title: A transposase-derived gene required for human brain development

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement, and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements. In the mouse cortex, loss of Pgbd5 leads to aberrant differentiation and gene expression of distinct neuronal populations, including multiple types of glutamatergic neurons, potentially explaining the features of PGBD5 deficiency in humans. Together, these studies nominate PGBD5 as the long-hypothesized neuronal DNA nuclease and transposase-derived gene required for brain function in mammals.

overall_design: Motor cortices from 21 days old Pgbd5wt/wt (n=3) and Pgbd5-/- (n=3) littermates were disected and subjected to nuclei extraction. 10x Multiome was performed in the samples with the goal to understand Pgbd5 roles on neuronal physiology and numbers.

first: Luz

last: Jubierre Zapater

first: Rodrigo

last: Lopez Gutierrez

first: Steven

last: Hébert

first: Alex

last: Kentsis


title: In vivo anti-FAP CAR T therapy reduces fibrosis and restores liver homeostasis in metabolic dysfunction-associated steatohepatitis

status: Public on Nov 05 2025

city: New York

first: Scott

last: Friedman

state: NY

address: 1425 Madison Ave

department: Liver Diseases

country: USA

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: In this study, we aimed to determine the efficacy of in vivo chimeric antigen receptor (CAR) T cell therapy, generated by targeted lipid nanoparticles (t-LNPs), as an anti-fibrotic in metabolic dysfunction-associated steatotic liver disease. Hepatic fibrosis is a key predictor of mortality in liver disease, driven by fibrogenic hepatic stellate cells (HSCs). In heart, chimeric antigen receptor (CAR) T cells targeting fibroblast activation protein alpha (FAP) reduce murine cardiac fibrosis. However, the value of this approach in liver is unknown. We explored the anti-fibrotic potential of in vivo-generated anti-FAP CAR T cells in metabolic dysfunction-associated steatohepatitis (MASH), a highly prevalent disease with no approved anti-fibrotic therapies. We first established that FAP expression in both human and murine MASH is specific to HSCs. We then used flow cytometry, Sirius Red morphometry, digital pathology analysis, and single nuclear RNA-sequencing to assess the impact of anti-FAP CAR T cell therapy on murine MASH. Anti-CD5 targeted-LNPs carrying anti-FAPCAR mRNA generate activated, transient anti-FAP CAR T cells, which significantly reduced fibrosis by depleting pro-fibrogenic HSCs, and by modulating immune cells, endothelial cells and hepatocytes in a non-cell autonomous manner to mitigate inflammation and restore hepatic homeostasis. These findings reinforce the potential of in vivo CAR T therapy to attenuate a highly morbid and pervasive liver disease through its integrated, multicellular salutary effects.

overall_design: Samples used were frozen minced murine liver (left lobe). There are four expeirmental groups: Chow diet + vehicle, FAT MASH model + vehicle, FAT MASH model + IgG-FAPCAR LNP, and FAT MASH model + CD5-FAPCAR LNP. About 10-15mg of snap frozen liver tissue from four representative mice per group were pooled. Samples were prepared via an established protocol for nuclei isolation from murine MASH tissue(36). Solutions used included 2xST buffer (292 mM NaCl (Thermo Fisher Scientific, cat. no. AM9759)), 20 mM Tris-HCl pH 7.5 (Thermo Fisher Scientific, cat. no.15567027), 2 mM CaCl2 (VWR International Ltd, cat. no. 97062-820) and 42 mM MgCl2 (Sigma Aldrich, cat. no. 1028) in DNA/RNAse free water. 0.03% TST was prepared by adding 5mL of 2xST, 83uL Ribolock,83uL 2%BSA, 300uL of 1% Tween20, 4.6mL of H2O. The samples used for snRNAseq Chromium 3’ GEX were from snap frozen Chow + saline, MASH + saline, MASH + IgG-FAPCAR, and MASH + CD5-FAPCAR livers, about 3 months after euthanasia and cryopreservation. Each sample was chopped for 10 minutes over ice and passed through a strainer with 1mL TST. Samples were spun down at 500xg for 5 minutes at 4oC, supernatant was aspirated. Pellet was resuspended by pipetting 30 times with P1000 tips in 200uL of 0.4% BSA/PBS and then brought to the Genetics Core.

first: Chittampalli

middle: N

last: Yashaswini

first: Li

last: Kenneth

middle: L


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for Cas9]

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. Our results demonstrate that CHANGE-seq-BE is highly sensitive than Digenome-seq to detect more bona fide off-targets with cellular activity ranging from 0.5% to 92.2%. Moreover, ABE exhibit more off-targets than Cas9 under same delivery conditions.

overall_design: Hybrid capture sequencing to validate bona fide off-targets sites nominated by CHANGE-seq-BE, CHANGE-seq, and Digenome-seq in primary human T-cells and hepatocytes.

first: Varun

last: Katta

first: Yichao

last: Li

first: Garret

last: Manquen


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for ABE targets]

summary: To assess CHANGE-seq-BE performance, we used it to characterize ABE8e-NRCH base editor activity targeting sickle mutation (HBBS) in the HBB gene and identified additional 29 (53% more) bona fide off-targets than CIRCLE-seq. Furthermore, CHANGE-seq-BE applied for ABE8e targeting five therapeutically relevant loci (B2M, CBLB, CD7, CIITA, and PDCD1) in human primary T-cells and compared with Digenome-seq. CHANGE-seq-BE is highly sensitive and capable of detecting bona fide off-targets while requiring approximately 20-fold less sequencing reads.

overall_design: CHANGE-seq-BE applied for ABE targeting MKSR, B2M, CBLB, CD7, CIITA, PDCD1, and PCSK9 in primary human cells (CD34+ HSPCs, T-cells, and hepatocytes)

first: Cicera

last: Lazzarotto

first: Elizabeth

last: Urbina

first: GaHyun

last: Lee


title: Nucleophosmin 1 lactylation in graft kidney induces ferroptotic trigger waves that exacerbate delayed graft function [RNA-Seq]

city: Chongqing

first: Xinyuan

address: Chongqing

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

summary: The effects of  NPM1 lactylation on transcriptional profiling in HK-2 cells

overall_design: We generated NPM1-knockout (NKO) HK-2 cells followed by reconstitution with WT NPM1 (NKO-NPM1 WT) or the K257R mutant (NKO-NPM1 K257R). RNA-sequencing analysis was performed to investigate the effect of NPM1-K257 lactylation on transcriptional profiling in HK-2 cells.

first: Xin

last: Gou

first: Tianxin

last: Lin

first: Weiyang

last: He


title: Strain Matters: Host Responses Reflect Symbiont Origin in the Squid-Vibrio Symbiosis

city: Pasadena

first: Vera

last: Beilinson

state: CA

address: 1200 E. California Blvd

department: Biology and Bioengineering

institute: Caltech

summary: Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses.

overall_design: Juvenile squid from the same clutch where exposed to 1 of 5 bacterial strains used in this study. Squid were considered part of the same clutch if their eggs were laid by the same parental pair at the same time and the hatchlings emerged synchronously. Clutch identity was tracked to account for genetic background in downstream analyses.

first: Grischa

middle: Y

last: Chen

first: Alexis

last: Hargadon

first: Edward

last: Ruby

first: Margaret

last: McFall-Ngai


title: Cryptococcus exploits delayed microglial activation, and microglial osteopontin (OPN/Spp1) impairs peripheral host control

status: Public on Nov 06 2025

city: Durham

first: Mari

middle: L.

last: Shinohara

state: NC

address: 207 Research Dr.

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: Cryptococcus, a neurotropic fungus and the World Health Organization (WHO) critical-priority pathogen, causes cryptococcal meningoencephalitis (CM), the second leading cause of death in HIV/AIDS patients. Despite the significance, host brain responses during CM remain underexplored. In a non-acute systemic mouse model, Cryptococcus infiltrates the brain within one day from circulation, yet full activation of microglia is delayed until 14 days post-infection. Microglia, regarded as sentinels of the central nervous system (CNS), exhibit slow responses, partly due to limited direct fungal recognition and reliance on T cells as a source of IFNg. Once activated, microglia upregulate Spp1, encoding osteopontin (OPN), a factor highly expressed in neurodegenerative diseases. Our findings demonstrate that microglia-derived OPN negatively impacts the host by altering peripheral immune responses. Thus, Cryptococcus exploits the delayed host response to establish brain infection, with activated microglia producing OPN in a host-detrimental manner.

overall_design: Age-matched female B6 WT and GeneX-/-mice were retro-orbitally infected with 10^6 yeasts/mouse of Cryptococcus neoformans (deneoformans) strain 52D; brains were collected at 0, 4, and 14 days post infection.  Samples from two mice were pooled for each time point, except 14-dpi which only had 1 sample. Brain cells were isolated using the Papain Dissociation Kit (Worthington Biochemical Corporation) and myelin was removed using Myelin Removal Beads II (Miltenyi Biotec). Live cells were enriched using the EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies).

first: Estefany

last: Reyes

first: Jae

last: Yong

first: Devon

middle: T

last: DiPalma

first: Jonathan

last: Messerschmidt

first: Miranda

last: Lumbreras

first: Hana

middle: H

last: Hendi

first: Danira

middle: R

last: Mukhamedyarova

first: Emily

middle: C

last: Troutman

middle: J

last: Wert


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for CBE targets]

first: Shengdar

last: Tsai

summary: To adapt and apply for cytosone base editors (CBEs), we perfomed CHANGE-seq-BE using eA3A-BE3 to target B2M, CBLB, CD7, CIITA and PDCD1 regions at different loci. CHANGE-seq-BE identified low frequency off-target editing rates ranging from 1.7% to 7.5%  that are not identified by Digenome-seq further implies CHANGE-seq-BE is highly sensitive and can identify true off-targets while requiring 20-fold fewer sequencing reads.

