About

After my master on microbial genetic diversity in oil contaminated arctic tundra, I suddenly found myself working in a cancer research lab. There, in the “Breast Cancer Group” at Haukeland University Hospital, I did a PhD focusing on therapy resistance to anthracyclines and the PI3K-Akt-PTEN signaling pathway. In my PhD I also did functional studies on the PTEN pseudogene to illuminate its biology as a ceRNA, and it´s possible effect on tumor growth and effect on therapy.

The rapid evolution of Next Generation Sequencing has made stuff possible that was pure science fiction during may master, opening up a new world of possibilities and problems to solve. Transitioning from a pure wet lab scientist into the realms of bioinformatics, required me to acquire a whole new skill set, including programming and statistics in R.

During my postdoc I was interested in therapy resistance in the context of DNA repair, and if faulty DNA repair in the tumor can predict if a patient responds to treatment or not. I worked with the phase 2 clincial trial PETREMAC during my entire PostDoc, doing 360 gene panel sequencing in matched tumor-blood samples, germline screening for pathogenic variants, building and maintaining the RNAseq pipeline with Dragen for WTS so that I could do i.e intrinsic subtyping and examine other gene signatures and cell type deconvolution from the gene expression data. I also worked with immunohistochemestry, established workflows for digital pathology for PD-L1 CPS score and other immune-markers. A great part of my time however, was also spent managing and organizing the clinical data from the PETREMAC trial, and doing statistics once the data was ready.

Currently I am working as a project-coordinator in a pink ribbon funded project focusing on the Arm A part of PETREMAC, the ER+ TP53wt patients. The patients in arm A that did not respond to endocrine therapy was given Palbociclib, a CDK4/6 inhibitor.
My aims during this project is to find predictive markers for response/resistance to Palbociclic.


The reason this webpage exists, is only because I thought that creating a webpage using R would be fun during the COVID lockdown.
So I made this site directly as a result from the inspirational workshop on Hugo and Blogdown hosted by R-Ladies Bergen, and later the excellent workshop on Apéro hosted by R-Ladies Tunis. Getting together digitally during lock-down, made the world a brighter place. So here I am, with a blog written in R, about doing stuff in R.

Blog

Timelapse video of IHC manual score vs digital score

Time lapse videos are fun to make. So I made a video of me scoring IHC slides the old fashion way by examining slides in the microscope, and by using digital pathology scoring the slides using machine learning with QuPath. The digital workflow consists of identifying tumor and immune cells, and counting all positive and negative cells. There was no way I was going to do that manually. This is where QuPath came for my rescue. Read more

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Publications

Papers

  1. Yndestad, S., C. Engebrethsen, A. Herencia-Ropero, O. Nikolaienko, O. K. Vintermyr, R. K. Lillestol, L. Minsaas, B. Leirvaag, G. T. Iversen, B. Gilje, E. S. Blix, H. Espelid, S. Lundgren, J. Geisler, H. S. Aase, T. Aas, E. G. Gudlaugsson, A. Llop-Guevara, V. Serra, E. A. M. Janssen, P. E. Lonning, S. Knappskog and H. P. Eikesdal (2023). Homologous Recombination Deficiency Across Subtypes of Primary Breast Cancer JCO Precis Oncol 7: e2300338.

  2. Nikolaienko, O., H. P. Eikesdal, E. Ognedal, B. Gilje, S. Lundgren, E. S. Blix, H. Espelid, J. Geisler, S. Geisler, E. A. M. Janssen, S. Yndestad, L. Minsaas, B. Leirvaag, R. Lillestol, S. Knappskog and P. E. Lonning (2023). Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development Genome Med 15(1): 104.

  3. Eikesdal, H. P., S. Yndestad, A. Elzawahry, A. Llop-Guevara, B. Gilje, E. S. Blix, H. Espelid, S. Lundgren, J. Geisler, G. Vagstad, A. Venizelos, L. Minsaas, B. Leirvaag, E. G. Gudlaugsson, O. K. Vintermyr, H. S. Aase, T. Aas, J. Balmana, V. Serra, E. A. M. Janssen, S. Knappskog and P. E. Lonning (2021). Olaparib monotherapy as primary treatment in unselected triple negative breast cancer Ann Oncol 32(2): 240-249.

  4. Yndestad, S., E. Austreid, K. O. Skaftnesmo, P. E. Lonning and H. P. Eikesdal (2018). Divergent Activity of the Pseudogene PTENP1 in ER-Positive and Negative Breast Cancer Mol Cancer Res 16(1): 78-89.

  5. Yndestad, S., E. Austreid, I. R. Svanberg, S. Knappskog, P. E. Lonning and H. P. Eikesdal (2017). Activation of Akt characterizes estrogen receptor positive human breast cancers which respond to anthracyclines Oncotarget.

  6. Yndestad, S., E. Austreid, S. Knappskog, R. Chrisanthar, P. K. Lilleng, P. E. Lonning and H. P. Eikesdal (2017). High PTEN gene expression is a negative prognostic marker in human primary breast cancers with preserved p53 function Breast Cancer Res Treat.

  7. Steinskog, E. S., S. J. Sagstad, M. Wagner, T. V. Karlsen, N. Yang, C. E. Markhus, S. Yndestad, H. Wiig and H. P. Eikesdal (2016). Impaired lymphatic function accelerates cancer growth Oncotarget.

