title: Aryl hydrocarbon receptor restricts axon regeneration of DRG neurons in response to injury [DRG_AN00024583]

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Injured neurons sense environmental cues to balance neural protection and axon regeneration, but the mechanisms are unclear. Here, we unveil aryl hydrocarbon receptor (AhR), a ligand-activated bHLH-PAS transcription factor, as a molecular sensor and key regulator of acute stress response at the expense of axon regeneration. We demonstrated responsiveness of DRG sensory neurons to AhR signaling, which functions to inhibit axon regeneration. Conditional neuronal Ahr deletion accelerated axon regeneration after sciatic nerve injury. Ahr deletion partially mimics the conditioning lesion in priming DRG to initiate axonogenesis gene programs; upon peripheral axotomy, Ahr ablation suppressed inflammation and stress signaling while augmenting pro-growth pathways. Moreover, comparative transcriptomics revealed signaling interactions between AhR and HIF-1α, two structurally related bHLH-PAS α units that share the dimerization partner Arnt/HIF-1β. Functional assays showed that the growth advantage of AhR-deficient DRG neurons requires HIF-1α; but in the absence of Arnt, DRG neurons can still mount a regenerative response. We further unveiled a link between bHLH-PAS transcription factors and DNA hydroxymethylation in response to peripheral axotomy, while RNA-seq of DRG neurons and neuronal single cell RNA-seq analysis revealed a link of AhR regulon to RNA regulation and integrated stress response (ISR), impacting global translation. Altogether, AhR activation favors stress coping and inflammation at the expense of axon regeneration; targeting AhR has the potential to enhance nerve repair.

overall_design: Ahr cKO (Ahr fl/fl Thy1CRE-ERT2/EYFP) or control (Ahr f/f or  f/+) male mice were injected with tamoxifen (once daily, 100 mg/kg i.p. for 5 consecutive days) at 17 weeks of age.  L4-L6 DRGs, both contralateral and ipsilateral were isolated from n=5 mice per group (DRGs from each mouse represents 1 sample) at 4 weeks post-tamoxifen treament. For the injury group, sciatic nerve transection lesion was performed on n=5 mice per group at 4 weeks post-tamoxifen treament and L4-L6 DRGs were isolated 1 day later.  DRGs were dissociated between ZT2 to 4 (ZT=0 when the light turns on in the mouse room).

first: Yiqun

last: Wang

first: Dalia

last: Halawani

first: Arthur

last: Sefiani

first: Aarthi

last: Ramakrishnan

first: Jiaxi

last: Li

first: Haofei

last: Ni

first: Daniel

last: Halperin

first: Li

last: Shen

first: Cedric

last: Geoffroy

first: Roland

middle: H

last: Friedel

first: Hongyan

last: Zou


title: Transcriptome analysis of Arabidopsis sqtl1 mutant

status: Public on Feb 05 2026

city: Heverlee

first: Zhi-Xing

last: Lau

address: Willem de Croylaan 42

country: Belgium

institute: KU Leuven

type: Expression profiling by high throughput sequencing

summary: Differential gene expression of Arabidopsis ribosome biogenesis related gene SQTL1, by comparing transcriptome of sqtl1 RNAi mutant with WT Col-0.

overall_design: Transcriptome comparison of mutant with WT (Col-0). Mutant of sqtl1 RNAi line and WT Col-0 were used, whole seedlings of mutant and Col-0 were collect at day-7 after stratification. 3 biological replicates were collected and sent for RNA-seq.

first: Ya-Huei

last: Chen

first: Donghui

last: Wei

first: Gu

last: Ying

first: Kai-Yin

last: Lo

first: Wan-Hsing

last: Cheng


title: Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity [tRF-seq]

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

country: Japan

institute: National institute of infectious diseases

summary: Bacteriophages must overcome diverse bacterial immune systems, yet the molecular principles enabling such escape remain poorly understood. Here, we show that the phage homing endonuclease SegB facilitates immune evasion by promoting the segmental amplification of anti-defense loci. The antiphage defense Septu inhibits phage T6 replication by cleaving the variable loop of tRNATyr. We show that SegB enables immune evasion by amplifying a genomic segment that contains the full-length tRNATyr gene. This repeat expansion increases tRNATyr expression, allowing the phage to overcome Septu immunity. Remarkably, SegB also mediates in trans amplification of distinct anti-defense genes that counteract OLD and toxin-antitoxin ToxIN defense systems. Collectively, our findings demonstrate that SegB-mediated segmental amplification represents a versatile mechanism by which phages rapidly adapt to and circumvent diverse bacterial antiphage defenses.

overall_design: Quantification of tRNA fragments through tRNA fragment sequencing (tRF-seq) in cells expressing either empty vector (pLG001) or Septu EcB88 (pKCN-069) in the presence or absence of T6 phage infection.

first: AaHaeruman

last: Azam

first: Egor

last: A. Syroegin

first: Ilya

last: Terenin

first: Masanori

last: Hashino

first: Koichi

last: Watashi

first: Kazuhiro

last: Horiba

first: Vasili

last: Hauryliuk

last: Kiga


title: Chikungunya virus persists in joint associated macrophages and promotes chronic disease.[Xenium]

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

country: USA

institute: University of Colorado Anschutz Medical Campus

summary: Arthritogenic alphaviruses including chikungunya, Mayaro, and Ross River viruses cause long-lasting musculoskeletal pain and inflammation. However, mechanisms driving chronic disease remain poorly understood. Here, we investigated joint-associated tissues in alphavirus-infected mice at a late stage of infection. Utilizing scRNA-seq, spatial transcriptomics, and flow cytometry we identified an accumulation of inflammatory macrophages in joint-associated tissues with elevated Tnf, Nlrp3, Il1b, and H2-Aa expression, and these cells harbored CHIKV RNA. Moreover, we identified accumulation of CD4+ T cells in joint-associated tissues, which express Ifng. Depletion of CD4+ T cells diminished MHC-II expression on joint macrophages, highlighting their potential role in inflammation. In addition, treatment with a small molecule inhibitor of CHIKV replication during chronic disease reduced viral RNA and joint inflammation, suggesting that viral RNA replication promotes chronic joint disease. Our data suggest that macrophages harbor replicating viral RNA and contribute to the sustained joint inflammation associated with chronic alphavirus disease.

overall_design: WT C57BL/6J mice were inoculated with the chikungunya virus strain AF15561, at 28 dpi joint-associated tissue was collected from the ipsilateral ankle, CHIKV RNA distribution was assessed using spatial transcriptomics.

first: Kristen

last: Zarrella

first: Brian

last: Ware

first: Bennett

last: Davenport

first: Aspen

last: Martin

first: Jay

last: Hesselberth

first: Thomas

last: Morrison


title: Gpc3 Selectively Suppresses Subcutaneous Adipogenesis in Diet-Induced Obesity

city: Beijing

first: Meng

last: Xie

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

summary: Subcutaneous and visceral adipose depots employ distinct expansion strategies in response to dietary cues, yet the molecular regulators underlying these depot-specific adaptations remain poorly understood. Through integrated proteomic profiling of human subcutaneous and visceral adipose tissues from paired obese/non-obese donors and temporal transcriptomic analysis of mouse adipose stem and progenitor cells (ASPCs) during diet switching, we identified Gpc3 as an obesity-responsive gene exhibiting reciprocal expression patterns between depots. ASPC-specific Gpc3 deletion in mice amplified high-fat diet (HFD)-induced weight and fat mass gain by selectively enhancing hyperplastic expansion in inguinal white adipose tissue (iWAT), without affecting epididymal WAT (eWAT). Mechanistically, Gpc3 loss biased ASPC fate toward proliferation over adipogenesis via depot-specific modulation of canonical Wnt signaling. These findings establish Gpc3 as a regulator for regional adipose plasticity, offering a molecular target for reprogramming pathological fat distribution in obesity and related metabolic disorders.

overall_design: SVF cells in the white adipose tissue were collected under different dietary conditions and sent for sequencing.

first: Yan

last: Li

first: Carlos

middle: F

last: Ibáñez


title: Profiling chromatin accessibility in Enteric Nervous System progenitors during neurogenic phases

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We utilized a Phox2b-H2BCerulean transgene that is expressed at low levels in Enteric Nervous System progenitors (ENPs) and enteric glia that is also expressed at notably higher levels in differentiating enteric neurons to capture these populations during neurogenic phases of ENS development. Collected tissues from 16.5 days post coitus developing mouse intestine included the stomach, small intestine, and colon that were dissociated to single cell suspensions for flow sort capture of Phox2b-H2BCerulaen+ cells. We applied differential gating in flow sorts to capture populations expressing low levels of the Phox2b-H2BCerulaen transgene (ENPs and enteric glia) and while concurrently collecting cells expressing high levels of the Phox2b-H2BCerulaen transgene (developing and maturing enteric neurons) from the same samples. Nuclei were generated from these Phox2b-H2BCerulaen “high” and “low” populations and encapsulated separately to produce single nucleus ATAC-Seq libraries using 10X Genomics chemistry.  Sequencing was performed on the Illumina NovaSeq6000 (S4) using PE150 Sequencing targeting >50,000 reads per nucleus. Comparison of the resulting sequence data from the “high” versus “low” cell populations allowed us to identify differentially accessible genome regions in developing enteric neurons compared to ENPs and enteric glia.

overall_design: 16.5 days post coitus (dpc) embryonic fetal guts derived from C3Fe.B6 Phox2b H2B-CFP transgenic lines were isolated and dissociated via cold-active protease, then flow sorted for low intensity CFP+ and high intensity CFP+ separately in two samples. Nuclei were isolated from viable, CFP+ cells.  10x Genomics' snATAC-seq platform was used for encapsulation and Illumina next-generation sequencing was performed to generate datasets. CellRanger was used to align FASTQ files to mm10. Two "dim" samples and one "bright" sample were processed further, while the other "bright" sample (4828-MS-16) was excluded due to quality concerns.

