Clinical and Translational Medicine最新文献

{"title":"LRH-1/NR5A2 targets mitochondrial dynamics to reprogram type 1 diabetes macrophages and dendritic cells into an immune tolerance phenotype","authors":"Nadia Cobo-Vuilleumier, Silvia Rodríguez-Fernandez, Livia López-Noriega, Petra I. Lorenzo, Jaime M. Franco, Christian C. Lachaud, Eugenia Martin Vazquez, Raquel Araujo Legido, Akaitz Dorronsoro, Raul López-Férnandez-Sobrino, Beatriz Fernández-Santos, Carmen Espejo Serrano, Daniel Salas-Lloret, Nila van Overbeek, Mireia Ramos-Rodriguez, Carmen Mateo-Rodríguez, Lucia Hidalgo, Sandra Marin-Canas, Rita Nano, Ana I. Arroba, Antonio Campos Caro, Alfred CO Vertegaal, Alejandro Martin Montalvo, Franz Martín, Manuel Aguilar-Diosdado, Lorenzo Piemonti, Lorenzo Pasquali, Roman González Prieto, Maria Isabel García Sánchez, Decio L. Eizirik, Maria Asuncion Martínez-Brocca, Marta Vives-Pi, Benoit R. Gauthier","doi":"10.1002/ctm2.70134","DOIUrl":"10.1002/ctm2.70134","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>The complex aetiology of type 1 diabetes (T1D), characterised by a detrimental cross-talk between the immune system and insulin-producing beta cells, has hindered the development of effective disease-modifying therapies. The discovery that the pharmacological activation of LRH-1/NR5A2 can reverse hyperglycaemia in mouse models of T1D by attenuating the autoimmune attack coupled to beta cell survival/regeneration prompted us to investigate whether immune tolerisation could be translated to individuals with T1D by LRH-1/NR5A2 activation and improve islet survival.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Peripheral blood mononuclear cells (PBMCs) were isolated from individuals with and without T1D and derived into various immune cells, including macrophages and dendritic cells. Cell subpopulations were then treated or not with BL001, a pharmacological agonist of LRH-1/NR5A2, and processed for: (1) Cell surface marker profiling, (2) cytokine secretome profiling, (3) autologous T-cell proliferation, (4) RNAseq and (5) proteomic analysis. BL001-target gene expression levels were confirmed by quantitative PCR. Mitochondrial function was evaluated through the measurement of oxygen consumption rate using a Seahorse XF analyser. Co-cultures of PBMCs and iPSCs-derived islet organoids were performed to assess the impact of BL001 on beta cell viability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>LRH-1/NR5A2 activation induced a genetic and immunometabolic reprogramming of T1D immune cells, marked by reduced pro-inflammatory markers and cytokine secretion, along with enhanced mitohormesis in pro-inflammatory M1 macrophages and mitochondrial turnover in mature dendritic cells. These changes induced a shift from a pro-inflammatory to an anti-inflammatory/tolerogenic state, resulting in the inhibition of CD4<sup>+</sup> and CD8<sup>+</sup> T-cell proliferation. BL001 treatment also increased CD4<sup>+</sup>/CD25<sup>+</sup>/FoxP3<sup>+</sup> regulatory T-cells and Th2 cells within PBMCs while decreasing CD8+ T-cell proliferation. Additionally, BL001 alleviated PBMC-induced apoptosis and maintained insulin expression in human iPSC-derived islet organoids.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>These findings demonstrate the potential of LRH-1/NR5A2 activation to modulate immune responses and support beta cell viability in T1D, suggesting a new therapeutic approach.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Key Points</h3>\u0000 \u0000 ","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noninvasive detection of twin zygosity using genome-wide linkage disequilibrium information","authors":"Lingrong Kong,&nbsp;Yingjun Yang,&nbsp;Chao Yuan,&nbsp;Xing Wei,&nbsp;Xinyao Zhou,&nbsp;Jia Zhou,&nbsp;Ya Xing,&nbsp;Gang Zou,&nbsp;Qianqian Sun,&nbsp;Luyao Cai,&nbsp;Qiufeng Liang,&nbsp;Yao Zhang,&nbsp;Hongkun Wang,&nbsp;Zesi Liu,&nbsp;Di Wu,&nbsp;Luming Sun","doi":"10.1002/ctm2.70130","DOIUrl":"10.1002/ctm2.70130","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <p>Dear Editor, in this study, we propose a novel linkage disequilibrium information-based noninvasive zygosity (LDNZ) assessment method in twin pregnancies. It combines fetus-specific allele frequency analysis with LD block to reduce the number of required single nucleotide polymorphism markers and experiment costs. LDNZ method offers a noninvasive, accurate, and cost-effective solution for zygosity assessment, addressing the need for precise obstetric care in twin pregnancies.