Biology subjects

Johansson, K.

Publications and source records attributed to Johansson, K..

7 recordsLinked to original sources

bioRxiv2026

Allergen-responsive T helper type 2 cells revealed by high-dimensional profiling in allergen challenged human airways

Asthma is a chronic inflammatory disease affecting over 300 million people worldwide. This disease has multiple underlying etiologies, and a major endotype of asthma is characterized by cellular and molecular signatures of type 2 (allergic) inflammation. In this study we conducted bronchoscopies with airway segmental allergen challenge in allergic asthmatics to dissect airway responses to allergen. Using mass cytometry and single-cell RNA sequencing, we characterized with high resolution the airway immune landscape before and after allergen challenge and the heterogeneity present between subjects. This heterogeneity generally falls along a type 1/ type 2 axis. In type 2 high individuals, we identified allergen-reactive Th2 cells by using TCR sequences to barcode clonal T cell populations in single-cell genomic and activation-induced marker expression assays. These potentially pathogenic Th2 cell clones were present systemically and expanded following allergen challenge, connecting local lung inflammation to systemic clonal Th2 cell dynamics. Th2 cell airway ingress was coordinated with myeloid cell expression of T cell chemoattractants including CCL17 and CCL22. This study provides insight into the molecular and cellular components of allergen-induced tissue inflammation in asthma. Deeper resolution of the T cell response to aeroallergens may inform novel diagnostic and therapeutic strategies for asthma and other allergic airway diseases.

immunology↗

bioRxiv2025

Smart Microscopy: Current Implementations and a Roadmap for Interoperability

Smart microscopy is transforming life sciences by automating experimental imaging workflows and enabling real-time adaptation based on feedback from images and other data streams. This shift increases throughput, improves reproducibility, and expands the functional capabilities of microscopes. However, the current landscape is highly fragmented. Academic researchers often develop custom solutions for specific scientific needs, while industry offerings are typically proprietary and tied to specific hardware. This diversity, while fostering innovation, also creates major challenges in interoperability, reproducibility, and standardization, which slows progress and adaption. This article presents a collaborative effort between academic and industry leaders to survey the current state of smart microscopy, highlight representative implementations, and identify common technical and organizational barriers. We propose a framework for greater interoperability based on shared standards, modular software design, and community-driven development. Our goal is to support collaboration across the field and lay the groundwork for a more connected, reusable, and accessible smart microscopy ecosystem. We conclude with a call to action for researchers, hardware developers, and institutions to join in building an open, interoperable foundation that will unlock the full potential of smart microscopy in life science research.

cell biology↗

bioRxiv2025

Proteomic analysis of bronchoalveolar lavage fluid after lung transplantation associates stable allograft function with less lung damage at 12 months

IntroductionFreedom from chronic lung allograft dysfunction (CLAD) is a key objective after lung transplantation, yet predicting its onset remains challenging. This study investigated whether early proteomic changes in bronchoalveolar lavage fluid (BALF) can differentiate between patients maintaining stable graft function at 36 months and those developing CLAD within the first year. Additionally, findings were compared to proteomic data from non-transplanted individuals. MethodsBALF samples were collected at one and twelve months post-transplant from 43 lung transplant recipients together with clinical parameters. Proteomic analysis was performed using mass spectrometry with label-free quantification for global protein profiling and heavy-labelled peptides for absolute quantification of mucins and related proteins. Differentially expressed proteins were identified and analyzed through pathway enrichment to explore biological mechanisms associated with CLAD. ResultsNo significant proteomic differences were detected at one month. By twelve months, 63 proteins were differentially expressed between patients who developed early CLAD and those with stable function. Mucin levels declined in stable patients but remained elevated in both groups compared to healthy controls. Cartilage acidic protein 1 was significantly higher in stable patients at twelve months and correlated with better pulmonary function. Pathway analysis linked several altered proteins in CLAD patients to networks associated with lung injury and remodelling. ConclusionProtein profiles in BALF that resemble those of healthy lungs are associated with sustained graft function, while persistent expression of lung injury markers is associated with early CLAD. This suggests an adaptive process is needed for long-term post-transplant success.

molecular biology↗

bioRxiv2025

Non-Physiological Potassium Concentrations in Commercial Culture Media Trigger Acute Epileptiform Activity in Human iPSC-Derived Neurons

Neuronal in vitro cultures are pivotal for studying brain electrophysiological function and dysfunction. Neuronal activity and communication are regulated by extracellular ion concentrations. Therefore, cell culture medium ion concentrations should ideally mimic those of cerebrospinal fluid (CSF) - considered as the milieu for brain cells in vivo. In this study, we demonstrate that commonly used cell culture media, including Neurobasal (+/- A), Neurobasal Plus, and BrainPhys media, do not accurately replicate human CSF ion concentrations. Using human iPSC-derived neuronal networks on microelectrode arrays, we show that the abnormally high potassium concentrations present in all tested cell culture media induce acute epileptiform activity, similar to that elicited by the convulsive drug 4- aminopyridine. These findings raise a critical question: How can human in vitro neuronal activity be defined as physiological and reliably distinguished from pathophysiological activity, if the routinely used ion concentrations in in vitro experiments are causing aberrant neuronal activity? SummaryThe neuronal activity in neuronal in vitro culture relies on extracellular ion concentrations, which should mimic cerebrospinal fluid (CSF). This study shows that common cell culture media and widely used artificial CSF composition in neuroscience research fail to replicate CSF ion levels, causing non-physiological and rather pathological neuronal activity.

