Tag Archives: #chromosomes

Mass of Human Chromosomes Measured For The First Time (Biology)

The mass of human chromosomes, which contain the instructions for life in nearly every cell of our bodies, has been measured with X-rays for the first time in a new study led by UCL researchers.

For the study, published in Chromosome Research, researchers used a powerful X-ray beam at the UK’s national synchrotron facility, Diamond Light Source, to determine the number of electrons in a spread of 46 chromosomes which they used to calculate mass.

They found that the chromosomes were about 20 times heavier than the DNA they contained – a much larger mass than previously expected, suggesting there might be missing components yet to be discovered.

As well as DNA, chromosomes consist of proteins that serve a variety of functions, from reading the DNA to regulating processes of cell division to tightly packaging two-metre strands of DNA into our cells.

Senior author Professor Ian Robinson (London Centre for Nanotechnology at UCL) said: “Chromosomes have been investigated by scientists for 130 years but there are still parts of these complex structures that are poorly understood.

“The mass of DNA we know from the Human Genome Project, but this is the first time we have been able to precisely measure the masses of chromosomes that include this DNA.

“Our measurement suggests the 46 chromosomes in each of our cells weigh 242 picograms (trillionths of a gram). This is heavier than we would expect, and, if replicated, points to unexplained excess mass in chromosomes.”

In the study, researchers used a method called X-ray ptychography, which involves stitching together the diffraction patterns that occur as the X-ray beam passes through the chromosomes, to create a highly sensitive 3D reconstruction. The fine resolution was possible as the beam deployed at Diamond Light Source was billions of times brighter than the Sun (ie, there was a very large number of photons passing through at a given time). 

The chromosomes were imaged in metaphase, just before they were about to divide into two daughter cells. This is when packaging proteins wind up the DNA into very compact, precise structures.

Archana Bhartiya, a PhD student at the London Centre for Nanotechnology at UCL and lead author of the paper, said: “A better understanding of chromosomes may have important implications for human health.

“A vast amount of study of chromosomes is undertaken in medical labs to diagnose cancer from patient samples. Any improvements in our abilities to image chromosomes would therefore be highly valuable.”

Each human cell, at metaphase, normally contains 23 pairs of chromosomes, or 46 in total. Within these are four copies of 3.5 billion base pairs of DNA.

The research was supported by Diamond Light Source, UKRI, the Biotechnology and Biological Sciences Research Council (BBSRC), the Engineering and Physical Sciences Research Council (EPSRC), the European Research Council, and the US Department of Energy.

Image

  • The spread of 46 chromosomes, with artificial colour added. Credit: Archana Bhatiya et al

Reference: Bhartiya, A., Batey, D., Cipiccia, S. et al. X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation. Chromosome Res 29, 107–126 (2021). https://doi.org/10.1007/s10577-021-09660-7


Provided by UCL

Discovery of 6 Sex Chromosomes in a Frog Species Offer Clues On Evolution of Complex XY Systems (Biology)

The O. swinhoana frog species is the first vertebrate known to retain descendant genes that now determine sex in mammals, birds, and fishes inherited from a common ancestor.

Scientists found six sex chromosomes in the Odorrana swinhoana frog species endemic in Taiwan, giving new insights into how complex XY systems evolve.

The discovery was a surprise to the international research team led by Associate Professor Ikuo Miura of Hiroshima University’s Amphibian Research Center. In 1980, the first reported instance of multiple sex chromosome systems in amphibians was found in the Taiwanese brown frog Raina narina — a synonym for O. swinhoana — which had a male-specific translocation between two chromosomes. Its sex chromosomes could be described as ♂X1Y1X2Y2-♀X1X1X2X2.

The finding suggested that translocation — a chromosomal abnormality that happens when a chromosome breaks and its fragment fuses to another — occurred between two potential sex-determining chromosomes. At that time, however, the identification of the chromosomes involved in the translocation was uncertain.

