Publisher Health

Scientists have discovered that the most widely-used class of antifungals in the world cause pathogens to self-destruct. The University of Exeter-led research could help improve ways to protect food security and human lives.
Fungal diseases account for the loss of up to a quarter of the world’s crops. They also pose a risk to humans and can be fatal for those with weakened immune systems.
Our strongest “weapon” against fungal plant diseases are azole fungicides. These chemical products account for to a quarter of the world agricultural fungicide market, worth more than £3 billion per year. Antifungal azoles are also widely used as a treatment against pathogenic fungi which can be fatal to humans, which adds to their importance in our attempt to control fungal disease.
Azoles target enzymes in the pathogen cell that produce cholesterol-like molecules, named ergosterol. Ergosterol is an important component of cellular bio-membranes. Azoles deplete ergosterol, which results in killing of the pathogen cell. However, despite the importance of azoles, scientists know little about the actual cause of pathogen death.
In a new study published in Nature Communications, University of Exeter scientists have uncovered the cellular mechanism by which azoles kill pathogenic fungi.
Funded by the BBSRC, the team of researchers, led by Professor Gero Steinberg, combined live-cell imaging approaches and molecular genetics to understand why the inhibition of ergosterol synthesis results in cell death in the crop pathogenic fungus Zymoseptoria tritic (Z. tritici). This fungus causes septoria leaf blotch in wheat, a serious disease in temperate climates, estimated to cause more than £250 million per year in costs in the UK alone due to harvest loss and fungicide spraying.
The Exeter team observed living Z. tritici cells, treated them with agricultural azoles and analysed the cellular response. They showed that the previously accepted idea that azoles kill the pathogen cell by causing perforation of the outer cell membrane does not apply. Instead, they found that azole-induced reduction of ergosterol increase the activity of cellular mitochondria, the “powerhouse” of the cell, required to produce the cellular “fuel” that drives all metabolic processes in the pathogen cell. While producing more “fuel” is not harmful in itself, the process leads to the formation of more toxic by-products. These by-products initiate a “suicide” programme in the pathogen cell, named apoptosis. In addition, reduced ergosterol levels also trigger a second “self-destruct” pathway, which causes the cell to “self-eat” its own nuclei and other vital organelles — a process known as macroautophagy. The authors show that both cell death pathways underpin the lethal activity of azoles. They conclude that azoles drive the fungal pathogen into “suicide” by initiating self-destruction.
The authors found the same mechanism of how azoles kill pathogen cells in rice-blast fungus Magnaporthe oryzae. The disease caused by this fungus kills up to 30 per cent of rice, an essential food crop for more than 3.5 billion people across the world. The team also tested other clinically relevant anti-fungal drugs that target the ergosterol biosynthesis, including Terbinafine, Tolfonate and Fluconazole. All initiated the same responses in the pathogen cell, suggesting that cell suicide is a general consequence of ergosterol biosynthesis inhibitors.
Lead author Professor Gero Steinberg, who holds a Chair in Cell Biology and is Director of the Bioimaging Centre at the University of Exeter, said: “Our findings rewrite common understanding of how azoles kill fungal pathogens. We show that azoles trigger cellular “suicide” programmes, which result in the pathogen self-destructing. This cellular reaction occurs after two days of treatment, suggesting that cells reach a “point of no return” after some time of exposure to azoles. Unfortunately, this gives the pathogen time to develop resistance against azoles, which explains why azole resistance is advancing in fungal pathogens, meaning they are more likely to fail to kill the disease in crops and humans.
“Our work sheds light on the activity of our most widely used chemical control agents in crop and human pathogens across the world. We hope that our results prove to be useful to optimise control strategies that could save lives and secure food security for the future.”

