bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2026–03–08
fourteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Dynamic subcellular proteomics identifies regulators of adipocyte insulin action.
  2. Phosphatidylinositol 4,5-bisphosphate mediates Arl4D self-interaction to promote Pak1 signaling.
  3. Structural and mechanistic basis of mTORC2 activation of protein kinase AKT/PKB.
  4. Phosphoinositide 3-kinase δ activity in patients with systemic lupus erythematosus.
  5. NSD1-Mediated PPARγ Methylation Enhances PTEN Activity to Suppress Glycolysis and Tumor Progression in Endometrial Cancer.
  6. Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants.
  7. Animal-origin-free method for generating blood vessel organoids.
  8. Genome-edited safe and immune-evasive human pluripotent cells: Potential solution for allogeneic therapies.
  9. Metabolic and behavioral effects of neurofibromin result from differential recruitment of MAPK and mTOR signaling.
  10. Integration of metabolomics and transcriptomics to reveal metabolic characteristics and the role of mTORC1 in β-cell proliferation induced by a short-term high-fat diet.
  11. Delayed forebrain excitatory and inhibitory neurogenesis in STRADA-related megalencephaly via mTOR hyperactivity.
  12. Protocol for single-cell optimization objective and trade-off inference.
  13. Large adipocytes increase vesicle-mediated lipid release and promote breast cancer malignancy.
  14. Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.
  1. Nat Commun. 2026 Feb 28.
    Dynamic subcellular proteomics identifies regulators of adipocyte insulin action.
    Olivia J Conway, Josie A Christopher, Lisa M Breckels, Hanqi Li, Dilip Menon, Meghna Birla, Bethan L Hawkins, Lu Liang, Satish Patel, Francoise Koumanov, David C Gershlick, David B Savage, Michael P Weekes, Kathryn S Lilley, Daniel J Fazakerley.
      Insulin acts on adipocytes to suppress lipolysis and increase glucose uptake to control whole-body glucose and lipid metabolism. Regulation of these processes by insulin signalling depends on changes in protein localisation. However, the extent of insulin-stimulated changes to the adipocyte spatial proteome, and the importance of these in the cellular insulin response, is unknown. Here, we use subcellular proteomics approaches to map acute insulin-stimulated protein relocalisation in adipocytes on a cell-wide scale. These data reveal extensive insulin-regulated protein redistribution, with hundreds of insulin-responsive proteins. These include the uncharacterised protein C3ORF18, which redistributes to the plasma membrane in response to insulin. Studies in C3ORF18-depleted adipocytes suggest this protein is required to maintain adipocyte insulin sensitivity. Overall, our data highlight the scale of protein relocalisation in the adipocyte insulin response, and provide an accessible resource to inform further studies into how changes in protein localisation contribute to cellular insulin responses.
    DOI:  https://doi.org/10.1038/s41467-026-70116-9
  2. Proc Natl Acad Sci U S A. 2026 Mar 10. 123(10): e2533102123
    Phosphatidylinositol 4,5-bisphosphate mediates Arl4D self-interaction to promote Pak1 signaling.
    Ting-Wei Chang, Fang-Jen S Lee.
      Self-association by small GTPases on membrane is critical for their signaling output and cellular function. However, a mechanistic understanding of how membrane components regulate this process remains incompletely understood. Here, we show that phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] promotes Arl4D self-association to potentiate downstream Pak1 signaling. We first show that Arl4D self-association is GTP-dependent and occurs at the plasma membrane. Fibronectin stimulation increases this self-association through two cooperative mechanisms: i) direct binding of PI(4,5)P2 by Arl4D via a conserved C-terminal polybasic motif, and ii) phosphorylation of Arl4D at Ser144 by its effector kinase Pak1. As a result, Arl4D membrane residency and protein stability are enhanced, with downstream signaling through Pak1 also amplified. Furthermore, pursuing structural prediction using AlphaFold, we generate an Arl4D mutant defective in self-association but retains GTP binding and membrane targeting, and find that this mutant fails to activate Pak1 for cell migration, while forced self-association of this mutant restores these downstream effects. Collectively, our findings reveal how an extracellular matrix cue leads to directional cell migration through Arl4D assembling into signaling-competent multimers at the plasma membrane, with cooperation between lipid recognition and kinase-mediated feedback playing critical roles.
