Mapping human tissues with highly multiplexed RNA in situ hybridization.

In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.

Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization.

In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical biopsies has been limited due to their large size, general lower tissue quality and high background autofluorescence. Here we report DART-FISH, a versatile padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections at cellular resolution. We introduced an omni-cell type cytoplasmic stain, dubbed RiboSoma that substantially improves the segmentation of cell bodies. We developed a computational decoding-by-deconvolution workflow to extract gene spots even in the presence of optical crowding. Our enzyme-free isothermal decoding procedure allowed us to image 121 genes in a large section from the human neocortex in less than 10 hours, where we successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. Additionally, we demonstrated the detection of transcripts as short as 461 nucleotides, including neuropeptides and discovered new cortical layer markers. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.

OsCRP1, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance.

Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that CHLOROPLAST RNA-BINDING PROTEIN 1 (OsCRP1), a rice (Oryza sativa) cpRNP gene, is essential for stabilization of RNAs from the NAD(P)H dehydrogenase (NDH) complex, which in turn enhances drought and cold stress tolerance. An RNA-immunoprecipitation assay revealed that OsCRP1 is associated with a set of chloroplast RNAs. Transcript profiling indicated that the mRNA levels of genes from the NDH complex significantly increased in the OsCRP1 overexpressing compared to non-transgenic plants, whereas the pattern in OsCRP1 RNAi plants were opposite. Importantly, the OsCRP1 overexpressing plants showed a higher cyclic electron transport (CET) activity, which is essential for elevated levels of ATP for photosynthesis. Additionally, overexpression of OsCRP1 resulted in significantly enhanced drought and cold stress tolerance with higher ATP levels compared to wild type. Thus, our findings suggest that overexpression of OsCRP1 stabilizes a set of mRNAs from genes of the NDH complex involved in increasing CET activity and production of ATP, which consequently confers enhanced drought and cold tolerance.

Ultraaccurate genome sequencing and haplotyping of single human cells.

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10-8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.

Capture and enumeration of mRNA transcripts from single cells using a microfluidic device.

Accurate measurement of RNA transcripts from single cells will enable the precise classification of cell types and characterization of the heterogeneity in cell populations that play key roles in normal cellular physiology and diseases. As a step towards this end, we have developed a microfluidic device and methods for automatic hydrodynamic capture of single mammalian cells and subsequent immobilization and digital counting of polyadenylated mRNA molecules released from the individual cells. Using single-molecule fluorescence imaging, we have demonstrated that polyadenylated mRNA molecules from single HeLa cells can be captured within minutes by hybridization to polydeoxyribothymidine oligonucleotides covalently attached on the glass surface in the device. The total mRNA molecule counts in the individual HeLa cells are found to vary significantly from one another. Our technology opens up the possibility of direct digital enumeration of RNA transcripts from single cells with single-molecule sensitivity using a single integrated microfluidic device.

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.

RNA-sequencing (RNA-seq) measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. In contrast, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq, our method enriches for context-specific transcripts over housekeeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d.

Fine-tuned grayscale optofluidic maskless lithography for three-dimensional freeform shape microstructure fabrication.

This article presents free-floating three-dimensional (3D) microstructure fabrication in a microfluidic channel using direct fine-tuned grayscale image lithography. The image is designed as a freeform shape and is composed of gray shades as light-absorbing features. Gray shade levels are modulated through multiple reflections of light in a digital micromirror device (DMD) to produce different height formations. Whereas conventional photolithography has several limitations in producing grayscale colors on photomask features, our method focuses on a maskless, single-shot process for fabrication of freeform 3D micro-scale shapes. The fine-tuned gray image is designed using an 8-bit grayscale color; thus, each pixel is capable of displaying 256 gray shades. The pattern of the UV light reflecting on the DMD is transferred to a photocurable resin flowing through a microfluidic channel. Here, we demonstrate diverse free-floating 3D microstructure fabrication using fine-tuned grayscale image lithography. Additionally, we produce polymeric microstructures with locally embedded gray encoding patterns, such as grayscale-encoded microtags. This functional microstructure can be applied to a biophysical detection system combined with 3D microstructures. This method would be suitable for fabricating 3D microstructures that have a specific morphology to be used for particular biological or medical applications.

Microfluidic devices with permeable polymer barriers for capture and transport of biomolecules and cells.

