bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1366: A novel stem cell memory T cell subpopulation intermediate to canonical stem cell memory and central memory T cells in human cancer
Authors: Powell Daniel J.
Published: June 2022

Stem memory T cells (Tscm) are integral for effective immunotherapy and antitumor responses, but little is known about Tscm immunobiology in solid human tumors. Here we identify self-renewing and multipotent Tscm tumor-infiltrating lymphocytes (TILs) in human cancer and present a novel Tscm subset which expresses CD45RO, is derived from CD45RO- Tscm T cells, and is capable of self-renewal and multipotency. From the analysis of CD45RO+ Tscm differentiation, phenotyping, gene expression, and the broader TCR repertoire, we find that CD45RO+ Tscm cells are hierarchically positioned in between canonical CD45RO- Tscm cells and central memory T cells. Notably, CD45RO+ Tscm cells exhibit a gene expression profile consistent with effector capabilities and a tumor-specific phenotype that is more similar to T cells associated with successful immunotherapy than canonical Tscm. Thus, we describe a novel Tscm subset in human cancer which has distinct phenotypic, transcriptional, and effector-like attributes that position it as an attractive subset for future basic and clinical research in the setting of cancer immunotherapy.

Citation Format: Daniel J. Powell. A novel stem cell memory T cell subpopulation intermediate to canonical stem cell memory and central memory T cells in human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1366.
Abstract 1370: Targeting LSD1 rescues MHC-I antigen presentation in small cell lung cancer
Authors: Nguyen Minh N. , Taniguchi Hirokazu , Chow Andrew , Zhan Yingqian A. , Sen Triparna , Rudin Charles M.
Published: June 2022

Purpose: Small cell lung cancer (SCLC) is a highly aggressive cancer with early primary resistance and modest clinical benefit to immune checkpoint blockade (ICB). Mutation or transcriptional repression of the major histocompatibility complex class I (MHC-I) is a key mechanism driving resistance to T cell-based therapies. Lysine Demethylase 1 (LSD1) regulates gene expression through modulating mono- and di- methylated lysine 4 and 9 of histone H3. LSD1 is a therapeutic target of interests in SCLC due to its oncogenic requirement for tumor growth, and there has been growing evidence pointing to LSD1 as a repressor of tumor-intrinsic immunogenicity. Here investigated the role of LSD1 as a transcriptional regulator of antigen presentation in SCLC.

Method: To perturb LSD1 function, we employed the pharmacological inhibitor ORY-1001 and shRNA-mediated knockdown. We then assessed changes in MHC-I expression on SCLC cell lines by flow cytometry and western blot. To analyze transcriptional changes following LSD1 inhibition, we performed RNA-seq on SCLC cells pre- and post-treatment with ORY-1001. To observe for antigen-specific T cell killing, we engineered SCLC cells to express endogenous antigens and co-cultured these cells with primary cognate CD8+ T cells. Finally, we treated genetically engineered mouse model (GEMM)-derived tumors on immunocompetent syngeneic mice with ORY-1001 with or without anti-PD-L1 blockade to assess for anti-tumor effects.

Results: We discovered a significant and strong negative correlation between expression of LSD1 and genes encoding the MHC-I antigen presentation pathway. Inhibition of LSD1 induces expression of MHC-I genes and restores expression of genes encoding the antigen presentation machinery. Perturbation of LSD1 further activates interferon signaling and interferon-inducible expression of NLRC5, a well-characterized transcriptional activator of MHC-I genes. We further showed that targeting LSD1 sensitizes SCLC cells to MHC-I-restricted T cell-dependent cytolysis and enhances ICB efficacy in refractory SCLC tumors.

Conclusion: Our data define a role for LSD1 as a potent negative regulator of MHC-I-mediated antigen presentation and provide rationale for the use of LSD1 inhibitors to augment response to immunotherapy in SCLC.

Citation Format: Minh N. Nguyen, Hirokazu Taniguchi, Andrew Chow, Yingqian A. Zhan, Triparna Sen, Charles M. Rudin. Targeting LSD1 rescues MHC-I antigen presentation in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1370.
Abstract 1373: PeptidePCR: Direct identification of cancer vaccine targets from scant clinical samples
Authors: Ramarathinam Sri H. , Faridi Pouya , Peng Angela , Szeto Pacman , Wong Nicholas C. , Behren Andreas , Shackleton Mark , Purcell Anthony W.
Published: June 2022

Background: Peptides presented by Human Leukocyte antigen (HLA) class I and II molecules form an important component of the adaptive immune response against tumors. Identifying HLA-bound peptides is therefore crucial to understand the specificity of T cell responses in cancer. Due to sample limitations, it is often difficult or impossible to confirm epitope presentation in clinical biopsy material. To develop truly personal medicine, target epitopes need to be directly identified or validated in patient tumors at the peptide antigen level.

Methodology: We have developed a microscale HLA immunoprecipitation protocol which when combined with a tandem mass tag (TMT)-based barcoding approach was able to identify HLA-bound peptides. HLA-complexes were affinity purified from either cultured cells, patient-derived xenograft or melanoma biopsies and the peptide cargo was tagged using TMT barcodes and analyzed using high-resolution mass spectrometry. Like primers in PCR, the carrier peptides and multiplexing of samples amplifies the signal enabling sensitive detection.

