A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy.

The accurate identification and prioritization of antigenic peptides is crucial for the development of personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration of mass spectrometry immunopeptidomics data, which can uncover antigenic peptides derived from various canonical and noncanonical sources. To address this, we present an end-to-end clinical proteogenomic pipeline, called NeoDisc, that combines state-of-the-art publicly available and in-house software for immunopeptidomics, genomics and transcriptomics with in silico tools for the identification, prediction and prioritization of tumor-specific and immunogenic antigens from multiple sources, including neoantigens, viral antigens, high-confidence tumor-specific antigens and tumor-specific noncanonical antigens.

Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma.

Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8 cells that preferentially infiltrated tumors post-ACT.

Complete genome of the Medicago anthracnose fungus, , reveals a mini-chromosome-like region within a core chromosome.

() is a phytopathogenic fungus causing significant economic losses on forage legume crops ( and species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.

Nudge theory and gambling: a scoping review.

Background: Gambling disorder (GD) is a pressing public health concern with significant societal costs. The recently developed nudge theory, which is rooted in behavioral economics, aims to influence the decision-making behaviors of individuals by implementing changes in the environment.

Aim: This scoping review aims to synthesize the literature on nudge theory as it relates to gambling.

Puberty Blocker, Leuprolide, Reduces Sex Differences in Rough-and-Tumble Play and Anxiety-like Behavior in Juvenile Rats.

We examined the effect of the puberty blocker, leuprolide acetate, on sex differences in juvenile rough-and-tumble play behavior and anxiety-like behavior in adolescent male and female rats. We also evaluated leuprolide treatment on gonadal and pituitary hormone levels and activity-regulated cytoskeleton-protein messenger RNA levels within the adolescent amygdala, a region important both for rough-and-tumble play and anxiety-like behavior. Our findings suggest that leuprolide treatment lowered anxiety-like behavior during adolescent development, suggesting that the maturation of gonadotropin-releasing hormone systems may be linked to increased anxiety.

Brain, behavior, and physiological changes associated with predator stress-An animal model for trauma exposure in adult and neonatal rats.

The use of predators and predator odor as stressors is an important and ecologically relevant model for studying the impact of behavioral responses to threat. Here we summarize neural substrates and behavioral changes in rats resulting from predator exposure. We briefly define the impact predator exposure has on neural targets throughout development (neonatal, juvenile, and adulthood).

Discovery of the Potent and Selective ATR Inhibitor Camonsertib (RP-3500).

ATR is a key kinase in the DNA-damage response (DDR) that is synthetic lethal with several other DDR proteins, making it an attractive target for the treatment of genetically selected solid tumors. Herein we describe the discovery of a novel ATR inhibitor guided by a pharmacophore model to position a key hydrogen bond. Optimization was driven by potency and selectivity over the related kinase mTOR, resulting in the identification of camonsertib (RP-3500) with high potency and excellent ADME properties.

Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction.

The accurate selection of neoantigens that bind to class I human leukocyte antigen (HLA) and are recognized by autologous T cells is a crucial step in many cancer immunotherapy pipelines. We reprocessed whole-exome sequencing and RNA sequencing (RNA-seq) data from 120 cancer patients from two external large-scale neoantigen immunogenicity screening assays combined with an in-house dataset of 11 patients and identified 46,017 somatic single-nucleotide variant mutations and 1,781,445 neo-peptides, of which 212 mutations and 178 neo-peptides were immunogenic. Beyond features commonly used for neoantigen prioritization, factors such as the location of neo-peptides within protein HLA presentation hotspots, binding promiscuity, and the role of the mutated gene in oncogenicity were predictive for immunogenicity.

Polygenic risk scores cannot make their mark on psychiatry without considering epigenetics.

We generally agree with Burt's thesis. However, we note that the author did not discuss epigenetics, the study of how the environment can alter gene structure and function. Given epigenetic mechanisms, the utility of polygenic risk scores (PRS) is limited in studies of development and mental illness.

Delayed estrogen actions diminish food consumption without changing food approach, motor activity, or hypothalamic activation elicited by corticostriatal µ-opioid signaling.

Mu-opioid receptor (μ-OR) signaling in forebrain sites including nucleus accumbens (Acb) and ventromedial prefrontal cortex (vmPFC) modulates reward-driven feeding and may play a role in the pathophysiology of disordered eating. In preclinical models, intra-Acb or intra-vmPFC μ-OR stimulation causes overeating and vigorous responding for food rewards. These effects have been studied mainly in male animals, despite demonstrated sex differences and estrogen modulation of central reward systems.

