Cesora

Welcome to the Centre of Excellence for Spatial Omics Research in Africa

About CESORA

Welcome to the Centre of Excellence for Spatial Omics Research in Africa (CESORA). CESORA, founded in 2023, is a pioneering interdisciplinary initiative integrating transcriptomics and tissue biology, based at the Africa Health Research Institute in South Africa. Our mission is to support and empower African-led research initiatives that aim to unravel the complexities of disease manifestation within specific tissue compartments. We are committed to accelerating access to cutting-edge spatial omics technology across the continent, fostering collaboration, and driving advancements in the field of spatial genomics. As the first research facility in Africa to possess the GeoMx DSP instrument, our programme is poised to overcome barriers of access to the spatial omics technology by African researchers.

We offer a range of services including:

  • Spatial Omics Project Design
  • Advanced Imaging
  • Next Generation Sequencing (NextSeq 2000)
  • Data analytics
  • nCounter

Leadership & Team

The CESORA is led by Professor Zaza Ndhlovu, faculty member at Africa Health Research Institute and the founding director and head of CESORA and its scientific programmes. Dr Bongiwe Mahlobo is the programme manager who oversees administrative and daily operations. The CESORA team includes spatial omics and imaging experts as well as administrative support.

Executive Committee

Prof Zaza Ndhlovu

Prof Zaza Ndhlovu

CESORA Executive Director View Bio

Professor Zaza Ndhlovu is an eminent HIV immunologist who has made significant contributions in the field of HIV pathogenesis research, vaccine, and cure research. He has numerous publications in top tier journals and has been awarded multiple competitive grants. Read more about Zaza and his research programme at Africa Health Research Institute (AHRI) here.

Dr Bongiwe Mahlobo

Dr Bongiwe Mahlobo

CESORA Programme Manager View Bio

Dr Bongiwe Mahlobo holds a PhD in HIV immunology. Her doctoral research delved into the complex realm of HIV and sought to gain insights into the role of regulatory CD4+ T cells in the lymphoid tissues of individuals with early treated HIV-1 infection. As the CESORA programme manager, Bongiwe is responsible for the day-to-day running of the centre.

Dr Andrea Papadopoulos

Dr Andrea Papadopoulos

CESORA Spatial Omics Support View Bio

Dr Andrea Papadopoulos is a postdoctoral research fellow at AHRI. She holds a PhD from Wits university. Her postdoctoral research focuses on characterising T cell responses to Covid-19 vaccines, and she is leveraging the first GeoMx platform in Africa to understand how spatial organisation of tissue immune microenvironments aids or restricts HIV reservoir persistence.

Thandeka Nkosi

Thandeka Nkosi

CESORA Administrative Support View Bio

Thandeka Nkosi completed her master’s degree in medical sciences at UKZN. Her research demonstrated that initiating antiretroviral (ART) treatment at an early stage is associated with a mitigated but measurable CD8+ T cell response that is functionally competent and durable. Thandeka oversees the daily operations of the Ndhlovu lab at AHRI.

Trevor Khaba

Trevor Khaba

CESORA Technical Support View Bio

Trevor Khaba is the senior research technician within the HIV Pathogenesis Programme (HPP) at UKZN. The focal point of Trevor’s research revolves around investigating the immunology of lymphoid tissue infected with HIV-1.

Scientific Advisory Board Members

Dr Alex K Shalek

Dr Alex K Shalek

Scientific Advisory Board Member View Bio

Alex K. Shalek, PhD, is the J. W. Kieckhefer Professor in the Institute for Medical Engineering & Science and the Department of Chemistry, and an Extramural Member of The Koch Institute for Integrative Cancer Research at MIT. He is also an Institute Member of the Broad Institute, a Member of the Ragon Institute, an Assistant in Immunology at MGB, and an Instructor in Health Sciences & Technology at HMS. Dr. Shalek received his bachelor’s degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT). 

