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Gene-regulatory networks are an abstract way of capturing the regulatory connectivity between transcription factors, microRNAs, and target genes in biological cells. Here, we address the problem of identifying enriched co-regulatory three-node motifs that are found significantly more often in real network than in randomized networks. First, we compare two randomization strategies, that either only conserve the degree distribution of the nodes’ in- and out-links, or that also conserve the degree distributions of different regulatory edge types. Then, we address the issue how convergence of randomization can be measured. We show that after at most 10 × |E| edge swappings, converged motif counts are obtained and the memory of initial edge identities is lost.

Introduction: Individuals with opioid use disorder are at elevated suicide risk, but systematic screening in this population is rarely done. This study assessed the effects of targeted clinical decision support prompts on structured suicide risk assessment completion., Methods: The study used a cluster-randomized controlled pragmatic pilot design. Adult primary care patients (aged 18-75 years) with or at risk for opioid use disorder or opioid overdose and suicide were eligible. Patients sought care from 15 Midwestern primary care clinics between July, 31, 2021 and July, 31, 2022. Data were analyzed between March and June 2023. Clinicians in intervention and control clinics received a printout from rooming staff, prompted by a clinical decision support-generated electronic health record alert, suggesting clinicians talk with patients about opioid risks. Intervention clinician handouts also alerted them to patients estimated to be at increased suicide risk and recommended completion of a Columbia Suicide Severity Rating Scale to further evaluate suicide risk. The handouts for control clinicians did not include suicide risk alerts. The main outcome measured the completion of the Columbia Suicide Severity Rating Scale in the 14 days following a visit., Results: A total of 115 eligible patients (69 intervention, 46 control) made at least 1 visit to a randomized clinic. Patients mean age was 39 years, and 57% were women; 48% of patients had a high risk of opioid use disorder or opioid overdose, 39% had an opioid use disorder diagnosis, 12% had an opioid use disorder in remission diagnosis, and 5% had a recent opioid overdose. Over a mean follow-up of 249 days, 20.3% of intervention patients and 17.4% of control patients had at least 1 Columbia Suicide Severity Rating Scale completed in the next 14 days ( p =0.70). Most (71%-75%) Columbia Suicide Severity Rating Scale scores were 0, indicating no risk., Conclusions: This pilot study did not increase the uptake of structured suicide risk assessments in primary care for patients at elevated risk for opioid use disorder and suicide. More robust interventions are likely needed to promote suicide risk assessment in primary care., (© 2024 The Authors.)

Background: Opioid-related deaths continue to rise in the U.S. A shared decision-making (SDM) system to help primary care clinicians (PCCs) identify and treat patients with opioid use disorder (OUD) could help address this crisis., Methods: In this cluster-randomized trial, primary care clinics in three healthcare systems were randomized to receive or not receive access to an OUD-SDM system. The OUD-SDM system alerts PCCs and patients to elevated risk of OUD and supports OUD screening and treatment. It includes guidance on OUD screening and diagnosis, treatment selection, starting and maintaining patients on buprenorphine for waivered clinicians, and screening for common comorbid conditions. The primary study outcome is, of patients at high risk for OUD, the percentage receiving an OUD diagnosis within 30 days of index visit. Additional outcomes are, of patients at high risk for or with a diagnosis of OUD, (a) the percentage receiving a naloxone prescription, or (b) the percentage receiving a medication for OUD (MOUD) prescription or referral to specialty care within 30 days of an index visit, and (c) total days covered by a MOUD prescription within 90 days of an index visit., Results: The intervention started in April 2021 and continues through December 2023. PCCs and patients in 90 clinics are included; study results are expected in 2024., Conclusion: This protocol paper describes the design of a multi-site trial to help PCCs recognize and treat OUD. If effective, this OUD-SDM intervention could improve screening of at-risk patients and rates of OUD treatment for people with OUD., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Summary: TFmiR2 is a freely available web server for constructing and analyzing integrated transcription factor (TF) and microRNA (miRNA) co-regulatory networks for human and mouse. TFmiR2 generates tissue- and biological process-specific networks for the set of deregulated genes and miRNAs provided by the user. Furthermore, the service can now identify key driver genes and miRNAs in the constructed networks by utilizing the graph theoretical concept of a minimum connected dominating set. These putative key players as well as the newly implemented four-node TF-miRNA motifs yield novel insights that may assist in developing new therapeutic approaches., Availability and Implementation: The TFmiR2 web server is available at http://service.bioinformatik.uni-saarland.de/tfmir2., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Common variants of about 20 genes contributing to AD risk have so far been identified through genome-wide association studies (GWAS). However, there is still a large proportion of heritability that might be explained by rare but functionally important variants. One of the so far identified genes with rare AD causing variants is ADAM10. Using whole-genome sequencing we now identified a single rare nonsynonymous variant (SNV) rs142946965 [p.R215I] in ADAM17 co-segregating with an autosomal-dominant pattern of late-onset AD in one family. Subsequent genotyping and analysis of available whole-exome sequencing data of additional case/control samples from Germany, UK, and USA identified five variant carriers among AD patients only. The mutation inhibits pro-protein cleavage and the formation of the active enzyme, thus leading to loss-of-function of ADAM17 alpha-secretase. Further, we identified a strong negative correlation between ADAM17 and APP gene expression in human brain and present in vitro evidence that ADAM17 negatively controls the expression of APP. As a consequence, p.R215I mutation of ADAM17 leads to elevated Aß formation in vitro. Together our data supports a causative association of the identified ADAM17 variant in the pathogenesis of AD.

