bluuebunny/crossref_metadata_2025 huggingface dataset:
Fuzzing vs SBST
Authors: Guizzo Giovani , Panichella Sebastiano
Published: January 2023

Search-Based Software Testing (SBST) is the application of SBSE for solving hard software testing problems. SBST has been the subject of discussion of our International SBST Workshop, colocated with the International Conference on Software Engineering (ICSE). In 2022 we hosted the 15th edition of our SBSTWorkshop, which brought together researchers and industrial practitioners to encourage the use of search-based and fuzz testing techniques and tools for addressing software engineering-specific challenges. In this 2022 edition, SBST held, among other exciting events, a discussion panel on the similarities and differences between SBST and Fuzzing. As it implies, the goal of the panel was to have a common ground for discussion on the main similarities and differences between the Fuzzing and SBST fields, focusing on how both communities can collaborate to advance the stateof- the-art on automated testing. This strong panel composed of researchers from both academia and industry was the highlight of SBST'22 and allowed the chairs of the workshop to make substantial changes for 2023. In this paper, we present the main take away messages from that seminal panel and highlight exciting new challenges in the field.
Software Engineering and AI for Data Quality in Cyber-Physical Systems/Internet of Things - SEA4DQ'22 Report
Authors: Nguyen Phu H. , Sen Sagar , Bretones-Cassoli Beatriz , Jourdan Nicolas , Magnanini Maria Chiara
Published: January 2023

Cyber-physical systems (CPS)/Internet of Things (IoT) are omnipresent in many industrial sectors and application domains in which the quality of the data acquired and used for decision support in common factor.
Don’t Need All Eggs in One Basket: Reconstructing Composite Embeddings of Customers from Individual-Domain Embeddings
Authors: Unger Moshe , Li Pan , Sen Sahana (Shahana) , Tuzhilin Alexander
Published: January 2023

Although building a 360-degree comprehensive view of a customer has been a long-standing goal in marketing, this challenge has not been successfully addressed in many marketing applications because fractured customer data stored across different “silos” are hard to integrate under “one roof” for several reasons. Instead of integrating customer data, in this article we propose to integrate several domain-specific partial customer views into one consolidated or composite customer profile using a Deep Learning-based method that is theoretically grounded in Kolmogorov’s Mapping Neural Network Existence Theorem. Furthermore, our method needs to securely access domain-specific or siloed customer data only once for building the initial customer embeddings. We conduct extensive studies on two industrial applications to demonstrate that our method effectively reconstructs stable composite customer embeddings that constitute strong approximations of the ground-truth composite embeddings obtained from integrating the siloed raw customer data. Moreover, we show that these data-security preserving reconstructed composite embeddings not only perform as well as the original ground-truth embeddings but significantly outperform partial embeddings and state-of-the-art baselines in recommendation and consumer preference prediction tasks.
Using Toulmin's Argumentation Model to Enhance Trust in Analytics-Based Advice Giving Systems
Authors: Rubin Eran , Benbasat Izak
Published: January 2023

Ecommerce websites increasingly provide
predictive analytics-based advice (PAA)
, such as advice about future potential price reductions. Establishing consumer-trust in these advice-giving systems imposes unique and novel challenges. First, PAA about future alternatives that can benefit the consumer appears to inherently contradict the business goal of selling a product quickly and at high profit margins. Second, PAA is based on mathematical models that are non-transparent to the user. Third, PAA advice is inherently uncertain, and can be perceived as subjectively imposed in algorithms. Utilizing Toulmin's argumentation-model, we investigate the influence of advice-justification statements in overcoming these difficulties. Based on three experimental studies, in which respondents are provided with the advice of PAA systems, we show evidence for the different roles Toulmin's statement-types play in enhancing various trusting-beliefs in PAA systems. Provision of warrants is mostly associated with enhanced competence beliefs; rebuttals with integrity beliefs; backings both competence and benevolence; and data statements enhance competence, integrity, and benevolence beliefs. Implications of the findings for research and practice are provided.
Rethinking Vision and Action
Authors: Nakayama Ken , Moher Jeff , Song Joo-Hyun
Published: January 2023

Action is an important arbitrator as to whether an individual or a species will survive. Yet, action has not been well integrated into the study of psychology. Action or motor behavior is a field apart. This is traditional science with its need for specialization. The sequence in a typical laboratory experiment of see → decide → act provides the rationale for broad disciplinary categorizations. With renewed interest in action itself, surprising and exciting anomalous findings at odds with this simplified caricature have emerged. They reveal a much more intimate coupling of vision and action, which we describe. In turn, this prompts us to identify and dwell on three pertinent theories deserving of greater notice.
Abstract A005: The aged tumor microenvironment influences tolerance to targeted therapy via NR2F1 overexpression in BRAF-mutant melanoma
Authors: Tiago Manoela , Purwin Timothy J. , Fane Mitchell E. , Chhabra Yash , Teh Jessica L. F. , Kadamb Rama , Cai Weijia , Chervoneva Inna , Rosenbaum Sheera , Chua Vivian , Hacohen Nir , Davies Michael A. , Villanieva Jessie , Weeraratna Ashani T. , Capparelli Claudia , Aguirre-Ghiso Julio A. , Aplin Andrew E.
Published: January 2023

