title: scRNA-seq and scATAC-seq reveal dual transcriptional and translational regulation in fiber cells in Upland and Pima cotton

city: Austin

first: Z Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Fiber cell initiation and development affect cotton fiber yield and quality. Cotton fiber develops from the ovular epidermis of a seed, and approximately 25-30% of protodermal cells in each cotton ovule develop into fiber. However, the molecular basis for fiber cell development remains elusive. Here, we analyzed single-cell RNA-seq (scRNA-seq) data from over 40,000 cells during early stages of fiber cell development in Upland and Pima cotton and in a naked seed mutant. We found concerted expression changes of 900-1,700 genes in fiber-cell clusters involving gene expression, translation, and peptide biosynthesis, which were substantially delayed or absent in the mutant. Expression of ∼500 and ∼300 genes in Upland and Pima cotton, respectively, was distinguishably different and consistent with overrepresentation of the genes in transcriptional and translational regulation, implying their roles in fiber yield and quality traits. Gene co-expression network analysis (GCNA) of scRNA-seq and scATAC-seq data revealed two modules of fiber gene co-expression networks. One module of the fiber co-expressed genes was associated with elevated chromatin accessibility for transcriptional regulation, whereas the other module of the genes was related to translational regulation and ribosome biogenesis. Indeed, expression of cotton putative translation factor genes was elevated in fiber cell clusters in both Upland and Pima cotton. Finally, cotton transgenic plants expressing promoter::GFP confirmed expression patterns of fiber-expressed GhRDL2_D5 during fiber cell initiation. These single-cell genomic resources provide insights into fiber cell development for breeding and biotechnological improvement of fiber yield and quality in Upland and Pima cotton.

overall_design: Whole ovules of Gossypium were collected and briefly digested using macerozyme and cellulase enzyme mix to release protoplasts from the epidermal surrface, including developing fiber cells. Ovules from Gossypium hirsutum TM1 at 0, 1 and 2 days post-anthesis, The protoplasts were purified using differential gradient centrifugation, lysed, and nuclei were then isolated and analyzed using via 10x scATAC sequencing.

first: Ryan

last: Kirkbride

first: Atsumi

last: Ando

first: Dayea

last: Park

first: Zhigang

last: Li

first: Sonika

last: Kumar

first: Christopher

last: Saski

first: Don

last: Jones

first: Z. Jeffrey


title: Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vivo]

status: Public on Dec 02 2025

city: St Lucia

first: Benjamin

middle: D

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

type: Expression profiling by high throughput sequencing

summary: The liver secretes most circulating proteins, which are critical for inter-organ communication and systemic energy homeostasis. However, the regulatory mechanisms governing hepatic protein secretion are largely unknown. Using proteomics approaches in humans and mice, we here demonstrate that hepatic protein secretion follows a 24-hour rhythm which is modulated by the timing of food intake. Rhythmic variations in the expression of secretory pathway proteins, involved in protein glycosylation and folding in the endoplasmic reticulum and Golgi apparatus, mediate this process. We find that feeding rhythms and the circadian clock protein BMAL1 regulate diurnal hepatic protein secretion by driving glycogen breakdown which generates glycosylation substrates. Rhythmic secretion was attenuated in a mouse model of obesity and affected by genetic variants associated with glycogen storage disease and congenital disorders of glycosylation. Our study reveals a mechanistic link between glycogen-derived metabolites and the protein secretion pathway, thereby connecting nutrient intake with fundamental liver functions.

overall_design: C57BL/6J mice (n=4 per treatment and timepoint) were exposed to 12-hour night-restricted feeding for four days before receiving a subcutaneous injection of CP-91149 (40 mg/kg; volume of 10 µl per g body weight) or vehicle at ZT0. Serum and liver tissues were collected at ZT3, ZT6, ZT9, ZT12, and ZT24.

first: Meltem

first: Benjamin D.

