Optimized nucleus isolation protocol from frozen mouse tissues for single nucleus RNA sequencing application DOI Creative Commons
Marie-Albane Minati,

Angeline Fages,

Nicolas Dauguet

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2023, Volume and Issue: 11

Published: Sept. 28, 2023

The single cell RNA sequencing technique has been particularly used during the last years, allowing major discoveries. However, widespread application of this analysis showed limitations. Indeed, direct study fresh tissues is not always feasible, notably in case genetically engineered mouse embryo or sensitive whose integrity affected by classical digestion methods. To overcome these limitations, nucleus offers possibility to work with frozen samples. Thus, can be performed after genotyping-based selection on samples stocked tissue bank and applicable retrospective studies. Therefore, opens field a wide range applications requiring adapted protocols for isolation according considered. Here we developed protocol from murine placenta pancreas. These two complex were submitted combination enzymatic manual dissociation before undergoing different steps washing centrifugation. entire was products usually present research lab. Before starting process, nuclei sorted flow cytometry. results obtained validate efficiency which easy set up does require use commercial kits. This specificity makes it adaptable organs species. association allows that resist lysis methods due presence fibrotic fatty tissue, such as kidney, tumors, embryonic

Language: Английский

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease DOI Open Access
Monika Piwecka, Nikolaus Rajewsky, Agnieszka Rybak‐Wolf

et al.

Nature Reviews Neurology, Journal Year: 2023, Volume and Issue: 19(6), P. 346 - 362

Published: May 17, 2023

Language: Английский

Citations

156
Single nuclei transcriptomics delineates complex immune and kidney cell interactions contributing to kidney allograft fibrosis DOI Creative Commons
Jennifer M. McDaniels, Amol C. Shetty, Cem Kuscu

et al.

Kidney International, Journal Year: 2023, Volume and Issue: 103(6), P. 1077 - 1092

Published: Feb. 28, 2023

Language: Английский

Citations

21
Advances in long-read single-cell transcriptomics DOI Creative Commons

Pallawi Kumari,

Manmeet Kaur, Kiran Dindhoria

et al.

Human Genetics, Journal Year: 2024, Volume and Issue: 143(9-10), P. 1005 - 1020

Published: May 24, 2024

Abstract Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The protocols developed for long-read sequencing platforms overcome these limitations by enabling characterization of full-length techniques initially suffered from comparatively poor accuracy compared short read scRNA-Seq. However, with improvements accuracy, accessibility, cost efficiency, long-reads gaining popularity field This review details advances scRNA-Seq, an emphasis on library preparation downstream bioinformatics analysis tools.

Language: Английский

Citations

6
A versatile and efficient method to isolate nuclei from low-input cryopreserved tissues for single-nuclei transcriptomics DOI Creative Commons

Cristopher Segovia,

Vincent Desrosiers,

Fatemeh Khadangi

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 15, 2025

Clinical samples are vital for understanding diseases, but their scarcity requires refined research methods. Emerging single-cell technologies offer detailed views of tissue heterogeneity need sufficient fully characterized tissues. We developed an optimized single-nuclei RNA sequencing (snRNA-seq) protocol to extract nuclei from just 15 mg cryopreserved human tissue. Applied four cancer tissues (brain, bladder, lung, prostate), it profiled 1550–7468 per tissue, revealing comparable public atlases. This method enhances the use and sharing rare, biospecimens, supporting where sample quantity is limited full characterization needed.

Language: Английский

Citations

0
Unraveling aging from transcriptomics DOI
Yuanfang Huang, Sheng Zhu, Shuai Yao

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

Citations

3
Application of single-cell sequencing technology and its clinical implications in Parkinson’s disease and Alzheimer’s disease: a narrative review DOI
Zhonghao Chen, Jing Shi, Longfei Li

et al.

Advanced technology in neuroscience ., Journal Year: 2025, Volume and Issue: 2(1), P. 9 - 15

Published: Feb. 6, 2025

Genetic materials, including DNA and RNA molecules in the nucleus cytosol, contain vital information related to protein production, metabolic regulation, signal transduction. Understanding these their expression levels is important for research different fields of biology, especially study human disease. Owing development next-generation sequencing technology, single-cell technology measures gene from mRNAs through process reverse transcription, allowing researchers gain insights into overexpression/low specific proteins various cells particular disease models, which could help explore signaling pathways associated with cellular molecular mechanisms diseases. For example, has revealed selective vulnerability dopamine neurons nuclear factor κB pathway progression Parkinson’s In Alzheimer’s research, helped identify subpopulations pathology provided inflammatory response Herein, we review application its clinical implications As life expectancy increases annually, incidence neurodegenerative diseases on rise. This trend underscores urgency relevance use anomalous pathogenic genes brain regions. paper introduces three subtypes total sequencing, namely, single-nucleus spatial sequencing. It also several advanced applications technologies At same time, this explores challenges contained methods discusses possible developments future. Overall, provides new tools research. Despite challenges, there great potential improve our understanding complex develop therapies.

