PACRI Research Programmes and Core Facilities

CO-CHAIRS/ASSOCIATE DIRECTORS

Population & Prevention Cancer Sciences (PPCS)

The PPCS Programme aims to keep people in a state of health and wellness, preventing them from crossing the threshold to disease and requiring treatment. Almost 70% of all cancers can be prevented, but significant data gaps exist in this field. Combined with an aging population and record success in survivorship, population-based cancer research is pivotal to health and wellbeing. To better support such primary and secondary prevention research, expertise in public health, cancer epidemiology and implementation research are being developed.

The population-based and context-specific research is in the following domains:

• Cancer registries, with the aim of developing a strong link to population-based cancer registration data

• Cancer information, with the aim of addressing context-specific issues e.g. on cancer beliefs and myths;

• Cancer statistics, as cancer control plans and lifestyle recommendations, can only be developed based on strong evidence-based setting-specific attributable causes, this part strongly encourages population-based studies of the attributable fractions for at least the major cancers causing premature mortality in each sex.
• Implementation research, In a developing country, improving cancer survival hinges upon accelerated pathways to diagnosis and access and adherence to treatment. Implementation studies of community-based interventions to address these weaknesses in the cancer journey may lead to more avoidable deaths than personalised approaches, at least at the present stage in the cancer profile.

Co-Chairs/Associate Directors: Dr Thulo Molefi (Medical Oncology), Prof Annie Joubert (Medical Physiology)

Clinical Cancer Research (CCR)

This Programme’s resolve pushes the envelope of early detection and treatment, personalised care, and immunotherapy and is crucial for achieving PACRI’s mission of  “Defeating Cancer Together”. This Programme’s focus is also on molecular-based approaches to cancer diagnosis and treatment and its emphasis is also on clinical trials that is aimed at implementing personalised cancer therapy and improving patient outcomes. The clinical research program aims at selecting emerging therapies and strategies to offer to our patients as experimental alternatives to routine care. It is about testing new drugs and new strategies developed by our PACRI researchers and in collaboration with colleagues throughout the world.

Co-Chairs/Associate Directors: Dr. Sheinaz Bassa (Radiation Oncology); Prof Mzubanzi Mabongo (Maxillofacial and Oral Surgery)

Translational Cancer Research (TCR)

This Programme unites investigators who study aspects of the human genome, that naturally contribute to genetic instability, investigators working on the genes, which play a primary role in maintaining or altering genomic stability, as well as investigators studying the mutagenesis process and the environmental contribution to mutagenesis. This is of relevance both in the diagnostic arena and in the identification of targets for therapeutic intervention. An understanding of aberrant signalling pathways in the tumour tissues represents ideal targets for therapeutic intervention in translational cancer research. Improved drugs to address resistance to chemotherapy and eventually to a recurrence of cancer are essential. Identifying microenvironment-specific mechanisms for resistance to chemotherapeutic agents and recurrence is of utmost importance. This Programme also aims to identify biomarkers that may be useful in identifying patients at high risk of recurrence.

Co-Chairs/Associate Directors: Prof Mike Sathekge (Nuclear Medicine); Dr. Kgomotso Mathabe (Urology)

Cancer Immunology, Viral Infection and Inflammation (CIVII)

This Programme aims at research that is related to interactions between the immune system and tumour cells and the association between infections and cancer which has become stronger over the last decade. PACRI investigators will be collaborating to translate their basic laboratory discoveries into clinical programs, including viral (HPV, HCV, EBV, HBV and HIV) bacterial (H pylori) and other infectious agents which will contribute to understanding how these chronic infections lead to certain cancers (cervical, aggressive tumours of the head and neck, etc.).

Co-Chairs/Associate Directors: Prof Pieter Meyer (Immunology); Dr Mankgopo Kgatle (Nuclear Medicine)

Cancer Health Disparities & Precision Oncology (CHDPO)

Diseases such as cancer do not affect all people equally. There are substantial differences in the screening rates, incidence, stage at diagnosis, prevalence, risk factors, morbidity, survival and mortality of cancer. These differences may be at a genetic level or molecular/biological level or immunological level due to racial/ethnic differences or may be due to differences in age of onset, gender, socio-economic status, literacy and educational level, regional/geographic location, cultural disparities, hormonal level disparities and many more. These disparities need to be tracked and investigated as they may result in increased risk and poorer outcomes in particular patient groups compared to the overall population.

Researchers in this programme aims to identify these adverse differences in biological, genetic, and social conditions that result in these cancer health disparities and generate the evidence and data necessary to identify oncologically targetable alterations or biomarkers for early diagnosis, optimal treatment and prognostication. This data will also be used to influence policy changes to enable equitable health provision and adequate education of the involved populations.

