Abstract
Background
No consensus germline testing guidelines currently exist for glioma patients, so the prevalence of germline pathogenic variants remains unknown. This study aims to determine the prevalence and type of pathogenic germline variants in adult glioma.
Methods
A retrospective review at a single institution with paired tumor/normal sequencing from August 2018–April 2022 was performed and corresponding clinical data were collected.
Results
We identified 152 glioma patients of which 15 (9.8%) had pathogenic germline variants. Pathogenic germline variants were seen in 11/84 (13.1%) of Glioblastoma, IDH wild type; 3/42 (7.1%) of Astrocytoma, IDH mutant; and 1/26 (3.8%) of Oligodendroglioma, IDH mutant, and 1p/19q co-deleted patients. Pathogenic variants in BRCA2, MUTYH, and CHEK2 were most common (3/15, 20% each). BRCA1 variants occurred in 2/15 (13%) patients, with variants in NF1, ATM, MSH2, and MSH3 occurring in one patient (7%) each. Prior cancer diagnosis was found in 5/15 patients (33%). Second-hit somatic variants were seen in 3/15 patients (20%) in NF1, MUTYH, and MSH2. Referral to genetics was performed in 6/15 (40%) patients with pathogenic germline variants. 14/15 (93%) of patients discovered their pathogenic variant as a result of their paired glioma sequencing.
Conclusions
These findings suggest a possible overlooked opportunity for determination of hereditary cancer syndromes with impact on surveillance as well as potential broader treatment options. Further studies that can determine the role of variants in gliomagenesis and confirm the occurrence and types of pathogenic germline variants in patients with IDH wild type compared to IDH mutant tumors are necessary.
Keywords: diffuse glioma, glioblastoma, pathogenic germline variants
Adult-type diffuse gliomas are an aggressive form of cancer with glioblastoma, IDH wild type being the most common and most deadly type.1,2 Recent molecular characterizations of gliomas have led to a greater understanding of the genetic events surrounding tumorigenesis, heterogeneity of tumors, and molecular signatures that have prognostic significance on treatment.3,4 While most tumors appear to arise de novo, a subset of tumors are related to inherited germline pathogenic variants increasing predisposition for glioma formation.5 Inherited gliomas are often caused by pathogenic variants in genes involved in key regulation of gliomagenesis, apoptosis, or DNA damage repair.5–8 Many of the inherited gliomas are associated with known hereditary cancer syndromes like Neurofibromatosis, Li-Fraumeni syndrome, and Lynch Syndrome where germline pathogenic variants increase the risk of primary brain cancer in addition to other cancers.9–11 Further characterization of a heritable risk for gliomas have identified pathogenic variants in candidate genes such as POT1 or found loci of increased risk for glioma formation through genome-wide association studies.12–16 Interestingly, familial and sporadic gliomas are molecularly similar wherein both the germline and somatic events converge on the same core pathways significant for gliomagenesis.17,18
Despite the known germline association for certain types of glioma, there are no consensus germline testing guidelines for glioma patients, leading to under-utilization of genetic testing. In order to quantify the prevalence and type of pathogenic germline variants present in gliomas, we conducted a retrospective review of 152 adult-diffuse glioma patients evaluated at a single institution with paired tumor and normal tissue sequencing.
Materials and Methods
Tumor Samples and Genetic Testing
Tumor specimens were surgically resected and patients gave informed consent for sequencing of their tumors. Targeted exome sequencing for cancer-related genes was conducted and annotated by Tempus Labs Inc. for single nucleotide variants, indels, and translocations measured by hybrid capture next-generation sequencing. The limit of detection of the assay is 5% variant allele fraction with sensitivity of 98.2% for single nucleotide variants, 91.8% for indels, and 91.7% for translocations (Supplementary Table 1). Patients had the option to consent to germline testing for inherited cancer syndromes. If patients consented, paired saliva or blood samples were submitted with tumors to determine germline variants. Saliva samples were used for all but one patient who had blood testing done. Germline variants were targeted from a panel of previously established genes associated with hereditary cancer syndromes (Supplementary Table 1). Germline variants were reported as pathogenic or as a variant of unknown significance (VUS) if the gene harbored a variant of unknown or unclassified biology based on guidelines put forth by the American College of Medical Genetics and Genomics (ACMG).19,20 Specifically, each variant was classified as pathogenic, likely pathogenic, uncertain significance, likely benign, or benign based on documented cases of the variant associated with disease in databases like ClinVar.21 Variants that were classified as pathogenic or likely pathogenic that were related to hereditary cancer syndromes were considered pathogenic variants. Variants classified as uncertain significance were classified as a VUS. Tumor mutational burden measures the quantity of somatic variants of any pathogenicity, including benign variants, carried in a tumor as the number of single nucleotides protein-altering variants per million coding base pairs. Tumor mutational burden calculation is based upon (1) both the tumor and normal sample if the lab had analyzed both at the time of the initial report, or (2) the tumor sample only if no normal sample had been analyzed at the time of the initial report. Expressed fusion transcripts are detected with whole transcriptome RNA-Seq in an unbiased (non-targeted) fashion. The fusion transcript detection bioinformatics pipeline analyzes and shows the positions of breakpoint spanning reads and split paired-end reads.
