Research in to Brain Tumours

Project Updates

March 2024

What have been your key achievements over the past few months?

A major focus of Yura’s work is in helping to unravel new subgroups of paediatric high grade glioma. Over the last year he has been heavily involved in the analysis of data relating to a large class of tumours which do not have the histone H3 mutations – so-called H3-wild-type. These may often present as being very diffusely spread throughout the brain, a variant known as gliomatosis cerebri (GC). Yura has worked to analyse data from a large European study on behalf of the SIOPE network to perform an integrated study on the pathology, radiology and biology of childhood GC. Within this study of 104 patients, we identified the presence of a GC-like growth pattern to be an independent poor prognosis factor, especially in tumours whose histology appeared to look like a tumour of lower risk. Most importantly, Yura’s analysis of the data derived from methylation array profiling highlighted for the first time that there was an enrichment of certain subgroups of gliomas for GC. Unlike previous studies which led to the exclusion of GC from the WHO brain tumour classification scheme, we identified a significant prevalence GC for subtypes called pedHGG_RTK2A/B and pedHGG_A/B, which frequently had mutations in a gene called EGFR.

This provides the first evidence for GCs to have a distinct biology to other gliomas, and also provides for a new therapeutic target in these tumours. Taking this work further, Yura has been involved in a collaboration between our lab, and that of Mariella Filbin (Boston), Mara Vinci (Rome) and David Castel (Paris). Here, working with our PhD student Shauna Crampsie, Yura has helped analyse data from our ‘single cell profiling’ of such specimens. We have identified particular gene signatures associated with how the cells spread through the brain, and are currently investigating these further in cell models derived from patients.

In another project with Mariella Filbin’s team, we have worked to understand another form of paediatric high grade glioma which have the H3G34 mutations. Here we have combined single cell analysis as above along with large ‘genetic screening’ experiments in which we take patients’ tumour cells and knock out every gene individually to see which ones are critical for tumour growth. Combining these analyses, Yura has helped to identify several genes which are important for tumour development as they reflect the cells from which these tumours arise, and may represent new targets for treating these children. One such target is CDK6, for which there are drugs already available in the clinic. We have been fortunate to work with our clinical colleagues at the Royal Marsden to treat one such child with a CDK6 inhibitor – having progressed on a second round of traditional chemotherapy, this patient remained well and with good quality of life for 18 months on this new drug, which gives us hope that it may represent a new treatment option for children with these types of tumours. We are now working towards identifying combinations of drugs that could enter clinical trial to test this.

Finally, Yura has also been working with Matt Clarke in our lab to specifically study the group of patients in the teenage and young adult population (TYA, 13-30 yrs) who develop high grade gliomas. Here by combining many different forms of molecular analyses, Yura has been able to tease out specific subgroups of the disease which are specifically associated with this age group for the first time. These subgroups are poorly defined, and do not have clear targetable alterations that we could think about using in the clinic. Yura is currently working to explore these data further in order to better refine these subgroup and identify exactly what makes them different from similar-looking tumours which occur in younger children and older adults.

What are the next steps?

Yura’s current priorities, in addition to the above projects, is finalising some analysis for our PhD student Molina Das. She has been looking at the emergence of drug resistance in diffuse midline glioma which are treated with inhibitors of the MAPK pathway, which we identified in a project a couple of years ago. She has combined single cell analysis and a way of ‘barcoding’ glioma cells to track the emergence of cells which can escape treatment with the drug. Molina recently spent 3 months with our collaborator Mimi Bandopadhayay in Boston, and Yura travelled there for discussions about how best to analyse these data with other bioinformaticians at the Dana Farber Cancer Institute. Yura is leading on this work and currently helping Molina prepare her findings for presentation at the upcoming ISPNO meeting in Philadelphia, and for publication.

