bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2026–02–08
thirteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU



  1. bioRxiv. 2026 Jan 16. pii: 2026.01.15.699774. [Epub ahead of print]
      Phosphatidylinositol 3-kinase (PI3K) integrates insulin/IGF signaling (IIS) and Ras inputs to control lifespan, metabolism and growth, yet the organismal consequences of selective structural perturbations remain poorly understood. Using structure-guided CRISPR/Cas9-dependent genome editing, we dissected functions of AGE-1, the sole Class IA PI3K catalytic subunit in Caenorhabditis elegans . An endogenously tagged AGE-1, containing a long flexible linker, epitope and fluorescent tag, retained full activity, enabling visualization of native protein dynamics in vivo . A constitutively active E630K substitution, modeled on oncogenic p110α alleles, markedly shortened lifespan and enhanced Ras-dependent induction of primary vulval precursor cell (VPC) fate, confirming evolutionary conservation of PI3K activation mechanisms that directly modulate longevity and development. Structural modeling further guided mutation of AGE-1 residues predicted to mediate Ras binding. Unexpectedly, a putative AGE-1 variant defective in Ras association, together with a complementary Ras effector-binding mutation, produced enlarged animals with reduced dauer formation. These phenotypes reveal a previously unrecognized Ras>PI3K signaling axis that restrains somatic growth and promotes entry into diapause, counter to canonical IIS models. Together, these structure-informed alleles show that discrete PI3K structural perturbations can differentially uncouple lifespan, growth, and developmental outcomes in vivo . By combining structural modeling with genome editing in a tractable aging model, this work establishes a framework for dissecting conserved signaling enzymes at single-residue resolution and uncovers unexpected organismal roles for PI3K structure in coordinating growth and longevity.
    DOI:  https://doi.org/10.64898/2026.01.15.699774
  2. Blood Vessel Thromb Hemost. 2026 Feb;3(1): 100133
      Vascular anomalies (VAs) are complex, highly morbid conditions that are increasingly managed by hematologists with targeted therapies. They are often driven by activating mutations in the phosphoinositide 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway. Alpelisib, a phosphoinositide 3-kinase-α (PI3Kα) inhibitor, is a key therapy for VAs; however, it is only approved for PIK3CA-related overgrowth spectrum (PROS), a VA diagnosis with multifaceted genotypic and phenotypic criteria, including a required PIK3CA mutation. Although there is a mechanistic rationale for alpelisib use in non-PROS VAs, published data supporting alpelisib use outside of PROS are limited. We conducted a single-center, retrospective study of 41 children and adults with VAs treated with alpelisib. Most patients failed prior therapies, including sirolimus. Alpelisib led to clinical improvement in 92% of the patients, 80% of whom did not meet PROS diagnostic criteria. There was no genetic testing in ∼50% of the responders, and ∼25% had mutations in non-PIK3CA genes in the PI3K/AKT/mTOR pathway (TEK, PIK3R1, and PTEN). Among patients with pre- and post-therapy imaging, 100% showed clinical improvement, but only 50% showed radiological improvement, highlighting discordance between imaging and clinical response. Our findings support expanding alpelisib use to VAs beyond PROS. In addition, they underscore the need for clinical trial end points based on clinical, not radiological, outcomes.
    DOI:  https://doi.org/10.1016/j.bvth.2025.100133
  3. Res Sq. 2026 Jan 29. pii: rs.3.rs-8279719. [Epub ahead of print]
      PTEN hamartoma tumor syndrome (PHTS) is a cancer predisposition disorder caused by germline PTEN variants, yet its full clinical spectrum remains poorly defined due to reliance on highly selected cohorts. Accordingly, PHTS is underrecognized and its prevalence underestimated. Leveraging genomic and electronic health record data from 414,830 participants in the All of Us (AoU) Research Program, we identified 55 individuals with pathogenic or likely pathogenic PTEN variants, the majority of whom lacked a prior PHTS diagnosis, underscoring underrecognition in the general population. PHTS affects ~ 1/7500 individuals in this US cohort, which is about 26-folds higher than historical estimates for PTEN -related disorder. Compared with carriers of other cancer-related gene variants and noncarriers, PTEN variant carriers exhibited the highest cancer prevalence and significantly younger ages at first cancer diagnosis. Phenotype enrichment revealed expected overgrowth-related features as well as previously unreported associations, including adenotonsillar hypertrophy, sleep apnea, acanthosis nigricans, and extreme obesity, suggesting broader systemic involvement than classically appreciated. Variant spectra were consistent across the population-based and clinically-ascertained PHTS cohorts. These findings demonstrate that PHTS is more prevalent, more heterogeneous, and more often undiagnosed than current clinical practice reflects, emphasizing the value of population-scale genomics for comprehensive characterization and earlier detection of PHTS.
