Harnessing the Potential of Multiomics Studies for Precision Medicine in Infectious Disease

Open Forum Infectious Diseases

2021 Sep 25

Ward, R;Aghaeepour, N;Bhattacharyya, R;Clish, C;Gaudillière, B;Hacohen, N;Mansour, M;Mudd, P;Pasupneti, S;Presti, R;Rhee, E;Sen, P;Spec, A;Tam, J;Villani, A;Woolley, A;Hsu, J;Vyas, J;
| DOI: 10.1093/ofid/ofab483

The field of infectious diseases currently takes a reactive approach, treating infections as they present in patients. Although certain populations are known to be at greater risk of developing infection (e.g., immunocompromised), we lack a systems approach to define the true risk of future infection for a patient. Guided by impressive gains in -omics technologies, future strategies to infectious diseases should take a precision approach to infection through identification of patients at intermediate and high-risk of infection and deploy targeted preventative measures (i.e., prophylaxis). The advances of high-throughput immune profiling by multiomics approaches (i.e., transcriptomics, epigenomics, metabolomics, proteomics) holds the promise to identify patients at increased risk of infection and enable risk-stratifying approaches to be applied in the clinic. Integration of patient-specific data using machine learning improves the effectiveness of prediction, providing the necessary technologies needed to propel the field of infectious diseases medicine into the era of personalized medicine.

Immunological mechanisms of vaccine-induced protection against COVID-19 in humans

Nature reviews. Immunology

2021 Aug 01

Sadarangani, M;Marchant, A;Kollmann, TR;
PMID: 34211186 | DOI: 10.1038/s41577-021-00578-z

Most COVID-19 vaccines are designed to elicit immune responses, ideally neutralizing antibodies (NAbs), against the SARS-CoV-2 spike protein. Several vaccines, including mRNA, adenoviral-vectored, protein subunit and whole-cell inactivated virus vaccines, have now reported efficacy in phase III trials and have received emergency approval in many countries. The two mRNA vaccines approved to date show efficacy even after only one dose, when non-NAbs and moderate T helper 1 cell responses are detectable, but almost no NAbs. After a single dose, the adenovirus vaccines elicit polyfunctional antibodies that are capable of mediating virus neutralization and of driving other antibody-dependent effector functions, as well as potent T cell responses. These data suggest that protection may require low levels of NAbs and might involve other immune effector mechanisms including non-NAbs, T cells and innate immune mechanisms. Identifying the mechanisms of protection as well as correlates of protection is crucially important to inform further vaccine development and guide the use of licensed COVID-19 vaccines worldwide.

Alpha oscillations and event-related potentials reflect distinct dynamics of attribute construction and evidence accumulation in dietary decision making

eLife

2021 Jul 15

HajiHosseini, A;Hutcherson, CA;
PMID: 34263723 | DOI: 10.7554/eLife.60874

How does regulatory focus alter attribute value construction (AVC) and evidence accumulation (EA)? We recorded electroencephalogram during food choices while participants responded naturally or regulated their choices by attending to health attributes or decreasing attention to taste attributes. Using a drift diffusion model, we predicted the time course of neural signals associated with AVC and EA. Results suggested that event-related potentials (ERPs) correlated with the time course of model-predicted taste-attribute signals, with no modulation by regulation. By contrast, suppression of frontal and occipital alpha power correlated with the time course of EA, tracked tastiness according to its goal relevance, and predicted individual variation in successful down-regulation of tastiness. Additionally, an earlier rise in frontal and occipital theta power represented food tastiness more strongly during regulation and predicted a weaker influence of food tastiness on behaviour. Our findings illuminate how regulation modifies the representation of attributes during the process of EA.

mRNA distribution in skeletal muscle is associated with mRNA size

Journal of cell science

2021 Jun 24

Pinheiro, H;Pimentel, MR;Sequeira, C;Oliveira, LM;Pezzarossa, A;Roman, W;Gomes, ER;
PMID: 34164679 | DOI: 10.1242/jcs.256388

Skeletal muscle myofibers are large and elongated cells with multiple and evenly distributed nuclei. Nuclear distribution suggests that each nucleus influences a specific compartment within the myofiber and implies a functional role for nuclear positioning. Compartmentalization of specific mRNAs and proteins has been reported at the neuromuscular and myotendinous junctions, but mRNA distribution in non-specialized regions of the myofibers remains largely unexplored. We report that the bulk of mRNAs is enriched around the nucleus of origin and that this perinuclear accumulation depends on recently transcribed mRNAs. Surprisingly, mRNAs encoding large proteins - giant mRNAs - are spread throughout the cell and do not exhibit perinuclear accumulation. Furthermore, by expressing exogenous transcripts with different sizes we found that size contributes to mRNA spreading independently of mRNA sequence. Both these mRNA distribution patterns depend on microtubules and are independent of nuclear dispersion, mRNA expression level and stability, and the characteristics of the encoded protein. Thus, we propose that mRNA distribution in non-specialized regions of skeletal muscle is size selective to ensure cellular compartmentalization and simultaneous long-range distribution of giant mRNAs.

