The Clinical Utility and Diagnostic Implementation of Human Subject Cell Transdifferentiation Followed by RNA Sequencing

Authors

Shenglan Li
Sen Zhao
Jefferson C Sinson
Aleksandar Bajic
Jill A Rosenfeld
Matthew B Neeley
Mezthly Pena
Kim C Worley
Lindsay C Burrage
Monika Weisz-Hubshman
Shamika Ketkar
William J Craigen
Gary D Clark
Seema Lalani
Carlos A Bacino
Keren Machol
Hsiao-Tuan Chao
Lorraine Potocki
Lisa Emrick
Jennifer Sheppard
My T T Nguyen
Anahita Khoramnia
Paula Patricia Hernandez
Sandesh Cs Nagamani
Zhandong Liu
Christine M Eng
Brendan Lee
Pengfei Liu

Publication Date

5-2-2024

Journal

American Journal of Human Genetics

DOI

10.1016/j.ajhg.2024.03.007

PMID

38593811

PMCID

PMC11080285

PubMedCentral® Posted Date

4-8-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Humans, Cell Transdifferentiation, Fibroblasts, Sequence Analysis, RNA, Neurons, Transcriptome, Reproducibility of Results, Nervous System Diseases, RNA-Seq, Female, Male, RNA sequencing, RNA-seq, transcriptome, transdifferentiation, induced neuron, genetic diagnosis, neurological disorder, clinically accessible tissue, fibroblast, isoform

Abstract

RNA sequencing (RNA-seq) has recently been used in translational research settings to facilitate diagnoses of Mendelian disorders. A significant obstacle for clinical laboratories in adopting RNA-seq is the low or absent expression of a significant number of disease-associated genes/transcripts in clinically accessible samples. As this is especially problematic in neurological diseases, we developed a clinical diagnostic approach that enhanced the detection and evaluation of tissue-specific genes/transcripts through fibroblast-to-neuron cell transdifferentiation. The approach is designed specifically to suit clinical implementation, emphasizing simplicity, cost effectiveness, turnaround time, and reproducibility. For clinical validation, we generated induced neurons (iNeurons) from 71 individuals with primary neurological phenotypes recruited to the Undiagnosed Diseases Network. The overall diagnostic yield was 25.4%. Over a quarter of the diagnostic findings benefited from transdifferentiation and could not be achieved by fibroblast RNA-seq alone. This iNeuron transcriptomic approach can be effectively integrated into diagnostic whole-transcriptome evaluation of individuals with genetic disorders.

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