Language: Английский

Citations

0
Optimized protocol for the multi-omics processing of cryopreserved human kidney tissue DOI
Sydney E. Gies, Sonja Hänzelmann, Dominik Kylies

et al.

AJP Renal Physiology, Journal Year: 2024, Volume and Issue: 327(5), P. F822 - F844

Published: Oct. 3, 2024

In this study, we addressed challenges in integrating clinically obtained kidney biopsies into everyday clinical routines. Using porcine kidneys, evaluated preservation media (RNAlater and CellCover) versus snap freezing for multi-omics processing. Our analyses highlighted RNAlater’s suitability single-nucleus RNA sequencing, proteome analysis histopathological evaluation. Only metabolomics are currently restricted to snap-frozen biopsies. research established a cryopreservation protocol that facilitates tissue biobanking advancing precision medicine nephrology.

Language: Английский

Citations

1
Effects of oxycodone on placental lineages: Evidence from the transcriptome profile of mouse trophoblast giant cells DOI Creative Commons

Zhen Lyu,

Jessica A. Kinkade,

Nathan J. Bivens

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(45)

Published: Oct. 30, 2024

Pregnant women are often prescribed or abuse opioid drugs. The placenta is likely the key to understanding how opioids cause adverse pregnancy outcomes. Maternal oxycodone (OXY) exposure of pregnant mice leads disturbances in layer invasive parietal trophoblast giant cells (pTGC) that forms interface between and uterus. These analogous extravillous trophoblasts human placenta. They crucial coordinating metabolic needs conceptus with those mother primary participants placenta-brain axis. Their large nuclear size, however, has precluded both single-cell (sc) single-nucleus (sn) RNA-seq analyses beyond embryonic day (E) 8.5. Here, we compared transcriptomes placentas from exposed OXY unexposed controls at E12.5, particular emphasis on pTGC. nonfluidic Parse snRNA-seq approach permitted characterization all major placental cell lineages their presumed progenitors E12.5. had a negligible effect components labyrinth, including two syncytial layers, but caused transcriptomic changes consistent stress throughout spongiotrophoblast. Most notably, there was loss majority pTGC, whose normal gene expression elevated energy demand relating biosynthesis multiple secretory products, especially hormones, endoduplication DNA. This unusual sensitivity pTGC presumably puts future health offspring risk exposure.

Language: Английский

Citations

1
Management of Dysglycemia in a Pregnancy Complicated by Fanconi–Bickel Syndrome DOI Creative Commons
Emily D. Szmuilowicz, Ellen Fruzyna,

Nigel Madden

et al.

AACE Clinical Case Reports, Journal Year: 2024, Volume and Issue: 10(6), P. 224 - 228

Published: July 27, 2024

Background/ObjectiveFanconi-Bickel Syndrome (FBS) is an inherited disorder of glucose metabolism resulting from functional loss transporter 2 (GLUT2) characterized by fasting hypoglycemia oscillating with postprandial hyperglycemia. Dysglycemia treatment strategies during FBS pregnancy have not been reported, and insulin therapy carries significant risk due to in FBS. We report for the first time: (1) glycemic profiles obtained via continuous monitoring (CGM), (2) CGM-guided cornstarch nutritional hyperglycemia, respectively, (3) placental GLUT isoform expression a pregnant individual FBS.Case ReportA 27-year-old woman presented at six weeks gestation management Cornstarch hyperglycemia were iteratively adjusted across based on CGM-derived patterns. Pregnancy-specific targets successfully achieved, she delivered healthy term infant. GLUT2 was detected tissue.DiscussionWe time patterns Glycemic achieved through stepwise optimization therapy, both guided CGM data. Our approach obviated need which amplified FBS.ConclusionFasting can be effectively treated adjustment polymer therapies pregnancy. More broadly, our case highlights novel application uncommon disorders

Language: Английский

Citations

1
Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development DOI Creative Commons

Steven Pregizer,

Thom Vreven,

Mohit Mathur

et al.

Frontiers in Molecular Biosciences, Journal Year: 2023, Volume and Issue: 10

Published: April 5, 2023

Single cell sequencing technologies have rapidly advanced in the last decade and are increasingly applied to gain unprecedented insights by deconstructing complex biology its fundamental unit, individual cell. First developed for measurement of gene expression, single approaches evolved allow simultaneous profiling multiple additional features, including chromatin accessibility within nucleus protein expression at surface. These multi-omic can now further be cells situ , capturing spatial context which their occurs. To extract from these datasets, new computational tools facilitated integration information across different data types use machine learning approaches. Here, we summarize current experimental methods generation datasets. We focus on opportunities augment therapeutic development kidney disease, applications biomarkers, disease stratification target identification.

Language: Английский

Citations

1