Drivers Of Differentiation Research Articles

Towards the understanding of genetic and morphological variations of a highly abundant seaweed-associated marine invertebrate

Unraveling the patterns of genetic structure and demographic history of marine species, as well as the factors that shape their genetic variations, is fundamental for informing conservation strategies for species and their environments. In this work, we investigate the current population structure and historical demographic patterns of the conspicuous seaweed-associated amphipod Hyale niger at a fine spatial scale in the subtropical SW Atlantic coast, in Brazil, by using both genome-wide and mitochondrial DNA markers. We also investigate how geographic distance, current oceanographic conditions, and variations in a key morphological trait contribute to the genetic variability of the amphipod. We observed an evident population genetic structure, even at a fine spatial scale, although genetic differentiation was lower than our expectations for a benthic direct brooder. Demographic history inferences were consistent across populations and showed two major demographic expansions on interglacial periods during the late Pleiostocene, before and after the last glacial maximum. We also demonstrated that isolation-by-environment (IBE) was the main driver of genetic differentiation, although we could not separate it from the effects of isolation-by-distance (IBD). Among environmental factors, nutrient concentrations in seawater were most relevant for explaining genetic structure. In addition, our data suggest that morphological variation in gnathopod 2 structure of males were not genetic-related and were probably plastic as a response to variations in macroalgae frond size. Our study reinforces the importance of using multiple molecular markers and analytical approaches to unveil patterns and processes generating genetic variation in natural populations.

Drivers of differentiation between EU Member‐states in the UN General Assembly

Drivers of differentiation between EU Member‐states in the UN General Assembly

Sporidiobolus pararoseus polysaccharides relieve rheumatoid arthritis by regulating arachidonic acid metabolism and bone remodeling signaling pathway

Rheumatoid arthritis (RA) is an autoimmune-mediated disease with the highest disability rate. Sporidiobolus pararoseus polysaccharides (SPP) have been demonstrated to have anti-rheumatoid and microbiota-modulatory effects; however, the underlying mechanisms remain unclear. This study employed collagen-induced arthritis (CIA) mice to explore the metabolic and genetic pathways. The results revealed SPP intervention significantly reduced the serum levels of rheumatoid and pro-inflammatory complement factors. SPP promoted the transition of macrophages of CIA mice toward the M2 phenotype (F4/80+/CD206+) from an inflammatory phenotype (F4/80+/CD86+) using flow cytometry analysis. A total of 44 metabolites were upregulated, and 110 metabolites were significantly downregulated by SPP compared to those in RA group. The decreased metabolites, 12(S)-HPETE, prostaglandin H2, 15-HETE, hepoxilin B3, and 15-keto-prostaglandin F2a, were mostly enriched in arachidonic acid metabolism (enrichment = 11.4 %), which was highly correlated with the anti-rheumatic activity of SPP. Gene expression analysis revealed that SPP significantly regulated OPG/RANKL/TRAF6 signaling pathway, stimulating osteogenic remodeling. Furthermore, arachidonic acid metabolism was identified as the critical metabolic driver of RA phenotypes and osteoclast differentiation, potentially associated with SPP-reshaped intestinal microbiota (i.e., Rikenellaceae_RC9_gut_group, Bacteroides, and Parabacteroides). Collectively, this study utilized an integrated approach of metabolomics and gene expression analysis to investigate the regulatory role of SPP in RA progression.

Genome-wide differentiation corresponds to climatic niches in two species of lichen-forming fungi.

