Stories of HCA|Organoid

What is your role in the HCA|Organoid team at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences?
Based in the laboratory of Christoph Bock at CeMM in Vienna, I am the scientific project manager of the HCA|Organoid project. I work closely together with all partners of our consortium to accomplish our goal to build an “Organoid Cell Atlas” based on massive-scale single-cell profiling of human organoids.

What are you currently working on? What’s your major research interest?
My work is centered on close collaboration with many leading scientists in the organoids and single-cell sequencing fields. I actively contribute to HCA|Organoid sample processing which includes single-cell sequencing of human brain and colon organoids. My research focuses on the validation of existing organoids as robust and faithful models of human biology and on the development of improved organoid models that include more cell types to make them better models for the study of human physiology and pathology.

What motivates you, personally? What made you go into science?
It’s the importance of the little things that fascinates me. In particular, I find it intriguing how the smallest molecular mechanisms, which cannot be observed with the naked eye, can make essential differences to the physiology and pathology of a multi-cellular organism. I think that understanding is key to exploiting knowledge, and this is what motivated me to go into life sciences.

Why do you think the HCA|Organoid research is important?
Organoids hold tremendous potential for biomedical applications since they recapitulate important aspects of in vivo organ development and biological function and they enable interventional studies in a human context. HCA|Organoid seeks to realize the full potential of human organoids by establishing a practically useful and readily extensible initial version of the “Organoid Cell Atlas”, which shall support researchers to functionally dissect and systematically perturb human biological systems.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it? The approach to understand complex human physiology and pathology by the characterization of single-cells is intriguing to provide a fundamentally new perspective for understanding biology with great potential to drive therapeutic advances. All HCA initiatives together create an open and inclusive research environment that facilitates collaboration among a broad range of interested researchers, bridging communities and integrating expertises – and this is key to achieving the overarching goal.

What is your role in the HCA|Organoid team at IMBA?
In the Knoblich lab we are responsible for the cerebral organoid branch of the HCA|Organoid team. Cerebral organoids are 3D tissues grown from induced pluripotent stem cells (iPSC) that recapitulate early human brain development, shedding light on a developmental process otherwise inaccessible. We grow cerebral organoids from some 100 iPSC lines that are characterized by scRNAseq in collaboration with Christoph Bock’s lab at CeMM to define natural phenotypic variation in human brain development.

What are you currently working on? What’s your major research interest?
What comprises normal human variation is a fascinating question. In a typical scRNAseq experiment, we compare a control sample to an experimental, say a patient sample. However, perfectly healthy humans are already quite different from one individual to another. Therefore, establishing what comprises normality – in this case in human brain development – is fundamental to also defining disease. Once we have defined normality, it will be a lot more informative defining exact disease phenotypes.

What motivates you, personally? What made you go into science?
I am really excited about my work because it allows me to ask so many interesting questions. Trying to understand the developing brain is a formidable task, as it is seemingly never-ending. Whenever we uncover a new process, a new set of questions arises. To answer these may even require the development of new experimental approaches. I find this constant cycle of answering and posing new questions extremely challenging but also rewarding. Of course, great teamwork is also a benefit.

Why do you think the HCA|Organoid research is important?
I think HCA|Organoid is vital to the exploding field of organoid research. In the past 10 years, in vitro systems of various human tissues collectively called organoids have been ever expanding. So far, these efforts were predominantly driven by a few individual labs. The HCA|Organoid effort establishes a solid basis, on which even more labs can enter the field. This will certainly advance the field and allow for new organoid applications such as disease modelling and drug screening.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it?
The Human Cell Atlas is a great initiative at the right time, because for the first time, we as a field are capable of charting every human cell in our bodies. This will lead to an unprecedented map of ourselves based on which we can study disease in much greater detail. The HCA|organoid effort is an important connection between human data and laboratory science because it bridges these two entities and will allow for even better modelling of human biology and pathologies.

What is your role in the HCA|Organoid team at CeMM?
I am a research technician in the lab of Christoph Bock and perform sample processing for the HCA|Organoid project, which includes the culturing as well as the single-cell characterization of various human organoids.

What are you currently working on? What’s your major research interest?
My work focuses on the transcriptomic and epigenomic characterization of human organoids at the single-cell level. We want to compare organoids with their primary tissue counterparts to explore differences and to improve future organoid technology to make them better models for the study of human physiology and pathology.

What motivates you, personally? What made you go into science?
I always wanted to follow my curiosity to understand how certain mechanisms work aiming to exploit my gained knowledge by contributing to new discoveries in life sciences.

