Microarrays of lentiviruses for gene function screens in immortalized and primary cells

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1 26 Nture Pulishing Group Microrrys of lentiviruses for gene function screens in immortlized nd primry cells Steve N Biley, Sirj M Ali, Anne E Crpenter, Citlin O Higgins & Dvid M Stini Here we descrie lentivirus-infected cell microrrys for the high-throughput screening of gene function in mmmlin cells. To crete these rrys, we cultured mmmlin cells on glss slides printed with lentiviruses pseudotyped s vesiculr stomtitis virus glycoprotein, which encode short hirpin RNA or cdna. Cells tht lnd on the printed fetures ecome infected with lentivirus, creting living rry of stly trnsduced cell clusters within monolyer of uninfected cells. The smll size of the fetures of the microrrys (3 lm in dimeter) llows high-density spotting of lentivirus, permitting thousnds of distinct prllel infections on single glss slide. Becuse lentiviruses hve wide cellulr tropism, including primry cells, lentivirus-infected cell microrrys cn e used s pltform for high-throughput screening in vriety of cell types. RNA interference (RNAi) technology llows for loss-of-function studies in mmmlin cells without the need for germline inctivtion of the gene eing studied 1. A roust, inexpensive RNAi-sed high-throughput screening pltform would fcilitte genome-scle loss-of-function studies in mmmlin cells. Drosophil cell-sed microrrys re effective for high-throughput RNAi-sed loss-offunction screens, ut cn only e used to study cell-iologicl phenomen tht tke plce in drosophil cell lines. To enle similr studies in mmmlin cells, severl groups hve developed cell-sed microrrys using smll interfering RNA or DNA plsmids. However, such microrrys rely on conventionl trnsfection methods nd thus re unlikely to e rodly comptile with mny different cell types 2 6. Becuse lentiviruses pseudotyped s vesiculr stomtitis virus glycoprotein (VSV-G) infect wide vriety of mmmlin cells with high efficiency 7, they void mny of the limittions of trnsfection for introducing over- or underexpression cssettes into cells. Such lentiviruses cn e used to overexpress cdna nd to express short hirpin RNA (shrna) tht silences gene expression through RNAi 8,9. Notly, lentiviruses cn infect nondividing cells, cpcity tht is prticulrly useful for the study of certin primry cell types 7. Here we descrie new type of cell-sed microrry whose fetures include clusters of mmmlin cells, ech trnsduced with single type of lentivirus. We refer to these s lentivirus-infected cell microrrys (LICMs). With these microrrys, we hve otined roust nd loclized infection of mmmlin cells with lentiviruses contining overexpression cssettes or RNAi cssettes. This technology provides pltform for loss-of-function nd overexpression screens in rod rnge of mmmlin cell types. RESULTS Development of the LCIM The fetures of LICMs comprise clusters of mmmlin cells, ech infected with distinct lentivirus nd surrounded y monolyer of uninfected cells. To mke the microrrys, we print on coted glss slide nnoliter volumes of solutions contining concentrted lentivirus. We plce dried printed slides in Petri dish nd dd dherent mmmlin cells in medi. After n incution of typiclly h, the LICM forms nd the cells cn e fixed nd processed with conventionl cell-sed ssy methods, such s immunofluorescence. Ech cell cluster on the microrry is then imged with utomted microscopy nd nlyzed for cellulr phenotypes of interest. To demonstrte this technology, we printed microrry with 3 fetures, ech contining either lentivirus encoding green fluorescent protein () or n shrna trgeting humn lmin A/C 8. We seeded HeL cells onto the rry nd, fter 72 h, processed it nd imged cells for expression of or lmin A/C nd DNA content. In pttern mtching tht of the lentivirus-contining fetures on the rry, cell clusters expressing or deficient in lmin A/C were clerly visile (Fig. 1). Ech cluster ws pproximtely 25 mm in dimeter nd contined out 15 cells. At this feture