Systems and methods for biodosimetry with biochip using gene expression signatures

• US 9,255,348 B2
• Filed: 08/24/2007
• Issued: 02/09/2016
• Est. Priority Date: 08/25/2006
• Status: Expired due to Fees

• Current Assignee: Trustees Of Columbia University In The City Of New York (Columbia University), Arizona Board of Regents (University of Arizona)
• Original Assignee: Trustees Of Columbia University In The City Of New York (Columbia University)
• Inventors: Zenhausern, Frederic, Orozco, Christine, Richards, Mark, Yamashiro, Carl, Amundson, Sally A., Lenigk, Ralf, Bittner, Michael L., Balagurunathan, Yoganand
• Primary Examiner(s): Beisner, William H
• Application Number:
  US12/438,944
• Publication Number:
  US 20100144558A1
• Time in Patent Office: 3,091 Days
• Field of Search: 435/287.2, 435/288.5
• US Class Current: 1/1
• 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. A portable biodosimetry device for detecting radiation exposure, comprising:

a microfluidic biochip comprising;

a biological sample collection channel module;

an oligonucleotide extraction biochannel module;

a hybridization channel module;

a plurality of fluidic actuators;

a pump, wherein the pump controls a fluid flow in at least one of the biological sample collection module, the oligonucleotide extraction biochannel module, or the hybridization channel module;

a power source; and

a microprocessor coupled to the power source, wherein the microprocessor controls activation of at least one module of the microfluidic biochip;

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 channel module, the oligonucleotide extraction biochannel module, and the hybridization channel module are fluidically coupled and wherein the plurality of fluidic actuators are each individually controlled by the microprocessor.

2. The device of claim 1 wherein the biological sample collection channel module, the oligonucleotide extraction biochannel module, and the hybridization channel module are operably and detachably coupled to the portable biodosimetry device.

3. The device of claim 2 wherein the biological sample collection channel module, the oligonucleotide extraction channel module, and the hybridization channel module are comprised in a cartridge and the cartridge is operably and detachably coupled to the portable biodosimetry device.

4. The device of claim 1 further comprising a reagent storage compartment module operably coupled to the portable biodosimetry device.

5. The device of claim 4 wherein the reagent storage compartment 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 compartment module.

6. The device of claim 1 further comprising a hybridization detector operably coupled to the portable biodosimetry device.

7. The device of claim 1 wherein the microfluidic biochip is a cyclo-olefinic co-polymer biochannel chip.

8. The device of claim 1 wherein the microfluidic biochip comprises a thermally actuated paraffin-based microvalve located in at least one of the biological sample collection channel module, the oligonucleotide extraction biochannel module, and the hybridization channel module.

9. The device of claim 1 wherein the biological sample collection channel module collects a blood sample from a mammalian subject.

10. The device of claim 1 wherein the biological sample collection channel module comprises at least one of a needle, a microneedle, a lasette, a capillary-force collection system, and a channel, a sample chamber, and a pump.

11. The device of claim 1 wherein the oligonucleotide extraction biochannel module extracts RNA from a biological sample.

12. The device of claim 1 wherein the oligonucleotide extraction biochannel 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, and (v) a magnetic separation system.

13. The device of claim 1 wherein the oligonucleotides of the array are immobilized with a 3-dimensional amino-reactive gel-coating of the hybridization channel module.

14. The device of claim 1 wherein the hybridization channel module comprises an electrochemical or thermopneumatic liquid pump for fluidically transporting a hybridization solution across the oligonucleotide array.

15. The device of claim 14 wherein detecting hybridization occurs in real-time.

16. The device of claim 1 wherein the oligonucleotide array is at least one of a printed low-density oligonucleotide microarray and a cDNA microarray.

17. The device of claim 1 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.

18. The device of claim 1 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, BCO22205, BCO23989, BCO39097, BC045174, BCO53363, 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, E124, 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, F1135348, FLJ36031, F1139575, FLJ40542, F1145445, FLRT2, FNDC3B, FOS, FOS, FPR1, FPRL1, FTSJ2, FXYD2, GOS2, 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, HIST1H2B0, HLA-DOA, HLA-DOB, HNRPC, HSF4, IBRDC3, IER5, IER5L, IFIH1, IFIT2, IFITM1, IGHA1, IGHM, IGHV1-69, IL1ORB, 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, LOCI 58830, 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, TP53I3, 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.