</p>\u0000 </section>\u0000 </div>","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics analysis of pyroptosis-related genes for prognosis and immune landscape in head and neck cancer","authors":"Shikang Zheng,&nbsp;Qinghua Liu,&nbsp;Cheng Wang,&nbsp;Rongqi Zhang,&nbsp;Xin Peng,&nbsp;Junda Fan,&nbsp;Haiming Xu,&nbsp;Xiazhi Pan,&nbsp;Nanxiang Chen,&nbsp;Mingbo Liu,&nbsp;Kai Zhao","doi":"10.1002/ctm2.70144","DOIUrl":"10.1002/ctm2.70144","url":null,"abstract":"&lt;p&gt;Dear Editor,&lt;/p&gt;&lt;p&gt;Despite the demonstrated efficacy of immunotherapy in various cancers, treating head and neck squamous cell carcinoma (HNSCC) continues to pose significant challenges.&lt;span&gt;&lt;sup&gt;1, 2&lt;/sup&gt;&lt;/span&gt; Pyroptosis, a distinct form of programmed cell death, is intricately associated with tumour progression and immune response modulation.&lt;span&gt;&lt;sup&gt;3, 4&lt;/sup&gt;&lt;/span&gt; This study undertakes a comprehensive multi-omics analysis to elucidate the complex role of pyroptosis-related genes (PRGs) in the context of HNSCC, with the objective of developing a robust prognostic signature that could substantially advance the understanding of the prognosis of HNSCC and its associated immune landscape.&lt;/p&gt;&lt;p&gt;Figure 1A provides a comprehensive overview of the study's workflow, delineating the principal steps and methodologies employed in our investigation. The study encompasses 528 cancer samples and 44 normal controls from the TCGA database, along with 270 cancer samples from the GEO database. We identified 64 PRGs, of which 51 were differentially expressed in HNSCC tissues (Figure S1A). Survival analysis showed that 33 of these genes were linked to patient outcomes (Figure S2). A prognostic network was developed to elucidate the interrelationships among these genes (Figure 1B). Analysis revealed that 409 of 510 samples had PRG mutations, an 80.2% mutation rate (Figure S1B). Additionally, PRGs often showed copy number variations (CNVs), with gains or losses illustrated in Figure S1C, and their chromosomal distribution was shown in Figure S1D.&lt;/p&gt;&lt;p&gt;Hierarchical clustering analysis identified two clusters in HNSCC (Figure 1C,D), with cluster B showing a significantly better prognosis than cluster A (Figure 1E). The clinical characteristics and PRGs expression profiles associated with these subtypes are presented in Figure 1F. Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA) analyses demonstrated that cluster B was associated with immune-related pathways, while cluster A was enriched in metabolic pathways (Figure 1G,H). This observation is further corroborated by ssGSEA, which revealed a higher degree of immune cell infiltration within cluster B (Figure 1I).&lt;/p&gt;&lt;p&gt;We further identified 717 differentially expressed genes (DEGs) related to pyroptosis subtypes (Figure 2A), with 169 DEGs significantly affecting prognosis (Figure S3A). The results of the enrichment analysis for the DEGs were presented in Figure S3B. We further performed a clustering analysis and found that &lt;i&gt;k&lt;/i&gt; = 3 was optimal (Figure 2B,C). Notably, patients in group C had a better prognosis than those in other groups (Figure 2D). Moreover, there is a notable overlap in clinical traits and DEG expression between geneCluster group C and PRGCluster cluster B (Figure 2E). To develop a novel prognostic signature for HNSCC, randomly selected patients were assigned to a training cohort for signature development and a validation cohort for evaluation. Through the app","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PARylation of HMGA1 desensitizes esophageal squamous cell carcinoma to olaparib","authors":"Xin-Yuan Lei,&nbsp;Kai-Yue He,&nbsp;Qiu-Tong Li,&nbsp;Lei Zhang,&nbsp;Dan-Hui Wu,&nbsp;Jing-Yu Yang,&nbsp;Jin-Rong Guo,&nbsp;Meng-Jie Liu,&nbsp;Zi-Long Zhao,&nbsp;Jun-Qi Li,&nbsp;Huai Liu,&nbsp;Yuan Zhao,&nbsp;Yu-Jia Li,&nbsp;Qian-Hui Sun,&nbsp;Chen-Guang Wu,&nbsp;Yun-Fan Wang,&nbsp;Geng-Sheng Cao,&nbsp;Gang Wang,&nbsp;Yong-Ping Jian,&nbsp;Zhi-Xiang Xu","doi":"10.1002/ctm2.70111","DOIUrl":"10.1002/ctm2.70111","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>As a chromatin remodelling factor, high mobility group A1 (HMGA1) plays various roles in both physiological and pathological conditions. However, its