Statistics
All graphs and statistics were conducted using the general-purpose statistical software package Stata 16.1 (Stata Corp, College Station, TX). Kaplan–Meier curves were used for progression-free and overall survival. Overall survival was computed from time of diagnosis to last available follow-up or death. Progression-free survival was computed from time of diagnosis to time of recurrence denoted by new surgical diagnosis. Kaplan–Meier curves were statistically compared using log-rank tests. Continuous variables were compared using a 2-sided students t-test and categorical variables were compared using a Fisher’s Exact test for independence.
Clinical Characteristics
The study was approved by the Institutional Review Board of Baylor College of Medicine. All patient information was de-identified before analysis. Patient clinical information was collected from review of the patient’s chart after paired tumor and saliva sequencing had been completed.
Results
Patient Demographics
In this study, we collected 152 patient tumor samples with matched germline testing during the time period. There were 71 female (46.7%) and 81 male (53.3%) patients with mean age of 51.75 years. The majority of samples were GBM, IDH wild type (n = 84), followed by astrocytoma, IDH mutant gliomas (n = 42), and oligodendrogliomas IDH mutant with 1p/19q co-deleted (n = 26) (Table 1). While all patients were offered tumor sequencing services with paired germline testing, 20 patients declined the germline testing but sequenced their tumors (Supplementary Table 2). The patients who did not receive germline testing were not statistically significantly different from the cohort with germline testing in terms of their age (P-value = .0901, 2-sided t-test), histopathology (P-value = .568, Fisher’s Exact), or gender (P-value = .635, Fisher’s Exact). These patients were not included in any subsequent analyses. On analyzing the paired germline samples, 15/152 (10%) patients had pathogenic germline variants. Of these, the majority of patients with germline pathogenic variants were in GBM, IDH wild type (n = 11), followed by astrocytoma, IDH mutant (n = 3), and oligodendroglioma, IDH mutant, 1p/19q co-deleted (n = 1). In addition to pathogenic germline variants, variants of unknown significance (VUS) were also reported. These VUS were found in 54/152 (36%) samples with the majority in GBM, IDH wild type (n = 31), followed by astrocytoma, IDH mutant (n = 14), and oligodendroglioma, IDH mutant, 1p/19q co-deleted(n = 9).
Table 1.
Patient Demographics
| GBM, IDH WT N = (%) | Astrocytoma IDH mutant N = (%) | Oligodendroglioma, IDH mutant, 1p/19q co-deleted N = (%) | Overall | |
|---|---|---|---|---|
| Number of patients | 84 (55) | 42 (28) | 26 (17) | 152 (100) |
| Age (SD) | 58.9 (11.5) | 40.9 (9.4) | 46.2 (11) | 51.75 (13.5) |
| Sex | ||||
| Female | 39 (46.43) | 19 (45.24) | 13 (50) | 71 (46.7) |
| Male | 45 (53.67) | 23 (54.76) | 13 (50) | 81 (53.3) |
| Grade | ||||
| II | 3 (3.57) | 20 (47.61) | 15 (57.69) | 38 (25) |
| III | 4 (4.76) | 12 (28.57) | 11 (42.31) | 27 (17.8) |
| IV | 77 (91.67) | 10 (23.81) | 0 (0.0) | 87 (57.2) |
| MGMT promoter methylation | ||||
| Unmethylated | 21 (25.0) | 2 (4.76) | 0 (0) | 23 (15.1) |
| Methylated | 23 (27.7) | 9 (21.42) | 4 (15.38) | 36 (23.7) |
| Not tested | 40 (48.19) | 31 (73.81) | 22 (84.62) | 93 (61) |
| IDH status | ||||
| Mutated | 0 (0) | 42 (100) | 26 (100) | 68 (44.7) |
| Wild type | 84 (100) | 0 (0) | 0 (0) | 84 (55.3) |
| Treatment | ||||
| Radiation alone | 2 (2.4) | 0 (0.0) | 2 (7.7) | 4 (2.63) |
| Concurrent Chemoradiation followed by adjuvant chemo | 70 (83.3) | 19 (45.2) | 4 (15.4) | 93 (61.2) |
| Radiation followed by Chemo | 5 (6.0) | 15 (35.7) | 15 (57.7) | 35 (23) |
| Chemo alone | 2 (2.4) | 0 (0.0) | 2 (7.7) | 4 (2.63) |
| Surveillance/ declined treatment | 5 (6.0) | 8 (19.0) | 3 (11.5) | 16 (10.5) |
| Pathogenic germline variants | 11 (13.1) | 3 (7.14) | 1 (3.85) | 15 (9.9) |
| Cancer related variants of unknown significance | 31 (36.9) | 14 (33.3) | 9 (34.62) | 54 (35.5) |
| Median progression free survival, months (SE) | 11.9 (1.4) | 57.9 (22.2) | 134.7 (4.5) | 25.1 (6.52) |
| Median overall survival, months (SE) | 21.1 (1.3) | 188.9 (3) | - | 84.1 (20.3) |
GBM, Glioblastoma; IDH, isocitrate dehydrogenase 1/2; SD, standard deviation; SE, standard error.
