IP Library › Granted Patent US 12,258,613

Granted Patent B2

US 12,258,613 · App. 16/492,588 · Granted Mar 25, 2025

Pairing antigen specificity of a T cell with T cell receptor sequences

Inventors: James R. Heath (Pasadena, CA); Songming Peng (San Mateo, CA); Alphonsus Hon-Chung Ng (Pasadena, CA)

Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY

C12Q1/6804 B01L3/502761 C12N15/1037 C12N15/1055 C12N15/1065 B01L2200/0652 B01L2300/0864 B01L2400/02

View Patent ↗

Loading inventors, assignments & file history…

Monitor This Case

Get email alerts when status or documents change.

Order Certified Copies

Most orders are placed with the USPTO same day — all within 24 business hours.

Order via The Patent Place →

Pre-filled with this patent's details

Quick Facts

Patent No.: US 12,258,613
App. No.: 16/492,588
Granted: Mar 25, 2025
Kind: B2

External Links

USPTO Patent Center↗ Full Patent PDF↗

Abstract

Compositions and methods for identifying antigen-specific T cells, including determining paired T cell receptor sequences for a specific antigen, are described. Compositions and methods for identifying neoantigen-specific T cells are also described. Microfluidic devices useful for identifying antigen-specific T cells, and methods of using the same, are also described.

Claims (225)

1. A composition comprising:

a) a major histocompatibility complex (MHC) display moiety comprising at least one antigenic peptide;

b) a first single-stranded polynucleotide sequence comprising in a 5′ to 3′ orientation:

1) a first universal target sequence;

2) a unique, defined barcode sequence, wherein the defined barcode sequence is operably associated with the identity of the antigenic peptide; and

3) a T cell receptor (TCR) a primer sequence, wherein the TCRα primer sequence is complementary to a TCRα RNA transcript; and

c) a second single-stranded polynucleotide sequence comprising in a 5′ to 3′ orientation:

1) the first universal target sequence;

2) the defined barcode sequence; and

3) a TCRβ primer sequence, wherein the TCRβ primer sequence is complementary to a TCRβ RNA transcript; and

d) a first particle; and

wherein the MHC display moiety, the first single-stranded polynucleotide sequence, and the second single-stranded polynucleotide sequence are independently attached to the first particle.

2. A composition comprising:

a) an MHC display moiety comprising:

a streptavidin core bound to four copies of a biotinylated MHC; and

four copies of at least one antigenic peptide, wherein the at least one antigenic peptide is a neoantigen, wherein each copy is independently bound to one of the biotinylated MHCs; and

a first polynucleotide hybridization domain;

b) a first single-stranded polynucleotide sequence comprising in a 5′ to 3′ orientation:

1) a biotin; and

2) a photocleaveable group;

3) a first universal target sequence;

4) a unique, defined barcode sequence, wherein the defined barcode sequence is operably associated with the identity of the neoantigen; and

5) a T cell receptor (TCR) a primer sequence, wherein the TCRα primer sequence is complementary to a TCRα RNA transcript; and

c) a second single-stranded polynucleotide sequence comprising in a 5′ to 3′ orientation:

1) a biotin;

2) a photocleaveable group;

3) the first universal target sequence;

4) the defined barcode sequence; and

5) a TCRβ primer sequence, wherein the TCRβ primer sequence is complementary to a TCRβ RNA transcript; and

d) a first particle that is a magnetic nanoparticle comprising:

streptavidin; and

a second polynucleotide hybridization domain complementary to the first polynucleotide hybridization domain,

wherein the MHC display moiety is attached to the at least one-magnetic nanoparticle by hybridization of the first and the second polynucleotide hybridization domains, and

wherein the first and the second single-stranded polynucleotide sequence are independently attached to the magnetic nanoparticle through a biotin-streptavidin interaction.

3. The composition of claim 1 or 2 , wherein the first universal target sequence is a polymerase chain reaction (PCR) primer target sequence.

4. The composition of claim 1 , wherein the first particle is selected from the group consisting of: a surface, a nanoparticle, a bead, and a polymer.

5. The composition of claim 4 , wherein the nanoparticle is a magnetic nanoparticle or a polystyrene nanoparticle.

6. The composition of claim 2 or 5 , wherein the magnetic nanoparticle comprises magnetic iron oxide.

7. The composition of claim 4 , wherein the first particle is the bead that is an agarose bead.

8. The composition of claim 1 or 2 , further comprising a fluorophore.

9. The composition of claim 8 , wherein the fluorophore is attached, with or without a linker, to the first particle.

10. The composition of claim 1 , wherein the first and the second single-stranded polynucleotide sequences are each independently and directly attached to the first particle.

11. The composition of claim 10 , wherein the first and the second single-stranded polynucleotide sequences each further comprise a cleavage moiety positioned between the first particle and the respective sequence.

12. The composition of claim 11 , wherein the cleavage moiety comprises a photocleavable group.

13. The composition of claim 2 or 12 , wherein the photocleavable group is cleavable by UV-light.

14. The composition of claim 2 or 12 , wherein the photocleavable group comprises the formula:

15. The composition of claim 1 , wherein the MHC display moiety is directly attached to the first particle.

16. The composition of claim 1 , wherein the first particle further comprises a first polynucleotide hybridization domain and the MHC display moiety further comprises a second polynucleotide hybridization domain.

