SYSTEMS AND METHODS FOR BIODOSIMETRY WITH BIOCHIP USING GENE EXPRESSION SIGNATURES

• US 20100144558A1
• Filed: 08/24/2007
• Published: 06/10/2010
• Est. Priority Date: 08/25/2006
• Status: Active Grant

• Current Assignee: Trustees Of Columbia University In The City Of New York (Columbia University), Arizona Board of Regents (University of Arizona)
• Original Assignee: Arizona Board of Regents (University of Arizona)
• Inventors: Lenigk, Ralf, Richards, Mark, Balagurunathan, Yoganand, Yamashiro, Carl, Orozco, Christine, Amundson, Sally A., Bittner, Michael L., Zenhausern, Frederic
• Granted Patent: US 9,255,348 B2
• Time in Patent Office: Days
• US Class Current: 506/39
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502723 characterised by venting arrangements
• CPC Class Codes: B01L 3/502738 characterised by integrated valves microvalves F16K99/0001
• CPC Class Codes: C40B 30/10 by measuring physical properties, e.g. mass
• CPC Class Codes: C40B 60/12 for screening libraries
• CPC Class Codes: G01T 1/02 Dosimeters G01T1/15 takes precedence

Abstract

Exposure to ionizing radiation can produce a well-defined dose dependent signature in terms of changes in gene expression. In approaches and devices described herein, such a signature can be used to generate and use a self-contained radiation biodosimeter device, based on, for example, a blood finger stick. Various aspects of the invention are directed to biodosimetry with a fully integrated biochip using gene expression signatures.

Claims

1-56. -56. (canceled)

57. A portable biodosimetry device for detecting radiation exposure, comprising:

a microfluidic biochip comprising;

a biological sample collection module;

an oligonucleotide extraction module;

a hybridization channel module;

a power module; and

a control module;

wherein,

the hybridization channel module comprises an oligonucleotide array;

the oligonucleotide array of the hybridization channel module comprises a plurality of oligonucleotides, where an oligonucleotide of the array will hybridize under stringent conditions to a gene expression product of a radiation responsive gene; and

the biological sample collection module, the oligonucleotide extraction module, and the hybridization channel module are fluidically coupled.

58. The device of claim 57 wherein the biological sample collection module, the oligonucleotide extraction module, and the hybridization channel module are operably and detachably coupled to the portable biodosimetry device.

59. The device of claim 58 wherein the biological sample collection module, the oligonucleotide extraction module, and the hybridization channel module are comprised in a cartridge and the cartridge is operably and detachably coupled to the portable biodosimetry device.

60. The device of claim 57 further comprising a reagent storage module.

62. The device of claim 60 wherein the reagent storage module comprises at least one of (i) aqueous reagents, (ii) a dry reagent and a means for solubilizing the dry reagent and (iii) a reagent pouch operably and detachably coupled to the reagent storage module.

65. The device of claim 57 further comprising a hybridization detection module.

67. The device of claim 57 wherein the microfluidic biochip is a cyclo-olefinic co-polymer biochannel chip.

68. The device of claim 57 wherein the microfluidic biochip comprises a thermally actuated paraffin-based microvalve.

70. The device of claim 57 wherein the biological sample collection module collects a blood sample from a mammalian subject.

72. The device of claim 57 wherein the biological sample collection module comprises at least one of (i) a means for collecting a biological sample from a mammalian subject, (ii) a needle, (iii) a microneedle, (iv) a lasette, (v) a capillary-force collection system, and (vi) a channel, a sample chamber, and a pump.

76. The device of claim 57 wherein the oligonucleotide extraction module extracts RNA from a biological sample.

77. The device of claim 57 wherein the oligonucleotide extraction module comprises at least one of (i) a means for cell capture, cell concentration, cell purification, and/or cell lysis, (ii) a means for isolating oligonucleotides of the biological sample, (iii) a means for amplifying the isolated oligonucleotides of the biological sample, (iv) an immunogenic separation system, (v) a magnetic separation system.

84. The device of claim 57 wherein the oligonucleotides of the array are immobilized with a 3-dimensional amino-reactive gel-coating of the hybridization channel module.

85. The device of claim 57 wherein the hybridization channel module comprises at least one of (i) an electrochemical or thermopneumatic liquid pump for fluidically transporting a hybridization solution across the oligonucleotide array and (ii) a means for detecting hybridization of oligonucleotides of a biological sample with oligonucleotides of the oligonucleotide array.

87. The device of claim 85 wherein detecting hybridization occurs in real-time.

88. The device of claim 57 wherein the oligonucleotide array is at least one of a printed low-density oligonucleotide microarray and a cDNA microarray.

