WO 2014/153651 A9 2 October 2014 (02.10.2014) P O P C T

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WO 2014/153651 A9 2 October 2014 (02.10.2014) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) CORRECTED VERSION (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2014/153651 A9 2 October 2014 (02.10.2014) P O P C T (51) International Patent Classification: 2038 Waycross Crescent, Mississauga, Ontario L5K 1H9 C12Q 1/02 (2006.01) G01N 33/48 (2006.01) (CA). DA COSTA, Daniel J.; 3844 West 11th, Van C12M 1/34 (2006.01) G01N 33/567 (2006.01) couver, British Columbia V6R 2K8 (CA). HANSEN, C12Q 1/68 (2006.01) Carl, L., G.; 6309 Larkin Drive, Vancouver, British Columbia V6T 1Z4 (CA). NELSON, Brad; 312-225 Men- (21) International Application Number: zies Street, Victoria, British Columbia (CA). NIELSEN, PCT/CA20 14/000304 Julie; 2410 Lee Avenue, Victoria, British Columbia V8R (22) International Filing Date: 6V5 (CA). LISAINGO, Kathleen; #402-1 10 Brew Street, 28 March 2014 (28.03.2014) Port Moody, British Columbia V3H 0E4 (CA). (25) Filing Language: English (74) Agent: MACINS, Andris; c/o C6 Patent Group Inc., oper ating as Carbon Patent Group, Unit 203A-1 16 Geary Aven English (26) Publication Language: ue, Toronto, Ontario M6H 4H1 (CA). (30) Priority Data: (81) Designated States (unless otherwise indicated, for every 61/806,329 28 March 2013 (28.03.2013) US kind of national protection available): AE, AG, AL, AM, (71) Applicant: THE UNIVERSITY OF BRITISH AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, COLUMBIA [—/CA]; University - Industry Liaison O f BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, fice, # 103 - 6190 Agronomy Road, Vancouver, BC V6T DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 1Z4 (CA). HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, (72) Inventors: RICICOVA, Marketa; 55 12 Victoria Drive, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, Vancouver, British Columbia V5P 3W1 (CA). HEYRIES, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, Kevin Albert; 305-6060 East Boulevard, Vancouver, Brit SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, ish Columbia (CA). ZAHN, Hans; Antweipener Strasse TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 21, 80805 Munich (DE). PETRIV, Oleh; 8271 Spires ZW. Road, Richmond, British Columbia V6Y 1W1 (CA). LE- CAULT, Veronique; 306-221 Union Street, Vancouver, (84) Designated States (unless otherwise indicated, for every British Columbia V6Z 3C2 (CA). SINGHAL, Anupam; kind of regional protection available): ARIPO (BW, GH, [Continued on nextpage] (54) Title: MICROFLUIDIC DEVICES AND METHODS FOR USE THEREOF IN MULTICELLULAR ASSAYS OF SECRE TION Figure 2 3 < (57) Abstract: Methods and devices are provided herein for identifying a cell population comprising an effector cell that exerts an extracellular effect. In one embodiment the method comprises retaimng in a microreactor a cell population comprising one or more effector cells, wherein the contents of the microreactor further comprise a readout particle population comprising one or more o readout particles, incubating the cell population and the readout particle population within the microreactor, assaying the cell popu - lation for the presence of the extracellular effect, wherein the readout particle population or subpopulation thereof provides a direct or indirect readout of the extracellular effect, and determining, based on the results of the assaying step, whether one or more effect o or cells within the cell population exerts the extracellular effect on the readout particle. If an extracellular effect is measured, the cell population is recovered for further analysis to determine the cell or cells responsible for the effect. w o 2014/153651 A9 1II III II II III I IIII II 1 1II III GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, (48) Date of publication of this corrected version: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 10 March 2016 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, (15) Information about Corrections: LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, see Notice of 10 March 2016 SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Previous Correction: GW, KM, ML, MR, NE, SN, TD, TG). see Notice of 6 November 2014 Published: M I CROFLU I DI C DEV I C ES A ND M ET HODS F O R USE T H EREOF I N M ULTI CEL L ULAR ASSAYS OF S ECRET I ON CROSS REFEREN E T O RELAT ED APPL CAT I ON [0001] This application claims priority from U.S. Provisional Application Serial No. 61/806,329, filed March 28, 2013, the disclosure of which is incorporated by reference in its entirety for all purposes. BAC KGROUND OF T H E I NV ENTI ON [0002] The cell is the fundamental unit of life and no two cells are identical. For example, differences in genotype, phenotype and/or morphological property can contribute