We report a method for fabricating permeable polymer microstructure barriers in polydimethylsiloxane (PDMS) microfluidic devices and the use of the devices to capture and transport DNA and cells. The polymer microstructure in a desired location in a fluidic channel is formed in situ by the polymerization of acrylamide and polyethylene diacrylate cross-linker (PEG-DA) monomer in a solution which is trapped in the location using a pair of PDMS valves. The porous polymer microstructure provides a mechanical barrier to convective fluid flow in the channel or between two microfluidic chambers while it still conducts ions or small charged species under an electric field, allowing for the rapid capture and transport of biomolecules and cells by electrophoresis. We have demonstrated the application of the devices for the rapid capture and efficient release of bacteriophage λ genomic DNA, solution exchange and for the transport and capture of HeLa cells. Our devices will enable the multi-step processing of biomolecules and cells or individual cells within a single microfluidic chamber.

Catalytic effects of ZnO nanorods grown by sonochemical decomposition of zinc acetate dihydrate.

In this study, we prepared ZnO nanorods by a sonochemical method using a zinc acetate dihydrate as a new precursor. Well-aligned high-quality ZnO nanorods were synthesized on FTO glass by the sonochemical decomposition of zinc acetate dihydrate using a ZnO thin-film as the catalytic layer. The ZnO thin-films were deposited on the FTO glass by a sputtering method. To investigate their catalytic effects on the ZnO nanorods, catalytic ZnO thin-films of 20 nm, 40 nm, and 60 nm thickness were prepared by adjusting the sputtering time. The ZnO nanorods grown on catalytic layers with different thicknesses were characterized by SEM, XRD, and PL. The ZnO nanorods grown on the catalytic layer of 40 nm thickness show the best crystal and spatial orientation and as a result display the best optical properties. It was found that a catalytic ZnO thin-film of 40 nm in thickness yields well-aligned high-quality ZnO nanorods, due to its small surface roughness and structural strain.

A single surgeon's experience with 54 consecutive cases of multivisceral resection for locally advanced primary colorectal cancer: can the laparoscopic approach be performed safely?

BACKGROUND: Laparoscopic resection for colorectal cancer has become popular. However, no previous studies have compared the laparoscopic and open approaches for colorectal cancer adherent to adjacent organs. This study analyzed the short- and long-term survival outcomes after laparoscopic multivisceral resection of the locally advanced primary colorectal cancer compared with open procedure in an effort to address appropriate patient selection. METHODS: From a prospectively collected database, 54 patients with locally advanced primary colorectal cancer who had undergone multivisceral resection from March 2001 to September 2009 were identified. Laparoscopic and open surgeries were selectively performed for 38 and 16 patients, respectively. RESULTS: The two groups had similar demographics, with no differences in age, sex, and comorbidity. However, five emergency or urgency operations were included in the open group. No differences existed between the two groups in terms of tumor node metastasis (TNM) staging, histologic tumor infiltration rates, or curative resection rates. Three patients (7.9%) in the laparoscopic group required conversion to open procedure. In the laparoscopic group, the operation time was longer (330 vs. 257 min; p = 0.018), the volume of blood loss was less (269 vs. 638 ml; p = 0.000), and the time until return of bowel movement was shorter (3.7 vs. 4.7 days; p = 0.029) than in the open group. The perioperative morbidity rates were similar in the two groups (21.1% vs. 43.7%; p = 0.107), and no perioperative mortality occurred in either group. The mean follow-up period after curative resection was 40 months in the laparoscopic group and 35 months in the open group. The two groups showed similar rates for local recurrence (7.7% vs. 27.3%; p = 0.144) and distant metastasis (15.4% vs. 45.5%; p = 0.091). The overall 5-year survival rate was 60.5% for the laparoscopic group and 47.7% for the open group (p = 0.044, log-rank test). In terms of TNM stages, the overall 5-year survival rate for pathologic stage 3 disease was 58.3% for the laparoscopic group and 25% for the open group (p = 0.022, log rank test), but no difference was noted for the stage 2 patients (p = 0.384). CONCLUSIONS: No adverse long-term oncologic outcomes of laparoscopic resection were observed in this study. Although inherent limitations exist in this nonrandomized study, laparoscopic multivisceral resection seems to be a feasible and effective treatment option for colorectal cancer for carefully selected patients. Patients with colon cancer should be much more carefully selected for laparoscopic multivisceral resection than patients with rectal cancer because anatomic uncertainty can make oncologic en bloc resection incomplete.