Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing.

Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a bioinformatics tool-LAMPrey-to process sequenced LAMP product. LAMPrey's concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.

Serial H3K27M cell-free tumor DNA (cf-tDNA) tracking predicts ONC201 treatment response and progression in diffuse midline glioma.

BACKGROUND: Diffuse Midline Glioma (DMG) with the H3K27M mutation is a lethal childhood brain cancer, with patients rarely surviving 2 years from diagnosis. METHODS: We conducted a multi-site Phase 1 trial of the imipridone ONC201 for children with H3K27M-mutant glioma (NCT03416530). Patients enrolled on Arm D of the trial (n = 24) underwent serial lumbar puncture for cell-free tumor DNA (cf-tDNA) analysis and patients on all arms at the University of Michigan underwent serial plasma collection. We performed digital droplet polymerase chain reaction (ddPCR) analysis of cf-tDNA samples and compared variant allele fraction (VAF) to radiographic change (maximal 2D tumor area on MRI). RESULTS: Change in H3.3K27M VAF over time ("VAF delta") correlated with prolonged PFS in both CSF and plasma samples. Nonrecurrent patients that had a decrease in CSF VAF displayed a longer progression free survival (P = .0042). Decrease in plasma VAF displayed a similar trend (P = .085). VAF "spikes" (increase of at least 25%) preceded tumor progression in 8/16 cases (50%) in plasma and 5/11 cases (45.4%) in CSF. In individual cases, early reduction in H3K27M VAF predicted long-term clinical response (>1 year) to ONC201, and did not increase in cases of later-defined pseudo-progression. CONCLUSION: Our work demonstrates the feasibility and potential utility of serial cf-tDNA in both plasma and CSF of DMG patients to supplement radiographic monitoring. Patterns of change in H3K27M VAF over time demonstrate clinical utility in terms of predicting progression and sustained response and possible differentiation of pseudo-progression and pseudo-response.

CHFR and Paclitaxel Sensitivity of Ovarian Cancer.

The poly(ADP-ribose) binding protein CHFR regulates cellular responses to mitotic stress. The deubiquitinase UBC13, which regulates CHFR levels, has been associated with better overall survival in paclitaxel-treated ovarian cancer. Despite the extensive use of taxanes in the treatment of ovarian cancer, little is known about expression of CHFR itself in this disease. In the present study, tissue microarrays containing ovarian carcinoma samples from 417 women who underwent initial surgical debulking were stained with anti-CHFR antibody and scored in a blinded fashion. CHFR levels, expressed as a modified H-score, were examined for association with histology, grade, time to progression (TTP) and overall survival (OS). In addition, patient-derived xenografts from 69 ovarian carcinoma patients were examined for CHFR expression and sensitivity to paclitaxel monotherapy. In clinical ovarian cancer specimens, CHFR expression was positively associated with serous histology (p = 0.0048), higher grade (p = 0.000014) and higher stage (p = 0.016). After correction for stage and debulking, there was no significant association between CHFR staining and overall survival (p = 0.62) or time to progression (p = 0.91) in patients with high grade serous cancers treated with platinum/taxane chemotherapy (N = 249). Likewise, no association between CHFR expression and paclitaxel sensitivity was observed in ovarian cancer PDXs treated with paclitaxel monotherapy. Accordingly, differences in CHFR expression are unlikely to play a major role in paclitaxel sensitivity of high grade serous ovarian cancer.

Electronic DNA Analysis of CSF Cell-free Tumor DNA to Quantify Multi-gene Molecular Response in Pediatric High-grade Glioma.

