25th Jun 2021
The ACGT hosted a webinar on the 28th of May 2021 presented by Dr Godfrey Kgatle and Ms Thabang Msimango from the University of Pretoria (UP). The webinar focused on how biotechnology can be used to curb the detrimental effects of micro-organisms in the Agricultural production sector.
Dr Kgatle, a plant pathologist based at UP’s Forestry and Agricultural Biotechnology Institute, is currently looking at creating baseline knowledge that is needed in order to address and refine management strategies for crop diseases. Dr Kgatle detailed how his work focuses on determining the distribution of crop diseases as well as surveilling potential emerging diseases. Dr Kgatle has been on 12 field trips so far in 2021. These field trips were aimed at building a collection of isolates associated with grain crops as well as building a catalogue of photographs of maize diseases. Dr Kgatle highlighted the need for a transdisciplinary research approach in combating plant diseases.
Ms Msimango’s presentation focused on how biotechnology can contribute to food safety. She presented her previous work that investigated the prevalence and characteristics of foodborne pathogens that were isolated from food that was supplied through school feeding programmes in South Africa. After analyzing samples from the water, fresh produce, soil, surfaces and hand swabs at the schools, Ms Msimango found the presence of E. coli and Staphylococcus aureus that exceeded normal levels. She also found that most of the E. coliisolates, detected mostly on fresh produce, were multi-drug resistant. Ms Msimango’s work indicated the need for improved food safety and sanitation strategies were food is prepared at the schools.
Following the discussions from the Q&A session after the presentations, Dr Kgatle emphasized the need for better non-invasive seed screening methods that would insure that the planted seeds are not diseased. The ACGT and Dr Kgatle will be looking at phenomics tools that could be utilized to screen seeds in order to give farmers a better yield.
Story by: ACGT
31st May 2021
Mortality in critically ill patients with COVID-19 is higher in African countries than reported from studies done in Asia, Europe, North America and South America. This is according to the findings of a study that was conducted by a team of African researchers, including experts from the University of Pretoria (UP), and recently published in peer-reviewed journal The Lancet.
Increased mortality was associated with insufficient critical-care resources, as well as comorbidities such as HIV/AIDS, diabetes, chronic liver disease and kidney disease, and the severity of organ dysfunction upon admission.
“Our study is the first to give a comprehensive picture of what is happening to people who are severely ill with COVID-19 in Africa, with data from multiple countries and hospitals,” says Professor Bruce Biccard of Groote Schuur Hospital in Cape Town and the University of Cape Town, who co-led the research. “Sadly, it indicates that our ability to provide sufficient care is compromised by a shortage of critical-care beds and limited resources within intensive-care units [ICU].”
Prof Biccard added that poor access to potential life-saving interventions such as dialysis, proning (turning patients onto their stomachs to improve breathing) and blood oxygen monitoring could be factors in the deaths of these patients, and could also partly explain why one in eight patients had therapy withdrawn or limited. “We hope these findings can help prioritise resources and guide the management of severely ill patients – and ultimately save lives – in resource-limited settings around the world.”
Until now, little had been known about how COVID-19 was affecting critically ill patients in Africa, as there have been no reported clinical outcomes data from Africa or any patient management data in low-resource settings. To address this evidence gap, the African COVID-19 Critical Care Outcomes Study (ACCCOS) aimed to identify which human and hospital resources, underlying conditions and critical-care interventions might be associated with mortality or survival in adults (aged 18 or older) admitted to intensive-care or high-care units in Africa.
The study focused on 64 hospitals in 10 countries (Egypt, Ethiopia, Ghana, Kenya, Libya, Malawi, Mozambique, Niger, Nigeria and South Africa). Between May and December 2020, about half (3 752 of 6 779) of patients with suspected or confirmed COVID-19 infection referred to critical care were admitted. Of those, 3 140 patients participated in the study. All received standard care and were followed up for at least 30 days unless they died or were discharged. Modelling was used to identify risk factors associated with death.
After 30 days, almost half (48% – 1 483/3 077) of the critically ill patients had died. The analysis estimates that death rates in these patients were 11% (in best-case scenarios) to 23% (in worst-case scenarios) higher than the global average of 31.5%.
“This collaborative landmark effort provides valuable information regarding the African COVID-19 experience among our critically ill patients,” says Prof Fathima Paruk, Clinical and Academic Head of the Critical Care Department at UP and the UP study site lead. “Unique findings – such as the high death rate, being male not being associated with a higher risk of death, ICU bed shortages, underuse of resources or a paucity of certain ICU resources – highlight the importance and need for our own data.”
