alpha-synuclein may promote melanoma progression by modulating the levels of tetraspanin proteins
Authors: Aloy Nirjhar Mandal , Graner Michael W. , Witt Stephan N.
Published: April 2023

Alpha-synuclein (α-syn; encoded by gene SNCA), which is an intrinsically disordered protein belonging to the synuclein family, is a common biological factor in Parkinson’s disease and melanoma. Aggressive melanomas express high levels of α-syn, but the precise biological role of this protein in melanoma progression is not known. Our group has previously reported that α-syn promotes the release of extracellular vesicles (EVs) and regulates the trafficking of transferrin receptor in melanoma cells. During our studies of exosomal/EV markers, we found that CD81 and CD9, two key members of the tetraspanin family, were significantly downregulated in SK-MEL-28 SNCA-knock out clones compared to control cells. In contrast, a robust upregulation of CD63, another tetraspanin protein, was observed in SNCA-KO cells, which might be due to a compensatory mechanism for the downregulation of CD81 and CD9. CD81 and CD9 have been proposed as potential therapeutic targets, and CD63 was proposed as a positive prognostic marker in melanoma in numerous studies. Our group has previously shown that knocking out α-syn causes decreased tumor growth in vivo and in vitro. We hypothesize that α-syn regulates the levels of these tetraspanins, possibly by sorting into heterogeneous multivesicular bodies and modulating the exosomal secretion and lysosomal degradation of these proteins. This might be one of the principal mechanisms by which α-syn promotes progression of melanoma. We also have initial evidence from transmission electron microscopy (TEM) that depletion of α-syn causes the morphological alterations of plasma-membrane structure in melanoma cells, and it is known that CD9, CD81 and CD63 are important transmembrane proteins involved in membrane organization. This is the very first report of α-syn as a regulator of cellular homeostasis of CD9, CD81 and CD63, and further work is needed to understand the underlying mechanism.

Citation Format: Nirjhar Mandal Aloy, Michael W. Graner, Stephan N. Witt. Alpha-synuclein may promote melanoma progression by modulating the levels of tetraspanin proteins [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 1357.
Abstract 143: A platform for deep evolutionary profiling of cancer resistance
Authors: Ravi Arvind , Sontha Sainikhil , Chowdhury Maisha , Smigiel Jacob , Rees Matthew , Danysh Brian , Roth Jennifer , Parida Laxmi , Lander Eric , Getz Gad
Published: April 2023

Despite the introduction of a number of new therapeutic classes including targeted inhibitors, immunotherapy, and antibody-drug conjugates, the ability to achieve long-term disease control in the majority of patients with advanced cancer remains elusive due to the emergence of resistance. While our understanding of resistance mechanisms continues to expand through preclinical and clinical sequencing efforts, comprehensive approaches to map the distribution of potential resistance mechanisms in a given cell line and drug context require the development of novel approaches.

Here, we describe the design of a platform for profiling cancer resistance at scale. Beginning with a single sensitive parental cancer cell line, the EGFR-mutant lung cancer line PC9, we optimize pre-existing diversity using a combination of single-cell subcloning and alkylator mutagenesis, and generate 50 independently evolved clones resistant to the EGFR inhibitor osimertinib. Profiling of this library via multiplexed whole genome sequencing (WGS) demonstrates convergent mutations in the MAPK pathway. Taking a similar approach, we profile the NTRK1-fusion-driven KM12 colon cancer cell line, yielding convergent, clinically observed, on-target resistance mutations to the NTRK inhibitor larotrectinib.

Taken together, these results provide an initial proof-of-concept for the high-throughput generation of viable drug-resistant cancer clones. Future efforts to increase mutational diversity as well as assess additional drug and disease contexts will broaden the utility of this approach.