Species-Specific -Glycomes and Methylation Patterns of Oysters and and Their Possible Consequences for the Norovirus-HBGA Interaction.

Noroviruses, the major cause of acute viral gastroenteritis, are known to bind to histo-blood group antigens (HBGAs), including ABH groups and Lewis-type epitopes, which decorate the surface of erythrocytes and epithelial cells of their host tissues. The biosynthesis of these antigens is controlled by several glycosyltransferases, the distribution and expression of which varies between tissues and individuals. The use of HBGAs as ligands by viruses is not limited to humans, as many animal species, including oysters, which synthesize similar glycan epitopes that act as a gateway for viruses, become vectors for viral infection in humans.

A call for qualitative and mixed-methods research on gambling and cannabis.

Gambling disorder and cannabis use disorder are both considered major public health issues. Despite the well-documented frequency of substance use disorders among people with gambling disorder, little is known about the experiences of those who both engage with gambling and cannabis. A scoping review was undertaken to investigate studies focusing on the experiences of people who gamble and use cannabis.

TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs.

T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires.

Small Molecule Inhibition of an Exopolysaccharide Modification Enzyme is a Viable Strategy To Block Pseudomonas aeruginosa Pel Biofilm Formation.

Biosynthesis of the Pel exopolysaccharide in Pseudomonas aeruginosa requires all seven genes of the operon. The periplasmic modification enzyme PelA contains a C-terminal deacetylase domain that is necessary for Pel-dependent biofilm formation. Herein, we show that extracellular Pel is not produced by a P.

Researchers' experiences with patient engagement in health research: a scoping review and thematic synthesis.

Context: Implicating patients in research is gaining popularity around the world and is now the reference of many funding agencies. Understanding these partnerships is necessary to grasp this new reality. The experiences of researchers who have involved patient-partners (PPs) in health research are important for a better understanding of these practices.

DNA topoisomerase Top3β is impacted by early life stress in the developing female and male rat brain.

DNA topoisomerases are essential for preserving genomic integrity. DNA topoisomerases induce breakage of DNA to facilitate replication and transcription by relaxing DNA and relieving supercoiling. Aberrant expression and deletions of topoisomerases are associated with psychiatric disorders such as schizophrenia and autism.

Qualitative Experience of Self-Exclusion Programs: A Scoping Review.

Gambling disorder is a major public health issue in many countries. It has been defined as a persistent, recurrent pattern of gambling and is associated with substantial distress or impairment, lower quality of life, and living with a plurality of psychiatric problems. Many people suffering from gambling disorder seek help in ways other than formal treatment seeking, including self-management strategies.

The experience of patient partners in research: a qualitative systematic review and thematic synthesis.

Context: Patient engagement in research consists in involving patients as partners across the research cycle. This practice has quickly become an international standard, with funding bodies actively encouraging it. As the increased incentive to engage patients can lead to tokenistic partnerships, it is important to consider the experiences of patient-partners.

Delayed but not immediate effects of estrogen curtail gamma-aminobutyric acid-mediated feeding responses elicited from the nucleus accumbens shell.

The present study investigated immediate versus delayed effects of estrogen replacement in ovariectomized (OVX) rats on hyperphagia elicited by gamma-aminobutyric acid (GABA)-A-agonist (muscimol) infusions into the nucleus accumbens shell (AcbSh). First, because intra-AcbSh muscimol-induced feeding has never been explored in OVX rats, a dose-effect curve was generated and compared to sham-operated males, the current point of reference in the literature. Muscimol (5, 10, 25, and 50 ng) increased food intake in both sexes, and both sexes reached the same asymptotic level of intake.

Examining frustration intolerance beliefs among adults with dyslexia or developmental coordination disorder.

Background: Research suggests that adults diagnosed with specific learning disorders, such as dyslexia or developmental coordination disorder (DCD), are at greater risk of emotional problems related to frustration and anger.

Aims: The purpose of this study was to investigate patterns of frustration intolerance beliefs among two groups of adults with a specific learning disorder (dyslexia or DCD), compared with typical adults.

Methods And Procedures: Participants were 235 French adults (students or in employment) with dyslexia (M = 35.

Expanded renal lymphatics improve recovery following kidney injury.

Acute kidney injury (AKI) is a major cause of patient mortality and a major risk multiplier for the progression to chronic kidney disease (CKD). The mechanism of the AKI to CKD transition is complex but is likely mediated by the extent and length of the inflammatory response following the initial injury. Lymphatic vessels help to maintain tissue homeostasis through fluid, macromolecule, and immune modulation.