Biology subjects

Langer, S.

Publications and source records attributed to Langer, S..

9 recordsLinked to original sources

bioRxiv2026

Plasma proteomics identifies an IL-6–associated SAA axis linked to muscle wasting in patients with cancer cachexia

Nearly half of patients with advanced lung cancer develop cachexia, a debilitating syndrome that worsens prognosis. We conducted longitudinal clinical and plasma proteomic profiling of 67 patients with non-small cell lung cancer, with and without cachexia, during first-line treatment. Patients with cachexia at diagnosis exhibited elevated risk of hospitalization and treatment-delaying toxicity. At diagnosis, 128 plasma proteins were upregulated and 67 downregulated in cachectic relative to non-cachectic patients. Longitudinal assessments of body composition, physical performance, metabolism, clinical outcomes, and nutritional risk revealed distinct fat and muscle wasting phenotype trajectories. 71 proteins were associated with fat loss, 92 with muscle loss, and 177 with concurrent muscle and weight loss. We identified and functionally validated 8 plasma proteins linked to muscle loss and adverse clinical outcomes. In a separate cohort of 147 patients with advanced pancreatic cancer receiving the interleukin-6 (IL-6) inhibitor tocilizumab, pharmacological suppression of serum amyloid A (SAA) levels following IL-6 inhibition suggests a systemic IL-6-SAA axis. These results collectively highlight SAA1 and SAA2 as IL-6-driven, cachexia-associated factors that reduce human myotube width. These findings uncover new potential therapeutic targets for cachexia.

Systems Biology↗

bioRxiv2026

Programmable Lipid Nanoparticle Targeting via Corona Engineering

Lipid nanoparticles (LNPs) are a versatile platform for in vivo delivery of biomolecules, yet systemically administered LNPs predominantly accumulate in the liver, limiting extrahepatic applications. This tropism arises from LNP adsorption of serum proteins, particularly apolipoprotein E (ApoE), which binds to LDL receptors (LDLR) on hepatocytes. Here, we overcome this tropism with two compatible strategies. First, we engineer dead ApoE mutants (dApoE) with five receptor-binding domain substitutions that selectively disrupt the ApoE-LDLR interaction but retain lipid binding. In cultured cells, pre-coating with these dApoE markedly inhibited LDLR-mediated uptake. Second, we pretreat cells with hyperactive PCSK9 (haPCSK9) to internalize surface LDLR, similarly reducing the LDLR-mediate uptake of LNPs. In vivo, both strategies substantially reduced liver LNP transduction without inducing redistribution to other major organs. To retarget LNP to new cell types we combined antibody conjugation with dApoE or haPCSK9, effectively engineering tropism to T cells, brain and lung tissues in vivo with substantially reduced hepatic background. In pilot studies, this strategy enabled specific delivery of reporter mRNAs to additional tissues, including megakaryocytes, hematopoietic progenitor cells, and cardiac tissue, and in aged T cells, to deliver miRNA cargos that produced a sustained reduction in DNA damage markers following a single systemic dose. dApoE coated CD5-targeted LNPs generated CAR+ T cells that retained cytotoxicity against CD19+ targets, while simultaneously reducing hepatocyte transduction by 90%. These findings establish a modular framework that integrates dApoE and haPCSK9-mediated detargeting with antibody-based retargeting, allowing for improvements in LNP specificity and broadening the therapeutic scope of LNPs.

bioengineering↗

bioRxiv2025

Tuning the open-close equilibrium of Cereblon with small molecules influences protein degradation

Most PROTACs and molecular glue degraders currently approved or in clinical trials recruit Cereblon (CRBN) as the ubiquitin E3 ligase. Upon binding ligands and molecular glues, CRBN undergoes a significant structural rearrangement from an open to closed state, defined by the positioning of the thalidomide-binding domain (TBD) with respect to the Lon domain. However, the exact molecular basis for this ligand-induced conformational change and its implication to neo-substrate degradation remain elusive. During our campaign to discover novel CRBN binders, we found hits exhibiting distinct biophysical behaviour from classical thalidomide-based ligands. By combining orthogonal biophysical methods of differential scanning fluorimetry, isothermal titration calorimetry, and small-angle X-ray scattering, supported by X-ray crystallography and cryo-EM structures of ligand-bound complexes, we classify CRBN binders between those that can induce CRBN closure, and those that cannot. Mutational studies identify key residues in the CRBN ligand binding pocket and N-terminal belt that are essential for the Lon and TBD domains to come together in the closed state. Finally, we show that the probability to yield active degrader molecules is greatly influenced by whether binders can or cannot induce CRBN closure. Together, our study reveals new molecular insights into the structural basis for how CRBN open-closed equilibrium is directly modulated by compound binding and impact target degradability by CRBN, with important implications to the design of PROTACs and molecular glue degraders.