Clinical services and critical care to patients revealed some important information. Prof Paruk and her team at UP’s Faculty of Health Sciences and Steve Biko Academic Hospital in Pretoria played a leading role in this important study. The impact of their findings will not only be seen on clinical training platforms, but will have an impact on patient care in Africa, says Prof Tiaan de Jager, Dean of UP’s Faculty of Health Sciences.
“Moving forward,” Prof Paruk adds, “the findings provide much-needed evidence in terms of guiding clinical management and in terms of the pressing need to ensure the appropriate provision, allocation and use of resources, so that we can save more lives in resource-limited settings. Furthermore, the high death rate among severely ill COVID-19 patients in Africa further strengthens the case for prevention through vaccination.”
“Africans are clearly at higher risk of more severe disease and death when COVID-19 positive,” adds Prof Robin Green, Chairman of the School of Medicine at UP. “This suggests that our population is desperately in need of better ICU resources and medications, but especially prevention through vaccination. The current vaccine roll-out in Africa is hopelessly ineffective. We would appeal to all humanitarian and health agencies to make vaccines for Africa a priority.”
“The Faculty of Health Sciences at UP, in particular our staff, has been at the forefront of the COVID-19 response,” says Prof De Jager. “The faculty has been preparing for this through the creation of research-driven teaching and learning platforms, informed by the demands of the fourth industrial revolution.”
Story by: Prof Fathima Paruk, for the University of Pretoria
31st May 2021
molecule made famous by its association with human heart disease and marine animals’ ability to survive high-pressure conditions turns out to be made by plants too, researchers report this week (May 19) in Science Advances. As it does in animals, trimethylamine N-oxide (TMAO) helps plants cope with stressful conditions, according to the study. The authors have already licensed the discovery to a company that is working to commercialize TMAO as a way to boost yields in agriculture.
“Nobody has published before that plants have TMAO in the tissues,” says study coauthor Rafael Catalá of the Centro de Investigaciones Biológicas (CIB) Margarita Salas in Madrid.
The new study grew out of earlier work in which Catalá and his colleagues looked for genes in the model plant Arabidopsis thaliana whose expression was changed by exposure to cold. One gene they found turned out to code for a type of enzyme called a flavin-containing monooxygenase (FMO) called FMOGS-OX5. In further analyses, reported in the current study, the team found that the expression of several other FMOgenes is also dialed up in Arabidopsis in response to cold.
FMOs are known to make TMAO in animals in response a variety of stressors. Wondering what the connection was between the FMOs and the plant’s cold response, the team used nuclear magnetic resonance to look for TMAO in wildtype Arabidopsis. They found it, and confirmed its presence with liquid chromatography–tandem mass spectrometry. The team also verified that FMOGS-OX5 can generate TMAO from its precursor, TMA, in vitro.
In animals, TMAO functions as an osmolyte, a type of molecule cells use to maintain the properties of their fluid and prevent proteins from becoming misfolded when confronted with conditions such as high salt concentrations. To see whether it plays a similar role in plants, Catalá and his colleagues treated Arabidopsisroots with tunicamycin, a compound that makes proteins unfold, as can happen under abiotic stress conditions such as cold or lack of water. The tunicamycin made the roots grow more slowly, but this effect was mitigated if the roots were grown in medium supplemented with TMAO, the researchers report.
When the researchers engineered Arabidopsis to overexpress FMOGS-OX5, the plant also increased the expression of 184 other genes, many of which had been previously linked to responses to abiotic stressors, the authors report. Applying TMAO to wildtype plants had a similar effect on gene expression, although it did not change FMOGS-OX5’s expression level, suggesting that TMAO acts downstream of FMO to enhance the expression of stress-response genes.
To find out whether TMAO is widespread in plant species, the team also looked for it in tomato, maize, barley, and a relative of tobacco, and found it was present in all of them. Moreover, their TMAO content rose when the plants were subjected to conditions of low water, high salt, or low temperatures (except barley, in which TMAO did not increase in the high-salt test but did in the other conditions). Spraying or watering tomato plants with a TMAO-containing solution made them visibly healthier, with more leaves, when they were exposed to each of the three stress conditions.