Why do you think the HCA|Organoid research is important?
The establishment of an Organoid Cell Atlas will lead to an enhanced characterization of organoids and will help to define quality standards and reference catalogues. Ultimately, this will guide the development of new organoid models that better recapitulate the heterogeneous complexity of primary tissues, and it will leverage the power of organoids for large-scale perturbations and functional studies in a human context.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it?
The generation of comprehensive reference maps of all human cells will be an important cornerstone for the understanding of human health and for diagnosing, monitoring, and treating disease. The individual HCA cluster projects are important to reach this ambitious goal since each of them provides a substantial amount of work to characterize the diverse human organs and primary tissues. The HCA|Organoid complements these efforts with the characterization of a readily perturbed model for functional studies to dissect human biology in vitro.

What is your role in the HCA|Organoid team at FMI?
I am coordinating the project and performing experiments. copyright: 'test'Together with Maurice Kahnwald we established a semi-automatic pipeline to culture, seed, stain, and image patient-derived colon and colorectal cancer organoids over time. This allows us to study cell type emergence over time for each patient and enables the assignment of individual pseudo-time trajectories. In parallel, we also provide mature organoids for single-cell multi-omics analyses conducted by our project partners at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna.

What are you currently working on? What’s your major research interest?
Currently, we are working on our second screening of patient-derived colon and colorectal cancer organoids. This takes up most of the time in my weekly schedule. My major research interest is and will be focused on looking into the differences between patients and the diversity of data that will result from the work of other groups within the HCA|Organoid consortium. For now, we can only judge about the visual differences based on our different pseudo-time trajectories and cell-type markers.

What motivates you, personally? What made you go into science?
Improving yourself by asking new questions that lead to learning new things, this is what I find motivating. Besides learning myself, I also like to teach other people new things on the work floor. Inspiring and engaging people with something you like is rewarding because you can also give something back that way. And, what made me go into science? Curiosity.

Why do you think the HCA|Organoid research is important?
With HCA|Organoid we aim to provide the research community with a robust platform for this relatively new and physiologically relevant model system. Sharing knowledge via this way is critical these days. The HCA|Organoid setup is almost impossible for a single group to manage.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it?
As I described above, I think it is critical these days to collaborate in order to achieve the goals set by the HCA Cluster.

What is your role in the HCA|Organoid team at Prinses Maxima Centrum?
My major role in the HCA|Organoid team is to apply single-cell technologies on organoids and matched tissue to provide highquality and quantity Next-Generation Sequencing (NGS) data for scientific analysis. Single-cell technology is one of the cutting-edge technologies of recent years, and its application in the HCA|Organoid project will lead to the construction of comprehensive reference cell map of human cell types and characteristics, in my case intestinal tissue. We are using the droplet based single cell technology from 10x Genomics, which requires good quality samples. Hence, the sample preparation optimization is key to guarantee high quality and quantity NGS data. Together with partners from Hubrecht Organoid Technology, we tested the combination of different enzyme digestion and storage conditions on primary tissue and organoid samples. Based on these pilot studies, we chose the best option for the project.

What are you currently working on? What’s your major research interest?
I am currently working on colorectal cancer tissue and intestinal organoids. Our goal is to unveil the mechanism behind the heterogeneity of cancer via building a comprehensive reference cell map to be able to eventually better monitor diagnosis and treatment. With the reference human cell map, we will gain a better overview on the molecular differences between different types of disease.

It is of great interest to determine the similarities and differences between health and cancer disease/models through analyses and milling valuable information from NGS data. Interpreting the acquired data will allow us to distinguish health and disease, monitor prediction and diagnosis, disentangle the development and progress processes of cancer, provide novel targets/methods for cancer treatment, and offer the possibility of personalized medicine. Despite the rapid development of computational tools for data annotation and interpretation, there are still numerous challenges like data storage, access, sharing, annotation, or integration that need to be overcome.

What motivates you, personally? What made you go into science?
I have always been amazed by the development processes from just a single cell to a highly intelligent creature, which is achieved via precise gene expression regulation. Now that I have acquired a deeper understanding of how the gene expression regulation actually works, I am even more fascinated by this complex, efficient, accurate, dynamic, and comprehensive regulatory system. This system includes layers like genome, transcriptome, epigenome, proteome, metabolome to name just a few. Hence, if a disorder occurs in any of those layers, this could break the harmony of the cell, tissue, or organism, which may lead to disease.

To me, the interesting part of doing science is using cutting-edge technologies. Plus, I like the process of plus deep-thinking combining smart and creative experimental design with powerful computational tools to test hypotheses, to unravel some of science's mysteries and get a better understanding of man and nature in general. This does not only give me a feeling of self-satisfaction and confidence, but also trains me to think, act, and study logically and scientifically, which are quite important skills for life - inside and outside science.