overall_design: CHANGE-seq-BE applied for eA3A-BE3 (CBE) targeting B2M, CBLB, CD7, CIITA, and PDCD1 in primary human T-cells

first: Garret

last: Manquen

first: Varun

last: Katta

first: Yichao

last: Li


title: A Single Day of Reduced Activity Alters the Next Day’s Transcriptomic and Metabolic Exercise Response

city: Cedarburg

first: Kevin

last: Gries

state: Wisconsin

address: W75N761 Tower Avenue Cedarburg, WI 5012

institute: Concordia University of Wisconsin

summary: Regular aerobic exercise decreases the risk of metabolic diseases, however reduced physical activity may attenuate these beneficial adaptations. This study investigated the influence of a single day of reduced activity on the skeletal muscle transcriptome (RNASeq) and systemic metabolism surrounding an acute bout of aerobic exercise. Utilizing a crossover design, subjects (n=9 [7M, 2F], 24±1y) exercised at 65% VO2max for 60-minutes following a day of reduced activity (IN; 3,581±1,185 steps) and normal activity (A; 11,069±3,631 steps). RNAseq from skeletal muscle biopsies was completed prior to and 4-hours post-exercise. Respiratory gas exchange analysis was completed at 20, 40, and 60 minutes of exercise. Blood samples for select metabolites were collected before, during, and throughout the 4-hour recovery. Inactivity resulted in nine Differentially Expressed Genes (DEG) at rest, while exercise altered 793 and 1,403 genes in A and IN, respectively. Gene set enrichment analysis revealed an interaction of exercise and trial that were related to inflammation, metabolism, cell cycle, and innate immunity. Respiratory exchange ratio (0.93±0.04 vs. 0.91±0.03; p<0.05) and carbohydrate utilization (2.16±0.79 vs. 1.96±0.72 g/min; p=0.09) was higher in the IN vs. A trial at 60-minutes of exercise. Triglycerides were higher in the IN trial (p<0.05),with no differences between trials observed in other measured metabolites. These findings indicate that a single day of reduced physical activity can elicit modest but significant changes in the metabolic and transcriptomic exercise response. Such alterations have implications for exercise guidelines and underscore the importance of controlling for daily step count when assessing exercise responses.

overall_design: RNAsequencing of human skeletal muscle before and 4 hours after exercise after a day of normal activity or inactivity.

first: Joseph

last: McGraw

last: Goetz-Sutinen

first: Jessica

last: Grimm

last: Baranowski

first: Mark

last: Berres


title: Serine tRNAs Compete to Regulate the mRNA Translation Of Serine-sensitive Codons

first: Robert

middle: S

last: Banh

address: 522 First Avenue, Smilow 907

department: Radiation Oncology

institute: New York University

summary: Differential mRNA translation efficiency (mTE) of codons is important in regulating protein synthesis, cellular states, and can change in response to amino acid (AA) availability. While the mTE of codons is canonically associated with their corresponding transfer RNA (tRNA) isoacceptors, its regulation by AAs in mammalian cells remains unexplored. We found that ELAC2, a 3’ tRNA maturation endonuclease, decreases the mTE of UC[U/C] serine (Ser) codons in response to Ser-limitation. Ablation of ELAC2 restored UC[U/C] mTE but reduced the mTE of AG[U/C] Ser codons. Among the tRNASer isoacceptors, tRNASer(GCU) decreased the most in ELAC2-deficient cells. Surprisingly, tRNASer(GCU) delivery restored AG[U/C] mTE and reduced UC[C/U] mTE in ELAC2-deficient cells. Finally, we deciphered the effects of Ser-sensitive codons on mRNA translation and the human proteome. Our study revealed that in response to Ser-limitation, regulation of tRNASer(GCU) levels fine-tune the mTE of UC[C/U] or AG[U/C] Ser-sensitive codons and shapes the proteome.

overall_design: Ribosome profiling and charged-tRNAseq was performed in PATU-8902 control (sgLUC) and ELAC2 KO (sgELAC2) cells grown with or without serine and glycine for 24hours.

first: Veronica

last: Costiniti

first: Wyatt

last: Tran

first: Nandhini

last: Rajesh Babu

first: Kanshin

last: Evgeny

first: Beatrix

last: Ueberheide

first: Alec

last: Kimmelman


title: Transcriptional network analysis of PTEN protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

city: Derio

first: Arkaitz

last: Carracedo

state: Biscay

address: Parque Científico Tecnológico de Bizkaia building 801A, POST-DOC Arkaitz, 4470

country: Spain

institute: CIC bioGUNE

summary: Among the extensive genomic alterations in prostate cancer, PTEN deletion stands out as one of the most consistently observed events. PTEN loss in prostate tumors is primarily associated with cancer cell proliferation and survival through the activation of the PI3K-AKT-mTOR signaling pathway. However, the use as a robust biomarker in clinical practice is hampered by its complex epigenetic, transcriptional, and post-translational regulation. In situ protein assessment by immunohistochemistry (IHC) captures PTEN protein status, but it does not report on associated tumor microenvironment remodeling.  Here, we undertook an approach that combined PTEN immunoreactivity analysis with high-throughput transcriptional analysis to gain insights into the downstream functional effects of PTEN protein loss in primary tumors. Our extensive bioinformatic analyses highlighted stromal remodeling as a prominent cancer cell-extrinsic process associated with PTEN loss. By extending our transcriptomic computational strategy to Pten-loss driven murine prostate cancer, we validated the causal role of Pten in the stromal reaction observed in clinical specimens. Mechanistically, we provide experimental evidence for the activation of a paracrine program that encompasses enhanced TGF-β signaling and that is compatible with the secretome of PTEN-deficient senescent cancer cells. Finally, our findings enable the sub-stratification of tumors with PTEN loss based on their senescence-associated stroma remodeling program to distinguish indolent from aggressive cases. Our study provides relevant biological context to the cellular and molecular alterations unleashed upon PTEN protein loss in prostate cancer.

overall_design: Transcriptomic profiles were generated from 197 primary prostate tumors to investigate molecular changes associated with PTEN protein loss, as determined by immunohistochemical (IHC) analysis.

first: Ivana

last: Rondon-Lorefice

first: Jose

middle: I

last: Lopez

first: Aitziber

last: Ugalde-Olano

first: Maite

last: Zufiaurre

first: Ianire

last: Astobiza

first: Natalia

last: Martin-Martin

first: Laura

last: Bozal-Basterra

first: Saioa

last: Garcia-Longarte

first: Amaia

last: Zabala

first: Sofia

last: Rey

first: Aida

last: Santos-Martin

first: Miguel

last: Unda

first: Ana

last: Loizaga-Iriarte

first: Mariona

last: Graupera

first: Paolo

last: Nuciforo

first: Isabel

last: Mendizabal


title: Nucleophosmin 1 lactylation in graft kidney induces ferroptotic trigger waves that exacerbate delayed graft function

first: Xinyuan

last: Li

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify the genome-wide binding sites of lactylated NPM1 and understand its role in transcriptional regulation.

overall_design: We generated NPM1-knockout (NKO) HK-2 cells followed by reconstitution with WT NPM1 (NKO-NPM1 WT) or the K257R mutant (NKO-NPM1 K257R).Fragmented chromatin was immunoprecipitated overnight at 4°C with anti-NPM1 antibody or rabbit IgG, followed by incubation with protein G-agarose beads.

first: Xin

last: Gou

first: Tianxin

last: Lin

first: Weiyang

last: He


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for CD40L target]

first: Shengdar

last: Tsai

summary: By CHANGE-seq-BE, we identified a total of 81 potential off-targets and confirmed 95.4% frequencies of on-target editing with no evident off-targets above the detection threshold compared to controls (rhAmp-seq, IDT).

overall_design: CHANGE-seq-BE applied as an IND-enabling assay to support an emergency FDA-cleared IND study to treat a patient with X-linked Hyper IgM syndrome due to CD40L mutation.

first: Garret

last: Manquen

first: Varun

last: Katta

first: Yichao


title: Multi-omics profiling of cachexia-targeted tissues reveals a spatio-temporally coordinated response to cancer

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

summary: Cachexia is a wasting disorder associated with high morbidity and mortality in patients with cancer. Tumour-host interaction and maladaptive metabolic reprogramming are substantial, yet poorly understood, contributors to cachexia. Here we present a comprehensive overview of the spatio-temporal metabolic reprogramming during cachexia, using integrated metabolomics, RNA sequencing and 13C-glucose tracing data from multiple tissues and tumours of C26 tumour-bearing male mice at different disease stages. We identified one-carbon metabolism as a tissue-overarching pathway characteristic for metabolic wasting in mice and patients and linked to inflammation, glucose hypermetabolism and atrophy in muscle. The same metabolic rewiring also occurred in five additional mouse models, namely Panc02, 8025, ApcMin, LLC and KPP, and a humanised cachexia mouse model. Together, our study provides a molecular framework for understanding metabolic reprogramming and the multi-tissue metabolite-coordinated response during cancer cachexia progression, with one-carbon metabolism as a tissue-overarching mechanism linked to wasting.

overall_design: RNA-seq profiling of liver (L), heart (H), gastrocnemius muscle (GC), epididymal (E) and inguinal (I) adipose tissues from healthy control mice (PBS-injected), non-cachectic NC26 tumor mice (NC), pre-cachectic (Pre) and cachectic (Cax) C26 tumor mice

first: Pauline

last: Morigny

first: Michaela

last: Vondrackova

first: Honglei

last: Ji

first: Konstantinos

last: Makris

first: Radka

last: Trubacova

first: Tuna

middle: F

last: Samanci

first: Doris

last: Kaltenecker

first: Sophia

middle: E

last: Chrysostomou

first: Anna

last: Bidovec

first: Mariana

last: Ponce-de-Leon

first: Tanja

last: Krauss

first: Claudine

last: Seeliger

first: Olga

last: Prokopchuk

first: Marc

last: Martignoni

first: Melina

last: Claussnitzer

first: Hans

last: Hauner

first: Martina

last: Schweiger

first: Laure

middle: B

last: Bindels

first: Mauricio

last: Berriel Diaz

first: Stephan

last: Herzig

first: Ondrej

last: Kuda

first: Maria

last: Rohm


title: scRNA seq of Pdgfra+ cells from the mouse intestine

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

summary: Sorted PDGFRA+cells  that were lineage-negative for other major intestinal cell type markers (EPCAM1, TER119, CD45, PECAM1) were obtained from the colon of 5 mice. Briefly, mice were given 2.0% (weight/volume) DSS (Thermo Fisher Scientific, #J14489-22) dissolved in water for 7 days for the acute model of DSS. In the chronic model, DSS-administration was followed by a water recovery phase lasting for another 7 days. This cycle was repeated 2 more times, with mice weights being recorded daily.