Catalá says externally applied TMAO has the potential to be “a very powerful tool for agriculture.” He and the paper’s senior author, Julio Salinas, also of the CIB Margarita Salas, have filed patents on the agricultural use of TMAO, which is being commercialized by the company Plant Response. The company’s field tests have had good results, Catalá adds.
Paul Verslues, who studies plant drought response at the Academia Sinica in Taipei, Taiwan, questions whether TMAO will be useful agriculturally. “TMAO protection of protein folding may be relevant to plant survival of severe stress but it is unknown whether it is also beneficial to protecting plant growth under less severe drought or salinity stress,” he writes in an email to The Scientist. The stresses the researchers subjected the plants to were too harsh to be reflective of agricultural conditions, and more experiments would be needed to determine whether TMAO also helps plants cope with milder stress conditions.
Verslues also notes other reservations about the study’s findings, including that Arabidopsis made to overexpress FMOGS-OX5 had greater stress tolerance than did wildtype plants but did not accumulate more TMAO, which he says suggests that FMOs may “also produce some other compound that promotes stress tolerance” apart from TMAO. Additionally, the authors did not take the step of knocking out all of a plant’s FMO genes to test whether those genes are truly required for TMAO production in plants.
Catalá argues that the study’s main finding, that TMAO exists in plants and has “a key role in plant tolerance to abiotic stress,” stands without testing such mutants. And he says it’s likely that FMOs do indeed produce other compounds involved in the stress response, but that the paper shows they are involved in making TMAO and that TMAO enhances stress tolerance.
Aleksandra Skirycz, a plant biologist at the Boyce Thompson Institute who was not involved in the study, calls it “a very nicely designed story.” For her, the “really exciting aspect of this work is that you have a molecule that would work as an osmolyte for protection [and] at the same time would probably have other signaling functions,” a phenomenon she calls “moonlighting.” It’s not yet clear how TMAO influences gene expression, Catalá says, and that will be an avenue for the group to pursue in the future.
In the biomedical literature, TMAO tends to come up in a negative context rather than a positive one, as high levels of it in patients’ blood have been linked to an elevated risk for blood clots. Studies have suggested that gut microbes break down choline, a nutrient present in high levels in meat, to generate TMAO and related compounds, providing a mechanistic link between a meat-heavy diet and risk of heart attack and stroke. Catalá says it’s not at all clear what implications, if any, the finding of TMAO in plants could have for human diet and health.
Story by: Shawna Williams for The Scientist
31st May 2021
Peter Mac researchers are developing a potential new way to make CAR T-cell therapy more effective against breast cancer and other solid cancers.
CAR T-cell therapy is a type of immunotherapy where a patient’s own immune cells are collected and reengineered, before being infused back into the patient to fight their cancer.
But CAR T-cells also contain a gene that can suppress this immune response. A Peter Mac-led study into this phenomenon has just been published in the scientific journal Nature Communications.
“Cancer hijacks these pathways to shut off an immune response that would otherwise be beneficial,” says Dr. Paul Beavis, one of the senior authors of the study.
Using a gene editing technique known as CRISPR, Dr. Beavis and his team were able to show that by knocking out this gene, CAR T-cell therapy was significantly more effective at fighting breast cancer.
While the research has so far only been conducted using mice and human CAR T-cells in mice models, Dr. Beavis is confident it has the potential to progress to clinical trials, particularly as the sort of procedures they’ve been using have been used in clinical trials elsewhere…
(To access the rest of the article please use the following link: MedicalXpress.com)
23rd Apr 2021
Among a group of cell surface proteins known as sialic-acid-binding immunoglobulin-like lectins (Siglecs), CD33-related Siglecs are found mainly on innate immune cells and are involved in cell signaling. One Siglec, however, appears to have “gone rogue” in humans, according to Ajit and Nissi Varki, a husband-and-wife team at the UC San Diego School of Medicine.
Siglec-XII, encoded by the gene SIGLEC12, no longer binds sialic acid and seems to be involved in abnormal cell signaling in humans, the researchers report. The Varkis argue that the protein plays a role in cancer progression and could help explain why humans have much higher rates of carcinoma—cancers that arise from epithelial cells, where Siglec-XII is abundant—than do other great apes.
