Ultrasmall InGa(As)P Dielectric and Plasmonic Nanolasers

Nanolasers have great potential for both on-chip light sources and optical barcoding particles. We demonstrate ultrasmall InGaP and InGaAsP disk lasers with diameters down to 360 nm (198 nm in height) in the red spectral range. Optically pumped, room-temperature, single-mode lasing was achieved from both disk-on-pillar and isolated particles. When isolated disks were placed on gold, plasmon polariton lasing was obtained with Purcell-enhanced stimulated emission. UV lithography and plasma ashing enabled wafer-scale fabrication of nanodisks with an intended random size variation. Silica-coated nanodisk particles generated stable subnanometer spectra from within biological cells across an 80 nm bandwidth from 635 to 715 nm.

Lost in transduction: Critical considerations when using viral vectors

The application of retroviral vectors in the laboratory requires considerations that often go overlooked but are often easy to circumvent. Here, we discuss the relationship between the observed transduction efficiency of a cell population and per-cell viral insertions-and describe how differential cell-type susceptibilities can confound results. We consider the math underlying this problem and review an alternative approach to the commonly used "multiplicity of infection" (MOI) method of titering and using viral vectors in the biomedical research laboratory.

A Cell Double-Barcoding System for Quantitative Evaluation of Primary Tumors and Metastasis in Animals That Uncovers Clonal-Specific Anti-Cancer Drug Effects

Simple Summary

The main problem in treating advanced cancers is a metastatic spread when individual cancer cells leave the primary tumor and colonize to distant organs. In drug development, it is important to quantitatively assess effects of novel drug candidates on both primary tumors and metastasis. Unfortunately, current methods of monitoring metastasis in mouse models have low sensitivity and are not quantitative. Here, we developed a methodology to monitor drug effects on metastasis that is quantitative and has a very high sensitivity and resolution. In fact, it allows monitoring effects of drugs on individual cancer cells in animals.

Abstract

Imaging in monitoring metastasis in mouse models has low sensitivity and is not quantitative. Cell DNA barcoding, demonstrating high sensitivity and resolution, allows monitoring effects of drugs on the number of tumor and metastatic clones. However, this technology is not suitable for comparison of sizes of metastatic clones in different animals, for example, drug treated and untreated, due to high biological and technical variability upon tumor and metastatic growth and isolation of barcodes from tissue DNA. However, both numbers of clones and their sizes are critical parameters for analysis of drug effects. Here we developed a modification of the barcoding approach for monitoring drug effects on tumors and metastasis that is quantitative, highly sensitive and highly reproducible. This novel cell double-barcoding system allows simultaneously following the fate of two or more cell variants or cell lines in xenograft models in vivo, and also following the fates of individual clones within each of these populations. This system allows comparing effects of drugs on different cell populations and thus normalizing drug effects by drug-resistant lines, which corrects for both biological and technical variabilities and significantly increases the reproducibility of results. Using this barcoding system, we uncovered that effects of a novel DYRK1B kinase inhibitor FX9847 on primary tumors and metastasis is clone-dependent, while a distinct drug osimertinib demonstrated clone-independent effects on cancer cell populations. Overall, a cell double-barcoding approach can significantly enrich our understanding of drug effects in basic research and preclinical studies.

Applications of high-resolution clone tracking technologies in cancer

Tumors are comprised of dynamic, heterogenous cell populations characterized by numerous genetic and non-genetic alterations that accumulate and change with disease progression and treatment. Retrospective analyses of tumor evolution have relied on the measurement of genetic markers (such as copy number variants) to infer clonal dynamics. However, these approaches neglect the critical contributions of non-genetic drivers of disease. Techniques that harness the power of prospective clone tracking via heritable barcode tags provide an alternative strategy. In this review, we discuss methods for high-resolution, quantitative clone tracking, including recent advancements to pair barcode-specific functionality with scRNA-seq, clonal cell isolation, and in situ hybridization and imaging. We discuss these approaches in the context of cancer cell heterogeneity and treatment resistance.

Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis

Fibroblast heterogeneity has been shown within the unwounded mouse dorsal dermis, with fibroblast subpopulations being identified according to anatomical location and embryonic lineage. Using lineage tracing, we demonstrate that paired related homeobox 1 (Prrx1)-expressing fibroblasts are responsible for acute and chronic fibroses in the ventral dermis. Single-cell transcriptomics further corroborated the inherent fibrotic characteristics of Prrx1 fibroblasts during wound repair. In summary, we identify and characterize a fibroblast subpopulation in the mouse ventral dermis with intrinsic scar-forming potential.

High-complexity extracellular barcoding using a viral hemagglutinin

While single-cell sequencing technologies have revealed tissue heterogeneity, resolving mixed cellular libraries into cellular clones is essential for many pooled screens and clonal lineage tracing. Fluorescent proteins are limited in number, while DNA barcodes can only be read after cell lysis. To overcome these limitations, we used influenza virus hemagglutinins to engineer a genetically encoded cell-surface protein barcoding system. Using antibodies paired to hemagglutinins carrying combinations of escape mutations, we developed an exponential protein barcoding system which can label 128 clones using seven antibodies. This study provides a proof of principle for a strategy to create protein-level cell barcodes that can be used in vivo in mice to track clonal populations.

Developmental barcoding of whole mouse via homing CRISPR

In vivo barcoding using nuclease-induced mutations is a powerful approach for recording biological information, including developmental lineages; however, its application in mammalian systems has been limited. We present in vivo barcoding in the mouse with multiple homing guide RNAs that each generate hundreds of mutant alleles and combine to produce an exponential diversity of barcodes. Activation upon conception and continued mutagenesis through gestation resulted in developmentally barcoded mice wherein information is recorded in lineage-specific mutations. We used these recordings for reliable post hoc reconstruction of the earliest lineages and investigation of axis development in the brain. Our results provide an enabling and versatile platform for in vivo barcoding and lineage tracing in a mammalian model system.

Rapidly evolving homing CRISPR barcodes

We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing. This integrated approach will have wide-ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.