Lichens can withstand fluctuating environmental conditions such as hydration-desiccation cycles. Many species distribute across climate zones, suggesting population-level adaptations to conditions such as freezing and drought. Here, we aim to understand how climate affects population genomic patterns in lichenized fungi. We analysed population structure along elevational gradients in closely related Umbilicaria phaea (North American; two gradients) and Umbilicaria pustulata (European; three gradients). All gradients showed clear genomic breaks splitting populations into low-elevation (Mediterranean zone) and high-elevation (cold temperate zone). A total of 3301 SNPs in U. phaea and 138 SNPs in U. pustulata were driven to fixation between the two ends of the gradients. The difference between the species is likely due to differences in recombination rate: the sexually reproducing U. phaea has a higher recombination rate than the primarily asexually reproducing U. pustulata. Cline analysis revealed allele frequency transitions along all gradients at approximately 0°C, coinciding with the transition between the Mediterranean and cold temperate zones, suggesting freezing is a strong driver of population differentiation. Genomic scans further confirmed temperature-related selection targets. Both species showed similar differentiation patterns overall, but different selected alleles indicate convergent adaptation to freezing. Our results enrich our knowledge of fungal genomic functions related to temperature and climate, fungal population genomics, and species responses to environmental heterogeneity.

Analysis of Temporal and Spatial Carbon Stock Changes and Driving Mechanism in Xinjiang Region by Coupled PLUS-InVEST-Geodector Model

Based on the goal of "dual-carbon" strategy, it is important to explore the impacts of land use change on carbon stock and the drivers of spatial differentiation of carbon stock in Xinjiang. Here, we predicted the land use types in Xinjiang in 2035 under different scenarios and analyzed the impacts of land use on carbon stock, which is of great theoretical and practical importance for policy formulation, land use structure adjustment, and carbon neutrality target achievement in Xinjiang. The coupled PLUS-InVEST-Geodector model was used to explore the spatial and temporal patterns of carbon stock change under the scenarios of rapid development, natural change, arable land protection, and ecological protection in Xinjiang in 2035 and to quantitatively reveal the attribution of influences on the changes in carbon stock from the perspectives of land use change and the combination of nature-socioeconomic-accessibility. The results showed that： ① From 1990 to 2020, the area of arable land and construction land in Xinjiang increased, and in terms of the transfer direction, it was mainly shifted from unutilized land to grassland. ② On the time scale, the carbon stock in Xinjiang showed the fluctuation of "decrease-increase-decrease," with an overall increasing trend. The transfer of unutilized land to grassland was the main reason for the increase in carbon stock； on the spatial scale, the carbon stock in the Altai Mountains in the north, the Tianshan Mountains in the middle, and the Kunlun Mountains in the south was higher, whereas the carbon stock in the Tarim Basin and the Junggar Basin was lower. ③ In 2035, the carbon stock of the natural development and rapid development scenarios decreased by 27.24 Tg and 71.17 Tg compared with 2020, respectively, and the ecological protection and arable land protection scenarios increased by 492.55 Tg and 46.67 Tg. The ecological protection scenario could significantly increase the carbon stock of the Xinjiang Region compared with that in the other scenarios, and the distribution pattern of the carbon stock in the four scenarios was more or less the same as that in 2020. In addition to land transformation, soil erosion intensity was the main driver of spatial differentiation of carbon stocks in Xinjiang （q value of 0.3501）, followed by net primary productivity of vegetation. The results of multifactor interactions showed that the spatial differentiation of carbon stocks in Xinjiang was the result of the joint action of multiple factors. All the factors had a synergistic enhancement under the interactions. The interaction between soil erosion intensity and the net primary productivity of vegetation was the main driver of the spatial differentiation of carbon stocks in Xinjiang.

Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish ecotype of Arabidopsis thaliana on contrasting soils.

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents of selection and quantifying their effects is key to understanding how populations adapt to local conditions. We performed a factorial reciprocal-transplant experiment using locally adapted ecotypes of Arabidopsis thaliana at their native sites to distinguish the contributions of adaptation to soil type and climate. Overall adaptive differentiation was strong at both sites. However, we found only very small differences in the strength of selection on local and non-local soil, and adaptation to soil type at most constituted only a few per cent of overall adaptive differentiation. These results indicate that local climatic conditions rather than soil type are the primary driver of adaptive differentiation between these ecotypes.

