Up or Down: Chroma Medicine Raises Stakes in Epigenetic Editing

With $135 million in new financing to draw upon, Chroma Medicine says it will spend this year presenting promising proof of concept data for its epigenetic genome editing platform, advancing its pipeline of single-dose therapies discovered through the platform, and growing its workforce.

Despite a chilly financing climate for early-stage biotechs, Chroma completed its $135 million Series B financing earlier this month, bringing the company’s total capital raised to $260 million.

The new capital, Chroma says, will help it build out a platform designed to develop programmable epigenetic editors that precisely turn genes on or off, or can alter the expression of several genes at once. By seamlessly silencing, activating, and multiplexing genes in a single platform intended to mimic the cell’s innate mechanisms for controlling gene expression, Chroma reasons, its epigenetic technology can become the leading approach for gene regulation.

“The technology can best address any disease where changes in the amount of gene expression are important to the pathogenesis of the disease,” Chroma CEO Catherine Stehman-Breen, MD, told GEN Edge. “We don’t correct genes. We change gene expression. We don’t need to change the sequence of the DNA in order to change gene expression. We can do this leveraging this endogenous system that was actually intended to regulate gene expression.”

Chroma’s programmable epigenetic editors—or epieditors—are designed to target genes and control chromatin conformation by coupling a DNA-binding domain with epigenetic effector domains. The DNA-binding domain specifically targets one or more genes to be silenced or activated, while the effector domains create specific and durable methylation patterns which control chromatin conformation and govern whether a gene is accessible or inaccessible for transcription.

“That pattern is the pattern of methyl marks that are added to cytosine residues when they’re in CG [cytosine-guanine] dinucleotides,” explained Vic Myer, PhD, Chroma’s president and CSO. “When C and G sit next to each other, there’s an entire system in every cell that says, ‘hey, should we put a methyl mark here?’ If yes, the methyl mark is put there.”

That methyl mark, Myer said, can open or close chromatin to make genes accessible or inaccessible for transcription—the latter by preventing DNA-binding proteins from interacting with the DNA and driving transcription. “This is the signal to the cell or to the contents of the cell to say, ‘don’t go here or go here,’” Myer said. “It’s like a stop sign.”

Chroma’s approach contrasts with current genome editing technologies that indirectly regulate gene expression by cutting DNA, as a result activating DNA repair pathways and potentially producing immunogenic truncated or mutant proteins, both potentially generating unpredictable results.

A different tune

Chroma is one of several companies pursuing the exciting field of epigenetic editing. Epicrispr Biosciences (Epic Bio), a startup founded by CRISPR pioneer Stanley Qi, PhD, uses the smallest-known Cas protein, Cas12f, to deliver genetic therapies that act on the epigenome. Gene expression in vivo is modified by its Gene Expression Modulation System (GEMS) platform, designed to dial gene expression up or down without permanently altering the DNA.

Epic Bio completed a $55-million Series A financing in July 2022. Three months later, the company presented its first data supporting its “persistent and tunable” approach to gene activation. Qi is Epic’s scientific advisor as well as a founding associate editor of The CRISPR Journal (a sister publication of GEN Edge).

A different approach to developing therapies based on epigenetic genome editing has been shown by Tune Therapeutics, whose TEMPO platform is also designed to deliver graded, tunable, and reversible editing of specific genes that avoids the deletions and knockouts applied in earlier gene editing approaches.

TEMPO consists of two switchable elements. One is a DNA-binding domain that enables the platform to bind to a tightly targeted region of the genome by recognizing specific DNA sequences that lie around the target gene. The DNA-binding domain guides the protein to specific genomic target sites—enhancers, which act to enhance or increase gene activity, or repressors which act to decrease gene activity. At the sites, effectors work to alter local epigenetic marks to either restrict or improve the ability of a cell’s transcription machinery to access and read the gene.

Based in Durham, NC, and Seattle, Tune was co-founded by Charles Gersbach, PhD, director of Duke University’s Center for Advanced Genomic Technologies and the company’s acting CSO; Akira Matsuno, a veteran executive with cell and gene therapy developers who serves as Tune’s president and CFO; and Fyodor Urnov, PhD, scientific director, technology and translation with the Innovative Genomics Institute, who chairs Tune’s Scientific Advisory Board.