Citation Format: Arvind Ravi, Sainikhil Sontha, Maisha Chowdhury, Jacob Smigiel, Matthew Rees, Brian Danysh, Jennifer Roth, Laxmi Parida, Eric Lander, Gad Getz. A platform for deep evolutionary profiling of cancer resistance [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 143.
Abstract 1452: Big data analysis revealed signalling activity and key regulators in human prostate cancer cell lines
Authors: Cheng Siyuan , Li Lin , Yu Xiuping
Published: April 2023

Background: Human prostate cancer (PCa) cell lines are the most used models for research. The commonly used PCa cell lines can be roughly categorized into 3 groups: androgen receptor (AR)+, neuroendocrine (NE)+ and double negative (AR- NE-) cell lines. However, although these cell lines have been extensively used in PCa research since their establishment decades ago, a global molecular characterization of these cell lines is still lacking, especially in the aspect of cell signaling activity and their clinical relevance, which requires a large scale of data mining.

Methods: The RNA-seq, DNA-seq and proteomic datasets were gathered from public cohort and our lab’s collection. From these data, a PCa cell line multi-omics database (PCMD) was established. Single sample gene set enrichment analysis (ssGSEA) was used to reveal the signaling pathways enriched in each PCa cell line. Additionally, human PCa patient single cell RNAseq data-based deconvolution and human PCa patient bulk RNAseq data-based nearest-neighbor (NN) graph analysis were used to evaluate the clinical relevance of each PCa cell line. The DNA-seq, ATAC-seq, DNase HS-seq and Bisulfite-seq datasets were used to annotate the key genes.

Results: The PCMD database was established by compiling more than 1000 RNASeq datasets derived from various PCa cell lines. The important signaling pathways and transcription factors were revealed for each PCa cell line. Further, the cell lines were annotated with relative clinical stages. Additionally, an interactive webApp was established for scientists to explore and visualize PCMD data.

Conclusion: our research characterized PCa cell lines using unbiased strategies and large sample number. It is our hope that this study would aid researchers to develop hypothesis and choose appropriate cell line to use.

Funding: This study is supported by: Feist-Weiller Cancer Center, LSU Health Shreveport.

Citation Format: Siyuan Cheng, Lin Li, Xiuping Yu. Big data analysis revealed signalling activity and key regulators in human prostate cancer cell lines [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 1452.
Abstract 1918: Reducing human papillomavirus associated cancers and disparities among Hispanics/Latinos through the adapted NCI NON CHE (National Outreach Network Community Health Education) program
Authors: Ramos Alejandra , Aristizabal Carolina , Baezconde-Garbanati Lourdes
Published: April 2023

While HPV vaccination has dramatically reduced HPV-related cancer incidences in certain demographic groups, it continues to disproportionately affect Hispanics/Latinos. The NON CHE program at (USC), (NCCC), aims to understand the gaps in Human Papillomavirus (HPV) knowledge and vaccination uptake, cervical cancer screenings, and addresses the barriers to participating in clinical trials (CT) by conducting culturally-sensitive educational workshops to the community.

Methods: Materials such as a PowerPoint presentation and Human Papillomavirus Vaccination (HPV) infographics were adapted by the NCI to ensure the message can influence the target audience. Educational workshops were conducted via Zoom. Recruitment of participants were facilitated by partnering with community organizations across Los Angeles County (LAC) which is NCCC’s catchment area. The effectiveness of the workshops was assessed by delivery of pre and post surveys that captured demographics and a series of true and false questions that measured HPV knowledge. 3- and 6-month follow-up surveys are distributed among participants of those of age 18 - 26 and to parents of children 9 - 18 years of age to assess vaccination intake.

Results: A total of 1,515 people have been reached during educational workshops, health fairs, and outreach events from October 2021 to September 2022. Our results demonstrate that the 236 participants, (55.6%) Spanish-speaking and (26.9%) English-speaking had not heard of HPV indicating the sparse availability and accessibility of information contributing to parents’

unfamiliarity of the HPV vaccine (79.5%) between the two groups. However, there was a positive distribution of likely to get vaccine (72.88%) and likely to vaccinate their children (47.88%.) Their lack of awareness stemmed from lack of provider motivation (44.2%) and limited health education (39.5%.)

Conclusion: Conducting culturally tailored educational workshops to disseminate information on Human Papillomavirus (HPV) has helped Hispanics/Latinos understand what HPV is and reduce the stigma. Effective dissemination of HPV education requires it to be inclusive, concise, and engaging to motivate community members to seek preventive care.

