Periodic Reporting for period 1 - HYMEDNA (Hypermethylated DNA detection using NanoGaps)
Reporting period: 2015-10-01 to 2016-09-30
Bladder cancer is one of the 10 most wide spread forms of cancer in males. It is also one of the most costly types of cancer due to its high recurrence rate. The current gold standard for monitoring bladder cancer uses cystoscopy and cytology. The check-up procedure is inconvenient for the patient and on top of that has low sensitivity for detection of early stage bladder cancer tumors. Early stage detection is of crucial importance since the 5-year survival rate drops from 98% when tumors are still confined to the muscosa, 48% when they become invasive, to 15% when they start to spread. A specific form of DNA called hypermethylated DNA (hmDNA) can be found in the early stages of bladder cancer and there are several techniques to check for this in blood or urine samples. Most of them are based on bisufite conversion coupled with PCR and optical detection techniques. This bisulfite-PCR procedure is time consuming and the process can lead to degradation of the DNA. So there is need for an alternative technique for early stage, non-invasive, and cheap bladder cancer detection. To circumvent the disadvantages of bisufite conversion and PCR we have different approach to capture hypermethylated DNA (hmDNA).
The HYMEDNA project aimed at commercialization of very sensitive point-of-care biosensors for early-stage cancer detection based on the electrical detection of hmDNA inside nanogaps.
Only recently the awareness has risen that local hypermethylation of DNA provides a generic marker for a wide range of cancers. A robust, simple and cheap method for detecting hmDNA at low concentrations would be a major step forward in the early-stage detection of cancer. Existing hmDNA detection relies on fluorescent read-out, which requires dedicated laboratory handling.
Our technology is based on electrodes separated by a tunable nanogap. The original idea was to trap hmDNA and highly concentrate it in between the electrodes using methyl binding domain (MBD) proteins. MBD binds specifically to methylated CpG sequences and thus provides the direct recognition of the targeted methylated moieties. During HYMEDNA we moved to a concept where hmDNA is first pre-concentrated, and afterwards detected in the nanogap using sequence-specific DNA trapping.
During HYMEDNA significant progress was made in the DNA metallization procedure. Multi-electrode sensors were realized with nanoscale gaps for trapping the DNA. Test DNA was prepared with relevant lengths of ~250 nm in combination with single-strand oligonucleotides that can be attached to the Au electrodes. Presently the effort concentrates on optimizing sensitivity and specificity of the nanoelectronic sensing method.
The HYMEDNA project aimed at commercialization of very sensitive point-of-care biosensors for early-stage cancer detection based on the electrical detection of hmDNA inside nanogaps.
Only recently the awareness has risen that local hypermethylation of DNA provides a generic marker for a wide range of cancers. A robust, simple and cheap method for detecting hmDNA at low concentrations would be a major step forward in the early-stage detection of cancer. Existing hmDNA detection relies on fluorescent read-out, which requires dedicated laboratory handling.
Our technology is based on electrodes separated by a tunable nanogap. The original idea was to trap hmDNA and highly concentrate it in between the electrodes using methyl binding domain (MBD) proteins. MBD binds specifically to methylated CpG sequences and thus provides the direct recognition of the targeted methylated moieties. During HYMEDNA we moved to a concept where hmDNA is first pre-concentrated, and afterwards detected in the nanogap using sequence-specific DNA trapping.
During HYMEDNA significant progress was made in the DNA metallization procedure. Multi-electrode sensors were realized with nanoscale gaps for trapping the DNA. Test DNA was prepared with relevant lengths of ~250 nm in combination with single-strand oligonucleotides that can be attached to the Au electrodes. Presently the effort concentrates on optimizing sensitivity and specificity of the nanoelectronic sensing method.