bluuebunny/crossref_metadata_2025 huggingface dataset:
A Graph‐Based Methodology for Optimal Design of Inerter‐Based Passive Vibration Absorbers With Minimum Complexity
Authors: He Haonan , Li Yuan , Wang Zixiao , Jiang Jason Zheng , Burrow Steve , Neild Simon , Conn Andrew
Published: November 2024

Passive vibration absorbers (PVAs) play a crucial role in mitigating excessive vibrations in engineering structures. Traditional PVA design typically begins with proposing a beneficial topological layout, incorporating stiffness, damping, and inertance elements, followed by optimal sizing of each element to minimise specific response of dynamically excited structures. An alternative approach involves first designing the impedance function of a PVA and then identifying a passive mechanical layout that replicates this impedance using network synthesis techniques. However, both methods struggle to identify the most efficient PVA layout using the minimum number of elements (referred to as “complexity”) for a given vibration suppression problem. To this end, this study introduces a graph‐based methodology for designing optimal configurations (i.e., layout + sizing) of two‐terminal spring‐damper‐inerter PVAs that achieve specified performance goals with minimum complexity. In this approach, a PVA is represented as a weighted coloured multigraph, enabling the application of a novel graph‐based enumeration technique to generate the full set of potential layouts from any given number of mechanical elements. This enumeration is followed by a performance assessment of all layouts to pinpoint the optimal absorber configuration for the given problem. The methodology’s automation capability and versatility make it suitable for various civil and mechanical engineering applications. The effectiveness of the proposed methodology is demonstrated through two case studies: a vibration absorber design for a wind‐excited tall building and a suspension design for a road vehicle. In both cases, the proposed methodology successfully identifies innovative PVA layouts that surpass traditional designs with minimum additional elements.
Abstract A005: APC mutations dysregulate alternative polyadenylation in cancer
Authors: Gabel Austin M , Belliville Andrea E , Thomas James D , Mario B Pineda Jose , Bradley Robert K
Published: November 2024

Alternative polyadenylation (APA) affects most human genes and is recurrently dysregulated in cancers. However, the mechanistic origins of this dysregulation are incompletely understood. We completed an unbiased computational analysis of molecular regulators of poly(A) site selection across The Cancer Genome Atlas and identified that colorectal adenocarcinoma is distinct from all other cancer subtypes. We linked this distinction to the frequent presence of loss-of-function APC mutations in colorectal adenocarcinoma, which were strongly associated with expression of long 3′ UTRs relative to tumors lacking APC mutations. APC knockout similarly dysregulated APA in human colon organoids, and reduced APC expression was associated with APA dysregulation in tumor types lacking APC mutations. Building on previous work that identified APC as an RNA-binding protein that preferentially binds 3′ UTRs during mouse neurogenesis, we found that APC binding is most significantly enriched just upstream of proximal poly(A) sites within 3′ UTRs. Our results suggest that APC promotes proximal poly(A) site use and that APC loss contributes to pervasive APA dysregulation in human cancers.

Citation Format: Austin M Gabel, Andrea E Belliville, James D Thomas, Jose Mario B Pineda, Robert K Bradley. APC mutations dysregulate alternative polyadenylation in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A005.
Abstract A007: Characterization of miR-141 and miR-145 expression in cancer stem cells of metastatic prostate cancer patients
Authors: Shukla Kamla Kant , Choudhary Gautam Ram
Published: November 2024

Background: Prostate cancer (PCA) is the second most prevalent cancer globally and the fifth leading cause of cancer-related mortality. However, effective prognostic biomarkers for metastatic PCA remain lacking. Recent research highlights the role of microRNAs (miRNAs) in regulating cancer stem cells (CSCs) and influencing tumour progression across various cancers. Therefore, in this we investigated the effects of miR-141 and miR-145 expression on the metastatic PCA of CSCs and assessed their potential role as biomarkers for metastatic PCA prognosis. Methods: The expression levels of miR-141 and miR-145 were quantified using real-time qPCR. Flow cytometry was employed to assess the levels of prostate cancer stem cells (PCSCs) in tissue samples from patients with localized (non-metastatic) and metastatic PCA. Results: Our findings revealed a significant increase in miR-141 expression, accompanied by elevated levels of CD44^high/CD24^low and CD133^high, in metastatic PCA compared to localized PCA. Conversely, reduced miR-145 expression was associated with enhanced stemness characteristics, as indicated by increased CD44^high/CD24^low and CD133^high levels, in metastatic PCA compared to localized PCA. Additionally, prostate-specific antigen (PSA) and testosterone levels exhibited a significant rise (p<0.001), while apoptosis rates decreased in both localized and metastatic PCA compared to localized PCA. Conclusions: The collective findings of this study suggest that miR-141 and miR-145, in conjunction with CSC markers, hold promise as diagnostic and prognostic tools for PCA. They may also be valuable for detecting minimal residual disease and improving therapeutic strategies for managing metastatic PCA.