Germline Pathogenic Variants and Variants of Unknown Significance
The pathogenic germline variants are summarized in Table 2 and VUS in Table 3. The most common pathogenic germline variants in our samples were in BRCA2, MUTYH, and CHEK2 with 3 patients each. Interestingly, the same CHEK2 variant was shared across all 3 patients who harbored a germline CHEK2 variant. Two of the three patients with MUTYH variants also harbored the same variant. Two patients had BRCA1 variants. Within the patients with germline pathogenic variants, we looked for second somatic hits, which occurred in MUTYH (n = 1), NF1 (n = 1), and MSH2 (n = 1), respectively. Of those with germline pathogenic variants, 5/15 (33%) had a prior history of cancer consistent with their germline variant. For example, one patient with a BRCA1 pathogenic variant had prior ovarian cancer, and another patient with a MSH2 variant had a prior colon cancer diagnosis. Many of the patients with germline variants had family members with prior cancer diagnoses with 8/15 (60%) having some direct family cancer diagnosis and 3/15 (20%) having a familial history of primary brain cancer (Table 2). The patients with germline pathogenic variants were largely found in World Health Organization (WHO) Grade IV tumors (n = 12) with some in WHO Grade II (n = 3). These patients had similar ages of presentation to the larger cohort and distribution of gender (Table 4). Forty percent of patients with germline pathogenic variants were referred to genetics of which 33% were seen by genetics and were counseled without further genetic testing. One patient declined the genetics visit after scheduling. The majority of the remaining 60% of patients declined the referral. Almost all (93%) of the cohort with germline variants were discovered as a consequence of the paired germline sequencing. The one patient who had previously been seen by genetics had a MSH2 variant and prior colon cancer, consistent with Lynch syndrome. Similarly, for cancer-related VUS, most patients had WHO Grade IV tumors (n = 32), with some in WHO Grade III (n = 10), and some WHO Grade II (n = 12) with comparable age and gender distributions. Many of the VUS were in the same genes as those found in the germline pathogenic cohort including ATM (n = 8), BRCA2 (n = 4), BRCA1 (n = 3), MUYTH (n = 3), CHEK2 (n = 1), MSH2 (n = 1), and MSH3 (n = 1) (Table 3). The demographics of the VUS group were similar to the germline pathogenic group with the exception of more grade III tumors (Table 4). Only 1 (3.7%) VUS patient was referred to and seen by genetics, and this patient had a concurrent germline pathogenic variant.
Table 2.
Summary of Germline Pathogenic Variants
| Specific Genes | N = (%) | Specific Variant Detected (ClinVar Classification) | Second Somatic Hit (%) | Personal History of Cancer | Family History of Cancer | Prior Cancer Diagnoses | Seen by Genetics Prior to Brain Cancer | Known Condition Prior to Brain Cancer | Variant Discovered by Paired Germline Sequencing |
|---|---|---|---|---|---|---|---|---|---|
| -BRCA2 | 3 (20) | - BRCA2- p.F2254fs (P) | 0 (0) | None documented | Parent: Colon Cancer | None documented | 0 (0) | 0 (0) | 3 (20) |
| - BRCA2- p.S1404fs (P) | Mother: Breast Cancer | ||||||||
| - BRCA2- p.T1673fs (P) | None | ||||||||
| -MUTYH | 3 (20) | - MUTYH-p.G396D (P/LP) | 1 (7) | None documented | Parent: Brain tumor | None documented | 0 (0) | 0 (0) | 3 (20) |
| - MUTYH-p.G396D (P/LP) | None | ||||||||
| - MUTYH-p.V493F (P/LP) | None | ||||||||
| -CHEK2 | 3 (20) | - CHEK2- p.I157T (P/LP) | 0 (0) | 1(7) | Sibling: GBM | Benign Colon and Gastric Polyps | 0 (0) | 0 (0) | 3 (20) |
| - CHEK2- p.I157T (P/LP) | Parent: Stomach cancer, Aunt: Uterine cancer, breast cancer Uncle: Skin cancer | ||||||||
| - CHEK2- p.I157T (P/LP) | None | ||||||||
| -BRCA1 | 2 (13) | - BRCA1- c.5277 + 1G>A (P) | 0 (0) | 1(7) | Parent: GBM | Ovarian Cancer | 0 (0) | 0 (0) | 2 (13) |
| - BRCA1- p.N1355fs (P) | None | ||||||||
| -NF1 | 1 (7) | - NF1-p.Y2285* (P) | 1 (7) | 1(7) | Aunts: Thyroid cancer, uterine cancer | Neurofibromas | 0 (0) | 0 (0) | 1 (7) |
| -ATM | 1 (7) | - ATM-p.T2333fs (P) | 0 (0) | None documented | Mother: Ovarian, Uncles: Prostate, Bladder, Gastric Grandmother/Aunts: Breast | None documented | 0 (0) | 0 (0) | 1 (7) |
| -MSH2 | 1 (7) | - MSH2-p.Q601* (P) | 1 (7) | 1(7) | Parent uterine cancer, brother colon cancer | Colon Cancer | 1 (7) | 1 (7) | 0 (0) |
| -MSH3 | 1 (7) | - MSH3-p.R715fs (P) | 0 (0) | 1(7) | None | Low Stage Breast Cancer | 0 (0) | 0 (0) | 1 (7) |
P, Pathogenic; LP, Likely Pathogenic.