17. The composition of claim 16 , wherein the first polynucleotide hybridization domain comprises the nucleotide sequence CTGAATCCTCGGGATGCCTA (SEQ ID NO: 8) and the second polynucleotide hybridization domain comprises the reverse complement TAGGCATCCCGAGGATTCAG (SEQ ID NO: 9).

18. The composition of claim 16 or 17 , wherein the MHC display moiety is attached to the first particle by hybridization of the first polynucleotide hybridization domain to the second polynucleotide hybridization domain.

19. The composition of claim 1 , wherein the first and the second single-stranded polynucleotide sequences further comprise an attachment moiety, and the first particle further comprises a complementary attachment moiety.

20. The composition of claim 19 , wherein the attachment moiety comprises biotin and the complementary attachment moiety comprises streptavidin, and wherein the first and the second single-stranded polynucleotide sequences are attached to the first particle through a biotin-streptavidin interaction.

21. The composition of claim 20 , wherein the streptavidin is a cysteine-modified streptavidin.

22. The composition of claim 19 , wherein the attachment moiety further comprises a fluorophore.

23. The composition of claim 19 , further comprising a cleavage moiety positioned between the attachment moiety and the first single-stranded polynucleotide sequence.

24. The composition of claim 19 , further comprising a cleavage moiety positioned between the attachment moiety and the second single-stranded polynucleotide sequence.

25. The composition of claim 1 or 2 , wherein the at least one antigenic peptide is selected from the group consisting of: a tumor antigen, a viral antigen, a phosphoantigen, a bacterial antigen, a microbial antigen, and combinations thereof.

26. The composition of claim 1 , wherein the at least one antigenic peptide is a neoantigen.

27. The composition of claim 2 or 26 , wherein the neoantigen is selected by analyzing tumor, viral, or bacterial sequencing data from a subject to identify one or more somatic mutations.

28. The composition of claim 27 , wherein the analyzing is performed using an in silico predictive algorithm.

29. The composition of claim 28 , wherein the predictive algorithm comprises an MHC binding algorithm to predict binding between the neoantigen and a MHC allele of the subject.

30. The composition of claim 29 , wherein the MHC display moiety is the MHC allele of the subject.

31. The composition of claim 1 or 2 , wherein the MHC display moiety comprises a mammalian MHC.

32. The composition of claim 31 , wherein the mammalian MHC comprises a human MHC.

33. The composition of claim 31 , wherein the mammalian MHC comprises a MHC class I molecule.

34. The composition of claim 33 , wherein the MHC class I molecule comprises a MHC molecule selected from the group consisting of: HLA-A, HLA-B, and HLA-C.

35. The composition of claim 33 , wherein the at least one antigenic peptide is 7-15, 7-10, 8-9, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acids in length.

36. The composition of claim 33 , wherein the at least one antigenic peptide is between 8-10 amino acids in length.

37. The composition of claim 31 , wherein the mammalian MHC comprises a MHC class II molecule.

38. The composition of claim 37 , wherein the MHC class II molecule comprises an MHC molecule selected from the group consisting of: HLA-DQ and HLA-DR.

39. The composition of claim 37 , wherein the at least one antigenic peptide is 11-30, 14-20, 15-18, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids in length.

40. The composition of claim 37 , wherein the at least one antigenic peptide is between 10 and 35, between 10 and 30, between 10 and 25, or between 10 and 20 amino acids in length.

41. The composition of claim 1 , wherein the MHC display moiety comprises a multimerized MHC.

42. The composition of claim 41 , wherein the multimerized MHC comprises a streptavidin core bound to multiple MHCs.

43. The composition of claim 42 , wherein the streptavidin core further comprises a fluorescent molecule.

44. The composition of claim 42 , wherein the streptavidin core is bound to four copies of biotinylated MHC.

45. The composition of claim 42 , wherein the streptavidin core is bound to three copies of biotinylated MHC.

46. The composition of claim 1 , wherein the MHC display moiety comprises a single chain trimer MHC.

47. The composition of claim 46 , wherein the single chain trimer comprises a disulfide trap.

48. The composition of claim 1 or 2 , wherein the first universal target sequence is between 10-50, between 15-40, between 15-35, between 15-30, between 20-40, between 25-40, or between 30-40 nucleotides in length.

49. The composition of claim 1 or 2 , wherein the first universal target sequence is between 25-35 nucleotides in length.

50. The composition of claim 1 or 2 , wherein the first universal target sequence is at least 15 nucleotides in length.

51. The composition of claim 1 or 2 , wherein the first universal target sequence comprises the sequence TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG (SEQ ID NO: 3).

52. The composition of claim 1 or 2 , wherein the defined barcode sequence is between 4-10 nucleotides in length.

53. The composition of claim 52 , wherein the defined barcode sequence is 6 nucleotides in length.

54. The composition of claim 52 , wherein the defined barcode sequence is 6 nucleotides in length.

55. The composition of claim 1 or 2 , wherein the TCRα primer sequence and the TCRβ primer sequence are between 10-50, between 15-40, between 15-35, between 15-30, between 15-25, between 15-20, or between 10-20 nucleotides in length.

56. The composition of claim 1 or 2 , wherein the TCRα RNA transcript sequence comprises a TCRα constant region sequence.

57. The composition of claim 56 , wherein the TCRα primer sequence comprises the nucleotide sequence TCTCTCAGCTGGTACACGGC (SEQ ID NO: 4).

58. The composition of claim 1 or 2 , wherein the TCRβ RNA transcript sequence comprises a TCRβ constant region sequence.

