Biology subjects

Shah, K.

Publications and source records attributed to Shah, K..

At least 19 recordsLinked to original sources

bioRxiv2026

DLL3 expression predicts response and long-term outcome in small cell lung cancer patients treated with tarlatamab

Background: Small cell lung cancer (SCLC) is an aggressive, high-grade neuroendocrine carcinoma (hgNEC) with poor prognosis. Tarlatamab, a DLL3-targeting T cell engager was approved in 2024 for relapsed SCLC, with almost doubled overall survival benefit compared to chemotherapy. However, over half of patients do not respond to tarlatamab and others develop resistance within months. With multiple DLL3-targeting therapies in clinical trials, there are currently no validated predictive biomarkers to identify patients most likely to benefit from tarlatamab. In this study, we evaluate baseline DLL3 IHC level in patients as a predictive biomarker to tarlatamab clinical outcome. Methods: We assembled a cohort of 138 patients within IRB-approved MD Anderson GEMINI database (PA13-0589) with DLL3 expression by CLIA-validated immunohistochemistry (IHC), and those treated with tarlatamab from 7/1/2024 to 3/30/2026. Only those with DLL3 IHC results and treated with tarlatamab were included in this predictive biomarker study. All DLL3 levels were reported as percentage cells with cytoplasmic or surface DLL3 expression, including 24 with additional intensity score and H-score calculation. demographic, clinical, and outcome data were collected. Systemic and intracranial response data were assessed by RECIST and mRANO BM criteria respectively. Longitudinal liquid biopsies were taken from a subset of patients for circulating tumor DNA (ctDNA) and (Cytometry by Time-of-Flight) CyTOF analyses. Results: In the predictive biomarker cohort of 54 patients with SCLC treated with tarlatamab, Median DLL3% level in tarlatamab treated cohort was 75%. Median follow-up time was 9.9 months, median time on tarlatamab treatment (ToT) was 5.8 months. At the data cut-off, 61% (33 out of 54) patients were alive. Kaplan-Meier curve stratified by DLL3 % of <=75% vs. >75 showed significant longer ToT and a trend toward longer median OS (mOS). In DLL3>75% compared to DLL3 <=75%: mToT was 10.1 months vs. 2.9 months (p=0.036), mOS: not reached vs. 9.5 months (p= 0.066). Among 41 patients who completed one cycle of tarlatamab treatment and were eligible for systemic (extra-cranial) response per RECIST criteria; we observed partial response (PR) in 51% (21) patients, stable disease (SD) in 22% (9) patients; and progressive disease (PD) in 27% (11) patients. The median DLL3 % in those with PR vs. PD were 80% vs. 40% (p=0.006); median DLL3% comparing PR and SD were 80% vs. 60% (p=0.051). Among 35 patients evaluable for intracranial response, best objective response prior to any brain radiation were 5 (14%) CR,11(31%) PR, 8 (23%) SD and 11 (31%) PD. 9 received brain radiation (8 SRS, 1 WBRT) during tarlatamab to achieve better intracranial control while systemic control is maintained. DLL3% does not appear to be correlated with intracranial response. Longitudinal ctDNA and CyTOF analyses showed persistent ctDNA positivity, as well as increasing NEUROD1 subtype cells in circulating tumor cells in post-tarlatamab progression samples. We additionally profiled DLL3 expression by IHC in 138 patients with SCLC and found heterogenous DLL3 expression, with Median DLL3% of 70% across different biopsy sites. Conclusions: Our data suggests DLL3 expression in patients with SCLC is heterogeneous and not ubiquitous, with median DLL3 IHC of 70%. DLL3 IHC predicts objective response and long-term outcome with tarlatamab. In addition, dynamic monitoring of ctDNA level and CTCs by CyTOF are suggestive of development of tarlatamab resistance, however further studies with larger cohort of paired longitudinal samples are needed to validate the novel blood-based biomarkers. To our knowledge, this study is the first to validate DLL3 IHC as a predictive biomarker for tarlatamab in SCLC, which leads the way for optimizing treatment selection and combinatorial therapies for the subset of patients less likely to respond to tarlatamab.

cancer biology↗

bioRxiv2026

BK Channels Orchestrate Cardiac Homeostasis Through Mitochondrial Uncoupling Proteins