first: Joseph

middle: T

last: Benthal

first: Justin

middle: A

last: Avila

first: Jeffrey

middle: R

last: Smith

first: Michelle


title: 6 week old KPPC mice treated with vehicle or Takinib (50mg/kg) for 14 days

city: ST LOUIS

first: KIAN

middle: HUAT

last: LIM

state: MO

address: 660 S. Euclid Avenue  Campus Box 8069, St. Louis

department: internal Medicine

institute: WashU

summary: We pooled three KPPC mice tumors into one sample for vehicle (n=3) or Takinib (n=3), prepared single cell suspension and performed  10X genomics scRNASeq to assess transcriptomic changes all cell populations

overall_design: scRNAseq analysis of KPPC tumors treated with vehcile or  takinib

first: Kian-Huat

last: Lim

first: Sapana

last: Bansod


title: Dynamic Antigen Expression and Intrinsic CTL Resistance in HIV-1 Reservoir Clones

city: New York

first: Alberto

last: Herrera

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary: Reservoirs of clonally expanded CD4+ T-cells harboring rebound-competent HIV-1 proviruses persist lifelong during ART. Latency is considered the principal barrier to viral eradication and has resisted pharmacological reversal, yet it appears that sustained immune pressure may still erode reservoirs. Recent advances have yielded glimpses into these exceptionally rare reservoir-harboring cells, implicating intrinsic pro-survival properties in their persistence. Here, we isolate and characterize populations of authentic reservoir clones (ARCs) that robustly proliferate and accumulate while producing infectious virus, without overtly succumbing to viral cytopathic effects. At any given moment, only small fractions of ARCs expressed HIV-1 proteins, a state remarkably unperturbed by potent TCR stimulation or latency-reversing agents. Nevertheless, sustained co-culture with cytotoxic T-lymphocytes (CTL) revealed extensive time-integrated antigenic vulnerability, culling clonal expansion of some ARCs by >90%. Notably, one regulatory T-cell ARC displayed pronounced cell-intrinsic resistance to CTL – a longstanding hypothesis we now directly demonstrate – linked to low oxidative stress and reversed with desferoxamine, a hypoxic stress inducer  and FDA-approved therapeutic. Overall, we provide novel insights into the vulnerabilities of reservoir clones to potent, sustained CTL pressure and highlight intrinsic resistance pathways as actionable therapeutic targets, opening opportunities for advancing immune-based HIV-1 cure strategies.

overall_design: 5' CITE-seq gene expression and antibody derived tag  libraries (from 6 authentic reservoir clones with matched uninfected clones) and TCR clonotype libraries (from 4 authentic reservoir clones and matched uninfected clones) were prepared from CD4+ T-cells from 4 donors living with HIV supressed on anti-retroviral therapy.

first: Richard

middle: B

last: Jones

first: Paul

last: Zumbo


title: Chikungunya virus persists in joint associated macrophages and promotes chronic disease.[scRNA-seq]

first: Ryan

last: Sheridan

overall_design: WT C57BL/6J mice were inoculated with the chikungunya virus strain AF15561, at 28 dpi joint-associated tissue was collected from the ipsilateral ankle, gene expression and CHIKV RNA distribution was assessed using single-cell RNA sequencing.

first: Kristen

last: Zarrella

first: Brian

last: Ware

first: Bennett

last: Davenport

first: Aspen


title: scRNAseq analysis of 8 week-old KPPC WT, MAP3K7ff   KPPC and MAP3K7fwt KPPC mice pancreatic tumor

summary: We pooled three 8 week-old KPPC WT (n=3), MAP3K7ff KPPC (n=3) and MAP3K7fwt KPPC (n=3) mice pancreatic tumor respectively into one sample, prepared single cell suspension and performed 10X genomics scRNASeq to assess transcriptomic changes all cell populations


title: In-vitro cellular tropism and immunomodulatory response to rVSVΔG-ZEBOV-GP in human cells derived from tissues associated with adverse events

city: Davos

first: Paola

middle: Andrey

last: Martinez Murillo

address: Herman-Burchard-Str 12

country: Switzerland

institute: CK-CARE

summary: The recombinant vesicular stomatitis virus–vectored Zaire Ebola virus glycoprotein (rVSVΔG-ZEBOV-GP) vaccine, while effective and well-tolerated, exhibits notable reactogenicity, manifesting in expected adverse events (AEs) such as fever, headache, and pain, along with rare, unexpected AEs like skin lesions, cutaneous vasculitis, and transient arthritis. The presence or absence of AEs following rVSVΔG-ZEBOV-GP vaccination is associated with a specific innate plasma signature. This study aims to elucidate in-vitro the tropism of the vaccine for different cell types derived from tissues previously reported to be involved in the unexpected AEs. Upon in-vitro infection with rVSVΔG-ZEBOV-GP, various cell types such as synoviocytes, fibroblast, keratinocytes and endothelial cells (except chondrocytes) demonstrate productive infection, which in dermal fibroblast triggered the release of many innate plasma signature markers, including keratinocytes’ proinflammatory and proapoptotic cytokines such as OSM and TRAIL. Infected monocytes from buffy coats, activated by infection, produce most innate plasma signature markers. In co-culture, rVSVΔG-ZEBOV-GP-infected monocytes serve as a source to synoviocytes infection, resulting in a distinct kinetics modulation in innate biomarkers (transcription and secretion) and upregulation of specific genes such as NEDD8 and SIGLEC-1, which have been associated with inflammatory arthritis in animal models. Altogether, our work based on in-vitro studies provide insights into the possible mechanisms of rVSVΔG-ZEBOV-GP observed reactogenicity by showing tropism of the vaccine for off target cells derived from AE affected compartments (skin, joints, vessels). Furthermore, in-vitro interaction with infected monocytes modulates the innate response of synoviocytes.

overall_design: Transcriptomic analysis was used to outline the response after rVSVΔG-ZEBOV-GP infection of Monocytes, Synoviocytes and co-culture of these two. Monocytes (CD14+) were isolated from fresh Peripheral Blood Mononucleate Cells (PBMCs) from healthy donors and synoviocytes isolated from a primary cell culture were used to set up different cell cultures: two mono-cultures and a co-culture. In the co-culture, monocytes were infected with rVSVΔG-ZEBOV-GP for 1h, extensively washed and plated together with the synoviocytes in fresh growth medium.  Cells were infected with rVSVΔG-ZEBOV-GP MOI 1 or mock stimulated.

last: Martinez

first: Simone

last: Lucchesi

first: Maria

last: Novedrati

first: Giorgio

last: Montesi

first: Chiara

last: Sonnati

first: Francesco

last: Santoro


title: Decoding glioblastoma invasion: single-cell profiling of environmental and cell cycle effects in tumour assembloids

city: Leeds

first: Heiko

last: Wurdak

address: Worsley Building, University of Leeds, Woodhouse

country: United Kingdom

institute: Leeds Institute of Medical Research (LIMR)

summary: Akhunbay-Fudge et al. develop two single-cell profiling techniques to dissect glioblastoma invasion phenotypes, focusing on the effects of lineage commitment (neural versus endodermal) and cell cycle progression within tumour assembloids. The study employs single-cell mRNA sequencing to compare tumour invasion into neural versus endodermal lineage assembloids and establishes the ‘DyPheT’ tracking algorithm to correlate cell cycle phases with malignant cell migration in cerebral organoids in real time. These complementary methods reveal glioblastoma-induced changes in environmental cells, identify cell-autonomous gene expression profiles of assembloid invasion in tumour cells, and emphasize a "go-and-grow" invasion paradigm, identifying highly migratory cells active during the S/G2 phase.

overall_design: Glioblastoma (GB) cells were introduced into neural and endodermal assembloids and analyzed by scRNA-seq, while real-time tracking (DyPheT) was used to link cell cycle phases with invasion dynamics in cerebral organoids.

first: Christopher

last: Akhunbay-Fudge

first: Bronwyn

middle: K

last: Irving

first: Alima

last: Ismail

first: Sabrina

last: Samuel

first: Emma

last: Smedley

first: Steven

last: Bagley

first: Alexander

last: Baker

first: Iain

middle: M

last: Hagan

first: Deena

last: Gendoo

first: Kevin

last: Critchley

last: Mathew


title: Engineered Living Systems with Self-Organizing Neural Networks: From Anatomy to Behavior and Gene Expression

city: Boston

first: Haleh

last: Fotowat

state: MA

address: 201 Brookline Ave

institute: Wyss Institute

summary: A great deal is known about the formation and architecture of biological neural networks in animal models, which have arrived at their current structure-function relationship through evolution by natural selection. Little is known about the development of such structure-function relationships in a scenario where neurons are allowed to grow within evolutionarily-novel, motile bodies. Previous work showed that ectodermal tissue excised from Xenopus embryos, develops into a three-dimensional (3D) mucociliary epidermal organoid ex vivo and exhibits movements distinct from age-matched tadpoles. These ‘biobots’ are autonomous, self-powered, and able to move through aqueous environments. Here we report a new type of biobot, the neurobot, composed of mucociliary epidermis and neural tissue. We show that neural precursor cells implanted in explanted Xenopus ectodermal tissue develop into mature neurons, extending processes both towards the surface and among each other. These self-organized neurobots exhibit unique morphology, more complex movements, and different responses to neuroactive drugs compared to non-neuronal counterparts. Calcium imaging confirms neuronal activity in neurobots. Transcriptomics reveals increased transcript variability, expression of genes related to nervous system development, a shift toward ancient genes, and up-regulation of neuronal genes linked to visual perception.

overall_design: These experiments were aimed to compare gene expression between various types of biological robots constructed out of ectodermal cells of Xenopus laevis. Biobots (XB1-4), are composed of xenopus epidermal cells, where as neurobots (NB1-4) are composed of epidermis as well as neurons derived from ectodermal cells, and sham neurobots (NN1-4) are built similar to neurobots, without the steps for neural differentiation (n=4).

first: Laurie

middle: E

last: O'Neill

first: Leo

last: Pio-Lopez

first: Megan

last: Sperry

first: Patrick

last: Erickson

first: Tiffany

last: Lin

first: Michael

last: Levin


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment. [P6]

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

institute: Saitama Medical University

summary: The priming, expansion, and function of CD8⁺ T cells are helped by CD4⁺ T cells via dendritic cells. Precursor exhausted T cells (Tpex) maintain self-renewal and supply cytotoxic CD8⁺ T cells in the tumor microenvironment (TME), but the identity of their CD4⁺ T-cell partners remains unclear. Here, we perform scRNA-seq, scTCR-seq, and mass cytometry analysis on peripheral blood, tumor, and lymph nodes derived from lung cancer patients and identify a population of IL-7Rhigh CCR6⁺ Th1-like CD4⁺ T cells, namedTh7R, that is numerically and spatially partnered with Tpex cells. Th7R cells express lymphotoxin-β and CXCL13, correlate with high endothelial venules, and co-localize with Tpex in tertiary lymphoid structures. Furthermore, Th7R cell abundance correlates with Tpex numbers in the TME and lymph nodes, and adoptive transfer of Th7R increases Tpex in a preclinical mouse model of skin cancer. In lung cancer patients, Th7R and Tpex in TME are associated with better response to neoadjuvant PD-1 blockade therapy. Thus, these results suggest that Th7R cells act as partners of Tpex CD8 T cells to sustain antitumor T-cell immunity.

overall_design: This study investigates the relationship between CD4+ and CD8+ T cells in tumor-infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells (PBMCs). Single-cell RNA sequencing, TCR repertoire profiling, and surface protein expression analysis were performed using the 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2. Matched TIL and PBMC samples were collected from each individual. Gene expression (GEX), TCR (V(D)J), and antibody-derived tag (ADT) libraries were generated from the same cells, enabling integrated analysis of transcriptomes, clonotypes, and surface markers to compare T cell phenotypes and clonal structures across compartments.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Largely distinct post-translational modifications differentiate skeletal muscle wasting induced by cancer, dexamethasone, and aging.