Only about 30 percent of humans produce this rogue protein; most people have a mutation that inactivates SIGLEC12. The Varkis and their colleagues found Siglec-XII in about 80 percent of carcinoma samples but in just 35 percent of normal tissues. When they forced production of Siglec-XII in a human prostate cancer cell line, the result was higher expression of cancer progression–related genes than in prostate cancer cells that lacked the protein. And comparing cohorts of cancer patients, the team found that functional SIGLEC12was associated with poor prognosis in late-stage colorectal cancer patients.
“The study proposes very interesting hypotheses,” says Jun Wang, an immunologist at NYU Langone Health who was not involved in the research. But, he says, more evidence is needed to confirm Siglec-XII’s role in cancer progression because artificial overexpression of the protein in prostate cancer cells could differ from how the protein behaves in tumors. He notes that it would also be interesting to examine how Siglec-XII in immune cells contributes to cancer. “The cancer cell is just part of the puzzle. The whole picture is cancer and the immune system.”
Story by: Asher Jones for The Scientist
20th Apr 2021
Ensuring COVID-19 vaccine access for refugee and displaced populations, and addressing health inequities, is vital for an effective pandemic response. Yet, vaccine allocation and distribution has been neither equitable nor inclusive, despite that global leaders have stressed this as a critical aspect to globally overcoming the pandemic, according to a paper published by Columbia University Mailman School of Public Health. Read “Leave No-one Behind: Ensuring Access to COVID-19 vaccines for Refugee and Displaced Populations” in the journal Nature Medicine.
As of April 1st, high and upper-middle-income countries received 86 percent of the vaccine doses delivered worldwide, while only 0.1 percent of doses have been delivered in low-income countries. Worldwide, over 80 percent of refugees and nearly all internally displaced persons are hosted by low and middle-income countries—nations at the end of the line for COVID-19 vaccine doses.
“As the world grapples with supply challenges and inequitable vaccine access on local and global scales, marginalized groups, particularly refugees, internally displaced persons and stateless persons, face a double burden of access, even within countries that are themselves marginalized on the global stage,” said Monette Zard, MA, Allan Rosenfield Associate Professor of Forced Migration & Health…
… To access the rest of the article please clink on the following link: medicalxpress.com
8th Apr 2021
The ACGT hosted a webinar for the plant phenomics community on the 4th of March 2021. The webinar was designed as a feedback session for the Wageningen University and Research (WUR) “Drones for Agriculture” online course, as well as to discuss the progress made on formation of the SA Phenomics Society and exploring collaborative funding opportunities.
The “Drones for Agriculture” course was attended by 20 participants (fully funded by the ACGT) associated with the University of Pretoria (UP), the Agricultural Research Council (ARC) and the South African Sugarcane Research Institute (SASRI). The course was a self-paced, three-week online course facilitated by WUR’s top professors from the ‘Information Technology Group’ and the ‘Laboratory of Geo-Information Science and Remote Sensing Group’. The course was ran through the edX platform. Three participants gave feedback on the course, including Mr Phinda Magagula (UP), Dr Tingmin Yu (ARC) and Ms Natalie Hoffman (SASRI). They gave an overview of the course and also shared their highlights from the course. The participants shared how each institution hopes to implement the drone technology in advancing the plant phenotyping in their institutions. The presentations from the participants can be accessed at the link below.
Dr John Becker from the ACGT chaired the sessions on the SA Phenomics Society formation and exploring collaborative funding opportunities for the community. It was highlighted that since the first Plant Phenotyping and Precision Agriculture meeting held in 2019, a Charter for the SA Phenomics Society was developed and has been circulated to a number of institutions for approval. More institutions were identified at this meeting and the Charter has been circulated to them.
In the last session of the webinar, the attendees were informed about the High-End Infrastructure grant application that will be submitted to the Department of Science and Innovation at the end of April 2021. This application is a collaborative effort by the ACGT, UP, the ARC and Stellenbosch University, from which national researchers stand to benefit. The community will be kept informed about the grant application progress.
From the discussions it was highlighted the ”Drones for Agriculture” course was useful for the community. The ACGT will thus investigate whether there is enough interest to fund more participants for the course in 2021. The ACGT will also look at identifying other courses that might be beneficial for the community. The ACGT was also tasked with establishing an online discussion forum, which has been completed in the interim. This discussion forum includes participants from UP, ARC, CSIR, SASRI and Stellenbosch University. This discussion forum will be utilized by the community as a communication tool (sharing ideas, seeking assistance, etc.) around any topic within the plant phenotyping field. The community highlighted the need for a large data storage facility. The ACGT volunteered to explore data storage platforms that the community could utilize.