BK channels, coded by the Kcnma1 gene, integrate voltage and intracellular Ca2+ signals and are recognized for their roles in smooth muscle and neuronal excitability. However, their contribution to baseline cardiac physiology remains poorly defined. Here we uncover a fundamental function for BK channels in maintaining normal cardiac performance, independent of pathological stress. Using non-invasive echocardiography, transcriptional profiling, and mechanistic analyses, we demonstrate that Kcnma1 deletion disrupts ventricular function, and remodels metabolic and stress-response pathways. Transcriptomic profiling revealed selective downregulation of mitochondrial uncoupling proteins (UCPs) and suppression of the PGC-1/FOXO3a axis, without broad loss of oxidative phosphorylation components. Enhancing UCP expression restored cardiac performance, indicating that mitochondrial uncoupling and redox control constitute key downstream effectors of BK signaling. Together, these results identify a physiological role for BK channels in maintaining myocardial function and define a mitochondrial BK-UCP axis, critical for cardiac homeostasis.

cell biology↗

bioRxiv2026

Compact adenine base editors to enable therapeutic rescue of Duchenne muscular dystrophy

Adenine base editors (ABEs) have emerged as a powerful gene-editing technology enabling precise and programmable adenine-to-guanine substitutions across the genome. However, their translation into in vivo therapeutics is limited by delivery challenges, as their size exceeds the packaging capacity of adeno-associated virus (AAV). Here, we report the discovery, structural characterization, and engineering of two compact, highly active ABEs built on novel deaminases and Cas9d nucleases, enabling all-in-one, single-vector AAV delivery. Applying these compact ABEs to Duchenne muscular dystrophy (DMD), we demonstrate efficient disruption of conserved splice-acceptor sites at dystrophin exons 45 and 51 in human skeletal muscle cells, enabling therapeutically relevant exon skipping. Together, these ABEs help expand the therapeutic reach of base editing towards diverse tissue types and disease targets.

bioengineering↗

bioRxiv2026

Targeting activated IL-23 signaling in Scleroderma by tildrakizumab

The pathogenesis of systemic sclerosis (SSc) involves immune system dysregulation and progressive multi-organ fibrosis. Aberrant interleukin-23 (IL-23) function is linked to many inflammatory conditions. Tildrakizumab, a humanized monoclonal antibody that binds to the p19 subunit of IL-23 to block its interaction with the IL-23 receptor, is FDA-approved for treating psoriasis. IL-23 levels are increased in SSc patients with lung involvement, but the pathogenic role of IL-23 in SSc fibrosis remains unclear. We examined IL-23 expression in SSc skin biopsies and assessed the effects of IL-23 inhibition in an in vivo fibrosis model. We found increased IL-23 expression in SSc compared to healthy skin biopsies. Pharmacological blockade of IL-23 signaling using tildrakizumab reversed experimental skin and lung fibrosis. Our findings support a pathogenic role of IL-23 in SSc and suggest that tildrakizumab could be a novel antifibrotic treatment strategy for SSc and related fibrotic disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/701821v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@777c8aorg.highwire.dtl.DTLVardef@9163f5org.highwire.dtl.DTLVardef@1399a54org.highwire.dtl.DTLVardef@c30ec2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

In the human brain, the dorsal anterior cingulate cortex (dACC) plays key roles in various components of cognitive control, and is particularly relevant for reward processing and conflict monitoring. The dACC regulates expression of fear and pain, and its dysfunction is implicated in a number of neuropsychiatric disorders. Compared to more recently specialized neocortical areas, such as the dorsolateral prefrontal cortex (dlPFC), the dACC is evolutionarily older. The regions agranular structure, and other evolutionary specializations, such as the presence of von Economo neurons (VENs), contribute to its specialized roles in cognitive and emotional processing. Here, we generated paired spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the dACC in ten adult neurotypical donors to define molecular profiles for dACC cell types and spatial domains. Using non-negative matrix factorization (NMF), we integrated these data by identifying gene expression patterns within the snRNA-seq data, which were projected onto the SRT data to infer the spatial localization. Combining these data with publicly available resources, we revealed insights about molecular profiles, spatial topography, enrichment of disease risk, and putative connectivity of spatially-localized dACC cell types, including VENs. Utilizing published dlPFC snRNA-seq and SRT data collected in the same neurotypical brain donors used here, we deployed cross-region comparison analyses between dACC and dlPFC to understand spatio-molecular specializations and laminar organization across human brain evolution. To make this comprehensive molecular resource accessible to the scientific community, we made both raw and processed data freely available, including through interactive web applications.

neuroscience↗

bioRxiv2024

Targeting Endoplasmic Reticulum Stress and Nitroso-Redox Imbalance in Neuroendocrine Prostate Cancer: The Therapeutic Role of Nitric Oxide

