Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity

Blood samples are frequently collected in human studies of the immune system but poorly represent tissue-resident immunity. Understanding the immunopathogenesis of tissue-restricted diseases, such as chronic hepatitis B, necessitates direct investigation of local immune responses. We developed a workflow that enables frequent, minimally invasive collection of liver fine-needle aspirates in multi-site international studies and centralized single-cell RNA sequencing data generation using the Seq-Well S3 picowell-based technology. All immunological cell types were captured, including liver macrophages, and showed distinct compartmentalization and transcriptional profiles, providing a systematic assessment of the capabilities and limitations of peripheral blood samples when investigating tissue-restricted diseases. The ability to electively sample the liver of chronic viral hepatitis patients and generate high-resolution data will enable multi-site clinical studies to power fundamental and therapeutic discovery. ### Competing Interest Statement N.C.N., J.A., and J.B. are employees of Janssen Pharmaceutical NV. N.H. holds equity in BioNTech and is a consultant for Related Sciences. J.F., R.J.D.K, and H.L.A.J., receive funding from AbbVie. J.F. and H.L.A.J. receive funding from Arbutus. J.F., R.J.D.K., H.L.A.J., A.B., and A.G. receive funding from Gilead Sciences. J.F., R.J.D.K., H.L.A.J., G.M.L., A.B., and A.G. receive funding from Janssen Pharmaceutical. J.F. receives funding from Eiger and Enanta. R.J.D.K. receives funding from BMS, Medtronic, Philips. H.L.A.J. receives funding from Merck, Myers-Squibb and Bristol. A.B. receives funding from Fujirebio. R.J.D.K. and H.L.A.J. receive funding from Roche. A.B. and A.G. receive funding from GSK. J.F. and R.J.D.K. report compensation for consulting from AbbVie. J.F., R.J.D.K., and H.L.A.J. report compensation for consulting from Gilead Sciences. J.F. and H.L.A.J. report compensation for consulting from Arbutus. J.F., H.L.A.J., and A.G. report compensation for consulting from GSK. R.J.D.K., H.L.A.J., and A.G. report compensation for consulting from Janssen Pharmaceutical and Roche. R.J.D.K., H.L.A.J., and A.K.S. report compensation for consulting from Merck/ Schering Plough. H.L.A.J., and A.G. report compensation for consulting from Vir Biotechnology Inc. R.J.D.K. reports compensation for consulting from BMS, Echosens, Medtronic and Norgine. H.L.A.J. reports compensation for consulting from Aligos, Arena, Eiger, Enyo, Regulus, VBI Vaccines and Viroclinics. A.K.S. reports compensation for consulting from Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, Third Rock Ventures, Hovione, Relation Therapeutics, FL82, and Dahlia Biosciences. A.G. reports compensation for consulting from Finch Therapeutics and SQZ BioTech. The other authors declare no competing interests.