Citation Format: Kamla Kant Shukla, Gautam Ram Choudhary. Characterization of miR-141 and miR-145 expression in cancer stem cells of metastatic prostate cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A007.
Abstract A008: Identification of EYA2 as a promising biomarker for DICER1-related tumor predisposition
Authors: Wu Mona , Zhou Shengmei , Kommoss Felix , Wang Yemin , Amatruda James F
Published: November 2024

Background: DICER1-related tumor predisposition (DRTP), also known as DICER1 syndrome, is a genetic condition associated with an increased risk of developing various tumors, including pleuropulmonary blastoma, thyroid gland neoplasia, ovarian tumors, and cystic nephroma. Currently, the diagnosis and surveillance of DRTP primarily relies on genetic testing for DICER1 mutations. There is a pressing need for surrogate diagnostic biomarkers to improve early detection and monitoring. Objective: To identify and validate EYA2 as a potential biomarker for DICER1-related tumor predisposition. Methods: Murine mesenchymal stromal cell lines were developed to model the consequences of DICER1 mutations, including the DICER1E1705K mutation found in DRTP. Both bulk RNA sequencing (RNAseq) and microRNA sequencing (miRNAseq) were employed to identify differentially expressed mRNAs in these cell lines. The RNA and protein levels of Eya2 were measured by qRT-PCR and Western blot, respectively. De-repression of Eya2 mRNA by miRNA was evaluated by dual luciferase assay to link overexpression with the DICER1 defect of DRTP. Then, immunohistochemistry staining of EYA2 was performed on a panel of DRTP tumors. Results: We found that more than 2000 mRNAs were derepressed in mesenchymal stromal cells expressing DICER1E1705K as compared to DICER1WT. Among these, Eya2 emerged as a top candidate. We observed elevated Eya2 mRNA and protein levels in DICER1E1705K -expressing mesenchymal stromal cells. Utilizing a reporter assay, we also observed de-repression of the 3’ UTR of Eya2 upon expression of DICER1E1705K as compared to DICER1WT. Strong nuclear EYA2 staining was observed in a subset of DRTP tumor samples. Conclusion: Elevated EYA2 expression in tumor tissues from DRTP patients supports its potential use in both diagnostic and surveillance contexts. Further studies are warranted to validate EYA2 as a clinical biomarker and explore its utility in improving early detection and monitoring strategies for individuals at risk of DRTP.

Citation Format: Mona Wu, Shengmei Zhou, Felix Kommoss, Yemin Wang, James F Amatruda. Identification of EYA2 as a promising biomarker for DICER1-related tumor predisposition [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A008.
Abstract A020: LncTransformer: Identifying novel prognostic long-noncoding RNA biomarkers for pancreatic cancer using deep learning
Authors: Singh Shivali
Published: November 2024

Pancreatic cancer remains a formidable challenge due to high mortality rates and limited therapeutic options due to late detection of the cancer. Recent literature has focused on investigating the potential of long noncoding RNAs (lncRNAs) as biomarkers in several cancers. To identify significantly altered expression of lncRNA in pancreatic cancer, I collected information from the Cancer Genome Atlas (TCGA) and extracted RNA- sequencing (RNA-seq) transcriptomic profiles of pancreatic carcinomas. Out of 60,660 gene transcripts shared between 151 pancreatic cancer patients, 38 lncRNAs were identified to be significantly differentially expressed. To find the lncRNAs related to metastatic progression of pancreatic cancer, different machine learning algorithms, including logistic regression (LR), support vector machine (SVM), random forest classifier (RFC), and a custom autoencoder model were trained to identify potential prognostic biomarkers. The custom deep learning model predicted metastatic prognostic biomarkers with a 92% accuracy, with the second-best accuracies coming from the SVM and RFC models, having an accuracy of 76%. Using the deep learning model, the following novel lncRNA and gene biomarkers were identified: LINC01300, SERPINB13, AC010789.1, TMPRSS15, DUSP5- DT, AL513128.3, MIR205HG, LINC00486, RF00019, LINC01115, and AC133530.1. Further investigating these results, specifically the identified lncRNA, the LINC01300 was identified to be potentially circulating in the blood. If further analysis proves this hypothesis correct then LINC01300 along with other identified genes could serve as biomarkers in a liquid biopsy. The identified biomarkers would be especially helpful in rural areas with lower accessibility to healthcare as it would allow for an easier, more efficient, and cost-effective method of pancreatic cancer detection. Based on these findings, further investigations of this gene panel in vitro and in vivo will be conducted, as they could be targeted for improved outcomes in pancreatic cancer patients and assist in the diagnosis of metastatic progression based on RNA-seq data of primary pancreatic tumors or the development of a liquid biopsy.