Despite the clinical success of targeted inhibitors, tumor responses to these agents are transient, and drug-tolerant residual cells seed resistance. Understanding the role of tumor-intrinsic mechanisms and effects of the tumor microenvironment in mediating drug tolerance will guide and optimize targeted therapies. Given similarities between drug tolerance and cellular dormancy, we studied the role of nuclear receptor subfamily 2 group F member 1 (NR2F1) in response to targeted therapy. We used BRAF-mutant cutaneous melanoma models treated with BRAF and MEK inhibitors (BRAFi + MEKi) since patients treated with this combination typically develop resistance. The aged tumor microenvironment has been shown to increase therapy resistance, and we find that melanoma cells in aged mice express higher levels of NR2F1 than when the same cells are injected into young animals. Transcriptomic analysis of melanoma patient samples treated with BRAFi + MEKi showed increased expression of NR2F1 post-treatment. Similarly, NR2F1 was highly expressed in minimal residual disease collected on BRAFi + MEKi treatment in patient- and xenograft-derived tumors. High expression of NR2F1 promotes tumor survival and invasion in the presence of BRAFi + MEKi in vitro leading to tolerance to BRAFi + MEKi efficacy in vivo. Depletion of NR2F1 in YUMM1.7 allografts grown in aged mice improved response to the combination therapy. Altogether, our findings suggest that NR2F1 promotes drug tolerance leading to minimal residual disease in melanoma and that NR2F1-high cells may be targeted with CDK4/6 inhibitors to improve targeted therapy outcomes in melanoma patients.

Citation Format: Manoela Tiago, Timothy J. Purwin, Mitchell E. Fane, Yash Chhabra, Jessica L. F. Teh, Rama Kadamb, Weijia Cai, Inna Chervoneva, Sheera Rosenbaum, Vivian Chua, Nir Hacohen, Michael A. Davies, Jessie Villanieva, Ashani T. Weeraratna, Claudia Capparelli, Julio A. Aguirre-Ghiso, Andrew E. Aplin. The aged tumor microenvironment influences tolerance to targeted therapy via NR2F1 overexpression in BRAF-mutant melanoma [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A005.
Abstract A023: Analysis of survival and prognostic factors for patients with non-small cell lung cancer and brain metastasis: 10-year experience in a single institution
Authors: Yang Seung Ho
Published: January 2023

The aims of the study were 1) to perform the review of non-small cell lung cancer (NSCLC) patients with brain metastasis in our institution, 2) to investigate the response and prognostic factor of brain metastasis after institution’s best treatment, and 3) to suggest the shift of treatment paradigms for brain metastasis. From Jan. 2007 to Oct. 2018, A total 214 NSCLC patients with brain metastasis were enrolled. Female to male ratio was 0.65 and median age at diagnosis of NSCLC was 64 years (range, 30-90). 54 patients had a solitary brain metastasis and 76 patients had more than 10 lesions. Supratentorial, infratentorial and both locations were 106, 17, and 91 patients, respectively. 116 patients (54%) had symptoms associated with brain metastasis at the diagnosis of brain metastasis. Radiation only, radiosurgery, craniotomy with whole brain radiotherapy (WBRT), and supportive care were given for brain metastasis in 111 (52%), 10 (5%), 13 (6%) and 61 (29%) patients, respectively. Overall survival (OS) was associated with age, treatment modality, histology, egfr mutation. Median OS of Radiation only, radiosurgery, craniotomy with WBRT, and supportive care was 13, 15, 15 and 9 months, respectively (P-value 0.044). Median OS of adenocarcinoma and squamous cell carcinoma was 15 and 4 months, respectively (P-value <0.05). Median OS of egfr mutation and wild type was 18 and 9 months, respectively (P-value 0.016). The number and location of brain metastasis, symptoms and sex were not associated with OS Serial brain imaging was performed in 99 patients. 61 out of them (62%) developed shrinkage of brain metastasis (response group). Median OS of response and non-response group were 23 and 17 months (p-value 0.618). Age is significantly associated with response of brain metastasis to the institution’s best treatment (p-value 0.047). Interestingly, 3 patients developed complete remission of brain metastasis following WBRT and chemotherapy. The response duration was 431, 390, 641 days, respectively. Our data show that the prognosis of brain metastasis primarily depends on the age of NSCLC patients rather than the number, location of brain metastasis, treatment modality. Survival of NSCLC patients with brain metastasis was about 15 months despite the institution’s best treatment. The authors suggest that we should update our institution’s treatment policy and provide the latest treatments for patients.

