MEDICINE
Scientists unravel key steps in the road to DNA repair
Insights into homologous recombination (HR) promise new insights into cancer
IMAGE:
TWO COMPETING MODELS EXIST FOR HOMOLOGOUS RECOMBINATION. THE RESULTS OF THIS STUDY SUPPORT A MODEL WHERE THE DOUBLE-STRANDED DNA IS NOT UNWOUND DURING THE HOMOLOGY SEARCH. (SHIBATA ET AL. NUCLEIC ACIDS RESEARCH, IN PRESS, DOI: 10.1093/NAR/GKAD1260, WITH MODIFICATION)
view moreCREDIT: TOKYO METROPOLITAN UNIVERSITY
Tokyo, Japan – Researchers from Tokyo Metropolitan University have been studying DNA repair by homologous recombination, where the RecA protein repairs breaks in double-stranded DNA by incorporating a dangling single-strand end into intact double strands, and repairing the break based on the undamaged sequence. They discovered that RecA finds where to put the single strand into the double helix without unwinding it by even a single turn. Their findings promise new directions in cancer research.
Homologous recombination (HR) is a ubiquitous biochemical process shared across all living things, including animals, plants, fungi, and bacteria. As we go about our daily lives, our DNA is subjected to all kinds of environmental and internal stress, some of which can lead to breakage of both strands in the double helix. This can be disastrous, and lead to imminent cell death. Luckily, processes like HR are continuously repairing this damage.
During HR, one of the two exposed ends of the break in the helix falls away, revealing an exposed single-stranded end; this is known as resection. Then, a protein known as RecA (or some equivalent) binds to the exposed single strand and an intact double strand nearby. Next, the protein “searches” for the same sequence. When it finds the right place, it recombines the single strand into the double helix in a process known as strand invasion. The broken DNA strand is subsequently repaired using the existing DNA as a template. HR enables accurate repair of double-strand breaks, as well as the exchange of genetic information, making it a key part of biodiversity. But the exact biochemical picture of HR, including what happens when RecA carries both the single and double strands, is not yet clear.
A team led by Professor Kouji Hirota of Tokyo Metropolitan University has been studying DNA repair mechanisms like HR. In their most recent work, they sought to test two competing models for what happens when HR occurs. In one, RecA unwinds a section of the double strand during the “homology search,” where it tries to find the right place for strand invasion to occur. In the second, there is no unwinding after the binding of RecA; only when strand invasion takes place does any unwinding occur.
The team, in cooperation with a team from the Tokyo Metropolitan Institute of Medical Science, adopted two approaches to tackle which of these actually happens. In the first, they used a mutant of RecA which cannot separate the double strands i.e. cannot unwind the strand, to see whether this affected DNA repair. It turns out that this has minimal effect. In the second, they tried to measure how much torsion was created in the strand at different stages of the process. They found that the only torsion due to unwinding they could detect occurred after the homology search was complete i.e. when strand invasion occurred. For the first time, the team clearly showed that the second model was correct.
Detailed insights into homologous recombination are vital to understanding what happens when things go wrong. For example, factors implicated in breast cancer (BRCA1 and BRCA2) are also responsible for the correct loading of single-stranded DNA onto RAD51, the human version of RecA. This suggests that problems with HR might underlie high incidences of breast cancer in patients with hereditary defects in BRCA1 or BRCA2. The team hopes findings like theirs will lead to new directions for research into cancer.
This work was supported by JSPS KAKENHI Grant Number JP22K06335.
