Signatures of copy number alterations in human cancer.

Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.

Leveraging single-cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers.

Intratumour heterogeneity (ITH) and tumour evolution are well-documented phenomena in human cancers. While the advent of next-generation sequencing technologies has facilitated the large-scale capture of genomic data, the field of single-cell genomics is nascent but rapidly advancing and generating many new insights into the complex molecular mechanisms of tumour biology. In this review, we provide an overview of current single-cell DNA sequencing technologies, exploring how recent methodological advancements have enumerated new insights into ITH and tumour evolution. Areas highlighted include the potential power of single-cell genome sequencing studies to explore evolutionary dynamics contributing to tumourigenesis through to progression, metastasis, and therapy resistance. We also explore the use of in situ sequencing technologies to study ITH in a spatial context, as well as examining the use of single-cell genomics to perform lineage tracing in both normal and malignant tissues. Finally, we consider the use of multimodal single-cell sequencing technologies. Taken together, it is hoped that these many facets of single-cell genome sequencing will improve our understanding of tumourigenesis, progression, and lethality in cancer, leading to the development of novel therapies. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Docosahexaenoic acid reduces microglia phagocytic activity via miR-124 and induces neuroprotection in rodent models of spinal cord contusion injury.

Microglia are activated after spinal cord injury (SCI), but their phagocytic mechanisms and link to neuroprotection remain incompletely characterized. Docosahexaenoic acid (DHA) has been shown to have significant neuroprotective effects after hemisection and compression SCI and can directly affect microglia in these injury models. In rodent contusion SCI, we demonstrate that DHA (500 nmol/kg) administered acutely post-injury confers neuroprotection and enhances locomotor recovery, and also exerts a complex modulation of the microglial response to injury. In rodents, at 7 days after SCI, the level of phagocytosed myelin within Iba1-positive or P2Y12-positive cells was significantly lower after DHA treatment, and this occurred in parallel with an increase in intracellular miR-124 expression. Furthermore, intraspinal administration of a miR-124 inhibitor significantly reduced the DHA-induced decrease in myelin phagocytosis in mice at 7 days post-SCI. In rat spinal primary microglia cultures, DHA reduced the phagocytic response to myelin, which was associated with an increase in miR-124, but not miR-155. A similar response was observed in a microglia cell line (BV2) treated with DHA, and the effect was blocked by a miR-124 inhibitor. Furthermore, the phagocytic response of BV2 cells to stressed neurones was also reduced in the presence of DHA. In peripheral monocyte-derived macrophages, the expression of the M1, but not the M0 or M2 phenotype, was reduced by DHA, but the phagocytic activation was not altered. These findings show that DHA induces neuroprotection in contusion injury. Furthermore, the improved outcome is via a miR-124-dependent reduction in the phagocytic response of microglia.

Raised Proinflammatory Cytokine Production Within Cerebrospinal Fluid Precedes Fever Onset in Patients With Neurosurgery-Associated Bacterial Meningitis.

OBJECTIVE: The objective of the present study was to determine whether selective inflammatory cytokine concentrations within cerebrospinal fluid are useful markers for the differential diagnosis of aseptic and bacterial meningitis within neurosurgical patients. DESIGN: Prospective, open-label, observational, cohort study. SETTING: Neurosurgical ICU, Chang Gung Memorial Hospital. PATIENTS: Thirty-two consecutive neurosurgical patients who had postoperative fever following external ventricular drain insertion for the treatment of brain injury underwent serial cerebrospinal fluid cytokine analysis pre and post fever to determine the value of such markers in ascertaining the differential diagnosis of meningitis. INTERVENTION: Cerebrospinal fluid samples were collected on the day of fever onset, as well as on day 2 and 4 pre and post fever development. Tumor necrosis factor-α, interleukin-1ß, interleukin-6, interleukin-8, transforming growth factor-ß, and procalcitonin were subsequently analyzed using enzyme-linked immunosorbent assay analysis techniques. MEASUREMENT AND MAIN RESULTS: Inflammatory marker levels were compared among febrile aseptic, bacterial, and nonmeningitis patients to determine cerebrospinal fluid inflammatory changes over time. Significant increases in cerebrospinal fluid tumor necrosis factor -α, interleukin-1ß, interleukin-6, and interleukin-8 levels were observed within patients with bacterial meningitis at fever onset, which was not evident in aseptic or nonmeningitis patients. Furthermore, significant increases in cerebrospinal fluid tumor necrosis factor-α, interleukin-1ß, interleukin-6, and interleukin-8 levels were detected as early as 4 days prior to fever onset within patients with bacterial meningitis when compared with both aseptic and nonmeningitis groups. Interestingly, procalcitonin was only significantly increased in patients with bacterial meningitis on the fourth day post fever. CONCLUSION: The present study suggests that raised cerebrospinal fluid tumor necrosis factor -α, interleukin-1ß, and interleukin-8 in a temporal manner may indicate early bacterial meningitis development in neurosurgical patients, enabling earlier diagnostic certainty and improved patient outcomes.

