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Dandapath I, Sahu S, Bhardwaj S, Mohan T, Chakraborty R, Singh J, Singh S, Garg A, Gupta D, Sharma MC, Suri V. Novel EGFR mutations in diffuse midline gliomas using cost-effective strategies: A report of 2 cases. Neurooncol Pract 2024; 11:358-363. [PMID: 38737618 PMCID: PMC11085830 DOI: 10.1093/nop/npae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Background Diffuse midline gliomas (DMGs) are malignant tumors predominantly affecting children, often leading to poor outcomes. The 2021 World Health Organization classification identifies 3 subtypes of DMGs, all characterized by the loss of H3K27 trimethylation. Here, we report 2 cases of DMG with Epidermal Growth Factor Receptor (EGFR) mutations within exon 20, contributing to the understanding of the molecular complexity of these pediatric brain tumors. Methods An economical immunohistochemical panel was designed to aid in the diagnosis of most DMGs in resource-constrained regions. Sanger sequencing was employed to identify rare EGFR mutations in exon 20 of 2 cases. Results Molecular analyses of 2 cases of DMG revealed novel EGFR mutations within exon 20. These mutations were identified using cost-effective diagnostic approaches. The presence of EGFR mutations expands the molecular landscape of DMGs and highlights the genetic heterogeneity within this tumor entity. Conclusions These findings underscore the molecular heterogeneity of DMGs and the significance of identifying novel mutations, such as EGFR mutations in exon 20. Further research into the molecular mechanisms underlying DMGs is warranted to advance therapeutic strategies and improve outcomes for pediatric patients.
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Affiliation(s)
- Iman Dandapath
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Saumya Sahu
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Supriya Bhardwaj
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Trishala Mohan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Rituparna Chakraborty
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotsna Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Garg
- Department of Neuroimaging and Interventional Neuroradiology, All India Institute of Medical Science, New Delhi, India
| | - Deepak Gupta
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
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Dandapath I, Das S, Charan BD, Garg A, Suri A, Kedia S, Sharma MC, Sarkar C, Khonglah Y, Ahmed S, Suri V. Evaluation of KIAA1549::BRAF fusions and clinicopathological insights of pilocytic astrocytomas. Ann Diagn Pathol 2024; 72:152318. [PMID: 38733671 DOI: 10.1016/j.anndiagpath.2024.152318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Pilocytic astrocytoma (PAs) represents a significant portion of childhood primary brain tumors, with distinct histological and radiological features. The prevalence of KIAA1549::BRAF fusion in PAs has been well-established, this study aims to assess the prevalence of KIAA1549::BRAF fusions and explore their associations with tumor characteristics, radiological findings, and patient outcomes in PAs. METHODS Histologically confirmed cases of PAs from a 5-year period were included in the study. Demographic, histopathological, and radiological data were collected, and immunohistochemistry was performed to characterize tumor markers. FISH and qRT-PCR assays were employed to detect KIAA1549::BRAF fusions. Statistical analyses were conducted to examine associations between fusion status and various other parameters. RESULTS Histological analysis revealed no significant differences in tumor features based on fusion status. However, younger age groups showed higher fusion prevalence. Radiologically, fusion-positive cases were distributed across different tumor subtypes SE, CWE and NCWE. Survival analysis did not demonstrate a significant impact of fusion status on overall survival, however most cases with recurrence and death harboured KIAA1549::BRAF fusion. Of 200 PAs, KIAA1549::BRAF fusions were detected in 64 % and 74 % of cases via qRT-PCR and FISH, respectively. Concordance between the two platforms was substantial (86 %). CONCLUSION KIAA1549::BRAF fusions are prevalent in PAs and can be reliably detected using both FISH and qRT-PCR assays. Cost considerations suggest qRT-PCR as a more economical option for fusion detection in routine clinical practice.
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Affiliation(s)
- Iman Dandapath
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Sumanta Das
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Bheru Dan Charan
- Department of Neuroradiology, All, India Institute of Medical Science, New Delhi, India
| | - Ajay Garg
- Department of Neuroradiology, All, India Institute of Medical Science, New Delhi, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Shweta Kedia
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar Chand Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Yookarin Khonglah
- Department of Pathology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya, India
| | - Shabnam Ahmed
- Department of Pathology, GNRC Hospitals, Dispur, Assam, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India.