Results: By using this strategy, we identified HLA-bound peptides from as few as ~1000 cultured cells. We demonstrate the clinical utility of this approach by confirming the presentation of around 1000 peptides from a challenging melanoma biopsy (~1-20mg in total), including 11 well-known T-cell response-inducing epitopes and other potential epitopes derived from Melanoma-associated antigens and neoantigens.

Conclusion: This strategy will be useful for studying peptidome subsets in other clinical samples where the amount of tissue available via sampling is limiting, including biopsies taken for autoimmune diseases and infections, or to sample rare cell types in tissue/cell samples, such as different antigen-presenting cell subsets. The approach can directly isolate antigens that are already presented by HLA molecules, thereby increasing the precision of personalized approaches to cancer treatment with less than 1-week turnaround times.

Citation Format: Sri H. Ramarathinam, Pouya Faridi, Angela Peng, Pacman Szeto, Nicholas C. Wong, Andreas Behren, Mark Shackleton, Anthony W. Purcell. PeptidePCR: Direct identification of cancer vaccine targets from scant clinical samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1373.
Abstract 1421: Non-invasive early detection of pancreatic ductal adenocarcinoma using methylation signatures in circulating tumor DNA
Authors: Gore Athurva J. , Dang Justin , Fung Alan , Xie Bin , Liu Rui
Published: June 2022

Background: Pancreatic ductal adenocarcinoma (PDAC) has a low overall survival rate primarily due to late onset of symptoms and rapid progression. Early symptoms, which include abdominal and back pain, diarrhea, weight loss, and jaundice are non-specific for PDAC and may be associated with other gastrointestinal diseases. PDAC lacks reliable and accurate tests for early detection. We aimed to discover biomarkers carrying a PDAC-specific DNA methylation signature in blood cell-free DNA, and to develop and validate a non-invasive test for PDAC detection.

Methods: Reduced representative bisulfite sequencing (RRBS) was previously performed on tissue and plasma samples from PDAC patients and healthy individuals to identify PDAC-specific methylation markers. These markers were combined with previously reported cancer methylation markers for a second round of marker screening. The resulting markers were utilized to develop a targeted methylation sequencing assay for plasma DNA, designated as PDACatch. The PDACatch assay was validated on an independent sample set to demonstrate its efficacy for pancreatic cancer methylation signature detection.

Results: The PDACatch assay was performed on 91 PDAC plasma and 84 healthy plasma samples obtained from commercial biobanks. In this independent verification sample set, the PandaX assay predicted PDAC from healthy with AUC of 0.91; accuracy remained high for classification of both stage I and early-stage (I/IIa) samples.

Conclusion: The PDACatch assay, a ctDNA methylation based blood test, achieved a high accuracy for detecting PDAC at early stages, indicating its potential in screening effectiveness.

Citation Format: Athurva J. Gore, Justin Dang, Alan Fung, Bin Xie, Rui Liu. Non-invasive early detection of pancreatic ductal adenocarcinoma using methylation signatures in circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1421.
Abstract 1443: Environmental heavy metal toxicity and mammographic breast density in a Mississippi Delta southern state
Authors: Fine Bobbie Dean , Stahr Shelbie , Rogers Lora J. , Runnells Gail A. , Chiang Tung-Chin , Su Lihchyun J.
Published: June 2022

Importance: Increased mammographic density (MD) is a strong independent risk factor for breast carcinoma. Ubiquitous environmental heavy metal (HM) exposure/toxicity appears pro-carcinogenic in several human cancers. However, studies in the current scientific literature have not elucidated specific connections between HM exposure and mammographically detected increases in breast density.

Objective: To determine whether increases in heavy metals (ie, chromium, arsenic and cadmium) measured in urine as a biomarker for long-term exposure, associate with increased MD in a female study cohort in Arkansas.

Design, Setting, Participants: One hundred thirty-nine participants in the Arkansas Rural Community Health (ARCH) study cohort, recruited through a mobile mammography unit at baseline, were included in this pilot study. Demographic/health history questionnaire data, urine, blood and saliva samples and incident mammograms classified by BI-RADS were ascertained after informed consent. Study protocol was approved by the Institutional Review Board at the University of Arkansas for Medical Sciences (UAMS).

Main Outcome and Measures: Urinary chromium, arsenic and cadmium levels were determined using inductively coupled plasma mass spectrometry. The concentrations of HM were adjusted for urinary creatinine and specific gravity and the results categorized into tertiles. Multivariable logistic regression models were used to evaluate the association between HM exposure and MD. Association of both continuous and categorical variables were examined. Confounding variables in the multivariable models including age, race, BMI, age at menarche and smoking history were determined by a priori knowledge and statistical assessment.

Results: Odds ratios (OR) and 95% confidence intervals (CI) for the association between each tertile of HM exposure and MD were used for the assessment. For the unadjusted model, increasing ORs for MD were noted with increased levels of both Chromium and Arsenic exposure. Increased ORs for MD were observed with increased levels of Chromium, Arsenic and Cadmium exposure in the multivariable adjusted model. However, none of these associations demonstrated statistical significance in this limited pilot study.

