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Kumar S, Sarmah DT, Paul A, Chatterjee S. Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastoma. Comput Biol Chem 2024; 109:108024. [PMID: 38335855 DOI: 10.1016/j.compbiolchem.2024.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
The conventional computational approaches to investigating a disease confront inherent constraints as they often need to improve in delving beyond protein functional associations and grasping their deeper contextual significance within the disease framework. Such context-specificity can be explored using clinical data by evaluating the change in interaction between the biological entities in different conditions by investigating the differential co-expression relationships. We believe that the integration and analysis of differential co-expression and the functional relationships, primarily focusing on the source nodes, will open novel insights about disease progression as the source proteins could trigger signaling cascades, mostly because they are transcription factors, cell surface receptors, or enzymes that respond instantly to a particular stimulus. A thorough contextual investigation of these nodes could lead to a helpful beginning point for identifying potential causal linkages and guiding subsequent scientific investigations to uncover mechanisms underlying observed associations. Our methodology includes functional protein-protein Interaction (PPI) data and co-expression information and filters functional linkages through a series of critical steps, culminating in the identification of a robust set of regulators. Our analysis identified eleven key regulators-AKT1, BRCA1, CAMK2G, CUL1, FGFR3, KIF3A, NUP210, PRKACB, RAB8A, RPS6KA2 and TGFB3-in glioblastoma. These regulators play a pivotal role in disease classification, cell growth control, and patient survivability and exhibit associations with immune infiltrations and disease hallmarks. This underscores the importance of assessing correlation towards causality in unraveling complex biological insights.
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Affiliation(s)
- Shivam Kumar
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Dipanka Tanu Sarmah
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Abhijit Paul
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Samrat Chatterjee
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India.
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Hönikl LS, Lange S, Butenschoen VM, Delbridge C, Meyer B, Combs SE, Illert AL, Schmidt-Graf F. The role of molecular tumor boards in neuro-oncology: a nationwide survey. BMC Cancer 2024; 24:108. [PMID: 38243190 PMCID: PMC10797778 DOI: 10.1186/s12885-024-11858-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND In neuro-oncology, the inclusion of tumor patients in the molecular tumor board has only become increasingly widespread in recent years, but so far there are no standards for indication, procedure, evaluation, therapy recommendations and therapy implementation of neuro-oncological patients. The present work examines the current handling of neuro-oncological patients included in molecular tumor boards in Germany. METHODS We created an online based survey with questions covering the handling of neuro-oncologic patient inclusion, annotation of genetic analyses, management of target therapies and the general role of molecular tumor boards in neuro-oncology in Germany. We contacted all members of the Neuro-Oncology working group (NOA) of the German Cancer Society (DKG) by e-mail. RESULTS 38 responses were collected. The majority of those who responded were specialists in neurosurgery or neurology with more than 10 years of professional experience working at a university hospital. Molecular tumor boards (MTB) regularly take place once a week and all treatment disciplines of neuro-oncology patients take part. The inclusions to the MTB are according to distinct tumors and predominantly in case of tumor recurrence. An independently MTB member mostly create the recommendations, which are regularly implemented in the tumor treatment. Recommendations are given for alteration classes 4 and 5. Problems exist mostly within the cost takeover of experimental therapies. The experimental therapies are mostly given in the department of medical oncology. CONCLUSIONS Molecular tumor boards for neuro-oncological patients, by now, are not standardized in Germany. Similarities exists for patient inclusion and interpretation of molecular alterations; the time point of inclusion and implementation during the patient treatment differ between the various hospitals. Further studies for standardization and harmonisation are needed. In summary, most of the interviewees envision great opportunities and possibilities for molecular-based neuro-oncological therapy in the future.
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Affiliation(s)
- Lisa S Hönikl
- Department of Neurosurgery, Klinikum rechts der Isar, Technical University of Munich (TUM), Ismaninger Str. 22, 81675, Munich, Germany.
- Center for Personalized Medicine (ZPM), Klinikum rechts der Isar, Technical Universitiy of Munich (TUM), Munich, Germany.