19. The device of claim 18 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, ACSL1, ADM, AK092942, AK097080, AK123446, AK123722, APOBEC3B, AQP9, ASB2, ASCC3, BAX, BBC3, BC068044, BCNP1, BE646426, B1828537, BLK, BLR1, C11orf54, C12orf5, C20orf24, C9orf102, CAMK2D, CARD6, CD19, CD24, CD79B, CDKN1A, CEBPB, CEBPE, CLEC4E, CR597075, CR627148, CSPP1, CXCL1, CXCL16, DDB2, DHRS7B, DKFZp434F142, ECE1, EGLN1, ENST00000323595, ENST00000355807, FAM113B, FBXO22, FDXR, FFAR2, FKSG44, FLJ11259, FLJ36031, F1139575, FLJ40542, F1145445, FOS, FPR1, FPRL1, FTSJ2, GOS2, GABRA3, GADD45A, GPR109A, GPR109B, HIP1R, HIST1H2BE, HIST1H2BF, HIST1H2B0, HLA-DOA, HLA-DOB, IBRDC3, IER5, IER5, IGHA1, IGHM, IL1ORB, IL1B, URN, IRAK3, ISG20L1, ITGA6, ITGAX, KCNJ15, KCNJ2, KIAA0963, KREMEN1, LOC283663, LOC339287, LOC349114, LOC399744, LOC401357, LRG1, MGC40499, MGC5370, MOBK1B, MXD1, NALP12, NEU1, 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, TP5313, TP53INP1, TREM1, TRIAP1, TRIM22, TRPM6, UPB1, WDFY3, XM_—

499519, XPC, and ZNF2.

20. The device of claim 18 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, BCO22205, BCO23989, BCO39097, BC045174, BCO53363, 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, E124, EIF2C3, ENST00000253048, ENST00000257897, ENST00000261569, ENST00000288074, ENST00000291567, ENST00000301749, ENST00000360329, EOMES, FAM105A, FAM62A, FAS, FASLG, FBS1, FBXL16, FBXO22, FBXW7, FCGBP, FCHO1, FCHSD2, FCRL2, FDXR, FHL2, FLIT, FLJ11259, FLJ20186, FLJ20647, F1135348, 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, LOCI58830, 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.

21. The device of claim 18 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.

22. The device of claim 1 further comprising at least one of a display for communicating information to the user, and an input and/or output connection for data transfer.

23. The device of claim 1 wherein the biological sample collection channel module comprises a means for collecting a biological sample from a mammalian subject.

24. The device of claim 1 wherein the hybridization channel module comprises a means for detecting hybridization of oligonucleotides of a biological sample with oligonucleotides of the oligonucleotide array.

25. The device of claim 1 wherein the control module further comprises a means for user input.

26. The device of claim 1 wherein each of the plurality of fluidic actuators has a heating element and a thermostat for controlling heating power.

27. The device of claim 26 wherein heat is transferred from at least one of the plurality of fluidic actuators to the materials through the placement and contact of the materials.

28. The device of claim 1 wherein each of the plurality of fluidic actuators may be individually energized.

29. The device of claim 1 wherein the plurality of fluidic actuators are self-controlled by an enable signal which does not power the fluidic actuator or influence temperature control.

30. The device of claim 1 wherein the plurality of fluidic actuators comprise a diode.

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

a microfluidic biochip comprising;

a biological sample collection channel module;

an oligonucleotide extraction biochannel module;

a hybridization channel module;

a fluidic actuator;

a pump, wherein the pump controls a fluid flow in at least one of the biological sample collection module, the oligonucleotide extraction biochannel module, or the hybridization channel module;

a power source; and

a processor, wherein the processor controls activation of at least one module of the microfluidic biochip;

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 channel module, the oligonucleotide extraction biochannel module, and the hybridization channel module are fluidically coupled, and wherein the fluidic actuator is controlled by the processor.