Biology subjects

Johnson, T.

Publications and source records attributed to Johnson, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Impaired loading following denervation elicits dynamic, differential growth trajectories of musculoskeletal tissues

Physical forces dictate the function and maintenance of adult musculoskeletal tissues. Yet, the impact of biophysical cues on the growth and maturation of these tissues, especially dense connective tissues, remains unclear. Here, we investigated the effects of neonatal mechanical loading on early postnatal growth of the musculoskeletal tissues of the lower limb, with particular focus on the Achilles tendon. We performed sciatic nerve resection (SNR) on one-day-old mice to denervate the hamstrings and distal hindlimb muscles. Sciatic Nerve Resection resulted in severe and sustained alterations in gait, accompanied by an altered transcriptional landscape in distal musculoskeletal tissues, with marked reductions in bone and tendon growth and smaller, fibrotic hindlimb musculature. Sciatic nerve resection impaired cumulative growth in the Achilles tendon, shifting cell proliferation and matrix-driven growth trajectories and altering mechanotransduction gene programs toward inflammation and matrix catabolism with age. This work highlights the essential role of mechanical loading in driving mechanosignaling and postnatal growth trajectories in musculoskeletal tissues of the developing limb, with implications for overall musculoskeletal health in adulthood.

bioengineering↗

bioRxiv2026

Moving object generates topographic responses in the majority of entorhinal neurons

Vision is crucial in generating a complex array of responses in rodents during spatial exploration and in humans during memory tasks. These tasks involve other variables too, e.g. multisensory cues in rodents and complex memories in humans. Further, there are major differences between the medial and lateral entorhinal cortical (MEC and LEC) functional cell types. To understand the contribution of purely visual information to entorhinal responses, we presented a simple, moving vertical bar of light to head-fixed mice, without any task or reward. Surprisingly, 66% (2391/3601) of the MEC broad spiking neurons were significantly modulated by the bar position on the screen. Visual tuning in MEC had a pronounced dorsoventral topography --the tuning strength dropped from 79% in the dorsal most quartile to 40% in the ventral most quartile. Unlike major differences in spatial and other codes between MEC and LEC during free foraging experiments, LEC cells showed very similar visual tuning (392/606, 65%), including the dorso-ventral gradient in LEC5. Additionally, the majority of putative interneurons, from MEC as well as LEC, showed similar, widespread visual tuning, unlike spatial tasks. Neurons also encoded the object motion direction (naso-temporal vs. temporo-nasal visual motion) with changes in mean rate, tuning strength and/or tuning location. Such directional nature of visual tuning indicates significant history-dependence or sequence encoding. Consistently, replacing the continuous motion by randomly flashing bar of light abolished bar-tuning in two-thirds of continuous bar-tuned cells and substantially altered tuning in the rest. These results reveal the contribution of purely visual inputs in generating anatomically organized responses in the majority of entorhinal neurons. The prevalence and similarity of visual tuning across all layers of MEC as well as LEC exceeds that of other known functional cell types (like grid cells in MEC or egocentric object tuning/time-cells in LEC) during spatial navigation tasks and could be foundational in understanding entorhinal complexity.

neuroscience↗

bioRxiv2026

A knockout screening platform for interferon-stimulated genes in respiratory cells identifies LY6E as a dominant antiviral effector against coronaviruses

Human coronaviruses (HCoVs) cause pathogenic outcomes ranging from mild illness to severe respiratory disease. Determining how respiratory cells coordinate an early antiviral response is necessary to understand successful control of HCoV replication. The Type I Interferon (IFN) response is a major component of innate viral immunity. IFN signaling leads to the upregulation of hundreds of interferon-stimulated genes (ISGs) that can have antiviral activity, though the individual ISGs that are responsible for restricting mildly pathogenic HCoVs in the respiratory epithelium are not clear. Here, we developed a targeted CRISPR-Cas9 knockout sgRNA library (termed the respISG library), focusing on ISGs that are upregulated across a panel of respiratory cells, to screen for innate host factors that restrict the mildly pathogenic human coronavirus, HCoV-OC43. We executed cell death-based screens in immortalized human small airway epithelial cells and identified lymphocyte antigen 6E (LY6E) as a top hit. We confirmed LY6E activity in validation studies and found it regulates entry of various SARS-CoV-2 Spike-pseudotyped lentiviruses. In addition to demonstrating a key role for LY6E in blocking a variety of HCoVs in small airway epithelial cells, this study establishes a loss-of-function CRISPR-Cas9 screening platform for identification of HCoV antiviral ISGs in respiratory cells.