| | - Sebastian Lange
- Center for Personalized Medicine (ZPM), Klinikum rechts der Isar, Technical Universitiy of Munich (TUM), Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - Vicki M Butenschoen
- Department of Neurosurgery, Klinikum rechts der Isar, Technical University of Munich (TUM), Ismaninger Str. 22, 81675, Munich, Germany
| | - Claire Delbridge
- Center for Personalized Medicine (ZPM), Klinikum rechts der Isar, Technical Universitiy of Munich (TUM), Munich, Germany
- Department of Neuropathology, Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Bernhard Meyer
- Department of Neurosurgery, Klinikum rechts der Isar, Technical University of Munich (TUM), Ismaninger Str. 22, 81675, Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - Anna Lena Illert
- Center for Personalized Medicine (ZPM), Klinikum rechts der Isar, Technical Universitiy of Munich (TUM), Munich, Germany
- Department of Medicine III, Faculty of Medicine, Klinikum Rechts der Isar, Technical University Munich (TUM), Munich, Germany
| | - Friederike Schmidt-Graf
- Center for Personalized Medicine (ZPM), Klinikum rechts der Isar, Technical Universitiy of Munich (TUM), Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
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Bedics G, Szőke P, Bátai B, Nagy T, Papp G, Kránitz N, Rajnai H, Reiniger L, Bödör C, Scheich B. Novel, clinically relevant genomic patterns identified by comprehensive genomic profiling in ATRX-deficient IDH-wildtype adult high-grade gliomas. Sci Rep 2023; 13:18436. [PMID: 37891325 PMCID: PMC10611758 DOI: 10.1038/s41598-023-45786-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023] Open
Abstract
Glioblastomas are the most common IDH-wildtype adult high-grade gliomas, frequently harboring mutations in the TERT gene promoter (pTERT) and utilizing the subsequent telomerase overexpression for telomere length maintenance. However, some rare cases show loss of ATRX and use alternative mechanisms of telomere lengthening. In this study, we performed the first complex genomic analysis specifically concentrating on the latter subgroup. Comprehensive genomic profiling of 12 ATRX-deficient and 13 ATRX-intact IDH-wildtype adult high-grade gliomas revealed that ATRX and pTERT mutations are mutually exclusive. DNMT3A alterations were confined to ATRX-deficient, while PTEN mutations to ATRX-intact cases. RAS-MAPK pathway alterations, including NF1 mutations, were more characteristic in the ATRX-deficient group. Variants of genes related to homologous recombination repair showed different patterns of affected genes. Two ATRX-deficient tumors with high tumor mutational burden and mismatch repair deficiency were found. One of these contained a novel fusion involving the NTRK2 and LRRFIP2 genes, while the other showed loss of MSH2 and MSH6 without genetic alterations in the encoding genes suggesting an epigenetic background. Genetic characteristics of ATRX-deficient IDH-wildtype adult high-grade gliomas suggest that these tumors are particularly intriguing targets of potential future therapeutic interventions including immunotherapies combined with MAPK pathway inhibition and DNA repair inhibitors.
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Affiliation(s)
- Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Péter Szőke
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Bence Bátai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Life Science Building, Debrecen, 4032, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Noémi Kránitz
- Department of Pathology, County Hospital Győr, Petz Aladár Hospital, Vasvári Pál út 2-4, Győr, 9024, Hungary
| | - Hajnalka Rajnai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Lilla Reiniger
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Bálint Scheich
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary.
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Stern E, Ben-Ami M, Gruber N, Toren A, Caspi S, Abebe-Campino G, Lurye M, Yalon M, Modan-Moses D. Hypothalamic-pituitary-gonadal function, pubertal development, and fertility outcomes in male and female medulloblastoma survivors: a single-center experience. Neuro Oncol 2023; 25:1345-1354. [PMID: 36633935 PMCID: PMC10326472 DOI: 10.1093/neuonc/noad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Endocrine deficiencies, including hypothalamic-pituitary-gonadal axis (HPGA) impairment, are common in survivors of childhood and adolescent medulloblastoma. Still, data regarding pubertal development and fecundity are limited, and few studies assessed HPGA function in males. We aimed to describe HPGA function in a large cohort of patients with medulloblastoma. METHODS A retrospective study comprising all 62 medulloblastoma patients treated in our center between 1987 and 2021, who were at least 2 years from completion of therapy. HPGA function was assessed based on clinical data, biochemical markers, and questionnaires. RESULTS Overall, 76% of female patients had clinical or biochemical evidence of HPGA dysfunction. Biochemical evidence of diminished ovarian reserve was seen in all prepubertal girls (n = 4). Among the males, 34% had clinical or biochemical evidence of gonadal dysfunction, 34% had normal function, and 29% were age-appropriately clinically and biochemically prepubertal. The difference between males and females was significant (P = .003). Cyclophosphamide-equivalent dose was significantly associated with HPGA function in females, but not in males. There was no association between HPGA dysfunction and other endocrine deficiencies, length of follow-up, weight status, and radiation treatment protocol. Two female and 2 male patients achieved successful pregnancies, resulting in 6 live births. CONCLUSIONS HPGA dysfunction is common after treatment for childhood medulloblastoma. This is seen more in females, likely due to damage to the ovaries from spinal radiotherapy. Our findings may assist in counseling patients and their families regarding risk to future fertility and need for fertility preservation.
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Affiliation(s)
- Eve Stern
- Pediatric Endocrinology and Diabetes Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Ben-Ami
- Pediatric Endocrinology and Diabetes Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noah Gruber
- Pediatric Endocrinology and Diabetes Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Toren
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Shani Caspi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Gadi Abebe-Campino
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Lurye
- Division of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Yalon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Dalit Modan-Moses
- Pediatric Endocrinology and Diabetes Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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