The Reactome Pathway Knowledgebase 2024

The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network.

Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells

Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to somatic mutations in myeloid malignancy-associated genes, such as TET2-mediated clonal hematopoiesis of indeterminate potential or CHIP, it represents increased risk for hematological malignancies and cardiovascular disease. IL1β is elevated in patients with CHIP, however, its effect is not well understood. Here we show that IL1β promotes expansion of pro-inflammatory monocytes/macrophages, coinciding with a failure in the demethylation of lymphoid and erythroid lineage associated enhancers and transcription factor binding sites, in a mouse model of CHIP with hematopoietic-cell-specific deletion of Tet2. DNA-methylation is significantly lost in wild type HSPCs upon IL1β administration, which is resisted by Tet2-deficient HSPCs, and thus IL1β enhances the self-renewing ability of Tet2-deficient HSPCs by upregulating genes associated with self-renewal and by resisting demethylation of transcription factor binding sites related to terminal differentiation. Using aged mouse models and human progenitors, we demonstrate that targeting IL1 signaling could represent an early intervention strategy in preleukemic disorders. In summary, our results show that Tet2 is an important mediator of an IL1β-promoted epigenetic program to maintain the fine balance between self-renewal and lineage differentiation during hematopoiesis.

Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma

Background

Uveal melanoma is the most common non-cutaneous melanoma and is an intraocular malignancy affecting nearly 7,000 individuals per year worldwide. Of these, approximately 50% will progress to metastatic disease for which there are currently no effective therapies. Despite advances in molecular profiling and metastatic stratification of uveal melanoma tumors, little is known regarding their underlying biology of metastasis. Our group has identified a disseminated neoplastic cell population characterized by co-expression of immune and melanoma proteins, circulating hybrid cells (hybrids), in patients with uveal melanoma. Compared to circulating tumor cells, which lack expression of immune proteins, hybrids are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression.

Methods

To ascertain mechanisms underlying enhanced hybrid cell dissemination we identified hybrid cells within primary uveal melanoma tumors using single cell RNA sequencing and evaluated their gene expression and predicted ligand-receptor interactions in relation to other melanoma and immune cells within the primary tumor. We then verified expression of upregulated hybrid pathways within patient-matched tumor and peripheral blood hybrids using cyclic immunofluorescence and quantified their protein expression relative to other non-hybrid tumor and disseminated tumor cells.

Results

Among the top upregulated genes and pathways in hybrid cells were those involved in enhanced cell motility and cytoskeletal rearrangement, immune evasion, and altered cellular metabolism. In patient-matched tumor and peripheral blood, we verified gene expression by examining concordant protein expression for each pathway category: TMSB10 (cell motility), CD74 (immune evasion) and GPX1 (metabolism). Both TMSB10 and GPX1 were expressed on significantly higher numbers of disseminated hybrid cells compared to circulating tumor cells, and CD74 and GPX1 were expressed on more disseminated hybrids than tumor-resident hybrids. Lastly, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting metastasis including GAS6-AXL, CXCL12-CXCR4, LGALS9-P4HB and IGF1-IGFR1.

Conclusion

These findings highlight the importance of TMSB10, GPX1 and CD74 for successful hybrid cell dissemination and survival in circulation. Our results contribute to the understanding of uveal melanoma tumor progression and interactions between tumor cells and immune cells in the tumor microenvironment that may promote metastasis.

Analysis of uveal melanoma scRNA sequencing data identifies neoplastic-immune hybrid cells that exhibit metastatic potential

Uveal melanoma (UM) is the most common non-cutaneous melanoma and is an intraocular malignancy that affects nearly 7,000 individuals per year worldwide. Of these, nearly 50% will progress to metastatic disease for which there are currently no effective therapies. Despite advances in the molecular profiling and metastatic stratification of class 1 and 2 UM tumors, little is known regarding the underlying biology of UM metastasis. Our group has identified a disseminated tumor cell population characterized by co-expression of immune and melanoma proteins, (circulating hybrid cells (CHCs), in patients with UM. Compared to circulating tumor cells, CHCs are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression. To identify mechanisms underlying enhanced hybrid cell dissemination we sought to identify hybrid cells within a primary UM single cell RNA-seq dataset. Using rigorous doublet discrimination approaches, we identified UM hybrids and evaluated their gene expression, predicted ligand-receptor status, and cell-cell communication state in relation to other melanoma and immune cells within the primary tumor. We identified several genes and pathways upregulated in hybrid cells, including those involved in enhancing cell motility and cytoskeleton rearrangement, evading immune detection, and altering cellular metabolism. In addition, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting cancer metastasis including IGF1-IGFR1, GAS6-AXL, LGALS9-P4HB, APP-CD74 and CXCL12-CXCR4. These results contribute to our understanding of tumor progression and interactions between tumor cells and immune cells in the UM microenvironment that may promote metastasis.

