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2.
bioRxiv ; 2024 Aug 17.
Article in English | MEDLINE | ID: mdl-39185156

ABSTRACT

Identifying the key molecular pathways that enable metastasis by analyzing the eventual metastatic tumor is challenging because the state of the founder subclone likely changes following metastatic colonization. To address this challenge, we labeled primary mouse pancreatic ductal adenocarcinoma (PDAC) subclones with DNA barcodes to characterize their pre-metastatic state using ATAC-seq and RNA-seq and determine their relative in vivo metastatic potential prospectively. We identified a gene signature separating metastasis-high and metastasis-low subclones orthogonal to the normal-to-PDAC and classical-to-basal axes. The metastasis-high subclones feature activation of IL-1 pathway genes and high NF-κB and Zeb/Snail family activity and the metastasis-low subclones feature activation of neuroendocrine, motility, and Wnt pathway genes and high CDX2 and HOXA13 activity. In a functional screen, we validated novel mediators of PDAC metastasis in the IL-1 pathway, including the NF-κB targets Fos and Il23a, and beyond the IL-1 pathway including Myo1b and Tmem40. We scored human PDAC tumors for our signature of metastatic potential from mouse and found that metastases have higher scores than primary tumors. Moreover, primary tumors with higher scores are associated with worse prognosis. We also found that our metastatic potential signature is enriched in other human carcinomas, suggesting that it is conserved across epithelial malignancies. This work establishes a strategy for linking cancer cell state to future behavior, reveals novel functional regulators of PDAC metastasis, and establishes a method for scoring human carcinomas based on metastatic potential.

3.
Orthop J Sports Med ; 12(8): 23259671241248457, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39135861

ABSTRACT

Background: Medial meniscal extrusion (MME) has been associated with knee osteoarthritis (OA). However, there is no standardized method to measure MME. Purpose/Hypothesis: The purpose of this study was to investigate the relationship between MME and outcome measures related to knee OA and discuss different magnetic resonance imaging (MRI) methods of measuring MME. It was hypothesized that MME would be associated with outcome measures of OA and that the distance extruded over the tibial plateau would be the most common MRI method to measure MME. Study Design: Systematic review; Level of evidence, 3. Methods: The MEDLINE, Embase, Cochrane Library, Scopus, Web of Science Core Collection, Global Index Medicus, and ClinicalTrials.gov databases were systematically searched. The inclusion criteria were studies that (1) measured MME on nonoperated knees using MRI; (2) evaluated knee OA with at least 1 knee OA grading scale, outcome measure, or direct characterization of cartilage or bone; (3) statistically evaluated the association between MME and knee OA outcome measure; (4) were randomized controlled trials, nonrandomized controlled trials, cohort studies, or case series; and (5) reported original results. Results: A total of 19 studies were included, of which 14 reported MME as the distance extruded over the tibial plateau, 7 reported MME as the volume extruded over the tibial plateau, and 1 reported MME as the percentage of the tibial plateau covered by the meniscus. All studies reported that MME was significantly associated with at least 1 OA outcome measure-including increased Kellgren-Lawrence grade, osteophytes, cartilage damage, varus alignment, knee pain, bone marrow lesions, and progression to arthroplasty. Eight studies found that MME was associated with worse OA outcomes over time (range, 2-10 years). Conclusion: All 19 reviewed studies reported that MME was associated with at least 1 knee OA outcome measure reflective of worsening arthritis, suggesting a strong association between OA and MME. Future research is needed to investigate this relationship and standardize the methods of measuring MME.

