Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14066107_1.fastq.gz | Fastqsanger.gz | |||
| SRR14066107_2.fastq.gz | Fastqsanger.gz | |||
| SRR14066108_1.fastq.gz | Fastqsanger.gz | |||
| SRR14066108_2.fastq.gz | Fastqsanger.gz | |||
| SRR14066109_1.fastq.gz | Fastqsanger.gz |
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Project description:We examine the global effect of hBD3 on transcription in TLR4-stimulated macrophages and for the first time show that hBD3 inhibits the transcription of critical pro-inflammatory genes. Among the repressed genes we detect significant enrichment of groups involved in the positive regulation of NFkappaB including components of Toll-like receptor signaling pathways. Total RNA obtained from bone marrow derived macrophages (BMDM) that have been subjected to 6 hour treatment with KLA, KLA&hBD3, hBD3 or untreated. There are 3 biological replicates per group.
2012-01-01 | E-GEOD-25871 | biostudies-arrayexpress
Project description:We performed a phase I clinical trial to assess the safety and feasibility of fecal microbiota transplantation (FMT) and re-induction of anti-PD-1 immunotherapy in patients with anti-PD-1-refractory metastatic melanoma. FMT donors were two metastatic melanoma patients who achieved a durable complete response. FMT recipient patients were metastatic melanoma patients who failed at least one anti-PD-1 line of treatment. Each recipient patient received FMT implants from only one of the two donors. FMT was conducted by both colonoscopy and oral ingestion of stool capsules, followed by anti-PD-1 re-treatment (Nivolumab, BMS). Recipient patients underwent pre- and post-treatment stool sampling, tissue biopsy of both gut and tumor, and total body imaging. Clinical responses were observed in three patients, including two partial responses and one complete response. Notably, treatment with FMT was associated with favorable changes in immune cell infiltrates and gene expression profiles in both the gut lamina propria and the tumor microenvironment.
2020-12-31 | GSE162436 | GEO
Project description:Multiple myeloma (MM) is a hematologic malignancy characterized by abnormal plasma cell proliferation, with lenalidomide emerging as a primary treatment. However, prolonged use often leads to drug resistance, underscoring the need to understand resistance mechanisms. Protein post-translational modifications (PTMs) play crucial roles in disease development, including chemoresistance. Here, we investigate the involvement of new types of PTMs, focusing on lysine lactylation (Kla), in lenalidomide resistance. We observed elevated Kla levels in lenalidomide-resistant MM cells, implicating its role in resistance. Through quantitative proteome, lactylome, and acetylome analysis, we identified 7493 proteins, 1241 Kla sites, and 9313 lysine acetylation (Kac) sites, thereby revealing differential protein expression and PTM profiles in lenalidomide-resistant cells. Proteomic analysis revealed that a serious of chemoresistance related proteins were upregulated, and a number of CRL4-CRBN regulatory factors were downregulated. Lactylome analysis revealed that numerous chemoresistance related proteins exhibited increased Kla levels in lenalidomide-resistant MM cells, suggesting that Kla played an important role in the development of lenalidomide-resistance in LenR MM cells. Notably, histone H4K8la were associated with upregulation of chemoresistance-related genes CDK6 and ECHS1. Our findings shed light on the epigenetic mechanisms underlying lenalidomide resistance in MM, offering insights for overcoming chemoresistance.
2026-04-09 | GSE294374 | GEO
Project description:Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. Interestingly, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on TSSs and the regulated Kla can facilitate in signaling pathways and progress of tumorigenesis. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.
2024-01-16 | GSE239656 | GEO
Project description:Hypoxia promotes tumorigenesis and lactate accumulation in esophageal squamous cell carcinoma (ESCC). Lactate can induce histone lysine lactylation (Kla, a recently-identified histone marks) to regulate transcription. However, the functional consequence of histone Kla under hypoxia in ESCC remains to be explored. Here, we reveal that hypoxia facilitates histone H3K9la to enhance LAMC2 transcription for proliferation of ESCC. We found that global level of Kla was elevated under hypoxia, and thus identified the landscape of histone Kla in ESCC by quantitative proteomics. Furthermore, we show a significant increase of H3K9la level induced by hypoxia. Next, MNseq ChIP-seq and RNA-seq analysis suggest that H3K9la is enriched at the promoter of cell junction genes. Finally, we demonstrate that the histone H3K9la facilitates the expression of LAMC2 for ESCC invasion by in vivo and in vitro experiments. Briefly, our study reveal a vital role of histone Kla triggered by hypoxia in cancer.