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open source, manually curated, peer-reviewed database of human biological pathways, provides annotations for over 4000 disease variants of close to 400 genes in the context of ∼800 disease reactions constituting ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics (ACMG). Reactome's pathway-based, reaction-specific disease variant dataset and data model provide a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.

Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal

Understudied or dark proteins have the potential to shed light on as-yet undiscovered molecular mechanisms that underlie phenotypes and suggest innovative therapeutic approaches for many diseases. The Reactome-IDG (Illuminating the Druggable Genome) project aims to place dark proteins in the context of manually curated, highly reliable pathways in Reactome, the most comprehensive, open-source biological pathway knowledgebase, facilitating the understanding functions and predicting therapeutic potentials of dark proteins. The Reactome-IDG web portal, deployed at https://idg.reactome.org, provides a simple, interactive web page for users to search pathways that may functionally interact with dark proteins, enabling the prediction of functions of dark proteins in the context of Reactome pathways. Enhanced visualization features implemented at the portal allow users to investigate the functional contexts for dark proteins based on tissue-specific gene or protein expression, drug-target interactions, or protein or gene pairwise relationships in the original Reactome's systems biology graph notation (SBGN) diagrams or the new simplified functional interaction (FI) network view of pathways. The protocols in this chapter describe step-by-step procedures to use the web portal to learn biological functions of dark proteins in the context of Reactome pathways. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Search for interacting pathways of a protein Support Protocol: Interacting pathway results for an annotated protein Alternate Protocol: Use individual pairwise relationships to predict interacting pathways of a protein Basic Protocol 2: Using the IDG pathway browser to study interacting pathways Basic Protocol 3: Overlaying tissue-specific expression data Basic Protocol 4: Overlaying protein/gene pairwise relationships in the pathway context Basic Protocol 5: Visualizing drug/target interactions.

Illuminating Dark Proteins using Reactome Pathways

Limited knowledge about a substantial portion of protein coding genes, known as "dark" proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehensive, open source, open-access pathway knowledgebase, to contextualize dark proteins within biological pathways. By integrating multiple resources and employing a random forest classifier trained on 106 protein/gene pairwise features, we predicted functional interactions between dark proteins and Reactome-annotated proteins. We then developed three scores to measure the interactions between dark proteins and Reactome pathways, utilizing enrichment analysis and fuzzy logic simulations. Correlation analysis of these scores with an independent single-cell RNA sequencing dataset provided supporting evidence for this approach. Furthermore, systematic natural language processing (NLP) analysis of over 22 million PubMed abstracts and manual checking of the literature associated with 20 randomly selected dark proteins reinforced the predicted interactions between proteins and pathways. To enhance the visualization and exploration of dark proteins within Reactome pathways, we developed the Reactome IDG portal, deployed at https://idg.reactome.org, a web application featuring tissue-specific protein and gene expression overlay, as well as drug interactions. Our integrated computational approach, together with the user-friendly web platform, offers a valuable resource for uncovering potential biological functions and therapeutic implications of dark proteins.