Why do you think the HCA|Organoid research is important?
As a contribution to the Human Cell Atlas project, HCA|Organoid is aiming to establish the human cell reference of organoids. Organoids are tiny, simplified version of organs which are self-organized, three-dimensional in-vitro cultures. There are four advantages to use organoids : 1) organoids are derived from human tissue; 2) the 3-D culture system and self-organizing properties largely mimic the real micro-anatomy; 3) their robustness characteristics enable scale-up; 4) establishing organoids from primary tissue holds great potential to help us discover novel ways towards personalised medicine.

These four advantages make organoids a unique and powerful model for disease-centric biomedical research. For instance, organoids can be used as a sample type for biobanking. From a basic research point of view, culturing organoids could be used for developmental biology research, or as the model for external stimulation and cell- cell interaction. And, organoids can also be used as a drug screening platform, in genetic engineering, and in cell therapy for precision medicine. Lastly, organoids serve as a good disease model for pathogen analyses or disease-related genetic variants screening. Hence, the establishing of human organoid cell reference is of high value as a unique system with broad applications.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it?
It has been a long time since the discovery of cells as the basic unit of structure and function in life. In the course of time and with the development of novel, disruptive technologies, researchers have been able explore many features of different cell types and states. We are lucky to live in the era of single-cell technology, which gives us the opportunity to investigate huge array of additional cell type components and different characteristics of human tissue.

The Human Cell Atlas set out to create comprehensive reference maps of all human cells aiming to further our understanding of human health and diagnosis, to improve disease monitoring and treatment (HCA whitepaper). And for me, this is exactly the right time for such a meaningful endeavour, considering that there are uncertainties of defining cell types and cell states. Moreover, cells are changing alongside the developmental trajectory, they are subject to different diseases, and we see complicated cell-cell interaction. A comprehensive human cell reference map is necessary for mapping and defining all the cell types, states, and their relationships in order to accelerate biomedical research for the sake of better diagnostics and drug discovery.

HCA|Organoid aims to establish a “Human Organoid Atlas” mainly on colon and brain of single cell transcriptomes, epigenomes and time-series imaging on thousands of organoids. The project thus do not only contribute to HCA by boosting the future disease-centric biomedical research, but also by expanding the knowledge and influence of the HCA.

What is your role in the HCA|Organoid team at HUB?
HUB is responsible for generating organoid biobanks from normal colon, colorectal cancer and normal liver tissues. Samples for single cell genomic and transcriptomic characterization are taken from the primary tissues and the derived organoid cultures. My main responsibility is the supervision of the laboratory team in their daily activities and keeping track of our progress. Our team has also developed protocols for the generation of both the organoid and tissue samples for characterization and I’ve been in charge of supervising this work as well.

What are you currently working on? What’s your major research interest?
Alongside the HCA|Organoid project I am involved on multiple research activities at HUB such as model development for Inflammatory Bowel Disease or optimization of assays for toxicity and immuno-oncology studies. Since organoid reflect in vivo physiology and patient to patient variation, patient derived organoids (PDOs) have a high potential to be used for disease modelling, drug testing and toxicity assays. At HUB we get to work on multiple projects and disease areas at the same time, which allows me to diversify my skill set, develop new expertise and stay up to date with all new developments in the field.

What motivates you, personally? What made you go into science?
My passion for science really flourished in secondary school when I was exposed to new subjects such as chemistry and biology, which I immediately found fascinating. The thing I love the most about science is to be able understand processes that cannot be seen with the naked eye. In addition, science is always moving forward, making new discoveries which makes it very interesting field to work in.

Why do you think the HCA|Organoid research is important?
PDOs are a relatively new field of research and have a high potential to fundamentally change the way we approach problem solving in disease modelling and toxicology as well as in drug discovery and development. Though organoids are currently been applied to multiple research areas, the HCA|Organoid research will further increase our understanding of the cellular composition of organoids and provide us with detailed characterization of the cell types. I expect that this increased knowledge will help to further develop existing protocols as well as new assays relevant for a variety of diseases.

What are your views on the Human Cell Atlas endeavour? Why do you think it is important, and how do HCAlOrganoid and the HCA Cluster contribute to it?
HCA will have a major impact on our understanding of the biology of human tissues. Though the main focus is on healthy tissue, I believe it will ultimately be translated into novel discoveries and applications in human disease. Since primary tissues and cells have numerous disadvantages (e.g. price, availability and in vivo resemblance), PDOs can be used for the development of such applications. Characterization within HCA|Organoid will facilitate the use of organoids for new applications.