Tag Archives: #braintumors

Scientists Can Detect Brain Tumours Using A Simple Urine Or Blood Plasma Test (Medicine)

Researchers from the Cancer Research UK Cambridge Institute have developed two tests that can detect the presence of glioma, a type of brain tumour, in patient urine or blood plasma.

The team say that a test for detecting glioma using urine is the first of its kind in the world.

Although the research, published in EMBO Molecular Medicine, is in its early stages and only a small number of patients were analysed, the team say their results are promising.

The researchers suggest that in the future, these tests could be used by GPs to monitor patients at high risk of brain tumours, which may be more convenient than having an MRI every three months, which is the standard method.

When people have a brain tumour removed, the likelihood of it returning can be high, so they are monitored with an MRI scan every three months, which is followed by biopsy.

Blood tests for detecting different cancer types are a major focus of research for teams across the world, and there are some in use in the clinic. These tests are mainly based on finding mutated DNA, shed by tumour cells when they die, known as cell-free DNA (cfDNA).

However, detecting brain tumour cfDNA in the blood has historically been difficult because of the blood-brain-barrier, which separates blood from the cerebrospinal fluid (CSF) that surrounds the brain and spinal cord, preventing the passage of cells and other particles, such as cfDNA.

Researchers have previously looked at detecting cfDNA in CSF, but the spinal taps needed to obtain it can be dangerous for people with brain tumours so are not appropriate for patient monitoring.

Scientists have known that cfDNA with similar mutations to the original tumour can be found in blood and other bodily fluids such as urine in very low levels, but the challenge has been developing a test sensitive enough to detect these specific mutations.

The researchers, led by Dr Florent Mouliere who is based at the Rosenfeld Lab of the Cancer Research UK Cambridge Institute and at the Amsterdam UMC, and Dr Richard Mair, who is based at Cancer Research UK Cambridge Institute and the University of Cambridge developed two approaches in parallel to overcome the challenge of detecting brain tumour cfDNA.

The first approach works for patients who have previously had glioma removed and biopsied. The team designed a tumour-guided sequencing test that was able to look for the mutations found in the tumour tissue within the cfDNA in the patient’s urine, CSF, and blood plasma.

A total of eight patients who had suspected brain tumours based on MRIs were included in this part of the study. Samples were taken at their initial brain tumour biopsies, alongside CSF, blood and urine samples.

By knowing where in the DNA strand to look, the researchers found that it was possible to find mutations even in the tiny amounts of cfDNA found in the blood plasma and urine.

The test was able to detect cfDNA in 7 out of 8 CSF samples, 10 out of the 12 plasma blood samples and 10 out of the 16 urine samples.

For the second approach the researchers looked for other patterns in the cfDNA that could also indicate the presence of a tumour, without having to identify the mutations.

They analysed 35 samples from glioma patients, 27 people with non-malignant brain disorders, and 26 healthy people. They used whole genome sequencing, where all the cfDNA of the tumour is analysed, not just the mutations.

They found in the blood plasma and urine samples that fragments of cfDNA, which came from patients with brain tumours were different sizes than those from patients with no tumours in CSF. They then fed this data into a machine learning algorithm which was able to successfully differentiate between the urine samples of people with and without glioma.

The researchers say that while the machine learning test is cheaper and easier, and a tissue biopsy from the tumour is not needed, it is not as sensitive and is less specific than the first tumour-guided sequencing approach.

MRIs are not invasive or expensive, but they do require a trip to the hospital, and the three-month gap between checks can be a regular source of anxiety for patients.

The researchers suggest that their tests could be used between MRI scans, and could ultimately be able to detect a returning brain tumour earlier.

The next stage of this research will see the team comparing both tests against MRI scans in a trial with patients with brain tumours who are in remission to see if it can detect if their tumours are coming back at the same time or earlier than the MRI. If the tests prove that they can detect brain tumours earlier than an MRI, then the researchers will look at how they can adapt the tests so they could be offered in the clinic, which could be within the next ten years.

“We believe the tests we’ve developed could in the future be able to detect a returning glioma earlier and improve patient outcomes,” said Mair. “Talking to my patients, I know the three-month scan becomes a focal point for worry. If we could offer a regular blood or urine test, not only will you be picking up recurrence earlier, you can also be doing something positive for the patient’s mental health.”

Michelle Mitchell, Chief Executive of Cancer Research UK said, “While this is early research, it’s opened up the possibility that within the next decade we could be able to detect the presence of a brain tumour with a simple urine or blood test. Liquid biopsies are a huge area of research interest right now because of the opportunities they create for improved patient care and early diagnosis. It’s great to see Cancer Research UK researchers making strides in this important field.”