433. UNRAVELLING THE MOLECULAR MECHANISMS BEHIND TUMOUR DIFFERENTIATION IN ESOPHAGEAL ADENOCARCINOMA

Abstract Background Esophageal adenocarcinoma tumors are divided into three grades based on the tumour’s histological differentiation: well, moderate and poor. Poorly differentiated tumours have a worse survival rate than moderate and well tumours. Understanding the molecular programs of this differentiation may lead to the identification of novel therapeutic interventions specific to tumour differentiation. We have utilized laser-capture microdissection to enrich tumour cells followed by gene expression profiling (RNA-seq) to identify gene expression programs and whole genome sequencing for differentiating specific mutations and copy number changes. Collectively, these results will enable us to unravel the molecular drivers of tumour differentiation. Methods Laser capture microdissection was applied to N=127 RNA-seq samples from N=74 patients and N=103 from N=81 patients from a mix of primary tumour biopsies, resections, and metastatic biopsies. Most samples have a matching RNA-seq and WGS sample. We used a standard pipeline to analyze the WGS data and produce somatic mutation, structural variant, and copy number calls. The gene expression data was segregated into two sets a test set consisting of N=74 samples and a test set of N=53 samples. Non-negative matrix factorization was used to identify eleven gene expression programs. Results Our testing RNA-seq cohort consisted of N=74 samples from N=74 patients with N=4 G1, N=26 G2, N=35 G3, and N=9 missing differentiation data. Our initial goal was to unravel the gene expression programs that correlate with tumour differentiation. Our non-negative matrix factorization analysis yielded 11 gene signatures, N=3 programs enriched in glandular gene expression, N=3 enriched in EMT pathways, N=2 with fibroblasts, and N=3 associated with immune / inflammation genes (not shown) (Figure 1). Moreover, the glandular signatures were associated with G1/G2 and the EMT and fibroblast signatures with G3. Moreover, the glandular 2 signature was associated with HER2 amplifications. Conclusion In this work we have begun to unravel the gene expression and genomic changes associated with tumour differentiation. We have found signatures enriched for both G1/G2 and G3 tumours and from these signatures we have observed gene expression heterogeneity within the different tumour differentiation categories. Moreover, the G3 tumours are enriched in fibroblasts despite our laser-capture microdissection. We are currently working on a classification model to predict tumor differentiation from these gene expression programs and are looking to further integrate our whole genome data to find additional genomic drivers.

CSF1R Ligands Expressed by Murine Gliomas Promote M-MDSCs to Suppress CD8+ T Cells in a NOS-Dependent Manner.

Glioblastoma (GBM) is the most common malignant primary brain tumor, resulting in poor survival despite aggressive therapies. GBM is characterized by a highly heterogeneous and immunosuppressive tumor microenvironment (TME) made up predominantly of infiltrating peripheral immune cells. One significant immune cell type that contributes to glioma immune evasion is a population of immunosuppressive cells, termed myeloid-derived suppressor cells (MDSCs). Previous studies suggest that a subset of myeloid cells, expressing monocytic (M)-MDSC markers and dual expression of chemokine receptors CCR2 and CX3CR1, utilize CCR2 to infiltrate the TME. This study evaluated the mechanism of CCR2+/CX3CR1+ M-MDSC differentiation and T cell suppressive function in murine glioma models. We determined that bone marrow-derived CCR2+/CX3CR1+ cells adopt an immune suppressive cell phenotype when cultured with glioma-derived factors. Glioma-secreted CSF1R ligands M-CSF and IL-34 were identified as key drivers of M-MDSC differentiation while adenosine and iNOS pathways were implicated in the M-MDSC suppression of T cells. Mining a human GBM spatial RNAseq database revealed a variety of different pathways that M-MDSCs utilize to exert their suppressive function that is driven by complex niches within the microenvironment. These data provide a more comprehensive understanding of the mechanism of M-MDSCs in glioblastoma.

