详细内容（前10条）

1. ⭐ GSE272190 髓系SRC家族激酶HCK通过激活肿瘤相关巨噬细胞介导的侵袭和抑制细胞毒性T细胞活性来调控乳腺癌生长

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、T cell、macrophage、kinase
• 📝 描述：Contributors : Michael W Murrey ; Ashleigh R Poh ; James H Steer ; Catherine Rinaldi ; Kellie A Mouchemore ; Amy R Dwyer ; Elena Denisenko ; Irina Kuznetsova ; Yen Yeow ; Matthew E Jones ; Khaing P Hmon ; Dáithí Ó Muirí ; Ya-Yu Liu ; Weitao Lin ; Alistair R Forrest ; Lesley G Ellies ; David A Joyce ; Matthias Ernst ; Fiona J PixleySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe normal developmental and homeostatic roles of tissue resident macrophages are subverted in tumor-associated macrophages to promote tumor progression. Pro-tumoral macrophage activities include immune suppression and promotion of invasion and metastasis. We used the Py8119 mouse mammary tumor model to investigate the role of Hck activity in tumor growth through therapeutic inhibition and genetic modification. Single cell RNA sequencing and immunohistochemistry approaches were used to investigate changes to the immune compartment.Loss of HCK activity reduced the growth of Py8119 mammary tumors by 70-80% while excessive HCK activity increased growth four-fold. Consistent with a role for HCK in macrophage invasiveness, plasma membrane-associated Src family kinase activity at the tumor margins was lost in the absence of HCK. Regarding immune evasion, HCK-deficient tumors contained increased CD8+ T cell numbers and, while CD8+ T cell depletion reduced survival in all mouse cohorts, CD8+ T cell-depleted HCK-deficient mice survived much longer than CD8+ T cell-replete control mice. Characterisation of the tumour microenvironment by single cell sequencing showed 5 major subtypes of TAMs (immunoregulatory (Folr2high ), inflammatory (MHC-IIhigh ), interferon-primed, angiogenic and tissue resident), which together made up 40% of cells in the tumour. While Hck activity did not affect the recruitment of TAMs or their subtype composition, pathway analysis showed that its loss decreased TAM motility and increased their interferon signalling and reduced EMT pathways in the Py8119 tumor cells.This study provides evidence that HCK activity in TAMs enhances tumour growth via promotion of invasive behaviour as well as suppression of anti-tumor immunity. These findings highlight HCK as a promising therapeutic target to limit tumor progression.
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2. ⭐ GSE289646 T细胞受体基因组分析为林奇综合征携带者的癌症免疫学提供了新的见解

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immunology、T cell、regex:immuno(logy|therapy|suppression)
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLynch Syndrome (LS) provides the perfect context to understand DNA mismatch repair deficient (MMRd) carcinogenesis. LS carriers develop MMRd tumors with high neoantigen loads, which are shared by different LS tumors and recognized by T-cell receptors (TCRs) to trigger adaptive immunity. However, the TCR landscape in LS remains unexplored. Therefore, we performed TCR-sequencing in 277 blood samples from 102 LS cancer survivors, 130 LS previvors, and 45 controls, as well as three LS colorectal cancers, and 11 pre-cancers. For the first time, we found that up to 41% of the most expanded TCRβs from colorectal cancers and pre-cancers are detectable in the blood of several LS carriers, whereas these TCRs have minimal or no expansion in the blood of controls. Additionally, we developed a classification model that distinguishes LS carriers from controls with excellent performance using a set of 1,114 TCRβs that associates with all LS carriers, regardless of MMRd cancer history, and a set of 2231TCRβs that associates with LS previvors who have never developed cancer. This study is the first to describe circulating TCRβs that recognize neoantigens derived from colorectal cancers and pre-cancers in LS carriers, moving the field towards the identification of a blood based TCRβ cancer biomarker.
