The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion.

Cystatin C (CyC) is a secreted cysteine protease inhibitor that is commonly used as a marker of renal function, and whose biological functions remain insufficiently characterized. Plasma CyC is elevated relative to renal function in many patients, including those receiving glucocorticoid (GC) treatment and patients with cancer. Endogenous GCs are essential for life and are appropriately upregulated in response to systemic stress. Here we empirically connect GCs with the systemic regulation of CyC. Using measurements of CyC and creatinine, another established marker of renal function, we used genome-wide association and structural equation modeling to determine the genetics of the latent trait CyC production in UK Biobank, thereby uncoupling CyC from renal function. CyC production and a polygenic score (PGS) capturing germline predisposition to CyC production predicted elevated all-cause and cancer-specific mortality. Using phenome-wide association, we further identified an association between germline predisposition to CyC production and accelerated onset of metabolic syndrome. As a potential explanation for these associations, we provide multiple lines of evidence that CyC is a direct transcriptional target of GC receptor, with GC-responsive CyC secretion exhibited by macrophages (cf. monocytes) and co-opted by multiple cancer cell lines, potentially explaining selective CyC elevations in disease states. Using isogenic CyC-knockout tumors (CRISPR-Cas9), we discovered a markedly attenuated tumor growth in vivo that was associated with a significantly reduced fraction of non-epithelial cells. To investigate whether depletion of specific non-epithelial cells could explain this, we performed single-cell RNA sequencing, which revealed abrogated recruitment of Trem2+ macrophages in knockout tumors, subsequently validated by Trem2 immunohistochemistry in a non-overlapping cohort. Trem2+ macrophages have previously been linked to immune suppression and failure of cancer immunotherapy. Consistent with this, we show that the CyC production PGS predicted checkpoint immunotherapy failure in a combined clinical trial cohort of 685 metastatic cancer patients. Taken together, our results demonstrate that CyC may be a direct effector of GC-induced immunosuppression, acting through the recruitment of Trem2+ macrophages, and therefore could be a target for combination cancer immunotherapy. Citation Format: Sam O. Kleeman, Breanna Demestichas, Nicholas Mourikis, Miriam Ferrer, Qing Gao, Dominik Loiero, Yosef J. Riazat-Kesh, Sean Bankier, Dimitrios Chantzichristos, Gudmundur Johannsson, Claire Regan, Jonathan Preall, Viktor H. Koelzer, Brian R. Walker, Hannah Meyer, Tobias Janowitz. Cystatin C is glucocorticoid-responsive, directs recruitment of Trem2+ macrophages and predicts failure of cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2891.

Claire Regan presents an ECG for you to analyse. The answer is given on page 45

Clare Regan presents an ECG for you to analyse. The answer is given on page 431

Claire Regan presents an ECG for you to analyse. The answer and management plan are given on page 303