Citation Format: Shivali Singh. LncTransformer: Identifying novel prognostic long-noncoding RNA biomarkers for pancreatic cancer using deep learning [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A020.
Abstract B002: A therapeutically targetable positive feedback loop between long noncoding RNA-HLX-2-7, HLX, and MYC that promotes childhood cancer group 3 medulloblastoma
Authors: Perera Ranjan R
Published: November 2024

Medulloblastoma (MB) is the most common malignant pediatric brain tumor. MB is categorized into four main molecular subgroups: wingless pathway (WNT)-activated, sonic hedgehog pathway (SHH)-activated, group 3 (G3), and group 4 (G4). Although the driver pathways for G3 and G4 MB are unclear, most of these tumors are characterized by c-Myc and MYCN signatures, respectively. Recent studies suggest that long non-coding RNAs (lncRNAs) contribute to medulloblastoma formation and progression. We have identified lncRNA, lnc-HLX-2-7, as an oncogene and a potential therapeutic target in group 3 (G3) medulloblastomas. lnc-HLX-2-7 RNA specifically accumulates in the promoter region of its host coding gene HLX, a sense overlapping gene of lnc-HLX-2-7, which activates HLX expression by recruiting multiple factors, including enhancer elements. RNA sequencing and chromatin immunoprecipitation reveal that HLX binds to and activates the promoters of several oncogenes, including TBX2, LIN9, HOXM1, and MYC. Intravenous treatment with cerium oxide nanoparticle–coated antisense oligonucleotides targeting lnc-HLX-2-7 (CNP-ASO-lnc-HLX-2-7) and lipid nanoparticle-coated HLX (LNP-si-HLX) inhibits tumor growth by 40-50% in an intracranial medulloblastoma xenograft mouse model (p<0.01). Combining nanoparticle-coated lnc-HLX-2-7 and HLX with standard-of-care cisplatin further inhibits tumor growth and significantly prolongs mouse survival compared with monotherapy (p<0.01). Thus, the lnc-HLX-2-7–HLX–MYC axis is important for regulating G3 medulloblastoma progression, providing a strong rationale for using lnc-HLX-2-7 and HLX as therapeutic targets for G3 MBs.

Citation Format: Ranjan R Perera. A therapeutically targetable positive feedback loop between long noncoding RNA-HLX-2-7, HLX, and MYC that promotes childhood cancer group 3 medulloblastoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B002.
Abstract B003: Systematic loss-of-function screens identify pathway-specific functional circular RNAs
Authors: Neve Matt , Liu Ling , Conn Simon , Goodall Gregory , Rosenbluh Joseph
Published: November 2024

Circular RNA (circRNA) is covalently closed, single-stranded RNA produced by back-splicing. A few circRNAs have been implicated as functional; however, we lack understanding of pathways that are regulated by circRNAs. Here we generated a pooled short-hairpin- RNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at different levels (ranging from low to high) in humans. We used this library for loss-of-function proliferation screens in a panel of 18 cancer cell lines from four tissue types harbouring mutations leading to constitutive activity of defined pathways. Both context-specific and non- specific circRNAs were identified. Some circRNAs were found to directly regulate their precursor, whereas some have a function unrelated to their precursor. We validated these observations with a secondary screen and uncovered a role for circRERE(4–10) and circHUWE1(22,23), two cell-essential circRNAs, circSMAD2(2–6), a WNT pathway regulator, and circMTO1(2,RI,3), a regulator of MAPK signalling. Our work sheds light on pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function.

Citation Format: Matt Neve, Ling Liu, Simon Conn, Gregory Goodall, Joseph Rosenbluh. Systematic loss-of-function screens identify pathway-specific functional circular RNAs [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B003.
Abstract B004: Ovarian cancer long intergenic noncoding RNA 1 is a potential therapeutic target in advanced ovarian cancer by promoting glycolytic pathway and hypoxic response
Authors: Horie Kuniko , Sato Wataru , Ikeda Kazuhiro , Inoue Satoshi
Published: November 2024

Ovarian cancer (OvC) is often diagnosed as an advanced disease because symptoms do not develop at earlier stages. Besides current treatments, alternative efficient therapies for OvC need to be established. We have previously identified that a novel long intergenic noncoding RNA (lincRNA) originated from chromosome 10q21 was predominantly expressed in clinical ovarian cancer tissues, designated as ovarian cancer lincRNA 1 (OIN1). Silencing of OIN1 in OvC cell lines substantially exhibited the inhibition of in vitro and in vivo cell proliferation, by upregulating apoptosis-related genes. In the present study, we aimed to evaluate whether OIN1 can be a therapeutic target in advanced OvC and how OIN1 drives the progression of OvC. We established long-term culturable spheroid cultures of OvC patient-derived cells (OvC-PDCs) from ascites of OvC patients as an advanced OvC model. The OvC-PDC spheroid cultures abundantly expressed OIN1 and stemness-related genes. OIN1-targeted siRNAs could suppress the spheroid growth and upregulate apoptosis-related genes such as RASSF5 and ADORA1 in OvC-PDC cultures. In a bloody ascites-generating xenograft in vivo model of mice intraperitoneally injected with OvC-PDC, OIN1-targeted siRNA treatment engineered by drug delivery system alleviated ascites production and prolonged the mice survival time. Based on transcriptomic analysis of OIN1 silencing in OvC-PDC cultures, we found that OIN1 inhibition exerts the downregulation of genes involved in glycolytic pathway and hypoxic response. We further demonstrated that OIN1 modulates HIF1a-mediated transcriptional regulation in OvC- PDCs. The present findings provide promising evidence that OIN1 can be a potential therapeutic target for advanced OvC.