PURPOSE: Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF), allowing for potential detection of tumor-associated mutations by CSF sampling. We hypothesized that direct, electronic analysis of cf-tDNA with a handheld platform (Oxford Nanopore MinION) could quantify patient-specific CSF cf-tDNA variant allele fraction (VAF) with improved speed and limit of detection compared with established methods. EXPERIMENTAL DESIGN: We performed ultra-short fragment (100-200 bp) PCR amplification of cf-tDNA for clinically actionable alterations in CSF and tumor samples from patients with pHGG (n = 12) alongside nontumor CSF (n = 6). PCR products underwent rapid amplicon-based sequencing by Oxford Nanopore Technology (Nanopore) with quantification of VAF. Additional comparison to next-generation sequencing (NGS) and droplet digital PCR (ddPCR) was performed. RESULTS: Nanopore demonstrated 85% sensitivity and 100% specificity in CSF samples (n = 127 replicates) with 0.1 femtomole DNA limit of detection and 12-hour results, all of which compared favorably with NGS. Multiplexed analysis provided concurrent analysis of H3.3A (H3F3A) and H3C2 (HIST1H3B) mutations in a nonbiopsied patient and results were confirmed by ddPCR. Serial CSF cf-tDNA sequencing by Nanopore demonstrated correlation of radiological response on a clinical trial, with one patient showing dramatic multi-gene molecular response that predicted long-term clinical response. CONCLUSIONS: Nanopore sequencing of ultra-short pHGG CSF cf-tDNA fragments is feasible, efficient, and sensitive with low-input samples thus overcoming many of the barriers restricting wider use of CSF cf-tDNA diagnosis and monitoring in this patient population.

Everolimus improves the efficacy of dasatinib in PDGFRα-driven glioma.

Pediatric and adult high-grade gliomas (HGGs) frequently harbor PDGFRA alterations. We hypothesized that cotreatment with everolimus may improve the efficacy of dasatinib in PDGFRα-driven glioma through combinatorial synergism and increased tumor accumulation of dasatinib. We performed dose-response, synergism, P-glycoprotein inhibition, and pharmacokinetic studies in in vitro and in vivo human and mouse models of HGG. Six patients with recurrent PDGFRα-driven glioma were treated with dasatinib and everolimus. We found that dasatinib effectively inhibited the proliferation of mouse and human primary HGG cells with a variety of PDGFRA alterations. Dasatinib exhibited synergy with everolimus in the treatment of HGG cells at low nanomolar concentrations of both agents, with a reduction in mTOR signaling that persisted after dasatinib treatment alone. Prolonged exposure to everolimus significantly improved the CNS retention of dasatinib and extended the survival of PPK tumor-bearing mice (mutant TP53, mutant PDGFRA, H3K27M). Six pediatric patients with glioma tolerated this combination without significant adverse events, and 4 patients with recurrent disease (n = 4) had a median overall survival of 8.5 months. Our results show that the efficacy of dasatinib treatment of PDGFRα-driven HGG was enhanced with everolimus and suggest a promising route for improving targeted therapy for this patient population.

Syringomyelia in children with closed spinal dysraphism: long-term outcomes after surgical intervention.

