PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

New open-source platform for high-resolution spatial transcriptomics

New open-source platform for high-resolution spatial transcriptomics
2024-08-06
(Press-News.org) Leuven, 6 August 2024 - A team of researchers from the lab of Prof. Stein Aerts (VIB-KU Leuven) presents Nova-ST, a new spatial transcriptomics technique that promises to transform gene expression profiling in tissue samples. Nova-ST will make large-scale, high-resolution spatial tissue analysis more accessible and affordable, offering significant benefits for researchers. The research was published in Cell Reports Methods.

Transcriptomics is the study of gene expression in a cell or a population of cells, but it usually does not include spatial information about where those genes were active. This hurdle limited our understanding of complex biological processes that rely on specific gene activity patterns within tissues. Thankfully, spatial transcriptomics has emerged as a powerful tool, allowing scientists to map gene expression across a tissue section with a spatial context. However, existing techniques often suffer from high costs, limited resolution, or compatibility issues.

Enter Nova-ST, a novel open-source spatial transcriptomics workflow developed by the lab of Prof. Stein Aerts and the Single-cell Microfluidics and Bioinformatics expertise units at VIB.AI and the VIB-KU Leuven Center for Brain & Disease Research. Nova-ST overcomes these limitations with its innovative approach, offering greater affordability, impressive resolution, and versatility.

Under the hood At the heart of Nova-ST lies a clever adaptation of Illumina NovaSeq 6000 S4 or the new generation Novaseq X sequencing flow cells, commonly used for large-scale DNA sequencing. These flow cells contain a dense nano-patterned surface riddled with tiny, randomly barcoded nanowells arranged in a hexagonal lattice. Each well acts as a capture site for mRNA molecules from a specific location within the tissue sample. This dense nano-patterned surface allows Nova-ST to achieve high spatial resolution, potentially capturing the footprint of single cells.

“We then use these capture sites to snag mRNA molecules while preserving their spatial coordinates,” explains Dr. Suresh Poovathingal, who led the experimental development and optimization. ”Sequencing these captured mRNA molecules reveals the gene expression profile for each capture site. By piecing together this information, we can reconstruct a detailed map of gene activity across the entire tissue section."

Advantages The new platform boasts several key advantages. Firstly, it is cost-effective. By leveraging readily available Illumina flow cells and employing a novel chip-cutting technique, multiple Nova-ST chips can be created from a single flow cell, significantly reducing costs compared to existing methods. Secondly, the dense nano-patterned surface allows Nova-ST to achieve high spatial resolution, potentially capturing gene expression at the single-cell level. Thirdly, Nova-ST is compatible with various tissue types, making it a versatile tool for studying diverse biological systems. Additionally, the compatibility with next-generation Illumina flow cells suggests that Nova-ST can benefit from advancements in sequencing technology.

“Importantly, Nova-ST’s open-source nature makes the protocol accessible to a wider range of researchers and allows for further customization,” Dr. Kristofer Davie, who led the data analysis, notes, "Our workflow is designed to be user-friendly and adaptable, ensuring that researchers can tailor the technique to their specific needs."

Impact Nova-ST is the latest example of broader efforts within the spatial transcriptomics research community to democratize access and build platforms that advance a wide range of biomedical research, including Seq-Scope and its recent variants developed at the University of Michigan, as well as the recently published Open-ST platform developed by scientists at Max Delbrück Center in Germany.

Stein Aerts' lab and the expertise units are already applying Nova-ST to advance their colleagues’ research in neurodegeneration and cancer biology. For example, they processed muscle samples for the Sandrine Da Cruz lab (VIB-KU Leuven) to study the effects of neurodegenerative diseases on neuromuscular junctions. Additionally, they are working with the Diether Lambrechts lab (VIB-KU Leuven) to expand the Nova-ST platform. This expansion will allow the simultaneous spatial analysis of immune cell receptors and gene expression, enabling the study of immune cell distribution in tumors undergoing immunotherapy. These collaborations highlight Nova-ST’s practical applications and its potential to impact various fields.

Prof. Stein Aerts emphasizes, “Nova-ST is a game-changer for research across multiple fields, from cancer biology to plant biology. By making this platform open source, we aim to empower scientists worldwide to explore and innovate.”

The detailed experimental protocols are available here and here. The computational pipeline is available on GitHub, where the entire scientific community can make use of it for implementing Nova-ST. Additional details can be found at nova-st.aertslab.org.