Citation Format: Kuniko Horie, Wataru Sato, Kazuhiro Ikeda, Satoshi Inoue. Ovarian cancer long intergenic noncoding RNA 1 is a potential therapeutic target in advanced ovarian cancer by promoting glycolytic pathway and hypoxic response [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B004.
Abstract B005: A robust NSCLC biomarker: miR-7-5p: in-silico validation and potential SPR- based probe for detection
Authors: Dhara Chandrajeet , Dhara Anindita , Gantayat Saumyatika
Published: November 2024

The abundance of micro RNAs as a specific biomarker for accurately detecting cancer metastasis has arisen recently. The expression levels of miRNA are analyzed to get insights into cancer tissue detection and subtypes. Similar to other cancer types, the miRNA shows high levels of target mRNA dysregulation in association with non-small cell lung carcinoma (NSCLC). Among many promising cancer biomarkers for NSCLC, miR-7-5p has shown significant downregulation in the NSCLC tissues and targets proto-oncogenes like PAK2 and NOVA2. The expression levels of different proto-oncogenes targeting the miR-7-5p in NSCLC show that the EGFR- mutated NSCLC has an experimental validation. And, the target validation of the miR-7-5p could be analyzed using SPR (Surface plasmon resonance) based sensors at a single nanoparticle level such as Au nanocube due to its high specificity and accountability. Despite being an accountable tool for cancer diagnosis, miRNA-based biomarkers sometimes cause poor diagnostic specificity and reproducibility due to their heterogenicity and immunogenicity in cancer detection. To overcome these shortcomings, the biomarkers need to be validated according to recent clinical studies.

Citation Format: Chandrajeet Dhara, Anindita Dhara, Saumyatika Gantayat. A robust NSCLC biomarker: miR-7-5p: in-silico validation and potential SPR- based probe for detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B005.
Abstract B007: Unlocking antiviral immunity against endogenous retroviruses in skin squamous cell carcinomas
Authors: Lyu Ying , Ge Yejing
Published: November 2024

Known as molecular parasites that invaded our genome through ancestors, transposons (mainly retrotransposons) are interspersed genomic repeats that constitute ∼40% of the mammalian genome. Primarily residing in the heterochromatin, retrotransposons exhibit dynamic expressions to orchestrate embryonic development and shape adult functions. Although rare, a cohort of evolutionarily young retrotransposons resisted extinction, whose selfish activities underlie polymorphic variations and genetic diseases including cancer. While the extraordinary molecular and functional heterogeneity of retrotransposons has been long recognized, mechanistic dissection remains challenging. To tackle this challenge, we use murine skin as our model, given its well-characterized, abundant, and highly accessible adult stem cells, not only mediating postnatal remodeling and tissue repair, but also serving as cell of origin for squamous cell carcinomas. By analyzing a genetic model lacking a known retrotransposon suppressor, histone methyltransferase Setdb1, which we found to be essential in the adult skin, we saw hair loss and hair follicle stem cell exhaustion phenotype, accompanied by a robust and selective surge of endogenous retroviruses (ERVs). When combined with squamous cell carcinoma drivers, Setdb1 loss significantly blocked tumor progression in vivo. We detected abundant retroviral peptides originated from its full-length copies through mass spectrometry and viral-like particles through transmission electron microscopy that are immunoreactive to previously reported ERV surface envelope (env) antibody. Similar viral-like particles were broadly evident across several epithelial tissues beyond skin, implicating its conserved function across squamous cancers. Mechanistically, epithelial originated ERVs elicit tissue wide inflammatory response, and can be ameliorated by pharmacological or genetic inhibition of retroviral activity. Moreover, ERV reactivation induced replication stress functionally accounts for stem cell exhaustion, therefore serving as a specific therapeutic vulnerability in squamous cancers. As an evolutionary conundrum, viral-coding ERVs pose a threat to host fitness and yet, they’ve resisted extinction persisting in the mammalian genome. Our findings suggest ERVs wrestle with the host surveillance programs to regulate adult tissue physiology and pathology, thus providing a key target in eliciting innate immunity in squamous cell carcinomas.

Citation Format: Ying Lyu, Yejing Ge. Unlocking antiviral immunity against endogenous retroviruses in skin squamous cell carcinomas [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B007.
Abstract B009: The RNA binding activity of the BRAF Kinase
Authors: Le Barch Alexia , Mennour Sabrina , Uguen Patricia , Vagner Stephan
Published: November 2024