The influence of plant traits on soil microbial communities varies between arid and mesic grasslands

Abstract Background and aims Both soil properties and plant traits shape the diversity, composition and functions of plant-associated soil microbial communities. However, the relative influence of these factors is poorly understood, as are interactive effects between factors and the degree to which their influence varies among climate zones. Methods To address this gap, we compared the diversity and composition of soil microbial communities associated with co-occurring C3 and C4 grasses from arid and mesic environments, and plant traits influencing them. Results Climate emerged as the main determinant of plant traits and microbial community properties. Within each climatic region, above- and below-ground traits and soil properties differentially affected microbial community composition, and their relative influence varied among communities. In both mesic and arid environments aboveground traits related to quantity and quality of leaf litter (e.g., specific leaf area, leaf C content) and nutrient availability were the most influential variables for community composition. However, in arid regions, belowground traits (i.e., root tissue density and specific root area) significantly contributed to structure the eukaryotic community, supporting the role of roots as important driver of eukaryotic differentiation in constrained environments. Further, the presence of C4 plants in the arid region resulted in higher relative abundance of ciliate protists and higher recruitment of potentially beneficial microbial community members from green algae mediated by drought adaptation traits (e.g. decreased abundance of fine roots). Conclusions Overall, our study revealed a differential response of microbial communities to environmental conditions, suggesting that soil microbial community composition is influenced by trade-offs between host adaptive traits across distinct climatic regions.

Divergent lineages in a young species: The case of datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula.

Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial-interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species. Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species. Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.

Ecological transcriptomics reveals stress response pathways of a ground-herb species in a waterlogging gradient of Amazonian riparian forests.

Environmental stress is a fundamental facet of life and a significant driver of natural selection in the wild. Gene expression diversity may facilitate adaptation to environmental changes, without necessary genetic change, but its role in adaptive divergence remains largely understudied in Neotropical systems. In Amazonian riparian forests, species distribution is predominantly influenced by species' waterlogging tolerance. The flooding gradient delineates distinct wetland forest types, shaping habitats and species characteristics. Here we investigated the molecular basis of environmental stress response in a tropical ground-herb species (Ischnosiphon puberulus) to environmental variation in Amazonian riparian forests. We compared environmental variables and gene expression profiles from individuals collected in two forest types: Igapó and Terra firme in the Amazonian riparian forests. Predictable seasonal flooding poses a significant challenge in Igapó compared to Terra firme environments, with the former presenting higher water column height and longer flooding duration. Our findings suggest that contrasting environmental conditions related to flooding regimes are important drivers of population genetic differentiation and differential gene expression in I. puberulus. Enriched gene ontology terms highlight associations with environmental stresses, such as defence response, water transport, phosphorylation, root development, response to auxin, salicylic acid and oxidative stress. By uncovering key environmental stress response pathways conserved across populations, I. puberulus offers novel genetic insights into the molecular basis of plant reactions to environmental constraints found in flooded areas of this highly biodiverse neotropical ecosystem.

Coupled zoning and spatial heterogeneity of human activities and natural endowments based on self-organizing map and random forest: A case study of the agro-pastoral ecotone in Gansu, China

Regional zoning is an important way for humans to understand geographical space，but the existing research on regional zoning focuses on natural conditions, ignoring the interdependent characteristics of human and nature, and the driving mechanism of regional differentiation is not sufficiently explained. In this study, using algorithms such as self-organizing feature map, clustering quality index, structural similarity index measure (SSIM) and random forest, the human activity (HA)–natural endowment (NE) coupled zoning in the agro-pastoral ecotone in Gansu, China (AEGC), was conducted to explore the driving mechanism of regional differentiation. Results show the following: (1) The HA-NE coupled zoning has the best clustering effect when implementing the partitioning scheme with a classification number of 4. Accordingly, the AEGC can be divided into four regions with significant differences between HAs and NEs. (2) From the perspective of spatial distribution, HA–NE coupled zoning, climate zoning, geographic zoning, and vegetation zoning are similar, whereas HA zoning is different. The results of SSIM showed that HA–NE coupled zoning takes all types of factors into consideration (SSIM mean 0.708), and the zoning results are better than single type zonings. HAs have strong independence (SSIM mean 0.576), and geographic conditions are closely related to all other factors (SSIM mean 0.671). (3) Elevation is the most important driver of regional differentiation in the AEGC, with a contribution degree of 22.36%; other important drivers include land use intensity, precipitation, and normalized difference vegetation index, with contribution degree distributions of 17.38%, 16.34%, and 15.79%. Furthermore, the dominant factors of regional differentiation in each sub-region are different. This study emphasizes that regional characteristic factors and uneven spatial distribution factors are important drivers of regional differentiation, and land use intensity has become an important force influencing geographic space. Policy recommendations for zonal governance are made based on the inherent conditions of different regions. This study may provide a reference for scientific regional zoning and cognitive regional differentiation.

