Biomarker Research最新文献

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Epigenetic signatures on plasma cell-free DNA to detect kidney allograft rejection in a non-invasive way: development of a 10-plex digital PCR assay. 无浆细胞DNA的表观遗传特征以非侵入性方式检测肾移植排斥反应:10 plex数字PCR测定的发展。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-09-26 DOI: 10.1186/s40364-025-00834-7
Yoan Velut, Geoffroy Poulet, Thomas Bersez, Pauline Boyer, Coraline Maujean, Stéphanie Gnanalingam, Camille Moniot, Jana Heneine, Dany Anglicheau, Marion Rabant, Renaud Snanoudj, Vincent Vuiblet, Gabriel Choukroun, Tristan de Nattes, François Audenet, Bastien Parier, Sophie Ferlicot, Virginie Verkarre, David Buob, Pierre Galichon
{"title":"Epigenetic signatures on plasma cell-free DNA to detect kidney allograft rejection in a non-invasive way: development of a 10-plex digital PCR assay.","authors":"Yoan Velut, Geoffroy Poulet, Thomas Bersez, Pauline Boyer, Coraline Maujean, Stéphanie Gnanalingam, Camille Moniot, Jana Heneine, Dany Anglicheau, Marion Rabant, Renaud Snanoudj, Vincent Vuiblet, Gabriel Choukroun, Tristan de Nattes, François Audenet, Bastien Parier, Sophie Ferlicot, Virginie Verkarre, David Buob, Pierre Galichon","doi":"10.1186/s40364-025-00834-7","DOIUrl":"10.1186/s40364-025-00834-7","url":null,"abstract":"<p><p>The standard of care for the follow-up of kidney allograft recipients combines non-invasive but non-specific biomarkers and kidney biopsies for the gold standard histology-based diagnosis, limited by the sampling bias, haemorrhagic risk, and low cost-effectiveness. We hypothesized that a targeted epigenetic analysis of cell-free DNA (cfDNA) would combine non-invasiveness and specificity for the diagnosis of kidney allograft rejection. We developed an in silico pipeline to identify 9 specific methylation signatures of epithelial or endothelial cell types in glomerular and tubular kidney compartments. Methylation-specific digital Polymerase Chain Reaction (dPCR) were designed and validated for these markers and combined in a 10-plex dPCR. In a retrospective cohort of 170 plasma cfDNA from adult kidney transplant recipients, we evaluated the diagnostic properties of our biomarkers for predicting rejection, evaluated on solid biopsy according to Banff 2022 classification. Combining the dedicated biomarkers with standard-of-care blood tests (donor-specific antibody (DSA), estimated glomerular filtration rate (eGFR)) produced a prediction model with an Area under the Curve (AUC) for biopsy-proven kidney transplant rejection vs. no rejection greater than with DSA and eGFR alone (AUC = of 0.884 vs. 0.776, p = 0.0005). In an alternative model for the prediction of any graft lesion of Banff classification vs. pristine biopsies (all Banff score = 0) epigenetic kidney biomarkers outperformed DSA (AUC = 0.754 vs. 0.596, p = 0.004). Thus, epigenetic signatures derived from the combination of kidney cell type specific methylation marker of cfDNA constitute a promising non-invasive diagnostic and theragnostic tool for kidney transplant patients.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"118"},"PeriodicalIF":11.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Long non-coding RNA PWRN4 associated with post-SVR hepatocellular carcinoma: a genome-wide association study. 长链非编码RNA PWRN4与svr后肝细胞癌相关:全基因组关联研究
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-09-24 DOI: 10.1186/s40364-025-00832-9
Goki Suda, Masaya Sugiyama, Hayato Hikita, Akira Nishio, Tomohide Tatsumi, Tetsuo Takehara, Miyako Murakawa, Mina Nakagawa, Yasuhiro Asahina, Masashi Mizokami, Tatsuhiko Kakisaka, Yuzuru Sakamoto, Akinobu Taketomi, Koji Miyanishi, Yoshiyuki Ueno, Hiroaki Haga, Shinya Maekawa, Nobuyuki Enomoto, Masayuki Kurosaki, Motoyuki Kohjima, Makoto Nakamuta, Yasuhito Tanaka, Yoshiya Yamamoto, Masaru Baba, Hisatoshi Hanamatsu, Jun-Ichi Furukawa, Masatsugu Ohara, Takashi Kitagataya, Naoki Kawagishi, Masato Nakai, Takuya Sho, Koji Ogawa, Naoya Sakamoto
