US 11,940,448 B2
Proteomic screening for lysosomal storage diseases
Sihoun Hahn, Clyde Hill, WA (US); Christopher Collins, Seattle, WA (US); Remwilyn Dayuha, Lynnwood, WA (US); and Fan Yi, Shoreline, WA (US)
Assigned to Seattle Children's Hospital, Seattle, WA (US)
Filed by Seattle Children's Hospital, Seattle, WA (US)
Filed on Mar. 31, 2021, as Appl. No. 17/219,776.
Claims priority of provisional application 63/002,992, filed on Mar. 31, 2020.
Prior Publication US 2021/0302435 A1, Sep. 30, 2021
Int. Cl. G01N 33/68 (2006.01)
CPC G01N 33/6854 (2013.01) [G01N 33/6848 (2013.01); G01N 2800/38 (2013.01)] 21 Claims
 
1. A method of detecting one or more signature peptides of Mucopolysaccharidosis Type I (MPSI) and/or Pompe Disease in a biological sample, the method comprising:
obtaining a biological sample from a subject;
digesting proteins from the biological sample with an enzyme to yield a digested biological sample comprising peptides;
enriching the digested biological sample for the one or more signature peptides by contacting the sample with an antibody or antigen binding fragment thereof for each of the one or more signature peptides, the enriching step comprising enriching for:
(A) an alpha-L-iduronidase enzyme (IDUA) signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the IDUA signature peptide and comprises: a heavy chain variable (VH) domain comprising a complementarity determining region (CDR)H1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a light chain variable (VL) domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27; and
an acid alpha-glucosidase enzyme (GAA) signature peptide of Pompe Disease of SEQ ID NO: 5 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 66, a CDRH2 as set forth in SEQ ID NO: 67, and a CDRH3 as set forth in SEQ ID NO: 68, and VL domain comprising a CDRL1 as set forth in SEQ ID NO: 69, a CDRL2 as set forth in SEQ ID NO: 70, and a CDRL3 as set forth in SEQ ID NO: 71; or
(B) a first IDUA signature peptide of MPSI of SEQ ID NO: 1 with an antibody or antigen-binding fragment thereof that binds the first IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 10, a CDRH2 as set forth in SEQ ID NO: 11, and a CDRH3 as set forth in SEQ ID NO: 12, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 13, a CDRL2 as set forth in SEQ ID NO: 14, and a CDRL3 as set forth in SEQ ID NO: 15; and
a second IDUA signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the second IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27; or
(C) a first IDUA signature peptide of MPSI of SEQ ID NO: 1 with an antibody or antigen-binding fragment thereof that binds the first IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 10, a CDRH2 as set forth in SEQ ID NO: 11, and a CDRH3 as set forth in SEQ ID NO: 12, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 13, a CDRL2 as set forth in SEQ ID NO: 14, and a CDRL3 as set forth in SEQ ID NO: 15;
a second IDUA signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the second IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27; and
a GAA signature peptide of Pompe Disease of SEQ ID NO: 5 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 66, a CDRH2 as set forth in SEQ ID NO: 67, and a CDRH3 as set forth in SEQ ID NO: 68, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 69, a CDRL2 as set forth in SEQ ID NO: 70, and a CDRL3 as set forth in SEQ ID NO: 71; or
(D) a first IDUA signature peptide of MPSI of SEQ ID NO: 1 with an antibody or antigen-binding fragment thereof that binds the first IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 10, a CDRH2 as set forth in SEQ ID NO: 11, and a CDRH3 as set forth in SEQ ID NO: 12, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 13, a CDRL2 as set forth in SEQ ID NO: 14, and a CDRL3 as set forth in SEQ ID NO: 15;
a second IDUA signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the second IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27; and
a GAA signature peptide of Pompe Disease of SEQ ID NO: 3 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 44, a CDRH2 as set forth in SEQ ID NO: 45, and a CDRH3 as set forth in SEQ ID NO: 46, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 47, a CDRL2 as set forth in SEQ ID NO: 48, and a CDRL3 as set forth in SEQ ID NO: 49; or
