Changes to pediatric brain tumors in 2021 World Health Organization classification of tumors of the central nervous system.

New tumor types are continuously being described with advances in molecular testing and genomic analysis resulting in better prognostics, new targeted therapy options and improved patient outcomes. As a result of these advances, pathological classification of tumors is periodically updated with new editions of the World Health Organization (WHO) Classification of Tumors books. In 2021, WHO Classification of Tumors of the Central Nervous System, 5th edition (CNS5), was published with major changes in pediatric brain tumors officially recognized including pediatric gliomas being separated from adult gliomas, ependymomas being categorized based on anatomical compartment and many new tumor types, most of them seen in children. Additional general changes, such as tumor grading now being done within tumor types rather than across entities and changes in definition of glioblastoma, are also relevant to pediatric neuro-oncology practice. The purpose of this manuscript is to highlight the major changes in pediatric brain tumors in CNS5 most relevant to radiologists. Additionally, brief descriptions of newly recognized entities will be presented with a focus on imaging findings.

SUFU haploinsufficiency causes a recognisable neurodevelopmental phenotype at the mild end of the Joubert syndrome spectrum.

BACKGROUND: Joubert syndrome (JS) is a recessively inherited ciliopathy characterised by congenital ocular motor apraxia (COMA), developmental delay (DD), intellectual disability, ataxia, multiorgan involvement, and a unique cerebellar and brainstem malformation. Over 40 JS-associated genes are known with a diagnostic yield of 60%-75%.In 2018, we reported homozygous hypomorphic missense variants of the SUFU gene in two families with mild JS. Recently, heterozygous truncating SUFU variants were identified in families with dominantly inherited COMA, occasionally associated with mild DD and subtle cerebellar anomalies. METHODS: We reanalysed next generation sequencing (NGS) data in two cohorts comprising 1097 probands referred for genetic testing of JS genes. RESULTS: Heterozygous truncating and splice-site SUFU variants were detected in 22 patients from 17 families (1.5%) with strong male prevalence (86%), and in 8 asymptomatic parents. Patients presented with COMA, hypotonia, ataxia and mild DD, and only a third manifested intellectual disability of variable severity. Brain MRI showed consistent findings characterised by vermis hypoplasia, superior cerebellar dysplasia and subtle-to-mild abnormalities of the superior cerebellar peduncles. The same pattern was observed in two out of three tested asymptomatic parents. CONCLUSION: Heterozygous truncating or splice-site SUFU variants cause a novel neurodevelopmental syndrome encompassing COMA and mild JS, which likely represent overlapping entities. Variants can arise de novo or be inherited from a healthy parent, representing the first cause of JS with dominant inheritance and reduced penetrance. Awareness of this condition will increase the diagnostic yield of JS genetic testing, and allow appropriate counselling about prognosis, medical monitoring and recurrence risk.

Imaging of Horner syndrome in pediatrics: association with neuroblastoma.

Neuroblastoma is the most common neoplasm associated with pediatric Horner syndrome. The laboratory and imaging evaluation of isolated pediatric Horner syndrome is controversial. We review the literature published in the last several decades and present the rationale for the imaging work-up in this patient cohort.

MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.

MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.

Expanding phenotype with severe midline brain anomalies and missense variant supports a causal role for FOXA2 in 20p11.2 deletion syndrome.

Rare individuals with 20p11.2 proximal deletions have been previously reported, with a variable phenotype that includes heterotaxy, biliary atresia, midline brain defects associated with panhypopituitarism, intellectual disability, scoliosis, and seizures. Deletions have ranged in size from 277 kb to 11.96 Mb. We describe a newborn with a de novo 2.7 Mb deletion of 20p11.22p11.21 that partially overlaps previously reported deletions and encompasses FOXA2. Her clinical findings further expand the 20p11.2 deletion phenotype to include severe midline cranial and intracranial defects such as aqueductal stenosis with hydrocephalus, mesencephalosynapsis with diencephalic-mesencephalic junction dysplasia, and pyriform aperture stenosis. We also report one individual with a missense variant in FOXA2 who had abnormal glucose homeostasis, panhypopituitarism, and endodermal organ dysfunction. Together, these findings support the critical role of FOXA2 in panhypopituitarism and midline defects.