90. The device of claim 57 wherein the oligonucleotide array comprises at least one of a glass non-porous solid support, a non-glass non-porous solid support, a silicon-based solid support produced by photolithographic masking, and a cyclo-olefinic copolymer solid support.

96. The device of claim 57 wherein the plurality of oligonucleotides of the oligonucleotide array comprise oligonucleotides that will hybridize under stringent conditions to gene expression products of radiation responsive genes selected from the group consisting of:

A_—

23_P255111, A_—

24_P127462, A_—

24_P15083, A_—

24_P585004, A_—

32_P140501, A_—

32_P198223, AA516273, ABTB2, ACSL1, ACTA2, ACTN1, ADA, ADM, AES, AF289562, AGRN, AK021751, AK024870, AK024898, AK055915, AK056245, AK092083, AK092875, AK092942, AK097080, AK123333, AK123446, AK123722, AK2, ALDH18A1, ALS2CR13, ANKRA2, ANXA11, ANXA2P1, ANXA4, AP1S2, APBA3, APBB1, APBB3, APOBEC3B, APOBEC3C, APOBEC3F, AQP9, ARHGEF3, ASB2, ASCC3, ASTN2, ATP2A3, ATP8B2, ATP9A, B3GNTL1, BANK1, BAX, BAZ1A, BBC3, BC014395, BC018597, BC022205, BC023989, BC039097, BC045174, BC053363, BC068044, BCL11A, BCL3, BCNP1, BE646426, BF511442, B1828537, BIRC3, BLK, BLR1, BM926530, BTG3, BU540282, BU595528, C11orf21, C11orf24, C11orf54, C12orf42, C12orf45, C12orf5, C14orf151, C16orf30, C17orf49, C19orf36, C1orf24, C1orf57, C20orf24, C3orf26, C8orf38, C9orf102, C9orf127, CA4, CAMK1D, CAMK2D, CARD6, CASP7, CCDC49, CCNB2, CCNG1, CCR7, CD19, CD24, CD40, CD40, CD511705, CD52, CD79A, CD79B, CD83, CD93, CDC25B, CDC42EP2, CDCA7L, CDKN1A, CDKN1A, CDKN1C, CEBPB, CEBPE, CENTB1, CENTG3, CHES1, CHRNA10, CIC, CLEC4E, CLIC3, CLIC4, CN271858, CNOT7, COL27A1, COL9A3, COMTD1, CR595983, CR597075, CR603437, CR616003, CR621698, CR623273, CR627148, CRLF3, CSPP1, CSPP1, CTAGE4, CXCL1, CXCL11, CXCL16, CXCL3, CXCR3, CYLD, DAPK2, DCP1B, DDB2, DDB2, DEF6, DEFA4, DHRS7, DHRS7B, DKFZp434F142, DPEP2, DZIP3, EBI3, EBPL, ECE1, ECE1, EFNB1, EGLN1, EHD1, EI24, EIF2C3, ENAM