Programmable endonuclease combined with isothermal polymerase amplification to selectively enrich for rare mutant allele fractions.

Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic acid fragments in body fluids but is challenged by the low abundance of nucleic acids of clinical interest and their sequence homology with the vast background of nucleic acids from healthy cells. Recently, programmable endonucleases such as clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas) and prokaryotic Argonautes have been successfully used to remove background nucleic acids and enrich mutant allele fractions, enabling their detection with deep next generation sequencing (NGS). However, the enrichment level achievable with these assays is limited by futile binding events and off-target cleavage. To overcome these shortcomings, we conceived a new assay (Programmable Enzyme-Assisted Selective Exponential Amplification, PASEA) that combines the cleavage of wild type alleles with concurrent polymerase amplification. While PASEA increases the numbers of both wild type and mutant alleles, the numbers of mutant alleles increase at much greater rates, allowing PASEA to achieve an unprecedented level of selective enrichment of targeted alleles. By combining CRISPR-Cas9 based cleavage with recombinase polymerase amplification, we converted samples with 0.01% somatic mutant allele fractions (MAFs) to products with 70% MAFs in a single step within 20 min, enabling inexpensive, rapid genotyping with such as Sanger sequencers. Furthermore, PASEA's extraordinary efficiency facilitates sensitive real-time detection of somatic mutant alleles at the point of care with custom designed Exo-RPA probes. Real-time PASEA' performance was proved equivalent to clinical amplification refractory mutation system (ARMS)-PCR and NGS when testing over hundred cancer patients' samples. This strategy has the potential to reduce the cost and time of cancer screening and genotyping, and to enable targeted therapies in resource-limited settings.

Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts.

Somatic mosaicism is a hallmark of malignancy that is also pervasively observed in human physiological aging, with clonal expansions of cells harboring mutations in recurrently mutated driver genes. Bulk sequencing of tissue microdissection captures mutation frequencies, but cannot distinguish which mutations co-occur in the same clones to reconstruct clonal architectures, nor phenotypically profile clonal populations to delineate how driver mutations impact cellular behavior. To address these challenges, we developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure and observed a clonal landscape dominated by a large number of clones with a single driver event, but only rare clones with two driver mutations. NOTCH1 mutants dominate the clonal landscape and are linked to stunted epithelial differentiation, while TP53 mutants and double-driver mutants promote clonal expansion through both differentiation biases and increased cell cycling. Thus, joint single-cell highly multiplexed capture of somatic mutations and mRNA transcripts enables high resolution reconstruction of clonal architecture and associated phenotypes in solid tissue somatic mosaicism.

Biphasic response of T cell activation to substrate stiffness.

T cell activation is sensitive to the mechanical properties of an activating substrate. However, there are also contrasting results on how substrate stiffness affects T cell activation, including differences between T cells of mouse and human origin. Towards reconciling these differences, this report examines the response of primary human T cells to polyacrylamide gels with stiffness between 5 and 110 kPa presenting activating antibodies to CD3 and CD28. T cell proliferation and IL-2 secretion exhibited a biphasic functional response to substrate stiffness, which can be shifted by changing density of activating antibodies and abrogated by inhibition of cellular contractility. T cell morphology was modulated by stiffness at early time points. RNA-seq indicates that T cells show differing monotonic trends in upregulated genes and pathways towards both ends of the stiffness spectrum. These studies provide a framework of T cell mechanosensing and suggest an effect of ligand density that may reconcile different, contrasting patterns of stiffness sensing seen in previous studies.

Enhanced activation and expansion of T cells using mechanically soft elastomer fibers.

Practical deployment of cellular therapies requires effective platforms for producing clinically relevant numbers of high-quality cells. This report introduces a materials-based approach to improving activation and expansion of T cells, which are rapidly emerging as an agent for treating cancer and a range of other diseases. Electrospinning is used to create a mesh of poly(ε-caprolactone) fibers, which is used to present activating ligands to CD3 and CD28, which activate T cells for expansion. Incorporation of poly(dimethyl siloxane) elastomer into the fibers reduces substrate rigidity and enhances expansion of mixed populations of human CD4+ and CD8+ T cells. Intriguingly, this platform also rescues expansion of T cells isolated from CLL patients, which often show limited responsiveness and other features resembling exhaustion. By simplifying the process of cell expansion, compared to current bead-based platforms, and improving T cell expansion, the system introduced here may accelerate development of cellular immunotherapy.