Analyzing the quality differences between healthy and moldy cigar tobacco leaves during the air-curing process through fungal communities and physicochemical components.

The air-curing process of cigar tobacco, as a key step in enhancing the quality of cigars, is often susceptible to contamination by mold spores, which severely constrains the quality of cigar tobacco. This study employed high-throughput Illumina sequencing technology and a continuous flow analysis system to analyze the differences between the microbial communities and physicochemical components of moldy and healthy cigar tobacco leaves. Furthermore, correlation analysis was performed to reveal the impact of mold on the quality of cigar tobacco. The differences between the microbial flora and physicochemical compositions of moldy (MC) and healthy (HC) tobacco leaves were analyzed, revealing significant disparities between the two groups. Aspergillus spp. represented the dominant mold in MC, with nine out of twelve isolated molds showing higher quantities on MC than on HC. Mold contamination notably decreased the total nitrogen (TN), total phosphorus (TP), total alkaloids (TA), starch, protein, and flavor constituents while increasing the total fatty acid esters (TFAA), which was accompanied by a shift towards weakly acidic pH in the leaves. Fungal community analysis indicated a significant reduction in the fungal operational taxonomic unit (OUT) numbers and diversity indices in MC, contrasting with the bacterial trends. Aspergillus exhibited significantly higher relative abundance in MC, with LEfSe analysis pinpointing it as the primary driver of differentiation. Furthermore, significant negative correlations were observed between Aspergillus and TP, starch, TA, and protein, while a significant positive association was evident with TFAA. Network analysis underscored the pivotal role of Aspergillus as the species influencing disparities between HC and MC, with its abundance serving as a critical determinant during the air-curing process. This study elucidated substantial quality distinctions between MC and HC during air-curing, with Aspergillus emerging as the key species contributing to leaf mold.

Critical role of Gα12 and Gα13 proteins in TGF-β-induced myofibroblast differentiation.

Myofibroblast differentiation, characterized by accumulation of cytoskeletal and extracellular matrix proteins by fibroblasts, is a key process in wound healing and pathogenesis of tissue fibrosis. Transforming growth factor-β (TGF-β) is the most powerful known driver of myofibroblast differentiation. TGF-β signals through transmembrane receptor serine/threonine kinases that phosphorylate Smad transcription factors (Smad2/3) leading to activation of transcription of target genes. Heterotrimeric G proteins mediate a distinct signaling from seven-transmembrane G protein coupled receptors, not commonly linked to Smad activation. We asked if G protein signaling plays any role in TGF-β-induced myofibroblast differentiation, using primary cultured human lung fibroblasts. Activation of Gαs by cholera toxin blocked TGF-β-induced myofibroblast differentiation without affecting Smad2/3 phosphorylation. Inhibition of Gαi by pertussis toxin, or siRNA-mediated combined knockdown of Gαq and Gα11 had no significant effect on TGF-β-induced myofibroblast differentiation. A combined knockdown of Gα12 and Gα13 resulted in a drastic inhibition of TGF-β-stimulated expression of myofibroblast marker proteins (collagen-1, fibronectin, smooth-muscle α-actin), with siGα12 being significantly more potent than siGα13. Mechanistically, a combined knockdown of Gα12 and Gα13 resulted in a substantially reduced phosphorylation of Smad2 and Smad3 in response to TGF-β, which was accompanied by a significant decrease in the expression of TGFβ receptors (TGFBR1, TGFBR2) and of Smad3 under siGα12/13 conditions. In conclusion, our study uncovers a novel role of Gα12/13 proteins in the control of TGF-β signaling and myofibroblast differentiation.

