TCR(alpha)-LCR-DERIVED GENE REGULATORY CASSETTES
20170240918 · 2017-08-24
Inventors
Cpc classification
C12N2830/46
CHEMISTRY; METALLURGY
C12N2740/15043
CHEMISTRY; METALLURGY
International classification
Abstract
A method of delivering a transgene to a cell is provided. The method uses a vector that contains a T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette having fewer than 5.0-kb. The method delivers the transgene with spatiotemporally specific gene expression and silencing-prevention controls to a cell such that a predetermined subset of progeny cell-types express a gene product from the transgene. Other progeny of the cell diminish, or silence, the expression of the gene product.
Claims
1. A method of delivering a gene to a cell such that progeny of the cell expresses a predetermined gene product with spatiotemporal specificity and resistance to silencing, the method comprising: introducing a vector to a cell, the vector comprising: (a) a T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette having fewer than 5.0-kb, the TCRαLCR derived gene regulatory cassette comprising a sequence that is at least 70% identical with SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3; and (b) a first transgene to be expressed.
2. The method as recited in claim 1, wherein the cell is a stem cell.
3. The method as recited in claim 1, wherein the cell is a multi-potent precursor cell.
4. The method as recited in claim 3, further comprising permitting the multi-potent precursor cell to proliferate and differentiate to form a population of T-cells and a population of non-T-cell progeny cells, wherein the population of T-cells differentiating from the multi-potent precursor cell expresses the first transgene with a first degree of expression and the population of non-T-cell progeny cells expresses the first transgene with a second degree of expression that is lower than the first degree of expression.
5. The method as recited in claim 4, wherein the second degree of expression is zero.
6. The method as recited in claim 1, wherein the first transgene is directly linked 5′ to the TCRαLCR derived gene regulatory cassette.
7. The method as recited in claim 1, wherein the first transgene is directly linked 3′ to the TCRαLCR derived gene regulatory cassette.
8. The method as recited in claim 1, wherein the first transgene is promoter-driven cDNA.
9. The method as recited in claim 1, wherein the vector further comprises a second transgene, wherein first transgene and the second transgene flank the T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette.
10. The method as recited in claim 1, wherein the vector further comprises a second transgene and the second transgene is a promoter-driven cDNA.
11. The method as recited in claim 1, wherein the vector further comprises a second transgene and the second transgene is a promoter-driven suicide cDNA.
12. The method as recited in claim 1, wherein the vector consists essentially of the T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette and the first transgene.
13. The method as recited in claim 1, wherein the vector consists essentially of the T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette and the first transgene and a second transgene.
14. The method as recited in claim 1, wherein the TCRαLCR derived gene regulatory cassette has fewer than 5.0-kb and the sequence within the TCRαLCR derived gene regulatory cassette is at least 70% identical with SEQ ID NO: 1.
15. The method as recited in claim 1, wherein the TCRαLCR derived gene regulatory cassette has fewer than 3.0-kb and the sequence within the TCRαLCR derived gene regulatory cassette is at least 70% identical with SEQ ED NO: 2.
16. The method as recited in claim 1, wherein the TCRαLCR derived gene regulatory cassette has fewer than 2.0-kb and the sequence within the TCRαLCR derived gene regulatory cassette is at least 70% identical with SEQ ID NO: 3.
17. The method as recited in claim 1, wherein the sequence is at least 80% identical with SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.
18. The method as recited in claim 1, wherein the sequence is at least 90% identical with SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.
19. The method as recited in claim 1, wherein the sequence is at least 90% identical with SEQ ID NO: 3.
20. A method of delivering a gene to a T cell such that the T cell expresses a predetermined gene product with resistance to silencing, the method comprising: introducing a vector to a T cell, the vector comprising: (a) a T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette having fewer than 5.0-kb, the TCRαLCR derived gene regulatory cassette comprising a sequence that is at least 70% identical with SEQ ID NO: 3; and (b) a first transgene to be expressed.
21. A vector for delivering a gene to a cell such that progeny of the cell expresses a predetermined gene product with spatiotemporal specificity and resistance to silencing, the vector comprising: (a) a T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette having fewer than 5.0-kb, the TCRαLCR derived gene regulatory cassette comprising a sequence that is at least 70% identical with SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3; and (b) a first transgene to be expressed.
22. The vector as recited in claim 21, wherein the vector further comprises a second transgene, wherein first transgene and the second transgene flank the T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette.