role in DNA damage response and DNA damage-based chemotherapy remains largely unexplored. In this study, we report the poly ADP-ribosylation (PARylation) of HMGA1 during DNA damage, leading to desensitization of esophageal squamous cell carcinoma (ESCC) cells to the poly(ADP-ribose) polymerase 1 (PARP1) inhibitor, olaparib. We found that HMGA1 accumulates at sites of DNA damage, where it interacts with PARP1 and undergoes PARylation at residues E47 and E50 in its conserved AT-hook domain. This modification enhances the accumulation of Ku70/Ku80 at the site of DNA damage and activates the DNA-dependent protein kinase catalytic subunit, facilitating nonhomologous end-joining repair. In both subcutaneous tumour models and genetically engineered mouse models of in situ esophageal cancer, HMGA1 interference increased tumour sensitivity to olaparib. Moreover, HMGA1 was highly expressed in ESCC tissues and positively correlated with PARP1 levels as well as poor prognosis in ESCC patients. Taken together, these findings reveal a mechanistic link between HMGA1 and PARP1 in regulating cell responses to DNA damage and suggest that targeting HMGA1 could be a promising strategy to increase cancer cell sensitivity to olaparib.</p>\u0000 </section>\u0000 </div>","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microenvironmental G protein-coupled estrogen receptor-mediated glutamine metabolic coupling between cancer-associated fibroblasts and triple-negative breast cancer cells governs tumour progression","authors":"Chongwu He,&nbsp;Meixi Peng,&nbsp;Xiaoqiang Zeng,&nbsp;Hanzhi Dong,&nbsp;Zhengkui Sun,&nbsp;Jiawei Xu,&nbsp;Manran Liu,&nbsp;Liyan Liu,&nbsp;Yanxiao Huang,&nbsp;Zhiqiang Peng,&nbsp;Yu-An Qiu,&nbsp;Chunling Jiang,&nbsp;Bin Xu,&nbsp;Tenghua Yu","doi":"10.1002/ctm2.70131","DOIUrl":"10.1002/ctm2.70131","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Background&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Triple-negative breast cancer (TNBC) is a particularly aggressive type of breast cancer, known for its lack of effective treatments and unfavorable prognosis. The G protein-coupled estrogen receptor (GPER), a novel estrogen receptor, is linked to increased malignancy in various cancers. However, its involvement in the metabolic regulation of cancer-associated fibroblasts (CAFs), a key component in the tumour microenvironment, remains largely unexplored. This study investigates how GPER influences the metabolic interaction between CAFs and TNBC cells, aiming to identify potential therapeutic targets.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Methods&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;The co-culture system is performed to examine the interaction between CAFs and TNBC cells, with a focus on GPER-mediated glutamine production and release by CAFs and its subsequent uptake and utilization by TNBC cells. The definite roles of microenvironmental GPER/cAMP/PKA/CREB signalling in regulating the expression of glutamine synthetase (GLUL) and lactate dehydrogenase B (LDHB) are further investigated.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Results&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Our findings reveal that estrogen-activated GPER in CAFs significantly upregulates the expression of GLUL and LDHB, leading to increased glutamine production. This glutamine is then secreted into the extracellular matrix and absorbed by TNBC cells, enhancing their viability, motility, and chemoresistance both in vitro and in vivo. TNBC cells further metabolize the glutamine through the glutamine transporter (ASCT2) and glutaminase (GLS1) axes, which, in turn, promote mitochondrial activity and tumour progression.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Conclusions&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;The study identifies GPER as a critical mediator of metabolic coupling between CAFs and TNBC cells, primarily through glutamine metabolism. Targeting the estrogen/GPER/glutamine signalling axis in CAFs offers a promising therapeutic strategy to inhibit TNBC progression and improve patient outcomes. This novel insight into the tumour microenvironment highlights the potential of metabolic interventions in treating TNBC.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Key points&lt;/h3&gt;\u0000 \u0000 &lt;div&gt;\u0000 &lt;ol&gt;\u0000 \u0000 &lt;li&gt;\u0000 &lt;p&gt;Estrogen-activated GPER in CAFs enhances GLUL and LDHB expression via the cAMP/PKA/CREB signalling, facilitating glutamine production and utilization.