Capillary-assisted microfluidic biosensing platform captures single cell secretion dynamics in nanoliter compartments
Publication date: Available online 19 February 2020Source: Biosensors and BioelectronicsAuthor(s): Amin Hassanzadeh-Barforoushi, Majid Ebrahimi Warkiani, David Gallego-Ortega, Guozhen Liu, Tracie BarberAbstractCancer cells continuously secrete inflammatory biomolecules which play significant roles in disease progression and tumor metastasis toward secondary sites. Despite recent efforts to capture cancer cells' intercellular secretion heterogeneity using microfluidics, the challenges in operation of these systems as well as the complexity of designing a biosensing assay for long-term and real-time measurement of single cell secretions have become grand research barriers. Here, we present a new capillary-based microfluidic biosensing approach to easily and reliably capture ∼500 single cells inside isolated dead-end nanoliter compartments using simple pipette injection, and quantify their individual secretion dynamics at the single cell resolution over a long period of culture (∼16 h). We first present a detailed investigation of the fluid mechanics underlying the formation of nanoliter compartments in the microfluidic system. Based on the measurement of single cell capture efficiency, we employ a one-step FRET-based biosensor which monitors the single cancer cells' protease activity. The sensor reports the fluorescent signal as a product of amino acid chain cleavage and reduction in its quenching capability. Using the single cell protease secretion data, we identifie...
We report the genome-wide effects of KAP1 loss on the transcriptome, the chromatin state, and on recruitment of various components of the transcription machinery in the colon colorectal cancer cell line HCT116.
Contributors : Junhang Luo ; Zhiping LiuSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensWe studied the alternative splicing function of KDM4B and found that KDM4B can act as a bona fide trans-acting splicing factor that binds RNA and signal-responsive scaffold protein that binds spliceosome.
Contributor : Yu ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDescription of breast cancer infiltrating lymphocyte through large scale single cell sequencing.While it has been well-recognized that T-cell mediated adaptive cellular immunity plays important roles in cancer immune response and tumor control, the roles of B lymphocytes in tumor development and therapy have only been proposed until recently, and are still mostly controversial. To gain mechanistic insights into the origin and dynamics of tumor infiltrated immune cells, especially B lymphocytes, we combined single ce...
Contributor : H F JuanSeries Type : Expression profiling by arrayOrganism : Homo sapiensCitreoviridin can suppress lung cancer cell growth by inhibiting the activity of ectopic ATP synthase, but has limited effect on normal cells. However, the mechanism of citreoviridin triggering dynamic molecular responses in cancer cells remains unclear. Here, we performed gene expression profiling to elucidate the dynamic changes after citreoviridin treatment in cells.
Contributor : Jesse RaabSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe carried out two sets of experiments to understand how the INO80 complex affected gene expression. Expression analysis following depletion of INO80 with two siRNAs to determine INO80 dependent transcription programs. In addition siMCRS1 or siNTG expression analysis with and without treatment with EZH2 inhibitor (EPZ-6438) was performed to determine what genes in HepG2 cells are de-repressed by EZH2 inhibition, and test the hypothesis that changes at INO80 autonomous sites would depdend on expression of other INO...
Contributors : Jesse R Raab ; Terry MagnusonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe mapped 4 subunits of the INO80 complex using ChIP-seq in HepG2 and Huh7 liver cancer cell lines. We found a subclass of sites occupied by the INO80 ATPase subunit, but not by any accessory subunits that we call 'Autonomous' INO80 sites. These sites are present in both HepG2 and Huh7 cells and are characterized by repressed chromatin. Relief of reprissive histone modifications thorugh EZH2 inhbiition led to the increase in H3K27ac at INO80 targets.
Contributors : Hiroshi Ishiguro ; Takashi KawaharaSeries Type : Expression profiling by arrayOrganism : Mus musculusVasectomy was thought to be a risk factor for prostate cancer. We investigated the mechanism on vasectomy using Affymetrix microarray.
Contributors : David Ulmert ; Robert J KleinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe used RNA sequencing to analyze the genomic signatures of prostate cancer that progressed after targeted alpha therapy.
Contributors : Lewis Liu ; Sonya A MacParland ; Jeff C Liu ; Gary D Bader ; Ian D McGilvraySeries Type : Expression profiling by high throughput sequencingOrganism : Marmota monaxWe characterized the identity of hepatic macrophages from the uninvolved liver of a WHV-positive (area with no visible tumor) tumor bearing woodchuck that take up NPs using RNA-sequencing (RNA-seq). Data from WHV-infected animal from experiment 3.
In this study, we identified reliable miRNA clusters that can be used to subclassify HNSCC tumors as well as other squamous tumors of other anatomic locations. An institutional discovery cohort was generated using miRNA expression data from microarrays, and this was validated using publicly available next-generation microRNA sequencing data from TCGA. Further analysis of these subtypes revealed distinct biological and clinical features of HNSCC tumors based on the miRNA expression profiles, which provides new insights into the pathogenesis and treatment of HNSCC.