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3. ⭐ GSE320273 microRNA-21 促进脂质代谢紊乱和肝细胞癌 [bulk RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、metabolism、RNA-seq
• 📝 描述：Contributors : Chad VanSant-Webb ; Jessye C Castro ; Audrey Y Su ; Kiandra Hawkins ; Aavrati Saxena ; Jillian Wright ; Richard Smith ; Marco Fragoso- García ; Yian A Chen ; Carrie Barton ; Chris Stubben ; Ryan M O’Connell ; Gregory S Ducker ; Kimberley J EvasonSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe prevalence of hepatocellular carcinoma (HCC) is rising in parallel with increasing obesity and metabolic dysfunction-associated steatohepatitis (MASH). MicroRNAs are key post-transcriptional regulators of gene expression and are attractive targets for HCC therapy. Here we sought to identify and characterize dysregulated microRNAs in MASH-driven HCC (MASH-HCC). We profiled microRNA expression in liver tissue from patients with MASH or MASH-HCC and in zebrafish HCC driven by activated β-catenin (ABC), one of the most commonly mutated oncogenes in MASH-HCC. We found overlap between dysregulated human and zebrafish miRNAs, including miR-21, which was increasingly upregulated from normal liver to MASH to MASH-HCC. We generated transgenic zebrafish that overexpress or sponge miR-21 in hepatocytes. We found that miR-21 overexpression caused larval liver overgrowth and increased HCC, while miR-21 sponge suppressed β-catenin-driven larval liver overgrowth. By performing histologic and lipidomic analysis, we found that overexpression of miR-21, like ABC, suppressed lipid accumulation in response to a high cholesterol diet and increased accumulation of acylcarnitines. Thus miR-21, which is similarly upregulated in human and zebrafish HCC, promotes lipid metabolic changes that may help drive hepatocarcinogenesis.
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4. ⭐ GSE318490 对来自 6 例晚期 HGSOC 患者的肿瘤样本进行单细胞 RNA 测序，涵盖治疗阶段（新辅助化疗前、新辅助化疗后和铂敏感复发）。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNA-seq、single-cell
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHigh-grade serous ovarian cancer (HGSOC) is characterized by pronounced cellular heterogeneity and dynamic changes during treatment and recurrence. In this study, we collected 10 tumor samples from six patients with advanced-stage HGSOC and performed single-cell RNA sequencing (scRNA-seq) to profile the tumor ecosystem across different treatment stages, including pre-neoadjuvant chemotherapy (pre-NACT), post-neoadjuvant chemotherapy (post-NACT), and platinum-sensitive recurrence. Single-cell libraries were prepared using the 10x Genomics platform followed by high-throughput sequencing. This dataset provides a resource for investigating transcriptional heterogeneity and cellular composition changes associated with treatment and recurrence in advanced HGSOC.
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5. ⭐ GSE291225 AF9/KLF2 基因调控回路将组蛋白乳酸化与乳腺癌转移联系起来 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、histone
• 📝 描述：Contributors : Huida Ma ; Ming Yuan ; Chenxuan Yang ; Yuchen Yuan ; Xin Wang ; Zhonghui Tang ; Haitao LiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHistone lysine L-lactylation (hereafter referred to as histone Kla) is a novel epigenetic mark induced by glycolytic metabolism, serving as a link between metabolic reprogramming and epigenetic regulation. In this study, we uncover an epigenetic-genetic transcriptional regulatory circuit involving AF9 and KLF2 that drives luminal breast cancer progression. AF9, identified as a reader of histone H3 lysine 9 lactylation (H3K9la), promotes KLF2 expression, while KLF2, functioning as a transcription factor for AF9, forms a positive feedback loop that amplifies lactylation-dependent effects. This circuit activates tumor-associated pathways, including TGFβ1, glucose and lactate transporters, and metabolic enzymes essential for glycolysis and serine biosynthesis, driving tumorigenesis and metastasis. Spatial and single-cell transcriptomics show AF9-positive tumor cells enriched in regions of active lactylation, correlated with immune evasion through interactions with M2 macrophages. Together, AF9, H3K9la, and KLF2 integrate metabolism, epigenetics, and signaling to promote tumor growth and metastasis, highlighting AF9’s central role as a histone lactylation reader and a potential therapeutic target in breast cancer.