So when the researchers set out to precisely identify the chromosomes involved, they were expecting only one translocation and not three. The three male-specific translocations created a system of six sex chromosomes, ♂X1Y1X2Y2X3Y3-♀X1X1X2X2X3X3. Their findings were published in the journal Cells last March 16, 2021.

A first among vertebrates

Cases of multiple chromosomes in amphibians are rare and their karyotypes, or collection of chromosomes, are generally highly conserved with little rearrangement among species. A majority are also homomorphic with undifferentiated sex chromosomes, unlike mammals and birds which have heteromorphic XY and ZW sex-determination systems. So far, there are only 10 known cases of multiple sex chromosome systems in amphibians.

What’s more, the research team uncovered that the potential sex-chromosomes involved in the translocations contained orthologs of the sex-determining genes in mammals, birds, and fishes. Orthologs are genes that evolved from an ancestral gene found in the shared ancestor of those species.

The researchers found the Dmrt1, the male determining gene in birds, and Amh, the male determining gene in fish and platypus, on the Y1 chromosome; the Sox3, the ancestral gene of SRY in therian mammals and the male determining gene in medaka fish, on the Y3 chromosome; and an unidentified sex-determining gene on the Y2 chromosome.

This is the first time that sex chromosomes containing orthologs of the sex-determining genes in mammals, birds, and fishes are found together in a vertebrate species.

Chance vs choice

Sex chromosomes evolve from an ordinary autosomal pair after acquiring a sex-determining gene. But the team has yet to figure out which of the three pairs is the original sex chromosome and which is the major sex-determining gene of the three candidates: Dmrt1Amh, and Sox3.

Miura explained that up to now, sex chromosome-autosome fusion has been documented as a chance occurrence. 

“In fact, it was like that in this frog, too. The break and fusion of the chromosomes may have occurred by chance,” he said. 

But the researchers believe that the chromosome members involved in the fusions were selected non-randomly or inevitably chosen as they probably share a common genomic region.

“To be so, the three may share a common DNA sequence on each of them, which makes them closely localized to each other, and this makes it possible to join the simultaneously occurring breakages and translocations.”

“This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system.”

Miura said identifying the genomic sequence common to the potential sex chromosomes would improve understanding of its evolution and turnover mechanisms.

Featured image: A graphical abstract showing the six sex chromosomes found in the Taiwanese frog species O. swinhoana. Mammal, bird, and fish sex-determining gene orthologs and another unidentified sex-determining gene were found in the frog’s three Y chromosomes. © Hiroshima University


Reference: Miura I, Shams F, Lin S-M, de Bello Cioffi M, Liehr T, Al-Rikabi A, Kuwana C, Srikulnath K, Higaki Y, Ezaz T. Evolution of a Multiple Sex-Chromosome System by Three-Sequential Translocations among Potential Sex-Chromosomes in the Taiwanese Frog Odorrana swinhoana. Cells. 2021; 10(3):661. https://www.mdpi.com/2073-4409/10/3/661 https://doi.org/10.3390/cells10030661


Provided by Hiroshima University

New Study Sheds Light on How X and Y Chromosomes Interact (Biology)

Researchers at Lund University in Sweden have investigated how the X and Y chromosomes evolve and adapt to each other within a population. The results show that breaking up coevolved sets of sex chromosomes could lead to lower survival rates among the offspring – something that could be of importance in species conservation, for example. The study is published in the journal PNAS.

The results provide new clues on how species are formed, and suggest it could be harmful to bring together individuals from different populations that have been separated for a long time. The reason is that the offspring have lower survival rates.

“This is something worth keeping in mind in conservation biology, where you want to see a population grow”, says Jessica Abbott, researcher in evolutionary ecology at Lund University.

It is previously known that hybrids between different species often do better if they are female (two X chromosomes) rather than male (X and Y chromosome).

In the study, the researchers crossed fruit flies from five different populations from different continents in order to combine X and Y chromosomes with different origins. They then followed and studied the subsequent generations.

The results show that males with X and Y chromosomes that don’t match had higher reproductive success than males with matching X and Y chromosomes. However, the higher male fertility was paired with lower survival rates among their offspring.