Tune launched in December 2021 with $40 million in financing co-led by New Enterprise Associates (NEA) and Emerson Collective, with Hatteras Venture Partners, Mission BioCapital, and other investors. (At deadline, a Tune Therapeutics spokesperson had not responded to GEN queries seeking additional information about the company.)

Up or down

While Chroma believes its platform can program genes to transcribe at varying speeds in addition to simply being “on” or “off,” that’s not an initial focus of the company.

“For our earliest set of programs, because we are learning the technology and developing the technology, we’re focusing on genes where there’s not really a limit to how much up or how much down we’d like to have. So, 100% down would be fine. A large overexpression would be fine,” Myer said.

“We’re not trying to thread the needle, if you will, for our first set of programs,” he added. “But as we add newer programs to our pipeline, we will be looking at circumstances where we’re trying to go slow.”

Because Chroma’s DNA methylation approach does not cut or nick the DNA, it avoids the risk of translocations and other naturally occurring events while enabling the company to focus on indications requiring multiplexing.

“When we go in and lay down methyl marks, we can actually do that at multiple genes simultaneously or frankly, at genes that are distributed broadly throughout the genome, without any worry of translocations,” Myer said. ”Where we really see the differentiation ultimately separating us from the pack, and then the differences versus the base editors or the cutters, are when we’re starting to get into modulating gene expression in multiple locations simultaneously. That’s where this is ultimately going to play a huge role.”

Private pipeline

Chroma has kept details about its pipeline under wraps, not disclosing what its lead candidates are or what therapeutic areas it is pursuing. Stehman-Breen said the company’s platform can develop therapies for diseases where delivery to cells has proven to be challenging.

“We’re focusing on diseases where we can deliver to the tissues effectively,” Stehman-Breen said. “The long arc of the company, though, is, we know that there’s a lot of diseases for which abnormalities in the epigenome play an important role in disease pathogenesis. As we learn more about the role of abnormalities in the epigenome and disease, we’re going to be extremely well positioned to be able to address those diseases.”

Chroma asserts that it has generated data that demonstrates the power and flexibility of the technology for a couple of its lead programs.

“Our primary goal to start with is to validate the platform, to demonstrate that this platform is highly effective,” Stehman-Breen said. “We’ve been able to generate some really exciting data since the company was formed that have demonstrated proof of concept, both in vitro and in vivo.” Those data, she and Myer said, will be presented later this year at upcoming conferences.

Chroma was established to commercialize discoveries of its scientific co-founders, who include many of the most prominent names in genome editing, including:

• Luke Gilbert, PhD—University of California, San Francisco
• J. Keith Joung, MD, PhD—Massachusetts General Hospital and Harvard Medical School
• David Liu, PhD—Harvard University and the Broad Institute
• Angelo Lombardo, PhD—the San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and San Raffaele University, Italy.
• Luigi Naldini, MD, PhD—SR-Tiget and San Raffaele University
• Jonathan Weissman, PhD—Whitehead Institute for Biomedical Research (MIT) and the Howard Hughes Medical Institute

On and off, hit and run

Chroma was formed to commercialize research published in 2020 by a 20-person research group led by Weissman and Gilbert. Their study, “Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing,” published in Cell and reported in GEN, detailed the development of a new gene editing technology called CRISPRoff, which was designed to control gene expression with high specificity, while leaving the sequence of the DNA unchanged.

CRISPRoff’s name comes from the silencing of methylated genes. Because the method does not alter the DNA sequence, researchers can reverse the silencing effect through the use of enzymes that remove the methyl groups, a method not unreasonably called CRISPRon.

“Transient expression of CRISPRoff writes a robust, specific, and multiplexable gene silencing program that is memorized by cells through cell division and differentiation, which can be rapidly reversed by CRISPRon,” Weissman, Gilbert, and colleagues observed. We show that CRISPRoff can specifically and robustly silence the large majority of human genes.”