city: Memphis

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Gene expression changes induced by LrpprcP27A vs. LrpprcWT in skeletal muscle

overall_design: RNA-sequencing data from mouse tibialis anterior skeletal muscles electroporated with wild-type LrpprcWT (control) or with the dihydroxylation-resistant LrpprcP27A variant.

first: Anna

last: Stephan

first: Fabio

last: Demontis


title: Overnutrition directly impairs thyroid hormone biosynthesis and utilization, causing hypothyroidism, despite remarkable thyroidal adaptations

first: Nancy

last: Carrasco

address: 2215 Garland Ave.

department: Molecular Physiology & Biophysics

institute: Vanderbilt University

summary: Thyroid hormones (THs: T3 and T4) are key regulators of metabolic rate and nutrient metabolism. They are controlled centrally and peripherally in a coordinated manner to elegantly match T3-mediated energy expenditure (EE) to energy availability. Hypothyroidism reduces EE and has long been blamed for obesity; however, emerging evidence suggests that, instead, obesity may drive thyroid dysfunction. Thus, we used a mouse model of diet-induced obesity to determine its direct effects on thyroid histopathology and function, deiodinase activity, and T3 action. Strikingly, overnutrition induced hypothyroidism within 3 weeks. Levels of thyroidal THs and the TH precursor protein thyroglobulin decreased, and ER stress was induced, indicating that thyroid function was directly impaired. We also observed pronounced morphological and vascular expansion in the thyroid. Overnutrition additionally suppressed T4 activation, rendering the mice resistant to T4 and reducing EE. Our findings collectively show that overnutrition deals a double strike to TH biosynthesis and action, despite large efforts to adapt—but, fortunately, thyroid dysfunction in mice can be reversed by weight loss. In humans, BMI correlated with thyroidal vascularization, importantly signaling initial translatability. These studies lay the groundwork for novel obesity therapies that tackle hypothyroidism—which are much-needed, as no current obesity treatment works for everyone.

overall_design: To investigate the effects of overnutrition on the thyroid, we placed C57Bl/6J mice on a high-fat diet and sucrose water, whereas control mice were given a chow diet. Thyroids were collected at two timepoints for differential gene expression analysis and gene set enrichment analysis based on bulk RNA-sequencing data from 4 mouse thyroids/group/timepoint.

first: Jessica

last: Rampy

first: Alejandra Paola

last: Torres-Manzo

first: Kendra

last: Hoffsmith

first: Matthew

last: Loberg

first: Quanhu

last: Sheng

first: Federico

last: Salas-Lucia

first: Antonio

middle: C

last: Bianco

first: Rafael

last: Arrojo e Drigo

first: Huiying

first: Vivian

middle: L

last: Weiss


title: Extensive enhancer crosstalk governs the induction of PPARG2 expression during adipogenic lineage commitment

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

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

overall_design: Refer to individual Series


title: LACTB inhibits lipid synthesis to suppress glioma growth by promoting Hsc70-mediated ERBB3 degradation

city: Chengdu

first: yanjia

last: Hu

state: Sichuan

address: No.37, Guoxue Lane, Wuhou District, Chengdu City

department: Cancer Center

institute: Sichuan University West China Hospital

summary: Abnormal lipid metabolism is a hallmark of tumor and represents an anti-cancer strategy. β-lactamase like protein (LACTB) is a novel tumor suppressor, but the biological function and the involved mechanism in glioma remain unclear. Here, we show that LACTB overexpression suppresses glioma growth while LACTB knockdown shows the opposite effect. By RNA-sequencing and untargeted lipidomics analysis, we find that LACTB overexpression inhibits the lipid synthesis of glioma cells. Mechanistically, LACTB downregulates ERBB3 and inhibits PI3K/AKT/mTOR signaling, which restrains the lipogenesis of tumor cells. We further uncover that LACTB overexpression decreases the protein stability of ERBB3 by lysosomal degradation. LACTB promotes the interaction of ERBB3 and Hsc70 to facilitate ERBB3 degradation in lysosome. Finally, we show that targeting LACTB/ERBB3 axis significantly suppresses glioma growth in the mouse model. Therefore, our study reveals the antitumoral role of LACTB in glioma and the LACTB/ERBB3 axis represents a potential new therapeutic target for this tumor.

overall_design: LN229 cells transduced with vector or LACTB were subject to RNA-seq to identify the differentially expressed genes and perform function enrichment analysis. The main goal of the RNA-seq is to reveal the biological function of LACTB on glioma cells.

first: Yanjia

first: Zhaoying

last: Zhu

first: Yeng

last: Ye

first: Xin

last: Qi

first: Yang

last: Wei

first: Denian

first: Meng

last: Tian


title: Pathobiont-triggered induction of epithelial IDO1 drives regional susceptibility to Inflammatory Bowel Disease

first: Ken

last: Lau

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

summary: Chelated proximal colon epithelium from wildtype and Tnf(dARE/+) mice in two murine housing facilities (CONV and SPF-B), where the CONV facility mice are naturally colonized with Chlamydia muridarum. Raw data contains all encapsulated cells, while processed data filtered out empty droplets, poor quality cells, and non-epithelial cells such as epithelia-associated or intraepithelial immune cells.

overall_design: For CONV facilility specimens, Tnf(dARE/+) datasets are young (6-7w, N = 4) and aged (20-24w, N = 4) conditions, while wildtype datasets are a mixture of young and aged (N = 2 aged, N = 1 young).  In SPF-B facility specimens, Tnf(dARE/+) datasets are young (6-7w, N = 5) as are wildtype datasets (N = 4).

first: Paige

last: Spencer

first: Alan

last: Simmons


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[multiome]

first: Satoshi

last: Yamasaki

overall_design: To investigate transcriptional and epigenetic heterogeneity among CD4+ T cell subsets, we performed single-nucleus RNA sequencing (snRNA-seq) and single-cell ATAC sequencing (scATAC-seq) using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform. CD4+ cells were isolated and subjected to multiomic profiling, enabling the simultaneous analysis of gene expression and chromatin accessibility from the same nuclei.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Inflammation- and resolution-programmed myeloid circuits govern therapeutic resistance in epithelial and mesenchymal triple-negative breast cancer

city: Houston

first: Xiang

last: Zhang

state: TEXAS

address: One Baylor Plaza, Alkek N1130

department: Breast Center

institute: Baylor College of Medicine

summary: Single-cell analysis of human triple-negative breast cancer revealed heterogeneous macrophage populations with opposing phenotypes—pro-inflammatory and pro-resolution of inflammation. Paradoxically, both subsets accumulated in therapy-refractory residual tumors but showed inverse correlations across patients, suggesting mutually exclusive resistance mechanisms. Inflammatory macrophages localized preferentially to epithelial-like tumors, whereas pro-resolution macrophages were enriched in mesenchymal-like tumors. Mouse models faithfully recapitulated these patterns. After chemo-immunotherapy, mesenchymal-like tumors expanded pro-resolution macrophages through phagocytosis/efferocytosis, ω-3 fatty-acid uptake, and resolvin production. Macrophage-secreted C1q emerged as a principal antagonist of T-cell function by targeting mitochondria and inducing metabolic dysfunction. By contrast, epithelial-like tumors accumulated inflammatory macrophages and neutrophils that produced prostaglandins via ω-6 fatty-acid pathways. Knocking down ELOVL5—an elongase involved in ω-3 and ω-6 metabolism—mitigated both neutrophil- and macrophage-mediated immunosuppression. These distinct axes, driven by dysregulated inflammation and resolution programs, converged to undermine therapy-induced immunosurveillance; however, targeting their shared upstream regulators may overcome these resistance mechanisms.

overall_design: Eighteen days post-tumor implantation, three tumors each from the E0771, E0771-Res1, and E0771-Res2 groups were harvested. CD45⁺ immune cells were isolated by sorting and subsequently subjected to single-cell RNA sequencing.

first: Liqun

last: Yu


title: KPPC cells cells treated with EphA2 inhibitor

first: SAPANA

middle: PRAKASHRAO

last: BANSOD

address: 4482 LINDELL BLVD, 608

department: INTERNAL MEDICINE

institute: WASHINGTON UNIVERSITY, ST LOUIS

summary: We treated KPPC cells with DMSO and EphA2 inhibitor for 24 hours and performed bulk RNAseq to assess transcriptomic changes KPPC cells

overall_design: Bulk RNAseq analysis of KPPC cells after DMSO and EphA2 inhibitor treatment

first: Kian-Huat

last: Lim

first: Sapana

last: Bansod


title: Spatial Transcriptomic Analysis of Early and Late Stages of Hidradenitis Suppurativa

city: Seoul

first: Seoyoon

last: Ham

address: Yonsei-ro 50-1, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

summary:
Background: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent inflammatory nodules, abscess formation, and sinus tract development. Current biologic therapies provide limited clinical benefit, underscoring the need for deeper understanding of the immune mechanisms driving HS pathogenesis. Objective: We sought to comprehensively characterize the immune landscape of early- and late-stage HS.
Methods: Skin biopsies from a total of 15 patients with early and late-stage HS were analyzed using spatial transcriptomics, with 6 samples from these patients further analyzed using single-cell RNA sequencing (scRNA-seq). Gene expression profiles were compared to the epidermal epithelium of acne conglobata in spatial transcriptomics and to psoriasis samples in scRNA-seq as controls.
Results: Spatial transcriptomics revealed extensive dermal immune activation from the early stage of HS, including a prominent B-cell signature (immunoglobulins, CD19, MS4A1), neutrophilic infiltration (CD177, MPO, ELANE), and robust IL-23/IL-17 axis, with enriched expression of T17-inducing transcripts (TGFB3, RUNX1, BATF) and T17 cytokines (IL17A, IL17F, IL21). ScRNA-seq confirmed marked plasma cell and B-cell expansion in HS and identified potentially multifunctional B-cells expressing pro-inflammatory cytokines (IL7, IL16) in addition to their role in antigen presentation and antibody production. Furthermore, T-cells were identified as the primary producers of the B-cell chemoattractant CXCL13.
Conclusions: HS exhibits early and sustained immune activation characterized by B-cell enrichment, IL-23/IL-17 axis activation, and neutrophilic inflammation extending into the deep dermis. These findings highlight the aggressive nature of HS from its onset, suggesting that early therapeutic targeting of the IL-23/IL-17 axis and B-cell-mediated inflammation may prevent disease progression.

overall_design: FFPE tissue sections (5 µm) were prepared on BOND Plus slides, followed by deparaffinization, rehydration, and antigen retrieval using Tris-EDTA and proteinase K treatment. The tissues were hybridized overnight with GeoMx WTA RNA probes (18,677 genes) and stained with morphology markers (panCK, CD45, CD31, and SYTO 13). ROIs were selected and categorized into four regions: epithelium epidermis (above dermis), epithelium dermis (sinus tracts), dermis superficial inflammation (immune cells near epidermis), and dermis deep inflammation (immune cells near epithelium dermis). Using the DSP instrument, ROIs were segmented into AOIs, and indexed oligonucleotides were UV-released and collected. Libraries were constructed following the NanoString GeoMx-NGS protocol, using Seq Code primers and AMPure XP bead purification. Sequencing was performed on Illumina NovaSeq 6000 (2 × 151 bp paired-end).