Conclusion: Positive associations between HM exposure and MD were noted after adjusting for age, sex, BMI, age at menarche and smoking history in this pilot study. However, the association did not reach statistical significance at α = 0.05.

Citation Format: Bobbie Dean Fine, Shelbie Stahr, Lora J. Rogers, Gail A. Runnells, Tung-Chin Chiang, Lihchyun J. Su. Environmental heavy metal toxicity and mammographic breast density in a Mississippi Delta southern state [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1443.
Abstract 1450: Interactions of DNMTs genetic variants associated with breast cancer risk
Authors: Lin Hui-Yi , Su L. Joseph , Rogers Lora J. , Runnells Gail A. , Hsu Ping-Ching , Stahr Shelbie D. , Chiang Tung-Chin
Published: June 2022

Background: DNA methyltransferases (DNMTs) control DNA methylation and impact gene expression. Many studies have demonstrated that genetic variants in DNMT genes play a role in cancer development, including breast cancer. However, the impact of SNP-SNP interactions for DNMTs associated with breast cancer risk is unclear. The objective is to evaluate SNP-SNP interactions associated with breast cancer risk.

Methods: We selected 14 SNPs in 3 DNMT genes (DNMT1, DNMT3A, and DNMT3B) for the 4,195 women (1:2 match for breast cancer cases and controls), including 1,085 African Americans (AAs) and 3,110 European Americans (EAs) in the Arkansas Rural Community Health (ARCH) cohort. We included different inheritance models (dominant, recessive, and additive) for individual SNP effects, using logistic regressions with breast cancer status (yes/no) as the outcome. Two-way SNP-SNP interactions associated with breast cancer risk were analyzed using the SNP Interaction Pattern Identifier (SIPI) approach developed by our research team.

Results: Out of the 14 DNMTs SNPs, we found two SNPs (rs7605753 and rs10196635 in DNMT3A) were individually associated with breast cancer risk (p<0.05) in EAs, however, none was statistically significant in AAs. Interestingly, we applied the SIPI approach, targeting SNP-SNP interactions,19 SNP-SNP interaction pairs for EAs, and 6 pairs for AAs associated with breast cancer risk. These promising SNP interaction pairs had an interaction p-value less than 0.05, far less than the p-values of the 2 constituent SNPs. Also, these promising SNP-SNP interaction pairs are different between races. For example, the EA women with the CC + AT/TT genotype in rs12991495 + rs10196635 (both in DNMT3A) had a higher risk of breast cancer risk than other genotype combinations (Odds ratio [OR]=2.2, p=0.011). On the other hand, the AA women with the TT+AA genotype in the SNP pair of rs2304429 (DNMT3A) + rs2290684 (DNMT1) tend to have a higher breast cancer risk than other genotype combinations in the same pair (OR=4.3, p=0.034). Notably, the individual effects of the two constituent SNPs are not significant (p=0.537 and 0.547).

Conclusion: Our findings support that the SNPs in DNMT genes play an essential role in breast cancer risk. SIPI is an excellent tool to evaluate SNP-SNP interactions, which can better predict breast cancer risk.

Citation Format: Hui-Yi Lin, L. Joseph Su, Lora J. Rogers, Gail A. Runnells, Ping-Ching Hsu, Shelbie D. Stahr, Tung-Chin Chiang. Interactions of DNMTs genetic variants associated with breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1450.
Abstract 1457: NELFE regulates chromatin accessibility to affect MYC induced transcription
Authors: Zhang Kai , Barry Anna , Lamm Ryan , Dang Hien
Published: June 2022

Liver cancer incidence rates have more than tripled in the last 40 years and is projected to increase more than 40% in the next decade. Although progress has been made, there is still limited therapeutic options. Due to the various etiological factors associated in HCC development and late stage in which it is diagnosed, the five-year survival rate is only 20%. Molecularly, more than 80% of HCC has an alteration in MYC signaling. Yet, MYC remains undruggable and studies over the recent years show that targeting proteins that regulate MYC is a promising approach in developing anti-cancer therapies. One such protein is the RNA binding protein (RBP) Negative Elongation Factor E (NELFE). We recently demonstrated for the first-time that NELFE recruits MYC via protein-protein interactions to the chromatin to control the expression of pro-survival genes. Consistent with the role of NELFE as a regulator of MYC in these cancers, we showed that patients with aberrant NELFE expression concurrently have active MYC signaling and poor outcome. These studies suggest that the NELFE/MYC interplay may be important for HCC maintenance. Thus, our hypothesis is that NELFE modulates the chromatin landscape to facilitate MYC-induced transcription to promote HCC. To investigate NELFE’s effect on MYC-induced transcription, we performed NELFE and MYC ChIP-sequencing and ATAC-sequencing analyses on CRISPR/Cas9-mediated NELFE knockout HCC cells. We found NELFE depletion resulted in significant reduction in nucleosomal accessibility and MYC binding to the chromatin near promoter-proximal regions. Although NELFE depletion alters the chromatin landscape, we found it rarely interacts with the chromatin, specifically within MYC bound regions, suggesting that the MYC/NELFE interaction is facilitated by a third protein. NELFE co-immunoprecipitation followed by mass spectrometry analyses identified the protein SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1 (SMARCB1) as a potential MYC cofactor that facilitates the NELFE/MYC interaction. Immunoblotting analyses show NELFE interacts with SMARCB1 and MYC and loss of NELFE significantly reduced SMARCB1/MYC interactions, indicating that NELFE facilitates chromatin accessibility through SMARCB1, which is required for MYC-induced transcription. Future studies include investigating SMARCB1’s oncogenic role in HCC through NELFE/MYC signaling.