overall_design: 3 Acute DSS treated vs. 2 Chronic DSS treated  samples from Il11mNG reporter mice

first: Vladislav

last: Pokatayev

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: Lack of Caspase 8 Directs Neuronal Progenitor-like reprogramming and Small Cell Lung Cancer Progression

city: Cologne

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

institute: University of Cologne, Medical Faculty and University Clinic Cologne

type: Methylation profiling by high throughput sequencing

summary: Mimicry of neuronal features is emerging as malignant regulator of cancer growth and metastasis. Neuroendocrine (NE) cancers including small cell lung cancers (SCLC) have been shown to share expression profiles marking various stages of neuronal differentiation. Yet, how these state changes are caused and malignant consequences thereof have remained unexplored.Here, we devise a novel mouse model of SCLC recapitulating low expression of caspase 8 as seen in humans and uncover that this allows for epigenetic reprogramming towards a more aggressive and metastasising stem-cell like neuronal state, resembling neuronal intermediate progenitor cells (nIPCs). Notably, transcriptional signatures of this cellular state are enriched in relapsed and metastatic human SCLC. Mechanistically, caspase 8 loss within the pre-tumoral niche promoted immunosuppression and metastasis via induction of immunogenic cell death. Inactivation of the necroptosis executioner Mixed lineage kinase domain-like protein (MLKL) neutralised caspase 8 loss-induced immunosuppression, metastasis and diminished the stem-cell like state providing genetic evidence for a role of necroptosis in promoting these effects. Collectively our data uncover an unexpected role for low expression of caspase 8 in directing neuronal-like reprogramming towards an immunosuppressive and highly metastatic state in SCLC.

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and inuced tumor by adeno cre inhalation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines (four of each genotype) and perfomed Methyl-seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor cells

first: Alicja

last: Pacholewska

first: Michal

first: Ariadne

last: Androulidaki

first: Silvia

last: von Karstedt


title: Identifying the molecular basis for functional divergence of duplicated SOX factors controlling endoderm formation and left-right patterning in zebrafish

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including liver and pancreas. Placement and patterning of these organs relies on the left-right organiser – known as Kupffer’s Vesicle (KV) in zebrafish. Transcription factors Sox32 and Sox17 are members of the zebrafish SoxF subfamily. Sox32 and sox17 arose from duplication of ancestral Sox17 in the teleost lineage. Sox32 induces sox17 expression in early embryos and is required for specification of endoderm and KV progenitors. Zebrafish Sox17 is implicated in KV morphogenesis. In mammals, Sox17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Phenotypic evidence therefore suggests functional similarities between zebrafish Sox32 and Sox17 with mammalian SOX17. We sought to explore the functional differences and potential similarities between these proteins in the early zebrafish embryo. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its HMG domain from its paralogue Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificity and divergence in mediating differential gene regulatory programmes. Finally, we establish that specific conserved peptides in the C-terminal domain are essential for the role of Sox17 in establishing correct organ asymmetry. Overall, our results provide novel insights into vertebrate endoderm development, left-right patterning, and the evolution of SoxF transcription factor function.

overall_design: To investigate the functional differences between SOX family transcription factors implicated in endoderm formation and left-right patterning (mammalian SOX17 and zebrafish Sox17 and Sox32) we injected equimolar quantities of mRNA encoding these factors into zebrafish embryos at the one-cell stage and performed RNA-seq analyses at 6 hours post-fertilisation.  To determine whether differences in the HMG domains between zebrafish Sox17 and Sox32 were critical to their distinct functions we produced mRNAs for Sox32 lacking the HMG domain, or where the Sox32 HMG domain had been substituted for that of Sox17.  We then performed RNA-seq analyses as previous.

first: Simaran

last: Johal

first: Randa

last: Elsayed

first: Kristen

middle: A

last: Panfilio


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for CBE and ABE]

first: Shengdar

last: Tsai

first: Varun

last: Katta

first: Yichao

last: Li

first: Garret

last: Manquen


title: GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [CLIP-seq]

city: Dortmund

first: Jeffrey

middle: Lesslie

last: Schloßhauer

address: Otto-Hahn-Straße 11

department: Chemical Genomics Centre

institute: Max Planck Institute of Molecular Physiology

summary:
Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells.
In acute myeloid leukemia (AML) RBPs are key regulators of tumor proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remains unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. We identified the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a pro-proliferative factor in AML cells. Based on cross-linking and immunoprecipitation (CLIP) we are defining the global targetome detecting novel RNA targets mainly located within 5’UTR including GAPDH, RPL13a, PKM and ENO1. The knockdown of GAPDH unveiled genetic pathways related to ribosome biogenesis, translation initiation, and regulation. Moreover, we were able to demonstrate a stabilizing effect through the GAPDH binding to target transcripts including its own mRNA, unveiling GAPDH’s pivotal role in cancer. The present findings provide new insights on the pathophysiological role of GAPDH in AML.

overall_design: To investigate the influence of GAPDH on RNA-binding we conducted CLIP-seq under low glucose,  normal glucose and galactose culturing conditions.


title: GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [GAPDH_KD_RNAseq]

overall_design: To investigate the influence of GAPDH depletion a knockdown of GAPDH was induced by shRNA under low glucose, normal glucose and galactose culturing conditions.


first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: Mimicry of neuronal features are emerging as malignant regulators of cancer growth and metastasis. Neuroendocrine (NE) cancers and small cell lung cancers (SCLC) in particular have been shown to share expression profiles marking various stages of neuronal differentiation. Yet, how these state changes are caused and malignant consequences thereof have remained unexplored.  Here, we devise a novel mouse model of SCLC recapitulating low expression of caspase 8 as seen in humans and uncover that this allows for epigenetic reprogramming towards a more aggressive and metastasising stem-cell like neuronal state. Notably, transcriptional signatures of this neuroendocrine cellular state are enriched in relapsed and metastatic human SCLC. Mechanistically, caspase 8 loss within the pre-tumoral niche promoted immunosuppression and metastasis via induction of immunogenic cell death. Inactivation of the necroptosis executioner Mixed lineage kinase domain-like protein (MLKL) neutralised caspase 8 loss-induced immunosuppression, metastasis and diminished the stem-cell like state providing genetic evidence for a role of necroptosis in promoting these effects. Collectively our data uncover an unexpected role for low expression of caspase 8 in directing neuronal-like reprogramming towards a highly metastatic stem cell-like state in SCLC.

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and inuced tumor by adeno cre inahlation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines  (four of each genotype) and perfomed RNA seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor  cells

first: Fanyu

last: Liu

middle: M

last: Bebber


title: Uncovering the Roles of PPARγ and the Immunoproteasome in ILC2 Regulation

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: ILC2 cells were discovered less than 10 years ago. The activation and regulation of these cells have been extensively studied and some mechanisms have been discovered, but certain regulatory pathways have yet to be defined. PPARg and the immunoproteasome seem to play a major role in this regulation, but their exact function is still unknown. The aim of this project is to study the role of both the immunoproteasome and the transcriptional factor PPARg in ILC2 physiology using RNAseq.

overall_design: ILC2 cells were divided into three treatment groups: untreated control, IL-33 stimulation alone, and combined treatment with IL-33 and the PPARγ antagonist PKS3053. RNA-seq was performed to assess transcriptional changes across conditions.

first: Paoline

last: Laurent

first: Franck

last: Barrat


title: GLIS3 RNA-seq

first: Alok

last: Jaiswal

summary: Define the transcriptome of fibroblasts perturbed for GLIS3 in response to fibrotic stimuli.

overall_design: IL-11mNG CRISPRko Ctrl/Glis3KO, and IL-11mNG CRISPRa Ctrl/Glis3A fibroblasts were treated with a combination of TGFb and IL1b (10ng/ml) over a timecourse of 24 hours. Cells were collected, RNA isolated, and submitted for bulk RNA-seq.

first: Vladislav

last: Pokatayev

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: GLIS3 ChIP-seq

summary: Define the DNA targets of fibroblast GLIS3 in response to fibrotic stimuli.

overall_design: IL-11mNG GLIS3-FLAG fibroblasts were treated with a combination of TGFb and IL1b (10ng/ml) over a timecourse of 24 hours. Cells were collected and ChIP Seq was performed. Sheared DNA lysate was incubated with anti-H3K4me3, -FLAG, or -IgG for the procedure.


title: Androgen receptor drives polyamine synthesis creating a vulnerability for prostate cancer

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: The androgen receptor (AR) enacts metabolic effects of the anabolic steroid testosterone, but how AR-directed metabolic changes affect prostate cancer progression is not well understood. Here, we show that the AR increases de novo polyamine synthesis by direct transcriptional regulation of ornithine decarboxylase (ODC) expression across cell types, including prostate cancer cells. Likewise, androgen treatment of prostate cancer models increased intracellular and secreted polyamines, a process that was critical for tumor development as both genetic and pharmacologic inhibition of AR-induced polyamine synthesis enhanced growth inhibition of prostate cancer by supraphysiological androgens. This polyamine reduction lessened negative feedback regulation of S-adenosylmethionine synthase 1 (AMD1), enhancing its utilization of S-adenosylmethionine (SAM), which reduced global protein methylation patterns and expression of the protooncogene MYC. The ODC inhibitor difluoromethylornithine (DFMO) was effective in reduction of polyamines in patients with metastatic CRPC even despite treatment with bipolar androgen therapy, supporting further study of this therapy combination. Thus, the AR is a critical regulator of polyamine synthesis, which may constitute a vulnerability in prostate cancer treated with bipolar androgen therapy.

overall_design: LNCaP cell line was obtained from American Type Culture Collection (ATCC) and grown in RPMI 1640 (Gibco; 11835-055) supplemented with 10% fetal bovine serum (Corning), sodium lactate 1.6mM, sodium pyruvate 0.5mM, L-alanine 0.43mM, 1% pen-strep (Gibco). The vector pCDH-puro-cMyc vector (Addgene; 46970, J Wang laboratory) and pCDH-EF1-FHC empty vector control (Addgene, 64874, R Wood laboratory) were transfected into 293T cells (ATCC) along with pMD2.G (Addgene; 12259) and psPAX2 (Addgene; 12260) packaging vectors using lipofectamine (Invitrogen) to produce cMyc-puro, control-puro, and Tet-On-shAR-puro lentivirus particles. Two days after transduction with indicated virus, vector-expressing cells were selected with puromycin 1ug/ml for 72 hours. Cells were maintained at 37 ⁰C in 5% CO2. They regularly tested negative for mycoplasma contamination using MycSensor PCR Assay kit (Agilent Technologies). R1881, DFMO, Putrescine and vehicle control were supplemented into the media of duplicate cultures and RNA obtained from the cells as processed as indicated.

