US2023375567A1PendingUtilityA1
Methods and compositions for assessing antibody specificities
Est. expiryNov 11, 2035(~9.3 yrs left)· nominal 20-yr term from priority
G01N 33/6854C07K 14/195C07K 14/315C07K 14/285C07K 14/43554C07K 14/44C07K 14/45G01N 33/6842G01N 33/56911G01N 33/56905G01N 33/56988G01N 33/56994G01N 33/56983G01N 33/53G01N 33/56944G01N 33/564G01N 33/569G01N 33/56966G01N 33/6845G01N 33/6878C12N 15/1037Y02A50/30C12Q 1/689G01N 2333/045G01N 2333/05G01N 2333/095G01N 2333/16G01N 2333/18G01N 2333/20G01N 2333/285G01N 2333/29G01N 2333/315G01N 2333/4353G01N 2570/00G01N 2800/24G01N 2800/26
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Claims
Abstract
The present invention provides compositions and methods that can be used to determine a peptide signature for an antibody repertoire in a sample comprising multiple antibodies. The method can be used to characterize a phenotype in a sample, such as providing a diagnosis, prognosis or theranosis of a medical condition.
Claims
exact text as granted — not AI-modifiedWhat is claimed is:
1 . A multiplex array for tick-borne infections, the multiplex array comprising an array surface and at least two peptide probes, wherein the at least two peptide probes extend from the array surface,
wherein a first peptide probe of the at least two peptide probes is capable of binding to an antibody associated with a first tick-borne infection and a second peptide probe of the at least two peptide probes is capable of binding to an antibody associated with a second tick-borne infection, wherein the first tick-borne infection and the second tick-borne infection are distinct tick-borne infections selected from the group consisting of: a Borrelia infection, an Ehrlichia infection, an Anaplasma infection, and a Babesia infection, wherein when the at least two peptide probes comprises a Borrelia -specific peptide probe, the Borrelia -specific peptide probe comprises a binding motif selected from the group consisting of:
(SEQ ID NO: 358)
VQQExxxxxP,
(SEQ ID NO: 359)
QQEGxxxx[YC],
(SEQ ID NO: 360)
QEG[IV]Q,
(SEQ ID NO: 361)
G[IV]QxEG,
(SEQ ID NO: 362)
[LI]xxA[ILV]xxRG,
(SEQ ID NO: 363)
[ATNSD]xxxxAI[LAM]xR,
(SEQ ID NO: 364)
Ix[LM]xGFxK,
(SEQ ID NO: 365)
LxGM[RQ]K,
(SEQ ID NO: 366)
[HR]xDxTNxF,
(SEQ ID NO: 367)
[DA]DPTN,
(SEQ ID NO: 368)
[KR]x[DE]xTNxF,
(SEQ ID NO: 369)
[ET][ML]HKF,
(SEQ ID NO: 370)
[ML]xxEFHK,
(SEQ ID NO: 371)
Q[TI]EQxxxxxK,
(SEQ ID NO: 372)
DxSP[IL]E,
(SEQ ID NO: 373)
PFx[AP]YxK,
(SEQ ID NO: 374)
VxxYFxx[LV]xK,
(SEQ ID NO: 375)
KxVDxDR,
(SEQ ID NO: 376)
[DN][AS]A[AG]F,
(SEQ ID NO: 377)
Cx[NA]xKFC,
(SEQ ID NO: 378)
Kx[GRST]AE[YF],
(SEQ ID NO: 379)
HQV[PA]xxx[DHE],
(SEQ ID NO: 380)
IPxxV[IF]xxR,
(SEQ ID NO: 381)
Cx[ALT]xWEx[CA],
(SEQ ID NO: 382)
CxxxCA[IL]xxR,
(SEQ ID NO: 383)
I[IV]Ixx[MT]xK,
(SEQ ID NO: 384)
QG[ITL]x[KN][FY],
(SEQ ID NO: 385)
KxxPPxIN,
(SEQ ID NO: 386)
G[YF][FY]FxxK,
(SEQ ID NO: 387)
DKNVx[IV],
(SEQ ID NO: 388)
[QE][KR][ND]xSG,
(SEQ ID NO: 389)
K[RK]PGD,
(SEQ ID NO: 390)
EGAxQP,
and
(SEQ ID NO: 391)
GSPEY;
wherein when the at least two peptide probes comprises a Ehrlichia -specific peptide probe, the Ehrlichia -specific peptide probe comprises a binding motif selected from the group consisting of:
(SEQ ID NO: 586)
YxxL[IV]xP[KR],
(SEQ ID NO: 587)
[SA]Nx[ML]FY,