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Mahajan S, Singh J, Dandapath I, Jha P, Chaturvedi S, Ahuja A, Bhardwaj M, Saran R, Garg A, Sharma MC, Manjunath N, Suri A, Sarkar C, Suri V. Analysis of Histomorphologic/Molecular Association and Immune Checkpoint Regulators in Epithelioid Glioblastoma and Pleomorphic Xanthoastrocytoma: Are These Tumors Potential Candidates for Immune Checkpoint Blockade? Appl Immunohistochem Mol Morphol 2024; 32:84-95. [PMID: 38158760 DOI: 10.1097/pai.0000000000001179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/12/2023] [Indexed: 01/03/2024]
Abstract
Accurate diagnosis of Epithelioid glioblastoma (eGB) and pleomorphic xanthoastrocytoma (PXA) is sometimes challenging owing to overlapping histologic and genetic features. There are limited reports on the immune profile of these tumors. In this study, we assessed 21 PXA [15 PXA Grade 2 (PXAG2); 6 PXA Grade 3 (PXAG3)] and 14 eGB for their histopathological and molecular association. Further, their immune profile was compared with GB, IDH1 wild-type (wt) (n-18). Morphologically, PXAG2 mostly differed from eGB; however, it was occasionally difficult to differentiate PXAG3 from eGB due to their epithelioid pattern and less obvious degenerative features. PXAG2 showed predominantly diffuse, whereas variable positivity for epithelial and glial markers was seen in PXAG3 and eGB. All cases showed retained nuclear ATRX and INI-1 . H3K27M or IDH1 mutation was seen in none. P53 mutation was more common in eGB, followed by PXAG3, and least common in PXAG2. BRAF V600E mutation was observed in 66.67% PXAG2, 33.33% PXAG3, and 50% eGB, with 100% concordance between immunohistochemistry (IHC) and sequencing. Thirty-six percent eGB, 33% PXAG3, and 61% PXAG2 harbored CDKN2A homozygous deletion. EGFR amplification was observed in 14% eGB and 66% of GB, IDH wt. PDL1 and CTLA-4 expression was higher in eGB (71.4% and 57.1%), PXAG3 (66.6% and100%), and PXAG2 (60% & 66.7%) as compared with GB, IDH wt (38.8% and 16.7%). Tumor-infiltrating lymphocytes were also observed in a majority of eGB and PXA (90% to 100%) in contrast to GB, IDH wt (66%). This analysis highlights the homogenous molecular and immune profile of eGB and PXA, suggesting the possibility that histologically and molecularly, these two entities represent 2 ends of a continuous spectrum with PXAG3 lying in between. Higher upregulation of PDL1, CTLA-4, and increased tumor infiltrating lymphocytes in these tumors as compared with GB, IDH wt suggests potential candidature for immunotherapy.
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Affiliation(s)
- Swati Mahajan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotsna Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Iman Dandapath
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Prerana Jha
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Chaturvedi
- Department of Pathology, Institute of Human Behaviour and Allied Sciences, New Delhi, India
| | - Arvind Ahuja
- Department of Pathology, PGIMER & Dr. RML Hospital, New Delhi, India
| | - Minakshi Bhardwaj
- Department of Pathology, PGIMER & Dr. RML Hospital, New Delhi, India
| | - Ravindra Saran
- Department of Pathology, G B Pant Institute of Postgraduate Medical Education and Research, New Delhi, India
| | - Ajay Garg
- Department of Neuroradiology, All India Institute of Medical Science, New Delhi
| | - Mehar C Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Niveditha Manjunath
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
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Kumari K, Dandapath I, Singh J, Rai HIS, Kaur K, Jha P, Malik N, Chosdol K, Mallick S, Garg A, Suri A, Sharma MC, Sarkar C, Suri V. Molecular Characterization of IDH Wild-type Diffuse Astrocytomas: The Potential of cIMPACT-NOW Guidelines. Appl Immunohistochem Mol Morphol 2022; 30:410-417. [PMID: 35708480 DOI: 10.1097/pai.0000000000001038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 04/25/2022] [Indexed: 11/26/2022]
Abstract
