PhD position in Biomarkers for Cancer in Biophotonic Images

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The Technical University of Denmark

The Department of Healthcare Technology at the Technical University of Denmark (DTU) is seeking a candidate for a PhD position on optical imaging systems for biomarkers for cancer in biophotonic Imaging.

The PhD student will join the 
Biophotonic Imaging group at the Department of Healthcare Technology (DTU Health Tech) consisting of ca 10 employees, including several PhD students and postdocs. Within the group, we are working on the advancement of optical imaging technologies for clinical and biological applications. Currently we have research projects on multimodal imaging combining optical coherence tomography, two-photon excitation fluorescence microscopy, lightsheet microscopy, fibre delivery of ultrashort pulses, as well as investigation of biomarkers relevant for cancer diagnosis using biophotonic imaging.

Background
Colorectal cancer is the second most common cause of cancer death in Europe, causing 225 000 deaths in 2012 (12% of the total) Current standard practice for diagnosing colorectal cancer is white light endoscopy, during which the colonoscopist assesses the appearance of polyps and tissue to identify possible neoplastic changes and decides whether to resect for further analysis using histopathology. To avoid a high number of undetected early stages of colorectal cancer, this procedure results in many unnecessary resections, posing higher risk for colon perforation requiring emergency surgery. On top of this, colonoscopy is not as effective in prevention of colorectal cancer in the right colon as in the left and provides sensitivity and specificity levels starting at 60% and 40%.

Therefore, a technology to assess the malignancy of suspect lesions in situ during colonoscopy would benefit both the patients and reduce healthcare costs. Optical imaging modalities have the ability to non-invasively probe tissue using non-ionizing radiation. This makes optical imaging an obvious choice for use as a diagnostic tool in many fields in healthcare, including oncology.

Optical Coherence Tomography
 (OCT) is already used worldwide on a daily basis in ophthalmology and in dermatology clinics to identify the structure of tissue in depth and thus characterise suspicious lesions. However, the technology still has an untapped potential, as the gathered data also contain information about optical properties of the tissue: these properties are linked to cell constituents. The diagnostic power of these additional biomarkers has only been skimmed thus far.

Two-Photon Excitation Fluorescence Microscopy
 (TPEFM), an established tool in the biosciences, is an emerging modality for clinical diagnostics. It is capable of probing endogenous fluorescent biomarkers inside the tissue with no or limited photodamage dealt. Two known endogenous fluorophores are NADH and FAD, providing insight into metabolic activity of the cells, thus enabling label free functional imaging.

Raman Spectroscopy
 provides a characteristic fingerprint identifying the molecules present in the probed sample, albeit only of the cells on the surface, i.e., only superficial cell layers of the tissue. It therefore allows assessment of the chemical composition and thus metabolic state of said cells.

As the metabolic state of cancerous cells is higher than of their non-cancerous equivalents, and the molecular composition and organelle contents of cells are different, all three modalities allow classification of cells and lesions. Additionally, as we have access to complementary classes of biomarkers, connected to structure from OCT and TPEFM and to function from optical properties, TPEFM and Raman, a multimodal assessment of cells or lesions taking all biomarkers into account will allow a more accurate diagnosis than each modality could provide on its own.

These optical modalities can readily be integrated into a colonoscope and thus have the potential to elevate sensitivity and specificity of cancer diagnosis in colonoscopy above current levels. To successfully apply OCT, TPEFM and Raman as diagnostic tools in oncology, we have to relate the above-mentioned biomarkers to early stages of colorectal cancer. Such biomarkers are challenging to characterise in complex environments such as biopsies due to their dependence on various environmental and disease specific influences. Therefore, we first have to turn to simple model systems where the environment can be tightly controlled. Spheroids, three-dimensional cell structures, can simulate the local conditions in a tumour better than two-dimensional cell cultures, due to the added cell-cell and cell-matrix interaction also present in an actual tumour, while still being easy to grow, handle and allowing control of the environment. Basic spheroids can be grown in well-plates, while more advanced structures can be built using solid scaffolds as a base for adherent cells, emulating 
in vivo situations even more closely. As such, we can simulate different tumour stages by growing spheroids from normal colon epithelial cells and from tumour cells, control the nutrition and oxygen supply to the spheroid or, in the case of scaffold-based technique, to individual parts of the spheroid, and investigate these tumour models using our optical modalities to establish relevant biomarkers differentiating tumours with malignant cells from tumours with benign cells.