Sue Humphreys, from Wallsall, a brain tumour patient, said: “If these tests are found to be as accurate as the standard MRI for monitoring brain tumours, it could be life changing.

If patients can be given a regular and simple test by their GP, it may help not only detect a returning brain tumour in its earliest stages, it can also provide the quick reassurance that nothing is going on which is the main problem we all suffer from, the dreaded Scanxiety.

The problem with three-monthly scans is that these procedures can get disrupted by other things going on, such as what we have seen with the Covid pandemic. As a patient, this causes worry as there is a risk that things may be missed, or delayed, and early intervention is the key to any successful treatment.”


Reference:
Florent Mouliere et al. ‘Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients.’ EMBO Molecular Medicine (2021). DOI: 10.15252/emmm.202012881


Provided by University of Cambridge

Blood Stem Cells Make Brain Tumors More Aggressive (Medicine)

For the first time, scientists from the German Cancer Consortium (DKTK) partner site in Essen/Düsseldorf have discovered stem cells of the hematopoietic system in glioblastomas, the most aggressive form of brain tumor. These hematopoietic stem cells promote division of the cancer cells and at the same time suppress the immune response against the tumor. This surprising discovery might open up new possibilities for developing more effective immunotherapies against these malignant brain tumors.

The DKTK is a consortium centered around the German Cancer Research Center (DKFZ) in Heidelberg, which has long-term collaborative partnerships with specialist oncological centers at universities across Germany.

Glioblastomas are the most common dangerous brain tumor in adults; they grow diffusely into healthy brain tissue and are therefore almost impossible to completely remove by surgery. They defy the combination of surgery, radiotherapy, and chemotherapy and usually continue to grow unchecked. Even immunotherapies, which achieve good results in some cases in other types of cancer, have had no effect on these malignant brain tumors to date.

“Glioblastomas apparently create an environment that actively suppresses the immune response,” explained Björn Scheffler, DKTK Professor of Translational Oncology at the West German Tumor Center in Essen, partner site Essen/Düsseldorf. “They produce immunosuppressive messengers, and in the immediate environment of the tumors we find certain types of immune cells that specifically suppress the immune defense.”

Researchers were not previously aware of the variety of immune cells in the microenvironment of glioblastomas in any detail. Yet Scheffler and his colleagues realized that a precise knowledge of the cellular composition of glioblastomas was necessary in order to be able to overcome tumor-related immunosuppression using appropriate treatments.

In tissue samples of 217 glioblastomas, 86 WHO grade II and III astrocytomas, and 17 samples from healthy brain tissue, the DKTK researchers used computer-assisted transcription analyses to draw up profiles of the cellular composition. The tissue samples were taken directly from the resection margins – where remaining tumor cells and immune cells meet.

The team were able to distinguish between signals from 43 cell types, including 26 different types of immune cells. To their great surprise, the researchers discovered hematopoietic stem and precursor cells in all the malignant tumor samples, while this cell type was not found in healthy tissue samples. “Blood stem cells are actually found in bone marrow, from where they supply the body with all kinds of mature blood cells – obviously including all the different types of immune cells. Blood stem cells of the brain tumor itself have never been described before now,” remarked lead author Celia Dobersalske.

An even more surprising observation was that these blood stem cells seem to have fatal characteristics: They suppress the immune system and at the same time stimulate tumor growth. When the researchers cultured the tumor-associated blood stem cells in the same petri dish as glioblastoma cells, cancer cell division increased. At the same time, the cells produced large amounts of the PD-L1 molecule, known as an “immune brake”, on their surface.

Tumor organoids – tiny tumors grown in a petri dish from the brain tumor cells of individual patients – reacted to the blood stem cells too. In the presence of these cells, the cancer cells formed a network of cell processes that connects them. Only a few years ago, scientists from the DKFZ and Heidelberg University Hospital discovered that glioblastoma cells communicate using these connections and can thus protect themselves against treatment-related damage.

All these observations suggested that the blood stem cells found in glioblastomas have a negative impact on the course of disease. This was confirmed in a study of 159 glioblastoma patients for whom data were available on the clinical course of disease. In this group of patients, it was consistently observed that the more blood stem cells a tumor contained, the more immunosuppressive messengers were released and the more immunosuppressive markers the cancer cells formed – and the lower the overall survival of the patients was.

In order to investigate brain tumor blood stem cells in more detail, the authors teamed up with the Department of Neurosurgery at Essen University Hospital (Director: Ulrich Sure) to extract individual cells from fresh patient tissue. Using gene expression sequencing in 660 individual cells, the researchers created a profile and compared it with cells from healthy bone marrow and blood. Analysis of these data led to several specific new suggestions as to how this tumor-promoting cell population could be made harmless.