“We were expecting the opposite, that males with different origin X and Y chromosomes would have lower reproductive success, so that was surprising”, says Jessica Abbott.


Reference: Katrine K. Lund-Hansen et al., “Sexually antagonistic coevolution between the sex chromosomes of Drosophila melanogaster”, PNAS February 23, 2021 118 (8) e2003359118; https://doi.org/10.1073/pnas.2003359118


Provided by Lund University

X Marks The Spot: How Genes On The Sex Chromosomes Are Controlled (Biology)

Researchers from the University of Tsukuba find that genes on the X chromosome in male fruit fly germ cells are regulated differently from other cells

Because human females have two X chromosomes and males have one X and one Y, somatic cells have special mechanisms that keep expression levels of genes on the X chromosome the same between both sexes. This process is called dosage compensation and has been extensively studied in the fruit fly Drosophila. Now, researchers at the University of Tsukuba (UT) continued work with Drosophila to show that dosage compensation does not occur in the germ cells of male flies.

In an article published in Scientific Reports, the UT researchers investigated this phenomenon in fly primordial germ cells (PGCs), which are present in embryos and are the precursor cells to what ultimately become sperm and eggs in adults. Previous reports on dosage compensation in this cell type were controversial.

Genetic research in somatic cells has shown that expression of X-linked genes in male fruit flies is upregulated to reach equivalent levels to that of their female counterparts. A group of proteins, called the male-specific lethal (MSL) complex, is responsible for carrying out this role. These findings made the UT group interested in if this mechanism also occurs in the male germ cells. Distinct molecular events occur in the PGCs during embryonic development between male and female fruit flies. Because results shown in earlier publications did not align, the researchers chose to address their main question differently.

“The MSL complex leaves a signature mark, called acetylation, on a specific amino acid of the histone H4 protein of the X chromosome,” says Professor Satoru Kobayashi, senior author of the study. “The acetyl group being added tells the cell to express the X-linked genes at a higher level, which results in dosage compensation.”

To address their questions, the researchers used a process called transcriptome analysis to compare gene expression levels between male and female fruit fly PGCs. They also examined the histone H4 protein to determine if acetylation had occurred.

“We found that X-linked gene expression in male PGCs was about half that of female PGCs,” describes Professor Kobayashi. “We also could not detect the acetylation signature of the MSL complex.”

The authors also determined that the main components of the MSL complex are only present in very low amounts in the fly PGCs. Interestingly, they then created transgenic flies that were engineered to express higher levels of the MSL complex proteins. Male PGCs in these flies showed greater activation of X-linked genes, as well as the acetylation signature.

The researchers believe that the findings of this study have high biological significance, possibly suggesting that the absence of dosage compensation affects sex determination in Drosophila PGCs. This work provides novel insight that will be crucial for further investigation of embryo development and germ cell maturation.


Reference: Ota, R., Hayashi, M., Morita, S. et al. Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos. Sci Rep 11, 4890 (2021). https://www.nature.com/articles/s41598-021-84402-7 https://doi.org/10.1038/s41598-021-84402-7


Provided by University of Tsukuba

Carp Genomes Uncover Speciation and Chromosome Evolution of Fish (Biology)

In a study published online in Molecular Ecology Resources, a research team led by Prof. HE Shunping from Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences, and the collaborators, revealed the evolutionary history of the East Asian cyprinids, and further explored the evolution and speciation of the silver carp and bighead carp, as well as genomic differentiation between the populations. 

By integrating short-read sequencing and genetic maps, Prof HE’s team presented chromosomal-level genome assemblies with high quality and contiguity for the silver carp and the bighead carp. 

They sampled 20 silver carp (seven from the Pearl River, four from the Amur River and nine from Yangtze River) and 22 bighead carp (eight from the Pearl River, four from the Amur River and 10 from Yangtze River) for re-sequencing, and found that an East Asian cyprinid genome-specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. The result suggested that the East Asian cyprinids may possess only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. 

