Landscape Of Alterations Research Articles

Analysis of single-cell RNA sequencing in human oocytes with diminished ovarian reserve uncovers mitochondrial dysregulation and translation deficiency.

Diminished ovarian reserve (DOR) is clinically characterized by a decrease in the number of available ovarian follicles and a decline in the quality of oocytes, accompanied by hormonal changes. Low quality of DOR oocyte leads to impaired embryo development, an increased risk of aneuploid pregnancies and miscarriages. However, the specific pathogenic mechanism remains unclear, posing a significant challenge for assisted reproductive technology. For the first time, our study employed single-cell RNA sequencing to reveal the altered transcriptomic landscape of DOR oocytes at GV stage after ovarian stimulation. Differentially expressed genes analysis (DEGs), functional enrichment analysis, weighted gene co-expression network analysis (WGCNA) and protein-protein interactions network analysis were performed. We found 132 up-regulated genes and 466 down-regulated genes in DOR oocytes, with the down-regulated genes primarily enriched in mitochondrial function and translation. Hub genes, identified through integrated analysis of WGCNA and DEGs, were further validated in DOR and control oocytes using RT-qPCR. By utilizing hub genes and employing transcription factor enrichment tools, it had been predicted that pleomorphic adenoma gene 1 (PLAG1) played a crucial role as a transcriptional regulatory factor in DOR oocytes. Additionally, we conformed the PLAG1-IGF2 axis was dysregulated in DOR oocytes. Transcriptome analysis revealed that DOR oocytes exhibited mitochondrial dysfunction and translational defects, and the PLAG1-IGF2 axis might be a potential contributor for the low quality of DOR oocytes.

Age-associated metabolic and epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes.

Heart disease is the leading cause of mortality in developed countries, and novel regenerative procedures are warranted. Direct cardiac conversion (DCC) of adult fibroblasts can create induced cardiomyocytes (iCMs) for gene and cell-based heart therapy, and in addition to holding great promise, still lacks effectiveness as metabolic and age-associated barriers remain elusive. Here, by employing MGT (Mef2c, Gata4, Tbx5) transduction of mouse embryonic fibroblasts (MEFs) and adult (dermal and cardiac) fibroblasts from animals of different ages, we provide evidence that the direct reprogramming of fibroblasts into iCMs decreases with age. Analyses of histone posttranslational modifications and ChIP-qPCR revealed age-dependent alterations in the epigenetic landscape of DCC. Moreover, DCC is accompanied by profound mitochondrial metabolic adaptations, including a lower abundance of anabolic metabolites, network remodeling, and reliance on mitochondrial respiration. Invitro metabolic modulation and dietary manipulation invivo improve DCC efficiency and are accompanied by significant alterations in histone marks and mitochondrial homeostasis. Importantly, adult-derived iCMs exhibit increased accumulation of oxidative stress in the mitochondria and activation of mitophagy or dietary lipids; they improve DCC and revert mitochondrial oxidative damage. Our study provides evidence that metaboloepigenetics plays a direct role in cell fate transitions driving DCC, highlighting the potential use of metabolic modulation to improve cardiac regenerative strategies.

Abstract B069: Spatial and single-cell proteomic landscaping of the hypoxic microenvironment in glioblastoma