His lab’s research is directed towards the development and application of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. Dr. Shalek and his work have received numerous honors including a NIH New Innovator Award, a Beckman Young Investigator Award, a Searle Scholar Award, a Pew-Stewart Scholar Award, the Avant-Garde (DP1 Pioneer) Award from the National Institute for Drug Abuse (NIDA), and an Alfred P. Sloan Research Fellowship in Chemistry, as well as the 2019-2020 Harold E. Edgerton Faculty Achievement Award at MIT and the 2020 HMS Young Mentor Award.

Dr Jacob Estes

Dr Jacob Estes

Scientific Advisory Board Member View Bio

Dr. Estes graduated from Brigham Young University with a B.S. in Microbiology and Molecular Biology in 1999. He continued his graduate education at Brigham Young University and obtained his Ph.D. in Immunology and HIV Pathogenesis in 2003 in the laboratory of Dr. Gregory Burton. From 2003 to 2007, he was a postdoctoral fellow in the laboratory of Dr. Ashley Haase in the Department of Microbiology at the University of Minnesota focusing on the in vivo immunopathology of lentiviral infections. 

Following postdoctoral training, Dr. Estes joined the AIDS and Cancer Virus Program at the Frederick National Laboratory for Cancer Research and was a Principal Investigator of the Retroviral Immunopathology Section and Senior Principal Scientist and Head of the Tissue Analysis Core. Dr. Estes was appointed an Adjunct Professor in the School of Health and Biomedical Sciences in the College of Science, Engineering and Health at RMIT University in Melbourne, Australia in 2017. In 2017, Dr. Estes accepted a dual appointment as Professor within the Vaccine and Gene Therapy Institute (VGTI) and Chief of the Division of Pathobiology & Immunology in the Oregon National Primate Research Center (ONPRC) at OHSU.

Dr Karen Makar

Dr Karen Makar

Scientific Advisory Board Member View Bio

Dr. Karen Makar is a PhD immunologist, molecular epidemiologist, and Deputy Director in the Discovery & Translational Sciences team in Global Health. She leads the Global Health Discovery Collaboratory, a grantee network program and domain in D&TS that brings the frontiers of technological innovation to priority global health problems by sourcing cutting-edge technologies, lowering barriers to accessing innovative technologies, and cultivating interdisciplinary partnerships between members to catalyze discovery of novel biomedical solutions. 

The Collaboratory Platforms, the flagship program of the Collaboratory, provide early access to best-in-class tools, technology platforms, and expertise to Collaboratory members to elevate the level of scientific rigor and accelerate discovery and translation efforts across the foundation. Karen has a 20+ year career cultivating and harvesting cutting-edge science and technology to advance innovative vaccines, biologics, diagnostics and other health interventions, first at Dendreon Corporation and then as Director of the Molecular Epidemiology Laboratory at the Fred Hutchison Cancer Research Center— prior to joining the D&TS team as a member of the Vaccines & Biologics domain in 2015.

Professor Thumbi Ndung’u

Professor Thumbi Ndung’u

Scientific Advisory Board Member View Bio

Thumbi Ndung’u is the Director for Basic and Translational Science at the Africa Health Research Institute (AHRI) in Durban, South Africa; Programme Director for the Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE); Professor of Infectious Diseases at University College London; Scientific Director of the University of KwaZulu-Natal’s HIV Pathogenesis Programme; and Associate Member of the Ragon Institute. He is Co-chair of the International AIDS Society (IAS) Towards an HIV Cure Advisory Board.

He has a Bachelor of Veterinary Medicine degree from the University of Nairobi, Kenya, completed a PhD in Biological Sciences in Public Health from Harvard University, USA and performed post-doctoral research in Virology at Harvard Medical School. He is a recipient of the South African Medical Research Council Gold award for scientific contributions that have impacted on the health of people and is a member of the Academy of Science of South Africa and an African Academy of Sciences Fellow. His research focuses on understanding how the immune system may be harnessed for HIV prophylactic or therapeutic strategies.