first: Dominic

last: Hoyle

first: Frédéric

last: Gachon


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [RNA-seq PDX]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: We have previously shown that IKKa coordinates the activation of several oncogenic and therapy-resistant pathways, including ATM/DDR, BRD4, and JAK/STAT3, independently of canonical NF-kB signaling. Here, we found that IKKa suppression, either genetically or pharmacologically, led to stabilization of ZO-1 protein and increased CLDN2 expression, resulting in altered tight junction distribution. IKKa KO cells showed a shift in their migratory mode towards collective migration, which is associated with superior metastatic capacity in vivo. Analysis of single-cell (sc)RNA-seq data from a mouse model of CRC revealed an accumulation of the tight junction signature, including ZO-1 and CLND2, in the metastatic populations. scRNA-seq analysis of patient-derived organoid (PDO5)  identified three distinct epithelial cell clusters (C2, C4 and C8) that show a significant enrichment for the metastasis-specific EpiHR signature and the tight junction signature. In particular, C2 and C8 display unique genetic signatures that are significantly upregulated in IKKa KO cells and enriched in the PDO5 IKKa KO-derived metastases. Analysis of human paraffin-embedded CRC specimens led to the identification of vascular tumor infiltrates with ZO-1 and CLDN2-positive cluster-like or glandular phenotypes. The concomitant presence of low CHUCK (IKKa)  and high TJP1 (ZO-1) RNA levels is sufficient to predict poor prognosis in CRC patients. These results suggest that the presence of collectively migrating cancer cells in the vascular infiltrates, characterized by high levels of tight junction proteins, could be standardized as a prognostic tool to predict metastasis. We anticipate the use of drugs targeting tight junction elements for metastasis prevention.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We analyzed bulk RNAseq samples obtained from hepatic metastasis (mouse PDX) derived from Patient Derived Organoid (Colorectal Tumoroid) in two different conditions: 3xWT untreated and 3xIKKa KO untreated.

first: Daniel

last: Alvarez-Villanueva

first: Mónica

last: Larrubia-Loring

first: María

last: Maqueda

first: Anna

last: Tramuns

first: Evelyn

last: Andrades

first: Teresa

last: Lobo-Jarne

first: Eric

last: Canton

first: Josune

last: Alonso-Marañón

last: Martínez-Iniesta

first: Luis

middle: G

last: Palma

first: Alberto

last: Villanueva

first: Mar

last: Iglesias

last: Bigas


title: Integrative transcriptome-wide association reveals PRKCG-linked GABAergic dysfunction in FXTAS

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

country: USA

institute: Emory University

summary: This SuperSeries is composed of the SubSeries listed below: GSE285979, GSE286170

overall_design: Refer to individual Series

first: Peng


title: Mixed-Chirality Prohibitin Peptide: D-(RLARLAR)2 Enhances Stability and In Vivo Effects on Obesity

first: Benjamin

last: Weger

summary: Obesity is a global epidemic and the primary risk factor for type 2 diabetes, ranking as the fifth leading cause of death worldwide. While lifestyle changes can address body fat accumulation, pharmacotherapies are essential for sustained weight loss. In this study, we report the design of a new generation of cationic-rich peptide-based therapeutics engineered to target white adipose tissues. Our findings demonstrate remarkable efficacy in significantly reducing body weight in a high-fat diet-induced mouse model. Notably, a prohibitin peptide substituted with D-arginine represents a paradigm shift by inducing mitochondrial uncoupling. This study heralds a promising avenue for developing the next generation of prohibitin-targeting peptides, capable of curbing adipocyte expansion and body weight, with favorable preclinical safety profiles. Altogether, these peptides hold immense potential for addressing obesity and metabolic syndrome.

overall_design: 2 organs (WAT and liver) of female (F) and male (M) mice that have been injected with vehicle or PTP-r.

first: Lai

middle: Y

last: Chan

first: Meltem

first: Junqiao

last: Du

first: Nicole

last: Lawrence

first: Marlon

middle: H

last: Cardoso

first: Samilla

middle: B

last: Rezende

first: Jéssica

last: AI Muller

first: Kuok

last: Yap

first: Brian

middle: C

last: Tse

first: Kamil

middle: A

last: Solowski

first: Robert

middle: P

last: Sullivan

first: Jennifer

last: Gunter

first: Octávio

middle: L

last: Franco

first: David

middle: J

last: Craik


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [scRNA-seq]

first: Lluis

last: Espinosa

overall_design: We analyzed 3x scRNAseq 10x samples obtained from Patient Derived Organoid (Colorectal Tumoroid) in three different conditions: 1xWT untreated, 1xIKKa KO untreated and 1xIKKa KO treated with CLDN2 inhibitor

