Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis ...with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease.
To classify PDAC according to distinct mutational processes, and explore their clinical significance.
We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium. The discovery cohort comprised 160 PDAC cases from 154 patients (148 primary; 12 metastases) that underwent tumor enrichment prior to whole-genome and RNA sequencing. The replication cohort comprised 95 primary PDAC cases that underwent whole-genome sequencing and expression microarray on bulk biospecimens.
Somatic mutations accumulate from sequence-specific processes creating signatures detectable by DNA sequencing. Using nonnegative matrix factorization, we measured the contribution of each signature to carcinogenesis, and used hierarchical clustering to subtype each cohort. We examined expression of antitumor immunity genes across subtypes to uncover biomarkers predictive of response to systemic therapies.
The discovery cohort was 53% male (n = 79) and had a median age of 67 (interquartile range, 58-74) years. The replication cohort was 50% male (n = 48) and had a median age of 68 (interquartile range, 60-75) years. Five predominant mutational subtypes were identified that clustered PDAC into 4 major subtypes: age related, double-strand break repair, mismatch repair, and 1 with unknown etiology (signature 8). These were replicated and validated. Signatures were faithfully propagated from primaries to matched metastases, implying their stability during carcinogenesis. Twelve of 27 (45%) double-strand break repair cases lacked germline or somatic events in canonical homologous recombination genes-BRCA1, BRCA2, or PALB2. Double-strand break repair and mismatch repair subtypes were associated with increased expression of antitumor immunity, including activation of CD8-positive T lymphocytes (GZMA and PRF1) and overexpression of regulatory molecules (cytotoxic T-lymphocyte antigen 4, programmed cell death 1, and indolamine 2,3-dioxygenase 1), corresponding to higher frequency of somatic mutations and tumor-specific neoantigens.
Signature-based subtyping may guide personalized therapy of PDAC in the context of biomarker-driven prospective trials.
Dysfunction of the ubiquitin proteasome system (UPS) has been implicated in the pathogenesis of many neurological diseases, including Alzheimer's, spinocerebellar ataxia, and several motor neuron ...diseases. Recent research indicates that changes in synaptic transmission may play a critical role in the progression of neurological disease; however, the mechanisms by which the UPS regulates synaptic structure and function have not been well characterized. In this report, we show that Usp14 is indispensable for synaptic development and function at neuromuscular junctions (NMJs). Usp14-deficient axJ mice display a resting tremor, a reduction in muscle mass, and notable hindlimb rigidity without any detectable loss of motor neurons. Instead, loss of Usp14 causes developmental defects at motor neuron endplates. Presynaptic defects include phosphorylated neurofilament accumulations, nerve terminal sprouting, and poor arborization of the motor nerve terminals, whereas postsynaptic acetylcholine receptors display immature plaque-like morphology. These structural changes in the NMJ correlated with ubiquitin loss in the spinal cord and sciatic nerve. Further studies demonstrated that the greatest loss of ubiquitin was found in synaptosomal fractions, suggesting that the endplate swellings may be caused by decreased protein turnover at the synapse. Transgenic restoration of Usp14 in the nervous system corrected the levels of monomeric ubiquitin in the motor neuron circuit and the defects that were observed in the motor endplates and muscles of the axJ mice. These data define a critical role for Usp14 at mammalian synapses and suggest a requirement for local ubiquitin recycling by the proteasome to control the development and function of NMJs.
To examine differences between male and female adolescents on measures of balance, vestibular and oculomotor function within 3 weeks of concussion among a group of pediatric patients presenting to a ...sports medicine clinic.
Medical record review.
Sports medicine clinic.
197 female (median age = 15.2 years) and 381 male (median age = 14.6 years) pediatric patients seen for a concussion, evaluated 9.3 ± 5.2 (mean ± SD) days post-concussion.
Patients completed Balance Error Scoring System (BESS), tandem gait, gaze stability, and near point of convergence (NPC) tests.
A higher proportion of female patients exhibited abnormal NPC (22% vs. 14%; p = 0.017), gaze stability (53% vs. 43%; p = 0.028), and tandem gait tests (20% vs. 13%; p = 0.026) compared to male patients. Multivariable analysis indicated an independent association between female sex and increased odds of abnormal NPC (adjusted odds ratio aOR = 1.79, 95% CI = 1.07–3.00), and tandem gait tests (aOR = 1.96, 95% CI = 1.12–3.41) following concussion.
Our results indicate that within the first three weeks of a concussion, female pediatric patients demonstrated increased odds of exhibiting abnormal near point of convergence, and tandem gait test performance compared to male patients.
