Biology subjects

Thompson, E.

Publications and source records attributed to Thompson, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Dual ecological-cultural pathways of sociocultural environment and resting state functional connectivity among Hispanic adolescents in the ABCD Study

Hispanic Americans face persistent health disparities rooted in complex sociocultural and bioecodevelopmental dynamics. Identifying early neurodevelopmental trajectories that confer risk or resilience during adolescence is critical for developing targeted health equity interventions. Grounded in the NIMHD Research Framework and bioecodevelopmental theory, data from 12- to 14-year-old Hispanic adolescents in the Adolescent Brain Cognitive Development (ABCD) Study were analyzed (n=236). Partial least squares correlation (PLSC) was used to evaluate multivariate associations between sociocultural measures, spanning individual, family, and community levels, and resting-state functional connectivity (rsFC) networks. Post hoc linear mixed-effects models examined how derived sociocultural-rsFC patterns predicted measures of physical and mental health, linking bioecodevelopmental patterns to adolescent well-being. PLSC revealed dual community- and family-level neural pathways of biological embedding, diverging from traditional nested bioecodevelopmental assumptions. The community pathway linked child opportunity and neighborhood disadvantage to connectivity across Cingulo-Opercular, Default, Dorsal Attention, Visual Networks. This community-rsFC profile was associated with lower respiratory functioning, reflecting an allostatic load marker of environmental stress. The family pathway linked caregiver ethnic identity and heritage acculturation to Default, Ventral Attention, Sensorimotor-Mouth, and Visual Networks connectivity, suggesting that the family system shapes neural systems underlying social attunement and identity formation. Structural community factors and familial culture impose distinct neurobiological demands on the adolescent connectome among Hispanic youth. Findings highlight respiratory health as a biological marker of environmental adversity and underscore the necessity of structural and culturally sustaining interventions to promote health equity among Hispanic youth.

neuroscience↗

bioRxiv2026

Sulforaphane targets Leishmania promastigotes to inhibit parasite motility and alters host autophagy to suppress parasite replication in macrophages

Visceral leishmaniasis (VL) is a neglected tropical disease caused by the protozoan parasites Leishmania infantum (LI) and Leishmania donovani (LD). VL disproportionately affects populations that live in extreme poverty and those affected by climate change. Treatment options are limited, fiscally prohibitive, and toxic to some that receive treatment. In cases where VL remains untreated, death is inevitable. Although disease prevalence is increasing in affluent countries with robust research capabilities, there remains little economic incentive to search for new, more accessible non-toxic treatments, emphasizing the neglected tropical aspect of this disease. Our previous results indicate that sulforaphane (SFN) inhibits VL promastigote and amastigote growth through an unknown mechanism. The current study extends the anti-parasitic effects of SFN establishing SFN's efficacy against multiple Leishmania parasites including L. tropica, L. mexicana, L. panamensis and L. amazonesis. Moreover, SFN was an effective therapy post-infection as stably infected macrophages treated with SFN (10 M for 48 hours) had a significant reduction in the number of infected cells and the number of amastigotes per cell against Leishmania species that cause both VL and cutaneous leishmaniasis (CL). Moreover, SFN led to a reduction of motility within 6 hours of treatment indicating a direct interaction with the parasite. Alkynyl SFN (A-SFN) was subsequently synthesized to determine the specific binding target of SFN. Interestingly, A-SFN was more effective than SFN in decreasing parasite viability and inhibiting motility against VL and CL parasite species at equivalent concentrations. Immunofluorescence analysis utilizing click chemistry indicated A-SFN binds to cytosolic promastigote components and colocalized only minimally with KMP-11. The binding of SFN to KMP-11 could not be confirmed in vitro. In terms of intracellular host effects, SFN treatment increased the induction of nonselective macroautophagy by increased lysosomal acidification as quantified by DALGreen and FITC-dextran staining in infected macrophages. The induction of autophagy occurred simultaneously with the upregulation of expression of cytoprotective, antioxidant and autophagy-related genes via the NRF2 transcription factor. These data provide robust evidence that SFN is an excellent lead compound against Leishmania that initiates multiple innate immune pathways that enable enhanced parasite killing. Future studies will focus on the in vivo efficacy of SFN against CL.