&lt;/p&gt;\u0000 &lt;/li&gt;\u0000 ","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A subtype of cancer-associated fibroblast expressing syndecan-2 (SDC2) predicts survival and immune checkpoint inhibitor response in gastric cancer","authors":"Ji-Yong Sung,&nbsp;Jae-Ho Cheong,&nbsp;Kihye Shin,&nbsp;Eui Tae Kim","doi":"10.1002/ctm2.70079","DOIUrl":"10.1002/ctm2.70079","url":null,"abstract":"&lt;p&gt;Dear Editor,&lt;/p&gt;&lt;p&gt;We explored the heterogeneity and clinical implications of cancer-associated fibroblasts (CAFs) within the gastric cancer microenvironment to understand their contributions to tumour progression and therapeutic resistance. CAFs, essential components of the tumour microenvironment, regulate tumour growth, immune responses, and therapeutic outcomes. We classified CAFs into three subtypes: myofibroblastic (myoCAF), immune-regulatory (irCAF), and inflammatory (infCAF), based on gene expression signatures and functional characteristics (Figure 1A–C). Each CAF subtype was characterized by unique marker genes from a literature review (Tables S1 and S2).&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; Gene ontology (GO) analysis revealed that transcription factors NFKB1, RELA, SP1, JUN, and transcriptional regulator HDAC2 are key in CAF subtype regulation (Figure 1B). Using the MCODE algorithm&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; for protein–protein interaction, we found myoCAFs were involved in blood vessel development and extracellular matrix modelling, while irCAFs were associated with peptide ligand-binding and chemokine receptors, indicating distinct roles in immune modulation (Figure 1D,E).&lt;/p&gt;&lt;p&gt;To further investigate CAF stemness, we employed the StemID tool on single-cell cohorts. Clusters 17 and 8 showed notably high entropy and stemness, indicating that these fibroblasts are highly activated and possess stem-like properties, contributing to tumour progression and treatment resistance (Figure 1F,G). These fibroblasts were enriched in pathways related to extracellular matrix organization,&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; including the NABA core matrisome and elastic fibre formation (Figure 1H).&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; Our analysis further revealed a strong correlation between irCAF signatures and stem-like signatures in bulk gastric cancer samples, suggesting that irCAFs play a key role in sustaining an aggressive tumour microenvironment (Figure 1I-L).&lt;span&gt;&lt;sup&gt;5&lt;/sup&gt;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;We evaluated the impact of these CAF subtypes on patient prognosis using data from the Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) dataset. High expression of infCAF, irCAF, and myoCAF signatures was linked to poor prognosis (Figure 2A). A combined analysis of all three CAF signatures also indicated poor outcomes for the high-expression group (Figure 2B). In the Yonsei Cancer Hospital cohort of 497 gastric cancer patients (Y497 dataset), these CAF subtypes were enriched in the stem-like type (Figure 2C). While the infCAF signature was not significantly linked to adverse outcomes, high expression of both irCAF and myoCAF signatures was consistently linked to worse clinical outcomes (irCAF: &lt;i&gt;p&lt;/i&gt; = .0022, myoCAF: &lt;i&gt;p&lt;/i&gt; = .0053) (Figure 2D). We classified patients into nine groups based on the CAF subtype signature via gene set enrichment test in the Y497 cohort. (Figure 2E). Furthermore, we confirmed that the CAF subtype signatures found in TCGA pan-cancer datasets act ","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From data to decision: Scaling artificial intelligence with informatics for epilepsy management","authors":"Nishant Sinha,&nbsp;Alfredo Lucas,&nbsp;Kathryn Adamiak Davis","doi":"10.1002/ctm2.70108","DOIUrl":"10.1002/ctm2.70108","url":null,"abstract":"&lt;p&gt;The integration of artificial intelligence (AI) into epilepsy research presents a critical opportunity to revolutionize the management of this complex neurological disorder.