microbiology↗

bioRxiv2026

Aryl Hydrocarbon Receptor (Ahr) Pathway Drives TBBPA Induced Cartilage Development Defects.

Tetrabromobisphenol A (TBBPA), is one the most widely produced brominated flame retardant, detected in human matrices including cord plasma, raising concern over its impact on embryonic development. Our previous work demonstrated that TBBPA disrupts craniofacial cartilage development in zebrafish; however, inhibition of bone morphogenetic protein (BMP) signaling did not rescue these defects, suggesting the involvement of alternative molecular mechanisms. Transcriptomic profiling revealed significant upregulation of aryl hydrocarbon receptor (Ahr) signaling genes, including cyp1a and cyp1c, as well as reactive oxygen species (ROS) responsive genes, such as nfe and gstp. Consistent with these findings, KEGG pathway enrichment analysis identified significant enrichment of pathways involved in xenobiotic metabolism, cytochrome P450-mediated metabolism, and molecular docking predicted stronger binding of TBBPA to Ahr2 than the Ahr2 agonist TCDD. Then we investigated the role of Ahr signaling and ROS in TBBPA-induced craniofacial cartilage defects using microinjection of Ahr2 translation-blocking morpholino and the antioxidant N-acetylcysteine (NAC), respectively. Immunohistochemistry confirmed concentration-dependent induction of Cyp1a and ROS at environmentally relevant concentrations (0.05;0.005 uM). Ahr2 knockdown using a translation-blocking morpholino rescued TBBPA-induced alterations in Cyp1a expression, ROS levels, DNA damage, the expression of chondrogenesis-related markers (Sox10 and Sox2), and epithelial to mesenchymal transition (EMT) markers (E-cadherin, N-cadherin, and Snail2). Furthermore, Ahr2 knockdown rescued several TBBPA-induced alterations in craniofacial cartilage parameters. Co-exposure of TBBPA with the antioxidant NAC rescued the ROS and DNA damage and rescued only ceratohyal cartilage length, whereas other cartilage parameters remained disrupted. These findings establish a causal role for the Ahr-Cyp1a axis in TBBPA-induced craniofacial cartilage developmental toxicity and identify ROS as an important downstream contributor, indicating that both ROS-dependent and ROS-independent Ahr mechanisms underlined the observed TBBPA induced craniofacial defects.

pharmacology and toxicology↗

bioRxiv2026

Psilocybin collapses visual change detection and drives cortical dynamics toward a state of surprise

Psilocybin profoundly alters visual perception, yet the neuronal mechanisms underlying these effects remain unclear. Here we combined large-scale Neuropixels recordings with cell-type specific optogenetics in head-fixed mice performing a visual change-detection task. Psilocybin severely impaired task performance without overt motor deficits. In cortex, the drug modestly suppressed activity of layer 5 neurons while preserving representations of image identity. By contrast, psilocybin imposed a 4-Hz oscillation on visually evoked activity that preferentially affected neurons encoding image change rather than image identity. Under psilocybin, expected image repetitions aberrantly recruited change-encoding ensembles and shifted cortical population dynamics towards trajectories normally evoked by genuine stimulus changes. These effects were strongest in somatostatin-expressing (SST) interneurons in visual cortex. The strength of this modulation depended on image structure and was greatest for images with clear, continuous contours, which preferentially recruited change-encoding ensembles. These findings demonstrate that psilocybin drives internally generated cortical surprise signals, providing a circuit mechanism for altered perception in the acute psychedelic state.

