Concussion is associated with a myriad of deleterious immediate and long-term consequences. Yet the molecular mechanisms and genetic targets promoting the selective vulnerability of different neural ...subtypes to dysfunction and degeneration remain unclear. Translating experimental models of blunt force trauma in
C. elegans
to concussion in mice, we identify a conserved neuroprotective mechanism in which reduction of mitochondrial electron flux through complex IV suppresses trauma-induced degeneration of the highly vulnerable dopaminergic neurons. Reducing cytochrome C oxidase function elevates mitochondrial-derived reactive oxygen species, which signal through the cytosolic hypoxia inducing transcription factor,
Hif1a
, to promote hyperphosphorylation and inactivation of the pyruvate dehydrogenase, PDHE1α. This critical enzyme initiates the Warburg shunt, which drives energetic reallocation from mitochondrial respiration to astrocyte-mediated glycolysis in a neuroprotective manner. These studies demonstrate a conserved process in which glycolytic preconditioning suppresses Parkinson-like hypersensitivity of dopaminergic neurons to trauma-induced degeneration via redox signaling and the Warburg effect.
Concussion is a type of traumatic brain injury that results from a sudden blow or jolt to the head. Symptoms can include a passing headache, dizziness, confusion or sensitivity to light, but experiencing multiple concussions can have drastic repercussions in later life.
Studies of professional athletes have shown that those who experience one or more concussions are prone to developing Alzheimer’s and Parkinson’s disease, two well-known neurodegenerative diseases. Both conditions involve the progressive loss or breakdown of nerve cells, called neurons. But exactly how this so-called neurodegeneration of brain cells stems from the original, physical injury remains unclear.
Head trauma may cause damage to the structural support of a cell or disrupt the flow of electrical impulses through neurons. Energy use and production in damaged cells could shift into overdrive to repair the damage. The chemical properties of different types of brain cells could also make some more vulnerable to trauma than others. Besides neurons, star-shaped support cells in the brain called astrocytes, which may have some protective ability, could also be affected.
To investigate which cells may be more susceptible to traumatic injuries, Solano Fonseca et al. modelled the impacts of concussion-like head trauma in roundworms (
C. elegans
) and mice. In both animals, one type of neuron was extremely vulnerable to cell death after trauma. Neurons that release dopamine, a chemical involved in cell-to-cell communication and the brain’s reward system, showed signs of cell damage and deteriorated after injury. Dopaminergic cells, as these cells are called, are involved in motor coordination, and the loss of dopaminergic cells has been linked to both Alzheimer’s and Parkinson’s disease.
Astrocytes, however, had a role in reducing the death of dopaminergic neurons after trauma. In experiments, astrocytes appeared to restore the balance of energy production to meet the increased energy demands of impacted neurons. Single-cell analyses showed that genes involved in metabolism were switched on in astrocytes to produce energy via an alternative pathway. This energetic shift facilitated via astrocytes may help mitigate against some damage to dopamine-producing neurons after trauma, reducing cell death.
This work furthers our understanding of cellular changes in the concussed brain. More research will be required to better characterise how this immediate trauma to cells, and the subsequent loss of dopaminergic neurons, impacts brain health long-term. Efforts to design effective therapies to slow or reverse these changes could then follow.
Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but little is known about its genetic etiology. We mapped the genomic ...landscape of canine melanoma through multi-platform analysis of 37 tumors (31 mucosal, 3 acral, 2 cutaneous, and 1 uveal) and 17 matching constitutional samples including long- and short-insert whole genome sequencing, RNA sequencing, array comparative genomic hybridization, single nucleotide polymorphism array, and targeted Sanger sequencing analyses. We identified novel predominantly truncating mutations in the putative tumor suppressor gene PTPRJ in 19% of cases. No BRAF mutations were detected, but activating RAS mutations (24% of cases) occurred in conserved hotspots in all cutaneous and acral and 13% of mucosal subtypes. MDM2 amplifications (24%) and TP53 mutations (19%) were mutually exclusive. Additional low-frequency recurrent alterations were observed amidst low point mutation rates, an absence of ultraviolet light mutational signatures, and an abundance of copy number and structural alterations. Mutations that modulate cell proliferation and cell cycle control were common and highlight therapeutic axes such as MEK and MDM2 inhibition. This mutational landscape resembles that seen in BRAF wild-type and sun-shielded human melanoma subtypes. Overall, these data inform biological comparisons between canine and human melanoma while suggesting actionable targets in both species.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer’s clinical management. Variation in driver mutation frequency between patients with ...the same tumor type as well as within an individual patients’ cancer can shape the use of mutations as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 43 dogs (27 HSA, 15 benign masses, and 1 stromal sarcoma) presenting for emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal targeted sequencing panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/27 (52%) HSAs. Among recurrent candidate driver mutations,
TP53
was most commonly mutated (30%) followed by
PIK3CA
(15%),
AKT1
(11%), and
CDKN2AIP
(11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspectives on the genomic landscape of this veterinary cancer and suggest a cross-species value for using HSA in pet dogs as a naturally occurring model of intratumoral heterogeneity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from ...59 dogs, including whole genome sequencing (
= 24) and whole exome sequencing (WES;
= 13) of primary tumors and matched normal tissue, WES (
= 10) of matched primary/metastatic/normal samples and RNA sequencing (
= 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent
(71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic
(42%) and
(50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.
