详细内容（全部8条）

1. ⭐ GSE315375 研究发现，智利人群甲状腺癌中 MALAT1 水平升高与代谢重编程和淋巴浸润相关

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:lymph(o|atic)?、metabolic
• 📝 描述：Contributors : Michelle Tobar-Lara ; Andrea Matamoros ; Marcelo Muñoz-González ; Diego Leiva ; Gunther Redenz ; Gino Nardocci ; Patricio Cabané ; Alvaro A Elorza ; Rodrigo AguilarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMetastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA (lncRNA) implicated in cancer progression. In thyroid cancer, MALAT1 has been proposed as a potential biomarker, but its role in disease progression remains incompletely understood. Here, we analyzed MALAT1 RNA levels in tumoral and non-tumoral paired-thyroid samples from a cohort of Chilean thyroid cancer patients. We found a positive correlation with lymphatic infiltration. RNA-seq analysis revealed upregulation of genes associated with epithelial-to-mesenchymal transition and downregulation of cell-adhesion molecules. Metabolism-associated genes were also altered.
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2. GSE308556 RNA-seq 分析了过表达组蛋白变体 H2BE 并用 BDNF 刺激的神经元。

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、histone
• 📝 描述：Contributor : Emily FeiermanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusA cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.
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3. GSE303428 胰岛细胞中线粒体miRNA的差异表达与母体蛋白质限制相关

• ✍️ 作者：未知作者
• 🏷️ 关键词：differential expression
• 📝 描述：Contributors : Cecile Jacovetti ; Romano RegazziSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Rattus norvegicusIn this study, we discovered cytosolic and mitochondrial small non-coding RNAs (tRNA-derived fragments, piRNAs and microRNAs) which may act as new regulators of cellular and metabolic functions. We analzyed the expression profile and function of tRNA-derived fragments in a previous study (https://doi.org/10.1016/j.molmet.2024.101955). In this current study, we focused our analysis on hundreds of microRNAs and piRNAs in the mitochondrial fractions versus whole cell lysates from pancreatic islets of progeny of rats exposed to a low-protein (LP) diet during in utero and lactation period and compared them to control rats. At 22 days of age, LP-exposed rats exhibit a reduced body weight and a decreased beta-cell mass. These animals are more prone to develop diabetes and display a glucose intolerance at adulthood. In our analysis, we identified 6164 tRFs, 543 microRNAs, 118 piRNAs and 32 other types of small non-coding RNAs in the islets of LP-exposed rats, among which 400 exhibited significant changes (total read counts ≥ 13 cutoff, p ≤ 0.05) compared to controls. Of these, 167 tRFs showed increased levels, while 233 small non-coding RNAs showed decreased levels in the LP-exposed rat islets. Analysis of mictochondrial content revealed the presence of 548 tRNA-derived fragments, 33 microRNAs, 18 piRNAs and 22 other types of small non-coding RNAs in the mitochondrial fractions of control rat islets while the mitochondrial fractions of LP-exposed rat islets contained 564 tRNA-derived fragments, 23 microRNAs, 9 piRNAs and 23 other types of small non-coding RNAs. Our analysis revaled 10 microRNAs that are concomitantly enriched in the mitochondria while being reduced in cytosol of LP-exposed islet cells. Our findings reveal a significant reshaping of mitochondrial small non-coding RNAs in pre-diabetic conditions, coinciding with a well-established mitochondrial metabolic defect under these conditions.
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4. GSE297297 血管生成素受体Tie2限制心脏内皮细胞的增殖和出芽

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac
• 📝 描述：Contributors : Andrey Anisimov ; Madeleine H Lackman ; Kari Alitalo ; Sinem KaramanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTie1 and Tie2 receptors are important in the maintenance of the vascular steady-state. We used scRNAseq to analyze how genetic deletion of Tie1 and Tie2 affects expression of proliferation-related genes in mouse endothelial cells.
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5. GSE308557 刺激神经元中组蛋白变体 H2BE 的 CUT&Tag seq 分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：histone
• 📝 描述：Contributor : Emily FeiermanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusA cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.
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6. GSE315445 MIC-Drop-seq：可扩展的突变脊椎动物胚胎单细胞表型分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell
• 📝 描述：Contributors : Clayton Carey ; Saba Parvez ; Zachary Brandt ; Brent Bisgrove ; Christopher Yates ; Randall Peterson ; James GagnonSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Danio rerioPooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, which combines high-throughput CRISPR gene disruption in zebrafish embryos with phenotyping by multiplexed single-cell RNAseq. In one MIC-Drop-seq experiment, we simultaneously identified changes in gene expression and cell abundance across 74 cell types resulting from loss of function of 50 transcription factors. These observations recapitulated many known phenotypes, while also uncovering novel functions in brain and mesoderm development. A key advantage of whole-animal screens is that they reveal how changes in one cell type affect the development of other cell types. Surprisingly, such cell-extrinsic phenotypes were abundant, indicating that transcription factors frequently exert effects beyond the cells where they are expressed to adjacent cells. We propose that MIC-Drop-seq will facilitate efforts to dissect the complete gene regulatory networks that guide animal development.
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7. GSE315475 研究表明，血管活性肠肽 (VIP) 基因靶向敲除的小鼠会出现自发性肺动脉高压，且缺氧会加剧这种高压。

