Cancer liquid biopsy
Our lab is focused on molecular biology, single-cell sequencing technologies and liquid biopsy in cancer. In particular, we are interested in pancreatic cancer diagnosis and treatment.
The lab is located at two sites: Lowy Cancer Research Centre (at University of New South Wales, UNSW) and Garvan Institute of Medical Research in Sydney, Australia. We are also affiliated to the Karolinska Institute in Stockholm, Sweden. We have access to cutting-edge instruments and facilities at UNSW and Garvan 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 Kinghorn Cancer Centre, 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. We will use this culture system for drug testing to obtain drug responses as accurately as possible. We name it the "Physiological Dynamic" (Ph.Dy.) culture system.
4. Precision medicine in pancreatic 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 pancreatic cancer patients? Pancreatic cancer is one of the world's most lethal cancers, with a 5-year survival rate of just ~10%. It is often diagnosed late when the tumour has spread out to the liver and other organs as metastases. Surgery cannot remove metastatic tumours, and chemotherapy is the only option. The question is, which chemotherapy drug works the best for each patient? In this project, we will develop and use various technologies to answer this question.
PhD position in precision oncology, novel tumour culture system and drug sensitivity assay, please contact firstname.lastname@example.org
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 and clinical students interested in doing a PhD in single cell technology, precision medicine, molecular biology and pancreatic cancer are encouraged to contact us.
Publications and Patents
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
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.
Omid Faridani , Group Leader
Mehdi Rafeie, Postdoc
Veena Gullapalli, PhD student
Roger Jiang, Honours student
Nageswara Rao Boggavarapu, Postdoc.
Gurjeet Kaur Virk, Research Assistant
Yun Cheah, Honours student
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)
Dr Hamid Alinejad-Rokny (UNSW, Australia)
Fundings and Awards
Cellular Genomics Futures Institute grant 2021
UNSW Medicine Cancer Research grant for Single-cell multi-omics of circulating tumour cells as a predictive biomarker in pancreatic cancer.
1. UNSW Lowy Cancer Research Centre, Cnr High and Botany St, Kensington 2033 NSW, Australia
2. Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst 2010 NSW, Australia
o.faridani [at] unsw.edu.au
o.faridani [at] garvan.org.au