Neuroendocrine prostate cancer (NEPC) is an aggressive and therapy-resistant subtype of prostate cancer. Current standard-of-care treatment for NEPC involves chemotherapies, which largely exert their cytotoxic effects by forming DNA crosslinks, disrupting DNA replication and transcription in NEPC cells. However, these therapies are often met with resistance, partly due to increased endoplasmic reticulum (ER) stress, which facilitates cancer cell survival and adaptive mechanisms. Despite its critical role, the molecular landscape underlying ER stress in NEPC remains inadequately understood. Here we showed that ER stress is intimately linked to the metabolic reprogramming of NEPC cells, a process that supports their transition from adenocarcinoma to a neuroendocrine phenotype. We identified MYCN as a key driver of this process, promoting unfolded protein response (UPR) elements that enhance ER stress by increasing the efflux of calcium ions through the ER which later is absorbed by the mitochondria and assist in increasing the overall glycolytic stress, thereby adding to the extended survival and metastatic potential of an NEPC cell. Our previous studies highlighted the importance of S-nitrosylation as a protein modification that is dysregulated in high-grade PCa. In this context, structural analysis of MYCN revealed potential S-nitrosylation sites at the positions Cys4, 186, and 464, respectively. However, similar to the castration-resistant stage, this modification is hindered in NEPC due to impaired nitric oxide (NO) production from dysregulated endothelial nitric oxide synthases (eNOS). We found that exogenous NO supplementation S-nitrosylates MYCN, reducing its binding to protein molecules which are essential to assist with increasing ER stress in NEPC cells. Exogenous supplementation of NO reduced the overall tumor burden in the mice harboring orthotopic NEPC cells and reduced the metastasis to the brain and liver. In conclusion, the findings from this study enrich our understanding of the mechanisms driving the ER stress responses in NEPC phenotype and how NO supplementation could pave the way as potential therapeutics for this challenging cancer. HIGHLIGHTSO_LIEndoplasmic reticulum (ER) stress is intricately linked to metabolic reprogramming, which supports the transition from prostate adenocarcinoma to neuroendocrine prostate cancer (NEPC). C_LIO_LIMYCN increases the ER stress in NEPC cells and is correlated with increased nitroso-redox imbalance. C_LIO_LIStructural analysis reveals potential S-nitrosylation sites on MYCN. Exogenous nitric oxide (NO) supplementation induces S-nitrosylation, disrupting MYCNs role in enhancing ER stress. C_LIO_LINO supplementation reduced tumor burden and metastasis in NEPC-bearing mice, highlighting its potential as a therapeutic avenue for NEPC. C_LIO_LIExogenous NO supplementation inhibits ER stress by targeting unfolded protein response (UPR) elements and decreasing calcium ion efflux, inhibiting the glycolytic stress in NEPC. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/624202v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1fb292forg.highwire.dtl.DTLVardef@4d00f7org.highwire.dtl.DTLVardef@17a7f43org.highwire.dtl.DTLVardef@1393286_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Branched actin networks in innate immune cells mediate host microbiota homeostasis.

Assembly of branched actin networks, driven by the Arp2/3 complex are essential for the function and integrity of the immune system. Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality. However, the mechanistic basis for these phenotypes remains obscure. Here we demonstrate that loss of Arpc5 in the murine hematopoietic system, but not the corresponding Arpc5l isoform causes early-onset intestinal inflammation after weaning. This condition is initiated by microbiota breaching the ileal mucosa, leading to local and systemic inflammation. Macrophage and neutrophils infiltrate into the ileum, but in the absence of Arpc5 fail to restrict microbial invasion. Loss of Arpc5 compromises the ability of macrophages to phagocytose and kill intra-cellular bacteria. Our results underscore the indispensable role of Arpc5, but not Arpc5l containing Arp2/3 complexes in mononuclear phagocytes function and host-microbiota homeostasis. One-Sentence SummaryArpc5 containing Arp2/3 complexes are essential for host-microbiota homeostasis

immunology↗

bioRxiv2024

STAG3 promotes exit from pluripotency through post-transcriptional mRNA regulation in the cytoplasm.

