iSciencePub Date : 2025-09-05DOI: 10.1016/j.isci.2025.113514
Wenhao Shi , Tianlong He , Nan Wang , Annan Qian , Yuqiao Liu , Shaojun Tang , Yiying Zhu
{"title":"Integrated multi-dimensional comparison of proteomic profiles across 54 cancer cell lines","authors":"Wenhao Shi , Tianlong He , Nan Wang , Annan Qian , Yuqiao Liu , Shaojun Tang , Yiying Zhu","doi":"10.1016/j.isci.2025.113514","DOIUrl":"10.1016/j.isci.2025.113514","url":null,"abstract":"<div><div>Human cancer cell lines are essential model systems in biomedical research. We conducted multi-level proteomics analyses on 54 widely used cancer cell lines derived from various tissues using two prominent proteomics technologies: mass spectrometry (MS) and reverse-phase protein array (RPPA). Our analysis identified 10,088 proteins, 33,161 phosphorylation sites across 7,469 phosphoproteins, and 56,320 site-specific glycans on 14,228 glycosylation sites from 5,966 glycoproteins, along with 305 drug-relevant protein and phosphoprotein targets. Analysis of this rich dataset yielded numerous biological insights, including protein features that distinguish tissue origins and cell line-specific kinase activation patterns, reflecting signaling diversity across cancer types. These findings may inform therapeutic strategies and support rational model system selection. Additionally, MS and RPPA showed consistent fold-change estimation and provided complementary views of proteome and signaling variation. This comprehensive resource facilitates biomarker discovery, signaling analysis, and translational oncology research across diverse human tumor types.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113514"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-05DOI: 10.1016/j.isci.2025.113509
Piyali Majumder , Arnab Dutta
{"title":"Closed-loop carbon management strategies for climate and energy-resilient India","authors":"Piyali Majumder , Arnab Dutta","doi":"10.1016/j.isci.2025.113509","DOIUrl":"10.1016/j.isci.2025.113509","url":null,"abstract":"<div><div>Climate change, primarily driven by excessive CO<sub>2</sub> emissions, poses urgent global challenges. India contributes over 2,600 Mt CO<sub>2</sub> annually, with ∼80% originating from hard-to-abate sectors, such as power, cement, petrochemical, chemical, and steel. This review highlights the importance of carbon capture, utilization, and storage (CCUS) and carbon dioxide removal (CDR) technologies as critical pathways to align India’s growth with climate goals. India prioritizes point-source capture from flue gases, reflecting its concentrated emission profile. Effective carbon management models must generate high-value marketable products, including fuels, fertilizers, aggregates, and construction materials, supporting a closed-loop carbon cycle. Mineralization pathways enable CO<sub>2</sub>-based building materials to strengthen Smart City and infrastructure initiatives, while CO<sub>2</sub>-derived fertilizers enhance agricultural productivity and food security. The manuscript also examines India’s emerging carbon market, recommending balanced compulsory and voluntary mechanisms, carbon credit incentives, and utilization-driven byproducts. Collectively, it provides an integrated CCUS framework for India that couples emission reduction with economic viability and offers scalable insights for other developing economies.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113509"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-05DOI: 10.1016/j.isci.2025.113513
Caroline Munini Muema , Belinda Kibii , Mingyue Zhong , Xinfeng Li , Paulina Miernikiewicz , Heng Xue , Yiyao Wang , Raphael Nyaruaba , Krystyna Dąbrowska , Hongping Wei , Hang Yang
{"title":"Transcriptomic analysis of phage-mammalian cell interaction reveals diverse phage immunobarcodes","authors":"Caroline Munini Muema , Belinda Kibii , Mingyue Zhong , Xinfeng Li , Paulina Miernikiewicz , Heng Xue , Yiyao Wang , Raphael Nyaruaba , Krystyna Dąbrowska , Hongping Wei , Hang Yang","doi":"10.1016/j.isci.2025.113513","DOIUrl":"10.1016/j.isci.2025.113513","url":null,"abstract":"<div><div>The phage-mammalian cell interactome is an emerging research frontier essential for uncovering the diverse impacts phages may have on humans. Here, we investigate the crosstalk of six distinct <em>Acinetobacter baumannii</em> phages with A549 epithelial cells and RAW264.7 