Citation Format: Seung Ho Yang. Analysis of survival and prognostic factors for patients with non-small cell lung cancer and brain metastasis: 10-year experience in a single institution [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A023.
Abstract B003: Causal effect of type II diabetes on prostate cancer in the East Asian population: A two-sample Mendelian randomization study
Authors: Guo Zhongyi
Published: January 2023

Type II diabetes, a metabolic disease, and prostate cancer are prevalent diseases in the elderly population. Whether type II diabetes has an association with prostate cancer has not been thoroughly studied. Limited research has been performed from a perspective of genetic level, especially among non-European populations. In this study, we used a two-sample Mendelian randomization (MR) approach to evaluate the causal effect between type II diabetes as an exposure and prostate cancer as an outcome in the East Asian population. For type II diabetes, we used 174 risk loci identified in a meta-analysis of 77,418 cases and 356,122 controls from 23 East Asian Genome-wide Association Studies (GWAS). For prostate cancer, summary statistics were extracted from the GWAS from BioBank Japan using 5,408 cases and 103,939 controls. We performed two-sample Mendelian randomization with the inverse variance weighted method while using MR Egger and weighted median methods as sensitivity analysis. For type II diabetes risk SNPs not directly present in the prostate cancer GWAS, we identified proxy SNPs in linkage disequilibrium (LD, r2  >  0.8) using the 1000 genome project. We used P-value < 0.05 as a threshold to determine statistical significance. Based on 152 out of 174 SNPs of type II diabetes in the East Asian population, we found that type II diabetes had a significant negative causal effect on prostate cancer [Odds Ratio (OR) = 0.76, 95% Confidence Interval (CI): 0.76 - 0.89, P = 2.26 x 10-6]. Results from sensitivity analysis using other weighting methods provided similar results. In conclusion, we observed an inverse relationship between type II diabetes and prostate cancer among the East Asian population. Patients with diabetes may have a lower risk of prostate cancer due to a reduced level of insulin and testosterone. To validate this association, further research is needed on those hormones and prostate cancer risk at the metabolic level.

Citation Format: Zhongyi Guo. Causal effect of type II diabetes on prostate cancer in the East Asian population: A two-sample Mendelian randomization study [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B003.
Abstract B008: Autoimmune disease and the risk of anal cancer in the U.S. elderly population
Authors: Song Minkyo , Engels Eric A. , Clarke Megan A. , Kreimer Aimée R. , Shiels Meredith S.
Published: January 2023

Background: Recently, anal squamous cell carcinoma (SCC) has increased rapidly over time, particularly among older women. As immunosuppression is associated with increased anal cancer risk, a parallel increase in autoimmune conditions may be contributing to this rising trend. Methods: We conducted a population-based case-control study using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database (years 2000-2017). Cases were individuals with first anal SCC diagnosed in SEER registries (N=4,505) and 199,566 cancer-free controls from a 5% random sample of Medicare beneficiaries. Using logistic regression, we calculated odds ratios (OR) and 95% confidence intervals (95%CI) for associations with 47 autoimmune conditions identified via Medicare claims. Models were adjusted for age (continuous), sex, race (white, others), year of selection (quartiles), average number of physician claims per year (quartiles), medicare coverage months (quartiles) and smoking status. The false discovery rate was used to correct for multiple comparisons. Results: 18% of cases and 15% of controls had any autoimmune condition diagnosed. Having any autoimmune condition was associated with an increased risk of anal SCC (OR 1.12, 95%CI 1.03-1.22). The strongest risk estimates were for sarcoidosis (OR 1.97, 95%CI 1.22-3.19), followed by systemic lupus erythematosus (1.86, 1.38-2.52) and psoriasis (1.31, 1.08-1.58). Stratified by sex, only women showed significant associations for systemic lupus erythematosus (OR 2.05, 95%CI 1.51-2.78) and men with psoriasis (1.72, 1.25-2.35) and polymyalgia rheumatica (0.33, 0.12-0.89). Conclusion: To date, this is the largest study of anal SCC exploring its association with autoimmunity, especially in this understudied old population. We report a weak to moderately increased risk of certain autoimmune diseases with anal SCC. Some associations differed by sex. Impact/Significance: Understanding the mechanism by which autoimmune diseases increase cancer anal cancer risk may guide better prevention and treatment strategies. Given the rarity of these conditions and their moderate associations with anal cancer, clinical diagnosis of autoimmune diseases cannot explain the rising trend in anal cancer. Future studies are warranted in addressing the underdiagnosis of these autoimmune conditions to better quantify the burden.

Citation Format: Minkyo Song, Eric A. Engels, Megan A. Clarke, Aimée R. Kreimer, Meredith S. Shiels. Autoimmune disease and the risk of anal cancer in the U.S. elderly population [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B008.
Abstract B010: Association between temporal muscle thickness and overall survival in non-small cell lung cancer patients with brain metastasis
Authors: Yang Seung Ho , Kim Young Il , Kim Hyun Ho , Shim Byoung Yong
Published: January 2023

Temporal muscle thickness (TMT) has recently been suggested as a novel biomarker of sarcopenia in head and neck malignancies. However, few studies have evaluated TMT as a prognostic marker in patients with brain metastasis. This study investigated the association of TMT with overall survival (OS) in non-small cell lung cancer (NSCLC) patients with brain metastasis. The records of all NSCLC patients with brain metastasis between 2009 and 2018 at St. Vincent’s Hospital were reviewed retrospectively. A total of 221 patients met our eligibility criteria. In the group with TMT thicker than the median, OS was longer than the group with TMT thinner than the median (240 days versus 139 days, p = 0.014). In multivariate analysis, the thicker TMT group had longer survival (HR 0.73 CI 0.56–0.96, p = 0.024). Male (HR 1.58 CI 1.19–2.09, p = 0.002) and older age (≥ 65 years) (HR 2.05 CI 1.53–2.74, p < 0.001) also showed statistical significance. We also performed subgroup analysis in older patients (≥ 65 years). In this subgroup of 107 patients, the thicker TMT group also showed longer OS than the thinner TMT group (209 days versus 82 days, p = 0.009). Our findings suggest that TMT can be a useful biomarker for OS in NSCLC patients with brain metastasis.