4.
medRxiv ; 2024 Aug 16.
Article in English | MEDLINE | ID: mdl-39185524

ABSTRACT

Background: Excessive daytime sleepiness (EDS) is a disabling symptom of Lewy body disorders (LBD). The hypothalamus is a key sleep-wake regulator, but its contribution to EDS in LBD remains unclear. Objectives: Use diffusion MRI to evaluate the relationship of hypothalamic microstructure to EDS symptoms in LBD. Methods: We studied 102 patients with clinically-defined LBD (Parkinson's disease, n=93; Parkinson's disease dementia, n=4; and dementia with Lewy bodies, n=5) and Epworth Sleepiness Scale (ESS) within 2 years of MRI. Mean diffusivity (MD) was compared between EDS+ (ESS≥10, n=37) and EDS- (ESS<10, n=65) groups in the whole hypothalamus and three subregions, covarying for age and sex. Secondary analyses tested correlations between subregion MD and continuous ESS, global cognition, and motor scores; and between subregion volume and continuous ESS. Results: MD was increased in EDS+ compared to EDS- only in the inferior tuberal subregion (Cohen's d=0.43, p=0.043, ß=0.117±0.057), with trend level differences in the whole hypothalamus (Cohen's d=0.39, p=0.064, ß=0.070±0.037) and superior tuberal subregion (Cohen's d=0.38, p=0.073, ß=0.063±0.035). No difference was seen in the posterior subregion (Cohen's d=0.1, p=0.628, ß=0.019±0.038). Significant correlations with continuous ESS were seen in MD of whole hypothalamus (r2=0.074, p=0.0057), superior tuberal (r2=0.081, p=0.0038), and inferior tuberal (r2=0.073, p=0.0059) subregions. There was no correlation of hypothalamic MD with global cognition or motor scores, and no correlation of whole/subregional hypothalamic volumes with ESS. Conclusions: Daytime sleepiness associates with increased MD in the inferior tuberal hypothalamus in an LBD cohort. This suggests degeneration within this region could contribute to EDS symptoms.

5.
Res Sq ; 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39149495

ABSTRACT

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.

6.
Nat Commun ; 15(1): 7054, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39147793

ABSTRACT

Pressure-induced phase transformations (PTs) in Si, the most important electronic material, have been broadly studied, whereas strain-induced PTs have never been studied in situ. Here, we reveal in situ various important plastic strain-induced PT phenomena. A correlation between the direct and inverse Hall-Petch effect of particle size on yield strength and pressure for strain-induced PT is predicted theoretically and confirmed experimentally for Si-I→Si-II PT. For 100 nm particles, the strain-induced PT Si-I→Si-II initiates at 0.3 GPa under both compression and shear while it starts at 16.2 GPa under hydrostatic conditions. The Si-I→Si-III PT starts at 0.6 GPa but does not occur under hydrostatic pressure. Pressure in small Si-II and Si-III regions of micron and 100 nm particles is ∼5-7 GPa higher than in Si-I. For 100 nm Si, a sequence of Si-I → I + II → I + II + III PT is observed, and the coexistence of four phases, Si-I, II, III, and XI, is found under torsion. Retaining Si-II and single-phase Si-III at ambient pressure and obtaining reverse Si-II→Si-I PT demonstrates the possibilities of manipulating different synthetic paths. The obtained results corroborate the elaborated dislocation pileup-based mechanism and have numerous applications for developing economic defect-induced synthesis of nanostructured materials, surface treatment (polishing, turning, etc.), and friction.

7.
Nature ; 632(8025): 614-621, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39048821

ABSTRACT

Western equine encephalitis virus (WEEV) is an arthropod-borne virus (arbovirus) that frequently caused major outbreaks of encephalitis in humans and horses in the early twentieth century, but the frequency of outbreaks has since decreased markedly, and strains of this alphavirus isolated in the past two decades are less virulent in mammals than strains isolated in the 1930s and 1940s1-3. The basis for this phenotypic change in WEEV strains and coincident decrease in epizootic activity (known as viral submergence3) is unclear, as is the possibility of re-emergence of highly virulent strains. Here we identify protocadherin 10 (PCDH10) as a cellular receptor for WEEV. We show that multiple highly virulent ancestral WEEV strains isolated in the 1930s and 1940s, in addition to binding human PCDH10, could also bind very low-density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), which are recognized by another encephalitic alphavirus as receptors4. However, whereas most of the WEEV strains that we examined bind to PCDH10, a contemporary strain has lost the ability to recognize mammalian PCDH10 while retaining the ability to bind avian receptors, suggesting WEEV adaptation to a main reservoir host during enzootic circulation. PCDH10 supports WEEV E2-E1 glycoprotein-mediated infection of primary mouse cortical neurons, and administration of a soluble form of PCDH10 protects mice from lethal WEEV challenge. Our results have implications for the development of medical countermeasures and for risk assessment for re-emerging WEEV strains.


