Defective post-transcriptional
gene regulation
Neil Renwick MD, PhD
Laboratory of Translational RNA Biology
Department of Pathology and Molecular Medicine
SEAMO Innovation Showcase 2015
Path to research independence in Translational RNA Biology
PhD
FCAP
MCTS
K08
DTMH
MBChB
Research theme: Using RNA to diagnose and treat disease
Post-transcriptional gene regulation
RBPs
RNA
DNA
miRNAs
PROTEIN
Post-transcriptional diseases
miRNA gene mutations
1) miR-96-related non-syndromic hearing loss
RNA-binding proteins
1)
2)
3)
4)
5)
FMR1 loss of expression resulting in Fragile X Syndrome
RBM20-related Dilated Cardiomyopathy
RBM10-related Cleft Palate
TDP43-related Amyotrophic Lateral Sclerosis
FUS-related Amyotrophic Lateral Sclerosis
RNAs
1) Likely many TBD
Post-transcriptional gene regulation
RBPs
RNA
DNA
miRNAs
PROTEIN
5 ng (or less)
sequence annotation and analysis
upload sequence file on RNAworld (300 mio reads)
barcode extraction (20 x 15 mio reads, validated)
small RNA annotation (iterative process)
miRNAs
none
rRNA
snoRNA
std cali
tRNA
13,300,000 (88.2%)
298,000 (2.0%)
382,000 (2.5%)
161,048 (1.1%)
254,941 (1.7%)
218,229 (1.3%)
clustering, heat map (log2 expression)
differential expression
discriminant analysis
Post-transcriptional gene regulation
RBPs
RNA
DNA
miRNAs
PROTEIN
Illustration of PAR-CLIP method
4-thiouridine
Library 5:TDP43 library annotation by read length.
non nannotated
mito_genome
18000000
genome
pET28a_plasmid
Redundant read count
pET16B_plasmid
RNL2_insert
16000000
BICC1_insert
concatamers
tRNA_prec
tRNA
14000000
std_cali
snRNA_prec
snRNA
12000000
snoRNA_prec
snoRNA
scRNA_prec
scRNA
10000000
scaRNA_prec
scaRNA
rRNA_prec
rRNA
8000000
plasmid
piRNA
other_ncRNA_prec
other_ncRNA
6000000
Ome_cali
mt_tRNA
mt_rRNA
4000000
mt_mRNA
mRNA_gene
mRNA
mirtron
2000000
miRNA
marker
long_cali
lincRNA_gene
0
lincRNA
5
7
9
doubtful_snoRNA
11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51doubtful_miRNA
Read length (nt)
circRNA
alt_cali
adapter
TDP-43 PAR-CLIP
Directions and plan
Projects
1)
2)
3)
4)
miRNA reannotation (other RNAs)
miRNA-based diagnostics for NETs (cancer biology)
RBP pathomechanisms (TDP-43)
Rare disease genetics (RNA-based mutation identification)
Yrs 1-2
Set up functional laboratory and recruit
Obtain preliminary funding
Write first and senior author manuscripts
Talk to senior investigators
Yrs 3-5
Develop collaborations (models)
Present nationally
Select topic for larger research award application
Acknowledgments
Lab members
Xiaojing Yang (research associate)
Kathrin Tyryshkin (data analyst)
Bryony Dorrington (path 499 student)
Betty Li (path 499 student)
Tiandra Ceyhan (summer student)
Dakota Gustafson (summer student)
Shane Mooney (summer student)
Francine Milone (volunteer)
Collaborators
Thomas Tuschl, The Rockefeller University (RNA biology)
Yao-Tseng Chen, Weill Cornell Medical College (rare tumors)
Lev Goldfarb, National Institutes of Health (genetics)
Fyodor Platonov, North-Eastern Federal University (rare diseases)
Andrew Craig, Queen’s University (cancer biology)
Funding
Start up
Department of Pathology and Molecular Medicine
QU School of Medicine
SEAMO
Competitive
AHSC AFP Innovation Fund
CFI JELF
MRI ORF-RI Program
QU KGH Clare Nelson Bequest Fund
QU SARC Grant
SFARI
neil.renwick@queensu.ca