OBJECTIVE: The nature of the relationship between spinal cord syrinx and tethered cord is not well known. It is unclear if surgical cord untethering results in resolution or improvement of an associated syrinx. The objective of this study was to report the response of spinal cord syrinx to surgical cord untethering. METHODS: The authors retrospectively reviewed all patients with a syrinx and tethered cord who presented to a single institution over an 11-year interval. Patients with open neural tube defects were excluded. Thirty-one patients were identified, 25 of whom had both clinical and imaging follow-up after surgery. Patients were grouped according to etiology of the tethered cord. Clinical outcomes and syrinx characteristics were recorded. RESULTS: Of the 25 patients with tethered cord, 68% (n = 17) were male. The average age at presentation was 2.5 years (0-10.1 years) and age at surgery was 3.7 years (range 1 day to 17 years). Etiologies of tethered cord were lipomyelomeningocele (n = 8), thickened/fatty filum (n = 7), intradural lipoma (n = 5), myelocystocele (n = 2), meningocele (n = 2), and diastematomyelia (n = 1). Twenty-three of the patients underwent primary untethering, whereas 2 patients had received untethering previously at another institution. The average syrinx length and width prior to surgery were 4.81 vertebral levels (SD 4.35) and 5.19 mm (SD 2.55 mm), respectively. Conus level ranged from L1 to S3. Patients were followed for an average of 8.4 years (1.35-15.85 years). Overall there was no significant change in syrinx length or width postoperatively; the average syrinx length increased by 0.86 vertebral levels (SD 4.36) and width decreased by 0.72 mm (SD 2.94 mm). Seven of 25 patients had improvement in at least one presenting symptom, including scoliosis, weakness, bowel/bladder dysfunction, and pain. Eight patients had stable presenting symptoms. Six patients were asymptomatic and 5 patients had new or worsening symptoms, which included scoliosis, pain, or sensory changes. CONCLUSIONS: Although some syrinxes improved after surgery for tethered cord, radiological improvement was not consistent and did not appear to be associated with change in clinical symptoms. The decision to surgically untether a cord should be focused on the clinical symptoms and not the presence of a syrinx alone. Further studies are needed to confirm this finding.

Morphometric changes at the craniocervical junction during childhood.

OBJECTIVE: Current understanding of how the pediatric craniocervical junction develops remains incomplete. Measurements of anatomical relationships at the craniocervical junction can influence clinical and surgical decision-making. The purpose of this analysis was to quantitatively define clinically relevant craniocervical junction measurements in a population of children with CT scans that show normal anatomy. METHODS: A total of 1458 eligible patients were identified from children between 1 and 18 years of age who underwent cervical spine CT scanning at a single institution. Patients were separated by both sex and age in years into 34 groups. Following this, patients within each group were randomly selected for inclusion until a target of 15 patients in each group had been reached. Each patient underwent measurement of the occipital condyle-C1 interval (CCI), pB-C2, atlantodental interval (ADI), basion-dens interval (BDI), basion-opisthion diameter (BOD), basion-axial interval (BAI), dens angulation, and canal diameter at C1. Mean values were calculated in each group. Each measurement was performed by two teams and compared for intraclass correlation coefficient (ICC). RESULTS: The data showed that CCI, ADI, BDI, and dens angulation decrease in magnitude throughout childhood, while pB-C2, PADI, BAI, and BOD increase throughout childhood, with an ICC of fair to good (range 0.413-0.912). Notably, CCI decreases continuously on coronal CT scans, whereas on parasagittal CT scans, CCI does not decrease until after age 9, when it shows a continuous decline similar to measurements on coronal CT scans. CONCLUSIONS: These morphometric analyses establish parameters for normal pediatric craniocervical spine growth for each year of life up to 18 years. The data should be considered when evaluating children for potential surgical intervention.

Molecular profiling and targeted therapy in pediatric gliomas: review and consensus recommendations.

As the field of neuro-oncology makes headway in uncovering the key oncogenic drivers in pediatric glioma, the role of precision diagnostics and therapies continues to rapidly evolve with important implications for the standard of care for clinical management of these patients. Four studies at major academic centers were published in the last year outlining the clinically integrated molecular profiling and targeting of pediatric brain tumors; all 4 demonstrated the feasibility and utility of incorporating sequencing into the care of children with brain tumors, in particular for children and young adults with glioma. Based on synthesis of the data from these studies and others, we provide consensus recommendations for the integration of precision diagnostics and therapeutics into the practice of pediatric neuro-oncology. Our primary consensus recommendation is that next-generation sequencing should be routinely included in the workup of most pediatric gliomas.

The Preventable Shunt Revision Rate: A Multicenter Evaluation.

