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1. ⭐ GSE329993 IRF1 rs2057656 多态性通过等位基因特异性表观遗传抑制调节 ARDS 中的 IRF1-AS1 转录和免疫功能障碍 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、ChIP-seq、epigenetic
• 📝 描述：Contributors : Shi Zhang ; Yuanyuan ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensAcute respiratory distress syndrome (ARDS) is a severe and life-threatening variant of respiratory failure. Effective targeted therapies are lacking, and patient heterogeneity is substantial. Interferon regulatory factor 1, a key inflammatory transcription factor implicated in ARDS pathogenesis, has poorly defined genetic regulation. By integrating clinical cohorts with genome-wide association studies, we identified a functional single-nucleotide polymorphism, rs2057656, in the antisense promoter of IRF1. The C allele significantly increased ARDS risk (odds ratio = 3.39). This variant modulates local DNA methylation, thereby regulating the expression of the antisense transcript IRF1-AS1, mediating histone deacetylation at the IRF1 promoter and establishing an epigenetic cascade, DNA methylation, antisense RNA, and histone modification that controls IRF1 transcription and pulmonary inflammation. Exogenous IRF1-AS1 delivery alleviated ARDS in C-allele mice. Our study systematically elucidates an epigenetic mechanism governing IRF1 expression and ARDS susceptibility, identifying a genotype-informed therapeutic target.
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2. GSE278494 BACH2 的双向调控协调系统性 CXCR5– 与 CXCR5+ CD4+ T 细胞分化 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、ATAC-seq
• 📝 描述：Contributors : Fangming Zhu ; Andrew R Schroeder ; Hui HuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusATAC-seq results of activated ThNone cells reveal chromatin accessibility changes following the deletion of Bach2 and Stat5.
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3. GSE306443 成纤维细胞中的 IL-10/IL-10Ra 轴通过抑制 I 型干扰素信号传导来限制大肠病理 [RNA-Seq，第 2 部分]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、regex:intestin(e|al)
• 📝 描述：Contributors : Bo Li ; Daisuke Motooka ; Hisako KayamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn the intestines, stromal cells are essential for epithelial homeostasis, supplying both stem cell niche signals and differentiation factors. Recent studies have shown that they play crucial roles not only in epithelial maintenance, but also in the immune system. However, the molecular mechanisms that control inflammatory response by stromal cells are poorly understood. We showed that stromal cells from Rag2 knock out (KO) mice highly express inflammatory cytokines and chemokines, and the IL10-IL10R axis is a key suppressor for those inflammatory mediators in fibroblasts. Fibroblast-specific Il10ra KO mice developed spontaneous colitis in aged mice. We performed (sc)RNA-seq on stromal cells from these mice and 16s rDNA-seq on the feces from those mice.
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4. GSE306442 成纤维细胞中的 IL-10/IL-10Ra 轴通过抑制 I 型干扰素信号传导来限制大肠病理 [scRNA-Seq，第 2 部分]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、regex:intestin(e|al)
• 📝 描述：Contributors : Takayoshi Ito ; Daisuke Okuzaki ; Hisako KayamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn the intestines, stromal cells are essential for epithelial homeostasis, supplying both stem cell niche signals and differentiation factors. Recent studies have shown that they play crucial roles not only in epithelial maintenance, but also in the immune system. However, the molecular mechanisms that control inflammatory response by stromal cells are poorly understood. We showed that stromal cells from Rag2 knock out (KO) mice highly express inflammatory cytokines and chemokines, and the IL10-IL10R axis is a key suppressor for those inflammatory mediators in fibroblasts. Fibroblast-specific Il10ra KO mice developed spontaneous colitis in aged mice. We performed (sc)RNA-seq on stromal cells from these mice and 16s rDNA-seq on the feces from those mice.
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5. GSE306433 成纤维细胞中的 IL-10/IL-10Ra 轴通过抑制 I 型干扰素信号传导来限制大肠病理 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、regex:intestin(e|al)
• 📝 描述：Contributors : Takayoshi Ito ; Daisuke Motooka ; Hisako KayamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn the intestines, stromal cells are essential for epithelial homeostasis, supplying both stem cell niche signals and differentiation factors. Recent studies have shown that they play crucial roles not only in epithelial maintenance, but also in the immune system. However, the molecular mechanisms that control inflammatory response by stromal cells are poorly understood. We showed that stromal cells from Rag2 knock out (KO) mice highly express inflammatory cytokines and chemokines, and the IL10-IL10R axis is a key suppressor for those inflammatory mediators in fibroblasts. Fibroblast-specific Il10ra KO mice developed spontaneous colitis in aged mice. We performed (sc)RNA-seq on stromal cells from these mice and 16s rDNA-seq on the feces from those mice.