JOURNAL
Nucleic Acids Research
ARTICLE TITLE
Homology recognition without double-stranded DNA-str and separ ation in D-loop f ormation b y RecA
ARTICLE PUBLICATION DATE
20-Jan-2024
Remodeling the immune system to fight tuberculosis
Collaborative team from UMass Amherst and Seattle Children’s Research Institute uncovers how prior exposure to bacteria changes the lung’s innate immune response—and what it might mean for vaccines
Peer-Reviewed PublicationIMAGE:
INFECTION OF THE ALVEOLAR MACROPHAGES IS TUBERCULOSIS’S FIRST STEP—WHAT IF WE COULD CHANGE THAT?
view moreCREDIT: ALISSA ROTHCHILD
AMHERST, Mass. – Tuberculosis, caused by the bacterium Mycobacterium tuberculosis (Mtb) kills upwards of 1.6 million people a year, making it one of the leading causes of death by an infectious agent worldwide—and that number is only growing larger. How, exactly, Mtb evades the immune system isn’t yet known, but a collaborative team of researchers from the University of Massachusetts Amherst and Seattle Children’s Research Institute recently discovered something surprising: prior exposure to a genus of bacteria called Mycobacterium seems to remodel the first-line defenders in the body’s immune system. Furthermore, how those cells are remodeled depends on exactly how the body is exposed. These results, published recently in PLOS Pathogens, suggest that a more integrated treatment approach that targets all aspects of the immune response could be a more effective strategy in the fight against tuberculosis.
“We breathe in thousands of liters of air every day,” says Alissa Rothchild, assistant professor in the Veterinary and Animal Sciences Department at UMass Amherst and the paper’s senior author. “This essential process makes us incredibly vulnerable to inhalation of all sorts of potentially infectious pathogens that our immune systems have to respond to.”
Systems, plural. When we think of immunity, we typically think of the adaptive immune system, which is when prior exposure to a pathogen—say, a weakened version of chickenpox—teaches the immune system what to guard against. Vaccination is the most common tool that we use to teach our adaptive immune systems what to look out for.
While the adaptive immune system is the major focus of most vaccine research (think protective antibodies induced by COVID-19 vaccines), it is not the body’s first responder—that would be the innate immune system and its ranks of macrophages. The macrophages are the first-line defenders in the tissues that recognize and destroy pathogens and also call for backup. One way they do this by turning on different inflammatory programs that can change the tissue environment.
In the case of the lungs, these macrophages are called alveolar macrophages (AMs). They live in the lung’s alveoli, the tiny air sacs where oxygen passes into the bloodstream—but, as Rothchild has shown in a previous paper, AMs don’t mount a robust immune response when they’re initially infected by Mtb. This lack of response seems to be a chink in the body’s armor that Mtb exploits to such devastating effect. “Mtb takes advantage of the immune response,” says Rothchild, “and when they infect an AM, they can replicate inside of it for a week or longer. They effectively turn the AM into a Trojan Horse in which the bacteria can hide from the body’s defenses.”
“But what if we could change this first step in the chain of infection?” Rothchild continues. “What if the AMs responded more effectively to Mtb? How could we change the body’s innate immune response? Studies over the last 10 years or so have demonstrated that the innate immune system is capable of undergoing long-term changes, but we are only beginning to understand the underlying mechanisms behind them.”
To test conditions where the innate immune response might be remodeled, Dat Mai, a research associate at Seattle Children’s Research Institute and the first author of the paper, Rothchild and their colleagues designed an experiment using two different mouse models. The first model used the BCG vaccination, one of the world’s most widely distributed vaccines and the only vaccine used for tuberculosis. In the second model, the researchers induced a contained Mtb infection, which they previously showed protects against subsequent infections in a form of concomitant immunity.
Weeks after exposure, the researchers challenged the mice with aerosolized Mtb and infected macrophages were taken from each mouse model for RNA sequencing. There were striking differences in the RNA from each set of models.
While both sets of AMs showed a stronger pro-inflammatory response to Mtb than AMs from unexposed mice, the BCG-vaccinated AMs strongly turned on one type of inflammatory program, driven by interferons, while the AMs from the contained Mtb infection turned on a qualitatively different inflammatory program. Other experiments showed that the different exposure scenarios changed the AMs themselves, and that some of these changes seem to be dependent on the greater lung environment.