Details of publications and upcoming publications:

Abstracts – ISPNO 2024, Philadelphia

1. Das M, Grabovska Y, Collins J, Rogers R, Burford A, Mackay A, Chang T, Beroukhim R, Bandopadhayay P and Jones C “Combining clonal tracking with single cell RNA sequencing reveals temporal shifts in cell states associated with trametinib resistance in MAPK altered diffuse midline glioma “

2. Kessler K, Grabovska Y, Carvalho D, Burford A, Temelso S, Tari H, Molinari V, Crampsie S, Yu L, Choudhary J,Proszek P, Hubank M, Mackay A, Jones C “Subclonal populations of diffuse midline glioma cells promote tumorigenesis through AP-1 transcription factor dysregulation”

3. Mackay A, Grabovska Y, Carvalho D, Burford A, Pereira R, Temelso S, Sejdiu D, Crampsie S, Molinari V, Rogers R, Kessler K, Bjerke L, Bridges L, Reisz Z, Al-Sarraj S, Singh N, Stapleton S, Bleil C, Hettige C, Zebian B, Cockle J, Carceller F, Clarke M and Jones C “Integrated molecular profiling of >2000 paediatric-type diffuse high-grade glioma tumours and 100 patient-derived models”

4. Rogers R, Grabovska Y, Mackay A, Carvalho D, Dobinson C, Pereira R, Sejdiu D, Burford A, Molinari V, Ruddle R, Gabel F, Raynaud F, Chew N, Tsui V, Sun C, Firestein R, Jones C “A novel role for ACVR1/ALK2 in regulating cholesterol biosynthesis provides a new combinatorial therapeutic approach for patients with DMG”

5. Perez-Somarriba M, Cherungonath A, Wasti A, Pace E, Benjamin P, Villacampa G, Reisz Z, Al-Sarraj S, Bridges L, Jacques T, Lavarino C, Gene N, Pereira R, Grabovoska Y, Mackay A, Kessler K, Clarke M, Santa-Maria V, Cruz O, Morales La Madrid A, Llort A, Lassaletta A, Vazquez-Gomez F, Carceller E, Garrido C, Solano-Paez P, Quiroga E, Zebian B, Hettige S, Cockle J, Mandeville M, Angelini P, Srivatsa K, Vaidya S, Marshall L, Jones C* and Carceller F “Clinical and molecular features of bithalamic gliomas in children and adolescents: multicentric study and meta-analysis?

6. Tauziède-Espariat A, Friker LL, NussbaumerG, Bison B, Dangouloff-Ros V, Métais A, SumerauerD, Zamecnik J, Benesch M, Perwein T, van Vuurden D, Wesseling P, Morales La Madrid A, Garre ML, Antonelli M, GiangasperoF, PietschT, JonesDTW, GrabovskaY, MackayA, Jones C, GrillJ, KrammCM, CastelD, GielenGH and Varlet P “Diffuse Pediatric-Type High-Grade Glioma Of Methylation-Based RTK2A And B Subclasses Present Distinct Radiological And Histomolecular Features”

7. Reisz Z, Pereira R, Nevis S, Mackay A, Bhaw L, Grabovska Y, Laxton R, Molinari V, Burford A, Barnaby C, Bleil C, Zebian B, Weiser A, Carceller F, Marshall L, King A, Bodi I, Al-Sarraj S, Jones C* and Clarke M “An exceptionally rare case of a diffuse midline glioma with concomitant H3.1 K27M and G34R mutations in the HIST1H3C gene”

Papers

1. Pereira R, Mackay A, Grabovska Y, Clarke A, Bloo, T, Nicoll J, Procter J, Moore A, Schagen J, Walker L, Roncaroli F, Ogunbigi O, van Dalen T, Ziegler D, Shi Z, Jacques TS, Hargrave D, Zebian B, Bleil C, Yates J, Norton E, Mandeville H, Creak A, Welsh L, Marshall L, Carceller F, Reisz Z, Al-Sarraj S, Mastronuzzi A, Carai A, Vinci M, Kurian K, Ng HK, Brandner S, Jones C* and Clarke M (submitted) “The spectrum of IDH- and H3-wildtype high-grade glioma subgroups occurring across teenage and young adult patient populations” Acta Neuropath

2. Nussbaumer G, Benesch M, Grabovska Y, Mackay A, Castel D, Grill J, Alonso MM, Antonelli M, Bailey S, Baugh JS, Biassoni V, Blattner-Johnson M, Broniscer A, Carai A, Colafati GS, Colditz C, Corbacioglu, S, Crampsie S, Entz-Werle N, Eyrich M, Friker LL, Frühwald MC, Garrè ML, Gerber NU, Giangaspero F, Gil-da-Costa MJ, Graf N, Hargrave D, Hauser P, Herrlinger U, Hoffmann M, Hulleman E, Izquierdo E, Jacobs S, Karremann M, Kattamis A, Kebudi R, Kortmann R-D, Kwiecien R, Massimino M, Mastronuzzi A, Miele E, Morana G, Noack CM, Pentikainen V, Perwein T, Pfister SM, Pietsch T, Roka K, Rossi S, Rutkowski S, Schiavello E, Seidel C, Štěrba J, Sturm D, Sumerauer D, Tacke A, Temelso S, Valentini C, van Vuurden D, Varlet P, Veldhuijzen van Zanten SEM, Vinci M, von Bueren AO, Warmuth-Metz M, Wesseling P, Wiese M, Wolff JEA, Zamecnik J, Morales La Madrid A, Bison B, Gielen GH, Jones DTW*, Jones C*, and Kramm CM* (in revision) “Gliomatosis cerebri in children: A poor prognostic, highly infiltrative phenotype of diffuse gliomas with a distinct molecular profile” Neuro-Oncol

3. Liu I, Bjerke L, Cruzeiro GAV, Rogers R, Grabovska Y, Panditharatna E, Mackay A, Barron T, Shaw ML, Hoffman SE, Hack OA, Quezada MA, Dempster J, Temelso S, Englinger B, Molinari V, Mire H, Jiang L, Madlener S, Mayr L, Dorfer C, Geyeregger R, Rota C, Alexandrescu S, Agnihotri S, Eisenstat DD, Carceller F, Stapleton S, Bleil C, Cole KA, Waanders A, Montero Carcaboso A, Vinci M, Hargrave D, Haberler C, Gojo J, Slavc I, Linnarsson S, Monje M, Jones C* and Filbin M* (in revision) “Early GABAergic neuronal lineage defines dependencies in histone H3 G34R/V glioma” Cancer Cell

June 2022

What have been your key achievements over the past few months?

A major piece of work over the last 6 months has been in the analysis of a genome-wide genetic screen aimed at identifying combination therapies alongside ACVR1 inhibitors in diffuse midline glioma. We had previously
identified mutations in ACVR1 to be present in around 25% of these tumours, and had published on using compounds directed against the receptor in our cell models. We are part of the CONNECT international
consortium, aiming to take an ACVR1 inhibitor into clinical trials, and have been working with 4 labs around the world to generate the necessary data to support this. In addition to screening a range of compounds in order to
determine which should be prioritised, we have been looking for new drug combinations which may be even more effective than any drug alone. Rebecca in the lab carried out a large ’CRISPR’ screen in ACVR1-mutant cells, knocking out every gene in the human genome alongside drug treatment, to look for which genes may kill these tumour cells more effectively alongside an ACVR1 inhibitor. This generates highly complex data which Yura has been analysing, generating ‘hits’ which can then be validated back in the lab. Rebecca and Yura have shown that targeting genes in the MAPK pathway, or specific processes associated with DNA repair, may be particularly effective. We are currently running and analysing large drug screens to validate these results, and working with our CONNECT colleagues to assess the combination of ACVR1 and MAPK inhibitors in vivo. This work is being presented at the upcoming ISPNO conference in Hamburg, the largest meeting for childhood brain tumour
research, and the first in-person for 4 years! Yura has also contributed substantially to three other abstracts from our lab, looking at specific subpopulations of glioma cells, and how we may use certain types of immunotherapy to alter the cellular landscape and kill the tumour cells.
It’s an incredibly exciting and productive time for the team, with Yura being central to so many advances and highlights.

What are the next steps?

In addition to validating the ACVR1 screening work, we are also carrying out similar experiments in gliomas which have MAPK alterations directly. Here we are specifically looking to establish a technique in the lab whereby we
can genetically label every individual tumour cell in our laboratory model, such that when we treat with drug we can identify the specific genetic make-up of any cells that are resistant to the inhibitor. This is currently being developed by our PhD student Molina along with collaborators in Boston, with Yura’s help in respect of the complex bioinformatics associated with the 20 million genetic ‘barcode’ library which needs to be introduced to our cell culture model, and then deconvoluted once the experiment is complete. Molina and Yura have this running for MAPK inhibitors, and if successful we will extend this to other glioma targets.