STAG proteins are key regulators of the cohesin complex and are often linked to alterations in cell identity and disease. Among the mammalian STAG paralogs, STAG3 has been less extensively studied beyond its known roles in meiosis. In this work, we demonstrate that STAG3 is expressed in mouse embryonic stem cells (mESCs) and primordial germ cell-like cells (PGCLCs), where it is required for cell fate decisions. Distinct from the other STAG proteins, STAG3 mediates its effects in the cytoplasm, facilitating the post-transcriptional regulation of gene expression. Furthermore, STAG3 localises to the centrosome independently of cohesin and interacts with proteins involved in mRNA localisation and stability. The knockdown of STAG3 in mESCs using siRNAs results in the destabilisation of the centrosome and the key P-body RNA-induced silencing complex (RISC) component TNRC6C, leading to the derepression of P-body localised mRNAs, such as DPPA3. Our results propose a model in which STAG3 collaborates with RNA-binding proteins (RBPs) and specific target mRNAs to control post-transcriptional gene expression and facilitate the transition from pluripotency in mESCs. Given that STAG3 is upregulated in various cancers, our results provide a novel perspective on how STAG proteins might contribute to cell identity and disease.

cell biology↗

bioRxiv2024

2.5D Actuating Substrates Enable Decoupling the Mechanical and Biochemical Effects of Muscle Exercise on Motor Neurons

Emerging in vivo evidence suggests that exercise impacts peripheral nerves, but the difficulty of isolating and studying the muscle-specific impact on motor neurons in vivo, as well as the inability to decouple the biochemical and mechanical impacts of exercise in this setting, motivate investigating this phenomenon in vitro. In this study, we show that tuning the mechanical properties of fibrin hydrogels can generate stable 2.5D motor neuron and contractile skeletal muscle cultures that enable long-term efficient secretome harvesting from exercised tissues. Motor neurons stimulated with muscle-secreted cytokines significantly upregulate neurite outgrowth and migration, with an effect size dependent on exercise intensity. Actuating magnetic microparticles embedded within 2.5D substrates enabled us to dynamically stretch motor neurons and non-invasively mimic the mechanical effects of exercise, revealing that dynamic stretch has an equally significant impact on axonogenesis. RNA sequencing revealed different transcriptomic signatures between groups, with biochemical stimulation having a significantly greater impact on cell signaling related to axon growth and development, neuron projection guidance, and neuron-muscle synapse maturation. Our study thus leverages 2.5D actuating substrates to robustly validate a hypothesized role for muscle exercise in regulating motor neuron growth and maturation through both mechanical and biochemical signaling.

bioengineering↗

bioRxiv2024

Identifying the genetic and epigenetic basis for asymmetric bZIP expression in temperature-stressed bread wheat

Asymmetric expression in the bread wheat (Triticum aestivum) genome refers to the differential expression of genes from A, B, and D parental genomes. Bread wheat is a hexaploid crop with six copies of each chromosome. This complexity can result in unequal expression of genes from each parental genome, leading to asymmetry in gene expression. In other polyploid crops like cotton, transcription factors (TF) exhibit genome-biased expression; however, there are no comparable studies for bread wheat. One of the most prominent TFs families in plants is the basic Leucine Zippers (bZIP) which are eukaryote-specific proteins and regulate various biological processes, including stress-related responses. bZIP proteins are dimeric and several heptads long. They exhibit typical coiled-coil structures with strategically placed amino acids in each heptad, responsible for their stability and specificity. Here, we aim to decipher the structural basis of the asymmetric expression of the bZIP TFs in wheat under low and high-temperature conditions. Furthermore, 19 highly expressed stress-related TabZIP TFs were analysed for their asymmetric expression profiles as plants were exposed to temperature-stress conditions. Two benchmarks were used to analyse the asymmetric gene expression of bZIPs, i.e., a) the promoters occupancy by the epigenetic marker histones, namely, H3K4me3, H3k9ac (active) and H3K27me3 (repressive), b) density and diversity of cis-regulatory elements in the promoters. Notably, the genetic basis of the differences in protein sequences of bZIP triads was explored, which may impart structural stability to a specific homeolog enabling the plant to endure the stress conditions better.

plant biology↗

bioRxiv2023

Exosome derived multi-gene biomarker panel identifies the risk of liver metastasis in lung cancer patients