{"title":"Long non-coding RNA PWRN4 associated with post-SVR hepatocellular carcinoma: a genome-wide association study.","authors":"Goki Suda, Masaya Sugiyama, Hayato Hikita, Akira Nishio, Tomohide Tatsumi, Tetsuo Takehara, Miyako Murakawa, Mina Nakagawa, Yasuhiro Asahina, Masashi Mizokami, Tatsuhiko Kakisaka, Yuzuru Sakamoto, Akinobu Taketomi, Koji Miyanishi, Yoshiyuki Ueno, Hiroaki Haga, Shinya Maekawa, Nobuyuki Enomoto, Masayuki Kurosaki, Motoyuki Kohjima, Makoto Nakamuta, Yasuhito Tanaka, Yoshiya Yamamoto, Masaru Baba, Hisatoshi Hanamatsu, Jun-Ichi Furukawa, Masatsugu Ohara, Takashi Kitagataya, Naoki Kawagishi, Masato Nakai, Takuya Sho, Koji Ogawa, Naoya Sakamoto","doi":"10.1186/s40364-025-00832-9","DOIUrl":"10.1186/s40364-025-00832-9","url":null,"abstract":"<p><p>A subset of patients still develops hepatocellular carcinoma (HCC) even after eradication of the hepatitis-C virus (HCV) by anti-HCV treatment. We conducted a genome-wide association study (GWAS) to identify host genetic factors associated with HCC development following HCV eradication in Japan. In this GWAS (n = 517), the discovery cohort included 118 patients without HCC and 67 who developed HCC following HCV eradication with interferon-based therapy. A genome-wide scan for HCC-associated variants was conducted. An independent cohort of 274 patients without HCC and 58 patients with post-eradication HCC was used for replication. The effects of candidate gene variants were assessed clinically and through in vitro cellular assays. The GWAS identified significant variants associated with HCC development following HCV eradication, including rs4778350, located near the long non-coding RNA Prader-Willi non-protein coding RNA 4 (PWRN4) on chromosome 15. In the combined analysis, rs4778350 remained significantly associated with HCC, showing a high odds ratio of 5.86 (95% CI, 3.63-9.44). The frequency of the A allele in rs4778350 differs across ethnic populations. Multivariate analysis revealed that female sex, high platelet count, and higher serum albumin levels were associated with reduced HCC risk, while fibrosis stage F4 and the AA genotype of rs4778350 were linked to increased risk. The AA genotype of rs4778350 enhanced PWRN4 expression, promoting cell proliferation, migration, and invasion. These findings suggest a role for PWRN4 in hepatocarcinogenesis through its association with rs4778350 in patients achieving HCV eradication.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"113"},"PeriodicalIF":11.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP. PKP1通过稳定PFKP调节能量代谢来促进肺癌。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-09-01 DOI: 10.1186/s40364-025-00815-w
Félix Ritoré-Salazar, Alberto M Arenas, Ana M Matia-González, Alessandra Zaza, Emil Aagaard Thomsen, Anne Bruun Rovsing, Jacob Giehm Mikkelsen, Nelida Ines Noguera, Pedro P Medina
{"title":"PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP.","authors":"Félix Ritoré-Salazar, Alberto M Arenas, Ana M Matia-González, Alessandra Zaza, Emil Aagaard Thomsen, Anne Bruun Rovsing, Jacob Giehm Mikkelsen, Nelida Ines Noguera, Pedro P Medina","doi":"10.1186/s40364-025-00815-w","DOIUrl":"10.1186/s40364-025-00815-w","url":null,"abstract":"","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"112"},"PeriodicalIF":11.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dual functionality of MDM2 in PROTACs expands the horizons of targeted protein degradation. MDM2在PROTACs中的双重功能扩展了靶向蛋白降解的范围。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-27 DOI: 10.1186/s40364-025-00826-7
Junyi Zhao, Hongzhen Chen, Chao Liang
