Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells

Abstract

Human induced pluripotent stem cells (iPSCs) represent a unique opportunity for regenerative medicine because they offer the prospect of generating unlimited quantities of cells for autologous transplantation, with potential application in treatments for a broad range of disorders. However, the use of human iPSCs in the context of genetically inherited human disease will require the correction of disease-causing mutations in a manner that is fully compatible with clinical applications. The methods currently available, such as homologous recombination, lack the necessary efficiency and also leave residual sequences in the targeted genome. Therefore, the development of new approaches to edit the mammalian genome is a prerequisite to delivering the clinical promise of human iPSCs. Here we show that a combination of zinc finger nucleases (ZFNs) and piggyBac technology in human iPSCs can achieve biallelic correction of a point mutation (Glu342Lys) in the α(1)-antitrypsin (A1AT, also known as SERPINA1) gene that is responsible for α(1)-antitrypsin deficiency. Genetic correction of human iPSCs restored the structure and function of A1AT in subsequently derived liver cells in vitro and in vivo. This approach is significantly more efficient than any other gene-targeting technology that is currently available and crucially prevents contamination of the host genome with residual non-human sequences. Our results provide the first proof of principle, to our knowledge, for the potential of combining human iPSCs with genetic correction to generate clinically relevant cells for autologous cell-based therapies.

Figure 1. Correction of the G290T mutation in the Tyr gene in mIPSCs

a, The strategy for precise genome modification using the piggyBac transposon. Top line, structure of the Tyr gene; red line, 5′ external probe for Southern blot analysis; open arrow, piggyBac transposon carrying a PGK-puroΔtk cassette; P1, P2 and P3, PCR primers; B, BamHI; E, EcoNI. b, c, Southern blot (b) and PCR analyses (c) showing insertion (c/PB) and excision (c/Rev) of the piggyBac transposon. ES, mouse ESCs as a control. d, e, Sequence analyses revealed correction of the G290T mutation (d) and seamless excision of the piggyBac transposon (e). Note that two silent mutations (A and T indicated by arrowheads) introduced near the TTAA site were also detected. f, A chimeric mouse generated by injecting corrected Tyr ^c/Rev mIPSCs (left) displays black coat color. Right, a non-injected albino mouse.

Figure 2. Correction of the Z mutation in A1ATD-hIPSCs

a, The strategy for precise genome modification using ZFNs and the piggyBac transposon. Top line, structure of the A1AT gene; blue lines, Southern blot probes; thin and thick boxes, non-coding and coding exons, respectively; open arrow, piggyBac transposon; B, BamHI; A, AflIII. b, Sequences of wild-type (Reference), Z, PB, and Rev alleles. Amino acid position 342 (blue), recognition sites for ZFNs (green), piggyBac excision site (red) are shown. Sequence changes in Rev allele from Z allele were indicated by asterisks. c, Surveyor nuclease assay showing the cleavage of Z mutation in ZFNs-transfected K562 cells. Non-transfected cells were used as a control. d, Southern blot analysis showing bi-allelic piggyBac insertion (B-16) and bi-allelic excision (B-16-C2, -C3 and -C6) during correction of the A1ATD-hIPSCs line B. Genomic DNA was digested by BamHI (5′ and PB probes) or AlfIII (3′ probe). Genotype: ZZ, homozygous for Z allele; PP, homozygous for insertion of piggyBac; RR, homozygous for reverted allele. e, Sequence analysis showing correction of Z mutation in 3 corrected hIPSC lines. Wild-type sequence (top line) and A1ATD-hIPSC (second line).

Figure 3. Functional analysis of restored A1AT in c-hIPSCs-derived hepatocyte-like cells

a, Immunofluorescence showing the absence of polymeric A1AT protein in hepatocyte-like cells generated from c-hIPSCs. All forms of A1AT (left panels) and misfolded polymeric A1AT (middle panels). b, c, ELISA to assess the intracellular (b) and secreted (c) levels of polymeric A1AT protein in hepatocyte-like cells derived from A1ATD-hIPSCs (ZZ), c-hIPSCs (RR) and control hIPSCs (++). d, Endoglycosidase H (E) and peptide:N-glycosidase (P) digestion of A1AT immunoprecipitated from uncorrected (ZZ), corrected (RR) and control (++) hIPSC-derived hepatocyte-like cells (upper panels) and corresponding culture medium (lower panels). e, Chymotrypsin ELISA showing that corrected cells (RR) have A1AT enzymatic inhibitory activity that is superior to uncorrected cells (ZZ) and close to adult hepatocytes. f, g, Immunofluorescence of transplanted liver sections detecting human albumin (f) and A1AT (g). DNA was counterstained with DAPI. h, ELISA read-out of human albumin in the mouse serum longitudinally followed for each mouse. Asterisk, the mouse was subjected to histology analysis. Scale bars, 100 μm. Data in b, c and e are shown as mean ± s.d. (n=3). Student’s t-test was performed. NS, not significant.