Glial injury in neurotoxicity after pediatric CD19-directed chimeric antigen receptor T cell therapy.

OBJECTIVE: To test whether systemic cytokine release is associated with central nervous system inflammatory responses and glial injury in immune effector cell-associated neurotoxicity syndrome (ICANS) after chimeric antigen receptor (CAR)-T cell therapy in children and young adults. METHODS: We performed a prospective cohort study of clinical manifestations as well as imaging, pathology, CSF, and blood biomarkers on 43 subjects ages 1 to 25 who received CD19-directed CAR/T cells for acute lymphoblastic leukemia (ALL). RESULTS: Neurotoxicity occurred in 19 of 43 (44%) subjects. Nine subjects (21%) had CTCAE grade 3 or 4 neurological symptoms, with no neurotoxicity-related deaths. Reversible delirium, headache, decreased level of consciousness, tremor, and seizures were most commonly observed. Cornell Assessment of Pediatric Delirium (CAPD) scores ≥9 had 94% sensitivity and 33% specificity for grade ≥3 neurotoxicity, and 91% sensitivity and 72% specificity for grade ≥2 neurotoxicity. Neurotoxicity correlated with severity of cytokine release syndrome, abnormal past brain magnetic resonance imaging (MRI), and higher peak CAR-T cell numbers in blood, but not cerebrospinal fluid (CSF). CSF levels of S100 calcium-binding protein B and glial fibrillary acidic protein increased during neurotoxicity, indicating astrocyte injury. There were concomitant increases in CSF white blood cells, protein, interferon-γ (IFNγ), interleukin (IL)-6, IL-10, and granzyme B (GzB), with concurrent elevation of serum IFNγ IL-10, GzB, granulocyte macrophage colony-stimulating factor, macrophage inflammatory protein 1 alpha, and tumor necrosis factor alpha, but not IL-6. We did not find direct evidence of endothelial activation. INTERPRETATION: Our data are most consistent with ICANS as a syndrome of systemic inflammation, which affects the brain through compromise of the neurovascular unit and astrocyte injury. ANN NEUROL 2019.

MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance.

To date, mutations in 15 actin- or microtubule-associated genes have been associated with the cortical malformation lissencephaly and variable brainstem hypoplasia. During a multicenter review, we recognized a rare lissencephaly variant with a complex brainstem malformation in three unrelated children. We searched our large brain-malformation databases and found another five children with this malformation (as well as one with a less severe variant), analyzed available whole-exome or -genome sequencing data, and tested ciliogenesis in two affected individuals. The brain malformation comprised posterior predominant lissencephaly and midline crossing defects consisting of absent anterior commissure and a striking W-shaped brainstem malformation caused by small or absent pontine crossing fibers. We discovered heterozygous de novo missense variants or an in-frame deletion involving highly conserved zinc-binding residues within the GAR domain of MACF1 in the first eight subjects. We studied cilium formation and found a higher proportion of mutant cells with short cilia than of control cells with short cilia. A ninth child had similar lissencephaly but only subtle brainstem dysplasia associated with a heterozygous de novo missense variant in the spectrin repeat domain of MACF1. Thus, we report variants of the microtubule-binding GAR domain of MACF1 as the cause of a distinctive and most likely pathognomonic brain malformation. A gain-of-function or dominant-negative mechanism appears likely given that many heterozygous mutations leading to protein truncation are included in the ExAC Browser. However, three de novo variants in MACF1 have been observed in large schizophrenia cohorts.

Establishment of normative values for the fetal posterior fossa by magnetic resonance imaging.

