Co-profiling (whole transcriptome and epigenome) of intact tissue to understand gene regulatory networks - Project Summary
The relation between structure and function in tissues is the cornerstone of tissue biology and pathology.
To address the need for analysis of intact tissue, many methods have emerged for spatial molecular
profiling. Unique among spatial biology platforms, AtlasXomics’ microfluidics-based platform helps basic
and translational researchers to understand and address the epigenetic dysregulation that underlies many
diseases including cancer and neurodegenerative diseases such as Alzheimer’s and ALS. The large data
sets generated by the new epigenomic assays can be integrated with data from single cell methods and
larger data sets describing disease states. These data sets are valuable because therapies for cancer and
neurodegenerative diseases are shifting from broad-brush approaches that have failed to meet
expectations due to patient heterogeneity. More targeted treatments for likely responders creates demand
for data that is presented in a form that informs disease mechanisms. Cell’s networks, phenotypic and
functional state is jointly regulated at multiple levels involving genome, epigenome, transcriptome,
proteome, and metabolome. Assessment of one modality at a time provides an incomplete representation
of cellular identity and is inadequate to understand biological systems and their underlying regulatory
mechanisms. There are no spatial epigenomics assays except for the one offered by AtlasXomics. This is
the first product to be developed from the Deterministic Barcoding in Tissue for spatial omics sequencing
(DBiT-seq) platform. The hypothesis is that the technology developed in an academic lab for co-profiling
can be transferred to other labs using the Company’s new chip designs that are easier to use. Reductions
in exposure to dust and required cleaning time by 90% should facilitate the democratized use of the assay.
The Company already has established a data portal with interactive visualization tools and website for
reviewers to access the processed data generated by DBiT-seq experiments from collaborators and
customers. Raw and processed data generated by this STTR will be made available through the data
portal tor reviewers (before publication) and the public to access data generated by this STTR (after
publication). Twenty investigators will be offered the opportunity to use the new software tools for co-
profiling service and to explore the curated data sets and provide feedback with a user satisfaction survey
(Likert scale) to assess the analysis and viewing of epigenome and transcriptome data. In Phase II, we aim
at launching commercial kits to existing customers of the single modality assay and to new customers.
These new products will enable dual and eventually tri-omic same-section spatial co-profiling
(transcriptome, epigenome, and proteome).
