scholarly journals Dissecting CLL through high-dimensional single-cell technologies

Blood ◽  
2019 ◽  
Vol 133 (13) ◽  
pp. 1446-1456
Author(s):  
Satyen H. Gohil ◽  
Catherine J. Wu

Abstract We now have the potential to undertake detailed analysis of the inner workings of thousands of cancer cells, one cell at a time, through the emergence of a range of techniques that probe the genome, transcriptome, and proteome combined with the development of bioinformatics pipelines that enable their interpretation. This provides an unprecedented opportunity to better understand the heterogeneity of chronic lymphocytic leukemia and how mutations, activation states, and protein expression at the single-cell level have an impact on disease course, response to treatment, and outcomes. Herein, we review the emerging application of these new techniques to chronic lymphocytic leukemia and examine the insights already attained through this transformative technology.

2019 ◽  
Vol 35 (20) ◽  
pp. 4063-4071 ◽  
Author(s):  
Tamim Abdelaal ◽  
Thomas Höllt ◽  
Vincent van Unen ◽  
Boudewijn P F Lelieveldt ◽  
Frits Koning ◽  
...  

Abstract Motivation High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore the full heterogeneity of a biological sample at the single-cell level is currently limited by the number of markers measured simultaneously on a single panel. Results To extend the number of markers per cell, we propose an in silico method to integrate CyTOF datasets measured using multiple panels that share a set of markers. Additionally, we present an approach to select the most informative markers from an existing CyTOF dataset to be used as a shared marker set between panels. We demonstrate the feasibility of our methods by evaluating the quality of clustering and neighborhood preservation of the integrated dataset, on two public CyTOF datasets. We illustrate that by computationally extending the number of markers we can further untangle the heterogeneity of mass cytometry data, including rare cell-population detection. Availability and implementation Implementation is available on GitHub (https://github.com/tabdelaal/CyTOFmerge). Supplementary information Supplementary data are available at Bioinformatics online.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yanjun Zhang ◽  
Yasufumi Takahashi ◽  
Sung Pil Hong ◽  
Fengjie Liu ◽  
Joanna Bednarska ◽  
...  

AbstractDynamic mapping of extracellular pH (pHe) at the single-cell level is critical for understanding the role of H+ in cellular and subcellular processes, with particular importance in cancer. While several pHe sensing techniques have been developed, accessing this information at the single-cell level requires improvement in sensitivity, spatial and temporal resolution. We report on a zwitterionic label-free pH nanoprobe that addresses these long-standing challenges. The probe has a sensitivity > 0.01 units, 2 ms response time, and 50 nm spatial resolution. The platform was integrated into a double-barrel nanoprobe combining pH sensing with feedback-controlled distance dependance via Scanning Ion Conductance Microscopy. This allows for the simultaneous 3D topographical imaging and pHe monitoring of living cancer cells. These classes of nanoprobes were used for real-time high spatiotemporal resolution pHe mapping at the subcellular level and revealed tumour heterogeneity of the peri-cellular environments of melanoma and breast cancer cells.


PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e57706 ◽  
Author(s):  
Ediz Sariisik ◽  
Denitsa Docheva ◽  
Daniela Padula ◽  
Cvetan Popov ◽  
Jan Opfer ◽  
...  

Lab on a Chip ◽  
2016 ◽  
Vol 16 (13) ◽  
pp. 2440-2449 ◽  
Author(s):  
Soo Hyeon Kim ◽  
Teruo Fujii

The electroactive double well-array consists of trap-wells for highly efficient single-cell trapping using dielectrophoresis (cell capture efficiency of 96 ± 3%) and reaction-wells that confine cell lysates for analysis of intracellular materials from single cells.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rita Ungai-Salánki ◽  
Eleonóra Haty ◽  
Tamás Gerecsei ◽  
Barbara Francz ◽  
Bálint Béres ◽  
...  

AbstractThe high throughput, cost effective and sensitive quantification of cell adhesion strength at the single-cell level is still a challenging task. The adhesion force between tissue cells and their environment is crucial in all multicellular organisms. Integrins transmit force between the intracellular cytoskeleton and the extracellular matrix. This force is not only a mechanical interaction but a way of signal transduction as well. For instance, adhesion-dependent cells switch to an apoptotic mode in the lack of adhesion forces. Adhesion of tumor cells is a potential therapeutic target, as it is actively modulated during tissue invasion and cell release to the bloodstream resulting in metastasis. We investigated the integrin-mediated adhesion between cancer cells and their RGD (Arg-Gly-Asp) motif displaying biomimetic substratum using the HeLa cell line transfected by the Fucci fluorescent cell cycle reporter construct. We employed a computer-controlled micropipette and a high spatial resolution label-free resonant waveguide grating-based optical sensor calibrated to adhesion force and energy at the single-cell level. We found that the overall adhesion strength of single cancer cells is approximately constant in all phases except the mitotic (M) phase with a significantly lower adhesion. Single-cell evanescent field based biosensor measurements revealed that at the mitotic phase the cell material mass per unit area inside the cell-substratum contact zone is significantly less, too. Importantly, the weaker mitotic adhesion is not simply a direct consequence of the measured smaller contact area. Our results highlight these differences in the mitotic reticular adhesions and confirm that cell adhesion is a promising target of selective cancer drugs as the vast majority of normal, differentiated tissue cells do not enter the M phase and do not divide.


2021 ◽  
Author(s):  
Wilson McKerrow ◽  
Shane A. Evans ◽  
Azucena Rocha ◽  
John Sedivy ◽  
Nicola Neretti ◽  
...  

