tbuckley/cabot-search huggingface dataset:
A population-based cohort study defined estimated glomerular filtration rate decline and kidney failure among Canadian immigrants
Authors: Ida-Ehosa Olaye, Chengchun Yu, Meltem Tuna, Ayub Akbari, Tim Ramsay, Peter Tanuseputro, Istvan Mucsi, Greg A Knoll, Manish M Sood, Gregory L Hundemer
Journal: Kidney International (2025)

The link between immigrant status, a key social determinant of health, and kidney disease remains uncertain. To evaluate this, we compared incident adverse kidney outcomes between immigrants and non-immigrants using Canadian provincial health administrative data. We conducted a population-based observational cohort study of all adult Ontario residents (immigrants and non-immigrants) with normal baseline kidney function (estimated glomerular filtration rate (eGFR) 70 mL/min/1.73m2 or more). Multivariable Cox proportional hazard regression modeling was used to evaluate the relationship between immigrant status and the composite adverse kidney outcome of 40% eGFR decline or kidney failure. The study cohort included 10,440,210 individuals with 22% immigrants and 78% non-immigrants. The mean (Standard Deviation) age and eGFR were 45 (17) years and 102 (16) mL/min/1.73m2, respectively. Immigrants experienced a 27% lower hazard for the composite adverse kidney outcome (adjusted hazard ratio 0.73 [95% Confidence Interval 0.72-0.74]) compared to non-immigrants which was primarily driven by 40% eGFR decline. However, immigrants also experienced a 12% lower hazard for incident kidney failure (0.88 [0.84-0.93]) compared to non-immigrants. Results were consistent upon accounting for the competing risk of death and adjusting for baseline albuminuria. As has been demonstrated with other chronic diseases, these novel findings suggest that a "healthy immigrant effect" also extends to kidney disease. Differential kidney disease outcomes were identified among immigrants based on refugee status and world region of origin which may inform health policy decision-making toward targeted screening strategies and more cost-effective resource allocation for immigrant populations.
Therapeutic Potential of Urinary Extracellular Vesicles in Delivering Functional Proteins and Modulating Gene Expression for Genetic Kidney Disease
Authors: Yi Huang, Ali Osouli, Hui Li, Megan Dudaney, Jessica Pham, Valeria Mancino, Taranatee Khan, Baishali Chaudhuri, Nuria M Pastor-Soler, Kenneth R Hallows, Eun Ji Chung
Journal: Biomaterials (2025)
eIF3f promotes tumour malignancy by remodelling fatty acid biosynthesis in hepatocellular carcinoma
Authors: Suiqing Zhou, Liren Zhang, Yue You, Kai Yu, Xiaofeng Tie, Yun Gao, Yining Chen, Feifan Yao, Ruizhi Zhang, Xiaopei Hao, Chunyao Fang, Xiangdong Li, Qing Li, Xuehao Wang
Journal: Journal of Hepatology (2025)
Tumor cells that resist neutrophil anticancer cytotoxicity acquire a prometastatic and innate immune escape phenotype
Authors: Jagoda Agnieszka Szlachetko, Francisca Hofmann-Vega, Bettina Budeus, Lara-Jasmin Schröder, Claudia Alexandra Dumitru, Mathias Schmidt, Eric Deuss, Sebastian Vollmer, Eva-Maria Hanschmann, Maike Busch, Jan Kehrmann, Stephan Lang, Nicole Dünker, Timon Hussain, Sven Brandau
Journal: Cellular and Molecular Immunology (2025)

