3DbioNet

ECR Club Kick off Social Lunch

ECR Social Lunch 3rd July 2020 12-1pm report by Jonathan Temple

The Early Career Researcher (ECR) social lunch was kicked off in a virtual session by a warm welcome by Dr. Bhumika Singh, the 3DbioNet manager, who introduced the ECR events organising committee to the participants. Currently, the committee members are Dr Caroline Taylor, University of Sheffield, Jonathan Temple, University of Liverpool and Sebastian Gilbert, University of Birmingham. Caroline outlined the aims of the session, and the overall aims of the ECR club.

Following a quick round of introduction from all the participants, we were split into two break out rooms for smaller discussion groups. Break out room 1 contained Sebastian Gilbert, Jonathan Temple, Manohar Prasad, Dr Rania Deranieh and Dr Pilar Aced: 1 Independent researcher, 1 PDRA and 3 PhD students with their year of study ranging from 1st to 4th year. Break out room 2 consisted of Dr Caroline Taylor, Dr Vijay Raghavendran, Dr Edi Tanase and Joseph Barnes: 2 PDRAs, 1 research fellow and 1 first year PhD student.

The discussion room atmosphere was very relaxed and it was soon apparent the groups contained people with a broad range of interests. From biomaterials for bone-assist medical implants and electrospun scaffolds for hepatotoxicity testing to oxygen level detecting biomolecules and pancreas and liver cell experts. The discussion was broad and everyone had lots to offer and even though highly varied, there was plenty of shared experience or interest in other people’s areas of research. We also found out there were plenty of keen bakers among us who had been baking up a storm during lockdown as well as others who loved being outdoors or playing various sports.

Next, it was time to discuss what people wanted from the network and how the network could help them. The discussion was informative and with a variety of input, people suggested coming together to discuss protocols and making standardised protocols along with other problems faced in the field. People who are new to the field or early in their career were keen to meet others in the field; possibly find collaborators, or even find experts in a different field to seek help. Many were also interested in the prospect of hearing from experts in different fields and industries on career progression and development. We received great feedback on what our attendees want from the committee and it will enable us to tailor our sessions to our members.

We finished the session with feedback from each room and the results of our online form before Caroline gave some concluding remarks. The first session was an exciting start for our ECR sessions and we had a number of PDRAs, PhD students and other ECRs from all over the country including The University of Liverpool, The University of Nottingham, The University of Sheffield, The University of Birmingham and University College London. We as the ECR committee now have a clearer direction and indication of the needs of our members. We are extremely looking forward to our future sessions and hope to see you there.

Respiratory organoid development via tailored three-dimensional macromolecular environments: a 3DbioNet funded project

Professor Ruth Cameron’s team at the University of Cambridge was awarded pump priming grant by 3DbioNet. The aim of the study is to produce alveolar organoid structures in highly defined 3D structures. This will allow transitioning away from current spherical organoid systems, typically cultured using Matrigel, to a 3D system that more appropriately reflects tissue organisation. The group propose to design ice –templated, collagen- and elastin-based, porous environments to supply the spatial, mechanical and biochemical cues of native tissue.Below is a video we filmed from our trip to their laboratory in Cambridge.

CARS microscopy for imaging 3D organoids: a 3DbioNet funded project

Dr Iestyn Pope’s team at Cardiff University was awarded pump priming grant for this project titled ”Incorporating deuterium into 3D organoids to identify cell types and track cellular metabolic rates using CARS microscopy”. In this study, Dr. Pope’s group intend to use CARS microscopy to image organoids that have been cultured in media containing deuterated water. The aim being to identify the different cell types that make up the organoid structures without the need for fluorescent markers. Similarly by feeding the cells with deuterated compounds we will be able to observe the uptake or metabolic rate of the individual cells and what effects different drugs have on this rate. This will allow us to study these complex systems with minimal interference or modification, allowing long term studies of the effect of therapeutic drugs on cell development and metabolism – a current unmet need within therapeutic design.

”We hypothesise that this grant by the network will allow us to perform two crucial experiments on 3D cell models:

1) As different types of cell make different biological molecules, we should be able to tell the cells apart simply by the way in which they use the deuterium from the heavy water.

2) Different types of cells metabolise material in different ways, and this heterogeneity could potentially affect their susceptibility to therapeutics. By studying the turnover of deuterium we should be able to understand the cells metabolism in more detail without using fluorescent markers”.

More information on this project.

3D model of ovarian cancer and metastasis: a 3DbioNet funded project

3DbioNet funded a range of projects, one of them was at Dr. Eirini Velliou’s group at the University of Surrey. The project aims to design a biomimetic 3D printed prototype of primary ovarian cancer.

”We want to see what happens when a patient develops resistance to a certain disease” ,
Dr. Priyanka Gupta, Velliou’s group, University of Surrey.

