Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

Abstract

The architecture of normal and diseased tissues strongly influences the development and progression of disease as well as responsiveness and resistance to therapy. We describe a tissue-based cyclic immunofluorescence (t-CyCIF) method for highly multiplexed immuno-fluorescence imaging of formalin-fixed, paraffin-embedded (FFPE) specimens mounted on glass slides, the most widely used specimens for histopathological diagnosis of cancer and other diseases. t-CyCIF generates up to 60-plex images using an iterative process (a cycle) in which conventional low-plex fluorescence images are repeatedly collected from the same sample and then assembled into a high-dimensional representation. t-CyCIF requires no specialized instruments or reagents and is compatible with super-resolution imaging; we demonstrate its application to quantifying signal transduction cascades, tumor antigens and immune markers in diverse tissues and tumors. The simplicity and adaptability of t-CyCIF makes it an effective method for pre-clinical and clinical research and a natural complement to single-cell genomics.

eLife digest

To diagnose a disease such as cancer, doctors sometimes take small tissue samples called biopsies from the affected area. These biopsies are then thinly sliced and treated with dyes to identify healthy and cancerous cells. However, clinicians and scientists often need to look into what happens inside individual cells in the tissues so they can understand how cancers arise and progress. This helps them to identify different types of tumor cells and to tailor the best treatment for the patient.

To do so, a number of proteins (the molecules involved in nearly all life’s processes) need to be tracked in healthy and diseased cells and tissues. This can be done thanks to a range of methods known as immunofluorescence microscopy, but following different proteins on the same slice of a sample is difficult. However, a new type of immunofluorescence known as t-CyCIF may be a solution.

With this technique, a fluorescent compound is applied that will bind to a specific protein of interest. A microscope can pick up the light from the compound when the sample is imaged, which reveals the protein’s location in the cell or tissue. Then, a substance is used that deactivates the fluorescence signal. After this, another compound that binds to a new type of protein is used, and imaged. This cycle is repeated several times to locate different proteins. Lastly, the individual images are processed and stitched together to reveal the cells and their internal structures.

Here, Lin, Izar et al. showed that t-CyCIF could be used to study biopsies and to obtain images that covered a large area of healthy human tissues and tumors. The technique helped to track over 60 different proteins in normal and tumor tissue samples from human patients. Several sets of experiments showed that t-CyCIF could uncover the molecular mechanisms that are disrupted during cancer, but also reveal the complexity of a single tumor. In fact, as shown with biopsies of brain cancer, cancerous cells in a tumor can be strikingly different, even when they are close to each other. Finally, the method helped to pinpoint which types of immune cells are involved in fighting a kidney tumor. Overall, such information cannot be obtained with conventional methods, yet is crucial for diagnosis and treatment.

Most laboratories can readily use t-CyCIF since the technique is open source and requires equipment that is easily accessible. In fact, the technique should soon be used to assess how well certain drugs help the immune system combat cancer. Ultimately, better use of biopsies is key to customizing cancer care.