IP Library › Granted Patent US 12,590,139
Granted Patent B2
US 12,590,139 · App. 17/631,821 · Granted Mar 31, 2026

MHC class II molecules and methods of use thereof

Inventors: Naoto Hirano (Toronto, CA); Kenji Sugata (Toronto, CA)
Assignee: University Health Network
C07K14/70539A61P35/00A61K38/00
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 12,590,139
App. No.
17/631,821
Granted
Mar 31, 2026
Kind
B2
Abstract

The present disclosure is directed to HLA class II molecules having a higher affinity for CD4 than naturally occurring HLA class II molecules. In certain aspects, the HLA class II molecule comprises a DQ beta chain having (i) an amino acid other than leucine at a position corresponding to amino acid residue 114 of SEQ ID NO: 1, (ii) an amino acid other than valine at a position corresponding to amino acid residue 143 of SEQ ID NO: 1, (iii) or both (i) and (ii). Certain aspects of the present disclosure are directed to nucleic acid molecules encoding the HLA class II molecules, vectors comprising the nucleic acid molecule, cells comprising the same, and methods of use thereof.

Claims (21)

1 . A DQ beta chain comprising an amino acid sequence with:

at least 80% identity to the amino acid sequence of SEQ ID NO: 3 and

(i) a tryptophan at the position corresponding to amino acid residue 114 of SEQ ID NO: 3;

(ii) a methionine at the position corresponding to amino acid residue 143 of SEQ ID NO: 3;

(iii) a glutamine at the position corresponding to amino acid residue 110 of SEQ ID NO: 3;

(iv) a valine at the position corresponding to amino acid residue 116 of SEQ ID NO: 3;

(v) a histidine at the position corresponding to amino acid residue 118 of SEQ ID NO: 3; and

(vi) an asparagine at the position corresponding to amino acid residue 146 of SEQ ID NO: 3.

2 . The DQ beta chain of claim 1 , comprising the amino acid sequence set forth in SEQ ID NO: 3.

3 . An HLA class II molecule comprising a DQ beta chain of claim 1 and a DQ alpha chain.

4 . The HLA class II molecule of claim 3 , wherein the DQ alpha chain comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 6 or 8.

5 . The HLA class II molecule of claim 4 , wherein the DQ alpha chain comprises the amino acid sequence set forth in SEQ ID NO: 6 or 8.

6 . A nucleic acid molecule encoding the HLA class II molecule of claim 3 .

7 . A cell comprising the HLA class II molecule of claim 3 .

8 . A complex comprising the HLA class II molecule of claim 3 and a peptide, wherein the peptide comprises DDX3Y 171-190 , HA 255-270 , GPC3 138-157 , or any combination thereof.

9 . The DQ beta chain of claim 1 comprising the amino acid sequence set forth in SEQ ID NO: 4.

10 . The cell of claim 7 , which is a mammalian cell or an insect cell.

11 . The cell of claim 7 , which is a K562 cell, T2, HEK293, HEK293T, A375, SK-MEL-28, Me275, COS, a fibroblast cell, or a tumor cell.

12 . The cell of claim 7 , which (i) lacks endogenous MHC class II DQ beta chain expression, (ii) lacks endogenous MHC class II DQ alpha chain expression, (iii) or both (i) and (ii).

13 . The HLA class II molecule of claim 3 , wherein the DQ beta chain comprises the amino acid sequence set forth in SEQ ID NO: 3.

14 . The HLA class II molecule of claim 13 , wherein the DQ beta chain comprises the amino acid sequence set forth in SEQ ID NO: 4.