first: Laura

last: Sena

first: David

last: Sanin


title: Genetic vulnerabilitis study in VHL mutant cells

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

summary: VHL has been known as a tumour suppressor gene, also is an essential gene for some proteolysis-targeting chimera (PROTAC) degraders. Here by using CRISPR-cas9 genome wide screening we find that VHL mutation results in strong proliferation defect by HIF1A . VHL MUT shows malfunction of mitochondria which can be restored by HIF1A inhibition. VHL MUT bear specific genetic vulnerabilities which are druggable and mainly HIF1A dependent. In OE33 and MCF7, additional HIF1A inhibition on VHL MUT allows a complete ARV-771 drug resistance acquisition. Our study reports the consequence of VHL mutation and HIF1A dependent druggable genetic vulnerabilities in VHL mutant renal epithelial cells and possible PROTAC resistance acquisition mechanism in breast and oesophageal cancers, provides potential therapeutic targets and strategies for early precancerous and established cancerous cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VHL WT HK2 clones (D-C8, D-C10, D-C35) and VHL KO HK2 clones (C8, C10, C35).

first: Sakari

last: Vanharanta


title: Single-cell transcriptomic analysis suggests potential differences in the developmental stage and quantity of adipose progenitor cells between bovine intramuscular and subcutaneous fat

status: Public on Nov 04 2025

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

summary: Background: Intramuscular fat (IMF), the white adipose tissue deposited between skeletal muscle fibers, is a key determinant of beef quality due to its contribution to meat, flavor, juiciness and tenderness. However, IMF develops later and grows more slowly, compared to other fat depots such as subcutaneous fat (SF) in cattle. The cellular and molecular mechanisms underlying the delayed development and slower growth of IMF compared to other fat depots remain poorly understood. Results: We performed single-cell RNA sequencing (scRNA-seq) on the stromal vascular fractions (SVFs) from IMF and SF of adult Angus crossbred steers as well as the mononuclear cell fractions (MCFs) from skeletal muscles of newborn Angus crossbred bull calves, with each tissue type collected from two animals. A total of 14,802 cells from 6 animals were sequenced. A clustering analysis revealed that these cells comprised ten cell types, including adipose progenitor cells (APCs), muscle satellite cells (MuSCs), myoblasts, smooth muscle cells, and various immune cell populations. The SF SVF from adult cattle harbored a significantly higher proportion of APCs than the IMF SVF. The MCFs from newborn calves did not contain detectable APCs. A subclustering analysis revealed that the APCs comprised six subpopulations (C0–C5), among which C3 and C5 were absent in the IMF SVF while C1 was markedly less abundant in the IMF SVF than the SF SVF. A gene set variation analysis and a pseudotime trajectory analysis showed that C1 and C3 represented more differentiated APCs, with higher expression of genes involved in adipogenesis, such as PPARG, ADAM12, and PPARGC1A, whereas subclusters C0 and C4 represented undifferentiated, uncommitted APCs, with higher expression of genes involved in DNA replication and cell adhesion, compared to the other subclusters. Conclusions:Overall, this single-cell transcriptomics study suggests two potential differences in APCs between IMF and SF in adult cattle: (1) IMF contains fewer APCs than SF; (2) APCs in IMF are adipogenically less committed and differentiated compared to APCs in SF. These differences may explain why IMF develops later and grows more slowly than SF in cattle. This study also suggests that, in cattle, intramuscular fat begins to develop postnatally, challenging the widely held belief that it forms during late gestation.

overall_design: Stromal vascular fractions (SVFs) were isolated from intramuscular fat (IMF) and subcutaneous fat (SF) of adult Angus crossbred steers (n = 2 per tissue type). Mononuclear cell fractions (MCFs) were isolated from longissimus dorsi skeletal muscles of newborn Angus crossbred bull calves (n = 2). Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 10x Genomics Chromium Single Cell 3’ platform and sequenced on an Illumina NovaSeq 6000. The study aimed to compare the abundance, subpopulation composition, and differentiation states of adipose progenitor cells (APCs) between IMF and SF, and to determine whether APCs are present in neonatal skeletal muscle.

first: Pengcheng

last: Lyu

first: Honglin

last: Jiang


title: IAF scRNA seq

summary: Human fibroblast cells were treated with a combination of fibrotic cytokines (TGF-b and IL-1b) over a time course of 0, 6, 12 and 24 hours. Live cells were collected and submitted to single cell sequencing.


title: Disparate Leukemia Mutations Converge on Nuclear Phase-Separated Condensates

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A, and mutations in NPM1. How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to recruit NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.

overall_design: NPM1WT/Degron OCI-AML3 cells were transduced with the lentiviral particles to induce FL-NPM1c, “C-body null”, or mCherry overexpression after endogenous NPM1c degradation with dTAG-13. mCherry positive cells were FACS isolated

first: Gandhar

middle: K

last: Datar

first: Elmira

last: Khabusheva

first: Archish

last: Anand

first: Joshua

last: Beale

first: Marwa

last: Sadek

first: Chun-Wei

last: Chen

first: Evdokiia

last: Potolitsyna

first: Nayara

last: Alcantara-Contessoto

first: Guangyuan

last: Liu

first: Josephine

last: De La Fuente

first: Christina

last: Dollinger

first: Anna

last: Guzman

first: Alejandra

last: Martell

first: Katharina

last: Wohlan

first: Abhishek

last: Maiti

first: Nicholas

last: Short

first: S. Stephen

last: Yi

first: Vibeke

last: Andresen

first: Bjørn Tore

last: Gjertsen

first: Brunangelo

last: Falini

first: Rachel

last: Rau

first: Lorenzo

last: Brunetti

first: Nidhi

last: Sahni

last: Riback


title: Transcriptional profile of Mycobacterium tuberculosis peptide-specific T cells in pulmonary granulomas

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The function of Mycobacterium tuberculosis peptide-specific T cells in granulomas is incompletely understood. Here we profiled rhesus macaque and human Mtb-specific T cells by performing single cell RNA sequencing on granuloma cells stimulated with Mtb peptide pools. Mtb-specific T cells express pro-inflammatory cytokines, chemokines, TNF superfamily molecules, SLAM family molecules, semaphorins, growth factors, proteases and collagen. Peptide recognition by Mtb-specific T cells also drives expression of FLT3LG, LTA and XCL1 in bystander and unconventional CD8 T cells. Granuloma T cells express transcripts encoding multiple cytotoxic molecules, while peptide-specific T cells primarily express granzyme B. In granulomas from a patient that underwent a pneumonectomy to remove tuberculosis-destroyed lung, we identify a population of peptide-specific T cells similar to macaque peptide-stimulated T cells. Thus, Mtb peptide-specific T cells may mediate protection against Mtb infection through the combined effects of many functions as well as the induction of bystander responses by neighboring T cells.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Scale Bio single-cell RNA seqsequencing of granulomas from human and Rhesus macaque

first: Christine

last: Nelson

first: Keith

middle: D

last: Kauffman

first: Kevin

last: Osum

first: Shunsuke

last: Sakai

first: Jay

last: Buchanan

first: Jean

last: Chanchu

first: Melanie

last: Cohen

first: Julie

last: Laux

first: Iyadh

last: Dougi

first: Katherine

last: Barrows

first: Ifeanyichukwu

middle: U

last: Anidi

first: Cecilia

last: Lindestam Arlehamn

first: Alessandro

last: Sette

first: April

last: Walker

first: Amirhossein

last: Shamsaddini

first: Justin

last: Lack

first: Joel

last: Ernst

first: Carl

middle: G

last: Feng

first: Laura

last: Via

middle: P

last: Fennelly

first: Shamus

last: Carr

first: Daniel

middle: L

last: Barber


first: Fanyu

last: Liu

address: Joseph-Stelzmann Str. 26

institute: CECAD

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and induced tumor by adeno cre inhalation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines (four of each genotype) and perfomed Methyl-seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor cells

first: Ariadne

last: Androulidaki

first: Pascal

last: Hunold

first: Vignesh

last: Sakthivelu

first: Ilmars

last: Kisis

first: Silvia

last: von Karstedt


title: APOBEC3 promotes squamous differentiation and metastases via IL1A/AP-1 signaling

city: Chapel Hill

first: William

last: Kim

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

summary: In urothelial carcinoma, up to 70% of mutations are caused by mutagenic activity of the APOBEC3 deaminases. To dissect the role of APOBEC3 in the progression of UC, we generated a mouse model UPPA with conditional knock out of Pten and Trp53 in addition to mouse Apobec3 (mA3) overexpression and scRNAseq was performed on the mouse bladder tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
UPPA and UPP mouse bladder tumors are anlyzed using scRNAseq
human bladder tumor scRNAseq

>>>Raw data for human samples are deposited in dbGaP due to patient privacy concerns<<<

first: Andrew

last: Truong

first: Mi

last: Zhou

middle: Y


title: The outcomes of caloric restriction are driven by enhanced glucocorticoid rhythms.