density, 5, different lentiviruses cn e printed on single slide. In the exmple ove, we printed the two different lentiviruses in n lternting pttern to ssess whether cells on one feture would ecome infected with viruses from vicinl fetures. This does not seem to e the cse, ecuse cells on the -lentivirus fetures hd high levels of green fluorescence ut expressed norml mounts of lmin A/C (Fig. 1). Conversely, the cells on fetures printed with the lmin A/C shrna lentivirus hd fivefold reduction in lmin A/C expression compred with cells growing either on nonprinted res of the slide or on the -lentivirus fetures. The numer of cells with knockdown of lmin A/C expression ws six times greter on fetures printed with the lmin A/C Whitehed Institute for Biomedicl Reserch nd Msschusetts Institute of Technology Deprtment of Biology, Nine Cmridge Center, Cmridge, Msschusetts 2142, USA. Brod Institute, 32 Chrles Street, Cmridge, Msschusetts 2141, USA. Correspondence should e ddressed to D.M.S. (stini@wi.mit.edu). RECEIVED 3 OCTOBER 25; ACCEPTED 19 DECEMBER 25; PUBLISHED ONLINE 23 JANUARY 26; DOI:1.138/NMETH848 NATURE METHODS VOL.3 NO.2 FEBRUARY

2 26 Nture Pulishing Group Men lmin A/C expression per cell (Cy3 signl) Men intensity per feture shrna lentivirus thn on the -lentivirus fetures or in feturesized nonprinted res of the slide. Our quntittive nlysis suggests tht fetures printed with lentiviruses infect smll clusters of cells in locl, virus-specific wy. In ddition, our exmple demonstrtes the use of overexpression nd shrna lentiviruses on the sme microrry. Use of primry dividing nd nondividing cells on LICMs Hving demonstrted the fesiility of LICMs, we explored their possile uses nd limittions in more detil. We first tested the Lmin A/C knockdown (% of cells/spot) Lmin A/C (Cy3) Fetures with cells infected with shlmin A/C lentivirus Fetures with cells infected with -expressing lentivirus Ares not spotted with virus effect of printing different mounts of lentivirus in ech spot. The typicl titer of printed lentivirl solution is infectious units (IFU)/ml. In ech feture we deposit out 3.9 nl of solution or 3,9 IFU/feture. Ech feture hs out 15 cells nd thus roughly 26 IFU/cell. We printed twofold seril dilutions of solution contining -encoding lentivirus (initil titer, IFU/ml) on multiple rrys nd quntified the susequent level of expression in the cells growing on those fetures. As seen with conventionl lentivirl infections, the mount of lentivirus deposited in ech spot ws proportionl to the mgnitude of the c Figure 1 LICMs mde with two different types of lentiviruses. () Microrry of 3 fetures printed with lentiviruses expressing either or shrna trgeting lmin A/C in n lternting pttern, nd seeded with HeL cells. Hoechst stining shows nuclei (lue), nti lmin A/C immunofluorescence shows lmin A/C (red) nd fluorescence is green. Right, higher mgnifiction imge of four fetures from the rry (oxed t left). Scle rs, 1 mm (left) nd 2 mm (right). () Quntifiction of nd lmin A/C expression in fetures of the rry nd nonspotted control res. For lmin A/C, we quntified oth men expression per cell (left; ritrry units) nd percent of cells in feture with reduced lmin A/C expression (knockdown; middle). For, we quntified men expression per feture (right; ritrry units). Mesurements re sed on n ¼ 16. Cy3, indocrocynine; shlmin A/C, shrna trgeting lmin A/C (see Supplementry Note). BJ firolsts Dendritic cells Men intensity n = 5 virus rry shlmin Incresing concentrtion of -expressing lentivirus One feture One feture 1 1 virus rry Men intensity HeL A549 HEK-293T DU145 Figure 2 LICMs re comptile with vriety of trnsformed nd primry cell lines. () A smll rry with incresing concentrtions of expressing lentivirus ws printed, seeded with HeL cells nd imged (top; scle r, 225 mm), nd the fluorescence in the fetures ws quntified (ottom). Results re derived from five fetures for ech condition. shlmin, shrna trgeting lmin A/C. () Arrys of 1 1 fetures were printed with -expressing lentivirus nd were seeded with HeL, A549, HEK-293T or DU145 cells. Top row, imges of entire rrys; middle nd ottom rows, imges of one feture from ech rry. Quntifiction of fluorescence in fetures (elow) shows tht comprle expression is otined with the four cell lines. Scle rs, 1 mm (top row) nd 1 mm (middlendottom rows). (c) Arrys were printed with -expressing lentivirus nd were seeded with primry humn BJ firolsts or primry mouse dendritic cells. Top row, imges of entire rrys; ottom row, imges of one feture from ech rry. Scle rs, 1 mm (top left), 225 mm (top right), 3 mm (ottom left) nd 1 mm (ottom right). 