Table 3.
Summary of Germline Variants of Unknown Significance
| Specific genes | N = (%) | Specific genes | N = (%) |
|---|---|---|---|
| -ATM | 8 (12.7) | -ATP7B | 1 (1.6) |
| -APOB | 4 (6.4) | -CDH1 | 1 (1.6) |
| -BRCA2 | 4 (6.4) | -CHEK2 | 1 (1.6) |
| -MYH11 | 4 (6.4) | -EGFR | 1 (1.6) |
| -RET | 4 (6.4) | -FLCN | 1 (1.6) |
| -MSH6 | 4 (6.3) | -LDLR | 1 (1.6) |
| -BRCA1 | 3 (4.8) | -MSH2 | 1 (1.6) |
| -LMNA | 3 (4.8) | -MSH3 | 1 (1.6) |
| -MUTYH | 3 (4.8) | -POLD1 | 1 (1.6) |
| -WT1 | 2 (3.2) | -RB1 | 1 (1.6) |
| -FH | 2 (3.2) | -RUNX1 | 1 (1.6) |
| -NBN | 2 (3.2) | -SMAD4 | 1 (1.6) |
| -PALB2 | 2 (3.2) | -TSC2 | 1 (1.6) |
| -RAD51D | 2 (3.2) | -VHL | 1 (1.6) |
| -TPM1 | 2 (3.2) |
Table 4.
Demographics of Germline Pathogenic and Variants of Unknown Significance
| Germline Pathogenic | VUS Associated with Other Cancers | |
|---|---|---|
| Number of patients | 15 | 54 |
| Age (SD) | 52 (11.4) | 52.1 (13.1) |
| Sex | ||
| Female | 7 (46.7) | 20 (37) |
| Male | 8 (53.3) | 34 (63) |
| Grade | ||
| II | 3 (20) | 12 (22.2) |
| III | 0 (0) | 10 (18.5) |
| IV | 12 (80) | 32 (59.3) |
| MGMT promoter methylation | ||
| Unmethylated | 1 (6.67) | 10 (18.5) |
| Methylated | 4 (26.7) | 11 (20.4) |
| Not Tested | 10 (66.7) | 33 (61.1) |
| IDH Status | ||
| Mutated | 5 (33.3) | 25 (46.3) |
| Wild type | 10 (66.7) | 29 (53.7) |
| Referred to genetics | 6 (40) | 2 (3.7) |
| Seen by genetics | 5 (33.3) | 2 (3.7) |
Progression-Free and Overall Survival of Patients With Germline Pathogenic Variants and Variants of Unknown Significance
While the germline pathogenic variants and VUS occurred in different genes, we sought to understand if there were differences in progression-free survival for the GBM, IDH wild-type group (Figure 1). Despite lower median progression-free survival for patients with germline pathogenic variants, there was no significant difference between the 2 groups (log-rank P = .34). For the germline cancer-related VUS, median progression-free survival was 14.1 months compared to 9 months for the rest of the cohort (Figure 2, log-rank P = .1). In addition to progression-free survival, we also determined if there was a difference in overall survival in the GBM, IDH wild-type group. There was lower median overall survival in the germline pathogenic group, but no significant difference between it and the rest of the groups (log-rank, P = .17). Similar to progression-free survival, there was no significant difference between the VUS group for overall survival either (log-rank, P = .17).
Figure 1.
IDH WT GBM progression-free survival. (A). Progression-free survival for IDH wild-type GBM with germline variants compared to the rest of the cohort. Median progression-free survival was 11.1 for germline variants versus 12.2 for the rest of the cohort. No significant difference between the 2 curves (log-rank, P = .34). (B). Progression-free survival for IDH wild-type GBM with germline cancer-related variants of unknown significance compared to the rest of the cohort. Median progression-free survival was 14.1 for germline variants of unknown significance versus 9.0 for the rest of the cohort. No significant difference between the 2 curves (log-rank, P = .1).