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6. GSE306432 成纤维细胞中的 IL-10/IL-10Ra 轴通过抑制 I 型干扰素信号传导来限制大肠病理 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、regex:intestin(e|al)
• 📝 描述：Contributors : Bo Li ; Daisuke Okuzaki ; Hisako KayamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn the intestines, stromal cells are essential for epithelial homeostasis, supplying both stem cell niche signals and differentiation factors. Recent studies have shown that they play crucial roles not only in epithelial maintenance, but also in the immune system. However, the molecular mechanisms that control inflammatory response by stromal cells are poorly understood. We showed that stromal cells from Rag2 knock out (KO) mice highly express inflammatory cytokines and chemokines, and the IL10-IL10R axis is a key suppressor for those inflammatory mediators in fibroblasts. Fibroblast-specific Il10ra KO mice developed spontaneous colitis in aged mice. We performed (sc)RNA-seq on stromal cells from these mice and 16s rDNA-seq on the feces from those mice.
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7. GSE279199 CBX4 通过招募 HDAC 抑制 Runx1 来促进急性单核细胞白血病的发展。

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia
• 📝 描述：Contributors : Yueying Zhang ; Yin Ye ; Wenqing Zhang ; Wei LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioAcute monocytic leukemia (AML-M5) is a type of acute myeloid leukemia, characterized by a dominance of monocytes in the bone marrow and peripheral blood. AML-M5 exhibits a poor prognosis compared to other AML subtypes, with a five-year long-term survival rate of less than 20% after diagnosis. Despite chromosomal aberrations and genetic mutations observed in AML-M5, its pathogenic mechanisms remain unclear. In this study, we uncovered a distinct and heightened expression of CBX4, a core component of PRC1, in the peripheral blood of individuals diagnosed with AML-M5. By generating cbx4 overexpression transgenic and deleted mutant zebrafish lines, we observed elevated cbx4 expression in macrophages, selectively modulating their production during zebrafish hematopoiesis. Notably, aging zebrafish with cbx4 overexpression exhibited a progression to AML-M5-like hematopoiesis. Further mechanistic analyses revealed that Cbx4 regulates the fate of macrophage lineage by suppressing runx1 expression. This suppression is achieved through the recruitment of HDAC to the runx1 promoter via the region2 of cbx4, resulting in the down-regulation of the H3K27 acetylation level of runx1. These findings offer novel insights, providing potential avenues for risk assessment and molecular diagnosis of AML-M5 leukemia. Moreover, CBX4 emerges as a promising target for the diagnosis and treatment of AML-M5 leukemia.
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8. GSE328123 WD40 蛋白的系统功能分析揭示了 Wcp1，一种环孢亲和素，它将 CO2/耐热性与新型隐球菌的酸性 pH 适应性联系起来 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Jin-Tae Choi ; Seong-Ryong Yu ; Jeeseok Oh ; Yu-Byeong Jang ; Yujin Lee ; Hyunjin Cha ; Doyeon Won ; Dohee Kim ; Sungmin Yu ; Soojin Yu ; Kyung-Ah Lee ; Jaeyoung Choi ; Won-Jae Lee ; Kyung-Tae Lee ; Yong-Sun BahnSeries Type : Expression profiling by high throughput sequencingOrganism : Cryptococcus neoformansWD40 domains are major protein–protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional expression and sporulation analyses identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We highlighted Wcp1, a WD40–cyclophilin fusion required for growth at 37 °C under 5% CO₂. Both modules supported CO₂/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1Δ mutants failed to grow under elevated temperature and CO₂ at acidic pH, exhibited enhanced intracellular acidification, reduced survival within macrophages and attenuated virulence in both Drosophila and murine models. Integrated transcriptomic and proteomic analyses revealed that Wcp1 acts as a central integrator of intracellular pH homeostasis by coordinating proton transport, metabolic adaptation and stress-buffering networks.