    Keywords:  Arf-like 4 GTPase; PI(4,5)P2; Pak; cell migration; fibronectin
    DOI:  https://doi.org/10.1073/pnas.2533102123
  3. Biochem J. 2026 Mar 04. 483(3): 375-389
    Structural and mechanistic basis of mTORC2 activation of protein kinase AKT/PKB.
    Nam Chu, Nhat Le, Ouada Nebie, Sammi Yang.
      The PI3K/AKT/mTOR signaling pathway is crucial for regulating essential cellular processes such as growth, survival, metabolism, and protein synthesis. Dysregulation of this pathway is strongly associated with diseases like cancer, where it drives uncontrolled cell proliferation and survival. The mTOR kinase forms two multiprotein complexes, mTORC1 and mTORC2, which govern distinct signaling pathways. mTORC1, regulated by nutrients, controls protein synthesis, cell growth, and autophagy, while mTORC2 acts as a central node in phosphoinositide 3-kinase (PI3K) and Ras signaling, often disrupted in cancer and diabetes. AKT, recruited by PIP3 to the plasma membrane, is phosphorylated by PDK1 and mTORC2, enabling it to regulate various cellular functions. Notably, mTORC2 selectively phosphorylates AKT and PKC but no other closely related kinases targeted by mTORC1, reflecting a high degree of substrate specificity. This specificity is due to structural elements in AKT that interact with the mTORC2 subunit mSin1 as revealed by recent studies using semisynthetic probes, paving the way for the design of mTORC2-specific inhibitors. Given the pathway's significant role in disease progression, particularly cancer, targeting the AKT/mTOR axis holds considerable therapeutic promise. However, challenges remain due to the complex regulation and feedback mechanisms in this pathway. Emerging combination therapies show promise in overcoming these obstacles. This review highlights the intricate regulation of the AKT/mTOR pathway and its potential for developing targeted therapies.
    Keywords:  AKT; cell signaling; mTOR; posttranslational modifications; protein kinase
    DOI:  https://doi.org/10.1042/BCJ20253108
  4. Front Immunol. 2026 ;17 1745692
    Phosphoinositide 3-kinase δ activity in patients with systemic lupus erythematosus.
    Elham Sadat Mirfazeli, Shalmalee Kharkar, Michel W P Tsang-A-Sjoe, Olivier Papapietro, Izabella Niewczas, Agner R Parra Sanchez, Anita Chandra, Klaus Okkenhaug, Irene E M Bultink, Reina E Mebius, Jonathan Clark, Alexandre E Voskuyl, Sergey Nejentsev.
       Introduction: New biomarkers are needed for better stratification and personalized treatment of Systemic Lupus Erythematosus (SLE). Phosphoinositide 3-kinase δ (PI3Kδ) has been implicated in SLE pathogenesis. Here, we investigated whether a subset of SLE patients has increased PI3Kδ activity after T cell activation.
    Methods: T cells were isolated from frozen PBMCs of 108 SLE patients, 19 healthy controls, and one patient with Activated PI3K Delta syndrome (APDS), which provided a benchmark of increased PI3Kδ activity. After 90-minute anti-CD3/CD28 stimulation, phosphatidylinositol 3,4,5-trisphosphate (PIP3) and phosphatidylinositol 4,5-bisphosphate (PIP2) were measured using high-performance liquid chromatography-mass spectrometry.
    Results: Higher levels of PIP3 (measured as the ratio of PIP3/PIP2) in stimulated T cells distinguished APDS patient from other subjects providing a useful biomarker of increased PI3Kδ activity. We observed no significant difference in T-cell PIP3 levels between SLE patients and healthy controls. However, a subset of SLE patients (n = 4) exhibited strong upregulation of PIP3 following T-cell stimulation, comparable to that observed in the APDS patient. PIP3 levels in stimulated T cells positively correlated with the frequency of CD4+ T cells and negatively correlated with the frequencies of CD8+, EMRA CD4+, and EMRA CD8+ T cells.
    Conclusions: We describe the range of variation of PI3Kδ activity in T cells from a large cohort of patients with SLE and from healthy subjects. Our findings suggest that increased PI3Kδ activity is not associated with SLE in general, although some SLE patients exhibit a particularly strong upregulation of PIP3 levels after T-cell stimulation. This subgroup of SLE patients warrants further investigation given the promising effect of PI3Kδ inhibitors in restoring normal immune regulation.
