Lactone structures are common in biologically active natural molecules; they can be found, for example, in vitamin C and in the bacterial-derived antibiotic erythromycin. Chemists have long had techniques for synthesizing lactones, but these techniques are quite limited in what they can produce. The achievement, reported May 26, 2022, in Science, makes the construction of diverse, complex lactones easier than ever.

“This method should be very broadly useful for developing new pharmaceuticals, polymer materials, perfumes and many other chemical products — we’re already getting queries from interested manufacturers,” says Jin-Quan Yu, PhD, the Frank and Bertha Hupp Professor of Chemistry at Scripps Research.

Yu and his laboratory are known for their innovations in molecule building, especially with regard to “C-H activation.” This involves the use of specially designed catalyst molecules to remove a hydrogen (H) atom from a carbon (C) atom on an organic molecule, and to replace the hydrogen atom with a more complex cluster of atoms.

The general goal is to develop a set of methods for doing C-H activation selectively to any chosen carbon atom on a starting molecule — and the dream is to use those methods to turn cheap and relatively simple molecules into complex and valuable drugs, plastics and other molecules.

In this case, Yu and his team aimed to perform particularly difficult, site-selective C-H activations to convert cheap and readily available dicarboxylic acids into highly valuable lactones. Dicarboxylic acids, despite their complicated-seeming name, are relatively simple molecules, and are ideal starting materials for many types of chemical synthesis. But chemists attempting C-H activation of dicarboxylic acids have traditionally faced steep hurdles.

“C-H activations at sites on a dicarboxylic acid that are far away from one of its carboxyl groups have been very difficult to date,” Yu says. “Being able to target distant carbons and/or nearer carbons, selectively by catalyst control, has seemed an impossible dream.”

The feat achieved by Yu and his team, including first author Sam Chan, PhD, a Croucher Foundation Postdoctoral Fellow in the Yu lab, was a set of methods employing palladium-based catalysts to freely achieve C-H activations on easy- and hard-to-reach carbons on a dicarboxylic acid.

“Over the past two decades, we managed to develop good methods for C-H activation two carbons away from a carboxyl, but now with our new methods we can also reach one more carbon away, and with the freedom to choose between the two sites, we can readily access new chemical space in drug discovery,” Yu says. “In addition, the remaining carboxyl group on the dicarboxylic acid can be used to make further modifications, so essentially with this approach one can build a very broad range of complex lactone compounds.”

Yu and his team demonstrated the ease and utility of their new methods by synthesizing — from cheap dicarboxylic acids — two complex natural lactones, a fungal molecule called myrotheciumone A, which has been investigated for anticancer properties, and the plant lactone pedicellosine.

The chemists are now using the new methods to generate hundreds of diverse lactone structures, whose properties — and potential to be developed into future pharmaceuticals — they are exploring in collaboration with the laboratory of Ben Cravatt, PhD, the Gilula Chair of Chemical Biology at Scripps Research.

“We are also using our methods to develop improved processes for ton-scale production of lactones used by chemical products manufacturers,” Yu says.

“Catalyst-controlled site-selective methylene C-H lactonization of dicarboxylic acids” was co-authored by Hau Sun Sam Chan, Ji-Min Yang and Jin-Quan Yu of Scripps Research.

Funding was provided by the National Institute for General Medical Sciences (2R01GM084019), and the Croucher Foundation.

In the study, published May 27 in Science, the researchers examined the molecular changes that occur within an advanced malignancy called castration-resistant prostate cancer, which arises when tumors evade treatment that deprives them of the hormones that drive their growth. Using samples derived from patients, they conducted a comprehensive survey of this cancer.

“Our data showed us that there are four groups of castration-resistant disease, two of which have not been defined before,” said co-senior author Dr. Ekta Khurana, WorldQuant Foundation Research Scholar and associate professor of physiology and biophysics at Weill Cornell Medicine.

One of these, which they call stem cell-like (SCL), accounts for approximately a quarter of castration-resistant prostate cancers, she and her collaborators estimated. Within SCL tumor cells, they identified a set of proteins that work together to fuel this treatment-resistant disease. Studies have shown that this same molecular pathway drives other solid tumors, including colorectal cancer and malignancies of the breast and lung, so scientists are already working to develop ways of interfering with their activity.

“For patients that fall into this SCL group, we have found very promising drug targets, which future studies will work to validate,” said Dr. Khurana, who is also co-leader of the Genetics and Epigenetics Program at the Sandra and Edward Meyer Cancer Center and a member of the Englander Institute for Precision Medicine at Weill Cornell Medicine. Dr. Khurana collaborated with co-senior author Dr. Yu Chen at Memorial Sloan Kettering Cancer Center on this study.