    DOI:  https://doi.org/10.21203/rs.3.rs-8279719/v1
  4. Res Sq. 2026 Jan 12. pii: rs.3.rs-8436616. [Epub ahead of print]
      Background Brain insulin resistance and cerebrovascular dysfunction emerge early in late-onset Alzheimer's disease, but how amyloid-β (Aβ) disrupts insulin signaling at the cerebrovascular blood-brain barrier-a major site of insulin receptor signaling and transport into the brain-remains unclear. Methods We exposed two distinct human blood-brain-barrier endothelial cell models to soluble Aβ40 or Aβ42 for 1 h, followed by 100 nM insulin for 10 min. Protein and phosphoprotein responses were quantified by reverse-phase protein array, and differential expression was evaluated using linear models. Results Aβ40 reduced insulin-stimulated Akt activation and converted insulin's normal inhibition of AMPK into modest stimulation. Aβ42 did not alter insulin-stimulated Akt signaling but moderately suppressed basal Akt activation. Conclusions These findings suggest that Aβ40 acutely impairs insulin signal transduction in BBB endothelial cells, supporting a model in which vascular Aβ exposure contributes directly to the early development of brain insulin resistance in AD.
    DOI:  https://doi.org/10.21203/rs.3.rs-8436616/v1
  5. Proc Natl Acad Sci U S A. 2026 Feb 10. 123(6): e2517889123
      Cell fates regulated by ERK respond to different thresholds of signaling strength. In mammalian cells, conditions that activate ERK to submaximal levels are sufficient to sustain proliferation, survival, and transformation, while stimuli that activate ERK to very high levels often lead to cell death or cell cycle arrest. But while this "Goldilocks effect" is well known, the mechanisms have never been fully explained. In particular, threshold responses have been shown at the level of transcription and cell state changes, but whether phosphorylation responses upstream of these events also respond to thresholds is unknown. Here, we used mass spectrometry-based phosphoproteomics to ask if molecular events in the ERK pathway respond to different thresholds of signaling strength, by quantifying changes in phosphorylation of pathway targets against the occupancy of the two activating phosphosites in ERK. The results show that most phosphorylation events track ERK activation faithfully, responding linearly with increasing 2P-ERK occupancy. But some sites respond nonlinearly, reaching maximal phosphorylation when 2P-ERK exceeds lower thresholds (10 to 40%), or increasing substantially after 2P-ERK exceeds higher thresholds (>60%). Low threshold sites are found on transcriptional repressors that facilitate proliferation when inactivated by ERK/ribosomal s6 kinase (RSK) phosphorylation. By contrast, high threshold sites are found on proteins that are recruited to double-stranded DNA breaks and mediate DNA repair. Measurement of phosphorylation occupancies also revealed unexpected differences between cell states not apparent from inhibitor fold-changes. Our findings demonstrate that signaling thresholds exist at the level of the phosphoproteome, providing potential mechanisms for regulating cellular responses to pathway strength.
    Keywords:  BRAF; ERK; MAP kinase; phosphorylation site occupancy; signaling thresholds
    DOI:  https://doi.org/10.1073/pnas.2517889123
  6. bioRxiv. 2026 Jan 18. pii: 2026.01.16.699909. [Epub ahead of print]
      Obtaining a precise genetic tuberous sclerosis diagnosis is a challenge as many missense TSC2 variants are variants of uncertain significance (VUS). VUS in TSC2 have been resolved by one-at-a-time functional assays, but these assays cannot scale to the 3,634 TSC2 missense VUS observed so far. To address this challenge, we used massively parallel sequencing to measure the steady-state abundance of almost 9,000 TSC2 missense variants and developed an mTOR pathway activity assay using genome editing and cell sorting to generate activity scores for 391 missense variants. 1,288 of 8,891 (14.49%) missense variants assayed had altered TSC2 abundance, and 69 of 391 (17.65%) missense variants assayed had altered mTOR pathway activity. Calibration and integration of these data into classification of variants identified in a clinical cohort putatively reclassified 212 of 276 (76.8%) TSC2 missense VUS. These datasets will lead to improved genetic diagnosis of tuberous sclerosis with potential positive impacts on the clinical management of patients and their families.
