bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1365: The spatially resolved host-microbiome sequencing platform reveals the interaction between bacteria and cancer stem cell microinches
Authors: Kim Gyeongjun 
Published: April 2023

Abstract
The tumor microbiome is a unique element that appears differently for each type of cancer in a person. Currently, intratumoral host-microbiome sequencing was only done by bulk tissue analysis which means little is understood when it comes to the spatial distribution of microbiota in the heterogeneous tumor microenvironment and the localized effect of the microbiota. Breast cancer is known to be one of the cancers rich in the microbiome. We focused on cancer stem cell-like microniches related to the tumor microenvironment of triple-negative breast cancer(TNBC). We adapted SLACS(Spatially resolved Laser activated Cell Sorter) which isolates the region of interest from immunofluorescence-stained samples using a laser, providing the spatial distribution of localized microbiota in rare cancer stem cell samples. By applying SLACS
to point out the breast cancer stem cell micro-niches, we discovered that more microbes flourished in ALDH1 high/CD44 high groups rather than normal cells. We also identified the composition of the microbiota was different in cancer stem cells depending on the degree of expression of the marker. Comparing RNA-seq data of host and microbiome sequencing with functional studies, we reveal the distribution of microbiota in breast tumors and interactions between cancer stem cells and microbiota. Collectively, we found the spatial pattern of the microbiota localized in cancer stem cell microniches and how cells and bacteria interact with each other more precisely.
Citation Format: Gyeongjun Kim. The spatially resolved host-microbiome sequencing platform reveals the interaction between bacteria and cancer stem cell microinches [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 1365.
Abstract 1372: NUDT16L1 promotes colon cancer progression via inhibition of ferroptosis
Authors: Lin Yi-Syuan , Tsai Ya-Chuan , Li Chia-Jung , Wei Tzu-Tang , Wu Ya-Na , Wu Shang-Rung , Lin Shin-Chin , Tsai Shaw-Jenq , Lin Shih-Chieh 
Published: April 2023

Abstract
Ferroptosis is an iron-dependent oxidative cell death with accumulation of lipid peroxidation and abnormal morphology of mitochondria. Although previous studies have shown that ferroptosis inducers have therapeutic potentials in several treatment-naive and drug-resistant cancer types, lacking systematic analysis of the ferroptosis sensitivity in different cancer types makes it difficult to know which cancer type is suitable for clinical usage and critical regulator determining the ferroptosis sensitivity during cancer progression is still not clear. In this study, colon cancer was identified as one of the ferroptosis-insensitive cancer types by dry and wet bench analyses. Importantly, our large-scale analysis also showed that NUDT16L1 was a novel ferroptosis repressor and overexpressed in colon cancer clinical specimens. Similar findings are also observed in the chemical-induced and genetic mouse models of colon cancer. Furthermore, NUDT16L1 loss-of-function and gain-of-function cell models and its conditional knock-in and knock-out mouse models are used to prove its crucial role in the development of colon cancer. In addition, loss of NUDT16L1 induced several key ferroptosis characteristics and impairment of mitochondrial functions while its restoration attenuated those phenomena in colon cancer cells. Mechanistically, our RNA-Seq and RIP-Seq analyses shown that NUDT16L1 directly interacted and positively regulated several crucial negative regulators of ferroptosis. More interestingly, loss of NUDT16L1 not only restores the sensitivity of ferroptosis inducer but also impairs the function of mitochondria. Finally, a specific NUDT16L1 inhibitor was shown to not only repress colon cancer growth in vitro and in vivo but also induce the ferroptosis in colon cancer. In conclusion, this is the first study to demonstrate that overexpression of NUDT16L1 promotes colon cancer progression by inhibition of ferroptosis and maintenance proper function of mitochondria. Furthermore, specific NUDT16L1 inhibitor might be a promising therapeutic strategy for colon cancer patient in the future.
Citation Format: Yi-Syuan Lin, Ya-Chuan Tsai, Chia-Jung Li, Tzu-Tang Wei, Ya-Na Wu, Shang-Rung Wu, Shin-Chin Lin, Shaw-Jenq Tsai, Shih-Chieh Lin. NUDT16L1 promotes colon cancer progression via inhibition of ferroptosis [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 1372.
Abstract 1382: Expression and intracellular translocation of cancer biomarkers in hepatocarcinoma cells induced by changes in mitochondrial metabolism
Authors: Larson Bradley R. , Gooz Monika , Maldonado Eduardo 
Published: April 2023