first: S

first: J

last: Lee

first: Y

last: Kim


title: Positional guidance for Schwann cells to build nerve bridge after injury requires Plexin-B1-mediated collision repulsion

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

institute: Mount Sinai School of Medicine

summary: Positional cues are critical to guide orientation of cell movement and morphological transformation during tissue morphogenesis. Positional guidance is particularly important in nerve repair after transection injury to build a new nerve bridge connecting the gap between the proximal and distal nerve stumps. However, the mechanisms governing longitudinal alignment of glial cells in the orientation of nerve axis remain unclear. Here, we reveal that in response to nerve injury, Schwann cells rely on guidance receptor Plexin B1 to orchestrate membrane/actin dynamics for morphological transformation and contact-based collision repulsion for spatial alignment during nerve repair, which requires contact with axons and regenerating growth cones. The Schwann cell alignment in turn provides positional guidance for the longitudinal alignment of macrophages and other stromal cells in the nerve bridge to safeguard axon pathfinding along the nerve axis. Collectively, our studies demonstrate the importance of axonal contacts and Plexin-B1 for providing positional guidance for Schwann cells to longitudinally align along the nerve axis to ensure correct orientation for axon regrowth during nerve regeneration.

overall_design: To unveil the function of Plexin-B1 for Schwann Cell (SC) physiology after SNI, we derived primary SCs from Plxnb1-/- mice and WT littermate controls. Transcriptomes of SCs, in triplicate samples of WT and Plxnb1-/- SCs, were sequenced using bulk RNA-seq.

first: Jiaxi

last: Li

first: Haofei

last: Ni

first: Dalia

last: Halawani

first: Aarthi

last: Ramakrishnan

first: Chrystian

middle: J

last: Alves

first: Li

last: Shen

first: Xijing

last: He

first: Roland

last: Friedel

first: Hongyan

last: Zou


title: Activating GCN2 and subsequently the Unfolded Protein Response with the small oral molecule NXP800 delays tumor growth in osteosarcoma.

city: Nantes

first: Anaïs

last: Postec

address: 1 Rue Gaston Veil

country: France

institute: Nantes University

summary: Osteosarcoma (OS) is the most common primary malignant bone tumor mainly affecting children and young adults. Despite current treatments combining polychemotherapy and surgery, survival rates have remained unchanged for decades, highlighting the need to identify novel therapeutic approaches. NXP800, a newly developed orally available molecule, represents a promising therapeutic option. The therapeutic efficacy of NXP800 was evaluated in vitro and in a preclinical murine xenograft model of OS. RNA-seq analysis and functional assays were conducted to investigate the mechanisms of action and molecular target of NXP800. NXP800 decreases the viability of OS cell lines by blocking proliferation and inducing apoptosis. Mechanistically, NXP800 activates the Unfolded Protein Response (UPR), as demonstrated by eIF2α phosphorylation and ATF4 upregulation. This effect is mediated through the engagement of the Integrated Stress Response (ISR) via the activation of GCN2 kinase. Inhibition of GCN2, either through molecular or pharmacological approaches, abolishes NXP800-induced eIF2α phosphorylation and partially restores OS cell viability. Furthermore, NXP800 activates the IRE1α/JNK/c-Jun pathway while increasing the expression of the pro-apoptotic protein Puma. Finally, NXP800 delays tumor growth in preclinical OS model by promoting apoptosis. This study is a preclinical proof-of-principle of therapeutic efficacy of NXP800 both in vitro and in vivo, highlighting the relevance of targeting GCN2, and consequently activating the ISR and UPR, to induce apoptosis and inhibit tumor progression in OS.

overall_design: mRNA differential expression between HOS-MNNG cells treated or not with NXP800, at 6h or 24h after treatment..

first: Emma

last: Racineau

first: Morgane

last: Lallier

first: Jérôme

last: Amiaud

first: Rose-Anne

last: Thépault

first: Régis

last: Brion

first: Séverine

last: Battaglia

first: Céline

last: Charrier

first: Marie-Anne

last: Colle

first: Bénédicte

last: Brounais-Le Royer

first: Marc

last: Baud’huin

first: Franck

last: Verrecchia

first: Benjamin

last: Ory

first: Steven

last: Georges

first: François

last: Lamoureux


title: IRE1α Regulates Macrophage Phagocytosis In Immune Thrombocytopenia Through NR1D1 mRNA Decay And Lysosomal Biogenesis

city: hangzhou

first: jue

last: xie

state: zhejiang

address: Qingchun road

department: Department of Blood Transfusion

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Introduction:Macrophage phagocytosis is crucial for cellular homeostasis and is tightly regulated by stress responses. The ER stress sensor IRE1α, a key unfolded protein response (UPR) regulator, is well-studied, but its role in phagocyte homeostasis remains unknown.Objectives:This study investigates whether IRE1α regulates phagocytosis in macrophages and explores its underlying mechanism, aiming to identify potential therapeutic targets for phagocytosis-related disorders.Methods:We examined IRE1α activation in macrophages during phagocytosis of dextran or platelets. Myeloid-specific IRE1α-knockout mice were used to assess phagocytic function. Mechanistic studies included RIDD analysis to identify IRE1α-dependent mRNA degradation. A mouse model of immune thrombocytopenia (ITP) was employed to evaluate platelet clearance, with pharmacological NR1D1 inhibition (SR8278) tested as a rescue strategy.Results:Phagocytosis specifically activates IRE1α in macrophages, where it maintains phagocytic homeostasis. IRE1α deficiency led to excessive phagocytosis due to uncontrolled lysosomal biogenesis. Mechanistically, IRE1α degrades Nr1d1 mRNA via its RNase activity, suppressing lysosomal expansion. In ITP mice, IRE1α deficiency worsened platelet clearance, while SR8278 treatment rescued this defect.

overall_design: Peritoneal macrophages were harvested from 8-week-old male Ern1(fl/fl) and Mac-Ern1(KO) mice three days after they received an intraperitoneal injection of 3% Brewer thioglycolate medium. Following isolation, the cells were co-cultured for two hours with platelets opsonized by the anti-CD42 antibody (R300) in a phagocytosis assay. To investigate transcriptional alterations resulting from these conditions, we then performed bulk RNA sequencing (bulk RNA-seq). The analysis included three biological replicates for each experimental cohort.


title: THE INTEGRATIVE GENOMIC AND FUNCTIONAL IMMUNOLOGICAL ANALYSES OF COLORECTAL CANCER INITIATING CELLS TO MODULATE STEMNESS PROPERTIES AND THE SUSCEPTIBILIY TO IMMUNE RESPONSES [RNA-seq]

city: Doha

first: Cristina

last: Maccalli

address: Doha

country: Qatar

institute: Sidra Medicine

summary: We conducted a Total RNAseq profiling of primary CICs-CRC and differentiated tumor cell lines-CRC (FBS), including autologous pairs.  A differential gene expression profile was detected in CICs vs. FBS tumor cells. Overall, N=1187 were detected out of a total of 15,913 genes with measured expression as differentially expressed with p<0.05. Through applying the threshold of p<0.01and LogFC of 1.5, N=132 genes resulted as significantly differentially expressed in CICs as compared to FBS tumor cells. In summary, 33 pathways were found to be signiﬁcantly impacted highlighting the hub function of differentially expressed genes (DEGs) (N=40) and significant pathways (N=26) (p<0.05). The differentially expressed genes include genes related to cancer development and progression, e.g., the unfolded protein response component CHAC1 as well as the hexokinase domain component 1, HKDC1 which promotes tumor immune evasion in hepatocellular carcinoma by coupling cytoskeleton to STAT1 activation and PD-L1 expression. Moreover, aldolase, fructose-bisphosphate C (ALDOC), that is associated with tumor cell spheroids formation, was 2.5-fold upregulated in CICs compared to FBS tumor cells while LCK kinase, implicated in various oncogenic processes, particularly in colorectal cancer was 5-fold upregulated in CICs. On the other hand, JUNB, a direct target of TGF-β-Smad signaling, which can act as tumor suppressor or oncogene depending on the cancer entity was found to be downmodulated in CRC-CICs vs. -FBS tumor cell lines.

overall_design: Total RNA profiling of 19 CICs primary cell lines or Colorectal cancer initiating cells (CICs) cell lines and 7 FBS (Colorectal cancer differentiated tumor cell lines). We evaluated A differential gene expression profile  detected in CICs vs. FBS tumor cells.

first: Alex

last: Tout

first: Salim

last: Bougarn


title: Unravelling the role of ASN1 gene in the model legume Lotus japonicus

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

country: Spain

institute: Universidad de Sevilla

summary: Asparagine constitutes the major form of nitrogen translocated within Lotus japonicus plants. Previous work had indicated that the different genes encoding for asparagine synthetase (ASN genes) show differential patterns of expression in different organs from plants grown under either symbiotic (S) or non-symbiotic (NS) conditions.  In this work we use knock out mutants deficient in LjASN1 gene, which is the most highly expressed ASN gene in NS conditions, but much less expressed under S conditions. The analysis of two different lines of LORE 1 Ljasn1 homozygous mutant plants grown in the presence complete nutrient medium (NS) or with Mesorhizobium loti (S) was comparatively examined with respect to the WT. The results obtained indicate that a much higher biomass was produced in Ljasn1 mutants grown under NS conditions compared to the WT, while little difference was observed in the mutant plants compared to the WT under S conditions. The results point out a relationship between the deficiency of the ASN1 gene and growth of L. japonicus plants mainly under NS conditions. Further metabolomic analysis revealed that Ljasn1 mutant plants are quite distinct to WT plants when grown under NS conditions, but not under S conditions, in accordance with previous results. Interestingly, asparagine level was considerably reduced in Ljasn1 mutant plants compared to the WT when plants were grown under NS but not under S conditions, thus confirming the crucial relevance of ASN1 in the asparagine levels found in the plants under NS conditions. The results from whole metabolomics analysis, together with other obtained by RNA seq analysis, indicate that ASN1 deficiency produce important changes in the C/N balance and metabolite allocation of  L. japonicus plants resulting in a higher biomass content.

overall_design: A comparative RNAseq analysis of WT and of Ljasn1_2 mutant, KO for the LjAsn1 gene encoding for one isoform of asparagine synthetase was carried out.Shoots, roots or nodulated roots were harvested from plants grown either with ammonium nitrate or under symbiotic conditions. WT and mutant tissues were harvested after 4 hours of the beginning of the light period after 40 days of growth under symbiotic or non-symbiotic (provided with ammonium nitrate) conditions.

