keyword
https://read.qxmd.com/read/38522139/single-cell-transcriptome-profiling-of-infrapatellar-fat-pad-highlights-the-role-of-interstitial-inflammatory-fibroblasts-in-osteoarthritis
#1
JOURNAL ARTICLE
Hongxu Pu, Chenghao Gao, Yi Zou, Liming Zhao, Guanghao Li, Changyu Liu, Libo Zhao, Meng Zheng, Gaohong Sheng, Xuying Sun, Xingjie Hao, Chaolong Wang, Ximiao He, Jun Xiao
OBJECTIVES: Osteoarthritis (OA) is a whole-joint disease in which the role of the infrapatellar fat pad (IFP) in its pathogenesis is unclear. Our study explored the cellular heterogeneity of IFP to understand OA and identify therapeutic targets. METHODS: Single-cell and single-nuclei RNA sequencing were used to analyze 10 IFP samples, comprising 5 from OA patients and 5 from healthy controls. Analyses included differential gene expression, enrichment, pseudotime trajectory, and cellular communication, along with comparative studies with visceral and subcutaneous fats...
March 23, 2024: International Immunopharmacology
https://read.qxmd.com/read/38517898/protocol-for-the-isolation-and-single-nuclei-multiomic-analyses-of-the-human-fetal-epicardium
#2
JOURNAL ARTICLE
Stanislao Igor Travisano, Ching-Ling Lien
The characterization of cell populations that reside in the outer layer of the heart has been hindered by difficulties in their isolation. Here, we present a protocol for isolation and single-nuclei multiomic analyses of the human fetal epicardium. We describe steps for microdissection, isolation, and enrichment of epicardial cells by mechanical dissociations and direct lysis. We then detail procedures for integrating transcriptome and chromatin accessibility datasets. This approach allows the analysis of diverse cell populations, marked by unique cis-regulatory elements...
March 21, 2024: STAR protocols
https://read.qxmd.com/read/38517229/a-cell-atlas-of-thoracic-aortic-perivascular-adipose-tissue-a-focus-on-mechanotransducers
#3
JOURNAL ARTICLE
Janice M Thompson, Stephanie W Watts, Leah Terrian, G Andres Contreras, Cheryl Rockwell, C Javier Rendon, Emma Wabel, Lizbeth Lockwood, Sudin Bhattacharya, Rance Nault
Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. However, major gaps remain in our understanding of the cells present in PVAT, as well as how different cells contribute to mechanotransduction. We hypothesized that snRNA seq would reveal expression of mechanotransducers, and test one (PIEZO1) to illustrate the expression and functional agreement between single-nuclei RNA sequencing (snRNAseq) and physiological measurements. To contrast two brown tissues, subscapular brown adipose tissue (BAT) was also examined...
March 22, 2024: American Journal of Physiology. Heart and Circulatory Physiology
https://read.qxmd.com/read/38463979/transcriptomic-analysis-of-the-human-habenula-in-schizophrenia
#4
Ege A Yalcinbas, Bukola Ajanaku, Erik D Nelson, Renee Garcia-Flores, Kelsey D Montgomery, Joshua M Stolz, Joshua Wu, Heena R Divecha, Atharv Chandra, Rahul A Bharadwaj, Svitlana Bach, Anandita Rajpurohit, Ran Tao, Joo-Heon Shin, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Louise A Huuki-Myers, Leonardo Collado-Torres, Kristen R Maynard
IMPORTANCE: Habenula (Hb) pathophysiology is involved in many neuropsychiatric disorders, including schizophrenia. Deep brain stimulation and pharmacological targeting of the Hb are emerging as promising therapeutic treatments. However, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in schizophrenia. OBJECTIVE: To define the molecular neuroanatomy of the human habenula and identify transcriptomic changes in individuals with schizophrenia compared to neurotypical controls...
February 27, 2024: bioRxiv
https://read.qxmd.com/read/38461411/protocol-to-dissect-and-dissociate-the-mouse-brainstem-for-single-cell-rna-seq-applications
#5
JOURNAL ARTICLE
Wiktor S Phillips, Naify Ramadan, Athina Samara, Eric Herlenius
Processing dissociated cells for transcriptomics is challenging when targeting small brain structures, like brainstem nuclei, where cell yield may be low. Here, we present a protocol for dissecting, dissociating, and cryopreserving mouse brainstem that allows asynchronous sample collection and downstream processing of cells obtained from brainstem tissue in neonatal mice. Although we demonstrate this protocol with the isolated preBötzinger complex and downstream SmartSeq3 cDNA library preparation, it could be readily adapted for other brainstem areas and library preparation approaches...
