IP Library › Granted Patent US 12,590,312
Granted Patent B2
US 12,590,312 · App. 17/612,934 · Granted Mar 31, 2026

NR4A super-repressors and methods of use thereof

Inventors: Michael Schlabach (Belmont, MA); Brian Alexander Sosa-Alvarado (Cambridge, MA)
Assignee: KSQ Therapeutics, Inc.
C12N15/635A61K40/11A61K40/31A61K40/4242A61P35/00C07K14/7051A61K2239/38C07K2319/03C07K2319/40
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Quick Facts
Patent No.
US 12,590,312
App. No.
17/612,934
Granted
Mar 31, 2026
Kind
B2
Abstract

The present disclosure provides super-repressors capable of inhibiting the transcription of NR4A1, NR4A2, and NR4A3 target genes. The super-repressors can be used to enhance the effector functions of immune cells, e.g., for adoptive cell therapy. Methods of treating disorders using the modified immune cells are also provided.

Claims (21)

1 . A method of treating cancer in a subject in need thereof comprising administering to the subject an effective amount of cells comprising a polynucleotide comprising a nucleic acid encoding a polypeptide comprising a DNA-binding domain that specifically binds to both the NBRE element and the NurRE element, wherein

(a) the polypeptide inhibits the activity of NR4A1, NR4A2, and NR4A3; or

(b) the polypeptide is capable of inhibiting transcription of a gene operably associated with both the NBRE element and the NurRE element.

2 . The method of claim 1 , wherein the polypeptide does not comprise a transcription activation domain.

3 . The method of claim 1 , wherein the cells are T cells.

4 . The method of claim 3 , wherein the cells further comprise an engineered immune receptor.

5 . A method of treating cancer in a subject in need thereof comprising administering to the subject an effective amount of cells comprising a polynucleotide comprising a nucleic acid encoding a polypeptide comprising a DNA-binding domain that specifically binds to both the NBRE element and the NurRE element, wherein the polypeptide does not comprise a transcription activation domain.

6 . The method of claim 5 , wherein the DNA-binding domain is a polypeptide comprising the amino acid sequence of the DNA-binding domain of NR4A1, NR4A2, or NR4A3.

7 . The method of claim 6 , wherein the DNA-binding domain comprises the amino acid sequence of the DNA-binding domain of NR4A3.

8 . The method of claim 7 , wherein the DNA-binding domain of NR4A3 is a polypeptide comprising the amino acid sequence of SEQ ID NO:4.

9 . The method of claim 5 , wherein the DNA-binding domain is a polypeptide comprising the amino acid sequence of any one of SEQ ID NOs: 4, 5, and 50-53.

10 . The method of claim 5 , wherein the DNA-binding domain comprises a TAL effector DNA binding domain, a zinc finger, or a DNA-binding domain from a meganuclease.

11 . The method of claim 5 , wherein the polypeptide further comprises the amino acid sequence of the ligand-binding domain (LBD) of NR4A1, NR4A2, or NR4A3.

12 . The method of claim 5 , wherein the polypeptide further comprises a dimerization domain, a transcriptional repressor domain, or a chromatin compaction domain.

13 . The method of claim 5 , wherein the polypeptide comprises the amino acid sequence of any one of SEQ ID NOs: 29-43.

14 . The method of claim 5 , wherein the polypeptide further comprises a Krüppel-associated box (KRAB) domain.

15 . The method of claim 5 , wherein the polypeptide further comprises NCOR1 or a fragment thereof.

16 . The method of claim 5 , wherein the DNA-binding domain is a polypeptide comprising the amino acid sequence of the DNA-binding domain of NR4A3.

17 . The method of claim 16 , wherein the DNA-binding domain of NR4A3 is a polypeptide comprising the amino acid sequence of SEQ ID NO:4.

18 . The method of claim 5 , wherein the cells are T cells.

19 . The method of claim 18 , wherein the cells further comprise an engineered immune receptor.