Subject(s)
Encephalitis Virus, Western Equine , Host Specificity , Protocadherins , Receptors, Virus , Animals , Female , Humans , Male , Mice , Birds/metabolism , Birds/virology , Communicable Diseases, Emerging/epidemiology , Communicable Diseases, Emerging/virology , Encephalitis Virus, Western Equine/classification , Encephalitis Virus, Western Equine/metabolism , Encephalitis Virus, Western Equine/pathogenicity , Encephalomyelitis, Equine/epidemiology , Encephalomyelitis, Equine/virology , LDL-Receptor Related Proteins/metabolism , Neurons/metabolism , Neurons/virology , Phenotype , Protocadherins/metabolism , Receptors, LDL/metabolism , Receptors, LDL/genetics , Receptors, Virus/metabolism , Viral Envelope Proteins/metabolism , Viral Zoonoses/epidemiology , Viral Zoonoses/virology
8.
J Neurosurg Pediatr ; : 1-11, 2024 Jul 26.
Article in English | MEDLINE | ID: mdl-39059425

ABSTRACT

OBJECTIVE: Posttraumatic headache (PTH) represents the most common acute and persistent postconcussive symptom (PCS) in children after concussion, yet there remains a lack of valid and objective biomarkers to facilitate risk stratification and early intervention in this patient population. Fixel-based analysis of diffusion-weighted imaging, which overcomes constraints of traditional diffusion tensor imaging analyses, can improve the sensitivity and specificity of detecting white matter changes postconcussion. The aim of this study was to investigate whole-brain and tract-based differences in white matter morphology, including fiber density (FD) and fiber bundle cross-section (FC) area in children with PCSs and PTH at 2 weeks after concussion. METHODS: This prospective longitudinal study recruited children aged 5-18 years who presented to the emergency department of a tertiary pediatric hospital with a concussion sustained within the previous 48 hours. Participants underwent diffusion-weighted MRI at 2 weeks postinjury. Whole-brain white matter statistical analysis was performed at the level of each individual fiber population within an image voxel (fixel) to compute FD, FC, and a combined metric (FD and bundle cross-section [FDC]) using connectivity-based fixel enhancement. Tract-based Bayesian analysis was performed to examine FD in 23 major white matter tracts. RESULTS: Comparisons of 1) recovered (n = 27) and symptomatic (n = 16) children, and those with 2) PTH (n = 13) and non-PTH (n = 30; overall mean age 12.99 ± 2.70 years, 74% male) found no fiber-specific white matter microstructural differences in FD, FC, or FDC at 2 weeks postconcussion, when adjusting for age and sex (family-wise error rate corrected p value > 0.05). Tract-based Bayesian analysis showed evidence of no effect of PTH on FD in 10 major white matter tracts, and evidence of no effect of recovery group on FD in 3 white matter tracts (Bayes factor < 1/3). CONCLUSIONS: Using whole-brain fixel-wise and tract-based analyses, these findings indicate that fiber-specific properties of white matter microstructure are not different between children with persisting PCSs compared with recovered children 2 weeks after concussion. These data extend the limited research on white matter fiber-specific morphology while overcoming limitations inherent to traditional diffusion models. Further validation of our findings with a large-scale cohort is warranted.

9.
Radiol Adv ; 1(1): umae005, 2024 May.
Article in English | MEDLINE | ID: mdl-38855428

ABSTRACT

Background: Medial meniscus root tears often lead to knee osteoarthritis. The extent of meniscal tissue changes beyond the localized root tear is unknown. Purpose: To evaluate if 7 Tesla 3D T2*-mapping can detect intrasubstance meniscal degeneration in patients with arthroscopically verified medial meniscus posterior root tears (MMPRTs), and assess if tissue changes extend beyond the immediate site of the posterior root tear detected on surface examination by arthroscopy. Methods: In this prospective study we acquired 7 T knee MRIs from patients with MMPRTs and asymptomatic controls. Using a linear mixed model, we compared T2* values between patients and controls, and across different meniscal regions. Patients underwent arthroscopic assessment before MMPRT repair. Changes in pain levels before and after repair were calculated using Knee Injury & Osteoarthritis Outcome Score (KOOS). Pain changes and meniscal extrusion were correlated with T2* using Pearson correlation (r). Results: Twenty patients (mean age 53 ± 8; 16 females) demonstrated significantly higher T2* values across the medial meniscus (anterior horn, posterior body and posterior horn: all P < .001; anterior body: P = .007), and lateral meniscus anterior (P = .024) and posterior (P < .001) horns when compared to the corresponding regions in ten matched controls (mean age 53 ± 12; 8 females). Elevated T2* values were inversely correlated with the change in pain levels before and after repair. All patients had medial meniscal extrusion of ≥2 mm. Arthroscopy did not reveal surface abnormalities in 70% of patients (14 out of 20). Conclusions: Elevated T2* values across both medial and lateral menisci indicate that degenerative changes in patients with MMPRTs extend beyond the immediate vicinity of the posterior root tear. This suggests more widespread meniscal degeneration, often undetected by surface examinations in arthroscopy.