Citation Format: Kai Zhang, Anna Barry, Ryan Lamm, Hien Dang. NELFE regulates chromatin accessibility to affect MYC induced transcription [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1457.
Abstract 1482: Efficient targeting of prostate cancer using ligand conjugated and chemically modified tumor suppressive miRNA
Authors: Abdelaal Ahmed M. , Kasireddy Sudarshan , Sohal Ikjot S. , Low Philip S. , Kasinski Andrea L.
Published: June 2022

MicroRNAs (miRNAs) inhibit the expression of genes through imperfect base pairing with target messenger RNAs (mRNAs), which allows a single miRNA the ability to regulate the expression of multiple genes, potentially acting as a multi-drug cocktail. In principle, tumor-suppressive miRNAs, such as miRNA-34a (miR-34a) are excellent anti-cancer agents; however, due to toxicity associated with currently used delivery vehicles and poor in vivo miRNA stability, the clinical application of miRNAs is thwarted. To overcome these challenges, we engineered two modifications to the miRNA. The first entails conjugating the miRNA to a ligand that promotes delivery specifically to cancer cells while the second involves using a fully chemically modified miRNA (FM-miR) to enhance miRNA stability. The ligand chosen for delivery, 2- [3-(1,3-dicarboxy propyl) ureido] pentanedioic acid (DUPA), is a high-affinity binding partner of the Prostate-Specific Membrane Antigen (PSMA), which is significantly upregulated on prostate cancer cells. We show that DUPA-miR-34a is specifically targeted to tumor cells overexpressing PSMA, is rapidly internalized by the cells, and induces target gene silencing. The binding and uptake of miR-34a by the tumor cells is dependent on conjugating the miRNA to DUPA. In vivo, DUPA-conjugates bind specifically to PSMA expressing prostate tumors with no significant uptake from normal organs or tumors with no PSMA expression. Additionally, Incorporation of the ionophore nigericin in the DUPA ligand enhances miR-34a silencing activity through facilitating its endosomal escape. However, since RNAs are inherently unstable a second modification was engineered to enhance the miRNA stability. Modifying miRNA through the inclusion of phosphorothioate linkages and 2′-fluoro and 2′-O-methyl modified ribose bases, enhances miRNA stability without compromising its activity. Fully modified miR-34a (FM-miR-34a) exhibits enhanced silencing activity of its target genes such as MET, and CD44 in comparison to partially modified miR-34a (PM-miR-34a). In addition, both PM-miR-34a and FM-miR-34a significantly inhibit cell proliferation in vitro, and the silencing of target genes requires the presence of argonaute 2 (AGO2) protein. We plan to identify the targeting differences between FM- and PM-miR-34a and will combine the DUPA ligand with FM-miR-34a to enhance both delivery and activity of miR-34a.

Citation Format: Ahmed M. Abdelaal, Sudarshan Kasireddy, Ikjot S. Sohal, Philip S. Low, Andrea L. Kasinski. Efficient targeting of prostate cancer using ligand conjugated and chemically modified tumor suppressive miRNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1482.
Abstract 1483: RNA interference seed-based approach to inhibit androgen signaling and induce prostate cancer cell death
Authors: Corbin Joshua M. , Ruiz-Echevarria Maria J.
Published: June 2022

The goal of this study is to identify RNA interference (RNAi) seed sequences that inhibit androgen signaling and induce toxicity in prostate cancer (PCa) cells. The high prevalence of acquired resistance to androgen deprivation therapy, as well as first and second generation androgen receptor (AR) antagonists, drives the development of lethal castration resistant prostate cancer (CRPC). As a result, PCa remains one of the leading causes of cancer related deaths in men. AR amplification, gain of function mutations and constitutively active splice isoforms of the AR, and the overexpression of AR coregulators, play considerable roles in promoting CRPC by sustaining AR activity in the presence of the low androgen environment and/or AR antagonists. The development of specific small molecule inhibitors of AR splice isoforms has been largely unsuccessful, and inhibitors of individual AR coregulators have not translated well into the clinic, likely due to their large number and functional redundancies. Therefore, novel therapeutic strategies for targeting androgen signaling in CRPC are necessary. Previous studies in our lab have demonstrated RNAi-mediated PCa cell death through seed region (nucleotides 2-8) complementarity of shRNA/siRNA guide strands to the 3’UTR of the AR and multiple AR coregulators and essential genes. In the current study, we used an unbiased novel seed-based shRNA screen to identify seed sequences that are toxic to different PCa cells, including CRPC cells expressing the clinically relevant constitutively active AR variant 7 (AR-V7). Common motifs were identified among toxic seed sequences, and the miRDB target prediction database was used to select those seeds that were predicted to target the AR and AR coregulators. Using RNA-seq analyses we confirmed that selected seed sequences inhibited global androgen signaling and identified potential direct targets known to be relevant to PCa. Conclusions: These studies have identified androgen signaling inhibitory sequences that have the potential to be used in RNAi-seed based therapies for PCa. The ability to inhibit the expression of the AR and multiple essential AR coregulators simultaneously with one agent, and the reduced likelihood of developed resistance, are considerable benefits of this approach.

