DNA Mechanisms in Cancer Immunotherapy

Nature Biotechnology paper (15 Apr 2026) closed the gap between knowing which gene matters and knowing which residue matters in cancer biology — and whether that residue matters the same way inside a living tumor as it does in a culture dish. 🔅 The researchers engineered a split-deaminase base editing system they call seBE, where the DNA mutating enzyme is divided into two inactive halves that only reconstitute when a small molecule — rapamycin — is administered. This simple but elegant design solves a long-standing problem: intact base editors cause persistent off-target deamination and transcriptional toxicity that destabilizes cells, perturbs gene expression, and makes in vivo functional screening practically impossible. With seBE, cells tolerate stable expression with virtually no toxicity, and editing is switched on precisely when and where the researcher wants it. 🔅 Using this system, the authors performed the first successful in vivo base editing functional genomics screen, identifying critical residues in 35 cancer immune genes inside established mouse tumors. A deep tiling screen of ADAR1 — a key mediator of cancer immunotherapy resistance — revealed that a single point mutation, R950C, nearly abolishes dsRNA editing activity and phenocopies full gene knockout in vivo while having no detectable effect in cell culture. The same screen uncovered a gain-of-function variant, A1000T, that confers resistance to interferon-mediated killing — a finding with direct implications for understanding why patients develop resistance to immune checkpoint blockade. 💟 To make this practical without requiring massive animal cohorts, the team developed LASER, an AI-guided sgRNA selection pipeline that integrates protein language models, evolutionary conservation scores, and base editor prediction tools. The top 20% of LASER-ranked guides captured 80% of experimental hits, reducing library size 3–5 fold and making residue-level in vivo screens feasible even in primary patient-derived material. Full Text: https://lnkd.in/gEPdzWmG Patent Document: https://lnkd.in/g9jJ7Gv7 #CRISPR #BaseEditing #FunctionalGenomics #CancerBiology #GeneEditing #Immunotherapy

T cell-specific non-viral DNA delivery and in vivo CAR-T generation using targeted lipid nanoparticles Methods Minicircle DNA (mcDNA) encoding a CAR construct and SB100x transposase mRNA were encapsulated within a novel lipid formulation which was functionalized with T cell-specific anti-CD7 and anti-CD3 binders. In vitro, we evaluated T cell specificity, mcDNA and mRNA transfection efficiency, transposon-mediated CAR integration and functionality of the resulting CAR-T cells. In vivo efficacy was assessed in peripheral blood mononuclear cell and CD34+ stem cell humanized murine xenograft models of B cell leukemia. Results In vitro, NCtx displayed high specificity and transfection efficiency with both mcDNA and mRNA in primary T cells. Transposase mRNA facilitated genomic integration of the CAR gene, leading to the generation of stable CAR-T cells that exhibited antigen-specific cytotoxicity and cytokine release. In vivo, a single intravenous dose of NCtx induced robust CAR-T cell generation resulting in effective tumor control and significantly improved survival in two distinct xenograft models. Conclusions Our findings demonstrate for the first time that targeted LNPs can be employed for efficient DNA delivery to T cells in vitro and in vivo. We show that when combined with transposase technology, this LNP-based system can efficiently generate stable CAR-T cells directly in vivo, inducing potent and durable antitumor responses. NCtx represents a novel non-viral gene therapy vector for in vivo CAR-T therapy, offering a scalable and potentially more accessible alternative to traditional approaches in CAR-T cell generation. Vertex Biopharm Consulting https://lnkd.in/ekCEXyBc

Cancer just showed us its playbook - and it’s nastier than we thought. UC San Diego scientists discovered why so many patients don’t respond to today’s most celebrated cancer drugs, immune checkpoint therapies. It isn’t random. Tumors are literally rewriting their own DNA to cut the phone lines that call in killer T-cells. No 9p arm of the chromosome. No interferon signals. No T-cells. No fight. That’s why so many tumors look “cold” and shrug off therapy. They’ve evolved an escape hatch. But here’s where it gets fascinating: the same team turned that weakness into an opening. They engineered a vaccine to flip the switch back on - restoring the immune signals, waking up the tumor microenvironment, and pulling T-cells back into the fight. In mice, it worked. Human trials are on the horizon. So what’s next? If this holds up, it doesn’t just patch a gap in cancer care. It rewrites the playbook - from testing who’s likely to resist therapy, to reprogramming tumors that were once untouchable. Imagine if “non-responders” became responders. How many lives, how many markets, how many clinical strategies does that change overnight?

