Multiple ongoing clinical trials use site-specific nucleases to disrupt T cell receptor (TCR) genes in order to allow for allogeneic T cell therapy [1][2][3][4][5] . In particular, the first U.S. clinical trial using CRISPR-Cas9 entailed the targeted disruption of the TCR chains and programmed cell death protein 1 (PDCD1) in T cells of refractory cancer patients 6 . Here, we used the same guide RNA sequences and applied single-cell RNA sequencing (scRNAseq) to more than 7000 primary human T cells, transfected with CRISPR-Cas9. Four days post-transfection, we found a loss of chromosome 14, harboring the TCRα locus, in up to 9% of the cells, and a chromosome 14 gain in up to 1.4% of the cells. We further identified truncations of chromosome 7, harboring the TCRβ locus, in 9.9% of the cells. Loss of heterozygosity (LOH) was further validated using fluorescence in situ hybridization (FISH) and the temporal dynamics of cleavage and incomplete repair were monitored using digital droplet PCR (ddPCR). Aneuploidy was found among all T cell subsets and was associated with transcriptional signatures of reduced proliferation and metabolism as well as with induced p53 activation and cell death. We conclude that aneuploidy and chromosomal truncations are frequent outcomes of CRISPR-Cas9 cleavage in clinical protocols. Monitoring and minimizing these aberrant products is crucial for future applications of genome editing in T cell engineering and beyond.

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Ehlers Danlos syndrome type IV is an often lethal disease caused by various mutations of type III collagen genes. It presents in infancy and childhood in several ways, and the symptoms and signs include low birth weight, prematurity, congenital dislocation of the hips, easy inappropriate bruising (sometimes suspected as child battering), and a diagnostic facial phenotype. These features predict a lethal adult disease often complicated by fatal arterial rupture in early or middle adult life. Most affected patients can be diagnosed from radiolabelled collagen protein profiles by polyacrylamide gel electrophoresis. Prenatal diagnosis by specific type III collagen restriction fragment length polymorphisms is possible in some families, and will become increasingly important. Prenatal diagnosis and prevention of the disease in selected families is already possible and will be widely available in the future.

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We evaluted measurement of urinary 4-hydroxyphenyl acetic acid as a potential screening method for small-bowel disease and bacterial overgrowth syndromes in 360 unselected acutely ill infants and children. Control data were obtained on 120 healthy children, ages 1.5 to 15 years, from a general medical practice, 48 healthy infants, ages one to five years, from local day nurseries, and 150 healthy babies, ages less than one to eight days. Comparative data were from 300 acutely ill hospitalized babies and children, ranging in age from less than one day to 15 years and without clinical evidence for small-bowel disease and bacterial overgrowth syndrome. No false-negative results and only 2% false-positive results were observed. Among the 10 patients whose urinary excretion of the analyte was considered to be abnormal were patients with Giardia lamblia infestation, ileal resection with blind loop, and other diseases of the small intestine associated with bacterial overgrowth. We conclude that measurement of 4-hydroxyphenylacetic acid excretion is useful in screening for such diseases.