•Female patients with concussion demonstrated more dysfunction than male patients.•Female patients demonstrated worse convergence and balance than male patients.•Sex may be a modifying factor for functional abilities after pediatric concussion.
Collagen peptides are analyzed using a low-cost, high-throughput method for assessing deamidation using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For each chosen ...peptide, the theoretical distribution is calculated and the measured distribution for each sample compared with this to determine the extent of glutamine deamidation. The deamidation of glutamine (Q) to glutamic acid (E) results in a mass shift of +0.984 Da. Thus, from the resolution of our data, the second peak in the isotope distribution for a peptide containing one glutamine residue coincides with the first peak of the isotope distribution for the peptide in which the residue is deamidated. A genetic algorithm is used to determine the extent of deamidation that gives the best fit to the measured distribution. The method can be extended to peptides containing more than one glutamine residue. The extent of protein degradation assessed in this way could be used, for example, to assess the damage of collagen, and screen samples for radiocarbon dating and DNA analysis.
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and ...setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
•Single/dual-task tandem gait performance after concussion was slower than in controls.•Tandem gait cut-points provided > 80% accuracy between concussion and control groups.•Dual-task tandem gait ...test performance may provide some prognostic value.
The tandem gait test has gained interest recently for assessment of concussion recovery. The purpose of our study was to determine the prognostic and diagnostic use of the single- and dual-task tandem gait test, alongside other clinical measures, within 10 days of pediatric concussion.
We assessed 126 patients post-concussion (6.3 ± 2.3 days post-injury, mean ± SD) at a pediatric sports medicine clinic and compared them to 58 healthy controls (age: 15.6 ± 1.3 years; 43% female). We also compared the 31 patients with concussion who developed persistent post-concussion symptoms (PPCS) (age = 14.9 ± 2.0 years; 48% female) to the 81 patients with concussion who did not develop PPCS following the initial assessment (age: 14.1 ± 3.0 years; 41% female). All subjects completed a test battery, and concussion patients were monitored until they experienced concussion-symptom resolution. The test battery included tandem gait (single-task, dual-task (performing tandem gait while concurrently completing a cognitive test) conditions), modified Balance Error Scoring System (mBESS), and concussion symptom assessment (Health and Behavior Inventory). We defined PPCS as symptom resolution time > 28 days post-concussion for the concussion group. Measurement outcomes included tandem gait time (single- and dual-task), dual-task cognitive accuracy, mBESS errors (single/double/tandem stances), and symptom severity.
The concussion group completed the single-task (mean difference = 9.1 s, 95% confidential interval (95%CI): 6.1–12.1) and dual-task (mean difference = 12.7 s, 95%CI: 8.7–16.8) tandem gait test more slowly than the control group. Compared to those who recovered within 28 days of concussion, the PPCS group had slower dual-task tandem gait test times (mean difference = 7.9 s, 95%CI: 2.0–13.9), made more tandem-stance mBESS errors (mean difference = 1.3 errors, 95%CI: 0.2–2.3), and reported more severe symptoms (mean difference = 26.6 Health and Behavior Inventory rating, 95%CI: 21.1–32.6).
Worse dual-task tandem gait test time and mBESS tandem stance performance predicted PPCS in pediatric patients evaluated within 10 days of concussion. Tandem gait assessments may provide valuable information augmenting common clinical practices for concussion management.
Display omitted
We examined post-concussion symptom presentation, exercise, and sleep among pediatric athletes who sustained concussion during the school year vs. summer months.
We evaluated athletes 6-18 years old ...within 21-days of concussion. They reported symptoms (Health and Behavior Inventory), with cognitive/somatic domain sub-scores calculated, and indicated if they had exercised or experienced sleep problems since injury. We grouped patients by injury season: summer months (June-August) vs. school year (September-May).
350 patients (14.4 ± 2.4 years old; 37% female; initial visit 8.8 ± 5.3 days post-concussion) were seen for care: 24% sustained a concussion during summer months, 76% during the school year. Lower cognitive (median = 7 IQR = 1, 15 vs. 9.5 4, 17;
= 0.01), but not somatic (7 2.5, 11 vs. 8 4, 13;
= 0.06), HBI scores were observed for patients injured during the summer. Groups were similar in proportion exercising (16% vs 17%) and endorsing sleep problems (29% vs 31%). After adjustments, sustaining a concussion during the summer predicted total (β=-3.43; 95%CI = -6.50, -0.36;
= 0.029) and cognitive (β = -2.29; 95%CI = -4.22, -0.36;
= 0.02), but not somatic (β=-1.46; 95%CI = -2.84, -0.08;
= 0.04), symptom severity.