23. The vector as recited in claim 21, wherein the vector further comprises a second transgene and the second transgene is a promoter-driven cDNA.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] So that the manner in which the features of the invention can be understood, a detailed description of the invention may be had by reference to certain embodiments, some of which are illustrated in the accompanying drawings. It is to be noted, however, that the drawings illustrate only certain embodiments of this invention and are therefore not to be considered limiting of its scope, for the scope of the in encompasses other equally effective embodiments. The drawings ate not necessarily to scale, emphasis generally being placed upon illustrating the features of certain embodiments of the invention. In the drawings, like numerals are used to indicate like parts throughout the various views. Thus, for further understanding of the invention, reference can be made to the following detailed description, read in connection with the drawings in which:
[0014]
[0015]
[0016]
[0017]
[0018]
[0019]
DETAILED DESCRIPTION OF THE INVENTION
[0020] Several T-cell receptor alpha (TCRα) locus control region (LCR)-derived gene regulatory cassettes are disclosed herein. Generally, these nucleotides range from 4.0-kbp to 1.3-kbp in DNA length. They contain various combinations of DNA from four functional regions of the TCRαLCR (as defined by studies in transgenic mouse models). These four functional regions refer to specific DNAse I hypersensitive sites (HS) within the TCRαLCR named as follows: HS1, HS1′, HS4, HS6. The combinations were made via recombinant DNA technology and were maintained/produced using bacterial plasmid vectors. These regulatory cassettes provide consistent, high-level transgene expression from gene transfer vectors that is: 1) spatiotemporally specific to T-cells and 2) resistant to the silencing effects of genomic heterochromatin spreading. Two cell culture-based assays, were developed to measure these two gene regulatory properties.
[0021] Finding the minimal amount of TCRαLCR DNA capable of supporting maximal TCRαLCR activity is desirable for incorporation into viral vectors, which typically have limited space for exogenous DNA sequences. The disclosed SEQ ID NO: 1 provides a robust 4.0-kb mini-LCR (TαLCR4.0) version that is 30% of the original DNA length of the full LCR in the genome (13-kb) but reproduces the qualities of the full-length version. The temporal activation pattern of this 4.0-kb mini-LCR is particularly well suited to driving a pattern of the expression of therapeutic antigen receptors that mimics the natural, physiological expression pattern of endogenous αβ T-cell receptor complex emergence in vivo. The early temporal activation kinetics of the small (1.3-kb) mini-LCR (TαLCR1.3) (SEQ ID NO: 3) is well suited for expressing therapeutic cargo genes to correct inherited, genetic T-cell immunodeficiency, or to express genes in T-cells that confer them with intracellular resistance to infection by T-cell tropic viruses (e.g. HIV). Like TαLCR4.0 and TαLCR1.3, the medium (2.4-kb) mini-LCR (TαLCR2.4) (SEQ ID NO: 2) possesses a strong capacity to insulate linked gene expression from silencing over time m the genuine T cells. A more detailed discussion follows.
[0022] Protection from Silencing (“Insulation Capacity”)
[0023] In pilot experiments (data not shown), data showing that the fall LCR possessed strong insulator-like activity in this assay was obtained, providing 100% protection of inked transgenes from silencing over time in all clones analyzed (n=7 single copy clones). For a description of the full LCR see B. D. Ortiz et al. Adjacent DNA elements dominantly restrict the ubiquitous activity of a novel chromatin-opening region to specific tissues The EMBO Journal, Vol. 16 No. 16 (1997) pp.5037-5045. in the absence of HS1′ through HS6 of the LCR sequences, the linked reporter gene experienced gradual silencing over time in all clones analyzed (11-6 single copy clones). Three TCRα-LCR constructions (SEQ ID NO. 1 (TαLCR4.0), SEQ ID NO: 2 (TαLCR2.4) and SEQ ID NO: 3 (TαLCR1.3) were designed to maintain the strong insulator-like activity.
[0024] As shown in
[0025] Each done was cultured in duplicate, one under drug selection, the second without drug selection (to permit detection of reporter gene silencing), YFP levels for all cultures were monitored over a 90-day period. The percent YFP maintenance in the absence of drug selection was calculated (YEP.sub.nodrug/YFP.sub.drug) for each done. All three mini-LCR versions were observed to offer substantial protection from reporter gene silencing by this measure.
[0026] The gradual gene silencing in enhancer-only clones has been linked to changes in historic modifications at the reporter gene locus. Chromatin immuno-precipitation (ChIP) studies show maintenance of euchromatin marks (e.g. diacetylated histone H3) at the reporter locus over time when the TαLCR4.0 (SEQ ID NO. 1) is present (
[0027] Spatiotemporal Specificity
[0028]
[0029]
[0030] As shown in
[0031] These mini-LCRs, in the context of lentiviral gene therapy vectors, can provide cargo gene transcription from lentiviral vectors with the requisite resilience and specificity to be used in gene therapy applications in which T-cells expressing a therapeutic gene product in a patient are derived from genetically engineered stem cell transplants.