118 VOL.3 NO.2 FEBRUARY 26 NATURE METHODS

3 26 Nture Pulishing Group /RFP (Cy3) Merged Higher mgnifiction Signl intensity (ritrry units) RFP Nucleus Edge of nucleus Cytoplsm RFP Edge of cell phenotypic chnge seen in cells growing on the corresponding feture (Fig. 2). Viruses pseudotyped s VSV-G redily infect mny different mmmlin cell types 7. To demonstrte this cpcity of lentiviruses in the rry formt, we printed four identicl, 1-feture rrys of the -encoding lentivirus nd cultured different cell type on ech (Fig. 2). Although the verge expression ws highest in A549 nd DU145 cells, ll four cell types tested hd levels of expression tht were well ove the ckground of uninfected cells. This result demonstrtes how LICMs cn e used with commonly used dherent, cultured cell lines, oth trnsformed nd nontrnsformed. To demonstrte the comptiility of LICMs with primry mmmlin cells, we cultured primry dividing humn BJ firolsts or primry nondividing one mrrow derived mouse dendritic cells on n rry printed with lentivirus contining -overexpression cssette (Fig. 2c). The rrys produced grids of -expressing fetures in the printed pttern, showing tht the microrrys re comptile with nondividing nd dividing primry cells nd tht cell division is not necessry for the formtion of LICMs. Quntifiction of high-content cellulr phenotypes We hve demonstrted tht LICMs re comptile with overexpression nd shrna-medited knockdown with lentiviruses. To ensure tht this functionlity is not specific to the lentivirl vectors or cdnas used, we tested severl different lentiviruses in c Phospho-S6 signl Intensity (ritrry units) Non stored rry Arry stored 15 months efore use Phospho-S6 (Cy3) Merged shmtor Percentge of cells in ech in of phospho-s6 intensity shmtor < >8 Phospho-S6 intensity Figure 3 LICMs re comptile with the detection of complex phenotypes. () These 3 3 rrys were printed with viruses using different promoters to overexpress, RFP nd. Hoechst stining shows nuclei; immunofluorescence with ntiody to shows memrne-loclized (red); fluorescence is green; RFP fluorescence is lso red. Ech feture ws lso imged t high mgnifiction (ottom row, representtive imges). Scle rs, 45 mm (min imges) nd 25 mm (higher mgnifiction). These imges were nlyzed to ssess the sucellulr distriution of ech protein (see Supplementry Note). Error rs, s.e.m.;, P o.1, sucellulr locliztion of versus nd RFP. () Experiments with rrys similr to tht in, ssyed on the dy of printing (top) or fter storge for 15 months t 8 1C (ottom). (c) Arrys were printed with lentiviruses expressing or or n shrna trgeting mtor (shmtor). Single fetures from the rry re presented. Scle r, 15 mm. Hoechst stining shows nuclei; immunofluorescence with ntiody to phosphorylted S6 (Phospho-S6) shows mtor pthwy ctivity (red); nd fluorescence is green. For quntifiction of S6 phosphoryltion, imges of six fetures for ech smple type (, nd shmtor) were nlyzed. For ech feture, the men fluorescence intensity of phospho-s6 stining in the cytoplsm ws mesured for every cell (see Supplementry Note). Bottom left, popultion-verged dt. Error rs, s.e.m.;, P o.1, versus s control. Bottom right, cells from those popultions were plced into ins sed on their men intensity vlues:redline,shmtor;greenline,; lue line,. the rry formt. We printed smll grids with lentiviruses contining overexpression cssettes of driven y the phosphoglycerte kinse promoter derived from trnsfection using the plsmid