PRKDC, formally known as the protein kinase, DNA-activated, catalytic polypeptide, encodes the catalytic subunit of the DNA-dependent protein kinase, a molecular machine central to non-homologous end joining, the cellular pathway that stitches double-strand DNA breaks back together. Because of this role, PRKDC has traditionally been studied in the context of genome stability, radiation sensitivity, and lymphocyte development. Yet accumulating evidence has implicated PRKDC in tumor progression across several cancer types, and the new study set out to determine whether the gene also shapes the tumor microenvironment in hepatocellular carcinoma, where tumor-associated macrophages are abundant and tend to adopt an immunosuppressive phenotype.

To test this, the researchers engineered mouse Hepa1-6 liver cancer cells that overexpressed PRKDC and implanted them into mice using both subcutaneous and orthotopic models, the latter recreating tumors within the liver itself. The results were clear: PRKDC overexpression enhanced malignant behaviors in vitro, including proliferation and other hallmarks of aggressive cancer, and accelerated tumor growth in vivo. This established PRKDC not merely as a passive correlate of tumor aggressiveness but as a driver of malignant phenotypes in hepatocellular carcinoma.

The next question was how a DNA repair kinase could exert such broad influence over tumor behavior. Using Olink proteomics, RNA sequencing, quantitative PCR, ELISA, and immunohistochemistry, the team found that PRKDC upregulated CSF1, also known as colony-stimulating factor 1, a secreted cytokine that acts as a key growth and differentiation factor for macrophages. Database analyses further supported CSF1R, the CSF1 receptor, as the primary receptor through which CSF1 signals, and single-cell analysis showed that CSF1R was enriched specifically in tumor-associated macrophages within the tumor microenvironment.

This finding reframed the biology of the tumor microenvironment in hepatocellular carcinoma. Rather than acting solely through intrinsic cancer cell pathways, PRKDC appeared to function as a signaling hub that recruits and reprograms immune cells. By secreting CSF1, PRKDC-overexpressing tumor cells could engage CSF1R on macrophages, nudging them toward an M2-like polarization state. M2 macrophages are known for promoting tissue repair and wound healing, but in the context of cancer they suppress antitumor immunity, support angiogenesis, and facilitate metastasis, making them one of the most treacherous components of the tumor microenvironment.

To validate this mechanism, the researchers performed CSF1R knockdown in mouse RAW264.7 macrophages, which reduced the expression of M2 markers induced by IL-4, a cytokine that normally drives M2 polarization. This demonstrated that CSF1R signaling is required for the M2 program in these macrophages. Immunohistochemistry, co-culture experiments, and flow cytometry then showed increased expression of M2-like tumor-associated macrophage markers in tumors overexpressing PRKDC, confirming that the PRKDC-CSF1 axis reshapes macrophage identity within the tumor microenvironment in living systems, not just in isolated cells.

Perhaps the most striking finding came from macrophage phagocytosis assays. Macrophages are professional phagocytes, capable of engulfing and digesting abnormal cells, including cancer cells that display eat-me signals. The study found that PRKDC-mediated CSF1 upregulation was associated with increased resistance of hepatocellular carcinoma cells to macrophage phagocytosis. In other words, by pushing macrophages toward an M2-like state, PRKDC-overexpressing tumor cells effectively disarmed the very immune cells that should be eliminating them, converting macrophages from attackers into supporters of tumor growth.

Collectively, the study proposes a coherent model: PRKDC promotes hepatocellular carcinoma progression by upregulating CSF1, activating the CSF1/CSF1R pathway, and inducing M2-like polarization of tumor-associated macrophages, thereby impairing phagocytosis and contributing to immune evasion. This PRKDC-CSF1/CSF1R-tumor-associated macrophage axis may represent a potential therapeutic target in hepatocellular carcinoma, a disease where immune checkpoint inhibitors have shown benefit but where many patients still fail to respond, partly because of the immunosuppressive tumor microenvironment.

The findings carry particular weight because hepatocellular carcinoma is highly lethal and immune evasion is a major barrier to treatment efficacy. Tumor-associated macrophages are abundant in hepatocellular carcinoma and tend to polarize toward an M2-like phenotype, contributing to immune evasion and limiting the impact of immunotherapy. By identifying PRKDC as an upstream regulator of this process, the study adds a new layer to the understanding of how liver tumors manipulate their surroundings and suggests that targeting the PRKDC-CSF1/CSF1R pathway could complement existing immunotherapeutic strategies.

