Standard BioTools

““We’ve shed some light on what is happening when tumors are being treated with a therapy specifically focusing on KRAS signaling, and how important it is in orchestrating the immune suppressive microenvironment,””

““It was beautiful to see the tumor with the normal tissue surrounding it and the way the cells were organized in the tissue. That was really an eye opener, and so using IMC became the default,””

““It was a real game changer for us because now we could run a whole cohort in one go, instead of manually dragging input files in and out of multiple software. The new approach, once optimized for the cohort, permitted us to run images directly from the Hyperion and get single-cell expression data out in the form of a spreadsheet. That was a big advantage for us,””

“Imaging Mass Cytometry with CyTOF™ technology is our method of choice for these studies because the limited samples are very valuable. CyTOF allows more than 30 markers in one panel, and we don’t have to worry about color compensation or background autofluorescence issues”

“Compared to other high-multiplex technologies, IMC excels at providing both spatial information and high multiplexity. It allows us to see spatial context more intuitively and enables accurate detection, treatment and prognosis of the disease by analyzing the immune system in the peripheral blood.”

“Using [the Standard BioTools] microfluidics workflow for DNA fingerprinting is allowing us to fulfill what these patients wanted, which is sharing their samples for the advancement of medical research.”

“DNA fingerprinting allows us to detect events that might otherwise lead to erroneous results. It helps us spot potential issues before we send samples to the requesting researcher.”

“Using DNA fingerprinting to assess samples prior to accession and distribution can save time and resources. Researchers who receive samples from the biorepository need to have confidence that the samples they receive have been correctly identified from the sample source. Additionally, researchers need to have confidence that the samples will yield interpretable data from their planned downstream analyses.”

“What makes the [Standard BioTools] microfluidics-based workflow unique is that it is high-throughput at a cost that is scalable to our process. It saves our customers and our lab time and resources.”

“Combining this data from the detection of chemokines, or of RNA in general, with detecting cell types in the tissues provides so much information,” Schulz says. “I think the field is wide open to take any target you want and investigate it. That’s the beauty and strength of this approach. You’re not dependent on the antibody and the antibody being available. Theoretically, it’s unlimited – you can detect what you want.”

“From our experience, the signals are fairly stable across measurements for TMAs because you have all your samples that have been processed in one batch and stained with the same antibodies in the exact same concentrations for the exact same time. So that really minimizes your experimental variation.”

“The Human Cell Atlas and CZ Biohub focus predominantly on single RNA-seq,” he said, “but looking at the epigenetic state using the methods we’ve developed in collaboration with [Standard BioTools], and other similar approaches, will be complementary and useful.”

“The key is that Script Builder software is easy to use,” he said. “You can design things in silico using computer modeling and then easily implement them in Script Builder.”

“CyTOF technology has a really unique niche for interrogating the tumor microenvironment,” said Newell. “It has relatively high throughput and high dimensionality, allowing us to open up a lot of doors.”

“A very important advantage to us was the ability to automate our analysis with Maxpar Pathsetter software. This is significant time savings and generates data that is much more reproducible and less impacted by the subjectivity that occurs with manual analysis.”

“We used the Maxpar Direct Immune Profiling Assay because we wanted a global approach to analyze the different immune cell types from both the innate and adaptive immune response. Most previous works on immune perturbations in autoimmune disease only analyzed the B cell compartment, the T cell compartment, or the regulatory T cells. A more comprehensive view is complicated using conventional flow cytometry, involving many different tubes to analyze one sample from a single patient. So, we wanted to use a more global approach facilitated by mass cytometry.”

“Mass cytometry is not just equal to the methods they’ve been using, it’s actually much, much better.”

“Mass cytometry has amazing potential. I don’t want to use the word ‘revolutionize’, but it’s close to it. This is the first time we can clearly monitor the whole immune system for a really broad view of what’s going on and what we should do.”

“It opens new areas for investigation. How would we have ever come to NK cells mimicking the immunosuppressive properties of decidual NK cells so essential for successful pregnancy, or to trogocytosis and CD9?”

“CyTOF is very powerful in leading you toward undiscovered secrets and mechanisms that you wouldn’t have seen otherwise.”

“CyTOF technology characterizes intact single cells in suspension based on protein co-expression patterns – about 60 parameters per cell – and measures hundreds of thousands to millions of cells. Its ability to work with intact single cells empowers us to discover previously unrecognized cell populations in multiparameter space,”

““We have been impressed by the quality of the data generated by C1 with a depth of interrogation that was on average beyond 10,000 genes per cell,””

“Perhaps other diseases like leukemias and myelomas can be affected. Essentially, we would like to understand how general this phenomenon is that we found.”

“We want to understand if this phenomenon is only related to this one type of therapy that we studied, or if it’s happening in other CAR T cell therapies. Is it only relevant to lymphoma?”

“Right now, the T regulatory cell fraction is variable, but if we remove these cells, therapy outcomes might actually be more consistent even though the dose perhaps could be slightly less.”