10.
Nat Commun ; 15(1): 4892, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38849329

ABSTRACT

Reducing disparities is vital for equitable access to precision treatments in cancer. Socioenvironmental factors are a major driver of disparities, but differences in genetic variation likely also contribute. The impact of genetic ancestry on prioritization of cancer targets in drug discovery pipelines has not been systematically explored due to the absence of pre-clinical data at the appropriate scale. Here, we analyze data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models to identify ancestry-associated genetic dependencies essential for cell survival. Surprisingly, we find that most putative associations between ancestry and dependency arise from artifacts related to germline variants. Our analysis suggests that for 1.2-2.5% of guides, germline variants in sgRNA targeting sequences reduce cutting by the CRISPR/Cas9 nuclease, disproportionately affecting cell models derived from individuals of recent African descent. We propose three approaches to mitigate this experimental bias, enabling the scientific community to address these disparities.


Subject(s)
CRISPR-Cas Systems , Germ-Line Mutation , Humans , Gene Editing/methods , RNA, Guide, CRISPR-Cas Systems/genetics , Germ Cells/metabolism , Genetic Variation , Neoplasms/genetics , False Negative Reactions , Genome, Human , Cell Line, Tumor , Cell Line
11.
Ecol Evol Physiol ; 97(1): 11-28, 2024.
Article in English | MEDLINE | ID: mdl-38717370

ABSTRACT

AbstractSeasonally breeding birds express variations of traits (phenotypic flexibility) throughout their life history stages that represent adaptations to environmental conditions. Changes of body condition during migration have been well studied, whereas alterations of skeletal and cardiac muscles, body mass, and fat scores have yet to be characterized throughout the spring or fall migratory stages. Additionally, we examined flexible patterns of muscle, body mass, and fat score in migrant white-crowned sparrows (Zonotrichia leucophrys gambelii) in comparison with those in a resident subspecies (Zonotrichia leucophrys nuttalli) during the stages they share to evaluate the influence of different life histories. Migrants showed hypertrophy of the pectoralis muscle fiber area on the wintering grounds in late prealternate molt, yet increased pectoralis muscle mass was not detected until birds readied for spring departure. While pectoralis profile and fat scores enlarged at predeparture in spring and fall, pectoralis, cardiac, and body masses were greater only in spring stages, suggesting seasonal differences for migratory preparation. Gastrocnemius mass showed little change throughout all stages, whereas gastrocnemius fiber area declined steadily but rebounded in fall on the wintering grounds, where migrants become more sedentary. In general, residents are heavier birds with larger leg structures, while migrants sport longer wings and greater heart mass. Phenotypic flexibility was most prominent among residents with peaks of pectoralis, gastrocnemius, and body masses during the winter stage, when local weather is most severe. Thus, the subspecies express specific patterns of phenotypic flexibility with peaks coinciding with the stages of heightened energy demands: the winter stage for residents and the spring stages for migrants.


Subject(s)
Animal Migration , Muscle, Skeletal , Phenotype , Seasons , Sparrows , Animals , Animal Migration/physiology , Muscle, Skeletal/physiology , Body Composition/physiology , Male , Pectoralis Muscles/physiology , Female
13.
EBioMedicine ; 104: 105151, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38728839