Citation Format: Joshua M. Corbin, Maria J. Ruiz-Echevarria. RNA interference seed-based approach to inhibit androgen signaling and induce prostate cancer cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1483.
Abstract 1500: Exonuclease 1 recruitment in human DNA mismatch repair
Authors: Knicely Breanna
Published: June 2022

DNA repair is the process by which cells identify and correct mutations present within the genome. These correction mechanisms maintain genomic stability and prevent the development of cancer. The DNA mismatch repair (MMR) pathway identifies and corrects small insertions, deletions, and misincorporations that arise within the genome as a result of errors during DNA replication. The process by which MMR corrects these mispairs includes recognition of the mispair by the MutS complex, recruitment of the MutL complex to the mutation site, excision of the mispair, and gap filling by DNA polymerase. MMR is also critical for inducing apoptosis after chemically induced mispairs, such as those from alkylating agents. Exonuclease 1 is the protein responsible for the excision step of MMR. However, MMR can occur in the absence of Exo-1. Thus, MMR can be separated into two subpathways: Exo1-dependent MMR and Exo1-independent MMR. In Exo1-dependent MMR Exo-1 binds to both the MutS complex and MutL complex. The MutL interaction is facilitated by an MLH1 interaction peptide (MIP) box. We recently identified a Msh2 interaction peptide (SHIP) box in yeast Exo1. This project aims to understand how MIP and putative human SHIP box motifs influence human Exo1 recruitment to MMR processes. We have created mutations within the predicted binding domains of human Exo1. We observe changes in localization of Exo1-mutant proteins within the cell, suggesting that changes in the overall MMR process may be present. We also observe changes in MMR-mediated apoptotic response when a subset of Exo1-mutations are expressed in the presence of endogenous wildtype Exo1, indicating a potential for a dominant negative interaction. Our ongoing studies are expected to shed more light upon how the changes in these interactions may affect the human MMR process and overall genomic stability.

Citation Format: Breanna Knicely. Exonuclease 1 recruitment in human DNA mismatch repair [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1500.
Abstract 1503: Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments
Authors: Rao Aakarsha , Ni Zijian , Wang Albert , Suresh Dhruthi , Mohanty Chitrasen , Kendziorski Christina , Iyer Gopal
Published: June 2022

Integration of human papillomavirus (HPV)16 genomes into host head and neck squamous cell carcinoma (HNSCC) DNA is an essential driver for cancer progression. Currently, there are no treatment strategies based on HPV integration status. We postulate that a conceptual advance in the treatment of HPV HNSCC cancer can be formalized by targeting transcriptional co-regulator - bromodomain and extra-terminal (BET) proteins which mediate viral and host transcription. HPV maintenance in the host environment is dependent on BET protein-BRD4. An additional function of BET proteins in regulating transcription of tumor suppressors and DNA damage repair (DDR) genes. Given that patient populations have viral integrations into their genomes and its maintenance depends on cellular Brd4, displacing Brd4 through novel second-generation BET inhibitors can abrogate HPV transcription. Through chemical and knockdown studies of BET proteins in integrated viral HNSCC cells, we show viral oncogenes E6 and E7 are directly regulated by Brd4, reactivate tumor suppressors p53, release E2F1-Rb cell cycle brake to induce G1 cell cycle arrest, and significantly converge towards downregulation of DDR pathways in disrupted viral genomes. In contrast, non-disrupted viral genomes diverge from DDR pathways towards downregulation of interferon signaling pathways. As a result of the intrinsic genomic instability caused by the downregulation of components of the DDR machinery, the addition of external beam radiation further delayed DNA repair kinetics quantified through H2AX foci formation in cells harboring disrupted viral genomes. Taken together, targeting BET proteins is not a viable monotherapy but creates genomic instability, which, when combined with radiation, has the potential to eradicate HPV-associated tumors.

Citation Format: Aakarsha Rao, Zijian Ni, Albert Wang, Dhruthi Suresh, Chitrasen Mohanty, Christina Kendziorski, Gopal Iyer. Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1503.
Abstract 1506: APOBEC3A a causative agent in cancer-related chromosomal instability and STING driven metastasis
Authors: Woermann Sonja Maria , Zhang Amy , Thege Fredrik I. , Gates Chris , Harris Reuben S. , Ross Susan R. , Notta Faiyaz , Maitra Anirban , Rhim Andrew D.
Published: June 2022