Citation Format: Seung Ho Yang, Young Il Kim, Hyun Ho Kim, Byoung Yong Shim. Association between temporal muscle thickness and overall survival in non-small cell lung cancer patients with brain metastasis [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B010.
Abstract B016: Aberrant age-related methylation leads to tumor predisposition in colorectal organoids
Authors: Petkovich Daniel A. , Powers Rachael , Tao Yong , Kang Byunghak , Patel Nibedita , Gabrielson Kathy , Cabo Rafael de , Baylin Stephen B. , Easwaran Hariharan P.
Published: January 2023

Aging is one of the greatest risk factors for cancers, and epigenetic changes involving DNA methylation show close similarities during age-related cellular processes and tumor development. We have shown orthogonal relationships between the accrual of aberrant DNA methylation changes associated with cell division cycles during senescence and transformation. Consequently, we have hypothesized that while both senescent and proliferative aging cells coexist in the same tissues, the risk for cancer most likely comes from, and due to, epigenetic changes occurring in the latter, long-term, self-renewing cells. Using colon organoid models, we have studied the importance of genes undergoing DNA methylation mediated silencing during aging and their role in predisposing to tumorigenesis. Analyses of the in vivo and ex vivo aging-associated epigenetic/expression changes indicate the importance of age-related aberrant methylation in tumor promoting states.

Citation Format: Daniel A. Petkovich, Rachael Powers, Yong Tao, Byunghak Kang Nibedita Patel, Kathy Gabrielson, Rafael de Cabo, Stephen B. Baylin, Hariharan P. Easwaran. Aberrant age-related methylation leads to tumor predisposition in colorectal organoids [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B016.
Abstract B026: SIWA318H, a novel advanced glycation end product (AGE) specific antibody, targets cancer and senescent cells in the tumor microenvironment and exhibits potent antitumor activity in a humanized mouse model for pancreatic cancer. [R]
Authors: Rossi Gabriela , Gruber Lewis , Gruber Misty , Han Haiyong
Published: January 2023

The aging-related and cancer cell derived oxidatively stressed tumor microenvironment drives cell senescence. Senescent cells (SCs), in turn, promote immune suppression, tumor progression, and metastasis. Hence, targeting SCs presents an attractive approach for cancer therapy. SIWA318H is a monoclonal antibody that selectively targets an advanced glycation end product biomarker on the surface of dysfunctional cells exhibiting both (a) aerobic glycolysis and (b) oxidative stress. The SIWA318H biomarker is associated with cancer cells, SCs, oxidatively damaged cells, and infected cells. SIWA318H has been shown to bind to an ADCC inducing human IgG FcγR3 receptor as a mechanism of action. SIWA318H exhibits strong binding to pancreatic cancer patient derived xenograft tumors as demonstrated by immunohistochemistry. In an in vivo study using a humanized mouse xenograft model for pancreatic cancer, we showed that treatment with SIWA318H (both high and low dose groups) statistically significantly reduced tumor growth compared to the isotype antibody control group (P < 0.0001). In addition, there was a significantly higher number of mice had complete remission in the treated groups compared to the isotype control group: 37.5% in high dose group (P = 0.0325) and 43.8% in low dose group (P = 0.0143). Moreover, mice treated with 318H had a median overall survival of > 45 days compared to 26 days for the isotype control mice. There was no difference in animal body weight between the SIWA318H-treated mice and the isotype control mice. Immunohistochemical analysis of tumor tissues taken from the in vivo study showed that SIWA318H treatment significantly reduced (a) tumor fibrosis as measured by the area of αSMA+ staining and (b) the number of senescent cells in the tumor stroma as measured by the number of p16INK4a positive cells in αSMA+ areas. In summary, our results demonstrate that SIWA318H is a novel senolytic antibody that exhibits potent preclinical antitumor activity against pancreatic cancer. SWA318H is currently under development for a first in human clinical trial.