Abstract
Hepatocarcinoma is one of the most common cancer types in the U.S. with limited treatment options and poor survival rate. Recently, cancer bioenergetics emerged as a promising source of targets to develop novel anticancer agents. The identification of biomarkers is essential for screening and validation of small molecules proposed as chemotherapeutic agents. In this regard, there is a great need for high-throughput/high-content methods, which require short and reproducible sample preparation. In this project, we used the erastin-like compound X1 in the well-characterized SNU-449 hepatocarcinoma cell line. Erastin initially enhances mitochondrial function and ROS formation leading to subsequent mitochondrial dysfunction. As readout, we employed directly and indirectly labeled fluorescent antibodies to visualize and quantify expression of proliferative and antiproliferative markers Ki-67 and cytoskeleton-associated protein 4/p63 (CKAP4/p63), as well as expression and intracellular translocation of the tumor suppressor protein p53. Using the Agilent BioTek Cytation 5 cell imaging multimode reader and Agilent BioTek Gen5 microplate reader and imager software, we successfully validated these markers and the corresponding antibodies as tools to study long-term effects of xenobiotics on mitochondrial bioenergetics. The method allows for fast and reliable screening of potential drug candidates. Acknowledgement: This work was supported in part by the Chan Zuckerberg Initiative, Silicon Valley Community Foundation, and the NIH S10 OD028663 to M.G. and by the U.S. National Institutes of Health (NIH/NCI) R01 CA184456, and South Carolina Translational Research Pilot Project UL1 TR001450-SCTR to E.N.M.
Citation Format: Bradley R. Larson, Monika Gooz, Eduardo Maldonado. Expression and intracellular translocation of cancer biomarkers in hepatocarcinoma cells induced by changes in mitochondrial metabolism [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 1382.
Abstract 1388: Non-thermal plasma-activated medium induces ferroptotic cell death by intracellular ferrous iron overload in head and neck cancer
Authors: Nguyen QuocKhanh , Oh Chan , Jung Seung-Nam , Piao Yudan , Lim Mi Ae , Kim Young Il , Jin Yanli , Kim Hae Jong , Koo Bon Seok 
Published: April 2023

Abstract
The notoriously high proliferation rate of cancer cells requires them to constantly deal with the balance adjustment between oxidative stress overload and upregulated protective antioxidant pathways. It puts them in a vulnerable state whenever one piece of this puzzle went out of control. Non-thermal plasma (NTP) is partially ionized gas operated at or around body temperature and has emerged as a new potential anti-cancer therapy due to its ability to release and induce ROS, RNS, and other free radicals as well as generate UV- photon and electromagnetic field; but the specific mechanism and its specificity to cancer cell are still controversial. Using transcriptomic analysis, we previously reported the link between NTP-activated media (NTPAM)and apoptosis; but the sequencing data also revealed a strong Ferroptotic response in all the 6Head and Neck cancer cell lines we checked. Ferroptosis is a newly identified oxidative-regulated cell death, characterized by the iron-dependent generation of lipid peroxidation. In this study, we found the prolonged treatment of NTPAM-induced cell death via the non-canonical ferroptosis pathway by directly increasing intracellular toxic ferrous Iron (Fe2+). We found that the excessive overexpression of HMOX1 under prolonged NTPAM-induced oxidative stress was actually responsible for the surge of intracellular Fe2+ due to the increase of heme degradation. Pharmacological inhibition or RNA silencing of HMOX1 was able to rescue 2 HNC cell lines from NTPAM-induced increased Iron concentration as well as ferroptosis cell death, both in vivo and in vitro. These results suggest NTP directly induces ferroptosis via an increase of Fe2+ concentration by triggering the over-responding of the NRF2 - HMOX1 antioxidant system. This finding could be exploited to develop future NTP-based cancer therapy as well as in combination with other Iron sensitive anti-neoplastic agents; and could be a potential method of overcoming conventional cancer treatment resistance.
Citation Format: QuocKhanh Nguyen, Chan Oh, Seung-Nam Jung, Yudan Piao, Mi Ae Lim, Young Il Kim, Yanli Jin, Hae Jong Kim, Bon Seok Koo. Non-thermal plasma-activated medium induces ferroptotic cell death by intracellular ferrous iron overload in head and neck 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 1388.
Abstract 139: Exploiting interactions between ploidy and host physiology
Authors: Andor Noemi 
Published: April 2023