Citation Format: Alejandra Ramos, Carolina Aristizabal, Lourdes Baezconde-Garbanati. Reducing human papillomavirus associated cancers and disparities among Hispanics/Latinos through the adapted NCI NON CHE (National Outreach Network Community Health Education) program [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 1918.
Abstract 1931: Racialized economic segregation and late-stage colorectal cancer in the United States, 2009-2017
Authors: Santiago-Rodriguez Eduardo J. , Shariff-Marco Salma , Bailey Zinzi D. , White Justin S. , Allen Isabel E. , Hiatt Robert A.
Published: April 2023

We examined the association between racialized economic segregation and late-stage colorectal cancer (CRC) in the US. All CRC cases diagnosed during 2009-2017 were identified using the United States Cancer Statistics database. Late-stage CRC was determined according to the presence of distant involvement (node or site) of the tumor at diagnosis. Racialized economic segregation was measured at the county level by the Index of Concentration at the Extremes (ICE) using the 2013-2017 American Community Survey estimates. ICE was calculated to show the extent to which individuals’ residence at diagnosis was located in counties of concentrated advantage or disadvantage. Four ICE metrics were considered, consisting of the difference between the number of households with White individuals reporting incomes in the top quintile of the US distribution, and the number of households with non-White (all people of color (POC), Black, Latino, or Asian American/Pacific Islander) individuals reporting incomes in the lowest quintile, divided by the total of households in the county. ICE metrics were further divided into quintiles based on the distribution of all counties in the US, with Q1 denoting least advantaged counties and Q5 the most advantaged counties. Multilevel logistic regression models accounting for clustering at counties were fit. Models were adjusted for age at diagnosis, sex, race and ethnicity, census region and year of diagnosis. A total of 1,356,053 cases were included in the analysis; mean age at diagnosis was 67 years, 52% were men, and 20% of cases had a late-stage diagnosis. In adjusted analysis for ICE-POC, people residing in less advantaged counties had higher odds of late-stage diagnosis than people residing in the most advantaged counties (OR [95% CI], Q1: 1.08 [1.05-1.11], Q2: 1.06 [1.04-1.09], Q3: 1.04 [1.02-1.07], Q4: 1.03 [1.01-1.05], Q5: reference). Similar results were observed on all four ICE metrics. Racialized economic segregation was associated with higher odds of late-stage CRC. These findings underscore the role of institutionalized racism as a driver of health inequities, with laws and policies that led to residential segregation also impacting the conditions for timely preventive care.

Citation Format: Eduardo J. Santiago-Rodriguez, Salma Shariff-Marco, Zinzi D. Bailey, Justin S. White, Isabel E. Allen, Robert A. Hiatt. Racialized economic segregation and late-stage colorectal cancer in the United States, 2009-2017 [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 1931.
Abstract 1934: Incidence and survival outcomes of younger adults with colorectal cancers by age group: a SEER analysis
Authors: Aqeel Sheeba Ba , Groman Adrienne , Attwood Kristopher , Iyer Renuka , Mukherjee Sarabjit , Vadehra Deepak
Published: April 2023

Background: The incidence of colorectal cancer (CRC) is increasing in younger adults (<50 years). Most cases occur between 40 and 49 years. Adolescents and young adults (AYA,15-39 years) with CRC have more aggressive disease. We sought to compare the incidence and outcomes of CRC in AYA with patients in the 40-49 age group.

Methods: Surveillance, Epidemiology, and End Result (SEER) was analyzed from 2000-2019. Survival outcomes were analyzed using Kaplan-Meier methods, and comparisons were made using the log-rank test. Cox regression models were used to evaluate univariate and multivariate associations with survival outcomes. SAS v9.4 (Cary, NC) and SEER*Stat v8.4 were used, with a significance level of 0.05.Results: A total of 13,877 AYA patients and 43,771 patients in the age group 40-49 years were identified. The annual incidence rate per 100,000 AYA patients increased from 3.1 in 2000 to 5.3 in 2019. In the 40-49 cohort, the annual incidence rate per 100,000 increased from 21.6 in 2000 to 28.0 in 2019. The annual percent change for incidence for the AYA cohort was higher 3.1% (95% CI 2.8,3.4) than the 40-49 cohort 1.4% (95% CI 1.2,1.6). The 2-year overall survival (OS) rate was not different among the two groups. Disease-specific survival (DSS) was slightly but significantly inferior in the AYA group, 83% (95%CI 0.82,0.83) compared to in the 40-49 cohort, 84% (95%CI 0.83,0.84). Factors associated with inferior DSS in the AYA group were male sex, black race, advanced stage, lack of chemotherapy, and longer time to treatment.