The history of chromosomal instability in genome doubled tumors.

Tumors frequently display high chromosomal instability and contain multiple copies of genomic regions. Here, we describe GRITIC, a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 6,091 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-doubled tumors. We measured chromosomal instability before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains often accumulate as punctuated bursts, commonly after genome doubling. We infer that genome duplications typically affect the landscape of copy number losses, while only minimally impacting copy number gains. In summary, GRITIC is a novel copy number gain timing framework that permits the analysis of copy number evolution in chromosomally unstable tumors.

Indirect Targeting of Subthalamic Deep Brain Stimulation Guided by Stereotactic Computed Tomography and Microelectrode Recordings in Patients With Parkinson's Disease.

Objective: Magnetic resonance imaging fusion techniques guided by frame-based stereotactic computed tomography and microelectrode recordings are widely used to target the subthalamic nucleus. However, MRI is not always available. The aim of this study was to determine whether the indirect targeting of the subthalamic nucleus for deep brain stimulation using frame-based stereotactic computed tomography and microelectrode recording guidance in patients with advanced idiopathic Parkinson's disease was an effective and safe treatment and to determine the factors that contributed to outcome. Methods: Thirty-four consecutive patients with Parkinson's disease who were treated from 2010 to 2012 were enrolled in this retrospective cohort study. The patients were assessed with the Unified Parkinson's Disease Rating Scale-part III (UPDRS-III) and other clinical profiles peri- and post-operatively. The horizontal and vertical distances between the midpoint of the head frame and the brain midline at the septum pellucidum level and the upper edge of the bilateral lens, respectively, on a thin-section brain computed tomography scan were defined as the horizontal and vertical deviations, respectively. Results: After the deep brain stimulation surgery, the patients' UPDRS-III scores improved 48 ± 2.8% (range, 20-81%) compared to the patients' baseline off-levodopa scores. No surgery-associated complications were found. The mean recorded length difference of the subthalamic nucleus between the initial and final single microelectrode recording trajectories was 5.37 ± 0.16 mm (range, 3.99-7.50). Multiple linear regression analyses revealed that the increased lengths of the vertical (regression coefficient [B]: -0.0626; 95% confidence interval [CI]: -0.113 to -0.013) and horizontal deviations (B: -0.0497; 95% CI: -0.083 to -0.017) were associated with less improvement in the patients' UPDRS scores. Conclusion: These results showed that the indirect targeting of the subthalamic nucleus for deep brain stimulation using frame-based stereotactic computed tomography and microelectrode recording guidance in patients with advanced idiopathic Parkinson's disease was effective and safe. Greater symmetry of the head frame fixation resulted in better outcomes of the deep brain stimulation of the subthalamic nucleus in patients with Parkinson's disease, especially when the horizontal deviation was 2 mm or less and the vertical deviation was 1 mm or less.

Neuroendoscopic surgery in children: does age at intervention influence safety and efficacy? A single-center experience.