Abstract
Whole-genome doubling facilitates rapid tumor evolution and is a hallmark of many cancers, including Glioblastoma (GBM) where it has an incidence of ~14%. GBM remains uniformly lethal, with a median overall survival of 14-16 months, despite aggressive therapy. In people aged 65 and above, prognosis is even more dismal, with median survival of less than 7 months. While comorbidities explain some of the increased age-related risk, age-related changes in the tumor microenvironment likely also contribute. Aging brains have higher incidence of polyploidy (Pearson r=0.80; P=0.031; Nandakumar et al., 2021), hypoxia related gene expression (Pearson r =0.22, P =0.008) and Glucose levels (Ding et al., 2021) as well as decreased stiffness (Hiscox et al., 2018). The average ploidy of 20 different cancer types correlates with the Oxygen levels recorded in their respective tissue of origin (Spearman r = 0.66, P = 0.002). Together these results suggest that availability of metabolic substrates in the GBM environment drives different cell fate decisions in cancer cells of different ploidy and shapes GBM disease initiation.
We address this hypothesis with integrated in-vitro and in-silico experiments and multi-omic and imaging analysis of primary and recurrent GBM. We genetically engineered cell lines to obtain diploid and tetraploid lineages for each and tested how exposure to variable gradients of glucose, hypoxia and phosphate affect their migratory patterns. We performed RNA-seq and WGS of multiple regions obtained from two patient-matched primary and recurrent GBM. Pre- and post-surgery MRI data was available from both surgeries and registered to a T1 map Atlas to quantify stiffness and oxygenation in the brain. This data was used to calibrate a Stochastic State-Space Model (S3MB) we developed to recapitulate re-growth of enhancing primary tumor margins into the respective recurrent tumor. The model domain is initiated from MRI data and consists of 4mm3 voxels. Each voxel state is defined by 8+ variables that are updated over time: Stiffness, Oxygen, Phosphate, Glucose, Vasculature, Dead cells, migrating cells and proliferating cells of various ploidies.
In-vitro results, multi-omics results and similarity between observed and simulated recurrent tumors were used to infer model parameters (resource consumption-, migration-, death and proliferation rates). Running the model backwards in time, we predict the local point of origin (LPO) of each GBM. We found that resource availability in the predicted LPO was correlated to WGD status, suggesting conditions in the local environment in which a GBM originates shape the outcome of an early competition between diploid and tetraploid cells.
Citation Format: Noemi Andor. Exploiting interactions between ploidy and host physiology [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 139.
Abstract 1397: Collagen COL26A1 promotes papillary thyroid cancer invasion and metastasis and correlates with poor survival and clinical outcomes
Authors: Carnazza Michelle , Quaranto Danielle , DeSouza Nicole , Dadafarin Sina , Moscatello Augustine , Geliebter Jan , Tiwari Raj K. 
Published: April 2023

