Rozenblatt-Rosen, O., Shin, J.W., Rood, J.E. et al. Building a high-quality Human Cell Atlas. Nat Biotechnol 39, 149–153, 2021. DOI:https://doi.org/10.1038/s41587-020-00812-4
Building the Human Cell Atlas (HCA) requires consistent and agile experimental designs, standardized operating protocols (SOPs), benchmarks and quality control metrics that can adapt to a rapidly evolving technological landscape. Here, the HCA Standards and Technology Working Group outlines pertinent technical challenges and their approach to defining benchmarks and quality control measures to ensure high-quality data for building a comprehensive and accurate human cell atlas and help guide other atlas projects in health and disease.
Luca Tosti, Yan Hang, Olivia Debnath, Sebastian Tiesmeyer, Timo Trefzer, Katja Steiger, Foo Wei Ten, Sören Lukassen, Simone Ballke, Anja A. Kühl, Simone Spieckermann, Rita Bottino, Naveed Ishaque, Wilko Weichert, Seung K. Kim, Roland Eils, Christian Conrad, Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas, Gastroenterology, 2020, DOI: https://doi.org/10.1053/j.gastro.2020.11.010.
Due to high autolytic activities, it is challenging to investigate the pancreas at the transcriptome level. In this paper, the authors overcame these limitations by using single-nuclei from frozen tissues, and generated a comprehensive human pancreas cell atlas including more than 120.000 cells, leading to the discovery of new cell states in health and disease. Moreover, in situ sequencing approaches revealed how cell types are spatially organised within pancreatic tissues. Taken together, this work provides new insights into how the pancreas works in homeostasis and it will open new avenues to better understand the aetiology of pancreatic diseases.
Dana Avrahami, Yue J. Wang, Jonathan Schug, Eseye Feleke, Long Gao, Chengyang Liu, Ali Naji, Benjamin Glaser, Klaus H. Kaestner, Single-cell transcriptomics of human islet ontogeny defines the molecular basis of β-cell dedifferentiation in T2D, Molecular Metabolism, Volume 42, 2020, 101057, DOI: https://doi.org/10.1016/j.molmet.2020.101057.
Recent evidence suggests that b-cell de-differentiation or even complete loss of identity contribute to reduced functional b-cell mass in T2D. However, evidence for the existence of compromised identity in human islet cells of patients with diabetes is limited and lacks a comprehensive characterization of the precise nature, level of plasticity, and functional outcome of this altered cellular state.
Since the main pancreatic cell types (α, β, δ, PP acinar and ductal cells) arise from common progenitor cells during embryonic development, a comparative analysis of the gene expression programs of adult pancreatic cells is useful to define their differentiated state in a developmental context and to investigate cellular processes such as maturation in health and loss of identity in disease. Using this strategy, we determined the postnatal maturation of human b and a cells at the transcriptome level using single cell transcriptome technology and demonstrated how this process is perturbed in T2D.
First, we show that maturation of a and b cells is associated with silencing of expression programs that characterize the other pancreatic cell types, repression of ‘disallowed’ genes, and activation of function genes. However, while both a and b-cells mature with age, adult a-cells achieve a less differentiated state, which might allow for cellular plasticity and self-renewal consistent with the increased regeneration and transdifferentiation processes previously reported in numerous models of diabetes. Moreover, our study describes the dramatic changes to the transcriptome of β-cells during the first year of life, concurrent with their improved function with age as previously reported. Specifically, we demonstrate changes in the expression levels of G6PC2, PCK1 and FABP5, which collectively contribute to the reduction of insulin secretion at low glucose levels or in response to pyruvate and fatty acids, thus preventing fasting hypoglycemia.
Second, our cell type-specific and age-related ‘immature’ gene signatures has revealed that a substantial fraction of T2D b cells revert to an immature expression profile characterized by de-repression of the geneset associated with neonatal islet cells. Interestingly, the promoters of these re-activated genes display a bivalent chromatin state in normal adult b-cells, suggesting that, while normal maturation is accompanied by repression of potentially harmful genes, this repression is tenuous and these genes remain poised to re-initiate expression when placed under metabolic stress. In summary, we demonstrated that in T2D both a and b-cells undergo a process of dematuration and identified several dysregulated genes that likely contribute to the a and b-cell phenotype observed in T2D, and thus could qualify as potential targets for the development of novel therapeutics.
Baron, M., et al., A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst, 2016. 3(4): p. 346-360 e4.
Enge, M., et al., Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell, 2017. 171(2): p. 321-330 e14.
Segerstolpe, A., et al., Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes. Cell Metab, 2016. 24(4): p. 593-607.