Multiprotein complexes are key molecular switches of oncogenic signal transduction pathways that relay the flux of information coming from transmembrane receptors and distribute signals to a myriad of effectors. As such the regulation of protein-protein interactions is crucial in signal transduction pathways. For instance, activation of the mitogen-activated protein kinases pathway (MAPK) occurs through a cascade of phosphorylation and protein-protein interactions (PPIs) and is often deregulated in cancer. RNA-protein interactions play key roles in biological processes. More than a thousand RNA binding proteins (RBPs) influence the fate of mRNAs and non-coding RNAs in different ways. It is however less described how RNAs can in turn influence the functions of proteins to which they bind. Here we propose that RNAs scaffold PPIs in the MAPK pathway, thereby fine-tuning oncogenic signaling. We focused our study on cutaneous melanoma for which the MAPK is activated in more than 70% of the cases due to activating mutations in BRAF and NRAS. Using UV-CrossLinking ImmunoPrecipitation (CLIP) experiments, we found that several proteins of the MAPK pathway, including BRAF (but not MEK and ERK) interact with RNAs in RAS-activated melanoma cells. In addition, using a PLA- based imaging technique that allows the visualisation of the proximity of two given proteins, we showed that RNAs promote the stabilisation of BRAF-PPIs, suggesting a scaffolding role of RNAs in the MAPK pathway. Loss of BRAF RNA binding activity (achieved with a single point mutation) is associated with decreased BRAF dimerization and signaling. The oncogenic mutant protein BRAF (V600E) also interacts with RNA in a variety of melanoma cell lines including a BRAF inhibitor-resistant melanoma cell line in which the dimerization of BRAF and CRAF is partly dependent on RNA. Identifying BRAF-bound RNAs will open new therapeutic strategies targeting RNA-protein interactions. We also envision that the level of BRAF-RNA interactions could serve as a predictive marker of response to BRAF (V600E) inhibitors.

Citation Format: Alexia Le Barch, Sabrina Mennour, Patricia Uguen, Stephan Vagner. The RNA binding activity of the BRAF Kinase [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B009.
Abstract B017: Discovery of cancer-specific small RNAs using a new unbiased analysis of cohort sequence data
Authors: Kalogeropoulos Panagiotis , Ulloa Maria Alejandra , Friedländer Marc
Published: November 2024

It is well-established that small RNAs such as microRNAs can have important roles as oncogenes or tumor suppressors. The majority of studies of small RNAs in cancer have focused on examining the often subtle deregulation of specific, well-characterized molecules, aiming to understand their role in tumorigenesis. However, these efforts have predominantly concentrated on known, well-annotated RNA sequences, potentially overlooking novel, cancer-specific molecules. In this study, we sought to apply a new computational approach to uncover small RNA molecules that are uniquely associated with cancer and are completely absent from all non- cancerous tissues. To achieve this, we developed an unbiased approach that can detect cancer- specific sequences even if they are lowly abundant, do not overlap with existing genome annotations and even if they do not map to the human reference genome. We applied our framework to hundreds of small RNA-seq samples across a diverse range of cancer types from two large-scale public resources: The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Through this comprehensive analysis, we identified a series of small RNA molecules that are exclusively present in tumor samples and completely absent in adjacent normal tissues across multiple cancer types. Furthermore, these molecules were not detected in a large cohort comprising over 2,500 non-cancerous public samples, underscoring their specificity to cancerous conditions. Some of these molecules are also associated with different patient metadata. For example, one of these candidates exhibited significant correlation with poor patient survival in both Lung Adenocarcinoma and Endometrial Carcinoma within both the TCGA and CPTAC datasets. The discovery of such cancer-specific small RNAs holds immense potential for clinical applications. These molecules could serve as highly specific diagnostic and prognostic biomarkers, aiding in the early detection and stratification of cancers. Moreover, their unique presence in cancer cells, positions them as promising targets for the development of novel therapeutic interventions. In summary, our findings highlight the importance of exploring the full spectrum of small RNAs in cancer research. By moving beyond the constraints of known annotations, we have uncovered previously unknown molecules that could improve cancer diagnostics, prognostics, and treatment.

Citation Format: Panagiotis Kalogeropoulos, Maria Alejandra Ulloa, Marc Friedländer. Discovery of cancer-specific small RNAs using a new unbiased analysis of cohort sequence data [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B017.
Abstract B018: miRNA-130a promotes Breast cancer progression by inhibiting multiple tumour suppressor genes as a Gene-TF-miRNA network
Authors: Reddy Gayam Prasanna Kumar , Mathew A Jesil , SM Fayaz
Published: November 2024

Cancer is a disease that has implications worldwide, including in developing countries. It is known for its notorious ways of adapting and gaining resistance to the therapies available. Breast cancer (BC) majorly affects women and leading cause of death in women worldwide. Despite studying BC for many decades, we are not yet certain about a definitive therapy that can cure it with confidence. One of the challenges associated with treating BC is its metastasis and resistance to available therapies. Non-cancerous cells exhibit a tightly regulated transcription profile. An altered transcription profile is considered one of the main causes of the origin of cancers and their progression, including resistance and metastasis. Tumor suppressor genes are associated with mitigating any oncogenic signals induced by external factors or internal dysregulation in oncogenic genes. Changes in the expression profiles of tumour suppressor and oncogenic genes are associated with BC progression and metastasis. Transcription factors (TFs) play a significant role in marinating the tight regulation of transcription. In this study, we have analyzed Genes(N=1057), TFs(N =233) and miRNAs (N = 246) that are promoting BC from literature and publicly available databases; we have analyzed the regulation of Gene-Gene, miRNA-miRNA, TF-TF, miRNA-Gene, miRNA-TF, TF-Gene, TF-miRNA as a network of three node Feed Forward Loops (FFLs). Upon constructing 3, 4,5 and 6 node FFLs, we have identified that the miRNA130a is promoting BC by inhibiting crucial Tumor suppressor genes like TGFBR1, TGFBR2, SOD2, PTEN, SMAD4, RUNX3 etc.