Conclusion: Our study shows that the annual percent change in incidence rate was higher in AYA patients compared to those in the 40-49 age group from 2000-2019. DSS was slightly lower in AYA patients; OS was similar in both groups. Further studies are needed to understand the discrepancies.

Table 1: Baseline characteristics of AYA and 40-49yr patients AYA 13877(24.1%) 40-49yr 43771(75.9%) Overall 57648(100%) P value Age at diagnosis Mean/Standard deviation 34/4.6 45.5/2.8 42.7/5.9 <0.001 Gender Male 51.9% 53.6% 53.2% <0.001 Race Non-Hispanic White 54.2% 59.4% 58.2% <0.001 Non-Hispanic Black 12.1% 13.3% 13% Asian or Pacific Islander 33% 26.7% 28.2% Unknown 0.6% 0.6% 0.6% Stage Localized 22.2% 26.5% 25.5% <0.001 Regional 31.6% 30.2% 30.6% Distant 20% 19.2% 19.4% Unstaged 1.8% 1.7% 1.7% Blank 24.4% 22.3% 22.8% Chemotherapy No/Unknown 33.8% 39.4% 38.1% <0.001

Citation Format: Sheeba Ba Aqeel, Adrienne Groman, Kristopher Attwood, Renuka Iyer, Sarabjit Mukherjee, Deepak Vadehra. Incidence and survival outcomes of younger adults with colorectal cancers by age group: a SEER analysis [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 1934.
Abstract 1935: Racial and ethnic disparities in survival among women with advanced-stage ovarian cancer who received systemic therapy: A National Cancer Database analysis
Authors: Washington Caretia J. , Karanth Shama D. , Braithwaite Dejana , Akinyemiju Tomi F.
Published: April 2023

Purpose: To evaluate the association between race and ethnicity and all-cause mortality among women with advanced-stage ovarian cancer who received systemic therapy.

Methods: We obtained data from the National Cancer Database on women diagnosed with advanced-stage ovarian cancer from 2004 to 2015. Multivariable Cox proportional hazards models were used to calculate hazard ratios (HR) and 95% confidence intervals (95% CI) by race and ethnicity groups (non-Hispanic (NH)-White, NH-Black, Hispanic, NH-Asian/Pacific Islander, and Other) and to examine the association of race/ethnicity with survival, stratified by age and comorbidity while adjusting for clinical and demographic variables.

Results: There were 53,367 women (52.4% ages ≥ 65 years, 8.7% NH-Black, 5.7% Hispanic, and 2.7% NH-Asian/Pacific Islander) included in the analysis. NH-Black women had a higher risk of death compared to NH-White women (HR: 1.13; 95% CI: 1.07,1.18), while Hispanic women had a lower risk of death compared to NH-White women (HR: 0.89; 95% CI: 0.82,0.97). The Black-White disparity persisted for women ages < 65 years and ≥ 65 years, and among women with no comorbidities (HR:1.14; 95% CI: 1.08,1.21).

Conclusion: Among women with advanced-stage ovarian cancer who received systemic therapy, NH-Black women experienced decreased survival compared with NH-White women, regardless of age and comorbidity status. Additional research is essential to identify drivers of ovarian cancer disparities, including racial differences in treatment response.