That study built upon research published four years earlier by a team of seven researchers led by Lombardo and Naldini. In “Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing,” a 2016 study published in Cell, the Italian researchers detailed their development of an alternative gene silencing modality that exploits epigenetics to instruct inheritable repression at selected genomic sites of somatic cells. The investigators repurposed the silencing machinery of endogenous retroviruses in embryonic stem cells to silence three highly expressed genes (B2M, IFNAR1, and VEGFA) in somatic cells, using what they called a “hit-and-run” approach to delivering combinations of engineered transcriptional repressors (ETRs).

“The hit-and-run action of the ETRs, which plug into endogenous processes to stably maintain gene silencing without relying on targeted mutagenesis or random genomic insertion, also makes our strategy attractive for the development of biomedical applications,” Lombardo, Naldini, and colleagues concluded. “Epigenetic inactivation of regulatory sequences might be readily adopted in gene and cell therapy.”

For example, they said, silencing the erythroid-restricted enhancer of BCL11A could reawaken fetal globin expression in patients affected by β-thalassemia or sickle cell disease.

Lombardo and Naldini set out to commercialize that and other research into epigenetic-based genome edited therapies as co-founders of Epsilen Bio. Founded in 2019, Epsilen was created to develop transformative therapies for patients affected by serious medical conditions, through stable and long-lasting epigenetic silencing of genes involved in pathological processes. The company was formed with seed financing from the Sofinnova Telethon Fund, the largest fund in Italy dedicated to early-stage biotech startups, and through a strategic partnership with SR-Tiget, a joint institution between Fondazione Telethon and Ospedale San Raffaele.

Taking an interest

Among those taking an interest in Epsilen’s work were Stehman-Breen and Myer, who had joined Chroma soon after it was founded in 2020. (Myer was previously with Editas Medicine, the first CRISPR-editing biotech company to turn public.)

“A really nice component for us here was that the founders actually knew each other. Keith [Joung] and Angelo [Lombardo], the founders of Epsilen, knew the founders of Chroma,” Myer recalled. “When we started talking about this, the founders were super helpful in terms of, they’re great to work with. They’re great people. They’re doing great science, etc.

“It was very easy making the argument that we should combine forces and work together—all the way from the founders to the scientists to our investors,” Myer added.

Chroma acquired Epsilen in 2021, then closed on its initial $125 million in financing within a few days of each other. Epsilen continues to operate as a wholly owned subsidiary of Chroma, and conducts epigenetic editing R&D in Milan. The initial financing included $100 million in Series A capital following on earlier seed and pre-Series A money.

The Series B financing was led by GV (Google Ventures), with participation from additional new investors including ARCH Venture Partners, DCVC Bio, Mubadala Capital, Sixth Street—as well as all existing investors. The existing investors included Alexandria Venture Investments, Atlas Venture, Casdin Capital, Cormorant Asset Management, Janus Henderson Investors, Newpath Partners, Omega Funds, Osage University Partners, Sofinnova Partners, T Rowe Price, and Wellington Management.

Chroma has beefed up its brainpower recently, appointing Jeffrey D. Marrazzo, PhD, and George Golumbeski, PhD, to its board and naming John Maraganore, PhD, as a strategic advisor. Marrazzo co-founded Spark Therapeutics—acquired by Roche in 2019 for $4.8 billion—and served as Spark’s CEO until stepping down last year. Golumbeski is a former executive vice president of business development at Celgene, which was acquired by Bristol-Myers Squibb in 2019 for $74 billion.

Maraganore was the founding CEO of Alnylam Therapeutics until he stepped down at the end of 2021, and shares insights on the industry through his numerous positions as a strategic advisor, venture capital executive, and board member.

From its launch, Chroma has grown its workforce to just over 80 people based at its new lab space in Boston’s Fenway section overlooking Fenway Park, home of the Boston Red Sox. Chroma moved into its 40,000-square-foot space in November.

“This is going to be a big year for us,” Stehman-Breen said. “We’ve demonstrated some really nice data in mouse models and are anticipating presenting that data. Of course, that’s allowing us to continue to move into more relevant models.”

“Our intent is to move as quickly as we can to bring what we think is an incredibly exciting advancement to patients that we think would really value from this approach,” Stehman-Breen added.

The post Up or Down: Chroma Medicine Raises Stakes in Epigenetic Editing appeared first on GEN – Genetic Engineering and Biotechnology News.

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