Citation Format: Prasanna Kumar Reddy Gayam, Jesil Mathew A, Fayaz SM. miRNA-130a promotes Breast cancer progression by inhibiting multiple tumour suppressor genes as a Gene-TF-miRNA network [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B018.
Abstract B020: The Ratio of Alternatively Spliced KRAS Isoforms Plays a Role in The Tumorigenesis of Colorectal Cancer
Authors: Pulipelli Harika Reddy , Hertel Dr. Klemens J.
Published: November 2024

One of the most frequently mutated oncogenes, KRAS, has two alternatively spliced isoforms, KRAS4A(4A) and KRAS4B(4B). The isoforms differ by the inclusion or exclusion of the fourth exon, resulting in 4A or 4B respectively. They undergo different post-transcriptional modifications, indicating the non-redundant nature of the two isoforms. Studies also show spatiotemporal regulation of 4A in the gastrointestinal tract of mice during development. Although 4B is considered the major isoform, the ratio of 4A to 4B is cell-type specific. We show 4A is more abundant in colorectal cancer (CRC) cells like CaCO2 and HCT116, compared to other cancer cell lines like HeLa cells and MDA-MB-468 cells. Differential splicing analysis on existing data from flow-sorted mouse colon-crypt cells (stem-like vs. differentiated) and murine intestinal organoids of colon cancer (WT vs. tumor) shows that while differentiated colon cells and WT organoids have decreased levels of 4A, stem-like cells and tumor cells show increased levels of 4A. This supports the stem-cell theory of cancer, indicating that the dysregulation of KRAS isoforms impacts colon cell differentiation in colon crypts and could lead to CRC. Interestingly, we also found that the 3’ splice site(3’SS) of exon 4A is highly conserved. RBM39, a 3’SS recognition homolog, and SRSF1 have also been shown to play a role in KRAS splicing. We hypothesize that RBM39 regulates KRAS splicing by binding the 3’SS, and SRSF1 may play a role either by binding the pre-mRNA directly or through its interaction with RBM39. Therefore, we propose a new model for alternative splicing of KRAS. The abundance of KRAS splice variants may determine the fate of colon cell differentiation and drive CRC tumorigenesis.

Citation Format: Harika Reddy Pulipelli, Dr. Klemens J. Hertel. The Ratio of Alternatively Spliced KRAS Isoforms Plays a Role in The Tumorigenesis of Colorectal Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B020.
Abstract B025: Redox reprogramming by SOD1 knockdown: A novel liposomal siRNA strategy to overcome platinum resistance in ovarian cancer
Authors: Szenasi Attila , Rocha Sonia , Wang Mu
Published: November 2024

Platinum resistance remains a significant obstacle in the treatment of advanced-stage ovarian cancer, frequently leading to therapeutic failure. Our previous research identified Superoxide Dismutase 1 (SOD1) as a key antioxidant target for re-sensitizing platinum-resistant ovarian cancer cells to platinum-based therapies through both enzymatic inhibition and RNA interference (RNAi) utilizing a graphene-based siRNA delivery platform. Building on these findings, we have now developed a liposomal formulation of chemically modified siRNA targeting SOD1, which demonstrates potent knockdown efficiency and significantly enhances the sensitivity of resistant ovarian cancer cells to cisplatin in vivo. While SOD1 inhibition or knockdown via RNAi effectively re-sensitizes resistant cells to cisplatin, the underlying redox-sensitive signaling pathways remain largely unexplored in ovarian cancer. Our current study reveals that SOD1 knockdown acts as a redox switch, triggering cellular reprogramming in drug-resistant cells through post-translational cysteine modifications. This reprogramming leads to the rewiring of critical cancer hallmarks, culminating in the restoration of a cisplatin-sensitive phenotype. These findings suggest that a liposomal, chemically modified SOD1 siRNA formulation could serve as a promising therapeutic approach for reversing platinum resistance in ovarian cancer by exploiting redox-mediated reprogramming of cancer hallmarks. This study not only underscores the therapeutic potential of targeting SOD1 but also highlights the broader implications of redox signaling in the etiology of platinum resistance, providing a novel avenue for therapeutic intervention.

Citation Format: Attila Szenasi, Sonia Rocha, Mu Wang. Redox reprogramming by SOD1 knockdown: A novel liposomal siRNA strategy to overcome platinum resistance in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B025.
Abstract I002: Alternative polyadenylation as a therapeutic target in cancer
Authors: Banjo Toshihiro , Kaito Satoshi , Gabel Austin M , Abdel-Wahab Omar , Bradley Robert K
Published: November 2024

Alternative polyadenylation (APA) is markedly dysregulated across cancer types. Although this phenomenon is well established and associated with altered patient prognosis, the functional importance of most dysregulated polyadenylation to cancer phenotypes remains unknown, as does the potential therapeutic impact of dysregulated APA. Recent work by our lab and others to address this gap has systematically identified specific APA events that alter key tumor phenotypes, including malignant cell growth and tumor recognition by cytotoxic T cells. Motivated by these studies, we sought to identify small molecules that modulate APA for therapeutic intent. We created a sensitive reporter of APA and used this reporter to conduct a molecular phenotypic reporter screen for APA-altering compounds. This screen revealed a diversity of compounds that altered APA transcriptome-wide. Phenotypic characterization of the strongest hit emerging from this screen revealed that it strongly induced cell differentiation and death of myeloid leukemia cells, with negligible toxicity for normal hematopoietic stem cells. Overall, these results highlight the untapped but promising therapeutic potential of targeting APA in cancer.

