How do you use the CiteAb reagent search engine? Interview with Dr. Andrea Radtke

By Skye Longworth

June 29, 2023

The author is supported by the Intramural Research Program of the NIAID, NIH. However, the views expressed in this piece are solely the private opinions of the author and do not reflect official policy of NIAID, NIH, DHHS, or any other component of the U.S. Federal Government.

This March, we celebrated ten years since the CiteAb reagent search engine went live. In this time, we have grown from an antibody search engine to cover five reagent types, over 13 million products and >75,000 users monthly. With each new user searching CiteAb to find reagents that work, our goal to help accelerate science is moved forward.

To reflect on this milestone, we have been talking with CiteAb users to find out a little more about their research and to understand how they use the reagent search engine. 

Today, we are thrilled to talk with Dr. Andrea Radtke. Dr. Radtke is an Associate Scientist at the NIAID/NIH, USA, with a focus on microscopy techniques. 

She began her research journey at the University of Wisconsin-Madison in the laboratory of Dr. Susan Paskewitz and completed her PhD in the laboratory of Dr. Fidel Zavala at the John Hopkins Malaria Research Institute. As a PhD student, Dr. Radtke developed a passion for immunology and began to teach herself multiplexed immunofluorescence imaging until graciously connecting with Drs. Wolfgang Kastenmuller and Michael Gerner in the laboratory of Dr. Ronald Germain at the National Institutes of Health. Passionate about open science, team science and mentoring, Dr. Radtke has carried the lessons from her early research experiences to her current work – namely sharing knowledge, successes, and failures.

Here’s what she had to say: 

What is your current work focused on?

‘I’ve spent the last 10 years, first as a postdoctoral fellow, then a Staff Scientist, and now Associate Scientist developing advanced microscopy techniques to explore the immune system within the Center for Advanced Tissue Imaging (CAT-I) led by Dr. Ronald Germain. In this role, I created a workflow for validating hundreds of antibodies on mouse and human tissues and developed IBEX [1,2], an open-source, versatile imaging method that enables highly multiplexed imaging in diverse human and mouse tissues. I’ve devoted more than a quarter of my life to building an extensive validated antibody catalog, optimizing imaging protocols, and applying quantitative multiplexed imaging to better understand normal and malignant tissue organization. I am grateful for the resources, support, and independence I have received in the Germain laboratory along with the amazing students, trainees, and colleagues who have enriched my life through their creativity, resilience, kindness, and substantial contributions to this work.’

Can you tell us a little more about the groups and initiatives you are involved in? 

All with a central theme of community, Dr. Radtke is involved in multiple initiatives: 

IBEX Imaging Community: 

‘Multiplexed tissue imaging has expanded in the last 20 years. These technologies offer incredible promise in characterizing the tissue microenvironments of normal and malignant tissues. However, the time, cost, and expertise required to find antibodies, validate in appropriate control tissues, and build panels are significant barriers for their adoption. The IBEX Imaging Community is an international group of scientists committed to sharing knowledge related to multiplexed imaging in a transparent and collaborative manner. This open, global repository is a central resource for reagents, protocols, panels, publications, software, and datasets.’

Additional methods are also supported by this community with guiding principles reflecting shared ownership and iterative improvement.

Here are some relevant resources: 

https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

https://zenodo.org/record/7693279#.ZAFfb3bMIuU

https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base/discussions

HuBMAP:

‘The Human BioMolecular Atlas Program is a consortium of over 300 researchers funded by the NIH Common Fund. Together, researchers are using cutting-edge techniques to map every cell of the human body in pursuit of a comprehensive Human Reference Atlas. Given the scope of the work, the HuBMAP consortium has several working groups focused on benchmarking technologies, developing standards, sharing expertise, and education and outreach. It’s an honor to be a member and co-chair of the Affinity Reagent Imaging and Validation Working Group, an international group of technology developers, reagent manufacturers, and domain experts in multiplexed tissue imaging. We are an open group spanning 9 time zones with members in academia, industry, and government. We first came together to author a primer in Nature Methods that outlined many of the challenges with spatial mapping approaches, principally the cost, time, and expertise required to acquire high quality imaging data using panels of antibodies. Over the last 2 years, we have worked to solve that problem by creating Organ Mapping Antibody Panels, collections of antibodies that can be used to map anatomical structures and cell types in human tissues. I am grateful for my incredible team leaders Ellen Quardokus, Diane Saunders, Neil Kelleher, Katy Borner, fellow co-chair Liz McDonough, and many others. The work will be published in Nature Methods in July 2023.’

It’s the year of open science, how is this important in the work you do? 

‘Yes, it’s exciting to see the U.S. Federal Government’s commitment to Open Science across its agencies. My dear friend, colleague, and chief architect of the IBEX Imaging Community, Dr. Ziv Yaniv, has been practicing open science for 20+ years in the open-source software community. Ziv has devoted his time and expertise to build an imaging community to share successes and failures.

Open Science is the how behind our why. Open Science instills confidence in the results, accelerates discovery, and makes the scientific enterprise more equitable by sharing datasets, software, and scientific findings with colleagues around the world. I will be honest…it’s not easy. You really must love it in order to do it as we don’t receive additional funds to support these initiatives. My mother, a retired public educator, volunteers her time to find antibody metadata for entries in the IBEX Knowledge-Base.’ 

So, how do you use the CiteAb platform in your work?

‘I’ve been using CiteAb almost daily for 5+ years. It’s integral to finding the best antibody candidates for our multiplexed tissue imaging studies. CiteAb is so critical for our work that searching CiteAb is a step in our protocol for building complex imaging panels. CiteAb allows my colleagues and me to search for the most highly cited antibody, with accompanying images, by application, reactivity, conjugate, and many other critical fields. As a result, we spend less time and money testing reagents that are likely to fail.’

What do you like about CiteAb?

‘We love the size and scope of CiteAb. It’s truly exhaustive. The page layout is attractive and intuitive, displaying reference data and citations for each result. We find the example images and links to papers with experimental details the most useful for validating potential candidates for our imaging studies. Using images from the literature, we can discern for ourselves if a reagent yields the appropriate labeling pattern prior to purchase. Whenever possible we try to select the most highly cited antibodies because, quite obviously, these candidates will have the greatest likelihood of success. ‘

Can you think of an example where you’ve found CiteAb to be useful?

‘Many times I have an established panel of antibodies and need an antibody with very specific properties (host species, isotype, conjugate) to be compatible with the entire panel. In those instances, I use CiteAb to find the most highly cited antibody that can fit into the empty roster spot, e.g., available in a particular conjugate or isotype (Chicken IgY). In many instances, we need to conjugate an antibody to a particular fluorophore to work in our panel. For this reason, I love that CiteAb allows searching by formulation (Carrier free) and suppliers that support custom conjugation services. Once I have identified a few candidates, I then search the accompanying papers for antigen retrieval conditions.’

Hear more from Dr. Radtke at the 4th International Antibody Validation Meeting

We want to extend our thanks to Dr. Andrea Radtke for speaking with us about her work and experience with CiteAb. It’s been a pleasure to learn more about her initiatives and the part CiteAb plays in this research. 

We are so excited that Dr. Radtke will also be speaking at the 4th International Antibody Validation Meeting this September, organised by CiteAb and the University of Bath. This unique meeting brings together experts in antibody validation across academia, the pharma/biotech sector and antibody suppliers with the aim of improving validation for the life science community. Register to hear her speak, alongside 13 other impressive individuals, here.

References

1.https://www.pnas.org/doi/abs/10.1073/pnas.2018488117

2.https://www.nature.com/articles/s41596-021-00644-9

About the author

Skye is the Scientific Communications Manager at CiteAb, with a background in Biochemistry.

More posts by Skye