OBJECTIVE: Suspected Dandy-Walker continuum anomalies constitute a significant percentage of prenatal cases evaluated by magnetic resonance imaging (MRI). To unify the description of posterior fossa malformations, we sought to establish objective measurements for the posterior fossa in normal fetuses between 18 and 37 weeks gestation. METHODS: T2-weighted images of normal fetal brains in sagittal projection were obtained from fetal magnetic resonance (MR) studies of normal brains performed from 2009 to 2017.121 fetal brains were included in the analysis. Three radiologists reviewed images and recorded the following for each case: superior posterior fossa angle (SPFA), posterior fossa perimeter, and tegmento-vermian angle (TVA). RESULTS: For each feature, the mean of the measurements, the percentage of absolute difference of the reader measurement compared with mean measurement, and the interclass correlation (ICC) were calculated. Values are reported as mean ± standard deviation. Perimeter increases linearly with age, whereas the SPFA and the TVA are independent of gestational age. For all included cases, the SPFA averaged 100.9° ± 8° and the TVA averaged 2.5° ± 2.3°. CONCLUSION: The superior posterior fossa angle, a novel measurement, and the posterior fossa perimeter can be used for establishing the expected size of the posterior fossa in second- and third-trimester fetuses by MRI.

The central nervous system manifestations of localized craniofacial scleroderma: a study of 10 cases and literature review.

BACKGROUND: Localized craniofacial scleroderma is a rare pediatric disease that involves a spectrum of discoloration, fibrosis and hemiatrophy of the face and scalp. Children with localized craniofacial scleroderma may have neurological symptoms, and in this context often undergo diagnostic imaging of the brain. OBJECTIVE: To catalogue neuroimaging abnormalities in patients with localized craniofacial scleroderma treated at our institution, review their clinical courses and compare this data with prior studies. MATERIALS AND METHODS: Following Institutional Review Board approval, an imaging database search identified 10 patients with localized craniofacial scleroderma and neuroimaging abnormalities treated at our institution. Neuroimaging exams and the electronic medical record were reviewed for each case. RESULTS: The most common indications for neuroimaging were headache or seizure (80% of cases). The most common neuroimaging abnormalities were T2-hyperintense, subcortical white matter lesions ipsilateral to the cutaneous lesion (90% of cases) on magnetic resonance imaging (MRI). Calcifications or blood products (50%), cysts (40%) and abnormal enhancement (20%) were also observed. A positron emission tomography (PET) scan obtained for a single case demonstrated diminished 18F-fluorodeoxyglucose (FDG) avidity corresponding to the dominant focus of signal abnormality on MRI. Progressive neuroimaging abnormalities were present in 30% of cases. There was no consistent relationship between changes in neurological symptoms following treatment and neuroimaging findings. CONCLUSION: Our results are similar to previously published data. In the absence of new or worsening neurological symptoms, the role of neuroimaging for follow-up of localized craniofacial scleroderma is unclear. Knowledge of intracranial neuroimaging abnormalities that are commonly associated with localized craniofacial scleroderma helps to distinguish these lesions from others that have similar appearance.

Pilocytic astrocytoma with leptomeningeal spread in a patient with incontinentia pigmenti presenting with unilateral nystagmus.

Incontinentia pigmenti (IP) is a genetic disorder caused by mutations in IKBKG, leading to functional loss of nuclear factor kappa B (NF-ĸB). We report the case of a 6-month-old female child with IP who presented with unilateral nystagmus and was found to have a pilocytic astrocytoma with leptomeningeal spread. Enhanced understanding of the relationship between NF-ĸB, along with its upstream regulators, and tumorigenesis may shed light on whether a subset of patients with IP may be at increased risk for neoplasia.

Primary choriocarcinoma of the bilateral basal ganglia presenting in a teenaged male.

Primary intracranial choriocarcinoma (PICCC), a type of germ-cell tumor, is a very rare primary tumor of the central nervous system that generally arises in the pineal or suprasellar region. We present a case of a teenage boy with PICCC of the bilateral basal ganglia, an anatomic site for which we were unable to find the previous reports. We offer discussion of the differential diagnosis, imaging characteristics, and prognosis of PICCC and germ-cell tumors of the basal ganglia, in the hope that it will increase awareness and allow for early detection.

Mind the gap: an unusual case of a cervical lipomyelocele.

