Profiling Approach Research Articles

Abstract IA15: What the surgeon has learned from pancreas cancer genomics, and vice versa

Abstract Recent advances in molecular profiling and fundamental science discoveries are impacting care of PDAC patients, including surgical decision making. Our multidisciplinary group at the Ontario Institute for Cancer Research and the Princess Margaret in Toronto has focused on elucidating both germline and somatic genomic changes in PDAC, with aims to understand genetic predisposition to the disease, foster early detection and conduct trials for improved selection of standard and novel therapies. Using laser capture microdissection overseen by expert pathologists, seamless tumor banking and aggressive biopsy of chemo-naïve and progressive metastases, we have generated high epithelial tumor cell content whole genomes and transcriptomes (WGTS) on over 600 PDAC patients with all stages of the disease. Germline sequencing of all PDAC patients should be considered standard of care to detect patients with uniquely actionable genomic changes due to less common mutational pathways. The genetic basis of familial pancreas cancer remains elusive and we continue to collaborate with the PACGENE Network spearheaded by colleagues at Mayo, Hopkins and McGill to discover novel genes in high risk cases. Our genomic work and others explains the clinical conundrum of late presentation of PDAC due to rapid punctuated evolution which challenges the ‘holy grail’ of early detection. Thus, screening high risk groups is still within the realm of investigational studies such as the PRECEDE consortium, of which we are an active member. Focused clinical trials (eg COMPASS and PASS-01) using WGTS has revealed both large scale changes in genomes (eg. HRD, tandem duplicators, etc) and transcriptomes (the Moffit ‘continuum’) and discreet mutations (eg BRAF mutations in Kras wild type tumors) that are important to identify as early as possible in the patient’s clinical course. Subspecialty PDAC surgeons need to keep abreast of recent developments of both prognostic and predictive transcriptomic biomarkers that will soon be important in selecting appropriate patients for appropriate neoadjuvant therapies. A few clinical vignettes will be shown to provide evidence for the importance of WGTS and other profiling approaches for almost all PDAC patients. Citation Format: Steven Gallinger. What the surgeon has learned from pancreas cancer genomics, and vice versa [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr IA15.

Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell Profiling.

Single-cell profiling, either in suspension or within the tissue context, is a rapidly evolving field. The purpose of this review is to outline recent advancements and emerging trends with a specific focus on studies in spondyloarthritis. The introduction of sequencing-based approaches for the quantification of RNA, protein, or epigenetic modifications at single-cell resolution has provided a major boost to discovery-driven research. Fluorescent flow cytometry, mass cytometry, and image-based cytometry continue to evolve. Spatial transcriptomics and imaging mass cytometry have extended high-dimensional analysis to cells in tissues. Applications in spondyloarthritis include the indexing and functional characterization of cells, discovery of disease-associated cell states, and identification of signatures associated with therapeutic responses. Single-cell TCR-seq has provided evidence for clonal expansion of CD8+ T cells in spondyloarthritis. The use of single-cell profiling approaches in spondyloarthritis research is still in its early stages. Challenges include high cost and limited availability of diseased tissue samples. To harness the full potential of the rapidly expanding technical capabilities, large-scale collaborative efforts are imperative.

Experimental study on conical flame transfer functions considering velocity profiles

This paper investigates the linear thermoacoustic dynamic response of laminar premixed stoichiometric propane/air flames under different oncoming flow velocity profiles. Experiments focused on four nozzle thickness-to-diameter ratios: 0.75, 1.5, 2.5 and 3.75, and three different mean bulk velocities: 1.1m/s, 1.2m/s and 1.3m/s. As the nozzle thickness-to-diameter ratio increases, the velocity profile transitions from a developing velocity profile to a fully developed velocity profile. The flame transfer function (FTF) gain exceeds unity at low frequencies. Notably, the effect of the velocity profile is mainly manifested in the moderate frequency range where the FTF gain decreases. When the velocity profile approaches the resonance frequency of the corresponding small orifice, the decline in FTF gain becomes less pronounced. For fully developed velocity profiles, the decrease in mean bulk velocity leads to an increase in FTF gain at low frequencies, but a more rapid decrease at higher frequencies. Additionally, this paper also investigates segmented flame transfer functions (segFTFs) at various axial positions along the flame. With the increase in frequency, the effect of flame front disturbance on FTF changes from the overall flame displacement caused by flame root stand-off distance, to the effect of flame front wrinkle counteracting effect. The different velocity profiles significantly impact the flame dynamic response, thereby affecting the flame heat release rate and consequently the FTF.