March 8, 2024: STAR protocols
https://read.qxmd.com/read/38438345/a-spatially-resolved-transcriptional-atlas-of-the-murine-dorsal-pons-at-single-cell-resolution
#6
JOURNAL ARTICLE
Stefano Nardone, Roberto De Luca, Antonino Zito, Nataliya Klymko, Dimitris Nicoloutsopoulos, Oren Amsalem, Cory Brannigan, Jon M Resch, Christopher L Jacobs, Deepti Pant, Molly Veregge, Harini Srinivasan, Ryan M Grippo, Zongfang Yang, Mark L Zeidel, Mark L Andermann, Kenneth D Harris, Linus T Tsai, Elda Arrigoni, Anne M J Verstegen, Clifford B Saper, Bradford B Lowell
The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially...
March 4, 2024: Nature Communications
https://read.qxmd.com/read/38435301/analysis-of-haemonchus-embryos-at-single-cell-resolution-identifies-two-eukaryotic-elongation-factors-as-intervention-target-candidates
#7
JOURNAL ARTICLE
Pasi K Korhonen, Tao Wang, Neil D Young, Joseph J Byrne, Tulio L Campos, Bill C H Chang, Aya C Taki, Robin B Gasser
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38416649/protocol-for-flow-cytometry-assisted-single-nucleus-rna-sequencing-of-human-and-mouse-adipose-tissue-with%C3%A2-sample-multiplexing
#8
JOURNAL ARTICLE
Anton Gulko, Adam Essene, Dylan Matthew Belmont-Rausch, Molly Veregge, Deepti Pant, Danielle Tenen, Benedicte Schultz Kapel, Margo P Emont, Tune H Pers, Evan D Rosen, Linus T Tsai
Adipocyte size and fragility and commercial kit costs impose significant limitations on single-cell RNA sequencing of adipose tissue. Accordingly, we developed a workflow to isolate and sample-barcode nuclei from individual adipose tissue samples, integrating flow cytometry for quality control, counting, and precise nuclei pooling for direct loading onto the popular 10× Chromium controller. This approach can eliminate batch confounding, and significantly reduces poor-quality nuclei, ambient RNA contamination, and droplet loading-associated reagent waste, resulting in pronounced improvements in information content and cost efficiency...
February 27, 2024: STAR protocols
https://read.qxmd.com/read/38405805/benchmark-of-cellular-deconvolution-methods-using-a-multi-assay-reference-dataset-from-postmortem-human-prefrontal-cortex
#9
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Sean K Maden, Nicholas J Eagles, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
BACKGROUND: Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Several deconvolution methods have been developed and they have been previously benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or cell type proportions derived from immunohistochemistry reference data. A major limitation preventing the improvement of deconvolution algorithms has been the lack of highly integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue block...
February 12, 2024: bioRxiv
https://read.qxmd.com/read/38405748/accessible-chromatin-maps-of-inflammatory-bowel-disease-intestine-nominate-cell-type-mediators-of-genetic-disease-risk
#10
Joseph A Wayman, Zi Yang, Elizabeth Angerman, Erin Bonkowski, Ingrid Jurickova, Xiaoting Chen, Anthony T Bejjani, Lois Parks, Sreeja Parameswaran, Alexander G Miethke, Kelli L VanDussen, Jasbir Dhaliwal, Matthew T Weirauch, Leah C Kottyan, Lee A Denson, Emily R Miraldi
Inflammatory Bowel Disease ( IBD ) is a chronic and often debilitating autoinflammatory condition, with an increasing incidence in children. Standard-of-care therapies lead to sustained transmural healing and clinical remission in fewer than one-third of patients. For children, TNFα inhibition remains the only FDA-approved biologic therapy, providing an even greater urgency to understanding mechanisms of response. Genome-wide association studies ( GWAS ) have identified 418 independent genetic risk loci contributing to IBD, yet the majority are noncoding and their mechanisms of action are difficult to decipher...
