Introduction to Protein Genomics Lecture Notes

Speaker Introduction

• Professor Frederick Ponton
  • Current position: Professor at Topsail Honesty, Sweden.
  • Topic: Human Protein Atlas (HPA) - a Swedish-based program aiming to map all human proteins.

Overview of Human Protein Atlas (HPA)

• Started: 2003
• Goal: Map human proteins in cells, tissues, and organs using various omics technologies:
  • Antibody-based imaging
  • Mass spectrometry-based proteomics
  • Transcriptomics
  • Systems biology
• Challenges: Success amidst various challenges, contributions from Indian pathologists and research collaborators.
• Focus of Lecture: Tissue Atlas of HPA

Project Background

• Funding: Generous support from the Valen By Foundation.
• First Draft Completion: 2015
• Vision: To add an information layer on the human genetic code published in 2001 by the Human Genome Project.
  • Aim to understand the relationship between genes and the proteins they encode.

Methodology

• Affirmative Probes: Development of antibodies to characterize the human proteome.
• Modules: Defined different modules with monthly goals.
• Data Production: All data produced is publicly available, as required by funding.

Gene Expression Profiling

• Techniques Used:
  • Immunofluorescence for cells and organelles.
  • Immunochemistry for tissues and organs.
  • RNA sequencing for quantitative data.

Tissue Microarrays

• Normal Tissues Studied: 46 different tissue types in triplicates from three individuals.
• Usage: Tissue microarrays allow profiling with reduced tissue waste.
• Development: Instrumentation for tissue microarrays was advanced at the end of the 90s.

Collaboration with Indian Pathologists

• Involvement: Key collaboration since 2006.
  • Focus on evaluating digital images of tissue samples.
• Volume of Work: Annotated over 12 million images, producing high-quality data.
• Outcome: High citation rate of collaborative publications in reputable journals.

Quantification of Data

• RNA Sequencing: Harvesting RNA from normal tissues for transcriptomics data.
• Results: Correlation observed between RNA levels and protein levels across different tissue types.
• Housekeeping Proteins: 44% expressed in all tissues; relevant in disease understanding.

Protein Atlas Structure

• Three Pillars:
  1. Tissue Atlas: Showcases gene expression in various tissues.
  2. Cell Atlas: Displays protein expression in different organelles.
  3. Pathology Atlas: Correlates gene expression with survival rates in cancer patients.

Accessing HPA Data

• Web Portal Navigation: Users can explore specific tissues and proteins; detailed summaries are available for each gene.
• Example: Data on colonic proteins and potential biomarker for colorectal cancer.

Conclusion

• Importance of HPA: Significant resource for understanding diseases and identifying biomarkers.
• Future Lectures: Focus on Cell Atlas and Pathology Atlas.

Final Notes

• Recommendation: Visit the HPA website for exploration and research purposes.