Pluripotent stem cells (PSCs) are a type of stem cells capable of developing into various cell types. Over the past few decades, scientists have been working towards the development of therapies using PSCs. Thanks to their unique ability to self-renew and differentiate (mature) into virtually any given type of tissue, PSCs could be used to repair organs that have been irreversibly damaged by age, trauma, or disease.
However, despite extensive efforts, regenerative therapies involving PSCs still have many hurdles to overcome. One being the formation of tumors (via the process of tumorigenesis) after the transplantation of PSCs. Once the PSCs differentiate into a specific type for stem cell therapy, there is a high probability of tumor formation after differentiated stem cells are introduced to the target organ. For the success of PSC-based therapies, the need of the hour is to minimize the risk of tumorigenesis by identifying potentially problematic cells in cultures, prior to transplantation.
Against this backdrop, a research team led by Atsushi Intoh and Akira Kurisaki from Nara Institute of Science and Technology, Japan, has recently achieved a breakthrough discovery regarding stem cell therapy and tumorigenesis. “Our findings present advancements that could bridge the gap between stem cell research and clinical application,” says Intoh, talking about the potential of their findings. Their study was published in Stem Cells Translational Medicine and focuses on a membrane protein called EPHA2, which was previously found to be elevated in PSCs prior to differentiation by the team.
Through several experiments involving both mouse and human stem cell cultures, the researchers gained insights into the role of EPHA2 in preserving the potency of PSCs to develop into several cell types. They found that EPHA2 in stem cells is co-expressed with OCT4 — a transcription factor protein which controls the expression of genes which are critically involved in the differentiation of embryonic stem cells. Interestingly, when the EPHA2 gene was knocked down from the cells, cultured stem cells spontaneously differentiated. These results suggest that EPHA2 plays a central role in keeping stem cells in an undifferentiated state.
The researchers thus theorized that EPHA2-expressing stem cells, which would fail to differentiate, might be responsible for tumorigenesis upon transplantation into the target organ.
To test this hypothesis, the researchers prepared PSC cultures and artificially induced their differentiation into liver cells. Using a magnetic antibody targeting EPHA2, they extracted EPHA2-positive cells from a group of cultures prior to transplantation into mice. Interestingly, the formation of tumors in mice receiving transplants from cultures from which EPHA2 had been removed was vastly suppressed.
Taken together, these results point to the importance of EPHA2 in emerging stem cell-based therapies. “EPHA2 conclusively emerges as a potential marker for selecting undifferentiated stem cells, providing a valuable method to decrease tumorigenesis risks after stem cell transplantation in regenerative treatments,” remarks Kurisaki.
Further in-depth studies on this protein may lead to the development of protocols that make PSCs safer to use. Luckily, however, these findings pave the way towards a future where we will be able to finally restore damaged organs and even overcome degenerative conditions.

Some 13% of older adults are diagnosed with traumatic brain injury (TBI), according to a study by UC San Francisco and the San Francisco VA Health Care System. These injuries are typically caused by falls from ground level.
Researchers followed about 9,200 Medicare enrollees, whose average age was 75 at the start of the study, and found that contrary to other studies of younger people, being female, white, healthier and wealthier was associated with higher risk of TBI.
The study publishes in JAMA Network Open on May 31, 2024.
The researchers, led by first author Erica Kornblith, PhD, of the UCSF Department of Psychiatry and the San Francisco VA Health Care System, tracked TBI Medicare claims of participants enrolled in the Health and Retirement Study, a long-term study of a representative sample of older Americans.
While TBI can be successfully treated, these injuries increase the likelihood of a number of serious conditions, including dementia, Parkinson’s disease and seizures, as well as cardiovascular disease and psychiatric conditions like depression and anxiety.
“The number of people 65 and older with TBI is shockingly high,” said senior author Raquel Gardner, MD, formerly of the UCSF Department of Neurology and the San Francisco VA Health Care System. “We need evidence-based guidelines to inform post-discharge care of this very large Medicare population, and more research on post-TBI dementia prevention and repeat injury prevention.”
The researchers sought to identify the factors that made some patients more vulnerable than others, during a follow-up period of up to 18 years.

