Auflistung nach Autor:in "Babrak, Lmar"

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Adaptive immune receptor repertoire (AIRR) community guide to TR and IG gene annotation
(Springer, 28.05.2022) Babrak, Lmar; Marquez, Susanna; Busse, Christian; Lees, William; Miho, Enkelejda; Ohlin, Mats; Rosenfeld, Aaron; Stervbo, Ulrik; Watson, Corey; Schramm, Chaim; Langerak, Anton W.
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
04A - Beitrag Sammelband
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
(Oxford University Press, 24.12.2019) Smakaj, Erand; Babrak, Lmar; Tosoni, Deniz David; Galli, Christa; Miho, Enkelejda
01A - Beitrag in wissenschaftlicher Zeitschrift
Kidins220 regulates the development of B cells bearing the λ light chain
(eLife Sciences Publications, 25.01.2024) Schaffer, Anna-Maria; Fiala, Gina Jasmin; Hils, Miriam; Natali, Eriberto; Babrak, Lmar; Herr, Laurenz Alexander; Romero-Mulero, Mari Carmen; Cabezas-Wallscheid, Nina; Rizzi, Marta; Miho, Enkelejda; Schamel, Wolfgang W.A.; Minguet, Susana
The ratio between κ and λ light chain (LC)-expressing B cells varies considerably between species. We recently identified Kinase D-interacting substrate of 220 kDa (Kidins220) as an interaction partner of the BCR. In vivo ablation of Kidins220 in B cells resulted in a marked reduction of λLC-expressing B cells. Kidins220 knockout B cells fail to open and recombine the genes of the Igl locus, even in genetic scenarios where the Igk genes cannot be rearranged or where the κLC confers autoreactivity. Igk gene recombination and expression in Kidins220-deficient B cells is normal. Kidins220 regulates the development of λLC B cells by enhancing the survival of developing B cells and thereby extending the time-window in which the Igl locus opens and the genes are rearranged and transcribed. Further, our data suggest that Kidins220 guarantees optimal pre-BCR and BCR signaling to induce Igl locus opening and gene recombination during B cell development and receptor editing.
01A - Beitrag in wissenschaftlicher Zeitschrift
Machine learning detects anti-DENV signatures in antibody repertoire sequences
(Frontiers, 11.10.2021) Horst, Alexander; Smakaj, Erand; Natali, Eriberto; Tosoni, Deniz David; Babrak, Lmar; Meier, Patrick; Miho, Enkelejda
Dengue infection is a global threat. As of today, there is no universal dengue fever treatment or vaccines unreservedly recommended by the World Health Organization. The investigation of the specific immune response to dengue virus would support antibody discovery as therapeutics for passive immunization and vaccine design. High-throughput sequencing enables the identification of the multitude of antibodies elicited in response to dengue infection at the sequence level. Artificial intelligence can mine the complex data generated and has the potential to uncover patterns in entire antibody repertoires and detect signatures distinctive of single virus-binding antibodies. However, these machine learning have not been harnessed to determine the immune response to dengue virus. In order to enable the application of machine learning, we have benchmarked existing methods for encoding biological and chemical knowledge as inputs and have investigated novel encoding techniques. We have applied different machine learning methods such as neural networks, random forests, and support vector machines and have investigated the parameter space to determine best performing algorithms for the detection and prediction of antibody patterns at the repertoire and antibody sequence levels in dengue-infected individuals. Our results show that immune response signatures to dengue are detectable both at the antibody repertoire and at the antibody sequence levels. By combining machine learning with phylogenies and network analysis, we generated novel sequences that present dengue-binding specific signatures. These results might aid further antibody discovery and support vaccine design.