Wafer‐Scale Manufacturing of Near‐Infrared Metalenses

AbstractMetalenses have revolutionized optical technologies with their superior ability to manipulate light and the potential to replace conventional, bulky optical components. However, their commercialization is hindered by limitations in conventional manufacturing techniques, such as small patterning areas, low throughput, and high cost. In this study, two methods are introduced for scalable and wafer‐scale manufacturing of metalenses operating in the near‐infrared region, aimed at overcoming the abovementioned challenges. The first type of metalens is polarization‐independent and constructed using hydrogenated amorphous silicon cylindrical structures fabricated through direct photolithography. This metalens has a diameter of 1 cm and numerical aperture (NA) of 0.53. The focusing efficiency is confirmed at a 940 nm wavelength, and the focal spot profile approaches the diffraction limit. The second metalens is polarization‐dependent and fabricated using silicon nanoparticle‐embedded‐resin rectangular structures through a cost‐effective nanoimprinting method. This process can produce metalenses with a diameter of 5 mm and an NA of 0.53. Both types of metalenses demonstrate high‐resolution capabilities when imaging a 1951 USAF resolution test target and bioimaging. This research offers innovative pathways for the mass production and large‐scale fabrication of metalenses. It is believed that the work will accelerate the industrialization of metalenses, fostering further advances in optical technology.

Air monitoring by nanopore sequencing.

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.

Categorical and latent profile approaches to temperamental infant reactivity and early trajectories of socioemotional adjustment.

This article examines the patterns, and consequences, of infant temperamental reactivity to novel sensory input in a large (N = 357; 271 in current analysis) and diverse longitudinal sample through two approaches. First, we examined profiles of reactivity in 4-month-old infants using the traditional theory-driven analytic approach laid out by Jerome Kagan and colleagues, and derived groups characterized by extreme patterns of negative reactivity and positive reactivity. We then used a theory-neutral, data-driven approach to create latent profiles of reactivity from the same infants. Despite differences in sample characteristics and recruitment strategy, we noted similar reactivity groups relative to prior cohorts. The current data-driven approach found four profiles: high positive, high negative, high motor, and low reactive. Follow-up analyses found differential predictions of internalizing, externalizing, dysregulation, and competence trajectories across 12, 18, and 24 months of life based on 4-month reactivity profiles. Findings are discussed in light of the initial formulation of early reactivity by Kagan and the four decades of research that has followed to refine, bolster, and expand on this approach to child-centered individual differences. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Supplemental Material for Categorical and Latent Profile Approaches to Temperamental Infant Reactivity and Early Trajectories of Socioemotional Adjustment

Supplemental Material for Categorical and Latent Profile Approaches to Temperamental Infant Reactivity and Early Trajectories of Socioemotional Adjustment

Concrete constructions or messy mangroves? How modelling contextual effects on constructional alternations reflect theoretical assumptions of language structure

Abstract Depending on the theory of language employed, the paradigmatic and lexical variation associated with a given composite form-meaning pair is treated in different ways. First, variation can be treated as independent of the constructional semantics, an approach typical of modular theories. Second, paradigmatic variation can be considered indicative of constructional semantics; its variation constituting networks of closely related families of constructions. This is a common approach in construction grammar. Third, there exists a trend in cognitive linguistics and construction grammar to treat grammatical constructions as non-discrete emergent clusters of many-to-many form-meaning mappings. This study explores the possibility of extending current methods for quantitatively modelling construction grammar to an approach that does not assume discrete grammatical constructions. The speaker choice examined consists of the English future constructions will and BE going to and their use in contemporary informal British English. The constructions are examined with the behavioural profile approach. Three different regression modelling methods are applied to the grammatical alternations, each operationalizing one of the theoretical assumptions. While the results show that all three approaches are feasible and comparable in predictive accuracy, model interpretation becomes increasingly difficult with added complexity.

Nanopore Sequencing of Cell-free DNA: An Emerging Liquid Biopsy Approach for Brain Tumor Molecular Profiling

