Tag Archives: Helix

Elucidating the function of BRCA2 gene offers insight into cancer development

A new study shows exactly how the gene BRCA2, linked to susceptibility to breast and ovarian cancer, functions to repair damaged DNA. By studying BRCA2 at the level of single molecules, researchers at the University of California, Davis, have generated new insights into the mechanisms of DNA repair and the origins of cancer. The work was published the week of March 27 in the Proceedings of the National Academy of Sciences.

Elucidating the function of BRCA2 is essential for understanding the molecular etiology of cancer development in breast and ovarian cells, as well as many other cell types including prostate.”

Stephen Kowalczykowski, distinguished professor of microbiology and molecular genetics, UC Davis College of Biological Sciences

By visualizing BRCA2 function at a single molecule level, Kowalczykowski’s team discovered that it acts as a molecular chaperone, delivering another protein, RAD51, to single-stranded DNA. It ensures formation of a functional filament of RAD51 and the repair of broken DNA.

“When BRCA2 is defective, broken DNA is not faithfully repaired, the genome loses integrity, and cancer ultimately ensues,” Kowalczykowski said.

Mutations in the BRCA2 gene are linked to an increased risk of cancer, especially breast and ovarian cancer. In 2010, teams led by Kowalczykowski and by Professor Wolf-Dietrich Heyer in the same department at UC Davis succeeded in purifying the BRCA2 protein and showed that it plays a key role in DNA repair.

The new work, using techniques developed in Kowalczykowski’s lab to image single proteins and DNA molecules in real time, gives new insight into the mechanics of this repair process.

Our DNA is under constant assault by both processes inside cells and by outside factors, such as sunlight or chemical exposures. Accumulating damage to DNA can cause cells to become cancerous. Fortunately, our cells have several mechanisms to repair DNA. One of these is homologous recombination to repair double-stranded breaks.

Repairing double-stranded breaks

When a break crosses both strands of the DNA double helix, one strand is trimmed back a little to leave a single exposed strand. This strand then goes hunting for its counterpart in the same gene in the matching paired chromosome. It inserts into the healthy DNA and uses it as a template for repair.

For this insertion to work, the single strand of DNA has to be coated with RAD51. Earlier work from Kowalczykowski’s lab measured how quickly RAD51 could be added onto DNA, like beads on a string.

The function of BRCA2 is to load up with RAD51 (each BRCA2 can carry up to six RAD51s), push another protein called RPA out of the way and put the proteins onto the DNA.

Postdoctoral researcher Jason Bell carried out the experiments observing RAD51 and BRCA2 working their way along the DNA. Bell manipulated pieces of DNA with a single-stranded gap and exposed them to RAD51 with and without BRCA2 under different conditions.

The resulting movies show how BRCA2 chaperones RAD51 onto single-stranded DNA, displacing RPA.

Understanding the role of BRCA2 in DNA repair has two important implications. First, it helps us understand why mutations of BRCA2 lead to an increased risk of cancer. Second, some drugs to treat cancer work by damaging DNA. By understanding how DNA repair works, we can develop new drugs to target it specifically in cancer cells.

Additional co-authors on the paper are Christopher Dombrowski and Jody Plank, both at UC Davis, and Ryan Jensen, formerly at UC Davis and now at the Yale University School of Medicine. The work was supported by grants from the National Institutes of Health.

Journal reference:

Bell, J. C., et al. (2023). BRCA2 chaperones RAD51 to single molecules of RPA-coated ssDNA. Proceedings of the National Academy of Sciences. doi.org/10.1073/pnas.2221971120.

Avanced genome editing technology could be used as a one-time treatment for CD3 delta SCID

A new UCLA-led study suggests that advanced genome editing technology could be used as a one-time treatment for the rare and deadly genetic disease CD3 delta severe combined immunodeficiency.

The condition, also known as CD3 delta SCID, is caused by a mutation in the CD3D gene, which prevents the production of the CD3 delta protein that is needed for the normal development of T cells from blood stem cells.

Without T cells, babies born with CD3 delta SCID are unable to fight off infections and, if untreated, often die within the first two years of life. Currently, bone marrow transplant is the only available treatment, but the procedure carries significant risks.

In a study published in Cell, the researchers showed that a new genome editing technique called base editing can correct the mutation that causes CD3 delta SCID in blood stem cells and restore their ability to produce T cells.