Services and Support

At CESORA we offer exciting collaborations and research opportunities for scientists across the continent. Our aim is to foster a vibrant, multi-disciplinary research community that is focused on developing novel and impactful solutions to key African challenges. We invite national and international researchers to work with us to understand disease manifestation in tissues. We welcome anyone interested in actively participating and contributing to this research community. We have several collaborative programmes in place. The scope of the projects is classified based on the following three-tiered framework:

Tier 1

This is an entry-level category which mainly caters for exploratory projects.

In this category, we provide service for up to 10 samples using the nCounter. This tier excludes next-generation sequencing (NGS) or bioinformatics support. No travel for investigators is needed and is free of charge or heavily subsidized. Importantly, CESORA helps to graduate some good Tier 1 projects to the second tier by offering technical assistance in study design and providing letters of support to potential funders.

Tier 2

This category offers mid-level service; this tier will cater for projects with sample numbers between 10 and 20 and addressing a substantive scientific question.

In Tier 2, we provide services, including assay design and histology services, multiparameter immunofluorescence microscopy and data analytics. Some Tier 2 projects will require NGS sequencing services and bioinformatics support. Investigators will typically be required to spend a few days at AHRI to conduct experiments alongside the CESORA core staff. Tier 2 projects are mostly funded by the project PI. CESORA may subsidize some reagent costs and bench fees depending on the rigour of science and the level of collaboration.

Tier 3

This category involves much larger projects.

This Tier is for large projects. Investigators will be required to travel and spend 1-3 months at AHRI to receive training and conduct their experiments. Most Tier 3 projects will require NGS and bioinformatics support from CESORA. Tier 3 projects are fully funded by the investigator’s grant.

Funding

CESORA aims to provide financial support for research projects seeking to advance knowledge within the field of spatial omics, as well as to encourage innovative multi-disciplinary collaborations between researchers of diverse backgrounds and varieties of experience. All funding calls are advertised under our ‘news and events’ section.

Education and Training

Our Centre of Excellence provides a range of education and training opportunities. Through hands-on training and project-based learning, participants will be able to gain a comprehensive understanding of spatial omics. These educational and training opportunities are aimed at equipping researchers with the necessary knowledge and skills to use, develop, and apply spatial omics technologies to study diseases in native tissue environments. As part of our education and training programme we offer annual in-person theory and practical workshops that cover the entire Spatial Omics research workflow. The inaugural spatial omics workshop was hosted in November 2023, in partnership with AMI, SANTHE and NanoString.

Technology Overview

What is Spatial Omics?

Spatial Omics is the study of gene expression and protein abundance in situ, meaning within the native tissue.

Using spatial omics techniques, scientists can visualize molecules in their unique tissue context within individual cells and tissues thus providing spatial context to decode functional biology.

Read More

Why is Spatial Omics relevant today?

Cells do not function in isolation but are strongly influenced by their spatial location and surroundings. Integrating... different scales of analysis from spatial omics and single‐cell analysis improves our understanding of tissue and cellular microenvironments in healthy and diseased samples.

Multi-omics data analysis along with spatial context are needed to capture biological function and gain a greater understanding of complex populations, and processes can be obtained which drive improved clinical diagnostics and therapies.

In particular, spatial omics technologies are being used to investigate:

  • Biomarker Discovery and Validation
  • Immune Profiling
  • Unbiased Pathway Analysis
  • Tissue and Cell Atlasing
  • Cellular Neighborhood Analysis
  • Receptor-Ligand Interactions
Read More

Spatial Transcriptomics Technologies

Biology is inherently spatial and cannot always be resolved by bulk analysis: cell fate decisions depend on... spatial relationships between cells in the same way that immune cells need to spatially interact with their target to exert their function at the tissue level.

Several new technologies have been developed that aim to combine gene and protein expression data with spatial context.

Read More

NGS-Based vs. Imaging-Based

Most of the spatial omics technologies available today have been built on in situ tissue analysis and can be... primarily categorized into:

(1) NGS-based approaches that encode positional information onto transcripts before sequencing and

(2) imaging approaches based either on in situ sequencing (ISS) where transcripts are amplified and sequenced in the tissue or fluorescence in situ hybridization (FISH) where imaging probes are sequentially hybridized in the tissue2.

