Transcriptional characterization of human postnatal and adult neural progenitors and of the stem cell niches.

Project Information

HUMANE

Grant agreement ID: 836027

DOI

10.3030/836027

Project closed

EC signature date 10 April 2019

Start date 1 August 2020

End date 31 July 2022

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 203 852,16

EU contribution

€ 203 852,16

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 1 - HUMANE (Transcriptional characterization of human postnatal and adult neural progenitors and of the stem cell niches.)

Reporting period: 2020-08-01 to 2022-07-31

Summary of the context and overall objectives of the project

The discovery of adult neurogenesis in mammals changed the long-lasting view of the brain as an immutable structure and raised new hope for brain regeneration. In the past fifty years adult neurogenesis was found in almost all mammals and has been extensively studied in rodents. Adult born neurons have special properties that significantly influence the activity of the networks into which they integrate, playing important roles in memory formation and cognitive flexibility. Furthermore, adult neurogenesis was shown to regulate affective state and to play a role in depression. Despite the vast body of knowledge regarding rodent adult neurogenesis, the data describing it in humans is scarce. Most studies investigating human adult neurogenesis rely on immunohistology, using biomarkers established in rodents. In this study we set out to test the existence of human adult neurogenesis in an unbiased manner by analysing the transcriptome of the cells present in the hippocampus using single nucleus RNA sequencing. One of the main goals of this project was to identify individual neural progenitors in the human brain and to characterize their transcriptome. We also aimed to characterize in detail the stem cell niches using spatial transcriptomics. The Frisén laboratory showed with the help of 14C-birthdating that adult born neurons are integrating not only in the human hippocampus but also in the striatum. However, it is not known where these neurons are originating from and in which striatal structures they are integrating. Thus, we also aim to analyze the human nucleus accumbens, nucleus caudatus and the putamen and to determine if newly generated neurons are present in these structures. Our project aimed to bring a detailed characterization of human neurogenesis, answering important outstanding questions in the field, and to create protocols and datasets that will be the starting points for numerous future studies investigating human adult neurogenesis in physiological and pathological contexts.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

One of the main difficulties in studying neural progenitors in the human brain is their scarcity amongst the large number of other cell types present in each structure. To be able to analyze the rare neural progenitors in adult human samples we set up enrichment methods and developed an analysis framework involving both supervised and unsupervised single cell RNA sequencing analysis methods that allows the identification of rare neural progenitors in teenage and adult human hippocampus datasets. Using these protocols, we prepared samples originating from early perinatal, adult, and aging donors and applied our analysis pipeline. We collected an impressive dataset of the human hippocampus including 26 samples ranging in age from 0 to 78 years and almost half a million nuclei including all cell types expected in the structure. The extensive dataset allows an in-depth study of the human hippocampus and of hippocampal neurogenesis throughout life. With the help of our analysis strategy, we identified neural progenitors not only in the childhood but also in the adult and aging human hippocampus and characterized for the first time the transcriptome of the adult human neural progenitors. Comparing the human progenitors with cells form other species, we found strong similarities with mouse, pig and and macaque progenitors with which they share not only the transcriptional differentiation program but also many neurogenic markers. We also identified new markers, some of them specific for the human progenitors or markers that show a characteristic expression pattern along the human neurogenic trajectory. The results are soon to be published and have been shared with the neurogenesis researcher’s community in several international meetings as well with the broad public during science communication events.
During this project we also generated a comprehensive dataset regarding the turnover of neurons and oligodendrocytes in the human striatum and have preliminary indications that neurogenesis is ongoing in human nucleus accumbent, putamen and nucleus caudatus. These results will better the understating of these structures and will brings us closer to building regenerative strategies for replacing the neurons lost during neurodegenerative diseases or stroke.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The identification and characterisation of the adult human hippocampal progenitors has mostly been realized using immunohistological and immunofluorescence methods based on very few markers characterized in rodents which are still disputed in the field. This study demonstrated ongoing neurogenesis in the human hippocampus based on single nucleus RNA sequencing, an unbiased method that allows the analysis of tens of thousands of genes simultaneously. We also characterize for the first time the transcriptome of the adult human neural progenitors and identify new neurogenic markers. The transcriptional patterns of the human neural progenitors will advance the understanding of human adult neurogenesis. Furthermore, the vast single nucleus RNA sequencing dataset generated including samples from 0 to 78 years of age will be invaluable for the field and constituting the starting point for numerous future studies targeting not only adult neurogenesis but also aging in the human hippocampus. A great obstacle in investigating human neurogenesis is the low number of progenitors present in the human hippocampus and striatum. The progenitor enrichment protocols and the analysis framework we developed will be valuable for isolating neural progenitors and will allow the study of neurogenesis in adult and aging human samples. The better understanding of human adult neurogenesis will not only deepen our knowledge regarding the human brain but will also teach us how to integrate neurons in adult brain structures which can be the starting point for future regenerative strategies.

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