Reprogramming The Tumor Microenvironment: Why RNA Immunotherapy Is Targeting Liver Metastases (Pt. 1)

A conversation with Art Krieg, MD, Founder, President, and Acting CEO/CSO, Zola Therapeutics

Immune checkpoint inhibitors have transformed cancer treatment, but patients whose tumors metastasize to the liver continue to face some of the poorest outcomes in immuno-oncology. Rather than focusing solely on activating T cells, a growing number of researchers are exploring whether reprogramming the liver's uniquely immunosuppressive microenvironment may unlock more durable responses. In Part 1 of his conversation with Life Science Connect Acquisition Editor Michael Soloway, Art Krieg, MD, discusses why liver metastases remain such a formidable challenge, how innate immunity and tumor-associated macrophages influence therapeutic resistance, and why his company's RNA/DNA immunotherapy platform is designed to restore antiviral interferon biology as a strategy for generating stronger anti-tumor immune responses.

ARNA: Immune checkpoint inhibitors have transformed oncology, yet patients with liver metastases often respond poorly. Why does the liver create such a uniquely immunosuppressive environment?

AK: When surgeons first started to transplant organs between animals and then humans, it quickly became clear that liver transplants were accepted more readily and that lower doses of immune suppressing medications were needed to prevent rejection, compared to transplants of other organs, such as kidney or heart.

From an immune perspective, the liver is considered to be a “tolerogenic” organ: it promotes immune tolerance to whatever proteins (antigens) are in the liver. Through decades of research, multiple mechanisms have been identified that contribute to the tolerogenic environment in the liver, but the relative importance of the various known pathways in maintaining health and contributing to disease are poorly understood. Perhaps this environment evolved because of the special role of the liver in taking up and processing food antigens from the gut, which are delivered to the liver before circulating to the rest of the body.

One role for the liver may be in preventing unnecessary immune responses to harmless food proteins that have been taken up in the gut. The gut has many defenses against invading pathogens, so if a protein taken up from the gut reaches the liver, then it can be “assumed” to be “safe” and to be sterile.

The liver also has a key role in taking up lipid/fat particles from the blood and preventing inappropriate immune responses to these. At the same time, the liver has many immune cells that have evolved to detect viruses or bacteria and to initiate protective responses if these are detected.

The relevance of this to cancer is that if a tumor succeeds in spreading to the liver, it seems to gain a great advantage in avoiding immune rejection, and patients are much less likely to respond to immunotherapy compared to patients whose tumors have not spread to the liver.

ARNA: What role do tumor-associated macrophages and innate immunity play in limiting the effectiveness of current immunotherapies?

AK: Over the past decades, it has become clear that tumors trick immune defenses such as macrophages into helping the tumors grow by releasing “damage molecules” (or damage associated molecular patterns – DAMPs). DAMPs are normally produced by stressed or injured cells in the body. DAMPs evolved as a way to repair wounds – they attract macrophages and other innate immune cells into the damaged tissue and induce gene expression programs that stimulate the growth of new blood vessels (angiogenesis), inhibiting immune defenses that could attack the tumor, such as T cells.

In fact, scientific studies have identified the mechanisms through which liver macrophages are induced by tumors to actively kill CD8+ T cells. Some approaches to tumor therapy have arisen to try to kill or block these immune suppressive macrophages and other myeloid cells or to block the effects of the DAMPs, either by preventing tumor cells from releasing these or blocking the ability of the immune cells to sense or respond to them. Other efforts have been directed at reprogramming these cells into an anti-tumor state often referred to as M1 (but this simple term doesn’t do justice to the complexity of these cells), but there has been no broad agreement over how to define the desired reprogramming.

The simplistic notion of “making cold tumors hot” by inducing inflammation has been resoundingly rebutted after multiple different failures in human clinical trials of therapies that showed outstanding efficacy in mouse models. In fact, gene signatures of inflammation are associated with resistance to immune therapies in humans, while gene expression signatures for interferons are associated with response.    

ARNA: Much of oncology has focused on activating T cells. Why do you believe reprogramming the innate immune system is becoming equally important?

AK: In the 1890s, William Coley figured out a way to destroy cancerous tumors by injecting patients with toxic bacteria. Debunked at the time, his treatments with a patient named Zola laid the groundwork for modern immunotherapy. Over 130 years later, the field of oncology has mostly retreated from the concept of stimulating innate immunity to treat cancer.

This may be seen as a rational response to the repeated clinical failures of most innate immune activators (e.g., STING, small molecule Toll-like receptor [TLR] 7/8 agonists) and to the clinical efficacy, regulatory approvals, and commercial success of T cell checkpoint inhibitors, TIL and CAR-T therapies, and more recently, T cell engagers. Activating T cells has achieved enough clinical success to build commercial momentum, encouraging further investment in these approaches. 

ARNA: Your platform combines RNA and innate immune signaling in a different way than many RNA therapeutics. What scientific gap are you trying to address?

AK: The scientific gap we are trying to address is the abject failure of the traditional scientific approach of incremental experimentalism to discover effective human therapies. The billions of wasted dollars spent by large pharma, and the toxicity (including death) and lack of efficacy suffered by tens of thousands of patients who have enrolled in various failed studies, demands a fresh approach. The usual approach of incremental experimentalism is doomed if we currently understand less than 1% of tumor immunology and because mouse models do not predict human efficacy.