59. The composition of claim 58 , wherein the TCRβ primer sequence comprises the nucleotide sequence GATGGCTCAAACACAGCGACCTC (SEQ ID NO: 5).

60. The composition of claim 1 or 2 , wherein the TCRα RNA transcript and the TCRβ RNA transcript comprise mammalian transcripts.

61. The composition of claim 60 , wherein the mammalian transcripts comprise human transcripts.

62. The composition of claim 1 or 2 , wherein the first and the second single-stranded polynucleotide sequences each further comprise a random nucleotide sequence.

63. The composition of claim 62 , wherein each of the random nucleotide sequences is between 6-20, between 6-15, between 6-12, between 6-10, or between 6-8 nucleotides in length.

64. The composition of claim 62 , wherein each of the random nucleotides sequence is 8 nucleotides in length.

65. The composition of claim 62 , wherein each of the random nucleotide sequences is positioned between the first universal target sequence and the defined barcode sequence.

66. The composition of claim 1 or 2 , wherein multiple copies of the first and the second single-stranded polynucleotide sequences are attached to the first particle.

67. The composition of claim 66 , wherein each of the multiple copies of the first and the second single-stranded polynucleotide sequences comprises a random nucleotide sequence, wherein each of the random sequences is unique for each of the multiple copies.

68. The composition of claim 1 or 2 , wherein the first particle is further bound to a TCR, wherein the TCR specifically binds the MHC display moiety.

69. The composition of claim 68 , wherein the TCR is on the surface of a T cell.

70. The composition of claim 69 , wherein the T cell is selected from the group consisting of: a CTL, a CD8+ T cell, a CD4+ T cell, a primary T cell, an ex vivo cultured T cell, a tumor infiltrating T cell, and an engineered T cell.

71. The composition of claim 69 , wherein the T cell is isolated from a subject.

72. The composition of claim 71 , wherein the subject is known or suspected to have cancer.

73. The composition of claim 1 or 2 , wherein the first particle is isolated within a droplet.

74. The composition of claim 73 , wherein the droplet is a water-in-oil emulsion.

75. The composition of claim 73 , wherein the droplet further comprises a lysis reagent.

76. The composition of claim 75 , wherein the lysis reagent comprises a surfactant.

77. The composition of claim 76 , wherein the surfactant comprises IGEPAL CA 630.

78. The composition of claim 73 , wherein the droplet further comprises one or more components for reverse transcription.

79. The composition of claim 78 , wherein the components for reverse transcription are selected from the group consisting of: reverse transcriptase, dNTPs, RNase inhibitors, buffering agents, chelators, DTT, and combinations thereof.

80. The composition of claim 79 , wherein the reverse transcriptase comprises a RNaseH positive recombinant reverse transcriptase.

81. The composition of claim 79 , wherein the final concentration of the DTT is 5 mM.

82. The composition of claim 73 , wherein the droplet further comprises components for DNA PCR amplification.

83. The composition of claim 82 , wherein the components for DNA PCR amplification are selected from the group consisting of: DNA polymerase, dNTPs, buffering agents, chelators, amplification primers, and combinations thereof.

84. The composition of claim 83 , wherein the DNA polymerase is a recombinant Thermococcus kodakaraensis KOD1 DNA polymerase.

85. The composition of claim 83 , wherein the amplification primers comprise a TCRα forward primer and a TCRβ forward primer.

86. The composition of claim 85 , wherein the TCRα forward primer and TCRβ forward primer are designed to amplify at least a portion of a TCR complementarity determining region (CDR) 3 sequence.

87. The composition of claim 85 , wherein the TCRα forward primer and TCRβ forward primer are multiplexed primers.

88. The composition of claim 87 , wherein each of the TCRα multiplexed primers comprises a sequence selected from SEQ ID NOs: 46-102 that hybridizes to a TCRα variable region (“Vα”), and each of the TCRβ multiplexed primers comprises a sequence selected from SEQ ID NOs: 103-167 that hybridizes to a TCRβ variable region (“Vβ”).

89. The composition of claim 73 , wherein the droplet has been exposed to a releasing stimulus.

90. The composition of claim 89 , wherein the releasing stimulus comprises a light stimulus.

91. The composition of claim 90 , wherein the light stimulus comprises UV light.

92. The composition of claim 89 , wherein the releasing stimulus comprises a releasing reagent introduced into the droplet.

93. The composition of claim 92 , wherein the releasing reagent is an enzymatic or chemical reagent.

94. The composition of claim 93 , wherein the releasing reagent comprises a reducing reagent.

95. The composition of claim 1 or 2 , further comprising:

a) a second particle;

b) a second MHC display moiety comprising at least one second antigenic peptide, wherein the second antigenic peptide has a distinct sequence relative to the at least one antigenic peptide of claim 1 or 2 ;

c) a third single-stranded polynucleotide sequence, comprising in a 5′ to 3′ orientation:

1) the universal target sequence;

2) a second unique, defined barcode sequence, wherein the second defined barcode sequence is operably associated with the identity of the second antigenic peptide, and wherein the second defined barcode sequence is distinct from the defined barcode sequence of any of claim 1 or 2 ; and

3) the T cell receptor (TCR) a primer sequence, and

d) a fourth single-stranded polynucleotide sequence comprising in a 5′ to 3′ orientation:

1) the first universal target sequence;

2) the second defined barcode sequence; and

3) The TCRβ primer sequence,

wherein the second MHC display moiety, the third single-stranded polynucleotide sequence, and the fourth single-stranded polynucleotide sequence are attached to the second particle.