Local antigen encounter promotes generation of tissue-resident memory T cells in the large intestine

Upon infection, CD8+ T cells that have been primed in the draining lymph nodes migrate to the invaded tissue, where they receive cues prompting their differentiation into tissue-resident memory cells (Trm), which display niche-specific transcriptional features. Despite the importance of these cells, our understanding of their molecular landscape and the signals that dictate their development remains limited, particularly in specific anatomical niches such as the large intestine (LI). Here, we report that LI Trm generated following oral infection exhibit a distinct transcriptional profile compared to Trm in other tissues. Notably, we observe that local cues play a crucial role in the preferential establishment of LI Trm, favoring precursors that migrate to the tissue early during infection. Our investigations identify cognate antigen recognition as a major driver of Trm differentiation at this anatomical site. Local antigen presentation not only promotes the proliferation of effector cells and memory precursors but also facilitates the acquisition of transcriptional features characteristic of gut Trm. Thus, antigen recognition in the LI favors the establishment of Trm by impacting T cell expansion and gene expression.

Unravelling the role of oceanographic connectivity in the distribution of genetic diversity of marine forests at the global scale

AbstractAimGenetic diversity of marine forests results from complex interactions of eco‐evolutionary processes. Among them, oceanographic connectivity driven by dispersal through water transport is hypothesized to play a pivotal role, yet its relative contribution has not been addressed at the global scale. Here, we test how present‐day oceanographic connectivity is correlated with the distribution of genetic diversity of marine forests across the ocean.LocationGlobal.Time periodContemporary.Major taxa studiedMarine forests of brown macroalgae (order: Fucales, Ishigeales, Laminariales and Tilopteridales).MethodsThrough literature review, we compiled a comprehensive dataset of genetic differentiation, encompassing 699 populations of 30 species. A biophysical model coupled with network analyses estimated multigenerational oceanographic connectivity and centrality across the marine forest global distribution. This approach integrated propagule dispersive capacity and long‐distance dispersal events. Linear mixed models tested the relative contribution of site‐specific processes, connectivity and centrality in explaining genetic differentiation.ResultsWe show that spatiality‐dependent eco‐evolutionary processes, as described by our models, are prominent drivers of genetic differentiation in marine forests (significant models in 91.43% of the cases with an average R2 of 0.50 ± 0.07). Specifically, we reveal that 18.7% of genetic differentiation variance is explicitly induced by predicted contemporary connectivity and centrality. Moreover, we demonstrate that long‐distance dispersal is key in connecting populations of species distributed across large water masses and continents.Main conclusionsOur findings highlight the role of present‐day oceanographic connectivity in shaping the extant distribution of genetic diversity of marine forests on a global scale, with significant implications for biogeography and evolution. This understanding can pave the way for future research aimed at guiding conservation efforts, including the designation of well‐connected marine protected areas, which is particularly relevant for sessile ecosystems structuring species such as brown macroalgae.