Long-lasting #mRNA-encoded interleukin-2 restores CD8+ T cell neoantigen immunity in MHC class I-deficient cancers:- •Major histocompatibility complex (MHC) class I antigen presentation deficiency is a common cancer immune escape mechanism, but the mechanistic implications and potential strategies to address this challenge remain poorly understood. •Studying β2-microglobulin (B2M) deficient mouse tumor models, we find that MHC class I loss leads to a substantial immune desertification of the tumor microenvironment (TME) and broad resistance to immune-, chemo-, and radiotherapy. •We show that treatment with long-lasting mRNA-encoded interleukin-2 (IL-2) restores an immune cell infiltrated, IFNγ-promoted, highly proinflammatory TME signature, and when combined with a tumor-targeting monoclonal antibody (mAB), can overcome therapeutic resistance. •Unexpectedly, the effectiveness of this treatment is driven by IFNγ-releasing CD8+ T cells that recognize neoantigens cross-presented by TME-resident activated macrophages. •These macrophages acquire augmented antigen presentation proficiency and other M1-phenotype-associated features under #IL-2 treatment. •Our findings highlight the importance of restoring neoantigen-specific immune responses in the treatment of cancers with #MHC class I deficiencies. #highlights :- •#MHC class I loss leads to immune desertification and resistance to therapy in tumors. •Tumor-targeting antibody and #IL-2 #mRNA overcomes this therapeutic resistance. •Therapeutic efficacy depends on M1-like macrophages, IFNγ, and CD8+ T cells. •IFNγ-releasing CD8+ T cells recognize neoantigens cross-presented by macrophages. #cancerresearch #cancertreatment #macrophages #mrnavaccines

What if cancer cells don’t just repair DNA damage, but actively decide when to stop? Our latest work in Nature Portfolio Cell Death & Disease uncovers a compelling systems-level mechanism linking metabolism to DNA repair: an ATM–AMPK–Wip1 feedback loop that dynamically controls how long DNA damage signals persist. Link: https://lnkd.in/giiWFrcF At first glance, DDR (DNA damage response) is often taught as a linear pathway. But biology rarely operates in straight lines. Instead, we show that: • DNA damage activates ATM • ATM engages AMPK, the cell’s metabolic sensor • AMPK stabilizes Wip1 • Wip1, in turn, shuts down ATM A closed loop. A regulatory circuit. A decision-making module. Why is this exciting? Because this loop acts like a molecular timer—fine-tuning how long a cell “keeps the alarm on” after DNA damage. And in cancer, this timing is everything. Under metabolic stress (a hallmark of tumors), this circuit can: → Accelerate DNA repair shutdown → Help cancer cells survive radiation and chemotherapy → Drive therapy resistance This also helps resolve a long-standing paradox: Why does AMPK sometimes suppress tumors, but in other contexts support their survival? The answer may lie not in AMPK alone, but in the network it participates in. From a translational perspective, one insight stands out: • Wip1 emerges as a precise therapeutic target Instead of broadly inhibiting metabolism (which comes with systemic toxicity), targeting Wip1 could selectively: • Prolong DNA damage signaling • Reinstate checkpoint control (p53, p38) • Sensitize tumors to treatment More broadly, this work reinforces a key idea in modern biology: Cells don’t just use pathways, they compute through circuits. Understanding these circuits is where the next breakthroughs in cancer therapy will come from. Curious to hear thoughts from others working at the intersection of metabolism, DDR, and systems biology. #CancerResearch #SystemsBiology #DNARepair #Metabolism #DDR #PrecisionOncology #Bioinformatics #TranslationalScience