(SEQ ID NO: 588)
WDGSx[IV],
(SEQ ID NO: 589)
PxxL[IV]KP,
(SEQ ID NO: 590)
KxDWDG,
(SEQ ID NO: 591)
RxxxxXxD[HY]D,
(SEQ ID NO: 592)
VDVMGN,
(SEQ ID NO: 593)
Ex[NQ][QN]xFY,
(SEQ ID NO: 594)
Vx[TS][TS]N,
(SEQ ID NO: 595)
KLHDP,
(SEQ ID NO: 596)
KxDxDT[GN],
(SEQ ID NO: 597)
Y[HA]GWx[SAE],
(SEQ ID NO: 598)
NPEH[DTE],
(SEQ ID NO: 599)
NPAxQ[HR],
(SEQ ID NO: 600)
[KR]MNKxx[TP],
(SEQ ID NO: 601)
DWxxx[FY][VK]K,
(SEQ ID NO: 602)
GVN[APTS]xK,
(SEQ ID NO: 603)
[IV]x[PR]EGxK,
(SEQ ID NO:604)
RVF[ST][MA],
(SEQ ID NO: 605)
NxRxx[VI]W[YF],
(SEQ ID NO: 606)
Yxx[MTL]xYNA,
(SEQ ID NO: 607)
Kx[VI]x[ND][IV]W,
(SEQ ID NO: 608)
[ED][YF]Q[LQ]H,
(SEQ ID NO: 609)
FGxPSI,
(SEQ ID NO: 610)
QLVGxxK,
and
(SEQ ID NO: 611)
YxxL[IV]xP[KR];
wherein when the at least two peptide probes comprises a Anaplasma -specific peptide probe, the Anaplasma -specific peptide probe comprises a binding motif selected from the group consisting of:
(SEQ ID NO: 612)
W[YK]Wx[PA]K,
(SEQ ID NO: 613)
KxExH[NK]F,
(SEQ ID NO: 614)
QxxxWPYxK,
(SEQ ID NO: 615)
YxFDxNxR,
(SEQ ID NO: 616)
FxWN[VI]P,
(SEQ ID NO: 617)
[FW][LM]EXAH,
(SEQ ID NO: 618)
DF[LI]xAT,
(SEQ ID NO: 619)
KxMSxFV,
(SEQ ID NO: 620)
W[YK]Wx[PA]K,
(SEQ ID NO: 621)
KxExH[NK]F,
(SEQ ID NO: 622)
QxxxWPYxK,
(SEQ ID NO: 623)
WPT[SF]T,
(SEQ ID NO: 624)
WP[TA]GR,
(SEQ ID NO: 625)
KNWPx[GF],
(SEQ ID NO: 626)
KxxP[LI]FA,
(SEQ ID NO: 627)
WPxGQV,
(SEQ ID NO: 628)
[VI][LR]KDF,
(SEQ ID NO: 629)
WPT[SF]T,
(SEQ ID NO: 630)
Kx[IM][VN]xWA,
(SEQ ID NO: 631)
[YW]TxEPF,
(SEQ ID NO: 632)
[AM][PTS]WExF,
(SEQ ID NO: 633)
R[PT][RTK]F[NS],
(SEQ ID NO: 634)
VY[SA]HW,
(SEQ ID NO: 635)
[WF]xxKPxWxxM,
(SEQ ID NO: 636)
KGx[SA]HxF,
(SEQ ID NO: 637)
KGxVxF[AS],
(SEQ ID NO: 638)
[IV]xHxTID,
(SEQ ID NO: 639)
MLSXXVN,
(SEQ ID NO: 640)
KxYSxxVR,
and
(SEQ ID NO: 641)
Kx[VK]VNP;
wherein when the at least two peptide probes comprises a Babesia -specific peptide probe, the Babesia -specific peptide probe comprises a binding motif selected from the group consisting of:
(SEQ ID NO: 558)
[ML]L[AS][TA]xK,
(SEQ ID NO: 559)
[VL]x[AS]xDPxxP,
(SEQ ID NO: 560)
[KR]x[IL]x[ST][MLF]N,
(SEQ ID NO: 561)
TG[KR]MxxxxQ,
(SEQ ID NO: 562)
GxPY[STA]xxxx[ML],
(SEQ ID NO: 563)
WE[EDA]x[PA]I,
(SEQ ID NO: 564)
E[IV]xHxxFxR,
(SEQ ID NO: 565)
Kxx[TS]HRxK,
(SEQ ID NO: 566)
TFExGxK,
(SEQ ID NO: 567)
WENx[RA]xxx[FI],
(SEQ ID NO: 568)
[NT][MF]FxxxxWxD,
(SEQ ID NO: 569)
[PA][GA][IV][MITV]xxP,
(SEQ ID NO: 570)
KxxRxS[YWH]D,
(SEQ ID NO: 571)
EKxxRxx[YF][DN],
(SEQ ID NO: 572)
DTxTPXE,
(SEQ ID NO: 573)
WL[DA]QW,
(SEQ ID NO: 574)
K[EN]xxDxWN,
(SEQ ID NO: 575)
[GT]GNGG,
(SEQ ID NO: 576)
G[YFW]Dxx[QT]P,
(SEQ ID NO: 577)
[IV]GxS[RK]x[CR],
(SEQ ID NO: 578)
[SAT]TPx[ML]E,
(SEQ ID NO: 579)
S[DQ]WxWE,
(SEQ ID NO: 580)
Dxx Y[IT]xx[HF]K,
(SEQ ID NO: 581)
K[YF]xxxL[IVT]K,
(SEQ ID NO: 582)
P[VI]xYMQ,
(SEQ ID NO: 583)
WPTGxxx[SN],
(SEQ ID NO: 584)
Kx[IM][VN]xWA,
and
(SEQ ID NO: 585)
W[AP]TG[KR].
2 . The multiplex array of claim 1 , further comprising a third peptide probe of the at least two peptide probes that is capable of binding to an antibody associated with a third tick-borne infection, wherein the first tick-borne infection, the second tick-borne infection, and the third tick-borne infection are distinct tick-borne infections.