Figure 2.
IDH WT GBM overall survival. (A). Overall survival for IDH wild-type GBM with germline variants compared to the rest of the cohort. Median overall survival was 16 for germline variants versus 21.8 for the rest of the cohort. No significant difference between the 2 curves (log-rank, P = .17). (B). Overall survival for IDH wild-type GBM with germline cancer-related variants of unknown significance compared to the rest of the cohort. Median overall survival was 26.5 for germline variants of unknown significance versus 21 for the rest of the cohort. No significant difference between the 2 curves (log-rank, P = .13).
Discussion
Our study quantified the prevalence and type of germline variants in different subtypes of adult-type diffuse glioma. Of the 152 glioma patients, we found 15 (10%) with pathogenic germline variants, 11/84 GBM, IDH wild type, 3/42 astrocytoma, IDH mutant, and 1/26 Oligodendroglioma, IDH mutant and 1p/19q co-deleted. The most common pathogenic variants were found in BRCA genes with 5/15 (33%) of germline pathogenic variants found in our cohort (3/15 BRCA2, 2/15 BRCA1). Germline variants also commonly seen were in MUTYH and CHEK2 (3/15 or 20% each), including variants shared across patients. Interestingly, second somatic variants were seen in NF1, MUTYH, and MSH2, which gives more credence to these holding significance for tumorigenesis in these patients.
Many of the germline pathogenic variants we identified are significant for tumorigenesis in other cancers; however, their role in gliomagenesis versus incidental findings in glioma patients is less clear. Germline BRCA pathogenic variants have been well characterized to increase risk of breast and ovarian cancer with approximately 5% and 11% of all breast and ovarian cancer patients having a BRCA germline variant.22,23 There have been documented cases of BRCA germline variants in GBM.24,25 The role of BRCA1 in GBM specifically has been thought to be not instrumental for tumor formation.26 Alternatively, BRCA2 has been more closely linked with different types of primary brain cancer including astrocytoma and medulloblastoma.27–30 In our study, we had a patient with a BRCA1 pathogenic variant that had ovarian cancer and an IDH wild-type GBM. BRCA genes function to repair genomic instability by homologous DNA recombination, making them therapeutically vulnerable to PARP inhibitors. Despite the murky role of BRCA1 in gliomagenesis, using PARP inhibitors in the context of germline or somatic pathogenic variants of BRCA1 is an unexplored opportunity in glioma patients.31,32 PARP inhibitors in conjunction with temozolomide for treatment of gliomas held promise preclinically but have failed to yield results in clinical trials.33–35 Three patients harbored the same CHEK2 pathogenic variant. CHEK2 variants found in one case of familial glioma were thought to be unrelated to their gliomagenesis; however, these results implicate a possible role in this specific variant in glioma biology.36CHEK2 is required for glioma response to ionizing radiation in mouse models, so patients with germline or somatic loss of function variants could be at a greater risk for accelerated tumor growth with less response to radiation.37ATM germline variants have also been previously documented in brain tumor patients38,39 In contrast to CHEK2, variants in ATM have been shown to improve radiosensitivity of gliomas.40,41 Another common variant in our cohort was MUTYH. Some recent reports have also noted germline MUTYH variants appear to be enriched in glioblastoma, possibly driving gliomagenesis due to its function to correct mismatch repair.42,43 One of our patients with a second somatic variant had it in MUTYH. The other 2 patients with second somatic hits had them in NF1 and MSH2. NF1 is a GTPase-activating protein that decreases RAS signaling, and germline variants of NF1 are associated with NF1. In our case, one patient had NF1 variants and neurofibromas but lacked café au lait spots.44 High-grade germline NF1 tumors harbor genetic alterations typical of GBM including those in TP53 and CDKN2A as well as PI3 kinase pathway alterations, while lower-grade tumors had over-represented MAP kinase genes.9 The second somatic hit in MSH2 is also not surprising as it has significant functions in DNA mismatch repair and pathogenic variants in it are found in Lynch Syndrome.45
Almost all of our patients (93%) discovered they had a pathogenic variant after receiving paired germline sequencing with their glioma; however, only 40% of our patients with pathogenic germline pathogenic variants were referred to genetics. Five of the patients with germline pathogenic variants had a prior personal history of cancer and only one patient had previously received genetic counseling. The other 10 patients had glioma first and were notified of their pathogenic germline status as a consequence of the paired testing. While there is no consensus for germline testing in glioma patients, the European Association of Neuro-Oncology guidelines recommend patients receive genetic counseling and subsequent molecular genetic testing on the basis of class IV, level C evidence.46 By these guidelines, we should have referred more of our own patients to genetics for management of their care. However, most of the patients were not referred for an official genetics consultation because they declined the referral. Some of the patients had serious progression of their disease and did not choose to continue with more evaluations. We found ~10% of patients in our cohort had a pathogenic germline variant and ~33% of patients had a VUS in cancer-related genes. The prevalence of germline variants in our study was similar to other studies with prior studies demonstrating rates of approximately 7%–15% for pathogenic or likely pathogenic germline variants in brain cancer.24,47 In fact, in a pan-cancer study about 15% of brain tumors had likely pathogenic or pathogenic germline variants, although this sample included brain metastases.24 Pairing germline sequencing with somatic tumor sequencing creates an opportunity for early identification of heritable cancer syndromes. Further evaluations by genetics can help with surveillance of other cancers as well as cascade testing for at-risk family members leading to optimal as well as tailored care for these patients.