neuroscience↗

bioRxiv2026

Deletion of TUBB4A mitigates the oligodendrocyte and neuronal deficits in human iPSCs derived from individuals affected by H-ABC

TUBB4A-related leukodystrophy (TUBB4A-LD) is a rare neurologic disorder with a broad spectrum of phenotypes, including severe early infantile encephalopathy, late infantile Hypomyelination with Atrophy of the Basal ganglia and Cerebellum (H-ABC), and milder late infantile forms. H-ABC is closely associated with a recurrent pathogenic variant, p.Asp249Asn, in the gene encoding tubulin beta class IVA (TUBB4A), a microtubule component. H-ABC presents with progressive dystonia, mobility loss, aphasia, and swallowing dysfunction in childhood. H-ABC results in cell-autonomous deficits in oligodendrocytes (OLs), cerebellar granule neurons, and medium spiny neurons (MSNs). Antisense oligonucleotides targeting Tubb4a can alleviate symptoms in H-ABC mouse models. However, the efficacy and safety of TUBB4A knockout in human cells remain poorly understood. We studied patient-derived TUBB4AD249N, TUBB4A KO, and control individual pluripotent stem cells (iPSCs). TUBB4AD249N iPSC-derived OLs failed to mature, showing less complexity and myelination, reduced microtubule acetylation and detyrosination. TUBB4AD249N iPSC-derived MSNs also showed impaired maturation and neurite extension. TUBB4A KO in mutant iPSCs reduced cellular deficits and was well tolerated. These findings support that suppression of TUBB4A could be a safe, effective therapy for TUBB4A-LD.

neuroscience↗

bioRxiv2026

Conserved and specialized features of thalamocortical wiring revealed by single-cell projection mapping in mouse and marmoset

Across mammals, brain regions can duplicate, expand, and diversify, requiring long-range connectivity to accommodate species-specific specializations while preserving globally ordered wiring. This challenge is especially pronounced in primate thalamocortical circuits, where select cortical fields and their thalamic partners have expanded disproportionately. Although gene expression in the thalamus follows broad and conserved gradients, how thalamocortical projections are organized at single-neuron resolution, and how this organization is reshaped by expansion, remain unknown. Here, we investigate thalamocortical projection organization by in situ sequencing and BARseq projection mapping in marmosets and mice. We profiled the gene expression of 1.5 million marmoset neurons and jointly measured gene expression and cortical projections in 708 marmoset and 1,518 mouse neurons that spanned multiple thalamic nuclei. In both species, projections of individual neurons targeted diverse areas that together spanned a large fraction of the cortex. Comparing projections at the single-neuron level and local neighborhood level revealed that marmoset thalamocortical projections were more spatially segregated, producing a point-to-point architecture. Strikingly, this local specialization coexisted with a conserved gradient that predominated over discrete anatomical borders: In the higher-order sensory thalamus of both species, gene expression and projections varied continuously across nucleus borders, and borders had only a small effect on projections. Furthermore, in both marmoset and mouse, gene expression gradients were associated with the anteroposterior locations of cortical targets. These results reconcile discrete nucleus and gradient-based models of thalamic organization and suggest that primate circuit specialization is superimposed on a conserved molecular-projection gradient.

neuroscience↗

bioRxiv2026

Tyrosine hydroxylase–mediated neuroimmune crosstalk regulates antitumor immunity in glioblastoma during oncolytic herpes virotherapy