In the tumor host, neutrophils may exhibit protumor or antitumor activity. It is hypothesized that in response to host-derived or therapy-induced factors, neutrophils adopt diverse functional states to ultimately execute these differential functions. Here, we provide an alternative scenario in which the response of an individual tumor cell population determines the overall protumor versus antitumor outcome of neutrophil‒tumor interactions. Experimentally, we show that human neutrophils, which are sequentially stimulated with bacteria and secreted factors from tumor cells, kill a certain proportion of tumor target cells. However, the majority of the tumor cells remained resistant to this neutrophil-mediated killing and underwent a functional, phenotypic and transcriptomic switch that was reminiscent of partial epithelial‒to-mesenchymal transition. This cell biological switch was associated with physical escape from NK-mediated killing and resulted in enhanced metastasis to the lymph nodes in a preclinical orthotopic mouse model. Mechanistically, we identified the antimicrobial neutrophil granule proteins neutrophil elastase (NE) and matrix metalloprotease-9 (MMP-9) as the molecular mediators of this functional switch. We validated these data in patients with head and neck cancer and identified bacterially colonized intratumoral niches that were enriched for mesenchymal tumor cells and neutrophils expressing NE and MMP-9. Our data reveal the parallel execution of tumor cytotoxic and prometastatic activity by activated neutrophils and identify NE and MMP-9 as mediators of lymph node metastasis. The identified mechanism explains the functional dichotomy of tumor-associated neutrophils at the level of the tumor target cell response and has implications for superinfected cancers and the dysbiotic tumor microenvironment.
Minimally invasive retrieval and characterisation of tenosynovial tissue in rheumatoid arthritis: a novel approach to study at-risk, active, and remission stages
Authors: Lavinia Agra Coletto, Hanna W van Steenbergen, Clara Di Mario, Marco Gessi, Barbara Tolusso, Denise Campobasso, Domenico Somma, Pierluigi Rizzuti, Dario Bruno, Pietro Rubortone, Beatrice Fresch, Tommaso Hubert, Natacha Goulas, Luca Petricca, Maria Rita Gigante, Viviana A Pacucci, Simone Perniola, Aziza Elmesmari, Carlo Tur, Roberta Benvenuto, Elisa Gremese, Mariola Kurowska-Stolarska, Marco Maria Lizzio, Maria Antonietta D'Agostino, Annette H M van der Helm-van Mil, Stefano Alivernini
Journal: Annals of the Rheumatic Diseases (2025)

Tenosynovial inflammation is a hallmark of rheumatoid arthritis (RA), even in the preclinical phase. However, tenosynovium retrieval and characterisation is beyond the current state-of-the-art. We aimed to (1) assess the rate of magnetic resonance imaging (MRI)-detected tenosynovitis in the wrists of patients with preclinical and clinical RA; (2) develop a technique for tenosynovium retrieval; and (3) characterise its cellular composition across disease phases, including the comparison to adjacent synovium. In total, 834 MRI wrist scans were analysed to assess extensor/flexor tendon tenosynovitis rate (168 autoantibody-positive clinical suspect arthralgia (CSA), 473 naïve to treatment RA, and 193 healthy controls). An ultrasound-guided minimally invasive technique was developed to collect tenosynovium from the wrist extensor tendons in an independent cohort: 16 autoantibody-positive CSA patients, 41 RA patients (14 of whom with adjacent synovium with comparable ultrasound-detected inflammation), and 8 osteoarthritis (OA) patients. Tissue representativity, lining hyperplasia, and inflammatory infiltrate degree were assessed by haematoxylin and eosin staining and immunohistochemistry (CD55, CD68, CD3, CD20, CD138, and CD21). Safety and tolerability were assessed. Tenosynovitis of the wrist extensors/flexor tendons was observed in 34% of CSA and 68% of RA patient compared to 8% in healthy. Tenosynovium was successfully retrieved in 89.7% of cases without severe adverse events. Tenosynovial lining hyperplasia and inflammatory infiltrate were significantly higher in active RA than CSA patients without ultrasound-detected subclinical inflammation and RA remission, and comparable to inflamed adjacent synovium. CSA patients with subclinical inflammation showed early CD3pos and CD55pos cells enrichment compared to OA controls. Tenosynovium is frequently inflamed and readily accessible in CSA and RA. Future molecular studies of tenosynovial biopsies will advance understanding of the transition from pre-RA to RA.
Continuous mechanical-gradient hydrogel with on-demand distributed Mn2+/Mg-doped hydroxyapatite@Fe3O4 for functional osteochondral regeneration
Authors: Junwei Xu, Yi Cui, Ping Li, Xuemei Sun, Zhiheng Chen, Jingxi Wang, Xuenan Gu, Xiaogang Wang, Yubo Fan
Journal: Bioactive Materials (2025)
Interpersonal problems as a predictor of treatment outcome in adult depression: An individual participant data meta-analysis
Authors: Juan Martín Gómez Penedo, Manuel Meglio, Christoph Flückiger, Frederik J Wienicke, Jasmijn Breunese, Marco Menchetti, Paola Rucci, Robert Johansson, Joel M Town, Allan A Abbass, Peter Lilliengren, R Michael Bagby, Lena C Quilty, Lotte H J M Lemmens, Suzanne C van Bronswijk, Michael Barkham, William B Stiles, Gillian E Hardy, Peter Fonagy, Patrick Luyten, Matthew P Constantinou, Jacques P Barber, Kevin S McCarthy, Nili Solomonov, Anthony S Joyce, Pim Cuijpers, Ellen Driessen
Journal: Clinical Psychology Review (2025)
Health-related quality of life in participants with advanced biliary tract cancer from the randomized phase III KEYNOTE-966 study
Authors: Changhoon Yoo, Makoto Ueno, Heinz-Josef Klümpen, Robin Kate Kelley, Arndt Vogel, Junji Furuse, Zhenggang Ren, Thomas Yau, Stephen Lam Chan, Masato Ozaka, Sang Cheul Oh, Shanzhi Gu, Joon Oh Park, Juan W Valle, Julien Edeline, Jong Gwang Kim, Shital Kamble, Josephine M Norquist, Li Yu, Usha Malhotra, Richard S Finn
Journal: Journal of Hepatology (2025)
HSR25-154: Treatment Patterns and Prognosis of Patients With HER2-Negative Early Breast Cancer and Germline Pathogenic Variants in BRCA1, BRCA2, ATM, CHEK2 and PALB2
Authors: Vishnu Prasath, Andrea Riner, Joanne Kim, Akia Clark, Brandon Slover, Bridget Oppong, Robert Wesolowski, Kai Johnson, Sagar Sardesai
Journal: Journal of the National Comprehensive Cancer Network (2025)

