CHICAGO—Inherited autoinflammatory and autoimmune diseases often display striking variability, even among family members with the same genetic mutation. This phenomenon, known as incomplete penetrance, has long intrigued researchers. At ACR Convergence 2025, in the session Old Dog, New Tricks: Regulation of Autoinflammation and Autoimmunity Informed by Inborn Errors of Immunity, Dusan Bogunovic, PhD, explored an emerging explanation: monoallelic expression (MAE). Drawing on his groundbreaking research as professor of pediatric immunology and director of the Center for Genetic Errors of Immunity at Columbia University, New York, Dr. Bogunovic described how MAE may shape the variable expression of autoimmune and autoinflammatory phenotypes.
Genetic Underpinnings of Disease
Dusan Bogunovic, PhD, Columbia University Medical Center
Dr. Bogunovic began by defining inborn errors of immunity (IEI) as genetic disorders that predispose to susceptibility to infections, autoinflammation, autoimmunity, allergy and malignancy. “Canonically, we used to think of them [inborn errors of immunity] as primary immunodeficiencies,” he said, but they are also capable of immune dysregulation. Therefore, patients with IEI may present to rheumatology clinics with various autoimmune and autoinflammatory phenotypes.
He recalled the most famous case of immunodeficiency, known to many as the “boy in the bubble.” The patient had severe combined immunodeficiency (SCID) and, effectively, no functioning immune system. The discovery of SCID was made in the 1960s, and since then, more than 600 unique, monogenic IEIs have been identified, accelerated by the advent of next-generation sequencing. Although these IEIs are thought of as rare, the collective group of monogenic diseases affects one in 800–1,000 people.
Dr. Bogunovic described forward genetics, the conventional pathway by which a new IEI is identified: a patient presents with a unique phenotype suspected of being monogenic, undergoes genetic sequencing and if a single causal mutation is identified, a new IEI is found. In the ideal situation, precision medicine facilitates development of a novel therapy directed to this single mutation.
He stated, however, that “medicine is complicated; it’s never linear and as dreamy as you want it to be.” This complexity is in part, due to incomplete penetrance, which means that a patient with a genetic variant does not manifest the disease clinically. Some patients carrying a mutation may have a partial phenotype or partial disease expressivity. Likewise, a sibling could carry the mutation without a single disease manifestation. Dr. Bogunovic highlighted that very few examples exist in the field of IEI that have 100% penetrance, such that all carriers of the mutation manifest the disease.
He acknowledged that ascertainment and reporting bias likely play a role because patients without disease manifestation won’t come to attention, thus he suspects this phenomenon is significantly under-identified.
Introducing Monoallelic Expression
Dr. Bogunovic noted several mechanisms by which genes are not expressed from both alleles—genomic imprinting, X-inactivation, transcriptional bursting and the focus of this talk, monoallelic expression.
To explain MAE, he explained that all cells have a paternal and maternal allele, meaning genetically they are heterozygous. However, somewhere during development, the cell commits to propagation of either the maternal or paternal allele. This commitment is stable through mitosis and only expressed in a single cell type, such as T cells. Merging the concepts of MAE and incomplete penetrance, he demonstrated a pedigree whereby a mother, father and son all carried a mutation. The son had fully penetrant disease, the father had partial expressivity and the mother did not express disease. The healthy mother dominantly expressed the healthy allele, and the father skewed toward mutant expression.
Dr. Bogunovic explained that the origin of this concept came from studying a patient from New York with immune dysregulation, found to have a de novo mutation in Janus kinase 1 (JAK1), which is downstream to more than 25 different cytokines. Single-cell RNA sequencing on JAK1 surprisingly found that 50% of cells only expressed the mutant allele and not the wild-type allele. This deviated from the traditional dogma that JAK1 should be fully expressed in a biallelic pattern. These findings led to the hypothesis that monoallelic expression can lead to phenotypic variability in IEIs.