Using the Reactome Database

Pathway databases provide descriptions of the roles of proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway-centric views of these roles may allow for the discovery of unexpected functional relationships in data such as gene expression profiles and somatic mutation catalogues from tumor cells. For this reason, there is a high demand for high-quality pathway databases and their associated tools. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, New York University Langone Health, the European Bioinformatics Institute, and Oregon Health & Science University) is one such pathway database. Reactome collects detailed information on biological pathways and processes in humans from the primary literature. Reactome content is manually curated, expert-authored, and peer-reviewed and spans the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm, and other model organisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Browsing a Reactome pathway Basic Protocol 2: Exploring Reactome annotations of disease and drugs Basic Protocol 3: Finding the pathways involving a gene or protein Alternate Protocol 1: Finding the pathways involving a gene or protein using UniProtKB (SwissProt), Ensembl, or Entrez gene identifier Alternate Protocol 2: Using advanced search Basic Protocol 4: Using the Reactome pathway analysis tool to identify statistically overrepresented pathways Basic Protocol 5: Using the Reactome pathway analysis tool to overlay expression data onto Reactome pathway diagrams Basic Protocol 6: Comparing inferred model organism and human pathways using the Species Comparison tool Basic Protocol 7: Comparing tissue-specific expression using the Tissue Distribution tool.

VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data

Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for users to efficiently and robustly analyze the host immune response gene expression data collected in the ImmPort/GEO databases. VIGET allows users to select vaccines, choose ImmPort studies, set up analysis models by choosing confounding variables and two groups of samples having different vaccination times, and then perform differential expression analysis to select genes for pathway enrichment analysis and functional interaction network construction using the Reactome's web services. VIGET provides features for users to compare results from two analyses, facilitating comparative response analysis across different demographic groups. VIGET uses the Vaccine Ontology (VO) to classify various types of vaccines such as live or inactivated flu vaccines, yellow fever vaccines, etc. To showcase the utilities of VIGET, we conducted a longitudinal analysis of immune responses to yellow fever vaccines and found an intriguing complex activity response pattern of pathways in the immune system annotated in Reactome, demonstrating that VIGET is a valuable web portal that supports effective vaccine response studies using Reactome pathways and ImmPort data.

Circulating Neoplastic-Immune Hybrid Cells Predict Metastatic Progression in Uveal Melanoma

Background: Uveal melanoma is an aggressive cancer with high metastatic risk. Recently, we identified a circulating cancer cell population that co-expresses neoplastic and leukocyte antigens, termed circulating hybrid cells (CHCs). In other cancers, CHCs are more numerous and better predict oncologic outcomes compared to circulating tumor cells (CTCs). We sought to investigate the potential of CHCs as a prognostic biomarker in uveal melanoma. Methods: We isolated peripheral blood monocular cells from uveal melanoma patients at the time of primary treatment and used antibodies against leukocyte and melanoma markers to identify and enumerate CHCs and CTCs by immunocytochemistry. Results: Using a multi-marker approach to capture the heterogeneous disseminated tumor cell population, detection of CHCs was highly sensitive in uveal melanoma patients regardless of disease stage. CHCs were detected in 100% of stage I-III uveal melanoma patients (entire cohort, n = 68), whereas CTCs were detected in 58.8% of patients. CHCs were detected at levels statically higher than CTCs across all stages (p = 0.05). Moreover, CHC levels, but not CTCs, predicted 3 year progression-free survival (p < 0.03) and overall survival (p < 0.04). Conclusion: CHCs are a novel and promising prognostic biomarker in uveal melanoma.

Pharmacological characterization of chemically synthesized monomeric phi29 pRNA nanoparticles for systemic delivery

Previous studies have shown that the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor folds into a compact structure, constituting a RNA nanoparticle that can be modularized with functional groups as a nanodelivery system. pRNA nanoparticles can also be self-assembled by the bipartite approach without altering folding property. The present study demonstrated that 2'-F-modified pRNA nanoparticles were readily manufactured through this scalable bipartite strategy, featuring total chemical synthesis and permitting diverse functional modularizations. The RNA nanoparticles were chemically and metabolically stable and demonstrated a favorable pharmacokinetic (PK) profile in mice (half-life (T(1/2)): 5-10 hours, clearance (Cl): <0.13 l/kg/hour, volume of distribution (V(d)): 1.2 l/kg). It did not induce an interferon (IFN) response nor did it induce cytokine production in mice. Repeat intravenous administrations in mice up to 30 mg/kg did not result in any toxicity. Fluorescent folate-pRNA nanoparticles efficiently and specifically bound and internalized to folate receptor (FR)-bearing cancer cells in vitro. It also specifically and dose-dependently targeted to FR(+) xenograft tumor in mice with minimal accumulation in normal tissues. This first comprehensive pharmacological study suggests that the pRNA nanoparticle had all the preferred pharmacological features to serve as an efficient nanodelivery platform for broad medical applications.