Cervical dysraphism is rare, and the 3 recognized subtypes manifest as cystic, skin-covered masses. To our knowledge, no case of cervical lipomyelocele has been reported in the literature so far. We present a case of surgically and pathologically confirmed cervical lipomyelocele in a patient with spondylocostal dysostosis and multiple other congenital anomalies and a brief review of the literature. In this case, magnetic resonance imaging demonstrates fat extension into a dysraphic cervical spinal canal, allowing for preoperative diagnosis. Computed tomography using 3-dimensional reconstruction serves to more clearly characterize the extensive spine malsegmentation characteristic of spondylocostal dysostosis. The use of this technique is suggested to benefit the orthopedic or neurologic surgeon confronted with such complex malformations.

Prenatal diagnosis of Chudley-McCullough syndrome.

Chudley-McCullough syndrome (CMS) is an autosomal-recessive disorder characterized by a complex brain malformation and profound congenital sensorineural hearing loss. Postnatal brain imaging findings include ventriculomegaly, partial agenesis of corpus callosum, inferior cerebellar dysplasia, arachnoid cysts, and malformations of cortical development including frontal subcortical heterotopia and polymicrogyria. Prenatal diagnosis of CMS is important due to the markedly less severe neurodevelopmental prognosis compared to disorders with similar brain imaging findings. We report prenatal imaging features that help distinguish CMS from other disorders, including slit-like frontal horns, agenesis of the corpus callosum, frontal subcortical heterotopia, arachnoid cysts, and cerebellar dysplasia. © 2016 Wiley Periodicals, Inc.

Cervicothoracic cystic dysraphism.

Cystic dysraphism of the cervical and upper thoracic spine is very rare. It differs from the much more common lumbosacral dysraphism in appearance and structure, and usually portends a better prognosis due to lack of functional neurological tissue in the dysraphic sac and absent or less severe intracranial anomalies. There is ambiguity in the literature regarding terminology because of the paucity of cases. We present cases of the most common type of cervicothoracic cystic dysraphism and emphasize differences from lumbosacral myelomeningocele. Patient outcome depends on the presence of associated anomalies and whether complete surgical resection is performed. Imaging plays a critical role in surgical planning, screening the central nervous system for additional anomalies, and in the postoperative setting for evaluation of retethering.

Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism.

IMPORTANCE: Focal cortical dysplasia (FCD), hemimegalencephaly, and megalencephaly constitute a spectrum of malformations of cortical development with shared neuropathologic features. These disorders are associated with significant childhood morbidity and mortality. OBJECTIVE: To identify the underlying molecular cause of FCD, hemimegalencephaly, and diffuse megalencephaly. DESIGN, SETTING, AND PARTICIPANTS: Patients with FCD, hemimegalencephaly, or megalencephaly (mean age, 11.7 years; range, 2-32 years) were recruited from Pediatric Hospital A. Meyer, the University of Hong Kong, and Seattle Children's Research Institute from June 2012 to June 2014. Whole-exome sequencing (WES) was performed on 8 children with FCD or hemimegalencephaly using standard-depth (50-60X) sequencing in peripheral samples (blood, saliva, or skin) from the affected child and their parents and deep (150-180X) sequencing in affected brain tissue. Targeted sequencing and WES were used to screen 93 children with molecularly unexplained diffuse or focal brain overgrowth. Histopathologic and functional assays of phosphatidylinositol 3-kinase-AKT (serine/threonine kinase)-mammalian target of rapamycin (mTOR) pathway activity in resected brain tissue and cultured neurons were performed to validate mutations. MAIN OUTCOMES AND MEASURES: Whole-exome sequencing and targeted sequencing identified variants associated with this spectrum of developmental brain disorders. RESULTS: Low-level mosaic mutations of MTOR were identified in brain tissue in 4 children with FCD type 2a with alternative allele fractions ranging from 0.012 to 0.086. Intermediate-level mosaic mutation of MTOR (p.Thr1977Ile) was also identified in 3 unrelated children with diffuse megalencephaly and pigmentary mosaicism in skin. Finally, a constitutional de novo mutation of MTOR (p.Glu1799Lys) was identified in 3 unrelated children with diffuse megalencephaly and intellectual disability. Molecular and functional analysis in 2 children with FCD2a from whom multiple affected brain tissue samples were available revealed a mutation gradient with an epicenter in the most epileptogenic area. When expressed in cultured neurons, all MTOR mutations identified here drive constitutive activation of mTOR complex 1 and enlarged neuronal size. CONCLUSIONS AND RELEVANCE: In this study, mutations of MTOR were associated with a spectrum of brain overgrowth phenotypes extending from FCD type 2a to diffuse megalencephaly, distinguished by different mutations and levels of mosaicism. These mutations may be sufficient to cause cellular hypertrophy in cultured neurons and may provide a demonstration of the pattern of mosaicism in brain and substantiate the link between mosaic mutations of MTOR and pigmentary mosaicism in skin.