Citation Format: Toshihiro Banjo, Satoshi Kaito, Austin M Gabel, Omar Abdel-Wahab, Robert K Bradley. Alternative polyadenylation as a therapeutic target in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr I002.
Abstract I003: Inhibitors of DHX9 RNA helicase as synthetic lethal cancer therapeutics
Authors: Silver Serena J
Published: November 2024

Over 100 modifications to RNA are known to occur in human cells, where they play critical roles in many aspects of normal cellular physiology, such as cell fate decisions and terminal differentiation, through effects on RNA biology such as protein and nucleic acid interactions. Our survey of human RNA-modifying enzymes suggests many are cancer essential enzymes with striking synthetic lethal profiles, including the DHX9 helicase. DHX9 is a multifunctional DExH-box RNA helicase which can unwind regions of double-stranded DNA and RNA helices but has a greater propensity for secondary structures such as DNA/RNA hybrids (R-loops) and DNA/RNA G-quadruplexes. DHX9 interacts with and regulates many proteins, including key members of DNA damage repair pathways. We have found that DHX9 knockdown is synthetic lethal in microsatellite high (MSI-H) or defective mismatch repair (dMMR) tumor models. A suite of assays was developed to identify and optimize potent and selective inhibitors of the DHX9 helicase, which recapitulate our findings with genetic tools. Profiling of DHX9 inhibitors across a broad panel of cancer cell lines reveals that tumor cells with mutations in the DNA damage repair genes BRCA1 and/or BRCA2 are also responsive to DHX9 inhibitor treatment in vitro and in vivo. DHX9 inhibition leads to increased RNA/DNA secondary structures such as R-loops and G-quadruplexes, resulting in subsequent DNA damage and increased replication stress, leading to cell cycle arrest and apoptosis. These results suggest that DHX9 inhibitors are a novel treatment modality for patients with defective DNA damage repair pathways such as dMMR and/or BRCA mutations.

Citation Format: Serena J Silver. Inhibitors of DHX9 RNA helicase as synthetic lethal cancer therapeutics [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr I003.
Abstract PR006: Target validation and drug discovery efforts on exoribonuclease XRN1
Authors: Lynes Maureen M. , Lockbaum Gordon J. , Sparling Brian A. , Shen Sophie A. , Nayak Sunaina P. , Knockenhauer Kevin , Grigoriu Simina , Buker Shane M. , Duncan Kenneth W. , Copeland Robert A. , Blakemore Stephen J. , Silver Serena J. , Boriack-Sjodin P. Ann
Published: November 2024

5′→3′ exoribonuclease 1 (XRN1) degrades single stranded mRNA and plays a key role in endogenous cellular mRNA turnover. XRN1 also degrades double-stranded RNA (dsRNA), thereby playing a role in innate immunity by preventing accumulation of dsRNA and pPKR induction in virus-infected cells. XRN1 was validated as a target with selective vulnerability in lung cancer cells with intrinsically elevated Type I interferon signaling, a cellular state that phenocopies viral infection. XRN1 knockout using CRISPR resulted in robust and selective antiproliferative effects in colony formation and proliferation assays. Analysis of Caspase 3/7 confirmed antiproliferation activity was due to apoptosis in sensitive cell lines. With genetic target validation activities completed, efforts to enable identification and characterization of XRN1 inhibitors were undertaken. Biochemical and biophysical assays and crystallography with human XRN1 were enabled. This assay suite allowed full characterization of a non-selective, nucleotide-based tool compound (pAp) as well as identification and validation of Compound 1, a selective, allosteric, RNA-competitive inhibitor of XRN1.

Citation Format: Maureen M. Lynes, Gordon J. Lockbaum, Brian A. Sparling, Sophie A. Shen, Sunaina P. Nayak, Kevin Knockenhauer, Simina Grigoriu, Shane M. Buker, Kenneth W. Duncan, Robert A. Copeland, Stephen J. Blakemore, Serena J. Silver, P. Ann Boriack-Sjodin. Target validation and drug discovery efforts on exoribonuclease XRN1 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR006.
Abstract PR008: Targeting Galectin-1 to enhance immuno-radiotherapy
Authors: Jiang Yuyan , Cao Hongbin , Deng Huaping , Guan Li , Langthasa Jimpi , Le Quynh-Thu
Published: November 2024

Galectin-1 is overexpressed in a wide range of malignant cancers and is strongly associated with immune suppression as well as cancer aggressiveness. However, effective therapeutics targeting Galectin-1 remain elusive in clinical practice. Herein, we report an activatable nano-system, termed Pr5S, to downregulate Galectin-1 through in vivo gene silencing. Pr5S features a bio-responsive lattice that can protect siRNA during circulation and efficiently break down for gene interference upon exposure to the elevated reductive pressure in the tumor microenvironment. When used independently, Pr5S significantly reduces Galectin-1 expression and mitigates T cell apoptosis, achieving tumor inhibition comparable to anti-Galectin-1 antibodies and superior to small molecule inhibitors. In combination with radiation, Pr5S enhances the anti-tumor immunity and results in significantly improved therapeutic outcome than clinical treatments such as chemoradiation or immune checkpoint blockade + radiation. Moreover, Pr5S strengthens the abscopal effect of radiation, efficiently abrogating unirradiated tumors. In summary, this work highlights a safe and efficient design of a gene silencing nanovector to improve personalized immuno-radiotherapy.