Abstract Glioblastoma (GBM) is a fatal adult solid tumour with median overall survival of 18-20 months post-diagnosis; contributing factors to therapeutic inefficacy include acquisition of genomic alterations post-therapy, immune evasion, deregulated hypervascularization, and tumor microenvironmental factors such as hypoxia. Combined with extensive inter- and intra-tumoral heterogeneity at bulk and single-cell level, hypoxia contributes to a gradient of molecular alterations that are specific to different cell populations that make up tumour bulk and reside in specific niches. Hitherto, high-dimensional histopathologic analyses of hypoxic regions within GBM tissue have not been performed. We took a combined spatial and single-cell proteomic profiling approach to investigate the histopathologic features of hypoxia by leveraging a unique clinical study wherein the exogenous hypoxia marker, pimonidazole (PIMO), was administered to GBM-patients preoperatively. Tissue specimens were subjected to imaging mass cytometry, high-resolution imaging, and serial immunohistochemistry using a panel of markers associated with cellular hallmarks of hypoxia, metabolism, proliferation, stemness, angiogenesis, and immune cell types. Our findings showed that PIMO staining is associated with histopathologic features of hypoxia and correlates with specific metabolic, immune, and stemness markers in GBM; specific lymphocyte populations were depleted from hypoxic regions alongside alterations in macrophagic and microglial landscape in a niche-specific manner; hypoxia reduced the proportion of proliferating glioma initiating cells and altered the proliferative, transcriptional, and translational capacity of different cell populations; microvessel density was reduced in hypoxic microenvironment. Cytometry by time-of-flight further validated the altered proportions of specific immune cell types enriched in hypoxic populations of GBM microenvironment. Our study is the first to report use of PIMO to interrogate spatial, single-cell, and phenotypic architecture associated with tissue hypoxia and altered expression of biomarkers associated with hypoxia/glycolysis, immune infiltration, proliferation, and stemness. Identification of targetable biomarkers and mediators of hypoxia-driven habitats in GBM may provide direction for future immunotherapeutic research. Citation Format: Shreya Gandhi, Sheila Mansouri, Olivia Singh, Mark Zaidi, Ronald Wu, Andrew Gao, Bradley Wouters, Gelareh Zadeh. Spatial and single-cell proteomic landscaping of the hypoxic microenvironment in glioblastoma [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B069.

Abstract PR011: Advance prostate cancer detection through epigenomic profiling of cell-free DNA

Abstract Introduction: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease which can be classified into clinically relevant subtypes based on the expression of genes, such as the androgen receptor (AR) and neuroendocrine markers. Neuroendocrine prostate cancer (NEPC), characterized by gain of stem-like and neuroendocrine features and lack of AR expression is a clinically aggressive variant. Due to the lack of adequate biomarkers, NEPC is usually detected at a very advanced stage. There is mounting evidence that molecular subtype changes seen in NEPC are enforced by widespread epigenetic alterations, in particular DNA methylation changes. In this study, we aim to devise a novel DNA methylation-based assay for molecular subtyping and disease monitoring from cell-free DNA (cfDNA). Methods: We analyzed genome wide methylation patterns in 56 prostate cancer patient-derived xenograft (PDX) and 128 mCRPC tumors using array- and sequencing-based assays. We integrated DNA methylation at promoters, gene bodies and transcription factor binding site (TFBS) to determine the landscape of methylation alterations at key lineage specific genes. Using whole genome methylation derived from tissue with matched expression data we developed a deep learning framework to predict gene expression directly from tissue or cfDNA. Using key marker genes, the model was used to discern tumor molecular phenotypes from tissue and cfDNA in three independent cohorts of mCRPC patients using whole genome bisulfite sequencing and low-pass Enzymatic Methyl-Seq (EM-seq). Results: We observed a tight association between promoter, gene body and TFBS methylation with gene expression. Inferring gene expression from methylation for lineage specific markers such as AR, KLK3, ASCL1, INSM1, SRRM4 and DLL3 we classified molecular subtypes from both tissue and cfDNA. Additionally, for AR and ASCL1, we identified core sets of TFBSs whose differential methylation allowed for accurate assay-independent molecular subtype quantification. Applying the optimized quantitative model to mCRPC patients who underwent comprehensive tissue sampling by rapid autopsy we observed accurate subtype classification from both tissue samples and cfDNA for all cases. A similar analytical performance was observed in additional clinical mCRPC cohorts with cfDNA. Conclusion: Whole-genome methylation analysis of cfDNA allows for the prediction of gene expression patterns in tumor tissues, enabling non-invasive tumor subclassification and assessment of therapeutic targets. Citation Format: Mohamed Adil, Brian Hanratty, Pallabi Mustafi, Chitvan Mittal, Helen Richards, Ilsa Coleman, Radhika Patel, Anna-Lisa Doebley, Robert Patton, Eden Cruikshank, Patricia Galipeau, Ruth Dumpit, Martine Roudier, Jin-Yih Low, Navonil Sarkar, Robert Montgomery, Eva Corey, Colm Morrissey, Peter Nelson, Gavin Ha, Michael Haffner. Advance prostate cancer detection through epigenomic profiling of cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR011.