Assignments (2)
CHANGE OF ADDRESS Recorded Sep 20, 2022
From: KSQ THERAPEUTICS, INC.
To: KSQ THERAPEUTICS, INC.
Reel/Frame 061479/0133 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 16, 2022
From: SCHLABACH, MICHAEL; SOSA-ALVARADO, BRIAN ALEXANDER
To: KSQ THERAPEUTICS, INC.
Reel/Frame 059141/0861 →
Continuity (2)
Provisional Application 62851554 · May 22, 2019
Related Publication 20220228155A1 · Jul 21, 2022
References Cited (38)
US 5981829A · Mountz et al. · 1999 [cited by applicant]
US 11608500B2 · Benson · 2023 [cited by examiner]
US 20060040298A1 · Schmidt et al. · 2006 [cited by applicant]
US 20060063727A1 · Chang · 2006 [cited by applicant]
US 20190284553A1 · Benson · 2019 [cited by examiner]
US 20220228155A1 · Schlabach · 2022 [cited by examiner]
KR 20150084469A · 2015 [cited by applicant]
WO WO2005017112A2 · 2005 [cited by applicant]
WO WO2019104245A1 · 2019 [cited by applicant]
Achatz, G., et al., “Functional Domains of the Human Orphan Receptor ARP-1/COUP-TFII Involved in Active Repression and Transrepression,” Molecular and Cellular Biology 17(9):4914-4932, Taylor & Francis, United States (S… [cited by applicant]
Beerli, R.R., and Barbas, C.F., “Engineering Polydactyl Zinc-finger Transcription Factors,” Nature Biotechnology 20(2):135-141, Nature America Publishing, United States (Feb. 2002). [cited by applicant]
Brudno, J.N., and Kochenderfer, J.N., “Chimeric Antigen Receptor T-cell Therapies for Lymphoma,” Nature Reviews Clinical Oncology 15(1):31-46, Nature Publishing Group, United Kingdom (Jan. 2018). [cited by applicant]
Chen, J., et al., “NR4A Transcription Factors Limit CAR T Cell Function in Solid Tumours,” Nature 567(7749):530-534, Nature Publishing Group, United Kingdom (Feb. 2019). [cited by applicant]
Choo, Y., and Isalan, M., “Advances in Zinc Finger Engineering,” Current Opinion in Structural Biology 10(4):411-416, Elsevier, Netherlands (Aug. 2000). [cited by applicant]
Choo, Y., et al., “In Vivo Repression by a Site-specific DNA-binding Protein Designed Against an Oncogenic Sequence,” Nature 372(6507):642-645, Nature Publishing Group, United Kingdom (Dec. 1994). [cited by applicant]
Fu, Y., et al., “NR4A Orphan Nuclear Receptors Modulate Insulin Action and the Glucose Transport System: Potential Role in Insulin Resistance,” The Journal of Biological Chemistry 282(43):31525-31533, Elsevier Inc. on b… [cited by applicant]
Gilbert, L.A., et al., “CRISPR-mediated Modular RNA-guided Regulation of Transcription in Eukaryotes,” Cell 154(2):442-451, Cell Press, United States (Jul. 2013). [cited by applicant]
Isalan, M., et al., “A Rapid, Generally Applicable Method to Engineer Zinc Fingers Illustrated by Targeting the HIV-1 Promoter,” Nature Biotechnology 19(7):656-660, Nature America Publishing, United States (Jul. 2001). [cited by applicant]
Johnson, L.A., et al., “Gene Therapy With Human and Mouse T-cell Receptors Mediates Cancer Regression and Targets Normal Tissues Expressing Cognate Antigen,” Blood 114(3):535-546, Elsevier, Netherlands (Jul. 2009). [cited by applicant]
Kochenderfer, J.N., et al., “B-cell Depletion and Remissions of Malignancy Along With Cytokine-associated Toxicity in a Clinical Trial of Anti-CD19 Chimeric-antigen-receptor-transduced T Cells,” Blood 119(12):2709-2720,… [cited by applicant]
Lamers, C.H., et al., “Treatment of Metastatic Renal Cell Carcinoma With CAIX Car-engineered T Cells: Clinical Evaluation and Management of on-target Toxicity,” Molecular Therapy 21(4):904-912, Cell Press, United States… [cited by applicant]