2024-05-22 | GSE255352 | GEO
Project description:Emerging evidence suggests that accumulated D-lactate (D-la) induces diverse effects in human intestinal injury diseases. However, the regulatory mechanism remain elusive. Here, we discover the lysine D-lactylation (D-Kla) induced by D-la and reveal the molecular mechanism underlying D-la-driven D-Kla for transcription regulation. We first discovered D-Kla in HepG2 cells stimulated by D-la from E. coli secretions. Next, we validated the existence of D-la-driven D-Kla by four approaches, especially including metabolic labelling experiments. Additionally, we uncover that SCOT1 catalyzes the transformation of D-la to D-lactyl-CoA, serving as a key donor for D-Kla. Furthermore, we identify the D-Kla landscape with 2895 sites by proteomics analysis and 34 histone D-Kla sites activated by D-la and further indicate the regulation of H3K18-Dla in transcription by CUT&Tag and RNA-seq assays. Finally, we show the effect of D-Kla on inhibiting the hepatocellular carcinoma cells proliferation. In summary, we uncover the D-la-driven D-Kla and reveal a D-Kla-mediated transcription regulation for tumor suppression, providing new insight into the protein modifications induced by microbiota secretions.
2026-07-15 | GSE269963 | GEO
Project description:As a novel post-translational modification of histone derived from lactate, lysine lactylation (Kla) links lactate metabolism to epigenetic regulation, playing a role in modulation of gene expression in tumor and immune microenvironment. Evidence so far indicates that HDAC1-3 can catalyze the removal of Kla. However, the regulated targets of HDACs for Kla and functional consequence remain elusive. Herein, we used an antibody-based proximity labeling approach to identify SIRT3 binding to histone H3K9la and catalytic removal of the lactylationoup. The molecular docking results further revealed the mechanism of the binding of Kla peptide to SIRT3. More importantly, SIRT3 can specifically modulate the gene transcription by regulating H3K9la, inhibiting the progression of esophageal cancer cells (ESCC). In conclusion, our work identifies the delactylase of H3K9la and reveal an H3K9la-mediated molecular mechanism catalyzed by SIRT3 for gene transcription regulation in ESCC, and our findings provide an opportunity to investigate the physiological significance of Kla and shed light on the unknown cellular mechanisms controlled by SIRT3.
2024-08-18 | GSE274648 | GEO
Project description:Multiple myeloma (MM) is a hematologic malignancy characterized by abnormal plasma cell proliferation, with lenalidomide emerging as a primary treatment. However, prolonged use often leads to drug resistance, underscoring the need to understand resistance mechanisms. Protein post-translational modifications (PTMs) play crucial roles in disease development, including chemoresistance. Here, we investigate the involvement of new types of PTMs, focusing on lysine lactylation (Kla), in lenalidomide resistance. We observed elevated Kla levels in lenalidomide-resistant MM cells, implicating its role in resistance. Through quantitative proteome, lactylome, and acetylome analysis, we identified 7493 proteins, 1241 Kla sites, and 9313 lysine acetylation (Kac) sites, thereby revealing differential protein expression and PTM profiles in lenalidomide-resistant cells. Proteomic analysis revealed that a serious of chemoresistance related proteins were upregulated, and a number of CRL4CRBN regulatory factors were downregulated. Lactylome analysis revealed that numerous chemoresistance related proteins exhibited increased Kla levels in lenalidomide-resistant MM cells, suggesting that Kla played an important role in the development of lenalidomide-resistance in LenR MM cells. Notably, histone H4K8la were associated with upregulation of chemoresistance-related genes CDK6 and ECHS1. Our findings shed light on the epigenetic mechanisms underlying lenalidomide resistance in MM, offering insights for overcoming chemoresistance.
2026-04-09 | GSE294373 | GEO
Project description:Mitochondria are not only the powerhouses of the cell. They are also dynamic signaling hubs, playing a key role in cellular metabolism and adaptation. Proper mitochondrial function depends largely on the import of proteins encoded by the nucleus. Using RNA immunoprecipitation and proximity labeling (TurboID), we show that Arabidopsis thaliana FRIENDLY (FMT) protein specifically recognizes the mRNAs of several organellar-destined proteins, mostly mitochondrial, and is in close proximity to these proteins during their translation. Remarkably, when FMT is absent, its target mRNAs lose their correct cellular localization. Our TurboID approach also confirms the interaction between FMT and the Nascent polypeptide Associated Complex (NAC), a ribosome-associated platform involved in the maturation and sorting of nascent peptides. Taken together, these results suggest that FMT, through its interaction with NAC and the ribosome, is involved in the spatial regulation of translation in the cell. FMT itself is under tight cellular control. It is rapidly degraded under stress but is overproduced in specific conditions, such as germination, impacting mitochondrial activity. Since mitochondria act as signaling hubs, this regulation of FMT could help the cell to quickly adapt to changing environments.
2026-03-05 | PXD061930 | Pride