Abstract B026: APOBEC3 promotes squamous differentiation via IL1A/AP-1 signaling

Abstract The APOBEC family of cytidine deaminase enzymes catalyze the conversion of cytosine to uracil in ssDNA and RNA substrates. The resulting C to U transition has been noted in the innate immune response to viral infection, and somatic hypermutation. However, APOBEC family members APOBEC3A (hA3A) and APOBEC3B (hA3B) have been implicated as drivers of the APOBEC3 mutational signatures in numerous cancer types. Notably, approximately 70% of single nucleotide variant mutations in bladder cancer can be attributed to APOBEC3 induced mutagenesis. Studies have implicated various APOBEC3 family members to be drivers of tumorigenesis, disease progression, and therapeutic resistance. To investigate APOBEC3’s role in bladder cancer, we have generated a novel, cre-inducible, pten and p53 knockout, to overexpress mouse Apobec3(mA3) in Upk3a+ cells (UPPA), compared to a model that does not overexpress mA3 (UPP). Apobec3 expression was shown to accelerate bladder tumor formation, indicated by a shorter median time of tumor latency in the UPPA model (43.3 weeks) compared to the UPP model (53.6 weeks). While both tumor models had presence of squamous differentiation, the extensiveness was more profound in the UPPA tumors. Transcriptional analysis of UPP and UPPA tumors, via scRNA sequencing, revealed an enrichment of squamous gene expression in the UPPA tumors. Utilizing mouse syngeneic bladder cancer cell lines and normal bladder urothelial cells, we overexpressed mA3 in a doxycycline inducible manner. Overexpression of mA3 was shown to prevent luminal differentiation. Additionally, mA3 overexpression resulted in the increase of IL-1a production. IL-1a production was sufficient to drive squamous differentiation in BBN963 and normal bladder urothelial cells. Blocking cFOS and IL-1R, individually, prevented expression of squamous genes. These results suggest that DNA damage induced by mA3 is sufficient to drive squamous differentiation via signaling through IL-1a resulting in AP-1 transcription factor activation. We then analyzed bladder cancer samples from The Cancer Genome Atlas and found that hA3A was the only APOBEC family member to be significantly associated with squamous gene expression. Interestingly, hA3A expression was enriched in the basal/squamous consensus subtype. To further interrogate the potential of hA3A being a driver of squamous differentiation in bladder cancer, we have also generated doxycycline inducible expression of hA3A and hA3B in syngeneic bladder cancer cell lines. Targeting IL-1a in various autoimmune diseases has resulted in FDA approval of antibodies targeting IL-1a and IL-1R. Given the clinical utility of targeting IL-1a, it is plausible to target this signaling axis for therapeutic benefit in bladder cancers with ongoing hA3A activity. In aggregate, our work demonstrates the promotion of an aggressive tumor state, driven by APOBEC mutagenesis and implicates hA3A as a possible driver of squamous differentiation in urothelial carcinoma. Citation Format: Andrew S. Truong, Michael S. Sturdivant, Mi Zhou, Wolfgang A. Beckabir, John Raupp, Ujjawal Manocha, Elliot D. Toomer, Ibardo A. Zambrano, Hung-Jui Tan, Marc A. Bjurlin, Angela B. Smith, Tracy L. Rose, Matthew I. Milowsky, Sara E. Wobker, Kathryn H. Gessner, Jeffrey S. Damrauer, William Y. Kim. APOBEC3 promotes squamous differentiation via IL1A/AP-1 signaling [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B026.

Osteomesopyknosis associated with a novel ALOX5 variant that impacts the RANKL pathway.

Bone tissue homeostasis relies on the coordinated activity of the bone-forming osteoblasts and bone-resorbing osteoclasts. Osteomesopyknosis is considered a distinctive rare sclerosing skeletal disorder of unelucidated pathophysiology and presumably autosomal dominant transmission. However, the causal genes are unknown. We present a case report encompassing clinical assessments, imaging studies, and whole-exome sequencing analysis, complemented by functional invitro experiments. This new case of osteomesopyknosis was associated with a missense ALOX5 variant predicted to induce protein misfolding and proteasomal degradation. Transfection experiments demonstrated that the variant was associated with reduced protein levels restored by proteasomal inhibition with bortezomib. Likewise, gene expression analysis showed that the mutated gene was associated with a decreased RANKL/OPG ratio, which is a critical driver of osteoclast precursor differentiation. Our data indicate impaired bone resorption as the underlying mechanism of this rare osteosclerosis, implicating ALOX5 pathogenic variants as potential etiological factors.