first: Daniel

last: Alvarez-Villanueva

first: Mónica

last: Larrubia-Loring

first: María

last: Maqueda

first: Anna

last: Tramuns

first: Evelyn

last: Andrades

first: Teresa

last: Lobo-Jarne

first: Eric

last: Canton

first: Josune

last: Alonso-Marañón

last: Martínez-Iniesta

first: Luis

last: Palma

first: Alberto

last: Villanueva

first: Mar

last: Iglesias


title: Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vitro]

first: Benjamin

last: Weger

overall_design: AML12 cells (300,000 cells/well) were seeded into sterile 6-well plates, and all washes were performed with 1x PBS. Treatments included 67 μM CP-91149 and vehicle (0.03% DMSO). Cell were collected at 3, 6, 14 and 24 h after treatment.

first: Meltem

first: Benjamin D.

first: Dominic

last: Hoyle

first: Frédéric

last: Gachon


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [RNA-seq Tumoroid]

first: Lluis

overall_design: We analyzed bulk RNAseq samples obtained from Patient Derived Organoid (Colorectal Tumoroid) in two different conditions: 2xWT untreated and 2xIKKa KO untreated.

last: Bigas


title: Mouse lung gene expression comparison between mesenchymal Flcn deletion and wild type control.

city: Los Angeles

first: Brendan

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Loss of functional FLCN mutations are known to be the cause of Birt-Hogg-Dubé (BHD) syndrome, in which pulmonary cysts are presented in up to 90% of the patients. Lack of the related disease models in vivo poses a significant barrier to understanding the pathogenic mechanisms, including how the cysts develop and what molecular signaling pathways are involved.   In this study, we selectively deleted Flcn specifically in lung mesenchymal cells using a Tbx4-rtTA/TetO-Cre driver. These mice exhibit defective postnatal lung alveolarization. Most strikingly, alveolar enlargement continues into adulthood in these mice, accompanied by bilateral pulmonary cyst formation that resemble human BHD. Interestingly, Flcn deletion in lung epithelial cells alone did not exhibit any alveolar enlargement. No synergistic or additive effects were detected in mouse lungs with combined Flcn deletion in both epithelial and mesenchymal compartments compared to the mice with lung mesenchymal Flcn knockout. We have compared differential gene expression of lung tissues between Flcn knockout in mesenchyme and wild type control mice by RNA-seq.

overall_design: The middle lobes of the de-blood lungs from the mice at postnatal day 7 and 4 months of ages were isolated and flash-frozen in liquid nitrogen. mRNAs from wild type and Flcn knockout lungs were prepared by using the TRIzol RNA extraction reagent (ThermoFisher, #15596026). The RNeasy Micro Kit (Qiagen, #74004) was then used to clean up the extracted mRNA. Total RNA quality was checked with a bioanalyzer (Agilent) with RIN greater than 7.0 being acceptable. RNA-sequencing was performed at Novogene (Sacremento, CA).

first: Wei

last: Shi

first: Yongfeng

last: Luo

first: Matthew

last: Thornton


title: Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Validation cohort

city: Antwerpen

first: Nicolaas

last: Van Renne

address: Universiteitsplein 1

country: Belgium

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)

summary: We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the validation cohort used to validate the predictive transcriptomic signature.

overall_design: Transcriptomic profiles of 51 patients with at least 1 million mapped reads were retained in the validation dataset.

first: Stijn

last: Van Hees

first: Bart

last: Cuypers

first: Arno

last: Furquim d’Almeida

first: Axelle

last: Vanderlinden

first: Pieter

last: Meysman

first: Jordan

last: Feld

first: Paloma

last: Sangro del Alcázar

first: Stefan

last: Bourgeois

first: Dirk

last: Sprengers

first: Geert

last: Robaeys

first: Luisa

last: Vonghia

first: Peter

last: Michielsen

first: Sven

last: Francque

first: Bruno

last: Sangro

first: Owen

last: Cain

first: Ahmed

middle: M

last: Elsharkawy

first: Rob

last: De Man

first: Andre

last: Boonstra

first: Harry

last: Janssen

first: Ann

last: Driessen

first: Kris

last: Laukens

first: Thomas

last: Vanwolleghem


title: Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Training cohort

first: Nicolaas

last: Van Renne

summary: We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the training cohort used to generate the predictive transcriptomic signature.