Co-Chairs/Associate Directors: Prof Llewellyn Padayachy (Neurosurgery); Dr Sikhumbuzo Mbatha (Surgery)

The Biostatistics Core (BC)

The mission of the Biostatistics Core is to provide biostatistical support to investigators in the study design, conduct, analysis and reporting of their research projects. Biostatistics support 1) ensures that public health and medical studies are designed appropriately with sufficient sample size and statistical power to solve the public health and medical questions in the research projects, 2) analyse the study data with appropriate and relevant quantitative statistical methods, 3) interpret the study findings correctly and 4) collaborate in reporting and writing of abstracts and presentations for professional meetings and conferences, manuscripts for peer-reviewed publications; policy brief and technical reports.

Co-Chairs/Associate Directors: Prof Din Chen, Biostatistics DST SARChI Chair; Prof Samuel Manda (SAMRC Biostatistics Unit Director and UP Extraordinary Professor in Statistics)

Histogenomics and Digital Pathology Cytometry Core Facility  (HDPCC)

The purpose of this core laboratory is to assist investigators requiring detection, imaging, and morphometric analysis of gene and protein expression in any type of cell and tissue. Expertise and state-of-the-art biomedical imaging services are provided with the aim of broadening and streamlining a wide variety of morphological and histogenomics based research. A core requirement in precision medicine is to understand the molecular mechanisms of diseases, with our focus being on the molecular oncology of various forms of cancer. Signal transduction cascades or dysregulation of such cascades are crucial for carcinogenesis as well as tumour progression.  As part of precision medicine, histogenomics identifies, characterises and quantifies multiple molecular markers in tumour cells as well as the tumour microenvironment. This helps us better understand patient-specific molecular mechanisms driving carcinogenesis, and provides key tools contributing to the development of targeted therapeutic interventions.

Co-Chairs/Associate Directors: Dr Minah Kgoebane-Maseko (Anatomical Pathology); Prof Meshack Bida (Anatomical Pathology) 

Biospecimen Core Facility (BCF)

The goal of the biobanking repository is to support PACRI programmatic research to further improve understanding of those molecular factors that contribute to cancer and that may lead to prevention, early detection, and cure. The mission of the BCF is to collect high-quality samples of normal and diseased human material (e.g., whole blood, cellular blood components, bone marrow, plasma, serum, urine, benign and tumour tissue) with appropriate clinical, pathological and demographic data and to make this material available to qualified researchers at PACRI while ensuring ethical informed consent, safety, donor anonymity, and all regulatory safeguards are in place. The Co-Chairs/Associate Directors of BCF should oversee this facility, with day-to-day procurement coordination and staff supervision provided. Access to biospecimens and corresponding data will be restricted to PACRI investigators who have successfully filed an online application to be reviewed by the Tissue Utilization Review Committee (TURC).

Co-Chairs/Associate Directors: Dr Meryl Oyomno (Surgery); Dr Tebogo Medupi (Anatomical Pathology)

Clinical Cancer Genome Analysis Core Facility (CCGAC)

The Clinical CCGA is being developed into a state-of-the-art facility capable of developing next-generation sequencing (NGS) protocols including whole-genome and whole-transcriptome sequencing (WGS and WTS), RNASeq, whole-exome sequencing and SNP analysis, and transcriptional profiling. The CCGA aims to serve multiple projects through the establishment of service contracts, collaborations at the institutional, local and international levels. CCGA plans to keep its services up-to-date and offer new platforms for ChIP-Seq optimization, single-cell sequencing, and single-molecule sequencing. These services will allow PACRI to increase the number of researchers and institutions using these facilities. Additionally, CCGA plans to enter the field of clinical genomics through a partnership with the New York Genome Centre (NYGC) and the Greek Genome Centre (GGC)-BRFAA and other major international players in this field. This will present a unique opportunity for genomic cancer medicine. CCGA’s long-term goal is to become the regional cancer genomics reference centre serving basic, translational and clinical researchers with state-of-the-art technology, training, and services which will lead to improved diagnosis/early diagnosis (inclusive of development of point of care (POC) cancer diagnosis kits), and better patient treatment with precision/personalised oncology. The CCGA will serve the PACRI scientific community studying the molecular mechanisms and genomic signatures in cancer and, at a later stage, other human diseases will be included. This Platform will become the site to generate genomic information for researchers, also from neighbouring universities including Sefako Makgatho Health Sciences University (SMU), University of Limpopo (UL), University of Johannesburg (UJ), Nelson Mandela University (NMU), Walter Sisulu University (WSU) and other African countries. In addition, this Platform will be instrumental for the establishment of national and international collaborations that would benefit our researchers and will further facilitate access to both national and international funding, train a critical mass of clinical cancer scientists and basic scientists in cutting-edge cancer research and improving patient care. This Platform will also form a basis for spin-out companies for cancer vaccine development, diagnostic kits including point of care diagnostics and precision/personalised drug formulations in collaboration with the University of Nottingham Cancer Sciences, United Kingdom and the Hellen Diller Family Comprehensive Cancer Center Global Cancer Program, San Francisco, USA, and the DKFZ German Cancer Center, Heidelberg, Germany. It will also provide service to raise funding for its future maintenance and future upgrades.

Co-Chairs/Associate Directors: Dr Rahaba Marima (Anatomical Pathology); Dr Rodney Hull (Anatomical Pathology)