"HSR25-154: Treatment Patterns and Prognosis of Patients With HER2-Negative Early Breast Cancer and Germline Pathogenic Variants in BRCA1, BRCA2, ATM, CHEK2 and PALB2" published on 28 Mar 2025 by National Comprehensive Cancer Network.
CRE25-040: A Case of Stage IV NSCLC With MET Exon 14 Mutation With Durable Response to MET Inhibitor Following Cessation of Therapy Due to Toxicity: Insights for Treatment Strategies
Authors: Chanmi Lee, Emmeline Academia, Page C. Widick
Journal: Journal of the National Comprehensive Cancer Network (2025)

"CRE25-040: A Case of Stage IV NSCLC With MET Exon 14 Mutation With Durable Response to MET Inhibitor Following Cessation of Therapy Due to Toxicity: Insights for Treatment Strategies" published on 28 Mar 2025 by National Comprehensive Cancer Network.
DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing
Authors: Junwei Song, Li-an Lin, Chao Tang, Chuan Chen, Qingxin Yang, Dan Zhang, Yuancun Zhao, Han-cheng Wei, Kepan Linghu, Zijie Xu, Tingfeng Chen, Zhifeng He, Defu Liu, Yu Zhong, Weizhen Zhu, Wanqin Zeng, Li Chen, Guiqin Song, Mutian Chen, Juan Jiang, Juan Zhou, Jing Wang, Bojiang Chen, Binwu Ying, Yuan Wang, Jia Geng, Jing-wen Lin, Lu Chen
Journal: Genome biology (2025)

Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m6A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.
Author Correction: Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer’s disease
Authors: Lynn van Olst, Brooke Simonton, Alex J. Edwards, Anne V. Forsyth, Jake Boles, Pouya Jamshidi, Thomas Watson, Nate Shepard, Talia Krainc, Benney MR Argue, Ziyang Zhang, Joshua Kuruvilla, Lily Camp, Mengwei Li, Hang Xu, Jeanette L. Norman, Joshua Cahan, Robert Vassar, Jinmiao Chen, Rudolph J. Castellani, James AR Nicoll, Delphine Boche, David Gate
Journal: Nature Medicine (2025)
Publisher Correction: The haplotype-resolved genome assembly of an ancient citrus variety provides insights into the domestication history and fruit trait formation of loose-skin mandarins
Authors: Minqiang Yin, Xiaochan Song, Chao He, Xiyuan Li, Mengyuan Li, Jiangbo Li, Hao Wu, Chuanwu Chen, Li Zhang, Zhenmei Cai, Liqing Lu, Yanhui Xu, Xin Wang, Hualin Yi, Juxun Wu
Journal: Genome biology (2025)
Author Correction: A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Authors: Johanna Klughammer, Daniel L. Abravanel, Åsa Segerstolpe, Timothy R. Blosser, Yury Goltsev, Yi Cui, Daniel R. Goodwin, Anubhav Sinha, Orr Ashenberg, Michal Slyper, Sébastien Vigneau, Judit Jané‐Valbuena, Shahar Alon, Chiara Caraccio, Judy Chen, Ofir Cohen, Nicole Cullen, Laura K. DelloStritto, Danielle Dionne, Janet Files, Allison Frangieh, Karla Helvie, Melissa E. Hughes, Stephanie Inga, Abhay Kanodia, Ana Lako, Colin MacKichan, Simon Mages, Noa Moriel, Evan Murray, Sara Napolitano, Kyleen Nguyen, Mor Nitzan, Rebecca Ortiz, Miraj Patel, Kathleen L. Pfaff, Caroline B. M. Porter, Asaf Rotem, Sarah Strauss, Robert Strasser, Aaron R. Thorner, Madison Turner, Isaac Wakiro, Julia Waldman, Jingyi Wu, Jorge Gómez Tejeda Zañudo, Diane Zhang, Nancy U. Lin, Sara M. Tolaney, Eric P. Winer, Edward S. Boyden, Fei Chen, Garry P. Nolan, Scott J. Rodig, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E. Johnson, Aviv Regev, Nikhil Wagle
Journal: Nature Medicine (2025)
MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models
Authors: Devlin C. Moyer, Justin Reimertz, Daniel Segrè, Juan I. Fuxman Bass
Journal: Genome biology (2025)

Genome-scale metabolic models (GSMMs) are used to predict metabolic fluxes, with applications ranging from identifying novel drug targets to engineering microbial metabolism. Erroneous or missing reactions, scattered throughout densely interconnected networks, are a limiting factor in these applications. We present Metabolic Accuracy Check and Analysis Workflow (MACAW), a suite of algorithms that helps to identify and visualize errors at the level of connected pathways, rather than individual reactions. We show how MACAW highlights inaccuracies of varying severity in manually curated and automatically generated GSMMs for humans, yeast, and bacteria and helps to identify systematic issues to be addressed in future model construction efforts.
Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset
Authors: Mei R. M. Du, Changqing Wang, Charity W. Law, Daniela Amann-Zalcenstein, Casey J. A. Anttila, Ling Ling, Peter F. Hickey, Callum J. Sargeant, Yunshun Chen, Lisa J. Ioannidis, Pradeep Rajasekhar, Raymond K. H. Yip, Kelly L. Rogers, Diana S. Hansen, Rory Bowden, Matthew E. Ritchie
Journal: Genome biology (2025)

Spatial transcriptomics allows gene expression to be measured within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics' Visium platform, a popular method which enables transcriptome-wide profiling of tissue sections. Visium offers a range of sample handling and library construction methods which introduces a need for benchmarking to compare data quality and assess how well the technology can recover expected tissue features and biological signatures. Here we present SpatialBenchVisium, a unique reference dataset generated from spleen tissue of mice responding to malaria infection spanning several tissue preparation protocols (both fresh frozen and FFPE, with either manual or CytAssist tissue placement). We note better quality control metrics in reference samples prepared using probe-based capture methods, particularly those processed with CytAssist, validating the improvement in data quality produced with the platform. Our analysis of replicate samples extends to explore spatially variable gene detection, the outcomes of clustering and cell deconvolution using matched single-cell RNA-sequencing data and publicly available reference data to identify cell types and tissue regions expected in the spleen. Multi-sample differential expression analysis recovered known gene signatures related to biological sex or gene knockout.
Carfilzomib prescribing patterns and outcomes for relapsed or refractory multiple myeloma: a real-world analysis
Authors: Sharlene Dong, Rahul Banerjee, Adeel M. Khan, Mengru Wang, Xiaoliang Wang, Anosheh Afghahi, Aimaz Afrough, Murali Janakiram, Bo Wang, Andrew J. Cowan, Adam S. Sperling, Larry D. Anderson, S. Vincent Rajkumar, Gurbakhash Kaur
Journal: Blood Cancer Journal (2025)