In the GBM, IDH wild-type group, our patients with germline pathogenic variants trended towards worse overall survival compared to the rest of the cohort, but it was not statistically significant (P = .17). One limitation is the small number of patients (11/84) limiting the statistical power of the mortality analysis. The age of onset of tumors in these patients also did not significantly differ from the rest of the cohort. Ultimately, the specific gene and specific variant likely have more to do with survival than the mere presence of a germline variant. Prior studies have sought to evaluate specific variants and in the case of POT1 found influence of survival influenced in a sexually dimorphic manner.13 While we did not study immune-related germline variants, some studies have indicated that most myeloid germline variants play little role, while a specific variant in the microglial and macrophage-related adhesion chemokine receptor gene (CX3CR1) appears to enhance glioma survival.48–50
Conclusion
Here we retrospectively analyzed a cohort of 152 patients with glioma and matched germline samples and found 15/152 had germline pathogenic variants, many of which likely played significant roles in tumorigenesis. Of those, 93% discovered they had a pathogenic variant after receiving paired germline sequencing with their glioma, and only 40% of them were referred to genetics. These findings suggest a possible overlooked opportunity for determination of hereditary cancer syndromes with impact on surveillance as well as potential broader treatment options. Further research to confirm the occurrence, frequency, and types of pathogenic germline variants in patients with Glioblastoma, IDH wild type compared to IDH mutant tumors is necessary.
Supplementary Material
Acknowledgments
M.F.M .would like to thank the McNair Medical Institute and BRASS (Baylor Research Advocates for Student Scientists) for their support.
Contributor Information
Malcolm F McDonald, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA.
Lyndsey L Prather, Department of Neurology, Baylor College of Medicine, Houston, Texas, USA.
Cassandra R Helfer, Department of Neurology, Baylor College of Medicine, Houston, Texas, USA.
Ethan B Ludmir, Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas, USA.
Alfredo E Echeverria, Department of Radiation Oncology, Baylor College of Medicine, Houston, Texas, USA.
Shlomit Yust-Katz, Department of Neurology, Rabin Medical Center, Petah Tikva, Israel.
Akash J Patel, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA; Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, USA.
Benjamin Deneen, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA.
Ganesh Rao, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA.
Ali Jalali, Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA.
Shweta U Dhar, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Internal Medicine, Baylor College of Medicine, Houston, Texas, USA.
Chris I Amos, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Jacob J Mandel, Department of Neurology, Baylor College of Medicine, Houston, Texas, USA.
Funding
National Institutes of Health [R01-CA217105 to B.D.].
Authorship statement
J.J.M. designed the study. M.F.M., L.L.P., CRH, and JJM performed the research. MFM, CIA, SUD, and J.J.M. analyzed the results. MFM, JJM, and SUD wrote the initial draft. EBL, AEE, SYK, AJP, B.D., GR, and AJ provided critical revisions to the manuscript.
Previous Presentation
This work was presented at the Society for Neuro-Oncology Meeting 2022.