Story by: the ACGT
17th Mar 2021
More than 1,200 people with rare diseases have received a diagnosis thanks to the integration of large-scale genomics into the Stockholm region’s healthcare system. This is according to a study from Karolinska Institutet in Sweden that analyzed the result of the first five years of collaboration on whole genome sequencing between Karolinska University Hospital and SciLifeLab. The work, published in Genome Medicine, constitutes a major leap forward in the emerging field of precision medicine.
“We’ve established a way of working where hospital and university collaborate on sequencing each patients’ entire genome in order to find genetic explanations for different diseases,” says the paper’s first author Henrik Stranneheim, researcher at the Department of Molecular Medicine and Surgery, Karolinska Institutet. “This is an example of how precision medicine can be used to make diagnoses and tailor treatments to individual patients.”
Large-scale whole genome sequencing technology, that is the process of determining an individual’s complete set of genetic material, has made rapid advances over the recent decade. Despite this, few clinics worldwide routinely use it to diagnose patients…
Please use the following link to access the rest of the article: ScienceX
17th Mar 2021
Two University of Pretoria (UP) researchers are among nine researchers in South Africa who have received funding grants from the South African Medical Research Council (SAMRC) as part of the Strategic Health Innovation Partnerships (SHIP) programme. The grants are worth approximately R3 million each and are to be used over a three-year period.
Professor Robert Millar and Dr Iman van den Bout, academics and researchers of the Centre for Neuroendocrinology in UP’s Faculty of Health Sciences, have received funding to support their research into cutting-edge solutions for the diagnosis and treatment of prostate cancer and breast cancer respectively.
Professor Tiaan de Jager, Dean of UP’s Faculty of Health Sciences, said he is delighted that two researchers from the Faculty are part of producing such important work. “At the Faculty of Health Sciences, we pride ourselves on using our research to solve today’s pressing issues in the communities we work and live in. Additionally, I am proud to hear that our Centre for Neuroendocrinology has received two grants of about R3 million each which will go into finding innovative and lasting solutions to the current challenges facing the diagnosis and treatment of cancer in SA.”
The announcement was made today (8 Feb) at a virtual ceremony. The MRC SHIP is a partnership between the SAMRC and the Department of Science and Technology that funds and manages innovative projects focused on the development of new drugs, treatments, vaccines, medical devices and prevention strategies. This partnership provides life-saving innovations to the health industry and the South African public through involvement in developing new and improved treatment options
An A-rated scientist with over 450 peer review publications, Prof Millar will continue his lifelong work by using the grant to test a new way to diagnose and stratify prostate cancer among South Africans, using a ‘liquid biopsy’ to improve outcomes.
“In South Africa, the age-standardised prostate mortality rate is one of the highest in the world. There is currently no systematic prostate cancer screening program in South Africa within the state-run healthcare system,” Professor Millar explained. “The standard diagnostic test for prostate cancer in South Africa consists of digital rectal examination and prostate specific antigen (PSA) and sometimes prostate biopsy. These tests are, however, characterised by high false-positive and false-negative values, leading to under- and over-diagnosis and consequent harm to patients, and increased costs to the healthcare system. My aim is to show that by utilising the novel state-of-the-art non-invasive genomic technology quantifying tumour mRNA in blood, PROSTATest and NETest, in South African black men, we can improve diagnosis and treatment selection and reduce costs to the healthcare system. Importantly, these tests have demonstrated the potential to identify new therapies for advanced prostate cancers which are not responsive to the major treatment – androgen deprivation therapy – thus addressing the SHIP call for a ‘pharmacogenomics approach to failed therapies.’”
For Dr van den Bout this project forms part of work that began 20 years ago. He will use his grant to initiate and develop the first breast cancer organoid biobank, which will be used to develop better prediction tools for South African women’s response to standard chemotherapy regimens offered in the public health system.
“As I keep developing the project, I feel very strongly that this project will establish a resource and knowledge base that will be of immense value to local cancer scientists in their quest to improve breast cancer patient care in our country,” Dr van den Bout said. “It is already known that a significant percentage of African breast cancer patients that are treated with the standard chemotherapies available in the public health system fail to respond well. In this study we seek to develop a way to test living cells from the tumours of these patients for their reaction to the therapies in the lab, and to see if this will predict how the patient will respond to the treatment. Eventually, we hope that our research will lead to clinical tools with which we can assess each incoming breast cancer patient to determine what therapies will be most effective for them.”