Despite the widespread use of carfilzomib (K) in relapsed/refractory multiple myeloma (RRMM), there is no consensus on optimal K dose in milligrams per square meter (mg/m2) or dosing schedule. We assessed three modern K prescribing patterns in RRMM using a large United States electronic health record-derived database. Our final cohort (n = 486) included 136 patients (28.0%) who received K 56 mg/m2 once weekly (K56-1x), 86 (17.7%) who received 56 mg/m2 twice weekly (K56-2x), and 264 (54.3%) who received 70 mg/m2 once weekly (K70-1x). Between 2016 and 2023, once-weekly dosing became more common: K70-1x proportions changed from 21.1% in 2016 to 50.6% in 2023, K56-1x from 15.8% to 37.0%, and K56-2x from 63.2% to 12.3%. Median progression-free survival was 13.0 months [95% confidence interval (CI) 11.2-20.7] for K56-1x, 13.2 months (95% CI 9.0-28.1 months) for K56-2x, and 10.9 months (95% CI 9.9-15.3 months) for K70-1x; these differences were not statistically significant (log-rank p = 0.46). Rates of heart failure was comparable (<5% in all cohorts). In summary, our findings do not support improved outcomes with twice-weekly carfilzomib in RRMM. K56-1x may provide the best balance of efficacy, safety, and avoidance of time toxicity from frequent infusions.
Clinicopathologic Attributes and Downstream Outcomes of Mucosal Melanomas: A Multi-Hospital Cohort Study
Authors: Sara Khattab, Emma Beagles, Matthew Tran, Cameron Moseley, Guihong Wan, Crystal Chang, Nga Nguyen, Maryam M Asgari, Marc S Hurlbert, Yevgeniy R Semenov
Journal: Journal of the American Academy of Dermatology (2025)
PATIENT PROFILE, FEASIBILITY, AND ACUTE SAFETY OF A SINOATRIAL NODE-SPARING HYBRID APPROACH FOR INAPPROPRIATE SINUS TACHYCARDIA (IST): FIRST RESULTS FROM AN INTERNATIONAL MULTI-CENTER IST PATIENT REGISTRY
Authors: Dhanunjaya R. Lakkireddy, Mark La Meir, Kun Kevin Xiang, Athanasios Thomaides, Paul Vesco, Chad Robbins Brodt, J. Michael Smith, Carlo De Asmundis
Journal: Journal of the American College of Cardiology (2025)
LEFT VENTRICULAR FIBROSIS ON T1 MAPPING IS ASSOCIATED WITH INCREASED RISK OF INCIDENT ATRIAL FIBRILLATION: RESULTS FROM THE MULTI-ETHNIC STUDY OF ATHEROSCLEROSIS (MESA)
Authors: Elnaz Ebrahimihoor, Takeki Suzuki, Konstantinos N. Aronis, Bharath Ambale Venkatesh, Gustavo J. Volpe, Masamichi Imai, Mohammadali Habibi, Anderson Costa Armstrong, Alvaro Alonso, Saman Nazarian, Joao A.C. Lima, Tarek Zghaib
Journal: Journal of the American College of Cardiology (2025)
DEVELOPMENT AND MULTINATIONAL VALIDATION OF A DEEP LEARNING ALGORITHM TO DETECT AND PREDICT ATRIAL FIBRILLATION AND FLUTTER FROM IMAGES OF 12-LEAD ELECTROCARDIOGRAMS IN SINUS RHYTHM
Authors: Arya Aminorroaya, Lovedeep Dhingra, Aline Pedroso Camargos, Veer Sangha, Evangelos K. Oikonomou, Rohan Khera
Journal: Journal of the American College of Cardiology (2025)
SPONTANEOUS ARRHYTHMIC EPISODES IN THE MODULAR ATP TRIAL: STUDY OF A MODULAR, COMMUNICATIVE, LEADLESS PACING-DEFIBRILLATOR SYSTEM
Authors: Michael Shane Lloyd, Lluís Mont, Carina Blomström-Lundqvist, Lucas V. Boersma, Maria Grazia Bongiorni, Martin C. Burke, Rahul N. Doshi, Paul A. Friedman, Daniel Gras, Steven P. Kutalek, Petr Neuzil, Paul Roberts, David J. Wright, Anish Amin, Jose Maria Tolosana, Lawrence M. Epstein, Amy Brisben, Elizabeth Matznick, Benjamin Speakman, Bryan Swackhamer, Julie West, Vivek Yerrapu Reddy, Reinoud Knops
Journal: Journal of the American College of Cardiology (2025)
Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments
Authors: Niels Holtgrefe, Katharina T Huber, Leo van Iersel, Mark Jones, Samuel Martin, Vincent Moulton
Journal: Molecular Biology and Evolution (2025)