Citation Format: Caretia J. Washington, Shama D. Karanth, Dejana Braithwaite, Tomi F. Akinyemiju. Racial and ethnic disparities in survival among women with advanced-stage ovarian cancer who received systemic therapy: A National Cancer Database analysis [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 1935.
Abstract 2069: ScNanoGPS: A robust tool for simultaneous calculation of same-cell genotypes and phenotypes from single cell long read transcriptomes
Authors: Shiau Cheng-Kai , Lu Lina , Kieser Rachel , Fukumura Kazutaka , Pan Timothy , Lin Hsiao-Yun , Yang Jie , Tong Eric L. , Lee GaHyun , Yan Yuanqing , Huse Jason T. , Gao Ruli
Published: April 2023

Single-cell Nanopore sequencing of full-length mRNAs is transforming single-cell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to compute same-cell genotype and phenotype without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long reads into single cells and single molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (single nucleotide variants) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms. In a kidney tumor, we identified 924 genes with distinct combinations of isoforms involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. In summary, scNanoGPS facilitates applications of single-cell long-read sequencing.

Citation Format: Cheng-Kai Shiau, Lina Lu, Rachel Kieser, Kazutaka Fukumura, Timothy Pan, Hsiao-Yun Lin, Jie Yang, Eric L. Tong, GaHyun Lee, Yuanqing Yan, Jason T. Huse, Ruli Gao. ScNanoGPS: A robust tool for simultaneous calculation of same-cell genotypes and phenotypes from single cell long read transcriptomes [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 2069.
Abstract 2070: Accelerated somatic mutation calling tool for whole-genome and whole-exome sequencing data from heterogenous tumor samples
Authors: Ji Shuangxi , Zhu Tong , Sethia Ankit , Montierth Matthew D. , Wang Wenyi
Published: April 2023

As constantly improving in capacity and reducing in price, genomic sequencing is becoming a routine part of medical practice for cancer patients. Variant calling in sequencing data is a fundamental prerequisite for any downstream analysis, thus playing a critical role in both basic research and clinical care of cancers. However, it remains notably time-consuming for most available tools (e.g., ~2 days for MuSE 1.0 and MuTect2 to complete running on one tumor-normal pair of whole-genome sequencing (WGS) data). Here, we launch MuSE 2.0, which maintains the same input and output as our previously released MuSE 1.0, but speeds up significantly for both whole-exome sequencing (WES) and WGS data. MuSE 2.0 employs a multithreaded producer-consumer model and the OpenMP library for parallel computing, including parsing and uncompressing reads from BAM files, detecting and filtering variants, and writing output. Using sample data from ICGC and TCGA, we have benchmarked the speed performance of MuSE 2.0 against MuSE 1.0, MuTect2, SomaticSniper and VarScan2, which are chosen as the somatic mutation callers in the GDC DNA-seq analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/). Compared to MuSE 1.0, MuSE 2.0 with 80 cores reduces the time cost of SNV calling from ∼40 hours per pair of tumor-normal WGS data down to less than 1 hour, and from 2-4 hours per pair of tumor-normal WES data down to 4-5 minutes (~50-60 times speedup). It is also faster than three other methods (up to 60 times), i.e., MuTect2, VarScan2 and SomaticSniper, for both WGS and WES data. These results show that MuSE 2.0 is a time-efficient tool and is expected to remove somatic mutation calling as a time-consuming obstacle for cancer genomic studies and clinicians decision making. MuSE 1.0 was adopted in multiple large-scale pipelines, including as a major contributing caller to reach final consensus calls by the TCGA PanCanAtlas project across 13,000 tumor samples, and the ICGC Pan-Cancer Analysis of Whole Genomes (PCAWG) initiative across 2,700 tumor samples. We therefore expect MuSE 2.0 to significantly accelerate the variant calling process and benefit the scientific and clinical communities. MuSE 2.0 is implemented in C++ and is freely available at GitHub https://github.com/wwylab/MuSE.

Citation Format: Shuangxi Ji, Tong Zhu, Ankit Sethia, Matthew D. Montierth, Wenyi Wang. Accelerated somatic mutation calling tool for whole-genome and whole-exome sequencing data from heterogenous tumor samples [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 2070.
Abstract 2077: Spatial analyses methods for visualization and interrogation of tumor immune micro-environment using multiplexed images
Authors: Kewale Vidhya , Das Komal
Published: April 2023

