Why we care about RNA

We developed the Valius workup to analyze tumor biology at every level: DNA, RNA, and protein.

Most of our patients are familiar with DNA testing before they start working with us. They've also typically done one or more protein stains for common targets in their indication.

However, few of our patients have received any RNA testing before engaging with us, and those that have often wonder why we think RNA is so useful.

We want to explain how RNA sequencing helps us estimate protein expression-and why that's a critical step to identifying treatment options.

Estimating protein expression with RNA sequencing

Put simply, RNA sequencing helps us measure the RNA expression-that is, the number of RNA transcripts-of each gene in a patient's tumor cells.

Think of RNA transcripts as "instruction manuals" for protein assembly; it makes sense that the amount of RNA encoding a given gene would proxy how much of that protein the cells produce.

Of course, human biology is never predictable, nor is the relationship between RNA and protein. Often, though, we've found that high RNA expression is indeed associated with high protein expression (the latter of which we measure by immunohistochemistry, or "IHC," stains).

Here's an example.

The chart below shows the RNA expression and protein expression of a common target, B7-H3, for seven of our patients. RNA expression (measured in transcripts per million) is on the x-axis, and protein expression (measured via the percentage of tumor cells staining positive at 3+ intensity) is on the y-axis. As you can see, the relationship between the two factors is not one-to-one, but it's clear that as RNA expression rises, protein expression often does too.

This relationship is the principal reason we care about RNA sequencing at Valius.

Why not just stain for everything?

You may wonder: if we mainly use RNA sequencing to estimate protein expression, why not skip the sequencing step and go directly to protein staining?

The answer is twofold.

First, whole transcriptome (RNA) sequencing allows us to measure the expression of every gene simultaneously. The number of therapeutically relevant targets is high-in the hundreds, even-and RNA sequencing allows us to understand their expression in one fell swoop.

Meanwhile, protein staining requires testing one target (or, at best, a handful of targets) at a time. Staining for each of these targets individually would be prohibitively expensive and slow for patients. And it would also require a much larger quantity of tissue.

In essence, RNA sequencing helps us narrow the list of targets we will stain for at the protein level.

Second, for some of the targets we look at, validated protein stains don't yet exist. In these cases, data from RNA sequencing is the best available indicator of the patient's target expression.

Where we're headed with RNA sequencing

As we continue to strengthen our analytical tools and deliver them to a wider group of patients, we're thinking a lot about which diagnostic technologies to continue performing and developing.

RNA sequencing is an absolutely essential input to our analysis today, and we expect it will continue to be. In fact, we plan to expand our portfolio of RNA-based assays by adding spatial RNA sequencing to our workup, which will help us understand how RNA expression varies spatially throughout a tumor.

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