96. The composition of claim 95 , further comprising a plurality of the first and the second particles.

97. A library comprising the composition of claim 95 , wherein the library comprises greater than or equal to two distinct particles, each distinct particle comprising a unique antigen and a unique, defined barcode sequence operably associated with the identity of each unique antigen.

98. A kit comprising the composition of claim 1 or 2 and instructions for use.

99. A method of manufacturing the composition of claim 1 or 2 , comprising:

(i) obtaining elements (a)-(d) of claim 1 or 2 , wherein one or more of elements (a)-(c) are optionally attached to the first particle prior to obtaining elements (a)-(d); and

(ii) attaching one or more of elements (a)-(c) to the first particle.

100. The method of claim 99 , wherein the at least one antigenic peptide is a cleavable peptide, and the method further comprises:

(iii) replacing the at least one antigenic peptide comprised in the MHC display moiety with another antigenic peptide of interest.

101. The method of claim 99 , wherein the obtaining step comprises:

synthesizing or having synthesized one or more of elements (a)-(c).

102. A method for isolating an antigen specific T cell, the method comprising the steps of:

(i) providing the composition of claim 1 or 2 ;

(ii) providing a sample known or suspected to comprise one or more T cells;

(iii) contacting the composition with the sample, wherein the contacting comprises providing conditions sufficient for a single T cell to bind the MHC display moiety attached to the first particle; and

(iv) isolating the single T cell associated with the first particle.

103. The method of claim 102 , wherein the isolating comprises magnetic separation when the first particle is magnetic.

104. The method of claim 103 , wherein the magnetic separation comprises capturing the first particle against a wall with a magnet and removing elements not captured against the wall.

105. The method of claim 102 , wherein the isolating comprises using fluorescence-activated cell sorting (FACS).

106. The method of claim 102 , wherein the isolating step comprises using a microfluidic device.

107. The method of claim 106 , wherein the microfluidic device comprises a flow cytometer.

108. The method of claim 106 , wherein the microfluidic device comprises a deterministic lateral displacement (DLD) device.

109. The method of claim 108 , wherein the DLD device that separates the single T cell associated with the first particle from unbound particles.

110. The method of claim 106 , wherein the microfluidic device comprises a droplet generating device that isolates the single T cell in a droplet, and the droplet does not contain another T cell or an unbound particle.

111. The method of claim 110 , wherein the droplet comprises an aqueous fluid encapsulated in an immiscible carrier fluid.

112. The method of claim 111 , wherein the immiscible carrier fluid comprises an oil.

113. The method of claim 112 , wherein the oil comprises a fluorinated oil.

114. The method of claim 113 , wherein the fluorinated oil comprises HFE-7500.

115. The method of claim 111 , wherein the immiscible carrier fluid further comprises a surfactant.

116. The method of claim 115 , wherein the surfactant comprises a fluorosurfactant.

117. The method of claim 116 , wherein the fluorosurfactant comprises a 5% w/w PEG-PFPE amphiphilic block copolymer.

118. The method of claim 110 , wherein the method further comprises adding a lysis reagent.

119. The method of claim 118 , wherein the lysis reagent is added immediately prior to isolating the single T cell in the droplet, such that the lysis reagent is contained within the droplet.

120. The method of claim 110 , wherein the method further comprises adding a RNA reverse transcriptase.

121. The method of claim 120 , wherein the RNA reverse transcriptase is added immediately prior to isolating the single T cell in the droplet, such that the reverse transcriptase is contained within the droplet.

122. The method of claim 120 , wherein the RNA reverse transcriptase comprises a RNaseH positive recombinant reverse transcriptase.

123. The method of claim 110 , wherein the method further comprises adding a DNA polymerase.

124. The method of claim 123 , wherein the DNA polymerase is added immediately prior to isolating the single T cell in the droplet, such that the DNA polymerase is contained within the droplet.

125. The method of claim 123 , wherein the DNA polymerase is a recombinant Thermococcus kodakaraensis KOD1 DNA polymerase.

126. The method of claim 110 , wherein the method further comprises adding:

a) a TCRα forward primer, the TCRα forward primer comprising a second universal target sequence and a sequence designed to hybridize to a TCRα variable region sequence;

b) a TCRβ forward primer, the TCRβ forward primer comprising the second universal target sequence and a sequence designed to hybridize to a known TCRβ variable region sequence;

wherein the TCRα forward primer and TCRβ forward primer are contained within the droplet.

127. The method of claim 126 , wherein the TCRα forward primer and TCRβ forward primer are added immediately prior to isolating the single T cell in the droplet, such that the TCRα forward primer and TCRβ forward primer are contained within the droplet.

128. The method of claim 126 , wherein the TCRα forward primer and TCRβ forward primer are designed to amplify at least a portion of a TCR complementarity determining region (CDR) 3 sequence.

129. The method of claim 126 , wherein the TCRα forward primer and TCRβ forward primer comprise TCRα multiplexed primers and TCRβ multiplexed primers.

130. The method of claim 129 , wherein each of the TCRα multiplexed primers comprises a sequence selected from SEQ ID NOs: 46-102 that hybridizes to a TCRα variable region (“Vα”), and each of the TCRβ multiplexed primers comprises a sequence selected from SEQ ID NOs: 103-167 that hybridizes to a TCRβ variable region (“Vβ”).