February 13, 2024: bioRxiv
https://read.qxmd.com/read/38380322/comparison-of-the-single-cell-and-single-nucleus-hepatic-myeloid-landscape-within-decompensated-cirrhosis-patients
#11
JOURNAL ARTICLE
Lukas Van Melkebeke, Jef Verbeek, Dora Bihary, Markus Boesch, Bram Boeckx, Rita Feio-Azevedo, Lena Smets, Marie Wallays, Eveline Claus, Lawrence Bonne, Geert Maleux, Olivier Govaere, Hannelie Korf, Diether Lambrechts, Schalk van der Merwe
BACKGROUND AND AIMS: A complete understanding of disease pathophysiology in advanced liver disease is hampered by the challenges posed by clinical specimen collection. Notably, in these patients, a transjugular liver biopsy (TJB) is the only safe way to obtain liver tissue. However, it remains unclear whether successful sequencing of this extremely small and fragile tissue can be achieved for downstream characterization of the hepatic landscape. METHODS: Here we leveraged in-house available single-cell RNA-sequencing (scRNA-seq) and single-nucleus (snRNA-seq) technologies and accompanying tissue processing protocols and performed an in-patient comparison on TJB's from decompensated cirrhosis patients (n = 3)...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38368983/tbx3-reciprocally-controls-key-trophoblast-lineage-decisions-in-villi-during-human-placenta-development-in-the-first-trimester
#12
JOURNAL ARTICLE
Cen Yi, Honglan Song, Hongxiu Liang, Yujie Ran, Jing Tang, Enxiang Chen, Fangfang Li, Lijuan Fu, Yaqi Wang, Fengming Chen, Yingxiong Wang, Yubin Ding, Youlong Xie
Human trophoblastic lineage development is intertwined with placental development and pregnancy outcomes, but the regulatory mechanisms underpinning this process remain inadequately understood. In this study, based on single-nuclei RNA sequencing (snRNA-seq) analysis of the human early maternal-fetal interface, we compared the gene expression pattern of trophoblast at different developmental stages. Our findings reveal a predominant upregulation of TBX3 during the transition from villous cytotrophoblast (VCT) to syncytiotrophoblast (SCT), but downregulation of TBX3 as VCT progresses into extravillous trophoblast cells (EVT)...
February 16, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38355308/differences-in-molecular-sampling-and-data-processing-explain-variation-among-single-cell-and-single-nucleus-rna-seq-experiments
#13
JOURNAL ARTICLE
John T Chamberlin, Younghee Lee, Gabor Marth, Aaron R Quinlan
A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing and analyzing single-cell and single-nucleus RNA sequencing experiments. Nuclei contain the same pre-mRNA population as cells, but they contain a small subset of the mRNAs. Nonetheless, early studies argued that single-nucleus analysis yielded results comparable to cellular samples if pre-mRNA measurements were included. However, typical workflows do not distinguish between pre-mRNA and mRNA when estimating gene expression, and variation in their relative abundances across cell types has received limited attention...
February 14, 2024: Genome Research
https://read.qxmd.com/read/38351133/single-nucleus-rna-seq-characterizes-the-cell-types-along-the-neuronal-lineage-in-the-adult-human-subependymal-zone-and-reveals-reduced-oligodendrocyte-progenitor-abundance-with-age
#14
JOURNAL ARTICLE
Sofía Puvogel, Astrid Alsema, Hayley F North, Maree J Webster, Cynthia Shannon Weickert, Bart J L Eggen
The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during post-natal life. In humans, the neurogenic potential of the SEZ declines after the first year of life. However, studies discovering markers of stem and progenitor cells highlight the neurogenic capacity of progenitors in the adult human SEZ, with increased neurogenic activity occurring under pathological conditions. In the present study, the complete cellular niche of the adult human SEZ was characterized by single-nucleus RNA sequencing, and compared between 4 youth (age 16-22) and 4 middle-aged adults (age 44-53)...