{"title":"Dual functionality of MDM2 in PROTACs expands the horizons of targeted protein degradation.","authors":"Junyi Zhao, Hongzhen Chen, Chao Liang","doi":"10.1186/s40364-025-00826-7","DOIUrl":"10.1186/s40364-025-00826-7","url":null,"abstract":"<p><p>The evolution of targeted protein degradation (TPD) has been significantly propelled by the advent of proteolysis-targeting chimeras (PROTACs), which utilize heterobifunctional molecules to facilitate the ubiquitination-mediated degradation of previously \"undruggable\" proteins. Mouse double minute 2 (MDM2), which is often overexpressed in various diseases and plays a crucial role in regulating key pathways like p53, emerges as an exemplary candidate for therapeutic exploitation within the TPD realm, serving both as an intrinsic E3 ligase and as a direct protein of interest (POI). By harnessing MDM2's inherent E3 ligase activity, PROTACs have been designed to efficiently degrade specific POIs, achieving substantial success in both in vitro and in vivo studies. Alternatively, PROTACs have been developed to directly target MDM2 itself, offering new approaches for therapeutic intervention. Recent research has yielded valuable strategies for optimizing MDM2-harnessing and MDM2-targeted PROTAC designs, concentrating on warhead selection of POI, linker length and composition optimization, and the choice among various E3 ligases and their corresponding recruiters. These advancements not only broaden the scope of PROTAC technologies but also expedite the development of MDM2-based therapies, inspiring approaches for disease treatment.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"111"},"PeriodicalIF":11.5,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12392632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crosstalk between lactylation and RNA modifications in tumorigenesis: mechanisms and therapeutic implications. 肿瘤发生中乳酸化和RNA修饰之间的串扰:机制和治疗意义。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-26 DOI: 10.1186/s40364-025-00824-9
Shantong Liu, Qianquan Ma, Chong Zeng, Haoyu Li, Jun Su, Zhihao Song, Ruyu Yan, Zijin Zhao, Songhai Tian, Wei Huang
{"title":"Crosstalk between lactylation and RNA modifications in tumorigenesis: mechanisms and therapeutic implications.","authors":"Shantong Liu, Qianquan Ma, Chong Zeng, Haoyu Li, Jun Su, Zhihao Song, Ruyu Yan, Zijin Zhao, Songhai Tian, Wei Huang","doi":"10.1186/s40364-025-00824-9","DOIUrl":"10.1186/s40364-025-00824-9","url":null,"abstract":"<p><p>Complex crosstalk occurs between protein and nucleic acid modifications, with lactylation, an emerging post-translational modification (PTM), being implicated in tumor progression. However, the mechanisms mediating the crosstalk between lactylation and RNA modifications and their roles in disease pathogenesis remain largely unresolved. In this review, we summarize current advances in the regulatory interactions between lactylation and RNA modifications, explore their functional implications in cancer biology, and discuss the therapeutic potential of targeting these modifications individually or in combination. This work aims to provide a comprehensive overview of their mechanistic involvement in cancer and to inform novel strategies for precision-targeted therapy.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"110"},"PeriodicalIF":11.5,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12382095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeting RPS6KC1 to overcome enzalutamide resistance in prostate cancer. 靶向RPS6KC1治疗前列腺癌enzalutamide耐药。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-23 DOI: 10.1186/s40364-025-00822-x
Fu-Hao Ji, Yu-Hang Qian, Xiu-Chen Guo, Hai-Hong Liao, Jia-Cheng Huang, Zi-Han Xu, Ming-Ming Yu, Yan-Yuan Wu, Jie-Wen Bao, Hao-Jie Chen, Yong-Jiang Yu, Lin Wang