Publication Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics. Poovathingal, Davie, et al. Cell Reports Methods, 2024. DOI: xxx

Funding The research (team) was supported by an ERC Advanced Grant and Aligning Science Across Parkinson’s through the Michael J. Fox Foundation for Parkinson’s Research.

END

[Attachments] See images for this press release:
New open-source platform for high-resolution spatial transcriptomics New open-source platform for high-resolution spatial transcriptomics 2 New open-source platform for high-resolution spatial transcriptomics 3

ELSE PRESS RELEASES FROM THIS DATE:

Targeted cancer therapy: initial high concentration may slow down selection for resistance

Targeted cancer therapy: initial high concentration may slow down selection for resistance
2024-08-06
BUFFALO, NY- August 6, 2024 – On July 28, 2024, Mikhail V. Blagosklonny M.D., Ph.D., from Roswell Park Comprehensive Cancer Center published a new editorial in Volume 16, Issue 14 of Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science), entitled, “Targeted cancer therapy: the initial high concentration may slow down the selection for resistance.” “Unfortunately, any targeted therapy is, always, started with low levels of the drug in the organism, selecting for drug resistance. One should propose that initial drug levels must be maximized, ...

Lehigh University researchers dig deeper into stability challenges of nuclear fusion—with mayonnaise

Lehigh University researchers dig deeper into stability challenges of nuclear fusion—with mayonnaise
2024-08-06
Mayonnaise continues to help researchers better understand the physics behind nuclear fusion. “We’re still working on the same problem, which is the structural integrity of fusion capsules used in inertial confinement fusion, and Hellmann’s Real Mayonnaise is still helping us in the search for solutions,” says Arindam Banerjee, the Paul B. Reinhold Professor of Mechanical Engineering and Mechanics at Lehigh University and Chair of the MEM department in the P.C. Rossin College of Engineering and Applied Science.  In simple terms, fusion reactions are what power the sun. If the process could ...

Texas Tech professor receives grant for printable semiconductors research

2024-08-06
Minxiang “Glenn” Zeng, an assistant professor in the Department of Chemical Engineering at Texas Tech University, has been awarded a $250,000 grant from the Launching Early-Career Academic Pathways in the Mathematical and Physical Sciences (LEAPS-MPS) award from the National Science Foundation (NSF) to further his research about printable semiconductors and electronics under extreme environments.   The grant supports Zeng’s work in understanding and controlling the thermal degradation pathways of printed metal chalcogenides, which are semiconductor materials including selenides, tellurides and sulfides. His goal is to develop strategies to enhance the thermal stability ...

Digital Olfaction Society 2024: Revolutionizing scent digitization and global transfer

Digital Olfaction Society 2024: Revolutionizing scent digitization and global transfer
2024-08-06
The 8th Annual Meeting of the Digital Olfaction Society (DOS) will take place on December 5-6, 2024, in Tokyo, Japan, and Online. The DOS meeting is uniquely aimed at digitizing scents, transferring them, and re-creating them in different parts of the world. The two-day event includes one day dedicated to talks and another day for demonstrations. Under the slogan "Olfaction to Digital Olfaction", the congress will explore the latest advances in olfaction science and digital olfaction technologies, highlighting their transformative impact across multiple fields. The first day of the congress will focus on olfaction science, scent-based diagnosis and treatment ...

New York City’s fireworks display prompts temporary surge of air pollution

2024-08-06
In 2023, roughly 60,000 firework shells exploded above Manhattan’s East River as part of Macy’s Fourth of July show. The resulting air pollutant levels were many times higher in the hours after the display than those seen when smoke from a Canadian wildfire had blanketed the area a month before. This is according to the results of a new study, led by researchers at NYU Langone Health, which measured air quality just before and after the Independence Day event, one of the largest in the United States. Tiny particles of hazardous metals and organic compounds peaked at 3,000 micrograms per cubic meter at an air sampling site ...

Smallest arm bone in human fossil record sheds light on the dawn of Homo floresiensis

Smallest arm bone in human fossil record sheds light on the dawn of Homo floresiensis
2024-08-06
A paper out today in Nature Communications reports the discovery of extremely rare early human fossils from the Indonesian island of Flores, including an astonishingly small adult limb bone.   Dated to about 700,000 years old, the new findings shed light on the evolution of Homo floresiensis, the so-called ‘Hobbits’ of Flores whose remains were uncovered in 2003 at Liang Bua cave in the island’s west by a team co-led by Australian-New Zealand archaeologist Professor Mike Morwood (1950–2013).   Archaeological evidence suggests these diminutive, small-brained humans inhabited Liang Bua ...