microbiology↗

bioRxiv2026

DUSP6 is transcriptionally upregulated by activated ALK and cooperates with ALK signaling to reduce lorlatinib sensitivity in neuroblastoma cells

Neuroblastoma is a pediatric, sympathoadrenal tumour accounting for 7-10% of childhood malignancies. Some neuroblastomas are driven by activating mutations in ALK kinase and inhibitors show promise in clinical trials. Nevertheless, with resistance an ever-present concern, it remains important to understand better the effectors and modulators of ALK signaling. Wild type ALK promotes ERK activation, raising expression of negative regulators such as the dual-specificity phosphatase (DUSP) DUSP6. DUSP6 though can be pro- or anti-oncogenic in different cancers and its role in neuroblastoma cells remains unclear. We sought to understand its role in cells with either wild type or mutated ALK. Mutated ALK strongly promotes DUSP6 transcription, but apparently not through the ERK pathway. DUSP6 also appears to promote neuroblastoma cell proliferation without affecting ERK. Additionally, when DUSP6 is lost, the cells become more sensitive to ALK inhibitors lorlatinib and crizotinib. Phosphoproteomic analysis of such cells demonstrates that mutated ALK cooperates with DUSP6 to maximise signaling through several potential pathways, but again not through ERK or AKT. Their cooperation may also maintain optimal levels of N-Myc in MYCN-amplified neuroblastoma cells. While key substrates of DUSP6 remain to be determined in neuroblastoma cells, our study defines a novel role for this phosphatase in supporting the action of oncogenic ALK.

Cancer Biology↗

bioRxiv2025

A Single Genomic Region Controls Primocane Fruiting in Tetraploid Blackberry

The fresh-market blackberry (Rubus subgenus Rubus) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 ([~]33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus Hillquist genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3' UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus, and deliver diagnostic markers that can be immediately deployed in breeding programs.

genetics↗

bioRxiv2025

Ethnic Identity Profiles Among Adolescents in the ABCD Study: Associations with Resting State Functional Connectivity and Perceived Discrimination

Ethnic identity refers to how individuals perceive and experience themselves in the context of social groups, racial background, or culture (Phinney & Ong., 2007). Ethnic identity is positively associated with psychological well-being (Rivas-Drake et al., 2014) and negatively associated with depression and anxiety (Forstmeier et al., 2021). Those with strong ethnic identity may display resiliency to the negative effects of discrimination on psychological well-being (Urzua et al., 2021). Phinneys model describes four profiles for how people put effort into, participate in, and reflect upon their ethnic identity (Phinney, 1989). Despite prior work addressing ethnic identity and psychosocial outcomes (for review, see Meca et al., 2023), few studies have considered its neurobiological underpinnings. In the current study, we identified profiles of ethnic identity among participants in The Adolescent Brain Cognitive Development Study (ABCD Study) using latent profile analysis. Next, we examined resting state functional connectivity differences across observed profiles and assessed the moderating effects of perceived discrimination. Results indicated heightened cingulo-parietal (CPAR) network connectivity among adolescents with highly diffuse ethnic identities; among moderately achieved ethnic identities, perceived discrimination moderated the association between ethnic identity and CPAR connectivity. We discuss how these findings may be related to attentional shift, error monitoring, autobiographical memory, and social judgements.

neuroscience↗

bioRxiv2025

Systematic molecular glue drug discovery with a high-throughput effector protein remodeling platform