biochemistry↗

bioRxiv2025

T-PGI: an engineered STITCHR system for scarless, programmable genome integration

Scarless, programmable insertion of defined DNA remains a central goal for therapeutic genome editing. We introduce T-PGI (Transposon-mediated programmable genomic integration), an engineered implementation of STITCHR that preserves target-primed reverse transcription (TPRT) while substantially improving efficiency, specificity, and modularity. T-PGI uses R2Tocc, a low-background ortholog that we further engineered through defined deletions, rational point mutations, and modular domain insertions to enhance performance. The system employs paired nCas9 nicks flanking homology arms and bicistronic co-expression with dual NLSs, together with optimized RNA donor designs. Using combinatorial guide-template screening, T-PGI achieves robust integration across diverse cargos, including precise cassette insertion following multi-kilobase deletions. Short- and long-read sequencing confirm high-fidelity insertion with minimal local indels or structural variants. Collectively, these advances establish T-PGI as a practical and adaptable platform for accurate, scarless genome integration and provide concise design principles spanning enzyme architecture, donor configuration, and guide pairing for next-generation therapeutic editing.

bioengineering↗

bioRxiv2024

Brain Structural Correlates of an Impending Initial Major Depressive Episode

BackgroundNeuroimaging research has yet to elucidate, whether reported gray matter volume (GMV) alterations in major depressive disorder (MDD) exist already before the onset of the first episode. Recruitment of presently healthy individuals with a known future transition to MDD (converters) is extremely challenging but crucial to gain insights into neurobiological vulnerability. Hence, we compared converters to patients with MDD and sustained healthy controls (HC) to distinguish pre-existing neurobiological markers from those emerging later in the course of depression. MethodsCombining two clinical cohorts (n=1709), voxel-wise GMV of n=45 converters, n=748 patients with MDD, and n=916 HC were analyzed in regions-of-interest approaches. By contrasting the subgroups and considering both remission state and reported recurrence at a 2-year clinical follow-up, we stepwise disentangled effects of 1) vulnerability, 2) the acute depressive state, and 3) an initial vs. a recurrent episode. ResultsAnalyses revealed higher amygdala GMV in converters relative to HC (pTFCE-FWE=.037, d=0.447) and patients (pTFCE-FWE=.005, d=0.508), remaining significant when compared to remitted patients with imminent recurrence. Lower GMV in the dorsolateral prefrontal cortex (pTFCE-FWE<.001, d=0.188) and insula (pTFCE-FWE=.010, d=0.186) emerged in patients relative to HC but not to converters, driven by patients with acute MDD. ConclusionBy examining one of the largest available converter samples in psychiatric neuroimaging, this study allowed a first determination of neural markers for an impending initial depressive episode. Our findings suggest a temporary vulnerability, which in combination with other common risk factors might facilitate prediction and in turn improve prevention of depression.

neuroscience↗

bioRxiv2022

SEMPAI: a Self-Enhancing Multi-Photon Artificial Intelligence for prior-informed assessment of muscle function and pathology

Deep learning (DL) shows notable success in biomedical studies. However, most DL algorithms work as a black box, exclude biomedical experts, and need extensive data. We introduce the Self-Enhancing Multi-Photon Artificial Intelligence (SEMPAI), that integrates hypothesis-driven priors in a data-driven DL approach for research on multiphoton microscopy (MPM) of muscle fibers. SEMPAI utilizes meta-learning to optimize prior integration, data representation, and neural network architecture simultaneously. This allows hypothesis testing and provides interpretable feedback about the origin of biological information in MPM images. SEMPAI performs joint learning of several tasks to enable prediction for small datasets. The method is applied on an extensive multi-study dataset resulting in the largest joint analysis of pathologies and function for single muscle fibers. SEMPAI outperforms state-of-the-art biomarkers in six of seven predictive tasks, including those with scarce data. SEMPAIs DL models with integrated priors are superior to those without priors and to prior-only machine learning approaches.