The TNF superfamily factor TWEAK promotes colonic inflammatory fibroblast differentiation and fibroblast-monocyte interaction

Background and Aims: Colonic fibroblasts have emerged as key players in inflammatory bowel disease (IBD) for their potential to acquire a pro-inflammatory phenotype, but the factors driving this process and how these fibroblasts interact with the immune system is incompletely understood. The TNF superfamily factor 12 (TNFSF12/TWEAK) has gained interest as a potential mediator of chronic inflammation and tissue remodelling in IBD. Here we explore its role as a driver of inflammatory fibroblast differentiation and as a modulator of fibroblast-monocyte interaction. Methods: Human primary colonic fibroblasts were stimulated with TWEAK or vehicle for 24 hours. fibroblasts were co-cultured with THP1 cells or primary monocytes for an additional 24 hours to investigate their interaction. RNA sequencing, immunoblotting, ELISA and flow cytometry were used for analysis. Results: TWEAK up-regulated the expression of >600 and down-regulated the expression of >500 genes in primary colonic fibroblasts (pAdj<0.05, fold>1.5). The up-regulated transcriptome was characterised by a pro-inflammatory programme including numerous cytokines, chemokines and immune receptors, which resembled an inflammatory stroma subpopulation previously identified in in ulcerative colitis (29% transcriptional alignment). The shared transcriptome included a marked signature of non-canonical NF-κB genes. At protein level, TWEAK inflicted changes in the expression of stromal markers (PDPN, PDGFRα); stimulated the secretion of IL-6, CCL2 and CXCL10; And enhanced the expression of surface adhesion molecules ICAM-1 and VCAM-1. Co-culture of THP1 cells with fibroblasts induced their adhesion and promoted a CD14high/ICAM-1high phenotype in THP1 cells, both of which were further enhanced when fibroblasts were pre-stimulated with TWEAK, while TWEAK did not directly affect adhesion or differentiation of THP1 cultured alone. Moreover, treatment of fibroblasts with a small molecule inhibitor of non-canonical NF-κB partially abrogated the fibroblast-mediated increase in CD14 expression on THP1 cells. In primary monocytes extracted from whole blood of 7 human donors, co-culture with TWEAK-treated fibroblasts promoted differentiation to a CD16intermediate, TREM-1high phenotype. Moreover, media from TWEAK-treated fibroblast-monocyte co-cultures displayed elevated levels of CXCL1 and IL-8 compared to vehicle-treated co-cultures, or to either cell type cultured alone, pointing towards reciprocal pro-inflammatory crosstalk. Conclusions: Our results indicate that TWEAK can promote pro-inflammatory polarisation in colonic fibroblasts and positions TWEAK as a mediator in the pro-inflammatory interaction between colonic fibroblasts and monocytes. This work is supported by funding from Science Foundation Ireland and The Irish Research Council under the Pathway program (21/PATH-S/9621), Enterprise Ireland, and the Conway Institute Director’s Strategic Award. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Quantitative analysis of body colouration in Sebastes rockfishes

Body colouration, a trait under strong selection, is influenced by the visual background of the environment. The stable influence of depth on visual background dynamics is due to light attenuation along the water column. Depth is also a key factor driving diversification in Sebastes rockfishes, influencing variations in several biological traits. Comparisons between closely related species suggest that brightly coloured species (red, orange, or yellow) tend to inhabit deeper waters and have slower growth rates compared to their shallow-water counterparts with dominance of dark colours (black, brown, or grey). Here, we used 377 photos from 100 Sebastes species, along with recently developed methods of colour quantification and phylogenetic comparative analyses, to assess this trend. Our analyses confirmed the separation of body colouration regarding depth, which was accompanied by differences in growth rates and morphological traits. This indicated that variations in body colourations are included in the ongoing correlational selection process dictated by depth. Analyses of closely related species indicated that depth is an initial driver of colour differentiation and that colour differences do not progressively increase with genetic divergences. We hypothesized that the bright-coloured rockfishes are found in deeper waters because in shallow environments they are more vulnerable to the potential negative effects of UV radiation and higher predation risk, while their predation successes are lessened, in comparison to dark-coloured rockfishes. Overall, this study emphasizes the intricate relationship between genetics, environment, adaptation, and the striking diversity of body colourations observed in Sebastes rockfishes.