Citation Format: Gabriela Rossi, Lewis Gruber, Misty Gruber, Haiyong Han. SIWA318H, a novel advanced glycation end product (AGE) specific antibody, targets cancer and senescent cells in the tumor microenvironment and exhibits potent antitumor activity in a humanized mouse model for pancreatic cancer. [R] [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B026.
Abstract IA003: Neuronal Genome Stability and Plasticity
Authors: Nussenzweig Andre
Published: January 2023

The DNA of neurons is continually damaged due to lifelong, high-level metabolic and transcriptional activity. In addition, recent studies have demonstrated extensive “programmed” DNA damage and somatic mutation in differentiating post-mitotic neurons. Here, we identify these endogenous lesions as single strand break intermediates of thymine DNA glycosylase (TDG)-mediated removal of oxidized methylcytosines during active DNA demethylation. Interrupting active DNA demethylation using anti-neoplastic cytosine analogs triggers TDG-dependent neuronal cell death. This suggests that the well-known neurotoxic side effects of certain chemotherapies, also called “chemobrain,” could be linked to DNA repair processes intrinsic to normal neuronal differentiation. In this presentation, we discuss the implications of these findings to neurodegeneration and cancer.

Citation Format: Andre Nussenzweig. Neuronal Genome Stability and Plasticity [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr IA003.
Abstract IA005: From hematopoiesis to immunity: Delineating the impact of aging on B-cell acute lymphoblastic leukemia progression
Authors: Henry Curtis J.
Published: January 2023

The world’s aging population, those 65 and older, is projected to increase from 703 million people to 1.5 billion people by 2050. This great accomplishment comes with the added obligation of providing adequate healthcare for this vulnerable population given the number of diseases that manifest with age, including cancer. Chronic inflammation is a well-established hallmark of aging, and we have demonstrated that this state compromises hematopoiesis, notably the function of B-progenitor cells. Furthermore, we have shown that aging-associated functional declines in B-progenitor cells can be rescued with the anti-inflammatory cytokine interleukin-37, which also reduces the expression of checkpoint proteins on aged innate immune cells and augments the function of aged lymphocytes. Importantly, interleukin-37-mediated improvements in hematopoiesis and immunity suppress B-cell acute lymphoblastic leukemia (B-ALL) progression and enhance the protective capacity of aged chimeric antigen receptor (CAR) T-cells in murine models of B-ALL. Our results highlight the therapeutic potential of anti-inflammatory agents in treating hematological malignancies and suggest that combining anti-inflammatory cytokine treatment with immunotherapy strategies may represent a novel approach for treating aging-associated blood cancers.

Citation Format: Curtis J. Henry. From hematopoiesis to immunity: Delineating the impact of aging on B-cell acute lymphoblastic leukemia progression [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr IA005.
Abstract IA006: Measuring the microbiome: Improving the predictive power of microbiome analysis in cancer outcomes
Authors: Bhatt Ami S.
Published: January 2023

More than 1,000 species of bacteria, archaea, viruses and fungi live in the human gut. Far from being passive passengers, these organisms strongly interact with one another and with their host’s metabolism and immune system. Compelling early experiments have demonstrated associations between the intestinal microbiome composition and obesity, cardiovascular diseases, and certain cancer chemotherapies’ efficacy. Yet teasing apart the mechanisms by which microbes impact host health has been challenging. To accelerate an otherwise challenging, slow and tedious process and to deconstruct mechanisms, we must critically examine our existing “tool kit” for studying the microbiome, and mature our measurement tools to meet these challenges. Our translational laboratory builds and designs observational and interventional clinical cohorts to study. We have also steadfastly worked to develop genomic tools to study strain level dynamics of the microbiome, how microbial genomes change over time and how microbes use hidden “microproteins” to communicate with each other and their human hosts. In this presentation, I will speak about three recent developments in our lab: (1) I will introduce the importance of absolute quantification in microbiome research, and our efforts toward that. This will form the basis of revised estimates of the number of microbial cells in a human body. (2) I will give an overview of a new computational workflow called “Phanta”, which enables simultaneous taxonomic profiling of eukaryotes, bacteria and viruses in a human gut metagenomic sample. (3) I will share unpublished work on how antibiotic exposure negatively impacts cancer outcomes in patients with triple-negative breast cancer.

Citation Format: Ami S. Bhatt. Measuring the microbiome: Improving the predictive power of microbiome analysis in cancer outcomes [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr IA006.
Abstract PR011: TXNRD1 drives innate immune response in senescent cells to promote tumor immune surveillance and age-associated inflammation
Authors: Hao Xue , Zhao Bo , Towers Martina , Liao Liping , Tang Hsin Yao , Havas Aaron , Kossenkov Andrew V. , Berger Shelley , Adams Peter D. , Speicher David W. , Zhang Rugang
Published: January 2023

Cellular senescence regulates cancer and tissue aging in part through the secretion of proinflammatory factors known as the senescence-associated secretory phenotype (SASP). For example, sterile inflammation or ‘inflammaging’ is a hallmark of tissue aging. Thioredoxin reductase 1 (TXNRD1) genetic variability is associated with aging and is often upregulated in human cancers. TXNRD1’s role in regulating tissue aging and cancer has been attributed to its enzymatic role in regulating cellular redox. Here we show that TXNRD1 drives the SASP and inflammation through the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) innate immune response pathway independently of its enzymatic activity. TXNRD1 localizes to cytoplasmic chromatin fragments (CCF) and interacts with cGAS in a senescence status dependent manner, which is required for the SASP. Biochemically, TXNRD1 enhances the enzymatic activity of cGAS. TXNRD1 is required for both the tumor-promoting and immune-surveillance functions of senescent cells, which are mediated by the SASP in vivo in mouse tumor models. Treatment of aged mice with a TXNRD1 inhibitor that disrupts its interaction with cGAS, but not an inhibitor of its enzymatic activity alone, downregulated inflammaging in several tissues. In summary, our results report TXNRD1 promotes inflammation via activating the innate immune response in a manner depending on its interaction with cGAS but not its enzymatic activity. Our findings have important implications for both tissue aging and cancer.