Besides, through phylogenetic analysis, the researchers found that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago. Population genetics and introgression indicated that silver carp and bighead carp were highly divergent, yet introgression between these species was detected in population analysis. They then identified the regions which might be associated with divergence or speciation.  

The result showed that genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics, and the divergent regions might have influence on early speciation, reproductive isolation and environmental adaptations between the two species. 

“These genomic data are important resource for further study of these East Asian cyprinids on their evolution, conservation and commercial breeding,” said YANG Liandong from Prof. HE’s team. 

Featured image: Carps jumping out of water (Image by IHB)


Reference: Jian, J, Yang, L, Gan, X, et al. Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation. Mol Ecol Resour. 2020; 00: 1– 12. https://doi.org/10.1111/1755-0998.13297


Provided by Chinese Academy of Sciences

Researchers Develop New Method to Revamp and Minimize Yeast Genome (Biology)

Researchers from the Shenzhen Institutes of Advanced Technology (SIAT) of the Chinese Academy of Sciences developed a method termed SCRaMbLE-based genome compaction (SGC) to revamp and minimize the yeast genome.

Schematic illustration of the SCRaMbLE-based genome compaction (SGC) method. (Image by SIAT)  

They showed that a synthetic chromosome arm (synXIIL) could be efficiently reduced by this method. Their study was published in Genome Biology on Jan 4. 

Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction removes sequences nonessential for given conditions. 

The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which has been proposed as an effective tool for genome minimization. 

As the Sc2.0 project is about to be completed, the researchers have begun to explore the application of the SCRaMbLE system in genome compaction. 

“With SGC, all the strains we identified harbor a reduced synthetic chromosome,” said Associate Professor LUO Zhouqing from SIAT, first author of the study. “The nonessential genes located approximate to the essential one could not be removed by SGC directly, if there is no loxP site in between.”

The researchers constructed an episomal essential gene array and introduced it prior to activate SCRaMbLE, which enhanced the deletion ability of SGC, not only by removing nonessential genes located close to the essential ones, but also by deleting more chromosomal sequences in a single SGC process. 

Further compaction was achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30°C in rich medium. 

“We developed iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome,” said Dr. DAI Junbiao from SIAT, the co-corresponding author of the study. 

Reference: Luo, Z., Yu, K., Xie, S. et al. Compacting a synthetic yeast chromosome arm. Genome Biol 22, 5 (2021). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02232-8 https://doi.org/10.1186/s13059-020-02232-8

Provided by Chinese Academy of Sciences

How Earth’s Oddest Mammal Got to be so Bizarre? (Biology)

Often considered the world’s oddest mammal, Australia’s beaver-like, duck-billed platypus exhibits an array of bizarre characteristics: it lays eggs instead of giving birth to live babies, sweats milk, has venomous spurs and is even equipped with 10 sex chromosomes. Now, an international team of researchers led by University of Copenhagen has conducted a unique mapping of the platypus genome and found answers regarding the origins of a few of its stranger features.

It lays eggs, but nurses, it is toothless, has a venomous spur, has webbed feet, fur that glows and has 10 sex chromosomes. Ever since Europeans discovered the platypus in Australia during the late 1700’s, the quirky, duck-billed, semiaquatic creature has baffled scientific researchers.

Modern day researchers are still trying to understand how the platypus — often considered to be the world’s oddest mammal — got to be so unique. Their understandings have now advanced, to a great degree. For the first time, an international team of researchers, led by University of Copenhagen biologists, has mapped a complete platypus genome. The study is published in the scientific journal, Nature.

“The complete genome has provided us with the answers to how a few of the platypus’ bizarre features emerged. At the same time, decoding the genome for platypus is important for improving our understanding of how other mammals evolved — including us humans. It holds the key as to why we and other eutheria mammals evolved to become animals that give birth to live young instead of egg-laying animals,” explains Professor Guojie Zhang of the Department of Biology.

The platypus belongs to an ancient group of mammals — monotremes — which existed millions of years prior to the emergence of any modern-day mammal.