macrophages. Our findings indicate that phage internalization rate varies depending on the phage type and the cell line. Notably, podovirus phage demonstrates the highest rate of internalization, while myovirus phage exhibits the lowest. Internalized phages maintain significant activity against intracellular bacteria. RNA sequencing revealed that phage-treated A549 cells display anti-inflammatory transcriptional signatures (immunobarcodes). Conversely, macrophages treated with siphovirus phage CK02 or podovirus phage CK21 demonstrate an anti-inflammatory profile, while those treated with myovirus phage CK12 maintain a pro-inflammatory response. Moreover, both phage-treated cells exhibit the downregulation of cellular reproduction and proliferation pathways, pointing to underexplored dimensions of phage-mammalian cell interactions. Altogether, our findings highlight the complexity of phage effects on mammalian cells.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113513"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-05DOI: 10.1016/j.isci.2025.113482
Yi Liu
{"title":"Efficient phenol removal by δ-MnO2 synthesized in situ on a self-supporting membrane","authors":"Yi Liu","doi":"10.1016/j.isci.2025.113482","DOIUrl":"10.1016/j.isci.2025.113482","url":null,"abstract":"<div><div>Manganese oxides are effective environmental coupling oxidants for the conversion of phenol; however, previous research has mainly focused on their powdered rather than immobilized forms. To address this gap, the oxidative removal of phenol from aqueous solutions was investigated using δ-MnO<sub>2</sub>, which was synthesized <em>in situ</em> and immobilized on a tailorable self-supporting membrane carrier (MnO<sub>2</sub>/M). The Freundlich isotherm provided the best fit for adsorption, whereas Sips successfully indicated the highest adsorption capacity. Kinetic analyses showed that the pseudo-second-order and electron transfer control models represented the reaction dynamics, with intra-particle diffusion and liquid film diffusion playing crucial roles. Physicochemical calculations confirmed the exothermic and spontaneous nature of the reaction (ΔG = −31.65 kJ/mol; 298 K). This research also clarifies and elucidates the two-electron direct oxidative transfer processes involved in the oxidative transformation of phenol by the MnO<sub>2</sub>/H<sup>+</sup> heterogeneous system, establishing a framework for advancing environmental remediation using Mn-based materials.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113482"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-05DOI: 10.1016/j.isci.2025.113505
Devesh U. Kapoor , Anil Pareek , Priyanka Uniyal , Bhupendra G. Prajapati , Kasitpong Thanawuth , Pornsak Sriamornsak
{"title":"Innovative applications of 3D printing in personalized medicine and complex drug delivery systems","authors":"Devesh U. Kapoor , Anil Pareek , Priyanka Uniyal , Bhupendra G. Prajapati , Kasitpong Thanawuth , Pornsak Sriamornsak","doi":"10.1016/j.isci.2025.113505","DOIUrl":"10.1016/j.isci.2025.113505","url":null,"abstract":"<div><div>Three-dimensional (3D) printing, or additive manufacturing, is transforming pharmaceutical and biomedical fields by enabling personalized medicine. This review highlights advances in 3D printing for customized drug delivery systems, including patient-specific dosage forms, multidrug polypills, and implantable devices that improve adherence and therapeutic outcomes—especially for pediatric and geriatric populations. The intersection of 3D printing with regenerative medicine is also explored, focusing on bioprinting technologies, stem cell-laden scaffolds, and smart biomaterials such as hydrogels and bioinks for localized therapy and tissue repair. These strategies reflect an expanded vision of personalized medicine, merging individualized pharmacotherapy with tissue engineering. Additionally, the review discusses the integration of artificial intelligence, nano-enabled platforms, and decentralized pharmaceutical manufacturing to accelerate development and access. Key regulatory and technical challenges are outlined, along with future directions to promote the clinical translation and scalability of 3D-printed pharmaceutical and regenerative systems.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113505"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-04DOI: 10.1016/j.isci.2025.113502
