Srinivas and his team study how our cells package and utilize their DNA

Everyone knows what it’s like to pack your bags for an upcoming flight. To avoid paying an extra fee to check a bag, you aim to fit everything into a small carry-on size piece of luggage. We all know it’s best to properly fold your clothes so you can fit as much as possible. You can even organize your suitcase strategically, so that your favorite outfits are on top and easily accessible. If you simply throw everything in without thought though, it’s a lot harder to find what you need once you reach your destination.

Dr. Srinivas Ramachandran runs a research lab at the University of Colorado, Anschutz in Aurora. His research group is studying a similar problem: how the tremendous amount of genetic instructions for life, called DNA, are packaged into our very small cells. Every cell in our bodies, from skin cells to stomach cells to lung cells, all contain the same DNA. What makes each cell unique is which parts of the DNA is accessed and used by each cell type. Skin cells only need to interpret the DNA that codes for information needed to become and maintain skin cells. Same goes for the stomach cells and lung cells. This means that a large amount of DNA will go unused or never be accessed within each cell. This is where Srinivas and his team come in. They are interested in learning more about how the DNA is accessed before it’s used by the cell and if tiny marks or ‘snapshots’ are left behind that would flag which sections of the DNA have been used. 

The ultimate storage problem! How do our cells package and utilize their DNA?

Each cell in our body individually contains nearly 7 feet of DNA, yet it must fit inside a nucleus that measures only a few micrometers across. In order for DNA to fit into the nucleus in an organized fashion, it must be very tightly and methodically packaged. To do this, DNA is wrapped around proteins called histones. Histones can be thought of as “beads on a string” because scientists have shown they really do look like individual beads on a long string. The string (DNA) is wrapped around the beads (the histones) as a way to package and organize the DNA.

Alt text: This diagram shows how DNA is packaged inside the nucleus through multiple levels of organization. DNA wraps around histone proteins to form nucleosomes, which fold into chromatin fibers and higher-order looped structures. These structures become increasingly condensed to form a tightly packed chromosome while allowing the genome to fit inside the cell nucleus.

visual credit: GeeksforGeeks

In order for DNA to be utilized and turned into RNA, the ‘recipe card’ for protein, a process called transcription must occur. The transcription of DNA into RNA is a key step in all biological processes that require proteins. The first step is that DNA needs to be open and accessible to the cellular machinery that perform transcription. If the DNA is tightly packaged though, the cellular machinery has a hard time reading the DNA to make RNA. It would be like if you had stored all your winter sweaters at the bottom of your drawer during the summertime under piles of warm weather clothes but then have a hard time getting to them when winter comes back around.

After it was discovered that cells package and organize their DNA in a distinct way, scientists then wanted to know how cells identify which DNA needs to be accessible to create the desired protein. Many scientists, including Srinivas and members of his lab, approached this question in organisms and cells that were easy to work with, like brewer’s yeast and cells taken from fruit flies. To ask how DNA is packaged, they would cut the DNA isolated from the yeast and fly cells with an enzyme that chewed up unpackaged DNA, but left behind DNA wrapped around proteins. Using the DNA left behind, they could make maps of which parts of the genome were open and which were closed.

One of the insights from Srinivas’ work in fly cells was that instead of completely unwrapping itself from its organized state, DNA can partially unwrap itself to become accessible to the transcription machinery. This partial unwrapping leaves behind a sort of “snapshot” that can be captured and used to further understand the cell and its potential disease state. For example, if you had to quickly rummage through your summer clothes at the top of your drawer to reach your winter clothes underneath at the bottom, you may leave behind a few ‘holes’ where the winter clothes had been pulled out. Someone might walk in later and see you had a rushed morning trying to dig quickly through the summer clothes at the top to get to the winter clothes below. This gives that person a “snapshot” of what happened earlier that day.

Srinivas and his team use “snapshots” in DNA to understand disease states

What Srinivas and his lab didn't know at the time was whether this same kind of snapshot, first seen in yeast and fly cells, would also show up in humans. It turned out it does. When a cell dies, its DNA doesn’t just disappear. When these dead cells break down, their genomes are chewed up by enzymes, in a manner similar to how scientists were cutting genomes to study their packaging for decades! The result of this cutting is that the DNA that is still wrapped around the histones can be found floating in the blood. These floating pieces of DNA are called cell-free DNA.

Srinivas and his team use cell-free DNA as a snapshot of what the cell was doing right before it died, and to analyze this cell-free DNA in the blood they use a technique called cell-free DNA sequencing. This technique allows them to identify which cell type, and therefore which tissue, the DNA came from and gives them clues about the disease state of the tissue. This approach allows scientists to study the potential disease state of tissues that lie deep within the body, without requiring invasive surgery to obtain a biopsy. This method can be thought of as a “liquid biopsy” because it uses blood samples instead of tissue samples.  

How can the findings of this research be used in a real-world example? 

Imagine someone sitting in an oncologist’s office, waiting to learn not just whether they have cancer, but which kind, because that answer determines which treatment gives them the best chance to overcome it. What the oncologists need is a molecular snapshot of the cancer, so they can choose the right treatment to attack it. One such molecular marker in breast cancer is estrogen receptor alpha, or ER. By knowing which form of breast cancer the individual has - ER+ or ER- breast cancer - it allows their healthcare team to better tailor their treatment.

Work done by Srinivas and his lab has shown how a “liquid biopsy” could potentially be used to understand the class and severity of ER+ breast cancer. By analyzing the cell-free DNA found in the blood of individuals with breast cancer, more information can be gathered about their ER status and allow scientists to understand the speed of tumor development and classify tumor subtypes. One day, this may allow for earlier cancer detection and more personalized treatment selection.

What’s next for the Ramachandran lab?

Srinivas and his lab are expanding this idea of a “liquid biopsy” into other fields of biology! They are currently working to understand how this technique could be used to understand the aging process of various tissues. For example, you may feel and appear healthy, but this technique may be able to identify early signs of an aging heart. By identifying heart problems early, you can intervene with lifestyle changes or other therapeutics to potentially slow, or even reverse, these signs of aging. Scientists are working hard to identify interventions that slow the effects of aging, but these studies take decades to tell if the interventions are beneficial. Srinivas and his team have a goal to develop blood tests that could tell in a matter of months if that lifestyle change or that new supplement is actually improving your health.

The implications of this work are very exciting! Instead of undergoing invasive surgical procedures to obtain biopsies of our tissues and organs, in the future, scientists can understand the health of our tissues simply looking at a blood sample. This technique gives us clues that help to determine how fast, or slow, a disease is progressing and understand if treatment options are working as expected. The basis of all this work started with brewer’s yeast and fruit fly cells, adding another example to the idea that the pursuit of fundamental knowledge of biology can unexpectedly help improve human health.