While the research was conducted in mouse models and cell lines, and further work will be needed to confirm the mechanism in human tumors and patients, the study offers a compelling example of how a gene with a well-established role in DNA repair can moonlight as a regulator of immune privilege in cancer. As the field of tumor immunology continues to uncover the complex crosstalk between cancer cells and their microenvironment, studies like this one highlight the importance of looking beyond intrinsic cancer cell pathways to understand how tumors co-opt the immune system for their own survival.

Subject of Research: PRKDC orchestrates immune evasion in hepatocellular carcinoma through CSF1/CSF1R-mediated M2 macrophage polarization

Article Title: PRKDC orchestrates immune evasion in hepatocellular carcinoma through CSF1/CSF1R-mediated M2 macrophage polarization

Article References: Wang, Y., Pang, W., Lu, X., Wu, H., Li, M., Pan, M., Tan, J., He, J., Luo, Y., Lin, H., Li, M., & Yu, Y. (2026). PRKDC orchestrates immune evasion in hepatocellular carcinoma through CSF1/CSF1R-mediated M2 macrophage polarization. Cancer Immunology, Immunotherapy. https://doi.org/10.1007/s00262-026-04600-y

Image Credits: AI Generated

DOI: 10.1007/s00262-026-04600-y

Keywords: hepatocellular carcinoma, PRKDC, CSF1, CSF1R, macrophage polarization, tumor microenvironment, immune evasion, phagocytosis, liver cancer, cancer immunology, orchestrates, immune

The case against conventional rodent models is now starkly quantitative. According to the review, approximately 41 percent of putative Alzheimer’s disease risk genes lack direct mouse orthologues, and even when a murine counterpart exists, protein sequence identity frequently falls below 60 percent. The APOE ε4 polymorphism, the single largest genetic risk factor for sporadic Alzheimer’s disease, is entirely absent in rodents, while genes such as CR1, CD33, TREM2 and members of the MS4A cluster either have multiple orthologues or poor sequence conservation. Human microglia also display greater transcriptional heterogeneity than their murine equivalents, expressing disease risk genes that are poorly conserved across species. For a disease field built on polygenic architecture, these discrepancies mean that findings in mice often cannot be translated to human biology, no matter how elegant the experiment.

The second problem is environmental. Microglia arise during early embryogenesis from yolk-sac-derived erythromyeloid progenitors and persist as a self-renewing population governed by CSF1R signalling and transcription factors such as PU.1 and IRF8. In the healthy brain they maintain homeostatic functions including complement-mediated synaptic pruning, apoptotic-cell clearance and support of oligodendrocyte maturation through IGF1 secretion, underpinned by signature genes like P2RY12, TMEM119 and CX3CR1. But when microglia are isolated from brain tissue and placed in standard culture dishes, thousands of genes change their expression. Cultured cells abandon their homeostatic surveillance programme and instead upregulate inflammatory cytokines such as IL1B, CXCL8 and CCL20, chemokine receptors, antigen presentation factors and NADPH oxidase components. In effect, removing a microglial cell from the brain pushes it into a chronic activation state that bears little resemblance to its in vivo identity, contaminating nearly every experiment performed on isolated cells.

The solution begins with human pluripotent stem cells, which can be steered into microglia through two complementary methodologies. Cytokine-based differentiation recapitulates embryonic ontogeny, sequentially exposing cells to morphogens such as BMP4, VEGF and stem-cell factor to generate primitive myeloid precursors, followed by terminal survival factors including TGFβ, M-CSF and IL-34. Modern iterations use chemically defined, serum-free conditions and even hypoxic incubation to mimic the oxygen environment of the developing embryonic niche, eliminating the need for manual sorting and feeder layers while improving reproducibility and scalability. Because these protocols mimic natural development, they yield cells whose homeostatic profiles align closely with primary human microglia, making them robust models for developmental and neuroimmune studies.