“Indeed, the platypus belongs to the Mammalia class. But genetically, it is a mixture of mammals, birds and reptiles. It has preserved many of its ancestors’ original features — which probably contribute to its success in adapting to the environment they live in,” says Professor Zhang.

Lays eggs, sweats milk and has no teeth

One of the platypus’ most unusual characteristics is that, while it lays eggs, it also has mammary glands used to feed its babies, not through nipples, but by milk — which is sweat from its body.

During our own evolution, we humans lost all three so-called vitellogenin genes, each of which is important for the production of egg yolks. Chickens on the other hand, continue to have all three. The study demonstrates that platypuses still carry one of these three vitellogenin genes, despite having lost the other two roughly 130 million years ago. The platypus continues to lay eggs by virtue of this one remaining gene. This is probably because it is not as dependent on creating yolk proteins as birds and reptiles are, as platypuses produce milk for their young.

In all other mammals, vitellogenin genes have been replaced with casein genes, which are responsible for our ability to produce casein protein, a major component in mammalian milk. The new research demonstrates that the platypus carries casein genes as well, and that the composition of their milk is thereby quite similar to that of cows, humans and other mammals.

“It informs us that milk production in all extant mammal species has been developed through the same set of genes derived from a common ancestor which lived more than 170 million years ago — alongside the early dinosaurs in the Jurassic period,” says Guojie Zhang.

Another trait that makes the platypus so unique is that, unlike the vast majority of mammals, it is toothless. Although this monotremes’ nearest ancestors were toothed, the modern platypus is equipped with two horn plates that are used to mash food. The study reveals that the platypus lost its teeth roughly 120 million years ago, when four of the eight genes responsible for tooth development disappeared.

Only animal with 10 sex chromosomes

Yet another platypus oddity investigated by the researchers was how their sex is determined. Both humans and every other mammal on Earth have two sex chromosomes that determine sex – the X and Y chromosome system in which XX is female and XY is male. The monotremes, however, including our duck-billed friends from Down Under, have 10 sex chromosomes, with five Y and five X chromosomes.

Thanks to the near-complete chromosomal level genomes, researchers can now suggest that these 10 sex chromosomes in the ancestors of the monotremes were organized in a ring form which was later broken away into many small pieces of X and Y chromosomes. At the same time, the genome mapping reveals that the majority of monotreme sex chromosomes have more in common with chickens than with humans. But what it shows, is an evolutionary link between mammals and birds.

PLATYPUS FACTS

  • The platypus is endemic to eastern Australia and Tasmania. It is a protected species and classified by the IUCN as near-threatened.
  • Among the reasons why platypuses are considered mammals: they have mammary glands, grow hair and have three bones in their middle ears. Each trait helps to define a mammal.
  • The platypus belongs to the mammalian order monotreme, so named because monotremes use a singular opening for urination, defecation and sexual reproduction.
  • The animal is an excellent swimmer and spends much of its time hunting for insects and shellfish in rivers.
  • Its distinctive beak is filled with electrical sensors which are used to locate prey in muddy river beds.
  • The male platypus has a venomous spur behind each of its hind legs. The venom is poisonous enough to kill a dog and is deployed when males fight for territory.
  • Another 2020 study demonstrated that platypus fur is fluorescent. The animal’s brown fur reflects a blue-green color when placed under UV light. (source: https://doi.org/10.1515/mammalia-2020-0027)

ABOUT THE STUDY

  • Advanced gene sequencing technology that combines numerous cutting-edge methods has allowed the research team to map a near-complete genome at the chromosomal level from both the platypus and its cousin, the echidna– the only two currently living types of monotreme animals. The gene data fills in 90 percent of the gaps in previous genetic mappings. Over 96% of the genome sequences are placed in the chromosomes now.
  • The researchers have compared the monotreme genes and genomes from chickens, humans, rats, Tasmanian devils and lizards.
  • In addition to Yang Zhou (lead author) and Guojie Zhang of the University of Copenhagen, the research was carried out by, among others: Linda Shearwin-Whyatt of The University of Adelaide (Australia) and Jing Li of Zhejiang University (China). A complete list of the authors can be found in the research article.
  • The study has just been published in the prestigious scientific journal, Nature.