“What this tells us,” says Rothchild, “is that there’s a great deal of plasticity in the macrophage response, and that there’s potential to therapeutically harness this plasticity so that we can remodel the innate immune system to fight tuberculosis.”
This research, which was supported by the National Institutes of Health and the National Institute of Allergy and Infectious Disease, is part of a much bigger, global, cross-species effort to comprehensively understand the immune responses to eliminate tuberculosis, called IMPAc-TB, for Immune Mechanisms of Protection Against Mycobacterium Tuberculosis.
Dr. Kevin Urdahl, professor of pediatrics at Seattle Children’s Research Institute, lead PI for this IMPAc-TB consortium, and one of the paper’s co-authors, says that “the overall goal of the program is to elucidate how the immune system effectively controls or eradicates the bacteria that causes tuberculosis so that effective vaccines can be developed. This is an important part of the larger IMPAc-TB program because we will be assessing the responses of human alveolar macrophages recovered from individuals who have recently been exposed to Mycobacterium tuberculosis in a TB endemic region. The findings of Rothchild’s team will help us interpret and understand the results we obtain from the human cells.”
Mycobacterium tuberculosis-infected alveolar macrophages at day 10 after infection. Mtb in green.
JOURNAL
PLoS Pathogens
ARTICLE TITLE
Exposure to Mycobacterium remodels alveolar macrophages and the early innate response to Mycobacterium tuberculosis infection
ARTICLE PUBLICATION DATE
18-Jan-2024
Semen microbiome health may impact male fertility
A new study finds that a small group of microorganisms may be influencing sperm motility
You may have heard about the gut microbiome and its influence on a person’s overall health and well-being. It turns out that the same may hold true for the semen microbiome.
According to researchers from the Department of Urology at UCLA, the semen microbiota might play a crucial role in influencing sperm parameters and enhancing male fertility. Considering recent studies highlighting the microbiome’s significance in overall human health, researchers investigated the semen microbiome to understand its potential impact on male infertility. Exploring the functions of these microorganisms in semen could potentially pave the way for developing treatments targeted at rectifying any issues with sperm parameters.
The study found that one microbe in particular, Lactobacillus iners, may have a direct negative impact on male fertility. Researchers found that men with more of this microbe were more likely to have issues with sperm motility. Previous research revealed that Lactobacillus iners can preferentially produce L-lactic acid, potentially leading to a pro-inflammatory environment locally, which could adversely affect sperm motility. The study authors point out that existing research has hinted at the link between this microbe and fertility, but most of the literature pertains to the vaginal microbiome and female factors. This is the first study to report a negative association between the microbe and male-factor fertility.
Researchers also discovered that three types of bacteria in the Pseudomonas group were present in patients with both normal and abnormal sperm concentrations. Microbes called Pseudomonas fluorescens and Pseudomonas stutzeri were more common in patients with abnormal sperm concentrations, while Pseudomonas putida was less common in samples with abnormal sperm concentrations. However, the findings indicate that not every member of the same closely related group may affect fertility in the same way, whether positively or negatively. In other words, even closely related microbes may not always have the same direct correlation to fertility.
“There is much more to explore regarding the microbiome and its connection to male infertility,” said Vadim Osadchiy, a resident in the Department of Urology at UCLA and the lead author of the study. “However, these findings provide valuable insights that can lead us in the right direction for a deeper understanding of this correlation. Our research aligns with evidence from smaller studies and will pave the way for future, more comprehensive investigations to unravel the complex relationship between the semen microbiome and fertility.”
Article: Semen microbiota are dramatically altered in men with abnormal sperm parameters, Published January 2024, https://doi.org/10.1038/s41598-024-51686-4.
JOURNAL
Scientific Reports
METHOD OF RESEARCH
Observational study
SUBJECT OF RESEARCH
People
ARTICLE TITLE
Semen microbiota are dramatically altered in men with abnormal sperm parameters
No benefit of physiotherapy over general advice after dislocated shoulder
Findings should help inform discussions about the best approach to rehabilitation
Routinely referring patients to a tailored programme of physiotherapy after a dislocated shoulder is no better than a single session of advice, supporting materials and the option to self-refer to physiotherapy, finds a clinical trial published by The BMJ today.