Background: Brain tumors exhibit significant molecular heterogeneity, complicating diagnosis, prognosis, and treatment. Traditional tissue biopsies are invasive and often fail to capture the full tumor landscape due to intratumoral heterogeneity. Liquid biopsy, which analyzes cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA), offers a minimally invasive alternative for tumor profiling. Nanopore sequencing, a novel long-read sequencing technology, is emerging as a valuable tool in this context. Purpose: This review explores the application of nanopore sequencing in molecular profiling of brain tumors using liquid biopsy, focusing on its ability to detect both genetic and epigenetic alterations with clinical relevance. Main body: Brain tumors, such as gliomas and medulloblastomas, are characterized by diverse molecular profiles, which influence patient outcomes and treatment strategies. Nanopore sequencing offers unique advantages for profiling cfDNA from biofluids like cerebrospinal fluid (CSF) and plasma, including the ability to generate long reads and detect structural variants, copy number alterations, and methylation patterns. Several studies have demonstrated its potential to identify key mutations (e.g., IDH1/2, H3K27 M) and track tumor evolution through serial cfDNA monitoring. However, challenges remain, including low ctDNA fractions in biofluids and bioinformatic complexities. Conclusion: Nanopore sequencing holds significant promise for advancing non-invasive molecular profiling of brain tumors, offering real-time insights into tumor genomics and evolution. This technology could revolutionize personalized brain tumor management, but further validation and optimization are needed before it can be routinely applied in clinical practice.

On person-community fit: Trait-, person-, and type-based approaches to measurement

Person-community fit is a timely and important concept in personality, social, and geographical psychology. The assessment of person-community fit poses statistical and conceptual challenges because there is inevitably greater variability among individuals than there is among communities. Leveraging data from the Synthetic Aperture Personality Assessment project involving 75,705 individuals across the US, we investigated the impact of fit on education, health, and well-being. We first assessed fit using variable-centered (response surface analysis) and person-centered (profile similarity) approaches. We then introduced a typological approach to person-community fit which is predicated on the idea that communities, like persons, are diverse, and can include multiple social and environmental niches. In this approach, persons are categorized into types, communities are described in terms of type-profiles, and fit is assessed as the proportion of people in the community sharing one's type. Using a rudimentary typology based on the five-factor model, this approach revealed striking differences between communities in their type profiles. For both the profile and type approaches, we found modest associations between person-community fit and outcomes, but these effects were due primarily to normativity (person-country fit) rather than to the distinguishing characteristics of communities. Taken together, our results highlight the benefits of using a multimethod approach for conceptualizing the personality of communities and assessing person-community fit.

Myeloid spatial and transcriptional molecular signature of ischemia-reperfusion injury in human liver transplantation.

Ischemia-reperfusion injury (IRI) is a significant clinical concern in liver transplantation, with a key influence on short-term and long-term allograft and patient survival. Myeloid cells trigger and sustain tissue inflammation and damage associated with IRI, but the mechanisms regulating these activities are unknown. To address this, we investigated the molecular characteristics of intragraft myeloid cells present in biopsy-proven IRI- and IRI+ liver transplants. RNA-sequencing was performed on 80 pre-reperfusion and post-reperfusion biopsies from 40 human recipients of liver transplantation (23 IRI+, 17 IRI-). We used transcriptional profiling and computational approaches to identify specific gene coexpression network modules correlated with functional subsets of MPO+, lysozyme+, and CD68+ myeloid cells quantified by immunohistochemistry on sequential sections from the same patient biopsies. A global molecular map showed gene signatures related to myeloid activation in all patients regardless of IRI status; however, myeloid cell subsets differed dramatically in their spatial morphology and associated gene signatures. IRI- recipients were found to have a natural corticosteroid production and response profile from pre-reperfusion to post-reperfusion, particularly among monocytes/macrophages. The pre-reperfusion signature of IRI+ recipients included acute inflammatory responses in neutrophils and increased translation of adaptive immune-related genes in monocytes/macrophages coupled with decreased glucocorticoid responses. Subsequent lymphocyte activation at post-reperfusion identified transcriptional programs associated with the transition to adaptive immunity found only among IRI+ recipients. Myeloid subset-specific genes and related signaling pathways provide targets for the development of therapeutic strategies aimed at limiting IRI in the clinical setting of liver transplantation.

Quantitative Proteomics of the Intracellular Bacterial Pathogen Salmonella enterica Serovar Typhimurium.

Mass spectrometry-based proteomics provides a wealth of information about changes in protein production and abundance under diverse conditions, as well as mechanisms of regulation, signaling cascades, interaction partners, and communication patterns across biological systems. For profiling of intracellular pathogens, proteomic profiling can be performed in the absence of a host to singularly define the pathogenic proteome or during an infection-like setting to identify dual perspectives of infection. In this chapter, we present techniques to extract proteins from the human bacterial intracellular pathogen, Salmonella enterica serovar Typhimurium, in the presence of macrophages, an important innate immune cell in host defense. We outline sample preparation, including protein extraction, digestion, and purification, as well as mass spectrometry measurements and bioinformatics analysis. The data generated from our dual perspective profiling approach provides new insight into pathogen and host protein modulation under infection-like conditions.