The potential therapy is the result of a collaboration between the laboratories of Dr. Donald Kohn and Dr. Gay Crooks, both members of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA and senior authors of the study.

Kohn’s lab has previously developed successful gene therapies for several immune system deficiencies, including other forms of SCID. He and his colleagues turned their attention to CD3 delta SCID at the request of Dr. Nicola Wright, a pediatric hematologist and immunologist at the Alberta Children’s Hospital Research Institute in Canada, who reached out in search of a better treatment option for her patients.

CD3 delta SCID is prevalent in the Mennonite community that migrates between Canada and Mexico.

Because newborns are not screened for SCID in Mexico, I often see babies who have been diagnosed late and are returning to Canada quite sick.”

Dr. Nicola Wright, pediatric hematologist and immunologist at the Alberta Children’s Hospital Research Institute

When Kohn presented Wright’s request to his lab, Grace McAuley, then a research associate who joined the lab at the end of her senior year at UCLA, stepped up with a daring idea.

“Grace proposed we try base editing, a very new technology my lab had never attempted before,” said Kohn, a distinguished professor of microbiology, immunology and molecular genetics, and of pediatrics.

Base editing is an ultraprecise form of genome editing that enables scientists to correct single-letter mutations in DNA. DNA is made up of four chemical bases that are referred to as A, T, C and G; those bases pair together to form the “rungs” in DNA’s double-helix ladder structure.

While other gene editing platforms, like CRISPR-Cas9, cut both strands of the chromosome to make changes to DNA, base editing chemically changes one DNA base letter into another -; an A to a G, for example -; leaving the chromosome intact.

“I had a very steep learning curve in the beginning, when base editing just wasn’t working,” said McAuley, who is now pursuing an M.D.-Ph.D. at UC San Diego and is the study’s co-first author. “But I kept pushing forward. My goal was help get this therapy to the clinic as fast as was safely possible.”

McAuley reached out to the Broad Institute’s David Liu, the inventor of base editing, for advice on how to evaluate the technique’s safety for this particular use. Eventually, McAuley identified a base editor that was highly efficient at correcting the disease-causing genetic mutation.

Because the disease is extremely rare, obtaining patient stem cells for the UCLA study was a significant challenge. The project got a boost when Wright provided the researchers with blood stem cells donated by a CD3 delta SCID patient who was undergoing a bone marrow transplant.

The base editor corrected an average of almost 71% of the patient’s stem cells across three laboratory experiments.

Next, McAuley worked with Dr. Gloria Yiu, a UCLA clinical instructor in rheumatology, to test whether the corrected cells could give rise to T cells. Yiu used artificial thymic organoids, which are stem cell-derived tissue models developed by Crooks’ lab that mimic the environment of the human thymus -; the organ where blood stem cells become T cells.

When the corrected blood stem cells were introduced into the artificial thymic organoids, they produced fully functional and mature T cells.

“Because the artificial thymic organoid supports the development of mature T cells so efficiently, it was the ideal system to show that base editing of patients’ stem cells could fix the defect seen in this disease,” said Yiu, who is also a co-first author of the study.

As a final step, McAuley studied the longevity of the corrected stem cells by transplanting them into a mouse. The corrected cells remained four months after transplant, indicating that base editing had corrected the mutation in true, self-renewing blood stem cells. The findings suggest that corrected blood stem cells could persist long-term and produce the T cells patients would need to live healthy lives.

“This project was a beautiful picture of team science, with clinical need and scientific expertise aligned,” said Crooks, a professor of pathology and laboratory medicine. “Every team member played a vital role in making this work successful.”

The research team is now working with Wright on how to bring the new approach to a clinical trial for infants with CD3 delta SCID from Canada, Mexico and the U.S.

This research was funded by the Jeffrey Modell Foundation, the National Institutes of Health, the Bill and Melinda Gates Foundation, the Howard Hughes Medical Institute, the V Foundation and the A.P. Giannini Foundation.

The therapeutic approach described in this article has been used in preclinical tests only and has not been tested in humans or approved by the Food and Drug Administration as safe and effective for use in humans. The technique is covered by a patent application filed by the UCLA Technology Development Group on behalf of the Regents of the University of California, with Kohn and McAuley listed as co-inventors.

Journal reference:

McAuley, G.E., et al. (2023) Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing. Cell. doi.org/10.1016/j.cell.2023.02.027.