Earlier TBI studies have found that males, non-whites and those of lower socio-economic status were more likely to be diagnosed with TBI. But the current study found that females and whites were overrepresented among the 1,148 participants with TBI. While 58% of the HRS participants were female and 84% were white, among those with TBI, the figures were 64% and 89%. In addition, 31% of those with TBI were in the highest quartile of wealth, while 22% were in the lowest.
Activities of healthier seniors may place them at higher risk
Participants who went on to be diagnosed with TBI were less likely when they enrolled in the study to have lung disease and to have trouble with the activities of daily living, like bathing, walking and getting out of bed. They also were more likely to have normal cognition.
“It’s possible that our findings reflect that adults who are healthier, wealthier and more active are more able or likely to engage in activities that carry risk for TBI,” said Kornblith, who is also affiliated with the UCSF Weill Institute for Neurosciences.
“While most TBIs in older people occur from falls at ground level, if you are in a wheelchair or bedbound, you don’t have as many opportunities for traumatic injuries,” she added. “It’s also possible that participants with cognitive impairment are more limited in their activity and have less opportunity to fall.”
But the findings may mask the true incidence of injury, since the data only reflect cases of TBI in which patients were diagnosed and received care. A 2007 study found that 42% of respondents to an online survey did not seek medical attention after TBI.
“We know that older adults who experience falls, the largest segment of Americans with TBI, as well as lower-resourced adults — including those subjected to racial and ethnic micro-aggressions in a medical setting — are less likely to seek care,” Kornblith said. “It’s possible that our data did not capture the true burden of TBI in this population.”
The study’s findings may raise questions at a time when physical activity is vigorously recommended to reduce or slow the development of dementia.
“The overall evidence still overwhelmingly sides with physical activity being neuroprotective,” said Gardner, who is now at the Sheba Medical Center in Israel. “However, taking measures to optimize safety and mitigate falls is critical. These measures need to change over the life-course as an individual accumulates physical or cognitive disabilities, or both.”

Investigators from Brigham and Women’s Hospital identified and assessed underlying mechanisms that may explain the Mediterranean diet’s 23 percent reduction in all-cause mortality risk for American women
The health benefits of the Mediterranean diet have been reported in multiple studies, but there is limited long-term data of its effects in U.S. women and little understanding about why the diet may reduce risk of death. In a new study that followed more than 25,000 initially healthy U.S. women for up to 25 years, researchers from Brigham and Women’s Hospital, a founding member of the Mass General Brigham healthcare system, found that participants who had greater Mediterranean diet intake had up to 23% lower risk of all-cause mortality, with benefits for both cancer mortality and cardiovascular mortality. The researchers found evidence of biological changes that may help explain why: they detected changes in biomarkers of metabolism, inflammation, insulin resistance and more. Results are published in JAMA.
“For women who want to live longer, our study says watch your diet! The good news is that following a Mediterranean dietary pattern could result in about one quarter reduction in risk of death over more than 25 years with benefit for both cancer and cardiovascular mortality, the top causes of death in women (and men) in the US and globally,” said senior author Samia Mora, MD, a cardiologist and the director of the Center for Lipid Metabolomics at the Brigham.
The Mediterranean diet is a plant-based diverse diet that is rich in plants (nuts, seeds, fruits, vegetables, whole grains, legumes). The main fat is olive oil (usually extra virgin), and the diet additionally includes moderate intake of fish, poultry, dairy, eggs, and alcohol, and rare consumption of meats, sweets, and processed foods.
The current study investigated the long-term benefit of adherence to a Mediterranean diet in a U.S. population recruited as part of the Women’s Health Study, and explored the biological mechanisms that may explain the diet’s health benefits. The study investigators evaluated a panel of approximately 40 biomarkers representing various biological pathways and clinical risk factors.
Biomarkers of metabolism and inflammation made the largest contribution, followed by triglyceride-rich lipoproteins, adiposity, insulin resistance. Other biological pathways relate to branched-chain amino acids, high-density lipoproteins, low-density lipoproteins, glycemic measures, and hypertension have smaller contribution.
“Our research provides significant public health insight: even modest changes in established risk factors for metabolic diseases — particularly those linked to small molecule metabolites, inflammation, triglyceride-rich lipoproteins, obesity, and insulin resistance — can yield substantial long-term benefits from following a Mediterranean diet. This finding underscores the potential of encouraging healthier dietary habits to reduce the overall risk of mortality,” said lead author Shafqat Ahmad, PhD, an associate professor of Epidemiology at Uppsala University Sweden and a researcher in the Center for Lipid Metabolomics and the Division of Preventive Medicine at the Brigham.
The current study identifies important biological pathways that may help explain all-cause mortality risk. However, the authors note some key limitations, including that the study was limited to middle aged and older well-educated female health professionals who were predominantly non-Hispanic and white. The study relied on food-frequency questionnaires and other self-reported measures, such as height, weight and blood pressure. But the study’s strengths include its large scale and long follow up period.
The authors also note that as the concept of the Mediterranean diet has gained popularity, the diet has been adapted in different countries and cultures.
“The health benefits of the Mediterranean diet are recognized by medical professionals, and our study offers insights into why the diet may be so beneficial. Public health policies should promote the healthful dietary attributes of the Mediterranean diet and should discourage unhealthy adaptations,” said Mora.