An estimated 268,000 men will develop prostate cancer this year. Researchers already knew that this type of cancer encompasses more than one disease. Some tumors may manage to resist the treatment, but still need testosterone and other hormones, which are called androgens collectively, to grow. Others, meanwhile, shed their dependence on androgens and take on an aggressive form known as neuroendocrine. The new study identified two additional types of this disease: SCL and WNT, named for the signaling pathways that is overactive in tumors of these types.

Scientists seeking to investigate castration-resistant prostate cancer have generally lacked enough cells derived from patients to capture its full diversity. For this study, however, the team had access to 40 tumor samples. Most of these came from a collection of organoids, which are tiny organ-like structures grown from tumor cells collected from patients at Weill Cornell Medicine and Memorial Sloan Kettering Cancer Center.

The researchers analyzed these cells’ DNA, RNA, and how compactly their DNA was packaged, a characteristic known as chromatin accessibility. Changes in this packaging contribute to cancer by altering genes’ availability for expression. The chromatin data led them to identify the four groups, including SCL and WNT.

To determine the proportion of cases they each may comprise, the researchers used RNA sequencing data to classify 100 patients from Weill Cornell Medicine and 266 from the organization Stand Up to Cancer. Depending on the set of patients, 22 to 30 percent fell into the SCL category, while WNT accounted for 5 or 7 percent.

Focusing on SCL, they used sophisticated computational tools to integrate the molecular data and identify the malfunctioning pathway at the heart of this cancer. These proteins, FOSL1, TEAD, YAP and TAZ, become overly active and alter chromatin accessibility to propel tumor growth. In experiments, the researchers found that two molecules known to interfere with these proteins slowed the growth of the SCL cells, but not that of androgen-dependent cells — a result that highlights the potential for a targeted treatment.

“Once you can identify which type of tumor patients have, that’s very powerful information,” Dr. Khurana said.

In particular, knowing the chemical composition of pigments and binders that Aboriginal Australian artists employ could allow archaeological scientists and art conservators to identify these materials in important cultural heritage objects. Now, researchers are turning to X-ray science to help reveal the composition of the materials used in Aboriginal Australian cultural heritage — starting with the analysis of century-old samples of plant secretions, or exudates.

Aboriginal Australians continue to use plant exudates, such as resins and gums, to create rock and bark paintings and for practical applications, such as hafting stone points to handles. But just what these plant materials are made of is not well known.

Therefore, scientists from six universities and laboratories around the world turned to high-energy X-rays at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory and the synchrotron SOLEIL in France. The team aimed X-rays at 10 well-preserved plant exudate samples from the native Australian genera Eucalyptus, Callitris, Xanthorrhoea and Acacia. The samples had been collected more than a century ago and held in various institutions in South Australia.

The results of their study were clearer and more profound than expected.

“We got the breakthrough data we had hoped for,” said Uwe Bergmann, physicist at University of Wisconsin-Madison and former SLAC scientist who develops new X-ray methods. “For the first time, we were able to see the molecular structure of a well-preserved collection of native Australian plant samples, which might allow us to discover their existence in other important cultural heritage objects.”

Researchers today published their results in the Proceedings of the National Academy of Sciences.

Looking below the surface

Over time, the surface of plant exudates can change as the materials age. Even if these changes are just nanometers thick, they can still block the view underneath.

“We had to see into the bulk of the material beneath this top layer or we’d have no new information about the plant exudates,” SSRL Lead Scientist Dimosthenis Sokaras said.

Conventionally, molecules with carbon and oxygen are studied with lower-energy, so-called “soft” X-rays, that would not be able to penetrate through the debris layer. For this study, researchers sent high-energy X-ray photons, called “hard” X-rays, into the sample. The photons squeezed past foggy top layers and into the sample’s elemental arrangements beneath. Hard X-rays don’t get stuck in the surface, whereas soft X-rays do, Sokaras said.

Once inside, the high-energy photons scattered off of the plant exudate’s elements and were captured by a large array of perfectly aligned, silicon crystals at SSRL. The crystals filtered out only the scattered X-rays of one specific wavelength and funneled them into a small detector, kind of like how a kitchen sink funnels water drops down its drain.

Next, the team matched the wavelength difference between the incident and scattered photons to the energy levels of a plant exudate’s carbon and oxygen, providing the detailed molecular information about the unique Australian samples.