overall_design: Transcriptomic profiles of 56 patients with at least 1 million mapped reads were retained in the training dataset.

first: Stijn

last: Van Hees

first: Bart

last: Cuypers

first: Arno

last: Furquim d’Almeida

first: Axelle

last: Vanderlinden

first: Pieter

last: Meysman

first: Jordan

last: Feld


title: CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial)

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D, has enabled effective targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics and CODEX-based spatial proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. MRTX1133 treatment was associated with increased CD11c+ cells, T cells, and tumor-restraining fibroblasts within proximity to cancer cells, suggesting that antigen presentation and remodeling of the local microenvironment is associated with an effective response to KRASG12D inhibition. In the context of emergence of MRTX1133 therapy resistance, CDK8, a multiprotein mediator complex associated kinase, was identified as a mediator of resistance in part through induction of downstream CXCL2 chemokine secretion, inhibition of FAS expression, and remodeling of the TME to promote immune evasion. Targeting CDK8 in combination with aCTLA-4 immunotherapy overcomes resistance to small molecule mediated targeted KRASG12D inhibition with prolonged survival of mice with PDAC.

overall_design: Pancreas tissue from mice treated with vehicle or MRTX1133 was collected in formalin and processed into paraffin blocks. HY19636 samples are orthotopic tumors and KC samples are from LSL-KrasG12D; Pdx1-Cre genetic models. 5 um thick sections were generated, stained with H&E, and scanned with an Zeiss Axio Scan.Z1.

first: Kathleen

last: McAndrews

first: Bingrui

last: Li

first: Raghu

last: Kalluri


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration

first: Lluis

last: Espinosa

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


title: CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (scRNA)

overall_design: Orthotopic PDAC models (PKC-HY19636 or KPC689 resistant) were treated with vehicle, or the KRASG12D inhibitor MRTX1133 alone or in combination with aCTLA4 and/or CDK8i for the indicated timeframes. 2-3 pancreata/tumors were pooled per sample.


title: Uterine epithelial ERα regulates preimplantation uterine luminal epithelial (LE) and uterine mRNAs

status: Public on Dec 01 2025

city: Athens

first: Xiaoqin

last: Ye

state: Georgia

address: 501 D.W. Brooks Drive

department: Physiology and Pharmacology

institute: The University of Georgia

summary: Uterine epithelial estrogen receptor α (ERα) deficiency in epiERα-/- (Esr1f/-Wnt7aCre/+) mice leads to dysregulated environment of uterine lumen, which is lined by uterine luminal epithelium (LE). We hypothesized that LE transcriptomes held molecular keys to understanding ERα in regulating preimplantation uterine environment. Day 0.5 post-coitum (D0.5) and D3.5 LE (isolated via enzymatic digestion), digested uterus (DU), and flash-frozen uterus (U) from Esr1f/- (control) and epiERα-/- mice were processed for mRNA-seq. There were minimal differentially expressed genes (DEGs, TPM>1, FC>2, FDR<0.05) between DU and U. Between D0.5 and D3.5 Esr1f/- LE, the top upregulated and downregulated GOBP pathways were on cellular processes and on innate immune responses, respectively, with the later also seen in Esr1f/- U. Compared to Esr1f/- LE, the most upregulated and downregulated pathways in D0.5 epiERα-/- LE were on innate immune responses and on biosynthesis and metabolism, respectively; while those in D3.5 epiERα-/- LE were on cell division and on signaling and metabolic processes, respectively. Na+ transmembrane transport was among shared upregulated pathways in D0.5 and D3.5 epiERα-/- LE. Between Esr1f/- and epiERα-/-, most DEGs in U were also DEGs in LE, limited DEGs in U only with higher expression than in LE were related to immune responses, implicating potential paracrine effects of uterine epithelial ERα. Selected DEGs were verified by realtime PCR and immunohistochemistry. This mRNA-seq dataset provides molecular keys to understanding temporal (e.g., innate immunity) and constituent (e.g., uterine fluid movement) functions, and potential paracrine effects of uterine epithelial ERα in regulating the preimplantation uterine environment.