01A - Beitrag in wissenschaftlicher Zeitschrift
Prospective artificial intelligence to dissect the dengue immune response and discover therapeutics
(Frontiers, 15.06.2021) Natali, Eriberto; Babrak, Lmar; Miho, Enkelejda
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1–5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
01A - Beitrag in wissenschaftlicher Zeitschrift
Real World Data - Technologies, Research Questions and Applications - Study in Cooperation - School of Business & School of Life Science
(Fachhochschule Nordwestschweiz FHNW, 2019) Grimberg, Frank; Asprion, Petra; Schneider, Bettina; Miho, Enkelejda; Babrak, Lmar; Habbabeh, Ali
In this research report of the University of Applied Sciences and Arts Northwestern Switzerland (FHNW), a classification of ‘Real World Data’ into the research landscape takes place. In addition, an identification of the still open research questions is done based on the fundamental principles and properties. The manifold potential of this relatively new data set is illustrated by a presentation of the already existing but also conceivable future application possibilities. Finally, the contribution of the FHNW, based on its specific competencies, to the further application of the dataset is shown.
05 - Forschungs- oder Arbeitsbericht
RWD-Cockpit. Application for quality assessment of real-world data
(JMIR Publications, 18.10.2022) Degen, Markus; Babrak, Lmar; Smakaj, Erand; Agac, Teyfik; Asprion, Petra; Grimberg, Frank; Van der Werf, Daan; Van Ginkel, Erwin Willem; Tosoni, Deniz David; Clay, Ieuan; Brodbeck, Dominique; Natali, Eriberto; Schkommodau, Erik; Miho, Enkelejda
Digital technologies are transforming the health care system. A large part of information is generated as real-world data (RWD). Data from electronic health records and digital biomarkers have the potential to reveal associations between the benefits and adverse events of medicines, establish new patient-stratification principles, expose unknown disease correlations, and inform on preventive measures. The impact for health care payers and providers, the biopharmaceutical industry, and governments is massive in terms of health outcomes, quality of care, and cost. However, a framework to assess the preliminary quality of RWD is missing, thus hindering the conduct of population-based observational studies to support regulatory decision-making and real-world evidence.
01A - Beitrag in wissenschaftlicher Zeitschrift
RWD-Cockpit: application for quality assessment of real-world data
(JMIR Publications, 2022) Babrak, Lmar; Smakaj, Erand; Agac, Teyfik; Asprion, Petra; Grimberg, Frank; Van der Werf, Daan; van Ginkel, Erwin Willem; Tosoni, Deniz David; Clay, Ieuan; Degen, Markus; Brodbeck, Dominique; Natali, Eriberto Noel; Schkommodau, Erik; Miho, Enkelejda
Background: Digital technologies are transforming the health care system. A large part of information is generated as real-world data (RWD). Data from electronic health records and digital biomarkers have the potential to reveal associations between the benefits and adverse events of medicines, establish new patient-stratification principles, expose unknown disease correlations, and inform on preventive measures. The impact for health care payers and providers, the biopharmaceutical industry, and governments is massive in terms of health outcomes, quality of care, and cost. However, a framework to assess the preliminary quality of RWD is missing, thus hindering the conduct of population-based observational studies to support regulatory decision-making and real-world evidence. Objective: To address the need to qualify RWD, we aimed to build a web application as a tool to translate characterization of some quality parameters of RWD into a metric and propose a standard framework for evaluating the quality of the RWD. Methods: The RWD-Cockpit systematically scores data sets based on proposed quality metrics and customizable variables chosen by the user. Sleep RWD generated de novo and publicly available data sets were used to validate the usability and applicability of the web application. The RWD quality score is based on the evaluation of 7 variables: manageability specifies access and publication status; complexity defines univariate, multivariate, and longitudinal data; sample size indicates the size of the sample or samples; privacy and liability stipulates privacy rules; accessibility specifies how the data set can be accessed and to what granularity; periodicity specifies how often the data set is updated; and standardization specifies whether the data set adheres to any specific technical or metadata standard. These variables are associated with several descriptors that define specific characteristics of the data set. Results: To address the need to qualify RWD, we built the RWD-Cockpit web application, which proposes a framework and applies a common standard for a preliminary evaluation of RWD quality across data sets—molecular, phenotypical, and social—and proposes a standard that can be further personalized by the community retaining an internal standard. Applied to 2 different case studies—de novo–generated sleep data and publicly available data sets—the RWD-Cockpit could identify and provide researchers with variables that might increase quality Conclusions: The results from the application of the framework of RWD metrics implemented in the RWD-Cockpit application suggests that multiple data sets can be preliminarily evaluated in terms of quality using the proposed metrics. The output scores—quality identifiers—provide a first quality assessment for the use of RWD. Although extensive challenges remain to be addressed to set RWD quality standards, our proposal can serve as an initial blueprint for community efforts in the characterization of RWD quality for regulated settings.