February 13, 2024: ENeuro
https://read.qxmd.com/read/38334607/single-cell-transcriptional-response-of-the-placenta-to-the-ablation-of-caveolin-1-insights-into-the-adaptive-regulation-of-brain-placental-axis-in-mice
#15
JOURNAL ARTICLE
Maliha Islam, Susanta K Behura
Caveolin-1 ( Cav1 ) is a major plasma membrane protein that plays important functions in cellular metabolism, proliferation, and senescence. Mice lacking Cav1 show abnormal gene expression in the fetal brain. Though evidence for placental influence on brain development is emerging, whether the ablation of Cav1 affects the regulation of the brain-placental axis remains unexamined. The current study tests the hypothesis that gene expression changes in specific cells of the placenta and the fetal brain are linked to the deregulation of the brain-placental axis in Cav1 -null mice...
January 24, 2024: Cells
https://read.qxmd.com/read/38328093/cell-type-specificity-of-mosaic-chromosome-1q-gain-resolved-by-snrna-seq-in-a-case-of-epilepsy-with-hyaline-protoplasmic-astrocytopathy
#16
Kun Leng, Cathryn R Cadwell, W Patrick Devine, Tarik Tihan, Zhongxia Qi, Nilika Singhal, Orit Glenn, Sherry Kamiya, Arun Wiita, Amy Berger, Joseph T Shieh, Erron W Titus, Mercedes F Paredes, Vaibhav Upadhyay
INTRODUCTION: Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathological finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. METHODS: We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA...
January 25, 2024: bioRxiv
https://read.qxmd.com/read/38325338/region-specific-transcriptomic-responses-to-obesity-and-diabetes-in-macaque-hypothalamus
#17
JOURNAL ARTICLE
Ying Lei, Xian Liang, Yunong Sun, Ting Yao, Hongyu Gong, Zhenhua Chen, Yuanqing Gao, Hui Wang, Ru Wang, Yunqi Huang, Tao Yang, Miao Yu, Longqi Liu, Chun-Xia Yi, Qing-Feng Wu, Xingxing Kong, Xun Xu, Shiping Liu, Zhi Zhang, Tiemin Liu
The hypothalamus plays a crucial role in the progression of obesity and diabetes; however, its structural complexity and cellular heterogeneity impede targeted treatments. Here, we profiled the single-cell and spatial transcriptome of the hypothalamus in obese and sporadic type 2 diabetic macaques, revealing primate-specific distributions of clusters and genes as well as spatial region, cell-type-, and gene-feature-specific changes. The infundibular (INF) and paraventricular nuclei (PVN) are most susceptible to metabolic disruption, with the PVN being more sensitive to diabetes...
February 6, 2024: Cell Metabolism
https://read.qxmd.com/read/38281016/a-transcriptomic-examination-of-encased-rotifer-embryos-reveals-the-developmental-trajectory-leading-to-long-term-dormancy-are-they-animal-seeds
#18
JOURNAL ARTICLE
Tamar Hashimshony, Liron Levin, Andreas C Fröbius, Nitsan Dahan, Vered Chalifa-Caspi, Reini Hamo, Oshri Gabai-Almog, Idit Blais, Yehuda G Assaraf, Esther Lubzens
BACKGROUND: Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied organisms exhibit seasonal or annual episodes of dormancy, but numerous less studied organisms enter long-term dormancy, lasting decades or even centuries. Intriguingly, many planktonic animals produce encased embryos known as resting eggs or cysts that, like plant seeds, may remain dormant for decades...
January 27, 2024: BMC Genomics
https://read.qxmd.com/read/38266791/unravelling-the-genetic-basis-of-schizophrenia
#19
REVIEW
Clara Casey, John F Fullard, Roy D Sleator
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain...
January 22, 2024: Gene
https://read.qxmd.com/read/38260567/loss-of-%C3%AE-ba-crystallin-but-not-%C3%AE-a-crystallin-increases-age-related-cataract-in-the-zebrafish-lens
#20
Mason Posner, Taylor Garver, Taylor Kaye, Stuart Brdicka, Madison Suttle, Bryce Patterson, Dylan R Farnsworth
The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein α-crystallins evolved to become key components of this lens, possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two α-crystallins, αA- and αB-crystallin, and mutations in each are linked to human cataract. In a mouse knockout model only the loss of αA-crystallin led to early-stage lens cataract...
January 3, 2024: bioRxiv
keyword
keyword
171814
1
2
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.