LKO.1, red fluorescent protein (RFP) driven y the uiquitin C promoter derived from trnsfection using the plsmid Lentilox 3.7, or (CD9) driven y the uiquitin C promoter derived from trnsfection using the plsmid LKO.2 (refs. 8,9; Fig. 3). All three lentiviruses produced loclized cell clusters expressing only the expected proteins, suggesting tht the microrrys re comptile with wide vriety of promoters for gene overexpression nd distinct virl ckones. At high mgnifiction, the memrne-trgeted locliztion of ws visily distinguishle from the sucellulr distriution of RFP nd (Fig. 3, ottom imges). We lso mesured the memrne locliztion of quntittively nd utomticlly on n individul cell sis (Fig. 3, grphs) using the CellProfiler imge nlysis softwre developed in our lortory ( Our results suggest tht lentiviruses printed in LICM fetures preserve the chrcteristics of VSV-G lentiviruses, including high efficiency infection of trnsformed nd primry mmmlin cells nd trnsduction of shrna 7. For use in screening formt, the rrys must e stle nd durle. We printed multiple copies of the microrrys descried ove nd stored the replicte rrys t 8 1C for 15 months. After storge, we thwed the slides, then seeded nd nlyzed them in the sme wy s the freshly ssyed rrys. The similrity of NATURE METHODS VOL.3 NO.2 FEBRUARY

4 26 Nture Pulishing Group shmtor shlmin Cell numer Four fetures One feture Higher mgnifiction Cell count Cell Cell minor Cell Zernike _ Cell extent re 12 xis Contr. shmtor Contr. shmtor Contr. shmtor Contr. shmtor Contr. shmtor Pixels/cell Four fetures One feture Higher mgnifiction the results otined with fresh nd stored rrys suggests tht the printed slides cn e stored for extended periods of time efore use (Fig. 3). We lso demonstrted tht LICMs cn e used to detect cellulr phenotypes cused y the knockdown of n endogenous gene. We seeded HeL cells onto n rry printed with lentivirus encoding n shrna trgeting humn mtor, centrl regultor of cell growth (cell size) nd prolifertion (cell numer) 1, in ddition to fetures printed with lentiviruses overexpressing or. We ssyed mtor ctivity through the phosphoryltion stte of its downstrem effector, the riosoml protein S6 (Fig. 3c). The cells in the fetures printed with lentivirus encoding shrna trgeting mtor hd visully ovious reduction in S6 phosphoryltion, which ws unffected in cells in the fetures with overexpression of or. Quntittive imge nlysis using CellProfiler s descried in the Supplementry Note online confirmed these results for the cell popultion (Fig. 3c, r grphs) nd on per-cell sis (Fig. 3c, histogrms). Finlly, we showed tht LICMs re comptile with the detection of cellulr phenotypes tht re not exclusively sed on fluorescence Nucler Zernike 4_ Nucler re Nucler eccentricity Nucler solidity Nucler Zernike _ Pixels/nucleus Contr. shlmin Contr. shlmin Contr. shlmin Contr. shlmin Contr. shlmin Figure 4 Complex cellulr phenotypes cn e detected y utomted imge nlysis of LICM fetures. (,) Arrys printed with lentiviruses expressing shrna trgeting mtor or lmin A/C were seeded with HeL cells nd processed for phospho-s6 () or lmin A/C () immunofluorescence. Hoechst stining shows nuclei (lue); immunofluorescence with ntiody to phosphorylted S6 nd ntiody to lmin A/C re cytoplsmic nd nucler stins, respectively (red). Scle rs, 15 mm (four fetures), 4 mm (one feture) nd 1 mm (higher mgnifiction). The smll rrow in indictes smll cell with decrese in phospho- S6 stining; the lrge rrow indictes n unffected cell. Automted shpe nd size mesurements were otined for every cell in the shmtor fetures nd every nucleus in the shlmin fetures (see Supplementry Note). Grphs present the popultion-verged dt for severl of these mesurements. Error rs, s.e.m.;, P o.1. Contr. (control), Thy1.1 overexpression () or overexpression (). See Supplementry Note for full description of the utomted imge nlysis protocols. intensity. We mesured 39 size nd shpe prmeters of the cytoplsms nd nuclei of HeL cells growing on fetures printed with lentiviruses expressing shrna