详细内容（前10条）

1. ⭐ GSE327056 利用10x Genomics Visium平台对人胰腺导管腺癌进行空间转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：10x、spatial、Visium、genomics
• 📝 描述：Contributors : Zhangyong Ren ; Bing Pan ; Fangfei Wang ; Shaocheng Lyu ; Jialei Zhai ; Xiumei Hu ; Zhe Liu ; Lixin Li ; Ren Lang ; Qiang He ; Xin ZhaoSeries Type : OtherOrganism : Homo sapiensIn this study, we performed spatial transcriptomics (ST) to investigate the gene expression features across one normal pancreatic tissue, PC tissue, adjacent tumor tissue, and tumor stroma using 10x Genomics Visium spatial gene expression platform. We generated high-quality spatial gene expression profiles combined with histomorphological information, aiming to reveal the spatial heterogeneity of pancreatic cancer microenvironment and identify spatially restricted gene signatures associated with tumor progression. Sequencing was performed on Illumina NovaSeq 6000 platform, and data processing was conducted using SpaceRanger software with hg38 reference genome. The results revealed that KRT13+FABP5+ malignant cell subpopulation had keratinization characteristics in the tumor tissue. Fibroblasts from adjacent tumor tissue exhibited a tumor-inhibiting role such as “B-cell activation” and “positive regulation of leukocyte activation.” The FGG+CRP+ inflammatory cancer-associated fibroblasts replaced the islets in tumor stroma. During PC progression, the damage to pancreatic structure and function was heavier in the pancreatic exocrine (AMYA2+PRSS1+) than in the endocrine (INS+GCG+). Our results revealed the spatial heterogeneity of dynamic changes and highlighted the significance of impaired exocrine function in PC.
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2. ⭐ GSE295600 对免疫排斥性肿瘤患者联合应用低剂量辐射和免疫疗法可有效增强同源重组修复缺陷肿瘤中 CD8+ T 细胞的功能 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、T cell、regex:immuno(logy|therapy|suppression)、scRNA
• 📝 描述：Contributors : Nicolas Rayroux ; Maria Ochoa-de-Olza ; Fernanda Herrera ; Denarda Dangaj-LanitiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImmune-checkpoint blockade (ICB) has shown significant efficacy across various tumor types. However, tumors with low intraepithelial T-cell infiltration, often referred to as “cold” tumors, are expected to yield poor responsiveness to ICB. We investigated the potential of LDRT to enhance immune-checkpoint blockade (ICB) responses in 25 patients with multimetastatic immune-excluded solid tumors through a multi-cohort phase I clinical trial (RACIN). Primary endpoint was to determine the safety and tolerability of the combination of a backbone treatment, comprising nivolumab, ipilimumab, aspirin/celecoxib, and low-dose cyclophosphamide in association with escalated LDRT. Secondary endpoints included among others disease control rate (DCR) and overall survival (OS). Exploratory endpoints included biomarkers and molecular correlates of response. The combination treatment showed a manageable safety profile, with Grade 3 or higher adverse events in 12% to 21% of patients across cohorts. The overall disease control rate (CR + PR + SD) was 41.6%. Progression free survival across all cohorts was 2.1 months (95% C.I.: 1.8 – 4.2 months), with the highest PFS observed in cohort 1 which received 0.5 Gy (5.7 months, (95% C.I.: 1.9 - 11.3 months). Median overall survival was 14.0 months (95% CI: 8.5–24.6 months), with one patient with ovarian cancer still maintaining a complete response at three years follow-up. Site-paired tumour biopsies collected for each patient at baseline and after LDRT +/- Cy enabled the comprehensive characterization of the dynamics of their excluded/desert tumour microenvironments (TME) at the single cell level. Response to LDRT and ICB was associated with DNA damage and repair responsiveness and the presence of detectable intratumoral PD1+CD8+ tumour infiltrating lymphocytes (TILs) at baseline. Our data revealed that LDRT amplified CD8+ TIL functionality in responding patients offering mechanistic insights on how LDRT improves ICB effectiveness. In contrast, we observed a radiosensitivity of TILs in tumours of non-responders. Detailed single cell immune profiling before LDRT also highlighted a lack of key immune stimulatory myeloid cells that can therefore limit ICB efficacy in excluded tumors. Collectively, this study represents the most comprehensive profiling of l…
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3. ⭐ GSE295599 对免疫排斥性肿瘤患者联合应用低剂量辐射和免疫疗法可有效增强同源重组修复缺陷肿瘤中 CD8+ T 细胞的功能 [bulk RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、T cell、regex:immuno(logy|therapy|suppression)、RNA-seq