to cellular heterogeneity. Indeed, "seemingly identical" clonal populations of cells have been shown to display phenotypic differences among cells within the population. Cellular differences exist across all levels of life, ranging from bacterial cells to partially differentiated cel ls (for example, adult stem and progen itor cells) to highly differentiated mammalian cells (for example, immune cells). Differences in cellular state, function and responses can arise from a variety of mechanisms including different histories, different differentiation states, epigenetic variations, cell cycle effects, stochastic variations, differences in genomic sequence, gene expression, protein expression and differing cell interaction effects. [0003] Conventional bulk cellular analyses, including measurements of expressed proteins or RNA, are performed by averaging very large numbers of cells, typically greater than 1000 cells per individual assay). This averaging of a cellular population masks the heterogeneity that exists within a cell population and obscures the underlying biological features of the individual cells within the population. There are many examples where such averaged measurements are inadequate. For example, measuring a cellular process in a cell population may be complicated by the responses of individual cells, which may be asynchronous, thus blurring the dynamics of the process. For example, the presence of dominant, yet phenotypically distinct subpopulations of cells can result in a population measurement that poorly reflects the internal states of the majority of cells in the population. See, e.g., Altschuler and Wu. (20 10). CellW, pp. 559-563. [0004] Existing methods for isolating populations of unique cell types are often limited in the purity of the population that is achievable. For example, enriched populations of primary multipotent stem cells rarely achieve better than 50% functional purity and are often well below 10 % pure, so that the molecular signatures of these cells are obscured by large, and often overwhelming contamination from other cell types. Many cell types interact with each other, both through direct contact and through secreted factors, to promote survival, death, differentiation or some other function, and these interactions are difficult to isolate and study in a mixture comprising a large number of cells. Additionally, cells may have differences in their genomic sequences and/or cellular state that result in different levels or types of expressed mRNA or proteins. If analyzed in a bulk population, the particular cell with a unique cellular state or having the expressed mRNA or protein of interest, although of high value for industrial purposes, is very difficult or impossible to isolate from the population. [0005] To overcome the deficiencies of bulk population cell analysis, single cell assay platforms have been developed. For example, microfluidic devices have been used to study single cells in the past (Lecault et a/. (20 12). Curr. Opin. Chem. Biol. 16, pp. 381-390). Ma et a/. (Nat Med, 17, pp. 738-743 (201 1)) applied a single cell barcode chip to simultaneously measure multiple cytokines (e.g., IL- 10, TNF- β, IFN-γ ) from human macrophages and cytotoxic T lymphocytes (CTLs) obtained from both healthy donors and a metastatic melanoma patient. Microfabricated chamber arrays have also been used to screen and select B cells secreting antigen-specific antibodies from both immunized humans and mice (Story et a/. (2009). Proc. Natl. Acad. Sci. U.S.A. 105, pp. 17902- 17907; Jin et a/. (2009). Nat. Med. 15, pp. 1088- 1092). In this approach, single B cells were arrayed on a surface containing tens of thousands of microfabricated wells (-1 0- 100 µιη deep), where the well surfaces were functionalized with capture antibodies. After incubation of cells on the well surfaces for less than 3 hours, the surfaces were washed with fluorescently labeled antigen and scanned in order to identify antigen-specific B cells. These cells were then manually recovered from the arrays by a microcapillary in order to amplify, sequence, and clone the antibody-encoding genes from these cells. [0006] Two-phase microfluidic devices have also been applied to the analysis of secreted proteins from single immune cells by encapsulating them in sub-nanoliter aqueous droplets separated by a stream of oil (Konry et a/. (20 11). Biosens. Bioelectron. 26, pp. 2702-27 10). These droplets can be analyzed in a flow-through format similar to FACS, and thus provide an opportunity for ultra-high throughput detection of secreted proteins from single cells. Water-in-oil emulsions have also been used to study cellular paracrine signaling by co- encapsulating cells in microfluidic-generated agarose beads (Tumarkin et at (201 1). Integr. Biol.
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