trgeting mtor or lmin A/C. Some ut not ll of the prmeters were ffected y knockdown of mtor or lmin A/C (suset, Fig. 4). For exmple, fetures printed with lentivirus encoding shrna trgeting mtor hd fewer nd smller cells thn did fetures printed with control lentivirus, consistent with the known involvement of mtor in cell size control 1.Some(for exmple, Zernike _) ut not ll (for exmple, extent) cell shpe prmeters were lso ffected y knockdown of mtor (Fig. 4). Cells in fetures printed with lentivirus encoding shrna trgeting lmin A/C showed chnge only in the Zernike 4_ shpe prmeter of the cell nucleus without n effect on nucler re or eccentricity (Fig. 4). DISCUSSION Like other cell-sed microrry formts, LICMs hve certin dvntges over microtiter plte sed screening methods. We print the microrrys on modified glss slides, which yields etter imge qulity for cellulr ssys thn do pltes with polystyrene ottoms. The rrys re comptile with the utomted detection of high-content phenotypes, such s the sucellulr locliztion of the memrne protein nd the size reduction of cells depleted of mtor. The scle of LICMs lso lends itself to svings in the numer of cells required for screen. A screen of 5, viruses using 384-well microtiter pltes requires out 13 pltes nd, depending on the cell type, t lest cells. At feture densities similr to those used in Figure 1, 5, different viruses cn e screened on single slide using fr fewer cells, n importnt chrcteristic for primry cells tht my e difficult to otin. Other cell-sed microrry methods use plsmids or smll interfering RNA to chieve overexpression or trnsient knockdown 2 6,11. Here, we hve demonstrted the ility to do oth using stle lentivirl trnsduction 8, highlighting the flexiility of LICM technology. Moreover, once printed, the rrys re comptile with vriety of cell types, including primry nondividing cells. We strongly suspect tht the formt will e dptle to other viruses pseudotyped s VSV-G, such s Moloney retroviruses. The microrrys my lso e comptile with other stle virl pseudotypes, ut this remins to e tested. The min hurdle for dpting LICM to genome-wide lossof-function screens is the requirement for high-titer virus otined y concentrting virus-contining superntnts. Ultrcentrifugtion is time consuming nd difficult to utomte, ut dvnces in the genertion of higher-titer lentivirl superntnts re likely. 12 VOL.3 NO.2 FEBRUARY 26 NATURE METHODS

5 26 Nture Pulishing Group In the men time, the production nd screening of focused lentivirl lirries (such s the genes encoding the kinome ) is prcticl, llowing the immedite ppliction of LICMs to mny cell iology prolems. METHODS Mterils. We otined immunofluorescence regents from the following sources nd used them t the dilutions in prentheses: mouse monoclonl ntiody to lmin A/C (636; 1:5 dilution; Snt Cruz Biotechnology), secondry ntiody to mouse indocrocynine (1:1, dilution; Jckson Lortories), ntiody to Thy-1 iotin (1:5 dilution; Phrmingen), streptvidin-indocrocynine secondry ntiody (1:1, dilution; Phrmingen), ntiody to phosphorylted S6 (ser24/4; 1:5 dilution; Cell Signling) nd Hoechst (1:1, dilution; Moleculr Proes). We used the following lentivirus plsmids: PRRL phosphoglycerte kinse 8 ; LKO.1 puro encoding lmin A/C or mtor shrna 12 ; Lentilox 3.7 CMV-RFP (C. Dillon); nd LKO.3 encoding mouse (N. Hcohen). Lentivirus production. To generte lentiviruses, we seeded HEK293T cells in 15-cm dishes nd, fter 48 h, cotrnsfected the cells with Fugene 6 using 9 mg lentivirl plsmid, 6 mg Delt VPR 8.9 nd 3 mg VSV-G 13. After 24 h, we removed the viruscontining superntnt, filtered it through.45-mm cellulose cette filter nd concentrted it y ultrcentrifugtion t 23, r.p.m. in n sw28 rotor in Beckmn ultrcentrifuge for 1.5 h (ref. 7). After ultrcentrifugtion, we resuspended virl pellets in microrry printing solution (.4 M HEPES, ph djusted to 7.4 with KOH, 12.5 mg/ml of Trehlose (625625; Cliochem), 6 mg/ml of protmine sulfte (P42; Sigm) nd 1.23 M KCL (3911; Sigm)). We stored concentrted lentivirus t 8 1C