Age vs Alzheimer's: a computational model of changes in representation

Previous research has demonstrated that the language of older adults leads to denser representations in a high dimensional model of memory than does the language of younger adults (Conley & Burgess, in press), and thus that density in the model (HAL or the hyperspace analogue to language) may constitute a useful metric in comparing memory for younger and older adults. This paper extends the previous research by examining the role of density in semantic representations that emerged from the language generated by adults with Alzheimer' s and comparing the results with age-matched normal controls. We found that, just as older adults have denser representations in semantic space than do younger adults, adults with Alzheimer's have still denser representations than normal older adults. These results support the hypothesis that greater density, normally associated in the model with good semantic depth, may in fact reach a "saturation point" and affect retrieval in older adults and especially adults with Alzheimer's.

The Psychology Graduate Applicant's Portal (www.psychgrad.org)

Applying to graduate school in psychology can be an intimidating process. Many obstacles must be overcome, such as applying to a program appropriate to the specific applicant, getting good GRE scores, submitting a clear and well-written statement of purpose, and obtaining letters of recommendation, to name just a few. Much information is available to assist applicants in these tasks, but finding this information can cause problems even for experienced Internet users. The goal of this project is to create an easily accessible Web clearing house of information on applying to graduate school in psychology. This Web site, called the Psychology Graduate Applicant's Portal (or PsychGrad.org), contains targeted links to other Web pages with valuable information, book recommendations on the applications process, polls to measure issues important to the graduate applicants, site-unique advice on graduate programs, a message board to exchange information and experiences, and other information relevant to the application process.

Age effects in a computational model of memory

Previous research demonstrates that semantic priming is relatively unaffected by age (Chiarello, Church, & Hoyer, 1985; Howard, 1988). To determine how age might affect representations in the HAL model of memory, the authors gathered text from older and younger adults and generated a global co-occurrence matrix for each. An analysis demonstrated that, as in humans, there was little difference in measures of semantic priming between memory matrices constructed from the two corpora. However, the authors discovered that semantic word neighborhoods generated by the older adult corpus were denser than corresponding neighborhoods derived from the younger adult corpus. This result has implications for changes in the semantic representation of words due to the aging process.

A computational approach to modeling population differences

Four experiments were conducted to determine whether the Hyperspace Analogue to Language (HAL) model of semantic memory could differentiate between two different populations. An analysis of the differences in densities (or average distances between word neighbors in semantic space) in HAL matrices--generated from text corpora derived from younger and older adults--confirmed that HAL was able to distinguish between the two age groups. This difference was again detected when structured interview data were used to build the corpora. A third experiment, designed to test the specificity of HAL in detecting differences between groups, did not detect any difference in the densities of the memory representations when older adults generated both the test corpora. The final experiment, conducted on the language of adults with Alzheimer's and normal adults, again demonstrated that HAL could discriminate between the two populations. These results suggest that HAL is capable of modeling, on the basis of changes in mean density, some of the differences between populations without modifying the model itself but, rather, by changing the text corpus from which the model creates its representations in semantic space.

Large-scale databases of proper names

Few tools for research in proper names have been available--specifically, there is no large-scale corpus of proper names. Two corpora of proper names were constructed, one based on U.S. phone book listings, the other derived from a database of Usenet text. Name frequencies from both corpora were compared with human subjects' reaction times (RTs) to the proper names in a naming task. Regression analysis showed that the Usenet frequencies contributed to predictions of human RT, whereas phone book frequencies did not. In addition, semantic neighborhood density measures derived from the HAL corpus were compared with the subjects' RTs and found to be a better predictor of RT than was frequency in either corpus. These new corpora are freely available on line for download. Potentials for these corpora range from using the names as stimuli in experiments to using the corpus data in software applications.

Harm reduction: concepts and practice. A policy discussion paper

This paper provides an overview of the context, definition, and key features of the harm reduction approach, and provides several examples of current programs in various countries. Both licit and illicit drugs are included in these illustrations. Some of the critical issues, and the strategies needed to advance harm reduction, are discussed. [Translations are provided in the International Abstracts Section of this issue.]