BACKGROUND: The Preventable Shunt Revision Rate (PSRR) was recently introduced as a novel quality metric. OBJECTIVE: To evaluate the PSRR across multiple centers and determine associated variables. METHODS: Nine participating centers in North America provided at least 2 years of consecutive shunt operations. Index surgery was defined as new shunt implantation, or revision of an existing shunt. For any index surgery that resulted in a reoperation within 90-days, index surgery information (demographic, clinical, and procedural) was collected and a decision made whether the failure was potentially preventable. The 90-day shunt failure rate and PSRR were calculated per institution and combined. Bivariate analyses were performed to evaluate individual effects of each independent variable on preventable shunt failure followed by a final multivariable model using a backward model selection approach. RESULTS: A total of 5092 shunt operations were performed; 861 failed within 90 days of index operation, resulting in a 16.9% combined 90-day shunt failure rate and 17.6% median failure rate (range, 8.7%-26.9%). Of the failures, 307 were potentially preventable (overall and median 90-day PSRR, 35.7% and 33.9%, respectively; range, 16.1%-55.4%). The most common etiologies of avoidable failure were infection (n = 134, 44%) and proximal catheter malposition (n = 83, 27%). Independent predictors of preventable failure (P < .05) were lack of endoscopy (odds ratio [OR] = 2.26), recent shunt infection (OR = 3.65), shunt type (OR = 2.06) and center. CONCLUSION: PSRR is variable across institutions, but can be 50% or higher. While the PSRR may never reach zero, this study demonstrates that overall about a third of early failures are potentially preventable.

Molecular characterization reveals NF1 deletions and FGFR1-activating mutations in a pediatric spinal oligodendroglioma.

Pediatric spinal oligodendrogliomas are rare and aggressive tumors. They do not share the same molecular features of adult oligodendroglioma, and no previous reports have examined the molecular features of pediatric spinal oligodendroglioma. We present the case of a child with a recurrent spinal anaplastic oligodendroglioma. We performed whole exome (paired tumor and germline DNA) and transcriptome (tumor RNA) sequencing, which revealed somatic mutations in NF1 and FGFR1. These data allowed us to explore potential personalized therapies for this patient and expose molecular drivers that may be involved in similar cases.

Intramedullary and Extramedullary Cervical Neurenteric Cyst Requiring Fixation and Fusion.

BACKGROUND: Spinal neurenteric cysts are rare in the literature, described by sporadic case reports and small case series. In the vast majority of cases, these lesions are intradural extramedullary. We report the novel case of a cervical neurenteric cyst that was simultaneously intramedullary and extramedullary. CASE DESCRIPTION: A 47-year-old man underwent C2 through C7 laminectomies for microsurgical resection of a large cystic intradural mass, with C1 through T1 instrumentation and fusion. Gross total resection was obtained. Fusion was necessary after removal of the posterior elements because the vertebrae were thinned extensively and remodeled around the tumor, a treatment paradigm that has not been described adequately for neurenteric cysts previously. CONCLUSIONS: A novel case of cervical intramedullary and extramedullary neurenteric cyst is presented with clinical, radiographic, and histologic details. Given the potential for bony remodeling around these developmental tumors, the possibility exists for instability after certain neurenteric cysts are resected. Thus, the present case adds fixation and fusion to the potential treatment paradigm for select spinal neurenteric cysts.

Control of centrin stability by Aurora A.

Aurora A is an oncogenic serine/threonine kinase which can cause cell transformation and centrosome amplification when over-expressed. Human breast tumors show excess Aurora A and phospho-centrin in amplified centrosomes. Here, we show that Aurora A mediates the phosphorylation of and localizes with centrin at the centrosome, with both proteins reaching maximum abundance from prophase through metaphase, followed by their precipitous loss in late stages of mitosis. Over-expression of Aurora A results in excess phospho-centrin and centrosome amplification. In contrast, centrosome amplification is not seen in cells over-expressing Aurora A in the presence of a recombinant centrin mutant lacking the serine phosphorylation site at residue 170. Expression of a kinase dead Aurora A results in a decrease in mitotic index and abrogation of centrin phosphorylation. Finally, a recombinant centrin mutation that mimics centrin phosphorylation increases centrin's stability against APC/C-mediated proteasomal degradation. Taken together, these results suggest that the stability of centrin is regulated in part by Aurora A, and that excess phosphorylated centrin may promote centrosome amplification in cancer.

