Breathing Life into the Fight Against Cancer
An Approach Towards Personalised Treatment for Lung Cancer Patients
Lung cancer is a major cause of death throughout the world with 1.3 million new cases diagnosed every year. The overall survival rate of lung cancer patients is about 16% within five years. Lung cancer occurs due to uncontrolled growth of aberrant cells across the epithelial lining of the breathing tubes and surface of the lungs. Main causes of lung cancer include cigarette smoking, which is responsible for 90% of cases, passive smoking and exposure to asbestos fibres.
Since a major category of lung cancer, non-small cell lung carcinoma (NSCLC), has subtypes with complex patterns of mutations in different genes, treatment is largely ineffective. Pharmaceuticals are typically targeted to individual proteins – for example, some drugs target epidermal growth factor receptors (EGFRs) to block EGF attachment. Moreover, tumours with similar clinical characteristics (location, pathology, size, stage) may respond differently to the same drug.
Pathway-targeted chemotherapeutic agents are new, more effective molecules for lung cancer treatment. A protein kinase inhibitor, AZD6244, is recommended for treating advanced NSCLC, where it inhibits mitogen-activated protein kinase (MEK) in a well-studied cellular survival pathway to cause apoptosis, thus killing off the cancer cells.
AZD6244 seems to be a godsend for some patients but not all NSCLC cases are sensitive to this drug. Scientists now think they know why.
One of the observable differences between AZD6244-sensitive cells and their insensitive counterparts is the high levels of phosphorylated AKT. AKT is activated by phosphorylation to inhibit cell apoptosis through a separate pathway. Since AZD6244 and AKT are involved in two parallel pathways, AZD6244 does not work on patients with abnormal constitutively active (phosphorylated) AKT.
The phosphorylation of AKT is negatively regulated by the phosphatase PTEN. Thus, an abnormally low level of expression of PTEN indicates the presence of constitutively active AKT, which leads to insensitivity to AZD6244.
Using SynaProbe™, oligonucleotide probes can be designed to evaluate the level of expression of PTEN in patients for quick prognosis of drug sensitivity. With this, a more personalised cancer treatment becomes possible, thus reducing the chances of erroneous prescriptions of drugs and improving more lives through the delivery of appropriate treatments. Instead of grasping at straws through trials with different therapeutic drugs, more lung cancer patients can now see hope in the near future.
Step 1 of 3
Click here, then click on .

Click on image to zoom
Step 2 of 3
Click to select the probe of interest. Here we selected Probe 1, which has the highest score.

Click on the SynaHybridise icon at the right corner.

Click on image to zoom
Step 3 of 3
The result shows that the probe has high specificity and uniquely matches PTEN.

Click on image to zoom
New Superbug Gene Could Spell Disaster
Imagine a world filled with indestructible germs.
If you think this nightmare scenario is straight out of a science fiction novel, think again. The ‘superbug’ is closer to reality than originally thought, and this has set alarm bells ringing within the life science community.
In August 2010, British researchers made public their discovery of new antibiotic-resistant enteric bacteria containing NDM-1. The findings, which were published in The Lancet, confirmed previous suspicions of the existence of microorganisms that are immune to available drugs and medication.
NDM-1, or New Delhi metallo-beta-lactamase, is an enzyme found inside different types of bacteria, including E. coli. The enzyme renders the bacteria resistant to antibiotics with beta-lactam rings, including carbapenems, a class of drugs often used in emergency cases as a last resort. The bacteria also have plasmid or chromosomal resistance to other forms of antibiotics such as aminoglycosides and streptomycin, thus making them superbugs.
Most of the cases involving these superbugs seem to be linked to patients who have travelled or sought medical treatment in the Indian subcontinent. A small number of cases have occurred in UK hospitals as well, thus increasing fears of a global endemic. The NDM-1 gene is reported to be able to jump from one strain of bacteria to another with ease, and researchers worry that infections from the multi-resistant strains of bacteria may be untreatable.
Using SynaTate™, we can highlight regions in the NDM-1 gene which code for antibiotic-resistant proteins. Researchers can then focus on these annotated regions to design drugs that could counteract the properties that accord resistance to the bacteria.
Source : BBC News
Step 1 of 4
Click here, then click on .
Step 2 of 4
In the Results page, scroll up using your mouse wheel to zoom in on the graph; this enables you to view the annotated gene in the selected region.