Reference: Zhou, Y., Shearwin-Whyatt, L., Li, J. et al. Platypus and echidna genomes reveal mammalian biology and evolution. Nature (2021). https://doi.org/10.1038/s41586-020-03039-0

Provided by Faculty of Science – University of Copenhagen

Discovery about How Cancer Cells Evade Immune Defenses Inspires New Treatment Approach (Medicine / Oncology)

Researchers at Memorial Sloan Kettering have learned how chromosomal instability allows cancer cells to avoid immune defenses and metastasize (spread). The discovery opens up potential new avenues for treatment.

Cancer cells are known for spreading genetic chaos. As cancer cells divide, DNA segments and even whole chromosomes can be duplicated, mutated, or lost altogether. This is called chromosomal instability, and scientists at Memorial Sloan Kettering have learned that it is associated with cancer’s aggressiveness. The more unstable chromosomes are, the more likely that bits of DNA from these chromosomes will end up where they don’t belong: outside of a cell’s central nucleus and floating in the cytoplasm.

Human metastatic melanoma cells in a lymph node. ENPP1, a protein involved in immune evasion, is shown in green. © MSKCC

Cells interpret these rogue bits of DNA as evidence of viral invaders, which sets off their internal alarm bells and leads to inflammation. Immune cells travel to the site of the tumor and churn out defensive chemicals. A mystery has been why this immune reaction, triggered by the cancer cells, does not spell their downfall.

“The elephant in the room is that we didn’t really understand how cancer cells were able to survive and thrive in this inflammatory environment,” says Samuel Bakhoum, a physician-scientist at MSK and a member of the Human Oncology and Pathogenesis Program.

“The elephant in the room is that we didn’t really understand how cancer cells were able to survive and thrive in this inflammatory environment.”, Samuel Bakhoum, physician-scientist.

According to a new study from Dr. Bakhoum’s lab published December 28 in the journal Cancer Discovery, the reason has to do, in part, with a molecule sitting on the outside of the cancer cells that destroys the warning signals before they ever reach neighboring immune cells.

The findings help to explain why some tumors do not respond to immunotherapy, and — equally important — suggest ways to sensitize them to immunotherapy.

Detecting Dangerous DNA

The warning system Dr. Bakhoum studies is called cGAS-STING. When DNA from a virus (or an unstable cancer chromosome) lands in a cell’s cytoplasm, cGAS binds to it, forming a compound molecule called cGAMP, which serves as a warning signal. Inside the cell, this warning signal activates an immune response called STING, which addresses the immediate problem of a potential viral invader.

In addition, much of the cGAMP also travels outside the cell where it serves as a warning signal to neighboring immune cells. It activates their STING pathway and unleashes an immune attack against the virally infected cell.

Previous work from the Bakhoum lab had shown that cGAS-STING signaling inside of cancer cells causes them to adopt features of immune cells — in particular, the capacity to crawl and migrate — which aids their ability to metastasize. This provided part of the answer to the question of how cancer cells survive inflammation and aid metastasis in the process. The new research shows how the cancer cells cope with the warning signals that activated cGAS-STING releases into the environment. A scissor-like protein shreds the signals, providing a second way the cells can thwart the threat of immune destruction.

Examples of human triple negative breast cancer staining negative (left) and positive (right) for ENPP1. ©MSKCC

The scissor-like protein that coats cancer cells is called ENPP1. When cGAMP finds its way outside the cell, ENPP1 chops it up and prevents the signal from reaching immune cells. At the same time, this chopping releases an immune-suppressing molecule called adenosine, which also quells inflammation.

Through a battery of experiments conducted in mouse models of breast, lung, and colorectal cancers, Dr. Bakhoum and his colleagues showed that ENPP1 acts like a control switch for immune suppression and metastasis. Turning it on suppresses immune responses and increases metastasis; turning it off enables immune responses and reduces metastasis.

