Biomarker Pipeline

Biomarker Pipeline

  • Overview

    • In the Whitaker lab we use the biomarker pipeline to identify, validate and develop novel biomarkers and therapeutics for cholangiocarcinoma and prostate, pancreatic, ovarian and bladder cancers. We focus on membranous and secreted proteins which can be detected in biological fluids or easily targeted for therapy.


    Biomarkers for early diagnosis are discovered by mining genomic and protein datasets using our knowledge of pathology to identify discriminatory molecules. Alternatively we do welcome approaches for collaborations with external groups.

    As much of the discovery work is completed in cell lines one of our key steps is test potential biomarkers on tissue at the earliest opportunity using our immunohistochemistry (IHC) pipeline. Using the appropriate resources we can use IHC to determine if a biomarker is also prognostic or predictive. If the IHC data is convincing we go on to develop ELISAs in-house and then convert them to the Mesoscale Discovery platform in collaboration with the Core Biochemistry Assay Laboratory

  • Mini TMA

    • Once a biomarker target has been identified we aim to test it on human tissue as quickly as possible using mini tissue microarrays (TMAs) that we make in-house. These arrays are made of 6mm cores of benign and tumour material (16 in total) and a marker core (liver tissue).

     

     

    Mini prostate TMA with a marker core positioned top left. This TMA was stained for AGR2 which stains prostate tumour cells (brown and blue) but not benign glands (blue only)

  • IHC Pipeline

    • IHC development in split into 2 streams dependent upon how much evidence exists that an antibody is proven to work for IHC. Evidence is gathered from the manufacturer, publications and Human Protein Atlas

  • Specificity controls

    • Specificity controls are made by knocking-down the target in a high expressing cell line using siRNA and running a Western blot for half of the sample to confirm knock-down. The remaining sample is made into a formalin fixed, paraffin embedded (FFPE) cell pellet for testing (to mimic tissue fixation). The method for producing an FFPE pellet can be found here

     

     

  • ELISA

    •  

    To determine the functional role of a biomarker in cancer cells we use a ‘molecular pathology’ approach where we overlay genomic level data from our involvement with the UK prostate ICGC consortium or from publically available TCGA data onto our biomarkers. Cancer-related mutations that cluster around functional motifs are recapitulated in cell lines to investigate changes in protein function.

      Membranous proteins which show low expression in normal tissue and high expression in tumours of interest are developed as biological therapeutics either in-house or through commercial partners in collaboration with Cancer Research Technology. 

     

In the Whitaker lab we use the biomarker pipeline to identify, validate and develop novel biomarkers and therapeutics for cholangiocarcinoma and prostate, pancreatic, ovarian and bladder cancers. We focus on membranous and secreted proteins which can be detected in biological fluids or easily targeted for therapy.


Biomarkers for early diagnosis are discovered by mining genomic and protein datasets using our knowledge of pathology to identify discriminatory molecules. Alternatively we do welcome approaches for collaborations with external groups.

As much of the discovery work is completed in cell lines one of our key steps is test potential biomarkers on tissue at the earliest opportunity using our immunohistochemistry (IHC) pipeline. Using the appropriate resources we can use IHC to determine if a biomarker is also prognostic or predictive. If the IHC data is convincing we go on to develop ELISAs in-house and then convert them to the Mesoscale Discovery platform in collaboration with the Core Biochemistry Assay Laboratory

Once a biomarker target has been identified we aim to test it on human tissue as quickly as possible using mini tissue microarrays (TMAs) that we make in-house. These arrays are made of 6mm cores of benign and tumour material (16 in total) and a marker core (liver tissue).

 

 

Mini prostate TMA with a marker core positioned top left. This TMA was stained for AGR2 which stains prostate tumour cells (brown and blue) but not benign glands (blue only)

IHC development in split into 2 streams dependent upon how much evidence exists that an antibody is proven to work for IHC. Evidence is gathered from the manufacturer, publications and Human Protein Atlas

Specificity controls are made by knocking-down the target in a high expressing cell line using siRNA and running a Western blot for half of the sample to confirm knock-down. The remaining sample is made into a formalin fixed, paraffin embedded (FFPE) cell pellet for testing (to mimic tissue fixation). The method for producing an FFPE pellet can be found here

 

 

 

To determine the functional role of a biomarker in cancer cells we use a ‘molecular pathology’ approach where we overlay genomic level data from our involvement with the UK prostate ICGC consortium or from publically available TCGA data onto our biomarkers. Cancer-related mutations that cluster around functional motifs are recapitulated in cell lines to investigate changes in protein function.

  Membranous proteins which show low expression in normal tissue and high expression in tumours of interest are developed as biological therapeutics either in-house or through commercial partners in collaboration with Cancer Research Technology.