With the increasing availability of genomic data, biologists aim to find more accurate descriptions of evolutionary histories influenced by secondary contact, where diverging lineages reconnect before diverging again. Such reticulate evolutionary events can be more accurately represented in phylogenetic networks than in phylogenetic trees. Since the root location of phylogenetic networks can not be inferred from biological data under several evolutionary models, we consider semi-directed (phylogenetic) networks: partially directed graphs without a root in which the directed edges represent reticulate evolutionary events. By specifying a known outgroup, the rooted topology can be recovered from such networks. We introduce the algorithm Squirrel (Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks) which constructs a semi-directed level-1 network from a full set of quarnets (four-leaf semi-directed networks). Our method also includes a heuristic to construct such a quarnet set directly from sequence alignments. We demonstrate Squirrel's performance through simulations and on real sequence data sets, the largest of which contains 29 aligned sequences close to 1.7 Mbp long. The resulting networks are obtained on a standard laptop within a few minutes. Lastly, we prove that Squirrel is combinatorially consistent: given a full set of quarnets coming from a triangle-free semi-directed level-1 network, it is guaranteed to reconstruct the original network. Squirrel is implemented in Python, has an easy-to-use graphical user-interface that takes sequence alignments or quarnets as input, and is freely available at https://github.com/nholtgrefe/squirrel.
Localised tissue-specific gene expression and gene duplications are important sources of social morph differences in a social bumblebee
Authors: Hongfei Xu, Thomas J Colgan
Journal: Molecular Biology and Evolution (2025)

Understanding the expression of multiple behaviourally and morphologically distinct phenotypes from a single genome represents a fundamental topic in evolutionary biology. Central to the complication of expressing phenotypes, which may differ in their optima, is the sharing of largely the same genome, which is predicted to manifest in conflict at the genomic level. This is particularly true for social insects where molecular mechanisms, such as differential gene expression, contribute to observed phenotypic differences between reproductive and non-reproductive morphs. In comparison, other mechanisms, such as tissue-specific expression and gene duplications, have been posited as contributing to social morph differences yet formal investigations are limited. Here, using a combination of transcriptomics for multiple tissues and comparative genomics, we show that in a social bumblebee, the strongest differences in gene expression are found in reproductive tissues, such as the spermatheca, an organ previously believed as vestigial in workers but recently shown as functional. In comparison, we find modest expression differences in genes between queens and workers for the brain, fat body, and ovary, which are traditionally investigated in social evolution. Interestingly, morph-biased genes in these three tissues display higher tissue-specificity suggesting that while social morphs may express a shared core transcriptome, localised expression profiles may contribute to phenotypic differences. We also find evidence of differential usage of duplicated genes by queens and workers, highlighting structural variants as a contributing factor to morph differences. Collectively, our findings highlight how social insects can utilise tissue-specific gene regulation and structural variants to contribute to phenotypic differences.