Abstract PR014: Robust disease monitoring using CSF liquid biopsies collected from children undergoing cellular therapy for malignant central nervous system tumors

Abstract Background: Central nervous system (CNS) tumors remain the leading cause of cancer-related mortality in children, necessitating more effective treatment options. Chimeric Antigen Receptor T-cells (CAR-T) have emerged as a promising strategy to treat CNS tumors, with B7H3 (CD276) representing an attractive target due to its high expression across a broad range of entities. B7H3-CAR-T therapy is currently being evaluated in a St. Jude Children’s Research Hospital Phase I clinical trial (NCT05835687) for the treatment of relapse/refractory pediatric CNS tumors. Monitoring disease progression after CAR-T infusion by magnetic resonance imaging (MRI) remains challenging, emphasizing the need for more sensitive biomarkers of treatment response. Detection of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) liquid biopsies holds tremendous potential for minimal residual disease (MRD) monitoring in the clinical setting. Here, we leverage CSF liquid biopsies for longitudinal disease profiling in pediatric CNS tumor patients receiving B7H3-CAR-T immunotherapy. Methods: CSF samples were collected from Ommaya reservoirs of 9 pediatric patients with relapse/refractory CNS tumors undergoing B7H3-CAR-T therapy. CSF was sampled at study enrollment, and weekly intervals pre- and post-infusion. Cell-free DNA (cfDNA) was extracted from 115 longitudinally collected CSF samples and subjected to enzymatic methylation sequencing (EM-seq). Implementation of a custom computational workflow enabled detection of tumor-derived copy number variations (CNVs), estimation of malignant vs. non-malignant fractions, and molecular classification of tumor entity. Results: Tumor-derived CNVs were detected in 7/9 (78%) CSF samples collected at enrollment, prior to immunotherapy. Liquid biopsy-inferred CNV profiles and entity classifications were highly concordant with matched tumor tissue profiles. Chromosomal alterations that were restricted to CSF profiles indicated clonal evolution. Increased ctDNA burden was repeatedly observed after B7H3-CAR-T infusions, suggesting subclinical antitumor activity. Transient subclonal alterations emerging in response to treatment were also identified in a subset of patients. Conclusions: EM-seq is a feasible method for serial tracking of ctDNA burden in patients receiving cellular immunotherapy. CSF liquid biopsies capture the global landscape of tumor heterogeneity and genetic alterations that arise during therapy, providing a sensitive platform for detecting clinical response and disclosing potential mechanisms of treatment resistance. Citation Format: Anna Kostecka, Kyle S Smith, Katie Han, Hong Lin, Deanna Langfitt, Tara Walhart, Stephen Gottschalk, Giedre Krenciute, Christopher DeRenzo, Kelsey Bertrand, Paul A Northcott. Robust disease monitoring using CSF liquid biopsies collected from children undergoing cellular therapy for malignant central nervous system tumors [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR014.

An investigation into the shifting landscape preferences of rural residents in Taiwan and their relationship with ecological indicators.

