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Chromosome Abnormalities And Cancer Cytogenetics

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New Insights Into Common Chromosomal Abnormality Revealed

Researchers from the University of Tennessee Health Science Center have made a foundational discovery about chromosome biology through their work on the first-ever human pangenome reference.

Published recently by the Human Pangenome Reference Consortium in the journal Nature, the draft pangenome uses complete genome assemblies to provide a diverse look at the genetic makeup of humans. Researchers in the UTHSC Department of Genetics, Genomics and Informatics created the technical tools to build the pangenome, and then used the tools to understand variation in parts of the genome that could not be seen before.

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The pangenome project aims to map the entirety of human genetic variation to create a comprehensive reference for geneticists to use to compare DNA sequences, which can aid in the study of connections between genes and diseases. The draft reference includes the genome sequences of 47 people, and the consortium aims to increase the number to 350 by mid-2024. The milestone comes more than 20 years after the first landmark draft genome was released.

"The first version of the reference project aimed to make a single, complete version that is representative of a typical genome, which was used in biomedical research to an incredible effect over the past 20 years," UTHSC's Erik Garrison, PhD, said.

According to Dr. Garrison, relating a genome to the original reference could cause bias, which was understood from the beginning but could not be technically addressed. "The differences between individual genomes can be quite significant. This causes a reference bias that makes most individual genomes look more like the reference than they really are," he said. "The goal with the human pangenome project is getting past that issue by having a reference that's a collection of many genomes."

In addition to Dr. Garrison, the UTHSC team included Associate Professor Pjotr Prins, PhD; Assistant Professor Vincenza Colonna, PhD; postdoctoral scholar Andrea Guarracino, PhD; PhD student Flavia Villani; postdoctoral scholar Silvia Buonaiuto, PhD; and IT analyst Christian Fischer.

The team's biological discovery was published in a separate paper in Nature alongside the draft pangenome reference. Dr. Guarracino, Dr. Colonna, and Dr. Garrison are credited as authors.

The discovery regards the recombination of the five acrocentric chromosomes, which have centromeres closer to one end rather than in the center. Humans have two copies of most chromosomes: one inherited from the mother, and the other from the father. Recombination, the exchange of genetic material between chromosomes, is generally believed to occur between equivalent chromosome pairs, but in a significant departure from this conventional understanding, the UTHSC researchers discovered different acrocentric chromosomes can recombine with each other to exchange DNA through their shorter arms.

Furthermore, the team showed how this observation was key to solving the most common type of chromosomal abnormality in humans. A portion of the short arm of chromosome 14 is inverted relative to the other acrocentric chromosomes, and recombination with it can result in a chromosomal abnormality known as Robertsonian translocation. A Robertsonian chromosome is a fusion of two acrocentric chromosomes in a head-to-head orientation. This can cause an abnormal number of chromosome copies, which causes reproductive issues for carriers of Robertsonian translocations.

"The presence of the extra chromosome copy will cause fertility issues and is related to Down syndrome," Dr. Garrison said. "We were able to actually provide a molecular description of why this is happening, resolving a question about the cause of Robertsonian translocations that has been open for 50 years. This will have ramifications for potential treatment, and it will help carriers understand the cause of their genetic condition."

Dr. Guarracino suggests their methods will unlock a new wave of sequence-based cytogenetic research. "Our work addresses limitations of previous studies and lays a strong foundation for future genomic and cytogenetic research, moving us closer to resolving persistent mysteries of human genetic evolution," he said.

The collaboration also paves the way toward considering these regions in biomedical and evolutionary studies that have previously overlooked them. "We haven't been able to account for variation in the short arms of the acrocentrics in past studies of genome-wide association and human evolution," Dr. Colonna said. "We show that these regions behave unusually genetically, and new approaches will be needed to leverage the information they contain into biomedical studies at the population level."

According to the researchers, the pangenome project is just beginning. Dr. Prins said the reference will keep growing, adding that the more people who are added to it from different backgrounds, the more valuable it becomes. Not only will the team's work apply to the study of humans, but Dr. Prins said it could also help animal researchers create a pangenome to help study species with far more variation than humans.