131. The method of claim 110 , wherein the method further comprises adding dithiothreitol (DTT).

132. The method of claim 131 , wherein the DTT is added immediately prior to isolating the single T cell in the droplet, such that the DTT is contained within the droplet.

133. The method of claim 131 , wherein the final concentration of the DTT is 5 mM.

134. The method of claim 110 , wherein the method further comprises adding additional components for nucleic acid amplification, wherein the additional components are selected from the group consisting of: dNTPs, DNase inhibitors, RNase inhibitors, buffering agents, chelators, divalent ions, and combinations thereof.

135. The method of claim 134 , wherein one or more of the additional components are added immediately prior to isolating the single T cell in the droplet such that the additional components are contained within the droplet.

136. The method of claim 110 , wherein the isolating step comprises collecting the droplet.

137. The method of claim 110 , wherein the isolating step comprises dispersing the droplet in tubing, followed by collecting the droplet in a collection tube.

138. The method of claim 110 , wherein the droplet is 70 micrometers or less, 65 micrometers or less, 60 micrometers or less, 55 micrometers or less, or 50 micrometers or less in diameter.

139. The method of claim 110 , wherein the droplet is 40-70 micrometers, 40-60 micrometers, or 50-60 micrometers in diameter.

140. The method of claim 110 , wherein the droplet is about 55 micrometers in diameter.

141. The method of claim 110 , wherein the droplet is 30-110 picoliters, 50-100 picoliters, 60-100 picoliters, 70-100 picoliters, 70-90 picoliters, or 75-85 picoliters in volume.

142. The method of claim 110 , wherein the droplet is about 80 picoliters in volume.

143. The method of claim 102 , further comprising releasing a portion of the first and a portion of the second single-stranded polynucleotide sequences from the first particle, each of the portions of the first and second single-stranded polynucleotide sequences comprising the first universal target sequence, the defined barcode sequence, and the respective TCRα or TCRβ primer sequence.

144. A method for isolating an antigen specific T cell, the method comprising the steps of:

(i) providing the composition of claim 11 ;

(ii) providing a sample known or suspected to comprise one or more T cells;

(iii) contacting the composition with the sample, wherein the contacting comprises providing conditions sufficient for a single T cell to bind the MHC display moiety attached to the first particle;

(iv) isolating the single T cell associated with the first particle;

(v) releasing a portion of the first and a portion of the second single-stranded polynucleotide sequences from the first particle, each of the portions of the first and second single-stranded polynucleotide sequences comprising the first universal target sequence, the defined barcode sequence, and the respective TCRα or TCRβ primer sequence, wherein the releasing comprises cleaving the cleavage moiety.

145. The method of claim 144 , wherein the cleaving comprises exposing the first particle to ultraviolet (UV) light.

146. The method of claim 144 , wherein the cleaving comprises exposing the first particle to a releasing agent.

147. The method of claim 146 , wherein the releasing agent comprises an enzymatic or chemical reagent.

148. The method of claim 147 , wherein the chemical cleavage reagent is a reducing agent.

149. The method of claim 146 , the method further comprises adding the releasing agent immediately prior to isolating the single T cell in a droplet, such that the releasing agent is contained within the droplet.

150. The method of claim 143 , wherein the releasing is performed in a collection tube.

151. The method of claim 143 , wherein the isolating step comprises collecting a droplet comprising the single T cell in a collection tube, and wherein the releasing is performed in tubing prior to collecting the droplet in the collection tube.

152. The method of claim 126 , further comprising generating or having generated a cDNA mixture, wherein the generating comprises reverse transcription, and the cDNA mixture comprises a sequence complementary to the TCRα RNA transcript and a sequence complementary to the TCRβ RNA transcript.

153. The method of claim 152 , further comprising extracting or having extracted the cDNA mixture from the droplet.

154. The method of claim 153 , wherein the extracting comprises the steps of:

A) adding a de-emulsification reagent;

B) collecting an aqueous solution, wherein the aqueous solution comprises the cDNA mixture.

155. The method of claim 154 , the method further comprising:

(v) contacting the resulting cDNA mixture with a forward amplification primer, the forward amplification primer comprising a third universal target sequence and a sequence capable of hybridizing to at least a portion of the first universal target sequence;

(vi) contacting the resulting cDNA mixture with a reverse amplification primer, the reverse amplification primer comprising a fourth universal target sequence and a sequence capable of hybridizing to at least a portion of the second universal target sequence; and

(vii) performing a DNA amplification to produce an amplified cDNA mixture.

156. The method of claim 155 , comprising purifying the amplified cDNA mixture, wherein the purifying comprises isolating the amplified cDNA mixture on an agarose gel.

157. The method of claim 152 , further comprising sequencing or having sequenced the cDNA mixture.

158. The method of claim 157 , wherein the sequencing comprises next generation sequencing.

159. The method of claim 157 , further comprising assigning or having assigned a paired TCRα sequence and TCR β sequence to the at least one antigenic peptide associated with the single T cell using the defined barcode sequence.

160. The method of claim 102 , wherein the antigen specific T cell is selected from the group consisting of: a primary T cell, an ex vivo cultured T cell, a tumor infiltrating T cell, and an engineered T cell.

161. The method of claim 102 , wherein the sample is selected from the group consisting of: blood, plasma, a peripheral blood mononuclear cell population, a tissue homogenate, a tumor homogenate, and an ex vivo T cell culture.