Temporal bone and cranial nerve findings in pontine tegmental cap dysplasia.

INTRODUCTION: Pontine tegmental cap dysplasia (PTCD) is a recently described brain malformation associated with multiple cranial neuropathies, most commonly congenital sensorineural hearing loss. The purpose of this study is to systematically characterize the cranial nerve and temporal bone findings in a cohort of children with this rare condition. METHODS: Sixteen patients with PTCD and diagnostic quality imaging were retrospectively reviewed. All patients had high-resolution MR of the brain and/or internal auditory canals, and seven patients had additional high-resolution CT of the temporal bones. Studies were evaluated by two pediatric neuroradiologists for cranial nerve and temporal bone anomalies. RESULTS: Fifteen of 16 patients (94%) had duplication of one or both internal auditory canals. Of the 24 total duplicated internal auditory canals, all 24 (100%) demonstrated stenosis or atresia of the vestibulocochlear nerve canal, as well as ipsilateral vestibulocochlear nerve aplasia. Of the non-duplicated internal auditory canals, 63% (5/8) were atretic or stenotic. Thirty-eight percent (3/8) were associated with absent vestibulocochlear nerve, and 38% (3/8) demonstrated isolated cochlear nerve aplasia. Twenty-five percent (2/8) demonstrated normal vestibulocochlear nerves, both in the same patient. Fifteen of 16 patients overall (94%) demonstrated bilateral cochlear nerve aplasia. Of the 32 total temporal bones, 4 (13%) demonstrated facial nerve aplasia. Seventy-nine percent (22/28) of facial nerves that were present demonstrated an aberrant origin or course. CONCLUSION: Patients with PTCD have highly characteristic temporal bone and cranial nerve findings on both CT and MR. Recognition of these findings is important for improved diagnosis of this rare disorder, particularly by CT.

Two Hundred Thirty-Six Children With Developmental Hydrocephalus: Causes and Clinical Consequences.

Few systematic assessments of developmental forms of hydrocephalus exist. We reviewed magnetic resonance images (MRIs) and clinical records of patients with infancy-onset hydrocephalus. Among 411 infants, 236 had hydrocephalus with no recognizable extrinsic cause. These children were assigned to 1 of 5 subtypes and compared on the basis of clinical characteristics and developmental and surgical outcomes. At an average age of 5.3 years, 72% of children were walking independently and 87% could eat by mouth; in addition, 18% had epilepsy. Distinct patterns of associated malformations and syndromes were observed within each subtype. On average, children with aqueductal obstruction, cysts, and encephaloceles had worse clinical outcomes than those with other forms of developmental hydrocephalus. Overall, 53% of surgically treated patients experienced at least 1 shunt failure, but hydrocephalus associated with posterior fossa crowding required fewer shunt revisions. We conclude that each subtype of developmental hydrocephalus is associated with distinct clinical characteristics, syndromology, and outcomes, suggesting differences in underlying mechanisms.

Recognizable cerebellar dysplasia associated with mutations in multiple tubulin genes.