IDH wild-type (wt) grade 2/3 astrocytomas are a heterogenous group of tumors with disparate clinical and molecular profiles. cIMPACT-NOW recommendations incorporated in the new 2021 World Health Organization (WHO) Classification of Central Nervous System (CNS) Tumors urge minimal molecular criteria to identify a subset that has an aggressive clinical course similar to IDH -wt glioblastomas (GBMs). This paper describes the use of a panel of molecular markers to reclassify IDH -wt grade 2/3 diffuse astrocytic gliomas (DAGs) and study median overall survival concerning for to IDH -wt GBMs in the Indian cohort. IDH -wt astrocytic gliomas (grades 2, 3, and 4) confirmed by IDHR132H immunohistochemistry and IDH1/2 gene sequencing, 1p/19q non-codeleted with no H3F3A mutations were included. TERT promoter mutation by Sanger sequencing, epidermal growth factor receptor amplification, and whole chromosome 7 gain and chromosome 10 loss by fluorescence in situ hybridization was assessed and findings correlated with clinical and demographic profiles. The molecular profile of 53 IDH -wt DAGs (grade 2: 31, grade 3: 22) was analyzed. Eleven cases (grade 2: 8, grade 3: 3) (20.75%) were reclassified as IDH -wt GBMs, WHO grade 4 ( TERT promoter mutation in 17%, epidermal growth factor receptor amplification in 5.5%, and whole chromosome 7 gain and chromosome 10 loss in 2%). Molecular GBMs were predominantly frontal (54.5%) with a mean age of 36 years and median overall survival equivalent to IDH -wt GBMs (18 vs. 19 mo; P =0.235). Among grade 2/3 DAGs not harboring these alterations, significantly better survival was observed for grade 2 versus grade 3 DAGs (25 vs. 16 mo; P =0.002). Through the incorporation of a panel of molecular markers, a subset of IDH -wt grade 2 DAGs can be stratified into molecular grade 4 tumors with prognostic and therapeutic implications. However, IDH -wt grade 3 DAGs behave like GBMs irrespective of molecular profile.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ajay Garg
- Neuroradiology, All India Institute of Medical Sciences, New Delhi, Delhi, India
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Dandapath I, Gupta R, Singh J, Shukla N, Jha P, Sharma V, Suri A, Sharma MC, Suri V, Sarkar C, Kulshreshtha R. Long Non-coding RNA and mRNA Co-expression Network Reveals Novel Players in Pleomorphic Xanthoastrocytoma. Mol Neurobiol 2022; 59:5149-5167. [PMID: 35674862 DOI: 10.1007/s12035-022-02893-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/18/2022] [Indexed: 11/25/2022]
Abstract
Histological interpretation of the rare pleomorphic xanthoastrocytoma (PXA) has been the holy grail for treatment options. However, no stand-alone clinical interventions have been developed owing to the lack of gene expression profiling data in PXA/APXA patients. We first time report the comprehensive analyses of the coding as well as long non-coding RNA (lncRNA) signatures of PXA/APXA patients. Several genes such as IGFBP2, NF1, FOS, ERBB2, and lncRNAs such as NEAT1, HOTAIRM1, and GAS5 known to play crucial roles in glioma patients were also deregulated in PXA patients suggesting the commonality in the molecular signatures. PPI network, co-expression, and lncRNA-mRNA interaction studies unraveled hub genes (such as ERBB2, FOS, RPA1) and networks that may play a critical role in PXA biology. The most enriched pathways based on gene profiles were related to TLR, chemokine, MAPK, Rb, and PI3K-Akt signaling pathways. The lncRNA targets were enriched in glucuronidation, adipogenesis, TGF-beta signaling, EGF/EGFR signaling, and cell cycle pathways. Interestingly, several mRNAs like PARVG, and ABI2 were found to be targeted by multiple lncRNAs suggesting a tight control of their levels. Some of the most prominent lncRNA-mRNA pairs were LOC728730: MRPL9, XLOC_l2_011987: ASIC2, lnc-C1QTNF5-1: RNF26. Notably, several lncRNAs such as lnc-CETP-1, lnc-XRCC3-1, lnc-RPL31-1, lnc-USP13-1, and MAPKAPK5-AS1, and genes such as RPA1, NTRK3, and CNRP1 showed strong correlation to the progression-free survival of PXA patients suggesting their potential as novel biomarkers. Overall, the findings of this study may facilitate the development of a new realm of RNA biology in PXA that may have clinical significance in the future.
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Affiliation(s)
- Iman Dandapath
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India
| | - Rahul Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Jyotsna Singh
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India
| | - Nidhi Shukla
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India
| | - Prerana Jha
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India
| | - Vikas Sharma
- All India Institute of Medical Sciences, CCRF, New Delhi, 110029, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - M C Sharma
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India
| | - Vaishali Suri
- Neuropathology Laboratory, All India Institute of Medical Sciences, Neurosciences Centre, New Delhi, 110029, India.
