Characterization of Loss-of-Imprinting in Breast Cancer at the Cellular Level by Integrating Single-Cell Full-Length Transcriptome with Bulk RNA-Seq Data.

Genomic imprinting, the parent-of-origin-specific gene expression, plays a pivotal role in growth regulation and is often dysregulated in cancer. However, screening for imprinting is complicated by its cell-type specificity, which bulk RNA-seq cannot capture. On the other hand, large-scale single-cell RNA-seq (scRNA-seq) often lacks transcript-level detail and is cost-prohibitive.

Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling.

Esophageal adenocarcinoma (EAC) is an aggressive cancer characterized by a high risk of relapse post-surgery. Current follow-up methods (serum carcinoembryonic antigen detection and PET-CT) lack sensitivity and reliability, necessitating a novel approach. Analyzing cell-free DNA (cfDNA) from blood plasma emerges as a promising avenue.

Image-guided patient-specific prediction of interstitial fluid flow and drug transport in solid tumors.

Tumor fluid dynamics and drug delivery simulations in solid tumors are highly relevant topics in clinical oncology. The current study introduces a novel method combining computational fluid dynamics (CFD) modeling, quantitative magnetic resonance imaging (MRI; including dynamic contrast-enhanced (DCE) MRI and diffusion-weighted (DW) MRI), and a novel ex-vivo protocol to generate patient-specific models of solid tumors in four patients with peritoneal metastases. DCE-MRI data were analyzed using the extended Tofts model to estimate the spatial distribution of tumor capillary permeability using the K parameter.

Poly(2-Hydroxymethyl-2-Oxazoline) as Super-Hydrophilic Antifouling Polymer.

Non-ionic "super-hydrophilic" polymers generally possess strong non-fouling characteristics and, therefore, can suppress non-specific and unwanted interactions with blood proteins when attached to in vivo nanomedicine ranging from drug or gene delivery to diagnostics. In this contribution, we revitalize a protected alcohol functionalized 2-oxazoline monomer, 2-acetoxymethyl-2-oxazoline, that was first reported almost fifty-five years ago and explore the possibility of making "super-hydrophilic" poly(2-oxazoline)s for biomedical applications. The synthesis of the 2-acetoxymethyl-2-oxazoline monomer and its cationic ring-opening homopolymerization and copolymerization kinetics are reported.

A human-like glutaminase-free asparaginase is highly efficacious in ASNS leukemia and solid cancer mouse xenograft models.

L-asparaginase (L-ASNase) is crucial in treating pediatric acute lymphoblastic leukemia (ALL), but its use is hampered by side effects from the immunogenicity and L-glutaminase (L-GLNase) co-activity of FDA-approved bacterial L-ASNases, often leading to treatment discontinuation and poor outcomes. The toxicity of these L-ASNases makes them especially challenging to use in adult cancer patients. To overcome these issues, we developed EBD-200, a humanized guinea pig L-ASNase with low Km and no L-GLNase activity, eliminating glutamine-related toxicity.

Depletion of the RNA binding protein QKI and circular RNA dysregulation in T-cell acute lymphoblastic leukemia.

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A spatial human thymus cell atlas mapped to a continuous tissue axis.

T cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus-the Cortico-Medullary Axis-and used it to perform a spatially resolved analysis.

ZEB2 drives intra-tumor heterogeneity and skin squamous cell carcinoma formation with distinct EMP transition states.

About 5% of patients with cutaneous squamous cell carcinoma (cSCC) have a poor prognosis which is associated with a loss of tumor differentiation, invasion and metastasis, all of which are linked to the process of epithelial-to-mesenchymal plasticity (EMP). Here, we showed that the EMP-associated transcription factor ZEB2 drives cSCC heterogeneity which resembles biphasic carcinosarcoma-like tumors. Single cell RNA sequencing revealed distinct subpopulations ranging from fully epithelial (E) to intermediate (EM) to fully mesenchymal (M), associated with the gradual loss of cell surface markers EPCAM, CDH1, ITGB4, and CD200.

Proteomics dataset of lysolecithin-induced demyelinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sham treatment.

This article presents a comprehensive proteomics dataset from a lysolecithin (LPC)-induced demyelination model in the corpus callosum of female Lewis rats. The LPC model, widely used in preclinical studies of toxic demyelination, serves as a valuable tool for investigating processes of demyelination and remyelination, as well as for testing potential remyelination therapies for diseases like Multiple Sclerosis. In this study, rats received either Vagus Nerve Stimulation (VNS) or a sham treatment.

Cytofluorometric analysis of the maturation and activation of bone marrow-derived dendritic cells to assess immunogenic cell death.