Chromosomal instability (CIN), a hallmark of cancer, has been associated with a highly metastatic phenotype in numerous cancers. Mechanisms by which these genomic events occur during the lifespan of a neoplasm have yet to be fully delineated. In our study we identified a novel function for APOBEC3A (A3A), a primate-specific cytidine deaminase upregulated in multiple cancers including Pancreatic ductal adenocarcinoma (PDAC), in the initiation of CIN.We demonstrate that A3A is not routinely detected in non-diseased pancreata; however, expression was detected in the epithelial and stromal compartments from patients with chronic pancreatitis and in precursor lesions of PDAC and is further significantly increased in invasive neoplasia. Strikingly, we found that A3A expression but not A3A-induced mutagenesis, was associated with a significantly reduced overall survival in PDAC. By employing a variety of genetic tools, we identified a novel function for A3A in initiating CIN, underscoring its potential role in driving the observed early metastatic propensity in PDAC. Using a series of in vivo and in vitro models, we demonstrate that A3A-induced CIN leads to aggressive cancer, featuring enhanced, STING-dependent, distant organ seeding and metastatic growth. As a consequence of aberrant A3A function and CIN-mediated upregulation of STING, NfkB and Stat3 pathways were activated. More importantly, all these effects were independent of the deaminase domain, underscoring a novel role of A3A beyond its established canonical function. Remarkably, in a novel autochthonous murine model of PDA expressing human A3A, we identified numerous copy number changes, homologous to those altered in A3A overexpressing patient tumors, including deletions in DNA repair pathway genes. While we showed that A3A-expressing PDAC cells do not fully phenocopy a BRCA mutation-like phenotype, A3A-expressing PDAC cells are exceptionally sensitive to PARP inhibition and DNA cross linking agents, recapitulating a state of “chemical BRCAness”. The combined effect of deletions in these genes has yet to be ascertained, and we hypothesize that these losses further add to ongoing DNA damage overall in PDAC. In summary, our study shows, that A3A drives metastasis and specific deletions through a deaminase-independent initiation of CIN, with potential implications for targeted treatment strategies in pancreatic cancer.

Citation Format: Sonja Maria Woermann, Amy Zhang, Fredrik I. Thege, Chris Gates, Reuben S. Harris, Susan R. Ross, Faiyaz Notta, Anirban Maitra, Andrew D. Rhim. APOBEC3A a causative agent in cancer-related chromosomal instability and STING driven metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1506.
Abstract 1508: Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin
Authors: Reimand Jüri , Ocsenas Oliver
Published: June 2022

Cancer genomes are shaped by mutational processes with complex spatial variation at multiple scales. However, the underlying mechanisms of this mutagenesis and its functional and genetic determinants remain poorly understood. Somatic regional mutagenesis is known to correlate with DNA replication timing and chromatin accessibility; however, these studies have used epigenetic information from common cell lines while the epigenomes of primary human cancers remain uncharacterized in this context.

Here we model megabase-scale mutation frequencies of single nucleotide variants (SNVs) in thousands of whole cancer genomes using hundreds of genome-wide profiles of chromatin accessibility and replication timing spanning primary cancer samples, normal tissues, and cell lines. Using a machine learning framework, we show that CA profiles of primary cancers, rather than those of normal cells, predict regional mutagenesis and single base substitution (SBS) signatures in most cancer types. Thus the majority of passenger mutations follow the epigenetic landscapes of transformed cells of matching cancer sites and tissues.

Mutational signatures associated with carcinogen exposure, as well as signatures of unknown origin, show the strongest associations with epigenomes while associations with endogenous signatures are weaker. In most cases, overall mutation burden and SBS signatures inversely correlate with chromatin accessibility, however certain signatures are instead enriched in chromatin-accessible elements.

Lastly, the genomic regions with excess mutations unexplained by the epigenetic profiles in our models likely represent a combination of localized mutagenesis and positive selection of functional oncogenic mutations. Our computational models highlight an enrichment of known driver mutations, point out novel intergenic regions with putative non-coding drivers, and indicate an over-representation of developmental and lineage-specific genes in these frequently mutated genomic regions.

These results characterize the complex interplay of mutational processes, genome function, and somatic evolution in cancer and its tissues of origin, and also outline strategies for distinguishing driver and passenger mutations.

Citation Format: Jüri Reimand, Oliver Ocsenas. Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1508.
Abstract 1513: FASN inhibition-induced BRCAness as a therapeutic option for castration-resistant prostate cancer (CRPC)
Authors: Ribeiro Caroline Fidalgo , Rodrigues Silvia D. , Bastos Debora C. , Pakula Hubert , Zadra Giorgia , Foiani Marco , Loda Massimo
Published: June 2022