Rapid urbanization has significantly altered landscape environments in both urban and rural regions, and these landscapes have been demonstrated to play a pivotal role in human well-being. This study develops a coherent framework that integrates landscape change, landscape ecological indicators, and landscape preferences within the context of the evolving landscape environments of rural communities in Taiwan. Four distinct types of rural communities were selected, and a quantitative methodology was employed to investigate the variations and transformations in landscape preferences among rural residents in the context of landscape change. A qualitative methodology was employed to investigate the relationship between landscape ecological indicators and landscape preferences. The study's findings indicate significant temporal variations in residents' landscape preferences, with landscape beauty, stewardship, and coherence emerging as key determinants in the evaluation of these preferences. Landscape ecological indicators were found to be significantly correlated with variables such as landscape complexity, landscape beauty, openness, naturalness, and comprehensive landscape assessment. The findings of this study indicate that design planners, land managers, and public sector organizations can employ multidimensional thinking in the management of rural landscapes to align with the visual aesthetic preferences of rural residents.

Monitoring Hazards in Dam Environments Using Remote Sensing Techniques: Case of Kulekhani-I Reservoir in Nepal

Maintaining the operability of a hydroelectric power station at a scale originally designed is being compromised by continuous reservoir sedimentation. The underlying factors include a complex mix of landscape alterations owing to natural and anthropogenic activities around dam areas, such as gully erosion, landslides, floods triggered by heavy rainfall, climate change, and construction activities. The hydropower projects in the low-to-mid mountain regions of Nepal are witnessing a combination of these phenomena, affecting their optimal performance in meeting long-term sustainable power supply targets. This paper presents a combination of geo-spatial analysis and field evaluations to identify the trends from Kulekhani-I, one of the oldest storage-type hydropower projects in Nepal, using long-term time series remote sensing satellite imagery from 1988 to 2020. Our analysis shows an expansion of the surface water content area over time, attributed mainly to high sedimentation deposition owing to multiple factors. This study has identified an urgent need for addressing the following two key contributory factors through an effective control mechanism to avoid rapid sedimentation in the reservoirs: natural—landslides and floods leading to mainly silt deposition during heavy rainfalls; and anthropogenic—road construction materials dumped directly in the reservoir. Effective implementation of a remote sensing monitoring scheme can safeguard future damages to dam environments of more recently built storage-type hydropower projects.

EPCO-25. TRANSPOSABLE ELEMENTS INDUCE ONCO-EXAPTATION EVENTS IN MALIGNANT ATRX-DEFICIENT GLIOMAS

Abstract Deficiency of ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a core member of SWI/SNF family chromatin regulator is altered in diffuse gliomas and coexist with IDH1/2 mutations in adults and histone G34R/V alterations in pediatric populations. Loss of ATRX has been associated with global alterations in chromatin accessibility and epigenomics landscape, however, the detail mechanism behind the oncogenic transformation remains elusive. Integrating transcriptomics and in-depth positional epigenome analysis over repetitive DNA sequences in progenitor and tumors models of murine and human gliomas, we describe ATRX-deficient gliomas is fundamentally a disease of altered Transposable Elements (TE’s) and regulates neuronal differentiation and cell motility in gliomas, as validated pharmacologically and genetically. Epigenome assessment reported de-repression of LINE-1 (Long interspersed nuclear elements-1), specifically at Lamina-Associated Domains (LADs) with gain of enhancer histone marks, with association in chromatin loops/topology in ATRX-deficient glioma cells. Moreover, our single cell-RNA seq analysis focusing on TE’s and molecular docking studies in human glioma stem cells demonstrated LINE-1 regulates oncogenic alternative splicing events and neuro-developmental signatures. Expanding the analysis, we identified a subset of evolutionary young regulatory TE’s to play critical role in ATRX-deficient gliomas involved in neuronal differentiation phenotype. To summarize, our cross-species analysis establishes tangible links between ATRX deficiency and multiscale dysregulated 3D-epigenomic architecture that hijack regulates onco-exaptation programs in gliomas. We further discover that enhancer-like TE’s fine-tune the transcriptional program with important clinical implications, that could help in developing treatment options in malignant gliomas.