The alternative approach trades developmental fidelity for speed. Direct lineage conversion uses forced expression of transcription factor cocktails, including PU.1, CEBPα, CEBPβ, IRF5, IRF8 and either MAFB or FLI1, to activate the microglial transcriptional network within days rather than weeks. Recent protocols have integrated these factor cassettes into genomic safe harbour loci such as AAVS1 and CLYBL, ensuring stable, uniform expression without random viral integration. The rapid induction kinetics and homogeneity of this strategy make it particularly well suited to pooled CRISPR screening, allowing researchers to systematically identify regulators of microglial disease states and validate polygenic risk variants at scale. High-resolution mapping of stage-specific regulatory networks, in which persistent core regulators like PU.1 act alongside fetal-state drivers and late-stage IRF, KLF and STAT families, now offers a conceptual route to overcoming the fetal-like limitations that currently constrain both approaches.

Whatever their origin, isolated microglia drift without company, so the field has progressively rebuilt the brain’s cellular ecosystem around them. Two-dimensional co-cultures and tri-cultures combining hPSC-derived neurons, astrocytes and microglia have already yielded fundamental insights: astrocytes sustain microglial survival by secreting CSF1, microfluidic devices reveal microglial migration toward amyloid-β and phosphorylated tau aggregates, and acute exposure to familial Alzheimer’s neurons suppresses the disease-associated microglial signatures otherwise induced by astrocytes. Yet monolayer systems impose artificial planar interactions and fail to reproduce the brain’s viscoelastic extracellular matrix, capping the physiological maturity the cells can achieve.

Three-dimensional brain organoids have pushed the modelling considerably further. When microglial progenitors are embedded within a neuroectodermal matrix containing diverse neural progenitors and glia, either by exogenous addition or by endogenous co-differentiation through targeted PU.1 overexpression, single-cell transcriptomics shows that the resulting cells preserve homeostatic states far better than in planar culture. The relationship is reciprocal: integrated microglia attenuate IRF gene expression and reduce stress markers such as double-stranded DNA breaks in radial glia, modulating the developmental trajectories of their neural neighbours. One striking mechanism involves lipid crosstalk, in which organoid-integrated microglia accumulate PLIN2-positive lipid droplets and export cholesterol that neural progenitor cells then take up, triggering metabolic reprogramming that limits excessive proliferation while promoting axonogenesis and neuronal maturation. In neurodegenerative contexts, microglia within organoids protect neural circuits from amyloid-β toxicity by mitigating ferroptosis, and these systems now support pooled CRISPR interference screening in situ. Multi-regional assembloids extend the paradigm further, showing that microglia adopt niche-specific identities, such as GABA(B) receptor enrichment in striatal regions, and that autism-associated SCN2A mutations trigger GABA(B) receptor-dependent microglial pruning of inhibitory synapses, a pathology reversible by targeted receptor inhibition.

Even organoids cannot fully reconstruct the intact central nervous system, which is why the review’s most consequential section concerns xenotransplantation. Human microglial progenitors can be injected into the brains of immunodeficient mice engineered to express human CSF1, since murine CSF1 binds poorly to the human receptor. Pre-treating neonates with a CSF1R inhibitor creates a permissive niche, and human cells come to constitute roughly 30 percent of all microglia within three weeks, expanding to 80 percent chimerism over three to six months as they outcompete residual murine cells. Within the mouse brain, the transplanted human cells transform: they restore canonical homeostatic genes including TMEM119, P2RY12, CX3CR1 and CSF1R, downregulate artefactually elevated activation markers such as SPP1, CTSB, CD9 and GPNMB, and acquire ramified morphology and surveillance motility matching endogenous cells. A newer refinement engineers a G795A point mutation into CSF1R, rendering the human cells resistant to pharmacological depletion and enabling near-complete replacement of the murine microglial compartment across the entire brain.

The disease applications of these chimeras are already substantial. In an Alzheimer’s model, xenografted human microglia adopt five distinct transcriptional programmes, including homeostatic, disease-associated, HLA antigen-presenting, cytokine-responsive and interferon-responsive states. In a frontotemporal dementia model driven by progranulin deficiency, wild-type human microglia restore progranulin levels, reduce lipofuscinosis and rescue thalamic circuit hyperexcitability and social behaviour deficits. In C9orf72-associated amyotrophic lateral sclerosis chimeras, hexanucleotide repeat expansions impair the microglial transition to disease-associated states and induce endolysosomal dysfunction. Chimeric platforms incorporating human neurons alongside human microglia reveal that autism-related neuronal defects drive abnormal microglial states in a cell-non-autonomous manner, while patient-derived microglia in Down syndrome models show aberrant synaptic pruning. Most strikingly for translational medicine, the FDA-approved antibody lecanemab significantly reduced amyloid plaques in chimeric mice only through Fc-mediated activation of human microglia, with Fc deletion abolishing the effect, a mechanism invisible in conventional mice because the antibody lacks cross-reactivity with murine targets.

