Serial tissue sampling has become essential in guiding modern targeted and personalized cancer treatments. An alternative to image guided core biopsies are fine needle aspirates (FNA) that yield cells rather than tissues but are much better tolerated and have lower complication rates. The efficient pathway analysis of such cells in the clinic has been difficult, time consuming and costly. Here we develop an antibody-DNA barcoding approach where harvested cells can be rapidly re-stained through the use of custom designed oligonucleotide-fluorophore conjugates. We show that this approach can be used to interrogate drug-relevant pathways in scant clinical samples. Using the PI3K/PTEN/CDK4/6 pathways in breast cancer as an example, we demonstrate how analysis can be performed in tandem with trial enrollment and can evaluate downstream signaling following therapeutic inhibition. This approach should allow more widespread use of scant single cell material in clinical samples.

The identification of patients with aggressive cancer who require immediate therapy is a health challenge in low-income and middle-income countries. Limited pathology resources, high healthcare costs and large-case loads call for the development of advanced standalone diagnostics. Here, we report and validate an automated, low-cost point-of-care device for the molecular diagnosis of aggressive lymphomas. The device uses contrast-enhanced microholography and a deep-learning algorithm to directly analyse percutaneously obtained fine-needle aspirates. We show the feasibility and high accuracy of the device in cells, as well as the prospective validation of the results in 40 patients clinically referred for image-guided aspiration of nodal mass lesions suspicious for lymphoma. Automated analysis of human samples with the portable device should allow for the accurate classification of patients with benign and malignant adenopathy.

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