(E) a first GAA signature peptide of Pompe Disease of SEQ ID NO: 3 with an antibody or antigen binding fragment thereof that binds the first GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 44, a CDRH2 as set forth in SEQ ID NO: 45, and a CDRH3 as set forth in SEQ ID NO: 46, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 47, a CDRL2 as set forth in SEQ ID NO: 48, and a CDRL3 as set forth in SEQ ID NO: 49; and
a second GAA signature peptide of Pompe Disease of SEQ ID NO: 5 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 66, a CDRH2 as set forth in SEQ ID NO: 67, and a CDRH3 as set forth in SEQ ID NO: 68, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 69, a CDRL2 as set forth in SEQ ID NO: 70, and a CDRL3 as set forth in SEQ ID NO: 71; or
(F) a first IDUA signature peptide of MPSI of SEQ ID NO: 1 with an antibody or antigen-binding fragment thereof that binds the first IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 10, a CDRH2 as set forth in SEQ ID NO: 11, and a CDRH3 as set forth in SEQ ID NO: 12, and VL domain comprising a CDRL1 as set forth in SEQ ID NO: 13, a CDRL2 as set forth in SEQ ID NO: 14, and a CDRL3 as set forth in SEQ ID NO: 15;
a second IDUA signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the second IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27;
a first GAA signature peptide of Pompe Disease of SEQ ID NO: 3 with an antibody or antigen binding fragment thereof that binds the first GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 44, a CDRH2 as set forth in SEQ ID NO: 45, and a CDRH3 as set forth in SEQ ID NO: 46, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 47, a CDRL2 as set forth in SEQ ID NO: 48, and a CDRL3 as set forth in SEQ ID NO: 49;
and a second GAA signature peptide of Pompe Disease of SEQ ID NO: 5 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 66, a CDRH2 as set forth in SEQ ID NO: 67, and a CDRH3 as set forth in SEQ ID NO: 68, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 69, a CDRL2 as set forth in SEQ ID NO: 70, and a CDRL3 as set forth in SEQ ID NO: 71; or
(G) a first IDUA signature peptide of MPSI of SEQ ID NO: 1 with an antibody or antigen-binding fragment thereof that binds the first IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 10, a CDRH2 as set forth in SEQ ID NO: 11, and a CDRH3 as set forth in SEQ ID NO: 12, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 13, a CDRL2 as set forth in SEQ ID NO: 14, and a CDRL3 as set forth in SEQ ID NO: 15;
a second IDUA signature peptide of MPSI of SEQ ID NO: 2 with an antibody or antigen-binding fragment thereof that binds the second IDUA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 22, a CDRH2 as set forth in SEQ ID NO: 23, and a CDRH3 as set forth in SEQ ID NO: 24, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 25, a CDRL2 as set forth in SEQ ID NO: 26, and a CDRL3 as set forth in SEQ ID NO: 27;
a first GAA signature peptide of Pompe Disease of SEQ ID NO: 3 with an antibody or antigen binding fragment thereof that binds the first GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 44, a CDRH2 as set forth in SEQ ID NO: 45, and a CDRH3 as set forth in SEQ ID NO: 46, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 47, a CDRL2 as set forth in SEQ ID NO: 48, and a CDRL3 as set forth in SEQ ID NO: 49; and
a second GAA signature peptide of Pompe Disease of SEQ ID NO: 5 with an antibody or antigen binding fragment thereof that binds the GAA signature peptide and comprises: a VH domain comprising a CDRH1 as set forth in SEQ ID NO: 66, a CDRH2 as set forth in SEQ ID NO: 67, and a CDRH3 as set forth in SEQ ID NO: 68, and a VL domain comprising a CDRL1 as set forth in SEQ ID NO: 69, a CDRL2 as set forth in SEQ ID NO: 70, and a CDRL3 as set forth in SEQ ID NO: 71;
and performing liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS) on the enriched peptides to determine a concentration of each enriched signature peptide, thereby detecting one or more signature peptide of MPSI and/or Pompe Disease in the biological sample.