Click on image to zoom
Step 3 of 4
Select the entire region of the first forward reading frame, F1, by left clicking and dragging across. Right clicking within the selection will display a list of options. Select ‘Annotate nucleotide sequence’.

Click on image to zoom
Step 4 of 4
The results indicate that the NDM-1 gene encodes for penicillin-insensitive protein, which is one of the proteins responsible for enabling resistance to antibiotics.

Click on image to zoom

Kuala Lumpur, 13 October 2010 – Malaysian Genomics Resource Centre Berhad (“MGRC” or the “Company”), Malaysia’s newly-listed genome sequencing and analysis service provider, announced today the appointment of Dr Stephen Rudd to the position of Chief Scientific Officer.

Dr Rudd specialises in bioinformatics and has been actively involved in projects relating to genome analysis, gene expression profiling, proteomics, toxicogenomics and pharmacogenomics. His primary responsibilities in MGRC include overseeing the development of new services and analysis pipelines.

Managing Director Robert Hercus said, “We are very pleased to welcome Dr Rudd, who is a highly experienced bioinformatician. In addition to our existing team of bioinformatics experts, I am confident that Dr Rudd will help to increase our capacity to take on new projects in genomics and bioinformatics.”

Dr Rudd said, “It is such a great opportunity for me to be working in Malaysia and especially with a company like MGRC. Over the years MGRC has successfully established itself as a proven and trusted player on the global bioinformatics stage. I am highly optimistic that MGRC will become a household name in the genomics and life science industry and I am looking forward to being part of the Company.”

Dr Rudd has a Ph.D. in molecular biology from the University of East Anglia in the UK. He was a Senior Bioinformatics Specialist at Orion Pharma in Finland. Prior to that, he was the Senior Scientist and the Head of Bioinformatics at the Turku Centre for Biotechnology in Finland. His other previous attachments include the John Innes Centre in the UK and GSF Research Centre in Munich, Germany. He has published more than 40 scientific articles, and co-authored the research paper on the Arabidopsis thaliana genome, the first plant genome in the world to be sequenced.

Kuala Lumpur, 27 September 2010 – Malaysia’s leading contract genomics services provider, Malaysian Genomics Resource Centre Berhad (“MGRC” or the “Company”), en-route for a listing on the ACE Market of Bursa Malaysia Securities Berhad, registered an oversubscription rate of 28.7 times for its 2 million shares made available to the Malaysian public.

A total of 4,529 applications for 59.4 million shares were received from the public. Another 16.5 million shares made available for private placement and 600,000 shares for subscription by eligible directors respectively were also fully subscribed.

MGRC’s listing exercise involved a Public Issue of 17.1 million new ordinary shares, and an Offer For Sale of 2.0 million existing MGRC Shares at an offer price of RM 1.08 per share. This exercise is expected to raise RM 18.468 million.

Of the 17.1 million shares offered, 2.0 million new shares were made available for public subscription, 14.5 million new shares were allocated for private placement to selected investors, and 600,000 new shares were for eligible directors of the Company.

Of the total proceeds, RM 6.90 million is allocated for capital expenditure, of which, a significant portion of that amount will be used to purchase two units of next generation sequencing machines. Other utilization of proceeds include RM 4.57 million for working capital, RM 2.0 million for marketing expenditure, RM1.51 million for Research and Development expenditure and the balance RM 3.49 million to defray listing expenses.

Commenting on the response, Robert George Hercus @ Abdul Karim Hercus, Managing Director of MGRC said, “We are delighted with the response to our IPO from the investment community at large, and the confidence the market has in the Company. Going forward, we believe MGRC will be able to leverage its position as a listed entity to capitalize on the business opportunities that present themselves in the genomics and bioinformatics space.”

The implied market capitalization of MGRC upon listing, based on its issue/offer price of RM1.08 a share, would be in excess of RM100 million. MGRC’s listing is expected be the first of its kind in South East Asia due to its niche market position and the high barriers of entry associated with commercial contract genomics sequencing.

MGRC is scheduled for a listing tentatively on 5 October 2010.

Kuala Lumpur, 08 September 2010 – Kuala Lumpur, 8 September 2010 – In conjunction with its proposed listing on the ACE Market of Bursa Malaysia Securities Berhad, Malaysian Genomics Resource Centre Berhad (“MGRC” or the “Company”), a leading contract genomics services player, launched its initial public offer (“IPO”) prospectus today.