overall_design: Virgin Esr1f/- and epiERα-/- female mice at ~2-6 months old were mated with wild type stud males (Esr1f/f or C57BL/6). They were checked every morning for the presence of a vaginal plug, an indication of mating activity during the previous night. The day of plug identification is defined as day 0.5 post-coitum (D0.5). The plugged females were separated from the stud males and randomly assigned into D0.5 and D3.5 time points, with same genotype littermates assigned into different timepoint groups. There were four groups of mice: D0.5 Esr1f/- group, D0.5 epiERα-/- group, D3.5 Esr1f/- group, and D3.5 epiERα-/- group. The mice were dissected at 11~12 h on both days. For each uterus, ¼ of one uterine horn was fixed in 10% formalin and ¼ of the other uterine horn was flash-frozen on dry-ice, designated as “U” (uterus), the remaining ¾ uterine horns connected by the cervix were slit open, immersed in 0.5% dispase (REF#17105-041, gibco, Waltham, MA, USA) in 1xHBSS buffer without calcium or magnesium (REF#1415-052, gibco, Waltham, MA, USA) for 30 min in a 6-cm culture dish, modified from our previous procedure (3-5). To determine the effects of enzymatic digestion process on uterine gene expression, we collected a small piece of digested uterine tissue prior to being processed for LE isolation. The small piece of digested uterine tissue was frozen on dry-ice and designated as “DU” (digested uterus). The LE layer in the remaining uterine tissue was gently scraped. The dislodged LE sheets were collected into a 1.5 ml microcentrifuge tube using a 200 μl pipette tip under a dissection microscope, centrifuged at 2000g for 3 minutes at 4C. Upon the removal of the buffer, 1 ml of TRIzol (REF# 15596018, Invitrogen, Carlsbad, CA, USA) was added to the LE pellet, which was gently vortexed to disperse the LE pellet, and kept at -20C. The U and DU tissues were carefully powdered in liquid N2 using a mortar and pestle, collected into a 1.5 ml microcentrifuge tube, in which 1 ml of TRIzol was added, and upon gentle vortexing to disperse the uterine powder, the tube was kept at -20C. At the conclusion of tissue collection, the LE, DU, and U samples in TRIzol were processed as one batch per tissue for total RNA isolation.

first: Jonathan

last: Hancock

first: Tong

last: Zhou

first: Yuehuan

first: Taylor

middle: E

last: Martin

first: Moya

last: Zhang


title: Investigating conjunctival immune pathways in Sjögren and non-Sjögren disease associated dry eye

first: Cintia

middle: Sade

last: de Paiva

address: One Baylor Plaza

department: Ophthalmology

institute: Baylor College of Medicine

summary: This study aimed to investigate changes in immune related genes on the ocular surface of patients with different diagnoses. We compared DEGs from 21 healthy controls, 12 aqueous tear deficient (ATD), and 12 Sjögren disease dry eye using the nanostring immunology v2 panel. We identified DEGs in immune pathways relating to viral response and adaptive immunity. We did not identify DEGs in comparison of ATD vs SjD, suggesting there are no differences in the immune response on the ocular surface, despite different diagnoses.

overall_design: 42 patient samples were submitted for Nanostring analysis. 25 healthy controls, 12 aqueous tear deficient dry eye, and 13 Sjögren disease dry eye. All samples were age and sex matched.

