August 20th
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Campbell et al. look at the role of NMD on DUX4 expression in facioscapulohumeral muscular dystrophy (FSHD), Chen, Yu & Wong look at m6A RNA modifications in colorectal cancer, and Pal et al. look at drug resilience in Mycobacterium tuberculosis.
Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression
Cell Reports, 2023
Campbell, A.E., Dyle, M.C., Albanese, R., Matheny, T., Sudheendran, K., Cortázar, M.A., Forman, T., Fu, R., Gillen, A.E., and Caruthers, M.H.
This study delved into the intricate dynamics of nonsense-mediated RNA decay (NMD), a crucial cellular process responsible for eliminating transcripts with premature termination codons (PTCs) caused by nonsense mutations or RNA processing errors. NMD not only safeguards transcript quality but also fine-tunes the expression of normal transcripts resembling NMD targets, thereby playing a pivotal role in gene regulation. This process has garnered therapeutic interest for genetic disorders in which truncated proteins with residual function could be beneficial.
The investigation was centered on facioscapulohumeral muscular dystrophy (FSHD), a myopathy driven by abnormal expression of the DUX4 transcription factor, where NMD inhibition occurs naturally. Employing a cellular FSHD model, the study explored the ramifications of NMD loss. By scrutinising RNA-seq and Ribo-seq data, the researchers unveiled the intricate interplay between DUX4 expression and the translation of target genes. Notably, DUX4’s influence on ZSCAN4, a target gene, led to increased translation over time.
The research also delved into the translation of aberrant SRSF3 transcripts prompted by DUX4 expression. Polysome profiling disclosed the intricacies of this translation, with a decrease in translation, augmented 80S ribosome presence, and an alignment with eIF2a phosphorylation and subsequent translation suppression. Examination of RNA fractions unveiled distinctive shifts in mRNA presence between ribosomes and monosomes.
These insights illuminated the widespread repercussions of NMD disruption on a genomic scale. The consequential production of truncated proteins, which can have potentially deleterious effects, has broad implications for understanding FSHD biology and could offer insights into addressing other genetic conditions where therapeutic modulation of NMD holds promise.
IDDF2023-ABS-0248 CRISPR/Cas9 screening of druggable targets in colorectal cancer with aberrant m6A regulation
Gut, 2023
Chen, D., Yu, J. and Wong, C.C.
Dysregulation of m6A, a prevalent RNA modification, often characterizes colorectal cancer (CRC), where the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) frequently exhibits elevated levels, contributing to tumor progression and immune evasion. Despite its significance, there are currently no drugs targeting YTHDF1. This study employed a systematic approach, integrating CRISPR/Cas9 screening and advanced molecular techniques to identify potential drug targets in CRC cases with heightened YTHDF1 expression.
Using Epi-drug CRISPR/Cas9 screening, RUVBL1/2 emerged as primary candidates for intervention, effectively inducing cell death in YTHDF1-overexpressing CRC cells. Elevated expression of RUVBL1/2 was validated in primary CRC samples from distinct cohorts, correlating with unfavorable prognosis. Depletion of RUVBL1/2 hindered growth in CRC cells with high YTHDF1 levels, human-derived CRC organoids, and xenografts. Mechanistically, a feedback loop between YTHDF1 and RUVBL1/2 was uncovered, enhancing oncogenic translation. YTHDF1 bonded with m6A-modified RUVBL1/2 mRNA, driving translation and protein expression. Remarkably, RUVBL1/2 proteins interacted with YTHDF1 in the translation initiation complex, while their knockout impeded YTHDF1-mediated translation, as confirmed by polysome profiling, HPG-immunofluorescence, and the SUnSET assay.
Ribosome profiling and RNA sequencing illuminated that RUVBL1/2 loss curtailed oncogenic MAPK, Ras, and PI3K signaling pathways driven by YTHDF1. Furthermore, inhibiting RUVBL1/2 using chemical inhibitors or vesicle-like nanoparticles (VNPs) encapsulating siRNA halted proliferation in YTHDF1-expressing CRC cells in vitro and triggered tumor regression in vivo. This comprehensive investigation elucidates YTHDF1’s role in CRC and identifies RUVBL1/2 as potent therapeutic targets, offering a promising avenue for combating CRC cases with heightened YTHDF1 expression.
ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis
Communications Biology, 2023
Pal, P., Khan, M.Y., Sharma, S., Kumar, Y., Mangla, N., Kaushal, P.S. and Agarwal, N.
The survival response of Mycobacterium tuberculosis (Mtb) to diverse cues relies on versatile transcription regulatory mechanisms involving transcription regulators (TRs). Among these, McdR, was linked to cell division upon overexpression in Mycobacterium smegmatis. Recently, reannotated as ResR, its role in antibiotic resilience and essentiality in Mtb remains unclear.
This study elucidates ResR/McdR’s importance encoded by ERDMAN_2020 in virulent Mtb Erdman for bacterial proliferation and vital metabolic functions. Ribosome profiling unveiled downregulation of expression of ribosomal genes and downregulation of protein synthesis in the resR/mcdR(−) strain, suggesting its involvement in bacterial protein translation machinery. Accumulation of tRNAs and amino acids due to abnormal protein synthesis, corroborating ribosome profiling data. Prolonged post-antibiotic effect (PAE) upon resR/mcdR knockdown, attributed to ribosome availability influencing recovery.
These findings underscore ResR/McdR’s pivotal role in antibiotic resilience and recovery post-treatment. By controlling rplN expression and protein synthesis machinery, it impacts the duration of tuberculosis (TB) treatment. Unveiling ResR/McdR’s role in protein translation and antibiotic resilience suggests promising therapeutic avenues for TB management. This study suggests that chemical inhibitors targeting ResR/McdR could be effective as adjunctive therapy, potentially reducing the duration of tuberculosis treatment.