miCF Research Centre

Welcome to the Molecular and Integrative Cystic Fibrosis (miCF) Research Centre. Our overall goal is to be at the forefront of translational research bridging between omic data to functional characterization and applied research in disease states (such as cystic fibrosis, asthma and COPD), and pharmacokinetics. Our lab is interested in understanding the processes at the cellular and molecular level in regulation of epithelial cell biology and how the breakdown of this regulation leads to pathogenesis of disease such as Cystic Fibrosis (CF).

The Lab

We are based at the Westfield Research Laboratories in Sydney Children's Hospital in Randwick, the second largest Paediatric hospital in the State of NSW. The Laboratory consists of PC2 wet laboratory spaces and associated office space. We have a range of specialized equipment to facilitate our research efforts. The Laboratory houses the Digital and Confocal Microscopy Unit and multiple ultra-freezers and Liquid Nitrogen tanks that are used for BioBanking services. The lab is well-equipped and configured to support a wide range of experiments making it possible to perform cytogenetic, epigenetics, and molecular and cell biology research.

We have access to the world class Genomics (Ramaciotti Centre for Genomics) and Proteomics facilities (Bioanalytical Mass Spectrometry Facility, BMSF at the Mark Wainwright Analytical Centre), which are based on UNSW Kensington campus. They help out greatly with all our sequencing and mass spectrometry needs. We also have a strong affiliation and collaboration with the Children's Cancer Institute of Australia (CCIA), the Drug Discovery Centre, to test and develop our new small molecule therapies.

Clinical Services

For more information on Cystic fibrosis services at Sydney Children's Hospital, please visit the Sydney Children's Hospitals Network website.

Acknowledgements

Our CF-related studies are supported by Sydney Children’s Hospital Foundation.

Staff/Team members 
image - Adam Jaffe2
Head of Discipline, Paediatrics & John Beveridge Chair of Paediatrics
Ph (02) 9382 5500
Conjoint Senior Lecturer
image - Keith Ooi 1
Senior Lecturer
Ph (02) 9382 1799
image - Unswphotoybfinal 0
Conjoint Senior Lecturer
Ph 61 2 9382 1246
image - Me 2017
Postdoctoral Fellow
Ph +61 (2) 9382 0243
Other team members 

Postgraduate Research Students

Chris Hewson
Dr Michael Coffey
Dr Bernadette Prentice

Research Assistants

Nino Turgutoglu
Sharon Wong
Lisa Corcoran

Clinical Team

Conjoint Prof Charles Verge
Dr Shihab Hameed
Dr Penny Field
Dr Sandra Chuang
Dr Louisa Owens
Dr Bernadette Prentice
Amanda Thomsen
Tamarah Katz
Carolyn Shalhoub
Michael Doumit
Holly Murphy
Meagan Lang
Jamie McBride
Leanne Plush
Rhonda Bell
Maria Lozano
Roxanne Strachan

Opportunities

We are looking for highly motivated and creative individuals to join the lab.
Current on Postdoctoral Research vacancies, please see Jobs@UNSW.
Expressions of interest can be sent to Prof Adam Jaffe, please email a Curriculum Vitae to discuss possible opportunities.

A baby is born with Cystic Fibrosis every four days, and most wont turn 40. CF is mostly caused by mutations in both copies of gene that encodes the Cystic Fibrosis transmembrane conductance regulator (CFTR) protein. CFTR is one of the major proteins involved in fluid and electrolyte transport, is translated from a low abundance mRNA in the plasma membrane of epithelial cells. Yet it is a principal anion channel that regulates chloride and bicarbonate, which control the volume and composition of secretions in the airway epithelial cells. As a result of inheritance of two defective copies of CFTR, people with CF suffer from improper fluid and electrolyte transport, which leads to salty sweat, extremely viscous mucus, and chronic lung disease.

Current Projects

  • Cystic fibrosis a model system for precision medicine

This project has a strong translational focus and aims to discover small molecules and peptides that are effective in correcting the trafficking and functional defects exhibited by CFTR mutation, while additionally addressing inter-individual human population variability. We are using an exciting and cutting edge technology to grow stem cell-derived human ‘mini organs’ (organoids) from the tissues of patients with CF. In cell culture, organoids not only mimic an organ’s structure and function; they stably recapitulate genetic and phenotypic characteristics of that diseased tissue. The organoids are characterized by genome sequencing, expression profiling and sensitivity to known drugs to establish a database linking genetic and transcriptional information to drug responsiveness. Thus, the organoids will allow us to predict a patient’s response to pre-clinical and clinical drugs.

For more information, contact: Dr Shafagh Waters

  • Specific targeted activation of cystic fibrosis transmembrane conductance regulator (CFTR)

We propose a novel approach to modulate CFTR function through the manipulation of a newly discovered endogenous long non-coding RNA (lncRNA) to be assessed using our developed ex vivo models. A human-specific long-non-coding RNA (lncRNA), BGas, was identified as an endogenous regulator of CFTR gene expression by our collaborator Prof. Kevin Morris (City of Hope, USA). It functions, independently of CFTR genotype, to reduce CFTR expression. Therefore, suppression of BGas leads to increased CFTR expression, and CFTR protein presentation on the cell surface. Methods that suppress BGas have the potential to be paradigm shifting in CF therapies.

There is now opportunity to develop entirely new RNA therapeutic molecules capable of rescuing CFTR function in individuals with the common delF508 mutation (along with other more rare trafficking mutations). LncRNAs have been successfully developed into RNA based therapeutic treatments for several disorders, including spinal muscular atrophy and amyotrophic lateral sclerosis. These studies have demonstrated the feasibility of RNA targeted therapies. They have paved the way, establishing drug delivery techniques that can be adopted to effectively translate BGas suppressing compounds into a novel CF therapy.This approach is highly novel, and could herald a new therapeutic approach in cystic fibrosis, independent of underlying genotype. We are currently using various methods to remove BGas from CF patient derived mini-organs.

