PMID- 34734208
OWN - NLM
STAT- MEDLINE
DCOM- 20230823
LR  - 20230904
IS  - 2667-2375 (Electronic)
IS  - 2667-2375 (Linking)
VI  - 1
IP  - 5
DP  - 2021 Sep 27
TI  - Systematic detection of m(6)A-modified transcripts at single-molecule and 
      single-cell resolution.
LID - 100061 [pii]
LID - 10.1016/j.crmeth.2021.100061 [doi]
AB  - Epigenetic modifications control the stability and translation of mRNA molecules. 
      Here, we present a microscopy-based platform for quantifying modified RNA 
      molecules and for relating the modification patterns to single-cell phenotypes. 
      We directly capture mRNAs from cell lysates on oligo-dT-coated coverslips, then 
      visually detect and sequence individual m(6)A-immunolabled transcripts without 
      amplification. Integration of a nanoscale device enabled us to isolate single 
      cells on the platform, and thereby relate single-cell m(6)A modification states 
      to gene expression signatures and cell surface markers. Application of the 
      platform to MUTZ3 leukemia cells revealed a marked reduction in cellular m(6)A 
      levels as CD34(+) leukemic progenitors differentiate to CD14(+) myeloid cells. We 
      then coupled single-molecule m(6)A detection with fluorescence in situ 
      hybridization (FISH) to relate mRNA and m(6)A levels of individual genes to 
      single-cell phenotypes. This single-cell multi-modal assay suite can empower 
      investigations of RNA modifications in rare populations and single cells.
FAU - Kim, Kyung Lock
AU  - Kim KL
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, 
      USA.
FAU - van Galen, Peter
AU  - van Galen P
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA.
FAU - Hovestadt, Volker
AU  - Hovestadt V
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215.
FAU - Rahme, Gilbert J
AU  - Rahme GJ
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, 
      USA.
FAU - Andreishcheva, Ekaterina N
AU  - Andreishcheva EN
AD  - SeqLL Inc., Woburn, MA 01801, USA.
FAU - Shinde, Abhijeet
AU  - Shinde A
AD  - SeqLL Inc., Woburn, MA 01801, USA.
FAU - Gaskell, Elizabeth
AU  - Gaskell E
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, 
      USA.
FAU - Jones, Daniel R
AU  - Jones DR
AD  - SeqLL Inc., Woburn, MA 01801, USA.
FAU - Shema, Efrat
AU  - Shema E
AD  - Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 
      Israel.
FAU - Bernstein, Bradley E
AU  - Bernstein BE
AD  - Department of Pathology and Center for Cancer Research, Massachusetts General 
      Hospital and Harvard Medical School, Boston, MA 02114, USA.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
AD  - Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, 
      USA.
AD  - Lead contact.
LA  - eng
GR  - F32 CA236432/CA/NCI NIH HHS/United States
GR  - R01 HG009269/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20210802
PL  - United States
TA  - Cell Rep Methods
JT  - Cell reports methods
JID - 9918227360606676
RN  - 0 (RNA, Messenger)
RN  - 0 (Antigens, CD34)
MH  - *In Situ Hybridization, Fluorescence
MH  - RNA, Messenger/genetics
MH  - Antigens, CD34
PMC - PMC8562683
MID - NIHMS1743828
COIS- DECLARATION OF INTERESTS B.E.B. declares outside interests in Fulcrum 
      Therapeutics, HiFiBio, Arsenal Biosciences, Cell Signaling Technologies, and 
      Chroma Medicine. D.R.J. declares interest in SeqLL as founding and current chief 
      executive officer and director.
EDAT- 2021/11/05 06:00
MHDA- 2021/11/05 06:01
PMCR- 2021/08/02
CRDT- 2021/11/04 06:32
PHST- 2021/11/04 06:32 [entrez]
PHST- 2021/11/05 06:00 [pubmed]
PHST- 2021/11/05 06:01 [medline]
PHST- 2021/08/02 00:00 [pmc-release]
AID - 100061 [pii]
AID - 10.1016/j.crmeth.2021.100061 [doi]
PST - ppublish
SO  - Cell Rep Methods. 2021 Sep 27;1(5):100061. doi: 10.1016/j.crmeth.2021.100061. 
      Epub 2021 Aug 2.