We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
Technopath Clinical Diagnostics

Download Mobile App




Events

ATTENTION: Due to the COVID-19 PANDEMIC, many events are being rescheduled for a later date, converted into virtual venues, or altogether cancelled. Please check with the event organizer or website prior to planning for any forthcoming event.

Spatial Tissue Profiled by Imaging-Free Molecular Tomography

By LabMedica International staff writers
Posted on 06 May 2021
Print article
Image: Schematic representation of sampling and reconstruction approach to resolve the spatial localization of genomics data (Photo courtesy of Swiss Federal Institute of Technology)
Image: Schematic representation of sampling and reconstruction approach to resolve the spatial localization of genomics data (Photo courtesy of Swiss Federal Institute of Technology)
Spatially resolved molecular atlases help scientists understand where different types of cells are located in the body and map their gene expression in specific locations in tissues and organs. However, many sequencing modalities lack spatial counterparts.

New technologies such as in situ hybridization can be used to map the expression of multiple genes on the same tissue sample and have accelerated the generation of new atlases. In situ hybridization allows for a target gene to be tagged ("hybridized") with a fluorescent marker within sections of a tissue ("in situ") and visualized under a specialized microscope. Several techniques are currently being developed for spatially resolved omics profiling, but each new method requires the setup of specific detection strategies or specialized instrumentation.

Life Scientists at the Swiss Federal Institute of Technology Lausanne (Lausanne, Switzerland) have created a computational algorithm called Tomographer that can transform gene-sequencing data into spatially resolved data such as images, without using a microscope. The framework uses a tissue sampling strategy based on multi-angle sectioning and an associated algorithm that enables the reconstruction of 2D spatial patterns.

The sampling technique involves cutting tissues into consecutive thin slices ("primary sections") that are subsequently further sliced along an orthogonal plane at predefined orientations ("secondary sections"), resulting in tissue strips spanning the entire tissue. Gene expression quantification of the sections is implemented using spatial transcriptomics by reoriented projections and sequencing (STRP-seq), a method that combines the sampling strategy presented above with a customized, low-input RNA-seq protocol based on single-cell tagged reverse transcription sequencing (STRT-seq) chemistry. The method produces parallel-slice projections for each gene by quantifying the reads that map to a transcript in each of the secondary sections.

The Tomographer framework was benchmarked for the ability to reconstruct transcriptome-wide spatial expression patterns against the Allen Adult Mouse Brain in situ hybridization atlas. First, the team measured 3,880 genes in the mouse brain. Then, they compared 923 reconstructed genes to the in situ hybridization data from the mouse brain atlas using Pearson's correlation coefficient and found that the Tomographer workflow was more than twice as accurate as iterative proportional fitting (IPF). They also compared Tomographer to the spatial reconstruction capabilities of IPF-based Tomo-seq.

The team noted that the quality of Tomographer's reconstructions depends on the balance between the number and width of the tissue strips sampled. They noted that four cutting angles provided results that are a fair compromise between the reconstruction quality and sample processing effort and cost. Also, the technique requires a distance of at least 1.15 times the secondary section width in order to discriminate between two distinct points of primary strips. The study was published on April 19, 2021 in the journal Nature Biotechnology.

Related Links:
Swiss Federal Institute of Technology

Gold Supplier
Blood Glucose Laboratory Analyzer
Nova Primary
New
Gold Supplier
SARS-CoV-2/Flu A/B & RSV Test
RespiBio Panel 3 (RBRP3)
New
Automated RNA Extraction & PCR Setup
Omnia LH 75 Pro
New
Next-Generation Sequencing Platform
Clear Dx

Print article

Channels

Pathology

view channel

Certest Offers Real-Time PCR Assays for Fast Detection of MDR Bacterial Infections

CerTest Biotec (Zaragoza, Spain) has joined the fight against multidrug resistant strains (MDR) bacterial infections by developing real-time PCR assays for the fast detection of genes or punctual mutations that confer resistance to antibiotics from both Gram-positive and Gram-negative pathogens. Resistance to antibiotics... Read more

Industry

view channel
Illustration

Thermo Fisher Launches World’s First Fully Integrated Digital PCR (dPCR) System

Thermo Fisher Scientific Inc. (Waltham, MA, USA) has launched the world’s first fully integrated digital PCR (dPCR) system designed to provide highly accurate and consistent results within 90 minutes.... Read more
Copyright © 2000-2021 Globetech Media. All rights reserved.