OBJECTIVE The aim of this study was to review the safety of pediatric intraventricular endoscopy across separate age groups and to determine whether intraventricular endoscopy is associated with an increased risk of complications or reduced efficacy in infants younger than 1 year. METHODS In this retrospective cohort study, 286 pediatric patients younger than 17 years underwent intraventricular endoscopy at Great Ormond Street Hospital between December 2005 and December 2014. The primary diagnosis, procedure, and complications were recorded. RESULTS Neuroendoscopic surgery was performed in 286 pediatric patients (51 neonates 0-6 months [Group 1]; 37 infants 6-12 months [Group 2]; 75 patients 1-5 years [Group 3]; 54 patients 5-10 years [Group 4]; and 69 patients ≥ 10 years [Group 5]; male/female ratio 173:113). The most common procedures included endoscopic third ventriculostomy (ETV) in 159 patients and endoscopic fenestration of intracranial cysts in 64 patients. A total of 348 consecutive neuroendoscopic procedures were undertaken. Nine different complications were identified, of which postoperative seizures (1.7%), CSF leak (3.1%), CSF infection (2.4%), and intracranial hemorrhage (1.7%) were the most common. Specifically, no significant difference in complication rate (11.9%) or infection rate (2.4%) was observed among age groups (p = 0.40 and p = 0.91, respectively). In addition, there were no perioperative deaths; 30-day mortality was 1.1%. After neuroendoscopy for CSF diversion (n = 227), a significantly higher rate of shunt insertion was observed in the youngest group (Group 1, 63.0%) when compared with older groups (Group 2, 46.4%; Group 3, 26.3%; Group 4, 38.6%; and Group 5, 30.8%; p = 0.03). Similarly, for patients who underwent ETV as their initial neuroendoscopic procedure or in combination with additional surgical interventions (n = 171), a significantly higher rate of shunt insertion was also observed within young infants (Group 1, 67.9%; Group 2, 47.6%; Group 3, 19.6%; Group 4, 27.3%; and Group 5, 23.3%; p = 0.003). CONCLUSIONS Intraventricular endoscopy is a safe neurosurgical intervention in pediatric patients of all ages, although it might be associated with increased shunt rates after endoscopic surgery, specifically ETV, in younger infants.

Effective Steroid Treatment in Traumatic Cervical Spinal Epidural Hematoma Presenting with Delayed Tetraparesis: Two Case Reports and Literature Review.

BACKGROUND: Traumatic spinal epidural hematoma (TSEH) is a rare neurosurgical condition that according to conventional treatment requires prompt surgical decompression. Recent reports, however, suggest that conservative management within the acute phase after trauma also can lead to similar long-term functional outcomes without the need for immediate neurosurgical intervention. CASE DESCRIPTION: In the present paper, we describe 2 cases of TSEH located in the ventral upper cervical spine, which presented with delayed neurologic deficits. In both cases, conservative management with steroid treatment was initiated before neurosurgical decompression, resulting in improved neurologic outcomes. CONCLUSIONS: Urgent surgical decompression may not be necessary acutely in patients with TSEH who respond well to conservative therapy. Although there is currently no consensus for the initial management strategies, steroid treatment could individually tailored and applied according to the clinical condition and evolving symptoms.

Modulating inflammatory cell responses to spinal cord injury: all in good time.

Spinal cord injury can have a range of debilitating effects, permanently impacting a patient's quality of life. Initially thought to be an immune privileged site, the spinal cord is able to mount a timely and well organized inflammatory response to injury. Intricate immune cell interactions are triggered, typically consisting of a staggered multiphasic immune cell response, which can become deregulated if left unchecked. Although several immunomodulatory compounds have yielded success in experimental rodent spinal cord injury models, their translation to human clinical studies needs further consideration. Because temporal differences between rodent and human inflammatory responses to spinal cord injury do exist, drug delivery timing will be a crucial component in recovery from spinal cord injury. Given too early, immunomodulatory therapies may impede beneficial inflammatory reactions to the injured spinal cord or even miss the opportunity to dampen delayed harmful autoimmune processes. Therefore, this review aims to summarize the temporal inflammatory response to spinal cord injury, as well as detailing specific immune cell functions. By clearly defining the chronological order of inflammatory events after trauma, immunomodulatory drug delivery timing can be better optimized. Further, we compare spinal cord injury-induced inflammatory responses in rodent and human studies, enabling clinicians to consider these differences when initiating clinical trials. Improved understanding of the cellular immune response after spinal cord injury would enhance the efficacy of immunomodulatory agents, enabling combined therapies to be considered.