The findings should help clinicians and patients have informed discussions about the best approach to non-operative rehabilitation, say the researchers.
The shoulder is the most frequently dislocated joint, with rates highest in men aged 16-20 years (805 per 100,000 person years) due to sporting injuries and in women aged 61-70 years (28 per 100,000 person years) due to falls.
Non-operative management is the most common treatment after a first dislocation. This can range from an advice sheet only to a programme of individually tailored physiotherapy over several months, but no previous trial evidence is available to inform the best approach.
To explore this further, researchers set out to assess the effects of two rehabilitation interventions in adults with a first time traumatic shoulder dislocation at 40 NHS hospitals across the UK between November 2018 and March 2022.
All participants (66% male; average age 45 years) initially had their arm supported in a sling and received a physiotherapy advice session within six weeks of their injury, which included a shoulder examination plus advice and support materials to aid self-management.
After this session, 240 participants were randomly assigned to advice only (no further treatment) and 242 were offered additional physiotherapy sessions, each lasting for up to 30 minutes over four months.
The main measure of interest was shoulder function on the Oxford shoulder instability score (a 0-48 point scale) reported by patients after six months.
No clinically relevant differences in shoulder scores were found between the two groups at six months or in other measures, including a questionnaire on physical function of the arm, shoulder and hand. Complications were also similar across the two groups
This is the largest trial on the topic to date, although the researchers acknowledge that just over a quarter of participants were lost to follow up. However, further analysis, accounting for missing data, gave similar results, providing reassurance that the conclusions are robust.
As such they say, until now, no strong evidence was available to guide rehabilitation management following an initial two weeks support in a sling. “We now know an additional programme of individually tailored physiotherapy is not superior to advice, supporting materials, and an option to self-refer to physiotherapy.”
“Knowing that an individually tailored programme of physiotherapy is not superior will enable clinicians and patients to have evidenced informed discussions about the best approach to non-operative rehabilitation,” they conclude.
This randomised clinical trial was well planned, executed, and reported, say researchers in a linked editorial.
The results show that physiotherapy-led rehabilitation, including generalised range of movement and strengthening exercises (mainly below shoulder height), plus patient advice, confers minimal advantage over advice and education alone.
However, they say caution is needed when extrapolating these results, particularly concerning younger patients wishing to return to sports, occupations, or activities with high shoulder loads.
JOURNAL
The BMJ
METHOD OF RESEARCH
Randomized controlled/clinical trial
SUBJECT OF RESEARCH
People
ARTICLE TITLE
Acute rehabilitation following traumatic anterior shoulder dislocation (ARTISAN): pragmatic, multicentre, randomised controlled trial
ARTICLE PUBLICATION DATE
17-Jan-2024
COI STATEMENT
All authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: all authors had financial support from National Institute for Health Research for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years. RSK is co-chair of the NIHR Programme Grants for Applied Research committee, a paid position in NIHR but unrelated to the trial. She is also a previous chair of the NIHR West Midlands Research for Patient Benefit ( committee and member of the NIHR Health Technology Assessment Clinical Evaluation and Trials Committee and NIHR Integrated Clinical Academic doctoral committee. RSK, DE, HP, AH, JM, HN, SD, CM, HB, DT, and MU have all been awarded current and previous NIHR research grants. HP, MU, and RSK are co-investigators on grants funded by the Australian NHMRC and NIHR funded studies receiving additional support from Stryker Ltd MU is a co-investigator on a grant funded by Norwegian Medical Research Council. He is a director and shareholder of Clinvivo Ltd that provides electronic data collection for health services research. He is part of an academic partnership with Serco Ltd, funded by the European Social Fund, related to return-to-work initiatives. They declare that there are no other relationships or activities that could appear to have influenced the submitted work
Concerns over new laws that could end use of Whatsapp in the NHS
Patient care will suffer, warn doctors
UK law changes pose a threat to the security of messaging apps – and therefore their use in the NHS. In The BMJ today, doctors warn that patient care will suffer if they can no longer use apps such asWhatsApp and Signal to share information.