Determination and validation of tiaprofenic acid in human plasma: A detailed LC-MS/MS-based analysis following ICH M10 guidelines and the accuracy profile approach

The validation of bioanalytical methods holds critical importance for regulatory agencies and organizations dedicated to ensuring the safety, efficacy, and quality of pharmaceuticals. In this context, the recent release of the ICH M10 guideline in May 2022 represents a significant milestone in standardizing bioanalytical method validation globally. However, this guideline lacks explicit experimental protocols for implementation. In this study, we address the practical implementation of the newly released ICH M10 guideline by providing a detailed validation protocol for a bioanalytical method. Our method specifically targets tiaprofenic acid, a widely used nonsteroidal anti-inflammatory drug. Tiaprofenic acid is a critical component in bioequivalence studies, underscoring the necessity for precise and accurate quantification within complex biological matrices. The integration of the accuracy profile approach, a statistical tool, enhances the significance of this work. This approach aids in assessing the accuracy and precision of bioanalytical methods, establishing confidence intervals around measured concentrations, and quantifying the level of accuracy and precision expected when using the validated method.

Improving susceptibility of neuroendocrine tumors to radionuclide therapies: personalized approaches towards complementary treatments.

Radionuclide therapies are an important tool for the management of patients with neuroendocrine neoplasms (NENs). Especially [131I]MIBG and [177Lu]Lu-DOTA-TATE are routinely used for the treatment of a subset of NENs, including pheochromocytomas, paragangliomas and gastroenteropancreatic tumors. Some patients suffering from other forms of NENs, such as medullary thyroid carcinoma or neuroblastoma, were shown to respond to radionuclide therapy; however, no general recommendations exist. Although [131I]MIBG and [177Lu]Lu-DOTA-TATE can delay disease progression and improve quality of life, complete remissions are achieved rarely. Hence, better individually tailored combination regimes are required. This review summarizes currently applied radionuclide therapies in the context of NENs and informs about recent advances in the development of theranostic agents that might enable targeting subgroups of NENs that previously did not respond to [131I]MIBG or [177Lu]Lu-DOTA-TATE. Moreover, molecular pathways involved in NEN tumorigenesis and progression that mediate features of radioresistance and are particularly related to the stemness of cancer cells are discussed. Pharmacological inhibition of such pathways might result in radiosensitization or general complementary antitumor effects in patients with certain genetic, transcriptomic, or metabolic characteristics. Finally, we provide an overview of approved targeted agents that might be beneficial in combination with radionuclide therapies in the context of a personalized molecular profiling approach.

All that glitters is not gold! Job insecurity and well-being in STEM research fellows: a latent profile analysis.

Job insecurity is now one of the major stressors affecting well-being at work. In academia, researchers appear to be in the most precarious position. To explore the relationship between job insecurity and well-being at work, we analyzed a sample of research fellows belonging to STEM disciplines in Italy. Using a latent profile approach, we identified three "hidden" subgroups: "Safe & Sound"; "Safe not so Sound" and "Neither Safe or Sound." Compared to previous studies, our results show that even within a population of STEM researchers that tends to have good levels of employability and mobility, there are subgroups of people characterized by greater job insecurity and low work commitment, who suffer from emotional exhaustion and cynicism at work level, i.e., more exposed to the risk of burnout.

High hypoxia status in pancreatic cancer is associated with multiple hallmarks of an immunosuppressive tumor microenvironment.

Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is a particularly lethal disease that is often diagnosed late and is refractory to most forms of treatment. Tumour hypoxia is a key hallmark of PDAC and is purported to contribute to multiple facets of disease progression such as treatment resistance, increased invasiveness, metabolic reprogramming, and immunosuppression. We used the Buffa gene signature as a hypoxia score to profile transcriptomics datasets from PDAC cases. We performed cell-type deconvolution and gene expression profiling approaches to compare the immunological phenotypes of cases with low and high hypoxia scores. We further supported our findings by qPCR analyses in PDAC cell lines cultured in hypoxic conditions. First, we demonstrated that this hypoxia score is associated with increased tumour grade and reduced survival suggesting that this score is correlated to disease progression. Subsequently, we compared the immune phenotypes of cases with high versus low hypoxia score expression (HypoxiaHI vs. HypoxiaLOW) to show that high hypoxia is associated with reduced levels of T cells, NK cells and dendritic cells (DC), including the crucial cDC1 subset. Concomitantly, immune-related gene expression profiling revealed that compared to HypoxiaLOW tumours, mRNA levels for multiple immunosuppressive molecules were notably elevated in HypoxiaHI cases. Using a Random Forest machine learning approach for variable selection, we identified LGALS3 (Galectin-3) as the top gene associated with high hypoxia status and confirmed its expression in hypoxic PDAC cell lines. In summary, we demonstrated novel associations between hypoxia and multiple immunosuppressive mediators in PDAC, highlighting avenues for improving PDAC immunotherapy by targeting these immune molecules in combination with hypoxia-targeted drugs.