A path for the future

Understanding the chemistries of each plant exudate will allow for a better understanding of identification and conservation approaches of Aboriginal Australian art and tools, Rafaella Georgiou, a physicist at Synchrotron SOLEIL, said.

“Now we can go ahead and study other organic materials of cultural importance using this powerful X-ray technique,” she said.

Researchers hope that people who work in cultural heritage analysis will see this powerful synchrotron radiation technique as a valuable method for determining the chemistries of their samples.

“We want to reach out to that scientific community and say, ‘Look, if you want to learn something about your cultural heritage samples, you can come to synchrotrons like SSRL,'” Bergmann said.

Led by experts at NYU Grossman School of Medicine and the NYU Langone Fertility Center, the new finding was based on 15 years of “real life” frozen egg thaw outcomes for women who had delayed childbearing and faced natural, age-related fertility decline.

Published online May 18 in Fertility and Sterility, the study also found that considerable number of the women studied had more than one child through egg preservation. In total the study reports 211 babies from egg freezing.

In comparison, and using fresh eggs or embryos from women trying to conceive, at age 40 fewer than 30 percent undergoing in vitro fertilization (IVF) become pregnant and fewer than 20 percent gave birth to live babies as a result, according to statistics gathered by the Centers for Disease and Prevention from the nation’s nearly 500 fertility clinics. Egg freezing and thawing at a later date provides a higher pregnancy success rate than using fresh embryos during assisted reproductive technology, say the study authors.

“Our findings shed light on the factors that track with successful births from egg freezing, which include careful screening of embryos to be thawed and implanted,” says study lead author Sarah Druckenmiller Cascante, MD, fellow in the Division of Reproductive Endocrinology and Infertility, within the Department of Obstetrics and Gynecology at NYU Langone. “A better understanding of the live birth rate from egg freezing for age-related fertility decline is necessary to inform patient decision-making.”

“Importantly, our study is based on actual clinical experience,” adds Cascante, “rather than mathematical modeling with limited data, which is most of what has been published on the chance of births from egg freezing thus far.” The number of U.S. women having children at older ages has been increasing for three decades, with evidence that the trend will continue. Birth rates have declined for women in their 20s and jumped for women in their late 30s and early 40s, according to the U.S. Census Bureau. The average age at first birth has risen from 19 years old in 1984 to 30 years old in 2021 and is higher in many metropolitan areas.

Specialists within the NYU Langone Fertility Center have been pioneers in the development of egg freezing technology, with the first baby born through via egg freezing at NYU Langone in July 2005. The Center has seen almost triple the number of women starting egg freezing cycles in 2022 in comparison to 2019. As this national trend increases, more data is needed to inform patients that seek to secure their reproductive futures.

Study Details

Within the study, 543 patients participated with an average age of 38 years old at the time of the first egg freeze, which is older than the optimal age to freeze eggs (35 years old or younger). These patients underwent 800 egg freezing cycles, 605 egg thaws, and 436 embryo transfers between 2005-2020.

The investigation found that overall, 39 percent of women between 27-44 years old, with a majority between 35-40 years old at egg freeze, had a least one child from their frozen eggs, which is comparable with age-matched IVF outcomes. Across all ages, women who thawed more than 20 mature eggs had a 58 percent live birth rate, which was profound and unexpected as this group included patients past their reproductive prime. In fact, 14 patients who froze eggs at the age of 41-43 years successfully had children from their frozen eggs. As noted, women under 38 years old who had 20 or more mature eggs thawed achieved a 70 percent live birth rate per patient. The length of frozen egg storage did not change the success rate.

Results also showed that preimplantation genetic screening with embryos from frozen and eventually thawed eggs resulted in lower miscarriage rates and higher live birth rates per transfer. Such screening also allows for single embryo transfers, yielding singleton pregnancies, which are safer for both the mother and child, say the authors.

“Our results provide realistic expectations for those considering oocyte preservation, and demonstrate that egg freezing technology empowers women with improved reproductive autonomy,” says study senior author James A. Grifo, MD, PhD, director of the Division of Reproductive Endocrinology and Infertility and the NYU Langone Fertility Center. “Freezing eggs at a young age becomes an option to be one’s own egg donor at advanced age. As younger patients freeze eggs and do more than one cycle, the success rates will be even higher than reported in this study.”

Dr. Grifo, also a professor in the Department of Obstetrics and Gynecology at NYU Langone, cautions that the study was limited by the number of patients. Future larger studies are under way to increase the data set from which patients can benefit and model their expected success rates. He adds that additional studies from a variety of geographic locations and center types are also necessary.