BackgroundThe lack of non-invasive methods for detection of early metastasis is a crucial reason for the poor prognosis of lung cancer (LC) liver metastasis (LM) patients. In this study, the goal was to identify circulating biomarkers based on a biomarker model for the early diagnosis and monitoring of patients with LCLM. MethodsAn 8-gene panel identified in our previous study was validated in CTC, cfRNA and exosomes isolated from primary lung cancer with & without metastasis. Further multivariate analysis including PCA & ROC was performed to determine the sensitivity and specificity of the biomarker panel. Model validation cohort (n = 79) was used to verify the stability of the constructed predictive model. Further, clinic-pathological factors, survival analysis and immune infiltration correlations were also performed. ResultsIn comparison to our previous tissue data, exosomes demonstrated a good discriminative value with an AUC of 0.7247, specificity (72.48 %) and sensitivity (96.87%) for the 8-gene panel. Further individual gene patterns led us to a 5-gene panel that showed an AUC of 0.9488 (p = <0.001) and 0.9924 (p = <0.001) respectively for tissue and exosomes. Additionally, on validating the model in a larger cohort a risk score was obtained (RS >0.2) for prediction of liver metastasis with an accuracy of 95%. Survival analysis and immune filtration markers suggested that four exosomal markers were independently associated with poor overall survival. ConclusionWe report a novel blood-based exosomal biomarker panel for early diagnosis, monitoring of therapeutic response, and prognostic evaluation of patients with LCLM.

cancer biology↗

bioRxiv2023

A paradigm for regulation at the effector interface with RNA-binding proteins

RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of dual-purpose peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.

molecular biology↗

bioRxiv2023

Dopamine functionalized, red carbon quantum dots for in vivo bioimaging, cancer therapeutics, and neuronal differentiation

One of the crucial requirements of quantum dots for biological applications is their surface modifications for very specific and enhanced biological recognition and uptake. Toward this, we present the green synthesis of bright, red-emitting carbon quantum dots derived from mango leaf extract (mQDs). These mQDs are conjugated electrostatically with dopamine to form mQDs-dopamine (mQDs: DOPA) bioconjugates. Bright red fluorescence of mQDs was used for bioimaging and uptake in multiple cell lines, tissues, and in vivo models like zebrafish. mQDs exhibited the highest uptake in brain tissue as compared to others. mQD:DOPA conjugate induced cellular toxicity only in cancer cells while showing increased uptake in epithelial cells and zebrafish. Additionally, the mQDs: DOPA promoted neuronal differentiation of SH-SY5Y cells to complete neurons. Both mQDs and mQDs: DOPA exhibited potential for higher collective cell migrations implicating their future potential as next-generation tools for advanced biological and biomedical applications. TOCmQDs were electrostatically conjugated with dopamine (DOPA) to form the mQDs: DOPA bioconjugate. mQDs are used to image cells, tissues, and zebrafish embryos. mQDs: DOPA kills cancer cells, differentiates neuronal cells, and increases the uptake of mQDs in zebrafish embryos. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/545347v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@f521a4org.highwire.dtl.DTLVardef@173a8f0org.highwire.dtl.DTLVardef@585271org.highwire.dtl.DTLVardef@8c959d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Cell specificity of adeno-associated virus (AAV) serotypes in human cortical organoids

Human-derived cortical organoids (hCOs) recapitulate cell diversity and 3D structure found in the human brain and offer a promising model for discovery of new gene therapies targeting neurological disorders. Adeno-associated viruses (AAVs) are the most promising vehicles for non-invasive gene delivery to the central nervous system (CNS), but reliable and reproducible in vitro models to assess their clinical potential are lacking. hCOs can take on these issues as they are a physiologically relevant model to assess AAV transduction efficiency, cellular tropism, and biodistribution within the tissue parenchyma, all of which could significantly modulate therapeutic efficacy. Here, we examine a variety of naturally occurring AAV serotypes and measure their ability to transduce neurons and glia in hCOs from multiple donors. We demonstrate cell tropism driven by AAV serotype and hCO donor and quantify fractions of neurons and astrocytes transduced with GFP as well as overall hCO health.

neuroscience↗

bioRxiv2023

Dietary environmental factors shape the defence against infection with Cryptosporidium

Cryptosporidium is a leading cause of diarrheal-related deaths in children, especially in resource-poor settings. It also targets the immunocompromised, chronically infecting people living with HIV and primary immunodeficiencies. There is no vaccine or effective treatment. While it is known from human cases and animal models that CD4+ T-cells play a role in curbing Cryptosporidium, the role of CD8+ cells remains to be defined. Using a Cryptosporidium tyzzeri mouse model, we show that gut-resident CD8+ intraepithelial lymphocytes (IELs) confer resistance to parasite growth. CD8+ IELs express, and are dependent on, the ligand-dependent transcription factor aryl hydrocarbon receptor (AHR). AHR deficiency reduced CD8+ IELs, decreased their cytotoxicity, and worsened infection. Transfer of CD8+ IELs rescued severely immunodeficient mice from death following Cryptosporidium challenge. Finally, dietary supplementation of the AHR pro-ligand indole-3-carbinol to new-born mice promoted resistance to infection. Therefore, common dietary metabolites augment the host immune response to cryptosporidiosis, protecting against disease.