    Keywords:  APDS; PI3Kδ; PIP3; SLE; T cells; autoimmunity; biomarker
    DOI:  https://doi.org/10.3389/fimmu.2026.1745692
  5. Cancer Res. 2026 Mar 02.
    NSD1-Mediated PPARγ Methylation Enhances PTEN Activity to Suppress Glycolysis and Tumor Progression in Endometrial Cancer.
    Han Tao, Ye Gu, Xiaojun Wang, Yeli Sun, Luhui Wang, Yilin Dai, Mengyue Zhu, Zhiyi Hu, Yiran Li, Mengwen Kong, Kun Gao, Xiaoping Wan.
      Metabolic reprogramming is a defining feature of endometrial cancer (EC). The upstream molecular mechanisms driving altered metabolism in EC represent potential therapeutic targets. Here, we identified the lysine methyltransferase NSD1-frequently mutated in EC-as a key epigenetic regulator of tumor metabolism. NSD1 directly monomethylated PPARγ at lysine 98 (K98), which enhanced the nuclear localization of PPARγ and promoted transcriptional activation of the tumor suppressor gene PTEN. The resulting elevated PTEN levels led to reduced glycolytic metabolism, cellular proliferation, and invasive potential in EC cells. Loss-of-function mutations in NSD1 abolished PPARγ K98 methylation, resulting in its cytoplasmic retention and impaired PTEN transcription. The consequent depletion of PTEN amplified glycolysis and drove tumor progression. Remarkably, restoration of PTEN expression or pharmacological inhibition of AKT effectively reversed the heightened glycolytic activity and malignant phenotype associated with NSD1 deficiency. Together, these findings reveal a critical epigenetic-metabolic axis in EC, wherein NSD1-mediated methylation of PPARγ at K98 orchestrates tumor-suppressive metabolic control via PTEN. These insights not only elucidate a regulatory pathway in EC pathogenesis but also highlight potential therapeutic targets for intervention in metabolically driven tumors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-3289
  6. Cancer Discov. 2026 Mar 06. OF1-OF20
    Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants.
    Carlos Stahlhut, Anna E Maciag, Kyle A Sullivan, Kanchan Singh, Nadege Gitego, Zuhui Zhang, Albert H Chan, Alok K Sharma, Patrick A Alexander, Jin Shu, Yue Yang, Megan Rigby, Roger Ma, Saman Setoodeh, Brian P Smith, Jun Pei, Dana Rabara, Erik K Larsen, David M Turner, Cathy Zhang, Cindy Feng, Siyu Feng, James P Stice, Rui Xu, Ken Lin, Andrew G Stephen, Felice C Lightstone, Chunmei Ji, Keshi Wang, Dhirendra K Simanshu, Dwight V Nissley, Eli Wallace, Bin Wang, Kerstin W Sinkevicius, Frank McCormick, Pedro J Beltran.
      Although KRASG12C-specific inhibitors have been introduced, no approved targeted therapies exist for other clinically significant KRAS mutants, including KRASG12D and KRASG12V. We discovered BBO-11818, a potent, selective, orally bioavailable noncovalent pan-KRAS inhibitor capable of targeting multiple KRAS mutants in both the inactive GDP-bound (OFF) and active GTP-bound (ON) states. BBO-11818 binds in the Switch-II/Helix 3 pocket, inducing conformational changes incompatible with effector binding, and demonstrates high-affinity binding to mutant KRAS with strong selectivity over NRAS and HRAS. BBO-11818 potently inhibited MAPK signaling and cellular viability specifically in KRAS-driven lines and produced tumor regressions in KRAS-mutant xenograft models. Combination studies with anti-PD-1, anti-EGFR antibodies, and a RAS:PI3Kα breaker compound showed enhanced efficacy. BBO-11818 has entered phase I clinical trials for patients with various KRAS mutations in colorectal, pancreatic, and lung cancers (NCT06917079).
    SIGNIFICANCE: We discovered BBO-11818, a potent and selective noncovalent KRAS inhibitor with activity against multiple KRAS mutants in both the active (ON) and inactive (OFF) states. BBO-11818 addresses the need for KRAS inhibitors targeting clinically relevant mutants such as KRASG12D and KRASG12V, either as monotherapy or in combination.
    DOI:  https://doi.org/10.1158/2159-8290.CD-25-1280
  7. Sci Rep. 2026 Mar 05.
    Animal-origin-free method for generating blood vessel organoids.
    Alexander Hoffmann, David Schorn, Jakob Thönig, Yu-Hsiang Teng, Jean-François Bisson, Teodor E Yordanov.
