Scalable single-cell workflow for multiomic analyses of chromatin interactions, accessibility, gene expression and cell surface proteins to unravel mechanisms of cellular diversity

Scalable single-cell workflow for multiomic analyses of chromatin interactions, accessibility, gene

expression and cell surface proteins to unravel mechanisms of cellular diversity

Arima Genomics

Project Summary/Abstract

All cells in the human body carry the same DNA sequence and yet individual cells are highly diverse in identity,

morphology, proliferation, and function, leading to enormous heterogeneity in the context of tissues, organs, and

organisms. Individual cells achieve this diversity via unique gene regulatory programs – where in, unique sets of

regulatory elements (REs) precisely instruct each cell which genes to express and when. Mapping such gene

regulatory programs are central to molecular biology and genomics, as mis-regulation is a major cause of disease

– mapping not only helps in diagnosis but also enables therapies that can intervene and correct mis-regulation.

Single cell ATAC sequencing (scATAC) has emerged as the popular mapping assay to delineate REs unique to

each cell. When scATAC is performed alongside single cell RNA sequencing (scRNA), the researcher has

access to both REs and gene expression, allowing them to obtain unprecedented insight into the gene regulatory

programs of living cells. There is only one problem – there are often multiple REs in the neighborhood of a gene

and without the ability to link specific REs to its target genes, a mechanistic view of gene regulation is lacking,

limiting our ability to enable precise diagnosis and drug discovery programs.

High throughput chromatin interaction capture assay and sequencing (HiC) presents a three-dimensional view

of the genome, often informing the missing link between RE and their target genes. Indeed, several KOLs – e.g.,

Dr. Tomi Pastinen calls scATAC, scRNA and scHiC as the “trifecta of modalities” that can truly delineate gene

regulatory programs of individual cells (see Dr. Pastinen’s letter and 30+ additional letters of support).

Recognizing the value, several academic labs have developed scHiC protocols, which has already unraveled

incredibly detailed mechanistic insights of gene regulation of complex microenvironments including breast

cancer, prostate cancer, hippocampus – several of these studies are discussed in this application. Despite the

enthusiasm around scHiC data, adoption has been restricted to a few labs because of (1) severe experimental

inefficiencies that result in exorbitant costs (upwards of $20,000 per sample), and (2) because current scHiC

protocols involve complex plate- or combinatorial indexing workflows that are challenging to setup and execute.

Via a self-funded phase-1 program, we tackled problem (1) to drastically improve efficiency of scHiC and

consequently, drive costs down from earlier $10 per cell, to 1,000 reactions of A-scHiC kits to tens of academic labs (despite no marketing activity

from Arima), who have embedded our kits within both the plate- and combinatorial indexing single cell workflows.

The scope of phase-2 program is to tackle problem (2) to enable widespread adoption. In particular, we propose

to build off the A-scHiC chemistry toward what we refer to as the sc3DGR chemistry that is performed upstream

of 10X genomics (10XG) Chromium – i.e., the output of sc3DGR kit will be an input into the 10X ATAC (flavor1)

or 10X Multiome (flavor2) kits, to concurrently capture scHiC and scATAC (flavor1), or, scHiC, scATAC and

scRNA (flavor2), respectively. Such a chemistry will not only solve the ease to use problem (2) given its

combability with the market leader 10XG, but importantly, it will enable multiomic analyses of the “trifecta” from

the same individual cell concurrently, thus enabling cell perturbation, characterization and screening use-cases

for precision mapping, diagnosis, and therapy. Once the sc3DGR chemistry is finalized, we translate it into robust

kits, to be validated by 14 KOLs (see letters of support) across academia and pharma (AbbVie, AstraZeneca &

Genentech). For Arima, the chemistry, the informatics, the easy end-to-end workflows, the overall workflow cost,

the KOL-based go-to-market strategy – all play major factors in a seamless commercialization process of this

leapfrog technology for delineating gene regulation programs of individual cells.