• 📝 描述：Contributors : Nicolas Rayroux ; Maria Ochoa-de-Olza ; Fernanda Herrera ; Denarda D LanitiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImmune-checkpoint blockade (ICB) has shown significant efficacy across various tumor types. However, tumors with low intraepithelial T-cell infiltration, often referred to as “cold” tumors, are expected to yield poor responsiveness to ICB. We investigated the potential of LDRT to enhance immune-checkpoint blockade (ICB) responses in 25 patients with multimetastatic immune-excluded solid tumors through a multi-cohort phase I clinical trial (RACIN). Primary endpoint was to determine the safety and tolerability of the combination of a backbone treatment, comprising nivolumab, ipilimumab, aspirin/celecoxib, and low-dose cyclophosphamide in association with escalated LDRT. Secondary endpoints included among others disease control rate (DCR) and overall survival (OS). Exploratory endpoints included biomarkers and molecular correlates of response. The combination treatment showed a manageable safety profile, with Grade 3 or higher adverse events in 12% to 21% of patients across cohorts. The overall disease control rate (CR + PR + SD) was 41.6%. Progression free survival across all cohorts was 2.1 months (95% C.I.: 1.8 – 4.2 months), with the highest PFS observed in cohort 1 which received 0.5 Gy (5.7 months, (95% C.I.: 1.9 - 11.3 months). Median overall survival was 14.0 months (95% CI: 8.5–24.6 months), with one patient with ovarian cancer still maintaining a complete response at three years follow-up. Site-paired tumour biopsies collected for each patient at baseline and after LDRT +/- Cy enabled the comprehensive characterization of the dynamics of their excluded/desert tumour microenvironments (TME) at the single cell level. Response to LDRT and ICB was associated with DNA damage and repair responsiveness and the presence of detectable intratumoral PD1+CD8+ tumour infiltrating lymphocytes (TILs) at baseline. Our data revealed that LDRT amplified CD8+ TIL functionality in responding patients offering mechanistic insights on how LDRT improves ICB effectiveness. In contrast, we observed a radiosensitivity of TILs in tumours of non-responders. Detailed single cell immune profiling before LDRT also highlighted a lack of key immune stimulatory myeloid cells that can therefore limit ICB efficacy in excluded tumors. Collectively, this study represents the most comprehensive profiling of longit…
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4. ⭐ GSE327129 利用空间转录组学解析组织间亚细胞mRNA定位模式

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Roy Novoselsky ; Ofra Golani ; Tal Barkai ; Merav Kedmi ; Inna Goliand ; Shalev ItzkovitzSeries Type : OtherOrganism : Mus musculusSubcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that leverages image-derived features to extract subcellular information from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures that can be readily obtained from standard high-definition spatial transcriptomics experiments. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.
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5. ⭐ GSE313334 肠道菌群影响营养免疫和对鲍曼不动杆菌肺炎的抵抗力

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、resistance、regex:intestin(e|al)
• 📝 描述：Contributors : Erin R Green ; Nicholas M Negretti ; Nicolas G Shealy ; Tess Brunner ; Felipe A Moser ; Sydney L Drury ; Kacie A Traina ; Valeria M Reyes Ruiz ; Tzushan S Yang ; Eric G Pamer ; Mariana X Byndloss ; Raf van de Plas ; Joseph P Zackular ; Samuel H Light ; Jennifer M Sucre ; Eric P SkaarSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBroad-spectrum antibiotics are frequently administered prophylactically to intensive care unit patients as part of empiric care. This treatment has been associated with subsequent infections by the emerging nosocomial pathogen Acinetobacter baumannii; however, the mechanisms underlying this association remain unclear. Here, we demonstrate in a murine model that prophylactic broad-spectrum antibiotic administration drives susceptibility to intranasal infections with A. baumannii, and that reconstitution of the intestinal microbiota by fecal microbiota transplant restores control of infection, implicating microbiota dysbiosis as a key driver of pulmonary disease. Using single-cell RNA sequencing, we determine that prophylaxis suppresses phagocyte effector functions in the lung, including nutritional immunity pathways that restrict pathogen access to essential nutrient metals. Depletion studies identify neutrophils and inflammatory monocytes as central mediators of microbiota-dependent protection, and infection of mice lacking nutritional immunity components lipocalin-2 or calprotectin abrogates the effects of prophylaxis, establishing a causal linkage between microbiota dysbiosis and impaired phagocyte-mediated nutritional immunity. Together, these findings provide a mechanism for the increased severity of A. baumannii pneumonia following antibiotic exposure and highlight the intestinal microbiota as a potential therapeutic target to prevent future nosocomial infections with this and other healthcare-associated pathogens.