It was already known from research reports that the blood stem cells in bone marrow tend to mature into immunosuppressive cell types during differentiation in the course of cancer. It appears that they are programmed by the tumor to do so. Expert and last author Igor Cima suspects that a similar phenomenon might be responsible for the observations in the glioblastoma-associated blood stem cells: “We can now see an opportunity to intervene in order to modify the differentiation process of the glioma-associated blood stem cells, for example through particular cell messengers, and hence prevent the immune system from being blocked as a result of the tumor. Immunotherapies would then have a better chance of being effective against glioblastomas.”

Featured image: The image shows a collage of fluorescently labeled tumor organoids grown from patient cells in the Scheffler lab as a “mini brain tumor” for research. © Source: K. Stratmann und C. Dobersalske


Reference: I-Na Lu, Celia Dobersalske, Laurèl Rauschenbach, Sarah Teuber-Hanselmann, Anita Steinbach, Vivien Ullrich, Shruthi Prasad, Tobias Blau, Sied Kebir, Jens T. Siveke, Jürgen C. Becker, Ulrich Sure, Martin Glas, Björn Scheffler and Igor Cima: Tumor-associated hematopoietic stem and progenitor cells positively linked to glioblastoma progression Nature Communications 2021, DOI: 10.1038/s41467-021-23995-z


Provided by DKFZ

Researchers Discover New Way to Starve Brain Tumours (Medicine)

Scientists from Queen Mary University of London, funded by the charity Brain Tumour Research and the Medical Research Council, have found a new way to starve cancerous brain tumour cells of energy in order to prevent further growth.

The pre-clinical research in human tissue samples, human cell lines and mice could lead to changes in the way that some children with medulloblastoma are treated in the future, if the findings are confirmed in human clinical trials.

Medulloblastoma is the most common high-grade brain tumour in children. Some 70 are diagnosed in the UK each year. Survival rate is 70 per cent for those whose tumour has not spread but it is almost always fatal in cases of recurrent tumour.

The research, published in the high impact journal Nature Communicationslooks at inositol hexaphosphate (IP6), a naturally occurring compound present in almost all plants and animals, and showed how it inhibits medulloblastoma and can be combined with chemotherapy to kill tumour cells.

Lead researcher Professor Silvia Marino from the Brain Tumour Research Centre of Excellence at Queen Mary University of London said: “Medulloblastoma occurs in four distinct subgroups (WNT, SHH, G3 and G4). Despite our growing knowledge of the molecular differences between these subgroups, current options are surgery together with radiotherapy and/or chemotherapy for all patients. We desperately need to understand the key molecular events driving tumour growth in each subgroup to design new, less toxic, targeted treatments.”

G4 medulloblastoma is the least understood of all subgroups, despite being the most common and associated with poor prognosis. We have identified a novel way that this type of medulloblastoma is able to adapt its metabolism and grow uncontrollably. Significantly, we have also shown how this energy supply can be blocked. These exciting results bring hope of developing new targeted treatments for patients with this aggressive paediatric brain tumour.”

Normal cells are able to switch specific genes on and off as required to control their growth. Known as epigenetics, this process can be disrupted in cancer, leading to over production of specific proteins that contribute to the development and growth of a tumour.

It is already known that epigenetic changes can contribute to the development of medulloblastoma. Furthermore, a protein involved in this process – known as BMI1 – is found in high levels in a broad range of cancers including brain tumours. In medulloblastoma, high levels of it are found in the G4 subgroup, where it sustains tumour growth.

Professor Marino’s team has previously demonstrated that, alongside high levels of BMI1, G4 medulloblastoma cells also lack a protein called CHD7. This combination of changes, or signature, is thought to contribute to the development of G4 medulloblastoma.

Now the team has shown that high levels of BMI1 enable the cancer cells to adapt their metabolism and grow aggressively. This change can be reversed by treating the cells with inositol hexaphosphate (IP6). The team also showed that when IP6 was combined with chemotherapy – in this case cisplatin – they observed an increased ability to kill the tumour cells in mice.

Hugh Adams, Head of Stakeholder Relations at Brain Tumour Research said: “These very exciting results reveal a new way for epigenetics to control metabolism within tumour cells. Clinical trials are now required to test the ability of combining IP6 with chemotherapy to treat G4 medulloblastoma, offering promise to a particularly vulnerable group of patients.

“It is great news and brings some much-needed hope for the future. There is still some way to go but we hope that a clinical trial could be up and running in the near future.

“Brain tumours kill more children and adults under the age of 40 yet, historically, just 1% of the national cancer spend has been allocated to this devastating disease. Brain Tumour Research is determined to change this.”