Neuroimmune crosstalk is increasingly recognized as a key regulator of tumor progression and therapeutic response, yet its role in central nervous system (CNS) tumors remains poorly understood. Here, we investigate tyrosine hydroxylase (TH)-mediated neuronal signaling in glioblastoma (GBM) and its impact on antitumor immunity and response to oncolytic virotherapy (OV). We show that TH cells are widely distributed within the GBM microenvironment, including neurons, astrocytes, and immune cells, and are enriched at the tumor margin. In addition, TH cells are present in the tumor-draining lymph nodes (TDLNs) of GBM, where they localize near lymphatic vessels and are associated with lymphangiogenesis. Notably, a subset of CD3TH T cells is detected within lymphatic structures of TDLNs, suggesting immune-intrinsic catecholamine signaling. Single-cell RNA sequencing reveals that noradrenergic signaling, particularly via {beta}2-adrenergic receptors (ADRB2), predominates in tumor-infiltrating myeloid cells and is dynamically regulated by therapy. Intratumoral administration of oncolytic herpes simplex virus (oHSV) upregulates ADRB2 expression in macrophages, whereas systemic chemo-immunotherapy induces distinct receptor modulation patterns in tumors and TDLNs. Functionally, pharmacologic {beta}-adrenergic blockade significantly enhances the efficacy of oHSV therapy in orthotopic GBM and subcutaneous melanoma models, resulting in reduced tumor growth, increased tumor cell death, and enhanced CD8 T cell infiltration. Similarly, direct inhibition of TH enzymatic activity suppresses tumor progression and further potentiates OV. Mechanistically, TH inhibition not only promotes tumor-infiltrated cytotoxic immune cells CD8, NK and {gamma}{delta} T cells, but also suppresses the activity of immunosuppressive myeloid cells, including transcriptional (Fos), and metabolism (Arg) modification in M2 macrophages and other immune cells. Collectively, these findings identify TH-mediated neuroimmune signaling as a critical regulator of tumor immunity in GBM and demonstrate that targeting catecholaminergic pathways or downstream neuroimmune crosstalk pathways can enhance the efficacy of OV. This study provides a rationale for integrating neural modulation into immunotherapeutic strategies for CNS malignancies.

Cancer Biology↗

bioRxiv2026

A Cross-Species Enhancer-AAV Toolkit for Cell Type-Specific Targeting Across the Basal Ganglia

The mammalian basal ganglia (BG) orchestrate motor, cognitive, and affective functions, yet cell type-specific genetic access remains limited, especially beyond rodents. Key structures implicated in movement and psychiatric disorders, including pallidum, subthalamic nucleus, and dopaminergic midbrain, lack scalable tools for cross-species targeting. Here, we present a comprehensive enhancer-AAV library enabling selective labeling and manipulation of major BG neuronal populations: striatal projection neuron subtypes, pallidal and subthalamic neurons, and midbrain dopaminergic and GABAergic populations. Using an evolutionarily informed discovery pipeline, we identified enhancers targeting canonical, non-canonical, and disease-relevant cell types, with validation demonstrating robust cross-species conservation of specificity between mouse and macaque. Computational modeling revealed sequence features predictive of in vivo performance, including motif grammar, chromatin accessibility, and evolutionary conservation, and identified distinct regulatory architectures across glial, projection, and interneuron lineages. This work establishes a comprehensive cross-species viral toolkit for the BG, unlocking previously inaccessible cell types for circuit dissection.

neuroscience↗

bioRxiv2025

Epiphyseal primary cilia axoneme are preferentially orientated, independent of centriolar position and irrespective of ambulatory limb loading.