Assignments (2)

CORRECTIVE ASSIGNMENT TO CORRECT THE THIRD INVENTOR'S NAME LISTED ON COVER SHEET FIRST NAME: ALPHONSUS MIDDLE NAME HON-CHUNG LAST NAME: NG PREVIOUSLY RECORDED ON REEL 065211 FRAME 0874. ASSIGNOR(S) HEREBY CONFIRMS THE ASSIGNMENT. Recorded Oct 18, 2023

From: HEATH, JAMES R.; PENG, SONGMING; NG, ALPHONSUS HON-CHUNG

To: CALIFORNIA INSTITUTE OF TECHNOLOGY

Reel/Frame 065265/0096 →

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 13, 2023

From: HEATH, JAMES R.; PENG, SONGMING; HON-CHUNG NG, ALPHONSUS

To: CALIFORNIA INSTITUTE OF TECHNOLOGY

Reel/Frame 065211/0874 →

Continuity (2)

Provisional Application 62468448 · Mar 8, 2017

Related Publication 20230069843A1 · Mar 9, 2023

References Cited (204)

US 4818680A · Collins et al. · 1989 [cited by applicant]

US 6037167A · Adelman et al. · 2000 [cited by applicant]

US 6100079A · Tajima · 2000 [cited by applicant]

US 6387622B1 · Siiman et al. · 2002 [cited by applicant]

US 6649378B1 · Kozwich et al. · 2003 [cited by applicant]

US 6730269B2 · Mirkin et al. · 2004 [cited by applicant]

US 6861221B2 · Mirkin et al. · 2005 [cited by applicant]

US 6969761B2 · Mirkin et al. · 2005 [cited by applicant]

US 6974669B2 · Mirkin et al. · 2005 [cited by applicant]

US 7094555B2 · Kwok et al. · 2006 [cited by applicant]

US 7098320B1 · Mirkin et al. · 2006 [cited by applicant]

US 7147687B2 · Mirkin et al. · 2006 [cited by applicant]

US 7169556B2 · Park et al. · 2007 [cited by applicant]

US 7186814B2 · Garimella et al. · 2007 [cited by applicant]

US 7208587B2 · Mirkin et al. · 2007 [cited by applicant]

US 7250499B2 · Mirkin et al. · 2007 [cited by applicant]

US 7259252B2 · Mirkin et al. · 2007 [cited by applicant]

US 7323309B2 · Mirkin et al. · 2008 [cited by applicant]

US 7381529B2 · Yamakawa et al. · 2008 [cited by applicant]

US 7531726B2 · Chan et al. · 2009 [cited by applicant]

US 7625702B2 · Cha · 2009 [cited by applicant]

US 7807372B2 · Mirkin et al. · 2010 [cited by applicant]

US 8323888B2 · Mirkin et al. · 2012 [cited by applicant]

US 8354231B2 · Kwong et al. · 2013 [cited by applicant]

US 8394590B2 · Kwong et al. · 2013 [cited by applicant]

US 8617884B2 · Berenson et al. · 2013 [cited by applicant]

US 8709722B2 · Tan et al. · 2014 [cited by applicant]

US 8993714B2 · Salemme et al. · 2015 [cited by applicant]

US 8999263B2 · Peterman et al. · 2015 [cited by applicant]

US 9011774B2 · Kim et al. · 2015 [cited by applicant]

US 9023650B2 · Farquar et al. · 2015 [cited by applicant]

US 9173840B2 · Amiji et al. · 2015 [cited by applicant]

US 10481158B2 · Heath et al. · 2019 [cited by applicant]

US 20020168663A1 · Phan et al. · 2002 [cited by applicant]

US 20030027234A1 · Murugan et al. · 2003 [cited by applicant]

US 20030219752A1 · Short · 2003 [cited by applicant]

US 20030223938A1 · Nagy et al. · 2003 [cited by applicant]

US 20040072231A1 · Mirkin et al. · 2004 [cited by applicant]

US 20040102369A1 · Wu et al. · 2004 [cited by applicant]

US 20040137642A1 · Erfle et al. · 2004 [cited by applicant]

US 20050019843A1 · Chen et al. · 2005 [cited by applicant]

US 20050048546A1 · Penn et al. · 2005 [cited by applicant]

US 20050287611A1 · Thomas, IV et al. · 2005 [cited by applicant]

US 20060014172A1 · Muller et al. · 2006 [cited by applicant]

US 20060040286A1 · Mirkin et al. · 2006 [cited by applicant]

US 20060240416A1 · Banerjee et al. · 2006 [cited by applicant]

US 20070264652A1 · Upadhyay et al. · 2007 [cited by applicant]

US 20080188374A1 · Chen et al. · 2008 [cited by applicant]

US 20080220982A1 · Vu · 2008 [cited by applicant]

US 20090017455A1 · Kwong et al. · 2009 [cited by applicant]

US 20090036324A1 · Fan et al. · 2009 [cited by applicant]

US 20100004138A1 · Sato et al. · 2010 [cited by applicant]

US 20110039717A1 · Kwong et al. · 2011 [cited by applicant]

US 20110166034A1 · Kwona et al. · 2011 [cited by applicant]

US 20110171749A1 · Alocilja et al. · 2011 [cited by applicant]

US 20110237449A1 · McMaster et al. · 2011 [cited by applicant]