Peter Gardiner, from Aston Clinton, near Aylesbury, lost his 13-year-old son to medulloblastoma in November 2017. Next month, May marks six years since his diagnosis.

“I can only describe our experience as a long hell. Firstly, Ollie was diagnosed, then he went through surgery and extensive treatment. When we were told there were no further options for him in the UK, we crowdfunded £500,000 so he could have immunotherapy in Germany. It was our only hope and, sadly, it didn’t work,” he said.

Ollie’s family generously donated £187,000 of the residue of their fundraising to Brain Tumour Research which is funding post-doctoral researcher Sara Badodi who works alongside Prof Marino.

Pete said: “We were overwhelmed by the support of friends, family and strangers who stood by us in our hour of need and came together to help us do the very best we could for our son. It means the world to think that, because of him and the love people showed to us, others might not have to go through what we did.”

Featured image: Professor Silvia Marino © Queensmary University of London


More information

  • Research paper: ‘Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation’. Sara Badodi, Nicola Pomella, Xinyu Zhang, Gabriel Rosser, John Whittingham, Maria Victoria Niklison-Chirou, Yau Mun Lim, Sebastian Brandner, Gillian Morrison, Steve M. Pollard, Christopher D. Bennett, Steven C. Clifford, Andrew Peet, M. Albert Basson and Silvia Marino. Nature Communications. DOI 10.1038/s41467-021-22379-7

Provided by Queensmary University of London

CNIO Scientists Discovered A Combination Therapy For Aggressive Brain Tumors (Medicine)

The researchers conducted an in-depth study of resistance to temozolomide, the first-line treatment for glioblastoma, to which many patients cease to respond over time

The combination of temozolomide and dianhydrogalactitol acts synergistically, overcomes this resistance and increases survival in mice with brain tumours

Treatments for glioblastoma have not improved in the last 20 years. The authors argue for the need to translate these results into clinical trials to study whether this combination therapy is also effective in patients with this disease

Glioblastomas are the most common and most aggressive brain tumours. Their survival rate has barely increased over the last 50 years, indicating an urgent need to develop new therapeutic strategies. In a paper published this week in the journal Molecular Cancer Therapeutics, a journal of the American Association for Cancer Research, the team led by Massimo Squatrito, Head of the Seve Ballesteros Foundation Brain Tumour Group at the Spanish National Cancer Research Centre (CNIO), proposes a novel therapeutic strategy based on the combination of temozolomide, the first-line treatment for these patients, and dianhydrogalactitol, a drug that is being tested in clinical trials and is already approved for the treatment of other tumours.

Currently, the main and virtually only treatment for glioblastomas is the combination of radiotherapy and the chemotherapy agent temozolomide, after surgical resection of the tumour mass.Like most chemotherapeutic agents used, temozolomide induces damage to the genetic material of tumour cells, causing them to break down and die.  However, in almost half of the patients, such tumours become resistant to the drug and the tumour continues to grow even while undergoing treatment.

“Although the incidence of glioblastoma is not excessively high in adults, they are the most common brain tumours, and there are no effective treatments or markers of response to treatment or of the generation of resistance,” says Squatrito.

DNA repair, the basis of resistance

Why do patients with glioblastoma stop responding to temozolomide? Squatrito and his team shed light on this central question last year in a paper published in the journal Nature Communications: some glioblastomas produce genomic rearrangements in the DNA repair gene MGMT, which increases its production and repairs the DNA damage induced by temozolomide so that the tumour manages to grow and evade treatment.

In the paper published now, the researchers studied temozolomide resistance in depth by using glioblastoma cell lines in which several key genes were silenced. The results show that this resistance not only depends on the MGMT gene but that it may also be mediated by failures in the MMR (DNA repair) pathway so that when any of its components are altered, tumour cells accumulate mutations that give them the ability to evade the effects of temozolomide.

Tumours are complex systems that use multiple tools to trick the body into supporting their growth and development. Combination therapies, targeting several components involved in the tumour process, are a revolution that brings hope to many patients. Advances in the understanding of the molecular biology of tumours allow the emergence of new therapies and targeted combinations thereof to fight the tumours and to avoid any type of resistance they may develop.

Combination therapy with dianhydrogalactitol

In the present study, the researchers focused on the drug dianhydrogalactitol, a chemotherapeutic agent that is able to cross the blood-brain barrier and reach the central nervous system, where it induces DNA damage in tumour cells. Dianhydrogalactitol is currently being tested in clinical trials for gliomas and other types of cancer such as ovarian cancer and is already approved in China for the treatment of acute myeloid leukaemia and lung cancer.