References
- 1. Ostrom QT, Cioffi G, Waite K, Kruchko C, Barnholtz-Sloan JS.. CBTRUS statistical report: Primary brain and other central nervous system tumors diagnosed in the United States in 2014–2018. Neuro Oncol. 2021;23(suppl_3):iii1–iii105. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Stupp R, Mason WP, van den Bent MJ, et al. ; European Organisation for Research and Treatment of Cancer Brain Tumor and Radiotherapy Groups. Radiotherapy plus concomitant and adjuvant Temozolomide for glioblastoma. N Engl J Med. 2005;352(10):987–996. [DOI] [PubMed] [Google Scholar]
- 3. Patel AP, Tirosh I, Trombetta JJ, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014;344(6190):1396–1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Louis DN, Perry A, Wesseling P, et al. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol. 2021;23(8):1231–1251. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Choi DJ, Armstrong G, Lozzi B, et al. The genomic landscape of familial glioma. Sci Adv. 2023;9(17):eade2675. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Kyritsis AP, Bondy ML, Xiao M, et al. Germline p53 gene mutations in subsets of glioma patients. J Natl Cancer Inst. 1994;86(5):344–349. [DOI] [PubMed] [Google Scholar]
- 7. Kyritsis AP, Bondy ML, Rao JS, Sioka C.. Inherited predisposition to glioma. Neuro Oncol. 2010;12(1):104–113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Tachibana I, Smith JS, Sato K, et al. Investigation of germline PTEN, p53, p16(INK4A)/p14(ARF), and CDK4 alterations in familial glioma. Am J Med Genet. 2000;92(2):136–141. [DOI] [PubMed] [Google Scholar]
- 9. D’Angelo F, Ceccarelli M, Tala, et al. The molecular landscape of glioma in patients with Neurofibromatosis 1. Nat Med. 2019;25(1):176–187. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Sloan EA, Hilz S, Gupta R, et al. Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features. Acta Neuropathol. 2020;139(5):953–957. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Alnahhas I, Rayi A, Ong S, Giglio P, Puduvalli V.. Management of gliomas in patients with Lynch syndrome. Neuro Oncol. 2021;23(1):167–168. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Bainbridge MN, Armstrong GN, Gramatges MM, et al. Germline mutations in Shelterin complex genes are associated with familial glioma. JNCI. 2015;107(1):dju384. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Jalali A, Yu K, Beechar V, et al. POT1 regulates proliferation and confers sexual dimorphism in glioma. Cancer Res. 2021;81(10):2703–2713. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Kinnersley B, Labussière M, Holroyd A, et al. Genome-wide association study identifies multiple susceptibility loci for glioma. Nat Commun. 2015;6:8559. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Kinnersley B, Houlston RS, Bondy ML.. Genome-wide association studies in glioma. Cancer Epidemiol Biomarkers Prev. 2018;27(4):418–428. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16. Melin BS, Barnholtz-Sloan JS, Wrensch MR, et al. ; GliomaScan Consortium. Genome-wide association study of glioma subtypes identifies specific differences in genetic susceptibility to glioblastoma and non-glioblastoma tumors. Nat Genet. 2017;49(5):789–794. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Jacobs DI, Fukumura K, Bainbridge MN, et al. Elucidating the molecular pathogenesis of glioma: Integrated germline and somatic profiling of a familial glioma case series. Neuro Oncol. 2018;20(12):1625–1633. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18. Ruiz VY, Praska CE, Armstrong G, et al. ; Gliogene Consortium. Molecular subtyping of tumors from patients with familial glioma. Neuro Oncol. 2018;20(6):810–817. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19. Richards S, Aziz N, Bale S, et al. ; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–424. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20. Kalia SS, Adelman K, Bale SJ, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): A policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017;19(2):249–255. [DOI] [PubMed] [Google Scholar]
- 21. ClinVar. https://www.ncbi.nlm.nih.gov/clinvar/. Accessed May 8, 2023.
- 22. Malone KE, Daling JR, Doody DR, et al. Prevalence and Predictors of BRCA1 and BRCA2 mutations in a population-based study of breast cancer in White and Black American Women ages 35 to 64 years. Cancer Res. 2006;66(16):8297–8308. [DOI] [PubMed] [Google Scholar]
- 23. Risch HA, McLaughlin JR, Cole DEC, et al. Prevalence and penetrance of germline BRCA1 and BRCA2 mutations in a population series of 649 women with ovarian cancer. Am J Hum Genet. 2001;68(3):700–710. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24. Stadler ZK, Maio A, Chakravarty D, et al. Therapeutic implications of germline testing in patients with advanced cancers. J Clin Oncol. 2021;39(24):2698–2709. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 25. Nageeb AM, Mohamed MM, Ezz El Arab LR, Khalifa MK, Swellam M.. Next generation sequencing of BRCA genes in glioblastoma multiform Egyptian patients: A pilot study. Arch Physiol Biochem. 2022;128(3):809–817. [DOI] [PubMed] [Google Scholar]