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Dandapath I, Mahajan DS, Sahu DS, Sharma DMC, Suri DA, Suri DV. LGG-53. Evaluation of KIAA-BRAF1549 fusions in pilocytic astrocytoma with clinicopathological correlation. Neuro Oncol 2022. [PMCID: PMC9164696 DOI: 10.1093/neuonc/noac079.365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Pilocytic astrocytomas (PAs) are the primary tumors most frequently found in children and adolescents, accounting for 5.4% of all gliomas. The overall prognosis of PAs is good, yet a substantial no of cases have a poor outcome, with recurrence, and ultimately death. The KIAA1549-BRAF fusion is a useful putative diagnostic marker for PAs and BRAF also is an important therapeutic marker. Aim and Objectives To study the frequency of KIAA1549-BRAF fusion (16-9, 15-9 and 16-11) in different locations of PAs using qRT-PCR technique in FFPE samples. Methodology Three different exon rearrangements of KIAA1549-BRAF (16-9, 15-9 and 16-11) fusions were assessed in 50 cases of PAs by using qRT-PCR (gold standard). FISH assay was also performed in all the cases. Results Out of 50 PAs, 32 were localised in midline structures such as the cerebellum, optic pathway, hypothalamus, and brain stem while 18 in non-midline regions like the cerebral hemispheres. Majority of the cases (35/50); 70% were positive for KIAA1549-BRAF fusion by RT-PCR. Of these, (16/35); 45.7% harboured 15-9 fusion, (15/35); 42.8% harboured 16-9 fusion, and only (4/35); 11.4% had 16-11 fusion. Only (24/30); 48% KIAA1549-BRAF showed fusion by FISH assay. There was 54.2% concordance between FISH and RT-PCR results. KIAA1549-BRAF fusion was observed in 78% of midline and 55.5% of non-midline cases. The frequency of KIAA1549-BRAF fusion decreased with increasing age, 77% in the age group <20, 54% in the age group 20-40 and 30% in the age group >40. Conclusion 15-9 and 16-9 KIAA1549-BRAF were the most frequently occurring fusions dominantly seen in the midline. The presence of fusion is inversely proportional to the age of patients. qRT-PCR is the gold standard technique and FISH assay has moderate concordance with qRT-PCR platform.
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Affiliation(s)
- Iman Dandapath
- All India Institute of Medical Sciences, South Delhi , New Delhi , India
| | - Dr Swati Mahajan
- All India Institute of Medical Sciences, South Delhi , New Delhi , India
| | - Dr Saumya Sahu
- All India Institute of Medical Sciences, South Delhi , New Delhi , India
| | | | - Dr Ashish Suri
- All India Institute of Medical Sciences, South Delhi , New Delhi , India
| | - Dr Vaishali Suri
- All India Institute of Medical Sciences, South Delhi , New Delhi , India
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Singh J, Dandapath I, Jha P, Shukla N, Gupta R, Katiyar A, Sharma V, Mahajan S, Chaturvedi S, Ahuja A, Bhardwaj M, Saran R, Garg A, Sharma MC, Manjunath N, Suri A, Kulshreshtha R, Sarkar C, Suri V. Gene expression based profiling of pleomorphic xanthoastrocytoma highlights two prognostic subgroups. Am J Transl Res 2022; 14:1010-1023. [PMID: 35273703 PMCID: PMC8902531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Pleomorphic xanthoastrocytomas (PXAs) are rare, accounting for less than 1% of astrocytomas, and commonly occur in young patients. The majority are WHO grade II. A fraction of tumors that present or recur with malignant change are classified as anaplastic (APXA, grade III). Limited data are available on their molecular characteristics. METHODOLOGY Genome-wide expression profiling of 14 PXA and 6 APXAs was performed by microarray. Among differentially expressed genes (DEGs), Cyclin-Dependent Kinase 14 (CDK14) and Mitochondrial Fission Process 1 (MTFP1) were validated by qRT PCR. RESULT Unsupervised hierarchical clustering revealed two distinct molecular clusters (Cluster 1: 10 PXA, 3 APXA and Cluster 2: 4 PXA, 3 APXA) with grade II and III tumors distributed in both highlighting molecular heterogeneity within the same grade. There was an insignificant difference in age, sex, immunohistochemical profile, frequency of BRAF mutation, or CDKN2A deletion among the two clusters. Significantly, worse progression-free survival was observed in cluster 2 (P=0.003). mRNA profiling-based prediction of recurrence was superior to and independent of histological grade, BRAF mutation, or CDKN2A deletion status. A total of 10 upregulated and 418 downregulated genes were identified between the PXA clusters. qRT-PCR validation of CDK14 (upregulated in cluster 2) and MTFP1 (upregulated in cluster 1) showed strong concordance with expression array data. CONCLUSION This is the first comprehensive study highlighting distinct molecular subgroups of PXA. The differentially expressed genes between two clusters may potentially be used for developing histology independent classification schemes, prognostication and may serve as prospective therapeutic targets for PXA patients.