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6. ⭐ GSE326883 TLR9激动剂通过B细胞-CD2共刺激轴增强过继性T细胞疗法在癌症治疗中的疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell、B cell
• 📝 描述：Contributors : Ayana Ruffin ; Chrystal PaulosSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAdoptive T cell transfer (ACT) therapy offers curative potential for some patients with cancer. Toll-like receptor (TLR) agonists improve the efficacy of ACT therapy, but the underlying mechanism of potency remains poorly understood. Here, we identify a previously unrecognized innate-adaptive circuit in which TLR9-activated B cells augment CD8 T cell fitness and antitumor activity through CD2-dependent costimulation. Among multiple TLR agonist tested, class B CpG uniquely programmed murine and human CD8⁺ T cells for superior effector differentiation, metabolic fitness and antitumor control. Disruption of CD2 signaling blunts the benefits of TLR9 agonism, including glycolytic capacity and tumor control. Independently, blocking CD86/CD80/CD28 or ICOS did not impair CpG conditioned CD8 T cell anti-tumor activity. Gain of function experiments revealed that CD2 stimulation recapitulated the effect of TLR9 agonism, bolstering the effector function of TIL and CAR T cells. Clinically, consistent with these findings, elevated CD2 expression in human tumors correlated with improved overall survival across multiple cancer cohorts, underscoring the importance of this signaling cue. Together, these data uncover a non-canonical B cell-CD2 costimulation axis through which TLR9 agonists potentiate ACT, revealing a targetable pathway to overcome resistance to cell therapy in solid tumors.
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7. ⭐ GSE326567 通过转录组分析解析长芒苋（Amaranthus palmeri S. Watson）对多种除草剂的代谢抗性

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、resistance、transcriptome
• 📝 描述：Contributors : Rishabh Singh ; Yaiphabi Kumam ; Mohit Mahey ; Eric Patterson ; Sanzhen Liu ; Sarah Lancaster ; Mithila JugulamSeries Type : Expression profiling by high throughput sequencingOrganism : Amaranthus palmeriMultiple herbicide resistance in Palmer amaranth (Amaranthus palmeri S. Watson) poses a serious threat to US crop production. A Palmer amaranth population (KCTR) from Kansas was found resistant to herbicides across six sites of action, including ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitors and synthetic auxins. Moreover, a predominance of metabolic resistance, possibly mediated by P450s or GSTs enzyme activity was reported in this population. This study aims to identify the specific genes involved in multiple herbicide metabolism in this Palmer amaranth population via transcriptome analysis. Vegetative clones were developed from three biological replicates of both resistant (KCTR/KCTR-G2) and susceptible (KSS) Palmer amaranth populations. Ten to 12 cm tall clones from each biological replicate were treated with labelled doses of chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione. Leaf samples were collected for RNA isolation at 6 hours after treatment with respective herbicides along with non-treated plants. Upon RNA sequencing, paired end reads generated were mapped to the Palmer amaranth transcriptome using HISAT2. Differential gene expression analysis revealed 414, 129, 529, 688 and 152 genes expressed differentially in resistant plants following chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione treatments, respectively. Isoforms of CYP72A219 or CYP704B1 and GST C-terminal were alternatively up-regulated expression across treatments. Transcripts for CYP72A219 and CYP704B1 show up-regulated expression of 3.4- to 6.6-fold and 5.9- to 12.4-fold in resistant plants as validated by qRT-PCR. Identification of genes involved in multiple herbicide metabolism in Palmer amaranth is crucial to predict the evolutionary course of herbicide resistance in weed species.
