The Landscape of Novel Expressed Chimeric RNAs in Rheumatoid Arthritis

Research Trends and Dynamics in Single-cell RNA Sequencing for Musculoskeletal Diseases: A Scientometric and Visualization Study

Background: Worldwide, approximately 1.7 billion people are afflicted with musculoskeletal (MSK) diseases, posing significant health challenges. The introduction of single-cell RNA sequencing (scRNA-seq) technology provides novel insights and approaches to comprehend the onset, progression, and treatment of MSK diseases. Nevertheless, there is a remarkable lack of analytical and descriptive studies regarding the trajectory, essential research directions, current research situation, pivotal research focuses, and upcoming perspectives. Therefore, the aim of this research is to present a comprehensive overview of the advancements made in scRNA-seq for MSK disorders over the past 15 years. Methods: It utilizes a robust dataset derived from the Web of Science Core Collection, encompassing January 1, 2009, through September 6, 2024. To achieve this, advanced analytical methodologies were applied to conduct thorough scientometric and visual analyses. Results: The findings underscore the preeminent role of China, which contributes 63.49% of the total publications, thereby exerting a substantial impact within this research domain. Notable contributions came from institutions such as Shanghai Jiao Tong University, Sun Yat-sen University, and Harvard Medical School, with Liu Yun being the leading contributor. Frontiers in Immunology published the greatest number of research papers in this field. This study identified joint diseases, bone neoplasms, bone fractures, and intervertebral disc degeneration as the main research focuses. Conclusion: This extensive scientometric analysis provides substantial benefits to both experienced and novice researchers by facilitating immediate access to critical data, thereby fostering innovation within this field.

Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction

Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions capable of generating chimeric transcripts even in normal tissues. In this study, we present a bottom-up approach targeting population-specific chimeric RNAs, identifying 58 such instances in the GTEx cohort, including notable cases such as SUZ12P1-CRLF3, TFG-ADGRG7 and TRPM4-PPFIA3, which possess distinct patterns across different ancestry groups. We provide direct evidence for an additional 29 polymorphic chimeric RNAs with associated structural variants, revealing 13 novel rare structural variants. Additionally, we utilize the All of Us dataset and a large cohort of clinical samples to characterize the association of the SUZ12P1-CRLF3-causing variant with patient phenotypes. Our study showcases SUZ12P1-CRLF3 as a representative example, illustrating the identification of elusive structural variants by focusing on those producing population-specific fusion transcripts.

Functional and regulatory impact of chimeric RNAs in human normal and cancer cells

Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients

The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the molecular mechanisms behind the development of disease severity are still not clearly understood. Recent studies demonstrated that SARS-CoV-2 alters the host cell splicing and transcriptional response to overcome the host immune response that provides the virus with favorable conditions to replicate efficiently within the host cells. In several disease conditions, aberrant splicing could lead to the development of novel chimeric transcripts that could promote the functional alternations of the cell. As severe SARS-CoV-2 infection was reported to cause abnormal splicing in the infected cells, we could expect the generation and expression of novel chimeric transcripts. However, no study so far has attempted to check whether novel chimeric transcripts are expressed in severe SARS-CoV-2 infections. In this study, we analyzed several publicly available blood transcriptome datasets of severe COVID-19, mild COVID-19, other severe respiratory viral infected patients, and healthy individuals. We identified 424 severe COVID-19 -specific chimeric transcripts, 42 of which were recurrent. Further, we detected 189 chimeric transcripts common to severe COVID-19 and multiple severe respiratory viral infections. Pathway and gene enrichment analysis of the parental genes of these two subsets of chimeric transcripts reveals that these are potentially involved in immune-related processes, interferon signaling, and inflammatory responses, which signify their potential association with immune dysfunction leading to the development of disease severity. Our study provides the first detailed expression landscape of chimeric transcripts in severe COVID-19 and other severe respiratory viral infections.

Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction

Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, including SUZ12P1-CRLF3 and TFG-ADGRG7 , whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal that SUZ12P1-CRLF3 results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize the SUZ12P1-CRLF3 chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts.

KEY POINTS

- Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions.

The landscape of differential splicing and transcript alternations in severe COVID-19 infection

Viral infections can modulate the widespread alternations of cellular splicing, favouring viral replication within the host cells by overcoming host immune responses. However, how SARS-CoV-2 induces host cell differential splicing and affects the landscape of transcript alternation in severe COVID-19 infection remains elusive. Understanding the differential splicing and transcript alternations in severe COVID-19 infection may improve our molecular insights into the SARS-CoV-2 pathogenesis. In this study, we analysed the publicly available blood and lung transcriptome data of severe COVID-19 patients, blood transcriptome data of recovered COVID-19 patients at 12-, 16- and 24-week postinfection and healthy controls. We identified a significant transcript isoform switching in the individual blood and lung RNA-seq data of severe COVID-19-infected patients and 25 common genes that alter their transcript isoform in both blood and lung samples. Altered transcripts show significant loss of the open reading frame, functional domains and switch from coding to noncoding transcript, impacting normal cellular functions. Furthermore, we identified the expression of several novel recurrent chimeric transcripts in the blood samples from severe COVID-19 patients. Moreover, the analysis of the isoform switching into blood samples from recovered COVID-19 patients highlights that there is no significant isoform switching in 16- and 24-week postinfection, and the levels of expressed chimeric transcripts are reduced. This finding emphasizes that SARS-CoV-2 severe infection induces widespread splicing in the host cells, which could help the virus alter the host immune responses and facilitate the viral replication within the host and the efficient translation of viral proteins.