3D spiral channels combined with flexible micro-sieve for high-throughput rare tumor cell enrichment and assay from clinical pleural effusion samples

The sieving and enrichment of rare tumor cells from large-volume pleural effusion(PE)samples is a promising technique for cell-based lung tumor diagnosis and drug tests,which features high throughput and recovery,purification,as well as viability rates of rare target cells as the prerequisites for high sensitivity,specificity,and accuracy of tumor cell analysis.In this paper,we propose a three-dimensional(3 D)sieving method for rare tumor cell enrichment,which effectively eliminates the"dead zones"in traditional two-dimensional(2 D)cell filters with a dimension-raising strategy to satisfy the requirements mentioned above.The prototype device was combined with a funnel-shaped holder,a flexible micropore membrane in the middle,and a3 D spiral fluid channel covered on the membrane as a three-layer ice-creaming cone composite structure.Driven by gravity alone,the device performed as follows:(1)20-fold throughput compared with the 2 D commercial planee hich was up to 20 mL/min for a threefold dilution of whole blood sample;(2)high recovery rates of 84.5%±21%,86%±25%,83%±14%for 100,1000,and 10000 cells/mL,respectively,in 30 mL phosphate buffer saline(PBS)sample,and a 100%positive detection rate in the case of≤5 A549 cells in 1 mL PBS;(3)a typical purification rate of 85.5%±9.1%;and(4)a viability rate of>93%.In the demonstration application,this device effectively enriched rare target cells from large volumes(>25 mL)of clinical pleural effusions.The following results indicated that tumor cells were easy-to-discover in the enriched PE samples,and the proliferation capability of purified cells was(>4.6 times)significantly stronger than that of unprocessed cells in the subsequent 6-day culture.The above evaluation indicates that the proposed easily reproducible method for the effective execution of rare cell enrichments and assays is expected to become a practical technique for clinical cell-based tumor diagnosis.

Effects of regenerated tissue extracts after liver injury on the proliferation,differentiation,migration and invasion of SK-HEP1 cells

Objective: To study the effects of regenerated tissue extracts after liver injury on the proliferation, differentiation, migration and invasion of SK-HEP1 cells. Methods: Regenerated tissue extracts after liver injury were used to induce SK-HEP1 cells after enrichment, their effects on the proliferation, differentiation, migration and invasion of SK-HEPI cells were observed through in vitro cell culture, MTT, flow cytometry and transwell assays. Results:In response to the action of regenerated tissue extracts after liver injury, SK-HEP1 cells were blocked in G_0/G_1 phase, their growth rate was distinctly reduced. The number of SK-HEP1^(-fj)colonies decreased. The migration ability of SK-HEPI cells showed a decreased trend on day7 and day 11 after induction. SK-HEPl's invasion ability clearly decreased on days 7 and11 after induction, especially on day 7. Conclusions: To a certain extent, regenerated tissue extracts after liver injury can inhibit the proliferation, differentiation, migration and invasion of hepatoma cells, showing an important potential of being a differentiating agent for the treatment of liver cancer.

Cell biomechanics and its applications in human disease diagnosis

Certain diseases are known to cause changes in the physical and biomechanical properties of cells.These include cancer,malaria,and sickle cell anemia among others.Typically,such physical property changes can result in several fold increases or decreases in cell stiffness,which are significant and can result in severe pathology and eventual catastrophic breakdown of the bodily functions.While there are developed biochemical and biological assays to detect the onset or presence of diseases,there is always a need to develop more rapid,precise,and sensitive methods to detect and diagnose diseases.Biomechanical property changes can play a significant role in this regard.As such,research into disease biomechanics can not only give us an in-depth knowledge of the mechanisms underlying disease progression,but can also serve as a powerful tool for detection and diagnosis.This article provides some insights into opportunities for how significant changes in cellular mechanical properties during onset or progression of a disease can be utilized as useful means for detection and diagnosis.We will also showcase several technologies that have already been developed to perform such detection and diagnosis.

Whole-blood sorting,enrichment and in situ immunolabeling of cellular subsets using acoustic microstreaming

Analyzing undiluted whole human blood is a challenge due to its complex composition of hematopoietic cellular populations,nucleic acids,metabolites,and proteins.We present a novel multi-functional microfluidic acoustic streaming platform that enables sorting,enrichment and in situ identification of cellular subsets from whole blood.This single device platform,based on lateral cavity acoustic transducers(LCAT),enables(1)the sorting of undiluted donor whole blood into its cellular subsets(platelets,RBCs,and WBCs),(2)the enrichment and retrieval of breast cancer cells(MCF-7)spiked in donor whole blood at rare cell relevant concentrations(10 mL^(−1)),and(3)on-chip immunofluorescent labeling for the detection of specific target cellular populations by their known marker expression patterns.Our approach thus demonstrates a compact system that integrates upstream sample processing with downstream separation/enrichment,to carry out multi-parametric cell analysis for blood-based diagnosis and liquid biopsy blood sampling.

Utilizing a microfluidic device to enrich and fluorescently detect circulating tumor cells

Circulating tumor cells(CTCs)are cancer cells that have propagated from primary tumor sites,spreading into the bloodstream as the cellular origin of fatal metastasis,and to secondary tumor sites.Capturing and analyzing CTCs is a kind of‘‘liquid biopsy'of the tumor that provides information about cancer changes over time and tailoring treatment[1].CTC enrichment and detection remains technologically challenging due to their extremely low concentra-

A highly efficient method for enriching TALEN or CRISPR/Cas9-edited mutant cells

In recent years,genome editing with site-specific nucleases,such as ZFN（zinc finger nuclease）,TALEN（transcription activatorlike effector nucleases）,and CRISPR/Cas9（the type II bacterial clustered,regularly interspaced,short palindromic repeats-associated protein 9）,has gained popularity for use in cell lines,animals,and plants（Urnov et al.,2010;Miller et al.,2011;Cong et al.

Role of bioinformatics databases and tools in radiation biology

Bioinformatics has become increasingly integral to radiation biology,also known as radiobiology,providing substantial support through data storage,conversion,visualization,and sharing.This review aims to deepen understanding of bioinformatics application in radiobiology by introducing key databases and analytical tools in radiobiology,including general bioinformatics databases,radiobiology-specific databases,data processing tools,and statistical analysis tools for differentially expressed genes(DEGs)and LC/MS analysis.This review also discusses bioinformatics applications in radiobiological fields,such as radioresistance and immune cell enrich-ment.Despite these advances,challenges such as data interoperability remain.Methods and projects to address these issues,such as GeCo and GMQL,are also examined.

deCS:A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and subjective.The increasing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference atlas.Here,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes.We used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different conditions,including reference panels,sequencing depth,and feature selection strategies.Our results demonstrate that expanding the references is critical for improving annotation accuracy.Compared to many existing state-of-the-art annotation tools,deCS significantly reduced computation time and increased accuracy.deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation.Finally,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cellular mechanisms underlying disease pathogenesis.