Citation Format: Xue Hao, Bo Zhao, Martina Towers, Liping Liao, Hsin Yao Tang, Aaron Havas, Andrew V. Kossenkov, Shelley Berger, Peter D. Adams, David W. Speicher, Rugang Zhang. TXNRD1 drives innate immune response in senescent cells to promote tumor immune surveillance and age-associated inflammation [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr PR011.
Abstract PR013: BH3 profiling of senescent cancer cells to identify mechanisms of resistance to ABT-263
Authors: Jochems Fleur , MacDonald Julie A. , Baltira Chrysiida , Daniels Veerle , Gooijer Mark de , Tellingen Olaf Van , Letai Anthony , Bernards René
Published: January 2023

Senescent cells rely on anti-apoptotic signaling for their survival, which can be targeted by senolytic agents. ABT-263 is a broad acting senolytic that targets anti-apoptotic proteins BCL-2, BCL-xL and BCL-W. Our group has shown that ABT-263 has a senolytic effect in most cancer cell lines, but not in all. This raised the question why certain senescent cancer cells undergo into apoptosis after treatment with ABT-263, while others remain refractory. To investigate this, we performed BH3 profiling, a technique that measures apoptotic priming (readiness to undergo into apoptosis) and apoptotic dependencies. We found that BH3 profiling in senescent cells requires specific optimization, and it determines that senescent ABT-263 sensitive cells highly depend on specific anti-apoptotic signaling, while ABT-263 resistant cells did not. Moreover, we found that ABT-263 sensitive cells were more primed to apoptosis compared to resistant cells. Intriguingly, this correlation was already apparent in the parental state. Nevertheless, we found that senescent cells were less primed to apoptosis than their parental counterparts, which was in contrast to what we expected. In conclusion, whether senescent cells will respond to ABT-263 is already determined in the parental state, and they become dependent on anti-apoptotic signaling for their survival. The observation that senescent cells were less primed to apoptosis was surprising, and we intend to further understand how it is possible that senescent cells are less primed to apoptosis, but still sensitive to ABT-263.

Citation Format: Fleur Jochems, Julie A. MacDonald, Chrysiida Baltira, Veerle Daniels, Mark de Gooijer, Olaf Van Tellingen, Anthony Letai, René Bernards. BH3 profiling of senescent cancer cells to identify mechanisms of resistance to ABT-263 [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr PR013.
Abstract A006: The NALCN channel regulates metastasis and non-malignant cell dissemination
Authors: Rahrmann Eric , Shorthouse David , Jassim Amir , Hu Linda , Ortiz Mariaestela , Mahler-Araujo Betania , Vogel Peter , Paez-Ribes Marta , Fatemi Atefeh , Hannon Gregory , Iyer Radhika , Blundon Jay , Lourenço Filipe , Kay Jonathan , Nazarian Rosaylnn , Hall Benjamin , Zakharenko Stanislav , Winton Douglas , Zhu Liqin , Gilbertson Richard
Published: January 2023

We identify the Sodium Leak Channel Non-Selective Protein (NALCN) as a key regulator of cancer metastasis and non-malignant cell dissemination. Among 10,022 human cancers, NALCN loss-of-function mutations were enriched in gastric and colorectal cancers. Deletion of Nalcn from gastric (Prom1CreERT2/LacZ;KrasG12D;Trp53Flx/Flx; n=269), intestinal (Villin1-CreERT2;KrasG12D;Trp53Flx/Flx; n=141) or pancreatic adenocarcinomas (Pdx1-Cre;KrasG12D;Trp53Flx/+; n=55) in mice did not alter tumor incidence, but markedly increased the number of circulating tumor cells (CTCs) and metastases. Treatment of these mice (Villin1-CreERT2;KrasG12D;Trp53Flx/Flx; n=28) with gadolinium–an imaging contrast agent and NALCN channel blocker–similarly increased CTCs and metastasis. Deletion of Nalcn from mice that lacked oncogenic mutations and never developed cancer(Prom1CreERT2/LacZ; n=174), caused shedding of epithelial cells into the blood at levels equivalent to those seen in tumor-bearing animals. These cells trafficked to distant organs to form normal structures including lung epithelium and kidney glomeruli and tubules. Thus, NALCN regulates cell shedding from solid tissues independent of cancer, divorcing this process from tumorigenesis and unmasking a potential new target for anti-metastatic therapies.