Pediatric patients with concussion may present with greater cognitive symptoms during the school year, compared to summer months.
To examine kinesiophobia (i.e. fear of movement) among adolescent athletes with concussion compared to controls, and correlations of kinesiophobia with symptoms and reaction time.
Prospective cohort ...study.
We evaluated 49 adolescent athletes twice. The concussion group was assessed within 14 days of injury and at return-to-play clearance. The control group was tested initially and approximately 28 days later. Participants completed Tampa Scale of Kinesiophobia, Post-Concussion Symptom Inventory, and clinical reaction time assessments.
We included 32 concussion participants (15 ± 2 years; 50% female) and 17 controls (16 ± 1 years; 47% female). Acutely (<14 days post-injury), the concussion group reported greater Tampa Scale of Kinesiophobia scores (38.5 ± 5.4 vs. 29.4 ± 6.7; p < 0.001; Cohen's d = 1.54), and a greater proportion of “high” (≥37) scores than controls (69% vs. 6%; p < 0.001). At return-to-play, there were no significant between-group differences (33.3 ± 6.5 vs. 30.8 ± 7.4; p = 0.23; Cohen's d = 0.36); 28% of the concussion group reported “high” Tampa Scale of Kinesiophobia scores. At return-to-play, kinesiophobia was significantly/moderately correlated with clinical reaction time for the concussion group (r = 0.50; p = 0.01).
Adolescents recovering from concussion commonly reported high kinesiophobia initially postconcussion, while 28% continued to report high kinesiophobia at return-to-play clearance. Additionally, a correlation between Tampa Scale of Kinesiophobia scores and clinical reaction time was observed for the concussion group. This finding would benefit from further study to determine potential perception–behavior relationships following concussion.
The ubiquitin-proteasome system (UPS) controls protein abundance and is essential for many aspects of neuronal function. In ataxia (ax(J)) mice, profound neurological and synaptic defects result from ...a loss-of-function mutation in the proteasome-associated deubiquitinating enzyme Usp14, which is required for recycling ubiquitin from proteasomal substrates. Here, we show that transgenic complementation of ax(J) mice with neuronally expressed ubiquitin prevents early postnatal lethality, restores muscle mass, and corrects developmental and functional deficits resulting from the loss of Usp14, demonstrating that ubiquitin deficiency is a major cause of the neurological defects observed in the ax(J) mice. We also show that proteasome components are normally induced during the first 2 weeks of postnatal development, which coincides with dramatic alterations in polyubiquitin chain formation. These data demonstrate a critical role for ubiquitin homeostasis in synaptic development and function, and show that ubiquitin deficiency may contribute to diseases characterized by synaptic dysfunction.
Co-occurrent KRAS and TP53 mutations define a majority of patients with pancreatic ductal adenocarcinoma (PDAC) and define its pro-metastatic proclivity. Here, we demonstrate that KRAS-TP53 ...co-alteration is associated with worse survival compared with either KRAS-alone or TP53-alone altered PDAC in 245 patients with metastatic disease treated at a tertiary referral cancer center, and validate this observation in two independent molecularly annotated datasets. Compared with non-TP53 mutated KRAS-altered tumors, KRAS-TP53 co-alteration engenders disproportionately innate immune-enriched and CD8
T-cell-excluded immune signatures. Leveraging in silico, in vitro, and in vivo models of human and murine PDAC, we discover a novel intersection between KRAS-TP53 co-altered transcriptomes, TP63-defined squamous trans-differentiation, and myeloid-cell migration into the tumor microenvironment. Comparison of single-cell transcriptomes between KRAS-TP53 co-altered and KRAS-altered/TP53
tumors revealed cancer cell-autonomous transcriptional programs that orchestrate innate immune trafficking and function. Moreover, we uncover granulocyte-derived inflammasome activation and TNF signaling as putative paracrine mediators of innate immunoregulatory transcriptional programs in KRAS-TP53 co-altered PDAC. Immune subtyping of KRAS-TP53 co-altered PDAC reveals conflation of intratumor heterogeneity with progenitor-like stemness properties. Coalescing these distinct molecular characteristics into a KRAS-TP53 co-altered "immunoregulatory program" predicts chemoresistance in metastatic PDAC patients enrolled in the COMPASS trial, as well as worse overall survival.
PDF