"People will forever be coming to us, because we wrote the tools," Dr. Prins said. "If you build a pangenome of 100 individuals, that's already pretty daunting, but of course in a few years, we'll be adding thousands. So, we'll need to improve the software that can handle these things and we may even need new methods."

Reference: Guarracino A, Buonaiuto S, de Lima LG, et al. Recombination between heterologous human acrocentric chromosomes. Nature. 2023;617(7960):335-343. Doi: 10.1038/s41586-023-05976-y

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

Unexpected Link Between Chromosomal Instability And Epigenetic Alterations

A graduate student's curiosity has uncovered a previously unknown link between two important hallmarks of cancer: chromosomal instability and epigenetic alterations.

The resulting study, which was published June 7 inNature, not only opens a fertile new area of basic science biology research, but has implications for clinical care as well.

Chromosomal instability has to do with changes to the number of chromosomes each cancer cell carries. Epigenetic alterations change which genes get turned on or off in a cell, but without modifying the cell's DNA code.

In his first year as a doctoral student in pharmacology at Weill Cornell Medicine, Albert Agustinus did a rotation in the lab of Samuel Bakhoum, MD, PhD, whose research group at Memorial Sloan Kettering Cancer Center (MSK) studies how alterations in the number and structure of chromosomes drive cancer. Albert is also co-mentored by epigenetics expert Yael David, PhD, whose lab at MSK's Sloan Kettering Institute takes a chemical-biology approach to studying the epigenetic regulation of transcription.

"He came to me and said, 'I'm interested in understanding the link between chromosomal instability and epigenetic modifications,'" Dr. Bakhoum recalls. "And my response to him was, 'Well, there isn't a known link, but you're welcome to find it!'"

And find one he did, expanding that initial inquiry into a 32-author, multi-institution collaboration published in one of science's top journals. The study was jointly overseen by Bakhoum and David.

Recently, Agustinus recounted his first big "aha" moment in the project, for which he also received a   drug discovery fellowship from the PhRMA Foundation.

He was sitting next to a lab mate and peering through the microscope. The cells he was looking at had abnormal little mini-nuclei scattered throughout the cell -- a common consequence of chromosomal instability. And they had been set up with fluorescent markers that would show the presence of epigenetic modifications.

"The micronuclei were glowing much brighter than the primary nucleus," Agustinus says. "My lab mate said to me, 'I've never seen you smile that wide before.'"

Chromosomes Gone Wild

Chromosomes are tightly packaged strands of DNA that carry our genetic information. Normally, each of our cells has 46 chromosomes -- half from one parent and half from the other. When a cell divides to make a new copy of itself, all those chromosomes are supposed to end up in the new cell, but in cancer the process can go dreadfully awry.

"The big question that my lab is trying to answer is how chromosomal instability drives cancer evolution, progression, metastasis, and drug resistance," Dr. Bakhoum says. "It's a feature of cancer, especially advanced cancers, where the normal process of cell division goes haywire. Instead of 46 chromosomes, you can have a cell with 69 chromosomes right next to a cell with 80 chromosomes."

The prevailing wisdom in the field has been that cancer cells increase their chance of survival by shuffling up their genetic material when they divide. This process increases the odds that some of the random changes will allow a cancer daughter cell to withstand the assaults of the immune system and medical interventions.

"This new research, however, suggests that's only part of the story," Bakhoum says.

That's because you can have two cancer cells, each with the same number of extra copies of a given chromosome, but each have different genes that are turned off or on. This is due to additional epigenetic changes.

"Our work further suggests that you don't actually need mutations in the genes that encode epigenetic-modifying enzymes for epigenetic abnormalities to happen. All you need is to have the ongoing chromosomal instability," Dr. Bakhoum says. "It's an unexpected finding, but really important. And it also explains why we often find chromosomal instability and epigenetic abnormalities in advanced, drug-resistant cancers, even when there is no evidence of the types of mutations that we would expect to create epigenetic havoc."

There and Back Again -- Or, What Micronuclei Have to Do With Cancer

Small, extra nuclei in cells -- known as micronuclei -- like the ones Agustinus saw through the microscope are usually rare and quickly get eliminated by the cell's natural repair mechanisms. When you get a bunch of them, it's a signal that something has gone horribly wrong, as happens in cancer.