first: Kaitlin

middle: K

last: Scholand

first: Laura

last: Schaefer

first: Zhiyuan

last: Yu

first: Stephen

last: Pflugfelder

first: Robert

last: Britton


title: Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

summary: Improper light focus on the retina, refractive error, is primarily caused by eye size differences and is the leading cause of vision loss worldwide. C-terminal variants in the Myelin Regulatory Factor (MYRF) gene, a retinal pigment epithelium (RPE)-derived transcription factor, lead to isolated nanophthalmos characterized by a small, though structurally sound eye. However, other MYRF loss-of-function variants cause syndromic disease. To address this discrepancy, in vitro and animal studies were performed on a pathogenic C-terminal variant dG-MYRF (p.Gly1126fs30*, c.3376-1G>A ). Human RPE-cells or primary RPE transduced with dG-MYRF showed reduced target gene expression, with decreased steady-state levels of the C-terminal cleavage product, but normal cleavage and localization. A homozygous humanized MYRF C-terminal mouse model (MyrfhumdG/humdG) was embryonic lethal by embryonic day (E) 18.5, while wildtype (MyrfhumWT/humWT) mice were viable. Single-cell RNA-seq from E17.5 MyrfhumdG/humdG and knockout RxCre;Myrffl/fl (E15.5 and P0) mice revealed shared differentially expressed genes, with decreased effect size in the MyrfhumdG/humdG  eyes. These findings support dG-MYRF as a hypomorphic allele. Additionally, two novel MYRF splicing variants creating nonfunctional isoforms were found in families with isolated nanophthalmos. Overall, hypomorphic MYRF alleles underlie isolated nanophthalmos, supporting a tissue-specific threshold effect and highlighting unique roles for the MYRF C-terminus in the RPE.

overall_design: Eyes were collected from e17.5 litters, the cornea, lens, and optic nerve were removed. Three MyrfhumWT/humWT and three MyrfhumdG/humdG samples were pooled for each time point, dissociated, and scRNAseq was performed.

first: Gabrielle

last: Rozumek

first: Michelle

last: Brinkmeier

first: SuQing

last: Wang

first: Ford

last: Hannum


title: RNA-sequencing of FACS-sorted hematopoietic stem and progenitor cells (LSK) from bone marrow of WT and Sucnr1 knock-out mice

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

summary: Succinate is a metabolic signal that links hypoxia to IL-1β and cell responses in myeloid cells through intracellular mechanisms, but also autocrine/paracrine processes through succinate receptor 1 (Sucnr1). Succinate and its receptor have been scarcely studied in the context of hematopoiesis under health or disease. We investigated the in vivo role and molecular mechanisms of succinate and Sucnr1 in normal and malignant hematopoiesis, using an in vivo knock-out (KO) of Sucnr1.

overall_design: We profiled FACS-sorted hematopoietic stem and progenitor cells (HSPC) identified as  Lin−Sca-1+c-Kit+ (LSK) from bone marrow (BM) of males C57BL6/J WT (n = 4) and Sucnr1-KO (n = 3) aged 7 months by RNA-sequencing (RNA-seq). 27000-75000 cells were FACS-sorted in Arcturus Picopure RNA isolation kit (Thermo Fisher) extraction buffer.

first: Aurora

last: BERNAL

first: Vincent

last: CUMINETTI

first: Ruth

last: PAULSSEN

first: Manuel

last: GÓMEZ

last: ARRANZ


title: Transcriptomic profiling of human saphenous veins during ex vivo culture–induced neointima proliferation

city: Augusta

first: David

middle: S

last: Kim

department: Vascular Biology Center

institute: Augusta University

summary: Vein graft failure is a major limitation of coronary and peripheral bypass surgery, driven by neointima proliferation and smooth muscle cell (SMC) phenotypic modulation. To investigate the early molecular events underlying this process, we cultured segments of human saphenous veins ex vivo for seven days. Bulk RNA sequencing and 10x Visium spatial transcriptomics  were performed on paired fresh (Day 0) and cultured (Day 7) samples. Differential gene expression analysis revealed significant downregulation of contractile SMC markers and cytoskeletal genes, and upregulation of extracellular matrix (ECM), inflammatory, and stress-response pathways. Integration of both datasets highlighted coordinated suppression of SMC contractile phenotype and activation of matrix remodeling programs, consistent with early neointima development. These results provide a multi-omics resource defining molecular transitions that drive human vein graft remodeling.

overall_design: Bulk RNA-seq profiling was performed on paired segments of human saphenous veins cultured ex vivo under serum-enriched conditions for 7 days (Day 7) compared with freshly isolated segments (Day 0).