Immunogenic cell death (ICD) has emerged as a pivotal form of cell death in anti-cancer therapy as it combines the ability to both eliminate cancer cells and simultaneously activate anti-tumor immunity, thereby contributing to the establishment of long-term immunological memory. Antigen-presenting cells (APCs), with an emphasis on dendritic cells (DCs), play a central role in bridging the innate and adaptive immune systems. DCs recognize and present antigens derived from the dying cancer cells to T cells in the lymph nodes, resulting in T cell activation.

Associations of the gut microbiome with outcomes in cervical and endometrial cancer patients treated with pembrolizumab: Insights from the phase II PRIMMO trial.

Background: The phase II PRIMMO trial investigated a pembrolizumab-based regimen in patients with recurrent and/or metastatic cervical (CC) or endometrial (EC) carcinoma who had at least one prior line of systemic therapy. Here, exploratory studies of the gut microbiome (GM) are presented.

Methods: The microbial composition of 77 longitudinal fecal samples obtained from 35 patients (CC, n = 15; EC, n = 20) was characterized using 16S rRNA gene sequencing.

Colibactin-driven colon cancer requires adhesin-mediated epithelial binding.

Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks Escherichia coli, which produces the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. However, it remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells to cause harm. Here, using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we demonstrate that the oncogenic potential of pks E.

A co-culture model to study modulators of tumor immune evasion through scalable arrayed CRISPR-interference screens.

Cancer cells effectively evade immune surveillance, not only through the well-known PD-1/PD-L1 pathway but also alternative mechanisms that impair patient response to immune checkpoint inhibitors. We present a novel co-culture model that pairs a reporter T-cell line with different melanoma cell lines that have varying immune evasion characteristics. We developed a scalable high-throughput lentiviral arrayed CRISPR interference (CRISPRi) screening protocol to conduct gene perturbations in both T-cells and melanoma cells, enabling the identification of genes that modulate tumor immune evasion.

A dual role for PSIP1/LEDGF in T cell acute lymphoblastic leukemia.

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Current intensified therapeutic protocols coincide with severe side effects, and no salvage therapy is available for primary therapy-resistant or relapsed patients. This highlights the need to identify new therapeutic targets in T-ALL.

Defining the optimal setting for transcriptomic analyses on blood samples for response prediction in immunotherapy-treated NSCLC patients.

Transcriptomic profiling of blood immune cells offers a promising alternative to invasive, sampling bias-prone tissue-based biomarker assays for predicting immune checkpoint inhibitor (ICI) therapy response in non-small cell lung cancer (NSCLC) patients. However, the optimal analytical approach to identify systemic correlates of response still needs to be explored. We collected peripheral blood mononuclear cells and whole blood (WB) samples from 33 ICI-treated NSCLC patients before ICI treatment and at the first response evaluation.

Assessing the impact of deep-learning assistance on the histopathological diagnosis of serous tubal intraepithelial carcinoma (STIC) in fallopian tubes.

In recent years, it has become clear that artificial intelligence (AI) models can achieve high accuracy in specific pathology-related tasks. An example is our deep-learning model, designed to automatically detect serous tubal intraepithelial carcinoma (STIC), the precursor lesion to high-grade serous ovarian carcinoma, found in the fallopian tube. However, the standalone performance of a model is insufficient to determine its value in the diagnostic setting.

Harnessing luciferase chemistry in regulated cell death modalities and autophagy: overview and perspectives.

Regulated cell death is a fate of cells in (patho)physiological conditions during which extrinsic or intrinsic signals or redox equilibrium pathways following infection, cellular stress or injury are coupled to cell death modalities like apoptosis, necroptosis, pyroptosis or ferroptosis. An immediate survival response to cellular stress is often induction of autophagy, a process that deals with removal of aggregated proteins and damaged organelles by a lysosomal recycling process. These cellular processes and their regulation are crucial in several human diseases.

Amplification of Protein Expression by Self-Amplifying mRNA Delivered in Lipid Nanoparticles Containing a β-Aminoester Ionizable Lipid Correlates with Reduced Innate Immune Activation.

Self-amplifying mRNA (saRNA) is witnessing increased interest as a platform technology for protein replacement therapy, gene editing, immunotherapy, and vaccination. saRNA can replicate itself inside cells, leading to a higher and more sustained production of the desired protein at a lower dose. Controlling innate immune activation, however, is crucial to suppress unwanted inflammation upon delivery and self-replication of RNA .

Characterizing the Cell-Free Transcriptome in a Humanized Diffuse Large B-Cell Lymphoma Patient-Derived Tumor Xenograft Model for RNA-Based Liquid Biopsy in a Preclinical Setting.

The potential of RNA-based liquid biopsy is increasingly being recognized in diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma. This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n = 171) derived from a DLBCL PDTX model, including 27 humanized (HIS) PDTX, 8 HIS non-PDTX, and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice.