This document summarizes molecular studies in central nervous system (CNS) tumors. It discusses the need for molecular studies to integrate histologic and molecular data in tumor classification. It then reviews molecular markers for various CNS tumors including gliomas, medulloblastoma, ependymal tumors, and meningioma. For each tumor type, key genetic alterations are identified that have diagnostic, predictive or prognostic significance such as IDH1/2 mutations, 1p/19q codeletion, MGMT methylation, and others.

1. MOLECULAR STUDIES
IN CNS TUMORS
DR. AMRITA RAKESH
(DNB RESIDENT)
Bhagwan Mahaveer Cancer Hospital And Research Centre
Jaipur.
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2. NEED OF MOLECULAR
STUDIES ?
• The WHO classification for CNS tumors was
revised in 2016 with a basis on the “integrated
diagnosis” incorporating histologic and molecular
advances.
• Diagnostic , predictive & prognostic
significance.
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3. 3

4. Cell of Origin For CNS
tumors
• Glial Cells
• Neural Stem Cells (NSCs)
• Genes that are expressed in NSCs are Nestin,
EGFR , PTEN , Hedgehog etc.
• Aberrant activation of developmental genetic
programs in NSC gives rise to CNS tumors.
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5. Gliomas
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6. • Gliomas are the most common intracranial
neoplasm.
• Astrocytoma , glioblastomas and oligodendrogliomas
accounting for more than 80%.
• Classified as grade I to IV.
• Grade I - JPA
• Grade II - fibrillary astrocytoma
• Grade III - anaplastic astrocytoma
• Grade IV - glioblastoma (most aggressive).
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7. • 1985 : Epidermal growth factor receptor (EGFR) gene
amplification in glioblastoma.
• Subsequent discoveries :
• Phosphate and tensin homolog (PTEN) gene.
• Mutations in the Tp53 gene.
• BRAF mutation
• MGMT gene
• IDH mutations.
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8. MOLECULAR MARKERS
:GLIOMA
• 1p/19q co-deletion in oligodendroglial tumors.
• Mutations in the IDH 1/2 genes in diffuse gliomas.
• Hypermethylation of the MGMT gene promoter
in glioblastomas.
• Alterations in the EGFR and PTEN genes , and
10q deletions in GBMs.
• BRAF alterations in pilocytic astrocytomas.
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9. 9

10. 1p/19q Co-Deletion
• A diagnostic , predictive and prognostic marker among the gliomas.
• Loss of short arm of chromosome 1 (1p)along with long arm of
chromosome 19 (19q) ; genetic signature of oligodendroglioma - early
genetic event.
• 80-90% in oligodendrogliomas (WHO grade II)
• 60% in anaplastic oligodendrogliomas (WHO grade III).
• 30 to 50% in oligoastrocytomas.
• Partial loss of 1p has opposite prognostic significance as compared
to complete loss.
• Almost all co-deletions also positive for IDH1 or 2 mutations.
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11. • The CIC gene (encoding for protein capicua homolog) is a tumor
suppressor gene present in Chr 19.
• Loss of CIC gene results in loss of transcription repressor
function.
• The status of 1p/19q loci detected by:
• FISH
• PCR
• LOH analysis
• Comparative genomic hybridization array
• Single nucleotide polymorphism array.
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12. • Associated with enhanced response to
radiochemotherapy.
• Cairncross et al.:(1998) : better response to
procarbazine-lomustine-vincristine chemotherapy and
a longer survival in patients with anaplastic
oligodendroglioma.
• Co-deletions of 9p or 10q may lead to poor outcome
independent of the 1p/19q status.
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13. IDH1 & IDH2 Mutations
• Diagnostic and prognostic marker among gliomas.
• Mutations in IDH1 are frequent (70-80%) in WHO grade II & III
astrocytomas and a small subset (5-10%) of GBMs (WHO grade
IV).
• IDH1 are completely absent in pilocytic astrocytomas.
• IDH2 genes mutations were detected in a similar proportion of
gliomas (5%) , mostly in oligodendroglial tumors.
• Presence of the mutation is associated with young age , a
secondary type GBM (60-90%) , and increased overall
survival.
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14. • IDH normally catalyses the action of isocitrate to a-
ketoglutarate, whereas the mutant forms of IDH1 & IDH2
lead to the production of the oncometabolite 2-
hydroxyglutarate, which inhibits function of numerous a-
ketoglutarate-dependent enzymes and leads to higher
levels of DNA methylation.
• IDH mutations identify a subset of gliomas with a slower rate
of growth and substantially improved prognosis, grade for
grade, compared with gliomas that are IDH wild type.
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15. MGMT Methylation
• The MGMT gene is located at chromosome 10q26 and
encodes for a DNA repair protein.
• Prognostic and predictive marker.
• Epigenetic silencing of this gene by promoter
hypermethylation leads to reduced expression of the
MGMT protein.
• MGMT gene silencing improves survival in patients
with glioblastoma who are treated concurrently
with alkylating drug temozolamide and radiation
therapy.
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16. • Hegi and colleagues (2005) : reported that 49%
of patients with glioblastoma and methylated
MGMT were alive at 2 yrs after treatment with
temozolamide and radiotherapy, as compared to
15% of patients with unmethylated MGMT.
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17. BRAF Mutation
• In gliomas : BRAF activation is by gene duplication or
point mutation.
• Fusion between the KIAA1549 and BRAF genes.
• Identified in 60-80% pilocytic astrocytomas ; rare in
diffuse astrocytic gliomas.
• Interphase FISH -currently the best method for testing
for this fusion.
• Prognostic significance is still under investigation.
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18. EGFR and PTEN
alterations
• EGFR gene : located on chromosome 7p12.
• Activation of EGFR signalling through gene amplification or
mutations is found in about 30 to 40% of primary glioblastomas.
• Mutant EGFR is indicative of high-grade glioma .
• PTEN gene located on long arm of chromosome 10.
• Counteracts PI3K-AKT signaling pathway.
• frequently found in high-grade gliomas.
• Poor prognostic marker for anaplastic astrocytomas and
glioblastomas.
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19. Ki-67
• Prognostic marker among grade II & III diffuse gliomas.
• Ki-67 is a nuclear antigen expressed in cells actively engaged in
the cell cycle but not expressed in the resting phase G0.
• Results expressed as percentage of positive staining cells.
• Among grade II and III diffuse gliomas, the Ki-67 index provides
prognostic value, as there is strong inverse relationship to
survival on multivariat analysis but not in GBM.
• Helpful in determining grade in histologically borderline cases.
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20. TP53
• Diagnostic marker among gliomas.
• TP53 mutation is a marker of astrocytoma lineage
in the setting of IDH mutation and occurs in
infiltrative astrocytomas,grade II;anaplastic
astrocytomas,grade III; and GBM,WHO grade IV.
• Extremely rare in Oligodendrogliomas with IDH
mutation and 1p/19q codeletion.
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21. ATRX
• ATRX (alpha thalassemia/mental retardation
syndrome X-linked) - diagnostic marker among
gliomas.
• Strongly associated with IDH mutation and TP53
mutation in infiltrating gliomas.
• Marker of astrocytic lineage.
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23. Medulloblastoma
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24. • Origin : stem cells located in the subependymal
matrix and the external granular layer of the
cerebellum.
• Medulloblastomas are tumors of the cerebellum ,
arising more frequently in the midline , especially
in the posterior vermis , adjacent to the roof of the
fourth ventricle.
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25. • Five histological subtypes :
• Classical type (CMB)
• Desmoplastic / Nodular type (DN)
• Medulloblastoma with extensive nodularity
(MBEN)
• Anaplastic type
• Large cell Medulloblastoma (LC)
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26. • 4 - MOLECULAR SUBGROUPS:
• WNT subgroup
• Sonic hedgehog subgroup
• Group 3
• Group 4
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27. • WNT subgroup - the WNT/b-catenin pathway
participates in the control of vertebrate development.
• Rarest subgroup of medulloblastoma, accounting for 11%
; includes mainly classic MB.
• Patients with Turcot Syndrome : predisposition to WNT
MB.
• Monosomy of chromosome 6 is present in about
100% of WNT tumors.
• Overall excellent long term prognosis (90% 5 yr
survival rate).
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28. • IHC : monoclonal antibodies against the C-
terminal domain of b-catenin.
• CTNNB1 (b-catenin encoding gene) mutation
analysis by direct gene sequencing.
• Cantharidin and noncantharidin : drugs on trial
against Wnt associated medulloblastoma.
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29. • SHH medulloblastomas - accounts for 28% of all
medulloblastomas ; intermediate prognosis.
• Dichotomous age distribution : <4 yrs and >16 yrs.
• Sonic Hedgehog (shh) pathway plays a key role in
normal cerebellar development, induces
proliferation of neuronal precursor cells in the
developing cerebellum and other tissues.
• Desmoplastic/nodular and MBEN are almost
exclusively associated with shh pathway
activation.
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30. • Group 3 Medulloblastomas - 28% of all medulloblastomas.
• associated with worst prognosis and frequently metastatic.
• predominantly found in infants/children.
• associated with MYC amplification.
• 3a-tumors — increased MYC expression and worse
prognosis.
• 3b-tumors — normal MYC expression and better prognosis.
• Mostly associated with classic or large cell/anaplastic
morphology.
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31. • Group 4 Medulloblastomas - most common “typical” subgroup
of medulloblastoma, accounting for around 34%.
• Rarely affect infants (0-3 yrs) and mainly affect children, with a
peak age of 10 years.
• intermediate prognosis.
• classic histology.
• 2/3rd cases associated with isochromosome 17q.
• associated with CDK6 & MYCN amplification but minimal MYC
over-expression.
• Chromosome X-loss is seen in 80% of females.
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34. EPENDYMAL
TUMORS
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35. • Taylor et al., aCGH profiles of 103
ependymomas, three molecularly distinct
subtypes of ependymomas depending on tumor
location :
• Supratentorial ependymomas : CDKN2A
deletion in >90% cases, poor prognosis.
• Spinal tumors : deletion of chromosome 22q12
• Posterior fossa ependymomas : chromosome
1q gain , good prognosis.
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36. • RELA fusion positive ependymomas : subset of
supratentorial ependymomas.
• amenable to targeted therapy.
• Methylation status of HIC-1 putative tumor
suppressor gene : down regulation in 81% of
cases , correlated with non-spinal localization and
paediatric age.
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37. MENINGIOMA
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38. • Most common CNS tumors in adults.
• Associated risk factors - deletions of the neurofibromatosis
type 2 (NF2) gene & ionising radiations.
• Benign meningiomas - slow growing & 5-yr recurrence rate
of 5% following gross-total resection.
• Atypical meningiomas have 5-yr recurrence rate of
40%.
• Anaplastic meningiomas have recurrence rates of up to
80%.
• Surgical resection and radiotherapy- mainstay of treatment.
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39. Cytogenetic Abnormality
• Monosomy 22 is the most frequent genetic
abnormality.
• Association between the long arm of chromosome
22 (22q) and meningiomas was first studied in
patients with NF-2.
• NF-2 codes for tumor suppressor merlin , which
has critical role in controlling cell growth and
motility.
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40. • Chr 1p deletions comprise the second most
common chromosomal abnormality.
• Loss of 1p also associated with a 30% recurrence
rate.
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41. PRIMARY CNS
LYMPHOMA
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42. • Accounts for less than 5% of all primary brain
tumours.
• 95-98% diagnosed as high-grade DLBCL.
• 70% are supratentorial
• Periventricular location , facilitating
leptomeningeal seeding.
• Extends across the corpus-callosum and involve
both cerebral hemispheres.
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43. • Gain on chromosome 12 — most frequent alteration.
• Gain in the region of 12q.
• MDM2 , CDK4 & GLI1 overexpression.
• EBV - immunocompromised individuals.
• BCA1 (CXCR13) - expressed at significant levels in PCNSL
tumors.
• Ectopic expression of Interleukin-4 : not expressed in the
vasculature of normal brain.
• Hypermethylation of CDKN2A gene - established molecular
event; produces p14ARF.
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44. • TO CONCLUDE - not only a morphological
diagnosis , but also molecular data is necessary
for prognosis and response to treatment.
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45. Thank You
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