The results of this study show that temozolomide and dianhydrogalactitol act synergistically on tumour cells in vitro, resulting in slower growth of these cells compared to when they are treated with each drug individually. The researchers observed similar results in mice with brain tumours, which survived longer when treated simultaneously with temozolomide and dianhydrogalactitol.

Furthermore, the results suggest that, unlike temozolomide, the anticancer effects of dianhydrogalactitol are independent of the MGMT DNA repair gene and the MMR pathway. “Our data show that dianhydrogalactitol could be an effective treatment that circumvents the resistance mechanisms that arise during temozolomide treatment,” explains Miguel Jiménez-Alcázar, first author of the paper.

“The results we obtained with this study are of great interest, as they could lead to a substantial improvement in the evolution of these patients,” says Squatrito. “It now becomes a matter of urgency to take these finding to clinical practice to see if this combination of drugs increases survival; both drugs are clinically available, which could accelerate the timeline of this new approach,” he concludes.

This study was funded by the Spanish Ministry of Science and Innovation, the Carlos III Health Institute, the Seve Ballesteros Foundation, the Spanish Association against Cancer (AECC) and the European Molecular Biology Organisation (EMBO).

Featured image: The combination of temozolomide (TMZ) with dianhydrogalactitol (DAG; culture dish on the right) is able to kill glioblastoma cells resistant to conventional therapy with temozolomide alone (TMZ; centre). /CNIO


Reference article

Dianhdrogalactitol overcomes multiple temozolomide resistance mechanisms in glioblastoma. Miguel Jiménez-Alcázar, Álvaro Curiel-García, Paula Nogales, Javier Perales-Patón, Alberto J. Schuhmacher, Marcos Galán-Ganga, Lucía Zhu, Scott W. Lowe, Fátima Al-Shahrour, Massimo Squatrito (Molecular Cancer Therapeutics, 2021). DOI: 10.1158/1535-7163.MCT-20-0319


Provided by CNIO

New Immunotherapy Target Discovered For Malignant Brain Tumors (Medicine)

Scientists say they have discovered a potential new target for immunotherapy of malignant brain tumors, which so far have resisted the ground-breaking cancer treatment based on harnessing the body’s immune system. The discovery, reported in the journal CELL, emerged from laboratory experiments and has no immediate implications for treating patients.

Scientists from Dana-Farber Cancer Institute, Massachusetts General Hospital, and the Broad Institute of MIT and Harvard said the target they identified is a molecule that suppresses the cancer-fighting activity of immune T cells, the white blood cells that seek out and destroy virus-infected cells and tumor cells.

The scientists said the molecule, called CD161, is an inhibitory receptor that they found on T cells isolated from fresh samples of brain tumors called diffuse gliomas. Gliomas include glioblastoma, the most aggressive and incurable type of brain tumor. The CD161 receptor is activated by a molecule called CLEC2D on tumor cells and immune-suppressing cells in the brain, according to the researchers. Activation of CD161 weakens the T cell response against tumor cells.

To determine if blocking the CD161 pathway could restore the T cells’ ability to attack the glioma cells, the researchers disabled it in two ways: they knocked out the gene called KLRB1 that codes for CD161, and they used antibodies to block the CD161-CLEC2D pathway. In an animal model of gliomas, this strategy strongly enhanced the killing of tumor cells by T cells, and improved survival of the animals. The researchers were also encouraged because blocking the inhibitory pathway appeared to reduce T-cell exhaustion – a loss of cell-killing function in T cells that has been a been a major hurdle in immunotherapy.

In addition, “we showed that this pathway is also relevant in a number of other major human cancer types,” including melanoma, lung, colon, and liver cancer, said Kai Wucherpfennig, MD, PhD, director of the Center for Cancer Immunotherapy Research at Dana-Farber. He is corresponding author of the report along with Mario Suva, MD, PhD, of Massachusetts General Hospital; Aviv Regev, PhD, of the Broad Institute, and David Reardon, MD, clinical director of the Center for Neuro-Oncology at Dana-Farber.

Many cancer patients are now being treated with immunotherapy drugs that disable “immune checkpoints” – molecular brakes exploited by cancer cells to suppress the body’s defensive response by T cells against tumors. Disabling these checkpoints unleashes the immune system to attack cancer cells. One of the most frequently targeted checkpoints is PD-1. However, recent trials of drugs that target PD-1 in glioblastomas have failed to benefit patients. In the current study, the researchers found that fewer T cells from gliomas contained PD-1 than CD161. As a result, they said, “CD161 may represent an attractive target, as it is a cell surface molecule expressed by both CD8 and CD4 T cell subsets [the two types of T cells involved in response against tumor cells] and a larger fraction of T cells express CD161 than the PD-1 protein.”