[0032] The TCRαLCR gives consistent, high-level expression beginning in late stage thymic T-cells and mature peripheral T-cells. This late stage timing is particularly suited to expression of exogenous antigen receptors, premature expression of which during T-cell development is known to cause abnormalities in mice. In contrast, the hCD2 LCR gives consistent high-level activity from early thymic T-cell stages on and is also consistently active in B-lineage cells. Thus the TCRαLCR is likely to be more specific in directing therapeutic gene expression to T-cells than the hCD2 LCR. The β-globin LCR is only active in erythroid lineage cells.
[0033] In other embodiments, cell lines are created to test agents affecting TCRα gene expression in cell culture. In still other embodiments, transgenic mouse models are created in which it is desired for the introduced gene's expression to be integration site-independent and directed to late stage thymic T cells and mature peripheral T cells.
[0034] The efficacy of the disclosed mini-TCR a LCRs in the context of a lend viral construct has been evaluated. A lentiviral gene transfer vector was obtained. A Vα-promoter-driven YFP reporter gene (creating lenti-VαYFP) was cloned into it and further linked this to each of the mini-LCRs.
[0035]
[0036] In one embodiment, a method of delivering gene product expressed from a genomically integrated vector to a biological cell is provided. The method comprises introducing a genomically integrated vector to a biological cell. The genomically integrated vector comprises (a) a T-cell receptor alpha locus control region (TCRαLCR) derived gene regulatory cassette having fewer than 5.0-kb, the TCRαLCR derived gene regulatory cassette being at least 70% identical with SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3; and (h) a first transgene to be expressed. In another embodiment, the TCRαLCR derived gene regulatory cassette is at least 80% identical with one of the above-referenced sequences. In yet another embodiment, the TCRαLCR derived gene regulatory cassette is at least 90% identical with one of the above-referenced sequences. In another embodiment, the TCRαLCR derived gene regulatory cassette consists essentially of one of the above-referenced sequences.
[0037] The term “transgene” refers to a sequence that includes a promotor and a gene that encodes for a predetermined gene product. The first transgene may be, for example, a short promoter-driven cDNA that encodes a gene product with therapeutic impact. For example, a cDNA may be used to produce a protein in T cells that would substitute for one that would have been produced by an endogenous gene that is congenitally non-functional (for examples, see Tasher et al., The genetic basis of severe combined immunodeficiency and its variants, Applications of Clinical Genetics, (Aug. 6, 2012) pp 67-80). Alternatively a cDNA encoding a TCR or chimeric antigen receptor directing T cells to target tumor cells may be used (see Porter et al., Chimeric Antigen Receptor-Modified T Cells in Chronic Lymphoid Leukemia, The New England Journal of Medicine, V. 365, (2011) pp725-33). Alternatively, a cDNA encoding a protein or a non-coding RNA (e.g. miRNA product) that inhibits the life cycle oft T-cell tropic virus inside a T cells may be used (for examples, see Tebas et al., Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV, The New England Journal of Medicine, vol. 370, no. 10 (Mar. 6, 2014) pp 901-910 and Tebas et al., Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV, Blood, vol. 121. no. 9, (Feb. 26, 2013), pp 1524-1533). The transgene may be linked 5′ or 3′ to the TCRαLCR derived gene regulatory cassette.
[0038] In one embodiment, a second transgene is also provided. The second transgene may, for example, attenuate or modulate the function of the first transgene. For example a first CAR cDNA can be coupled with a second inhibitory CAR cDNA to divert off-target T cell responses (ref: Federov, et. al. Sci. Transl. Med. 2013 Dec. 11; 5(215):215ra172.). Alternatively, the first and second transgenes may co-express a set of two incomplete but complementary CAR encoding cDNAs to increase target cell specificity by requiring recognition of two antigens to induce a T cell response (Kloss, et. al. 2013. Nat. Biotechnol. 31:71-5). Alternatively, a first CAR/TCR transgene can be co-expressed with a second transgene expressing a “suicide cDNA” (e.g. thymidine kinase) that will enable elimination of therapeutic gene expressing cells upon administration of a specific drug (e g. acyclovir). In another embodiment, the first and second transgenes provide intracellular resistance to two T cell tropic viruses at once (e,g. HIV and HTLV-1). The first and second transgenes, in some embodiments, flank the TCRαLCR derived gene regulatory cassette.
[0039] In one embodiment, the TCRαLCR derived gene regulatory cassette has fewer than 5.0-kb and is at least 90% identical with SEQ ID NO: 1. In another embodiment, the TCRαLCR derived gene regulatory cassette has fewer than 3.0-kb and is at least 90% identical with SEQ ID NO: 2. In yet another embodiment, the TCRαLCR derived gene regulatory cassette has fewer than 2.0-kb and is at least 90% identical with SEQ ID NO: 3.