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

institute: helmholtz munich

summary: Caloric restriction extends lifespan and healthspan across species, with feeding times synchronized to circadian rhythms further maximizing its benefits. However, the mechanisms linking diet, diurnal rhythms, and lifespan are not fully understood. In mice, the time point most strongly tied to dietary effects on lifespan coincides with the peak of glucocorticoid secretion (ZT12, lights-off). Caloric restriction raises circulating glucocorticoid hormone levels, but their functional relevance remains untested. We show that the glucocorticoid receptor (GR) is critical for the effects of caloric restriction. Hepatocyte-specific GR mutant mice fail to respond to caloric restriction indicating that increased glucocorticoid amplitudes support its benefits. Using multiomics techniques in murine liver, we find that nutrient deprivation elicits a nuclear switch from active STAT signaling to increased FOXO1 activity, enabling the GR to activate a unique diet-specific gene expression program. Taken together, our results suggest that glucocorticoid rhythms are crucial for caloric restriction-induced metabolic reprogramming.

overall_design: Wild-type and glucocorticoid receptor hepatocyte-specific knock-out (GR-LKO) mice were treated to 40% caloric restriction (CR) or night-restricted fed (NRF) as control. Then we harvested their liver, and isolation the liver nuclei through centrifugation.

first: Konstantinos

last: Makris

first: Ioannis

last: Deligiannis

first: Liwei

last: Zhang

first: Fania

last: Feby Ramadhani

first: Celia

last: Martinez-Jimenez

first: Fabiana

last: Quagliarini

first: Nina Henriette

last: Uhlenhaut


title: Transcriptomics insights into the functional role of tick Ixodes ricinus midgut proteins metalloprotease and antigen p23

city: Ciudad Real

first: Rita

last: Vaz-Rodrigues

address: Ronda de Toledo 12

department: SaBio

institute: Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM)

summary: Ticks are hematophagous ectoparasites that impact human and animal health worldwide. Tick saliva contains multiple biomolecules capable of disrupting host immunity, occasionally causing emergent tick-borne allergies like the alpha-Gal syndrome (AGS). Current results highlight a knowledge gap in characterizing tick salivary biomolecules, without alpha-Gal modifications, that influence host response to alpha-Gal and may be implicated in the AGS. This study aimed to functionally characterize biomolecules antigen p23 (A0A0K8RKR7) and metalloprotease (A0A0K8RCY8) based on their role in Ixodes ricinus tick feeding and reproduction, determined after gene knockdown by RNA interference and further transcriptomics analysis. Silencing the expression of antigen p23 and metalloprotease did not result in any significant differences in tick engorgement and egg batch weights compared to the GFP control group. Transcriptomics analysis revealed a total of 438 differentially expressed genes (DEGs) were found in the antigen p23-silenced group, including 149 upregulated and 78 downregulated genes. GSEA analysis following antigen p23 gene knockdown identified significantly upregulated pathways associated with protein production and suppressed routes mostly correlated with ion transport, lipid metabolism, catalytic activity, protein modification, and G-protein activity. Partially silencing metalloprotease in tick midguts led to the identification of 182 DEGs, comprising 104 upregulated and 78 downregulated genes. Ablation of endogenous metalloprotease led to the upregulation of several biological and functional pathways associated with RNA splicing and significantly suppressed routes connected with detoxification, protein modification, catalytic activity and molecule binding. These findings provide valuable insights into tick physiology, providing a foundation for further research on tick-host interactions and AGS pathogenesis.

overall_design: Total RNA from 3 groups (antigen p23, metalloprotease and GFP control) was submitted to RNA-seq anaysis. Samples included the midguts of nine Ixodes ricinus female ticks per group divided into three biological replicates, each containing three ticks per pool.

first: Vincent

middle: C

last: Duru

first: Ard

last: Nijhof

first: José

last: de la Fuente


title: Global characterization of Dictyostelium discoideum gene expression changes under hypoxic conditions

city: Villeubanne

first: Julie

last: hesnard

state: FRANCE

address: HESNARD

country: France

institute: Institut Lumière Matière

summary: Aerobic eukaryotes utilize oxygen (O2) to oxidize metabolites and generate ATP. The protist kingdom lacks the Hypoxia Inducible Factor-dependent transcriptional response network to accommodate low O2 though possesses a HIF prolyl hydroxylase that initially mediates the response. To address the scale and scope of hypoxic responses in protists, we characterized transcriptomic and proteomic changes when the social amoeba Dictyostelium is subjected to low (1%) O2 under nutritive conditions over 24 h followed by reoxygenation. Remarkably, 32% of the transcripts quantified were differentially expressed during hypoxia, with greatest changes associated with early (1 h) and late phases (24 h). Protein changes were modestly correlated with and generally lagged behind transcriptional changes. Correlated changes were observed for transcripts and proteins associated with various metabolic, anabolic, and catabolic pathways, as well as chromosome organization, cell cycling, vesicular trafficking, and signaling. Analysis of 4 marker genes showed extremely rapid responses that were graded over a range of O2 levels, with differential responses to inhibitors affecting protein synthesis and mitochondria. Overall, the amoebal response to a low but non-toxic O2-level resulted in massive remodeling of the transcriptome and proteome.

overall_design: Dictyostelium AX3 cells were placed under hypoxic conditions (1% O2) for 24 hours and then reoxygenated for 5 hours (20% O2). Cells were collected for transcriptomic (and proteomic) analysis at 1h, 5h, and 24h of hypoxia, and at 1h and 5h of reoxygenation. Cells were also collected from the culture tube at t0 (21% O2).Transcripts sequencing, alignment with the reference genome, and bioinformatic processing to obtain differential expressions (compared to t0) with a relative FDR were performed by the company GenXpro (GenXpro GmbH, Germany).

last: Hesnard

first: Hanke

last: van der Wel

first: Olivier

last: Cochet-Escartin

first: Stephane

last: Joly

first: Elisabet

last: Gas-Pascual

first: Jean-Paul

last: Rieu

first: Christopher

last: West

first: Christphe

last: Anjard


title: Radon Exposure Delays the Development of Skin Lesions in a Mouse Model of Psoriasis

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: We used transgenic mice that spontaneously develop chronic psoriatic skin lesions inflicted (CD11c-IL-17Aind/ind mice) to investigate effects induced by multiple radon exposures. Comprehensive transcriptome profiling of non-lesional skin showed downregulation of genes associated with psoriasis initiation, while anti-inflammatory genes were upregulated. Pathway enrichment analysis revealed immunosuppressive effects related to T cell regulation, similar to UV radiation-induced response.

overall_design: Investigation of plaque formation (skin) throughout the observation period; cytokine release (serum), immune status and proliferation marker after sacrification. Transcriptome profiling (skin) was performed.

first: Sylvie

last: Lerchl

first: Julia

last: Wiedemann

first: Andreas

last: Maier

first: Franziska

last: Papenfuß

first: Anna

last: Brand

first: Björn

last: Clausen

first: Claudia

last: Fournier


title: Chameau (HBO1) regulates starvation in a temperature-dependent manner in Drosophila melanogaster

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

institute: MDC-Berlin

summary: The body temperature of Drosophila melanogaster depends on the extrinsic temperature. Numerous studies show that environmental temperature influences metabolism, lifespan, and starvation resilience. We have previously shown that Chameau (Chm), a MYST-domain acetyltransferase, promotes aging but also increases starvation resilience. Strikingly, the metabolic increase associated with a 2°C temperature rise was sufficient to bypass the requirement for Chm in starvation resilience, suggesting that Chm modulates metabolism in a temperature-dependent manner. The increase in temperature also rescued the dampened expression of genes involved in starvation response, the weight loss, and the misregulation of trehalose, which we observed in chm mutants at 23°C. Thus, Chm regulates starvation at ≤23°C but becomes obsolete at higher temperatures, likely because of efficient acetyl-CoA generation ensuring similar acetylation despite lower Chm. Supporting this, citrate supplementation increased starvation resilience of chm mutants at lower temperatures. Our finding that a gene's role manifests only under specific environments has important implications in light of global climate change

overall_design: 2 genotypes at 2 different conditions in 5 biological replicates per genotype and condition

middle: V

first: Axel

last: Imhof


title: Charting the Multi-Level Molecular Response to Palbociclib in ER-Positive Breast Cancer

first: Archishma

last: Kavalipati

state: North Carolina

address: 120 Mason Farm Rd

department: Pharmacology

summary: The addition of CDK4/6 inhibitors to endocrine therapy has significantly improved outcomes in HR+/HER2- breast cancer. However, variable patient responses and acquired resistance remain a clinical challenge. We therefore defined the comprehensive molecular response to palbociclib, the most clinically used CDK4/6 inhibitor. Global analyses of gene expression, protein abundance, splicing, and chromatin accessibility revealed broad patterns and specific changes that result from CDK4/6-inhibition in breast cancer cells. We uncovered unexpected feedback between CDK4/6 and estrogen-response signaling, which has clear clinical implications. We also revealed a widespread alternative splicing program that partially overlapped with genes whose expression is regulated, and which is expected to impact protein function. These molecular changes nominated combination therapies that interfere with the activation of CDKs or ERα. Accordingly, co-targeting CDK7, which regulates CDK2, CDK4/6 and ERα, additively impacted cell fitness.  Collectively, these data reveal a complex, multi-tiered response to CDK4/6 inhibition, with implications for therapeutic efficacy.

overall_design:
6 RNA-seq samples total. 3 biological replicates of T-47D treated with 1 uM palbociclib for 24 hours and 3 biological replicates of T-47D treated with DMSO (control) for 24 hours.
6 ATAC-seq samples total. 3 biological replicates of T-47D treated with 1 uM palbociclib for 24 hours and 3 biological replicates of T-47D treated with DMSO (control) for 24 hours

first: Daniel

last: Dominguez

first: Michael

middle: J

last: Emanuele


title: Rise in KRT17 sensitizes platinum-resistant ovarian cancer organoids to targeted therapies

first: Mirjana

last: Kessler

address: Pettenkoferstrasse 8a

department: Department of Obstetrics and Gynecology

institute: Ludwig Maximilian University Munich

summary: Variable responses to platinum chemotherapy and the development of resistant disease drive high mortality in high-grade serous ovarian cancer (HGSOC), the deadliest gynecological malignancy. Here, we developed the organoid drug resistance assay (ODR-test) to quantify the patient-specific efficacy of platinum treatment and generated post-platinum lines (ptGPC) as an in vitro model of platinum-resistant ovarian cancer (PROC). We observed a gradual increase in resistance of ptGPC lines, mirroring the clinical outcomes of patients. We have performed RNA-seq analysis from two different donor organoid lines, before carboplatin exposure and paired ptGPC lines of long-term expandable organoids that successfully overcame in vitro drug treatment. By differential expression analysis, we have identified target genes that mediate the cellular response to platinum and play a role in the development of resistant phenotype in ovarian cancer. We have found that carboplatin treatment triggers sustained reprogramming and ptGPC organoids from different donors show common changes in cell adhesion and cytoskeletal organization, indicating the existence of conserved mechanisms that lead to an increase in resistance.

overall_design:
Total mRNA Isolated from ovarian cancer patient-derived organoids, wt, and ptGPC lines (obtained through ODR-testing- after carboplatin challenge and reseeding ) has been sequenced and analyzed. In parallel, phenotypic changes in ptGPC organoids have also been investigated on the proteome level. Regulation of candidate mediator genes was validated by qPCR, while global changes in cellular architecture and tissue organization were visualized by confocal imaging. An increase in resistance of ptGPC lines has been demonstrated by repeated carboplatin challenge and quantification of organoid forming efficiency. Direct involvement of the rise in KRT17 levels in promoting platinum resistance, and altering the sensitivity of organoids to targeted testing was demonstrated by the generation of genetically modified organoids and in parallel ODR testing.   Raw sequences are not provided due to data protection concerns. Their release would require special approval from the relevant regulatory authority.