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6. GSE322536 外周血单核细胞来源的microRNA作为急性淋巴细胞白血病诊断/疾病相关生物标志物的差异表达和靶基因分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、differential expression
• 📝 描述：Contributors : Hadil Alahdal ; Ghaida Almuneef ; Fatemah Basingab ; Kawther A Zaher ; Alia M AldahlawiSeries Type : Expression profiling by arrayOrganism : Homo sapiens ; synthetic constructClinical specimens were collected from patients with Acute Lymphoblastic Leukemia (ALL) and from non-leukemic controls. Total RNA (including small RNA) was profiled using the Affymetrix GeneChip miRNA 4.0 array to identify differentially expressed miRNAs between ALL and controlsRaw CEL files were generated using standard Affymetrix GeneChip scanning and feature extraction (AGCC or equivalent). Expression values were obtained in R using RMA normalization, followed by probe filtering was applied. Differential expression was assessed with limma using an ALL vs CTRL contrast with Benjamini–Hochberg FDR correction.
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7. GSE322503 LKB1 在肠神经系统发育过程中作为神经元-胶质细胞平衡的检查点发挥作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：nervous、Neuronal
• 📝 描述：Contributors : Chantal Thibert ; Jordan AllardSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHow the energy status of enteric progenitors controls neurogliogenesis and the subsequent formation of the complex enteric nervous system (ENS) remains poorly understood. We previously showed that the tumor suppressor kinase LKB1 is essential for postnatal ENS maintenance through amino acid homeostasis. Here, we investigated LKB1’s functions during embryonic ENS formation using a genetically engineered mouse model with conditional Lkb1 inactivation in neural crest progenitors during gut colonization. Using advanced 3D imaging techniques on cleared tissue including lightsheet microscopy and adaptive optics confocal microscopy, we found that Lkb1 loss impairs early neuronal differentiation followed by progressive glial degeneration, leading to hypoganglionosis and compromised digestive tissue integrity. Notably, Lkb1 inactivation induced a transient upregulation of the glial stress marker S100 at mid-gestation, suggestive of a reactive glial state preceding glial loss. Consistent with this response, Lkb1 loss elevated oxidative stress in the digestive tract and in neural crest progenitors and their glial derivatives, triggering DNA damage and p53 activation. Although p53 ablation rescued glial specification in vitro and glial maintenance in vivo, it only partially restored ENS architecture in vivo without rescuing enteric neuron numbers. Together, these findings establish LKB1 as a critical metabolic checkpoint governing neuronal-glial balance during ENS development and suggest that dysregulated LKB1 signaling may contribute to human enteric neurogliopathies.
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8. GSE320272 microRNA-21 促进脂质代谢紊乱和肝细胞癌 [miRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、metabolism
• 📝 描述：Contributors : Chad VanSant-Webb ; Jessye C Castro ; Audrey Y Su ; Kiandra Hawkins ; Aavrati Saxena ; Jillian Wright ; Richard Smith ; Marco Fragoso- García ; Yian A Chen ; Carrie Barton ; Chris Stubben ; Ryan M O’Connell ; Gregory S Ducker ; Kimberley J EvasonSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Danio rerioThe prevalence of hepatocellular carcinoma (HCC) is rising in parallel with increasing obesity and metabolic dysfunction-associated steatohepatitis (MASH). MicroRNAs are key post-transcriptional regulators of gene expression and are attractive targets for HCC therapy. Here we sought to identify and characterize dysregulated microRNAs in MASH-driven HCC (MASH-HCC). We profiled microRNA expression in liver tissue from patients with MASH or MASH-HCC and in zebrafish HCC driven by activated β-catenin (ABC), one of the most commonly mutated oncogenes in MASH-HCC. We found overlap between dysregulated human and zebrafish miRNAs, including miR-21, which was increasingly upregulated from normal liver to MASH to MASH-HCC. We generated transgenic zebrafish that overexpress or sponge miR-21 in hepatocytes. We found that miR-21 overexpression caused larval liver overgrowth and increased HCC, while miR-21 sponge suppressed β-catenin-driven larval liver overgrowth. By performing histologic and lipidomic analysis, we found that overexpression of miR-21, like ABC, suppressed lipid accumulation in response to a high cholesterol diet and increased accumulation of acylcarnitines. Thus miR-21, which is similarly upregulated in human and zebrafish HCC, promotes lipid metabolic changes that may help drive hepatocarcinogenesis.