Immunotherapies are new and promising treatments but work only for a small subset of patients. IHC staining is the current standard technique for diagnosing and a commonly used research technique but only allows for evaluation of one, or maximum two, biomarkers at a time. Multiplexed immunofluorescence assays and multispectral imaging technology can label up to six biomarkers on the same tissue section to capture the tumor-immune tissue environment complexity at the single-cell level. These images are very data-rich, but the crowding of information on the tissue can make it difficult to derive meaning directly from the multiplexed images. Current commercial and open-source software has the capability to segment each cell and quantify each biomarker; however, there are not yet any computational tools to capture spatial relationships. With R programming, we developed a toolkit to quantify and visualize multiplexed imaging data for detailed quantification and spatial analysis. Using our computational toolkit, novel questions about the tissue behavior can be addressed, such as tissue heterogeneity, different cell types, cell functional status (naïve, exhausted, experienced, etc.), spatial visualization and quantification of expression level of biomarkers across the tissue, proximity and interaction of different cell types at the single cell level, and much more. We plan to release this toolkit as a web-based R-Shiny app to allow biologists and clinicians to upload their multiplexed imaging data and choose combinations of cell characteristics they would like to analyze. The power of multiplex imaging is the detailed spatial data it provides, and our data analytics methods can be used to effectively extract relevant information about single-cell level relationships.

Citation Format: Vidhya Kewale, Komal Das. Spatial analyses methods for visualization and interrogation of tumor immune micro-environment using multiplexed images [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 2077.
Abstract 2165: Identification and characterization of Karyopherin α2 (KPNA2), a member of the nucleocytoplasmic transporter family, in lung cancer
Authors: Kim Seoree , Lee Heejin , Yoon Jung-Sook , Lee Hyun Woo , Kang Seok Yun , Lee Ji Hyun , Chun Sang Hoon , Won Hye Sung , Hong Soon Auck , Kang Keunsoo , Ahn Young-Ho , Ko Yoon Ho
Published: April 2023

Introduction: Many oncologists began to make sense, that the Karyopherin a-2 (KPNA2), a nucleocytoplasmic transport protein, regulates the nuclear import of macromolecules and changes in cellular phenotype. In particular, it can be a poor prognostic marker by causing aberrant subcellular localization of DNA damage response proteins or OCT4-c MYC pathway molecules depending on the type of carcinoma. An association with the p53 oncogenic pathway has been reported, showing good prognostic values in other types. We aimed to investigate the clinical significance and metabolic pathway of stable CAF and cancer cells for KPNA2

Method: We retrospectively analyzed the data from NSCLC patients receiving curative resection in Uijeongbu and Bucheon St. Mary’s Hospitals (n=165). IHC staining was performed on the tumor microarray samples using antibodies against KPNA2. The positivity was defined as median value of H-score.

Result: Based on the TMA staining, mean KPNA2 score was 36.5 [0-240] and median value was 10. Table 1. Scatter plots and correlation between KPNA2 expression levels and tumor invasiveness markers reveals that high KPNA2 expressor was related to lymphatic invasion (p = 0.00782), advanced stage (p = 0.0202) and current smoker (p = 0.0074). KPNA2 expression was higher in squamous cell carcinoma(SqCC) histotype than in adenocarcinoma (SqCC ratio (%), 13.5 vs 43.4 in Low exp vs High exp; p = 0.007). Patients with high expression of KPNA2 showed shorter survival than other patients (median OS (mo), 72.8 vs 42.2, P < 0.0001; median RFS (mo), 72.8 vs 32.1, P < 0.0011) and relevant to high recurrence (recurrence rate (%), 24.7 vs 44.7, p = 0.007).

Conclusion: Taken together, our results suggest that KPNA2 protein expression has a poor prognostic association, revealed by its association with survival outcome or invasiveness markers. Its clinical significance as an oncogenic target molecule is emerging, and further evaluation using an organoid model is in progress.

