Abstract 1147: RNA-targeting approaches to modulate alternative RNA splicing in cancer

Alternative RNA splicing (AS) is a critical step in gene expression regulation. This differential inclusion of sequences in the mRNA is a source of functional transcriptomic diversity that allows multiple RNA isoforms to be expressed from the same gene. Dysregulation of AS is hallmark of cancer and leads to the expression of RNA isoforms that promote tumor initiation and maintenance. Understanding how tumor-associated RNA isoforms impact cancer biology is needed for the development of cancer therapies targeting AS. Here, we describe two approaches to modulate AS in cancer cells. First, we utilize CRISPR-Artificial Splicing Factors (CASFx), splicing factor domains fused to catalytically inactive Cas13 proteins, to direct splicing activity to a specific site using a guide RNA (gRNA). We demonstrate that this approach can be used to promote either exon inclusion or skipping in mRNA from several cancer-associated genes (e.g., HRAS, EP400, TRA2β, SRSF3) depending on the gRNA binding location and the splicing-factor domain fusion. Second, we develop antisense oligonucleotides (ASOs) that target a non-coding poison exon in the oncogenic splicing factor TRA2β. This exon functions as a regulatory “poison exon”, which induces RNA degradation when included, and is differentially spliced in multiple tumor types compared to their corresponding adjacent normal tissue. TRA2β-targeting ASOs promoting poison exon inclusion cause decreased TRA2β protein expression, increased cell death, and decreased proliferation across multiple cancer cell lines. Additionally, compared to cancer cells, normal cell lines were less affected by TRA2β-targeting ASO toxicity, demonstrating a therapeutic window for using this technology to specifically target cancer cells.

Citation Format: Nathan K. Leclair, Laura Urbanski, Mattia Brugiolo, Marina Yurieva, Brenton R. Graveley, Albert Cheng, Olga Anczukow. RNA-targeting approaches to modulate alternative RNA splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1147.

Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis

The RNA isoform repertoire is regulated by splicing factor (SF) expression, and alterations in SF levels are associated with disease. SFs contain ultraconserved poison exon (PE) sequences that exhibit greater identity across species than nearby coding exons, but their physiological role and molecular regulation is incompletely understood. We show that PEs in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. We uncover an extensive cross-regulatory network of SR proteins controlling their expression via alternative splicing coupled to nonsense-mediated decay. We define sequences that regulate PE inclusion and protein expression of the oncogenic SF TRA2β using an RNA-targeting CRISPR screen. We demonstrate location dependency of RS domain activity on regulation of TRA2β-PE using CRISPR artificial SFs. Finally, we develop splice-switching antisense oligonucleotides to reverse the increased skipping of TRA2β-PE detected in breast tumors, altering breast cancer cell viability, proliferation, and migration.

Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis

Misregulation of alternative splicing is a hallmark of human tumors, yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer and uncover differences and redundancies in their targets and biological functions. We identify splicing factors frequently altered in human breast tumors and assay their oncogenic functions using breast organoid models. We demonstrate that not all splicing factors affect mammary tumorigenesis in MCF-10A cells. Specifically, the upregulation of SRSF4, SRSF6, or TRA2β disrupts acinar morphogenesis and promotes cell proliferation and invasion in MCF-10A cells. By characterizing the targets of these oncogenic splicing factors, we identify shared spliced isoforms associated with well-established cancer hallmarks. Finally, we demonstrate that TRA2β is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo, and its levels correlate with breast cancer patient survival.

Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics

Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

Angiocentric gliomas are pediatric low-grade gliomas (PLGGs) without known recurrent genetic drivers. We performed genomic analysis of new and published data from 249 PLGGs including 19 Angiocentric Gliomas. We identified MYB-QKI fusions as a specific and single candidate driver event in Angiocentric Gliomas. In vitro and in vivo functional studies show MYB-QKI rearrangements promote tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression, and hemizygous loss of the tumor suppressor QKI. This represents the first example of a single driver rearrangement simultaneously transforming cells via three genetic and epigenetic mechanisms in a tumor.