A submaximal treadmill test for developing target ratings of perceived exertion for outpatient cardiac rehabilitation

For patient populations whose heart rates cannot be used to regulate exercise intensity, the Borg Rating of Perceived Exertion (RPE) Scale is the preferred way to prescribe exercise intensity. Individual perceptual variations are best quantified by measuring perceptual intensity during maximal exercise testing; however, many situations require a submaximal protocol. Here, a submaximal treadmill procedure for establishing individualized target Ratings of Perceived Exertion is described. Target ratings of exertion were developed for outpatient cardiac rehabilitation patients using the new method and compared to target Ratings of Perceived Exertion obtained using standard techniques. A total of 144 target ratings at intensities ranging from 50% to 85% VO2max were compared. Over-all, the average difference between the two methods was 0.27 units and was not significant at any intensity. Therefore, the Treadmill Slope Method appears to be a valid submaximal test for generating target Ratings of Perceived Exertion for outpatient cardiac rehabilitation patients.

Three-point method of prescribing exercise with ratings of perceived exertion is valid for cardiac patients

It is often difficult to use heart rate to prescribe exercise for cardiac patients due to the effects of medications and procedures such as cardiac transplantation. Ratings of Perceived Exertion (RPE) is the preferred method of regulating exercise intensity in these situations. An RPE-based exercise prescription has previously depended on perceptual data from a maximal Graded Exercise Test (GXT). Recently, using 13 healthy subjects, we validated a Three-point RPE for prescribing exercise using RPE which can be used when ratings from a GXT are not available Currently, we examined the accuracy of this method for developing target RPEs for patients in Phase II cardiac rehabilitation. Such target RPEs did not differ from those obtained using standard procedures. We conclude that the Three-point Method is valid for preparing RPE-based exercise prescriptions for Phase II cardiac rehabilitation patients.

Responses of 3-dimensional arch wires to vertical v-bends: comparisons with existing 2-dimensional data in the lateral view

The mechanics of V-bends in orthodontic arch wires have been described almost exclusively in terms of bending forces in two-dimensional (2-D) single plane terms. When a rectangular arch wire enters a third dimension, a more complex wire deformation pattern develops from both torsion and bending during the activation of the V-bends. The necessity for a rectangular three-dimensional (3-D) arch wire to undergo torsion during activation results in a greater resistance to deformation at those points in the wire where the torsion is greatest. This is especially apparent with 2 x 2 long span arch wires. This study used finite element analysis to model the force systems produced by activation of V-bends in 3-D arch wires. In both 2-D and 3-D data, greater moments are present as any V-bend is moved toward either adjacent bracket. In 3-D systems, however, a V-bend at the molar produces significantly less moment and associated equilibrium forces than the same V-bend located the same distance from the incisor. Moreover, the reversal of the direction of the moments at either bracket does not occur when the V-bend location is two thirds of the distance toward that tooth as reported with 2-D studies.

Structure and expression of the human slow twitch skeletal muscle troponin I gene

The contractile protein troponin I is encoded by a multigene family whose members are expressed differentially in various classes of muscle fibers. In vertebrates, the "slow" isoform of troponin I is expressed during early heart and skeletal muscle development but is restricted to slow twitch skeletal muscle in the adult. This diverse expression pattern offers an opportunity to study the regulation of a single gene within different developmental contexts. To initiate such studies, we have cloned the gene encoding the human slow twitch skeletal muscle isoform of troponin I and have identified 5'-flanking sequences required for its expression in skeletal muscle cells. The slow troponin I gene spans 12.5 kilobases and is divided into nine exons. In contrast to many muscle-specific genes, the troponin I promoter does not contain consensus CCAAT or TATA elements. Moreover, the sequence from -9 to +11 resembles an "initiator element" previously shown to direct transcription of some tissue-specific genes lacking TATA boxes (Smale, S. T., and Baltimore, D. (1989) Cell 57, 103-113; Brand, N. J., Petkovich, M., and Chambon, P. (1990) Nucleic Acids Res. 18, 6799-6806; Weis, L., and Reinberg, D. (1992) FASEB J. 6, 3300-3309). A transcriptional fusion construct, comprising 4.2 kilobases of troponin I 5'-flanking DNA linked to the bacterial chloramphenicol acetyl-transferase gene, exhibited cell type-specific and developmentally regulated expression. A muscle-specific enhancer regulated slow troponin I promoter activity.