For more information, contact: Dr Shafagh Waters

  • Harnessing protective and antiapoptotic function of stress granules (SGs) in CF

SGs contributes to cell survival and are formed in response to certain cellular stress including oxidative stress, and ER stress, caused by protein misfolding. Both of which play predominant roles in CF pathogenesis, , as a result of failure of CFTR protein folding in ER. SG assembly in CF epithelial cells is unknown. In this study we test if oxidative stress contributes to epithelial cell death by inhibiting SG formation. SG-promoting compounds targeted to TIA1 protein, will be assessed.

For more information, contact: Dr Shafagh Waters

  • Early Origins Study of cystic fibrosis related diabetes (EOS)

The EOS study, led by Dr John Widger, investigates the endocrine pancreas in CF.  Pancreatic disease in Cystic Fibrosis manifests as growth failure from exocrine enzyme insufficiency and defective insulin secretion. Insulin deficiency occurs from birth, is progressive and results in Cystic Fibrosis-Related Diabetes which causes a more rapid clinical deterioration, shortening the life expectancy of patients. It is crucial that a better understanding of how glucose abnormalities develop over time and the early impact they have on children with Cystic Fibrosis in order to optimise clinical care.

The aim of this project is to determine the prevalence of glucose abnormalities in children with CF, in the first decade of life using Continuous Glucose Monitoring and to correlate glucose tolerance with clinical status (e.g. anthropometrics, lung function, inflammation and microbiology). The study will also evaluate the relationship between early glucose abnormalities and pulmonary inflammation and microbiome diversity in bronchoalveolar lavage samples.

For more information, contact: Dr John Widger or Dr Bernadette Prentice

  • Serum biomarkers of Cystic Fibrosis Related Diabetes

Biomarkers for identification of individuals at risk of developing complications such as cystic fibrosis related diabetes would greatly improve the care and long-term outcome of CF patients. This study will ascertain the protein and RNA content of exososmes isolated from blood collected from CF and healthy people. Small non-coding RNAs (sncRNAs) such as microRNAs (miRNAs) control gene expression and participate in many physio-pathological processes. Hundreds of miRNAs are released in the blood and can be used to evaluate health status and disease progression. This project aims at identifying sncRNAs that can be exploited as novel biomarkers in CFRD and develop new and more accurate composite predictive models.

For more information, contact: Dr Shafagh Waters or Dr John Widger

  • Modelling the Alimentary TRact using eX vivo systems in Cystic Fibrosis (The “MATRIX-CF” Study)

The primary aims of this project are to establish and benchmark a protocol for the culture of intestinal organoids in a hypoxic chamber and microinjection with patient-derived intestinal microbial communities; determine the response of CF and healthy control (HC) intestinal organoids to co-culture with CF and HC intestinal microbial communities by analysing the microbiome (16s rRNA), its functional consequences (proteomics and metabolomics) and inflammatory mediators. This will help to elicit the complex interactions between host (genetic, immune and mucosal) factors, microbial communities and intestinal inflammation.  Secondary aims are to test the effects of drugs or interventions which have theoretical or potential anti-inflammatory effects on the intestinal model in CF.

For more information, contact: Dr Keith Ooi  or Dr Shafagh Waters

  • Cystic Fibrosis Gut Research Program

Dr Keith Ooi’s research group are studying the unique but altered environment that exists in the gastrointestinal tract of children with cystic fibrosis, particularly alterations in the gut microbiota and development of intestinal inflammation. Our work is focused on the understanding the pathogenesis, clinical impact and developing potential therapies. One of the current studies include “Probiotics and the EARly Life effects on intestinal bacteria and inflammation in children with Cystic Fibrosis (PEARL-CF)”, which is a randomized placebo-controlled trial of probiotics in young children with CF. 

For more information, contact: Dr Keith Ooi

  • Dietary Intake Study in cHildren with Cystic Fibrosis (DISH-CF)

This study comprehensively evaluates the dietary intake of children with CF, which has major implications in: (1) disease severity in relation to lung function and survival; (2) development of complication(s) from specific nutritional deficiencies; and (3) development of future comorbidities in the context of increasing survival of CF patients. The outcomes will lead to the identification of optimal contemporary eating patterns to support health and wellbeing, and to inform future global nutritional recommendations in CF. This study will also help identify dietary patterns associated with socioeconomic factors and provide a rationale for support based on disadvantage.

For more information, contact: Dr Keith Ooi

  • INternational Study Group of Pediatric Pancreatitis: In search for a cuRE (INSPPIRE) a.k.a. “Acute recurrent or chronic pancreatitis study”

Dr Ooi’s research focus extends into both the exocrine and endocrine pancreas in CF, and studying the links between these two components. INSPPIRE is a group of 22 pediatric gastroenterology centres in North America, Europe and Australia. The INSPPIRE study builds a database of information from children with pancreatitis to help researchers determine the prevalence of this condition, understand the causes and risk factors for disease progression, and review laboratory and imaging findings as well as responses to any treatments given. We hope this will help us better understand pancreatitis in children and, in turn, develop better tests and treatments. A further aim of the study is to identify novel genetic susceptibility genes for the development of pancreatitis in childhood.

For more information, contact: Dr Keith Ooi

We are currently recruiting PhD, Masters, and Honours students.
Please contact Dr Shafagh Waters for further information about current projects.

Further information on enrolment and scholarships can be found on the UNSW Sydney Graduate Research School website.

 

 

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