Invited Article: Progress in coherent lithography using table-top extreme ultraviolet lasers

Compact (table top) lasers emitting at wavelengths below 50 nm had expanded the spectrum of applications in the extreme ultraviolet (EUV). Among them, the high-flux, highly coherent laser sources enabled lithographic approaches with distinctive characteristics. In this review, we will describe the implementation of a compact EUV lithography system capable of printing features with sub-50 nm resolution using Talbot imaging. This compact system is capable of producing consistent defect-free samples in a reliable and effective manner. Examples of different patterns and structures fabricated with this method will be presented.

Defect-tolerant extreme ultraviolet nanoscale printing

We present a defect-free lithography method for printing periodic features with nanoscale resolution using coherent extreme ultraviolet light. This technique is based on the self-imaging effect known as the Talbot effect, which is produced when coherent light is diffracted by a periodic mask. We present a numerical simulation and an experimental verification of the method with a compact extreme ultraviolet laser. Furthermore, we explore the extent of defect tolerance by testing masks with different defect layouts. The experimental results are in good agreement with theoretical calculations.

The complete blood count and reticulocyte count--are they necessary in the evaluation of acute vasoocclusive sickle-cell crisis?

OBJECTIVE

To assess the usefulness of the complete blood count (CBC) and the reticulocyte count in the evaluation of adult patients with acute vasoocclusive sickle-cell crisis (SCC) presenting to the ED.

METHODS

A 2-part study was performed. Part 1 was retrospective chart review of patients with a sole ED diagnosis of acute SCC. Part 2 was a prospective evaluation of consecutive patients presenting in SCC. In both parts of the study, patients with coexisting acute disease were excluded. The remaining patients were divided into 2 groups: admitted and released. The mean values for white blood cell (WBC) count, hemoglobin (Hb) level, and reticulocyte count were compared. In Part 2, the change (delta) from the patient's baseline in WBC count, Hb level, and reticulocyte count also was determined. Data were analyzed by 2-tailed Student's t-test.

RESULTS

Part 1: There was no difference between the admitted (n = 33) and the released (n = 86) groups in mean WBC count (p = 0.10), Hb level (p = 0.25), or reticulocyte count (p = 0.08). Part 2: There was no difference between the admitted (n = 44) and the released (n = 160) groups in mean Hb level (p = 0.88), reticulocyte count (p = 0.47), delta Hb level (p = 0.88), and delta reticulocyte count (p = 0.76). There was a difference in mean WBC counts (15.8 +/- 4.9 x 10(9)/L admitted vs 12.8 +/- 4.9 x 10(9)/L released, p = 0.003) and delta WBC counts (5.1 +/- 4.6 x 10(9)/L admitted vs 1.8 +/- 4.6 x 10(9)/L released, p < 0.002).

CONCLUSION

Determination of the Hb level and the reticulocyte count do not appear useful in the evaluation of acute SCC in the ED. Admission decisions appear associated with elevations in the WBC count. Further study is required to determine the true value of the WBC count in such decisions.

Sociocultural and psychological factors in American Indian drug use: implications for treatment

Use of alcohol and other drugs has been acknowledged as a serious problem among American Indian populations. This study was designed to 1) compare female and male American Indian substance users in residential treatment on psychological (self-esteem, depression, attributional style) and sociocultural (demographics, personal drug use history, family history, acculturation) variables, and 2) examine relationships of the psychological and sociocultural variables with program completion. Results showed that females experienced more family dysfunction (family members misuse of substances, and emotional, physical, and sexual abuse) than males. Both females and males showed positive change on the psychological measures from treatment entry to treatment completion. The factors predicting dropout before program completion were divorce, use of cocaine and depressants, and living in foster care as a child. Implications for prevention, intervention, and training of treatment service providers are discussed.