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:intestin(e|al)
• 📝 描述：Contributors : Akash Gupta ; Mohamed Ahmed ; Anthony N SzemaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe earlier reported spontaneous moderate pulmonary arterial hypertension in Vasoactive Intestinal Peptide (VIP) gene knockout mice. In the current study, we show accelerated pulmonary artery pressure changes associated with vascular and cardiac remodeling changes in VIP KO mice subjected to hypoxia compared to control wild-type C57BL/6 mice in hypoxia chambers. There is differential whole-lung RNA sequencing expression between baseline normoxia wild-type and VIP KO mice groups. Under conditions of hypoxia vs. normoxia, we observe upregulation of spatial biology expression of CD45 in VIP KO mice with hypoxia, but not in wild-type mice with hypoxia. Moreover, wild-type hypoxia mice express alpha-actin and CD31, which is not seen in the VIP KO hypoxia cohort. Human lung tissue from pediatric patients with idiopathic pulmonary arterial hypertension (PAH) lacks immunohistochemical evidence of VIP, supporting the concepts that VIP plays a critical role in the immunopathogenesis of pulmonary hypertension and VIP or its analogues may potentially be used to treat PAH.
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8. GSE293983 香烟烟雾和生物年龄诱导视网膜色素上皮退行性异质性[scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA
• 📝 描述：Contributors : Yang Jin ; Krishna Singh ; Jiang Qian ; James T HandaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEnvironmental exposure such as cigarette smoke induces epigenetic changes that can induce degenerative heterogeneity and accelerate aging. In early age-related macular degeneration (AMD), the leading worldwide cause of blindness among the elderly, retinal pigment epithelial (RPE) cell heterogeneity is a key change. Since smoking is the strongest environmental risk factor for AMD, we hypothesized that cigarette smoke induces degenerative RPE heterogeneity through epigenetic changes that are distinct from aging, and that with aging, the RPE becomes vulnerable to cigarette smoke insult. We administered cigarette smoke condensate (CSC) intravitreally to young and aged mice and performed snRNA-seq and snATAC-seq on the RPE/choroid. This analysis identified separate cell clusters corresponding to healthy and abnormal, dedifferentiated RPE in both aged vehicletreated and young CSC-treated mice. The dedifferentiated RPE were characterized by a global decrease in chromatin accessibility and decreased expression of genes in functional categories that were linked to hallmarks of aging. Notably, young, dedifferentiated RPE also exhibited a compensatory upregulation of hallmarks of aging-related genes, specifically those related to mitochondrial function and proteostasis. In contrast, aged dedifferentiated RPE did not express these compensatory changes, and did not survive CSC treatment, as experimentally verified with TUNEL labeling. These changes are relevant to early AMD because we identified through scRNA-seq, similar dedifferentiated and healthy macular RPE clusters in a donor who smoked and another with early AMD, but not from a nonsmoker. Degenerative cellular heterogeneity can include an abnormal cluster that jeopardizes cell survival and may represent an additional hallmark of ocular aging.
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详细内容（全部3条）

1. 科学家们测试了不减少食物摄入量的间歇性禁食，发现它对新陈代谢没有益处。

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic
• 📝 描述：Time-restricted eating has been widely promoted as a simple way to boost metabolic health, but new research paints a more complicated picture. When calorie intake stayed the same, an eight-hour eating window did not improve insulin sensitivity or cardiovascular markers. What did change was the body’s internal clock, which shifted based on meal timing and altered sleep patterns. The results suggest calorie reduction, not the eating window itself, may be the real driver of health benefits.
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2. 潜在的脑部问题可能是阿尔茨海默病的早期预警信号。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Researchers discovered that clogged brain “drains” show up early in people at risk of Alzheimer’s disease. These blockages, easily seen on standard MRI scans, are tied to toxic protein buildup linked to memory loss and cognitive decline. In some cases, they may signal Alzheimer’s earlier than other commonly used brain markers. This could help physicians detect the disease earlier, before irreversible damage sets in.
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3. 糖尿病药物可能正在以令人惊讶的方式改变癌症。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Common diabetes drugs may do more than regulate blood sugar—they could also influence how cancers grow, spread, or slow down. Researchers are now unraveling how these medications affect immune function, inflammation, and tumor biology, with intriguing but still uncertain implications.
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