Mao Hagihara , Makoto Yamashita , Tadashi Ariyoshi , Ayaka Minemura , Chika Yoshida , Seiya Higashi , Kentaro Oka , Motomichi Takahashi , Akinobu Ota , Akihiro Maenaka , Kenta Iwasaki , Jun Hirai , Yuichi Shibata , Takumi Umemura , Takeshi Mori , Hideo Kato , Nobuhiro Asai , Hiroshige Mikamo
{"title":"Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120","authors":"Mao Hagihara , Makoto Yamashita , Tadashi Ariyoshi , Ayaka Minemura , Chika Yoshida , Seiya Higashi , Kentaro Oka , Motomichi Takahashi , Akinobu Ota , Akihiro Maenaka , Kenta Iwasaki , Jun Hirai , Yuichi Shibata , Takumi Umemura , Takeshi Mori , Hideo Kato , Nobuhiro Asai , Hiroshige Mikamo","doi":"10.1016/j.isci.2025.113502","DOIUrl":"10.1016/j.isci.2025.113502","url":null,"abstract":"<div><div>We previously reported that orally administered <em>Clostridium butyricum</em> enhances anti-influenza virus effects through the interferon-λ upregulation in mice lungs; however, the precise mechanism remains unclear. Orally administered <em>C. butyricum</em> promotes the proliferation of <em>Bifidobacterium</em> species in the lung microbiome, and this enhances <em>C. butyricum</em> induced anti-influenza effects. Among the <em>Bifidobacterium</em> species, <em>B. longum</em> effectively enhanced the sensitivity of the lung epithelial cells to long-chain fatty acids through the G-protein-coupled receptor120 upregulation. Oral administration of <em>C. butyricum</em> altered long-chain fatty acid metabolism and promoted interferon-λ production through G-protein-coupled receptor120. We hypothesized that these effects enhance anti-influenza virus responses through interferon-λ upregulation via collaboration between long-chain fatty acid metabolism alterations and the lung microbiome moderation. This study identified a gut-lung axis mechanism and provides insights into viral respiratory infection treatment and prophylaxis.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113502"},"PeriodicalIF":4.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparison of immunogenicity and protection efficacy of self-amplifying and circular mRNA vaccines against SARS-CoV-2","authors":"Oinam Ningthemmani Singh , Umang Berry , Garima Joshi , Tejeswara Rao Asuru , Kannan Chandrasekar , Sriram Narayanan , Puneet Srivastava , Mahima Tiwari , Souvick Chattopadhyay , Farha Mehdi , Bhisma Narayan Panda , Debasis Nayak , Shailendra Mani , Tripti Shrivastava , Gaurav Batra , C.T. Ranjith-Kumar , Prasenjit Guchhait , Milan Surjit","doi":"10.1016/j.isci.2025.113498","DOIUrl":"10.1016/j.isci.2025.113498","url":null,"abstract":"<div><div>Recent advances in vaccine technology have positioned messenger RNA (mRNA) vaccines as safe and reliable options for human use. Conventionally, mRNA vaccines were designed using linear or self-amplifying mRNA (SAM), the latter considered to be superior. Subsequent studies on Circular mRNA (Circ-RNA) vaccines proved their efficacy. Here, we compared the efficacy of SAM- and Circ-RNA vaccines using the SARS-CoV-2-RBD (receptor binding domain) antigen. Both SAM-RBD and Circ-RBD induced a comparable anti-RBD IgG titer and virus-neutralizing antibody titer. However, the latter induced a higher memory T cell response. The Circ-RBD vaccine is stable for 4 weeks at 4°C. A bivalent vaccine containing Circ-RBD of both delta and omicron SARS-CoV-2 variants potently neutralized these viruses. These findings demonstrate Circ-RNA-RBD as an excellent vaccine candidate against COVID-19 and also provide a platform for developing bivalent Circ-RNA vaccine candidates against SARS-CoV-2 or other viruses with rapidly emerging variants.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113498"},"PeriodicalIF":4.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-04DOI: 10.1016/j.isci.2025.113508
Yaqi Jiao , Weirong Lu , Xiaohua Wang , Wenxing Sun , Baoying Hu , Jianya Zhao , Jinghao Fang , Ying Lu , Chunhua Wan