Androgen deprivation therapy (ADT) is the primary treatment for prostate cancer. However, resistance to ADT invariably develops, leading to castration-resistant prostate cancer (CRPC). Prostate cancer progression is marked by overexpression of fatty acid synthase (FASN) and increased de novo synthesis of fatty acids. Importantly, the majority of normal tissues have low expression of FASN and rely mostly on exogenous lipids, making FASN an interesting therapeutic target for prostate cancer. Previously our group evaluated the effects of inhibiting FASN in prostate cancer, with especially promising results in CRPC models. We observed that FASN inhibition decreases DNA damage repair capability by transcriptionally modulating homologous recombination (BRCAness) and non-homologous end joining repair pathways, which leads to increased DNA damage and apoptosis. Key enzymes involved in DNA repair pathways are reduced at the protein level, and the addition of exogenous palmitate, the product of FASN, is able to rescue their expression to normal levels. Interestingly, genes involved in the synthesis of ceramide are upregulated after FASN blockade, with consequent increased cellular levels of ceramides, dihydroceramides and sphingomyelin. Additionally, we observed increased acyl chain unsaturation levels in these lipid species, in line with the uptake of polyunsaturated fatty acids (PUFA) observed when de novo lipogenesis is blocked. The inhibition of ceramide synthesis, both through genetic knock-down with siRNA or pharmacologically with an inhibitor of serine palmitoyltransferase, is capable of partially rescuing the DNA damage induced by FASN inhibition, suggesting a role of ceramides in DNA damage response modulation. Next, we investigated the synergistic effect of combining FASN inhibitor with PARP inhibitor and observed a higher inhibition of cell growth in prostate cancer cell lines in comparison to either drug alone. Human CRPC organoids when treated with PARP and FASN inhibitor in combination showed reduced diameter, as well as reduced cell proliferation, when compared with each agent alone. Overall, our data demonstrate that targeting de novo lipogenesis can increase the therapeutic efficacy of PARP inhibitors and benefit prostate cancer patients that do not harbor BRCA mutations, by pharmacologically downregulating DNA damage repair pathways, particularly HR.

Citation Format: Caroline Fidalgo Ribeiro, Silvia D. Rodrigues, Debora C. Bastos, Hubert Pakula, Giorgia Zadra, Marco Foiani, Massimo Loda. FASN inhibition-induced BRCAness as a therapeutic option for castration-resistant prostate cancer (CRPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1513.
Abstract 1516: The role of protein tyrosine kinases in DNA mismatch repair
Authors: Daniels Hannah , Knicely Breanna , Goellner Eva M.
Published: June 2022

The DNA mismatch repair (MMR) pathway and its regulation are necessary for genomic stability. Cells deficient in MMR exhibit increased expansion and contraction of short repeat sequences in the genome, termed microsatellite instability (MSI). Loss of MMR also results in resistance to certain classes of DNA damaging chemotherapeutics. The standard treatment option for most patients includes chemotherapy, which has toxic side effects. Immunotherapy has recently been utilized as a treatment for various cancers. MSI-high cancers respond better to immunotherapy treatment compared to microsatellite stable (MSS) cancers. This increased response is believed to be due to the higher mutation frequencies associated with the MSI-high tumors, which lead to greater neoantigen production. The primary proteins required for MMR are known, however regulation of the pathway is not well understood. The MLH1 protein is critical for MMR and is required for the excision licensing of the daughter DNA strand. Loss or mutation of MLH1 leads to defective MMR, increased mutation frequency, and MSI. Recent studies by our laboratory and others have shown that treatment with a tyrosine kinase inhibitor, Imatinib, leads to decreased MLH1 protein expression, and resistance to MMR-dependent apoptosis. These observations suggest a link between Imatinib-sensitive protein tyrosine kinases (PTKs) and the regulation of MMR. We show that MLH1 protein reduction is not occurring at the mRNA level and is thought to be post-transcriptional. We have identified the Imatinib sensitive target most likely responsible for the MLH1 reduction phenotype. We show that the target protein and MLH1 have a physical interaction that likely prevents degradation targeting of MLH1 by the Hsp70 chaperone. A detailed understanding of MMR regulation by PTKs would significantly advance the knowledge in the field of MMR and have important implications for immunotherapy strategies.

Citation Format: Hannah Daniels, Breanna Knicely, Eva M. Goellner. The role of protein tyrosine kinases in DNA mismatch repair [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1516.
Abstract 152: Discovery and characterization of GSK3 allosteric activators
Authors: Varghese Reeba P. , Thorne Curtis A.
Published: June 2022

The intestinal epithelium undergoes constant regeneration and is tightly regulated. Disruption of its homeostasis can result in the development of colorectal cancer (CRC). Glycogen synthase kinase 3 (GSK3) is a kinase that plays a central role in multiple signaling pathways, including cellular proliferation, where it inhibits the activity of its substrates. GSK3 dynamics can be described as a multiple input multiple output system. Numerous upstream growth factors can regulate and thus inhibit GSK3 from acting on its many substrates. Mutations in these growth signaling pathways (e.g., Wnt and KRAS) have been well established to have a role in CRC progression. Therefore, aberrantly activated signaling due to these proteins are presumed to result in the constitutive inhibition of GSK3 activity in CRC, thus making it an ideal therapeutic target. The aim of this study is to discover an allosteric GSK3 small molecule activator that can restore GSK3 kinase activity within CRC. Method: We screened 50,000 small molecule compounds using a luciferase-based in-vitro kinase assay. We are further confirming our top hits using both chemical and cell-based assays. For the cell-based assays, we test the compounds in human colonic epithelial cells (HCEC) and its three isogenic cell lines, which mimic CRC progression, and monitor changes in GSK3 kinase activity indirectly, via changes in its substrate protein levels, and directly via a live-cell GSK3 specific reporter. In addition, the top hits are also tested in both normal colon and CRC organoids. Results: Prior to running our large screen, we performed various optimization steps to determine the ideal condition for our screening assay. Our screening assay scored a Z-Score of 0.5 and higher, which indicated that it was a high-quality screening assay. Additionally, we have developed two cell-based orthogonal HTS assays. One using immunofluorescence and single-cell quantification of 24 GSK3 substrates from various pathways in our cell lines. Second, we engineered a GSK3 live-cell reporter and expressed it in the HCEC cells and three isogenic cell lines and organoid models. Impact: There is a need for advancements in preventative or therapeutic targets against CRC. Research indicates that suppression of GSK3 enzymatic activity decreases sensitivity to certain chemotherapeutic and targeted therapies. Therefore, restoring GSK3 enzymatic activity in CRC may re-sensitize tumors to other targeted therapies and establish GSK3 as a potential therapeutic target.