IGJ, ENST00000253048, ENST00000257897, ENST00000261569, ENST00000288074, ENST00000291567, ENST00000301749, ENST00000323595, ENST00000355807, ENST00000360329, EOMES, FAM105A, FAM113B, FAM62A, FAS, FASLG, FBS1, FBXL16, FBXO22, FBXO22, FBXW7, FCGBP, FCGR1A, FCHO1, FCHSD2, FCRL2, FDXR, FFAR2, FGL2, FHL2, FKSG44, FLII, FLJ11259, FLJ20186, FLJ20647, FLJ35348, FLJ36031, FLJ39575, FLJ40542, FLJ45445, FLRT2, FNDC3B, FOS, FOS, FPR1, FPRL1, FTSJ2, FXYD2, G0S2, GABRA3, GADD45A, GADD45A, GAMT, GCH1, GDF15, GHRL, GLIPR1, GLS2, GNG7, GNG8, GPR109A, GPR109B, GPR160, GPR18, GPR84, GRIPAP1, GRPEL2, GSK3A, GSS, GTF2I, H2-ALPHA, HEBP1, HIP1R, HIST1H2BE, HIST1H2BF, HIST1H2BO, HLA-DOA, HLA-DOB, HNRPC, HSF4, IBRDC3, IER5, IER5L, IFIH1, IFIT2, IFITM1, IGHA1, IGHM, IGHV1-69, IL10RB, IL1B, IL1RN, IL21R, IL8, IRAK3, ISG20L1, ITGA6, ITGAX, JAK3, JMJD2A, KCNJ15, KCNJ2, KCNN4, KCTD12, KENAE, KIAA0284, KIAA0963, KIF2, KIR2DS4, KLF2, KREMEN1, LAMP3, LBR, LEPROTL1, LHPP, LIF, LIG1, LILRA2, LILRB3, LIMK2, LMBRD1, LMNA, LMNB2, LOC158830, LOC201229, LOC256021, LOC283663, LOC284184, LOC339287, LOC349114, LOC399744, LOC401357, LOC649791, LRG1, LY9, MAMDC4, MANSC1, MAP4K2, MAP4K4, MAPKAPK2, MARCKS, MDM2, MDS025, METTL7A, MGAT3, MGC16207, MGC17624, MGC2463, MGC40499, MGC5370, MGST1, MLX, MOBK1B, MPEG1, MPP1, MR1, MXD1, MYC, MYOM2, N28017, NALP12, NBN, NBPF15, NEBL, NEU1, NFKB1, NFKB2, NPAL2, NRBP1, OPLAH, OSBPL3, P2RX5, PACSIN1, PCNA, PDLIM5, PELO, PGCP, PHLDA3, PHPT1, PIK3CD, PKLR, PLAGL2, PLAUR, PLK2, PLK3, PLXNA1, PLXNA2, PLXNB2, PMAIP1, POLH, POPDC2, POU2AF1, PPM1D, PRG1, PRKAB1, PRMT7, PSD4, PTGIR, PTP4A1, PTPN7, PTPNS1, PTPRCAP, PXN, PYCRL, PYGL, RAFTLIN, RALGPS2, RARRES3, RASA3, RASGEF1A, RASGRP2, RBM14, RBPSUH, RELB, RGS12, RGS14, RGS16, RGS3, RNF24, RP11-298P3.3, RP4-742C19.3, RPS19, RPS27L, RRAD, RRAGD, RUFY3, SAC3D1, SACS, SCN1B, SDCBP, SDF2, SELPLG, SEMA4C, SERPINB1, SERPING1, SERTAD1, SESN1, SESN2, SGK, SH2D1B, SIGIRR, SIGLEC9, SIRPB2, SIT1, SLA, SLBP, SLC11A1, SLC13A2, SLC25A15, SLC27A1, SLC27A3, SLC35F2, SLC4A11, SLC7A6, SLCO4A1, SOCS1, SOD2, SPIB, SPPL2A, SRA1, SRPK2, SSPN, STAT1, SYNGR2, TACC3, TAPBP, TBC1D1, TBXAS1, TCF2, TCF3, TCF4, TCF7, TCL1A, TESK2, TFE3, THC2292160, THC2305303, THC2340838, THC2342491, THC2347909, THC2364440, THC2380864, THC2397697, THC2429167, THC2439183, THC2442819, TKT, TM7SF3, TM9SF4, TMC8, TMEM30A, TMEM68, TNF, TNFAIP2, TNFAIP3, TNFAIP6, TNFRSF10B, TNFRSF12A, TNFRSF18, TNFSF10, TNFSF12, TNFSF4, TNFSF7, TNIP1, TP53AP1, TP5313, TP53INP1, TRAF4, TRAF5, TREM1, TRIAP1, TRIB2, TRIM22, TRIM32, TRPM6, TSC22D3, TSPAN32, TTC21A, TYMS, UBE2H, UBE2L6, UNQ501, UPB1, UROD, VAT1, VSIG4, WARS, WDFY3, WIG1, XM_—