Citation Format: Eric Rahrmann, David Shorthouse, Amir Jassim, Linda Hu, Mariaestela Ortiz, Betania Mahler-Araujo, Peter Vogel, Marta Paez-Ribes, Atefeh Fatemi, Gregory Hannon, Radhika Iyer, Jay Blundon, Filipe Lourenço, Jonathan Kay, Rosaylnn Nazarian, Benjamin Hall, Stanislav Zakharenko, Douglas Winton, Liqin Zhu, Richard Gilbertson. The NALCN channel regulates metastasis and non-malignant cell dissemination [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A006.
Abstract A013: Loss of MLL3 epigenetic regulator drives metastasis by promoting a hybrid epithelial-mesenchymal transition state
Authors: Cui Jihong , Zhang Chi , Lee Ji-Eun , Bartholdy Boris , Yang Dapeng , Liu Yu , Erler Piril , Galbo Phillip , Hodge Dayle Q. , Huangfu Danwei , Zheng Deyou , Ge Kai , Guo Wenjun
Published: January 2023

Phenotypic plasticity associated with the hybrid epithelial-mesenchymal transition (EMT) state is crucial to metastatic seeding and outgrowth. However, the mechanisms controlling the induction of hybrid EMT remain poorly defined. We showed that deletion of the epigenetic regulator MLL3, a tumor suppressor frequently altered in human cancer, promoted the acquisition of the hybrid EMT state in both epithelial and mesenchymal breast cancer cells by facilitating EMT and mesenchymal-epithelial transition, respectively, distinct from other known EMT regulators mediating unidirectional changes. Consequently, MLL3 deletion greatly increased metastasis by enhancing metastatic colonization. MLL3 loss led to increased IFNg signaling, which is required for the induction of hybrid EMT cells and the enhanced metastatic capacity. Mechanically, MLL3 loss enhanced IFNg signaling by increasing H3K27ac intensity in the enhancers of a subset of IFNg response genes in both epithelial and mesenchymal tumor cells. We further showed that MLL3-deficient cells were sensitive to BET inhibition, which effectively suppressed the growth of MLL3-mutant primary tumors and metastases. These results uncovered a key driver of the hybrid EMT state in breast cancer that could be targeted therapeutically.

Citation Format: Jihong Cui, Chi Zhang, Ji-Eun Lee, Boris Bartholdy, Dapeng Yang, Yu Liu, Piril Erler, Phillip Galbo, Dayle Q. Hodge, Danwei Huangfu, Deyou Zheng, Kai Ge, Wenjun Guo. Loss of MLL3 epigenetic regulator drives metastasis by promoting a hybrid epithelial-mesenchymal transition state [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A013.
Abstract A018: Phosphorylated nuclear DICER1 promotes open chromatin state and lineage plasticity of lung adenocarcinomas
Authors: Reyes-Castro Raisa A. , Chen Shin-Yu , Seemann Jacob , Arur Swathi
Published: January 2023

DICER1 controls micro(mi)RNA-mediated epithelial-to-mesenchymal transition (EMT) to regulate tumorigenesis of lung adenocarcinomas (LUADs). We discovered that DICER1 is phosphorylated by ERK and nuclear translocated and phospho-DICER1 contributes to tumorigenesis. Mechanisms through which phospho-DICER1 regulates tumor progression remain undefined. We show that phospho-nuclear DICER1 associates with invasive human LUADs with oncogenic KRAS mutations and promotes late-stage tumor progression in mice with oncogenic Kras mutations. Surprisingly, phosphomimetic DICER1 regulates LUAD progression independent of miRNAs and EMT. Integrating single-cell RNA sequencing, fluorescent in situ RNA hybridization, immunofluorescence, and ATAC-sequencing, in mice,we discovered that phosphomimetic DICER1 generates an open chromatin state in the lung tumor alveolar cells leading to expression of gastrointestinal genes and altered AT2 cell identity. Strikingly, we also observe the gastric gene signature in human LUADs with phospho-DICER1 and KRAS mutations. We propose that phosphorylated nuclear DICER1 regulates chromatin remodeling leading to tumor cell reprogramming which drives lung cancer progression.

Citation Format: Raisa A. Reyes-Castro, Shin-Yu Chen, Jacob Seemann, Swathi Arur. Phosphorylated nuclear DICER1 promotes open chromatin state and lineage plasticity of lung adenocarcinomas [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A018.
Abstract A036: Juxtacrine signaling between macrophage and cancer cell inhibits radiation-induced ferroptosis in syngeneic colon cancer
Authors: Kim Sang Wha , Chung Hyewon , Seok Seung Hyeok
Published: January 2023

Although radiotherapy (RT) is one of the most common modalities for cancer treatment, radioresistance remains an intractable challenge. RT induces intratumoral infiltration of macrophages for the clearance of injury debris, but rather tumor-associated macrophages confer fitness advantages to cancer cells after RT. Here, we report that tumor-associated macrophage instigates radioresistance by inhibiting RT-induced cell death in a contact-dependent manner. Mechanistically, RT increases receptor tyrosine kinases (RTKs) expression in cancer cells to enable direct interaction with macrophages, resulting in reduced cancer cell ferroptosis triggered by RT. Unbiased RNA-seq analysis of RTK-dependent juxtacrine signaling in macrophages further reveals a profound remodeling of the irradiated tumor microenvironment (TME) via regulation of macrophage polarization and cytotoxic T cell-mediated antitumor responses. Using a syngeneic colon cancer model, we found that ablation of RTK-induced juxtacrine signaling sensitized tumor to RT through increasing cancer cell ferroptosis and impairing macrophages-mediated TME. Collectively, our study supports the RTKs as a new radiosensitizing target via attenuation of the interaction between cancer cells and macrophages during RT.