Cryo-electron microscopy reveals atomic structure of Staphylococcus epidermidis bacteriophage

Cryo-electron microscopy by University of Alabama at Birmingham researchers has exposed the structure of a bacterial virus with unprecedented detail. This is the first structure of a virus able to infect Staphylococcus epidermidis, and high-resolution knowledge of structure is a key link between viral biology and potential therapeutic use of the virus to quell bacterial infections.

Bacteriophages or “phages” is the terms used for viruses that infect bacteria. The UAB researchers, led by Terje Dokland, Ph.D., in collaboration with Asma Hatoum-Aslan, Ph.D., at the University of Illinois Urbana-Champaign, have described atomic models for all or part of 11 different structural proteins in phage Andhra. The study is published in Science Advances.

Andhra is a member of the picovirus group. Its host range is limited to S. epidermidis. This skin bacterium is mostly benign but also is a leading cause of infections of indwelling medical devices. “Picoviruses are rarely found in phage collections and remain understudied and underused for therapeutic applications,” said Hatoum-Aslan, a phage biologist at the University of Illinois.

With emergence of antibiotic resistance in S. epidermidis and the related pathogen Staphylococcus aureus, researchers have renewed interest in potentially using bacteriophages to treat bacterial infections. Picoviruses always kill the cells they infect, after binding to the bacterial cell wall, enzymatically breaking through that wall, penetrating the cell membrane and injecting viral DNA into the cell. They also have other traits that make them attractive candidates for therapeutic use, including a small genome and an inability to transfer bacterial genes between bacteria.

Knowledge of protein structure in Andhra and understanding of how those structures allow the virus to infect a bacterium will make it possible to produce custom-made phages tailored to a specific purpose, using genetic manipulation.

The structural basis for host specificity between phages that infect S. aureus and S. epidermidis is still poorly understood. With the present study, we have gained a better understanding of the structures and functions of the Andhra gene products and the determinants of host specificity, paving the way for a more rational design of custom phages for therapeutic applications. Our findings elucidate critical features for virion assembly, host recognition and penetration.”

Terje Dokland, professor of microbiology at UAB and director of the UAB Cryo-Electron Microscopy Core

Staphylococcal phages typically have a narrow range of bacteria they can infect, depending on the variable polymers of wall teichoic acid on the surface of different bacterial strains. “This narrow host range is a double-edged sword: On one hand, it allows the phages to target only the specific pathogen causing the disease; on the other hand, it means that the phage may need to be tailored to the patient in each specific case,” Dokland said.

The general structure of Andhra is a 20-faced, roundish icosahedral capsid head that contains the viral genome. The capsid is attached to a short tail. The tail is largely responsible for binding to S. epidermidis and enzymatically breaking the cell wall. The viral DNA is injected into the bacterium through the tail. Segments of the tail include the portal from the capsid to the tail, and the stem, appendages, knob and tail tip.

The 11 different proteins that make up each virus particle are found in multiple copies that assemble together. For instance, the capsid is made of 235 copies each of two proteins, and the other nine virion proteins have copy numbers from two to 72. In total, the virion is made up of 645 protein pieces that include two copies of a 12th protein, whose structure was predicted using the protein structure prediction program AlphaFold.

The atomic models described by Dokland, Hatoum-Aslan, and co-first authors N’Toia C. Hawkins, Ph.D., and James L. Kizziah, Ph.D., UAB Department of Microbiology, show the structures for each protein -; as described in molecular language like alpha-helix, beta-helix, beta-strand, beta-barrel or beta-prism. The researchers have described how each protein binds to other copies of that same protein type, such as to make up the hexameric and pentameric faces of the capsid, as well as how each protein interacts with adjacent different protein types.

Electron microscopes use a beam of accelerated electrons to illuminate an object, providing much higher resolution than a light microscope. Cryo-electron microscopy adds the element of super-cold temperatures, making it particularly useful for near-atomic structure resolution of larger proteins, membrane proteins or lipid-containing samples like membrane-bound receptors, and complexes of several biomolecules together.

In the past eight years, new electron detectors have created a tremendous jump in resolution for cryo-electron microscopy over normal electron microscopy. Key elements of this so-called “resolution revolution” for cryo-electron microscopy are:

  • Flash-freezing aqueous samples in liquid ethane cooled to below -256 degrees F. Instead of ice crystals that disrupt samples and scatter the electron beam, the water freezes to a window-like “vitreous ice.”
  • The sample is kept at super-cold temperatures in the microscope, and a low dose of electrons is used to avoid damage to the proteins.
  • Extremely fast direct electron detectors are able to count individual atoms at hundreds of frames per second, allowing sample movement to be corrected on the fly.
  • Advanced computing merges thousands of images to generate three-dimensional structures at high resolution. Graphics processing units are used to churn through terabytes of data.
  • The microscope stage that holds the sample can also be tilted as images are taken, allowing construction of a three-dimensional tomographic image, similar to a CT scan at the hospital.