Nordzell, M., et al., “Defining an N-terminal Activation Domain of the Orphan Nuclear Receptor Nurr1,” Biochemical and Biophysical Research Communications 313(1):205-211, Elsevier, Netherlands (Jan. 2004). [cited by applicant]
Pabo, C.O., et al., “Design and Selection of Novel Cys [cited by applicant]
Paulsen, R.F., et al., “Three Related Brain Nuclear Receptors, NGFI-B, Nurr1, and NOR-1, as Transcriptional Activators,” Journal of Molecular Neuroscience 6(4):249-255, Humana Press, United States (Dec. 1995). [cited by applicant]
Philips, A., et al., “Novel Dimeric Nur77 Signaling Mechanism in Endocrine and Lymphoid Cells,” Molecular and Cellular Biology 17(10):5946-5951, Taylor & Francis, United States (Oct. 1997). [cited by applicant]
Radvanyi, L.G., et al., “Specific Lymphocyte Subsets Predict Response to Adoptive Cell Therapy Using Expanded Autologous Tumor-infiltrating Lymphocytes in Metastatic Melanoma Patients,” Clinical Cancer Research 18(24):6… [cited by applicant]
Safe, S., et al., “Nuclear Receptor 4A (NR4A) Family—Orphans No More,” The Journal of Steroid Biochemistry and Molecular Biology 157:48-60, Pergamon, United Kingdom (Mar. 2016). [cited by applicant]
Segal, D.J., and Barbas 3rd, C.F., “Custom DNA-Binding Proteins Come of Age: Polydactyl Zinc-Finger Proteins,” Current Opinion in Biotechnology 12(6):632-637, Elsevier, Netherlands (Dec. 2001). [cited by applicant]
Song, C-H., et al., “Testicular Steroidogenesis is Locally Regulated by Androgen via Suppression of Nur77,” Biochemical and Biophysical Research Communications 422(2):327-332, Elsevier, Netherlands (Jun. 2012). [cited by applicant]
Thakore, P.I., et al., “Editing the Epigenome: Technologies for Programmable Transcription and Epigenetic Modulation,” Nature Methods 13(2):127-137, Nature Publishing Group, United Kingdom (Feb. 2016). [cited by applicant]
UniProtKB, “NR4A2_Human,” Accession No. P43354, accessed at https://www.uniprot.org/uniprotkb/P43354/entry, accessed on Mar. 25, 2025, 10 pages. [cited by applicant]
UniProtKB, “NR4A3_Human,” Accession No. Q92570, accessed at https://www.uniprot.org/uniprotkb/Q92570/entry, accessed on Mar. 25, 2025, 12 pages. [cited by applicant]
UniProtKB, “NR4A1_Human,” Accession No. P22736, accessed at https://www.uniprot.org/uniprotkb/P22736/entry, accessed on Mar. 25, 2025, 17 pages. [cited by applicant]
Warren, R.S., et al., “Clinical Studies of Regional and Systemic Gene Therapy with Autologous CC49-zeta Modified T Cells in Colorectal Cancer Metastatic to Liver,” Cancer Gene Therapy 5:S1-S2, pp. 1-3, Springer Nature, … [cited by applicant]
Wilson, T.E., et al., “Participation of Non-zinc Finger Residues in DNA Binding by Two Nuclear Orphan Receptors,” Science 256(5053):107-110, American Association for the Advancement of Science, United States (Apr. 1992). [cited by applicant]
Yeo, N.C., et al., “An Enhanced CRISPR Repressor for Targeted Mammalian Gene Regulation,” Nature Methods 15(8):611-616, Nature Publishing Group, United Kingdom (Aug. 2018). [cited by applicant]
Nakagawara, K., “NR4A Ablation Improves Mitochondrial Fitness for Long Persistence in Human CAR-T Cells Against Solid Tumors,” Journal for Immunotherapy of Cancer 12(8):e008665, pp. 1-16, BMJ Publishing Group Ltd., Unit… [cited by applicant]
Srirat, T., et al., “NR4a1/2 Deletion Promotes Accumulation of TCF1+ Stem-like Precursors of Exhausted CD8+ T Cells in the Tumor Microenvironment,” Cell Reports 43(3):113898, pp. 1-25, Cell Press, United States (Mar. 20… [cited by applicant]