IL-1R1-dependent signaling coordinates epithelial regeneration in response to intestinal damage

Science immunology

2021 May 07

Cox, CB;Storm, EE;Kapoor, VN;Chavarria-Smith, J;Lin, DL;Wang, L;Li, Y;Kljavin, N;Ota, N;Bainbridge, TW;Anderson, K;Roose-Girma, M;Warming, S;Arron, JR;Turley, SJ;de Sauvage, FJ;van Lookeren Campagne, M;
PMID: 33963061 | DOI: 10.1126/sciimmunol.abe8856

Repair of the intestinal epithelium is tightly regulated to maintain homeostasis. The response after epithelial damage needs to be local and proportional to the insult. How different types of damage are coupled to repair remains incompletely understood. We report that after distinct types of intestinal epithelial damage, IL-1R1 signaling in GREM1+ mesenchymal cells increases production of R-spondin 3 (RSPO3), a Wnt agonist required for intestinal stem cell self-renewal. In parallel, IL-1R1 signaling regulates IL-22 production by innate lymphoid cells and promotes epithelial hyperplasia and regeneration. Although the regulation of both RSPO3 and IL-22 is critical for epithelial recovery from Citrobacter rodentium infection, IL-1R1-dependent RSPO3 production by GREM1+ mesenchymal cells alone is sufficient and required for recovery after dextran sulfate sodium-induced colitis. These data demonstrate how IL-1R1-dependent signaling orchestrates distinct repair programs tailored to the type of injury sustained that are required to restore intestinal epithelial barrier function.

Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer

Cancer cell

2021 Apr 27

Hornburg, M;Desbois, M;Lu, S;Guan, Y;Lo, AA;Kaufman, S;Elrod, A;Lotstein, A;DesRochers, TM;Munoz-Rodriguez, JL;Wang, X;Giltnane, J;Mayba, O;Turley, SJ;Bourgon, R;Daemen, A;Wang, Y;
PMID: 33961783 | DOI: 10.1016/j.ccell.2021.04.004

Distinct T cell infiltration patterns, i.e., immune infiltrated, excluded, and desert, result in different responses to cancer immunotherapies. However, the key determinants and biology underpinning these tumor immune phenotypes remain elusive. Here, we provide a high-resolution dissection of the entire tumor ecosystem through single-cell RNA-sequencing analysis of 15 ovarian tumors. Immune-desert tumors are characterized by unique tumor cell-intrinsic features, including metabolic pathways and low antigen presentation, and an enrichment of monocytes and immature macrophages. Immune-infiltrated and -excluded tumors differ markedly in their T cell composition and fibroblast subsets. Furthermore, our study reveals chemokine receptor-ligand interactions within and across compartments as potential mechanisms mediating immune cell infiltration, exemplified by the tumor cell-T cell cross talk via CXCL16-CXCR6 and stromal-immune cell cross talk via CXCL12/14-CXCR4. Our data highlight potential molecular mechanisms that shape the tumor immune phenotypes and may inform therapeutic strategies to improve clinical benefit from cancer immunotherapies.

The role of EBV in hematolymphoid proliferations: Emerging concepts relevant to diagnosis and treatment

Histopathology

2021 Apr 07

Ababneh, E;Saad, AM;Crane, GM;
PMID: 33829526 | DOI: 10.1111/his.14379

Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus with >90% of the adult population worldwide harboring latent infection. A small subset of those infected develop EBV-associated neoplasms including a range of lymphoproliferative disorders (LPD). The diagnostic distinction of these entities appears increasingly relevant as our understanding of EBV-host interactions and mechanisms of EBV-driven lymphomagenesis improves. EBV may lower the mutational threshold for malignant transformation, create potential vulnerabilities related to viral alteration of cell metabolism and allow for improved immune targeting. However, these tumors may escape immune surveillance by affecting their immune microenvironment, limiting viral gene expression or potential loss of the viral episome. Methods to manipulate the latency state of the virus to enhance immunogenicity are emerging as well as the potential to detect so-called "hit and run" cases where EBV has been lost. Finally, measurement of EBV DNA remains an important biomarker for screening and monitoring of LPD. Methods to distinguish EBV DNA derived from virions during lytic activation from latent, methylated EBV DNA present in EBV-associated neoplasms may broaden the utility of this testing, particularly in patients with compromised immune function. We will highlight some of these emerging areas relevant to the diagnosis and treatment of EBV-associated LPD with potential applicability to other EBV-associated neoplasms. This article is protected by

Top-Down Control of Sweet and Bitter Taste in the Mammalian Brain

Cell

2021 Jan 07

Jin, H;Fishman, ZH;Ye, M;Wang, L;Zuker, CS;
PMID: 33417862 | DOI: 10.1016/j.cell.2020.12.014

Hardwired circuits encoding innate responses have emerged as an essential feature of the mammalian brain. Sweet and bitter evoke opposing predetermined behaviors. Sweet drives appetitive responses and consumption of energy-rich food sources, whereas bitter prevents ingestion of toxic chemicals. Here we identified and characterized the neurons in the brainstem that transmit sweet and bitter signals from the tongue to the cortex. Next we examined how the brain modulates this hardwired circuit to control taste behaviors. We dissect the basis for bitter-evoked suppression of sweet taste and show that the taste cortex and amygdala exert strong positive and negative feedback onto incoming bitter and sweet signals in the brainstem. Finally we demonstrate that blocking the feedback markedly alters responses to ethologically relevant taste stimuli. These results illustrate how hardwired circuits can be finely regulated by top-down control and reveal the neural basis of an indispensable behavioral response for all animals.

