High Impact Articles by Malaysian Scientists

High Impact Articles by Malaysian Scientists

A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry

Yong, SC, Roversi, P, Lillington, J, Rodriguez, F, Krehenbrink, M, Zeldin, OB, Garman, EF, Lea, SM & Berks, BC (2014). A complex iron-calcium cofactor catalyzing phosphotransfer chemistry. Science, 345:1170-1173.

Yong Shee Chien (SC) has since left academia and currently works for Sunway Berhad, Malaysia.

Fig. 1. Phosphorus cycle in the ocean. Phosphorus is required by all living organisms to make DNA, RNA, ATP (energy molecules), and other essential organic compounds. The most abundant phosphorus exists in the form of phosphate (PO43-) ions. In the ocean, phytoplankton utilize phosphate for growth under high phosphate conditions. After assimilation, a fraction of the phosphorus is released back to the ocean pool as dissolved organic phosphorus, which is in turn converted back to phosphate by bacteria. However, under low phosphate conditions, phytoplankton and other marine organisms will utilize dissolved organic phosphorus and/or scavenge for phosphate by releasing phosphate from organic molecules using alkaline phosphatase.

Fig. 1. Phosphorus cycle in the ocean. Phosphorus is required by all living organisms to make DNA, RNA, ATP (energy molecules), and other essential organic compounds. The most abundant phosphorus exists in the form of phosphate (PO43-) ions. In the ocean, phytoplankton utilize phosphate for growth under high phosphate conditions. After assimilation, a fraction of the phosphorus is released back to the ocean pool as dissolved organic phosphorus, which is in turn converted back to phosphate by bacteria. However, under low phosphate conditions, phytoplankton and other marine organisms will utilize dissolved organic phosphorus and/or scavenge for phosphate by releasing phosphate from organic molecules using alkaline phosphatase.

(i) Impact of this work to the society

SC: Phosphate-containing molecules such as DNA and ATP (the energy currency of life) are essential for living cells. Under phosphate-deficient conditions, microorganisms produce alkaline phosphatase enzymes to release phosphate from phosphate-containing organic molecules. PhoX is one of the most widely distributed alkaline phosphatases amongst ocean microbes living  in low phosphate environments found in much of the world’s oceans. Structural analysis of PhoX also identified a new catalytic cofactor containing iron and calcium, whose mechanism of action is not seen in other phosphatases. Hence, understanding the PhoX structure has implications not only in microbial ecology but also in chemistry.

(ii) Efforts required

SC: The key to the success of this study was the cross discipline collaborations. The discoveries about PhoX came about because the enzyme is a substrate of a protein transporter that my supervisor, Professor Ben Berks, is studying. The unexpected purple colour of PhoX piqued our interest. As a biochemistry lab, we conducted biochemical assays to understand its biochemical properties. Structural analysis was done in collaboration with renowned structural biologists Dr Pietro Roversi and Professor Susan Lea. To further investigate the metal ion content in PhoX, we enlisted the help of Professor Elspeth Garman, who pioneered an approach known as Micro-PIXE which allowed for the identification of all metals and relative amounts in any molecule.

(iii) What’s next?

SC: I have since left academia but I keep in touch with Professor Berks and my collaborators regularly. As this is a novel mechanism, we are constantly receiving comments and suggestions for more detailed studies of PhoX. Professor Berks’ lab is constantly finding new collaborators and tap into their expertise to find out more about PhoX. As in any research, there will always be new discoveries to be made and new possibilities to explore, even if it is only for a small protein.


Genetic Variability In The Regulation Of Gene Expression In Ten Regions Of The Human Brain

Ramasamy, A, Trabzuni, D, Guelfi, S, Varghese, V, Smith, C, Walker, R, De, T, UK Brain Expression Consortium, North American Brain Expression Consortium, Coin, L, de Silva, R, Cookson, MR, Singleton, AB, Hardy, J, Ryten, M & Weale, ME (2014). Genetic variability in the regulation of gene expression in ten regions of the human brain. Nat. Neurosci, 17:1418-1428.

Adaikalavan Ramasamy (AR) currently heads the transcriptomics core facility at the Jenner Institute, University of Oxford.

(i) Impact of this work to the society

AR: Neurological diseases such as Alzheimer’s and Parkinson’s diseases are complex and poorly understood. They significantly reduce the quality of patient’s life and the burden is set to increase with aging populations.

In recent years, large scale collaborations have identified some genetic variants (mutations in the DNA) associated with neurological diseases. The mechanism on how these genetic variants cause diseases is still largely unknown.

