Researchers are using RNA-Seq to study fetal development

from Scientific American by Claire Ainsworth –

Probing fetal development starts, naturally enough, with DNA, the recipe for life. Developmental biologists have already gathered a trove of information here, through studies of laboratory animals from worms to mice, identifying many genes and processes that have human equivalents. Painstaking detective work on families with inherited genetic diseases has yielded even more insight.

DNA is but the start of the story of human development. Researchers are keen to understand how instructions in the genome are deployed in time and space as a fetus grows, and how this goes wrong during disease. Many are therefore focusing on the molecule RNA, which the cell uses to copy—and then act on—a given set of DNA instructions. And that presents fresh challenges. RNA breaks down very quickly, so it is harder to work with than DNA, especially when trying to untangle a fetus’s output of RNA—its transcriptome—from the mother’s.

To simplify things, clinician and geneticist Diana Bianchi, now director of the National Institute of Child Health and Human Development in Bethesda, Maryland, began by studying the transcriptome of amniotic fluid, which contains freely floating RNA from fetus and placenta. Over the past decade, her team has built up intriguing snapshots of gene activity through the second and third trimesters (from discarded samples taken during amniocentesis tests), and at term (from samples gleaned during Caesarean sections), as well as some work with maternal blood, which bears free-floating RNA fragments from fetus, mother and placenta.

She has shown how a full-term fetus switches on just the sorts of genes that might be expected for a baby gearing up to be born—including ones involved in lung and gut physiology, energy metabolism, the immune system and the eye. Genes involved in smell ramp up, too, “which we think has some evolutionary advantage”, says Bianchi, “because the baby needs to know the smell of its own mother, for survival reasons”.

Much of Bianchi’s work has focused on amniotic-fluid samples from fetuses affected by chromosomal abnormalities, such as Down’s syndrome (an extra chromosome 21) and Edward’s syndrome (an extra chromosome 18). She finds that gene activity is abnormal across the whole genome, not just on the extra chromosome, and even in genes needed for brain development. She’s also found that cells of fetuses with Down’s incur damage from the by-products of metabolism, a condition known as oxidative stress.

This raises the provocative possibility of treating fetuses in the womb to ameliorate the cognitive impairment associated with Down’s. To explore this, Bianchi’s team compared transcriptome data from fetuses with and without Down’s, and mouse models of the syndrome, to pinpoint patterns associated with the condition. Then they scoured a database for molecules that might reverse some of the abnormal patterns, including some drugs that are already approved for human use.

They fed one of these molecules, called apigenin, to pregnant ‘Down’s syndrome’ mice and in unpublished data found that the offspring had improved memory and met developmental milestones sooner than those whose mothers did not get the compound. “It’s not that everything gets better, but certain areas do improve,” says Bianchi. “We are very encouraged.”

Bianchi and others in the field are now seeking ways to get more detailed information, non-invasively, about fetal RNA. Until recently, the work has been done using devices called microarrays, which allow scientists to detect known RNA sequences. Although valuable, they offer limited insight because much about the transcriptome remains mysterious. A version of next-generation DNA sequencing called RNA-seq reveals the transcriptome in all its complex glory, and quantifies each RNA type much more accurately.

Researchers have shown that such an approach is possible. In 2014, for example, Quake’s team examined blood samples from pregnant women using RNA-seq, in combination with other methods, to detect RNAs that probably originated in the fetus and placenta. They could track the ebbs and flows of transcripts through all three trimesters, including the activity of genes that are crucial for normal brain development. Now they are hunting for transcripts that could yield insight into conditions associated with pregnancy such as pre-eclampsia, in which problems with the placenta cause dangerously high blood pressure in the mother.

The placenta is also the focus of an RNA-seq project led by Williams and RNA biologist Thomas Tuschl at the Rockefeller University in New York City. They are focusing on microRNA (miRNA), a kind of RNA that’s known to control the activity of genes, in the hope of uncovering insight into placental biology and devising early-warning tests for pre-eclampsia and other pregnancy conditions. Existing tests, such as looking for protein in the mother’s urine, don’t reveal the disease until the mother has already started to develop organ damage, says Williams. His team hopes to use miRNA to monitor the placenta non-invasively, and detect pre-eclampsia before damage takes hold.

But such methods still need more work to ensure accuracy and reproducibility before their full potential can be realized, he says.

(read more at Scientific American…)

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