Integrated In Silico Analysis of the Splicing Effects TMSB4X c.-16-1G>A Variant and Prime Editing Design for Splicing Correction in Diffuse Large B- Cell Lymphoma

Zahwa, Eca Desriana; Sutandyo, Noorwati; Paramita, Rafika Indah

Volume 18, Issue 2 (June-2026 2026) Iranian Journal of Blood and Cancer 2026, 18(2): 70-87 | Back to browse issues page

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Zahwa E D, Sutandyo N, Paramita R I. Integrated In Silico Analysis of the Splicing Effects TMSB4X c.-16-1G>A Variant and Prime Editing Design for Splicing Correction in Diffuse Large B- Cell Lymphoma. Iranian Journal of Blood and Cancer 2026; 18 (2) :70-87
URL: http://ijbc.ir/article-1-1906-en.html

Integrated In Silico Analysis of the Splicing Effects TMSB4X c.-16-1G>A Variant and Prime Editing Design for Splicing Correction in Diffuse Large B- Cell Lymphoma

Eca Desriana Zahwa ^*¹

, Noorwati Sutandyo²

, Rafika Indah Paramita³

1- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia. , eca.desriana@ui.ac.id
2- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia & Department of Hematology and Medical Oncology, Dharmais National Cancer Center Hospital, Jalan Letjen S.Parman, Jakarta, 11420, Indonesia. & Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia.
3- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia & Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia. & Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta, 10430, Indonesia

Abstract: (18 Views)

Diffuse Large B-Cell Lymphoma (DLBCL) is an aggressive lymphoid malignancy characterized by diverse genetic alterations, including variants that disrupt pre-mRNA splicing. The TMSB4X c.-16-1G>A variant is a splice-site alteration reported in DLBCL; however, its molecular consequences and potential correction using prime editing have not been comprehensively investigated. This study aimed to evaluate the impact of the TMSB4X c.-16-1G>A variant on splicing, characterize its effects on transcript and protein products, and design an in silico prime editing strategy for variant correction. Variant characterization was performed through genomic, clinical, and population frequency annotation. Splicing effects were assessed using dbscSNV, MaxEntScan, SpliceAI, Pangolin, Human Splicing Finder (HSF), RNA Disease Cryptic Splicing Code (RDCC), and SAI-10k-calc. Transcript and protein consequences were analyzed through open reading frame prediction and protein translation. Prime editing design included sgRNA selection, pegRNA optimization, and off-target assessment. The TMSB4X c.-16-1G>A variant was identified as a splice_acceptor_variant, absent from population databases, and reported in COSMIC as a somatic mutation associated with hematological malignancies. All prediction tools consistently indicated a high probability of splicing disruption, predicting both a 155-bp intron retention event and exon 2 skipping. These aberrant transcripts were predicted to generate truncated proteins compared with the wild-type protein (44 amino acids), producing proteins of 32 and 22 amino acids, respectively. Furthermore, two candidate prime editing systems were successfully designed for targeted correction of the variant. These findings suggest that TMSB4X c.-16-1G>A may induce aberrant splicing and provide a foundation for future experimental validation of prime editing-based correction strategies in DLBCL.

Keywords: TMSB4X, DLBCL, Splicing, Splice-site variant, Prime editing, Bioinformatics

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: Original Article | Subject: Genetics
Received: 2026/03/19 | Accepted: 2026/06/20 | Published: 2026/06/30

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