MGRC’s IPO entails a public issue of 17.1 million new ordinary shares and offer for sale of 2.0 million existing ordinary shares at an issue/ offer price of RM 1.08 per share. Of the 19.1 million total shares, 16.5 million shares were earmarked for private placement, 2.0 million shares will be made available via balloting and 0.6 million shares were offered to eligible directors.

Speaking at the prospectus launching ceremony, which was held earlier today, Robert [George?] Hercus @ Abdul Karim Hercus, Managing Director of MGRC said, “Over the past 8 years there has been a 9,000 fold increase in the volume of sequence data that can be generated in a single day. Bioinformatics analysis is needed to extract meaningful biological information from this data and more research institutions are looking to outsource such expertise to bioinformatics service providers such as MGRC. This listing is timely as it will allow us to tap into the capital market to expand our resources and capitalize on the growing demand for cutting edge bioinformatics solutions and analysis services.”

The Company is raising close to RM18.5 million from this IPO exercise, of which RM6.9 million (37.4%) will be used for capital expenditure, RM4.6 million (24.7%) for working capital, and the remainder for marketing expenditure, research and development activities as well as listing expenses.

A significant portion of MGRC’s capex will be utilized to purchase two next generation-sequencing machines which is expected to enhance the Company’s service offering, increase the speed of generating DNA sequence data, and reduce project costs.

Independent market research consultant, Frost & Sullivan Malaysia Sdn Bhd foresees that the global bioinformatics industry will grow from an estimated USD19.0 billion in 2009 to USD50.1 billion by 2014.

“We are very excited to ride on the growth of this emerging industry. Leveraging on our track record and technical expertise, we are confident of strengthening our market presence further”, said Hercus.

For the financial year ended 31 May 2009, MGRC recorded net profit of RM12.0 million on the back of RM17.1 million revenue. For its audited 10 month financial period (1) ended 31 March 2010, the Company posted net attributable profit of RM9.3 million against RM14.3 million revenue.

Applications for the subscription of MGRC’s public issue will open from today, 8 September 2010 and will close at 5 pm on 23 September 2010. Trading of MGRC shares on the ACE Market of Bursa Malaysia Securities Berhad is expected to commence at 9 am on 5 October 2010.

Spread of HIV Infection Linked to Smallpox Demise
Researchers from the George Mason University in Virginia have discovered that the vaccine which was used to wipe out smallpox also offers some protection against HIV. They theorise that HIV has flourished now that the smallpox vaccine is no longer used. The researchers also suggest that smallpox vaccination offers cross-protection through long-term alterations in the immune system. This may include the expression of a receptor called CCR5 on the surface of white blood cells, which is recognised by both smallpox and HIV.
The CCR5 gene encodes for a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. This protein is expressed by T-cells and macrophages, and is known to be an important co-receptor for macrophage-tropic viruses, including HIV, that enables pathogens to enter host cells. Defective alleles of this gene have been associated with HIV infection resistance. Two splice variants have been found for this gene, and the functional and structural characteristics of each splice variant can be analysed with SynaTate™.
SynaTate is a sequence mining tool which can be used to find putative regions of ‘importance’ or SIGNIFICANCE in a given sequence. This application analyses patterns within sequences. It subsequently associates keywords and annotations to those patterns. Using SynaTate, we are able to see that the two transcripts are coded in different reading frames. Both show a region that has the keyword ‘transmembrane receptor’ highlighting a domain which is involved in pathogen entry into host cells. With this information, researchers could design entry inhibitor drugs that disrupt this region in order to prevent interaction between CCR5 and pathogens such as HIV.
Source : BBC News
Step 1 of 6
Click here for transcript A then click on .
Step 2 of 6
In the results page, right click and drag the peak in F1 to select a region. Right click on the region and select ‘Annotate nucleotide sequences’.

Click on image to zoom
Step 3 of 6
This page shows the potential proteins coded by transcript A of CCR5.

Click on image to zoom
Step 4 of 6
Click here for transcript B then click on .
Step 5 of 6
In the results page, right click and drag the peak in F3 to select a region. Right click on the region and select ‘Annotate nucleotide sequences’.

Click on image to zoom
Step 6 of 6
This page shows the potential proteins coded by transcript B of CCR5.

Click on image to zoom
Back to Archives