Continuity (3)
Provisional Application 63029114 · May 22, 2020
Provisional Application 62880501 · Jul 30, 2019
Related Publication 20220275051A1 · Sep 1, 2022
References Cited (59)
US 20030064915A1 · Strominger et al. · 2003 [cited by applicant]
US 20050042624A1 · Itoh et al. · 2005 [cited by applicant]
US 20060084116A1 · Muchhal · 2006 [cited by applicant]
US 20060228758A1 · Muchhal et al. · 2006 [cited by applicant]
US 20130287748A1 · June et al. · 2013 [cited by applicant]
US 20220281948A1 · Hirano et al. · 2022 [cited by applicant]
US 20220281949A1 · Hirano et al. · 2022 [cited by applicant]
US 20220291215A1 · Hirano et al. · 2022 [cited by applicant]
CA 2995838A1 · 2017 [cited by applicant]
CN 1244804A · 2000 [cited by applicant]
CN 1902313A · 2007 [cited by applicant]
CN 101001868A · 2007 [cited by applicant]
CN 109476727A · 2019 [cited by applicant]
WO WO02077030A2 · 2002 [cited by applicant]
WO WO2008109075A2 · 2008 [cited by applicant]
WO WO2016135363A1 · 2016 [cited by applicant]
WO WO2019126818A1 · 2019 [cited by applicant]
National Library of Medicine (US), National Center for Biotechnology Information;—. Accession No. XP_012517264, Predicted: HLA class II histocompatibility antigen, DQ beta 1 chain-like [Propithecus coquereli]; [cited Ju… [cited by examiner]
Gustafsson et al. Class II Genes of Miniature Swine. Journal of Immunology, vol. 145, 1946-1951, No. 6, Sep. 15, 1990 (Year: 1990). [cited by examiner]
Anczurowski, M., et al., “Mechanisms underlying the lack of endogenous processing and CLIP-mediated binding of the invariant chain by HLA-DP84Gly,” Sci. Rep. 8:4804, Springer, Germany (Mar. 2018). [cited by applicant]
Butler, M.O., et al., “Ex vivo expansion of human CD8+ T cells using autologous CD4+ T cell help,” PloS One 7:e30229, PLOS, United States (Jan. 2012). [cited by applicant]
Butler, M.O., et al., “Long-lived antitumor CD8+ lymphocytes for adoptive therapy generated using an artificial antigen-presenting cell,” Clin Cancer Res 13:1857-1867, American Association for Cancer Research, United St… [cited by applicant]
De Jong, W., and Borm, P., “Drug delivery and nanoparticles:applications and hazards,” Int. J Nanomedicine 3(2):133-49, Dove Medical Press, United Kingdom (Jun. 2008). [cited by applicant]
Fleury, S., et al., “HLA-DR Polymorphism Affects the Interaction with CD4,” J Exp Med 182(3):733-741, Rockefeller University Press, United States (Sep. 1995). [cited by applicant]
Genbank, “HLA class II histocompatibility antigen, DP beta 1 chain [ [cited by applicant]
Genbank, “HLA class II histocompatibility antigen, DP beta 1 chain-like,” Accession No. XP_023576849, accessed at https://www.ncbi.nlm.nih.gov/protein/XP_023576849.1/, Jan. 2018, accessed on Dec. 18, 2024, 2 pages. [cited by applicant]
Genbank, “HLA class II histocompatibility antigen, DQ beta 1 chain,” Accession No. XP_008260979, accessed at https://www.ncbi.nlm.nih.gov/protein/XP_008260979.2/, Jun. 23, 2016, accessed on Dec. 18, 2024, 2 pages. [cited by applicant]
Genbank, “MHC class II antigen [ [cited by applicant]
Genbank, “MHC class II antigen, partial,” Accession No. AUZ41832, accessed at https://www.ncbi.nlm.nih.gov/protein/AUZ41832.1/, Feb. 2018, accessed on Dec. 18, 2024, 2 pages. [cited by applicant]
Genbank, “Predicted: boLa class II histocompatibility antigen, DQB*0101 beta chain,” Accession No. XP_005879777, accessed at https://www.ncbi.nlm.nih.gov/protein/XP_005879777.2/ Nov. 2015, accessed on Dec. 18, 2024, 2 p… [cited by applicant]
Genbank, “Predicted: HLA class II histocompatibility antigen, DQ beta 1 chain-like [Propithecus coquereli],” Accession No. XP_012517264, accessed at https://www.ncbi.nlm.nih.gov/protein/XP_012517264.1/, Jun. 2015, acces… [cited by applicant]
GenBank, “T-cell surface glycoprotein CD4 isoform 1 precursor [ [cited by applicant]
Hasan, A.N., et al., “Artificial Antigen Presenting Cells: An Off the Shelf Approach for Generation of Desirable T-Cell Populations for Broad Application of Adoptive Immunotherapy,” Adv. Genet. Eng. 4(3):130, (Oct. 2015… [cited by applicant]
Heemskerk, M.H., et al., “Redirection of antileukemic reactivity of peripheral T lymphocytes using gene transfer of minor histocompatibility antigen HA-2-specific T-cell receptor complexes expressing a conserved alpha j… [cited by applicant]
Hirano, N., et al., “Efficient presentation of naturally processed HLA class I peptides by artificial antigen-presenting cells for the generation of effective antitumor responses,” Clin Cancer Res 12:2967-2975, American… [cited by applicant]
Hirano, N., et al., “Engagement of CD83 ligand induces prolonged expansion of CD8+ T cells and preferential enrichment for antigen specificity,” Blood 107:1528-1536, American Society of Hematology, United States (Feb. 2… [cited by applicant]