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9. GSE330859 人类巨噬细胞对新型隐球菌的差异性识别引发截然不同的免疫反应（男性和女性）。

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：Contributor : Erin E McClellandSeries Type : Expression profiling by high throughput sequencingOrganism : Cryptococcus neoformans ; Homo sapiensCryptococcus neoformans (Cn) is a pathogenic yeast and the cause of cryptococcosis, a life-threatening fungal disease. Strikingly, ~70% of patients that develop cryptococcosis are male. Here, we investigated decreased Cn recognition by male macrophages and the impact on the subsequent innate immune response. Human PBMCs were isolated from healthy male and female donors, differentiated into macrophages, and tested for immune response differences. Cn incubated with female serum showed increased binding of the opsonin serum amyloid P component, possibly explaining the increased Cn phagocytosis in female macrophages. Cytokine analysis showed increased secretion of proinflammatory cytokines at 24 h in male macrophages that substantially decreased by 48 h. In contrast, female macrophages secreted fewer proinflammatory cytokines at both 24 and 48 h but had increased secretion of CCL5 (24 and 48 h) and IL-18 (48 h). As male macrophages rapidly downregulated proinflammatory immune responses after 24 h; we investigated the macrophage activation state. Male macrophages were alternatively activated at 48 h, with increased secretion of arginase 1 whereas female macrophages were classically activated, with increased secretion of nitric oxide at 24 and 48 h. Cn genes related to glucuronoxylomannan (GXM) biosynthesis were increased in Cn grown in male serum at 48 h. These data suggest that female macrophages better recognize Cn and become classically activated whereas male macrophages initiate an inflammatory response that is markedly reduced after 24 h, possibly due to testosterone-induced GXM secretion. Therefore, antifungal therapeutics targeting testosterone-induced GXM release may improve outcomes in male patients with cryptococcosis.
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10. GSE330780 人类 THP1 细胞状态下先天免疫配体和干扰素蛋白介导的转录反应解析

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：Contributors : Lama Lodoe ; Morozov PavelSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInterferon regulatory factors (IRFs) are essential for transcription of interferons (IFNs), interferon-stimulated genes (ISGs), and pro-inflammatory cytokines. We profile the transcriptome of human monocyte THP1 cells challenged with cGAMP, LPS, or IFNB1 protein as a function of knockout (KO) or overexpression (OE) of IRFs or KO of IFNAR2. We define distinct gene expression groups, reflecting the transcription factors responsible for their induction including subgroups activated by more than one pathway or feed-forward regulation. We compare IRF3- and IRF7-induced gene signatures and note the strong direct induction of a subset of antiviral-acting ISGs by IRF3 or IRF7. LPS treatment induces NF-kB responses in monocyte and macrophage state cells, however, IFNs and ISGs are only co-induced in the macrophage state requiring IRF3. IRF1, IRF2, IRF5, and IRF8 are largely dispensable for IFN-stimulated or innate-immune-mediated gene induction. This study provides a valuable resource for dissecting complex inflammatory gene signatures and their underlying transcription factors thereby anticipating the effects of selectively drugging the underlying pathways.
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1. ⭐ 科学家发现微小的肠道颗粒可能与衰老和慢性疾病有关。

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、gut、regex:gut(-?microbiome)?
• 📝 描述：A new study suggests microscopic particles from the gut may actively drive inflammation and chronic diseases associated with aging. Remarkably, gut particles from young animals appeared to counter some aging-related damage in older animals, hinting at new possibilities for future treatments.
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• GSE330687 PD-L1驱动非小细胞肺癌细胞的代谢重编程和线粒体重塑
• GSE330529转录组分析表明GPNMB是胃癌侵袭性的关键驱动因素
• GSE297199 黑色素瘤功能获得和功能丧失突变的图谱 [RNA-seq]
• GSE268133 对筛选出的高侵袭性（KAP-INV）和高转移性（KAP-MTS）小鼠结直肠癌细胞与亲代（KAP-P）对照细胞系进行转录组分析
• GSE328092 新一代测序技术促进了郑氏58背景中野生型和apl突变体转录组的定量分析
• GSE325756 成纤维细胞中的IL-10/IL-10Ra轴通过抑制I型干扰素信号传导来限制大肠病理
• GSE318880 MC3T3-E1细胞中RUNX2转录靶点的全基因组鉴定
• GSE260675 新一代测序技术促进了W22背景下野生型和edf1突变体转录组的定量分析