US 2023/0375567 A1Published application

Methods and compositions for assessing antibody specificities

AssigneeSerimmune Inc.

InventorsPatrick Sean Daugherty, Kathryn Vinaya Louise Kamath, Jack Ryan Reifert

Life of this patent

Estimating the term…

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.

Claims20

Dependent claims

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].

361 more elements

Dependencies are inferred from the claim text.

Facts

Application: 18/122,527Filed 16 Mar 2023
Priority: 11 Nov 2015
Published: 23 Nov 2023
Term ends: Not estimatedThe source records don’t support an estimate.

Classification41 codes

G01N 33/6854
Involving proteins, peptides or amino acids: immunoglobulins
C07K 14/195
Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof: from bacteria
C07K 14/285
From bacteria: from Pasteurellaceae , e.g. Haemophilus influenza
C07K 14/315
From bacteria: from Streptococcus , e.g. Enterococci

Family

Application62/253,926Us provisional application · filed 11 Nov 2015
Application62/339,644Us provisional application · filed 20 May 2016
Application15/775,363Continuation · filed 10 May 2018
Application15/991,982Continuation · filed 29 May 2018
Application16/544,652Continuation · filed 19 Aug 2019
Application17/096,890Continuation · filed 12 Nov 2020
Application18/122,527Continuation
US 10,386,373 B2Related patent
US 10,871,494 B2Related patent
US 11,828,762 B2Related patent
US 2018/0267056 A1Published application
US 2019/0369118 A1Published application
US 2021/0011025 A1Published application
US 2021/0156873 A1Published application
US 2023/0375567 A1This patent

From the US filing history. Foreign family members aren’t listed.

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Abstract

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].

361 more elements

Facts

Application

18/122,527Filed 16 Mar 2023

Priority

11 Nov 2015

Published

23 Nov 2023

Term ends

Not estimatedThe source records don’t support an estimate.

Classification41 codes

G01N 33/6854
Involving proteins, peptides or amino acids: immunoglobulins
C07K 14/195
Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof: from bacteria
C07K 14/285
From bacteria: from Pasteurellaceae , e.g. Haemophilus influenza
C07K 14/315
From bacteria: from Streptococcus , e.g. Enterococci

Family

Application62/253,926Us provisional application · filed 11 Nov 2015

Application62/339,644Us provisional application · filed 20 May 2016

Application15/775,363Continuation · filed 10 May 2018

Application15/991,982Continuation · filed 29 May 2018

Application16/544,652Continuation · filed 19 Aug 2019

Application17/096,890Continuation · filed 12 Nov 2020

Application18/122,527Continuation

US 10,386,373 B2Related patent

US 10,871,494 B2Related patent

US 11,828,762 B2Related patent

US 2018/0267056 A1Published application

US 2019/0369118 A1Published application

US 2021/0011025 A1Published application

US 2021/0156873 A1Published application

US 2023/0375567 A1This patent

From the US filing history. Foreign family members aren’t listed.