Excited by this possibility, Dr. Bogunovic and his team decided to take peripheral blood mononuclear cells (PBMCs) from 10 healthy donors in New York, sorted the cells into T cells, made large populations of T cell clones and validated a mechanism to determine if allelic bias was somatically acquired and stable. Using this clonal population, the team found evidence of MAE in IEI genes (e.g., JAK1, STAT1, NFKB1) even in healthy individuals. They found that about 5% of all genes and about 4% of IEI genes undergo MAE.
To validate their findings, the team examined JAK1 MAE via digital droplet polymerase chain reaction (PCR) for six different clones, as well as for a heterozygous variant in PLCG2 from one of the ten donors, repeating what they saw in RNA sequencing. Importantly, they found that PLCG2 MAE is stable in clones cultured over weeks.
Dr. Bogunovic and his team then asked, why is this happening and what is the underlying mechanism? They performed digital droplet PCR using a reference allele (PLCG2) expressed in a monoallelic pattern. By introducing JMJD1 short non-coding RNA, which perturbs H3K27 trimethylation, they produced a biallelic clone. Likewise, using a biallelic PLCG2 clone, they were able to promote monoallelic expression by manipulating DNA methylation. Dr. Bogunovic explained that these results are somewhat misleading in that they have not fully elucidated the mechanism of MAE. For unexplained reasons, even in the same individual, some clones did not respond to the above perturbations, although others did, suggesting multiple mechanisms are involved in regulation of MAE.
MAE as a Driver of Clinical Phenotypes
Dr. Bogunovic returned to the patient from New York with the mutation in JAK1 that inspired this work. His laboratory colleague Conor Gruber, MD, PhD, was able to demonstrate that JAK1 was a gain-of-function mutation, with downstream signaling even in the absence of cytokines. Given that this particular patient had a de novo mutation, they could use this case to test for incomplete penetrance; however, they have since discovered hundreds of JAK1 gain-of-function patients, including some with incomplete penetrance.
To this point, he highlighted the pedigree of another family with gain of function mutations in JAK1. The grandfather was an asymptomatic carrier of the mutation, and the mother—the index case—was a 34-year-old woman who had been healthy until a toxoplasmosis infection at age 28. She then developed common variable immune deficiency (CVID), hyper IgM syndrome, splenomegaly and pancytopenia. This patient has a daughter who was a carrier of the variant, but also completely healthy. His team took PBMCs from the daughter and the mother and used digital droplet PCR to look for allelic bias.
They found the healthy carrier—the daughter—only had 22% of the mutant allele expressed, and the affected carrier—the mother—expressed 36% of the mutant allele. They sorted PBMCs into cell types and noted a propensity to suppress the gain of function allele, except in maternal T cells. “This was really the first example, telling us that monoallelic expression or expressional bias in heterozygous disease correlates well with disease penetrance,” Dr. Bogunovic said.
Dr. Bogunovic and his team wondered how widespread this mechanism was. Is it common? They then looked to PLCG2 mutations in a large family pedigree. They examined two cousins—patient A and patient B—with normal and low IgG production, respectively. Dr. Bogunovic wondered if monoallelic expression might be at play.
To explore this further, they isolated B cells from the cousins carrying the mutation, as well as healthy controls, then sorted B cells based on calcium flux, a functional outcome measure. They found that the B cells with negative calcium flux were only expressing the mutant allele, and the cousin with normal IgG levels expressed both alleles. This was the second example of monoallelic expression correlating with phenotypic output.
In Sum
Monoallelic expression occurs naturally in all humans and explains some instances of incomplete penetrance in inborn errors of immunity. Why this occurs remains an unanswered question; however, Dr. Bogunovic closed by framing MAE in the broader context of human evolution: genes deemed bad get kicked out, and those that are good are passed down over generations. MAE, he proposed, allows for a form of personal evolution, allowing genetic flexibility and tonality to the genome.
Dr. Bogunovic speculated that patients with rheumatic disease may have skewed biallelic expression during an active disease flare—a question that his laboratory continues to investigate. He also highlighted the invaluable contributions of his colleagues, including Conor Gruber, O’Jay Stewart and Haley Randolph, PhD, whose work was instrumental in advancing their research.
Michael Cammarata, MD, RhMSUS, is an assistant professor of medicine at the Johns Hopkins University School of Medicine in Baltimore.