The scientists also looked at ENPP1 in samples of human cancers. ENPP1 expression correlated with both increased metastasis and resistance to immunotherapy.

Empowering Immunotherapy

From a treatment perspective, perhaps the most notable finding of the study is that flipping the ENPP1 switch off could increase the sensitivity of several different cancer types to immunotherapy drugs called checkpoint inhibitors. The researchers showed that this approach was effective in mouse models of cancer.

Several companies — including one that Dr. Bakhoum and colleagues founded — are now developing drugs to inhibit ENPP1 on cancer cells.

Dr. Bakhoum says it’s fortunate that ENPP1 is located on the surface of cancer cells since this makes it an easier target for drugs designed to block it.

It’s also relatively specific. Since most other tissues in a healthy individual are not inflamed, drugs targeting ENPP1 primarily affect cancer.

Finally, targeting ENPP1 undercuts cancer in two separate ways: “You’re simultaneously increasing cGAMP levels outside the cancer cells, which activates STING in neighboring immune cells, while you’re also preventing the production of the immune-suppressive adenosine. So, you’re hitting two birds with one stone,” Dr. Bakhoum explains.

The pace of the research has been incredibly fast, he says. “One of the things I would be really proud of is if this research ends up helping patients soon, given that we only just started this work in 2018.”

He hopes there will be a phase I clinical trial of ENPP1 inhibitors within a year.

This study received financial support from the National Institutes of Health (grants DP5OD026395, K08CA222663, and U54CA225088), the NCI Breast Cancer SPORE (P50CA247749), the Burroughs Wellcome Fund Career Award for Medical Scientists, the Parker Institute for Immunotherapy at MSKCC, the Josie Robertson Foundation, and the MSKCC core grant (P30-CA008748); the Breast Cancer Research Foundation, the Louis V. Gerstner, Jr. Scholars Program, an HICCC core grant (P30CA013696), the Oxford Institute for Radiation Oncology, the Prostate Cancer Foundation, the American Society of Clinical Oncology, the Academy of Medical Sciences, HSC Research Development Division of the Public Health Agency in Northern Ireland and the Friends of the Cancer Centre, Swim Across America, Ludwig Cancer Research, and Nonna’s Garden Foundation. Dr. Bakhoum holds a patent related to some of the work described targeting chromosome instability and the cGAS-STING pathway in advanced cancer. He owns equity in, receives compensation from, and serves as a consultant and on the Scientific Advisory Board and Board of Directors of Volastra Therapeutics Inc. He has also consulted for Sanofi, received sponsored travel from the Prostate Cancer Foundation, and both travel and compensation from Cancer Research UK.

Reference: Jun Li, Mercedes A Duran, Ninjit Dhanota, Walid K. Chatila, Sarah E Bettigole, John Kwon, Roshan K Sriram, Matthew Philip Humphries, Manuel Salto-Tellez, Jacqueline A. James, Matthew G Hanna, Johannes C. Melms, Sreeram Vallabhaneni, Kevin Litchfield, Ieva Usaite, Dhruva Biswas, Rohan Bareja, Hao Wei Li, Maria Laura Martin, Princesca Dorsaint, Julie-Ann Cavallo, Peng Li, Chantal Pauli, Lee Gottesdiener, Benjamin J DiPardo, Travis J Hollmann, Taha Merghoub, Hannah Y Wen, Jorge S. Reis-Filho, Nadeem Riaz, Shin-San Michael Su, Anusha Kalbasi, Neil Vasan, Simon N Powell, Jedd D. Wolchok, Olivier Elemento, Charles Swanton, Alexander N Shoushtari, Eileen E Parkes, Benjamin Izar and Samuel F Bakhoum, “Metastasis and immune evasion from extracellular cGAMP hydrolysis”, Cancer Discovery, 2020. DOI: 10.1158/2159-8290.CD-20-0387 https://cancerdiscovery.aacrjournals.org/content/early/2020/12/23/2159-8290.CD-20-0387

Provided by MSKCC

Ludwig Cancer Research Study Reveals How ecDNA Forms And Drives Cancer Drug Resistance (Medicine)

Researchers led by Ludwig San Diego Member Don Cleveland and Peter Campbell of the Sanger Center have solved the mystery of how free-floating circular DNA fragments, which are almost exclusively found in cancer cells, drive gene amplification to generate drug resistance in cancer. The research, published on December 23 in the journal Nature, provides new insights into how cancers evolve to adapt to changing environments and suggests ways to reduce drug resistance by combining therapies.