AbstractLINE-1 retrotransposons are known to be expressed in early development, in tumors and in the germline. Less is known about LINE-1 expression at the single cell level, especially outside the context of cancer. Because LINE-1 elements are present at a high copy number, many transcripts that are not driven by the LINE-1 promoter nevertheless terminate at the LINE-1 3’ UTR. Thus, 3’ targeted single cell RNA-seq datasets are not appropriate for studying LINE-1. However, 5’ targeted single cell datasets provide an opportunity to analyze LINE-1 expression at the single cell level. Most LINE-1 copies are 5’ truncated, and a transcript that contains the LINE-1 5’ UTR as its 5’ end is likely to have been transcribed from its promoter. We developed a method, L1-sc (LINE-1 expression for single cells), to quantify LINE-1 expression in 5’ targeted 10x genomics single cell RNA-seq datasets. Our method confirms that LINE-1 expression is high in cancer cells, but low or absent from immune cells. We also find that LINE-1 expression is elevated in epithelial compared to immune cells outside of the context of cancer and that it is also elevated in neurons compared to glia in the mouse hippocampus.


2018 ◽  
Vol 54 (67) ◽  
pp. 9317-9320 ◽  
Author(s):  
Chen-chen Li ◽  
Yan Zhang ◽  
Wen-jing Liu ◽  
Chun-yang Zhang

We develop a triple-amplification strategy for sensitive detection of telomerase from cancer cells at the single-cell level.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1114-1114
Author(s):  
Kyoung-Eun Lee ◽  
Hyun Ae Woo ◽  
Seung Ha Yang ◽  
Jung-Won Huh ◽  
Jee-Young Ahn ◽  
...  

Abstract Abstract 1114 Poster Board I-136 Background : It has been proposed that treating cancer cells with vectors that cause the over expression of MnSOD and catalase could inhibit tumor cell growth by disrupting the redox signaling involved with cell division as well as, therapeutically, by providing protection for normal cells. These results support the hypotheses that increasing the dismutation of mitochondrial superoxide alters redox signaling in cancer cells that can result in growth suppression. Peroxiredoxins (Prxs) are a ubiquitous family of multifunctional antioxidant thioredoxin-dependent peroxidases that have roles in the reversible inactivation of PTPs and PTEN in cells stimulated by growth factors and protect cells against oxidative stress and modulate intracellular signaling cascades (Rhee et al, Cell Biology 17:183-189, 2005). In our study, we investigated the changes of the levels of H2O2-removing enzymes (ie Prxs, glutathione peroxidase 1 (Gpx1), and catalase) on a single cell during IM therapy in newly diagnosed CML. Patients and Methods Six paired CML samples (two blast crisis, one accelerated phase, three chronic phases) were analyzed in a study was approved by the institutional review board. Patients gave written informed consent according to institutional guidelines. 400 mg or 600 mg of imatinib was given to the chronic phase and accelerated/blast crisis samples respectively. Following encircling cells from marrow BM aspiration from patients or normal individuals with the Dako Pen (Dako, Denmark) on a dry slides, cells were incubated with blocking solution (10% FBS in PBS) for 30minutes to block non-specific staining. Then, cells were incubated with specific primary antibodies to antioxidant enzymes in 0.2% TritonX-100/10% FBS/PBS solution overnight (1:100). After washing with PBS, cells were incubated with Alexa-488 or 594-conjugated goat antibodies to mouse or rabbit IgG, respectively for an hour. Confocal fluorescence images of cells were obtained with an LSM510 microscope (Carl Zeiss, Tornwood, NJ). Results Samples of newly diagnosed CML patients showed significantly decreased levels of Prx 2, but revealed increased level of catalase on single cell level. The immunohistochemical expression was well correlated with western blot results. As the level of Philadelphia chromosomes decreased with IM treatment, the expression levels of Prx II and catalase were restored to the levels of normal individuals. Using our technique, we are able to quantify the changes of Prx and catalase on each myeloid, erythroid and megakaryocytic lineages at the single cell level. Conclusions Decreased Prx 2 and elevated catalase levels at the time of diagnosis are closely correlated with the elevated bcr/abl kinase level in CML at the each single cell level. The aberrant expression of those antioxidant enzymes were back to the level of normal individuals after IM treatment. This method might be accurate and convenient to assess the changes of the level of Prx and Catalase especially in the situation of cytopenia with IM treatment. Understanding the molecular mechanisms of changes on antioxidant might be potent tools to develop more effective new drugs in CML patients especially for Imatinib resistant patients. Disclosures No relevant conflicts of interest to declare.


Micromachines ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 149 ◽  
Author(s):  
Adam Snider ◽  
Ileana Pirozzi ◽  
Anubhav Tripathi

Analysis at the single cell level has becoming an increasingly important procedure to diagnose cancer tissue biopsies. These tissue samples are often heterogeneous and consist of 1000–15,000 cells. We study the use of centrifugal microfluidics to isolate single cells into micro chambers. We describe the optimization of our microfluidics flow device, characterize its performance using both polystyrene beads as a cell analogue and MCF-7 breast cancer cells, and discuss potential applications for the device. Our results show rapid isolation of ~2000 single cell aliquots in ~20 min. We were able to occupy 65% of available chambers with singly occupied cancer cells, and observed capture efficiencies as high as 80% using input samples ranging from 2000 to 15,000 cells in 20 min. We believe our device is a valuable research tool that addresses the unmet need for massively parallel single cell level analysis of cell populations.


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