&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; Despite significant advancements in developing AI algorithms to diagnose and manage epilepsy, their translation into clinical practice remains limited. This gap underscores the urgent need for scalable AI and neuroinformatics approaches that can bridge the divide between research and real-world application.&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; The ability to generalize AI models from controlled research environments to diverse clinical settings is crucial. Current efforts have made substantial progress, but they also reveal common pitfalls, such as overestimation of model performance due to data leakage and the challenges of small sample sizes, which hinder the generalization of these models.&lt;/p&gt;&lt;p&gt;To address these challenges and fully realize the potential of AI in epilepsy care, a robust framework for data sharing and collaboration across research centres is essential. Cloud-based informatics platforms offer a promising solution by enabling the aggregation and harmonization of large, multisite datasets. These platforms can facilitate the development of AI models that are not only powerful but also scalable and generalizable across different patient populations and clinical scenarios. In this commentary, we will explore the common methodological errors that lead to overly optimistic AI models in epilepsy research and propose strategies to overcome these issues. We will also discuss the importance of collaborative data sharing in building robust, clinically relevant AI tools and highlight the role of advanced neuroinformatics infrastructures in supporting the translational pathway from research to clinical practice (Figure 1).&lt;/p&gt;&lt;p&gt;The promise of AI in epilepsy research is often hampered by methodological errors that lead to overly optimistic performance metrics. One of the most significant issues is &lt;i&gt;data leakage&lt;/i&gt;, which occurs when information from outside the training dataset influences the model, resulting in an overestimation of its predictive power. This can happen when features are derived from the entire dataset rather than just the training subset.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; To mitigate this, strict separation between training and test datasets is essential and feature selection must be performed within each fold of the cross-validation process independently. Nested cross-validation, where model selection and performance estimation are conducted separately, further reduces the risk of data leakage.&lt;/p&gt;&lt;p&gt;Another common error is the &lt;i&gt;improper application of cross-validation&lt;/i&gt; techniques. Often, researchers perform feature selection or hyperparameter tuning on the entire dataset before cross-validation, leading to inflated performance metrics. The correct approach is to embed these steps within each fold of the cross-validation process to ensure","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic conditioning of porcine kidney grafts with extracellular vesicles derived from urine progenitor cells: A proof-of-concept study","authors":"Perrine Burdeyron,&nbsp;Sébastien Giraud,&nbsp;Maryne Lepoittevin,&nbsp;Nina Jordan,&nbsp;Sonia Brishoual,&nbsp;Maïté Jacquard,&nbsp;Virginie Ameteau,&nbsp;Nadège Boildieu,&nbsp;Estelle Lemarie,&nbsp;Jonathan Daniel,&nbsp;Frédéric Martins,&nbsp;Nicolas Mélis,&nbsp;Marine Coué,&nbsp;Raphaël Thuillier,&nbsp;Henri Leuvenink,&nbsp;Luc Pellerin,&nbsp;Thierry Hauet,&nbsp;Clara Steichen","doi":"10.1002/ctm2.70095","DOIUrl":"10.1002/ctm2.70095","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt;  &lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Among strategies to limit ischemia/reperfusion (IR) injuries in transplantation, cell therapy using stem cells to condition/repair transplanted organs appears promising. We hypothesized that using a cell therapy based on extracellular vesicles (EVs) derived from urine progenitor cells (UPCs) during hypothermic and normothermic machine perfusion can prevent IR-related kidney damage.&lt;/p&gt;\u0000 \u0000 &lt;p&gt;We isolated and characterized porcine UPCs and their extracellular vesicles (EVs). Then these were used in an &lt;i&gt;ex vivo&lt;/i&gt; porcine kidney preservation model. Kidneys were subjected to warm ischemia (32 min) and then preserved by hypothermic machine perfusion (HMP) for 24 h before 5 h of normothermic machine perfusion (NMP). Three groups were performed (&lt;i&gt;n&lt;/i&gt; = 5–6): Group 1 (G1): HMP/vehicle + NMP/vehicle, Group 2 (G2): HMP/EVs + NMP/vehicle, Group 3 (G3): HMP/EVs + NMP/EVs.