The altered landscape as heterotopia

ABSTRACT This paper considers the contemporary photographic practices of the authors, aligning their conceptual ideas and working methodology with notions of heterotopia. It argues for a positioning within contemporary altered landscape photography that considers place as a heterotopia, a networked system or process that modifies and makes an alternative ‘territory’. In dialogue with a range of relevant authors and artists, the paper contextualises heterotopia and altered landscape spaces as layers of both cultural and ecological intervention. It asserts that an artist in a state of mobility, transit and movement, can effectively employ notions of heterotopia to inform a creative photographic practice. We build on existing heterotopologies through the photographic practices of the authors, altered landscape photography by Australian artist Shane Hulbert, and the cultural investigations of expatriation by Greek artist Ioannis Galanopoulos Papavasileiou. The artists, through phenomenology, lens-based practice and noetic synthesis, approach altered landscape photography from two divergent cultural perspectives; one through the lens of postcolonial national imaging, the other through a trans-national experience of expatriation. We propose that both the cultural and geographic counter-site of an altered landscape, and the social and psychological state of expatriation, are informed by notions of heterotopia, and therefore build on existing heterotopologies.

The Evolving Molecular Landscape and Actionable Alterations in Urologic Cancers

The genetic landscape of urologic cancers has evolved with the identification of actionable mutations that impact diagnosis, prognosis, and therapeutic strategies. This narrative review consolidates existing literature on genetic mutations across key urologic cancers, including bladder, renal, prostate, upper tract urothelial, testicular, and penile. The review highlights mutations in DNA damage repair genes, such as BRCA1/2 and PTEN, as well as pathway alterations like FGFR and PD-L1 overexpression. These mutations influence tumor behavior and therapeutic outcomes, emphasizing the need for precision oncology approaches. Molecular profiling, through tools like next-generation sequencing, has revolutionized patient care by enabling targeted treatment strategies, especially in cancers with distinct molecular subtypes such as luminal or basal bladder cancer and clear cell renal carcinoma. Emerging therapies, including FGFR inhibitors and immune checkpoint blockade, offer new treatment avenues, although resistance mechanisms remain a challenge. We also emphasize the importance of biomarker identification for personalized management, especially in metastatic settings where treatment intensification is often required. Future research is needed to further elucidate our understanding of the genetics affecting urologic cancers, which will help develop novel, individualized therapies to enhance oncologic outcomes.

Enhancing Ecological Education: Utilizing Agent-Based Modeling to Simplify the Impacts of Deforestation on Amphibians

Understanding how deforestation and changes in habitat boundaries affect biodiversity is essential for developing conservation solutions. These topics are central to biology and ecology programs, where students learn to apply their knowledge in real-world conservation efforts. Higher education plays a crucial role in strengthening this understanding, particularly in life sciences programs. Given the complexity of ecological processes in altered landscapes, agent-based modeling provides an interactive and engaging way to simplify and visualize the effects of land use changes. In this study, we integrate Amazonian anurans, highly sensitive to temperature and humidity fluctuations, with an Agent-based model to simulate the impacts of deforestation, habitat restoration, and land abandonment on species survival and movement. Their ectothermic nature and dependence on pulmocutaneous respiration make them especially vulnerable to the drier and more variable conditions caused by deforestation. Integrating this model into conservation biology courses has enhanced learning by encouraging independent exploration, both in and out of the classroom. This tool, an agent-based model, is particularly suited for university-level ecology and conservation courses, and can also serve as an effective awareness tool in environmental education and decision-making workshops, highlighting the negative effects of human-made habitat changes on biodiversity.