Details of publications and upcoming publications:

Abstracts – ISPNO 2022, Hamburg

1. Rebecca Rogers, Yura Grabovska, Diana Carvalho, Elisabet Fernandez, Elisa Izquierdo, Alan Mackay, Chris Jones “Combined pharmacological and genetic screening to identify dependencies and combinations in ACVR1-mutant diffuse midline glioma”
2. Ketty Kessler, Yura Grabovska, Anna Burford, Sara Temelso, Haider Tari, Valeria Molinari, Shauna Crampsie, Lu Yu, Jyoti Choudhary, Paula Proszek, Mike Hubank, Alan Mackay, Chris Jones “Multi-omic profiling of patient-derived subclones identifies aggressive cellular subpopulations in paediatric diffuse high grade gliomas (PDHGGs)”
3. Julia V Cockle, Lynn Bjerke, Alan Mackay, Yura Grabovska, Anna Burford, Valeria Molinari, Rita Pereira, Jessica Boult, Diana Martins Carvalho, Ian Titley, Erika Yara, Alan Melcher, Erik Wennerberg, Chris Jones “Exploring and modulating the tumour immune microenvironment to facilitate the selection of immunotherapies for paediatric-type diffuse high-grade glioma”
4. Alan Mackay, Sara Temelso, Diana Martins Carvalho, Ketty Kessler, Jessica Boult, Elisa Izquierdo, Rita Pereira, Elisabet Fernandez, Anna Burford, Valeria Molinari, Lynn Bjerke, Yura Grabovska, Rebecca Rogers, Shauna Crampsie, Molina Das, Simon Robinson, Matthew Clarke, Chris Jones “Evolutionary selection of key oncogenic alterations in patient-derived models of paediatric diffuse high grade glioma (PDHGG) subtypes in vitro and in vivo”

Papers

1. Izquierdo E, Carvalho DM, Mackay A, Temelso S, Boult JKR, Pericoli G, Potente EF, Das M, Molinari V, Grabovska Y, Rogers R, Ajmne-Cat MA, Proszek P, Stubbs M, Depani S, O’Hare P, Yu L, Choudhary J, Clarke M, Fairchild AR, Jacques TS, Grundy R, Howell L, Picton S, Adamski J, Wilson S, Gray J, Zebian B, Marshall LV, Carceller F, Grill J, Vinci M, Robinson SP, Hubank M, Hargrave D and Jones C (2021) “DIPG harbour alterations targetable by MEK inhibitors, with acquired resistance mechanisms overcome by combinatorial inhibition” Cancer Discov 12(3):712-729
2. Carvalho DM, Temelso S, Mackay A, Pemberton HN, Rogers R, Kessler K, Izquierdo E, Bjerke L, Fazal Salom J, Clarke M, Grabovska Y, Burford A, Proszek P, Potente EF, Boult JKR, Molinari V, Taylor KR, Fofana M, Chandler C, Zebian B, Bhangoo R, Martin AJ, Dabbous B, Stapleton S, Hettige S, Marshall LV, Carceller F, Mandeville H, Vaidya S, Saran F, Bridges LR, Al-Sarraj S, Johnston R, Cryan J, Crimmins D, Caird J, Pears J, Mastronuzzi A, Carai A, Robinson SP, Hubank M, Moore AS, Lord CJ, Carcaboso AM, Vinci M, and Jones C (in revision) “Drug screening linked to molecular profiling identifies novel dependencies in patient-derived primary cultures of paediatric high grade glioma and DIPG” Nature Commun
3. Liu I, Bjerke L, Cruzeiro GAV, Rogers R, Grabovska Y, Panditharatna E, Mackay A, Barron T, Shaw ML, Hoffman SE, Hack OA, Quezada MA, Dempster J, Temelso S, Englinger B, Molinari V, Mire H, Jiang L, Madlener S, Mayr L, Dorfer C, Geyeregger R, Rota C, Alexandrescu S, Agnihotri S, Eisenstat DD, Carceller F, Stapleton S, Bleil C, Cole KA, Waanders A, Montero Carcaboso A, Vinci M, Hargrave D, Haberler C, Gojo J, Slavc I, Linnarsson S, Monje M, Jones C* and Filbin M* (in revision) “Early GABAergic neuronal lineage defines dependencies in histone H3 G34R/V glioma” Nature Cancer