first: Sara

last: Rosa-Téllez

first: Marco

last: Betti

first: Alisdair

last: Fernie

first: Antonio

last: Márquez

first: Margarita

last: García-Calderón


title: The role of Decctin-2 in DSS induced colitis

city: Guangzhou

first: Haiyang

last: Sun

address: Zhongshan road

department: The first affiliated hosptial

institute: Sun Yat-sen university

summary: Isolating commensal fungi from mouse intestines has been challenging, limiting our understanding of their role in intestinal immune homeostasis and diseases. Using an Fc fusion protein of the C-type lectin Dectin-2, we successfully purified the commensal Ascomycota fungus Engyodontium sp. from mouse feces. Engyodontium enhances the antimicrobial activity of colonic neutrophils via CARD9 pathway, and exacerbates colitis by impairing the colonization of intestinal Lactobacillus johnsonii WXY strain. L. johnsonii produces high levels of L-glutamic acid by expressing the glutaminase-encoding gene glsA to facilitate Treg expansion via enhancing IL-2 receptor signaling.

overall_design: Fecal form wt and Dectin-2 ko mice,16S seq

first: Xinying

last: Wang

first: Ying

last: Tan

first: Ce

last: Tang


title: Boosting TrkA+ Sensory Nerve-to-Bone Interactions Enhances Calvarial Bone Repair and Hedgehog Signaling Activation

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: The neuroregulatory effects of sensory nerves in bone repair have recently begun to be elucidated, principally through loss of function studies. However, the potential therapeutic efficacy of boosting nerve-to-bone interactions, as well as the elucidation of downstream signaling pathways remains poorly studied. Here, two parallel approaches were utilized to enhance sensory nerve-to-bone interactions using a mouse calvarial bone defect model system.  Pharmacologic activation of TrkA with gambogic amide induced bone-associated nerve ingrowth and markedly improved calvarial bone healing. Single-cell RNA sequencing analysis of cells derived from the defect site revealed shifts in cluster proportions, with enrichment of immune cell populations in TrkA agonist-treated mice. Within the skeletal cell lineage, TrkA agonism enhanced osteoblast differentiation while suppressing fibroblastic differentiation. Pathway analysis showed increased activity of Hedgehog, Wnt, BMP, and other osteogenic pathways. Further investigation of intercellular communication identified elevated Hedgehog signaling pathway specifically from DRG neurons. In summary, activation of TrkA-positive sensory nerves stimulates hedgehog pathway activity in local mesenchymal stem and progenitor cells, promoting osteoblast differentiation and bone formation. Our study thus elucidates signaling mechanisms underlying neurogenically-enhanced bone repair.

overall_design: 2 samples were analyzed comparing mRNA from mice. One is a control group which received intraperitoneal (IP) injection of vehicle control (10% DMSO). The other is a GA group which received IP injection of gambogic amide. Gambogic amide (GA)  was used to activate TrkA. Mice received intraperitoneal (IP) injection of either 100 μL vehicle control (10% DMSO) or GA (1.2 mg/kg in 10% DMSO). Treatment began 24h prior to calvarial injury, and continued daily thereafter for 1 week. Skulls were microdissected 7 days after defect creation. Cranial bone with a defect at the center, with an approximate edge length of 3mm, was minced and subjected to six sequential enzymatic digestions with a mixture containing collagenase type I (1 mg/ml) and collagenase type II (1 mg/ml).

first: Zhao

last: Li

first: Xin

last: Xing

middle: W


title: A synergistic interaction between PRMT5 and LSD1 inhibitors in AML

city: NYC

first: Nayeli

last: Gutierrez

state: NYC

address: Hess CSM Building, 1470 Madison Ave, 6, 108

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Acute myeloid leukemia (AML) is a hematopoietic malignancy caused by abnormal proliferation and differentiation of blasts. PRMT5, a methyltransferase that catalyzes symmetric di-methylation of arginine residues, has been implicated in cancer stem cell homeostasis and shown to be a potential therapeutic target in MLL-fusion AMLs. However, given the toxicity of complete PRMT5 inhibition, there is a need to identify effective synergistic therapies. Through a targeted screen of compounds that inhibit key nodes of pathways either regulated by PRMT5 or known to be relevant for AML (e.g. intracellular signaling, splicing and transcription), we have identified a synthetic lethality between inhibition of LSD1, a lysine demethylase known to affect AML blast differentiation, and PRMT5. The two inhibitors broadly reshape the transcriptome of targeted cells and synergize to promote AML differentiation and eventually growth inhibition and apoptosis, in a p53-dependent manner. To leverage this synthetic lethal interaction, we have generated a new set of dual compounds that inhibit both PRMT5 and LSD1. Mechanistically, we show that these dual compounds elicit transcriptional and post-transcriptional (splicing) defects that recapitulate the combination therapy. Last, we were able to solve the X-ray co-crystal structure of one of the designed inhibitors with LSD1, thus elucidating its binding mode and providing a structural basis for the rational design of further inhibitors. In summary, our findings identify a novel drug combination strategy for the treatment of AML.

overall_design: To understand the mechanism underlying the synergistic cytotoxic effects of combinatorial PRMT5 and LSD1 inhibition, we performed RNA-sequencing on MV4-11 cells treated with DMSO, PRT220 (3nM), GSK-LSD1 (10nM) or both drugs combined for 3 days. Analysis of gene expression was performed to determine if there were changes in expression patterns that can explain the synergistic phenotype seen upon PRT220 and GSK-LSD1 combination in MV4-11.

first: Ernesto

last: Guccione

first: Antonello

last: Mai

first: Luca

last: Pignata


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[P5]

first: Satoshi

last: Yamasaki

summary: The priming, expansion, and function of CD8⁺ T cells are helped by CD4⁺ T cells via dendritic cells. Precursor exhausted T cells (Tpex) maintain self-renewal and supply cytotoxic CD8⁺ T cells in the tumor microenvironment (TME), but the identity of their CD4⁺ T-cell partners remains unclear. Here, we perform scRNA-seq, scTCR-seq, and mass cytometry analysis on peripheral blood, tumor, and lymph nodes derived from lung cancer patients and identify a population of IL-7Rhigh CCR6⁺ Th1-like CD4⁺ T cells, namedTh7R, that is numerically and spatially partnered with Tpex cells. Th7R cells express lymphotoxin-β and CXCL13, correlate with high endothelial venules, and co-localize with Tpex in tertiary lymphoid structures. Furthermore, Th7R cell abundance correlates with Tpex numbers in the TME and lymph nodes, and adoptive transfer of Th7R increases Tpex in a preclinical mouse model of skin cancer. In lung cancer patients, Th7R and Tpex in TME are associated with better response to neoadjuvant PD-1 blockade therapy. Thus, these results suggest that Th7R cells act as partners of Tpex CD8 T cells to sustain antitumor T-cell immunity.

overall_design: This study investigates the relationship between CD4+ and CD8+ T cells in tumor-infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells (PBMCs). Single-cell RNA sequencing, TCR repertoire profiling, and surface protein expression analysis were performed using the 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2. Matched TIL and PBMC samples were collected from each individual. Gene expression (GEX), TCR (V(D)J), and antibody-derived tag (ADT) libraries were generated from the same cells, enabling integrated analysis of transcriptomes, clonotypes, and surface markers to compare T cell phenotypes and clonal structures across compartments.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes

city: Aurora

first: Srinivas

last: Ramachandran

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Facultative heterochromatinization of genomic regulators by Polycomb repressive complex (PRC) 1 and 2 is essential in development and differentiation; however, the underlying molecular mechanisms remain obscure. Using genetic engineering, molecular approaches, and live-cell single-molecule imaging, we quantify the number of proteins within condensates formed through liquid-liquid phase separation (LLPS) and find that in mouse embryonic stem cells (mESCs), approximately 3 CBX2 proteins nucleate many PRC1 and PRC2 subunits to form one non-stoichiometric condensate. We demonstrate that sparse CBX2 prevents Polycomb proteins from migrating to constitutive heterochromatin, demarcates the spatial boundaries of facultative heterochromatin, controls the deposition of H3K27me3, regulates transcription, and impacts cellular differentiation. Furthermore, we show that LLPS of CBX2 is required for the demarcation and deposition of H3K27me3 and is essential for cellular differentiation. Our findings uncover new functional roles of LLPS in the formation of facultative heterochromatin and unravel a new mechanism by which low-abundant proteins nucleate many other proteins to form compartments that enable them to execute their functions.

overall_design: CUT&RUN of tagged CBX2 and Ezh2, and CUT&Tag of H3K27me3 in mESCs (WT and CBX2 KO) in two biological replicates.

first: Steven

last: Ingersoll

first: Abby

last: Trouth

first: Xinlong

last: Luo

first: Axel

last: Espinoza

first: Joey

last: Wen

first: Joseph

last: Tucker

first: Kalkidan

last: Astatike

first: Christopher

last: Phiel

first: Tatiana

middle: G

last: Kutateladze

first: Tao

middle: P

last: Wu

first: Xiaojun

last: Ren


title: Identification of differentiated expressed genes in cold storage associated kidney transplantation

city: yichang

first: huimin

last: Li

state: hubei

address: Wujiagang District, Yichang City, Hubei Province

institute: Yichang Central People's Hospital

summary: Background: Though it is acknowledged that ischemia reperfusion injury is the primary pathology of cold storage associated kidney transplantation, its underlying mechanism is not well elucidated. Method: To extend the understanding of molecular event and mine hub genes post-transplantation, we performed bulk RNA-sequencing at different time points (24h, day7 and 14) on a murine kidney transplantation model with prolonged cold storage (10h). Result: In the present study, we showed that genes related to regulation of apoptotic process, DNA damage response, cell cycle/proliferation and inflammatory response were steadily elevated at 24h and day7. The upregulated gene profiling delicately transformed to extracellular matrix organization and fibrosis at day 14. It is prominent that metabolic associated genes persistently took the first place among downregulated genes. The gene ontology terms of particular note to enrich are fatty acid oxidation and mitochondria energy metabolism. Correspondingly, the key enzymes of the above processes were the products of hub genes as recognized. Moreover, we highlighted the proximal tubular cell specific increased genes at 24h by combining the data with public RNA-seq performed on proximal tubules. We also focused on ferroptosis related genes and fatty acid oxidation genes to show profound gene dysregulation in kidney transplantation. Conclusion: The comprehensive characterization of transcriptomic analysis may help provide diagnostic biomarkers and therapeutic targets in kidney transplantation.

overall_design: Comparative gene expression profiling analysis of rna-seq data from difference groups

first: Jiefu

last: Zhu

first: Xiang

last: Xiaohong

first: Lang

last: Shi

first: Zhixia

last: Song


title: mTOR signaling regulates demand-adapted hematopoiesis and metabolic reprogramming required for an effective cellular immune response in Drosophila melanogaster larvae

city: Tampere

first: Laura

last: Vesala

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: The evolutionarily conserved mechanistic Target of Rapamycin (mTOR) pathway connects energy and nutrient availability to growth, proliferation, differentiation, immunity and survival. Here, we investigated the role of the mTOR pathway in Drosophila hematopoiesis and immunity using genetic and transcriptomic analyses of peripheral blood cells (hemocytes) from larvae. We show that blood cell-directed mTor expression induced lamellocyte differentiation as seen after parasitoid wasp infection. Genetic epistasis revealed that lamellocyte hematopoiesis downstream of mTor is mediated by the JNK and p38 pathways. Transcriptomic profiling showed largely similar changes in gene expression patterns of wasp infected and mTor overexpressing hemocytes. While mTOR signaling is necessary for proper lamellocyte differentiation, mTOR Complex 1 (mTORC1) activity is suppressed in mature lamellocytes. Our gene expression data indicated that hemocyte activation is accompanied by a shift in metabolism towards aerobic glycolysis for energy production, the oxidative pentose phosphate pathway for NADPH recycling, ROS production and detoxification as well as glutaminolysis for glutathione production. Our data highlight the key role of mTOR in controlling blood cell fate in Drosophila.

