Research

First responders to the World Trade Center attacks carry elevated rates of premalignant and malignant blood cells, decades after the collapse. That fact is established. What it has not yet told us is how — which mutational processes a complex environmental exposure actually leaves behind in the blood, and why they land where they do.

Rutgers hosts a World Trade Center Health Program Clinical Center of Excellence, so the population this research concerns is one our own institution monitors and treats.

Our retrospective study of this cohort points toward somatic hypermutation at genes associated with clonal hematopoiesis. In clonal hematopoiesis, somatic mutations at a defined set of loci give hematopoietic stem cells a fitness advantage and allow them to expand clonally. It is not always harmful, but it is a recognized precursor state for leukemia, and because differentiated blood cells circulate throughout the body, it also carries elevated cardiovascular risk.

These mutations recur at a strikingly small number of loci — DNMT3A, TET2, ASXL1, JAK2, PPM1D, SF3B1 — and are thought to accumulate in response to endogenous and exogenous stress across a lifetime. What remains unexplained is why these particular loci. Why does a diffuse, whole-body exposure converge on the same few regions, in the same cell type, again and again? The recurrence is usually treated as a given rather than as something requiring explanation.

Beyond clonal hematopoiesis itself, the answer may help explain why individuals with genome instability disorders such as Fanconi anemia are predisposed to blood cancers.

A virus enters a cell and, rather than killing it, settles in and alters it — its replication, its chromatin, its capacity to repair damage. This project concerns the mechanics of that persistence, and it begins with the virus that does it most aggressively.

Human T-cell lymphotropic virus type 1 integrates its genome into the host’s and commandeers the cell’s machinery from within, and the adult T-cell leukemia that follows carries a heavy burden of somatic mutation alongside sweeping transcriptional and epigenetic change. We are working out where the virus inserts, including at fragile sites and other disease-defining loci, how integration reorganizes topologically associating domains and how that destabilizes the host genome.

Our hypothesis is that integration sites are hotspots of replication stress — that a virus lands where the genome is already difficult to copy. We are testing whether integrated viral DNA then stays put or remodels, expanding into tandem arrays or breaking away as extrachromosomal DNA, and which host DNA repair pathways decide between those outcomes. Which mechanism engages at an integration site may determine whether the virus is contained or becomes a persistent driver of instability — a question human papillomavirus, which takes the same approach, gives us a second system to ask in.

Not every virus integrates. Earlier work in the lab centered on Kaposi’s sarcoma-associated herpesvirus, which during latency persists as an episome. By visualizing viral DNA replication directly in host cells, we identified a way to break that latency: blocking replication of the viral genome itself.

Replication forks stall constantly, at lesions and at sequences the polymerase cannot easily read through. Getting past these obstacles requires a handoff: translesion synthesis polymerase η takes over from the replicative polymerase, working alongside the Fanconi anemia pathway protein FANCD2. We are mapping how that handoff is coordinated, and what happens when it isn’t.

Using single-molecule analysis of replicated DNA, we follow replication through fragile sites and repeat structures at the exact loci where the handoff fails. The consequences are visible and severe: chromosomal breaks, micronuclei, the kind of instability that seeds tumors. This work has a direct clinical edge, because translesion synthesis is how tumor cells survive the DNA damage that chemotherapy is designed to inflict, making it one of the main routes to chemoresistance.

The same question extends to proteins not previously thought to have any role in replication. PHF6 is the most frequently mutated gene in pediatric T-cell acute lymphoblastic leukemia, altered in roughly 16% of cases. It is classified as a tumor suppressor and known to work with the NuRD complex, UBF1 and PAF1 to influence chromatin accessibility, ribosome biogenesis and transcription. Those functions do not account for what actually happens when PHF6 is lost: profound genomic instability, disrupted proliferation, G2/M arrest.