Professor Tawana Kupe, UP Vice-Chancellor and Principal, said the two researchers embody UP’s vision of being the leading research-intensive university on the African continent. “Cancer in South Africa and on the African continent remains one of the most devastating diseases. I am proud that two of our researchers are leading the quest to find lasting and more effective solutions in the diagnosis and treatment of breast cancer and prostate cancer. It proves that at UP, we are committed to producing research that is relevant, innovative and that will improve the lives of ordinary people across Africa and the world.”
19th Feb 2021
For decades, researchers have viewed synonymous mutations as inconsequential quirks of the genome. Due to the way the genetic code is set up—where multiple three-base-pair codons can encode the same amino acid—mutations can arise that don’t change a protein’s amino acid sequence. Scientists have largely dismissed these anomalies as harmless oddities.
But like other historically underappreciated aspects of the genome, scientists are realizing that many “silent” mutations might not be so silent after all. Research suggests they’re often subject to selective pressure and could play a role in cancer, autism, and schizophrenia.
A study published online last week (February 12) in iScience adds to the mounting evidence that synonymous variants can have consequences. The authors describe a synonymous mutation in the gene BAP1 that was associated with a worse-than-expected prognosis in a kidney cancer patient. Their subsequent experiments suggest that the mutation has this effect by disrupting cells’ RNA splicing process, by which freshly transcribed messenger RNA (mRNA) is converted into digestible fragments ready to be translated into protein. Because the cancer patient lacked a second healthy copy of the gene, the silent mutation may have resulted in a complete loss of function of BAP1.
“To my knowledge, tying a specific synonymous mutation [to] a clinical outcome [in cancer] is a novelty,” remarks Fran Supek, a cancer geneticist at the Institute for Research and Biomedicine in Barcelona who wasn’t involved in the study. “I’m always glad to see that researchers are thinking a bit outside the box . . . and looking at understudied classes of genetic changes that may help us solve a certain number of patients with genetic diseases or with cancer.”
While combing through The Cancer Genome Atlas(TCGA)—a public database of genomic samples from more than 11,000 patients around the world—Samuel Peña-Llopis and his colleagues discovered an entry from a patient with an unusual course of disease. The 73-year-old Caucasian woman had clear-cell renal cell carcinoma, the most common form of kidney cancer, with a mutation in PBRM1, a gene involved in chromatin remodeling.
Although PBRM1 mutations are normally associated with relatively good clinical outcomes in such patients—with a median survival of 117 months, according to TCGA data—the patient died only 56 months after diagnosis, says Peña-Llopis, a cancer geneticist specializing in kidney cancer and uveal melanoma with the German Cancer Consortium at the University Hospital Essen in Germany.
The team noticed that she also had a synonymous mutation in BAP1, which encodes an enzyme involved in regulating the degradation of proteins. The mutation changes a thymine to a guanine, which still results in the same amino acid, glycine, encoded both by GGT and GGG. Curiously, the patient also had very low abundance of BAP1 protein, in fact, it was on par with renal cell carcinoma patients who have nonsynonymous loss-of-function mutations in BAP1, which tend to be linked to severe outcomes. The team suspected that the silent BAP1 mutation might somehow affect the gene’s transformation into protein.
The path by which DNA turns into protein is a long and winding one. First, double-stranded DNA is teased apart and the strands are individually transcribed into single strings of pre-mRNA, a rough draft of the instructions needed to turn it into protein. Then it must be spliced, whereby various proteins bind to different sites across the pre-mRNA and cut out noncoding nucleotide sequences—introns—and fuse the coding parts—exons—together. Only then is the mRNA ready for other cellular machinists to translate into protein.
One way by which synonymous mutations can perturb this process, previous research suggested, is by altering the specific binding sites of RNA splicing proteins, which are required to properly integrate different exons. If they can’t bind—or the altered codon causes the wrong proteins to bind—they might end up skipping over important bits of genetic code—called “exon skipping”—which can result in a dysfunctional protein. Because the synonymous mutation located in BAP1’s exon 11 was close to a splice site critical for joining this exon to the next, “we thought that maybe the splicing system was affected,” Peña-Llopis recalls.
To find out, the team conducted a series of experiments with genetic constructs containing BAP1’s exon 11, into which they had inserted fluorescent proteins. They expressed the construct in a human cancer cell line. Based on the color that emerged under a microscope, they could tell if the exon was being integrated or skipped. They observed nearly 100 percent skipping when the construct contained the synonymous mutation, significantly more than when using the construct based on the unmutated version of BAP1.