Objective: The aim of this study was to identify variants associated with familial late-onset Alzheimer disease (AD) using whole-genome sequencing., Methods: Several families with an autosomal dominant inheritance pattern of AD were analyzed by whole-genome sequencing. Variants were prioritized for rare, likely pathogenic variants in genes already known to be associated with AD and confirmed by Sanger sequencing using standard protocols., Results: We identified 2 rare ABCA7 variants (rs143718918 and rs538591288) with varying penetrance in 2 independent German AD families, respectively. The single nucleotide variant (SNV) rs143718918 causes a missense mutation, and the deletion rs538591288 causes a frameshift mutation of ABCA7 . Both variants have previously been reported in larger cohorts but with incomplete segregation information. ABCA7 is one of more than 20 AD risk loci that have so far been identified by genome-wide association studies, and both common and rare variants of ABCA7 have previously been described in different populations with higher frequencies in AD cases than in controls and varying penetrance. Furthermore, ABCA7 is known to be involved in several AD-relevant pathways., Conclusions: We conclude that both SNVs might contribute to the development of AD in the examined family members. Together with previous findings, our data confirm ABCA7 as one of the most relevant AD risk genes.

Maintenance of cell pluripotency, differentiation, and reprogramming are regulated by complex gene regulatory networks (GRNs) including monoallelically-expressed imprinted genes. Besides transcriptional control, epigenetic modifications and microRNAs contribute to cellular differentiation. As a model system for studying the capacity of cells to preserve their pluripotency state and the onset of differentiation and subsequent specialization, murine hematopoiesis was used and compared to embryonic stem cells (ESCs) as a control. Using published microarray data, the expression profiles of two sets of genes, pluripotent and imprinted, were compared to a third set of known hematopoietic genes. We found that more than half of the pluripotent and imprinted genes are clearly upregulated in ESCs but subsequently repressed during hematopoiesis. The remaining genes were either upregulated in hematopoietic progenitors or in differentiated blood cells. The three gene sets each consist of three similarly behaving gene groups with similar expression profiles in various lineages of the hematopoietic system as well as in ESCs. To explain this co-regulation behavior, we explored the transcriptional and post-transcriptional mechanisms of pluripotent and imprinted genes and their regulator/target miRNAs in six different hematopoietic lineages. Therewith, lineage-specific transcription factor (TF)-miRNA regulatory networks were generated and their topologies and functional impacts during hematopoiesis were analyzed. This led to the identification of TF-miRNA co-regulatory motifs, for which we validated the contribution to the cellular development of the corresponding lineage in terms of statistical significance and relevance to biological evidence. This analysis also identified key miRNAs and TFs/genes that might play important roles in the derived lineage networks. These molecular associations suggest new aspects of the cellular regulation of the onset of cellular differentiation and during hematopoiesis involving, on one hand, pluripotent genes that were previously not discussed in the context of hematopoiesis and, on the other hand, involve genes that are related to genomic imprinting. These are new links between hematopoiesis and cellular differentiation and the important field of epigenetic modifications., Competing Interests: The authors have declared that no competing interests exist.

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Breast cancer is a genetically heterogeneous type of cancer that belongs to the most prevalent types with a high mortality rate. Treatment and prognosis of breast cancer would profit largely from a correct classification and identification of genetic key drivers and major determinants driving the tumorigenesis process. In the light of the availability of tumor genomic and epigenomic data from different sources and experiments, new integrative approaches are needed to boost the probability of identifying such genetic key drivers. We present here an integrative network-based approach that is able to associate regulatory network interactions with the development of breast carcinoma by integrating information from gene expression, DNA methylation, miRNA expression, and somatic mutation datasets., Results: Our results showed strong association between regulatory elements from different data sources in terms of the mutual regulatory influence and genomic proximity. By analyzing different types of regulatory interactions, TF-gene, miRNA-mRNA, and proximity analysis of somatic variants, we identified 106 genes, 68 miRNAs, and 9 mutations that are candidate drivers of oncogenic processes in breast cancer. Moreover, we unraveled regulatory interactions among these key drivers and the other elements in the breast cancer network. Intriguingly, about one third of the identified driver genes are targeted by known anti-cancer drugs and the majority of the identified key miRNAs are implicated in cancerogenesis of multiple organs. Also, the identified driver mutations likely cause damaging effects on protein functions. The constructed gene network and the identified key drivers were compared to well-established network-based methods., Conclusion: The integrated molecular analysis enabled by the presented network-based approach substantially expands our knowledge base of prospective genomic drivers of genes, miRNAs, and mutations. For a good part of the identified key drivers there exists solid evidence for involvement in the development of breast carcinomas. Our approach also unraveled the complex regulatory interactions comprising the identified key drivers. These genomic drivers could be further investigated in the wet lab as potential candidates for new drug targets. This integrative approach can be applied in a similar fashion to other cancer types, complex diseases, or for studying cellular differentiation processes.