***************************************************************
Raw sequences from patients underlies strict privacy lows and requires institutional approval and restricted acces.
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first: Juliane

last: Reichenbach

first: Juliana

last: Schmid

first: Sophia

last: Hierlmayer

first: Tingyu

last: Zhang

last: Sophia Geweniger

first: Tobias

last: Straub


title: Glucocorticoid Receptor cistromic reprogramming by caloric restriction and corticosterone treatments.

first: fabiana

last: quagliarini

summary: In order to examine the impact of two separate corticosterone surges on liver physiology, we conducted genome-wide mapping of GR binding profiles at 6 pm (ZT12) through ChIP-sequencing. This was done using liver samples from mice subjected to either short-term caloric restriction or corticosterone injections. Our findings reveal that both interventions yield unique binding profiles.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Glucocorticoid Receptor (GR) in mouse liver in caloric restriction. In the case of GR, we have ChIP-seq between three different conditions (night-restricted feeding/NR, caloric restriction/CR, and cort-supplementation + NR/CORT+NR).

first: Konstantinos

last: Makris

first: Fania

last: Feby Ramadhani

first: Fabiana

last: Quagliarini

first: Nina

middle: H

last: Uhlenhaut


title: Hepatic Glucocorticoid Receptor (GR) drives the diurnal adaptation to Caloric Restriction

summary: We examined the gene expression profiles of liver samples throughout the day/night cycle (ZT0-ZT4-ZT8-ZT12-ZT16-ZT20) from control mice (night-restricted fed) and mice under short-term caloric restriction.

overall_design: Bulk RNA sequencing (RNA-seq) from livers of WT and hepatocyte-deleted for Glucocorticoid Receptor mice (GR liver KO ) upon night restricted feeding (NR) and caloric restriction (CR) with sampling every 4hours at 6 different timepoints (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20), ZT corresponds to Zeitgeber Time, 6 a.m :ZT0 & ZT12: 6 p.m. Additionally, bulk RNA sequencing (RNA-seq) from livers of night-restricted fed (NR) and caloric restricted (CR) WT mice at Zeitgeber 12 (ZT12; 6 p.m).


overall_design: This project consist of several bulk RNA-seq datasets, ChIP-seq datasets, and single nuclei multiome dataset. All datasets comes from murine liver samples.

first: Liwei

first: Ioannis

last: Deligiannis

first: Celia

last: Martinez-Jimenez

first: Nina Henriette


title: CFAP20 salvages arrested RNAPII from the path of co-directional replisomes

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Fine-tuning DNA replication and transcription is crucial to prevent collisions between their machineries, especially at promoters where RNA polymerase II (RNAPII) initiates transcription and forms R-loops. Arrested RNAPII can obstruct DNA replication, which often starts near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes are unknown. Here, we identify CFAP20 as a key player in rescuing arrested RNAPII in promoter-proximal regions, preventing conflicts with co-directional replisomes. CFAP20-deficient cells accumulate R-loops near promoters and exhibit defects in replication origin firing and fork progression. Co-depleting the Mediator coactivator complex or removing RNAPII engaged with R-loops rescues these defects. Thus, CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.

overall_design: Wild-type and CFAP20-KO RPE-1 cells were subjected to scEdU-seq as previously described by van den Berg 2024

first: J


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq2: Differential activation of Immune cell types by IL2-Immunocytokines]

status: Public on Nov 03 2025

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: IL2 is an immune-regulatory cytokine that activates both effector and T regulatory cells—a dual function leveraged in immunotherapy. However, pure IL2 induces both activation and suppression, and requires toxic doses due to its short half-life. To address this, the Spangler Lab at Johns Hopkins developed IL2 immunocytokines (IL2-ICs)—antibody-conjugated IL2 fusion proteins targeting IL2Ra (Tregs) or IL2Rb (effector cells), with extended serum half-life. We tested IL2-ICs in Foxp3IRES-GFP mice, harvesting cells at 4, 24, and 64 hours post-injection for bulk RNA-seq. Transcriptomic analysis showed IL2-ICs induced sustained IL2 responses with partial cell-type bias.

overall_design: Five treatments were tested: 1: F5111 IL2-IC, which targets IL-2 activity to Treg cells. 2: F10 IL2-IC, which targets IL-2 activity to NK cells. 3 and 4: Two FITC-IL2 controls, in which IL-2 is bound to a biologically irrelevant antibody that does not direct activity to any specific cell type. To match the N297A mutation present in F10 IL2-IC, the corresponding FITC control also included this mutation. 5: PBS, as a negative control. Each treatment was administered to 20 mice: 10 were injected 24 hours before tissue harvest and 10 were injected 4 hours before. Thus, each treatment group included both time points. Spleens were harvested at 4 and 24 hours post-injection. Treg cells, B cells, and NK cells were sorted for low-input bulk RNA sequencing. B cells, which do not respond to IL2-ICs, served as a reference to distinguish differential responses in Treg and NK cells.

first: Kumba

last: Seddu

first: Kaitavjeet

last: Chowdhary

first: Odhran

last: Casey

first: Molly

last: Henderson

first: Yi

last: Cao

first: Jakub

last: Tomala

first: Liang

last: Yang

first: Jamie

last: Spangler

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Single-cell RNA-sequencing of ChAT-eGFP+ adipose stromal vascular cells

city: St Louis

first: Alexander

last: Knights

state: MO

address: 4515 McKinley Ave

institute: Washington University

summary: ChAT-eGFP mice were housed at thermoneutrality for three weeks then either kept at thermoneutrality or exposed to acute cold challenge, then inguinal adipose stromal vascular cells were harvested and scRNAseq performed on sorted ChAT-eGFP+ cells. This study represents the first single-cell transcriptomic profiling of cholinergic cells in fat and seeks to understand the regulation of these cells in response to acute cold exposure and thermogenic activation.

overall_design: At five weeks of age, male ChAT-eGFP mice were housed at thermoneutrality (30C) for three weeks, then either kept at thermoneutrality or exposed to acute cold challenge (4C) for 4h. Two biological replicates per condition were used, with each biological replicate comprised of cells from four pooled mice. Inguinal subcutaneous white adipose tissue was harvested then stromal vascular cells were isolated following tissue digestion. Live, single ChAT-eGFP+ cells were FACS-sorted then ~10,000 cells per biological replicate were submitted for 10x Genomics scRNAseq (3' GEX v3).

first: Jun

last: Wu


title: MNX1 prevents somatostatin expression in human beta cells by repressing PERCC1

city: Paris

first: Farah

last: Kobaisi

address: 123 Bvd Port Royal

institute: Institute Cochin

summary: A highly specific mosaic transcriptional environment guides the fate of pancreatic progenitors during development and next maintains the identity of mature endocrine cells. In mice, one of such transcription factors is MNX1 (motor neuron and pancreas homobox1). It is essential for beta cell development and identity as its deletion in mature beta cells increases their somatostatin expression via an unknown mechanism. Here, we asked whether MNX1 plays a similar role in human beta cells and dissected the molecular players involved in its function. We used the human beta cell line EndoC-BH1, knocked down MNX1 expression using siRNA and performed bulk RNA sequencing searching for MNX1 targets. We next performed loss- (siRNA) and gain- (transduction with lentivectors and lipofections) of function to determine how MNX1 regulates gene expression in human beta cells. SiRNA-mediated downregulation of MNX1 in EndoC-BH1 cells induced the upregulation of somatostatin as well as its transcriptional activator HHEX. RNAseq revealed PERCC1 (Proline and Glutamate Rich with Coiled Coil 1) as being among the highest upregulated genes. SiRNA-mediated loss of PERCC1 upon MNX1 knockdown impaired the upregulation of both SST and HHEX expression, while PERCC1 overexpression upregulated the expression of both HHEX and SST. PERCC1 expression was tightly regulated by HHEX and by its own expression in a positive feedback mechanism. Moreover, NKX2.2 downregulation, whose knockout in mice induces somatostatin upregulation, led to the upregulation of PERCC1, HHEX and SST in EndoC-BH1. Finally, over-expression of PERCC1 in primary mouse beta cells revealed an upregulation of both mouse Hhex and Sst. We discovered a novel MNX1-PERCC1-HHEX regulatory axis in human beta cells. There, MNX1 protects beta cell identity by inhibiting PERCC1, an activator of HHEX and SST expression. PERCC1 might thus be considered as a sharply tuned central hub for SST regulation. Our results increase our knowledge of beta cell plasticity and may have implications for therapeutic strategies aimed at protecting beta cell identity.

overall_design: RNA seq profiling of EndoCBH1 cells that were transfected with MNX1 siRNA to knock down its expression or transfected with a non-targeting (NT) control

first: Alicia

last: Maugein

first: Alexis

last: Fouque

first: Olivier

last: Albagli-Curiel

first: Philippe

last: Ravassard

first: Raphael

last: Scharfmann


title: Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

summary: This study aimed to elucidate how epithelial–macrophage interactions contribute to pulmonary fibrosis. Using bleomycin-induced and genetic mouse models (Mif-2 KO, SPC-Cul3 KO, SPC-Mif KO, CX3CR1-Cd74 KO, PF4-Cd74 KO, and TGF-β transgenic mice), we performed single-cell transcriptomic profiling of lung cells and compared them with wild-type controls.

overall_design: Single-cell RNA sequencing was performed on lung cells from wild-type and genetically modified mice, including Mif-2 KO, SPC-Cul3 KO, SPC-Mif KO, CX3CR1-Cd74 KO, PF4-Cd74 KO, and doxycycline-inducible TGF-β transgenic mice. Pulmonary fibrosis was induced by intratracheal bleomycin, with lung tissues collected at day 10 and 14  or by two weeks of doxycycline administration to activate TGF-β transgene expression. Gene expression profiles were compared across models and wild-type controls to identify cell type–specific changes associated with fibrosis progression.