The hippocampus supports many facets of cognition, including learning, memory, and emotional processing. Anatomically, the hippocampus runs along a longitudinal axis, posterior to anterior in ...primates. The structure, function, and connectivity of the hippocampus vary along this axis. In human hippocampus, longitudinal functional heterogeneity remains an active area of investigation, and structural heterogeneity has not been described. To understand the cellular and molecular diversity along the hippocampal long axis in human brain and define molecular signatures corresponding to functional domains, we performed single-nuclei RNA sequencing on surgically resected human anterior and posterior hippocampus from epilepsy patients, identifying differentially expressed genes at cellular resolution. We further identify axis- and cell-type-specific gene expression signatures that differentially intersect with human genetic signals, identifying cell-type-specific genes in the posterior hippocampus for cognitive function and the anterior hippocampus for mood and affect. These data are accessible as a public resource through an interactive website.
•Analysis of single-nuclei transcriptomes along the human hippocampal longitudinal axis•Excitatory neurons show transcriptional heterogeneity across the axis•Cell-type- and axis-specific enrichment of disease-associated genes
Ayhan et al. examine single-nuclei gene expression profiles from distinct regions of human hippocampus. Integrating these results with human genetic data reveals differential involvement of these regions in brain disorders. Comparisons between human and rodent data show that the results are partially conserved.
3062
Background: The regulatory approval of TRK tyrosine kinase inhibitors (TKIs) represented a landmark in tissue-agnostic drug development. Adult and pediatric patients harboring NTRK fusions ...derive meaningful clinical benefits from the first-generation TRK TKIs larotrectinib and entrectinib. However, characterizing NTRK fusions and resistance mechanisms to TRK TKIs by circulating tumor DNA (ctDNA) remains to be studied. Methods: Patients with NTRK-fusion-positive tumors who received TRK TKIs and had ctDNA analyzed using next-generation sequencing (NGS) were retrospectively identified. Samples were collected at multiple time points, including pre-TRK TKI, on-treatment, and post-progression. Mechanisms of resistance to TRK TKIs were examined when post-progression ctDNA samples were available. Results: Twenty-seven patients, with a median age of 57 years (range 28-81) and 11 different cancer types were identified. Twenty-two patients (81%; 22/27) had at least one ctDNA-positive sample (tumor burden greater than 0). A total of 67 ctDNA samples were analyzed by MSKCC ACCESS ctDNA pipeline, of which 10 samples (15%; 10/67) were collected before any TRK TKI. Forty-two samples (63%; 42/67) had positive ctDNA and NTRK fusion was detected in 16 ctDNA samples (24%; 16/67), including 9 (56%) NTRK1 fusions and 7 (44%) NTRK3 fusions. Among the pre-TRK TKI samples (n=10), 2 samples (20%, 2/10) had NTRK fusions detected. A total of 8 patients had post-progression samples with a resistance mechanism identified, of which 5 patients received larotrectinib and 3 entrectinib. The ctDNA samples revealed 7 patients (88%; 7/8) with on-target resistance and 1 patient (12%; 1/8) with off-target resistance. Among on-target mutations identified, the most common involved the solvent front residue (86%, n=6/7: n=2 NTRK3 G623R, n=2 NTRK1 G595R, n=1 NTRK3 G623E, n=1 NTRK3 623L) followed by the xDFG motif (14%, n=1/7: n=1 NTRK1 G667C). Regarding off-target alterations, one patient developed a BRAF V600E mutation. Conclusions: The use of plasma ctDNA can improve the identification of NTRK fusions through non-invasive techniques and potentially identify subsequent resistance mechanisms after the administration of the TRK TKIs.
Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral ...lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural variation and absence of UV-derived mutation signatures. Only 38% of patients demonstrated driver
mutations. In contrast with CM, we observed
copy gains in 15% of patients, and somatic
translocations, copy gains, and missense and promoter mutations, or germline events, in 41% of patients. We further show that in vitro TERT inhibition has cytotoxic effects on primary ALM cells. These findings provide insight into the role of
in ALM tumorigenesis and reveal preliminary evidence that TERT inhibition represents a potential therapeutic strategy in ALM.