New research shows that people who develop dementia often begin falling behind on bills years earlier.Long before people develop dementia, they often begin falling behind on mortgage payments, credit card bills and other financial obligations, new research shows.A team of economists and medical experts at the Federal Reserve Bank of New York and Georgetown University combined Medicare records with data from Equifax, the credit bureau, to study how people’s borrowing behavior changed in the years before and after a diagnosis of Alzheimer’s or a similar disorder.What they found was striking: Credit scores among people who later develop dementia begin falling sharply long before their disease is formally identified. A year before diagnosis, these people were 17.2 percent more likely to be delinquent on their mortgage payments than before the onset of the disease, and 34.3 percent more likely to be delinquent on their credit card bills. The issues start even earlier: The study finds evidence of people falling behind on their debts five years before diagnosis.“The results are striking in both their clarity and their consistency,” said Carole Roan Gresenz, a Georgetown University economist who was one of the study’s authors. Credit scores and delinquencies, she said, “consistently worsen over time as diagnosis approaches, and so it literally mirrors the changes in cognitive decline that we’re observing.”The research adds to a growing body of work documenting what many Alzheimer’s patients and their families already know: Decision-making, including on financial matters, can begin to deteriorate long before a diagnosis is made or even suspected. People who are starting to experience cognitive decline may miss payments, make impulsive purchases or put money into risky investments they would not have considered before the disease.“There’s not just getting forgetful, but our risk tolerance changes,” said Lauren Hersch Nicholas, a professor at the University of Colorado School of Medicine who has studied dementia’s impact on people’s finances. “It might seem suddenly like a good move to move a diversified financial portfolio into some stock that someone recommended.”Tell us about your family’s challenges with money management and Alzheimer’s.

Some say that becoming as dull as a rock is an effective way to disengage.Take a moment to imagine a small gray rock sitting in the palm of your hand. It’s silent, smooth and otherwise unremarkable.Are you bored yet? If so, that’s kind of the point.Most people will eventually lose interest in a dull piece of granite. So there’s a theory percolating online that if you adopt the qualities of a stone, becoming impassive and bland, then you will repel the argumentative, antagonistic people in your life who are itching for conflict.It’s called the “gray rock” method, and over the last decade it has spread on social media, including among TikTok influencers, who have shared strategies to channel your inner rock. It even surfaced on a recent episode of the reality show “Vanderpump Rules,” when a cast member, Ariana Madix, said that using the technique had helped her avoid toxic interactions with her ex-boyfriend, Tom Sandoval, who had been unfaithful.The goal of the gray rock technique is to disengage without ending contact, said Ramani Durvasula, a clinical psychologist and the author of “It’s Not You: Identifying and Healing From Narcissistic People.” People who gray rock remain neutral, keep their interactions “trim and slim,” and avoid sharing information that could potentially be turned against them, she added.But while some psychologists say that the method is helpful under certain circumstances, it isn’t always the right solution.How does ‘gray rocking’ work?There isn’t an official set of rules for gray rocking. The method has not been studied, nor is it derived from an evidence-based psychological practice.We are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber? Log in.Want all of The Times? Subscribe.