      Blood vessel organoids (BVOs) represent a promising tool for modeling vascular diseases, drug screening, and regenerative therapies. However, current protocols for BVO generation are complex, labor-intensive, and reliant on animal-derived extracellular matrices (ECM) such as Matrigel, limiting reproducibility, scalability, and clinical applicability. We developed a simplified, animal-origin-free protocol for BVO generation that addresses current limitations and enables high-throughput automated workflows. The method employs ultra-low attachment 96-well U-bottom plates for standardized aggregation and differentiation of human induced pluripotent stem cells (hiPSCs) in a human derived collagen-based extracellular matrix. Unlike conventional protocols where aggregates are embedded in a two-layer ECM, our approach utilizes a single-layer, which we termed "sitting drop". This innovative approach requires considerably fewer materials and handling steps and is compatible with high-throughput automated machines. BVO generation utilizing the here described optimized protocol resulted in the formation of BVOs with reproducible morphology and cellular composition. Flow cytometry confirmed the presence of CD31⁺ endothelial cells and PDGFRβ⁺ pericytes in BVOs, generated in sitting drops in ultra-low adhesive U-bottom shaped 96 well plates, with cell population percentages comparable to those observed in traditional two-layer BVO cultures. In vivo transplantation of mature BVOs in a mouse full-thickness skin wound model demonstrated integration of BVO derived cells into host vessels, highlighting their potential in cell-based therapies. Our study presents a robust and animal-origin-free method for BVO generation based on single-layer "sitting drop" cultures. This protocol maintains cellular integrity while enhancing reproducibility and automation-readiness, paving the way for high-throughput screening and clinical translation of vascular organoid technology.
    Keywords:  Bioengineering; Blood vessel organoids (BVO); Collagen; Extracellular matrix (ECM); High-throughput; Organoids
    DOI:  https://doi.org/10.1038/s41598-026-42977-z
  8. Stem Cell Reports. 2026 Mar 05. pii: S2213-6711(26)00061-5. [Epub ahead of print] 102850
    Genome-edited safe and immune-evasive human pluripotent cells: Potential solution for allogeneic therapies.
    Vivian Tam, Nicole Ching Man Wong, Andrew Chung Hin Poon, Mengxia Zhu, Ting Mei, Janette Kwok, Patrick Chu, Eric D Jong, Jean Kit Tang, Andras Nagy, Danny Chan.
      We used an embryonic stem cell line (H1) engineered for immune-evading properties to avoid rejection ("AlloAccept") and equipped with a "SafeCell" (SC) kill-switch to eliminate aberrantly proliferating cells. Utilizing a humanized immune system mouse model, we demonstrated the successful generation of allogeneic tissues from SafeCell-AlloAccept (SC-AlloAccept) cells in immunocompetent humanized mice in the immune-active subcutaneous region. These cells formed various tissue types, and their growth can be controlled with pro-drug ganciclovir to activate the kill switch, which eliminated proliferating cells and rendered the remaining tissue dormant. Strikingly, SC-AlloAccept-derived grafts survived for 5 months, underscoring their potential for long-term engraftment. Importantly, neither prior rejection of immunogenic parental H1 cells (sensitization) nor the presence of immune-evasive H1-derived tissue (potential immunocompromising) affected the immune response to a subsequent second transplant. This study validated the utility of SC-AlloAccept human cells in transplantation and enhanced the safety and efficacy of stem cell-based regenerative therapies.
    Keywords:  AlloAccept; allogeneic transplantation; cell therapy; human pluripotent stem cell; humanized immune system; immune evasion; kill switch; long-term engraftment; regenerative medicine; universal cell source
    DOI:  https://doi.org/10.1016/j.stemcr.2026.102850
  9. PLoS Genet. 2026 Mar 05. 22(3): e1012061
    Metabolic and behavioral effects of neurofibromin result from differential recruitment of MAPK and mTOR signaling.
    Valentina Botero, Jenifer Barrios, Anneke Knauss, Greta Dahlen, Ethan Rosendahl, Kenneth J Colodner, Seth M Tomchik.