In its place, we have employed teleological deduction, which we believe is far more powerful. Our use of this process starts from the universally agreed fact that the goal of cancer immunotherapy is to induce anti-tumor CD8+ T cells. We can deduce that CD8+ T cells evolved, at least in part, for the purpose of killing retroviral-infected cells. Therefore, innate immunity had to evolve receptors to detect such cells or the particles they release (more powerful).

The only plausible receptors able to distinguish retroviral particles from normal cellular debris are TLR7/8/9, so we reasoned that optimizing our activation of these receptors, by mimicking the natural structures of retroviral replicative complexes, should have increased efficacy in cancer immunotherapy compared to prior approaches. This led us to combine RNA and DNA sequence motifs in structures known to characterize retroviral and DNA viral genomes and to our lead program, Z-007.

ARNA: Interferon signaling appears central to your approach. Why is restoring interferon biology so important for generating durable anti-tumor immunity?

AK: Decades ago, interferons were discovered for their ability to interfere with viral infection of human cells. Once CD8+ T cells were discovered, it was realized that type I interferon (IFN) is critical for induction of maximal CD8+ T cell responses and that T cell production of type II IFN is critical in the efficacy of control of infections. The role of type I IFN in mediating response to cancer immunotherapies is well established, yet the type I IFN system is quite complex and widely misunderstood by scientists working in cancer immunotherapy. (As an aside, I have not met a single scientist working in biotech or pharma who was aware of these differences and their implications!)

There are 17 type I IFNs, including 13 genes for IFN-α and one for IFN-β, all of which bind and act through a single receptor, called IFNAR. These genes have been independently maintained through evolution. In mice, these have similar biologic effects, so many investigators have assumed they likewise are interchangeable in humans. However, striking differences emerged early in the human clinical development of recombinant IFN-α2 and IFN-β.

Recombinant IFN-α2 has been approved for the treatment of chronic viral infections (hepatitis B virus, hepatitis C virus) and some forms of cancer. IFN-β was approved to treat patients with multiple sclerosis but failed in the treatment of chronic viral infections or cancer. These distinct therapeutic applications most likely reflect distinct biologic roles of the individual IFNs that remain poorly understood. IFN-β can be secreted by essentially all nucleated cells activated through most pattern recognition receptors (PRRs). By contrast, IFN-α is predominantly secreted by a subset of plasmacytoid dendritic cells (pDCs) in response to only two PRRs: TLR7 or TLR9.

ARNA: How do you envision RNA therapeutics complementing checkpoint inhibitors rather than competing with them?

AK: Checkpoint inhibitors work by taking the brakes off anti-tumor CD8+ T cells in patients where these are already present. A minority of patients respond to these agents, which is believed to be largely due to the lack of adequate effective CD8+ T cells in most patients and most types of cancer.

Our RNA/DNA therapeutics function in a completely different manner, activating innate immune pathways that evolved for the purpose of inducing CD8+ T cells to dangerous viral infections and empowering these to kill infected host cells throughout the body. We expect our RNA/DNA therapeutics to transform cancer immunotherapy by providing a universal inducer for endogenous anti-tumor CD8+ T cells. Based on prior clinical trials with the CpG-A TLR9 agonist vidutolimod, we expect Z-007 to have monotherapy clinical efficacy.

Ultimately, Z-007 is likely to be used widely in combination therapies, augmenting checkpoint inhibitors and bispecific antibodies, depending on the presence of anti-tumor T cells. By inducing endogenous anti-tumor CD8+ T cells through the antiviral pathway, Z-007 provides a universal therapy, making personalized tumor vaccines, TIL, and CAR-T approaches obsolete. Beyond oncology, our drugs also should be useful for treating viral infections such as chronic hepatitis B virus.

ARNA: Liver metastases are common across multiple tumor types. Could this strategy ultimately have applications beyond colorectal cancer?

AK: Yes! One of the most exciting aspects of innate immune activation is that, in principle, it should be agnostic to the tumor type. In reality, there are sure to be some tumors that suppress TLR7/8/9 stimulation.

For example, in our early trials of Z-007 therapy in pet dogs with spontaneous cancer, we have seen no benefit in three dogs with mucosal melanoma, a type of tumor that is generally resistant to immunotherapy in humans. Colorectal cancer has been widely believed to be resistant to immune therapies, but recent studies have identified multiple different transcriptional signatures, or gene expression programs, whose presence in a tumor predicts response to immunotherapy. In tumor-associated immune cells from humans with colorectal cancer (CRC), Z-007 induces the expression of multiple different transcriptional signatures that have been associated with human clinical response and survival in CRC and other tumor types.

We expect Z-007 to be effective in many tumor types, especially if it is combined with other agents that reverse TLR7/8/9 suppression, assuming this turns out to be present in some tumors. During clinical development of Z-007, translational studies will be performed to confirm whether patients are showing the expected induction of response-associated gene signatures and to determine mechanisms of resistance.

About The Expert

Art Krieg, MD, founded Zola Therapeutics in 2023 and serves as CEO. Previously, Krieg founded Checkmate Pharmaceuticals, until its acquisition by Regeneron in 2022; RaNA Therapeutics (subsequently Translate Bio, acquired by Sanofi); and Coley Pharmaceutical Group until its acquisition by Pfizer in 2008. Krieg served as CSO of Pfizer’s Oligonucleotide Therapeutics Unit from 2008 to 2011 and cofounded the first antisense journal, Nucleic Acid Therapeutics and the Oligonucleotide Therapeutics Society, for which he recently served as president. Krieg has published more than 250 scientific papers and is an inventor on over 50 U.S.-issued patents covering oligonucleotide technologies. He is currently an adjunct professor in the UMass Chan Medical School RNA Therapeutics Institute.