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Affiliation(s)
- Jyotsna Singh
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Iman Dandapath
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Prerana Jha
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Nidhi Shukla
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Rahul Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology DelhiNew Delhi, India
| | - Amit Katiyar
- CCRF, All India Institute of Medical SciencesNew Delhi, India
| | - Vikas Sharma
- CCRF, All India Institute of Medical SciencesNew Delhi, India
| | - Swati Mahajan
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Sujata Chaturvedi
- Department of Pathology, Institute of Human Behaviour and Allied SciencesNew Delhi, India
| | - Arvind Ahuja
- Department of Pathology, PGIMER & Dr. RML HospitalNew Delhi, India
| | | | - Ravindra Saran
- Department of Pathology, GB Pant Institute of Postgraduate Medical Education and ResearchNew Delhi, India
| | - Ajay Garg
- Department of Neuroradiology, All India Institute of Medical SciencesNew Delhi, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Niveditha Manjunath
- Department of Neurosurgery, All India Institute of Medical SciencesNew Delhi, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical SciencesNew Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology DelhiNew Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical SciencesNew Delhi, India
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Dandapath I, Chakraborty R, Kaur K, Mahajan S, Singh J, Sharma MC, Sarkar C, Suri V. Molecular alterations of low-grade gliomas in young patients: Strategies and platforms for routine evaluation. Neurooncol Pract 2021; 8:652-661. [PMID: 34777834 PMCID: PMC8579091 DOI: 10.1093/nop/npab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, it has been established that molecular biology of pediatric low-grade gliomas (PLGGs) is entirely distinct from adults. The majority of the circumscribed pediatric gliomas are driven by mitogen-activated protein kinase (MAPK) pathway, which has yielded important diagnostic, prognostic, and therapeutic biomarkers. Further, the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT) Steering Committee in their fourth meeting, suggested including a panel of molecular markers for integrated diagnosis in "pediatric-type" diffuse gliomas. However, a designated set of platforms for the evaluation of these alterations has yet not been mentioned for easier implementation in routine molecular diagnostics. Herein, we have reviewed the relevance of analyzing these markers and discussed the strategies and platforms best apposite for clinical laboratories.
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Affiliation(s)
- Iman Dandapath
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Kavneet Kaur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotsna Singh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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Singh M, Kaur K, Sharma A, Kaur R, Joshi D, Chatterjee M, Dandapath I, Kaur A, Singh H, Singh P. Genome-wide characterization of peptidyl-prolyl cis-trans isomerases in Penicillium and their regulation by salt stress in a halotolerant P. oxalicum. Sci Rep 2021; 11:12292. [PMID: 34112860 PMCID: PMC8192932 DOI: 10.1038/s41598-021-91602-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Peptidyl-prolyl cis-trans isomerases (PPIases) are the only class of enzymes capable of cis-trans isomerization of the prolyl peptide bond. The PPIases, comprising of different families viz., cyclophilins, FK506-binding proteins (FKBPs), parvulins and protein phosphatase 2A phosphatase activators (PTPAs), play essential roles in different cellular processes. Though PPIase gene families have been characterized in different organisms, information regarding these proteins is lacking in Penicillium species, which are commercially an important fungi group. In this study, we carried out genome-wide analysis of PPIases in different Penicillium spp. and investigated their regulation by salt stress in a halotolerant strain of Penicillium oxalicum. These analyses revealed that the number of genes encoding cyclophilins, FKBPs, parvulins and PTPAs in Penicillium spp. varies between 7-11, 2-5, 1-2, and 1-2, respectively. The halotolerant P. oxalicum depicted significant enhancement in the mycelial PPIase activity in the presence of 15% NaCl, thus, highlighting the role of these enzymes in salt stress adaptation. The stress-induced increase in PPIase activity at 4 and 10 DAI in P. oxalicum was associated with higher expression of PoxCYP18. Characterization of PPIases in Penicillium spp. will provide an important database for understanding their cellular functions and might facilitate their applications in industrial processes through biotechnological interventions.
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Affiliation(s)
- Mangaljeet Singh
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Kirandeep Kaur
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Avinash Sharma
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rajvir Kaur
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Dimple Joshi
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Megha Chatterjee
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Iman Dandapath
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Amarjeet Kaur
- grid.411894.10000 0001 0726 8286Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Harpreet Singh
- grid.506003.00000 0004 1778 5641Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab 144008 India
| | - Prabhjeet Singh
- grid.411894.10000 0001 0726 8286Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
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