01A - Beitrag in wissenschaftlicher Zeitschrift
Single Cell Gene Expression analysis in a 3D microtissue liver model reveals cell type-specific responses to pro-fibrotic TGF-β1 stimulation
(MDPI, 22.04.2021) Messner, Catherine; Babrak, Lmar; Titolo, Gaia; Caj, Michaela; Miho, Enkelejda; Suter-Dick, Laura
3D cell culture systems are widely used to study disease mechanisms and therapeutic interventions. Multicellular liver microtissues (MTs) comprising HepaRG, hTERT-HSC and THP-1 maintain multicellular interactions and physiological properties required to mimic liver fibrosis. However, the inherent complexity of multicellular 3D-systems often hinders the discrimination of cell type specific responses. Here, we aimed at applying single cell sequencing (scRNA-seq) to discern the molecular responses of cells involved in the development of fibrosis elicited by TGF-β1. To obtain single cell suspensions from the MTs, an enzymatic dissociation method was optimized. Isolated cells showed good viability, could be re-plated and cultured in 2D, and expressed specific markers determined by scRNA-seq, qRT-PCR, ELISA and immunostaining. The three cell populations were successfully clustered using supervised and unsupervised methods based on scRNA-seq data. TGF-β1 led to a fibrotic phenotype in the MTs, detected as decreased albumin and increased αSMA expression. Cell-type specific responses to the treatment were identified for each of the three cell types. They included HepaRG damage characterized by a decrease in cellular metabolism, prototypical inflammatory responses in THP-1s and extracellular matrix remodeling in hTERT-HSCs. Furthermore, we identified novel cell-specific putative fibrosis markers in hTERT-HSC (COL15A1), and THP-1 (ALOX5AP and LAPTM5).
01A - Beitrag in wissenschaftlicher Zeitschrift
The real-world data challenges radar: a review on the challenges and risks regarding the use of real-world data
(Karger, 2021) Grimberg, Frank; Asprion, Petra; Schneider, Bettina; Miho, Enkelejda; Babrak, Lmar; Habbabeh, Ali
Background: The life science industry has a strong interest in real-world data (RWD), a term that is currently being used in many ways and with varying definitions depending on the source. In this review article, we provide a summary overview of the challenges and risks regarding the use of RWD and its translation into real-world evidence and provide a classification and visualization of RWD challenges by means of the RWD Challenges Radar. Summary: Based on a systematic literature search, we identified 3 types of challenges – organizational, technological, and people-based – that must be addressed when deriving evidence from RWD to be used in drug approval and other applications. It further demonstrates that numerous different aspects, for example, related to the application field and the associated industry, must be considered. A key finding in our review is that the regulatory landscape must be carefully assessed before utilizing RWD. Key Messages: Establishing awareness and insight into the challenges and risks regarding the use of RWD will be key to taking full advantage of the RWD potential. As a result of this review, an “RWD Challenges Radar” will support the establishment of awareness by providing a comprehensive overview of the relevant aspects to be considered when employing RWD.
01A - Beitrag in wissenschaftlicher Zeitschrift
Traditional and Digital Biomarkers: Two Worlds Apart?
(Karger, 2019) Babrak, Lmar; Miho, Enkelejda
The identification and application of biomarkers in the clinical and medical fields has an enor - mous impact on society. The increase of digital devices and the rise in popularity of health- related mobile apps has produced a new trove of biomarkers in large, diverse, and complex data. However, the unclear definition of digital biomarkers, population groups, and their in - tersection with traditional biomarkers hinders their discovery and validation. We have identi - fied current issues in the field of digital biomarkers and put forth suggestions to address them during the DayOne Workshop with participants from academia and industry. We have found similarities and differences between traditional and digital biomarkers in order to synchronize semantics, define unique features, review current regulatory procedures, and describe novel applications that enable precision medicine.
01A - Beitrag in wissenschaftlicher Zeitschrift