Ludwig San Diego Members Don Cleveland and Ofer Shoshani © Ludwig Cancer Research

“Drug resistance is the most problematic part of cancer therapy,” said Ofer Shoshani, a postdoctoral researcher in Cleveland’s lab and the study’s first author. “If not for drug resistance, many cancer patients would survive.”

Extrachromosomal DNAs (ecDNA) are distinct circular units of DNA that are unassociated with chromosomes, which package genomic DNA in the cell’s nucleus. ecDNA can contain many copies of cancer genes that help tumors grow and survive. Understanding the biology and origins of ecDNA took on some urgency after a team led by Ludwig San Diego Member Paul Mischel and his colleague Vineet Bafna at the University of California San Diego School of Medicine first reported in 2017 that it is found in nearly half of all tumor types and that it plays a major role in the growth and diversity of cancer cells.

In the new study, Shoshani, Cleveland, Campbell and colleagues show that chromothripsis, the shattering of chromosomes and their reassembly in shuffled order, initiates the formation of ecDNA.

Chromothripsis was first described in 2011 by a team led by Campbell. Scientists hypothesized at the time that chromosomal shattering could produce DNA snippets that circularize to form ecDNA, but this has not been proven until now. “What we were able to show is the link between chromosomal shattering and the formation of ecDNA,” Cleveland said. The team also showed that ecDNA can itself undergo successive rounds of chromothripsis to spawn rearranged ecDNAs that provide even higher drug resistance.

“We’ve watched these pieces evolve with time as they get shattered and reshattered,” Cleveland said. “That means if an ecDNA fragment acquires a gene that encodes for a product that directly counters an anticancer drug, it can make more and more of it, leading to drug resistance. We have now established this in three different cell lines forming resistance to methotrexate and in biopsies from human colorectal cancer patients forming resistance to BRAF therapy.”

While chromothripsis occurs naturally in cancer cells, the researchers found that it can also be induced by chemotherapeutic drugs such as methotrexate, which kill dividing cells by damaging their DNA. Moreover, the particular kind of DNA damage these drugs cause–breaking both strands of the DNA double helix–provides an opening for ecDNA to reintegrate back into chromosomes.

“We show that when we break a chromosome, these ecDNAs have a tendency to jump into the break and seal them, serving almost like a ‘DNA glue,'” Shoshani said. Thus, some of the very drugs used to treat cancers might also be driving drug resistance by generating double-stranded DNA breaks.

The researchers found that such ecDNA formation can be halted by pairing chemotherapeutic drugs with molecules that prevent the DNA fragments created by chromosomal shattering from closing to form circles. Shoshani showed that when applied together to cancer cells, this strategy inhibited the formation of ecDNA and reduced the emergence of drug resistance.

“This means that an approach in which we combine DNA repair inhibitors with drugs such as methotrexate or vemurafenib could potentially prevent the initiation of drug resistance in cancer patients and improve clinical outcomes,” Shoshani said.

Cleveland added, “I think the field has accepted that combination therapy is how we’re going to generate better outcomes for cancer patients, but here’s a specific example of what kinds of combinations should be tested.”

This study was supported by Ludwig Cancer Research, US National Institutes of Health and the Wellcome Trust.

In addition to his Ludwig post, Don Cleveland chairs the Department of Cellular and Molecular Medicine and is a professor of Medicine, Neurosciences and Cellular and Molecular Medicine at UC San Diego.

Provided by Ludwig Cancer Research