Accelerating discovery and integration from RNA to Protein with R2T2P
- 1Human Technopole, Milan, Italy
Abstract
Integrating transcriptomics and proteomics data remains an unmet challenge in the post-genomics era, discouraging researchers from pursuing integrative approaches to molecular biology research. Leveraging the power of translation profiling, we present RNA to Translation to Protein (R2T2P), a computational platform integrating genome-guided transcriptome assembly with identification of translation and proteins, including a tailored differential analysis framework and support for multiple reference transcriptomes. We applied R2T2P to investigate a cellular model of facioscapulohumeral muscular dystrophy (FSHD), where ectopic expression of the DUX4 retrogene in skeletal muscle triggers significant alterations in transcription and RNA metabolism. We uncovered hundreds of uncharacterized, highly overexpressed RNAs, including antisense and alternative transcripts, and quantified their contribution to translatome and proteome. Re-analysis of expression datasets from patient-derived myotubes and muscle biopsies validated this alternative transcriptome in FSHD patients, adding a reservoir of bona-fide novel molecular actors in a rare disease. Available at https://github.com/nfdata-omics/R2T2P/, R2T2P is a flexible and powerful workflow in modern integrative biology.
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BibTeX
@misc{albanese2026accelerating,
title = {{Accelerating discovery and integration from RNA to Protein with R2T2P}},
author = {R. Albanese and A. E. Campbell and M. Bonfanti and A. S. Ali and C. T. James and A. Graziadei and G. Tasca and A. Riva and J. Krijgsveld and S. Jagannathan and L. Calviello},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.05.764226},
url = {https://www.biorxiv.org/content/10.64898/2026.11.05.764226v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Accelerating discovery and integration from RNA to Protein with R2T2P
AU - R. Albanese
AU - A. E. Campbell
AU - M. Bonfanti
AU - A. S. Ali
AU - C. T. James
AU - A. Graziadei
AU - G. Tasca
AU - A. Riva
AU - J. Krijgsveld
AU - S. Jagannathan
AU - L. Calviello
PY - 2026
DA - 2026/11/05
PB - bioRxiv
DO - 10.64898/2026.11.05.764226
UR - https://www.biorxiv.org/content/10.64898/2026.11.05.764226v1
AB - Integrating transcriptomics and proteomics data remains an unmet challenge in the post-genomics era, discouraging researchers from pursuing integrative approaches to molecular biology research. Leveraging the power of translation profiling, we present RNA to Translation to Protein (R2T2P), a computational platform integrating genome-guided transcriptome assembly with identification of translation and proteins, including a tailored differential analysis framework and support for multiple reference transcriptomes. We applied R2T2P to investigate a cellular model of facioscapulohumeral muscular dystrophy (FSHD), where ectopic expression of the DUX4 retrogene in skeletal muscle triggers significant alterations in transcription and RNA metabolism. We uncovered hundreds of uncharacterized, highly overexpressed RNAs, including antisense and alternative transcripts, and quantified their contribution to translatome and proteome. Re-analysis of expression datasets from patient-derived myotubes and muscle biopsies validated this alternative transcriptome in FSHD patients, adding a reservoir of bona-fide novel molecular actors in a rare disease. Available at https://github.com/nfdata-omics/R2T2P/, R2T2P is a flexible and powerful workflow in modern integrative biology.
ER -