The analysis of Andhra virion structure by the UAB researchers started with 230,714 particle images. Molecular reconstruction of the capsid, tail, distal tail and tail tip started with 186,542, 159,489, 159,489 and 159,489 images, respectively. Resolution ranged from 3.50 to 4.90 angstroms.

Journal reference:

Hawkins, N.C., et al. (2022) Structure and host specificity of Staphylococcus epidermidis bacteriophage Andhra. Science Advances. doi.org/10.1126/sciadv.ade0459.

$2.5 million CDC contract to fund one of the largest SARS-CoV-2 surveillance programs in the U.S.

A team led by Scripps Research scientists has been awarded a contract by the U.S. Centers for Disease Control & Prevention (CDC) in support of one of the largest SARS-CoV-2 surveillance programs in the United States.

The two-year, $2.5 million contract will fund the large-scale, near real-time sequencing of SARS-CoV-2 isolates from hospitals and local public health agencies in San Diego and nearby northwestern Mexico, and the development of software for tracking the evolution and geographical spread of SARS-CoV-2 variants.

The contract, an extension of one originally awarded in 2020, will be carried out by the San Diego Epidemiology and Research for COVID Health (SEARCH) Alliance, which was co-founded by Scripps Research, the University of California San Diego (UC San Diego), and Rady Children’s Hospital-San Diego.

CDC’s support for SEARCH’s genomic surveillance program has already led to significant COVID-19 public health advances as well as new science on SARS-CoV-2, and we expect much more progress in both areas as a result of this new award.”

Kristian Andersen, PhD, Principal Investigator, Professor, Department of Immunology and Microbiology at Scripps Research

Since the start of the pandemic, SEARCH has been conducting genomic surveillance of SARS-CoV-2 using clinical samples collected at San Diego hospitals and from sources across the border in Baja California. SEARCH has also developed key protocols and analysis tools to track the emergence and spread of SARS-CoV-2 variants in wastewater. Moreover, SEARCH investigators are actively involved in understanding the emergence of SARS-CoV-2, and in several high-profile publications have found evidence for an initial spread from animals sold at the Huanan Market in Wuhan, China.

SEARCH’s efforts involve multiple collaborations, including with the CDC, San Diego County’s Health & Human Services Agency, the California Department of Public Health, Sharp Health, Scripps Health, the viral surveillance company Helix, and the Salud Digna healthcare network in Mexico. Since the start of the pandemic, these efforts have yielded publications and analyses of more than 70,000 SARS-CoV-2 sequences.

Under the new contract, SEARCH will accelerate its virus-sequencing workflow to produce more timely and actionable information on local virus spread and evolution-;including the emergence of new variants and subvariants of concern.

“The current process of sampling, sequencing and analyzing a batch of virus samples from local hospital cases and wastewater treatment plants can take several weeks,” says Mark Zeller, PhD, project scientist in the Andersen lab. “We’re aiming to get that down to a matter of days, which would enable us to monitor the transmission chains in local outbreaks in near real-time.”

Working with the County of San Diego, the state of California and Mexican public health labs, the researchers will also continue to analyze the transmission of SARS-CoV-2 across the busy California-Baja border. Additionally, they’ll expand their genomic surveillance efforts to additional Mexican border states and popular tourist destinations, including Puerto Vallarta. The team will continue to post their analyses on SEARCH’s online dashboards.

The project includes the further development of open-source software tools to support the tracking of local SARS-CoV-2 evolution and transmission.

“The tools we’ve developed in recent years are already being used widely by the public health community for SARS-CoV-2 sequencing and analysis,” says Joshua Levy, PhD, postdoctoral research associate in the Andersen lab. “Under this new contract, we will be developing the technology to permanently transform how genomic surveillance will be used to strengthen our public health response.”

These open-source software tools are available at https://andersen-lab.com/secrets/code/. The SEARCH Alliance’s SARS-CoV-2 surveillance dashboards are at https://searchcovid.info/Dashboards/.