Funding support for the foundational scientific studies that led to NYU Langone’s clinically successful oocyte cryopreservation program was provided by the Carolyn and Malcom Wiener Foundation.

In addition to Dr. Cascante and Dr. Grifo, other clinician-scientists in the study were Jennifer K. Blakemore, MD; Shannon M. DeVore, MD; Brooke Hodes-Wertz, MD, MPH; Elizabeth Fino, MD; Alan S. Berkeley, MD; Carlos M. Parra, MD; and Caroline McCaffrey, PhD. The entire team of embryologists, doctors, nurses and support staff at the NYU Langone Fertility Center contributed to the success presented in this study.

In new research, Cornell scientists provide an explanation for how this problem is solved by nature: they define with atomic precision how a transposon-derived system edits DNA in RNA-guided fashion. Transposons are mobile genetic elements inside bacteria. A lineage of transposon encodes IscB, which is less than half the size of Cas9 but equally capable of DNA editing. Replacing Cas9 with IscB would definitively solve the size problem.

The researchers used cryo-electron microscopy (Cryo-EM) to visualize the IscB-ωRNA molecule from a transposon system in high resolution. They were able to capture snapshots of the system in different conformational states. They were even able to engineer slimmer IscB variants, by removing nonessential parts from IscB. 

“Next-generation fancy applications require the gene editor to be fused with other enzymes and activities and most Cas9s are already too big for viral delivery. We are facing a traffic jam at the delivery end,” said corresponding author Ailong Ke, professor of molecular biology and genetics in the College of Arts and Sciences. “If Cas9s can be packaged into viral vectors that have been used for decades in the gene therapy field, like AAV, then we can be confident they can be delivered and we can focus research exclusively on the efficacy of the editing tool itself.”

CRISPR-Cas9 systems use an RNA as a guide to recognize a sequence of DNA. When a match is found, the Cas9 protein snips the target DNA at just the right place; it’s then possible to do surgery at the DNA level to fix genetic diseases. The cryo-EM data gathered by the Cornell team show that the IscB-ωRNA system works in a similar way, with its smaller size achieved by replacing parts of the Cas9 protein with a structured RNA (ωRNA) which is fused to the guide RNA.  By replacing protein components of the larger Cas9 with RNA, the IscB protein is shrunken to the core chemical reaction centers which snip the target DNA.

“It’s about understanding the molecules’ structure and how they perform the chemical reactions,” said first author Gabriel Schuler, a doctoral student in the graduate field of microbiology. “Studying these transposons gives us a new starting point to generate more powerful and accessible gene editing tools.”

It is believed that transposons — mobile genetic elements — were the evolutionary precursors to CRISPR systems. They were discovered by Nobel Laureate Barbara McClintock ’23, M.A. ’25, Ph.D. ’27.

“Transposons are specialized genetic hitchhikers, integrating into and splicing out of our genomes all the time,” Ke said. “The systems inside bacteria in particular are being selected constantly — nature has basically tossed the dice billions of times and come up with really powerful DNA surgical tools, CRISPR included. And now, by defining these enzymes in high resolution, we can tap into their powers.”

As small as IscB is compared to CRISPR Cas9, the researchers believe they will be able to shrink it even smaller. They’ve already removed 55 amino acids without affecting IscB’s activity; they hope to make future versions of this genome editor even smaller and hence even more useful.

Better understanding the function of the companion guide RNA was another motivation behind the study, said co-first author Chunyi Hu, a postdoctoral researcher in the Department of Molecular Biology and Genetics. “There’s still a lot of mystery — like why do transposons use an RNA-guided system? What other roles this RNA may be playing?”

 One challenge that yet remains for the researchers is that while the IscB-ωRNA is extremely active in test tubes, it was not as efficient at altering DNA in human cells. The next step in their research will be to use the molecular structure to explore the possibilities they have identified for the cause of the low activity in human cells. “We have some ideas, a lot of them actually, that we are eager to test in the near future,” Schuler said.

The research was funded by grants Ke received from the National Institutes of Health. Schuler is supported by the Department of Defense through the National Defense Science and Engineering Graduate Fellowship Program. The Cryo-EM work was assisted by the Cornell Center for Materials Research and the Brookhaven National Laboratory. 

Story Source:

Materials provided by Cornell University. Original written by Linda B. Glaser, courtesy of the Cornell Chronicle. Note: Content may be edited for style and length.