bioinformatics↗

bioRxiv2022

Integrative metabolomics reveal the organisation of alkaloid biosynthesis in Daphniphyllum macropodum

Daphniphyllum alkaloids are structurally diverse nitrogen-containing compounds with polycyclic, stereochemically rich carbon skeletons. Understanding how plants biosynthesise these compounds may lead to greater access to allow exploration of bioactivities; however, very little is known about their biosynthetic origins. Here, we integrated metabolomics approaches to map alkaloid distribution across Daphniphyllum macropodum plants and tissues. We generated a novel untargeted metabolomics workflow to highlight trends in alkaloid distribution across tissues, using a holistic approach that does not rely on ambiguous peak annotations. Both liquid-chromatography-mass spectrometry and mass-spectrometry imaging analyses independently revealed that alkaloids have a pattern of spatial distribution based on their skeletal subtypes. The distinct alkaloid subtype localisation suggests the biosynthetic pathway is controlled spatially with intermediates transported from the phloem to the epidermis where they undergo additional derivatization. This study sets the stage for the future work on Daphniphyllum alkaloid biosynthesis and highlights how integrating different metabolomics strategies can reveal valuable insights on these compounds distribution within the plant.

plant biology↗

bioRxiv2021

Sodium accumulation in breast cancer predicts malignancy and treatment response

Breast cancer is the leading cause of cancer-related death in women worldwide. Development of novel noninvasive diagnostic and predictive pathophysiological biomarkers would represent a significant clinical improvement. Here, we explored the utility of non-invasive 23Na MRI to profile tumour physiology using preclinical mouse models of breast cancer. We establish that tissue Na+ concentration ([Na+]) is elevated vs non-tumour regions across multiple different tumour models. Ex vivo SBFI fluorescence imaging corroborated that this elevation in tumour [Na+] is due to increased intracellular [Na+]. Effective treatment with cytotoxic chemotherapy reduced tumour tissue [Na+], but was not detected by 1H diffusion-weighted imaging (DWI). Moreover, combining 23Na MRI and DWI measurements enabled superior classification accuracy of tumour vs non-tumour regions compared to either parameter alone. Quantification of breast tumour tissue [Na+] using 23Na MRI thus represents a novel, accurate, non-invasive diagnostic and predictive imaging biomarker.

cancer biology↗

bioRxiv2021

A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor

The HIV-1 accessory protein Vpu modulates membrane protein trafficking and degradation to provide evasion of immune surveillance. Targets of Vpu include CD4, HLAs, and BST-2. Several cellular pathways co-opted by Vpu have been identified, but the picture of Vpus itinerary and activities within membrane systems remains incomplete. Here, we used fusion proteins of Vpu and the enzyme ascorbate peroxidase (APEX2) to compare the ultrastructural locations and the proximal proteomes of wild type Vpu and Vpu-mutants. The proximity-omes of the proteins correlated with their ultrastructural locations and placed wild type Vpu near both retromer and ESCRT-0 complexes. Hierarchical clustering of protein abundances across the mutants was essential to interpreting the data and identified Vpu degradation-targets including CD4, HLA-C, and SEC12 as well as Vpu-cofactors including HGS, STAM, clathrin, and PTPN23, an ALIX-like protein. The Vpu-directed degradation of BST-2 required PTPN23 but not the retromer subunits. These data suggest that Vpu directs targets from sorting endosomes to degradation at multi-vesicular bodies via ESCRT-0 and PTPN23. Author SummaryVpu triggers the degradation or mis-localization of proteins important to the hosts immune response. Vpu acts as an adaptor, linking cellular protein targets to the ubiquitination and membrane trafficking machinery. Vpu has been localized to various cellular membrane systems. By fusing wild type Vpu and Vpu-mutants to the enzyme ascorbate peroxidase, we defined the cellular proteome in proximity to Vpu and correlated this with the proteins location. We found that wild type Vpu is proximal to ESCRT proteins, retromer complexes, and sorting and late endosomal proteins. Functionally, we found that the Vpu-mediated degradation of the innate defense protein BST-2 required PTPN23, an ALIX-like protein, consistent with our observation of Vpus presence at the limiting membranes of multi-vesicular bodies.

microbiology↗