first: Sang-Hun

last: Kim

first: Jessica

last: Nouws


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2  [scATAC-seq1: IL2 2h and PBS Ctl]

first: CBDM

last: Lab

summary: We investigated early effects of IL2 treatment on mouse Treg chromatin accessibility by performing scATAC-seq on splenic Tregs isolated from mice 2h after treatment with recombinant IL2 or PBS vehicle control.

overall_design: Mouse CD4+ regulatory Tregs were isolated from Foxp3-IRES-GFP reporter mice exactly 2h after treatment with 10 μg of recombinant mouse IL2 (PeproTech, 212-12) or PBS vehicle control (in 110 μl volume). Tregs were isolated from the spleen by FACS for scATAC-seq.

first: Kaitavjeet

last: Chowdhary

first: Kumba

last: Seddu


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [scRNA-seq: IL2/JES6-1 timecourse]

summary: Interleukin-2 (IL2) is the key trophic factor for T Regulatory (Treg) cells, regulating both their differentiation and homeostasis. To understand how temporally regulated responses to IL2 unfold in Tregs, we performed fine time-course analyses at single-cell level induced by IL2 in Tregs in vivo. The data revealed responses that were largely uniform in resting Treg, but diverse among activated or effector Tregs, matching different STAT5 signal transduction efficiency. Individual Tregs displayed divergences in the preponderance of changes downstream of STAT1 or STAT5.

overall_design: We investigated how temporal interleukin-2 stimulation affect regulatory T cell gene expression. To do so, we stimulated FOXP3-GFP mice in vivo with IL2-JES6-1 complex at different time points between 1 to 128hrs and isolated splenic Tregs for each timepoints with PBS control.  Cells were encapsulated using the Chromium Single Cell 5’ v3 platform (10X Genomics). TotalSeq-A hashtag antibodies and samples (0.5 μl per sample for 20 min, BioLegend; hashtag 2, 128hr IL2-treated; hashtag 4, 128hr PBS-treated; hashtag 5, 64hr IL2-treated; hashtag 6, 24hr IL2-treated; hashtag 8, 16hr IL2-treated; hashtag 9, 8hrs IL2-treated; hashtag 10, 4hr IL2-treated; hashtag 11, 2hr IL2-treated; hashtag 12, 2h PBS-treated; hashtag 13, 1hr IL2-treated.

first: Molly

last: Henderson

first: Jakub

last: Tomala

first: Odhran

last: Casey

first: Yi

last: Cao

first: Jamie

last: Spangler


title: Human Placenta–Derived Mesenchymal Stem Cells Attenuate Hippocampal Aging-Associated Transcriptomic Profiles in Aged Mice

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

country: South Korea

institute: CHA University

summary: Background Intravenous human placenta–derived mesenchymal stem cells (hpMSCs) can improve tissue function through paracrine effects, but their impact on normal brain aging is not well defined.  Methods Aged female mice (18–19 months) received three intravenous infusions of hpMSCs or PBS at six-week intervals. Hippocampal tissue was collected after the behavioral tests for RNA sequencing.  Results RNA sequencing showed hpMSCs' effectiveness in modulating aging-related neural pathways, particularly by downregulating age-specific genes in the hippocampus, indicative of neural reactivation.  Conclusions Systemic hpMSC administration modulates neural pathways in aged mice.

overall_design: RNA-Seq profiling of hippocampal tissue from hpMSC-treated and PBS-treated aged mice


title: Single-cell RNA Sequencing Reveals Multiple Pathways Involving Pulmonary Immune and Epithelial Cells Through which Aryl Hydrocarbon Receptor Activation Attenuates Acute Respiratory Distress Syndrome

city: Columbia

first: Chloe

last: Weyer-Nichols

state: South Carolina

address: 6311 Garners Ferry Rd

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary: Acute Respiratory Distress Syndrome (ARDS) is a severe inflammatory lung disorder triggered by pneumonia, sepsis, trauma, and COVID-19, leading to high mortality. In this study, we investigated the effect of Aryl Hydrocarbon Receptor (AhR) activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a potent ligand, on LPS-induced ARDS in mice using single-cell RNA sequencing (scRNA-seq). scRNA-seq revealed sixteen transcriptionally distinct cell clusters in the lungs. AhR activation reversed the decreased pulmonary functions caused by LPS, and significantly reduced pulmonary infiltration of monocytes, neutrophils, and macrophages. Interestingly, AhR activation during ARDS led to increased proportions of alveolar macrophages, and angiogenic and quiescent endothelial cells (AECs and QECs, respectively). Among the downregulated pathways, prostaglandin signaling was the most broadly suppressed across many cell types in the LPS+TCDD group. AhR activation suppressed the neutrophil chemotaxis pathway involving Cxcl2, Cxcl3, and Cxcl10. The damage to endothelial and epithelial cells induced during ARDS was also blocked by AhR activation. This was associated with decreased expression of S100a8 and S100a9. Notably, multiple pathways related to cellular junction organization were enriched following AhR activation. Additionally, Scgb1a1, also called Club cell protein 16 (CC16), primarily secreted by Club cells in the respiratory epithelium, was highly upregulated following AhR activation accounting for lung homeostasis. Together, these findings demonstrate that AhR activation mitigates key inflammatory and barrier-disruptive processes involving multiple cell types in LPS-induced ARDS. These data identify AhR as a central regulator of pulmonary inflammation and epithelial–endothelial integrity and support the future evaluation of AhR-targeted therapeutics as potential treatment for ARDS.

overall_design: Mice were treated with either Vehicle or 30 ug/kg TCDD (i.p.) at 0 hours followed by 10 mg/kg LPS (i.t.) at 24 hours. After 48 hours, whole lungs were collected and prepared for scRNA-seq.

first: Mitzi

last: Nagarkatti


title: Non-canonical functions of UGT2B17 promote castrate-resistant prostate cancer progression

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

summary: When prostate cancer (PCa) overcomes the androgen receptor (AR) target therapy and progresses to the castrate-resistant prostate cancer (CRPC) stage, it becomes curable. UDP glucuronosyltransferase 2B17 (UGT2B17) is the key enzyme determining androgen bioavailability to AR inside PCa cells. However, whether UGT2B17 promotes CRPC progression remains poorly understood. Here, we report that anti-AR therapy increases UGT2B17 protein stability. UGT2B17 is localized in both the cytoplasm and nucleus to exert multiple non-enzymatic functions. In the cytoplasm, UGT2B17 activates unfolded protein response (UPR) to counteract endoplasmic reticulum (ER) stress for cell survival. UGT2B17 can exert its nuclear functions by stimulating c-Src kinase to activate AR in the absence of androgens. The UGT2B17-Src axis confers PCa cells resistant to DNA damage and promotes cell cycling by passing the G2 checkpoints through de-activating ATM and ATR kinases. We conclude that these non-enzymatic functions of UGT2B17 activate multiple survival pathways to allow CRPC progression.

overall_design: RNA-seq analysis comparing the transcriptome between LNCaP95 and LNCaP(UGT2B17 KO) cell lines

first: Xuesen

last: Dong

first: Tunc

last: Morova


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq1: IL2/JES6-1 timecourse]

summary: IL2 is an immune-regulatory cytokine that is crucial for the development and maintenance of Tregs. Here we investigate how temporal IL2 stimulation affects Treg gene expression and chromatin landscape via RNASeq and ATACSeq

overall_design: We tested IL2/JES6 and IL2 immunocytokines F10 and F511 compared to PBS in Foxp3IRES-GFP mice, harvesting cells at 1 to 128 hours post-injection for bulk RNA-seq.

first: Liang

last: Yang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Activation of Piezo1 induces heterogeneity in LSK cells leading to HSC proliferation and myelopoiesis [scRNA-seq]

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

summary: Bone marrow haematopoietic stem cells (HSCs) are mobilised into blood under various stresses.  Although they are exposed to shear stress during circulation, the role of mechanical stimulation in regulating HSCs remains unknown. Piezo1, a mechanosensory ion channel, was implicated in regulation of haematopoietic cells. We analysed the transcriptional heterogeneity of LSK cells from mice treated with the Piezo1 agonist Yoda1 for 2 weeks. Our study demonstrated that activation of Piezo1 promoted HSC proliferation and differentiation toward the myeloid lineage, as evidenced by an increase in HSC numbers and the upregulation of myeloid transcription factors.

overall_design: LSK cells were sorted from the bone marrow of control and Yoda1-treated mice.

first: Tongyao

last: Shang

first: Li

last: Zhao

first: Shibo

last: Ying


title: The ORB2 RNA-binding protein negatively regulates its target transcripts during the Drosophila maternal-to-zygotic transition via its functionally conserved Zinc-binding 'ZZ' domain

city: Toronto

first: Howard

last: Lipshitz

state: ON

address: 661 University Ave

department: Molecular Genetics

institute: University of Toronto

summary: RNA-binding proteins (RBPs) are key components of the post-transcriptional regulatory machinery. We show that the ORB2 RBP, the Drosophila ortholog of vertebrate Cytoplasmic Polyadenylation Element Binding Protein 2 (CPEB2), binds to hundreds of maternally provided mRNAs in early embryos, identify a U-rich motif enriched in ORB2’s targets, and show that this motif confers ORB2 binding and repression to a luciferase reporter mRNA in S2 tissue culture cells. ORB2’s target transcripts are translationally repressed and unstable during the maternal-to-zygotic transition (MZT), a developmental phase during which a large proportion of maternally provided mRNAs are repressed and cleared.  We show that, when tethered to a luciferase reporter, ORB2 and its human homolog CPEB2 (but not ORB and CPEB1) repress translation and that the C-terminal Zinc-binding (‘ZZ’) domain of ORB2 is sufficient for repression. ORB2 interacts with a suite of post-transcriptional regulators in early embryos; a subset of these interactions is lost upon deletion of the ZZ domain, notably with the Cup repressive complex. Analysis of the early embryo’s translatome in the presence or absence of the endogenous ZZ domain, shows that ORB2’s targets move onto polysomes upon ZZ domain deletion, indicating that this domain mediates translational repression of ORB2’s targets during the MZT. Together, our results assign a function to the ZZ domain and support a significant role for ORB2 in post-transcriptional regulation of maternal mRNAs during the Drosophila MZT.