overall_design: METHODS: We utilized the GAL4-UAS system to target mTor overexpression to hemocytes. We used the combination of two hemocyte GAL4 lines (He-GAL4 and Hml[delta]-GAL4, HH-GAL4 for short) to drive a wild-type Tor (UAS-TOR.WT) in hemocytes. As a control, we crossed the w1118 line to the HH-GAL4. Both, the HH-GAL4; UAS-TOR.WT and the control larvae were subjected to L. boulardi parasitoid wasps for two hours, and hemocyte samples were collected 48 h after infection start. Hemocytes were also collected from uninfected, age-matched larvae.

first: Ines

last: Anderl

first: Jens-Ola

last: Ekström

first: Tea

last: Tuomela

first: Mika

last: Rämet

first: Tiina

last: Salminen


title: Immunosuppressive monocytes are enriched in hepatocellular carcinoma patients with liver dysfunction in a phase II trial of combination sorafenib and nivolumab

status: Public on Feb 04 2026

city: San Francisco

first: Bridget

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

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

overall_design: Refer to individual Series


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[S1-S3]

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

institute: Saitama Medical University

overall_design:
To examine differences in gene expression and clonal repertoire, scRNA-seq and scTCR-seq analyses were performed on Th1, Th7R, and Th17 CD4+ T cells sorted according to surface protein expression using Dynabeads and SH800Z before library construction.
These sorted libraries were then analyzed to find signature genes for Th1, Th7R, and Th17 T cells. By examining the expression patterns of these signature genes in other samples derived from lung cancer patients, we can now accurately make annotations for them.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Single-cell RNA-sequencing of bronchoalveolar lavage cells from humans with bronchiectasis

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

summary: Bronchiectasis is a lung disease characterized by irreversible dilation of the large airways (bronchodilatation), which often causes recurrent airway infection and non-resolving inflammation. In this study, we performed single-cell RNA-sequencing (scRNA-seq) to determine the heterogeneity of immune cells in the airways of bronchiectasis patients.

overall_design:
Bronchoalveolar lavage (BAL) fluid was obtained by bronchoscopy from 6 individuals with bronchiectasis. BAL cells were isolated by density gradient centrifugation and cell aliquots frozen.  For single-cell RNA-sequencing, frozen BAL cells were thawed and treated with 50 U/ml Benzonase Endonuclease (Merck) for 20 minutes at 37°C. Human immune cells (excluding neutrophils) were then purified by cell sorting as live CD45+CD66- BAL cells.

***As Swedish legislation and GDPR prevent unrestricted distribution of raw sequencing data, raw sequence data cannot be provided, including through controlled access databases.***

first: Elza

last: Evren


title: Lung cancer-enriched p53 mutants occupy canonical p53 target genes without activating transcription, revealing a distinct loss-of-function behavior [ChIP-Seq]

city: Philadelphia

first: Steven

last: McMahon

state: PA

address: 233 S 10th St

institute: Thomas Jefferson University

summary: Lung cancer is the most common cause of cancer-related death in the U.S. and globally. Cigarette smoking remains the leading risk factor for lung cancer, in part by inducing loss-of-function mutations in tumor suppressor genes, including TP53. While most cancers share a set of common “hotspot” mutations in p53, lung cancer exhibits an additional, distinct cluster of hotspot mutations. This cluster is typified by the missense mutations TP53:p.V157F and TP53:p.R158L. While canonical hotspot mutations cause broad misfolding of p53 or eliminate specific DNA contact residues, mechanistic studies of the lung cancer mutants reported here demonstrate that they retain the ability to bind the same genomic sites as wild-type p53. Despite actively binding to traditional p53 target genes, the lung cancer mutants are defective in activating transcription. To our knowledge, this represents the first demonstration of functional inactivation of the p53 tumor suppressor at a point after DNA binding, but prior to target gene activation. Relevant to the sequential inactivation of each p53 allele during cancer progression, the lung cancer mutants block the activity of a wild-type p53 allele when co-expressed in a dominant negative manner. Identification of this loss-of-function mechanism has key implications for therapeutic strategies aimed at restoring p53 function in lung cancer.

overall_design:
ChIP-seq was performed on H460 (WT p53), H2087 (V157F p53), and H661 (R158L p53) cells following 6 hours of camptothecin treatment or left untreated.
ChIP-seq was performed on H1299 cells containing a tetracycline-inducible plasmid for WT, V157F, or R158L p53. Cells were treated with tetracycline alone or with tetracycline followed by camptothecin for an additional 6 hours prior to collection.

first: Mason

last: Tracewell

first: Hailey

middle: N

last: Shankle

first: Samantha

last: Barnada

first: Khushali

last: Vyas

first: Kevin

last: Kim

first: Theodhora

last: Qyshkollari

first: Jonathan

last: Karlin

first: Julie

last: Barta


title: Lung cancer-enriched p53 mutants occupy canonical p53 target genes without activating transcription, revealing a distinct loss-of-function behavior [RNA-Seq]

overall_design: RNA-seq was performed on H1299 cells containing a tetracycline-inducible plasmid for WT, V157F, or R158L p53. Cells were treated with tetracycline alone or with tetracycline followed by camptothecin for an additional 24 hours prior to RNA extraction (3 replicates per condition).

middle: A


title: CMS subtypes correlate with complete response in trial of neoadjuvant Galunisertib plus chemoradiation in rectal cancer

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

summary: Improving response to neoadjuvant therapy for patients with locally advanced rectal cancer has the potential to improve organ preservation and disease-free survival. Knowing which patients may need therapeutic escalation or de-escalation from standard-of-care treatment remains an area of investigation. We previously reported the primary and secondary endpoints of our single-arm study combining transforming growth factor beta receptor inhibitor, Galunisertib, with neoadjuvant chemoradiation in patients with locally advanced rectal cancer. Here we analyze RNA sequencing data obtained from tissue biopsies at baseline and after 2 weeks of galunisertib. Differences in expression of pathways associated with MYC, inflammation, and epithelial-to-mesenchymal transition were observed between complete responders (CR) and <CR, with galunisertib upregulating MYC pathway expression in CR. Radiosensitivity and TGFβ response scores demonstrated limited ability to predict for response to galunisertib + chemoradiation. Typically treatment resistant consensus molecular subtype 4 (CMS4), characterized by TGFβ expression, was associated with response to galunisertib + chemoradiation. Differences in correlations between RNA based measures of cell composition and immunohistologic quantification of infiltrates and extracted MRI parameters were observed for CIBERSORT, MCPcounter, and Xcell methodologies. Based on these data, we hypothesize that the stromal radioresistant phenotype driven by TGFβ can be overcome by the addition of galunisertib to chemoradiation in rectal cancer.

overall_design:
RNA sequencing data obtained from tissue biopsies at baseline and after 2 weeks of galunisertib

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Venkatesh

last: Rajamanickam

first: Kristina

last: Young


title: IL1A enhances TNF-induced retinal ganglion cell death

city: Bar Harbor

first: Michael

last: MacLean

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Introduction: A growing body of literature suggests a role for neuroinflammation in retinal ganglion cell (RGC) death in glaucoma. For instance, deficiency of three proinflammatory cytokines, complement component 1, subcomponent q (C1q), interleukin 1 alpha (Il1a), and tumor necrosis factor (Tnf), resulted in significant protection of RGCs after glaucoma-relevant insults. While TNF and C1Q have been extensively investigated in glaucoma-relevant model systems, the role of IL1A in RGCs is not well defined.  Methods: Eyes of 2-4 month-old C57BL/6J mice or mice deficient in either Jun or Sarm1 were intravitreally injected with IL1A alone, TNF alone, or IL1A and TNF together. Retinal flat mounts were assessed for RGC survival using immunostaining of RBPMS. Bulk RNA-sequencing and differential expression analyses of retinal tissue was performed to determine molecular changes in response to IL1A, TNF, and IL1A combined with TNF within C57BL/6J and Sarm1 deficient mice.  Results: Intravitreal injection of IL1A did not result in RGC death at either 14 days or 12 weeks. Consistent with previous studies, TNF injection did not cause significant RGC loss at 14 days but did after 12 weeks. Together, IL1A+TNF resulted in a relatively rapid RGC death, driving significant loss two weeks after injection. We identified molecular changes which occur in response to IL1A and to combined IL1A+TNF treatment with limited changes identified in TNF alone treated eyes. Using mice deficient in Jun or Sarm1, we showed RGC loss after IL1A+TNF insult is JUN-independent and SARM1-dependent. Furthermore, RNA-seq analysis showed Sarm1 deficiency does not stop the neuroinflammatory response to IL1A+TNF.  Discussion: We identified a novel role of IL1A, we found that IL1A acted as a sensitizer to TNF-induced death. Co-injection of IL1A and TNF resulted in rapid RGC death, with significant RGC loss 14 days after injection. TNF+IL1A-induced RGC death did not depend on JUN activation and was rather SARM1 dependent.  Also, RNA-seq analyses indicated that while Sarm1 deficiency protected from IL1A+TNF induced RGC loss it did not significantly alter microglia and astrocyte responses. Altogether, these findings indicate that IL1A potentiates SARM1-dependent TNF-induced RGC death in vivo.

overall_design: Eyes of 2-4 month-old C57BL/6J mice or mice deficient in either Jun or Sarm1 were intravitreally injected with IL1A alone, TNF alone, or IL1A and TNF together.  Retinas were dissected after 2, 14, or 35 days and subjected to tissue processing and RNA-sequencing.

first: Katherine M.

last: Andersh

first: Gareth R.

last: Howell

first: Richard T.

last: Libby


title: Sox9-dependent acquisition of a drug resistant "memory state" induces reciprocal expression of Sox6 and Sox7 in BRAF melanoma

city: Ottawa

first: Luc

last: Sabourin

state: Ontario

address: 501 Smyth Rd

department: Cancer Research

country: Canada

institute: Ottawa Hospital Research Institute

summary: In melanoma, SOX9 and SOX10 are markers of the mesenchymal and melanocytic state, respectively. Using a panel of BRAFV600E positive YUMM lines, we find that, following chronic vemurafenib treatment, SOX10 is lost whereas SOX9 is induced. Overexpression or knock-down of either SOX9 or SOX10 had no impact on vemurafenib sensitivity. However, we find that SOX9 is necessary to program a vemurafenib-resistance memory state following a drug holiday in vitro. RNA-Seq studies show that the loss of Sox10 represents an intermediate state that is accompanied by the loss of Sox6 and the induction of Sox7, Sox9 and other phenotype switching markers. However, SOX7 expression is not sufficient to induce vemurafenib resistance. Upon acquired drug resistance, we observed differential chromatin accessibility in the Sox9 and Sox10 upstream regions, supporting their activation and repression, respectively. Overall, our data show that the loss of SOX10 and SOX9 induction are critical to program drug resistance. Furthermore, we show that the YUMM cell lines represent a good murine model to investigate transitions to an acquired drug resistant state.