Realising the promise of new medicines that operate through a targeted molecular glue-induced degradation mechanism requires systematic tools that can uncover the relevant principles of neomorphic protein-protein interactions. Whilst some monovalent glue degraders have been found through serendipity, the rules for small molecule attributes and the pairs or complexes of proteins that are amenable to drug-induced proximity control remain poorly articulated. Here we introduce a new approach to address this by using programmed libraries of intramolecularly edited proteins to expand protein surface landscapes and trigger new druggable interactions. We show that effector proteins, such as the E3 ligase Cereblon, can be engineered to provoke neomorphic activity by inducing the degradation of new client proteins and that these de novo interactions provide a blueprint from which new small molecule degraders can be built. As a demonstration of the approach, we use the platform to identify new non-IMiD molecular glue degraders of the oncology target GSPT1. SUMMARYO_LIMolecular glues are a highly important and promising new form of therapeutic agent, but rationalising their discovery has so far been impossible C_LIO_LIGlueSEEKER screening enables prospective monovalent drug discovery by using high-throughput deep mutational scanning to re-engineer the function of effector proteins like E3 ligases C_LIO_LIWe used this approach to enable the computational discovery of small molecule glues which degrade the oncology target GSPT1 and show how the technology can be used across new targets C_LI

bioengineering↗

bioRxiv2024

Genetic Control of Prickles in Tetraploid Blackberry

Prickle-free blackberry (Rubus subgenus Rubus) canes are strongly preferred by growers due to food and worker safety concerns and damage to fruit from mechanical injury by prickles. This project was conducted to identify the genetic region responsible for prickle-free canes derived from the recessive Merton Thornless source in autotetraploid blackberry using a genome-wide association study, develop diagnostic KASP markers for prickle-free canes, and determine the effects of allele dosage at the prickle-free locus on prickle density in two biparental populations. The prickle locus was located on chromosome Ra04 from 30.48 to 36.04 Mb in an extensive LD block, with the peak SNP located at 33.64 Mb. Two diagnostic KASP markers were developed that correctly predicted the phenotype of 97% and 96% of 626 diverse fresh-market blackberry genotypes from multiple breeding programs, respectively. Allele dosage at the prickle-free locus had a significant impact on prickle density, with duplex prickly genotypes having significantly higher prickle density than simplex genotypes in both biparental populations studied. Five potential candidate genes with functional annotations related to epidermal, trichome, and/or prickle development were identified within the prickle-free locus, but no nonsynonymous polymorphism within these genes were identified. Article SummaryBlackberry cultivars with prickle-free canes are strongly preferred by growers and shipper marketers. The objectives of this study were to map the prickle-free locus in tetraploid fresh- market blackberries using a genome-wide association approach and develop diagnostic molecular markers that breeders can use to plan crosses and screen seedlings for prickle-free canes. The prickle-free locus was mapped to a 5.6 Mb region on chromosome Ra04. Two molecular markers developed in this region correctly predicted the phenotype of 96% or more of the breeding selections and cultivars in a large validation panel composed of germplasm from three breeding programs.

genetics↗

bioRxiv2024

The ancestry of a genome

Motivated originally by the increasing number of examples where a lone member of a once thriving population or even species now survives, we investigate what genomes of that population the survivor may represent. More generally it is of interest to consider what genomes of our ancestry each of us may represent. We consider only diploid dioecious organisms, and consider primarily the ancestry of a haploid genome, for example the maternal autosomes of the focal individual. Our ancestors are many and, in an unbounded population, increase exponentially in number. Our genetic ancestors are few, bounded by the number of ancestral genome segments which increases linearly over past generations. First we show that the major loss of potential ancestral lineages is at 8-11 generations, and that thereafter the number of genetic ancestors increases approximately linearly, but does not approach the upper bound. Over many generations, there remain tightly linked but not contiguous segments that result from the same ancestral lineage. Second we analyze the process of these "repeated" ancestral segments that continue to be formed in distant ancestry, even as others are lost by recombination. Thirdly, we consider the effect of a finite population, with one model of a geographically structured population. Ancestors are many, and soon fill the entire species range even with low migration rates. Genetic ancestors are not only few, but remain geographically local.

