Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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A Workflow for Full Traceability of AI Decisions
arXiv:2511.11275v2 Announce Type: replace Abstract: An ever increasing number of high-stake decisions are made or assisted by automated systems employing brittle artificial intelligence technology. There is a substantial risk that some of these decision induce harm to people, by infringing their well-being or their fundamental human rights. The state-of-the-art in AI systems makes little effort with respect to appropriate documentation of the decision process. This obstructs the ability to trac
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cs.AI, q-bio.NC updates on arXiv.org
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MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
arXiv:2510.27671v1 Announce Type: new Abstract: Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring alignment between generated drugs and their pharmacological properties, remains a critical challenge. To address these challenges, we propose MolChord, which integrates two key techniques: (1) to align protein and
MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
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Nature Biotechnology - Issue - nature.com science feeds
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Scaling DNA synthesis with a microchip-based massively parallel synthesis system
Nature Biotechnology, Published online: 01 October 2025; doi:10.1038/s41587-025-02844-0A microchip-based DNA synthesis method enables scalable production of complex DNA constructs.
Scaling DNA synthesis with a microchip-based massively parallel synthesis system
Nature Biotechnology, Published online: 01 October 2025; doi:10.1038/s41587-025-02844-0
A microchip-based DNA synthesis method enables scalable production of complex DNA constructs.-
(Multiomics OR Omics) AND (Pancreatic)
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Fatty acid-binding proteins in cancers
Int J Surg. 2025 Jul 15. doi: 10.1097/JS9.0000000000003049. Online ahead of print.ABSTRACTFatty acid-binding proteins (FABPs) are intracellular lipid chaperones with molecular weights of approximately 14-15 kDa. By binding and transporting fatty acids and lipid-related molecules, FABPs precisely regulate metabolic pathways, signal transduction, and gene expression, playing a central role in cancer initiation and progression. The 11 identified subtypes (FABP1-FABP12; FABP11 is identical to FABP3)
Fatty acid-binding proteins in cancers
Int J Surg. 2025 Jul 15. doi: 10.1097/JS9.0000000000003049. Online ahead of print.
ABSTRACT
Fatty acid-binding proteins (FABPs) are intracellular lipid chaperones with molecular weights of approximately 14-15 kDa. By binding and transporting fatty acids and lipid-related molecules, FABPs precisely regulate metabolic pathways, signal transduction, and gene expression, playing a central role in cancer initiation and progression. The 11 identified subtypes (FABP1-FABP12; FABP11 is identical to FABP3) exhibit tissue-specific expression and influence tumor progression through metabolic reprogramming, immune microenvironment modulation, and therapy resistance. Metabolically, FABPs enhance fatty acid uptake, β-oxidation, and synthesis, meeting the high proliferative demands of tumors. In immune regulation, FABP4+ macrophages secrete IL-6 to suppress T cell activity, while FABP6 downregulates MHC-I molecule expression to reduce CD8+ T cell infiltration, fostering an immunosuppressive microenvironment. Regarding therapy resistance, FABP4 enhances mitochondrial β-oxidation to reduce apoptosis in ovarian cancer, and FABP5 promotes chemoresistance in HCC via the HIF-1α pathway. Functional heterogeneity exists among subtypes: FABP7 drives glioblastoma stem cell migration via RXRα signaling, while FABP5 exhibits context-dependent roles, promoting HCC progression but suppressing colorectal cancer (CRC) through mTOR-mediated autophagy. Clinically, FABPs serve as diagnostic biomarkers and therapeutic targets. However, challenges such as insufficient target specificity, cross-cancer heterogeneity, and normal tissue toxicity remain. Future studies should integrate multi-omics and single-cell technologies to elucidate cell-specific mechanisms and develop precise combination therapies for clinical translation.
PMID:40717587 | DOI:10.1097/JS9.0000000000003049
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Cell
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Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors
This study demonstrates that extrachromosomal DNA (ecDNA) replication induces DNA double-strand breaks and activates the DNA damage response (DDR). The DDR pathways, such as alt-NHEJ, are critical for ecDNA maintenance in tumor cells. Mechanistic insights into ecDNA replication and maintenance unveil a therapeutic approach for treating tumors harboring ecDNA.
Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Pan-cancer analysis uncovered the prognostic and therapeutic value of disulfidptosis
NPJ Precis Oncol. 2025 Feb 24;9(1):50. doi: 10.1038/s41698-025-00834-8.ABSTRACTDisulfidptosis, a newly discovered cell death mode distinct from other programmed cell death in lung and kidney cancer cells, is defined as extensive disulfide bonds to actin cytoskeleton proteins, leading to actin contraction and cytoskeletal disruption cell death. New cell death pattern discoveries often drive advances in tumor research. Therefore, the present study attempted to decipher the manifestation and import
Pan-cancer analysis uncovered the prognostic and therapeutic value of disulfidptosis
NPJ Precis Oncol. 2025 Feb 24;9(1):50. doi: 10.1038/s41698-025-00834-8.
ABSTRACT
Disulfidptosis, a newly discovered cell death mode distinct from other programmed cell death in lung and kidney cancer cells, is defined as extensive disulfide bonds to actin cytoskeleton proteins, leading to actin contraction and cytoskeletal disruption cell death. New cell death pattern discoveries often drive advances in tumor research. Therefore, the present study attempted to decipher the manifestation and importance of disulfidptosis in pan-cancer. Combining Clinical specimen immunofluorescence staining, single-cell analyses, and spatial transcriptome analyses, we demonstrated the manifestation of disulfidptosis in pan-cancer. Multi-omics analysis has revealed that genomic variants and DNA methylation in DRGs can affect the prognosis of patients with pan-cancer. The nomogram based on the DRGs Score model could accurately predict the prognosis of patients with pan-cancer. PF-562271, EHT-1864, and IPA-3 are potential therapeutic agents targeting disulfidptosis. Collectively, this study deciphered for the first time the importance of disulfidptosis for pan-cancer and developed the DRGs Score model that can assist clinicians in accurately predicting the prognosis and guiding individualized treatment of pan-cancer patients.
PMID:39994355 | DOI:10.1038/s41698-025-00834-8
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses
Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.ABSTRACTImmune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (
Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses
Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.
ABSTRACT
Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.
PMID:39909032 | DOI:10.1016/j.cmet.2024.12.013
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Oncogenesis - nature.com science feeds
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Methylation of HBP1 by PRMT1 promotes tumor progression by regulating actin cytoskeleton remodeling
Oncogenesis, Published online: 08 August 2022; doi:10.1038/s41389-022-00421-7Methylation of HBP1 by PRMT1 promotes tumor progression by regulating actin cytoskeleton remodeling
Methylation of HBP1 by PRMT1 promotes tumor progression by regulating actin cytoskeleton remodeling
Oncogenesis, Published online: 08 August 2022; doi:10.1038/s41389-022-00421-7
Methylation of HBP1 by PRMT1 promotes tumor progression by regulating actin cytoskeleton remodeling-
Most Recent Articles: Clinical Epigenetics
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Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer
Lung cancer is one of most common cancers worldwide, with a 5-year survival rate of less than 20%, which is mainly due to late-stage diagnosis. Noninvasive methods using 5-hydroxymethylation of cytosine (5hmC)...