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How lungs develop

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  • Premature babies often have problems with lung development
  • Imaging cross-sections of mouse lungs helps researchers identify where genes are expressed
  • Mapping gene activity improves understanding and may lead to improved treatments for lung disease

Imaging cross-sections of mouse lungs about half the thickness of a human hair enabled researchers to identify precise locations where specific genes are expressed, furthering our understanding of the genetic component of healthy lung development. 

<strong>Premature children</strong> are often born with lungs that aren’t fully mature. Studying how healthy lungs develop could lead to improved treatments for lung disease in children. Courtesy US Army, Suzanne Oval.The research is part of a larger project called LungMAP, which is funded by the National Heart, Lung, and Blood Institute of the National Institutes of Health, and aims to map normal cell structure of mouse and human lungs in late gestation around the time of birth and during early postnatal development.

“This project has a basic science interest to understand biology, but we’re also interested because one of the problems for premature children is lung development—being born so early the lungs don’t have a chance to mature in utero,” said Cecilia Ljungberg, assistant professor at the Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital and Baylor College of Medicine.

She continued, “If we could understand more about how lungs develop normally, that knowledge could help to develop treatments for lung diseases of babies.” 

<strong>Making genes visible.</strong> An in situ cross section of a mouse lung – one of over 10,000 images processed for the study through the BisQue image analysis platform hosted by CyVerse. Courtesy lungmap.netLjungberg is also a specialist in the technique called RNA in situ hybridization, which combines molecular genetics and histology, the study of the microscopic structure of tissues.

“A benefit of looking at a section is that you can actually see the location where a gene is expressed,” she noted. “It could be in different cell types; it could be in blood vessels or alveoli.”

“A gene isn’t necessarily expressed everywhere, but with traditional RNA-Seq you can’t tell where it’s expressed and where it’s not.” (The traditional method involves grinding up the tissue in a test tube and sequencing the genes; this tells you what genes are present but not where they express.)

To pinpoint the genes she is looking for, Ljungberg makes fragments of messenger-RNA, or mRNA, the molecule that conveys genetic information from DNA to the cellular machinery that organizes amino acids, and labels the fragments with a little tag. She then affixes the mRNA to the lung sections that have been frozen and dried on glass slides, and looks for the tag under a microscope.

Using this process, the researchers looked at over 10,000 images of over 500 genes, which were suggested to them as genes of particular interest by experts in lung development and genetics. “For each slide we can only look at one type of mRNA, which is why we need so many slides,” Ljungberg explained.

<strong>BisQue, which stands for Bio-Image Semantic Query User Environment</strong>, allows researchers to store, visualize, organize, and analyze images in a cloud environment. BisQue is hosted through CyVerse’s computational infrastructure and integrated with CyVerse Data Store.Ljungberg uploaded the images to the BisQue image analysis platform at CyVerse, whereby several collaborators, including project Co-PI James Carson and undergraduate researcher associates at the Texas Advanced Computing Center, curated and analyzed images prior to their upload onto the LungMAP website for public access.

“Key characteristics of BisQue that made it suitable for this project include convenient methods for uploading and downloading images, easy sharing with collaborators, the ability to make images publicly accessible, and the ability to interactively view and analyze images,” said Carson.

“When we originally applied to LungMAP, we intended to ship hard drives to move the large number of gigapixel images around,” he added. “That is how terabytes of data had been moved in the past.  I joined TACC just before the start of LungMAP and became aware of CyVerse's capabilities including BisQue, and I realized that this would provide a much more elegant and convenient option for sharing and viewing large images.” 

“Sharing the images through BisQue allows us to move the images easily and keep them secure,” Ljungberg added. 

Carson and his team curated the images of tissue just 20 micrometers thick by viewing them at full resolution in BisQue. The suitable images were then sent to the LungMAP Data Coordinate Center to download from the CyVerse.

“In this paper we’re really presenting what we have finished for the LungMAP Consortium when it comes to the mouse,” Ljungberg said. “We started off looking at mice because there are things you can learn in mice that you can’t learn from humans.” 

Ongoing phases of the project will involve looking at mRNA markers in cross sections of human lung tissue from donors. The researchers anticipate compiling the results to develop a much clearer understanding of genetic and functional aspects of healthy lung development that could eventually improve treatment of lung disease in children. 

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