overall_design: Vemurafenib-resistant YUMM1.1 cell lines (ResA) were generated by treating wildtype/naive YUMM1.1 cells at their IC50 for 6 weeks. Guide RNA targeting the N-terminal region of Sox10 (sgSox10) was used for CRISPR/Cas9-mediated Sox10 knockout in wildtype/naive YUMM1.1 cells. Control cell lines were generated using a non-targetting control guide RNA (NTC). Gene expression profiles for control (NTC), Vemurafenib-resistant (ResA), and Sox10-deficient (sgSox10) cell lines were compared using bulk RNA sequencing.

first: Samuel

last: Delisle

first: John

last: Abou-Hamad


title: RNA-seq of human aortic smooth muscle cells treated with recombinant sST2 and angiotensin II

city: Shanghai

first: Chenfeng

last: Wang

address: West Huaihai Road

institute: Shanghai Chest Hospital

summary: Soluble ST2 (sST2) is a well-established prognostic biomarker for aortic aneurysm (AA); however, its direct contribution to AA pathogenesis remains obscure. While traditionally characterized as a decoy receptor for IL-33, whether sST2 exerts independent biological functions in vascular remodeling is unknown. Here, we demonstrate that elevated sST2 levels actively drive AA progression. Using gain-and loss-of-function ApoE-/- mouse models infused with Angiotensin II (Ang II), we found that sST2 overexpression significantly exacerbated aortic rupture, dissection, and mortality, whereas sST2 deficiency conferred robust protection against aneurysm formation. Mechanistically, transcriptomic profiling and molecular validation revealed that sST2 triggers phenotypic switching, inflammation, and extracellular matrix degradation in vascular smooth muscle cells (VSMCs). We identified a novel, IL-33-independent signaling axis wherein sST2 rapidly activates STAT3 phosphorylation, subsequently upregulating the expression and secretion of the chemokine CXCL1 from VSMCs. This sST2-STAT3-CXCL1 axis orchestrates medial degeneration. Furthermore, pharmacological inhibition of STAT3 using Cryptotanshinone (CPT) effectively blocked the sST2-induced upregulation of CXCL1 and reversed maladaptive aortic remodeling in vivo and in vitro. Collectively, our findings challenge the canonical view of sST2 as solely a decoy receptor, uncovering a distinct pathogenic role in AA. Targeting the sST2-STAT3-CXCL1 axis represents a promising therapeutic strategy, with Cryptotanshinone emerging as a potential candidate for clinical intervention.

overall_design: To elucidate the mechanism by which sST2 contributes to aortic disease, human aortic smooth muscle cells were exposed to recombinant sST2 and angiotensin II. Cells were allocated to two 24-hour treatment groups(n = 3): angiotensin II alone or the combination of recombinant sST2 plus angiotensin II, followed by RNA-seq analysis.

first: Shengyan

last: Pu

first: Ruogu

last: Li


title: Optimized Protocol for Culturing Porcine Retinal Explants and RNA Isolation

city: Biberach

first: Siavash

last: Khosravi

address: Birkendorfer Strasse 65

country: Germany

institute: Boehringer Ingelheim

summary: The culture of porcine retinal explants serves as a valuable cellular model for studying retinal pathologies and their underlying molecular mechanisms. This protocol provides a detailed, step-by-step guide for dissecting the eye, isolating retina, and culturing primary porcine retinal explants for extended periods. Additionally, we outline procedures for RNA isolation and sequencing from cultured retinal explants, enabling molecular analysis of retinal biology.

overall_design: RNA-seq proifle of organotypic culture of retina from sus scrofa for a dutation of 10 days

first: siavash

last: khosravi

first: Nina

last: Zipple


title: Gene Expression profiling of TgCRND8 brains at 18 months

city: Atlanta

first: Karen

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

summary: Tau tangles and amyloid plaques are pathological hallmarkes of Alzheimer's disease (AD). To understand transcriptomics changes that occur in response to amyloid deposition, we have analyzed the brains of 18 month old mice from the TgCRND8 transgenic line which overexpresses APP and develop Thioflavin S-positive amyloid plaques beginning at 3 months of age.

overall_design: Gene expression profiling of RNA from the forebrains of CRND8 transgenic (Tg) and non-transgenic (NTg) litter mates aged to 18 months.

first: Yona

last: Levites

first: Todd

last: Golde


title: Global knockout of VEGFB improves lipoprotein lipase activity leading to an improved lipid profile during diabetes

city: Vancouver

first: Hualin

state: BC

address: 2405 Wesbrook Mall

department: Faculty of Pharmaceutical Sciences

institute: University of British Columbia

summary: Diabetes affects over half a billion people worldwide, with cardiovascular disease Q7 being its leading cause of death, either occurring secondary to atherosclerosis or due to an intrinsic defect in heart muscle (diabetic cardiomyopathy, DbCM). One instigator for DbCM is impaired cardiac metabolism characterized by excessive fatty acid (FA) delivery and utilization by the heart, causing oxidative stress and toxic lipid accumulation. Inhibition of vascular endothelial growth factor B (VEGFB) has been shown to counter these factors associated with abnormal cardiac metabolism by inducing metabolic flexibility and preventing cardiac lipid accumulation in Type 2 diabetes. However, its impact on lipoprotein lipase (LPL) and the sources of FA for cardiac use in Type 1 diabetes is unknown. Global Vegfb knockout (VegfbKO) in rats caused limited phenotype and cardiac transcriptome changes under normal conditions but notably reduced cardiac LPL activity, probably by impeding LPL translocation from cardiomyocyte to the coronary vasculature. Under streptozotocin (STZ)-induced diabetes, VegfbKO rats exhibited increased cardiac LPL activity, protecting animals from dyslipidemia, decreased plasma saturated FA, and provided a safer cardiac FA source, LPL-derived FA. Knockout of Vegfb also protected animals from DbCM by inhibiting excess FA oxidation, preserving angiogenesis and alleviating cell death in the heart. Inhibiting VEGFB may offer a promising therapeutic approach to address the current lack of mechanism-based treatments for DbCM.

overall_design: VEGFB knockout (KO) rats were created on a Sprague Dawley background rats by inserting a beta-glucosidase gene to disrupt the VEGFB gene using zinc-finger nucleases. Wildtype and global VEGFB KO rats were housed until 7 weeks of age. Diabetes was induced by intravenous administration of streptozotocin (55 mg/kg) to kill insulin production beta cell. Given the sex differences in the susceptibility to STZ diabetes, only male rats were used for this study. All animals injected with STZ developed hyperglycemia and hypoinsulinemia within 24 hours. Animals were monitored for 4 days. On day 4 of diabetes, cardiac tissue was collected from diabetic rats and their littermate-matched controls. So we have four experimental groups: wildtype control (WTC), wildtype diabetic (WTD), VEGFB KO control (KOC), and VEGFB KO diabetic (KOD)(n = 5 for each group).  Total RNA was extracted from frozen ventricular tissue using TRIzol reagent according to the manufacturer’s protocol. The concentration and purity of the RNA samples were checked by Qubit fluorometer. And the RNA integrity of the RNA samples was checked by Bioanalyzer. Then, we sent our qualified RNA sample to Sequencing Core Facility for library preparation and sequencing. The sequencing library was prepared using NEBNext Ultra II Directional RNA library Prep Kit and sequenced using Illumina Nextseq 500 platform to generate paired-end reads.

first: Rui

last: Shang

first: Chae Syng

last: Lee

first: Bahira

last: Hussein

first: Brian

last: Rodrigues


title: RNA-seq of the aorta from sST2-knockout mice in angiotensin II-induced aortic disease model

overall_design: To investigate the impact of sST2 on aortic disease progression, 6-month-old apolipoprotein E-deficient (Apoe -/-) mice were assigned to two groups (n = 3 per group): wild-type littermates and sST2-knockout littermates. Both groups received angiotensin II via osmotic minipump for 28 days to induce aortic disease, after which aortas were harvested for RNA-seq analysis


title: Multi-omics identification of key targets for the osteogenic differentiation of human bone marrow mesenchymal stromal cells under oxidative stress

city: guiyang

first: dong

last: wentao

state: guizhou

address: No. 28, Guiyi Street

institute: The Affliated Hospital of Guizhou Medical University

summary:
Background: Human bone marrow mesenchymal stromal cells (hBMSCs) are multipotent stromal cells capable of osteogenic differentiation, making them a promising cell source for bone tissue engineering and regenerative medicine. Identifying key factors that regulate hBMSCs osteogenic differentiation is crucial for enhancing bone regeneration strategies.
Objective: This study aims to identify target genes underlying impaired osteogenic differentiation of hBMSCs under oxidative stress (OS) through integrated transcriptomic and proteomic approaches, and delineate the role of proenkephalin (PENK) in this process.
Methods: OS model and impaired osteogenic differentiation model were established in hBMSCs using hydrogen peroxide (H2O2). Cellular oxidative stress levels were assessed using Dihydroethidium (DHE) fluorescent probes and JC-1 staining. Osteogenic differentiation was evaluated by alkaline phosphatase (ALP) activity and Alizarin Red staining (ARS). Key genes and proteins were predicted via integrated transcriptomic and proteomic analyses. The role of PENK in osteogenic differentiation was validated using lentiviral transfection.
Results: This study established 400 μM H2O2 as the optimal concentration for inducing impaired osteogenic differentiation in hBMSCs. Integrated transcriptomic and proteomic analysis identified 18 pivotal regulatory genes that orchestrate impaired osteogenic differentiation of hBMSCs under OS. Among these, PENK was identified as a potential therapeutic target involved in regulating oxidative stress-impaired osteogenic differentiation of hBMSCs. Functional validation confirmed that PENK overexpression promotes osteogenic differentiation in hBMSCs.
Conclusion: OS contributes to impaired osteogenic differentiation in hBMSCs. PENK regulates osteogenic differentiation of hBMSCs under OS and holds promise as a novel therapeutic target for bone regeneration and repair.

