Biology subjects

Hirankarn, N.

Publications and source records attributed to Hirankarn, N..

4 recordsLinked to original sources

bioRxiv2026

PiggyBac transposon and transposase delivered in trans, in cis, and as mRNA for engineering CAR-T cells: a multi-objective optimization

Chimeric antigen receptor (CAR)-T cell therapy has become a revolutionary strategy in cancer immunotherapy. However, conventional manufacturing strategies, which rely on viral vectors to deliver genetic material to host genomes, are hindered by many obstacles that have limited their widespread clinical application. This study aims to optimize the delivery of piggyBac transposon for simple and cost-effective manufacturing of CAR-T cells. We tested three different piggyBac delivery strategies: (i) conventional two-plasmid system (CONV), (ii) helper and donor one-plasmid system (ONE), and (iii) mRNA transposase in combination with a DNA donor plasmid (MRNA). Each method was evaluated for transfection efficiency, cell viability, and transgene copy number. The results demonstrated that, without enrichment, ONE approach generated CAR-T cells with the highest gene delivery efficiency at the cost of lower viability and higher transgene copy number, while transfection using MRNA offered a reduction in transgene copy numbers at the cost of lower efficiency. Interestingly, with enrichment by autologous feeder, the shortcoming in viability was completely overcome while retaining higher efficiency and higher transgene copy number. The result of this study lays the groundwork for a more efficient and safer piggyBac-engineered CAR T cell manufacturing process, and it should facilitate the decision in method selection for further optimization and clinical scale-up.

synthetic biology↗

bioRxiv2026

Mass Spectrometry-Based Profiling of Personalized Immunopeptidomes in Thai Renal Cell Carcinoma

This study profiles the personalized immunopeptidomes of 13 Thai patients with renal cell carcinoma (RCC), addressing a critical knowledge gap in Southeast Asian populations characterized by distinct HLA allele distributions. We combined whole-exome sequencing (WES)-based personalized proteome construction with liquid chromatography-tandem mass spectrometry (LC-MS/MS), using both database-driven searches and de novo peptide sequencing. HLA typing identified seven alleles not previously represented in major immunopeptidome databases, with HLA-A*11:01 being the most frequent (69%). Database-based analysis identified a single tumor-specific neoantigen derived from a mutant JADE2 peptide in the patient with the highest tumor mutational burden, which was validated by a mutant-specific ELISPOT response. In contrast, de novo sequencing revealed numerous non-canonical peptides, a subset of which were supported by proteogenomic validation using PepQuery and detected exclusively in cancer proteomes but not in normal tissue datasets, indicating their potential as tumor-associated antigens. Together, these results establish an integrated and scalable framework for identifying HLA-presented tumor-derived peptides and provide a foundational immunopeptidome resource to support personalized cancer immunotherapy development in Southeast Asia.

systems biology↗

bioRxiv2025

Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations

Using genotype data consisting of 8,316 individuals, we systematically evaluated imputation performance across six state-of-the-art reference panels for Chinese and Thai populations. A substantial proportion of variants identified through whole-genome sequencing, especially low-frequency variants, remained undetected by existing reference panels. In the Chinese population, the TOPMed panel required an R2 threshold of 0.60-0.70 to achieve comparable imputation accuracy of the ChinaMAP panel without R2 filtering, challenging the standard practice of applying a fixed R2 threshold for downstream analyses. Regional analysis highlighted the role of recent selection in imputation discrepancies and revealed an enrichment of immune-related genes in poorly imputed regions. In addition, we showed that the selection of reference panels and R2 thresholds could significantly influence estimation of polygenic risk score for disease prediction. These findings underscore the importance of developing ancestrally diverse reference panels and provide valuable guidelines for improving genotype imputation in East and Southeast Asian populations.

genomics↗

bioRxiv2023

Optimisation of a DNA extraction protocol for improving the bacterial and fungal classification based on Nanopore sequencing

Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Long-read nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimised protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and long-amplicon PCR-based approaches using Nanopore sequencing. Three sample lysis conditions were applied to a mock microbial community, including known bacterial and fungal species; the 96 MagBead DNA lysis buffer (ML) alone, incorporating bead-beating (MLB) or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). Profiling of bacterial comparison, MLB had more statistically different bacterial phyla and genera than the others. For fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, the principal coordinates analysis (PCoA) plot by the Bray-Curtis index showed a significant difference among groups for bacterial (p = 0.033) and fungal (p = 0.012) profiles. Overall, the microbial profiling and diversity analysis revealed that ML and MLBE have more similarity than MLB for both bacteria and fungi, therefore, bead-beating is not recommended for long-read amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human microbiome and mycobiome studies.

microbiology↗