{"title":"Targeting RPS6KC1 to overcome enzalutamide resistance in prostate cancer.","authors":"Fu-Hao Ji, Yu-Hang Qian, Xiu-Chen Guo, Hai-Hong Liao, Jia-Cheng Huang, Zi-Han Xu, Ming-Ming Yu, Yan-Yuan Wu, Jie-Wen Bao, Hao-Jie Chen, Yong-Jiang Yu, Lin Wang","doi":"10.1186/s40364-025-00822-x","DOIUrl":"10.1186/s40364-025-00822-x","url":null,"abstract":"<p><p>The androgen receptor signaling inhibitor enzalutamide (Enz) is one the primary therapeutic drugs for advanced prostate cancer (PCa). Nevertheless, most of patients ultimately develop resistance to Enz. Through an integrated analysis of CRISPR genome-wide and kinome-wide screens, coupled with observations of elevated expression levels in Enz-resistant cell lines and PCa tumor tissues, our study identified RPS6KC1 as a novel essential gene implicated in Enz resistance. Mechanistically, our research indicates that the Warburg effect induces H3K18 lactylation, which regulates the expression of RPS6KC1 via the transcription factor P65. Elevated expression of RPS6KC1 was found to recruit PRDX3 to the mitochondria, thereby mitigating ferroptosis. These findings suggest that the H3K18la/NF-κB/RPS6KC1/PRDX3 axis is important for the development of resistance to Enz. Our results suggest that the combination of Enz with targeted RPS6KC1 inhibition or a ferroptosis inducer may represent a promising therapeutic strategy to overcome Enz resistance.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"109"},"PeriodicalIF":11.5,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12375275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Salvage therapy containing sorafenib and donor lymphocyte infusion is associated with improved outcomes for FLT3 wild-type acute myeloid leukemia relapsing after allogeneic hematopoietic stem cell transplantation. 含有索拉非尼和供体淋巴细胞输注的补救性治疗与同种异体造血干细胞移植后FLT3野生型急性髓性白血病复发的改善结果相关。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-20 DOI: 10.1186/s40364-025-00816-9
Zhonghui Jiang, Ya Zhou, Yuxin Bai, Fang Dai, Menglin Fan, Tian Zhang, Danian Nie, Yunxin Zeng, Yirong Jiang, Ping Zhu, Zhiping Fan, Na Xu, Fen Huang, Ren Lin, Min Dai, Xiaojun Xu, Zhangkun Li, Hua Jin, Jing Sun, Qifa Liu, Li Xuan
{"title":"Salvage therapy containing sorafenib and donor lymphocyte infusion is associated with improved outcomes for FLT3 wild-type acute myeloid leukemia relapsing after allogeneic hematopoietic stem cell transplantation.","authors":"Zhonghui Jiang, Ya Zhou, Yuxin Bai, Fang Dai, Menglin Fan, Tian Zhang, Danian Nie, Yunxin Zeng, Yirong Jiang, Ping Zhu, Zhiping Fan, Na Xu, Fen Huang, Ren Lin, Min Dai, Xiaojun Xu, Zhangkun Li, Hua Jin, Jing Sun, Qifa Liu, Li Xuan","doi":"10.1186/s40364-025-00816-9","DOIUrl":"10.1186/s40364-025-00816-9","url":null,"abstract":"<p><strong>Background: </strong>There is no established standard treatment for acute myeloid leukemia (AML) patients with FLT3 wild-type relapsing after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Multi-kinase inhibitor sorafenib has been widely explored in the treatment of AML patients with FLT3 internal tandem duplication (FLT3-ITD) mutations. Some studies have revealed that the addition of sorafenib to standard chemotherapy could improve outcomes in newly diagnosed AML regardless of FLT3 status. However, the application of sorafenib in FLT3 wild-type AML patients experiencing relapse after allo-HSCT remains minimally investigated.</p><p><strong>Methods: </strong>We retrospectively compared the effects of conventional treatment combined with or without sorafenib on the outcomes of these patients. The study mainly focused on the treatment response of salvage therapy and survival.</p><p><strong>Results: </strong>Sixty-two AML patients with FLT3 wild-type who relapsed after allo-HSCT were enrolled in this study, including 38 with sorafenib and 24 without sorafenib. Fifty patients received 68 doses of donor lymphocyte infusion (DLI). The rate of composite complete remission was 65.8% in the sorafenib group, compared with 29.2% in the non-sorafenib group (P = 0.005). With a median follow-up of 13.2 months (IQR, 3.2-43.5) after relapse, the 2-year overall survival (OS) was 47.4% (95%CI, 33.9%-66.2%) and 16.7% (6.8%-40.8%) in the sorafenib and non-sorafenib groups (P = 0.006). The 2-year event-free survival (EFS) was 44.7% (31.4%-63.7%) and 16.7% (6.8%-40.8%) in the two groups (P = 0.012). Multivariable analysis revealed that salvage therapy including sorafenib was the protective factor for longer OS and EFS (HR = 0.395, 95% CI: 0.209-0.746, P = 0.004; HR = 0.406, 95% CI: 0.218-0.754, P = 0.004). The incidences of acute graft-versus-host disease (GVHD) and chronic GVHD were similar between the two groups (P = 0.806, P = 0.908).