27 minutes agoFergus Walsh

Amphetamine is a psychostimulant that has been used to treat a variety of brain dysfunctions. However, it is a highly abused drug. In fact, amphetamine and amphetamine-derived compounds such as methamphetamine (Meth) are among the most abused psychostimulants in the world.
The neurological effects caused by acute or chronic use of amphetamine have been broadly investigated and several studies have shown that proteins involved in the synthesis, storage, release and reuptake of dopamine (DA), a neurotransmitter that plays a role as in the “reward” center, are either direct targets of or are indirectly affected by these drugs.
During pregnancy, the effects of therapeutical doses of amphetamine have been investigated on birth outcomes in humans. However, a thorough investigation of the mechanisms underlying the long-term effects of embryonal exposure to addictive doses of amphetamine remains largely unexplored.
Using a tiny worm, C. elegans, Florida Atlantic University researchers are the first who investigate the underlying mechanisms within the embryo after exposure to high concentrations of amphetamines, uncovering their long-lasting effects.
For the study, researchers examined whether exposure to high doses of amphetamine throughout embryogenesis causes changes in the expression and function of two major dopaminergic proteins, tyrosine hydroxylase (TH) and vesicular monoamine transporter (VMAT). TH and VMAT both play important roles in the synthesis, storage and release of dopamine — critical for various brain functions and behaviors.
Results of the study, published in the International Journal of Molecular Sciences, show that following exposure to high doses of amphetamine during embryogenesis, the expression of specific genes in the dopaminergic system (dopamine transporter, TH and VMAT) is altered in adult C. elegans via epigenetic mechanisms. These modifications in gene and, consequently, proteins expression cause behavioral changes in adult animals such that animals that received amphetamine during embryogenesis were more susceptible to amphetamine-induced behaviors.
“The dopaminergic response to amphetamines and the mechanisms underlying histone methylation are highly conserved across diverse species, which is why we used C. elegans to examine the long-term effects caused by embryonal exposure to amphetamines,” said Lucia Carvelli, Ph.D., senior author and an associate professor of neuroscience, FAU Harriet L. Wilkes Honors College and a member of the FAU Stiles-Nicholson Brain Institute. “Importantly, although we used C. elegans as a model system, our goal is to understand how amphetamine works in humans.”
One advantage of the model the researchers used is that C. elegans embryos can develop outside the uterus and in the absence of maternal care.

“Our results were not influenced by possible amphetamine-induced epigenetic or behavioral modifications passed through maternal care, but they are a direct consequence of biological alterations at the embryo,” said Carvelli.
Behavioral data from the research show that, following embryonic exposure to amphetamine, adult animals exhibit an increased response to amphetamines. This suggests that the altered expression of TH and VMAT caused by continuous exposure to amphetamines during embryogenesis generates animals that are hypersensitive to amphetamines.
“Since our results are in agreement with data showing that mice overexpressing TH exhibit enhanced amphetamine-induced behaviors, and that rats chronically treated with amphetamine exhibit a long-lasting increase in striatal reuptake of dopamine, our findings establish C. elegans as an efficient and inexpensive model to study the long-lasting physiological modifications caused by prenatal exposure to amphetamine,” said Carvelli.
Study co-authors are Tao Ke, Ph.D., a post-doctoral researcher in the Carvelli lab; Kate E. Poquette, an undergraduate FAU student; and Sophia L. Amro Gazze, a student at FAU High School.
This research was funded by the National Institute on Drug Abuse, National Institutes of Health (grant No. DA042156), awarded to Carvelli.

UC Santa Barbara researchers are building out the repertoire of chemical reactions, using light. In a paper published in the journal Nature, chemistry professor Yang Yang and collaborators at the University of Pittsburgh report a method using photobiocatalysis to produce non-canonical (not naturally occurring) amino acids that are valuable building blocks of peptide therapeutics, bioactive natural products and novel functional proteins.
“So many efforts have been made in the field of biocatalysis, and we are now at a point where we can rationally design entirely new enzymatic reactions which are unprecedented in either chemistry or biology,” Yang said.
Most efforts in the field of biocatalysis, or the acceleration of chemical reactions via enzymes — nature’s privileged catalysts — have leaned toward optimizing natural enzyme functions that are useful to synthetic chemistry, or repurposing natural enzymes to facilitate unnatural reactions known to synthetic chemistry. Despite a decade of extensive research, there are only a handful of examples of enzymatic reactions that are both new-to-nature and new-to-synthetic chemistry. “What we are interested in is essentially to discover entirely new enzymatic reactions and general modes of enzyme catalysis,” he added.
Enter photobiocatalysis, in which light is used to excite enzymes to generate energy (often in the form of free radicals) to convert one molecule into another. A relatively young field of chemistry, photobiocatalysis takes advantage of the selectivity and efficiency of enzymes and combines that with the versatility and sustainability of light to create new processes, and in this case, non-canonical amino acids.
Interacting catalytic processes
For this study, the research team focused on pyridoxal-phosphate (PLP)-dependent enzymes, a large family of enzymes that are responsible for the metabolism of amino acids. They developed an interacting, triple catalytic cycle in which a photocatalyst — an iridium-based compound — is exposed to light, initiating a process that generates a transient free radical, while a second cycle using light regenerates the photocatalyst.
Concurrently, the biocatalysis cycle using a PLP enzyme modifies the amino acid substrate via a series of activation steps unique to PLP biochemistry. The free radical generated from photochemistry comes into play here, entering the enzyme active site and engaging the enzymatic intermediate to enable new chemistry. This cooperation between the enzyme and the photocatalyst allows the production of non-canonical amino acid product.
The altering of, in this case, common amino acid molecular structures, adds new features and capabilities to these acids. In creating a new carbon-carbon bond to the critical “alpha carbon,” of the amino acid, Yang said, it becomes possible to use this “backbone” to design a range of novel amino acids that could in turn perform new, unique and desirable functions as the basis of new therapeutics and natural products. “This is the first demonstration of pyridoxical biocatalysis via radical-mediated alpha functionalization of abundant amino acid substrates,” Yang pointed out.
Additionally, the highly efficient process is both stereoselective, meaning it can select for a preferred three-dimensional “shape” of the resulting amino acid, and it eliminates the extra steps of adding and removing “protecting groups,” or compounds that mask certain reactive areas on molecules to prevent unwanted chemical reactions in those regions.
“We’ve uncovered interesting interactions between the photocatalyst and the enzyme,” said Yang, whose group is studying how to further improve the interactions between the two catalysts. “I think this is going to lead to new fundamental science, both from a synthetic chemistry standpoint and also an enzymology standpoint.”

