Finding Host Proteins Required for HIV Replication
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Transcript of Finding Host Proteins Required for HIV Replication
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Finding Host ProteinsRequired for HIV Replication
Abe Brass
Partners AIDS Research Center and GI Unit Mass. General HospitalHarvard Medical School
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How do we find what HIV needs to replicate?
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Rationale• Employ new methods in mammalian
genetics to find host factors that HIV depends upon (HDFs).
• HDFs provide targets for anti-retroviral therapy and chemical prophylaxis.
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Rationale• HIV may be hard pressed to evade
HDF-directed therapies.
• Comprehensive information about the lifecycle of the virus will benefit the HIV research community.
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Overview• RNAi Mechanism• RNAi Tools• Finding HIV-dependency factors• Three HIV siRNA Screens• TNPO3
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RNAi Mechanism
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RNAi Tools
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Genetic Screens
• Deplete protein expression with shRNAs or siRNAs.
• Test how depletion impacts phenotype with simple in vitro functional assay.
• Unbiased whole genome screens bring new targets into the “pipeline”.
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Genetic Screens
• The way a genetic screen is designed can profoundly influence which genes are uncovered
• Different screen platforms yield different results (i.e. libraries, viruses, cell lines, transfection conditions and efficiencies, readouts)
• Some weak hits may be the most important unlike small molecule screens (knockdown efficiency unknown).
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Caveats• False positives (OTEs). Present, but
minimized through bioinformatic functional clustering, expression studies and reagent redundancy.
• False negatives. Why didn’t this host factor score? Saturation is the goal, but hard to obtain by generating hypomorphs with the current siRNA technology. Optimized validated reagents will help.
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shRNA Libraries
•Whole genome, 3 shRNAs/gene
•Packaged into Retroviral Pools, Stable knockdown
•Focused Libraries: Kinases, Ubiquitin pathway
•shRNAs have unique barcodes
•Formats : MSCV, lentivirus, Inducible.
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mir30-5’ mir30-3’ barcode LTR
mir30-shRNARetrovirus
Integration mir30-
shRNA
Phenotype
Processing of shRNA Target
mRNA-single copy knockdown
LTR
shRNA Libraries
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shRNA Libraries
Barcode: unique 60 nt sequences that allow the abundance of any particular retroviral shRNA in a complex population to be followed using microarray hybridization.
Control Experimental
PCR recovery of and color label of barcode
Competitive hybridization
to barcode microarray
shRNA dropped out following selection shRNA enriched
following selection
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siRNA Libraries
• Arrayed format-”one gene per well”• High throughput whole genome screens
done with liquid handling robotics.• Transiently transfect siRNAs, RISC
active for 6 days post transfection.• Image based=scanning microscope.• Reporter gene=plate reader.
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Finding HIV-dependency factors
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CD4
Tat
Luciferase
Part two
Part one
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siRNA Library• Dharmacon: SMARTpool library, 4
siRNAs per pool, whole human genome (21,121 genes).
• Initial screen done with pools.• Validation round done with the four
individual siRNAs.
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Screen Results• Out of 21,121
genes, 386 scored 2 SD below control
• 1.8% hit rate
• Each of the four individual siRNA were retested
• 16 genes scored with 4/4 individual siRNAs
• 44 genes 3/4• 99 genes 2/4• 115 genes 1/4• 273 of 386 siRNA pools
were confirmed by at least 1 siRNA (71%)
• Reagent Redundancy tries to minimize OTEs, but some of the ¼ are “knowns”.
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Known Host Factors Found in the ScreenA4GALT (2/4 siRNAs) DDX3X (2) PSME2 (1)
AKT1 (2) ERCC3 (3) PURA (2)
AP2M1 (1 ) FBXW11 (4) Rab9p40 (3)
Arf1 (2) GCN5L2 (1) RANBP1 (1)
CD4 (2) H3F3A (1) RelA (4)
CD147 (3) HRS (SP) SIP1 (1)
CRTC2 (1 ) HTATSF1 (1) ST3GAL5 (1)
CRTC3 (3 ) IKBG (2) TFAP4 (3)
CTDP1 (1) La Autoantigen (2) TFE3 (2)
CXCR-4 (2) FAPP1 (1) VPRBP (1)
CyclinT1 (1) NMT1 (3 ) ZNRD1 (2)
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Biologic Processes
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Enzymes Found in the ScreenADAM10 (3/4 siRNAs) WNK1 (3) Jak1 (1)
DDX55 (3) PSPHL (2) USP26 (2)
DDX49 (2) DPM1 (2) OTUD3 (2)
ATPV0A1 (2) OST48 (3) LPL (2)
GAPVD1(2) PRKX1 (1) HUWE1 (2)
PIGH (1) STT3A (2) HERC3 (3)
PIGY (2) RNF170 (3) EXOD1(2)
ABGL5 (2) FNTA(4) HERC6 (2)
FLJ32569 (2) ALKBH8 (2) DDX33 (2)
ITPKA (2) NMT1 (3) SET7 (3)
MOS (2) DIMT1L(4) ARF1 (2)
PIP5K1C (3) C14orf125 (3) CENTG1 (3)
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Three HIV siRNA Screens
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Cells KD Virus Infection Readout Hits
Zhou et al
HeLa-Bgal 24 h HXB2 48 hr; 96 hrβ-gal
reporter activation
207
Konig et al
293T 48 h
NL 4.3 luc
vector, VSV-G
24 hr Luc reporter 295
Brass et al
TZM-bl,HeLa 72 h HIV-1-
IIIB48 hr; 48 hr in
new cells
p24 ; reporter
activation 280
Comparison of Three HIV siRNA Screens
Stephen Goff Cell 135 2008
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1813
9 207
280
295
Brass et al
Zhou et alKonig et al
RelAMed6Med7
783total
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HDFs Found by Two Independent ScreensADRBK1 DDX3X Med7
AKT1 DMXL1 MID1IP1ANAPC2 IDH1 (1) Mre11A
ANKRD30A (1) Jak1 (1) Nup153Cav2 MAP4 Nup155CD4 Med14 Rab28 (1)
CHST1 Med19 RanBP2CTDP1 (1) Med28 RelA
CXCR4 Med4 RNF26 (1)CyclinT1 (1) Med6 TCEB3
WNK1 TRIM55 TNPO3
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Why so little overlap?
• Different screen platforms yield different results.
• Technology caveats: False positives (OTEs) and false negatives (reagents not validated).
• High throughput methodologies• Secondary filters of the primary data
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TNPO3
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SR
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Virion RTC PIC ProvirusPIC
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Conclusions• Functional enrichment, finding known factors, and
confirmation studies suggests the majority of the genes found in the screens impact HIV replication.
• Clearly conventional validation work is required, but host factor discovery has been accelerated (33+ functionally confirmed host factors in 10 months).
• Two screens yielded TNPO3, which is very likely the factor that permits HIV-1, HIV-2, EIAV, and SIV access to their host’s genomes.
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Thank You
• Stephen J. Elledge, HHMI, BWH, HMS• Judy Lieberman, Nan Yan, Derek Dykxhoorn,
IDI, Childrens Hospital• Ramnik Xavier, Yair Benita, CCIB, MGH• Caroline Shamu and staff, ICCB-L HMSFelipe
Diaz-Griffero, DFCI, HMS• Bill and Melinda Gates Foundation• Harvard CFAR