US 20120121649A1 · Santamaria · 2012 [cited by applicant]

US 20120157329A1 · Castellano et al. · 2012 [cited by applicant]

US 20120276109A1 · Fraser et al. · 2012 [cited by applicant]

US 20130130364A1 · Seo et al. · 2013 [cited by applicant]

US 20130260447A1 · Link · 2013 [cited by examiner]

US 20130330414A1 · Santamaria · 2013 [cited by applicant]

US 20140272972A1 · Lee · 2014 [cited by applicant]

US 20150044672A1 · Stojanovic et al. · 2015 [cited by applicant]

US 20150050747A1 · Alocilja et al. · 2015 [cited by applicant]

US 20150051089A1 · Robins et al. · 2015 [cited by applicant]

US 20150132758A1 · Medina-Llamas et al. · 2015 [cited by applicant]

US 20150157737A1 · Gu et al. · 2015 [cited by applicant]

US 20150166997A1 · Messmer · 2015 [cited by applicant]

US 20150290611A1 · Pine et al. · 2015 [cited by applicant]

US 20150322494A1 · Garcia et al. · 2015 [cited by applicant]

US 20160271237A1 · Santamaria · 2016 [cited by applicant]

US 20160282255A1 · Irimia et al. · 2016 [cited by applicant]

US 20160287152A1 · Schwartz et al. · 2016 [cited by applicant]

AU 2007100888A4 · 2007 [cited by applicant]

AU 2010202492A1 · 2010 [cited by applicant]

AU 2016203838A1 · 2016 [cited by applicant]

CN 1464070A · 2003 [cited by applicant]

CN 101684503A · 2010 [cited by applicant]

CN 101852808A · 2010 [cited by applicant]

CN 102072931A · 2011 [cited by applicant]

CN 102147414A · 2011 [cited by applicant]

CN 102168066A · 2011 [cited by applicant]

CN 102234682A · 2011 [cited by applicant]

CN 102321762A · 2012 [cited by applicant]

CN 103266170A · 2013 [cited by applicant]

CN 103276087A · 2013 [cited by applicant]

CN 103333967A · 2013 [cited by applicant]

CN 104962570A · 2015 [cited by applicant]

CN 105648069A · 2016 [cited by applicant]

CN 105651992A · 2016 [cited by applicant]

CN 105755118A · 2016 [cited by applicant]

DE 102008013715 · 2010 [cited by applicant]

EP 1328540B1 · 2005 [cited by applicant]

EP 0837946B1 · 2009 [cited by applicant]

EP 1747295B1 · 2012 [cited by applicant]

EP 2842570A1 · 2015 [cited by applicant]

JP 2004354164A · 2004 [cited by applicant]

JP 2006158276A · 2006 [cited by applicant]

JP 2006328032A · 2006 [cited by applicant]

JP 2007262114A · 2007 [cited by applicant]

JP 2009068869A · 2009 [cited by applicant]

JP 2013092501A · 2013 [cited by applicant]

JP 2014514331A · 2014 [cited by applicant]

JP 2015173626A · 2015 [cited by applicant]

KR 100823684B1 · 2008 [cited by applicant]

KR 20110133843A · 2011 [cited by applicant]

KR 20130114932A · 2012 [cited by applicant]

KR 20130121550A · 2013 [cited by applicant]

KR 20140097679A · 2014 [cited by applicant]

KR 20150049697A · 2015 [cited by applicant]

KR 20150144644A · 2015 [cited by applicant]

WO WO1991017265 · 1991 [cited by applicant]

WO WO1992007952 · 1992 [cited by applicant]

WO WO1993025660 · 1993 [cited by applicant]

WO WO1995005399 · 1995 [cited by applicant]

WO WO1999002728 · 1999 [cited by applicant]

WO WO2000028088 · 2000 [cited by applicant]

WO WO2000040750 · 2000 [cited by applicant]

WO WO2001096023 · 2001 [cited by applicant]

WO WO2002031501 · 2002 [cited by applicant]

WO WO2002083292 · 2002 [cited by applicant]

WO WO2003035829 · 2003 [cited by applicant]

WO WO2004003142 · 2004 [cited by applicant]

WO WO2004015395 · 2004 [cited by applicant]

WO WO2004033497 · 2004 [cited by applicant]

WO WO2004053163 · 2004 [cited by applicant]

WO WO2004067742 · 2004 [cited by applicant]

WO WO2004106546 · 2004 [cited by applicant]

WO WO2005001113 · 2005 [cited by applicant]

WO WO2005021800 · 2005 [cited by applicant]

WO WO2005108612 · 2005 [cited by applicant]

WO WO2005111624 · 2005 [cited by applicant]

WO WO2006031883 · 2006 [cited by applicant]

WO WO2006076793 · 2006 [cited by applicant]

WO WO2007014267 · 2007 [cited by applicant]

WO WO2007024676 · 2007 [cited by applicant]

WO WO2007024840 · 2007 [cited by applicant]

WO WO2007133807 · 2007 [cited by applicant]

WO WO2008001376 · 2008 [cited by applicant]

WO WO2008016680 · 2008 [cited by applicant]

WO WO2008017507 · 2008 [cited by applicant]

WO WO2008030071 · 2008 [cited by applicant]

WO WO2008090557 · 2008 [cited by applicant]

WO WO2008091364 · 2008 [cited by applicant]

WO WO2008157649 · 2008 [cited by applicant]

WO WO2009003492 · 2009 [cited by applicant]