first: Vy

last: Ong

first: Jiang

last: Zhou

first: Yang

last: Shi

first: Austin

middle: W

last: Chang

first: Neal

last: Weintraub


title: Intestinal Stem and Progenitor Cells Exhibit Distinct Adaptive Responses to Inflammatory Stress in IBD

city: Nottingham

first: Brinda

last: Balasubramanian

address: University Park

country: United Kingdom

institute: University of Nottingham

summary: Intestinal epithelial stem cells (SCs) and their transit-amplifying (TA) progeny are critical for mucosal repair and regeneration. However, their behaviour under chronic inflammatory conditions, such as those observed in Inflammatory Bowel Disease (IBD), remains incompletely understood. We investigated the impact of chronic inflammation on intestinal stem/progenitor cells by integrating bulk RNA sequencing from the largest IBD biopsy cohort to date with single-cell transcriptomic analysis and experimental assays using patient-derived intestinal organoids. Active inflammation was associated with a reduction in canonical LGR5⁺ intestinal stem cells and a concurrent expansion of OLFM4⁺ populations, consistent with an inflammation-induced epithelial repair program. Notably, SC/TA cells from both inflamed and non-inflamed IBD tissues exhibited persistent transcriptional changes that were distinct from those in healthy controls. Single-cell analysis identified transcriptionally heterogeneous SC/TA subpopulations, including a previously uncharacterized inflammation-associated cluster enriched in immune signalling pathways. Pseudotime trajectory analysis demonstrated a shift in differentiation toward deep crypt secretory (Paneth-like) cell lineages under inflammatory conditions. Chronic intestinal inflammation reshapes the epithelial stem/progenitor cell compartment, promoting altered differentiation and the emergence of immune-responsive epithelial states. These findings highlight the plasticity of the human intestinal epithelium in IBD and point to new avenues for therapeutic strategies aimed at maintaining epithelial integrity during chronic inflammation.

overall_design: RNA-seq profiling of patient derived organoids from healthy donors and IBD patients.

first: Balasubramanian

last: Brinda

first: Patel

last: Shivam

first: Ordonez-Moran

last: Paloma


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [H3K4me1 CUT&RUN]

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

institute: johns hopkins university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response.

overall_design: H3K4me1 CUT&RUN was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li


title: Multimodal integration of epigenetics, spatial transcriptomics and immune microenvironment in sacral chordoma

city: New York City

first: Yee Hoon

last: Foong

state: NY

address: NYU Grossman School of Medicine

department: Department of Medicine

institute: New York University

type: Methylation profiling by genome tiling array

summary: Multimodal study elucidated the complex epigenetic and immunological landscape in sacral chordomas

overall_design: Bisulfite converted DNAs from 29 sacral chordoma tissues  were analyzed on Illumina EPIC platforms (21 on EPICv1 and 8 on EPICv2)

first: Yee

first: George

last: Jour

first: Garima

last: Sinha

first: Jamal

last: Benhamida

first: Nathan

last: Aleynick

first: Yanyun

first: Travis

last: Hollmann

first: Mrinal

last: Gounder

first: Rohan

last: Sardana

first: Carla

last: Saoud

first: Max

last: Vaynrub

first: Patrick

last: Boland

first: Rami

last: Vanguri

first: Meera

last: Hameed


title: Signaling and mechanistic insights into folate binding protein induced cytotoxicity in KB cancer cells

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

institute: Monash University

summary: To investigate the mechanism(s) underlying FBP-induced cytotoxicity and apoptosis in FR-overexpressing KB cancer cells, using next-generation sequencing (NGS), followed by bioinformatics analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KB cells treated with 50 µM FBP for 0, 6, 12, and 24 hours.

first: Hajar

last: Samadian

first: Mark

last: Banaszak Holl

first: Jennifer

last: Dyson

first: Manuel

last: Rosa-Garrido

first: Rujula

last: Pradeep


title: Conditional Fibroblast BCL-2 Expression Promotes Persistent Pulmonary Fibrosis, which is Reversible by Therapeutic BCL-2 Inhibition

city: Denver

first: Elizabeth

last: Redente

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease that develops in response to chronic epithelial injury. Unlike injury-induced homeostatic lung repair during which fibroblasts undergo apoptosis and clearance, the lungs of IPF patients continue to accumulate apoptosis-resistant, pro-fibrotic, extracellular matrix-producing fibroblasts. Here, we show that prevention of PDGFRα+ fibroblast apoptosis by conditional BCL-2 expression leads to the emergence and persistence of senescent, pro-fibrotic fibroblasts along with enduring, pathologic fibrotic lung remodeling. Additionally, spatial transcriptomic studies of human IPF lungs confirmed the presence of senescent, BCL-2 expressing α-smooth muscle actin+ myofibroblasts in fibrotic regions. Of translational significance, selective BCL-2 inhibition with ABT-199 in fibrotic mice re-engaged the apoptotic pathway in fibroblasts, reduced senescence, and promoted fibrosis resolution and lung regeneration. Our findings suggest that sustained BCL-2 expression in fibroblasts prevents homeostatic lung repair, drives persistent fibrosis and is a therapeutically relevant target to reverse persistent pulmonary fibrosis.