Citation Format: Reeba P. Varghese, Curtis A. Thorne. Discovery and characterization of GSK3 allosteric activators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 152.
Abstract 1523: Beta-2 adrenergic receptor and mu opioid receptor interact to increase the aggressiveness in triple negative breast cancer cells through activation of GSK3 signaling
Authors: Rousseau Bénédicte , Murugan Sengottuvelan , Palagani Ajay , Sarkar Dipak K.
Published: June 2022

Breast cancer is the world’s leading cause of cancer mortality in women worldwide. It has been shown that body stress hormones, such as norepinephrine, and opioid peptides interact to control the growth and progression of this cancer. Opioid and beta-adrenergic receptors are recently shown to cross talk via formation of receptor heterodimers to control cellular functions in various cell systems. However, the underlying cell signaling mechanism remains unclear. To determine the effect of the interaction of the two systems in breast cancer, we employed triple-negative breast cancer (TNBC) cell lines MDA-MB-231 and MDA-MB-468, CRISPR, chemical inhibition or activation and, PCR Array technology to study aggressive tumor phenotype and signaling cascades. We found that knock down of the beta-adrenergic (B2AR) or mu-opioidergic receptor (MOR) system via the CRISPR technique or pharmacological agents induces a less aggressive phenotype in triple negative breast cancer cells both in vitro and in vivo, with the effect being potentiated when both receptor systems were inhibited together. The mRNA expression study using a PCR Array targeting Cancer Stem Cell genes shows that B2AR or MOR activated the glycogen synthase kinase 3 (GSK3) signaling cascade. The GSK3 inactivation in MDA-MB-231 and MDA-MB-468 cells induced similar phenotypic changes as was done by the inhibition of B2AR and/or MOR, while a GSK3 activation by wortmannin reversed the effects of B2AR and/or MOR knockdown on these cells. GSK3 inactivation also prevents B2AR agonist norepinephrine or MOR agonist DAMGO from affecting MDA-MB-231 and MDA-MB-468 cell proliferation. These data identify a role of B2AR and MOR interaction in the control of breast cancer cell growth and establish a possible role of the GSK3 signaling system in mediation of these two receptors’ cross talk. (Supported by NIH grant R01 CA20863201).

Citation Format: Bénédicte Rousseau, Sengottuvelan Murugan, Ajay Palagani, Dipak K. Sarkar. Beta-2 adrenergic receptor and mu opioid receptor interact to increase the aggressiveness in triple negative breast cancer cells through activation of GSK3 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1523.
Abstract 1524: Expression of GDNF and its receptors in glioblastoma
Authors: Ewald Jesper D. , Knudsen Arnon M. , Kristensen Bjarne W.
Published: June 2022

Introduction: Glioblastoma is the most aggressive primary brain cancer and one of the most lethal types of cancer overall. Despite multimodal treatment strategies, the prognosis is poor with a median survival of approx. 15 months. Although neurotrophic factors are of major importance in the nervous system, their role in brain cancer is still not fully understood. We focused on the glial cell line-derived neurotrophic factor (GDNF), which has been shown to play a role in growth and migration in glioblastoma. The aim of this study was to investigate the expression of GDNF and it primary receptor GFRA1, as well as the other GDNF family receptors GFRA2-4 and RET.

Methods: Tissue sections from 10 glioblastoma patients were stained with antibodies against GDNF and each of the receptors. GDNF stainings were performed on frozen tissue slides, while receptor stainings were performed on formalin-fixed paraffin-embedded tissue sections. The area fractions of positive staining were quantified with a software-based classifier. Double immunofluorescence stainings with the different markers and Iba1 as well as GFAP were performed to assess expression in microglia/macrophages and tumor cells, respectively.

Results: GDNF staining was observed in five of ten patient specimens, whereas GFRA1 and GFRA2 staining was observed in all samples. GFRA1 and GFRA2 staining was seen in the membrane and cytoplasm with a mean area fraction of GFRA1 staining at 31% (range: 7-56%), and a mean area fraction of GFRA2 staining at 3% (range: 0.2-7%). GFRA3, GFRA4 and RET were not expressed in glioblastoma tissue. Double immunofluorescence stainings demonstrated co-expression of GFRA1 and GFAP, while co-expression of GFRA1 and IBA1 was limited.

Conclusion and perspectives: Our results suggest that GDNF and GFRA1 are widely expressed in glioblastoma tumor tissue, but GFRA2 is also expressed and may play a role in glioblastoma biology. Additional stainings are being established to clarify cellular expression and expression levels of GDNF and its receptors.

Citation Format: Jesper D. Ewald, Arnon M. Knudsen, Bjarne W. Kristensen. Expression of GDNF and its receptors in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1524.