Significant challenges remain before these platforms reach their full potential. Current protocols yield microglia retaining fetal or early postnatal signatures, necessitating epigenetic ageing or senescence induction to capture the dystrophic, lipid-accumulating phenotypes that drive late-onset neurodegeneration. Organoid systems suffer from batch variability, inconsistent microglial distribution and survival losses during extended culture, while immunodeficient hosts preclude analysis of adaptive immune contributions to neurodegeneration. The rodent brain may also impose species-specific constraints on human microglial behaviour. Nevertheless, the trajectory is clear: monolayer cultures provide the tractability for genome-wide screening, organoids restore the neuroglial crosstalk that reverses transcriptomic drift, and chimeric models serve as a translational bridge embedding human cells in living systems with systemic circulation and progressive ageing. Together they form a continuous pipeline from high-throughput discovery to in vivo preclinical validation, one that Lee and Yoo argue will ultimately guide clinical trial design and biomarker discovery for neuroinflammation, and bring precision therapies for microglia-driven neurological diseases within realistic reach.

Subject of Research: Human pluripotent stem cell-based modelling of microglia for neurological disease research

Article Title: Translational modelling of human microglia from cultures to chimeras

Article References: Lee, J., & Yoo, Y. (2026). Translational modelling of human microglia from cultures to chimeras. Experimental & Molecular Medicine. https://doi.org/10.1038/s12276-026-01866-1

Image Credits: AI Generated

DOI: 10.1038/s12276-026-01866-1

Keywords: microglia, human pluripotent stem cells, brain organoids, xenotransplantation, Alzheimer's disease, neuroinflammation, CRISPR screening, chimeric mouse models, CSF1R, neurodegeneration, synaptic pruning, disease-associated microglia

The research team, led by Professor Wang Chuanxin of Shandong University, tackled the problem with a dual-technology strategy that has become the gold standard for dissecting complex tissues: single-cell RNA sequencing to resolve the identities and states of individual cells, combined with spatial transcriptomics to preserve the crucial information that conventional dissociation destroys — where each cell sits relative to its neighbors. Applying this integrative approach to human tissue samples spanning the disease trajectory from non-atrophic gastritis through atrophic gastritis to early gastric cancer, the investigators constructed a spatially resolved transcriptional atlas of gastric carcinogenesis at its most biologically ambiguous stage.

The central finding is conceptually striking. Early gastric cancer, the team demonstrates, arises from an inflammation-driven, highly coordinated microenvironmental state that they term the inflammation-associated spatial niche. This is not merely inflamed tissue; it is a structured ecological unit in which three features converge in the same physical location. First, epithelial cells within the niche selectively maintain stem-like transcriptional programs, retaining a developmental plasticity that most differentiated gastric epithelium has surrendered. Second, the niche emits enhanced inflammatory chemotactic signaling, continuously recruiting immune cells from the surrounding microvasculature. Third, the recruited immune landscape is skewed, with immunosuppressive cell populations becoming regionally enriched precisely where the pre-malignant epithelium resides.

This spatial colocalization is the key insight. Stemness, chemoattraction, and immune evasion are often studied as separate hallmarks of cancer, each with its own literature and its own molecular candidates. The new data show that in early gastric tumorigenesis these programs are not parallel events happening in the same place by coincidence; they are mutually reinforcing components of a single niche. The epithelial cells secrete inflammatory chemokines that draw in myeloid cells, and the resulting immune milieu in turn supports the epithelium’s undifferentiated state. The niche behaves as a self-sustaining engine, and its physical integrity — the precise adjacency of its cellular components — appears to be a prerequisite for malignant progression.

Mechanistically, the study identifies the SOX9-CXCL axis as the regulatory module that knits the niche together. SOX9, a transcription factor best known for its roles in development and stem cell maintenance, emerges here as a downstream effector of the inflammatory niche within the epithelial compartment. Its activity is linked to the expression of CXCL-family chemokines, which are the ligands for CXCR2-bearing receptors on myeloid cells. In practical terms, the axis converts epithelial stemness into a recruitment signal: the more the pre-malignant epithelium holds onto its stem-like identity, the more strongly it summons macrophages and other myeloid cells, and the more the local immune environment is remodeled toward a tumor-permissive configuration. This provides a concrete molecular bridge between two phenomena — epithelial plasticity and immune microenvironment reshaping — that have historically been investigated in isolation.