Citation Format: Sang Wha Kim, Hyewon Chung, Seung Hyeok Seok. Juxtacrine signaling between macrophage and cancer cell inhibits radiation-induced ferroptosis in syngeneic colon cancer [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A036.
Abstract A042: Differences in gain-of-function and inhibitory effects amongst p53 mutants in vivo
Authors: Xiong Shunbin , Chachad Dhruv , Zhang Yun , Gencel-Augusto Jovanka , Sirito Mario , Pant Vinod , Yang Peirong , Sun Chang , Lozano Guillermina
Published: January 2023

The majority of p53 missense mutations identified in cancer patients are in the DNA-binding domain and are characterized as either structural or contact mutations. These missense mutations exhibit inhibitory effects on wild-type p53 activity. More importantly, these mutations also demonstrate gain-of-function (GOF) activities characterized by increased metastasis, poor prognosis, and drug resistance. To better understand the activities by which TP53 mutations, identified in Li-Fraumeni syndrome, contribute to tumorigenesis in vivo, we generated a novel germline p53R245W allele (contact mutation) and compared it to existing p53R172H (structural mutation) and p53R270H (contact mutation) alleles. Thymocytes from heterozygous mice showed all three hot-spot mutations exhibited similar inhibitory effects on wild type p53 transcription in vivo and tumors from these mice had similar levels of loss of heterozygosity. However, the overall survival of p53R245W/+ and p53R270H/+ mice, but not p53R172H/+ mice, was significantly shorter than that of p53+/- mice, demonstrating p53 mutation-specific GOF contributions to tumor development. Furthermore, p53R245W/+ and p53R270H/+ mice had more osteosarcoma metastases than p53R172H/+ mice, indicating that these two contact mutants have stronger GOF in driving osteosarcoma metastasis. Omics analyses using RNA-sequencing data from p53R172H/+, p53R245W/+, and p53R270H/+ primary osteosarcomas in comparison to p53+/- indicated GOF was mediated by distinct pathways among the three mutations. Thus, both the inhibitory effect of mutant over WT p53, and GOF activities of mutant p53 contributed to tumorigenesis in vivo. Targeting p53 mutant-specific pathways may be important for therapeutic outcomes in osteosarcomas.

Citation Format: Shunbin Xiong, Dhruv Chachad, Yun Zhang, Jovanka Gencel-Augusto, Mario Sirito, Vinod Pant, Peirong Yang, Chang Sun, Guillermina Lozano. Differences in gain-of-function and inhibitory effects amongst p53 mutants in vivo [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A042.
Abstract B019: Identify features of fibroblast and macrophage which regulate metastasis of triple-negative breast cancer
Authors: Lee Woochan , Chung Hyewon , Heo Woohang , Moon Hyeong-Gon , Seok Seung Hyeok , Kim Jong-Il
Published: January 2023

The tumor microenvironment (TME), which the cancer is known to remodel, can interact with cancer in various ways, such as promoting or hindering metastasis. The challenge with comprehending TME is that each patient's individual variance makes it difficult to carry out a consistent analysis. We used the PDX model to analyze the alterations entirely brought about by cancer cells of each patient in the same environment exclusively. In 121 breast cancer patients, we created a PDX model and performed WES and RNA-seq. We repeatedly performed metastatic induction tests on the models of 26 TNBC patients among the PDX models we generated. The replicated experiments confirmed that cancer cells with frequent metastasis usually spread well, while cancer cells with seldom metastases rarely metastasize. For each of the five samples that had the greatest and worst rates of metastasis, the pre-metastatic xenograft tumor was analyzed using scRNA-seq. Metastasis could not be predicted by only cancer cells because there was no difference between the two groups. Still, fibroblasts and macrophages had distinct gene markers before metastasis which can predict metastasis. To explore TME that develops pre-metastatic niches (PMN) in organs that would be metastasis targets, we developed a metastatic model using 4T1 cell lines. Daily lung macrophage RNA-seq, lung WES, and lung scRNA-seq procedures were carried out for four weeks to examine the precise timing of metastasis and the daily changes in the transcriptome. Surprisingly, a few days before the presence of any cancer cells, the gene expression of lung macrophages had already undergone significant modification. Additionally, only injections of tumor-conditioned media that mimicked metastasis could activate PMN in lung macrophages.

Citation Format: Woochan Lee, Hyewon Chung, Woohang Heo, Hyeong-Gon Moon, Seung Hyeok Seok, Jong-Il Kim. Identify features of fibroblast and macrophage which regulate metastasis of triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr B019.