The first step is to understand how genetic variants control gene expression. To answer this, we analysed post-mortem brain samples from 134 healthy individuals. As gene expression varies by cell and tissue type, we sampled ten brain regions for each individual.

We found that many genes are under genetic controls and some of these were replicated in externally generated datasets. About half of the signals identified were common to all brain regions and many code for different gene isoforms. We also observed that about half of the signals operate on neighbouring gene instead of the nearest gene.

There are many more insights that one can gain by mining this rich resource. Therefore, we made this resource publicly available through Braineac (http://www.braineac.org) in order to encourage public re-use and re-analysis. We also created a simple webtool to help scientist to quickly query and visualise the results.

(ii) Efforts required

AR: A huge number of people contributed to the success of this project: the generous individuals who donated their brain tissues, the coroners who collected the brain tissues and the staff of the brain bank who carefully preserved them over the years.

Several of my co-authors deserve special mention here. Daniah Trabzuni and Mina Ryten spent two years of intensive and careful work in the laboratory to assay the brain tissues and generate the data that I had the privilege to analyse. Sebastian Guelfi worked tirelessly on the website development and preparation of the graphs for manuscript. Mike Weale provided statistical guidance that forms the foundation for this paper. Mike and Mina along with Prof. John Hardy successfully guided this project since its beginning.

Finally, the reviewers and editors who provided unbiased comments that strengthened this paper.

(iii) What’s next?

AR: We applied for and were awarded £1.3 million of research funding from the Medical Research Council, UK. This money was used to generate Next Generation Sequencing (NGS) data on four selected brain tissues that allow us to understand gene structures and isoforms more directly. We also isolated pure populations of cells (e.g. dopamine neurons) using laser capture microscopy for NGS analysis. This is important because a brain tissue is a mix of cells that behave differently.

Thanks to the experience gained from this project, I was appointed to a more senior research role at the University of Oxford. I am currently still part of the continuing work but mainly in an advisory capacity.


Whole-genome sequencing analysis of phenotypic heterogeneity and anticipation in Li-Fraumeni cancer predisposition syndrome

Ariffin, H, Hainaut, P, Puzio-Kuter, A, Choong, SS, Chan, AS, Tolkunov, D,  Rajagopal, G, Kang, W,  Lim, LL,  Krishnan, K, Chen, KS, Achatz, MI, Karsa, M, Shamsani, J, Levine, AJ &  Chan CS (2014). Whole-genome sequencing analysis of phenotypic heterogeneity and anticipation in Li-Fraumeni cancer predisposition syndrome. Proc Natl Acad Sci USA, 111: 15497 – 15501.

Professor Hany Ariffin (HA) is a paediatric oncologist based in University of Malaya, Kuala Lumpur.

(i) Impact of this work to the society

HA: This study addresses the phenomenon of anticipation and heterogeneity seen in families with Li-Fraumeni syndrome (LFS). LFS is a cancer predisposition condition defined by germline mutations in the TP53 gene, the so-called guardian of the genome. A novel hypothesis has been proposed where germline TP53 mutation carriers who develop cancer only at a late age may have a form of “genetic resistance” to early cancer. Our findings provide insights into mechanisms of inheritance in the context of the evolutionary tolerability of germline p53 mutations in an important familial cancer syndrome.

(ii) Efforts required

HA: Our team and collaborators analysed p53 mutations in a large international database of LFS families as well as performed genome-wide sequencing on members of a Malaysian LFS kindred who showed acceleration in ageing at the onset of cancer  and increased severity of the syndrome over two generations. Using a unique sample set and  comprehensive sequencing analysis, we managed to address challenging and understudied genetic predisposition mechanisms. The findings are supported by both human data as well as p53 knock-out mouse models.

(iii) What’s next?

HA: Following on from this work, the collaborative teams are working on several related projects to understand heterogeneity in disease presentation in individuals who have inherited TP53 mutations and are at increased risk of developing malignancies. This knowledge will improve accuracy and efficiency of cancer screening efforts  as well as counselling strategies for affected individuals.

Please consult the Li-Fraumeni Syndrome Association (http://www.lfsassociation.org/) for further information.

Please consult the Li-Fraumeni Syndrome Association
(http://www.lfsassociation.org/) for further information.

This article first appeared in the Scientific Malaysian Magazine Issue 11. Check out other articles in Issue 11 by downloading the PDF version for free here: Scientific Malaysian Magazine Issue 11 (PDF version)