How cells and their organelles are positioned in three-dimensional, organ level, anatomical context, is rarely investigated. Here we focus on cells, centrioles and primary cilia in the growing limb. Through the ciliums mechanobiological role in skeletal development, we explored the mechanobiology of morphogenesis. A transgenic mouse model (Centrin 2-GFP.ARL13B-mCherry), combined with an image analysis pipeline, can map cellular size, positions and orientations, centriole position and ciliary axoneme orientation, all with respect to the anatomy of the epiphysis or growth plate. The line was crossed with an ift88fl/flCreERT2 line to enable ciliary ift88 deletion. We used limb immobilization, to test for a role of mechanical forces associated with ambulatory loading, in the organization of these elements and transcriptomics to understand the role of forces in regulating growth plate morphogenic programs. The pipeline can accurately quantify expected patterns of cell orientation and size through zones of the growth plate. Analysis across thousands of cells, through regions and zones of multiple murine growth plates, reveals cilia prevalence is increased in the periphery, highest in the resting zone in the outer limb, harboring stem cells. Cilia length is greatest in the hypertrophic cells about to die or transdifferentiate, as part of the formation of bone from cartilage by endochondral ossification. The inducible and cartilage-specific, deletion of ciliary gene ift88, alters cell orientation and sizes and reduces ciliation in the areas where endochondral ossification is most disrupted, the periphery and expanded hypertrophic zones, linking changes in structure to function. Most strikingly, centriole position, including that of the basal body, from which the ciliary axoneme is extended, is not preferentially organised. In contrast, cilia axoneme orientation is preferentially organised. Axonemes are directed posterior or anterior, 45 degrees to the axis of the limb, irrespective of their position, which is defined by basal body position. Immobilization of the limb for 2 weeks markedly alters the transcriptomic profile of the growth plate, with changes to size and orientation of cells and alterations in matrix and cytoskeletal profiles. Within altered genes, primary cilia genes themselves are regulated, including those indicative of altered cilia signaling such as hedgehog signaling. However, despite the role of cilia in mechanobiology of the growing limb, and ciliary signature within changes to loading of the limb, cilia orientation is unaltered by the removal of ambulatory associated forces. Patterns of ciliation in control and IFT88cKO mice help reconcile the previously observed anisotropic effects of cilia perturbation, focusing study on stem cell-resting chondrocytes and hypertrophy, when considering the mechanobiological role of cilia in limb development. Endochondral ossification is apparently highly sensitive to ambulatory loading at transcriptomic level, including effects on ciliary genes and signaling. A highly organized orientation of these putative antennae is governed by centriole position-independent mechanisms and is independent to changes to ambulatory loading, indicating a cell intrinsic mechanism. The resilient position of axonemes in the limb, points to mechano-regulatory mechanisms for how cilia integrate biophysical signals. We propose that predominant ventral or dorsal orientation at 45 degrees to horizonal plane but never parallel to cranial-chordal or medial-lateral axis, ensures multiple signal integration and avoids single signal blindness.

cell biology↗

bioRxiv2025

Biosynthesis, Structure, and Antibiotic Properties of Gelatinamin A, a Triculamin-like Lasso Peptide

Lasso peptides are structurally unique natural products endowed with high thermal and proteolytic stability, making them attractive as scaffolds for drug discovery. Recently, a new class of lasso peptides containing a second macrocycle, formed between a lysine sidechain and the C-terminus, was discovered, resulting in an even more compact architecture. Here, we report the first NMR structure of the class V lasso peptide, gelatinamin A. Using heterologous expression of the gelatinamin biosynthetic gene cluster (BGC) in Bacillus subtilis, we delineated the biosynthetic pathway through targeted gene deletions. We expressed and characterized the predicted transpeptidase, GelP, that catalyzes the formation of an isopeptide bond between Lys2 and the C-terminus and mediates the reversible conversion of gelatinamin B to gelatinamin A. In addition, we characterize GelT, an N-acetyltransferase that inactivates lasso peptide antimicrobial activity by acetylating a key lysine residue. Furthermore, we demonstrate that gelatinamin is highly potent against several important pathogens and that the activity is strongly bicarbonate-dependent. Finally, we propose a complete biosynthetic pathway for gelatinamin. The structural insight of gelatinamin A and the functional characterization of GelP provide the foundation for future discovery of class V lasso peptides and for engineering transpeptidases to modify other lasso peptide scaffolds.

biochemistry↗

bioRxiv2025

Surface-by-temperature interactions shape the relationship between viral free-living survival and reproduction