</p><p><strong>Conclusion: </strong>Our results suggest that salvage therapy including sorafenib and DLI is associated with improved outcomes for AML patients with FLT3 wild-type relapsing after allo-HSCT.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"106"},"PeriodicalIF":11.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144884294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Trans-omics analyses identify the biochemical network of LPCAT1 associated with coronary artery disease. 反式组学分析确定了与冠状动脉疾病相关的LPCAT1的生化网络。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-20 DOI: 10.1186/s40364-025-00821-y
Paul Wei-Che Hsu, Chi-Hsiao Yeh, Chi-Jen Lo, Tsung-Hsien Tsai, Yun-Hsuan Chan, Yi-Ju Chou, Ning-I Yang, Mei-Ling Cheng, Wayne Huey-Herng Sheu, Chi-Chun Lai, Huey-Kang Sytwu, Ting-Fen Tsai
{"title":"Trans-omics analyses identify the biochemical network of LPCAT1 associated with coronary artery disease.","authors":"Paul Wei-Che Hsu, Chi-Hsiao Yeh, Chi-Jen Lo, Tsung-Hsien Tsai, Yun-Hsuan Chan, Yi-Ju Chou, Ning-I Yang, Mei-Ling Cheng, Wayne Huey-Herng Sheu, Chi-Chun Lai, Huey-Kang Sytwu, Ting-Fen Tsai","doi":"10.1186/s40364-025-00821-y","DOIUrl":"10.1186/s40364-025-00821-y","url":null,"abstract":"<p><strong>Background: </strong>Coronary artery disease (CAD) remains a leading cause of mortality in developed nations. While previous genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) linked to CAD, their impact on disease progression requires trans-omics validation.</p><p><strong>Methods: </strong>This study merges whole genome SNP analysis and metabolomic profiling to distinguish CAD patients from high-risk and healthy individuals. A cross-sectional study was conducted, enrolling participants from the Northeastern Taiwan Community Medicine Research Cohort, which spans the period between August 2013 and November 2020. A total of 781 participants were included in the study and categorized into three groups: control (n = 271), high-risk (n = 363), and CAD (n = 147) groups, following a stratification protocol. The study integrated K-clustering of metabolomics and SNP datasets. Subsequently, a machine-learning (ML)-assisted prediction model was developed specifically for CAD identification.</p><p><strong>Results: </strong>Four significant findings emerged. Firstly, plasma levels of phospholipids decline from healthy controls to high-risk individuals and then decline further among CAD patients. This indicates that plasma phospholipids have potential as biomarkers and implies that they have a role in CAD progression. Secondly, five genes are linked to lipidomic alterations via their top-ranking among CAD-associated SNPs. Thirdly, a specific LPCAT1 haplotype is associated with CAD using a trans-omics approach. Lastly, an ML-assisted trans-omics prediction model for CAD was developed, which achieves an area under the curve of 0.917, with LPCAT1 among the 16 top-ranked predictive features.</p><p><strong>Conclusion: </strong>This study highlights the usefulness of a multi-omics signature when discriminating CAD patients and suggests that abnormalities in phospholipid metabolism are influenced by LPCAT1 genetic variants. Our findings underscore the potential of multi-omics approaches to our understanding and identification of critical factors in CAD development.</p><p><strong>Trial registration number and date of registration: </strong>ClinicalTrials.gov Identifier: NCT04839796; Aug 2013.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"107"},"PeriodicalIF":11.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144884301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The distinct landscape of tumor immune microenvironment in homologous recombination deficient cancers. 同源重组缺陷癌中肿瘤免疫微环境的独特景观。
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-20 DOI: 10.1186/s40364-025-00814-x