immunology↗

bioRxiv2023

Immunoreactivity against SLC3A2 in high grade gliomas displays positive correlation with glioblastoma patient survival: Potential target for glioma diagnosis and therapy

Immunity against cancer cells is at the forefront of fight against highly malignant tumors like glioblastomas (GBM). Autoantibodies and their autoantigen cooperators are one of the promising biomarkers linked to the immune responses and have been reported as having an initiative or prognostic role for certain types of paraneoplastic disorders. Nevertheless, immunoreactivity against antigens expressed in GBM are poorly studied. To date, autoantibodies were identified by pursuing targeted approaches. By contrast, in this study, we collected human GBM tissue and sera samples and by applying proteomics analysis, we determined autoantigen candidates for GBM. Subsequent immunohistochemistry and immunoprecipitation experiments revealed that a solute carrier; SLC3A2 is widely overexpressed in GBMs and therefore, immunoreactivity against SLC3A2 is present in high grade GBM, and SLC3A2 expression is altered in GBMs. No antibody interaction was detected in SLC3A2 expressors of low grade gliomas. Furthermore, autoantibody presence was correlated with prolonged survival of GBM patients. Taken together, for the first time, we reported that the SLC3A2 immunoreaction exists in high grade gliomas with a distinct GBM profile. In conclusion, our findings may open up new avenues for our understanding of glioma prognosis in the context of autoimmunity. This may eventually lead to diagnostic and therapeutic inventions that can be utilized for prevention of the disease progression.

immunology↗

bioRxiv2023

Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer

Patient-derived xenograft (PDX) models involve the engraftment of tumour tissue in immunocompromised mice and represent an important pre-clinixtcal oncology research. A limitation of non-small cell lung cancer (NSCLC) PDX model derivation in NOD-scid IL2Rgammanull (NSG) mice is that a subset of initial engraftments are of lymphocytic, rather than tumour origin. In the lung TRACERx PDX pipeline, lymphoproliferations occurred in 17.8% of lung adenocarcinoma and 10% of lung squamous cell carcinoma transplantations, despite none of these patients having a prior or subsequent clinical history of lymphoproliferative disease. Lymphoproliferations were predominantly human CD20+ B cells and had the immunophenotype expected for post-transplantation diffuse large B cell lymphoma. All lymphoproliferations expressed Epstein-Barr-encoded RNAs (EBER). Analysis of immunoglobulin light chain gene rearrangements in three tumours where multiple tumour regions had resulted in lymphoproliferations suggested that each had independent clonal origins. Overall, these data suggest the presence of B cell clones with lymphoproliferative potential within primary NSCLC tumours that are under continuous immune surveillance. Since these cells can be expanded following transplantation into NSG mice, our data highlight the value of quality control measures to identify lymphoproliferations within xenograft pipelines and support the incorporation of strategies to minimise lymphoproliferations during the early stages of xenograft establishment pipelines. To present the histology data herein, we developed a Python-based tool for generating patient-level pathology overview figures from whole-slide image files; PATHOverview is available on GitHub (https://github.com/EpiCENTR-Lab/PATHOverview).

cancer biology↗

bioRxiv2023

Neuroimmune cortical organoids overexpressing C4A exhibit multiple schizophrenia endophenotypes

Elevated expression of the complement component 4A (C4A) protein has been linked to an increased risk of schizophrenia (SCZ). However, there are few human models available to study the mechanisms by which C4A contributes to the development of SCZ. In this study, we established a C4A overexpressing neuroimmune cortical organoid (NICO) model, which includes mature neuronal cells, astrocytes, and functional microglia. The C4A NICO model recapitulated several neuroimmune endophenotypes observed in SCZ patients, including modulation of inflammatory genes and increased cytokine secretion. C4A expression also increased microglia-mediated synaptic uptake in the NICO model, supporting the hypothesis that synapse and brain volume loss in SCZ patients may be due to excessive microglial pruning. Our results highlight the role of C4A in the immunogenetic risk factors for SCZ and provide a human model for phenotypic discovery and validation of immunomodulating therapies.

neuroscience↗