neuroscience↗

bioRxiv2024

Engineering multivalent Fc display for FcγR blockade

Autoimmune diseases, driven by Fc{gamma} receptor (Fc{gamma}R) activation through autoantibody immune complexes (IC), present a complex therapeutic challenge of achieving pharmacological blockade of Fc{gamma}R without triggering receptor activation. The assembly of ICs into polydisperse, higher-order structures is required for Fc{gamma}R activation. However, engineered multimeric, monodisperse Fc assemblies have been reported to prevent Fc{gamma}R activation, suggesting that Fc spatial organization determines Fc{gamma}R activation. In this study, we engineered a functional single-chain Fc domain protein (scFc) for unidirectional, multivalent presentation by virus-like particles (VLPs), used as a display platform. We found that the multivalent display of scFc on the VLPs elicited distinct cellular responses compared with monovalent scFc, highlighting the importance of the structural context of scFc on its function. scFc-VLPs had minimal impact on the nanoscale spatial organization of Fc{gamma}R at the cell membrane and caused limited receptor activation and internalization. In contrast, the monovalent scFc acted as an Fc{gamma}R agonist, inducing receptor clustering, activation, and internalization. Increasing scFc valency in scFc-VLPs was associated with increased binding to monocytes, reaching a plateau at high valencies. Notably, the ability of scFc-VLPs to block IC-mediated phagocytosis in vitro increased with scFc valency. In a murine model of passive immune thrombocytopenia (ITP), a high valency scFc-VLP variant with a desirable immunogenicity profile induced attenuation of thrombocytopenia. Here we show that multivalent presentation of an engineered scFc on a display platform can be tailored to promote suppression of IC-mediated phagocytosis while preventing Fc{gamma}R activation. This work introduces a new paradigm that can contribute to the development of therapies for autoimmune diseases.

bioengineering↗

bioRxiv2023

An essential role for miR-15/16 in Treg suppression and restriction of proliferation

The miR-15/16 family is a highly expressed group of tumor suppressor miRNAs that target a large network of genes in T cells to restrict their cell cycle, memory formation and survival. Upon T cell activation, miR-15/16 are downregulated, allowing rapid expansion of differentiated effector T cells to mediate a sustained immune response. Here, using conditional deletion of miR-15/16 in immunosuppressive regulatory T cells (Tregs) that express FOXP3, we identify new functions of the miR-15/16 family in T cell immunity. miR-15/16 are indispensable to maintain peripheral tolerance by securing efficient suppression by a limited number of Tregs. miR-15/16-deficiency alters Treg expression of critical functional proteins including FOXP3, IL2R/CD25, CTLA4, PD-1 and IL7R/CD127, and results in accumulation of functionally impaired FOXP3loCD25loCD127hi Tregs. Excessive proliferation in the absence of miR-15/16 inhibition of cell cycle programs shifts Treg diversity and produces an effector Treg phenotype characterized by low expression of TCF1, CD25 and CD62L, and high expression of CD44. These Tregs fail to control immune activation of CD4+ effector T cells, leading to spontaneous multi-organ inflammation and increased allergic airway inflammation in a mouse model of asthma. Together, our results demonstrate that miR-15/16 expression in Tregs is essential to maintain immune tolerance. HighlightsO_LITreg-specific miR-15/16 expression is essential to prevent systemic tissue inflammation C_LIO_LImiR-15/16 restrict Treg proliferation and regulate expression of the key functional Treg molecules FOXP3, IL2R, CTLA4, PD-1 and IL7R C_LIO_LImiR-15/16 limit formation of effector Tregs and is necessary for high suppressive capacity C_LI

molecular biology↗

bioRxiv2020

Flow cytometric analysis and purification of airway epithelial cell subsets

The human airway epithelium is essential in homeostasis, and epithelial dysfunction contributes to chronic airway disease. Development of flow cytometric methods to characterize subsets of airway epithelial cells will enable further dissection of airway epithelial biology. Leveraging single cell RNA-sequencing (scRNA-seq) data in combination with known cell type-specific markers, we developed panels of antibodies to characterize and isolate the major airway epithelial subsets (basal, ciliated, and secretory cells) from human bronchial epithelial cell cultures. We also identified molecularly distinct subpopulations of secretory cells and demonstrated cell subset-specific expression of low abundance transcripts and micro-RNAs that are challenging to analyze with current scRNA-seq methods. These new tools will be valuable for analyzing and separating airway epithelial subsets and interrogating airway epithelial biology.

cell biology↗