In March 2020, in the face of the pandemic, clinicians were officially allowed to use messaging services such as WhatsApp “where the benefits outweigh the risk,” reversing years of caution about their use in patient care – provided the apps used encryption, explains journalist Stephen Armstrong.
The most recent NHS England advice continues that policy, advising healthcare workers to use two-step verification and disable message notifications on the lock-screen.
And yet two recent pieces of legislation – one passed and one pending – threaten the use of any end-to-end encrypted messaging in the NHS.
October’s Online Safety Act instructs the UK communications regulator Ofcom to monitor user-to-user apps and software, while an amendment to the Investigatory Powers Act – expected in the spring – says technology companies can’t introduce new security software or make any significant changes to the security of their existing service without UK government approval.
What this means, in effect, is that the government will have installed surveillance of all encrypted messaging, making it impossible to be sure patient data is secure, writes Armstrong.
Not only that, but the app providers – including major tech companies such as Meta, owner of WhatsApp and Facebook, Apple and Signal – have warned that the new requirements may force them to withdraw services from the UK if it unduly impacts their ability to innovate and introduce new security features.
Marcus Baw, an emergency medicine and general practice doctor in Yorkshire, says if WhatsApp were to disappear, “we’d have an NHS wide problem immediately.”
Ross Anderson, professor of security engineering at Cambridge University, also points out that “as Signal and WhatsApp upgrade their software a number of times a week to deal with bugs or new threats, the UK would have to be treated like Burma or North Korea and simply avoided rather than wait for GCHQ approval – which could take months”.
“The combination of the IPA reforms and the online safety Act presents the possibility of a shocking level of state interference,” says Meredith Whittaker, president of Signal Foundation. “If the choice came down to adulterating the security features that allow us to keep the privacy promises we make to the people who rely on Signal in the NHS or leaving, we would leave.”
An Ofcom spokesperson told the BMJ they will use their new online safety powers “in a way that is compatible with rights to privacy and freedom of expression” and “won’t be reviewing all harmful online material or be able to read private online messages.”
But Mike Grocott, professor of anaesthesia and critical care medicine at the University of Southampton, argues that tech companies are not prepared to subject their apps to this level of government surveillance. If encrypted messaging apps withdraw from the UK, patient care would suffer, he says.
“Care is better when doctors can talk to each other,” agrees Sam Smith from patient privacy group MedConfidential. “For a range of situations doctors find themselves in, only a general app like WhatsApp is easy to use.”
For Marcus Baw, the entire problem could have been avoided if NHS IT leaders had had the vision to build an end-to-end encrypted NHS approved app linked to NHS mail.
His hope is that someone in government is going to realise the electoral foolishness of the two pieces of legislation. “The tech companies are serious,” he says. “Can you imagine the outcry from the population if WhatsApp withdraws from the UK? It would be an act of catastrophic self-harm by any government. Perhaps for once common sense will prevail.”
JOURNAL
The BMJ
METHOD OF RESEARCH
News article
SUBJECT OF RESEARCH
People
ARTICLE TITLE
What will happen if doctors can’t use WhatsApp?
ARTICLE PUBLICATION DATE
17-Jan-2024
COI STATEMENT
Stephen Armstrong is a journalist and author. He is paid to write about technology, medicine, science, politics, and culture for Wired, the Sunday Times, and the Daily Telegraph, among others. He has written books on the private security industry, the rise of oligarchs in the developing world, and poverty in the UK. He is a trustee of the Orwell Foundation and a fellow of the Royal Society of Arts. He owns no stock options or shares in any pharmaceutical, IT, or healthcare companies. He has a personal pension, which may invest in these types of companies.