Qiuyang Xu, Yuanjia Wen, Taiyuan Huang, Huayi Li, Xingzhe Liu, Shen-Nan Shi, Wenjian Gong, Gordon B Mills, Ding Ma, Qinglei Gao, Yong Fang
{"title":"The distinct landscape of tumor immune microenvironment in homologous recombination deficient cancers.","authors":"Qiuyang Xu, Yuanjia Wen, Taiyuan Huang, Huayi Li, Xingzhe Liu, Shen-Nan Shi, Wenjian Gong, Gordon B Mills, Ding Ma, Qinglei Gao, Yong Fang","doi":"10.1186/s40364-025-00814-x","DOIUrl":"10.1186/s40364-025-00814-x","url":null,"abstract":"","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"108"},"PeriodicalIF":11.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144884295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeting degradation of IKZF1 and IKZF3 through modulation of the E3 ligase substrates in the context of cellular therapies for multiple myeloma. 通过调节E3连接酶底物靶向IKZF1和IKZF3在多发性骨髓瘤细胞治疗中的降解
IF 11.5 2区 医学
Biomarker Research Pub Date : 2025-08-15 DOI: 10.1186/s40364-025-00825-8
David Kegyes, Anamaria Bancos, Adrian Bogdan Tigu, Ioana Rus, Delia Dima, Diana Cenariu, Madalina Nistor, Raluca Munteanu, Diana Gulei, Alina Tanase, Anca Colita, Anca Buzoianu, Cristina Iuga, Mihnea Zdrenghea, Evangelos Terpos, Stefan O Ciurea, Aaron Ciechanover, Hermann Einsele, Ciprian Tomuleasa
{"title":"Targeting degradation of IKZF1 and IKZF3 through modulation of the E3 ligase substrates in the context of cellular therapies for multiple myeloma.","authors":"David Kegyes, Anamaria Bancos, Adrian Bogdan Tigu, Ioana Rus, Delia Dima, Diana Cenariu, Madalina Nistor, Raluca Munteanu, Diana Gulei, Alina Tanase, Anca Colita, Anca Buzoianu, Cristina Iuga, Mihnea Zdrenghea, Evangelos Terpos, Stefan O Ciurea, Aaron Ciechanover, Hermann Einsele, Ciprian Tomuleasa","doi":"10.1186/s40364-025-00825-8","DOIUrl":"10.1186/s40364-025-00825-8","url":null,"abstract":"<p><p>Multiple myeloma (MM) is a blood cancer characterized by the clonal evolution of plasma cells. In 2022, there were an estimated 118 000 MM cases and 121 000 deaths worldwide. The treatment landscape of MM has undergone a dramatic transformation in recent decades, shifting from conventional chemotherapy to more targeted approaches. In order to overcome intrinsic and acquired resistance mechanisms that frequently restrict the efficacy of single-agent therapies, drug combination strategies have been developed to simultaneously target multiple pathogenetic pathways. Building on the success of immunomodulatory agents, CRBN E3 ligase modulators (CELMoDs), iberdomide (CC-220) and mezigdomide (CC-92480), have been designed as promising and more selective agents. CELMoDs demonstrate a 10-20 times higher binding capacity and they promote a more profound and rapid breakdown of Ikaros and Aiolos compared to traditional immunomodulatory agents. According to the National Cancer Institute Surveillance Program, the median survival for fit patients is greater than ten years, and the 5-year survival for the general MM patient population in the US approaches 60%. Despite these encouraging numbers, MM is still an incurable disease, and the majority of patients eventually relapse and require additional lines of therapy. Combining CELMoDs with cellular therapies significantly improves the response rate in MM patients. In this paper, based on the literature presented at the Annual Meeting of the American Society of Hematology (ASH), the American Society of Clinical Oncology (ASCO), the International Myeloma Society (IMS), and the European Hematology Association (EHA) in the 2020-2025 timeframe, we explore the rationale and emerging evidence of combining CELMoDs with immunotherapies, and their use as a bridge to transplant or as post-ASCT maintenance therapy in MM.</p>","PeriodicalId":54225,"journal":{"name":"Biomarker Research","volume":"13 1","pages":"105"},"PeriodicalIF":11.5,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12357425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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