- 26. Boukerroucha M, Josse C, Segers K, et al. BRCA1 germline mutation and glioblastoma development: report of cases. BMC Cancer. 2015;15:181. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 27. Offit K, Levran O, Mullaney B, et al. Shared genetic susceptibility to breast cancer, brain tumors, and Fanconi anemia. J Natl Cancer Inst. 2003;95(20):1548–1551. [DOI] [PubMed] [Google Scholar]
- 28. Frappart PO, Lee Y, Lamont J, McKinnon PJ.. BRCA2 is required for neurogenesis and suppression of medulloblastoma. EMBO J. 2007;26(11):2732–2742. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 29. Dodgshun AJ, Sexton-Oates A, Saffery R, Sullivan MJ.. Biallelic FANCD1/BRCA2 mutations predisposing to glioblastoma multiforme with multiple oncogenic amplifications. Cancer Genet. 2016;209(1-2):53–56. [DOI] [PubMed] [Google Scholar]
- 30. Wilson BT, Douglas SF, Polvikoski T.. Astrocytoma in a breast cancer lineage: Part of the BRCA2 phenotype? J Clin Oncol. 2010;28(30):e596–e598. [DOI] [PubMed] [Google Scholar]
- 31. Gorodetska I, Kozeretska I, Dubrovska A.. BRCA genes: the role in genome stability, cancer Stemness and therapy resistance. J Cancer. 2019;10(9):2109–2127. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 32. Noordermeer SM, van Attikum H.. PARP Inhibitor resistance: A tug-of-war in BRCA-mutated cells. Trends Cell Biol. 2019;29(10):820–834. [DOI] [PubMed] [Google Scholar]
- 33. Wu S, Li X, Gao F, et al. PARP-mediated PARylation of MGMT is critical to promote repair of temozolomide-induced O6-methylguanine DNA damage in glioblastoma. Neuro Oncol. 2021;23(6):920–931. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 34. Higuchi F, Nagashima H, Ning J, et al. Restoration of Temozolomide sensitivity by PARP inhibitors in mismatch repair deficient glioblastoma is independent of base excision repair. Clin Cancer Res. 2020;26(7):1690–1699. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35. Sarkaria JN, Ballman KV, Kizilbash SH, et al. Randomized phase II/III trial of Veliparib or placebo in combination with adjuvant Temozolomide in newly diagnosed glioblastoma (GBM) patients with MGMT promoter Hypermethylation (Alliance A071102). J Clin Oncol. 2022;40(Suppl. 16): abstr. 2001. [Google Scholar]
- 36. Sallinen SL, konen T, Haapasalo H, Schleutker J.. CHEK2 mutations in primary glioblastomas. J Neurooncol. 2005;74(1):93–95. [DOI] [PubMed] [Google Scholar]
- 37. Squatrito M, Brennan CW, Helmy K, et al. Loss of ATM/Chk2/p53 pathway components accelerates tumor development and contributes to radiation resistance in gliomas. Cancer Cell. 2010;18(6):619–629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 38. Miyagi K, Mukawa J, Kinjo N, et al. Astrocytoma linked to familial ataxia-telangiectasia. Acta Neurochir (Wien). 1995;135(1-2):87–92. [DOI] [PubMed] [Google Scholar]
- 39. Malmer BS, Feychting M, Lönn S, et al. Genetic variation in p53 and ATM haplotypes and risk of glioma and meningioma. J Neurooncol. 2007;82(3):229–237. [DOI] [PubMed] [Google Scholar]
- 40. Kim N, Kim SH, Kang SG, et al. ATM mutations improve radio-sensitivity in wild-type isocitrate dehydrogenase-associated high-grade glioma: Retrospective analysis using next-generation sequencing data. Radiat Oncol. 2020;15(1):184. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 41. Qin T, Mullan B, Ravindran R, et al. ATRX loss in glioma results in dysregulation of cell-cycle phase transition and ATM inhibitor radio-sensitization. Cell Rep. 2022;38(2):110216. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 42. Kline CN, Joseph NM, Grenert JP, et al. Inactivating MUTYH germline mutations in pediatric patients with high-grade midline gliomas. Neuro Oncol. 2016;18(5):752–753. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 43. Bedics G, Kotmayer L, Zajta E, et al. Germline MUTYH mutations and high-grade gliomas: Novel evidence for a potential association. Genes Chromosomes Cancer. 2022;61(10):622–628. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 44. Martin GA, Viskoohil D, Bollag G, et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell. 1990;63(4):843–849. [DOI] [PubMed] [Google Scholar]
- 45. Fishel R, Lescoe MK, Rao MRS, et al. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell. 1993;75(5):1027–1038. [DOI] [PubMed] [Google Scholar]
- 46. Weller M, van den Bent M, Preusser M, et al. EANO guidelines on the diagnosis and treatment of diffuse gliomas of adulthood. Nat Rev Clin Oncol. 2021;18(3):170–186. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 47. Yap TA, Ashok A, Stoll J, et al. Prevalence of germline findings among tumors from cancer types lacking hereditary testing guidelines. JAMA Network Open. 2022;5(5):e2213070. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 48. Jacobs DI, Liu Y, Gabrusiewicz K, et al. Germline polymorphisms in myeloid-associated genes are not associated with survival in glioma patients. J Neurooncol. 2018;136(1):33–39. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 49. Lee S, Latha K, Manyam G, et al. Role of CX3CR1 signaling in malignant transformation of gliomas. Neuro Oncol. 2020;22(10):1463–1473. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 50. Rodero M, Marie Y, Coudert M, et al. Polymorphism in the microglial cell-mobilizing CX3CR1 gene is associated with survival in patients with glioblastoma. J Clin Oncol. 2008;26(36):5957–5964. [DOI] [PubMed] [Google Scholar]
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