IntroductionStable genetic modification of hematopoietic stem/progenitor cells (HSPCs) is achieved with retroviral vectors (RVs) that integrate into the cell genome and express a therapeutic transgene. 1 Transplantation of genetically modified autologous HSPCs provides a therapeutic option for patients with genetic disorders. [1][2][3] However, in clinical trials for X-linked severe combined immunodeficiency (X-SCID) and chronic granulomatous disease (CGD) oncogenesis triggered by ␥RV-mediated insertional mutagenesis has occurred. Leukemic or myelodysplastic cell clones in patients from these trials harbored RV integrations at common insertion sites (CISs) targeting recurrently LMO2 or MDS1-EVI1, PRDM16, SETBP1, and other genes. [4][5][6][7] Alternative to ␥RVs, HIV-derived self-inactivating lentiviral vectors (LVs) transduce human HSPCs efficiently and display a superior safety profile with respect to ␥RVs as shown in in vitro and in vivo preclinical mouse models. [8][9][10][11] Moreover, good efficacy and safety of LVs has also been documented in a recent HSPC-based clinical trial for X-linked adrenoleukodystrophy (ALD). 3 However, a careful LV integration site analysis in derived cells from patients with ALD showed that relevant numbers of CISs were present. 3 This observation raises concerns 12 because the detection of CISs is a well-established hallmark of insertional mutagenesis in mice 13,14 and clinical trials. 5,7,15 Thus, it is possible that the occurrence of CISs in the ALD clinical trial is a still silent effect of genotoxicity. To understand whether CISs generated by LV integrations are the product of genotoxicity we generated our own dataset of LV integrations in human HSPCs and their progeny after engraftment in immunodeficient mice and studied the integration pattern and the clonal repertoire of vector-marked cells in in vitro culture and in vivo. Moreover, we performed an extensive comparison between our dataset and the integrations found in the ALD clinical trial and in other gene therapy trials that reported insertional leukemogenesis, as well as in mice subjected to RV-mediated oncogene tagging. From our own integration data and the meta-analysis of the other integration datasets we provide evidence that the driving force leading to the appearance of CISs in LV-transduced HSPCs from the ALD clinical trial reflects a previously unappreciated bias of LVs in integration site selection rather oncogenic selection. Methods LV production and isolation and transduction of human HSPCsLV.ARSA (arylsulfatase A) and LV.GFP (green fluorescent protein) were produced with the use of the pCCLsin.cPPT.hPGK.hARSA.WPREmut6 and the pCCLsin.cPPT.hPGK.GFP.Wpre transfer plasmids. 16 Vesicular stomatitis virus-pseudotyped LV-concentrated stocks were produced and titered as described. 17 Human HSPCs were obtained by positive selection of CD34-expressing cells (CD34 progenitor cell isolation kit, MACS; Miltenyi Biotec) from BM aspirates, mobilized peripheral blood (MPB), or CB of healthy donors on collection with info...

Gamma-retroviral/lentiviral vectors (γRV/LV) with self-inactivating (SIN) long terminal repeats (LTRs) and internal moderate cellular promoters pose a reduced risk of insertional mutagenesis when compared with vectors with active LTRs. Yet, in a recent LV-based clinical trial for β-thalassemia, vector integration within the HMGA2 gene induced the formation of an aberrantly spliced mRNA form that appeared to cause clonal dominance. Using a method that we developed, cDNA linear amplification-mediated PCR, in combination with high-throughput sequencing, we conducted a whole transcriptome analysis of chimeric LV-cellular fusion transcripts in transduced human lymphoblastoid cells and primary hematopoietic stem/progenitor cells. We observed a surprising abundance of read-through transcription originating outside and inside the provirus and identified the vector sequences contributing to the aberrant splicing process. We found that SIN LV has a sharply reduced propensity to engage in aberrant splicing compared with that of vectors carrying active LTRs. Moreover, by recoding the identified vector splice sites, we reduced residual read-through transcription and demonstrated an effective strategy for improving vectors. Characterization of the mechanisms and genetic features underlying vector-induced aberrant splicing will enable the generation of safer vectors, with low impact on the cellular transcriptome.

SUMMARY The epigenetic mechanisms that enable lifelong neurogenesis from neural stem cells (NSCs) in the adult mammalian brain are poorly understood. Here we show that JMJD3, a histone H3-lysine 27 (H3K27) demethylase, acts as a critical activator of neurogenesis from adult subventricular zone (SVZ) NSCs. JMJD3 is upregulated in neuroblasts, and Jmjd3-deletion targeted to SVZ NSCs in both developing and adult mice impairs neuronal differentiation. JMJD3 regulates neurogenic gene expression via interaction at not only promoter regions, but also neurogenic enhancer elements. JMJD3 localizes at neural enhancers genome-wide in embryonic brain, and in SVZ NSCs, JMJD3 regulates the I12b enhancer of Dlx2. In Jmjd3-deleted SVZ cells, I12b remains enriched with H3K27me3, and Dlx2-dependent neurogenesis fails. These findings support a model in which JMJD3 and the poised state of key transcriptional regulatory elements comprise an epigenetic mechanism that enables the activation of neurogenic gene expression in adult NSCs throughout life.

Oncogenesis induced by insertional mutagenesis with gene therapy vectors occurs mainly by activation of proto-oncogenes found at or nearby the insertion site. This activation often occurs by an enhancer-mediated mechanism or by a process of splicing capture which generates chimeric transcripts comprising portions of vector and cellular mRNAs. Although the activation of oncogenes may be reduced by the use of self-inactivating design and moderate cellular promoters, how to reduce genotoxic splicing capture events and aberrant transcript formation triggered by vector integration is still unclear.We developed a modified Linear Amplification-Mediated (LAM) PCR technique, named cDNA LAM PCR (cLAM-PCR), aimed at retrieving, from the whole transcriptome of LV-transduced cells aberrantly spliced mRNAs that contain lentiviral vector (LV) sequences fused with cellular transcripts in a high-throughput fashion. The sequences of cLAM-PCR products were obtained by 454 pyrosequencing and analyzed by dedicated high-throughput computational pipeline running in a computer cluster that use a dynamic analysis process composed by different steps based on a map-reduce parallelization model. Thus, chimeric LV-genome sequences are recognized, the nucleotide position of the fused sequence is identified (the splice site), and the remaining portion mapped on the appropriate genome assembly by BLAST.We identified several established and previously unknown splice sites within the LV backbone that parti-cipate in the aberrant splicing process with variable efficiency. Results obtained with different LV designs show that integrated LVs can perturb the processing of cellular transcripts by interacting with the cellular splicing machinery and fusing with its own splice sites to cellular splice sites both upstream and downstream the integration site. So far, 70 different fusion transcripts could be identified in total, 84% of which were fused to known splice sites of gene exons, 6% were fused to uncharacterized cryptic splice sites located in introns and the remaining 10% were fused to genomic sequences not corresponding to any annotated gene. This analysis allows identifying also several different slice sites within the LV backbone that participated to the aberrabt splicing process. Quantitative PCR on different LV portions within the LV backbone allow measuring the relative contribution to the aberrant splicing process of each splice site identified. Interestingly, the amount of transcription occurring in regions outside the expression cassette reaches the 3% of the entire transgene expression.The cLAM-PCR technique, coupled to high-throughput sequencing and the computational power of our specialized data analysis pipeline allows gaining insights into the biology of vector-mediated splicing alteration. Since this process could induce neoplastic transformation by the generation of aberrant oncogenic protein, its in-depth characterization is instrumental in the development of next-generation LV with a higher safety profile.