This classification is not clear-cut as some technologies may incorporate elements of both categories.

Read More

Additional resources

Links to external resources about Spatial Omics.

Webinar: Spatial Biology 101

How can you set up a spatial biology experiment? How is it different from multiplex immunofluorescence staining? Learn the answers to these questions and more by connecting to this on-demand webinar.

Get an overview of the GeoMx DSP system, how it works, what you can do with it, what kinds of assays are available, and how you can analyze your data. Plus, get a sneak peek of the single cell spatial imaging platform the CosMx™ Spatial Molecular Imager and how GeoMx and CosMx complement each other.

Spatial Organ Atlas

Get access to open-source whole transcriptome GeoMx DSP data of selected mouse and human organs: pancreas, brain, colon, lymph node, liver, mouse embryo etc.

Browse the Minerva stories as they help reveal the complex molecular mechanisms underlying organ development and function by combining whole transcriptome data with spatial context.

GeoMx Tissue Book

The GeoMx Tissue Book is a repository of images, data, and region of interest (ROI) selection and segmentation strategies for different tissue types and diseases that have been analyzed through the GeoMx Digital Spatial Profiling (DSP) Technology Access Program. Each individual PDF page of the GeoMx Tissue Book includes images of the tissue and is annotated by the disease(s) studied, species of interest, and type of assay performed.

Read More

News and events

Call for applications: CESORA funding opportunity

CESORA is offering up to $40,000 in direct funding for a one-year grant that aims to provide access to their GeoMx DSP technology. If you are an African researcher interested in incorporating spatial omics into your research, this could be for you!

Inaugural CESORA Spatial Omics Workshop 2023

The inaugural Centre of Excellence for Spatial Omics Research in Africa (CESORA) introduction to spatial omics research meeting and workshop took place from November 6-9, 2023. AHRI faculty member Prof Zaza Ndhlovu - who leads CESORA - opened the workshop with an intro to spatial biology talk.

GeoMx Practical Session:

Photos of CESORA's GeoMx Practical Session, led by Dr. Aida Freire Valls and Dr. Vasileios Kampanis from NanoString, along with Dr. Andrea Papadopoulos from AHRI. These practicals were designed to familiarise participants with the GeoMx DSP workflow, covering everything from slide preparation to oligo collection.

AHRI’s CESORA programme hosts its first intern

The Centre of Excellence for Spatial Omics Research in Africa (CESORA), based at Africa Health Research Institute (AHRI), recently hosted its first intern as part of its broader education and training programme.

AHRI’s CESORA at the Grand Challenges Annual Meeting

Africa Health Research Institute’s Professor Zaza Ndhlovu and Dr Bongiwe Mahlobo were privileged to participate in the 2023 Grand Challenges Annual Meeting, which took place in Dakar, Senegal from October 8 – October 11, 2023.

Register now: intro to Spatial Omics Workshop 2023

This intensive, interactive, and hands-on workshop – hosted by the Centre of Excellence for Spatial Omics Research in Africa (CESORA) at Africa Health Research Institute – will focus primarily on the theory and practice of spatial biology.

Register now: 2nd intro to Spatial Omics Workshop 2024

The workshop aims to provide participants with a comprehensive introduction to spatial omics, offering a general overview of multiple omics approaches and assist researchers understand how they can integrate spatial omics into their research initiatives. With hands-on practical sessions, the course will teach participants how to conduct spatial omics experiments focusing on the GeoMx DSP technology. It will cover all experimental stages, including sample/slide preparation, image processing, oligo barcode collection and data analysis.

Contact Us

Postal Address

Africa Health Research Institute
Private Bag X7
Congella
Durban
4013

Physical Address

Africa Health Research Institute
719 Umbilo Road
Nelson R. Mandela School of Medicine University of KwaZulu-Natal, Durban
4001
South Africa

Direct

031 521 0569

cesora@ahri.org

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