Multi-Institutional Clinical Review
A retrospective chart review was performed on 38 patients with newly diagnosed H3 G34-mutant DHG between 2006 and 2024. Twenty-four patients were treated at St. Jude Children’s Research Hospital, and 14 patients were treated at collaborating institutions (The University of Oklahoma Health Sciences Center, Akron Children’s Hospital, The University of North Carolina School of Medicine, The University of Texas Health San Antonio, Children’s Mercy Kansas City, American University of Beirut Medical Center, Kaiser Permanente Los Angeles Medical Center, and Lucile Packard Children’s Hospital Stanford). Collected data included patient demographics, tumor location, molecular alterations, surgical resection status, treatment details, and survival outcomes. Frontline TMZ use was defined as the receipt of at least ten doses of TMZ during RT and/or at least one completed maintenance cycle of TMZ (any dose). Institutional review board approval was obtained at St. Jude (IRB# 19–0338, 22-1199, 24-1699) and external institutions based on local guidelines.
Systematic Review of Literature
An electronic search of PubMed was performed using the terms “H3 G34-mutant OR G34 OR H3 G34 OR G34R OR H3 G34R OR H3.3 G34R” AND “Brain Tumor OR Glioma OR PNET OR Brain OR Diffuse Hemispheric Glioma” to yield articles discussing H3 G34-mutant DHG. One hundred fifty-four articles were identified and independently reviewed by two investigators (J.T.R. and D.T.). Thirty-four articles reporting patient-level survival data and associated molecular findings were included in our meta-analysis cohort. Patient data duplicated across articles was identified and subsequently removed prior to analysis. Based on the initial identification of histone H3 mutations in pHGG in 2012, only articles published between January 1, 2012, and March 15, 2024, were considered. Non-peer-reviewed preprint articles and abstracts were excluded from the review. The systematic review and meta-analysis were conducted in accordance with PRISMA reporting guidelines.
Whole genome sequencing
Genomic DNA was extracted from snap-frozen tumor tissue using an automated Maxwell RSC Instrument (Promega), as previously described [7, 14, 16]. DNA quality was assessed on a 4200 TapeStation (Agilent). Paired-end sequencing was conducted on the Illumina HiSeq platform with a 100- or 125-bp read length or NovaSeq with a 150-bp read length. Sequencing results were analyzed using an institutionally established pipeline for alignment and calling of single nucleotide variants (SNVs). Insertions or deletions (indels) were annotated and ranked by putative pathogenicity using a workflow named “medal ceremony” and subsequently manually reviewed [37].
Whole exome sequencing
Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using a QIAamp DNA FFPE Tissue Kit (Qiagen), as previously described [7, 9, 14, 16]. The genomic libraries were generated using the SureSelectXT kit (Agilent Technologies), followed by exome enrichment using the SureSelectXT Human All Exon V8 bait set (Agilent Technologies). The resulting exon-enriched libraries were then subjected to the paired-end, 100-cycle sequencing performed on a NovaSeq X Plus (Illumina). Sequencing results were analyzed as mentioned above.
Methylation array analysis
Genomic DNA was extracted as stated above and subjected to genome-wide methylation profiling on an Illumina Infinium MethylationEPIC platform, as previously described [7–10, 16, 20]. Copy number variation analysis was performed using conumee, as previously described [13]. MGMT promotor methylation was assessed using MGMT-STP27, as previously described [2, 3].
Histopathology review and immunohistochemistry
Hematoxylin and eosin-stained 5 µm sections of FFPE tissue specimens of all tumor samples were centrally reviewed by a board-certified neuropathologist specialized in pediatric CNS tumors (JC) to confirm the diagnosis. The following antibodies were used on 5 µm FFPE tissue sections: p53 (Zeta Corp, Z2029M, clone DO-7, 1:200) and ATRX (Sigma, HPA001906, 1:600).
Imaging
For each patient, the baseline MRI (before any therapy) and all the following scans were reviewed by a neuroradiologist (AKB) until evidence of recurrence. Each scan consisted of pre- and post-contrast T1-weighted sequence, T2-weighted sequence, FLAIR, and diffusion-weighted sequences. Blood-sensitive sequences, gradient recalled echo (GRE), or susceptibility weighted sequence (SWI) were used to evaluate intra-tumoral hemorrhage when available. Non-contrast CT scans at the time of presentation were also reviewed for evaluation of hemorrhage. At presentation, scans were categorically evaluated for a) location of the tumor, midline vs. lobar vs. multi-lobar; b) patterns of tumor margins, well defined vs. infiltrative; c) focality of the tumor, focal vs. multifocal; d) presence of hemorrhage; e) presence of enhancement; f) patterns of diffusion restriction; and g) presence of metastasis throughout the neuraxis. A focal lesion was defined as a single lesion with well-defined margins on postcontrast T1-weighted sequence with or without proportionate T2 abnormality suggestive of peritumoral edema surrounding the T1-enhancing lesion. An infiltrative lesion is defined as a lesion with either poorly defined T1 enhancing margins, abnormal disproportionate T2 signal around the T1 enhancing lesion, or ill-defined margin in tumors with no enhancing component. Infiltrative lesions were further evaluated for contiguous multiple lobar involvement. Recurrence was defined as the development of a new lesion or worsening of a previously treated lesion and was evaluated for either local or distant recurrence, as defined below. The focality of the recurrence was also assessed, as was the extent of recurrence with respect to crossing midline and the presence of subventricular spread. A gross total resection (GTR) was defined as a clean, well-defined surgical margin with no evidence of residual tumor on any sequence. A near-total resection (NTR) was defined when imaging appearance across all sequences resembled a focal residual tumor (~ 5% of the initial mass), predominantly along well-defined and clean surgical margins. A subtotal resection (STR) was defined as substantial residual tumor.
Radiation Dosimetry and Pattern of Failure Analysis
For radiotherapy dosimetric assessment, complete CT data sets of RT treatment plans were transferred to MIM software (MIM Software Inc, Cleveland, OH), and composite radiation dose data were assembled. MRI scans at progression were co-registered to CT data sets with standard vendor-supplied software, and the anatomic tumor extent at progression was manually delineated based on T2-weighted fluid-attenuated inversion recovery and T1 postcontrast abnormalities on MRI. Dose-volume histograms were calculated for the progression volumes, and progression with respect to radiation dose distribution was categorized as previously done for adult and pediatric patients with HGG [5, 33].
Statistical Analysis
Progression-free survival (PFS) was defined as the time interval from the date of first surgery to the date of disease progression or death from any cause or to the date of last contact for patients without events. Overall survival (OS) was defined as the time interval from the date of first surgery to the date of death from any cause or to the date of last contact for survivors. The Kaplan-Meier (KM) method was used to estimate survival outcomes. The difference between survival curves was compared by log-rank test. Fisher’s exact tests were used to investigate associations between categorical variables. A p-value < 0.05 was considered significant.