Researchers develop cheaper method to identify aggressive tumours

In a recent study conducted by the researchers at Karolinska Institute in Sweden, a new cheap method has been developed that can identify highly heterogeneous tumours which can become very aggressive in future and therefore needs to be treated more aggressively.

A common feature of cancer cells is alterations in the number of copies in which each chromosome or gene is present in the genome - a phenomenon known as copy number alterations or CNAs. Within the same tumour, cells belonging to different anatomical parts of the tumour may carry different CNAs. Tumours with many CNAs are typically very aggressive and tend to reform more often, even after harsh treatments.

The Bienko-Crosetto Laboratory at Karolinska Institute and Science for Life Laboratory in Sweden have developed a new genomic method, named CUTseq, which can assess the amount and type of CNAs in many different parts of the same tumour, at a much lower cost than existing technologies.
 
A senior researcher at the Department of Medical Biochemistry and Biophysics, said, "I expect that CUTseq will find many useful applications in cancer diagnostics. Multi-region tumour sequencing is going to be increasingly used in the diagnostic setting, in order to identify patients with highly heterogeneous tumours that need to be treated more aggressively. I believe that our method can play a leading role here."

The method works with DNA extracted from multiple biopsies and even from very small portions of thin tissue sections - the type of sample that pathologists commonly rely on to make a diagnosis of cancer under the microscope.

By tagging the DNA extracted from multiple regions of the same tumour sample with unique molecular barcodes, a comprehensive picture of the heterogeneity of CNAs in a tumour can be obtained with a single sequencing experiment.

Applications of CUTseq are not only limited to cancer diagnostics, according to the researchers behind the new method.

"For example, CUTseq could be used as a platform for cell line authentication and to monitor genome stability in large cell line repositories and biobanks," said a senior researcher at the same department. "It could also be applied in ecology, as an alternative to other reduced representation genome sequencing methods, such as RAD-seq, to assess biodiversity in a cost-effective way," the researcher added.  

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Substance in brown coal may aid in combating viruses

Scientists have identified biologically active molecular components of humic substances extracted from coal and discovered substances with antiviral activity against the tick-borne encephalitis virus.

Natural multicomponent mixtures, such as humic substances found in soil, peat and coal are a significant source of biologically active compounds. Understanding their composition and extracting active components can be a great help in creating new drugs. However, finding a specific compound in these environments is a highly challenging task that requires advanced methods capable of differentiating and separating one substance from another.

The study was jointly conducted by researchers from different  research institutes.

We made an attempt at understanding the structural reasons behing the antiviral activity of the molecular components of humic substances. Aware that standard methods of complex mixture separation do not work for humic substances, we looked at some known structures matching the molecular compositions determinable by mass spectrometry and noticed that some structures correspond to compounds often extracted from natural sources, for e.g., flavonoids, said one of the authors of the study.

We undertook further mass spectometry experiments, which suggest that there can indeed be a match between the types of structures we found in the databases and the molecular components of humic systems, he added.

The study revealed that humic substances inhibit the reproduction of a dangerous human pathogen, tick-borne encephalitis virus. The authors relied in high-resolution mass spectometry to study the composition of humic samples and chemoinformatics to analyse their findings.

They compared the results against extensive databases of chemical compounds and identified the compounds' structural features which may be responsible for their virucidal activity. The data analysis results clearly attest to the importance of natural central fragments of flavonoids and polyphenols, 2 classes of natural compounds with wide-ranging biological activity.

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