SenPred: A single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden
Background - Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled increased understanding of senescent cell heterogeneity. Methods - Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D. Results - Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (>99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not senescence of lung fibroblasts or whole skin. Conclusions - We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets.  The development of SenPred has allowed for detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities. Overall design: 10x 3' scRNA-seq of primary human dermal fibroblasts isolated from facelift skin of a 42-year-old donor. Cells were grown in 2D in 6-well culture plates, or in 3D in a matrigel/collagen 1 dermal matrix. Sample Type - DS2D, Barcode Suffix -1 Sample Type - DS3D, Barcode Suffix -2 Sample Type - EP2D, Barcode Suffix -3 Sample Type - EP3D, Barcode Suffix -4