Baseline clinical and pathological characteristics

Citation Format: Seoree Kim, Heejin Lee, Jung-Sook Yoon, Hyun Woo Lee, Seok Yun Kang, Ji Hyun Lee, Sang Hoon Chun, Hye Sung Won, Soon Auck Hong, Keunsoo Kang, Young-Ho Ahn, Yoon Ho Ko. Identification and characterization of Karyopherin α2 (KPNA2), a member of the nucleocytoplasmic transporter family, in lung cancer [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 2165.
Abstract 2350: Role of ECM hyaluronic acid in the tumor-promoting functions of TIMP-1
Authors: Thorenoor Nithyananda , Xiao Wei , Rojiani Amyn M. , Rojiani Mumtaz V.
Published: April 2023

Non-small cell lung carcinoma (NSCLC) is responsible for the most significant number of lung cancer deaths with over 85% of lung cancers falling in this category. The dismal outcomes of this disease are augmented by advanced disease at initial presentation and ongoing development of chemoresistance following standard chemotherapeutic interventions. Tissue Inhibitor of metalloproteinase-1 (TIMP-1), one of the natural inhibitors of matrix degrading enzymes, is classically regarded as a tumor suppressor. However, there is much evidence that has established this molecule as having tumorigenic functions and has been shown to be upregulated in multiple cancers as well as in the development of fibrosis. In earlier studies we have demonstrated the tumor-promoting role of TIMP-1 in multiple biological interactions including angiogenesis, apoptosis, chemoresistance and cancer metabolism in NSCLC. The ECM plays an important role in providing structural support and as a depot for growth factors and cytokines critical for cell signaling. As TIMP-1 remains a vital molecule facilitating and modulating multiple elements of the ECM, we have sought to further define its role in the tumor microenvironment ECM in NSCLC cells. Our investigations have shown that TIMP-1 protein accumulates in the culture medium over long incubation periods. We have also found TIMP1 mRNA upregulation during this incubation period and correlated this as a function of cell density. As high cell density led to increased upregulation of TIMP1 mRNA, we postulated that factors secreted in the culture were responsible for this upregulation. We have identified that hyaluronic acid (HA), a component of the ECM, was accumulating in the culture media, resulting in the above response. HA is a critical matrix molecule of the tumor pericellular stroma and its upregulation is associated with poor prognosis. It is synthesized by hyaluronic acid synthetase (HAS) isoforms 1,2 and 3. We have also found that HAS2 was strongly expressed in high TIMP1 expressing NSCLC cells. Several studies have shown increased HAS2 expression in tumor tissue. We found that knocking down TIMP1 resulted in lower HA levels and decreased expression of HAS2. In a 3D coculture spheroid assay utilizing A549 cells and MRC5, we have shown increased expression of TIMP-1 and HA, which was also confirmed in archived NSCLC patient samples. The role of HA in the tumor-promoting functions of TIMP1 will be discussed further.

Citation Format: Nithyananda Thorenoor, Wei Xiao, Amyn M. Rojiani, Mumtaz V. Rojiani. Role of ECM hyaluronic acid in the tumor-promoting functions of TIMP-1 [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 2350.
Abstract 2352: ALDOC interplays with KIAA1409 to reduce m6A modifications and cancer-associated fibroblast characteristics in gliomas
Authors: Li Chien-Hsiu , Chan Ming-Hsien , Chang Yu-Chan
Published: April 2023

The abundance and regulatory mechanisms of tumor microenvironment in gliomas remain unclear. We have previously demonstrated that aldolase c (ALDOC) has tumor suppressor function and prognostic value in the progression of glioma. In this study, we used immune infiltration algorithms to identify the immune response events that ALDOC modulates in gliomas and found that they were particularly strongly associated with cancer-associated fibroblasts (CAFs). Our transcriptomic and proteomic profiles infer that ALDOC is involved in the methylation status of N6-methyladenosine (m6A) and binds to KIAA1429, which in turn affects the assembly of the assembly of the m6A-METTL complex. We show that ALDOC can interact with KIAA1429 and trap it in the cytoplasm and then interfere with the modification of m6A. In malignant cells and ALDOC knockdown models, we observed loss of ALDOC function, KIAA1429 was responsible for the ‘writer’ of m6A and stabilized expression levels of various CAF-related features. Through the MeRIP-Seq/m6A-seq approach, we found that the RNA-binding protein, IGF2BP2, can be directly stabilized with multiple CAF-related genes. We examined ALDOC and KIAA1429, CAF-related genes (FAP, α-SMA, S100A4 and VIM) in available cohorts and tissue microarrays and were statistically inversely correlated. Furthermore, ALDOC colocalized with KIAA1429 and CAF genes in the surrounding microenvironment was significantly reduced in tissue sections from orthotopic animal models by multiplex immunohistochemistry.