    DOI:  https://doi.org/10.64898/2026.01.16.699909
  7. Proc Natl Acad Sci U S A. 2026 Feb 10. 123(6): e2505182123
      Current single-cell profiling technologies enable the capture of multiple cellular modalities, providing valuable insights into complex biological systems. While a substantial amount of single-cell multimodal data has been generated and accumulated, most of these datasets are unpaired, characterized by distinct feature spaces and a lack of cell-wise correspondence. The absence of explicit linkages between modalities poses a fundamental challenge for data integration and interpretation. To address this, we introduce SuperMap, a statistical learning method designed for the integrative analyses of unpaired multimodal data. SuperMap directly learns cross-modal mappings from unpaired data to effectively bridge and link different modalities, facilitating a variety of downstream analysis tasks. Comprehensive benchmarking and real-world applications demonstrate the superior performance of SuperMap in enhancing cell-type identification, improving diagonal integration, enabling regulatory analysis, and revealing epigenomic priming events to specify cell differentiation directions for trajectory inference.
    Keywords:  cross-modality data integration; gene activity score; regression with unlinked data
    DOI:  https://doi.org/10.1073/pnas.2505182123
  8. bioRxiv. 2026 Jan 17. pii: 2026.01.16.699948. [Epub ahead of print]
      CRISPR screens have become essential tools for systematically probing gene function from basic biology to drug discovery, yet important frontiers remain beyond genome scale. Probing regulatory elements, interpreting genetic variants, and mapping genetic interactions all challenge the sensitivity and scalability of existing approaches. Here we introduce two synergistic technologies to address these limitations. PORTAL (Perturbation Output via Reporter Transcriptional Activity in Lineages) shifts pooled genetics toward quantitative RNA phenotypes, encoding perturbation effects in expressed transcripts to enable single-molecule measurements with lineage or single-cell resolution. CAP cloning (Covalently closed Assembly Products) bypasses bacterial transformation to enable construction of ultrahigh-complexity lentiviral libraries. Combining these advances, we construct a genetic interaction map spanning 665,856 pairwise perturbations across 46 million clonal lineages-the largest exhaustive map in human cells and the first at this scale using a non-fitness phenotype. More broadly, this work charts a path toward comprehensive genetic interaction mapping in human cells.
    DOI:  https://doi.org/10.64898/2026.01.16.699948
  9. Science. 2026 Feb 05. eadz1884
      Site-specific insertion of gene-sized DNA fragments remains an unmet need in the genome editing field. IS110-family serine recombinases have recently been shown to mediate programmable DNA recombination in bacteria using a bispecific RNA guide (bridge RNA) that simultaneously recognizes target and donor sites. Here, we show that the bridge recombinase ISCro4 is highly active in human cells, and provide structural insights into its enhanced activity. Using plasmid- or all-RNA-based delivery, ISCro4 supports programmable multi-kilobase exisions and inversions, and facilitates donor DNA insertion at genomic sites with efficiencies exceeding 6%. Finally, we assess ISCro4 specificity and off-target activity. These results establish a framework for the development of bridge recombinases as next-generation tools for editing modalities that are beyond the capabilities of current technologies.
    DOI:  https://doi.org/10.1126/science.adz1884
  10. bioRxiv. 2026 Jan 17. pii: 2026.01.16.699963. [Epub ahead of print]
      Mitogenic signals are understood to license cell cycle progression and the metabolic reprogramming required for cell division, with acquired nutrients serving as permissive substrates. Here, we show that nutrient availability instead functions as a mitogen-independent regulatory input that dynamically controls CD8+ T cell proliferative potential. Activating stimuli have been shown to set T cell expansion capacity through their control of c-Myc expression, with the rate of c-Myc decay functioning as a division timer. We demonstrate that nutrient availability is sufficient to control c-Myc expression dynamics and dictates how division potential is stored and later actualized. Glucose-restricted T cells sustain proliferative potential and exhibit high AKT and ERK phosphorylation, despite limited growth. Upon glucose restoration, these cells rapidly increase c-Myc expression, accelerate through the cell cycle, and return to the expansion potential of glucose-replete controls, even after days of enforced restriction. Glucose restriction thus maintains a latent metabolic and mitogenic signaling state that is rapidly realized upon recovery. Mechanistically, mTOR signaling is required for this glucose recovery-driven proliferation, despite c-Myc and pERK remaining elevated following mTOR inhibition, indicating that glucose and mitogen signals operate through parallel rather than hierarchical control points. Altogether, these findings reveal that nutrient availability is not merely rate-limiting for proliferation but dictates the kinetics at which mitogenic signals are dissipated and realized. While mitogenic and nutrient cues converge on a shared anabolic network, they operate through distinct regulatory arms to coordinate the tempo and magnitude of clonal expansion, with implications for protective immunity and immunotherapy.