WO WO2009055068 · 2009 [cited by applicant]

WO WO2009083856 · 2009 [cited by applicant]

WO WO2009106322 · 2009 [cited by applicant]

WO WO2009124296 · 2009 [cited by applicant]

WO WO2009149091 · 2009 [cited by applicant]

WO WO2010037395 · 2010 [cited by applicant]

WO WO2010037397 · 2010 [cited by applicant]

WO WO2011090445 · 2011 [cited by applicant]

WO WO2011100669 · 2011 [cited by applicant]

WO WO2011104497 · 2011 [cited by applicant]

WO WO2012044999 · 2012 [cited by applicant]

WO WO2012062904 · 2012 [cited by applicant]

WO WO2012111685 · 2012 [cited by applicant]

WO WO2012111686 · 2012 [cited by applicant]

WO WO2012111687 · 2012 [cited by applicant]

WO WO2012148960 · 2012 [cited by applicant]

WO WO2013071520 · 2013 [cited by applicant]

WO WO2013119793 · 2013 [cited by applicant]

WO WO2014124543 · 2014 [cited by applicant]

WO WO2014144892 · 2014 [cited by applicant]

WO WO2014189257 · 2014 [cited by applicant]

WO WO2014192937 · 2014 [cited by applicant]

WO WO2014197840 · 2014 [cited by applicant]

WO WO2015060417 · 2015 [cited by applicant]

WO WO2015100373 · 2015 [cited by applicant]

WO WO2015135856 · 2015 [cited by applicant]

WO WO2015161173 · 2015 [cited by applicant]

WO WO2015174862 · 2015 [cited by applicant]

WO WO2015200384 · 2015 [cited by applicant]

WO WO2016015027 · 2016 [cited by applicant]

WO WO2016075172 · 2016 [cited by applicant]

WO WO2016090115 · 2016 [cited by applicant]

WO WO2016115500 · 2016 [cited by applicant]

WO WO2016127158 · 2016 [cited by applicant]

WO WO2016160908 · 2016 [cited by applicant]

WO WO2016196691 · 2016 [cited by applicant]

WO WO2016196691A2 · 2016 [cited by examiner]

WO WO2018057051A1 · 2018 [cited by examiner]

WO WO2018165475 · 2018 [cited by applicant]

Bentzen et al. Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes. Nature Biotechnology. 34(10), 2016, 1037-1045. (Year: 2016). [cited by examiner]

Bakker, Arnold H. et al.; “Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -87”; PNAS; Mar. 11, 2008; vol. 105; No. 10; pp. 3825-3830. [cited by applicant]

Coulie, Pierre G. et al.; “Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy”; Nature Reviews Cancer; vol. 14; Feb. 2014; pp. 135-146. [cited by applicant]

Extended European Search Report, European Application No. 16804369.3, Dec. 13, 2018, 10 pages. [cited by applicant]

Fritsch, Edward F. et al.; “HLA-binding properties of tumor neoepitopes in humans”; Cancer Immunol Res.; Jun. 2014; 2(6); pp. 522-529. [cited by applicant]

International Search Report and Written Opinion mailed Nov. 29, 2016 in corresponding International Application No. PCT/US2016/035357, 10pp. [cited by applicant]

International Search Report and Written Opinion mailed Aug. 3, 2018 in corresponding International Application No. PCT/US2018/021611, 10pp. [cited by applicant]

Kwong, Gabriel A. et al.; “Modular nucleic acid assembled p/MHC microarrays for multiplexed sorting of antigen-specific T cells”; J Am Chem Soc.; Jul. 22, 2009; 131(28); pp. 9695-9703. [cited by applicant]

Novak, Erik J. et al.; “MHC class II tetramers identify peptide-specific human CD4+ T cells proliferating in response to influenza A antigen”; J Clin Invest.; Dec. 5, 1999; 104(12); pp. R63-R67. [cited by applicant]

Rodenko, Boris et al.; “Generation of peptide-MHC class I complexes through UV-mediated ligand exchange”; Nature Protocols; vol. 1; No. 3; 2006; pp. 1120-1132. [cited by applicant]

Sano, Takeshi et al.; “Expression of a cloned streptavidin gene in [cited by applicant]

Stoeva, S.I. et al., “Multiplexed Detection of Protein Cancer Markers with Biobarcoded Nanoparticle Probes,” Journal of the American Chemical Society, Jul. 5, 2006, vol. 128, No. 26, pp. 8378-8379. [cited by applicant]

Stone, D.J. et al., “HLA-restricted epitope identification and detection of functional Tcell responses by using MHC-peptide and costimulatory microarrays,” Proceedings of the National Academy of Sciences of the United S… [cited by applicant]

Toebes, Mireille et al.; “Design and use of conditional MHC class I ligands”; Nature Medicine; vol. 12; No. 2; Feb. 2006; pp. 246-251. [cited by applicant]

Andersen, Rikke Sick et al.; “Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers”; Nature Protocols; vol. 7; No. 5; 2012; pp. 891-902. [cited by applicant]

File History of U.S. Appl. No. 15/170,919, filed Jun. 1, 2016 in 478 pages. [cited by applicant]

File History of U.S. Appl. No. 16/347,559, filed May 3, 2019 in 775 pages. [cited by applicant]

International Search Report and Written Opinion mailed Mar. 6, 2018 in International Application No. PCT/US2017/059598, in 15 pages. [cited by applicant]