New study is one of first to show people with evidence of any remission of diabetes from weight-loss trial had a 40% lower rate of cardiovascular disease and 33% lower rate of chronic kidney disease
DIABETOLOGIA
While several trials have shown that substantial weight loss using diet and lifestyle can reverse type 2 diabetes, new research published in Diabetologia (the journal of the European Association of the Study of Diabetes [EASD]) is among the first to show the subsequent impact of remission on cardiovascular outcomes. The study is by Professor Edward Gregg, Head of the School of Population Health, RCSI University of Medicine and Health Sciences, Dublin, Ireland, and colleagues.
The new study shows that in patients that took part in the Look AHEAD study, those with any evidence of remission had a 40% lower rate of cardiovascular disease (CVD) and 33% lower rate of chronic kidney disease (CKD).
The Look AHEAD study was a multi-centre RCT that compared the effect of a 12-year intensive lifestyle intervention (ILI) with that of diabetes support and education (DSE) on CVD and other long-term health conditions. The study, carried out between 2001 and 2016, recruited and randomised 5145 adults with overweight or obesity (BMI >25 kg/m2 for non-insulin users or BMI >27 kg/m2 for insulin users) aged 45–76 years with type 2 diabetes. The authors conducted an observational post hoc analysis of participants in both groups, classified them based on remission status, and then compared long-term outcomes (described below) based on any remission, and the duration of remission, over a period of 12 years. They compared the incidence of CVD and CKD among more than 4000 participants, respectively, based on achievement and duration of diabetes remission.
Participants were 58% female, and had a mean age of 59 years, a mean duration of diabetes of 6 years, and a mean BMI of 35.8 kg/m2 (in the range of severe obesity). The authors applied an epidemiological definition of remission: taking no diabetes medications and having a glycated haemoglobin (HbA1c – a measure of blood sugar control) of <48 mmol/mol (6.5%) at a single point in time.
The team defined high-risk or very high-risk CKD based on the Kidney Disease Improving Global Outcomes (KDIGO) criteria, and CVD incidence as any occurrence of non-fatal acute heart attack, stroke, admission for angina or CVD death.
Participants with evidence of any diabetes remission during follow-up had a 33% lower rate of CKD and a 40% lower rate of CVD in analyses adjusting for HbA1c, blood pressure, blood fats, CVD history, diabetes duration and intervention arm, compared to participants without remission. The magnitude of risk reduction was greatest for participants with evidence of longer-term remission.
The authors say they observed three main findings related to the implications of achieving diabetes remission. First, although 18% of participants achieved remission at some point during follow-up, the percentage of participants with current remission had decreased to 3% by the 8th year of the study, underlining the challenges of keeping weight off using lifestyle interventions. Second, despite the relatively short-lived durations of most episodes of remission, they found that any achievement of remission was associated with 33% and 40% lower rates of CKD and CVD, respectively, compared with participants who did not achieve remission, and risk reduction was even greater (55% and 49%, respectively) among those who had evidence of at least 4 years of remission (see table 2 and figure 2 of full paper) Third, participants with a short duration of diabetes, low starting HbA1c and a large magnitude of weight loss were most likely to experience remission. The authors conclude that the associations they found “may be explained by post-baseline improvements in weight, fitness, HbA1c and LDL (bad) cholesterol.”
Professor Gregg says: “As the first intervention study to associate remission with reduction of diabetes-related complications, this is encouraging news for those who can achieve remission from type 2 diabetes. While our study is also a reminder that maintenance of weight loss and remission is difficult, our findings suggests any success with remission is associated with later health benefits.”
JOURNAL
Diabetologia
ARTICLE TITLE
Impact of remission from type 2 diabetes on long‑term health outcomes: findings from the Look AHEAD study
ARTICLE PUBLICATION DATE
18-Jan-2024
COI STATEMENT
See full paper for disclosures