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8. ⭐ GSE302811 RNA测序分析了乳腺癌术后放疗或单纯手术后伤口渗出液中分离的单核免疫细胞。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、RNA-seq
• 📝 描述：Contributors : Nikko Brix ; Benedek Dankó ; Martin SelmansbergerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis dataset comprises RNA-seq profiles from mononuclear immune cells purified from wound fluid of breast cancer patients who received intraoperative radiotherapy (IORT) or surgery only (control). Samples were collected on postoperative day 2 and processed for total RNA extraction and 3′-end mRNA sequencing. The study aims to characterize the transcriptional immune landscape in the early wound-healing phase following IORT.
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9. GSE291273 胎盘特异性组蛋白 H3.4 促进生殖细胞发育和生殖适应性 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、histone
• 📝 描述：Contributors : Antoine H F.M. Peters ; Pavel A. KomarovSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGenes involved in chromatin remodeling during sperm development are under strong evolutionary pressure to optimize reproductive fitness In mice, the histone H3.4 variant, encoded by the single copy H3f4 gene, is essential for spermatogenesis. H3.4 is highly expressed in spermatogonia and replaces progressively canonical H3 histones during spermatogonial expansion and differentiation. Phylogenetic analysis shows that H3f4 is specific to the placental lineage and originates from an ancestral H3.2 gene existing prior to the divergence of placental and marsupial mammals over 100 million years ago. Situated in a majorly truncated histone cluster, placental H3f4 orthologs show increased synonymous and non-synonymous substitution rates compared to analogous marsupial H3.2 genes. H3f4 carries four non-synonymous substitutions relative to H3.2 genes. To understand the impact of evolutionary sequence divergence on reproductive fitness, we reverted three of four non-synonymously substituted residues in H3f4 to those present in H3.1 (H3f4V24A, H3f4H42R, H3f4S98A) while leaving H3f4C96 intact which is identical to H3.1C96. When expressed from both alleles, neither single nor triple reversion of diverged residues affected spermatogenesis much. In contrast, hemizygous expression of the triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed that residues V24 and H42 of H3.4 promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.
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10. GSE291272 胎盘特异性组蛋白 H3.4 促进生殖细胞发育和生殖适应性 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、histone
• 📝 描述：Contributors : Antoine H F.M. Peters ; Pavel A. KomarovSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusGenes involved in chromatin remodeling during sperm development are under strong evolutionary pressure to optimize reproductive fitness In mice, the histone H3.4 variant, encoded by the single copy H3f4 gene, is essential for spermatogenesis. H3.4 is highly expressed in spermatogonia and replaces progressively canonical H3 histones during spermatogonial expansion and differentiation. Phylogenetic analysis shows that H3f4 is specific to the placental lineage and originates from an ancestral H3.2 gene existing prior to the divergence of placental and marsupial mammals over 100 million years ago. Situated in a majorly truncated histone cluster, placental H3f4 orthologs show increased synonymous and non-synonymous substitution rates compared to analogous marsupial H3.2 genes. H3f4 carries four non-synonymous substitutions relative to H3.2 genes. To understand the impact of evolutionary sequence divergence on reproductive fitness, we reverted three of four non-synonymously substituted residues in H3f4 to those present in H3.1 (H3f4V24A, H3f4H42R, H3f4S98A) while leaving H3f4C96 intact which is identical to H3.1C96. When expressed from both alleles, neither single nor triple reversion of diverged residues affected spermatogenesis much. In contrast, hemizygous expression of the triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed that residues V24 and H42 of H3.4 promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.