      Neurofibromatosis type 1 results from mutations in the NF1 gene and its encoded neurofibromin protein. This condition produces multiple symptoms, including tumors, behavioral alterations, and metabolic changes. Molecularly, neurofibromin mutations affect Ras activity, influencing multiple downstream signaling pathways, including MAPK (Raf/MEK/ERK) and PI3K/Akt/mTOR signaling. This pleiotropy raises the question of which pathways could be targeted to treat the disease symptoms, and whether different phenotypes driven by neurofibromin mutations exhibit similar or diverging dependence on the signaling pathways downstream of Ras. To test this, we examined metabolic and behavioral alterations in the genetically tractable Drosophila neurofibromatosis type 1 model. In vivo genetic analysis revealed that behavioral effects of neurofibromin were mediated by MEK signaling, with no necessity for Akt. In contrast, metabolic effects of neurofibromin were mediated by coordinated actions MEK/ERK and Akt/mTOR/S6K/4E-BP signaling. At the systemic level, loss of neurofibromin dysregulated metabolism via molecular effects in interneurons and muscle. These changes were accompanied by altered muscle mitochondria morphology, with no concomitant changes in neuronal ultrastructure or neuronal mitochondria. Overall, this suggests that neurofibromin mutations affect multiple signaling cascades downstream of Ras, which differentially affect metabolic and behavioral neurofibromatosis type 1 phenotypes.
    DOI:  https://doi.org/10.1371/journal.pgen.1012061
  10. PeerJ. 2026 ;14 e20871
    Integration of metabolomics and transcriptomics to reveal metabolic characteristics and the role of mTORC1 in β-cell proliferation induced by a short-term high-fat diet.
    Jiajia Wang, Jing Li, Yunshan Li, Mengran Liu, Shan Huang, Wenyi Li.
       Background: Pancreatic β-cell proliferation is essential for maintaining the balance of β-cell mass, and an elevated metabolic load can stimulate their proliferation. Numerous studies have shown that a short-term high-fat diet increases metabolic load without affecting insulin sensitivity, thereby promoting the proliferation of pancreatic β-cells. However, the underlying mechanisms of this effect remain to be fully elucidated.
    Results: A model has been constructed in our study to emulate pancreatic β-cell proliferation induced by a short-term high-fat diet, aiming to scrutinize the underlying mechanisms. Integrated transcriptomic and metabolomic analyses suggest that the mTORC1 signaling pathway may be crucial in this induced proliferation. Further analysis revealed that rapamycin, a specific inhibitor of the mTORC1 pathway, can inhibit proliferation induced by the short-term high-fat diet.
    Conclusion: Our study confirms the significant role of the mTORC1 signaling pathway in pancreatic β-cell proliferation induced by a short-term high-fat diet.
    Keywords:  Short-time high-fat diet; Transcriptomics and metabolomics; mTORC1; β cell proliferation
    DOI:  https://doi.org/10.7717/peerj.20871
  11. Stem Cell Reports. 2026 Mar 05. pii: S2213-6711(26)00044-5. [Epub ahead of print] 102833
    Delayed forebrain excitatory and inhibitory neurogenesis in STRADA-related megalencephaly via mTOR hyperactivity.
    Tong Pan, Grace Lin, Xuan Li, Debora VanHeyningen, John C Walker, Sahej Kohli, Aiswarya Saravanan, Amrita Kondur, Daniel C Jaklic, Saul Pantoja-Gutierrez, Shivanshi Vaid, Julie Sturza, Ken Inoki, Tomozumi Imamichi, Weizhong Chang, Louis T Dang.
      Biallelic pathogenic variants in STRADA (STE20-related adaptor alpha), an upstream regulator of the mechanistic target of rapamycin (mTOR) pathway, result in megalencephaly, drug-resistant epilepsy, and severe intellectual disability. This study explores how mTOR pathway hyperactivity alters cell fate specification in dorsal and ventral forebrain development using STRADA knockout human stem cell-derived brain organoids. In both dorsal and ventral forebrain STRADA knockout organoids, neurogenesis is delayed, with a predilection for progenitor renewal, increased proliferation and an expanded outer radial glia population. Ventrally, interneuron subtypes shift to an increase in neuropeptide Y-expressing cells. Inhibition of the mTOR pathway with rapamycin rescues most phenotypes. When mTOR pathway variants are present in all cells of the developing brain, overproduction of interneurons and altered interneuron cell fate may underlie mechanisms of megalencephaly, epilepsy, and cognitive impairment. Our findings suggest that mTOR inhibition during fetal brain development could be a potential therapeutic strategy in STRADA deficiency.
