Research Article: Integrating environmental health and genomics research in Africa: challenges and opportunities identified during a Human Heredity and Health in Africa (H3Africa) Consortium workshop

Date Published: August 27, 2019

Publisher: F1000 Research Limited

Author(s): Bonnie R. Joubert, Kiros Berhane, Jonathan Chevrier, Gwen Collman, Brenda Eskenazi, Julius Fobil, Cathrine Hoyo, Chandy C. John, Abera Kumie, Mark Nicol, Michèle Ramsay, Joshua Smith, Adrie Steyn, Desire Tshala-Katumbay, Kimberly McAllister.


Individuals with African ancestry have extensive genomic diversity but have been underrepresented in genomic research. There is also extensive global diversity in the exposome (the totality of human environmental exposures from conception onwards) which should be considered for integrative genomic and environmental health research in Africa. To address current research gaps, we organized a workshop on environmental health research in Africa in conjunction with the H3Africa Consortium and the African Society of Human Genetics meetings in Kigali, Rwanda. The workshop was open to all researchers with an interest in environmental health in Africa and involved presentations from experts within and outside of the Consortium. This workshop highlighted innovative research occurring on the African continent related to environmental health and the interplay between the environment and the human genome. Stories of success, challenges, and collaborative opportunities were discussed through presentations, breakout sessions, poster presentations, and a panel discussion. The workshop informed participants about environmental risk factors that can be incorporated into current or future epidemiology studies and addressed research design considerations, biospecimen collection and storage, biomarkers for measuring chemical exposures, laboratory strategies, and statistical methodologies. Inclusion of environmental exposure measurements with genomic data, including but not limited to H3Africa projects, can offer a strong platform for building gene-environment (G x E) research in Africa. Opportunities to leverage existing resources and add environmental exposure data for ongoing and planned studies were discussed. Future directions include expanding the measurement of both genomic and exposomic risk factors and incorporating sophisticated statistical approaches for analyzing high dimensional G x E data. A better understanding of how environmental and genomic factors interact with nutrition and infection is also needed. Considering that the environment represents many modifiable risk factors, these research findings can inform intervention and prevention efforts towards improving global health.

Partial Text

The Human Heredity and Health in Africa (H3Africa) initiative began as a joint effort of the National Institutes of Health (NIH) Common Fund Global Health Program and the Wellcome Trust, in partnership with the African Society of Human Genetics. H3Africa aims to support the establishment of a sustainable African research infrastructure for the study of the genetic and environmental contributors to disease and health
1. The work of this Consortium includes common diseases such as cardiovascular
2, neurological
3, respiratory
4, kidney
5, and other non-communicable diseases, as well as research in infectious diseases. Developments in pharmacogenomics
6 and the human microbiome
7 are underway, and many studies incorporate information about HIV, malaria, and tuberculosis. The Consortium also promotes opportunities for training in bioinformatics
10, supports three biorepositories on the African continent, and facilitates policy development and guidelines with recommendations on ethical issues

The workshop was opened by Dr. Gwen Collman, Director of the NIEHS Division of Extramural Research and Training. Dr. Collman described the long history of NIEHS-supported environmental health research in Africa and the unique exposures and health challenges. She described the commitment of NIEHS to global environmental health and involvement in the H3Africa consortium. Dr. Kim McAllister, Program Administrator at NIEHS, provided brief remarks on the charge of the workshop, on behalf of the NIEHS organizing team. She highlighted the opportunity for H3Africa projects to expand exploration for both genomic and environmental risk factors of complex diseases in Africa. The objectives of the workshop were to highlight current and innovative research occurring on the African continent related to the interplay between the environment and the human genome. The workshop was designed to enable face to face interactions between Consortium members and environmental health experts to facilitate collaborative opportunities and global networking. Sharing of expertise, research recommendations for study design, biospecimen collection and storage practices, and statistical methodologies were discussed, as well as the current research challenges and needs of existing H3Africa projects.

To better understand the data and interests of existing H3Africa projects, a short survey including fifteen questions was sent to all H3Africa project PIs by the coordinating center, to collect information on environmental exposures in H3Africa projects. Data collected on questionnaires, biomarkers of environmental exposures, monitoring data, or related information was reported. Characteristics of the H3Africa project study populations were collected including life stage, location, important co-morbidities, key health outcomes, and current environmental data. The survey also asked about interests in collecting more environmental exposure data in existing study populations. Nine projects completed the survey prior to the workshop (
Figure 1;
Table 1). The study populations of these projects represented West Africa (40%), Central Africa (6.7%), Eastern Africa (26.7%), and Southern Africa (26.7%). (There were no study populations from Northern Africa represented by projects completing the survey). The primary outcomes of interest from these projects were cardiovascular disease, infectious disease, and psychosocial or mental health disorders. DNA was the most commonly reported biospecimen collected and stored (
Figure 2), and approximately 55% of respondents stated that additional biospecimen collection was not possible for their study population(s). This indicated some limitations in the scope of environmental data that can be added using biospecimens (for example, biomarkers measured in urine samples).