Environmental factors play a critical role in viral persistence, yet the combined effects of temperature and surface chemistry on viral fitness are not fully understood. We examined bacteriophages T4 and{varphi} X174 across copper, stainless steel, and polypropylene plastic surfaces at 4{degrees}C and 37{degrees}C to assess how these variables influence survival and reproduction. Both phages exhibited marked differences in survival across surfaces: copper at 37{degrees}C caused rapid inactivation, and cooler conditions promoted persistence. Reproductive capacity varied independently of survival, indicating that viral stability and replication are partially decoupled traits shaped by environmental context. Linear modeling and correlation analyses confirmed significant, non-additive interactions between surface type and temperature. These findings suggest that abiotic factors can act synergistically to determine viral fitness outside the host. More broadly, they refine our understanding of the mechanisms that govern the environmental ecology of viruses and the canonical relationship between survival and transmission.

ecology↗

bioRxiv2025

Map of spiking activity underlying change detection in the mouse visual system

Visual behavior requires coordinated activity across hierarchically organized brain circuits. Understanding this complexity demands datasets that are both large-scale (sampling many areas) and dense (recording many neurons in each area). Here we present a database of spiking activity across the mouse visual system--including thalamus, cortex, and midbrain--while mice perform an image change detection task. Using Neuropixels probes, we record from >75,000 high-quality units in 54 mice, mapping area-, cortical layer-, and cell type-specific coding of sensory and motor information. Modulation by task-engagement increased across the thalamocortical hierarchy but was strongest in the midbrain. Novel images modulated cortical (but not thalamic) responses through delayed recurrent activity. Population decoding and optogenetics identified a critical decision window for change detection and revealed that mice use an adaptation-based rather than image-comparison strategy. This comprehensive resource provides a valuable substrate for understanding sensorimotor computations in neural networks.

neuroscience↗

bioRxiv2025

Variable information across SNPs in GWAS data can cause false rejections of colocalisation which can be resolved by proportional colocalisation tests

Fine-mapping is now a standard post-GWAS analysis, but it has been shown to be potentially inaccurate for large meta-analysis GWAS. We show how this can be caused by variable amounts of statistical information between variants, e.g. due to variable sample sizes, which arise widely in meta-analyses, or due to variable imputation accuracy or call rate. This effect becomes more pronounced as sample sizes become larger, such that small differences in information available at different variants can lead to large errors in credible set predictions. Here, we show this inaccuracy propagates to the colocalisation method coloc, yielding confident but incorrect inference. We propose an adaptation of the proportional colocalisation test, which avoids any fine-mapping inference as an alternative to fine-mapping based colocalisation. This method was originally superseded by coloc because the null hypothesis is colocalization, and because it can have low power in genetic regions with many variants. Our adaptation resolves this second issue, and simulations demonstrate that our approach accurately resolves false coloc inferences. However, the first issue remains, such that we suggest proportional colocalisation is used as an accompaniment to fine-mapping-based coloc. Our findings also emphasize the need for new methodologies in fine-mapping, particularly as GWAS sample sizes grow, to ensure accurate fine-mapping inference.

bioinformatics↗

bioRxiv2025

The RNA splicing factor Prp45 directs histone H2B ubiquitination through its C-terminal domain

While chromatins influence on co-transcriptional splicing is well established, the reciprocal model, that spliceosomal components actively shape chromatin, has lacked mechanistic support. Here we show that the C-terminal intrinsically disordered region (IDR) of the yeast splicing factor Prp45 (mammalian SKIP) promotes histone H2B ubiquitination, a hallmark of active transcription. The Prp45 IDR binds and stabilizes Lge1, the scaffold of the H2B ubiquitin ligase complex, enabling its function with the ubiquitin ligase Bre1. When this interaction is disrupted, Lge1 is degraded by the SUMO-targeted ubiquitin ligase Slx5, Bre1 is mislocalized, H2B ubiquitination is lost, and cells become enlarged. Deleting SLX5 restores Lge1 stability, H2B ubiquitination, and normal cell morphology. Although its sequence diverges across eukaryotes, the IDRs structural properties are conserved, and the disordered regions of Arabidopsis and human SKIP functionally replace the yeast domain. These findings reveal a conserved IDR-mediated mechanism by which a splicing factor directs chromatin modification.