  8. Knappskog, S., E. O. Berge, R. Chrisanthar, S. Geisler, V. Staalesen, B. Leirvaag, S. Yndestad, E. de Faveri, B. O. Karlsen, D. C. Wedge, L. A. Akslen, P. K. Lilleng, E. Lokkevik, S. Lundgren, B. Ostenstad, T. Risberg, I. Mjaaland, T. Aas and P. E. Lonning (2015). Concomitant inactivation of the p53- and pRB- functional pathways predicts resistance to DNA damaging drugs in breast cancer in vivo Mol Oncol.

  9. Yndestad S, Eikesdal HP, PI3K-Akt-mTOR signallering og Anthracyclinresistens. Onkonytt. 2014(1).


Scientific meeting posters

  1. Synnøve Yndestad. “Digital PD-L1 CPS score: A workflow for Positive cell detection and classification using QuPath.” Bringing AI and Precision Medicine to Patient Care, The Sixth Annual MMIV Conference Bergen (2023).

  2. PS07-09 Prenatal BRCA1 epimutations is a major cause of triple-negative breast cancer. Per Lonning, Hans Petter Eikesdal, Elisabet Ognedal, Bjornar Gilje, Steinar Lundgren, Egil Blix, Helge Espelid, Jürgen Geisler, Stephanie Geisler, Emiel Janssen, Synnøve Yndestad, Laura Minsaas, Beryl Leirvaag, Reidun Lillestol, Stian Knappskog, Oleksii Nikolaienko. SABC (2023).

  3. S. Yndestad, Engebrethsen, C., A. Herencia-Ropero, O. Nikolaienko, O. K. Vintermyr, R. K. Lillestøl, L. Minsaas, B. Leirvaag, G. Iversen, B. Gilje, E. Blix, H. Espelid, S. Lundgren, J. Geisler, L. J. Vassbotn, H. S. Aase, T. Aas, A. Llop-Guevara, V. Serra, P. E. Lønning, S. Knappskog and H. P. Eikesdal. “Abstract P6-10-04: Homologous recombination deficiency across subtypes of primary breast cancer.” Cancer Research 83(5_Supplement): P6-10-04-P16-10-04. (2023)

  4. Eikesdal, H. P., Yndestad, S., Blix, E. S., Lundgren, S., Vagstad, G., Espelid, H., Gilje, B., Janssen, E. A., Geisler, J., Aas, T., Aase, H., Knappskog, S., Lønning, P. E.Neoadjuvant olaparib monotherapy in primary triple negative breast cancer. Annals of Oncology 2019; 30.

  5. Synnøve Yndestad, Eilin Austreid, Ida R. Svanberg, Per E. Lønning, Hans P. Eikesdal. “The Role of Akt in Anthracyclin Resistance in Patients with Locally Advanced Breast Cancer.” 4rth CCBIO symposium, Solstrand (2016).

  6. Synnøve Yndestad, Eilin Austreid, Kai Ove Skaftnesmo, Per Eystein Lønning, Hans Petter Eikesdal. “Introduction of Pten Pseudogene in Murine Breast Cancer Upregulates Pten, P53 and Activating Protein 2 Gamma and Delays Tumor Growth.”. AACR 106th Annual Meeting 2015; Apr 18–22, 2015; Philadelphia, PA, no. Poster Presentation, Abstract number 3986 (2015).

  7. Yndestad Synnøve, Austreid Eilin, Eikesdal Hans Petter. “The Non-Coding Pten Pseudogene Influences Pi3k Signaling and Inhibits Breast Cancer Progression.” AACR 105th Annual Meeting 2014; Apr 5–9, 2014; San Diego, CA, no. Poster presentation, Abstract number 3539 (2014). 8. Austreid, E. Yndestad, S. Knappskog, S. Lønning, P.E. Eikesdal, H.P. “The Influence of Doxorubicin on Pten and Pi3k-Akt-Mtor Signaling in Human Breast Cancer.” San Antonio Breast Cancer Symposium Poster Presentation (2013).

  8. Eikesdal Hans Petter, Austreid Eilin, Yndestad Synnøve, Knappskog Stian, Lonning Per Eystein. “Pten Pseudogene Downregulates Pten in Human Breast Cancer.” Keystone Poster presentation (2012).

  9. Yndestad Synnøve, Roiha Irja Sunde, Torsvik Vigdis, Brandvik Per Johan, Øvreås, Lise. Microbial community analysis of a hydrocarbon-contaminated arctic soil from Svalbard. 1st Workshop on Microbial ecology and bioremediation in cold climate (MECBIO). Bergen (2002) UiB UNIS

  10. Yndestad Synnøve, Roiha Irja Sunde, Torsvik Vigdis, Brandvik Per Johan, Øvreås Lise. Microbial community analysis of a hydrocarbon-contaminated arctic soil from Svalbard. 7th Symposium on Bacterial Genetics and Ecology (BAGECO-7) (2002) UiB UNIS.

  11. Yndestad Synnøve, Roiha Irja Sunde, Øvreås Lise, Brandvik Per Johan. Oil pollution in the Arctic and its effect on microbial diversity and ecology. Mikrobiologisk vintermøte (2002) UiB UNIS

PhD thesis

The role of PTEN, PI3K-Akt-mTOR signaling and pseudogene PTENP1 in breast cancer 2018 University of Bergen Lint to thesis

Master/Cand. Scient thesis

Mikrobiell diversitet i oljeforurenset og uberørt tundra på Svalbard https://bora.uib.no/bora-xmlui/handle/1956/17687

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Synnøve Yndestad

I just needed the data, I wasn’t supposed to be doing this.
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