The therapeutic implications follow directly from the mechanism. Because the niche depends on chemokine-mediated recruitment and on macrophage survival and polarization signals, the team tested whether dismantling those dependencies could collapse the niche. Their experiments indicate that concurrent targeting of the CXCR2-mediated chemokine signaling pathway and the CSF1R-mediated macrophage pathway effectively disrupts the structural integrity of the inflammatory niche, and that this dual intervention significantly suppresses early gastric cancer progression. The logic is elegant: CXCR2 blockade cuts the recruitment lines that keep the niche stocked with pro-tumor myeloid cells, while CSF1R inhibition undermines the differentiation and maintenance of the macrophages already embedded in the tissue. Neither pathway alone achieves what the combination does, mirroring a principle well established in oncology — that microenvironmental dependencies are most effectively broken in parallel.

For clinicians, the work offers a reframing of risk. Current surveillance of patients with atrophic gastritis and intestinal metaplasia relies largely on histological grading and endoscopic detection of visible lesions, an approach that can miss the spatial cues that precede overt neoplasia. If the inflammation-associated spatial niche can be identified — through spatially resolved biomarkers, molecular imaging, or targeted biopsy strategies — it could serve as an earlier and more precise indicator of which regions of the stomach are genuinely committed to malignant transformation. Risk stratification would shift from asking whether a patient has metaplasia to asking where, within the mucosa, the coordinated niche state has taken hold. The study’s authors position this as a novel framework for early gastric cancer risk stratification and intervention, one that targets the niche rather than isolated tumor cell populations.

Conceptually, the paper contributes to a broader movement in cancer research away from reductionism. The dominant paradigm of the past two decades has been cell-autonomous: identify the driver mutation, the clonal expansion, the checkpoint escape. That framework has produced extraordinary therapies, but it struggles with cancers like gastric carcinoma, which arise on a foundation of chronic inflammation and evolve within a densely social tissue environment. By elevating the spatial niche to the status of a fundamental regulatory unit — a unit with its own composition, signaling logic, and vulnerability — the study aligns gastric carcinogenesis with ecological and evolutionary models of cancer in which the microenvironment is not a passive backdrop but an active participant in initiation. The methodological corollary is equally important: without spatial transcriptomics, the colocalization of stemness, chemotaxis, and immunosuppression would have been invisible, averaged away in bulk sequencing or decontextualized in single-cell suspensions.

The translational horizon extends beyond treatment into prevention. Chronic Helicobacter-associated inflammation affects enormous populations worldwide, yet only a minority progress to cancer, and predicting which patients will do so remains imprecise. A niche-based model suggests that the decisive variable may be the emergence of this coordinated spatial state, potentially detectable years before dysplasia becomes endoscopically visible. Interventions that prevent niche assembly — or that dissolve it once formed — could in principle arrest the process at a stage where the epithelium is still plastic rather than irreversibly transformed. The SOX9-CXCL axis, sitting at the junction of epithelial intrinsic programming and extrinsic immune recruitment, is an obvious candidate for biomarker development and, eventually, pharmacological targeting.

As with any study built on human tissue sampling and multi-omic correlation, the causal chain from niche assembly to malignant transformation will require further experimental validation, and the therapeutic disruption of CXCR2 and CSF1R pathways demonstrated here will need to be tested in appropriate models and, ultimately, clinical settings. But the conceptual contribution is already clear. Early gastric cancer, the most critical and least understood stage of gastric carcinogenesis, now has a spatial address: an inflammation-associated niche in which stemness is maintained, macrophages are recruited, and immune surveillance is locally disarmed. Mapping that address — and learning to demolish it — may prove to be one of the more consequential shifts in how the field approaches inflammation-driven cancers.

Subject of Research: Spatial niche mechanisms driving early gastric cancer initiation

Article Title: How does early gastric cancer arise? The key role of the spatial niche

Article References: How does early gastric cancer arise? The key role of the spatial niche. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: early gastric cancer, spatial transcriptomics, single-cell RNA sequencing, inflammation, SOX9-CXCL axis, tumor microenvironment, macrophages, CXCR2, CSF1R, epithelial stemness, gastric carcinogenesis, immunosuppression