Prior to the current study, the researchers said little was known about the expression of genes and the molecular circuits of immune T cells that infiltrate glioma tumors, but fail to halt their growth. To open a window on these T cell circuits, the investigators took advantage of new technologies for reading out the genetic information in single cells – a method called single-cell RNA-seq. They applied RNA-seq to glioma-infiltrating T cells from fresh tumor samples from 31 patients and created an “atlas” of pathways that regulate T cell function. In analyzing the RNA-seq data, the researchers identified the CD161 protein, encoded by the KLRB1 gene, as a potential inhibitory receptor. They then used CRISPR/Cas9 gene-editing technology to inactivate the KLRB1 gene in T cells and showed that CD161 inhibits the tumor cell-killing function of T cells.

“Our comprehensive atlas of T cell expression programs across the major classes of diffuse gliomas thus identifies the CD161-CLEC2D pathway as a potential target for immunotherapy of diffuse gliomas and other human cancers,” the authors of the report said.

This strategy was tested in two different animal models created by implanting “gliomaspheres” – 3-dimensional clusters of tumor cells from human patients – into rodents, which developed aggressive tumors that invaded the brain. The scientists subsequently injected T cells with the KLRB1 gene edited out into the cerebrospinal fluid of some of the animals, and T cells that hadn’t had the KLRB1 gene deleted. Transfer of the gene-edited T cells slowed the growth of the tumors and “conferred a significant survival benefit,” in both of the animal models of gliomas, the scientists said.

The research was supported by a grant from the Ben and Catherine Ivy Foundation and the Bridge project, along with National Institutes of Health grants R01 CA238039, P01 CA236749, R37CA245523, and others. Wucherpfennig is a member of the Parker Institute for Cancer Immunotherapy.

Wucherpfennig is a co-founder and advisory board member of Immunitas Therapeutics. He serves on the scientific advisory board of TCR2 Therapeutics, T-Scan Therapeutics, SQZ Biotech, and Nextechinvest and received sponsored research funding from Bristol-Myers Squibb and Novartis.

Featured image: Kai Wucherpfennig, MD, PhD, Dana-Farber Cancer Institute © Dana-Farber Cancer Institute


Reference: Nathan D. Mathewson, Orr Ashenberg et al., “Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis”, Cell, 2021. https://doi.org/10.1016/j.cell.2021.01.022


Provided by Dana Farber Cancer Institute

New Approach Emerges to Better Classify, Treat Brain Tumors (Psychiatry)

A look at RNA tells us what our genes are telling our cells to do, and scientists say looking directly at the RNA of brain tumor cells appears to provide objective, efficient evidence to better classify a tumor and the most effective treatments.

Dr. Jin-Xiong She and MD/PhD student Paul Tran. © Kim Ratliff, Augusta University Photographer

Gliomas are the most common brain tumor type in adults, they have a wide range of possible outcomes and three subtypes, from the generally more treatable astrocytomas and oligodendrogliomas to the typically more lethal glioblastomas.

Medical College of Georgia scientists report in the journal Scientific Reports that their method, which produces what is termed a transcriptomic profile of the tumor is particularly adept at recognizing some of the most serious of these tumors, says Paul M.H. Tran, MD/PhD student.

Gliomas are currently classified through histology, primarily the shape, or morphology, pathologists see when they look at the cancerous cells under a microscope, as well as identification of known cancer-causing gene mutations present.

“We are adding a third method,” says Dr. Jin-Xiong She, director of the MCG Center for Biotechnology and Genomic Medicine, Georgia Research Alliance Eminent Scholar in Genomic Medicine and the study’s corresponding author. Tran, who is doing his PhD work in She’s lab, is first author.

While most patients have both the current classification methods performed, there are sometimes inconsistent findings between the two groups, like traditional pathology finding a cancer is a glioblastoma when the mutation study did not and vice versa, and even when two pathologists look at the same brain tumor cells under a microscope, the scientists say.

To more directly look at what a cancer cell is up to, they opted to look at relatively unexplored gene expression, more specifically the one-step downstream RNA, which indicates where the cell is headed. DNA expression equals RNA since DNA makes RNA, which makes proteins, which determine cell function. One way cancer thrives is by altering gene expression, turning some up and others way down or off.

They suspected the new approach would provide additional insight about the tumor, continue to assess the efficacy of existing classification methods and likely identify new treatment targets.

“RNA would be a snapshot of what is high and what is low currently in those glial cells as they are taken out of the body,” Tran says. “They are actually looking at how many copies of RNA relevant genes are making. Normally that gene expression determines everything from your hair color to how much you weigh,” She says. “The transcriptomic profile counts the number of copies of each gene you have in the cell.”