Like a cell's primary nucleus, these micronuclei contain packages of genetic material. And when these micronuclei burst -- which they frequently do -- it causes even more problems, the research team found.

Dr. Bakhoum uses the metaphor of a traveler who picks up a foreign accent and brings it back home. The research demonstrated that the sequestration of chromosomes into micronuclei disrupts the organization of chromatin -- a complex of genetic components that get packaged into chromosomes during cell division.

This leads to ongoing epigenetic dysregulation, which continues long after a micronucleus is reintegrated into a cell's primary nucleus.

And the repeated formation and reincorporation of micronuclei over many cycles of cell division leads to the buildup of epigenetic changes. These, in turn, lead to greater and greater differences between individual cancer cells.

The more variation between individual cancer cells within the same tumor, the more likely it is that some of the cells will be resistant to whatever treatment is being thrown at them -- allowing them to survive and continue their runaway growth.

Analyzing Epigenetic Changes

To understand and quantify the epigenetic changes happening inside the cells, the researchers use a series of sophisticated experiments to isolate the micronuclei and examine changes occurring in them compared to the cells' primary nuclei. This allowed them to see patterns of histone modification -- changes to the spools around which DNA winds, which, in turn, change access to the underlying genes.

"This allowed us to ask some important questions, like do we actually get transcription of genes that are important in specific pathways?" Dr. David says. "And the answer is 'yes.'"

They also compared intact versus ruptured micronuclei -- revealing an even greater level of changes in the ones that had burst open.

"We also found there were a lot more accessible promoter regions in the micronuclei than in the primary nuclei," she adds -- promoter regions being DNA sequences near the beginning of a gene that help to initiate transcription, a critical step in gene expression.

In one key experiment, the researchers forced a chromosome to go out into a micronucleus and then allowed it to get reintegrated into the primary nucleus. They compared this adventuresome chromosome to one that stayed put.

"Our model chromosome, which happened to be chromosome Y, showed substantial changes in its epigenetic landscape and accessibility of its DNA," Dr. David says. "This has major implications because of the significant impact the journey of a chromosome into a micronucleus have on the epigenetic changes of the primary nucleus, which we know play a role in tumor progression and evolution."

The work, she adds, opens whole new avenues of study.

"Now that we've demonstrated that chromosomal instability and epigenetic changes are closely linked, we can go deeper and ask questions about precisely how and why," Dr. David says.

Findings by another research team from Harvard University and the Dana-Farber Cancer Institute, and published in Nature at the same time found additional evidence that supports the MSK team's discoveries.

Clinical Implications

More than just shedding light on the changes happening inside cancer cells, the research holds promise for treating patients, as well, the researchers note.

Epigenetic changes are a reversible form of gene regulation -- and several classes of drugs have already been developed to work on them.

So, to begin with, chromosomal instability and the presence of micronuclei might be used as a biomarkers to help identify which patients might be more likely to be helped by epigenetic modifying drugs, Dr. Bakhoum says.

Additionally, the findings may pave the way for new therapeutic approaches.

"There's a question of whether we should be treating chromosomally unstable cells with these epigenetic modifying therapies," he says. "This research demonstrates epigenetic changes can occur without those mutations being present."

Moreover, the study also suggests that ongoing research into drugs to target chromosomal instability directly might benefit from being combined with efforts to suppress epigenetic alternations, Dr. Bakhoum adds.

Longer term, another potential avenue would be to explore ways of targeting the micronuclei to preventing them from rupturing, which the research showed was a big driver of epigenetic changes, Dr. David notes.

"I think this is a great example of a fundamental, basic science research discovery that, over the next five years, will open multiple interesting avenues for exploration and potential translation to the clinical setting," she says.

Agustinus, whose curiosity kicked off the entire project and who led the research effort, sums it up this way, "Chromosomal instability and epigenetic alterations help cancer achieve a population diversity that gives them a better chance to survive and develop. But armed with a new understanding of the relationship between these two phenomena, we should be better able to target them therapeutically."

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