Type 2 diabetes and fracture risk in older women

2024-08-06
About The Study: The results from this study suggest that the higher fracture risk among older women with type 2 diabetes may be due to impaired physical function and not skeletal characteristics.  Corresponding Author: To contact the corresponding author, Mattias Lorentzon, MD, PhD, email mattias.lorentzon@medic.gu.se. To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ (doi:10.1001/jamanetworkopen.2024.25106) Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and ...

AI for early detection of pediatric eye diseases using mobile photos

2024-08-06
About The Study: In this cross-sectional study, the artificial intelligence (AI) model demonstrated strong performance in accurately identifying myopia, strabismus, and ptosis using only smartphone images. These results suggest that such a model could facilitate the early detection of pediatric eye diseases in a convenient manner at home. Corresponding Authors: To contact the corresponding authors, email Lin Li, MD, PhD (jannetlee130@gmail.com), and Jie Xu, DHM (xujie@pjlab.org.cn). To access the embargoed ...

Demographic representation of generative AI images of physicians

2024-08-06
About The Study: This study identifies demographic biases in artificial intelligence (AI)-generated images of physicians with disproportionate representation of white and male physicians and concerning underrepresentation of other races and ethnicities (Asian and Latino) and female physicians in some platforms. This bias has the potential to reinforce stereotypes and undermine diversity, equity, and inclusion initiatives within health care.  Corresponding Author: To contact the corresponding author, Sang Won Lee, MSc, email sangwon_lee@hms.harvard.edu. To access the embargoed ...

When faster is not better: New study links premature development of human neurons to brain developmental disorders

When faster is not better: New study links premature development of human neurons to brain developmental disorders
2024-08-06
Leuven, 7 August 2024—The mechanisms underlying intellectual disabilities or autism remain largely unknown. Researchers in the labs of Prof. Pierre Vanderhaeghen and Prof. Vincent Bonin at the VIB-KU Leuven Center for Brain & Disease Research and NERF have discovered that mutations in a gene called SYNGAP1 disrupt the prolonged development of human neurons, which is thought to be essential for normal cognitive function. Their work has interesting implications for our understanding and treatment ...

LAST 30 PRESS RELEASES:

Opening borders for workers: Abe’s profound influence on Japan’s immigration regime

How skills from hospitality and tourism can propel careers beyond the industry

Research shows managers of firms handling recalls should review media scrutiny before deciding whether to lobby

New model system for the development of potential active substances used in condensate modifying drugs

How to reduce social media stress by leaning in instead of logging off

Pioneering research shows sea life will struggle to survive future global warming

In 10 seconds, an AI model detects cancerous brain tumor often missed during surgery 

Burden of RSV–associated hospitalizations in US adults, October 2016 to September 2023

Repurposing semaglutide and liraglutide for alcohol use disorder

IPK-led research team provides insights into the pangenome of barley

New route to fluorochemicals: fluorspar activated in water under mild conditions

Microbial load can influence disease associations

Three galactic “red monsters” in the early Universe

First ever study finds sexual and gender minority physicians and residents have higher levels of burnout, lower professional fulfillment

Astronomers discover mysterious ‘Red Monster’ galaxies in the early Universe

The secrets of fossil teeth revealed by the synchrotron: a long childhood is the prelude to the evolution of a large brain

Obesity-fighting drugs may reduce alcohol consumption in individuals with alcohol use disorder

Does AI improve doctors’ diagnoses? Study puts it to the test

Extreme weather accelerates nitrate pollution in groundwater

Burden of liver cancer attributable to hepatitis B and alcohol globally, in China, and for five sociodemographic index regions from 1990 to 2021

Lehigh partners with North Carolina A&T to enhance flood damage mapping with AI and advanced radar

2024 AAAS Kavli Science Journalism Award winners named

Collaborative of prominent academic institutions launches groundbreaking healthcare AI challenge

American Federation for Aging Research announces 2024 AFAR grants for junior faculty

Potential single-dose smallpox and mpox vaccine moves forward

Mass General Brigham Gene and Cell Therapy Institute names Spark Grant recipients

New discovery may lead to more effective treatment for cardiovascular disease

Developing advanced recycling technology to restore spent battery cathode materials

An advance toward inhalable mRNA medications, vaccines

A step toward safer X-rays with new detector technology

[Press-News.org] New open-source platform for high-resolution spatial transcriptomics