The glial cells, whose job is to support neurons, have a tightly regulated gene expression that enables them to do just that. With cancer, one of the first things that happens is how many RNA copies of each gene the cells are making changes and the important cell function changes with it. “You change gene expression to become something different,” She says.

Transcriptomic profiling starts like the other methods with a tumor sample from the surgeon, but then it goes through an automated process to extract RNA, which is put into an instrument that can read gene expression levels for the different genes. The massive amounts of data generated then is fed into a machine learning algorithm Tran developed, which computes the most likely glioma subtype and a prognosis associated with it.

They started with The Cancer Genome Atlas (TCGA) program and the Repository of Molecular Brain Neoplasia Data (REMBRANDT), two datasets that had already done the work of looking at RNA and also provided related clinical information, including outcomes on more than 1,400 patients with gliomas. Tran, She and their colleagues used their algorithm to discover patterns of gene expression and used those patterns to classify all glioma patients without any other input. They then compared the three major glioma subtypes that emerged with standard classification methods.

Their transcriptomic classification had about 90% agreement with the traditional approach looking at cells under a microscope and about 93% agreement with looking at genetic mutations, She says. They found about a 16% discrepancy between the two standard measures.

“All three methods don’t agree on about 10-15% of patients,” She says, but notes the most accurate analysis among the three should be theirs because their method is better than the others at predicting survival.

And the discrepancies they found between classification methods could be significant for some patients despite close percentages.

“We found our method may have some advantages because we found some patients actually had a worse prognosis that could be identified by our method, but not by the other approaches,” Tran says.

As an example, patients with a mutation in a gene called IDH, or isocitrate dehydrogenase, most typically have an astrocytoma or oligodendroglioma, which are generally more responsive to treatment and have better survival rates than glioblastomas. However they also found that even some lower-grade gliomas with this IDH mutation can progress to what’s called a secondary glioblastoma, something which may not be found by the other two methods. The IDH mutation is rare in primary glioblastomas, Tran notes.

Using the standard techniques, which look at a snapshot in time, these astrocytomas that progress to more lethal glioblastomas were classified as a less serious tumor in 27 patients. “That progression phenomenon is known but our technique is better at identifying those cases,” Tran says.

Further analysis also found that about 20% of the worse-prognosis patients had mutations in the promoter region of the TERT gene. The TERT gene is best known for making telomerases, enzymes that enable our chromosomes to stay a healthy length, a length known to decrease with age. TERT function is known to be hijacked by cancer to enable the endless cell proliferation that is a cancer hallmark. This mutation is not usually present in a glioma that starts out as a more aggressive glioblastoma, and implicates a mutation in the TERT promoter is important in glioma progression, they say.

“The implication would be that if we have inhibitors or something else that target the TERT gene, then you may be able to prevent some of those cases from having a worse prognosis,” Tran says.

These findings also point to strengths of the different classification methods, in this case suggesting that classification by mutation may not pick up these most aggressive brain tumors rather their new transcriptomic method, as well as the older approach of looking at the cancer cells under a microscope, are better at making this important distinction.

“It is known that a certain proportion of your lower-grade gliomas can progress to become a glioblastoma and those are some of the ones that can sometimes be misidentified by the original techniques,” Tran says. “Using our gene expression method, we found them even though some of them have the IDH mutation.”

All these variations have groups like the World Health Organization asking for better ways to determine poor prognosis IDH patients, they write. Other variations include some glioblastomas with the normal IDH gene carry one of the worse prognoses for gliomas, but there is a subgroup of glioblastomas that act more like astrocytes and tend to carry a better prognosis.

Now that the MCG team has a better indication of which patients will have a worse prognosis, next steps including finding out why and maybe what can be done.

In addition to accuracy of prognosis, a second way to assess a tumor classification method is whether it points you toward better treatment options, She says, which they are now moving toward. He notes that most drugs and many of our actions, like exercise and what we eat, alter RNA expression.

“Right now, if anyone gives us RNA expression data from patients anywhere in the world, we can quickly tell them which glioma subtype it most likely is,” Tran says. The fact that equipment that can examine RNA expression is becoming more widely available, should make transcriptomic profiling more widely available, they say.

Gliomas are tumors of glial cells — which include astrocytes, oligodendrocytes and microglial cells — brain cells which outnumber neurons and whose normal job is to surround and support neurons.

Identification of IDH gene mutations in the cells has already made standard glioma classification more systematic, the scientists say. The mutation can be identified by either staining the biopsy slide or by sequencing for it.