A Stanford Medicine study of thousands of breast cancers has found that the gene sequences we inherit at conception are powerful predictors of the breast cancer type we might develop decades later and how deadly it might be.
The study challenges the dogma that most cancers arise as the result of random mutations that accumulate during our lifetimes. Instead, it points to the active involvement of gene sequences we inherit from our parents — what’s known as your germline genome — in determining whether cells bearing potential cancer-causing mutations are recognized and eliminated by the immune system or skitter under the radar to become nascent cancers.
“Apart from a few highly penetrant genes that confer significant cancer risk, the role of heredity factors remains poorly understood, and most malignancies are assumed to result from random errors during cell division or bad luck,” said Christina Curtis, PhD, the RZ Cao Professor of Medicine and a professor of genetics and of biomedical data science. “This would imply that tumor initiation is random, but that is not what we observe. Rather, we find that the path to tumor development is constrained by hereditary factors and immunity. This new result unearths a new class of biomarkers to forecast tumor progression and an entirely new way of understanding breast cancer origins.”
Curtis is the senior author of the study, which will be published May 31 in Science. Postdoctoral scholar Kathleen Houlahan, PhD, is the lead author of the research.
“Back in 2015, we had posited that some tumors are ‘born to be bad’ — meaning that their malignant and even metastatic potential is determined early in the disease course,” Curtis said. “We and others have since corroborated this finding across multiple tumors, but these findings cast a whole new light on just how early this happens.”
A new take on cancer’s origin
The study, which gives a nuanced and powerful new understanding of the interplay between newly arisen cancer cells and the immune system, is likely to help researchers and clinicians better predict and combat breast tumors.

Currently, only a few high-profile cancer-associated mutations in genes are regularly used to predict cancers. Those include BRCA1 and BRCA2, which occur in about one of every 500 women and confer an increased risk of breast or ovarian cancer, and rarer mutations in a gene called TP53 that causes a disease called Li Fraumeni syndrome, which predisposes to childhood and adult-onset tumors.
The findings indicate there are tens or hundreds of additional gene variants — identifiable in healthy people — pulling the strings that determine why some people remain cancer-free throughout their lives.
“Our findings not only explain which subtype of breast cancer an individual is likely to develop,” Houlahan said, “but they also hint at how aggressive and prone to metastasizing that subtype will be. Beyond that, we anticipate that these inherited variants may influence a person’s risk of developing breast cancer.”
The genes we inherit from our parents are known as our germline genome. They’re mirrors of our parents’ genetic makeup, and they can vary among people in small ways that give some of us blue eyes, brown hair or type O blood. Some inherited genes include mutations that confer increased cancer risk from the get-go, such as BRCA1, BRCA2 and TP53. But identifying other germline mutations strongly associated with future cancers has proven difficult.
In contrast, most cancer-associated genes are part of what’s known as our somatic genome. As we live our lives, our cells divide and die in the tens of millions. Each time the DNA in a cell is copied, mistakes happen and mutations can accumulate. DNA in tumors is often compared with the germline genomes in blood or normal tissues in an individual to pinpoint which changes likely led to the cell’s cancerous transformation.
Classifying breast cancers
In 2012, Curtis began a deep dive — assisted by machine learning — into the types of somatic mutations that occur in thousands of breast cancers. She was eventually able to categorize the disease into 11 subtypes with varying prognoses and risk of recurrence, finding that four of the 11 groups were significantly more likely to recur even 10 or 20 years after diagnosis — critical information for clinicians making treatment decisions and discussing long-term prognoses with their patients.

