Nanoimaging, Spectroscopy, and Biosensor Assays for Alternatively Spliced RNA Isoforms in Disease Diagnostics
4 affiliations
- 1Gyeongsang National University , , ,
- 2Cleveland Clinic , , , ,
- 3University of Illinois Urbana−Champaign , , , ,
- 4Eulji University , , ,
Abstract
Alternative splicing (AS) generates distinct mRNA isoforms, and frequently distinct proteins, from single genes; its dysregulation is established in cancer, neurodegeneration, and immune disease. Sequencing now nominates candidate splice events at scale, but a nominated event does not become a usable measurement until an isoform-discriminating sequence has been converted into a physical signal. Existing AS reviews concentrate on sequencing workflows, computational event calling, or disease catalogs; the assay-engineering step that follows target nomination remains comparatively underserved, and it is where most translational failures occur. This review addresses that gap. We group postsequencing detection into five classes defined by the physical origin of the signal: (i) fixed-tissue in situ localization, (ii) live-cell RNA imaging, (iii) plasmonic and spectroscopic readouts, (iv) label-free nanophotonic biosensing combined with site-specific RNA processing, and (v) protein-level proteogenomic confirmation. These classes are compared on target definition, reported analytical performance, multiplexing, matrix compatibility, perturbation risk, and clinical readiness. The reported performance spans single-copy imaging of splice variants in living cells to label-free detection at 580 fM in under 30 min without cDNA synthesis or PCR. Three conclusions follow. First, assay selection should be governed by the class of claim being made rather than by platform novelty. Second, analytical sensitivity measured on synthetic targets systematically overstates readiness in clinical matrices; therefore, matrix-matched validation is not optional. Third, cross-laboratory comparison is currently obstructed by inconsistent reporting, which we address by proposing a minimum performance-reporting set and explicit platform-selection criteria. We close with emerging directions, including CRISPR-based isoform detection, biosensor integration with nanopore sequencing, AI-assisted probe design, and digital and microfluidic formats.
Related
- Human adenine nucleotide translocator isoforms mediate functionally redundant mitochondrial ADP/ATP exchange
- Subcellular Localization and Cell Cycle-Associated Expression of Human dUTPase Isoforms
- 1142 Basescope™ duplex assay enables same-slide detection of short RNA targets including isoforms
- Identification and functional characterization of novel murine DIS3L2 isoforms
- Biomolecular Identification and Analyte Charge Measurement Using Drain-Current Readings from a Single Transistor: An Asymmetric Dual-Gate a-IGZO FET Biosensor
BibTeX
@article{kadam2026nanoimaging,
title = {{Nanoimaging, Spectroscopy, and Biosensor Assays for Alternatively Spliced RNA Isoforms in Disease Diagnostics}},
author = {Ulhas S. Kadam and Zhongwu Zhou and Joseph Irudayaraj and Il-Hoon Cho and Jong Chan Hong},
journal = {ACS Omega},
year = {2026},
month = oct,
doi = {10.1021/acsomega.6c07239},
url = {https://pubs.acs.org/acsodf/article/11/42/64324/5451997/Nanoimaging-Spectroscopy-and-Biosensor-Assays-for},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Nanoimaging, Spectroscopy, and Biosensor Assays for Alternatively Spliced RNA Isoforms in Disease Diagnostics
AU - Ulhas S. Kadam
AU - Zhongwu Zhou
AU - Joseph Irudayaraj
AU - Il-Hoon Cho
AU - Jong Chan Hong
PY - 2026
DA - 2026/10/15
JO - ACS Omega
DO - 10.1021/acsomega.6c07239
UR - https://pubs.acs.org/acsodf/article/11/42/64324/5451997/Nanoimaging-Spectroscopy-and-Biosensor-Assays-for
AB - Alternative splicing (AS) generates distinct mRNA isoforms, and frequently distinct proteins, from single genes; its dysregulation is established in cancer, neurodegeneration, and immune disease. Sequencing now nominates candidate splice events at scale, but a nominated event does not become a usable measurement until an isoform-discriminating sequence has been converted into a physical signal. Existing AS reviews concentrate on sequencing workflows, computational event calling, or disease catalogs; the assay-engineering step that follows target nomination remains comparatively underserved, and it is where most translational failures occur. This review addresses that gap. We group postsequencing detection into five classes defined by the physical origin of the signal: (i) fixed-tissue in situ localization, (ii) live-cell RNA imaging, (iii) plasmonic and spectroscopic readouts, (iv) label-free nanophotonic biosensing combined with site-specific RNA processing, and (v) protein-level proteogenomic confirmation. These classes are compared on target definition, reported analytical performance, multiplexing, matrix compatibility, perturbation risk, and clinical readiness. The reported performance spans single-copy imaging of splice variants in living cells to label-free detection at 580 fM in under 30 min without cDNA synthesis or PCR. Three conclusions follow. First, assay selection should be governed by the class of claim being made rather than by platform novelty. Second, analytical sensitivity measured on synthetic targets systematically overstates readiness in clinical matrices; therefore, matrix-matched validation is not optional. Third, cross-laboratory comparison is currently obstructed by inconsistent reporting, which we address by proposing a minimum performance-reporting set and explicit platform-selection criteria. We close with emerging directions, including CRISPR-based isoform detection, biosensor integration with nanopore sequencing, AI-assisted probe design, and digital and microfluidic formats.
SN - 2470-1343
ER -