Our lab focuses on molecular biology, cellular technologies, and liquid biopsy in cancer. In particular, we are interested in precision oncology of paediatric cancers.
We are located at the Children's Cancer Institute in Sydney, Australia. We are working with ZERO Childhood Cancer Program, a world-leading precision medicine program for children with cancer in Australia and New Zealand.
We have access to cutting-edge instruments and facilities at UNSW and Children's Cancer Institute including next-generation sequencing, long-read sequencing (Nanopore Oxford Technology and PacBio), FACS, liquid handling robotics, automated micromanipulator, microfluidics, 3D printing, and microscopy. We collaborate closely with the Sydney Children's Hospital, The Ramaciotti Centre for Genomics, and Kinghorn Centre for Clinical Genomics.
We are interested in single-cell analysis to characterise the diversity of cell types in the human body. Studying a tissue in a single-cell resolution provides a more precise picture of its behaviour in health and disease.
We are also studying circulating tumour cells (CTCs), a diverse cell population that is released by solid tumours into the circulation in the form of single cells or cell clusters. CTCs can be used as a liquid biopsy to obtain information from tumours in a minimally invasive way. Our lab aims to investigate CTCs with single-cell technology to test whether they can potentially serve as a predictive/prognostic biomarker in solid cancers.
To reach these aims, we use the latest technology and when there is none, we develop it.
1. Single-cell technology. Is it more informative to look at gene expression in a whole tissue or every single cell of a tissue? Single-cell molecular analysis has been gaining momentum in various biological disciplines. We have developed some trendy single-cell transcriptomics technologies (also known as single-cell RNA sequencing) such as Smart-seq2, Small-seq and recently Smart-seq3. However, a method that detects and measures several molecular types in a single cell has been highly demanded. In this project, we develop a single-cell multi-omics technology to simultaneously profile several molecular types, including DNA, RNA, and proteins, in an individual cell.
2. Liquid Biopsy. Can we follow up on cancer patients' progress continuously and accurately? Can we have multiple biopsies from a patient at various time points and perform molecular analyses on biopsies? Liquid biopsy (circulating tumour cells and circulating tumour DNA) is the answer. However, isolation and preparation of circulating tumour cells (CTCs) have been traditionally established for enumeration purposes, and it is not optimised for molecular analysis. Here, we aim to design a protocol for isolating viable CTCs from patients' blood using microfluidics to analyse with single-cell RNA sequencing.
3. A whole new tissue culture system. Have we cultured the tumour tissue correctly? How is the culture medium defined currently? Do we have physiological conditions in the dish and incubator? These are the ideas that trigger us to rethink tissue culture again. We are developing an entire tissue culture system near physiological conditions, considering the natural body fluids and circulation. We will use this culture system for drug testing to obtain drug responses as accurately as possible. Our culture device, called "Phynamix", was developed by Dr Mehdi Rafeie, and our physiological medium, called "PhysiLife", was developed by Roger Jiang.
4. Precision medicine in paediatric cancer. Every patient's tumour is different! So, not the same drug works for all patients. Can we find the right drug for the right patient, especially for young cancer patients? The question is, which chemotherapy drug works the best for each patient? We use various technologies we have developed above to answer this question.
PhD position in precision oncology, and single-cell sequencing technology, please contact o.faridani@ccia.org.au
We are always looking for enthusiastic and brilliant students and postdocs who care about science and improving cancer patients' lives. Please send us your CV if you are interested in joining us.
Honour students interested in doing a PhD in single-cell technology, precision medicine, molecular biology and paediatric cancer are encouraged to contact us.
Selected publications
Faridani OR, Abdullayev I, Hagemann-Jensen M, Schell JP, Lanner F, Sandberg R.
Nat Biotechnol. 2016 Dec;34(12):1264-1266.
Hagemann-Jensen M, Abdullayev I, Sandberg R, Faridani OR.
Nat Protoc. 2018 Oct;13(10):2407-2424.
Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, Segerstolpe Å, Rivera CM, Ren B, Sandberg R.
Nature. 2019 Jan;565(7738):251-254.
Full publication list in Pubmed
Patents
Methods and Compositions for cDNA Synthesis and Single-Cell Transcriptome Profiling Using Template Switching Reaction. (PCT/US2014/052233) 2015. This patent was licensed to Clontech/Takara for Smart-Seq V4 kit.
Methods of small-RNA transcriptome sequencing and applications thereof (PCT/US2017/037620).
Method and kit for preparing complementary DNA.(2019, application number: SE 1851672-4) 2019. This patent was also licensed to Clontech/Takara.
Dr Omid Faridani , Group Leader
Dr Mehdi Rafeie, Postdoc
Veena Gullapalli, PhD student
Ali Afrasiabi, PhD student
Roger Jiang, PhD student
Anushree Lavendra, Honours student
Hafsah Atif, Honours student
Alumni:
Dr Nageswara Rao Boggavarapu, Postdoc.
Dr Hossein Tavassoli, Postdoc.
Dr Gurjeet Kaur Virk, Research Assistant
Yun Cheah, Honours student
Dev Saldanha, Honours student
Ruiyi Zhang, Honours student
Dr Md Imtiazul Islam, Postdoc
Professor Kristina Gemzell Danielsson (Karolinska, Sweden)
Professor Claudia Spits (VIB, Belgium)
Professor Andres Salumet (University of Tartu, Estonia)
Associate Professor Joseph Powell (Garvan, Australia)
Professor John Pimanda (UNSW, Australia)
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Cellular Genomics Futures Institute grant 2021
Single-cell multi-omics of circulating tumour cell clusters.
UNSW Medicine Cancer Research grant for Single-cell multi-omics of circulating tumour cells as a predictive biomarker in pancreatic cancer.
Address. Level 4, Health Translation Hub, 55 Botany Street, Randwick NSW 2031, Australia
Email. ofaridani [at] ccia.org.au