499519, XPC, YWHAB, YWHAZ, ZC3H12A, ZC3H7A, ZFAND2B, ZNF195, ZNF25, ZNF337, ZNF541, ZNF625, ZNF79, ZNF92, ZUBR1, and α

H2AX.

97. The device of claim 96 wherein the plurality of oligonucleotides of the oligonucleotide array comprise oligonucleotides that will hybridize under stringent conditions to gene expression products of radiation responsive genes selected from the group consisting of:

A_—

23_P255111, A_—

24_P127462, A_—

24_P127462, A_—

24_P15083, A_—

24_P15083, A_—

24_P585004, A_—

32_P140501, A_—

32_P198223, AA516273, ACSL1, ADM, AK092942, AK092942, AK097080, AK097080, AK123446, AK123722, APOBEC3B, AQP9, ASB2, ASCC3, ASCC3, ASCC3, BAX, BAX, BAX, BAX, BBC3, BBC3, BBC3, BBC3, BC068044, BCNP1, BE646426, BE646426, B1828537, BLK, BLR1, C11orf54, C12orf5, C12orf5, C20orf24, C20orf24, C9orf102, CAMK2D, CARD6, CD19, CD24, CD79B, CDKN1A, CDKN1A, CEBPB, CEBPE, CLEC4E, CR597075, CR627148, CSPP1, CSPP1, CXCL1, CXCL16, DDB2, DDB2, DHRS7B, DKFZp434F142, ECE1, EGLN1, ENST00000323595, ENST00000355807, ENST00000355807, FAM113B, FBXO22, FBXO22, FDXR, FDXR, FFAR2, FKSG44, FLJ11259, FLJ11259, FLJ36031, FLJ39575, FLJ40542, FLJ45445, FOS, FPR1, FPRL1, FTSJ2, G0S2, GABRA3, GADD45A, GADD45A, GPR109A, GPR109B, HIP1R, HIST1H2BE, HIST1H2BF, HIST1H2BO, HLA-DOA, HLA-DOB, IBRDC3, IER5, IER5, IGHA1, IGHM, IL10RB, IL10RB, IL1B, IL1RN, IRAK3, ISG20L1, ISG20L1, ITGA6, ITGAX, ITGAX, KCNJ15, KCNJ2, KIAA0963, KREMEN1, LOC283663, LOC339287, LOC349114, LOC349114, LOC349114, LOC399744, LOC399744, LOC401357, LOC401357, LRG1, MGC40499, MGC5370, MOBK1B, MOBK1B, MXD1, NALP12, NEU1, OPLAH, OPLAH, P2RX5, PCNA, PHLDA3, PHPT1, PLAUR, PLK2, PLK3, POU2AF1, PPM1D, PRG1, PTP4A1, PTPNS1, PXN, RNF24, RPS27L, RRAGD, SDCBP, SDF2, SEMA4C, SERPINB1, SGK, SIGLEC9, SIRPB2, SLA, SPIB, TCF7, TCL1A, THC2340838, THC2397697, THC2429167, THC2439183, TNFAIP6, TNFRSF10B, TNFSF7, TP53I3, TP53INP1, TREM1, TRIAP1, TRIM22, TRPM6, UPB1, WDFY3, XM_—

499519, XPC, XPC, and ZNF2.

98. The device of claim 96 wherein the plurality of oligonucleotides of the oligonucleotide array comprise oligonucleotides that will hybridize under stringent conditions to gene expression products of radiation responsive genes selected from the group consisting of:

ABTB2, ACTA2, ACTN1, ADA, AES, AF289562, AGRN, AK021751, AK024870, AK024898, AK055915, AK056245, AK092083, AK092875, AK123333, AK123722, AK2, ALDH18A1, ALS2CR13, ANKRA2, ANXA11, ANXA2P1, ANXA4, AP1S2, APBA3, APBB1, APBB3, APOBEC3C, APOBEC3F, ARHGEF3, ASCC3, ASTN2, ATP2A3, ATP8B2, ATP9A, B3GNTL1, BANK1, BAX, BAZ1A, BBC3, BC014395, BC018597, BC022205, BC023989, BC039097, BC045174, BC053363, BCL11A, BCL3, BCNP1, BE646426, BF511442, BIRC3, BM926530, BTG3, BU540282, BU595528, C11orf21, C11orf24, C12orf42, C12orf45, C12orf5, C14orf151, C16orf30, C17orf49, C19orf36, C1orf24, C1orf57, C3orf26, C8orf38, C9orf127, CA4, CAMK1D, CASP7, CCDC49, CCNG1, CCPG1, CCR7, CD40, CD511705, CD52, CD79A, CD83, CD93, CDC25B, CDC42EP2, CDCA7L, CDKN1A, CDKN1C, CENTB1, CENTG3, CHES1, CHRNA10, CIC, CLIC3, CLIC4, CN271858, CNOT7, COL27A1, COL9A3, COMTD1, CR595983, CR603437, CR616003, CR621698, CR623273, CRLF3, CTAGE4, CXCR3, CYLD, DAPK2, DCP1B, DDB2, DEF6, DHRS7, DPEP2, DZIP3, EBI3, EBPL, ECE1, EFNB1, EHD1, EI24, EIF2C3, ENST00000253048, ENST00000257897, ENST00000261569, ENST00000288074, ENST00000291567, ENST00000301749, ENST00000360329, EOMES, FAM105A, FAM62A, FAS, FASLG, FBS1, FBXL16, FBXO22, FBXW7, FCGBP, FCHO1, FCHSD2, FCRL2, FDXR, FHL2, FLII, FLJ11259, FLJ20186, FLJ20647, FLJ35348, FLJ40542, FNDC3B, FTSJ2, FXYD2, GADD45A, GAMT, GDF15, GHRL, GLIPR1, GLS2, GNG7, GNG8, GPR160, GPR18, GPR84, GRIPAP1, GRPEL2, GSK3A, GSS, GTF2I, H2-ALPHA, HEBP1, HNRPC, IER5, IER5L, IFIH1, IFITM1, IGHM, IGHV1-69, IL21R, ISG20L1, JAK3, JMJD2A, KCNJ2, KCNN4, KCTD12, KENAE, KIAA0284, KIR2DS4, KLF2, LAMP3, LBR, LEPROTL1, LHPP, LIF, LIG1, LIMK2, LMBRD1, LMNA, LMNB2, LOC158830, LOC201229, LOC256021, LOC284184, LOC649791, LY9, MAMDC4, MANSC1, MAP4K2, MAP4K4, MAPKAPK2, MARCKS, MDM2, MDS025, METTL7A, MGAT3, MGC16207, MGC17624, MGC2463, MGC5370, MGST1, MLX, MPEG1, MPP1, MR1, MYC, MYOM2, N28017, NBN, NBPF15, NFKB1, NFKB2, NPAL2, NRBP1, OSBPL3, P2RX5, PACSIN1, PCNA, PDLIM5, PELO, PGCP, PHLDA3, PHPT1, PIK3CD, PLAGL2, PLK2, PLK3, PLXNA1, PLXNA2, PLXNB2, PMAIP1, POLH, POPDC2, PPM1D, PRKAB1, PRMT7, PSD4, PTGIR, PTP4A1, PTPN7, PTPRCAP, PYCRL, PYGL, RAFTLIN, RALGPS2, RASA3, RASGEF1A, RASGRP2, RBM14, RBPSUH, RELB, RGS12, RGS14, RGS16, RGS3, RP11, 298P3.3, RP4-742C19.3, RPS19, RPS27L, RRAD, RUFY3, SAC3D1, SACS, SELPLG, SERPINB1, SERTAD1, SESN1, SESN2, SH2D1B, SIGIRR, SIT1, SLBP, SLBP, SLC11A1, SLC13A2, SLC25A15, SLC27A1, SLC27A3, SLC35F2, SLC4A11, SLC7A6, SLCO4A1, SOCS1, SOD2, SPPL2A, SRA1, SRPK2, SSPN, SYNGR2, TACC3, TAPBP, TBC1D1, TBXAS1, TCF3, TCF4, TCL1A, TESK2, TFE3, THC2292160, THC2305303, THC2340838, THC2342491, THC2347909, THC2364440, THC2380864, THC2397697, THC2429167, THC2439183, THC2442819, TKT, TM7SF3, TM9SF4, TMC8, TMEM30A, TMEM68, TNFAIP2, TNFAIP3, TNFAIP6, TNFRSF10B, TNFRSF12A, TNFRSF18, TNFSF12, TNFSF4, TNFSF7, TNIP1, TP53AP1, TRAF4, TRAF5, TRIAP1, TRIB2, TRIM22, TRIM32, TSC22D3, TSPAN32, TTC21A, TYMS, UBE2H, UNQ501, UROD, VAT1, VSIG4, WIG1, XPC, YWHAB, YWHAZ, ZC3H12A, ZC3H7A, ZFAND2B, ZNF195, ZNF337, ZNF541, ZNF625, ZNF79, ZNF92, and ZUBR1.

99. The device of claim 96 wherein the plurality of oligonucleotides of the oligonucleotide array comprise oligonucleotides that will hybridize under stringent conditions to gene expression products of radiation responsive genes selected from the group consisting of:

CDKN1A, CD40, NEBL, GADD45A, CXCL11, HSF4, CXCL3, FLRT2, TNFSF10, IL8, TNF, ENAM IGJ, XPC, KIF2, SERPING1, DDB2, IFIT2, LILRB3, GCH1, FOS, CCNB2, LILRA2, RARRES3, SCN1B, UBE2L6, FCGR1A, FGL2, VSIG4, PKLR, STAT1, WARS, TCF2, DEFA4, and α

H2AX.

100. The device of claim 57 wherein the control module comprises at least one of a means for user input, a display for communicating information to the user, and an input and/or output connection for data transfer.

61. (canceled)

63-64. -64. (canceled)

66. (canceled)

69. (canceled)

71. (canceled)

73-75. -75. (canceled)

78-83. -83. (canceled)

86. (canceled)

89. (canceled)

91-95. -95. (canceled)

101-104. -104. (canceled)