&lt;/p&gt;\u0000 \u0000 &lt;p&gt;Porcine UPCs were successfully isolated from urine and fully characterized as well as their EVs which were found of expected size/phenotype. EVs injection during HMP alone, NMP alone, or both was feasible and safe and did not impact perfusion parameters. However, cell damage markers (LDH, ASAT) were decreased in G3 compared with G1, and G3 kidneys displayed a preserved tissue integrity with reduced tubular dilatation and inflammation notably. However, renal function indicators such as creatinine clearance measured for 5 h of normothermic perfusion or NGAL perfusate's level were not modified by EVs injection. Regarding perfusate analysis, metabolomic analyses and cytokine quantification showed an immunomodulation signature in G3 compared with G1 and highlighted potential metabolic targets. In vitro, EVs as well as perfusates from G3 partially recovered endothelial cell metabolic activity after hypoxia. Finally, RNA-seq performed on kidney biopsies showed different profiles between G1 and G3 with regulation of potential IR targets of EVs therapy.&lt;/p&gt;\u0000 \u0000 &lt;p&gt;We showed the feasibility/efficacy of UPC-EVs for hypothermic/normothermic kidney conditioning before transplantation, paving the way for combining machine perfusion with EVs-based cell therapy for organ conditioning.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Highlights&lt;/h3&gt;\u0000 \u0000 &lt;div&gt;\u0000 &lt;ul&gt;\u0000 \u0000 &lt;li&gt;&lt;span&gt;· &lt;/span&gt;UPCs from porcine urine can be used to generate a cell therapy product based on extracellular vesicles (pUPC-EVs).&lt;/li&gt;\u0000 \u0000 &lt;li&gt;&lt;span&gt;· &lt;/span&gt;pUPC-EVs injection during HMP and NMP decreases cell damage markers and has an immunomodulatory effect.&lt;/li&gt;\u0000 \u0000 &lt;li&gt;&lt;span&gt;· &lt;/span&gt;pUPC-EVs-treat","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chitinase 3-like 1 is neurotoxic in multiple sclerosis patient-derived cortical neurons","authors":"Rucsanda Pinteac,&nbsp;Jordi Soriano,&nbsp;Clara Matute-Blanch,&nbsp;José M Lizcano,&nbsp;Anna Duarri,&nbsp;Sunny Malhotra,&nbsp;Herena Eixarch,&nbsp;Gloria López Comellas,&nbsp;Xavier Montalban,&nbsp;Manuel Comabella","doi":"10.1002/ctm2.70125","DOIUrl":"10.1002/ctm2.70125","url":null,"abstract":"&lt;p&gt;Dear Editor,&lt;/p&gt;&lt;p&gt;We are pleased to present our latest findings regarding the neurotoxic role of Chitinase 3-like 1 (CHI3L1) in multiple sclerosis (MS). CHI3L1, a 40 kD glycoprotein, is primarily produced by activated astrocytes and microglia in the central nervous system (CNS), and it has garnered considerable attention due to its implications in inflammation and tissue remodelling.&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; It is notably increased in several conditions, including MS, and accumulating evidence supports CHI3L1 as a biomarker in early MS, with elevated cerebrospinal fluid (CSF) levels associated with increased disability risk.&lt;span&gt;&lt;sup&gt;2, 3&lt;/sup&gt;&lt;/span&gt; This association led us to investigate whether CHI3L1 simply reflects glial activation or if it exerts direct neurotoxicity. Our prior work in murine neurons demonstrated CHI3L1's neurotoxic effects,&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; prompting us to explore its impact on MS patient-derived human induced pluripotent stem cells (hiPSC). Here, we aim to characterize these effects at both molecular and functional levels, further exploring CHI3L1's potential as a biomarker and therapeutic target for MS.&lt;/p&gt;&lt;p&gt;The first step in our investigation involved refining a human neuronal model using two MS-derived hiPSC lines (Table S1), MS-10 and MS-6, matured for 28 and 40 days (Figure S1A). To ensure the model's suitability, we meticulously characterized the neuronal cultures through immunofluorescence and calcium imaging, evaluating neuronal and astrocytic proportions (Figure S1B–E,J,L), cortical fate (Figure S1F–I,K,M), dendrite growth (Figure S2A), synaptic (Figure S2B) and neurotransmitter markers (Figure S3) and the onset of sporadic and synchronous neuronal activity (Figure S4). The neuronal cultures exhibited varying percentages of astrocytes, which increased over time for both cell lines (Figure S1J,L). Cortical fate was delineated by robust Tbr1 immunoreactivity alongside limited CTIP2 expression (Figure S1K,M). Notably, dendritic growth persisted until day 28 (Figure S2A), coinciding with the expression of synaptic markers like synapsin and PSD-95 (Figure S2B). By day 28, most neurons from each line co-expressed glutamatergic and GABAergic markers, but by day 40, the loss of vGAT immunoreactivity suggested a predominant population of glutamatergic cells (Figure S3). Additionally, fluorescence calcium imaging revealed a progressive increase in spontaneous and synchronous neuronal activity over time, culminating in a sporadic and synchronous pattern by day 40 (Figure S4).