Dr. Eirini Velliou’s group at University of Surrey, received funding from 3DbioNet network to develop a 3D model of ovarian cancer. Ovarian cancer is a deadly gynaecological disease. Currently, there are not many screening platforms for this cancer, other than simple 2D models which are not very effective. The 3D model to be developed by the Velliou group is a complex and advanced model of spread and development of the ovarian cancer. It will capture the tumour microenvironment including structural integrity and interstitial flow, and utilise patient derived cancer cells leading the way for development of personalised therapy. Video courtesy Cal Strode.

Early Career Researchers Committee

3DbioNet have started an initiative to promote learning and training among the early career researchers interested in 3D biology. A committee has been set up to lead the activities, some of which would be around training in techniques, new methods, as well as career mentorship. Dr. Caroline Taylor, University of Sheffield, and Jonathan Temple, University of Liverpool have been appointed as the ECR committee members. If you would like to become a member of the ECR committee, or to contribute, please email at 3dbionet@liverpool.ac.uk.

Imaging and modelling 3D cell culture systems

Our latest workshop was a joint event with another Technology Touching Life network, IBIN (Integrated Biological Imaging Network) in London. This was our first joint IBIN-3DBioNet workshop where over 100 attendees from all over the UK met during two days in January. IBIN‘s focus is on developing new methods of taking high-resolution images of living cells in 3D systems and tissues. So, the complementarity with 3DbioNet is obvious. The first day included a session on mental health organised and chaired by early career researchers. The power of combining experimental and mathematical modelling approaches was on full display during the two days through several excellent talks. Our colleagues from the industry sector brought important insights on what is needed to develop future applications and how collaborations with academia will be essential. Overall, a highly successful event, which, we hope, triggered many new ideas and collaborations. You can check out the Twitter reporting from the event. Below is the full video from the event. Thanks a lot to Cal Strode who made this fantastic video.

Funded Project Summary:

Dr Iestyn Pope’s team at Cardiff University was recently awarded £53,950 to take the following project forward:

Incorporating deuterium into 3D organoids to identify cell types and track cellular metabolic rates using CARS microscopy

Organoids are 3D microtissues that reproduce more accurately how a tissue behaves compared to a 2D culture on plastic. This is because it allows the cells to interact with each other and to organise their own microenvironment. Recently, we and others have shown that patient-derived cancer organoids retain the cellular diversity that matches that of the tumours from which they are derived. Thus 3D cell culture has the potential to revolutionise technical approaches in personalised medicine and drug discovery.

Typically, identification of different cell types within cancer organoids, and many of the experiments undertaken on them are performed by first tagging the cells or molecules of interest with a fluorescent marker, which can then be visualised on a microscope. However, using this technique there is always the potential that the addition of the fluorescent marker alters the behaviour of the cell or molecule you are interested in following.

Over recent years, Coherent anti-Stokes Raman Scattering (CARS) microscopy has emerged as a powerful label-free way of rapidly imaging live cells and tissues with high 3D spatial resolution and quantitative chemical information. Rather than looking at a fluorescent marker, CARS directly probes the bonds of the molecules that make up the cells and tissues of interest. One such bond that is frequently probed is the bond between carbon and hydrogen (CH2) since it is present in large numbers within biological components. Recent work has demonstrated how the addition of deuterated water (also known as heavy water, since the hydrogen atoms that make up the water contain an extra neutron compared to regular hydrogen) can be used to generate carbon–deuterium (C–D) bonds in molecules within cells. Owing to the heavier isotopic mass, deuterated bonds can be easily distinguished from other cellular signatures when imaged with CARS microscopy.

We hypothesise that this will allow us to perform two crucial experiments on 3D cell models:

1) As different types of cell make different biological molecules, we should be able to tell the cells apart simply by the way in which they use the deuterium from the heavy water.

2) Different types of cells metabolise material in different ways, and this heterogeneity could potentially affect their susceptibility to therapeutics. By studying the turnover of deuterium we should be able to understand the cells metabolism in more detail without using fluorescent markers.

In this study we intend to use CARS microscopy to image organoids that have been cultured in media containing deuterated water. The aim being to identify the different cell types that make up the organoid structures without the need for fluorescent markers. Similarly by feeding the cells with deuterated compounds we will be able to observe the uptake or metabolic rate of the individual cells and what effects different drugs have on this rate. This will allow us to study these complex systems with minimal interference or modification, allowing long term studies of the effect of therapeutic drugs on cell development and metabolism – a current unmet need within therapeutic design.