until use. Microrry printing. We used microrrying root (Pixsys 55; Genomic Solutions) with SMP1 pins (Arryit SMP1; Telechem) to deposit virl solutions on glss slides coted with g-mino propyl silne (UltrGAPS; 415; Corning). We used UltrGAPS slides ecuse the surfce llowed for the printing of smll, well-formed spots nd they were comptile with cell culture. Before printing the microrry, we loded 2 ml of virl solution into round-ottomed, 384-well polypropylene microtiter plte nd centrifuged it t 1, r.p.m. for 3 s. We did ll printing t 23 1C with 55% humidity. The titer of typicl concentrted virus solution is roughly IFU/ml. An SMP1 pin deposits out 3.9 nl of solution to generte spots with dimeter of 2 3 mm. After printing, we stored the slides t 8 1C in seled irtight gs. In the experiments in Figures 1, 2, 2 nd 3, the center-to-center distnce etween fetures ws 5 mm. In Figure 2c, the center-to-center distnce etween fetures ws 1.5 mm nd 5 mm for the rrys seeded with the very lrge BJ firolsts nd mouse dendritic cells, respectively. Lentivirus microrry seeding. We desiccted stored rrys t 25 1C for 1 h efore use. All slides were then locked for exctly 3 min t 25 1C in 15-cm dish in Dulecco s modified Egle s medium with 1% inctivted fetl clf serum. During the locking, the slides were positioned so tht the printed re on the slide ws fce down nd ws not in contct with nything other thn the medi. After locking, slides were plced rry side up in 1-mm 1-mm 1-mm squre tissue culture dish. We used ctively growing mmmlin cells in 25 ml of culture medium (A549 cells: Dulecco s modified Egle s medium with 1% fetl ovine serum, 5 units/ml of penicillin nd 5 mg/ml of streptomycin; HeL, HEK-293T, DU145 nd BJ firolsts: Dulecco s modified Egle s medium with 1% inctivted fetl clf serum, 5 units/ml of penicillin nd 5 mg/ml of streptomycin) for seeding the rrys. We incuted seeded rrys t 37 1C inn tmosphere of 5% CO 2.ForFigure 2c, we seeded rrys with humn BJ firolsts, followed y incution for 72 h, or seeded rrys with mouse dendritic cells, followed y incution for 92 h. We plced mouse dendritic cells on the slide s loosely ttched ggregte t dy 6 fter purifiction from one mrrow 14. This loosely ttched ggregte then relesed mture, nonproliferting dendritic cells s finl stge of development. For the experiments in Figures 1, 2, 3 nd 4, we seeded rrys with HeL cells nd incuted for 72 h. After culture for the specified mount of time, we removed slides from medi nd fixed them for 2 min t 25 1C in 3.7% prformldehyde plus 4% sucrose in PBS. Immunofluorescence. After fixtion, we proed cells with primry nd secondry ntiodies s descried 12. Imge cpture nd nlysis. We cptured imges of rrys with n Axiovert 2 microscope (Crl Zeiss) nd nlyzed them with custom softwre designed on the KS4 pltform for ll figures. Photos of lrge rrys were cptured t 5 mgnifiction, imges of single fetures were cptured t 1 nd the imge of the feture contining lentivirus expressing n shrna trgeting mtor ws cptured t 4. For Figures 3 nd 4, we used CellProfiler imge nlysis softwre developed in our lortory ( See Supplementry Note for full description of the imge nlysis protocols used. Note: Supplementry informtion is ville on the Nture Methods wesite. ACKNOWLEDGMENTS We thnk S.A. Stewrt (Wshington University; St. Louis, Missouri) for the gift of LKO.1 puro; C. Dillon (Msschusetts Institute of Technology, Cmridge, Msschusetts) for the gift of Lentilox 3.7-CMV-RFP; nd N. Hcohen (Msschusetts Generl Hospitl; Boston, Msschusetts) for the gift of LKO.3 nd primry mouse dendritic cells. A.E.C. is Novrtis fellow of the Life Sciences Reserch Foundtion; S.M.A. is Howrd Hughes Medicl Institute predoctorl fellow. This work ws supported y funds from the Whitehed Institute nd Pew Chritle Trusts. COMPETING INTERESTS STATEMENT The uthors declre tht they hve no competing finncil interests. Pulished online t Reprints nd permissions informtion is ville online t 1. Brummelkmp, T.R. & Bernrds, R. 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