&lt;/p&gt;&lt;p&gt;Our investigation progressed to examine the impact of CHI3L1 on neuronal morphology and synaptic plasticity by treating MS-10 and MS-6 neuronal cultures at day 28 with CHI3L1 (300 ng/mL) or vehicle (PBS) for 24 and 72 h (Figure 1A). The analysis revealed a 17.5% reduction in dendritic arborization by 24 h and a 19% reduction by 72 h, along with a 16.5% decrease in dendrite length at 72 h (Figure 1B–D). Additionally, synaptic plastic","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating intra-tumoural heterogeneity and microenvironment diversity in primary cardiac angiosarcoma through single-cell RNA sequencing","authors":"Jingyuan Huo,&nbsp;Zhen Wang,&nbsp;Wenting Zhao,&nbsp;Miao Chen,&nbsp;Haoyang Li,&nbsp;Fengpu He,&nbsp;Xiao Tian,&nbsp;Yaqi Ma,&nbsp;Firyuza Husanova,&nbsp;Liang Ma,&nbsp;Yiming Ni,&nbsp;Hongda Ding,&nbsp;Weidong Li,&nbsp;Hongfei Xu","doi":"10.1002/ctm2.70113","DOIUrl":"10.1002/ctm2.70113","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Background&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Primary cardiac angiosarcoma (PCAS) is a rare and aggressive heart tumour with limited treatment options and a poor prognosis. Understanding cellular heterogeneity and tumour microenvironment (TME) is crucial for the development of effective therapies. Here, we investigated the intratumoural heterogeneity and TME diversity of PCAS using single-cell RNA sequencing (scRNA-seq).&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Methods&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;We performed scRNA-seq analysis on tumour samples from four patients with PCAS, supplemented with multicolour immunohistochemistry for identification. We used scRNA-seq data from five normal cardiac tissue samples downloaded from public databases for comparative analyses. Bioinformatic analyses, including Cell Ranger, Seurat, Monocle2, hdWGCNA, SCENIC and NicheNet, were utilized to identify distinct cell populations, transcriptional patterns, and co-regulating gene modules.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Results&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Our analysis revealed significant intratumoural heterogeneity in PCAS driven by diverse biological processes such as protein synthesis, degradation, and RIG-I signalling inhibition. The SCENIC analysis identified three primary transcription factors' clusters (&lt;i&gt;CEBPB&lt;/i&gt;, &lt;i&gt;MYC&lt;/i&gt; and &lt;i&gt;TAL1&lt;/i&gt;). T-cell subset analysis showed exhausted antigen-specific T-cells, complicating the efficacy of immune checkpoint blockade. Furthermore, we observed suppressive macrophages (SPP1+ and OLR1+) and reduced mitochondrial gene &lt;i&gt;MT-RNR2&lt;/i&gt; (MTRNR2L12) expression in TME-infiltrating cells, indicating impaired mitochondrial function.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Conclusion&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;This study elucidates the complex cellular landscape and immune microenvironment of PCAS, highlighting potential molecular targets for the development of novel therapies. These findings underscore the importance of a multifaceted therapeutic approach for addressing the challenges posed by PCAS's heterogeneity and immune evasion.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Key points&lt;/h3&gt;\u0000 \u0000 &lt;div&gt;\u0000 &lt;ul&gt;\u0000 \u0000 &lt;li&gt;Insights into the heterogeneity and transcriptional patterns of sarcoma cells may explain the challenges in treating primary cardiac angiosarcoma (PCAS) using the current therapeutic modalities.&lt;/li&gt;\u0000 \u0000 &lt;li&gt;Characterization of the immune microenvironment revealed significant immunosuppression mediated by specific myeloid cell","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}