Molecular characterization of gliomas and glioneuronal tumors amid Noonan syndrome: cancer predisposition examined.

In the setting of pediatric and adolescent young adult cancer, increased access to genomic profiling has enhanced the detection of genetic variation associated with cancer predisposition, including germline syndromic conditions. Noonan syndrome (NS) is associated with the germline RAS pathway activating alterations and increased risk of cancer. Herein, we describe our comprehensive molecular profiling approach, the association of NS with glioma and glioneuronal tumors, and the clinical and histopathologic characteristics associated with the disease. Within an institutional pediatric cancer cohort (n = 314), molecular profiling comprised of paired somatic disease-germline comparator exome analysis, RNA sequencing, and tumor classification by DNA methylation analysis was performed. Through the implementation of paired analysis, this study identified 4 of 314 (1.3%) individuals who harbored a germline PTPN11 variant associated with NS, of which 3 individuals were diagnosed with a glioma or glioneuronal tumor. Furthermore, we extend this study through collaboration with a peer institution to identify two additional individuals with NS and a glioma or glioneuronal tumor. Notably, in three of five (60%) individuals, paired genomic profiling led to a previously unrecognized diagnosis of Noonan syndrome despite an average age of cancer diagnosis of 16.8 years. The study of the disease-involved tissue identified signaling pathway dysregulation through somatic alteration of genes involved in cellular proliferation, survival, and differentiation. Comparative pathologic findings are presented to enable an in-depth examination of disease characteristics. This comprehensive analysis highlights the association of gliomas and glioneuronal tumors with RASopathies and the potential therapeutic challenges and importantly demonstrates the utility of genomic profiling for the identification of germline cancer predisposition.

A Perspective Review of Cancer Therapy (Part I): Immunotherapy, Gene Therapy, and Nanotechnology

The application of genomic profiling approaches has propelled the advancement of precision medicine, enabling the development of personalized treatment programs that are specifically customized for each particular patient. This method considers the distinct genetic composition of each tumor, allowing for the detection of crucial driver mutations and possible weaknesses that might be targeted for therapeutic purposes. Furthermore, immunotherapy has emerged as a promising approach in cancer treatment, utilizing the potential of the immune system to identify and eradicate cancerous cells. Medical breakthroughs like CAR-T cell therapy have already demonstrated exceptional efficacy in treating hematologic malignancies. Moreover, state-of-the-art technologies such as CRISPR-Cas9 gene editing offer potential for directly altering tumor cells or augmenting the efficacy of current treatments. The future of cancer therapy is focused on developing more precise and targeted techniques to enhance patient outcomes and ultimately overcome this destructive illness. This involves continual research and cooperation among scientists, physicians, and pharmaceutical corporations on a worldwide level.

Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.

Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3' end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA polymerase II at the end of a gene, and faster cleavage leads to quicker degradation of downstream readthrough RNA. Our findings shed light on the features important for efficient 3' end cleavage and the regulation of transcription termination.

A latent profile approach to the study of conspiracy belief: Identifying the role of executive functioning

The proliferation of conspiracy theories has coincided with advancement in communication technologies. Research has consistently identified the social determinants of conspiracy beliefs, such as social media exposure and peer influence, the impact of cognitive abilities, especially executive function (EF), remains unexplored. This study aimed to explore whether conspiracy beliefs varied with different EF profiles. A sample of 194 participants (M = 35.56; SD = 10.01) completed a questionnaire covering beliefs in six common conspiracy theories and tasks assessing working memory (N-Back), cognitive flexibility (Modified Card Sorting Task), and affective decision-making (Iowa Gambling Task). Latent profile analysis on the cognitive tests identified three distinct EF profiles: Low Cool EF, Moderate Cool EF, and High EF. Notably, the Low Cool EF cohort displayed significantly stronger beliefs in five of the six conspiracy theories than the High EF profile. The Moderate Cool EF profile also showed significantly stronger beliefs in conspiracies relating to personal wellbeing, and Covid-19 compared to the High EF profile. Executive functioning plays a pivotal role in shaping an individual's inclination towards or resistance against conspiracy beliefs. Enhanced cognitive flexibility and working memory enables individuals to critically assess information rather than rigidly subscribing to a singular viewpoint, likely fostering resistance to conspiratorial thinking.