A promising approach for treatment of tumor-induced bone diseases: utilizing bisphosphonate derivatives of nucleoside antimetabolites.

Despite palliative treatments, tumor-induced bone disease (TIBD) remains highly debilitating for many cancer patients and progression typically results in death within two years. Therefore, more effective therapies with enhanced anti-resorptive and cytotoxic characteristics are needed. We developed bisphosphonate-chemotherapeutic conjugates designed to bind bone and hydrolyze, releasing both compounds, thereby targeting both osteoclasts and tumor cells. This study examined the effects of our lead compound, MBC-11 (the anhydride formed between arabinocytidine (AraC)-5'-phosphate and etidronate), on bone tumor burden, bone volume, femur bone mineral density (BMD), and overall survival using two distinct mouse models of TIBD, the 4T1/luc breast cancer and the KAS-6/1-MIP1alpha multiple myeloma models. In mice orthotopically inoculated with 4T1/luc mouse mammary cells, MBC-11 (0.04 microg/day; s.c.) reduced the incidence of bone metastases to 40% (4/10), compared to 90% (9/10; p=0.057) and 100% (5/5; p=0.04) of PBS- or similarly-dosed, zoledronate-treated mice, respectively. MBC-11 also significantly decreased bone tumor burden compared to PBS- or zoledronate-treated mice (p=0.021, p=0.017, respectively). MBC-11 and zoledronate (0.04 microg/day) significantly increased bone volume by two- and four-fold, respectively, compared to PBS-treated mice (p=0.005, p<0.001, respectively). In mice systemically injected with human multiple myeloma KAS-6/1-MIP1alpha cells, 0.04 and 4.0 microg/day MBC-11 improved femur BMD by 13% and 16%, respectively, compared to PBS (p=0.025, p=0.017, respectively) at 10 weeks post-tumor cell injection and increased mean survival to 95 days compared to 77 days in mice treated with PBS (p=0.047). Similar doses of zoledronate also improved femur BMD (p< or =0.01 vs PBS) and increased mean survival to 86 days, but this was not significantly different than in PBS-treated mice (p=0.53). These results demonstrate that MBC-11 decreases bone tumor burden, maintains bone structure, and may increase overall survival, warranting further investigation as a treatment for TIBD.

Breast cancer and aneusomy 17: implications for carcinogenesis and therapeutic response.

Abnormalities of chromosome 17, recognised over two decades ago to be important in tumorigenesis, often occur in breast cancer. Changes of specific loci on chromosome 17 including ERBB2 amplification, P53 loss, BRCA1 loss, and TOP2A amplification or deletion are known to have important roles in breast-cancer pathophysiology. Numerical aberrations of chromosome 17 are linked to breast-cancer initiation and progression, and possibly to treatment response. However, the clinical importance of chromosome 17 anomalies, in particular the effect on ERBB2 protein expression, is unknown. Reports are conflicting regarding the association of copy gain of chromosome 17 (polysomy 17) with strong ERBB2 protein expression in the absence of true ERBB2 gene amplification. Copy-number anomalies in chromosome 17 seem to be common in tumours that show discrepant ERBB2 expression and in tumours with discordant ERBB2-protein and ERBB2 gene copy number measurements. The mechanisms of ERBB2 dosage changes-gene amplification versus chromosome gain and loss-probably differ in primary and metastatic disease; however, a correction for chromosome 17 copy-number is necessary to completely distinguish between these mechanisms. A better understanding of how polysomy 17 affects gene-copy number and protein expression will help to select patients who will respond to therapies targeting ERBB2 and other protein products of chromosome 17 loci.