    Significance Statement: CD8+ T cells rapidly proliferate to fight infections and cancer, often in variable nutrient environments. Activation signals are understood to control T cell expansion potential by setting c-Myc expression and its subsequent decay, with nutrients providing fuel. Here we find that glucose availability functions as an independent regulatory switch. Glucose-restricted T cells remain proliferatively poised for days, keeping pro-growth signaling and metabolic capacity primed. Upon glucose restoration, cells undergo a proliferative burst and catch up to glucose-replete counterparts. Although c-Myc expression rises upon glucose restoration, accelerated division kinetics instead require mTOR activity. These findings reveal that nutrient availability operates in parallel with mitogenic signaling, tuning the rate at which T cells store and realize their expansion potential.
    DOI:  https://doi.org/10.64898/2026.01.16.699963
  11. Nat Commun. 2026 Feb 06.
      Blood vessels near injury sites rapidly dilate, become permeable, and release serum and leukocytes into the wounded tissue to support healing and regeneration. How the vasculature senses distant homeostatic tissue perturbations within seconds-to-minutes remains incompletely understood. Using high-speed imaging of live zebrafish larvae, we monitor two hallmark vascular responses to injury: vessel dilation and serum exudation. By genetic, pharmacologic, and osmotic perturbation along with leukocyte depletion, we show that the cPla2 nuclear membrane mechanotransduction pathway converts a ~ 50 μm/s osmotic wound signal into rapid vessel-permeabilization via perivascular macrophages, 5-lipoxygenase (Alox5a), and leukotriene A4 hydrolase (Lta4h). By revealing a previously undescribed physiological function of nuclear membrane mechanotransduction, we provide real-time insights into the long-range communication of wounds and blood vessels in intact tissue.
    DOI:  https://doi.org/10.1038/s41467-026-68520-2
  12. Biochem J. 2026 Feb 03. pii: BCJ20253428. [Epub ahead of print]483(2):
      The Forkhead box O (FOXO) class of transcription factors is evolutionary conserved both structurally and at least in part also functionally. FOXO activation results in transcriptional programs that provide cellular resilience toward exogenous and endogenous challenges, especially challenges that provoke cellular oxidative stress. This FOXO-dependent mechanism of resilience explains by and large the observed longevity phenotype in model organisms where increased FOXO activity extends lifespan. This may even hold for human lifespan as genome-wide association studies show a strong linkage between FOXO3 and human lifespan. Despite decades of studies on FOXOs, there are still many unresolved questions. Here, we discuss some of these knowledge gaps, related to our general understanding of transcriptional control by FOXOs, the role of the intrinsically disordered regions that constitute over 50% of FOXOs sequence, the role of cellular context in determining isoform specificity, and finally, the importance of resilience in understanding FOXO function. The latter, we think, provides context to the evolutionary role of FOXOs. So, rather than providing an exhaustive summary of literature findings, we focus on some of the omissions in our knowledge of FOXO function. Resolving these outstanding questions, we think, will help to provide the necessary insight to know how and when to manipulate FOXO function in a manner that will contribute to healthy aging.
    Keywords:  Forkhead proteins; aging; insulin signaling; intrinsically disordered proteins; signal transducers and activators of transcription; transcription factors
    DOI:  https://doi.org/10.1042/BCJ20253428
  13. Res Sq. 2026 Jan 30. pii: rs.3.rs-8697220. [Epub ahead of print]
      Primary liver cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), arise from the neoplastic transformation of hepatocytes and cholangiocytes, respectively. Loss or downregulation of PTEN, a tumor suppressor negatively regulating the PI3K/AKT pathway, is frequently observed in CCA and HCC. Notably, PTEN mutations are observed at nearly twice the frequency in combined CCA-HCC tumors than either HCC or CCA alone. Using lineage-specific liver-targeted PTEN-deficient mouse models, we demonstrate that PTEN loss drives cellular dedifferentiation and tumorigenesis, a process that is critically dependent on AKT2. Mechanistically, PTEN deficiency induces activation of NOTCH and upregulation of transcriptional factor SOX9, which plays a central role in tumor cell transformation. In parallel, PTEN loss increases SMAD4 expression and sensitizes the tumor cells to TGFβ signaling, with TGFβ treatment repressing SOX9 expression in tumor cells lacking PTEN. Together, our study defined a critical role for PTEN-AKT2 signaling in maintaining liver epithelial lineage fidelity and revealed how its disruption promotes the conversion of mature hepatocytes or cholangiocytes into liver cancer stem-like cells (LCSCs). Furthermore, we identify a PTEN-dependent crosstalk between NOTCH and TGFβ pathways that governs liver tumor development. Together, this work provides mechanistic insight into lineage plasticity in liver cancer with implications for pathway-directed therapy.
    DOI:  https://doi.org/10.21203/rs.3.rs-8697220/v1