The workshop presenters covered experimental design, exposures of interest, exposure measurements, biospecimen collection and storage, and laboratory and statistical methodologies. They also discussed training needs and other challenges, populations at risk, health outcomes of interest for represented populations, and collaborative opportunities. The scientific content of the presentations is organized here by exposure category.

Participants gathered in smaller groups in the afternoon to discuss common and emerging environmental exposures of interest to H3Africa researchers. Breakout group discussions were focused on exposures of interest including: electronic waste, ambient and indoor air pollution (including tobacco smoke), metals and mycotoxins, pesticides and nutrition/toxicodietary exposures, and biomarkers of chemical exposures and infectious diseases. Each group was asked to comment on the important health outcomes associated with the exposure category, what could be done now to measure exposures of interest in existing studies, example research they may be involved in, training needs to build environmental health research capacity, critical issues for biorepositories storing/managing samples for environmental analysis, and ethical, legal, and social implications. General themes of interest across the breakout group discussions were: identifying what exposures should be measured when studying specific health outcomes, clinical training to recognize symptoms related to hazardous environmental exposures, access to existing data/records/biological samples to assess exposures, use of questionnaires to determine suitability of existing samples for biomarkers of environmental exposures, and biobanking of samples. Key points and discussion from select breakout sessions are provided below.

Panelists included Dr. Mark Nicol, from University of Cape Town, Dr. Michèle Ramsay from the University of the Witwatersrand, Dr. Kiros Berhane from University of Southern California, Dr. Brenda Eskenazi, University of California Berkeley, and Dr. Adrie Steyn from the Africa Health Research Institute and University of Alabama Birmingham.

Fifteen poster presentations by trainees covered environmentally focused research efforts that emphasized some of the unique challenges for this field in Africa. Topics highlighted in the posters included: indoor and outdoor air pollution, coal mining exposures, respiratory microbiota, and pesticide exposures. Research presented by these trainees covered topics such as multidrug-resistant
Plesiomonas shigelloides in surface waters in Southwest Nigeria, traffic-related air pollution exposure and health outcomes in street vendors in Cape Coast, Ghana, PM2.5 concentrations in Kampala, Uganda, household air pollution and stroke in Ghana and Nigeria, inhaled air pollution and the microbiota of children in the Gambia, pesticide residues in fruits and vegetables in Kampala, Uganda, and characterization of PM2.5 in Addis Ababa. Abstracts for all posters are included in the
workshop meeting book posted on the workshop website.

To address the environmental research needs of the H3Africa Consortium, a new H3Africa working group was initiated in 2018, referred to as the H3Africa Environmental Health Working Group. In the coming years, this working group hopes to continue to build on the momentum from the workshop to explore ideas of individual and collaborative projects facilitating the incorporation of environmental risk factors into H3Africa studies. These may include identification of potential collaborative opportunities or joint publications relating to common environmental exposures across different H3Africa study populations. This group will investigate ways to strengthen capacity to measure environmental exposures and expand research in environmental epidemiology, including research on the epigenome and microbiome, and related G x E mechanisms. The group will also discuss ways investigators can expand their work in existing study populations by collecting environmental data through questionnaires, analyzing stored biospecimens for biomarkers of exposures, planning the collection of new biospecimens, or integrating data from air and personal monitors as well as satellite-based environmental data. Attention to the current issues of environmental health research such as mixtures, where multiple environmental/chemical exposures are measured in a sample/individual is also important. Education on the most appropriate statistical methodology for analyzing mixtures data, rather than traditional epidemiology models, has been discussed and ongoing training through webinars, other virtual methods, and in-person meetings is anticipated.

With developments in technologies to measure environmental exposures, there is opportunity for global progress in environmental health research. In Africa, important environmental research has enabled interventions to reduce harmful exposures (e.g., aflatoxin). However, much more could be addressed. One of the most pressing concerns identified through this workshop was the underlying need for further characterization of key environmental exposures across varying geographies and populations in Africa. Against the backdrop of challenges of malnutrition, infectious diseases, and limited environmental regulations, the environmental exposure burden of Africans appears to be high, and likely contributes substantially to disease. Importantly, the prevalence of cardiovascular disease, obesity, and diabetes is increasing in African populations, particularly in some geographic regions such as southern Africa, impacting both children and adults
34. Leadership by African researchers on studies evaluating multiple environmental exposures, gene-environment interactions, and comparative biology is important and timely. The H3Africa Consortium, with accomplishments in genomic research infrastructure, trained staff, research productivity, and extensive clinical and demographic data across African study populations, represents an ideal platform for advancing African-led environmental health science across the continent. Considering that the environment is a modifiable risk factor, this research has viable application to important intervention and prevention efforts.

The views expressed in this article are those of the authors and are not meant to be representative of the affiliated institutions. Publication in AAS Open Research does not imply endorsement by the AAS.

Data relating to the survey completed by nine projects prior to the workshop is available in
Table 1.




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