{"title":"Nucleolar stress facilitates islet β cell senescence via hijacking the DNA damage response pathways","authors":"Yaqi Jiao , Weirong Lu , Xiaohua Wang , Wenxing Sun , Baoying Hu , Jianya Zhao , Jinghao Fang , Ying Lu , Chunhua Wan","doi":"10.1016/j.isci.2025.113508","DOIUrl":"10.1016/j.isci.2025.113508","url":null,"abstract":"<div><div>Senescence is a crucial contributor to pancreatic β cell dysfunction during diabetes progression. Herein, we demonstrated that nucleolar stress, a stress event resulting from disrupted ribosomal RNA (rRNA) synthesis, drives β cell senescence. Senescent β cells exhibited altered nucleolar morphology and redistribution of the nucleolar protein nucleophosmin (NPM) <em>in vivo</em>. Exposure to nucleolar stress inducers CX-5461 and actinomycin D (ActD) resulted in senescence-associated β-gal staining (SA-β-gal) activity in cultured β cells. This was accompanied by upregulation of senescence markers p53, p21, and p16 and a senescence-associated secretory phenotype (SASP). Notably, nucleolar stress also induced γ-H2AX foci formation and Ataxia telangiectasia mutated (ATM) activation independently of DNA double-strand breaks (DSBs). Pharmacological inhibition of ATM with KU60019 strongly attenuated nucleolar stress-induced β cell senescence. Collectively, these findings identify nucleolar stress as a key upstream event in β cell senescence and highlight the γ-H2AX-ATM axis as a critical mediator of this process.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113508"},"PeriodicalIF":4.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iSciencePub Date : 2025-09-04DOI: 10.1016/j.isci.2025.113506
Yao Wang , Yu-Ru Liu , Peng-Ye Wang , Hui Li , Ping Xie
{"title":"Mechanism of spindle stability and poleward flux regulating spindle length during the metaphase","authors":"Yao Wang , Yu-Ru Liu , Peng-Ye Wang , Hui Li , Ping Xie","doi":"10.1016/j.isci.2025.113506","DOIUrl":"10.1016/j.isci.2025.113506","url":null,"abstract":"<div><div>During metaphase, the spindle stabilizes chromosomes and maintains its size despite continuous microtubule poleward flux. To investigate the mechanism of the spindle stability and how the poleward flux regulates the spindle size, we establish a minimal spindle model that incorporates kinetochores, microtubules, spindle poles, and microtubule sliding proteins such as kinesin-5, microtubule depolymerizing proteins such as kinesin-13, and microtubule crosslinking proteins such as NuMA. We find that the poleward flux stabilizes the spindle by regulating the spindle length and the length of antiparallel microtubule overlaps to achieve equal rates of microtubule sliding, plus-end polymerization, and minus-end depolymerization. We reveal the underlying mechanism of how the poleward flux rate scales linearly with the spindle length and microtubule overlap length in small cells and how microtubule nucleation affects spindle dynamics in large cells.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113506"},"PeriodicalIF":4.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Developmental changes in upper limb muscle synergies during throwing: A comparison between preschoolers and schoolers","authors":"Hiroki Saito , Ayane Kusafuka , Taishi Okegawa , Saki Takao , Naotsugu Kaneko , Hikaru Yokoyama , Ken Takiyama , Kenji Takaki , Kimitaka Nakazawa","doi":"10.1016/j.isci.2025.113497","DOIUrl":"10.1016/j.isci.2025.113497","url":null,"abstract":"<div><div>Throwing is a fundamental motor behavior that undergoes marked refinement during childhood, yet the neuromuscular mechanisms underlying this process remain unclear. We compared upper limb muscle synergies in preschool-aged (3–5 years; <em>n</em> = 13) and school-aged (6–9 years; <em>n</em> = 8) children during overarm throwing. Participants threw balls toward a fixed target while electromyographic activity from 16 upper limb muscles and ball kinematics were recorded. Muscle synergies, extracted using non-negative matrix factorization, were analyzed for structure and sparseness. School-aged children exhibited higher ball velocity, improved accuracy, and greater synergy sparseness, reflecting more selective muscle recruitment. Cluster analysis identified eight synergy clusters in schoolers versus six in preschoolers, with several preschooler synergies fractionated into functionally specialized components in schoolers. These refinements—across the upper limb—likely enhance energy transfer efficiency and release control. The findings highlight fractionation-driven specialization as a key developmental adaptation that supports improved throwing performance.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 10","pages":"Article 113497"},"PeriodicalIF":4.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145107374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}