MSGID: 1:317/3 6279eac7   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    Methylation of tRNA-derived fragments regulates gene-silencing activity   
   in bladder cancer    
      
     Date:   
         May 9, 2022   
     Source:   
         University of Alabama at Birmingham   
     Summary:   
         Researchers describe a novel form of gene regulation that is altered   
         in bladder cancer, leading to the boosting of a gene pathway that   
         helps the cancer cells survive during rapid growth. The work focuses   
         on a 22-base fragment of transfer RNA, tRF-3b, which is modified   
         by the enzyme complex TRMT6/61A. In bladder cancer, the levels of   
         TRMT6/61A -- a methyltransferase -- are elevated. The methylation   
         modification prevents tRF-3bs from silencing the expression of   
         various genes in the unfolded protein response pathway in the   
         cancer cells.   
      
      
      
   FULL STORY   
   ==========================================================================   
   Anindya Dutta, MBBS, Ph.D., and colleagues have described a novel form of   
   gene regulation that is altered in bladder cancer, leading to the boosting   
   of a gene pathway that helps the cancer cells survive during rapid growth.   
      
      
   ==========================================================================   
   Their work focuses on a 22-base fragment of transfer RNAs known as a   
   tRF-3b, which is modified by an enzyme complex called TRMT6/61A. In   
   bladder cancer, the levels of TRMT6/61A -- a methyltransferase enzyme   
   that adds a methyl group onto the fourth base of the tRF-3bs --   
   are elevated. This modification prevents tRF- 3bs from silencing the   
   expression of various genes in the unfolded protein response pathway in   
   the cancer cells, resulting in increased expression of those genes.   
      
   "To the best of our knowledge, this is the first example of   
   microRNA-like gene silencing being regulated by the TRMT6/61 based on   
   an N1-methyladenosine modification, and our report provides a mechanism   
   by which the elevation of TRMT6/61A seen in cancers can impact gene   
   expression," Dutta said. "Fast proliferating cancer cells synthesize and   
   fold many more proteins than normal cells and thus need to upregulate the   
   unfolded protein response pathway to maintain protein homeostasis. We   
   find that one way bladder cancer cells activate the pro-survival   
   unfolded protein response to alleviate endoplasmic reticulum stress   
   is by preventing tRFs from silencing the expression of genes involved   
   in this unfolded protein response."  "The unfolded protein response is   
   tightly linked to many aspects of cancer progression and has emerged as a   
   promising therapeutic target," Dutta said. "It has been previously noted   
   that unfolded protein response-related genes are globally upregulated   
   in several cancer types, including bladder cancer, and so our results   
   suggest that inhibiting the TRMT6/61A enzyme may be a new approach to   
   treat bladder cancer."  The study by Dutta and co-corresponding author   
   Rune Ougland, M.D., Ph.D., included analysis of bladder cancer tissue   
   obtained from patients undergoing transurethral resection of bladder   
   tumors. It is published in the journal Nature Communications.Dutta is   
   chair of the University of Alabama at Birmingham Department of Genetics,   
   and Ougland is a urologic surgeon and senior research investigator at   
   Oslo University Hospital Rikshospitalet, Oslo, Norway.   
      
   An important advance in the study was the workflow used to create   
   a library from human cells of small RNAs with an N1-methyladenosine   
   modification, or m1A.   
      
   The workflow combined two independent approaches -- enrichment by   
   m1A-antibody, followed by small RNA-sequencing and m1A-induced mismatch   
   signature by sequencing.   
      
      
      
   ==========================================================================   
   The UAB researchers found that a reverse transcriptase enzyme,   
   ProtoScriptII, commonly used for short RNA sequencing, did a poor job of   
   detecting small RNAs that contain m1A; but the use of two other reverse   
   transcriptases in the workflow revealed that tRNA-derived fragments,   
   including tRF-3b, were enriched among short RNAs. This suggested that   
   small RNAs with an m1A modification are under-represented in most small   
   RNA-sequence libraries that commonly have used ProtoScriptII.   
      
   With the improved workflow, the researchers found that the m1A   
   modification existed mostly on tRFs among the human small RNAs. They also   
   found that the m1A modification was highly specific and prevalent on both   
   nuclear-encoded tRFs and mitochondria-encoded tRFs, and the m1A found on   
   tRF-3b from nuclear-encoded tRNAs was mediated by the TRMT6/61A complex.   
      
   How does the m1A-tRF-3b impede gene silencing? The answer involves an   
   even deeper dive into molecular genetics, but the key appears to be   
   that the N1- methyladenosine modification disrupts regular Watson-Crick   
   base pairing.   
      
   MicroRNAs are known to silence genes by binding to the RNA-induced   
   silencing complex, or RISC. There they act as a template to bind   
   complementary messenger RNAs, and the messenger RNA is then silenced   
   and degraded by RISC. Similar to microRNAs, tRF-3s have been found   
   in diverse biological pathways, in particular gene-silencing pathways   
   that rely on base pairing between the small RNAs, in this case tRF-3s,   
   and the target RNAs.   
      
   The researchers created a luciferase reporter assay and found that an   
   unmodified tRF-3 triggered gene silencing, whereas the m1A-modified   
   tRF-3b abolished the gene silencing. "Since m1A interrupts canonical   
   base pairing, we hypothesize the weakened base pairing by m1A in the   
   tRF-3 with target messenger RNA explains the lowered gene-silencing   
   activity observed for m1A-containing tRF-3s," Dutta said.   
      
   Co-authors with Dutta and Ougland in the study, "TRMT6/61A-dependent base   
   methylation of tRNA-derived fragments regulates gene-silencing activity   
   and the unfolded protein response in bladder cancer," are Zhangli Su,   
   UAB Department of Genetics; Ida Monshaugen and Arne Klungland, Oslo   
   University Hospital Rikshospitalet; and Briana Wilson and Fengbin Wang,   
   University of Virginia.   
      
   Support came from National Institutes of Health grants CA044579, CA254134,   
   AR067712 and CA259526; Vestre Viken Hospital (Gjettum, Norway) Trust   
   grant 25C003; and Norwegian Cancer Society grant 216115.   
      
      
   ==========================================================================   
   Story Source: Materials provided by   
   University_of_Alabama_at_Birmingham. Original written by Jeff   
   Hansen. Note: Content may be edited for style and length.   
      
      
   ==========================================================================   
   Journal Reference:   
      1. Zhangli Su, Ida Monshaugen, Briana Wilson, Fengbin Wang, Arne   
      Klungland,   
         Rune Ougland, Anindya Dutta. TRMT6/61A-dependent base methylation   
         of tRNA-derived fragments regulates gene-silencing activity and the   
         unfolded protein response in bladder cancer. Nature Communications,   
         2022; 13 (1) DOI: 10.1038/s41467-022-29790-8   
   ==========================================================================   
      
   Link to news story:   
   https://www.sciencedaily.com/releases/2022/05/220509171056.htm   
      
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