overall_design: This study aims to elucidate the transcriptomic landscape underlying the impaired osteogenic differentiation of human bone marrow mesenchymal stromal cells (hBMSCs) under oxidative stress (OS). A multi-group comparison design was employed: Experimental Groups: Control: hBMSCs in standard growth medium. OS: hBMSCs treated with 400 μM H₂O₂. Osteogenic Differentiation (OD): hBMSCs in osteogenic induction medium. OS+OD (Key Model): hBMSCs treated with 400 μM H₂O₂ and cultured in osteogenic induction medium (model of impaired osteogenesis). PENK OE + OS+OD (Functional Validation): PENK-overexpressing hBMSCs subjected to the OS+OD condition. Primary Comparison: The core analysis compares the OS+OD group versus the OD group to directly pinpoint genes specifically dysregulated during osteogenesis under OS conditions. Replication: Each group was analyzed with 3 biological replicates to ensure statistical robustness. Validation: Key candidate genes identified from transcriptomic analysis (prioritizing PENK) were functionally validated using lentiviral overexpression.

first: Wentao

last: Dong

first: Yangyang

last: Zheng

first: Yongfang

last: Zhou

first: Tao

first: Jiexin

last: Yang

first: Huaying

first: Wuxun

last: Peng


title: Functional analysis of antitumor and antiviral effects associated with changes in FAH expression in HBV-stably transfected HepG2 cells

city: Yoshida-gun

first: Shouichi

last: Namikawa

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: The Department of Gastroenterology

institute: University of Fukui

summary: HBV-stably transfected HepG2 cells were subjected to both FAH overexpression and siRNA-mediated FAH knockdown, and global gene expression changes were assessed by RNA microarray analysis to identify host pathways associated with FAH-dependent antitumor and antiviral effects. Comprehensive transcriptomic profiling revealed distinct FAH-regulated gene signatures linked to tumor-related biological processes and HBV regulation, providing mechanistic insights into how FAH modulates both tumor biology and antiviral responses in this in vitro system.

overall_design: RNA microarray was performed in HBV-stably transfected HepG2.D11 cells under FAH overexpression and FAH knockdown conditions. HepG2.D11 cells were seeded on day 0 and transfected on day 1 with either a FAH expression vector or an empty vector control, or with siRNA targeting FAH (siFAH) or a non-targeting control siRNA (si Nontarget). Cells were collected on day 4. The comparison combinations used in this analysis were 1) FAH Vector and Empty vector, 2) siFAH and si Nontarget, and 3) FAH Vector and siFAH.

first: Takuto

last: Nosaka

first: Lyu

last: Juan

first: Yosuke

last: Murata

first: Yu

last: Akazawa

first: Tomoko

last: Tanaka

first: Kazuto

last: Takahashi

first: Tatsushi

last: Naito

first: Masahiro

last: Ohtani

first: Lihong

last: Zhang

first: Tsutomu

last: Nishizawa

first: Hiroaki

last: Okamoto

first: Yasunari

last: Nakamoto


title: Epigenome‐wide association study, meta‐analysis, and multiscore profiling of whole blood in Parkinson's disease

city: Oslo

first: Lasse

last: Pihlstrøm

address: Sognsvannsveien 20

department: Department of Neurology

country: Norway

institute: Oslo University Hospital

type: Methylation profiling by genome tiling array

summary: We aimed to further elucidate the role of dysregulated DNA methylation in Parkinson's disease and to evaluate the biomarker potential of methylation-based profiling. We conducted an epigenome-wide association study (EWAS) in whole blood, including 280 Parkinson's disease and 279 control participants from Oslo, Norway. Data were later meta-analysed with data from other sources.     Methods: We conducted an epigenome-wide association study (EWAS) in whole blood, including 280 Parkinson's disease and 279 control participants from Oslo, Norway. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in postmortem human frontal cortex samples from European donors in the Netherlands Brain Bank. Following quality checks, sample filtering and normalization, association between CpG methylation and Braak alpha-synuclein stage was assessed using linear models.

overall_design: Bisulphite converted DNA from whole blood samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip v. 1.0

first: Mathias

last: Toft


title: Effects of diet, paarsite infection, and antibiotic treatment on the mouse intestinal transcriptome

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

institute: University of Copenhagen

summary: Diets rich in whole grains and fermentable fibers may promote gut health, whilst processed foods can lead to inflammation and increased susceptibility to pathogens. Here, we show that mice infected with the roundworm Heligmosomoides polygyrus exhibited increased resistance to infection when fed fiber-deprived semi-synthetic diets (SSD), relative to mice fed fibre-rich isoenergetic chow. SSD-fed mice had augmented transcription of type-2 immune-related genes during infection, and worm fitness (fecundity) was reduced. Enhanced anti-helminth immunity in SSD-fed mice was associated with suppression of gene pathways related to xenobiotic metabolism and aryl-hydrocarbon receptor (AhR) activation in the gut mucosa. However, inclusion of synthetic AhR agonists in SSD did not recapitulate the effect of chow. Moreover, whilst diet composition regulated host gut microbiota (GM) changes in response to H. polygyrus, infection resistance in SSD-fed mice was independent of the GM as antibiotic depletion of the GM failed to attenuate diet-mediated effects on parasite fecundity. Thus, in contrast to well-known health-promoting effects of whole-grain diets, synthetic diet components directly enhance resistance to helminth infection in the small intestine. These findings emphasize the role of the physicochemical structure of diet in regulating host defense at mucosal surfaces.

overall_design: Female C57BL/6 mice aged 6 weeks on arrival were used for all experiments and purchased from Envigo (The Netherlands). Mice were housed in cages of six with individual ventilation, wood chips, nesting material and ad libitum water and diet in each cage. At arrival, mice were fed either a standard grain-based diet,standard chow; a semisynthetic open-source diet (13 kJ% fat (#E15051); ssniff Spezialdiäten GmbH, Germany), SSD; or the an SSD diet containing 200 mg/kg indole-3-carbinol (#E0241). Mice were fed their respective diets for two weeks before infection with approximatively 200 L3 stage larvae of Hp. Infections were obtained by dispensing 0.2 mL/mouse of a water-larvae suspension by oral gavage. Mice were euthanized by cervical dislocation at 7-, 14-, or 28-days post infection (DPI). Mice treated with antibiotics were treated 14 days prior to and throughout infection. The treatment was administered through drinking water ad libitum. The drinking water contained 1 mg/mL Ampicillin sodium salt (Sigma-Aldrich #A9518), 1 mg/mL Neomycin trisulfate salt hydrate (Sigma #N1876), and 0.5 mg/mL Gentamycin (Sigma #G1272).

middle: R


title: Arsenic-induced transcriptional interference generates arm-wide γH2A, with distinct telomeric and centromeric responses

city: Wrocław

first: Ireneusz

middle: Bernard

last: Litwin

address: Kanonia 6/8

department: Department of Genetics and Cell Physiology

country: Poland

institute: University of Wroclaw

summary: Arsenic is a widespread environmental carcinogen, yet how exposure promotes tumorigenesis remains unclear. Prevailing models attribute arsenic genotoxicity to reactive oxygen species and replication-associated DNA breaks. Using calibrated γH2A mapping and genetics in budding yeast, we show that As(III) rapidly elicits a diffuse, chromosome-arm-spanning γH2A response that is replication-independent and occurs without oxidative stress. Instead, arsenic reduces RNA polymerase II chromatin occupancy and promotes loss of the Rpb1 subunit, consistent with acute transcriptional interference. We propose that transcription stress generates transient ssDNA intermediates that activate DNA damage signaling and require homologous recombination (HR) for resolution. Notably, the response is domain-specific: As(III) dampens subtelomeric γH2A while increasing telomere-proximal HR, and it promotes HR-factor recruitment together with Pol ε accumulation at centromeres. In human cells, short-term As(III) activates ATR and induces RPA foci and γH2AX. Together, these findings shift the early trigger of arsenic genotoxicity from ROS-driven breaks to transcription-linked ssDNA signaling.

overall_design:
ChIP–seq profiling of S129-phosphorylated histone H2A (γH2A) in wild-type Saccharomyces cerevisiae cells in log phase or arrested in G1 and G2/M, in the presence or absence of As(III).
ChIP–seq profiling of S129-phosphorylated histone H2A (γH2A) in log-phase wild-type Saccharomyces cerevisiae cells  in the presence or absence of phleomycin.
ChIP–seq profiling of S129-phosphorylated histone H2A (γH2A) in log-phase H2A S129A mutant Saccharomyces cerevisiae cells  in the presence or absence of As(III).
ChIP–seq profiling of S129-phosphorylated histone H2A (γH2A) in G1-arrested Saccharomyces cerevisiae cells lacking KU70 in the presence or absence of As(III).
ChIP–seq profiling of S129-phosphorylated histone H2A (γH2A) in log-phase rpb1-1 Saccharomyces cerevisiae cells grown at 25°C or shifted to 37°C.
ChIP–seq profiling of Tel1-12Pk in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of RPA in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Rad52-YFP in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Rad51 in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Rad59-13cMyc in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Rpb1 in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Rap1-13cMyc in G2/M-arrested wild type Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Cdc13-18cMyc in G2/M-arrested wild type Saccharomyces cerevisiae cells in the presence or absence of As(III).
ChIP–seq profiling of Pol2-3HA in wild-type log-phase Saccharomyces cerevisiae cells in the presence or absence of As(III).

first: Adrianna

last: Nawrot

first: Paulina

last: Tomaszewska

first: Ewa

last: Maciaszczyk-Dziubinska

first: Karol

last: Kramarz

first: Aleksandra

last: Domaradzka


title: β-Lapachone Antagonizes Ubiquitin-Specific Protease 18 Activity to Elicit Anti-Neoplastic Effects

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

summary: The deubiquitinase (DUB) Ubiquitin-Specific Protease 18 (USP18) is as an antineoplastic  target.  USP18 inhibitors are needed. To address this unmet need, we engineered an enzymatically active human recombinant USP18 protein for high-throughput screening. This found β-lapachone was an inhibitor of USP18-ISG15 activity. Independent β-Lapachone treatments of murine and human lung cancer cell lines statistically-significantly reduced proliferation and increased apoptosis. Gain of USP18 expression opposed these effects. β-Lapachone treatments statistically- significantly repressed growth of H1299 human lung cancer xenografts in athymic mice and also in syngeneic mice transplanted with murine 344SQ lung cancers. β-Lapachone increased reactive oxygen species (ROS) but antineoplastic effects proceeded at concentrations having little ROS production.  ROS scavenger treatments did not rescue anti-cancer effects, indicating an ROS-independent anti-neoplastic mechanism was engaged. To identify this an Interferon-Stimulated Response Element (ISRE) reporter assay was used. β-Lapachone treatment activated this reporter activity as expected for a USP18 inhibitor. β-Lapachone treatment increased global ISG15 conjugation. Proteomic analysis and immunoprecipitation assays revealed known and new ISG15ylated proteins. RNA sequencing of parental lung cancer cells engineered with or without gain of USP18 expression found differentially expressed genes and pathways after β-lapachone treatments. Taken together, β-lapachone is a novel USP18 inhibitor and cancer biology tool.

overall_design: A549 lung cancer cells stably expressing USP18 or empty vector treated with vehicle as a control or β-Lapachonefor 48 hours were harvested to extract total RNA for sequencing.

first: Blessing

last: Ogunlade

first: Xi

last: Liu

first: Ethan

last: Dmitrovsky