Much progress also has been made in using machine learning to automate and objectify cancer diagnosis and subtyping they write, including glioblastomas. Glioblastomas have been characterized using transcriptome-based analysis but not all gliomas, like the current study.

Like most genes, the IDH gene normally has many jobs in the body, including processing glucose and other metabolites for a variety of cell types. But when mutated, it can become destructive to cells, producing factors like reactive oxygen species, which damage the DNA and contribute to cancer and other diseases. These mutations can result with age and/or environmental exposures. IDH inhibitors are in clinical trials for a variety of cancers including gliomas.

Increasing insight also is emerging into the significant DNA methylation that occurs in cancer, which alters gene expression, resulting in changes like silencing tumor suppressor genes and producing additional cancer-causing genetic mutations.

Reference: Tran, P.M.H., Tran, L.K.H., Nechtman, J. et al. Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas. Sci Rep 10, 20651 (2020). https://www.nature.com/articles/s41598-020-77777-6 https://doi.org/10.1038/s41598-020-77777-6

Provided by Medical College of Georgia at Augusta University

Breakthrough Blood Test Developed For Brain Tumors (Medicine)

Genetic mutations that promote the growth of the most common type of adult brain tumors can be accurately detected and monitored in blood samples using an enhanced form of liquid biopsy developed by researchers at Massachusetts General Hospital (MGH).

Comparing blood samples from patients with gliomas with tumor biopsy tissues from the same patients, Leonora Balaj, PhD, Bob S. Carter, MD, and other MGH investigators in the Department of Neurosurgery found that a novel digital droplet polymerase chain reaction (ddPCR) blood test they pioneered could accurately detect and monitor over time two mutations of the gene TERT. The mutations, labeled C228T and C250T, are known to promote cancer growth and are present in more than 60 percent of all gliomas, and in 80 percent of all high-grade gliomas, the most aggressive and life-threatening type.

Their discovery, which has the potential to substantially improve the diagnosis and monitoring of gliomas, is reported in the journal Clinical Cancer Research.

Gliomas are tumors of glia, central and peripheral nervous system cells that support and protect neurons, the cells that transmit electrical impulses.

Liquid biopsy is a method for detecting cancer by looking for fragments of tumor DNA that circulate in blood. The technique has been shown to be sensitive at detecting the presence of some forms of cancer, but brain tumors have until now posed a formidable barrier.

“Liquid biopsy is particularly challenging in brain tumors because mutant DNA is shed into the bloodstream at much lower level than any other types of tumors,” Balaj says.

“By ‘supercharging’ our ddPCR assay with novel technical improvements, we showed for the first time that the most prevalent mutation in malignant gliomas can be detected in blood, opening a new landscape for detection and monitoring of the tumors,” she says.

The researchers first tested the performance of the ddPCR assay in tumor tissue and found that the results were in perfect agreement with the results from an independently performed clinical laboratory assessment of TERT mutations in the tumor specimens.

They then looked at samples of blood plasma matched to patient tumors and found that the ddPCR assay could detect TERT mutations both in samples from MGH as well as from similarly matched plasma and tumor samples from collaborators at other institutions.

The ddPCR assay has an overall sensitivity (ability to detect the presence of a glioma) of 62.5 percent, which is a tenfold improvement over any prior assay for TERT mutations in the blood for brain tumors, compared to the standard of tissue-based detection of TERT mutations.

The test is easy to use, quick, and low cost, and could be performed in most laboratories, Balaj says. Importantly, the test can also be used to follow the course of disease. “We envision the future integration of tests like this one into the clinical care of our patients with brain tumors,” says Carter, chief of Neurosurgery and co-director of the MGH Brain Tumor Center. “For example, if a patient has a suspected mass on MRI scanning, we can take a blood sample before the surgery and assess the presence of the tumor signature in the blood, and then use this signature as a baseline to monitor as the patient later receives treatment, both to gauge response to the treatment and gain early insight into any potential recurrence.”

The team’s goal is to expand this blood test to be able to differentiate many types of brain tumors.

References: Koushik Muralidharan, Anudeep Yekula, Julia L. Small, Zachary S. Rosh, Keiko M. Kang, Lan Wang, Spencer Lau, Hui Zheng, Hakho Lee, Chetan Bettegowda, Michael R Chicoine, Steven Kalkanis, Ganesh M. Shankar, Brian V Nahed, William T. Curry, Pamela S. Jones, Daniel P. Cahill, Leonora Balaj and Bob S Carter, “TERT promoter mutation analysis for blood-based diagnosis and monitoring of gliomas”, Clinical Cancer Research, 2020. DOI: 10.1158/1078-0432.CCR-20-3083

Provided by Massachusetts General Hospital