Pump-priming awardees confirmed:

3DbioNet received 21 eligible applications in total, and had a final ranking review call with our advisory board on Friday August 30th, the outcome of which we are pleased to share. We were only able to fund four projects in this round, there are many more we would have liked to have funded. The four successful projects are as follows:

Award amount: £45,750
Principal Investigator:
 Dr Ipsita Roy 
Institution: University of Sheffield, Material Science and Engineering
Project title: A natural and sustainable biomaterial-based 3D model of healthy cardiac tissue

Award amount: £63,980
Principal Investigator: Prof Ruth Cameron
Institution: Cambridge Centre for Medical Materials / Materials Science and Metallurgy
Project title: Directing respiratory organoid development via tailored three-dimensional macromolecular environments

Award amount: £57,906
Principal Investigator: Dr Eirini Velliou
Institution: Bioprocess and Biochemical Engineering group (BioProChem), Department of Chemical and Process Engineering
Project title: On the design of a biomimetic 3D printed metastasis prototype of primary ovarian cancer – towards Personalised Healthcare

Award amount: £53,950
Principal Investigator: Dr Iestyn Pope
Institution: Cardiff University, School of Biosciences
Project title: Incorporating deuterium into 3D organoids to identify cell types and track cellular metabolic rates using CARS microscopy.

Funded Project Summary:

Professor Ruth Cameron’s team at the University of Cambridge was recently awarded £63,980 to take the following project forward:

Directing respiratory organoid development via tailored three-dimensional macromolecular environments

Our aim is to produce alveolar organoid structures in highly defined 3D structures. This will allow us to transition away from current spherical organoid systems, typically cultured using Matrigel, to a 3D system that more appropriately reflects tissue organisation. We propose to design ice –templated, collagen- and elastin-based, porous environments to supply the spatial, mechanical and biochemical cues of native tissue.

The self-organisation of alveolar-derived co-cultures in 3D cell scaffolds will be studied in structures possessing a range of density, porosity and composition, identifying conditions that promote cellular organisation to closely match native lung. Critically these tailorable structures permit systematic decoupling and assessment of extracellular matrix (ECM) attributes that are crucial for lung cell organisation which is not possible using current homogeneous supports (e.g. transwell inserts and Matrigel) or decellularised lung tissue. Instead our system will allow the study of cells in a native-ECM structure with systematically altered properties to address specific, hypothesis-driven, questions such as the influence of architecture, biochemical cues and stiffness.

We will use ice-templating methodology to fabricate highly porous, completely interconnected 3D structures of biologically-derived collagen I and elastin with precisely tailored architectural cues. These are highly cell conductive and can be used for the formation of complex self organised cell structures, developed from multiple cell types. We will explore the effects of pore architecture, mechanics, the ratio of collagen and elastin and the use of synthetic peptide motifs to direct the cellular phenotype.

This project will provide proof of concept of a system replicating lung cell self-organisation with the flexibility to decouple, assess and address environmental attributes crucial for lung development and disease progression.

Funded project summary:

Dr Eirini Velliou’s team at the University of Surrey was recently awarded £57,906 to take the following project forward:

On the design of a biomimetic 3D printed metastasis prototype of primary ovarian cancer – towards personalised healthcare

Ovarian cancer is a silent gynecological killer with late stage diagnosis, relatively low survival rate, high resistance to chemotherapy and high recurrence rate. While research is being conducted to answer, and solve many of its associated problems, the lack of a robust, high throughput in vitro model for the disease and its metastasis puts a dent on research success.

Most studies for ovarian cancer use either animal models or simplistic 2D cell culture systems. However, animal studies are expensive, difficult to reproduce and have ethical issues associated with their use. At the same time, 2D models are unable to mimic the complexities of the human body in terms of cellular arrangement, presence 3D structure, cell- cell and cell-matrix interactions, interstitial flow etc. Tissue engineering and the emerging of 3D tissue culture models can mitigate many of the problems associated with animal models and 2D cell culture. 3D models provide a 3-dimensional growth environment able to mimic spatially and biochemically an actual tissue, they allow for cell-cell and cell-Extracellular Matrix (ECM) interactions, they provide structural integrity and can be incorporated in bioreactors to mimic the interstitial flow. Additionally, they are less expensive and devoid of ethical challenges associated with animal models.

Due to the above benefits, researchers have started using 3D models for ovarian cancer research. However, most models are single cell based and do not capture the biological complexity of a real tumour. Furthermore, the models of omentum, which is the primary metastasis site, are also relatively simplistic and do not capture the complexity of the organ. Overall, to date, there is no model of ovarian cancer that integrates the complex tumour biological structure coupled with a robust omentum structure. Here, we aim to bridge that gap via developing for the first time a robust dynamic multicellular model of a human primary ovarian tumour and its primary metastasis site (omentum). This novel model involves multicellular tumour aggregates from fresh human ovarian cancer tissue coupled with a complete omentum model.

For the integrated model development, a multidisciplinary group of scientists will work together using human derived tissues and techniques such as 3D-printing, novel materials and bioreactors to mimic the interstitial flow. The model will enable advanced studies on the disease progression, treatment response as well as the screening of novel treatment methods. Therefore, it will be of benefit to clinicians, academics and the industry. Most importantly, it will facilitate faster development of personalised treatment protocols, accelerating appropriate individualized therapies for the disease from bench to bedside.