Keywords: Aldolase C, m6A modification, cancer-associated fibroblasts, gliomas

Citation Format: Chien-Hsiu Li, Ming-Hsien Chan, Yu-Chan Chang. ALDOC interplays with KIAA1409 to reduce m6A modifications and cancer-associated fibroblast characteristics in gliomas [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 2352.
Abstract 2353: PTGES is involved in the myofibroblast differentiation
Authors: Yang Yi-Fang , Lee Yi-Chen , Lin Min-Hsi
Published: April 2023

Lung cancer is the leading cause of cancer-related death worldwide, and patients usually have poor prognoses and low 5-year survival rates. Idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are both chronic and dysfunction of lung refers to lung fibrosis and increased risk of lung cancer. Myofibroblasts contribute to the procession of asthma, COPD, and IPF, leading to fibrosis of the airway and lung. Accumulating evidence has shown metabolic reprogramming has been considered a major hallmark of fibrosis and plays an important role in the fibrosis process. In this study, we identified Prostaglandin E Synthase (PTGES) was upregulated in lung fibroblast after being treated with IL-4, IL-13, and TNF-α, respectively. We found that PTGES increased the levels of myofibroblast markers α-SMA, FAP, and Vimentin, and promoted lung fibroblast cell migration and invasion. Further, in vivo lung fibrosis model demonstrated that PTGES was upregulated in lung fibrosis rats. PTGES induces phosphorylation of ERK1/2 and HIF-1α expression in lung fibroblast cells. Based on our findings, PTGES increases the expression of myofibroblast markers to modulate the myofibroblast differentiation.

Citation Format: Yi-Fang Yang, Yi-Chen Lee, Min-Hsi Lin. PTGES is involved in the myofibroblast differentiation [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 2353.
Abstract 2355: Transcription factor EB modulates fibrotic response in pancreatic ductal adenocarcinoma
Authors: Alcalde Alejandra Diaz , Vallariello Edoardo , Astanina Elena , Middonti Emanuele , Bussolino Federico
Published: April 2023

Pancreatic ductal adenocarcinoma (PDAC), which comprises 85% of all the pancreatic cancers, is one of the most aggressive and deadly tumor that exists today with less than 8% of survival 5 years after diagnosis. It is predicted to become the second cause of cancer death by 2030. A typical characteristic of this tumor is the presence of prominent stroma component mainly produced by Pancreatic Stellate Cells (PSCs) in response to soluble factors released by cancer cells. PSCs activation and differentiation into CAF (Cancer-associated fibroblasts) is a reversible process, which impacts on both tumor progression and drug resistance. Transcription factor EB (TFEB) is mostly known as a master regulator of autophagy and lysosomal biogenesis. A recent study demonstrated that TFEB inhibits epithelial-to-mesenchymal transition (EMT) and myofibroblast differentiation in epicardial cells by upregulating TGIF1, a TGFβ pathway repressor. Based on this observation, we investigated if TFEB might have an inhibitory role in PSCs activation, taking into consideration the crucial role of TGFβ signaling in this process. The TFEB expression, measured by immunostaining, was significantly downregulated in CAFs in human PDAC samples compared to PSCs in healthy pancreas. In PSCs, co-cultured with PDAC cell lines, CAF markers were upregulated while TFEB expression was downregulated. The overexpression of TFEB in PSCs suppressed CAF markers upregulation induced by co-culture with PDAC cells at both mRNA and protein levels. The bulk RNAseq analysis showed the differential expression of genes required for extracellular matrix production, fibrotic response and inflammation in PSCs co-cultured with PDAC cell lines versus PSCs alone, with and without TFEB overexpression. These in vitro data suggest a role for TFEB in PSCs activation and stroma formation which will be further investigated in PDAC mouse models.

Citation Format: Alejandra Diaz Alcalde, Edoardo Vallariello, Elena Astanina, Emanuele Middonti, Federico Bussolino. Transcription factor EB modulates fibrotic response in pancreatic ductal adenocarcinoma [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 2355.