Cytoplasmic biomarkers, including circulating nucleic acids and tumour cells, have significant potential for monitoring patient responses during treatment for malignant squamous cell carcinoma (SCC). The development of liquid biopsy markers is crucial for patient subgroups at higher risk of aggressive SCC who are unable to tolerate frequent skin biopsies. One such group includes individuals with recessive dystrophic epidermolysis bullosa (RDEB), an inherited genetic disorder characterized by skin fragility, frequent blistering, and impaired wound healing. Due to the increased risk of complications from invasive tissue biopsy procedures, there is a pressing need for non-invasive diagnostic alternatives. Here, we report on the use of liquid biopsy in association with the microRNA tumour marker (miR-10b) and ScreenCell® filtration system for assessing malignancy in inoperable or difficult to treat SCCs. Initial analyses were conducted in cultured patient-derived and commercial cell lines, data was collected with Zeiss Confocal Microscope, following multiplex fluorescent in situ hybridisation. Data was then analysed to examine the expression profile of different patient cell lines. Following this, a size-filtration method (ScreenCell®) was used to capture putative circulating tumour cells (CTCs) in blood samples from RDEB patients. To distinguish putative CTCs from hematopoietic cells, epithelial markers (pan-cytokeratin) and leukocyte markers (CD45) were utilized. Through precise miR-10b targeting, we observed significantly higher expression levels in cell lines exhibiting greater malignancy compared to controls. This trend suggests a strong correlation between miR-10b expression and SCC aggressiveness. Additionally, we demonstrated feasibility of multiplexing miR-10b with an internal negative control, effectively reducing cell-to-cell signal variation and increasing diagnostic reliability. Putative SCC-derived CTCs were successfully identified from both spiked-in blood samples and patient samples, reinforcing the potential of this approach. To expand on this work, we have also begun examining CTC-like cells (the non-adherent fraction in culture) from the cultured patient derived cell lines to assess their similarity to naturally disseminating CTCs from patients. In this way, we have demonstrated differential expression of miR-10b in malignant patient derived aggressive SCC cell lines from RDEB and non-RDEB patients, and shown miR-10b is differentially expressed in putative CTCs captured from patients. These results confirmed previously published work from the Mellick Lab in breast, colon and prostate cancer and are the basis of ongoing work in the Mellick laboratory for the development of a minimally invasive method for tracking malignancy in difficult to treat SCCs.