Abstract
Papillary thyroid cancer (PTC) is the most common cancer in women under 25 years of age and is increasing in incidence. While PTC is often slow-growing and surgically resectable, recurrence years to decades after initial surgery occurs in ~20% of patients (now only in their 40s/50s), with mortality of 38-69%. The identification of both prognostic biomarkers and actionable therapeutic targets for high-risk PTC at diagnosis is critically important and an unmet need. RNASeq analysis of 45 PTC and matched normal patient tissues from our biobank identified collagen 26A1 (COL26A1) as significantly upregulated in patients with higher risk extrathyroidal extension, lymph node metastasis, and multifocal tumors, compared to those with localized disease. Kaplan Meier survival curves of The Cancer Genome Atlas (TCGA) data confirmed that increased COL26A1 expression significantly decreases survival probability by 25% (p=0.0086). Further analyses of TCGA data indicated that COL26A1 expression significantly correlated with clinical attributes including MACIS score (q=0.001), differentiation score (q=0.025), and tumor stage (q=0.025). Data from our in vitro culture PTC model system indicated that COL26A1 expression was increased 3X in PTC cell line K1, compared to immortalized “normal” thyroid epithelial cells, NThy-ori-3-1. Two CRISPR guides designed to target COL26A1 introduced into K1 resulted in repression of COL26A1 RNA and protein levels by 50% and 70%, respectively. COL26A1 repression decreased critical tumor phenotypes of aggressiveness and metastasis including proliferation (30%), clonogenicity (33%), anchorage-independent growth (37%), cell motility (43%), invasion (30%) and migration (33%). Cell-to-cell adhesion and cell-matrix adhesion also decreased (36% and 25%, respectively). Thus, COL26A1 may have use as a prognostic marker and actionable target for small molecule inhibitors in PTC.
Citation Format: Michelle Carnazza, Danielle Quaranto, Nicole DeSouza, Sina Dadafarin, Augustine Moscatello, Jan Geliebter, Raj K. Tiwari. Collagen COL26A1 promotes papillary thyroid cancer invasion and metastasis and correlates with poor survival and clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1397.
Abstract 1404: A functional genetic polymorphism of mitochondrion-associated DNAJA3 in nonalcoholic steatohepatitis-related hepatocellular carcinoma
Authors: Shiode Yuto , Chang Ching-Wen , Wang Xin Wei 
Published: April 2023

Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease worldwide and may progress to nonalcoholic steatohepatitis (NASH). Although emerging evidence suggests that NASH would be an important driver of hepatocellular carcinoma (HCC), molecularly what drives the transition of NAFLD to NASH and then HCC has not been clearly defined. Since NASH is a mitochondrial disease, we aimed to determine genetic variants associated with mitochondrial dysfunction linked to NASH and NASH-related HCC. We performed an integrative genomics analysis by analyzing a large-scale genome-wide association study of the body fat distribution-related variants in 344,369 individuals from multiple ancestries. And we linked these results to the top 24 significant variants to NASH and NASH-related HCC in 1,009 individuals from the NCI-UMD cohort. We also performed the expression quantitative trait loci (eQTL) analysis on candidate variants. We analyzed the 3D genome architecture especially chromatin topology based on UCSC Genome Browser that influences the expression of candidate variants. As a result, we identified rs3747579-TT, an eQTL to a mitochondrial chaperone Hsp40, also known as DNAJA3 rather than a coding variant, as a risk allele linked to NASH-related HCC. HCC patients with rs3747579-TT variant had a poor prognosis compared to HCC patients with rs3747579-CT or CC variant. We confirmed that HCC with rs3747579-TT had a reduced expression of DNAJA3, encoding a protein that maintains mitochondrial homeostasis. Consistently, HCC patients with low DNAJA3 expression had a poor prognosis. We found a specific site based on chromatin topology that may influence rs3747579 to regulate the expression of DNAJA3. In summary, we identified rs3747579-TT as a functional polymorphic variant of DNAJA3 that may be responsible for the development of NASH and NASH-related HCC.
Citation Format: Yuto Shiode, Ching-Wen Chang, Xin Wei Wang. A functional genetic polymorphism of mitochondrion-associated DNAJA3 in nonalcoholic steatohepatitis-related hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1404.
Abstract 1414: The role of chromosome arm 3p and human papillomavirus on proliferation, differentiation, and metastasis in squamous cancers
Authors: Mallick Samyukta , Taylor Alison M. 
Published: April 2023