3 . The multiplex array of claim 2 , further comprising a fourth peptide probe of the at least two peptide probes that is capable of binding to an antibody associated with a fourth tick-borne infection, wherein the first tick-borne infection, the second tick-borne infection, the third tick-borne infection, and the fourth tick-borne infection are distinct tick-borne infections.
4 . The multiplex array of claim 1 , wherein the array surface comprises a solid surface.
5 . The multiplex array of claim 4 , wherein the solid surface comprises a microparticle.
6 . The multiplex array of claim 1 , wherein the array surface comprises a biological particle.
7 . The multiplex array of claim 6 , wherein the biological particle comprises a cell, a virus, or a bacteriophage.
8 . The multiplex array of claim 7 , wherein the biological particle is an Escherichia coli cell.
9 . The multiplex array of claim 6 , wherein the array surface comprises a plurality of the biological particles, wherein each of the plurality of the biological particles comprises a single species of the at least two peptide probes.
10 . The multiplex array of claim 1 , wherein the at least two peptide probes comprises at least a portion of an Escherichia coli eCPX scaffold.
11 . The multiplex array of claim 1 , wherein the at least two peptide probes further comprise a label.
12 . A method of diagnosing a tick-borne infection in a subject comprising:
contacting the multiplex array of claim 1 with a biological sample from the subject, wherein the biological sample comprises a plurality of antibodies; incubating the biological sample and the array under conditions sufficient for binding of each of the at least two peptide probes to its target antibody if present in the biological sample; and measuring the binding of the at least two peptide probes to its target antibody in the biological sample.
13 . The method of claim 12 , wherein the method further comprises contacting the biological sample with at least one reagent configured to remove antibodies that bind to array components other than the at least two peptide probes before contacting the multiplex array of claim 1 with a biological sample from the subject.
14 . The method of claim 13 , wherein the at least one reagent is the array surface free of the at least two peptide probes.
15 . The method of claim 12 , wherein the measuring comprises an ELISA assay.
16 . The method of claim 12 , wherein the measuring comprises a peptide library display system.
17 . The method of claim 16 , wherein the peptide library display system comprises an E. Coli display system.
18 . The method of claim 12 , wherein the measuring comprises calculating the sum of z-scores for the at least two peptide probes.
19 . The method of claim 12 , wherein the biological sample comprises a bodily fluid, optionally wherein the bodily fluid is peripheral blood, lymphatic fluid, sweat, saliva, or mucus.
20 . A kit for diagnosing a tick-borne infection, comprising the multiplex array of claim 1 and a system for detecting the binding of each of the at least two peptide probes to its target antibody, optionally wherein the kit further comprises an agent for removing antibodies that bind to array components other than the at least two peptide probes.Cited by (0)
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