Mosaic Chromosomal Alterations Drive Cancer Risk via Chromatin Topology Disruption and Inflammaging Feedback
Hypothesis
Mosaic chromosomal alterations (mCAs) drive age‑related cancer risk not only by altering gene dosage but by perturbing three‑dimensional chromatin architecture, leading to ectopic enhancer‑promoter contacts that increase transcriptional noise and inflammasome activation.
Mechanistic Model
- Structural destabilization – mCAs such as copy‑number‑neutral loss of heterozygosity (CN‑LOH) or focal gains create abrupt changes in chromatin fiber flexibility, altering topologically associating domain (TAD) boundaries.
- Enhancer hijacking – When a TAD boundary is lost, enhancers normally restricted to neighboring domains gain access to oncogenes (e.g., MYC on 8q) or tumor suppressors, producing stochastic bursts of transcription.
- Transcriptional noise → inflammaging – Increased expression variability triggers chronic low‑level NF‑κB signaling and inflammasome priming, creating a microenvironment that favors clonal expansion of mCAR‑positive cells.
- Feedback loop – Inflammatory cytokines (IL‑6, TNF‑α) exacerbate replication stress, further increasing mCA formation in hematopoietic stem cells (HSCs).
This model extends the observed dose‑response (≥10% mCA fraction → OR 1.61 for lung cancer) by proposing that the functional impact scales with the proportion of cells harboring architecturally disruptive mCAs, not merely their presence.
Testable Predictions
- Prediction 1: Single‑cell multi‑omics (scDNA‑seq + scATAC‑seq + scRNA‑seq) from aged donors will show that cells with mCAs exhibit increased chromatin accessibility at ectopic enhancer‑promoter loops and higher transcriptional variance of oncogenic pathways compared with mCA‑negative cells from the same individual.
- Prediction 2: Pharmacological reduction of NF‑κB signaling (e.g., using IKKβ inhibitors) will decrease the selective advantage of mCA‑positive HSCs in vitro, measured by reduced clonal expansion in competitive transplantation assays.
- Prediction 3: Inducing a defined CN‑LOH event on chromosome 13q in human HSCs using CRISPR‑mediated mitotic recombination will increase TAD boundary loss at the 13q14 locus, detectable by Hi‑C, and lead to elevated BCL2 expression noise.
Experimental Design
- Cohort: Obtain peripheral blood mononuclear cells from 30 donors aged >65 y, stratified by mCA burden (<5 %, 5‑10 %, >10 % as determined by DLP+ single‑cell CNV profiling) [6].
- Single‑cell multi‑omics: Perform simultaneous scDNA‑seq (for mCA detection), scATAC‑seq (chromatin accessibility), and scRNA‑seq on 5 k cells per donor. Compute ectopic loop scores using tools like Cicero and calculate gene expression variance (Fano factor) for oncogene sets.
- Statistical test: Linear mixed‑effects model linking mCA fraction to ectopic loop score and expression variance, adjusting for age, sex, smoking. Falsify if no significant association (p > 0.05).
- Intervention: Treat CD34⁺ HSCs from high‑mCA donors with an IKKβ inhibitor (e.g., BMS‑345541) or DMSO control for 7 days, then perform competitive repopulation assays in immunodeficient mice. Measure donor chimerism over 16 weeks.
- Expected outcome: Significant reduction in chimerism of mCA‑positive cells under IKKβ inhibition supports the inflammaging feedback loop; lack of effect refutes it.
- Engineered CN‑LOH: Use CRISPR‑Cas9 to create a tandem duplication that triggers mitotic recombination on 13q in healthy CD34⁺ cells, isolate clones, perform promoter‑capture Hi‑C to assess TAD integrity at 13q14, and quantify BCL2 allele‑specific expression noise via smFISH.
- Outcome: Engineered CN‑LOH clones showing increased ectopic contacts and BCL2 noise validate the architectural mechanism; absence of changes would challenge the model.
If predictions hold, mCA burden could be reframed as a modulator of chromatin topology, offering new intervention avenues (e.g., TAD‑boundary stabilizers or anti‑inflammatory therapies) to attenuate cancer risk in aging populations.
References