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1. RNA测序正朝着基因表达的绝对测量方向发展

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing calibration using standardized references enables absolute quantification of gene expression, improving cross-study comparisons and reducing bias across experiments and laboratories…
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2. 科学家利用RNA测序来识别克罗恩病肠道瘢痕的诱因

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing reveals interactions between immune and endothelial cells that drive fibrosis in Crohn’s disease, identifying new pathways that could guide targeted therapies…
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3. Parse Biosciences推出与FFPE兼容的条形码技术，用于全转录组单细胞分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Parse Biosciences enables RNA sequencing of FFPE samples at single cell resolution, unlocking archived tissues for whole transcriptome analysis and deeper insights into gene…
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• GSE327152 心脏三级免疫微环境驱动免疫检查点抑制剂心肌炎中的免疫激活
• GSE327033 HyDRA：用于整合长读长和短读长 RNA 测序数据以进行自定义转录组组装的流程
• GSE326904 心脏三级免疫微环境驱动免疫检查点抑制剂心肌炎中的免疫激活 [CosMx]
• GSE312823 结肠癌在克隆水平上对整合应激反应 (IRS) 的抵抗力
• GSE326833 利用单细胞测序研究保加利亚乳杆菌在微生物液体、冻干和冻干储存条件下的群体异质性
• GSE231474 单核细胞来源细胞的浸润扰乱中枢神经系统代谢，促进精氨酸分解代谢，加剧神经炎症
• GSE326853 膀胱癌治疗组和对照组样本的转录组分析
• GSE242697 UHOMi003-A 细胞系来源的 iALI 上皮细胞和间充质细胞的单细胞 RNA 测序
• GSE196044 外周血单核细胞单细胞转录组和染色质可及性图谱揭示杜洛克猪和梅山猪的免疫细胞异质性和品种特异性特征
• GSE326978 人类转录组中的必需长链非编码RNA [CRISPR]
• GSE319117 通过单个 CRISPR-Cas9 多功能编辑器同时进行正交细胞工程 [RNA-seq T 细胞 B2M/TET2/TGFBR2]
• GSE319115 通过单个 CRISPR-Cas9 多功能编辑器同时进行正交细胞工程 [RNA-seq T 细胞 CD3D]
• GSE309821 基于保守表皮因子的增强子导向基因递送用于手指再生 [scRNA-seq]
• GSE293141 利用单个 CRISPR-Cas9 多功能编辑器同时进行正交细胞工程 [RNA-seq K562]
• GSE316271：Runx1和/或Rb1缺失驱动的p53缺陷型乳腺肿瘤的批量RNA测序分析
• GSE309461：T-bet WT 与诱导型 Ncr1-T-bet Δ/Δ 小鼠肝脏 NK 细胞和 ILC1 细胞的批量 RNA 测序
• GSE304838 小鼠神经突生长中干细胞衍生神经元培养模型
• GSE294864 工程化细胞因子分泌细胞以防止对植入物的异物反应
• GSE267579 MRE11 近端多聚腺苷酸化位点介导的环化影响转录和基因组稳定性 [RNA-seq]
• GSE252183 小鼠神经突生长中干细胞衍生神经元培养模型
• GSE326820 ChREBPα：驱动小鼠植入前胚胎脂滴更新的中心代谢传感器
• GSE326798 CDK4/6抑制增强CAR-T细胞疗法在实体瘤中的疗效
• GSE326758 韩国小型猪（Sus scrofa）从头转录组组装[I]
• GSE326599：识别克服克隆进化导致的获得性硼替佐米耐药性的潜在治疗策略
• GSE324735 PEPITEM 在免疫介导的炎症性关节炎期间调节滑膜微环境以限制疾病进展
• GSE293993 核肌球蛋白1调节小鼠血小板活化和免疫反应
• GSE293509 Effect of Rnf111 S254D mutant on gene expression at intestine tissues
• GSE326929 人类非肌层浸润性膀胱癌细胞系 MGH-U3 衍生的不同表型肿瘤的单细胞水平染色质可及性分析
• GSE326928 人类非肌层浸润性膀胱癌细胞系衍生的不同表型肿瘤的系统发育信息
• GSE326854 人类非肌层浸润性膀胱癌细胞系衍生的不同表型肿瘤的单细胞水平基因表达谱
• GSE311960 tRF 和 tiRNA 测序
• GSE307959 25-羟基胆固醇抑制登革病毒期间的膜融合抑制、免疫调节和胆固醇合成失调
• GSE264636 淋巴瘤样丘疹病与晚期皮肤T细胞淋巴瘤：单细胞谱分析揭示自限性疾病与侵袭性疾病行为的标志物