ABSTRACT

BACKGROUND: People living with HIV (PLWH) with multidrug-resistant (MDR) viruses have limited therapeutic options and present challenges regarding clinical management. Recent studies have shown that passive transfer of combination broadly neutralizing antibodies (bNAbs) against HIV and anti-domain 1 CD4 antibody UB-421 can sustain virologic suppression in PLWH in the absence of antiretroviral therapy (ART). Yet studies addressing the therapeutic potential of these antibodies and/or detailed characterization of immunologic and virologic parameters in PLWH with MDR HIV are lacking. METHODS: We examined levels of immune activation and exhaustion markers on CD8+ T cells and the intact HIV proviral DNA burden in 11 PLWH with MDR viruses. For comparison purposes, we included a control group consisting of 27 ART-naïve viremic PLWH. In addition, we determined the sensitivity of infectious viral isolates obtained from the participants against eight bNAbs (3BNC117, 10-1074, VRC01, VRC07, N6, 10E8, PGDM1400, and PGT121) and two anti-CD4 antibodies (ibalizumab and UB-421) using a TZM-bl-based neutralization/suppression assay. FINDINGS: The level of intact HIV proviral DNA was comparable between the two groups (P = 0.29). The levels of activation and exhaustion markers PD-1 (P = 0.0019), TIGIT (P = 0.0222), 2B4 (P = 0.0015), CD160 (P = 0.0015), and CD38+/HLA-DR+ (P = 0.0138) were significantly lower in the MDR group. The infectious viral isolates from each study participant with MDR HIV were resistant to at least 2 bNAbs; however, they were sensitive to at least one of the CD4-binding and non-CD4-binding site antibodies. The majority of participants had ibalizumab-sensitive viruses although the isolates from some participants showed reduced sensitivity to ibalizumab. Notably, none of the 93 viral isolates obtained from the participants were resistant to UB-421. INTERPRETATION: Our data suggest that combination therapy with HIV-specific bNAbs and/or UB-421 in the presence of optimized background therapy could potentially provide sustained virologic suppression in PLWH with MDR HIV. However, this therapeutic strategy needs to be evaluated in human clinical trials. FUNDING: Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health.


Subject(s)
Antibodies, Neutralizing , Broadly Neutralizing Antibodies , HIV Antibodies , HIV Infections , HIV-1 , Humans , HIV Infections/immunology , HIV Infections/virology , HIV Infections/drug therapy , HIV-1/immunology , Male , Female , Adult , Antibodies, Neutralizing/immunology , Middle Aged , Broadly Neutralizing Antibodies/immunology , HIV Antibodies/immunology , CD4 Antigens/metabolism , CD4 Antigens/immunology , Drug Resistance, Multiple, Viral , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Viral Load , Antibodies, Monoclonal/therapeutic use , Antibodies, Monoclonal/pharmacology , Antibodies, Monoclonal/immunology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism
14.
J Appl Lab Med ; 9(4): 704-715, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38767175

ABSTRACT

BACKGROUND: The COVID-19 pandemic emphasized an urgent need for devices used in the self-collection of biospecimens in an evolving patient care system. The mailing of biospecimen self-collection kits to patients, with samples returned via mail, provides a more convenient testing regimen, but could also impart patient sampling variabilities. User compliance with device directions is central to downstream testing of collected biospecimens and clear instructions are central to this goal. METHODS: Here, we performed an evaluation of 10 oral DNA collection devices involving either swab or saliva self-collection and analyzed ease of use and comfort level with a device, as well as DNA recovery quantity/quality and sample stability. RESULTS: We show that while these DNA quality/quantity metrics are comparable between devices, users prefer direct saliva collection over swab-based devices. CONCLUSIONS: This information is useful in guiding future experiments including their use in human RNA, microbial, or viral sample collection/recovery and their use in clinical testing.


Subject(s)
COVID-19 , SARS-CoV-2 , Saliva , Specimen Handling , Humans , Specimen Handling/methods , Specimen Handling/instrumentation , Saliva/virology , COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2/isolation & purification , SARS-CoV-2/genetics , DNA/analysis , DNA/isolation & purification
15.
bioRxiv ; 2024 Jul 28.
Article in English | MEDLINE | ID: mdl-38746332

ABSTRACT

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.

16.
Commun Biol ; 7(1): 426, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589567

ABSTRACT

Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies remains challenging in part due to the lack of faithful preclinical in vitro models. Here we establish twelve patient-derived WT cell lines and demonstrate that these models faithfully recapitulate WT biology using genomic and transcriptomic techniques. We then perform loss-of-function screens to identify the nuclear export gene, XPO1, as a vulnerability. We find that the FDA approved XPO1 inhibitor, KPT-330, suppresses TRIP13 expression, which is required for survival. We further identify synergy between KPT-330 and doxorubicin, a chemotherapy used in high-risk FHWT. Taken together, we identify XPO1 inhibition with KPT-330 as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo.