The Prominent Role of the Matrix in Ecology, Evolution, and Conservation

As the Anthropocene proceeds, the matrix in which remaining habitats are embedded is an increasingly dominant component of altered landscapes. The matrix appears to have diverse and far-reaching effects, yet our understanding of the causes and consequences of these effects remains limited. We first synthesize the broad range of perspectives on the matrix, provide a generalized framing that captures these perspectives, and propose hypotheses for how and why the matrix matters for ecological and evolutionary processes. We then summarize evidence for these hypotheses from experiments in which the matrix was manipulated. Nearly all experiments revealed matrix effects, including changes in local spillover, individual movement and dispersal, and use of resources in the matrix. Finally, we discuss how the matrix has been, and should be, incorporated into conservation and management and suggest future issues to advance research on and applications of the matrix in ecology, evolution, and conservation.

Epigenomic Reprogramming in Gout

Gout is a crystal-induced arthropathy in which monosodium urate (MSU) crystals precipitate within joints as a result of persistent hyperuricemia and elicit an inflammatory response. An intriguing aspect is the occurrence of gout in only 10–15% of hyperuricemic individuals, suggesting the presence of additional risk factors. Although MSU crystal deposition is widely recognized as the cause of gout flares, the variability in initiating the inflammatory response to hyperuricemia and MSU deposition is not well understood. Several studies bring up-to-date information about the environmental and genetic influences on the progression towards clinical gout. Elevated urate concentrations and exposure to different external factors precipitate gout flares, highlighting the potential involvement of epigenetic mechanisms in gouty inflammation. A better understanding of the alteration of the epigenetic landscape in gout may provide new perspectives on the dysregulated inflammatory response. In this review, we focus on understanding the current view of the role of epigenomic reprogramming in gout and the mechanistic pathways of action.

Determining the effect of long non-coding RNA maternally expressed Gene 3 (lncRNA MEG3) on the transcriptome profile in cervical cancer cell lines

This study investigates the role of the long non-coding RNA Maternally Expressed Gene3 (lncRNA MEG3) gene in cervical cancer, as evidenced by its downregulation in cancerous cell lines. The study demonstrates the effects of the overexpression of lncRNA MEG3 in cervical cancer cell lines, particularly in C33A and CaSki. Through comprehensive analyses, including Next-Generation Sequencing (NGS), alterations in global mRNA expression were analyzed. In C33A cells, 67 genes were upregulated, while 303 genes were downregulated. Similarly, in CaSki cells, 221 genes showed upregulation and 248 genes displayed downregulation. Gene ontology and KEGG pathway analyses were conducted to gain insight into potential mechanisms. Furthermore, the study delves into gene regulatory networks, uncovering intricate interactions among genes. The RNA sequencing data were confirmed for eight genes: PAX3, EGR2, ROR1, NRP1, OAS2, STRA6, CA9, and EDN2 by Real-time PCR. The findings illuminate the complex landscape of gene expression alterations and pathways impacted by the overexpression of lncRNA MEG3. The impact of MEG3 on the overall cervical cancer cells' mRNA profile is reported for the first time. New biomarkers for the prognosis of cervical cancer are also reported in this study. Moreover, identifying specific genes within the regulatory networks provides valuable insights into potential therapeutic targets for managing cervical cancer.

RUNX1::CBFA2T2 rearranged acute myeloid leukemia transformed from JAK2 V617F mutated primary myelofibrosis

AbstractAcute myeloid leukemia (AML) with RUNX1::CBFA2T2 fusion is rare with largely unknown clinicopathological features and genomic characterization. We present one such case of AML transformed from JAK2 V617F mutated primary myelofibrosis and review the literature on this topic. The immunophenotype and the landscape of cooperative gene alterations in AML with RUNX1::CBFA2T2 resemble those of AML with RUNX1::RUNX1T1, including expression of CD19, cooperative gene alterations in signaling pathway (JAK2), epigenetic/chromatin and cell cycle regulation (TET2, SMC3, and CDKN2A/B), and additional chromosomal abnormalities (trisomies 8 and 15). This case study provides insights into the pathogenesis of this rare subtype of AML.

NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes

BackgroundNF1 inactivation is associated with sensitivity to MEK inhibitor targeted therapy in low-grade and some high-grade gliomas. NF1 loss may also be a harbinger of exploitable vulnerabilities in IDH-wildtype glioblastoma (GBM). Accurate and consistent detection of NF1 loss, however, is fraught given the large gene size, challenges with complete coverage and variant calling upon sequencing, and mechanisms of mRNA and protein regulation that result in early degradation in the absence of genomic alterations. Here, we seek to perform a composite analysis for NF1 loss accounting for genomic alterations and protein expression via immunohistochemistry. We also characterize the landscape of NF1 alterations in GBM.MethodsWe assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. We performed NF1 immunohistochemistry using two different NF1 antibodies (NFC, Sigma-Aldrich; and iNF-07E, iNFixion Bioscience) and correlated results with clinical, genomic, and other immunohistochemical features.ResultsIn our retrospective cohort, we identified 88 IDH-wildtype GBM with NF1 alterations (16%). NF1 alterations were mutually exclusive with EGFR and MDM2 alterations (p-adj < 0.001, 0.05, respectively), but co-occurred with PIK3R1 alterations (Log2(OR) = − 1.6, p-adj = 0.03). Of the 63 scorable sporadic GBMs in the TMA, 14 harbored NF1 inactivating alterations and of those, 12 (86%) demonstrated minimal NF1 immunoreactivity by NFC antibody, compared to 8 (57%) by iNF-07E antibody. Among the 42 scorable NF1-wildtype GBM in the TMA, NF1 immunostaining was minimal in 18 (43%) by NFC antibody compared to 4 (10%) by iNF-07E antibody, potentially reflecting false positives or differential protein regulation. Minimal immunoreactivity by NFC antibody was associated with decreased median overall survival (8.5 vs. 16.4 months, p = 0.011). Cox proportional hazards model correcting for prognostic variables in this subset revealed HR 3.23 (95% CI 1.29–8.06, p = 0.01) associated with decreased NF1 expression by IHC.ConclusionNF1 immunostaining may serve as a sensitive surrogate marker of NF1 genomic inactivation and a valuable extension to next-generation sequencing for defining NF1 status. Minimal NF1 immunoreactivity is a poor prognostic marker, even in IDH-wildtype glioblastoma without apparent NF1 genomic alterations, but the underlying molecular mechanism requires further investigation.

Comprehensive structure-function analysis reveals gain- and loss-of-function mechanisms impacting oncogenic KRAS activity.

To dissect variant-function relationships in the KRAS oncoprotein, we performed deep mutational scanning (DMS) screens for both wild-type and KRAS G12D mutant alleles. We defined the spectrum of oncogenic potential for nearly all possible KRAS variants, identifying several novel transforming alleles and elucidating a model to describe the frequency of KRAS mutations in human cancer as a function of transforming potential, mutational probability, and tissue-specific mutational signatures. Biochemical and structural analyses of variants identified in a KRAS G12D second-site suppressor DMS screen revealed that attenuation of oncogenic KRAS can be mediated by protein instability and conformational rigidity, resulting in reduced binding affinity to effector proteins, such as RAF and PI3-kinases, or reduced SOS-mediated nucleotide exchange activity. These studies define the landscape of single amino acid alterations that modulate the function of KRAS, providing a resource for the clinical interpretation of KRAS variants and elucidating mechanisms of oncogenic KRAS inactivation for therapeutic exploitation.