overall_design: polysome gradient RNA-seq profiling of embryo of wild type and orb2∆zz D. melanogaster at 0-1hr, 1-2hr and 2-3hr of post egg-lay.

first: Timothy

last: Low

first: Hua

last: Luo

first: Chalini

last: Weerasooriya

first: Sichun

last: Lin

first: Stephane

last: Angers

first: Craig

last: Smibert

first: Zhuyi

last: Wang


title: Single-cell and single-nucleus transcriptomic profiling of mouse models and human lung tissues to study pulmonary fibrosis

first: Maor

last: Sauler

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Single-nucleus RNA sequencing of ex vivo precision-cut lung slices from normal human lung tissue

overall_design: Samples were inflated by injecting 3% low-melting agarose followed by cutting samples into 5x5 mm cubes. Peripheral slices (300 μm) were cut with a vibratome. Sections were placed into 1 mL 10% DMEM with 1% pen-strep in a 24 well plate. hPCLS were washed with HBSS x 2 h, rocking, at 37 degrees, and then treated with vehicle (DMSO) or Fibrotic cocktail (FC) [5 ng/ml recombinant transforming growth factor-β (TGF-β) (240-B, R&D Systems), 5 μM platelet-derived growth factor-AB (PDGF-AB) (PHG0134, GIBCO), 10 ng/ml tumor necrosis factor-α (TNF-α) (210-TA, R&D Systems), and 5 μM 1-Oleoyl lysophosphatidic acid (LPA) (62215, Cayman Chemical)] +/- 50μM 4-IPP drugs in 500 ul of 0.25% DMEM w 1% pen-strep. Every 2 days, the media was changed and treated again. At the end of the 5 days, PCLS were washed in cold PBS x 2 then placed in RNAlater solution (Thermo). Nuclei were isolated from frozen tissue and profiled with snRNAseq.

first: Sang-Hun

last: Kim

first: Jessica

last: Nouws


overall_design:
For each replicate of RIP-seq, 1mL of 0-3h embryo extract (prepared as described above) was supplemented with Triton X-100 to 0.1% final concentration, then diluted in an equal volume of lysis buffer with 0.1% Triton X-100 and cleared again by centrifugation at 4°C, 13 000 RPM for 15 minutes. The supernatant was incubated for 3 to 4 hours at 4°C with end-over-end rotation with 100μL of anti-FLAG M2 affinity gel beads (Sigma) which had been pre-incubated at 4°C with 50μg of purified anti-ORB2 E8 synthetic antibodies blocked with 5μg/μL BSA. After incubation, the lysates were decanted and beads were washed four times with lysis buffer supplemented with 0.1% Triton X-100 and then three times with equilibration buffer: 100 mM NaCl, 100 mM HEPES-NaOH (pH 7.4), 1 mM MgCl2. Fabs and associated RNPs were eluted from the beads with 200 μL of 200μg/μL FLAG-peptide (Sigma) suspended in equilibration buffer at 4°C for 20 minutes. RNA was isolated from the eluate using TRI Reagent (Sigma) according to the manufacturer’s instructions.
RNA was prepared for sequencing using Ribo-Zero Gold rRNA depletion kit and TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to manufacturer’s instructions. Libraries were sequenced using the HiSeq 2500 System, V4 Chemistry (Illumina), with paired-end reads 125nt in length.


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [scATAC-seq2: IL2/JES6-1 timecourse]

first: CBDM

last: Lab

summary: We investigated the dynamic effects of IL2 exposure on Treg chromatin accessibility over time by performing scATAC-seq on splenic Tregs isolated from mice at mulitple timepoints (1,2,4,8,16,32,64,128hours) after treatment with IL2/JES6-1 complexes or PBS vehicle control.

overall_design: Mouse CD4+ regulatory Tregs from Foxp3-IRES-GFP reporter mice treated with PBS or IL2/JES6-1 complexes and isolated from the spleen by FACS for scATAC-seq at multiple timepoints (1, 2, 4, 8, 16, 32, 64 and 128hours after injection)

first: Kaitavjeet

last: Chowdhary

first: Kumba

last: Seddu


overall_design: Total RNA-seq profiling of embryo of wild type and orb2-delta-zz D. melanogaster at 0-1hr, 1-2hr and 2-3hr of  post egg-lay.

first: Timothy CH

first: Craig A


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2


title: Single cell transcriptomics of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [scRNA-seq cART+3HP]

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We studied components of TB immunity that remain impaired after cART in the lung compartment, versus those that are restored by concurrent 3 months of once weekly isoniazid and rifapentine (3HP) and cART in the rhesus macaque (RM) model of LTBI and Simian Immunodeficiency Virus (SIV) co-infection. Concurrent administration of cART+3HP did improve clinical and microbiological attributes of Mtb/SIV co-infection compared to cART-naïve or -untreated RMs. While RMs in the cART+3HP group exhibited significantly lower granuloma volumes after treatment, they, however, continued to harbor caseous granulomas with increased FDG uptake. cART only partially restores the constitution of CD4+ T cells to the lung compartment in co-infected macaques. Concurrent therapy did not further enhance the frequency of reconstituted CD4+ T cells in BAL and lung of Mtb/SIV co-infected RMs compared to cART, and treated animals continued to display incomplete reconstitution to the lung. Furthermore, the reconstituted CD4+ T cells in BAL and lung of cART+3HP treated RMs exhibited an increased frequencies of activated, exhausted and inflamed phenotype compared to LTBI RMs. cART+3HP failed to restore the effector memory CD4+ T cell population that was significantly reduced in pulmonary compartment post SIV co-infection. Concurrent therapy was associated with the induction of Type I IFN transcriptional signatures and led to increased Mtb-specific TH1/TH17 responses correlated with protection, but decreased Mtb-specific TNF responses, which could have a detrimental impact on long term protection.

overall_design: These cells were isolated from bronchoalveolar lavage of rhesus macaques co-infected with Mtb/SIV and treated with cART+3HP

first: Riti

last: Sharan

first: Yi

last: Zou

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Deepak

last: Kaushal


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [RNAseq_DMSO_SGC]

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

summary: Insights into the epigenetic mechanisms of CD8 T cell differentiation are delivering novel opportunities for modulating fate decisions and immune responses. The histone methyltransferase DOT1L is emerging as a central epigenetic regulator in immune cells. However, its cell-intrinsic role in CD8 T cell programming remains unclear as positive as well as negative roles have been ascribed to DOT1L. Here, we determined the cell-intrinsic role of DOT1L in mouse CD8 T cells using conditional ablation. In contrast to deletion of Dot1L early in the T cell lineage, conditional ablation of Dot1L in isolated mature CD8 T cells in vitro did not compromise the in vivo proliferative capacity and anti-tumor reactivity. In vitro, Dot1L knock-out CD8 T cells showed accelerated and enhanced antigen-specific cytotoxic activity towards tumor cells. Mechanistically, transcriptome and proteome profiling revealed that loss of DOT1L results in an altered cell-identity program with loss of T-cell and gain of NK-cell features. This role of DOT1L was linked to its catalytic activity since treatment with specific DOT1L inhibitors phenocopied genetic deletion of Dot1L. Our findings show that ablation of DOT1L activity is well-tolerated in mature CD8 T cells, rewires their cell identity in a tunable way towards the NK-cell lineage and enhances their cytolytic activity cell intrinsically.

overall_design: RNAseq on expanded murine CD8 T cells (day 8) to investigate the effect of loss of DOT1L catalytic activity on the transcriptome. Cells (n=4 biological replicates) were treated for 8 days with either SGC-0946 (DOT1L inhibitor; 10 mM) or DMSO (vehicle control).

first: Muhammad

last: Aslam

first: Muddassir

last: Malik

first: Willem-Jan

last: de Leeuw

first: Tibor

last: van Welsem


title: Piezo1 deficiency induces transcriptomic changes in HSCs [RNA-seq]

first: Xinjiang

last: Lu

summary: We found that haematopoietic cell-specific Piezo1 knockout (KO) inhibits HSC proliferation and myeloid differentiation. To identify the underlying mechanism, we analysed the gene expression profiles of long-term haematopoietic stem cells (LT-HSCs) from Piezo1 KO mice and compared them with those from control mice. Our study demonstrated that the tight junction pathway was one of the enriched terms among downregulated genes in Piezo1 KO HSCs, with a decrease in JAM3 expression.

overall_design: We performed transcriptional profiling using RNA-seq in sorted LT-HSCs from the bone marrow of control and Piezo1 KO mice.

first: Tongyao

last: Shang

first: Li

last: Zhao

first: Shibo

last: Ying


title: Normocaloric Diet induces represión on immune response genes in liver of C57BL/6 mice

city: Juarez

first: Isui Abril

last: Garcia Montoya

state: Chihuahua

address: Plutarco Elias Calles  1210

department: Químico Biológicas

country: Mexico

institute: Universidad Autónoma de Ciudad Juárez

summary: Gene expression profiles in the Liver of C57BL/6 mice with DIO   vs. those who received a Normocaloric diet . Normocaloric diet induce  the downexpression of inflammation-related genes and signaling pathways.

overall_design:
M22K_14_14: Pools of total RNA were made per study group (five mouse per group): Normocaloric   mice (test group) and obese mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Normocaloric) or Cy3 (Obesity.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.
M22K_14_15: Pools of total RNA were made per study group (five mouse per group): Symbiotic  mice (test group) and Normocaloric mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Symbiotic) or Cy3 (Normocaloric.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.
M22K_14_16: Pools of total RNA were made per study group (five mouse per group): Symbiotic  mice (test group) and Obese mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Symbiotic) or Cy3 (Obesity.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

last: García-Montoya

first: Florinda

last: Jiménez-Vega


title: miRNA-Seq of Extracellular Vesicles from Human Placenta–Derived Mesenchymal Stem Cells

first: Jae Hyun

last: Park

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) released by human placenta–derived mesenchymal stem cells (hpMSCs) are thought to mediate paracrine effects. To characterize their small-RNA cargo, we isolated hpMSC-derived EVs (hpEVs) from conditioned media using size-exclusion chromatography and performed miRNA sequencing.

overall_design: small RNA profiling of EVs released from human placenta-derived mesenchymal stem cells