Hirano, N., et al., “Identification of an immunogenic CD8+ T-cell epitope derived from gamma-globin, a putative tumor-associated antigen for juvenile myelomonocytic leukemia,” Blood 108:2662-2668, American Society of He… [cited by applicant]
Huang, B., et al., “Analysis of the contact sites on the CD4 molecule with class II MHC molecule: co-ligand versus co-receptor function,” J Immunol 158(1):216-25, American Association of Immunologists, United States (Ja… [cited by applicant]
Huang, S., and Kamihira, M., “Development of hybrid viral vectors for gene therapy,” Biotechnol. Adv. 31(2):208-23, Elsevier, Netherlands (May 2013). [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/IB2020/057176, Canadian Intellectual Property Office, Quebec, mailed on Nov. 10, 2020, 11 pages. [cited by applicant]
Janeway, C., et al., “Recognition of MHC Class II Antigens by the CD4: T Cell Receptor Complex,” In: H-2 Antigens. NATO ASI Series (Series A: Life Sciences), David C.S., eds., pp. 441-449, Springer, United States (1987). [cited by applicant]
Nakatsugawa, M et al., “Specific roles of each TCR hemichain in generating functional chain-centric TCR,” J Immunol 194:3487-3500, American Association of Immunologists, United States (Apr. 2015). [cited by applicant]
Nakatsugawa, M., et al., “CD4(+) and CD8(+) TCRβ repertoires possess different potentials to generate extraordinarily high-avidity T cells,” Sci Rep 6:23821, Springer, Germany (Mar. 2016). [cited by applicant]
Ochi, T., et al., “Optimization of T-cell Reactivity by Exploiting TCR Chain Centricity for the Purpose of Safe and Effective Antitumor TCR Gene Therapy,” Cancer Immunol Res 3:1070-1081, American Association for Cancer … [cited by applicant]
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs, R., et al., “Evolutionary and biomedical insights from the rhesus macaque genome,” Science 316(5822):222-34, American Association for the Advancement of S… [cited by applicant]
Su, L.F., et al., “Virus-specific CD4(+) memory-phenotype T cells are abundant in unexposed adults,” Immunity 38:373-383, Cell Press, United Kingdom (Feb. 2013). [cited by applicant]
Umeshappa, C., et al., “Suppression of a broad spectrum of liver autoimmune pathologies by single peptide-MHC-based nanomedicines,” Nat. Commun. 10(1):2150, Springer, Germany (May 2019). [cited by applicant]
Wang, X.X., et al., “Affinity Maturation of Human CD4 by Yeast Surface Display and Crystal Structure of a CD4-HLA-DR1 Complex,” PNAS, 108(38):15960-15965, National Academy of Sciences, United States (Sep. 2011). [cited by applicant]
Weber, K.S., et al., “Class II-restricted T cell receptor engineered in vitro for higher affinity retains peptide specificity and function,” PNAS 102(52):19033-19038, National Academy of Sciences, United States (Dec. 20… [cited by applicant]
Wooldridge, L., et al., “Anti-coreceptor antibodies profoundly affect staining with peptide-MHC class I and class II tetramers,” Eur J Immunol 36:1847-1855, Wiley-VCH, United States (Jun. 2006). [cited by applicant]
Yamashita, Y., et al., “HLA-DP84Gly constitutively presents endogenous peptides generated by the class I antigen processing pathway,” Nat. Commun. 8:15244, Springer, Germany (May 2017). [cited by applicant]
Yao, X., et al., “Isolation and Characterization of an HLA-DPB1*04: 01-restricted MAGE-A3 T-Cell Receptor for Cancer Immunotherapy,” J Immunother. 39:191-201, Lippincott Williams and Wilkins Ltd., United States (Jun. 20… [cited by applicant]
Feng, S., et al., “QM/MM Molecular Dynamics Simulation for the MHC class I Molecule Interacting with Antigen Peptide,” Acta Chimica Sinica 71(9):1313-1320, SIOC Journals, China (Jun. 2013). [cited by applicant]
Kremer, A.N., et al., “Natural T-cell ligands that are created by genetic variants can be transferred between cells by extracellular vesicles,” Eur J Immunol 48(10):1621-1631, Wiley, United States (Oct. 2018). [cited by applicant]
Sugata, K., et al., “Affinity-matured HLA class II dimers for robust staining of antigen-specific CD4+ T cells,” Nature biotechnology 39(8):958-967, Nature Portfolio, Germany (Aug. 2021). [cited by applicant]
UniProt, “MHC class II antigen,” Accession No. XP_093087560, accessed at https://www.uniprot.org/uniprotkb/F8LFW2/entry, accessed on Dec. 18, 2024, 6 pages. [cited by applicant]
UniProt, “MHC class II antigen,” Accession No. XP_093087727, accessed at https://www.uniprot.org/uniprotkb/Q7YPT7/entry, accessed on Dec. 18, 2024, 7 pages. [cited by applicant]
International Search Report and Written Opinion for International Application No. PCT/IB2020/057173, Canadian Intellectual Property Office, Canada, mailed on Nov. 10, 2020, 21 pages. [cited by applicant]
Marsh, S.G.E., et al., “Nomenclature for factors of the HLA system, 2010,” [cited by applicant]