From Bench Backlog to Breakthrough: How Bridge Informatics Accelerated Spatial Transcriptomics Analysis for a Pharmaceutical Giant

From Bench Backlog to Breakthrough: How Bridge Informatics Accelerated Spatial Transcriptomics Analysis for a Pharmaceutical Giant

Table of Contents

 Case study

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A large pharmaceutical company aimed to understand immune reactions after pathogen exposure and uncover the spatial signature of immune cell subtype involvement. Their research and development (R&D) team identified potential gene biomarkers. To verify these markers and explore additional targets, they designed an investigative transcriptomic experiment. However, conducting the analysis internally would take months for their small team. The Principal Scientist also planned to integrate spatial transcriptomics data but was unsure which platform to use. The company turned to Bridge Informatics (BI) for outsourcing.


Within a week, BI’s data scientists proposed and began executing on a statement of work in line with Client’s delivery timeline, which included:

  • Conducting a detailed review of various spatial omics technologies, including hybridization-based (e.g., MERFISH), barcode-based (e.g., SlideTag, Slide-seq), and spot-based methods (e.g., Visium, Xenium), exploring the advantages and disadvantages of each technology to determine suitability.
  • Pre-processing spatial transcriptomics data to account for variations in detection efficiency and background noise specific to each spatial technology.
  • Performing dimensional reduction and spatial clustering to identify distinct spatial gene expression patterns and cellular composition within the tissue context.
  • Implementing cell-type annotation using reference-free and/or reference-based methods.
  • Transferring labels from Client’s transcriptomic data and checking the quality of cell type annotation.
  • Conducting downstream analysis in spatial data, including differential gene expression within cell types across conditions.
  • Identifying spatially variable genes, spatial gene set enrichment analysis, pathway analysis (using KEGG and Reactome) to interpret biological pathways influenced by spatial variability.
  • Performing cell proximity and niche analysis to understand cellular microenvironments and the functional dynamics that occur in situ, which can be crucial for deciphering complex biological processes and disease mechanisms.
  • Investigating cell-cell communication with spatial resolution through ligand-receptor interactions.
  • Creating spatial maps and detailed visualizations to illustrate findings.
  • Listing candidate genes in a spatially informed manner for further validation through in situ hybridization or immunohistochemistry.
  • Assisting in integrating spatial transcriptomics data with other omics data types to provide a comprehensive view of the molecular and cellular landscape, aiding in a multi-omic integration approach.


Within two months of receiving the sequencing data from Client, BI conducted a comprehensive analysis, integrated the data, and summarized the most compelling findings. Notably, specific immune cell subtypes were identified in distinct spatial niches within the tissue following pathogen exposure. Furthermore, the characterization of specific molecular pathways mediated by these immune cell subtypes illuminated intricate molecular interactions crucial for the client’s pathway of interest.

Following these findings, both the client’s Bioinformatics Scientist and Principal Scientist were able to swiftly extract insights and postulate mechanisms underlying disease progression and pathogenesis. BI also played a crucial role in educating the client’s scientists on the specific spatial transcriptomics analysis workflows and corresponding visualizations, enabling them to effectively present the analysis to their non-technical colleagues.

Interested in partnering with Bridge Informatics? Contact us to learn more about our team of bioinformaticians with experience at the bench whose core specialty is understanding and analyzing biological data.

Jessica Corrado, Head of Business Development & Commercial Operations, Bridge Informatics

As the Head of Business Development & Commercial Operations, Jessica is responsible for driving strategic growth initiatives and overseeing the company’s commercial activities. She has both a keen understanding of the life sciences industry and a strong track record in building successful partnerships.

Prior to joining Bridge, Jessica held a number of leadership roles across sales, marketing, and communications. Outside of work, Jessica is responsible for the majority of marketing and event planning for Shore Saves, a non-profit animal rescue. She enjoys reading and is often reading at least two books of various genres at a time. If you’re interested in reaching out, please email [email protected] or [email protected]

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