Prior studies had shown that people with inherited BRCA1 or BRCA2 mutations tend to develop a subtype of breast cancer known as triple negative breast cancer. This correlation implies some behind-the-scenes shenanigans by the germline genome that affects what subtype of breast cancer someone might develop.
“We wanted to understand how inherited DNA might sculpt how a tumor evolves,” Houlahan said. To do so, they took a close look at the immune system.
It’s a quirk of biology that even healthy cells routinely decorate their outer membranes with small chunks of the proteins they have bobbing in their cytoplasm — an outward display that reflects their inner style.
The foundations for this display are what’s known as HLA proteins, and they are highly variable among individuals. Like fashion police, immune cells called T cells prowl the body looking for any suspicious or overly flashy bling (called epitopes) that might signal something is amiss inside the cell. A cell infected with a virus will display bits of viral proteins; a sick or cancerous cell will adorn itself with abnormal proteins. These faux pas trigger the T cells to destroy the offenders.
Houlahan and Curtis decided to focus on oncogenes, normal genes that, when mutated, can free a cell from regulatory pathways meant to keep it on the straight and narrow. Often, these mutations take the form of multiple copies of the normal gene, arranged nose to tail along the DNA — the result of a kind of genomic stutter called amplification. Amplifications in specific oncogenes drive different cancer pathways and were used to differentiate one breast cancer subtype from another in Curtis’ original studies.
The importance of bling
The researchers wondered whether highly recognizable epitopes would be more likely to attract T cells’ attention than other, more modest displays (think golf-ball-sized, dangly turquoise earrings versus a simple silver stud). If so, a cell that had inherited a flashy version of an oncogene might be less able to pull off its amplification without alerting the immune system than a cell with a more modest version of the same gene. (One pair of overly gaudy turquoise earrings can be excused; five pairs might cause a patrolling fashionista T cell to switch from tutting to terminating.)
The researchers studied nearly 6,000 breast tumors spanning various stages of disease to learn whether the subtype of each tumor correlated with the patients’ germline oncogene sequences. They found that people who had inherited an oncogene with a high germline epitope burden (read: lots of bling) — and an HLA type that can display that epitope prominently — were significantly less likely to develop breast cancer subtypes in which that oncogene is amplified.
There was a surprise, though. The researchers found that cancers with a large germline epitope burden that manage to escape the roving immune cells early in their development tended to be more aggressive and have a poorer prognosis than their more subdued peers.
“At the early, pre-invasive stage, a high germline epitope burden is protective against cancer,” Houlahan said. “But once it’s been forced to wrestle with the immune system and come up with mechanisms to overcome it, tumors with high germline epitope burden are more aggressive and prone to metastasis. The pattern flips during tumor progression.”
“Basically, there is a tug of war between tumor and immune cells,” Curtis said. “In the preinvasive setting, the nascent tumor may initially be more susceptible to immune surveillance and destruction. Indeed, many tumors are likely eliminated in this manner and go unnoticed. However, the immune system does not always win. Some tumor cells may not be eliminated and those that persist develop ways to evade immune recognition and destruction. Our findings shed light on this opaque process and may inform the optimal timing of therapeutic intervention, as well as how to make an immunologically cold tumor become hot, rendering it more sensitive to therapy.”
The researchers envision a future when the germline genome is used to further stratify the 11 breast cancer subtypes identified by Curtis to guide treatment decisions and improve prognoses and monitoring for recurrence. The study’s findings may also give additional clues in the hunt for personalized cancer immunotherapies and may enable clinicians to one day predict a healthy person’s risk of cancer from a simple blood sample.
“We started with a bold hypothesis,” Curtis said. “The field had not thought about tumor origins and evolution in this way. We’re examining other cancers through this new lens of heredity and acquired factors and tumor-immune co-evolution.”
The study was funded by the National Institutes of Health (grants DP1-CA238296 and U54CA261719), the Canadian Institutes of Health Research and the Chan Zuckerberg Biohub.