genetics↗

bioRxiv2024

Replay of procedural experience is independent of the hippocampus

Sleep is critical for consolidating all forms of memory1-3, from episodic experience to the development of motor skills4-6. A core feature of the consolidation process is offline replay of neuronal firing patterns that occur during experience7,8. This replay is thought to originate in the hippocampus and trigger the reactivation of ensembles of cortical and subcortical neurons1,3,9-18. However, non-declarative memories do not require the hippocampus for learning or for sleep-dependent consolidation19-26 meaning what drives their consolidation is unknown. Here we show, using an unsupervised method, that replay occurs in the dorsal striatum of mice during offline consolidation of a non-declarative, procedural, memory and that this replay is generated independently of the hippocampus. Replay occurred at both real-world and time-compressed speeds and was also prioritised both at the level of the individual neurons and the type of neural sequence. Complete bilateral lesions of the hippocampus had no effect on any feature of this replay. Our results demonstrate that procedural replay during consolidation of a non-declarative memory is independent of the hippocampus. These results support the view that replay drives active consolidation of all types of memory during sleep but challenges the idea that the hippocampus is the source of this replay.

neuroscience↗

bioRxiv2024

Clonal evolution of hematopoietic stem cells after cancer chemotherapy

Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies1. The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D. Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D. Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.

cancer biology↗

bioRxiv2024

Sodium/Potassium ATPase Alpha 1 Subunit Fine-tunes Platelet GPCR Signaling Function and is Essential for Thrombosis

BackgroundThrombosis is a major cause of myocardial infarction and ischemic stroke. The sodium/potassium ATPase (NKA), comprising and {beta} subunits, is crucial in maintaining intracellular sodium and potassium gradients. However, the role of NKA in platelet function and thrombosis remains unclear. MethodsWe utilized wild-type (WT, 1+/+) and NKA 1 heterozygous (1+/-) mice, aged 8 to 16 weeks, of both sexes. An intravital microscopy-based, FeCl3-induced carotid artery injury thrombosis model was employed for in vivo thrombosis assessment. Platelet transfusion assays were used to evaluate platelet NKA 1 function on thrombosis. Human platelets isolated from healthy donors and heart failure patients treated with/without digoxin were used for platelet function and signaling assay. Complementary molecular approaches were used for mechanistic studies. ResultsNKA 1 haplodeficiency significantly reduced its expression on platelets without affecting sodium homeostasis. It significantly inhibited 7.5% FeCl3-induced thrombosis in male but not female mice without disturbing hemostasis. Transfusion of 1+/-, but not 1+/+, platelets to thrombocytopenic WT mice substantially prolonged thrombosis. Treating WT mice with low-dose ouabain or marinobufagenin, both binding NKA 1 and inhibiting its ion-transporting function, markedly inhibited thrombosis in vivo. NKA 1 formed complexes with leucine-glycine-leucine (LGL)-containing platelet receptors, including P2Y12, PAR4, and thromboxane A2 receptor. This binding was significantly attenuated by LGL>SFT mutation or LGL peptide. Haplodeficiency of NKA 1 in mice or ouabain treatment of human platelets notably inhibited ADP-induced platelet aggregation. While not affecting 10% FeCl3-induced thrombosis, NKA 1 haplodeficiency significantly prolonged thrombosis time in mice treated with an ineffective dose of clopidogrel. ConclusionNKA 1 plays an essential role in enhancing platelet activation through binding to LGL-containing platelet GPCRs. NKA 1 haplodeficiency or inhibition with low-dose ouabain and marinobufagenin significantly inhibited thrombosis and sensitized clopidogrels anti-thrombotic effect. Targeting NKA 1 emerges as a promising antiplatelet and antithrombotic therapeutic strategy.

cell biology↗

bioRxiv2024

Psychobiological regulation of plasma and saliva GDF15 dynamics in health and mitochondrial diseases