Variation in species-specific responses to habitat fragmentation and land cover structure in urban small mammal communities

Abstract Urbanization is a key driver of habitat loss and fragmentation worldwide, yet many urban ecosystems contain vegetated habitat patches that support diverse wildlife communities. Managing urban systems to support robust wildlife communities requires us to understand the mechanisms that drive the response of species to the urban environment. Small mammals are key components of terrestrial ecosystems (e.g., seed predators, prey) and likely also carry out these roles in urban ecosystems; however, the effects of urbanization on small mammal communities are understudied. To identify how species-specific responses to urban environments shape community composition, we quantified both overall community and species-specific changes in small mammal abundance across an urbanization gradient in a Midwestern US metropolitan area. We combined small mammal trapping and land cover data to generate a hierarchical community abundance model. Species diversity increased with increasing proportional cover of human-modified land cover (i.e., impervious surfaces and turfgrass). This finding is driven by high species diversity on sites bordering streams in mowed parks and low diversity on sites with high tree canopy closure. Additionally, modeling results indicated that species responded differently to landscape attributes, leading to variation in small mammal community composition across the urbanization gradient: prairie-associated species tended to be more abundant in tall vegetation bordering mowed parks while habitat generalists tended to be more abundant on sites with greater canopy closure and shrub cover. Our results suggest that studies that focus on community-level responses (e.g., species richness) to urbanization may miss important species-specific responses. It may be particularly important to assess both species-specific and community-level responses in cities at ecotones (e.g., between forest and grassland) where species with different habitat requirements may replace one another in different types of green spaces, thereby changing community composition without affecting species diversity or richness. Our findings also indicate that vegetated urban patches, especially patches with tall vegetation cover and low canopy cover, are important habitat for prairie-associated small mammal communities, providing conservation options in heavily altered landscapes.

Carbon Sequestration and Landscape Influences in Urban Greenspace Coverage Variability: A High-Resolution Remote Sensing Study in Luohe, China

Urbanization has significantly altered urban landscape patterns, leading to a continuous reduction in the proportion of green spaces. As critical carbon sinks in urban carbon cycles, urban green spaces play an indispensable role in mitigating climate change. This study aims to evaluate the carbon capture and storage potential of urban green spaces in Luohe, China, and identify the landscape factors influencing carbon sequestration. The research combines on-site data collection with high-resolution remote sensing, utilizing the i-Tree Eco model to estimate carbon sequestration rates across areas with varying levels of greenery. The study reveals that the carbon sequestration capacity of urban green spaces in Luohe City is 1.30 t·C·ha−1·yr−1. Among various vegetation indices, the Enhanced Vegetation Index (EVI) explains urban green space carbon sequestration most effectively through an exponential model (R2 = 0.65, AIC = 136.5). At the city-wide scale, areas with higher greening rates, better connectivity, and more complex edge morphology exhibit superior carbon sequestration efficiency. The explanatory power of key landscape indices on carbon sequestration is 78% across the study area, with variations of 71.5%, 62%, and 84.9% for low, medium, and high greening rate areas, respectively. Moreover, when greening rates reach a certain threshold, maintaining and optimizing the quality of existing green spaces becomes more critical than simply expanding the green area. These insights provide valuable guidance for urban planners and policymakers on enhancing the ecological functions of urban green spaces during urban development.

Implications of Coalfield Dynamics on Associated Ecosystems: A Tangential Review

Traditionally, the coal has stood as a resourceful entity for the energy demands of the society. The coalmines are the driving forces in the sufficing the energy and economy of the nation. Certainly, the existence of coal and its excavation is a much aspired endeavours for the development of any society. There are numerous prospective, functional and abandoned coalmines all over the world. Along with the intrinsic worth of the coal excavations, many studies have decisively elucidated the associated environmental complications. The ecological devastation is one of them. The ecological sphere whether it be macro or micro, is a fragile entity and must be taken care of accordingly. The process of coal excavations involves large scale landscape alteration where the entire native vegetation is removed. The ecological domain developed through an extensive period over the landscape vanishes in no time. The hydrological fluctuation also in terms of water chemistry destroys the aquatic habitat prominently known as hydroecology. The microclimatic shift is also a factor affecting drastically on the associated ecologies. The present review article strives to understand the various influencers in the coalfields dominating over the accompanying ecologies through selective endeavours executed all over the world. It also deliberates the probable measures to be taken to shield the associated ecologies in and around coalfields including the sensitization drives for protecting ecologies.