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9. GSE311521：泛癌细胞系的单细胞多模态分析揭示了细胞内在状态和环境特征背后的基因调控原理

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell
• 📝 描述：Contributors : Zihan Xu ; Aileen Ugurbil ; Joshua Kwan ; Chloe Schaefer ; Abdulraouf Abdulraouf ; Ziyu Lu ; Wei Zhou ; Junyue CaoSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCancer arises from somatic mutations whose effects are executed through dysregulated gene-regulatory programs that reshape chromatin, transcription, and malignant phenotypes. To uncover gene regulatory principles underlying heterogeneous cancer cell states and their linked environmental features, here we present a pan-cancer single-cell, multi-omic atlas of human cancer cell lines, including a compendium of 240,957 transcriptomes and 223,347 chromatin-accessibility profiles from primary cancers spanning 20 tumor types. We revealed extensive pan-cancer cell-state heterogeneity, core gene-regulatory networks, and consensus epithelial–mesenchymal transition (EMT) trajectories that transcend tissue of origin and are governed by conserved epigenomic and transcriptomic features. In addition, our copy-number variation analysis implicated transcription factor amplification, followed by hyperactive downstream regulation, as a major driver of malignant states. Further focused analysis of acral versus cutaneous melanoma cell lines uncovers a universal inflammation-suppressive program in acral melanoma versus an inflamed regulatory landscape in cutaneous melanoma, highlighting the JAK–STAT axis as a key discriminator. Finally, by integrating single-cell and bulk datasets across models and patient cohorts, we revealed tumor–microenvironment co-adaptation in vivo, and this was associated with immunotherapy responsiveness.
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10. GSE291664 乳酸和组蛋白 H3K18 乳酸化与视网膜基因表达的代谢控制相关 [timecourse_CUT&Tag]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、histone
• 📝 描述：Contributors : Mohita Gaur ; Matthew J Brooks ; Xulong Liang ; Milton English ; Laura Campello ; Claire Marchal ; Anand SwaroopSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHigh aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a key product of glycolysis, is implicated in epigenetic regulation through histone lactylation in cancer. Here, we demonstrate that increased ATP production during retinal development is achieved primarily through augmented glycolysis. Histone lactylation, especially H3K18La, parallels enhanced glycolysis and its product, lactate, in developing retina and in retinal explants. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in euchromatin at promoters of active retinal, especially photoreceptor, genes. H3K18La and gene expression also correspond to glucose metabolism in retinal explants. Evaluation of accessible chromatin at H3K18La promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating specificity of H3K18La-mediated gene regulation. Our results highlight glycolysis/lactate/H3K18La as a regulatory axis in fine-tuning gene expression in developing and mature retina.
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1. Ultima Genomics推出UG200系列和Solaris 2.0工作流程，实现可扩展测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、genomics
• 📝 描述：Ultima Genomics launches the UG200 Series and Solaris 2.0 workflows, expanding high-throughput RNA sequencing and whole genome sequencing with higher output…
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2. 科学家揭示了一种流行的抗衰老化合物为何也可能促进癌症发生。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、aging
• 📝 描述：Polyamines—natural molecules found in every living cell—have become stars in the longevity world for their ability to boost cellular cleanup and support healthy aging. But there’s a dark twist: high levels of these same molecules are consistently seen in cancer, where tumors grow aggressively.