Growth Differentiation Factor 15 (GDF15) is a protein that reflects mitochondrial energetic stress and is linked to physical and mental health symptoms, aging, and mortality. Here, we tested the hypothesis that GDF15 is a stress-responsive biomarker through a series of observational and experimental studies. We report four main findings. First, in the UK Biobank (n=53,026) and Framingham Heart Study (FHS) Offspring (n=3,460) cohorts, plasma GDF15 levels were elevated in individuals with symptoms of depression and anxiety. In the FHS cohort, GDF15 was also higher in participants exposed to chronic psychosocial stressors, including lower educational attainment, lower family income, and higher job strain. Second, plasma GDF15 levels in the FHS cohort correlated positively with epigenetic clocks measuring biological aging and effect sizes of GDF15 associations with psychosocial stressors were comparable to those observed for the clocks. Third, in a two-participant intensive-sampling study (n=112 days), saliva GDF15 showed a robust awakening response similar to established stress-related hormones. However, it exhibited a distinct negative pattern, peaking at waking and declining by 42-92% within 30-45 minutes. Finally, in two laboratory experiments (n=148), acute social-evaluative stress significant increased GDF15 levels in plasma and saliva within minutes. Together, these findings suggest that psychosocial stress may contribute to mitochondrial energetic stress indexed by GDF15, with implications for aging and health. This work opens new avenues for using GDF15 as a non-invasive biomarker to study the biological embedding of stress and its impact on aging trajectories. Significance statementGrowth Differentiation Factor 15 (GDF15) is a circulating protein elevated with mitochondrial energetic stress, aging, and diseases. Our findings show that GDF15 is elevated with depressive and anxiety symptoms and in those exposed to chronic psychosocial stress. Elevated plasma GDF15 also correlates with accelerated biological aging, as measured by epigenetic clocks. The effect sizes linking GDF15 to psychosocial stressors were comparable to those observed for the epigenetic clocks. Saliva GDF15 shows a robust negative awakening response characterized by elevated levels at awakening before declining within 30-45 minutes. Acute social-evaluative stress induced increase in plasma and saliva GDF15. Together, these findings suggest GDF15 can be used to study the energetic mechanisms for the biological embedding of stress across the lifespan.

physiology↗

bioRxiv2024

Morphological, pathological and phylogenetic analyses identify a diverse group of Colletotrichum spp. causing leaf, pod, and flower diseases on the orphan legume African yam bean

African yam bean (AYB; Sphenostylis stenocarpa Hochst. Ex A. Rich.) is an underutilized legume indigenous to Africa. The crop has great potential as it can enhance food security and its chemical composition offers nutritional and medicinal opportunities. However, the low grain yield caused by fungal diseases, including pod blight and leaf tip dieback, deters farmers from large-scale cultivation. The causal agents of pod and leaf tip dieback on AYB are largely uncharacterized. To determine the prevalence of fungal diseases affecting leaves, pods, and flowers of AYB, a survey was conducted in 2018 and 2019 in major AYB-growing areas in Nigeria. Leaf tip dieback, flower bud rot, and pod blight were the most common symptoms. Morphological and molecular assays were conducted to identify the causal agents of the observed diseases. In all the samples examined, fungi from eight genera were isolated from leaves and pods showing disease symptoms. However, Kochs postulates were fulfilled only for fungi belonging to the Colletotrichum genus. Fungi from the other seven genera did not produce disease symptoms in healthy AYB tissues. Several Colletotrichum isolates were characterized by sequencing the ITS, glyceraldehyde-3-phosphate dehydrogenase, calmodulin, and ApMAT loci. A combined phylogenetic analysis revealed four Colletotrichum species: C. siamense, C. theobromicola, and C. fructicola, which were recovered from the diseased leaves, and C. truncatum, which was recovered from diseased pods and buds. Our results are useful to gear efforts to develop integrated management strategies to control diseases affecting AYB in Nigeria and other parts of Africa. The availability of such strategies may stimulate greater cultivation of AYB to contribute to diet diversification, which has been repeatedly advocated by a range of stakeholders to increase food security and the prosperity of smallholder farmers.