molecular biology↗

bioRxiv2025

Development of a Pharmacokinetic (PK) Mouse Serum GLP ELISA for an Anti-CD19-AntiCD3 Diabody

GP101 is a single chain diabody composed of Fv regions of antibodies directed to CD3 and CD19. It is designed to mimic commercial blinatumomab (Blincyto(R)) that simultaneously co-engages patient T lymphocytes and CD19 positive B cell leukemias and lymphomas, facilitating their targeted destruction. This study details the purification of GP101 protein and development of a highly sensitive ELISA for its detection, achieving a sensitivity of 15pg/mL in 25% mouse serum. This ELISA has been validated according to GLP standards.

immunology↗

bioRxiv2025

A novel deep optimal transport framework reveals prostate cancer risk heterogeneity, Alzheimers disease risk heterogeneity, and myeloma cells associated with a short-term sham bortezomib response and progressive disease

Leveraging single-cell gene expression profiles can significantly enhance our understanding of diseases by associating single cells with traits such as disease subtypes, prognosis, and drug response. Although previous efforts have linked single cell clusters and groups with these attributes, they have primarily focused on changes in cell proportions while overlooking transcriptional changes at the single cell level. To further unravel cell heterogeneity with clusters and reveal the nuanced behaviors of cellular subtypes, it is essential to assess the disease associations of individual cells. Previous methods often fail to capture complex patterns that are only discernible through summarizing non-linear relationships across multiple genes. The Diagnostic Evidence GAuge of Single-cells/Spatial-transcriptomics (DEGAS) framework advances these efforts by aligning single cells and/or spatial transcriptomics regions with patients through a unified latent space using non-linear transformations learned from deep neural networks (DNNs). DEGAS achieves superior performance in analyzing single cell and spatial transcriptomics datasets, including Alzheimers disease (AD), multiple myeloma (MM), and prostate cancer (PDAC). Here we present DEGAS version 2, which has been updated with optimial transport based transfer learning and improved time-to-event loss functions, more advanced model architecture, and improved model baseline evaluations. DEGASv2 outperformed other methods in both single cell and spatial transcriptomic baseline comparisons. On the multiple myeloma discovery dataset, DEGASv2 enabled us to discover cell types that exhibited distinct drug response patterns over various time frames and were validated with time series single cell multiomic data that we generated, demonstrating a dangerous subtype of cell and novel therapeutic target.

bioinformatics↗

bioRxiv2025

Utilizing Genomics to Identify Novel Immunotherapeutic Targets in Multiple Myeloma High-Risk Subgroups

Immunotherapy is now standard of care for multiple myeloma, where the most common targets are B cell maturation antigen, CD38, and G protein-coupled receptor class C group 5 member D but strategies to identify additional targets are needed. We have utilized two large datasets of genomic data and integrated them with existing databases to identify expressed cell surface targets in myeloma patients. Importantly, we also identify targets specific to genomic defined subgroups of patients including primary translocations and high-risk subgroups. Examples of subgroup targets include ROBO3 in t(4;14), CD109 in t(14;16), CD20 in t(11;14), GPRC5D in 1q+, and ADAM28 in biallelic TP53 samples. Expression was validated by flow cytometry and CRISPR-Cas9 knock out models. Sub-clonal differences in expression were noted, as was alternative splicing of existing immunotherapy targets such as FCRL5. These results highlight the use of genomic stratification to identify novel therapeutic targets. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=157 HEIGHT=200 SRC="FIGDIR/small/635544v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@6965e6org.highwire.dtl.DTLVardef@1a0e567org.highwire.dtl.DTLVardef@34fc30org.highwire.dtl.DTLVardef@98c3d4_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