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• GSE291663 乳酸和组蛋白 H3K18 乳酸化与视网膜基因表达的代谢控制相关 [explant_CUT&Tag]
• GSE291661 乳酸和组蛋白 H3K18 乳酸化与视网膜基因表达的代谢控制相关 [explant_RNA-seq]
• GSE277999 利用脑膜炎球菌蛋白微阵列鉴定免疫原性外膜囊泡疫苗抗原成分
• GSE322468 人类发育中基底神经节和抑制性神经元的单细胞和空间三维表观基因组图谱
• GSE291806 c-Rel 通过纤连蛋白-整合素信号通路诱导的隔离应激抵抗和上皮间质转化 (EMT) 驱动胰腺癌转移。
• GSE247801：野生型和LDB1条件性敲除小鼠E14.5胎肝成红细胞1期细胞的转录组测序
• GSE312838 miR-130b/301b簇的缺失促进巨噬细胞吞噬作用和脂肪组织炎症的消退
• GSE292106 热应激触发核内陷和蛋白质代谢的空间区室化
• GSE291224 AF9/KLF2 基因调控回路将组蛋白乳酸化与乳腺癌转移联系起来 [CUT&Tag]
• GSE291079 RANK信号通路抑制干扰巨噬细胞的免疫抑制作用，从而增强乳腺癌的肿瘤免疫力
• GSE290919 巨噬细胞极化过程中 Kdm7a 缺陷型 RAW264.7 细胞的转录组分析。
• GSE243298 B细胞发育和B细胞急性淋巴细胞白血病中的3D染色质重塑[Hi-C]
• GSE243276 B细胞发育和B细胞急性淋巴细胞白血病中的3D染色质重塑[RNA-seq]
• GSE243272 B细胞发育和B细胞急性淋巴细胞白血病中的3D染色质重塑[ChIP-seq]
• GSE243271 B细胞发育和B细胞急性淋巴细胞白血病中的3D染色质重塑[ATAC-seq]
• GSE320263 神元丹胶囊通过抑制METTL3介导的m6A甲基化来恢复自噬稳态并减轻心肌梗死后心力衰竭
• GSE316445 通过人中性粒细胞-血管内皮细胞相互作用阐明炎症消退的强效促消退介质
• GSE309947 RNA编辑蛋白敲低重塑HepaRG转录组和药物基因表达
• GSE308173 表达野生型、E76K 或 E76R H2B 的 IMR-90 SV40-T 细胞的单细胞转录组分析
• GSE307377 对来自年轻和老年供体的原代人真皮成纤维细胞进行批量 RNA-seq 分析
• GSE305125 链球菌感染后牙髓外周和中央亚群的分子特征：一项批量RNA测序分析
• GSE301981 自然环境下野生拟南芥种质生命周期全基因组基因表达的多时间尺度分析
• GSE302111 PTX治疗后后爪皮肤成纤维细胞、角质形成细胞和免疫细胞的生物学过程（短期模型）
• GSE287841 内在无序区抑制哺乳动物和植物中RNA和组蛋白去甲基化酶的基因组靶向作用
• GSE144813 线粒体外泌体转移重编程慢性气道炎症中的T辅助细胞功能
• GSE322664 靶向尤文氏肉瘤 EWS::FLI1 转录因子：曲贝替定联合低剂量伊立替康 (SARC037) 的 1/2 期研究 - RNA-Seq
• GSE313506 Centromeres are hotspots of DNA methylation epimutations that are transmitted and occur at high rates in a filamentous fungus
• GSE248375 Aldh1a3 通过增强肿瘤细胞与肺上皮细胞之间的 Sema4d-Plxnb1 和 Sema3a-Nrp1 信号通路相互作用，加速 PDAC 的肺转移
• GSE322631 患有疼痛性糖尿病神经病变的大鼠中央杏仁核的 RNA 测序
• GSE320327 逆转录转座子驱动的共转录染色质重塑重新连接 Ash2l 亚型的使用以启动发育启动子 [ChIP-seq]
• GSE306415 B细胞发育和急性淋巴细胞白血病中的3D染色体重塑[HiChIP]
• GSE300277 大象诱导多能干细胞的获得 [短读长 RNA 测序]
• GSE300148 抗CD137激动性抗体治疗后肝脏中KLRG1+CD127-CD8 T细胞的转录组分析
• GSE290953 基于蛋白聚糖模拟物的生物活性微针，具有调节炎症微环境和脂质代谢的能力，可用于痤疮治疗
• GSE290920 从博来霉素诱导的野生型和 Kdm7a KO 小鼠肺纤维化模型中提取的整个肺的单细胞 RNA 测序。
• GSE283468 大象诱导多能干细胞的获得 [RNA-seq]
• GSE283467 Derivation of elephant induced pluripotent stem cells [ATAC-seq]
• GSE276054 ESCRT介导的机制直接驱动心脏T小管的形成
• GSE275879 ESCRT介导的机制直接驱动心脏T小管的形成
• GSE261128 OsCCT22- OsSh1-OsCAD2 模块通过抑制水稻木质素生物合成促进种子脱落 [RNA-seq]
• GSE261122 OsCCT22- OsSh1-OsCAD2 模块通过抑制水稻木质素生物合成促进种子脱落 [ChIP-seq]
• GSE243299 B细胞发育和B细胞急性淋巴细胞白血病中的3D染色质重塑
• GSE226704 COQ6 D316Y纯合性对BMDM转录组的影响