抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

https://www.cell.com/cell/pdf/S0092-8674(15)00549-8.pdf

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system’s technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system’s ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients. Single-cell gene expression analysis is challenging. This work describes a new droplet-based single cell RNA-seq platform capable of processing tens of thousands of cells across 8 independent samples in minutes, and demonstrates cellular subtypes and host–donor chimerism in transplant patients.

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Massively parallel digital transcriptional profiling of single cells

Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

During cancer progression and treatment, multiple subclonal populations of tumour cells compete with one another, with selective pressures leading to the emergence of predominant subclones that replicate and spread most proficiently, and are least susceptible to treatment. At present, the molecular landscapes of solid tumours are established using surgical or biopsy tissue samples. Tissue-based tumour profiles are, however, subject to sampling bias, provide only a snapshot of tumour heterogeneity, and cannot be obtained repeatedly. Genomic profiles of circulating cell-free tumour DNA (ctDNA) have been shown to closely match those of the corresponding tumours, with important implications for both molecular pathology and clinical oncology. Analyses of circulating nucleic acids, commonly referred to as 'liquid biopsies', can be used to monitor response to treatment, assess the emergence of drug resistance, and quantify minimal residual disease. In addition to blood, several other body fluids, such as urine, saliva, pleural effusions, and cerebrospinal fluid, can contain tumour-derived genetic information. The molecular profiles gathered from ctDNA can be further complemented with those obtained through analysis of circulating tumour cells (CTCs), as well as RNA, proteins, and lipids contained within vesicles, such as exosomes. In this Review, we examine how different forms of liquid biopsies can be exploited to guide patient care and should ultimately be integrated into clinical practice, focusing on liquid biopsy of ctDNA - arguably the most clinically advanced approach.

Integrating liquid biopsies into the management of cancer

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ∼2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100 000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associat...

/pdf/high-throughput-droplet-digital-pcr-system-for-absolute-49l18zmi9e.pdf

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

System, including methods and apparatus, for forming droplets of an emulsion. The system may include a channel junction at which a stream of sample fluid is divided into droplets by a dividing flow of carrier fluid. The system also may include one or more features configured to position sample fluid for reduced contact between the sample fluid and one or more surface regions of the channel junction, which may improve the consistency of droplet formation. In exemplary embodiments, sample fluid may be positioned by a step member produced by an increase in channel depth, and/or by directing flow of carrier fluid to form a barrier layer between sample fluid and a wall region, such as a ceiling region or floor region, of a channel network.

Droplet generation system with features for sample positioning

System, including methods and apparatus, for spacing droplets from each other and for detection of spaced droplets.

System for detection of spaced droplets

Method of making a droplet-generating device. In the method, a first droplet-generating device may be produced. The first droplet-generating device may include a molded portion created at least in part with a mold and also may include a plurality of droplet generators each formed at least in part by the molded portion. A set of droplets may be generated with each of one or more of the droplet generators. A property of at least one set of generated droplets may be determined. The mold may be modified based on the property. A second droplet-generating device may be produced that includes a molded portion created at least in part with the modified mold.

Method of making a droplet-generating device

Sample holding system, including methods and apparatus, including a holder defining a well having a wicking promoter that encourages flow of a sample to the bottom of the well. Methods of making and using the holder are also disclosed.

Thomas H. Cauley

Papers

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

Droplet generation system with features for sample positioning

System for detection of spaced droplets

Method of making a droplet-generating device

Sample holder with a well having a wicking promoter