Quantitative Analysis of Inflammatory Uterine Lesions of Pregnant Gilts with Digital Image Analysis Following Experimental PRRSV-1 Infection

Animals : an open access journal from MDPI

2023 Feb 24

Horváth, DG;Abonyi-Tóth, Z;Papp, M;Szász, AM;Rümenapf, T;Knecht, C;Kreutzmann, H;Ladinig, A;Balka, G;
PMID: 36899686 | DOI: 10.3390/ani13050830

Reproductive disorders caused by porcine reproductive and respiratory syndrome virus-1 are not yet fully characterized. We report QuPath-based digital image analysis to count inflammatory cells in 141 routinely, and 35 CD163 immunohistochemically stained endometrial slides of vaccinated or unvaccinated pregnant gilts inoculated with a high or low virulent PRRSV-1 strain. To illustrate the superior statistical feasibility of the numerical data determined by digital cell counting, we defined the association between the number of these cells and endometrial, placental, and fetal features. There was strong concordance between the two manual scorers. Distributions of total cell counts and endometrial and placental qPCR results differed significantly between examiner1's endometritis grades. Total counts' distribution differed significantly between groups, except for the two unvaccinated. Higher vasculitis scores were associated with higher endometritis scores, and higher total cell counts were expected with high vasculitis/endometritis scores. Cell number thresholds of endometritis grades were determined. A significant correlation between fetal weights and total counts was shown in unvaccinated groups, and a significant positive correlation was found between these counts and endometrial qPCR results. We revealed significant negative correlations between CD163+ counts and qPCR results of the unvaccinated group infected with the highly virulent strain. Digital image analysis was efficiently applied to assess endometrial inflammation objectively.

Evaluation of the Antiseizure Activity of Endemic Plant Halfordia kendack Guillaumin and Its Main Constituent, Halfordin, on a Zebrafish Pentylenetetrazole (PTZ)-Induced Seizure Model

International journal of molecular sciences

2023 Jan 30

Skiba, A;Kozioł, E;Luca, SV;Budzyńska, B;Podlasz, P;Van Der Ent, W;Shojaeinia, E;Esguerra, CV;Nour, M;Marcourt, L;Wolfender, JL;Skalicka-Woźniak, K;
PMID: 36768918 | DOI: 10.3390/ijms24032598

Epilepsy is a neurological disease that burdens over 50 million people worldwide. Despite the considerable number of available antiseizure medications, it is estimated that around 30% of patients still do not respond to available treatment. Herbal medicines represent a promising source of new antiseizure drugs. This study aimed to identify new drug lead candidates with antiseizure activity from endemic plants of New Caledonia. The crude methanolic leaf extract of Halfordia kendack Guillaumin (Rutaceae) significantly decreased (75 μg/mL and 100 μg/mL) seizure-like behaviour compared to sodium valproate in a zebrafish pentylenetetrazole (PTZ)-induced acute seizure model. The main coumarin compound, halfordin, was subsequently isolated by liquid-liquid chromatography and subjected to locomotor, local field potential (LFP), and gene expression assays. Halfordin (20 μM) significantly decreased convulsive-like behaviour in the locomotor and LFP analysis (by 41.4% and 60%, respectively) and significantly modulated galn, and penka gene expression.

Nucleic Acid Pharmaceutical Agents

Haschek and Rousseaux's Handbook of Toxicologic Pathology, Volume 2 : Safety Assessment Environmental Toxicologic Pathology

2023 Feb 27

Kohnken, R;Harbison, C;Klein, S;Engelhardt, J;
| DOI: 10.1016/B978-0-12-821047-5.00017-8

Nucleic acid pharmaceutical (NAP) agents are a relatively recent class of therapeutics that are uniquely capable of inhibiting protein translation through direct interaction with RNA. These classes of pharmaceuticals have demonstrated clinical benefit for diseases previously considered untreatable by small molecules and biologics by their theoretical ability to target any cellular RNA associated with disease. This chapter provides an overview of the major types of NAPs and the types of indications for which they are being developed, with examples of therapeutics on the market and in clinical development. The reader is also provided with a review of the most common delivery systems and chemical modifications that enable the biodistribution and efficacy of these drugs. A brief discussion of the nonclinical safety package is provided, and finally the most common toxicities that have been observed in preclinical species are discussed.

Reagents for Mass Cytometry

Chemical reviews

2023 Jan 25

Arnett, LP;Rana, R;Chung, WW;Li, X;Abtahi, M;Majonis, D;Bassan, J;Nitz, M;Winnik, MA;
PMID: 36696538 | DOI: 10.1021/acs.chemrev.2c00350

Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm2 spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.

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	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

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