If exon 11 is skipped, that likely causes a loss of BAP1 for that gene copy, Peña-Llopis explains. Because that exon has 185 base pairs—which is not a multiple of three—losing it will cause a shift of the three-base-pair reading frame that enzymes use for protein translation. That, in turn, would cause a codon further down the line to be misread as a stop codon, signaling the protein translation machinery to terminate. mRNA transcripts containing premature stop codons are typically degraded by the cell. In this particular patient, this likely led to a complete loss of BAP1 because she had lost her second copy due to a deletion of a small chromosome segment, which is common in that cancer subtype.
Synonymous mutations in kidney cancer patients
Back in the TCGA database, which includes nearly 500 clear-cell renal cell carcinoma patients, the team found another eight patients who had synonymous mutations in BAP1 exons near sites important for splicing, two of which were located inside the sites necessary for gluing exons 10 and 11 together. Considering that there are 32 splicing sites across the 17 exons that make up BAP1, finding two out of eight is a significant number, Peña-Llopis says, “suggesting that this is a hotspot for inactivation of BAP1.” However, the two patients had very different clinical outcomes, suggesting that other genetic alterations also play a role in the prognosis.
“I think this is an important finding,” remarks James Brugarolas, a physician-scientist and oncologist who directs the kidney cancer program at the University of Texas Medical Center. BAP1 is mutated in around 10–15 percent of all clear-cell renal cell carcinomas, mostly through nonsynonymous alterations. “The study provides relatively convincing evidence that . . . mutations that do not affect the protein sequence in BAP1could be pathogenic driver mutations, leading to the inactivation of the tumor suppressor protein,” adds Brugarolas, who has collaborated with Peña-Llopis in the past but wasn’t involved in the new research.
Brugarolas says that the data would have been even more convincing had there been more RNA sequencing and immunohistochemistry data from the patients’ tumor available, which could yield more definitive evidence of exon skipping. And, of course, such findings can always be better supported by larger sample sizes and replication in independent datasets, Supek adds. That said, “I think the in vitro experiments that they [did] suggest that the mutation they’ve identified has the potential to alter splicing. And clearly, exon 11 escaping would result in a nonfunctional protein due to a premature stop codon. One could make a very convincing argument for that,” Brugarolas says.
The clinical relevance of the finding is not yet apparent. Targeting loss-of-function mutations in tumor suppressor genes such as BAP1 has lagged behind targeting gain-of-function mutations, for instance, in enzymes that control cell growth and function, Brugarolas says; it’s generally easier to inhibit misfit proteins than to correct something that has been already abolished by mutation. It’s also unclear if BAP1 mutations could be used as biomarkers to predict patients’ responsiveness to therapies. “How mutations in BAP1[should] be leveraged for therapy remains unknown,” Brugarolas adds.
On the whole, the findings indicate that researchers should be paying more attention to synonymous mutations, notes Thomas Mitchell, a clinician-scientist focusing on kidney cancer at the Wellcome Sanger Institute in the UK. “[There is] little awareness of synonymous mutations and their role in cancer. In general, they are ignored in sequencing studies as it has been felt that they are very unlikely to be drivers.”
Nevertheless, larger studies in the past have predicted that synonymous mutations could have pathogenic effects. In 2014, Supek and colleagues estimated that around 6–8 percent of pathogenic single-nucleotide mutations in cancer genes are synonymous mutations. Taken together with other studies, research seems to converge on an estimate of 5 percent of all driver mutations being synonymous mutations—a “non-negligible amount” that may be quite significant for some individual cancer patients, Supek says. Exon skipping is one mechanism by which such mutations could have deleterious effects, “but it’s probably going to be different for every synonymous mutation.”
Understanding silent mutations, along with other overlooked genetic alterations, could help unlock the underlying causes of disease for many individual patients for whom mutations don’t clearly fall into the nonsynonymous bucket, and open the door to finding treatments. “The human genome is a very complex thing, and there are many ways in which it can break and result in disease,” Supek says.
J. Niersch et al., “A BAP1 synonymous mutation results in exon skipping, loss of function and worse patient prognosis,” iScience, doi:10.1016/j.isci.2021.102173.
Story by: Kararina Zimmer, for The Scientist