Citation Format: Yuyan Jiang, Hongbin Cao, Huaping Deng, Li Guan, Jimpi Langthasa, Quynh-Thu Le. Targeting Galectin-1 to enhance immuno-radiotherapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR008.
Abstract PR015: Decoding RNA metabolism by RNA-linked CRISPR screening in human cells
Authors: Nugent Patrick J , Park Heungwon , Subramaniam Arvind Rasi
Published: November 2024

RNAs undergo a complex choreography of metabolic processes in human cells that are regulated by thousands of RNA-associated proteins. While the effects of individual RNA-associated proteins on RNA metabolism have been extensively characterized, the full complement of regulators for most RNA metabolic events remain unknown. Here we present a massively parallel RNA-linked CRISPR (ReLiC) screening approach to measure the responses of diverse RNA metabolic events to knockout of 2,092 human genes encoding all known RNA-associated proteins. ReLiC screens highlight modular interactions between gene networks regulating splicing, translation, and decay of mRNAs. When combined with biochemical fractionation of polysomes, ReLiC reveals striking pathway-specific coupling between growth fitness and mRNA translation. Perturbing different components of the translation and proteostasis machineries have distinct effects on ribosome occupancy, while perturbing mRNA transcription leaves ribosome occupancy largely intact. Isoform-selective ReLiC screens capture differential regulation of intron retention and exon skipping by SF3b complex subunits. Chemogenomic screens using ReLiC decipher translational regulators upstream of mRNA decay and uncover a role for the ribosome collision sensor GCN1 during treatment with the anti-leukemic drug homoharringtonine. Our work demonstrates ReLiC as a versatile platform for discovering and dissecting regulatory principles of human RNA metabolism.

Citation Format: Patrick J Nugent, Heungwon Park, Arvind Rasi Subramaniam. Decoding RNA metabolism by RNA-linked CRISPR screening in human cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR015.
Supplementary Figure S.9 from Mathematical Modeling Unveils Optimization Strategies for Targeted Radionuclide Therapy of Blood Cancers
Authors: Kuznetsov Maxim , Adhikarla Vikram , Caserta Enrico , Wang Xiuli , Shively John E. , Pichiorri Flavia , Rockne Russell C.
Published: November 2024

Supplementary Figure S.9
Supplementary Figure S.30 from Mathematical Modeling Unveils Optimization Strategies for Targeted Radionuclide Therapy of Blood Cancers
Authors: Kuznetsov Maxim , Adhikarla Vikram , Caserta Enrico , Wang Xiuli , Shively John E. , Pichiorri Flavia , Rockne Russell C.
Published: November 2024

Supplementary Figure S.30
Delayed return of gastrointestinal function after partial hepatectomy: a single-center cross-sectional study
Authors: Piazza Giulia , Labgaa Ismail , Uldry Emilie , Melloul Emmanuel , Halkic Nermin , Joliat Gaëtan-Romain
Published: November 2024

Introduction
Partial hepatectomy (PH) remains associated with complication rates around 30-50%. Delayed return of gastrointestinal function (DRGF) has been reported in 10-20%. This study aimed to assess DRGF predictors after PH.
Aim
This retrospective study aimed to assess DRGF predictors after PH.
Methods
All patients who underwent PH between 01/2010 and 12/2019 were included. DRGF was defined as need of postoperative nasogastric tube (NGT). Independent DRGF predictors were identified with multivariable logistic binary regression.
Results
Overall, 501 patients were included. DRGF occurred in 82 patients (16%). A hundred-and-twelve patients (22%) underwent a minimally invasive approach and DRGF incidence was significantly lower in this group (p <0.001). DRGF was more frequent after major PH (p<0.001).
DRGF occurred more often in patients with preoperative embolization (p<0.001), biliary anastomosis (p<0.001) and extrahepatic resection (p<0.001). Patients with DRGF had longer median operation duration (p<0.001), more biliary leaks/bilomas (p<0.001) and higher median blood loss (p<0.001). DRGF patients developed more pneumonias (p<0.001) and had longer median length of stay (p<0.001).
On multivariable analysis, operation duration (p<0.001), major hepatectomy (p<0.001) and postoperative biloma/biliary leak (p<0.001) were independently associated with DRGF occurrence.
Conclusion
Postoperative DRGF occurred in 16% of the patients and was associated with longer length of stay. Surgery duration, major PH and postoperative biloma/biliary leak were found as independent predictors of DRGF.