Abstract
Squamous Cell Carcinoma (SCC) is an aggressive form of cancer that develops in the mucosal epithelium of the digestive and respiratory tracts as well as on the skin. Two major risk factors for development of SCC are carcinogen exposures, such as alcohol and tobacco, and Human Papillomavirus (HPV) infection. Viral- and carcinogen-driven SCCs have differential responses to radiation, chemotherapy, and immunotherapy, with HPV+ SCCs responding better to these treatments than HPV- carcinomas. Analysis of aneuploidy patterns of genomic samples from The Cancer Genome Atlas (TCGA) have shown that squamous cancers cluster together and are characterized by gain of chromosome arm 3q gain and loss of chromosome arm 3p. However, while HPV+ SCCs show similar rates of 3q gain, they have significantly lower rates of 3p loss, suggesting that 3p deletion and HPV infection might have overlapping roles in cancer initiation and/or progression. In addition, the degree to which these two paths of tumor development contribute to differences in disease progression and outcome has been largely unexplored. We have identified a strong correlation between 3p deletion and high epithelial-mesenchymal transition (EMT) gene signature across all cancer types. Interestingly, interferon signaling has been found to be upregulated in non-squamous cancers upon 3p deletion but downregulated in squamous cancers with 3p deletion. SCCs positive for HPV infection show decreased expression of EMT genes and increased expression of genes in interferon signaling and cell cycle checkpoint pathways. Together, the results of these TCGA analyses suggest mechanisms by which chromosome 3p deletion and HPV infection may affect cancer progression and are currently being validated in vitro in a panel of squamous cancer cell lines. Additionally, we will use a targeted CRISPR-Cas9 system developed in our lab to delete chromosome 3p, as well as transfect HPV oncoproteins, in normal keratinocytes to create isogenic models. With these models, we will study the role of individual aneuploidy events in tumorigenesis, tumor development, and metastasis in the context of HPV positive and negative SCC.
Citation Format: Samyukta Mallick, Alison M. Taylor. The role of chromosome arm 3p and human papillomavirus on proliferation, differentiation, and metastasis in squamous cancers [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 1414.
Abstract 1415: The search for molecular biomarkers of relapse in early stage lung adenocarcinoma
Authors: Ke Honggang , Jing Zhongying 
Published: April 2023

Abstract
Background: Recurrence cannot be completely prevented by resection or chemotherapy. Molecular biomarkers reported in previous studies have the potential to predict the recurrence risk of lung adenocarcinoma (LUAD), but the results were controversial.
Methods: We retrospectively analyzed the molecular characteristics of the 218 early-stage patients with lung adenocarcinoma based on 599 gene-panel target sequencing. All the patients received no neoadjuvant therapy and no EGFR-TKI treatment. The follow-up information on recurrence was complete. Univariate and multivariate analyses were performed using the Cox proportional hazard models to investigate whether the common alterations in EGFR and KRAS were prognostic factors for relapse-free survival(RFS).
Results: Among all the enrolled patients, the mutation rates of EGFR and KRAS were 47.6% and 9.3%, respectively. EGFR mutation was not proved to be a prognostics signature of relapse for lung adenocarcinoma regardless univariate and multivariate analysis (univariate: HR, 1.11; 95%CI, 0.82-1.50, P = 0.49; multivariate: HR, 1.18; 95%CI, 0.86-1.64, P = 0.31). The univariate and multivariate analysis identified KRAS alteration as an independent prognostic factor for a shorter RFS (univariate: HR, 1.64; 95%CI, 0.75-2.43, P &lt; 0.05; multivariate: HR, 1.66; 95%CI, 1.19-2.32, P &lt;0.05). For patients in pathological stage I, the patients with KRAS alterations showed significant recurrent risk compared with wild-type patients (HR, 2.02; 95%CI, 1.38-2.96; P &lt;0.0.01).
Conclusion: KRAS alterations rather than EGFR alterations were prognostic biomarkers of relapse for early-stage lung adenocarcinoma, especially for patients in pathological stage I.
Citation Format: Honggang Ke, Zhongying Jing. The search for molecular biomarkers of relapse in early stage lung 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 1415.