Subject(s)
Hydrazines , Kidney Neoplasms , Triazoles , Wilms Tumor , Humans , Exportin 1 Protein , Active Transport, Cell Nucleus , Karyopherins/genetics , Karyopherins/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Cytoplasmic and Nuclear/metabolism , Cell Line, Tumor , Apoptosis , Neoplasm Recurrence, Local , Doxorubicin/pharmacology , Wilms Tumor/drug therapy , Wilms Tumor/genetics , Kidney Neoplasms/drug therapy , Kidney Neoplasms/genetics , ATPases Associated with Diverse Cellular Activities/metabolism , Cell Cycle Proteins/metabolism
17.
Cancer Discov ; 14(4): 563-568, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38571417

ABSTRACT

SUMMARY: Here, we define a future of cancer team science adopting "radical collaboration"-in which six "Hallmarks of Cancer Collaboration" are utilized to propel cancer teams to reach new levels of productivity and impact in the modern era. This commentary establishes a playbook for cancer team science that can be readily adopted by others.


Subject(s)
Cooperative Behavior , Neoplasms , Humans , Interdisciplinary Research , Neoplasms/therapy
18.
Proc Natl Acad Sci U S A ; 121(17): e2318596121, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38621142

ABSTRACT

While there is increasing recognition that social processes in cities like gentrification have ecological consequences, we lack nuanced understanding of the ways gentrification affects urban biodiversity. We analyzed a large camera trap dataset of mammals (>500 g) to evaluate how gentrification impacts species richness and community composition across 23 US cities. After controlling for the negative effect of impervious cover, gentrified parts of cities had the highest mammal species richness. Change in community composition was associated with gentrification in a few cities, which were mostly located along the West Coast. At the species level, roughly half (11 of 21 mammals) had higher occupancy in gentrified parts of a city, especially when impervious cover was low. Our results indicate that the impacts of gentrification extend to nonhuman animals, which provides further evidence that some aspects of nature in cities, such as wildlife, are chronically inaccessible to marginalized human populations.


Subject(s)
Biodiversity , Residential Segregation , Animals , Humans , Cities , Mammals , Animals, Wild , Ecosystem
19.
Sci Rep ; 14(1): 9456, 2024 04 24.
Article in English | MEDLINE | ID: mdl-38658588

ABSTRACT

Migration is one of the most energy-demanding behaviors observed in birds. Mitochondria are the primary source of energy used to support these long-distance movements, yet how mitochondria meet the energetic demands of migration is scarcely studied. We quantified changes in mitochondrial respiratory performance in the White-crowned Sparrow (Zonotrichia leucophrys), which has a migratory and non-migratory subspecies. We hypothesized that the long-distance migratory Gambel's subspecies (Z. l. gambelii) would show higher mitochondrial respiratory performance compared to the non-migratory Nuttall's subspecies (Z. l. nuttalli). We sampled Gambel's individuals during spring pre-migration, active fall migration, and a period with no migration or breeding (winter). We sampled Nuttall's individuals during periods coinciding with fall migration and the winter period of Gambel's annual cycle. Overall, Gambel's individuals had higher citrate synthase, a proxy for mitochondrial volume, than Nuttall's individuals. This was most pronounced prior to and during migration. We found that both OXPHOS capacity (state 3) and basal respiration (state 4) of mitochondria exhibit high seasonal flexibility within Gambel's individuals, with values highest during active migration. These values in Nuttall's individuals were most similar to Gambel's individuals in winter. Our observations indicate that seasonal changes in mitochondrial respiration play a vital role in migration energetics.


Subject(s)
Animal Migration , Mitochondria , Sparrows , Animals , Animal Migration/physiology , Sparrows/physiology , Mitochondria/metabolism , Seasons , Oxidative Phosphorylation , Cell Respiration , Energy Metabolism
20.
Chem Commun (Camb) ; 60(40): 5298-5301, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38660776

ABSTRACT

We demonstrate that an ionic liquid 1-ethyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide combined with propylene carbonate and lithium bis(trifluoromethanesulfonyl)imide yields a hybrid electrolyte that enables a wide operational temperature window (-20 °C to 60 °C). When integrated into a lithium titanate‖lithium cobalt oxide full-cell configuration, high-rate capability is achieved at -20 °C with >40% retention at a C/2 cycling rate, and negligible capacity fade is observed during rate capability tests and long-term cycling at 60 °C.

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