microbiology↗

bioRxiv2024

Islands of genomic stability in the face of genetically unstable metastatic cancer

AbstractO_ST_ABSIntroductionC_ST_ABSMetastatic cancer affects millions of people worldwide annually and is the leading cause of cancer-related deaths. Most patients with metastatic disease are not eligible for surgical resection, and current therapeutic regimens have varying success rates, some with 5-year survival rates below 5%. Here we test the hypothesis that metastatic cancer can be genetically targeted by exploiting single base substitution mutations unique to individual cells that occur as part of normal aging prior to transformation. These mutations are targetable because [~]10% of them form novel tumor-specific "NGG" protospacer adjacent motif (PAM) sites targetable by CRISPR-Cas9. MethodsWhole genome sequencing was performed on five rapid autopsy cases of patient-matched primary tumor, normal and metastatic tissue from pancreatic ductal adenocarcinoma decedents. CRISPR-Cas9 PAM targets were determined by bioinformatic tumor-normal subtraction for each patient and verified in metastatic samples by high-depth capture-based sequencing. ResultsWe found that 90% of PAM targets were maintained between primary carcinomas and metastases overall. We identified rules that predict PAM loss or retention, where PAMs located in heterozygous regions in the primary tumor can be lost in metastases (private LOH), but PAMs occurring in regions of loss of heterozygosity (LOH) in the primary tumor were universally conserved in metastases. ConclusionsRegions of truncal LOH are strongly retained in the presence of genetic instability, and therefore represent genetic vulnerabilities in pancreatic adenocarcinomas. A CRISPR-based gene therapy approach targeting these regions may be a novel way to genetically target metastatic cancer.

cancer biology↗

bioRxiv2023

Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming

Axon guidance molecules were found to be the gene family most frequently altered in pancreatic ductal adenocarcinoma (PDA) through mutations and copy number changes. However, the exact molecular mechanism regarding PDA development remained unclear. Using genetically engineered mouse models to examine one of the axon guidance molecules, semaphorin 3D (SEMA3D), we found a dual role for tumor-derived SEMA3D in malignant transformation of pancreatic epithelial cells and a role for nerve-derived SEMA3D in PDA development. This was demonstrated by the pancreatic-specific knockout of the SEMA3D gene from the KRASG12D and TP53R172H mutation knock-in, PDX1-Cre (KPC) mouse model which demonstrated a delayed tumor initiation and growth comparing to the original KPC mouse model. Our results showed that SEMA3D knockout skews the macrophages in the pancreas away from M2 polarization, providing a potential mechanistic role of tumor-derived SEMA3D in PDA development. The KPC mice with the SEMA3D knockout remained metastasis-free, however, died from primary tumor growth. We then tested the hypothesis that a potential compensation mechanism could result from SEMA3D which is naturally expressed by the intratumoral nerves. Our study further revealed that nerve-derived SEMA3D does not reprogram macrophages directly, but reprograms macrophages indirectly through ARF6 signaling and lactate production in PDA tumor cells. SEMA3D increases tumor-secreted lactate which is sensed by GPCR132 on macrophages and subsequently stimulates pro-tumorigenic M2 polarization in vivo. Tumor intrinsic- and extrinsic-SEMA3D induced ARF6 signaling through its receptor Plexin D1 in a mutant KRAS-dependent manner. Consistently, RNA sequencing database analysis revealed an association of higher KRASMUT expression with an increase in SEMA3D and ARF6 expression in human PDAs. Moreover, multiplex immunohistochemistry analysis showed an increased number of M2-polarized macrophages proximal to nerves in human PDA tissue expressing SEMA3D. Thus, this study suggests altered expression of SEMA3D in tumor cells lead to acquisition of cancer-promoting functions and the axon guidance signaling originating from nerves is "hijacked" by tumor cells to support their growth. Other axon guidance and neuronal development molecules may play a similar dual role which is worth further investigation. One sentence summaryTumor- and nerve-derived SEMA3D promotes tumor progression and metastasis through macrophage reprogramming in the tumor microenvironment. STATEMENT OF SIGNIFICANCEThis study established the dual role of axon guidance molecule, SEMA3D, in the malignant transformation of pancreatic epithelial cells and of nerve-derived SEMA3D in PDA progression and metastasis. It revealed macrophage reprogramming as the mechanism underlying bothroles. Together, this research elucidated how inflammatory responses promote invasive PDA progression and metastasis through an oncogenic process.