    Keywords:  PMSE syndrome; STRADA; brain organoid; cell fate specification; epilepsy; interneuron development; mTOR; mTORC1; mammalian target of rapamycin; mechanistic target of rapamycin
    DOI:  https://doi.org/10.1016/j.stemcr.2026.102833
  12. STAR Protoc. 2026 Mar 05. pii: S2666-1667(26)00026-2. [Epub ahead of print]7(1): 104373
    Protocol for single-cell optimization objective and trade-off inference.
    Da-Wei Lin, Cara Teixeira, Carolina Chung, Sayan Saha Roy, Amit Ghosh, Sriram Chandrasekaran.
      Single-cell optimization objective and trade-off inference (SCOOTI) is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs in biological systems. Here, we present a protocol for installing and running SCOOTI, using transcriptomics, proteomics, and metabolomics data to constrain metabolic models. We describe steps to interpret metabolic priorities across different cell states or conditions through clustering, dimensionality reduction, and trade-off analysis.
    Keywords:  Bioinformatics; Metabolism; Systems biology
    DOI:  https://doi.org/10.1016/j.xpro.2026.104373
  13. Cell Rep. 2026 Mar 05. pii: S2211-1247(26)00139-7. [Epub ahead of print]45(3): 117061
    Large adipocytes increase vesicle-mediated lipid release and promote breast cancer malignancy.
    Garrett F Beeghly, Irina Kopyeva, Jenny Deng, Marlee I Pincus, Rohan R Varshney, Dilip D Giri, Domenick J Falcone, Michael C Rudolph, Marc A Antonyak, Neil M Iyengar, Claudia Fischbach.
      Primary adipocytes exhibit striking variability in size, yet the functional consequences of adipocyte hypertrophy remain unclear due to insufficient experimental approaches to control for cell size. Here, we establish methods to culture large and small primary adipocytes isolated from the same adipose depot, enabling size-resolved analyses independent of systemic obesity. Using transcriptomic, lipidomic, and functional profiling across two mouse models of obesity, as well as human clinical samples, we show that adipocyte size-rather than body weight-drives distinct phenotypic cell states. Notably, large adipocytes increase extracellular vesicle-mediated lipid release. In coculture assays, this shift enhances lipid uptake, migration, and proliferation of breast cancer cells through fatty acid oxidation. Consistent with these findings, individuals with larger mammary adipocytes exhibit elevated fasting triglycerides independent of body mass index. Together, our results identify adipocyte size as a key determinant of adipose tissue function with implications for both metabolic disease and cancer progression.
    Keywords:  CP: cancer; CP: metabolism; adipocyte; adipose tissue; breast cancer; extracellular vesicles; hypertrophy; lipid metabolism; obesity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2026.117061
  14. Nat Commun. 2026 Mar 02.
    Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.
    Hui-Yin Chang, Yamei Deng, Ruohong Li, Dmitry Avtonomov, Bo Wen, Sarah E Haynes, Felipe da Veiga Leprevost, Bing Zhang, Fengchao Yu, Alexey I Nesvizhskii.
      Isobaric mass tags, such as isobaric tags for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT), are widely utilized for peptide and protein quantification in multiplex quantitative proteomics. We present TMT-Integrator, a bioinformatics tool for processing quantitation results from TMT and iTRAQ experiments, offering integrative reports at the gene, protein, peptide, and post-translational modification site levels. We demonstrate the versatility of TMT-Integrator using five publicly available TMT datasets: clear cell renal cell carcinoma (ccRCC) whole proteome and phosphoproteome datasets from the Clinical Proteomic Tumor Analysis Consortium, an E. coli dataset with 13 spike-in proteins, and two human cell lysate datasets showcasing the latest advances with the Thermo Orbitrap Astral mass spectrometer and TMTpro 35-plex reagents. Integrated into the widely used FragPipe computational platform (https://fragpipe.nesvilab.org/), TMT-Integrator is a core component of TMT and iTRAQ data analysis workflows. We evaluated the performance of FragPipe coupled with TMT-Integrator analysis pipeline against MaxQuant and Proteome Discoverer with multiple benchmarks, facilitated by the bioinformatics tool OmicsEV. Our results show that FragPipe coupled with TMT-Integrator quantifies more proteins in the E. coli and ccRCC whole proteome datasets, quantifies more phosphorylated sites in the ccRCC phosphoproteome dataset, and overall delivers more robust quantification performance compared to other tools.
    DOI:  https://doi.org/10.1038/s41467-026-70118-7
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