Abstract
Background: Osteosarcoma (OS), the most common malignant bone tumor in humans and dogs, shares several features in both species including clinical presentation and molecular alterations. ...Despite numerous efforts there have been no improvements in outcome: 30% of people and 90% of dogs still die of metastasis. While the genomic landscape of human OS has been interrogated, limited data exist regarding that of dogs. Using whole genome sequencing (WGS) we identified the presence of mutations in DMD, the gene encoding dystrophin, in canine OS. The purpose of this work was to expand upon these findings and begin to interrogate the functional consequences of these mutations. Methods: Whole-genome sequencing (WGS) of 24 canine primary OS tumor samples was completed on an Illumina platform. Somatic single nucleotide and structural variants, and germline variants were identified using Cerberus, a canine cancer genomics pipeline. Expression of the Dp71 DMD isoform was modulated using CRISPR-Cas9 and lentiviral overexpression approaches; the biologic significance of DMD loss was characterized using Co-IP, western blotting, Matrigel invasion and proliferation assays. Results: Our prior data found that canine OS recapitulates several genetic features of human OS including high structural complexity and translocation burden withTP53 (71%) the most frequently mutated gene. In addition to inactivating SETD2 mutations 42% of cases, we found that 50% of tumors possessed large somatic intragenic deletions and copy number loss of DMD, the gene encoding dystrophin. Building upon these data we found that truncated dystrophin isoforms (Dp260, Dp140, Dp71, Dp40) predominate in canine OS cell lines, with only Dp40 expressed in normal osteoblasts. Deletion of Dp71 in OS lines using CRISPR-Cas9 resulted in increased cell proliferation and markedly enhanced invasion through Matrigel. Consistent with the published literature, dystrophin and β-dystroglycan co-associated in the OS lines, and phosphorylation of β-dystroglycan was increased when dystrophin expression was downregulated. Lastly, dasatinib, a small molecule inhibitor of Src, inhibited β-dystroglycan phosphorylation and cell proliferation in the canine OS lines. Conclusions: These data provide important new information regarding the genomic profile of canine OS and suggest that aberrations in dystrophin expression may contribute to OS pathophysiology in dogs by promoting a metastatic phenotype. Future work will dissect exactly how altered dystrophin isoforms contribute to OS tumor biology with the goal of developing approaches for therapeutic intervention that target this pathway.
Citation Format: Heather L. Gardner, Karthigayini Sivaprakasam, Natalia Briones, William Hendricks, Cheryl A. London. The genomic landscape of canine osteosarcoma implicates DMD as a therapeutic vulnerability abstract. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B026. doi:10.1158/1535-7163.TARG-19-B026
Cancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer's clinical management. Variation in driver mutation frequency between patients with ...the same tumor type as well as within an individual patients' cancer can shape the use of mutations as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 43 dogs (27 HSA, 15 benign masses, and 1 stromal sarcoma) presenting for emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal targeted sequencing panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/27 (52%) HSAs. Among recurrent candidate driver mutations, TP53 was most commonly mutated (30%) followed by PIK3CA (15%), AKT1 (11%), and CDKN2AIP (11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspectives on the genomic landscape of this veterinary cancer and suggest a cross-species value for using HSA in pet dogs as a naturally occurring model of intratumoral heterogeneity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Essential tremor (ET) is a common, progressive neurological disease characterized by an 8–12-Hz kinetic tremor. Despite its high prevalence, the patho-mechanisms of tremor in ET are not fully known. ...Through comprehensive studies in postmortem brains, we identified major morphological changes in the ET cerebellum that reflect cellular damage in Purkinje cells (PCs), suggesting that PC damage is central to ET pathogenesis. We previously performed a transcriptome analysis in ET cerebellar cortex, identifying candidate genes and several dysregulated pathways. To directly target PCs, we purified RNA from PCs isolated by laser capture microdissection and performed the first ever PC-specific RNA-sequencing analysis in ET versus controls. Frozen postmortem cerebellar cortex from 24 ETs and 16 controls underwent laser capture microdissection, obtaining ≥2000 PCs per sample. RNA transcriptome was analyzed via differential gene expression, principal component analysis (PCA), and gene set enrichment analyses (GSEA). We identified 36 differentially expressed genes, encompassing multiple cellular processes. Some ET (13/24) had greater dysregulation of these genes and segregated from most controls and remaining ETs in PCA. Characterization of genes/pathways enriched in this PCA and GSEA identified multiple pathway dysregulations in ET, including RNA processing/splicing, synapse organization/ion transport, and oxidative stress/inflammation. Furthermore, a different set of pathways characterized marked heterogeneity among ET patients. Our data indicate a range of possible mechanisms for the pathogenesis of ET. Significant heterogeneity among ET combined with dysregulation of multiple cellular processes supports the notion that ET is a family of disorders rather than one disease entity.
PDF