cancer biology↗

bioRxiv2023

Epidermal Growth Factor potentiates EGFR(Y992/1173)-mediated therapeutic response of triple negative breast cancer cells to cold atmospheric plasma-activated medium

Cold atmospheric plasma (CAP) holds promise as a cancer-specific treatment that selectively kills basal-like breast cancer cells. We used CAP-activated media (PAM) to capture the multi-modal chemical species of CAP. Specific antibodies, small molecule inhibitors and CRISPR/Cas9 gene-editing approaches showed an essential role for receptor tyrosine kinases, especially epidermal growth factor (EGF) receptor, in mediating triple negative breast cancer (TNBC) cell responses to PAM. EGF also dramatically enhanced the sensitivity and specificity of PAM against TNBC cells. Site-specific phospho-EGFR analysis, signal transduction inhibitors and reconstitution of EGFR-depleted cells with EGFR-mutants confirmed the role of phospho-tyrosines 992/1173 and phospholipase C gamma signaling in upregulating levels of reactive oxygen species above the apoptotic threshold. EGF-triggered EGFR activation enhanced the sensitivity and selectivity of PAM effects on TNBC cells, such that a strategy based on the synergism of CAP and EGF therapy may provide new opportunities to improve the clinical management of TNBC.

cancer biology↗

bioRxiv2023

Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma

The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer. One-Sentence SummaryAggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.

immunology↗

bioRxiv2022

Quantitative analyses of T cell motion in tissue reveals factors driving T cell search in tissues

T cells are required to clear infection, moving first in lymph nodes to interact with antigen bearing dendritic cells leading to activation. T cells then move to sites of infection to find and clear infection. T cell motion plays a role in how quickly a T cell finds its target, from initial naive T cell activation by a dendritic cell to interaction with target cells in infected tissue. To better understand how different tissue environments might affect T cell motility, we compared multiple features of T cell motion including speed, persistence, turning angle, directionality, and confinement of motion from T cells moving in multiple tissues using tracks collected with microscopy from murine tissues. We quantitatively analyzed naive T cell motility within the lymph node and compared motility parameters with activated CD8 T cells moving within the villi of small intestine and lung under different activation conditions. Our motility analysis found that while the speeds and the overall displacement of T cells vary within all tissues analyzed, T cells in all tissues tended to persist at the same speed, particularly if the previous speed is very slow (less than 2 {micro}m/min) or very fast (greater than 8 {micro}m/min) with the exception of T cells in the villi for speeds greater than 10 {micro}m/min. Interestingly, we found that turning angles of T cells in the lung show a marked population of T cells turning at close to 180o, while T cells in lymph nodes and villi do not exhibit this "reversing" movement. Additionally, T cells in the lung showed significantly decreased meandering ratios and increased confinement compared to T cells in lymph nodes and villi. The combination of these differences in motility patterns led to a decrease in the total volume scanned by T cells in lung compared to T cells in lymph node and villi. These results suggest that the tissue environment in which T cells move can impact the type of motility and ultimately, the efficiency of T cell search for target cells within specialized tissues such as the lung.

immunology↗