SBIR-STTR Award

Direct to Phase II

A scalable kit-based assay for multi-omic analyses of transcriptional protein binding and chromatininteractions from ultra-low input frozen and FFPE samples at single-cell resolutionArima Genomics/Precise regulation of gene expression is paramount to establishing cellular identities, and mis-regulation of genescauses human disease. Cells regulate gene expression using regulatory elements (REs), short DNA sequencesembedded throughout the genome, who are bound by transcriptional proteins (TBPs) to facilitate their regulatoryfunction. Molecular mapping tools, such as Chromatin immunoprecipitation with sequencing (ChIP-seq), produce"maps" of REs along the genome and have been a ubiquitous approach towards understanding gene regulation.However, REs mapped using ChIP-seq are only understood in context of a linear genome. In reality, REs executegene control within a three dimensional (3D) genome. Therefore to truly understand gene regulation - generegulation must be mapped in 3D. Indeed, high throughput chromatin interaction capture (HiC) was developedto produce 3D interaction maps of all 3 billion bases in the human genome, however, HiC does measuretranscriptional protein binding, nor whether an interaction is regulatory, thus having limited utility in advancingour understanding of 3D gene regulation. To truly obtain 3D gene regulation maps, a multi-omic assay thatconcurrently captures the binding of transcriptional proteins and their mediated interactions is necessary.Recently, novel approaches attempt to combine the molecular steps of ChIP-seq and chromatin interactioncapture to measure transcriptional protein binding and mediated chromatin interactions in a single, multi-omicassay. However these approaches, termed ChIA-PET and HiChIP, do not efficiently capture chromatininteractions or transcriptional protein binding, respectively. Consequently, there is need for improved assays thatproduce true multi-omic maps of 3D gene regulation.To satisfy this unmet need, we have developed and commercialized our optimized minimal viable product (MVP)Arima-HiChIP (A-HiChIP) solution. This phase-1 product incorporates innovations designed to meet the needsof early adopter customers, achieving efficient multi-omic mapping of TBP and chromatin interactions in higherinput frozen cells and tissues, and a defined subset of transcriptional proteins. We have also developed ourphase-1 product for workflow integration, leveraging industry and academic partnerships to reduce barriers inChIP and bioinformatics components of the workflow, respectively. Our team has deep expertise in the scienceof chromatin interaction capture, gene regulation, and its commercialization. In 2018, we commercialized Arima-HiC kits for studying general principles of chromatin interactions and within 2 years have accumulated 500+customers, providing tools to enable published discoveries across a host of basic science and disease research.Based on VOC analytics, we shifted our focus to develop the A-HiChIP kit - a more relatable product to the generegulation market that customers wanted and that represented a larger market opportunity. Indeed, after ourself-funded phase-1 R&D and product developments, we launched our MVP A-HiChIP solution into the marketand have seen remarkable success - measured by an increase in our revenue contributions, increased qualityof revenue, and traction with key opinion leaders (KOLs), large consortia, and COVID research. However, ourphase-1 A-HiChIP has known limitations. In particular, the product falls short of meeting the needs of researchersutilizing common clinical samples types or quantities in their research, or seeking single-cell resolution in theiranalyses of heterogeneous tissues.As part of this direct-2-phase II program, we propose to further develop our technology to overcome theselimitations, meet customer need, and enable broader adoption and application of this powerful multi-omic assayin the form of our second-generation A-HiChIP solution. Specifically, we propose assay developments to enablecompatibility with pervasive clinical sample characteristics - ultra-low cell inputs (<100K cells) and FFPE tissues.Further, we propose development of a first-of-its-kind single-cell HiChIP assay and companion bioinformaticstools. We also propose essential product developments, to ensure commercialization of a robust, premium-performance kit-based product that is optimally integrated into the bulk and single-cell sequencing ecosystems.Upon successful completion of these technical and product-oriented aims, we propose to benchmark andvalidate our phase-2 A-HiChIP solution through collaboration and prototype (beta) kit and bioinformaticsevaluations with KOLs across customer segments.

Public Health Relevance Statement:
A scalable kit-based assay for multi-omic analyses of transcriptional protein binding and chromatin interactions from ultra-low input frozen and FFPE samples at single-cell resolution Arima Genomics Project Narrative Precise gene regulation plays an essential role in specifying the unique functions of cells and tissues throughout the human body. When genes are mis-regulated, human disease can result. To regulate gene expression, cells utilize binding of transcriptional proteins to define regulatory elements, and precise physical interactions between regulatory element and their target genes folded within the 3D genome of a cell. Most genomics assays to study these two key mechanisms are "single-omic" - they independently map regulatory elements or 3D interactions, but they do not inform which regulatory elements regulate which genes at any given point in time. "Multi-omic" assays have been developed to concurrently map regulatory elements and their interactions, but remain inefficient, necessitating improved assays. Arima has overcome these challenges to develop an integrated kit- based solution for true multi-omic mapping of regulatory elements and their interactions. Building off this, Arima proposes to develop a new integrated kit-based solution that enables access to previously inaccessible clinical samples. Importantly, the proposed kit also enables multi-omic mapping of regulatory elements and their interactions at single-cell resolution. The development and application of this kitted solution builds new inroads for gene regulation studies toward improving the human condition via improved discovery, diagnosis and therapy.

Project Terms:
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