Caimano, M. | bioRxiv Science

bioRxiv2026

An IGF2-anchored oncofetal state and relapse-associated transcriptomic module define systemic progression risk in early-onset colorectal cancer

The epidemiological surge of early-onset colorectal cancer (EOCRC) is characterized by accelerated biological kinetics and disproportionately high rates of systemic relapse following curative-intent surgery. Because standard anatomical staging (TNM) lacks the resolution to accurately capture the intrinsic regenerative capacity of microscopic residual disease, we investigated the transcriptomic architecture of post-surgical failure in a strictly defined, curative-intent clinical pan-cohort. Unbiased transcriptomic profiling of the localized (M0) discovery sub-cohort identified IGF2 as the most significantly upregulated correlate of metachronous relapse. High-resolution isoform analysis revealed that this transcriptional output is predominantly driven by the embryonic (P4) and placental (P5) promoters. Systematic allele-specific expression (ASE) analysis supported widespread biallelic IGF2 expression consistent with relaxation of imprinting-domain control. This signal was not restricted to relapsing tumors, suggesting a recurrence-independent oncofetal baseline across the EOCRC spectrum. Because this foundational epigenetic unlocking is functionally insufficient on its own to execute systemic metastasis, we distilled the additional transcriptional plasticity required for dissemination into an internally derived and bootstrap-stabilized 5-gene recurrence-risk module Multivariable analysis across the combined pan-cohort supported an independent association between the high-risk module and systemic relapse (p < 0.001), capturing prognostic dimensions completely unresolved by classical pathological covariates and baseline staging. Ultimately, our findings reframe EOCRC aggressiveness as the product of a dual-hit architecture. This framework resolves the clinical paradox of widespread IGF2 LOI co-existing with heterogeneous outcomes, offering a biologically grounded basis for molecular risk stratification beyond anatomical boundaries.

cancer biology↗

bioRxiv2019

Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and - independent phagosomal signals that contribute to phagocytosis and inflammation

Lyme disease is a tick-borne illness caused by the spirochete Borrelia burgdorferi (Bb). It is believed that the robust inflammatory response induced by the hosts innate immune system is responsible for the clinical manifestations associated with Bb infection. The macrophage plays a central role in the immune response to many bacterial infections and is thought to play a central role in activation of the innate immune response to Bb. Previous studies have shown that following phagocytosis of spirochetes by macrophages, phagosome maturation results in degradation of Bb and liberation of bacterial lipoproteins and nucleic acids, which are recognized by TLR2 and TLR8, respectively, and elicit MyD88-mediated phagosome signaling cascades. Bone marrow-derived macrophages (BMDMs) from MyD88-/- mice show significantly reduced spirochete uptake and inflammatory cytokine production when incubated with Bb ex vivo. Paradoxically, additional studies revealed that Bb-infected MyD88-/- mice exhibit inflammation in joint and heart tissues. To determine the contribution of MyD88 to macrophage-mediated spirochete clearance, we compared wildtype (WT) and MyD88-/- mice using a murine model of Lyme disease. MyD88-/- mice showed increased Bb burdens in hearts 28 days post infection, while H&E staining and immunohistochemistry showed significantly increased inflammation and greater macrophage infiltrate in the hearts of MyD88-/- mice. This suggests that Bb triggers MyD88-independent inflammatory pathways in macrophages to facilitate cell recruitment to tissues. Upon stimulation with Bb ex vivo, WT and MyD88-/- BMDMs exhibit significant differences in bacteria uptake, suggesting that MyD88 signaling mediates cytoskeleton remodeling and the formation of membrane protrusions to enhance bacteria phagocytosis. A comprehensive transcriptome comparison in Bb-infected WT and MyD88-/- BMDMs identified a large cohort of MyD88-dependent genes that are differentially expressed in response to Bb, including genes involved in actin and cytoskeleton organization (Daam1, Fmnl1). We also identified a cohort of differentially-expressed MyD88-independent chemokines (Cxcl2, Ccl9) known to recruit macrophages. We identified master regulators and generated networks which model potential signaling pathways that mediate both phagocytosis and the inflammatory response. These data provide strong evidence that MyD88-dependent and -independent phagosomal signaling cascades in macrophages play significant roles in the ability of these cells to phagocytose Bb and mediate infection.\n\nAUTHOR SUMMARYMacrophages play prominent roles in bacteria recognition and clearance, including Borrelia burgdorferi (Bb), the Lyme disease spirochete. To elucidate mechanisms by which MyD88/TLR signaling enhances clearance of Bb by macrophages, we studied Bb-infected wildtype (WT) and MyD88-/- mice and Bb-stimulated bone marrow-derived macrophages (BMDMs). Bb-infected MyD88-/- mice show increased bacterial burdens, macrophage infiltration and altered gene expression in inflamed heart tissue. MyD88-/- BMDMs exhibit impaired uptake of spirochetes but comparable maturation of phagosomes following internalization of spirochetes. RNA-sequencing of infected WT and MyD88-/- BMDMs identified a large cohort of differentially expressed MyD88-dependent genes involved in re-organization of actin and cytoskeleton during phagocytosis along with several MyD88-independent chemokines involved in inflammatory cell recruitment. We computationally generated networks which identified several MyD88-independent master regulators (Cxcl2 and Vcam1) and MyD88-dependent intermediate proteins (Rhoq and Cyfip1) that are known to mediate inflammation and phagocytosis respectively. These results provide mechanistic insights into MyD88-mediated phagosomal signaling enhancing Bb uptake and clearance.

immunology↗