@article {70134, title = {COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 30}, pages = {8373}, abstract = {

Covalent inhibitors are an emerging class of therapeutics, but methods to comprehensively profile their binding kinetics and selectivity across the proteome have been limited. Here we introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), an unbiased method for quantifying irreversible covalent inhibitor binding kinetics on a proteome-wide scale. COOKIE-Pro uses a two-step incubation process with mass spectrometry-based proteomics to determine k and K values for covalent inhibitors against both on-target and off-target proteins. We validated COOKIE-Pro using BTK inhibitors spebrutinib and ibrutinib, accurately reproducing known kinetic parameters and identifying both expected and unreported off-targets. The method revealed that spebrutinib has over 10-fold higher potency for TEC kinase compared to its intended target BTK. To demonstrate the method{\textquoteright}s utility for high-throughput screening, we applied a streamlined two-point strategy to a library of 16 covalent fragments. This approach successfully generated thousands of kinetic profiles, enabling the quantitative decoupling of intrinsic chemical reactivity from binding affinity at scale and validating the method{\textquoteright}s broad applicability. By providing a comprehensive view of covalent inhibitor binding across the proteome, COOKIE-Pro represents a powerful tool for optimizing the potency and selectivity of covalent drugs during preclinical development.

bioRxiv preprint: https://doi.org/10.1101/2025.06.19.660637

}, keywords = {Adenine, Agammaglobulinaemia Tyrosine Kinase, High-Throughput Screening Assays, Humans, Kinetics, Mass Spectrometry, Piperidines, Protein Binding, Protein Kinase Inhibitors, Proteome, Proteomics, Pyrazoles, Pyrimidines}, issn = {2041-1723}, doi = {10.1038/s41467-025-63491-2}, url = {https://doi.org/10.1038/s41467-025-63491-2}, author = {Lin, Hanfeng and Yang, Bin and Ding, Lang and Yang, Yen-Yu and Holt, Matthew V and Jung, Sung Yun and Zhang, Bing and Wang, Meng C and Wang, Jin} } @article {69613, title = {Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction in Caenorhabditis elegans}, journal = {PLoS Genet}, year = {2025}, month = {2025 May 30}, abstract = {

Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology.

Preprint:\ https://doi.org/10.1101/2024.09.12.612591

}, doi = {10.1371/journal.pgen.1011425}, url = {https://doi.org/10.1371/journal.pgen.1011425}, author = {Guan, Youchen and Yu, Yong and Gao, Shihong Max and Ding, Lang and Zhao, Qian and Wang, Meng} } @article {69803, title = {TEMI: Tissue Expansion Mass Spectrometry Imaging}, journal = {Nat Methods}, year = {2025}, month = {2025 Apr 22}, abstract = {

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here, we developed a Tissue Expansion method compatible with matrix-assisted laser desorption/ionization Mass spectrometry Imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

Preprint:\ 10.1101/2025.02.22.639343

}, doi = {10.1101/2025.02.22.639343}, url = {https://doi.org/ 10.1038/s41592-025-02664-9.}, author = {Zhang, Hua and Ding, Lang and Hu, Amy and Shi, Xudong and Huang, Penghsuan and Lu, Haiyan and Tillberg, Paul W. and Wang, Meng C. and Li, Lingjun} } @article {70192, title = {Tissue expansion-enhanced mass-spectrometry imaging decodes biomolecular landscapes.}, journal = {Nat Rev Mol Cell Biol}, year = {2025}, month = {2025 Nov 17}, issn = {1471-0080}, doi = {10.1038/s41580-025-00931-3}, url = {https://doi.org/10.1038/s41580-025-00931-3}, author = {Ding, Lang} } @article {69482, title = {Aging atlas reveals cell-type-specific effects of pro-longevity strategies.}, journal = {Nat Aging}, year = {2024}, month = {2024 May 30}, abstract = {

Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.

}, issn = {2662-8465}, doi = {10.1038/s43587-024-00631-1}, author = {Gao, Shihong Max and Qi, Yanyan and Zhang, Qinghao and Guan, Youchen and Lee, Yi-Tang and Ding, Lang and Wang, Lihua and Mohammed, Aaron S and Li, Hongjie and Fu, Yusi and Wang, Meng C} } @article {68998, title = {Mitochondrial GTP metabolism controls reproductive aging in C.~elegans.}, journal = {Developmental Cell}, year = {2023}, month = {2023 Sep 07}, abstract = {

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.08.019}, author = {Lee, Yi-Tang and Savini, Marzia and Chen, Tao and Yang, Jin and Zhao, Qian and Ding, Lang and Gao, Shihong Max and Senturk, Mumine and Sowa, Jessica N and Wang, Jue D and Wang, Meng C} } @article {69103, title = {Mitochondrial GTP metabolism controls reproductive aging in C.~elegans.}, journal = {Developmental Cell}, volume = {58}, year = {2023}, month = {2023 Dec 04}, pages = {2718-2731.e7}, abstract = {

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.

}, keywords = {Aging, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Guanosine Triphosphate, Longevity, Mitochondria, Mitochondrial Dynamics, Reproduction}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.08.019}, author = {Lee, Yi-Tang and Savini, Marzia and Chen, Tao and Yang, Jin and Zhao, Qian and Ding, Lang and Gao, Shihong Max and Senturk, Mumine and Sowa, Jessica N and Wang, Jue D and Wang, Meng C} }