We can then use these newly established biomarkers on colon biopsies to probe the state of those cells, and we can also use the same biomarkers and spheroids for testing the effects of medications on the cells in preclinical trials.

Description of the PhD project
This PhD project would entail the steps laid out above: in collaboration with Bioneer A/S, we have already established protocols for growing spheroids from healthy and cancerous colon epithelial cells, and we have done preliminary tests on recording and analysing of OCT and TPEFM biomarkers. This PhD will perform extended studies on scaffold-free and scaffold-based spheroids grown from different cell lines in different environments. The PhD student will characterise the cells’ states in the spheroids using immunohistochemistry. OCT, TPEFM and Raman data will be recorded and analysed to provide the new biomarkers: For OCT, the PhD student will use a mathematical model and fitting procedure previously developed in our group to extract the optical properties and show their diagnostic value on a fundamental level, by connecting these properties to the underlying biological features present in the cell lines. In TPEFM, our existing system provides recording of spectrally resolved data: this allows the identification of new fluorescence spectral bands most relevant for diagnosis. The PhD student will build a Raman system on our existing two-photon platform, both for collection of the Raman data from the surface, but also using spatially offset Raman and novel light-sheet Raman to enable data collection from deeper layers in the spheroids, thus allowing fast, co-registered multimodal imaging on the samples. To analyse the Raman data acquired from the different cell line spheroids, the PhD student will work closely together with the University of St. Andrews to extract the spectral features specific for cancerous cells.

Finally, the PhD student will extract the biomarkers established through this study from biopsies acquired from colon in an existing collaboration with the University Hospital Freiburg, to show the diagnostic capabilities of this all-optical, potentially minimally invasive multimodal approach.

Tasks and Expected Publications
 

  • Model and fitting procedure for OCT data to extract optical properties from spheroids
  • Optical properties are established as OCT biomarkers by comparing data and immunohistochemical assays from different spheroid types and states.
  • TPEFM biomarkers are identified by comparing two-photon excited auto-fluorescence signals and immunohistochemical assays of different spheroid types and states.
  • Raman signatures for cancerous and non-cancerous spheroids of cells are established.
  • OCT, TPEFM and Raman biomarkers are recorded in a multimodal setup to study spheroids and biopsies of colon, and the diagnostic accuracy is shown.

Qualifications
The candidate should have a master’s degree in applied physics, biophotonics, photonics engineering or a similar degree with an academic level equivalent to the master’s degree. A solid background in optics, photonics, optical imaging and data processing is an asset, and knowledge of microscopy is an advantage. Previous experience in working with cells and cells cultures is required. We expect the candidate to have strong laboratory skills in the above areas. Good communication skills in written and spoken English is a must. Starting date is spring 2020.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and only candidates with an above the average marks are accepted in the program. We recommend the applicants to contact the supervisors in advance to assess the suitability of the application.

Candidates will be enrolled in one of the general degree programs of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the 
DTU PhD Guide.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

Part of the project is expected to be carried out at one of our collaborator’s abroad, as an external research stay.

You can read more about 
career paths at DTU here.

Further information
Further information may be obtained from Dr. Peter E. Andersen, tel. +45 4677 4555, email peta@dtu.dk, or Dr. Dominik Marti, tel. +45 4677 4568, email domar@dtu.dk.

You can read more about Department of Healthcare Technology on 
www.healthtech.dtu.dk/english.

Application
Please submit your application as soon as possible and no later than 6 March 2020 (23:59 local time)Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link “Apply online”, fill out the online application form, and attach all your materials in English in one PDF file. The file must include: 

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)
Candidates may apply prior to obtaining their master’s degree but cannot begin before having received it.

Applications and enclosures received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.


DTU Health Tech engages in research, education, and innovation base on technical and natural science for the healthcare sector. The Healthcare sector is a globally expanding market with demands for the most advanced technological solutions. DTU Health Tech creates the foundation for companies to develop new and innovative services and products which benefit people and create value for society. DTU Health Techs expertise spans from imaging and biosensor techniques, across digital health and biological modelling, to biopharma technologies. The department has a scientific staff of about 175 persons, 130 PhD students and a technical/administrative support staff of about 80 persons.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 11,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.

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Turani Z et al.: Optical Radiomic Signatures Derived from OCT Images to Improve Identification of Melanoma. Cancer Res 79(8), 2021-2030 (2019).
Chang S, Bowden AK: Review of methods and applications of attenuation coefficient measure-ments with optical coherence tomography. J. Biomed. Opt. 24 (9), 090901 (2019).

To apply for this job please visit www.dtu.dk.