Periodic Reporting for period 2 - ESPACE (Human Cell Atlas of the Pancreas)
Periodo di rendicontazione: 2021-07-01 al 2022-06-30
The Human Cell Atlas (HCA) is a worldwide initiative with the mission to create comprehensive reference maps of all human cells – the fundamental units of life – as a basis for both understanding human health and diagnosing, monitoring, and treating disease. The ESPACE consortium pursues the goal to generate the first version of the HCA of the pancreas already with an emphasis on specific pancreatic diseases.
The human pancreas is a physiologically unique organ involved in the secretion of several hormones. The organ regulates blood sugar levels as well as the secretion of enzymes for the digestive tract. Several human diseases are associated with the pancreas: Pancreatic adenocarcinoma (PDAC) is one of the most aggressive cancers in humans and pancreatitis is a common potentially life-threatening disorder related to adverse lifestyle conditions. A very common chronical disease affecting the pancreas is type 2 diabetes (T2D), a metabolic disorder that is characterized by high blood sugar levels due to the lack of insulin produced in the pancreas endocrine islets. Despite its high physiological importance, the high autolytic activity makes the pancreas a very challenging tissue to study. Furthermore, diabetes plays an important role as risk factor in COVID-19 disease severity or possibly as long-COVID-19 symptom. We have generated molecular profiles on cellular level, including transcriptome and epigenomics data from more than 1 million single nuclei jointly together with tissue proteomics allowing to address fundamental questions of cell state and phenotype in healthy adults and during foetal development. Thus, we intend to present a first version of an open single-cell repository of the pancreas that sufficiently describes all cell types in healthy tissue, in T2D and changes during aging. Probably, most interesting are the many different micropathological lesions studied in healthy human pancreata of the fifth decade. Towards publication of the data, we implemented a cloud-based analysis platform which will serve as data portal of ESPACE.
The human pancreas is a physiologically unique organ involved in the secretion of several hormones. The organ regulates blood sugar levels as well as the secretion of enzymes for the digestive tract. Several human diseases are associated with the pancreas: Pancreatic adenocarcinoma (PDAC) is one of the most aggressive cancers in humans and pancreatitis is a common potentially life-threatening disorder related to adverse lifestyle conditions. A very common chronical disease affecting the pancreas is type 2 diabetes (T2D), a metabolic disorder that is characterized by high blood sugar levels due to the lack of insulin produced in the pancreas endocrine islets. Despite its high physiological importance, the high autolytic activity makes the pancreas a very challenging tissue to study. Furthermore, diabetes plays an important role as risk factor in COVID-19 disease severity or possibly as long-COVID-19 symptom. We have generated molecular profiles on cellular level, including transcriptome and epigenomics data from more than 1 million single nuclei jointly together with tissue proteomics allowing to address fundamental questions of cell state and phenotype in healthy adults and during foetal development. Thus, we intend to present a first version of an open single-cell repository of the pancreas that sufficiently describes all cell types in healthy tissue, in T2D and changes during aging. Probably, most interesting are the many different micropathological lesions studied in healthy human pancreata of the fifth decade. Towards publication of the data, we implemented a cloud-based analysis platform which will serve as data portal of ESPACE.
In the first funding period and as the ubiquitous starting point for all downstream approaches, we started with the procurement of pancreatic tissues. Here, we focused on full-organs from brain-dead organ donors as well as pancreatic slices from pancreatectomies (unaffected regions of the organ). The pandemic did only slightly delay the procurement from organ donors, but finally provide more procurements due to less transplantations (The Netherlands), while the dramatic COVID-19 situation in Italy diminished the sample procurement of pancreatic tissues from pancreatectomies. Instead of procured T2D samples, we received bio-banked islet samples from North American resources. Here, we still aim for the comparison of the molecular profiles form T2D and unaffected individuals. In addition, we also overachieved procured foetal pancreatic tissues (foetuses from abortion without medical indication) to explore cell maturation.
In particular, the ESPACE Human Cell Atlas project provides multiomic characterization of pancreas organ including proteomics and genomics. We conducted separate sequencing of single-cells or -nuclei and spatial proteomics technologies, including 16 different individuals and 4 different locations in the respective donated pancreatic organs. Due to quality issues, we explicitly decided to run single nuclei RNA and epigenetics sequencing separately to achieve most precise outputs from the different experimental branches.
Due to the pandemic and corresponding delays, the consortium was also affected in exchange and communication within. This will further delay the first comprehensive cell atlas of the pancreas, although all the projected data is stored, we worked on cloud-based analysis and dissemination output (joined publications).
On the other hand, single-nuclei sequencing pancreas protocols really helped to study post-mortem respiratory, brain and lung COVID-19 samples. This should be considered as a wider societal and scientifical impact in the pandemic.
In particular, the ESPACE Human Cell Atlas project provides multiomic characterization of pancreas organ including proteomics and genomics. We conducted separate sequencing of single-cells or -nuclei and spatial proteomics technologies, including 16 different individuals and 4 different locations in the respective donated pancreatic organs. Due to quality issues, we explicitly decided to run single nuclei RNA and epigenetics sequencing separately to achieve most precise outputs from the different experimental branches.
Due to the pandemic and corresponding delays, the consortium was also affected in exchange and communication within. This will further delay the first comprehensive cell atlas of the pancreas, although all the projected data is stored, we worked on cloud-based analysis and dissemination output (joined publications).
On the other hand, single-nuclei sequencing pancreas protocols really helped to study post-mortem respiratory, brain and lung COVID-19 samples. This should be considered as a wider societal and scientifical impact in the pandemic.
The integrative analysis which was planned within the framework of the DCP initiative in the HCA as central portal did not materialize. However, we and other European HCA consortia established independently state-of-the-art cloud solutions for data sharing and collaborative analysis. We will probably see more bottom-to-top initiatives in other single cell and multiomic projects. In our experience, the gene count matrices defining cell types without any patient information serve as an excellent scientific repository for further studies. In the biological context we envision to provide the base for cell understanding and regeneration in diabetic diseases, where fine mapping of epigenetic differences and demethylation of endocrine cell types play pivotal role. Moreover, findings of micro pathologies in ‘healthy’ pancreatic tissue (e.g. inflammation or fibrosis) may lead to better monitoring of the pancreas and early therapy intervention.
Our single-nuclei RNA sequencing pancreas protocols greatly helped to study post-mortem respiratory, brain and lung COVID-19 samples. Using this expertise, we were able to support the efforts of the scientific community in understanding the molecular mechanisms activated during/after the SARS-CoV-2 infection.
Our single-nuclei RNA sequencing pancreas protocols greatly helped to study post-mortem respiratory, brain and lung COVID-19 samples. Using this expertise, we were able to support the efforts of the scientific community in understanding the molecular mechanisms activated during/after the SARS-CoV-2 infection.