[0040] Three mini-TCRαLCRs (SEQ ID NO: 1; SEQ ID NO: 2 and SEQ ID NO: 3) were constructed from portions of the endogenous mouse TCRαLCR that had been determined to be functional cis-acting gene regulatory elements. These elements were assembled in the pBlueScript SK I (PBSK) cloning vector (Stratagene) as follows.
[0041] Construction of the “small” mini-LCR (TαLCR1.3) cassette (SEQ ID NO: 1)
[0042] pS-HS11′ PvuII/Sca 1: The smallest version of the mini TCRαLCR contains segments of the HS1, HS1′ and HS6 functional regions of the full LCR. To isolate the HS1 and 1′ region, a PCR scheme was developed to amplify an 804-bp fragment spanning from the Pvu II site located at the 5′-border of the Eα transcriptional enhancer located in HS1 to the Sea site (3 border) located in HS1′. This region contains Eα and ends right after the identified CTCF sites within HS1′. The forward primer included an artificial Xho 1 site on the 5′-end and the reverse primer included an artificial Cla I site on the 3′ end. The sequence for the forward primer was: 5′-GACCTGCTCGAGCTGCACCCTGAAATGGT-3′ (SEQ ID NO: 4). The reverse primer sequence was: 5′-CGAGTCATCGATACTGCTGCCCCCGTGTG-3′ (SEQ ID NO: 5). The insertion of these two unique restriction enzyme target sites enabled the insertion of the PCR product into the Xho 1 and Cla I sites of pBSK. This plasmid contained the functional regions of Eα and HS1′ and was termed pS-HS11′ PvuII/Sac I.
[0043] pS-LCR: To complete the construction of the small LCR, a 554-bp Bcl I to Bgl II fragment of the HS6 region was placed into the BamIII site of pvuII/Sca I. Since digestions of DNA with Bcl I and Bgl II leave both ends compatible with ligation into Bam HI sites, the resulting plasmids was analyzed for clones bearing the fragment in the correct natural genomic orientation. This was confirmed by restriction analysis. The correct plasmid was termed pSLCR, containing the TαLCR1.3 cassette.
[0044] Construction of the “medium” mini-LCR (TαLCR2.4) cassette
[0045] pM-LCR: The medium version of the mini TCRαLCR (TαLCR2.4) has the same regions HS1, HS1′ and HS6 as the small LCR with the addition of an 1127-bp region containing the HS4 element. This ApaL I to Dra I region of HS4 was blunted and ligated into a unique EcoR V site within pSLCR in between the HS1/HS1′ and HS6 regions in the natural genomic orientation.
[0046] Construction of the “large” mini-LCR (TαLCR4.0) cassette
[0047] pL-HS11′ PvuII/BamHI: To isolate the enhancer (HS1) and complete HS1′ region of the TCRαLCR, a PCR primer pair was designed to amplify a 1052-bp genomic fragment spanning from a Pvu II site located at the 5′ border of the the Eα transcriptional enhancer in HS1 to a Ban site located at the 3′-border of HS1′. The forward primer included an artificial Xho I site on the 5′ end and reverse primer included an artificial Cla I site on the 3′ end. The sequence for the forward primer was: 5′-GACCTGCTCGAGCTGCACCCTGAAATGGT-3′ (SEQ ID NO: 4), while the sequence for the reverse primer was: 5′-CGAGTCATCGATACTGCTGCCCCCGTGTGG-3′ (SEQ ID NO: 5). The PCR product was digested with Xho I and Cla I and placed in to their corresponding sites in PBSK. Once assembled, this PBSK plasmid contained the complete HS1 and HS1′ region and was termed pL-HS11′ PvuII/BamH I.
[0048] pL-HS11′/L-HS6: A 1786-bp Mfe I to Ec136 II fragment containing the complete HS6 region was excised. This fragment was inserted 3′ of the HS1/HS1′ DNA in pL-HS11′ PvuII/BamH I using the EcoR I site and Sma I sites.
[0049] pL-LCR: The 1127-bp ApaL I to Dra I fragment containing the HS4 region was blunted and inserted into the EcoR V site of pL-HS11′/L-HS6 in a position in between the HS1/HS1′ and the HS6 DNA to complete pL-LCR containing the (TαLCR4.0) cassette.
[0050] This written description uses examples to disclose the invention, including the best mode, and also to enable any person skilled in the art to practice the invention, including making and using any devices or systems and performing any incorporated methods. The patentable scope of the invention is defined by the claims, and may include other examples that occur to those skilled in the art. Such other examples are intended to be within the scope of the claims if they have structural elements that do not differ from the literal language of the claims, or if they include equivalent structural elements with insubstantial differences from the literal language of the claims.