Mutations in alpha- and beta-tubulins are increasingly recognized as a major cause of malformations of cortical development (MCD), typically lissencephaly, pachygyria and polymicrogyria; however, sequencing tubulin genes in large cohorts of MCD patients has detected tubulin mutations in only 1-13%. We identified patients with a highly characteristic cerebellar dysplasia but without lissencephaly, pachygyria and polymicrogyria typically associated with tubulin mutations. Remarkably, in seven of nine patients (78%), targeted sequencing revealed mutations in three different tubulin genes (TUBA1A, TUBB2B and TUBB3), occurring de novo or inherited from a mosaic parent. Careful re-review of the cortical phenotype on brain imaging revealed only an irregular pattern of gyri and sulci, for which we propose the term tubulinopathy-related dysgyria. Basal ganglia (100%) and brainstem dysplasia (80%) were common features. On the basis of in silico structural predictions, the mutations affect amino acids in diverse regions of the alpha-/beta-tubulin heterodimer, including the nucleotide binding pocket. Cell-based assays of tubulin dynamics reveal various effects of the mutations on incorporation into microtubules: TUBB3 p.Glu288Lys and p.Pro357Leu do not incorporate into microtubules at all, whereas TUBB2B p.Gly13Ala shows reduced incorporation and TUBA1A p.Arg214His incorporates fully, but at a slower rate than wild-type. The broad range of effects on microtubule incorporation is at odds with the highly stereotypical clinical phenotype, supporting differential roles for the three tubulin genes involved. Identifying this highly characteristic phenotype is important due to the low recurrence risk compared with the other (recessive) cerebellar dysplasias and the apparent lack of non-neurological medical issues.

KIAA0586 is Mutated in Joubert Syndrome.

Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. JS is part of a group of disorders called ciliopathies based on their overlapping phenotypes and common underlying pathophysiology linked to primary cilium dysfunction. Biallelic mutations in one of 28 genes, all encoding proteins localizing to the primary cilium or basal body, can cause JS. Despite this large number of genes, the genetic cause can currently be determined in about 62% of individuals with JS. To identify novel JS genes, we performed whole exome sequencing on 35 individuals with JS and found biallelic rare deleterious variants (RDVs) in KIAA0586, encoding a centrosomal protein required for ciliogenesis, in one individual. Targeted next-generation sequencing in a large JS cohort identified biallelic RDVs in eight additional families for an estimated prevalence of 2.5% (9/366 JS families). All affected individuals displayed JS phenotypes toward the mild end of the spectrum.

PI3K/AKT pathway mutations cause a spectrum of brain malformations from megalencephaly to focal cortical dysplasia.

Malformations of cortical development containing dysplastic neuronal and glial elements, including hemimegalencephaly and focal cortical dysplasia, are common causes of intractable paediatric epilepsy. In this study we performed multiplex targeted sequencing of 10 genes in the PI3K/AKT pathway on brain tissue from 33 children who underwent surgical resection of dysplastic cortex for the treatment of intractable epilepsy. Sequencing results were correlated with clinical, imaging, pathological and immunohistological phenotypes. We identified mosaic activating mutations in PIK3CA and AKT3 in this cohort, including cancer-associated hotspot PIK3CA mutations in dysplastic megalencephaly, hemimegalencephaly, and focal cortical dysplasia type IIa. In addition, a germline PTEN mutation was identified in a male with hemimegalencephaly but no peripheral manifestations of the PTEN hamartoma tumour syndrome. A spectrum of clinical, imaging and pathological abnormalities was found in this cohort. While patients with more severe brain imaging abnormalities and systemic manifestations were more likely to have detected mutations, routine histopathological studies did not predict mutation status. In addition, elevated levels of phosphorylated S6 ribosomal protein were identified in both neurons and astrocytes of all hemimegalencephaly and focal cortical dysplasia type II specimens, regardless of the presence or absence of detected PI3K/AKT pathway mutations. In contrast, expression patterns of the T308 and S473 phosphorylated forms of AKT and in vitro AKT kinase activities discriminated between mutation-positive dysplasia cortex, mutation-negative dysplasia cortex, and non-dysplasia epilepsy cortex. Our findings identify PI3K/AKT pathway mutations as an important cause of epileptogenic brain malformations and establish megalencephaly, hemimegalencephaly, and focal cortical dysplasia as part of a single pathogenic spectrum.