overall_design: Naive, 3wk bleomycin hBcl2, 3wk bleomycin Wild Type/CO, 6wk bleomycin hBcl2, 6wk bleomtcin Wild Type/CO

middle: F

first: Tengyao

last: Song

first: Nomin

last: Javkhlan

first: Benjamin

last: Edelman

first: Daniel

last: Foster

first: Jasmine

last: Wilson

first: Sangita

last: Chakraborty

first: Joseph

last: Cooley

first: Rohit

last: Gaurav

first: Satria

last: Saguthi

first: Max A

last: Seibold

first: Rachel

middle: Z

last: Blumhagen

first: David

last: Schwartz

first: Ivana

middle: V

last: Yang

last: Matsuda

first: James

last: Bridges

last: Zemans

first: Rubin

last: Tuder

last: Riches


title: ROS Activated NETosis of Bone Marrow CD55+ Intermediate Mature Neutrophils Through HIF1α-PADI4 Pathway to Initiate Bone Aging.

city: Beijing

first: Yutong

last: Guo

address: No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100081, PR China.

country: China

institute: Peking University

summary: Bone marrow neutrophils are highly heterogeneous cells and we used sing cell RNA-sequencing to analyze the diversity of BM neutrophils of SAMP6 and SAMR1 mice femur bone.

overall_design: Femour of 3-month male SAMP6 and SAMR1 mice were separately flushed out, and after lysing red cells, BM cells were analyzed by sc-RNA seq.


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [CUT&Tag]

city: San Diego

first: Christopher

last: Hartl

address: Pacific Heights Blvd

department: Cell Biology

institute: Epigenome Technologies

summary: Aging disrupts genome organization and transcriptional fidelity, but the role of non-canonical DNA structures in the aging process remains unclear. G-quadruplexes (G4s), stable guanine-rich DNA and RNA structures are established regulators of gene expression and genome integrity, yet their contribution to physiological aging is unknown. Using primary human astrocytes derived from individuals spanning early to late adulthood (22–73 years) and fluorescent imaging, we observed increased G4 accumulation and reduced nuclear expression of the G4-resolving helicase DDX5 in older cells. To investigate how these changes relate to genome architecture, we performed ATAC-seq and G4 CUT&Tag across all astrocyte cultures. Older cells exhibited global chromatin compaction and focal G4 enrichment, with gains occurring in both accessible and closed chromatin regions, indicating locus-specific and context-dependent regulation. To determine whether DDX5 modulates these features, we overexpressed DDX5 in young astrocytes and identified transcriptional targets involved in chromatin organization and genome maintenance. Acute DDX5 knockout caused focal G4 accumulation without widespread chromatin changes, indicating that DDX5 maintains and modulates G4 dynamics at defined genomic regions. Together, these findings reveal G4s as dynamic, age-sensitive features of the genome with potential roles in epigenetic regulation and establish DDX5 as a modulator of G4 dynamics and genome integrity during human brain aging.

overall_design: RNA-seq, ATAC-seq, G4 Quadruplex CUT&Tag in resection-derived human astrocytes across the human age span, and with DDX5 over-expression and knockout

first: Vijay

last: Kumar

first: Rocio

middle: D

last: Escarcega

first: Ellery

last: Wheeler

first: Nitin

last: Tandon

last: Monchaud

first: Andrey

last: Tvetkov


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [FOSL1 ChIP-Seq]

first: Yangzhenyu

last: Gao

overall_design: FOSL1 ChIP-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li


title: Effect of Recombinant ApoE on Gene Expression During Osteoblast Differentiation of Mouse Bone Marrow Stromal Cells (BMSCs)

city: Durham

first: Gurpreet

last: Baht

state: North Carolina

address: 300 North Duke Street

department: Orthopaedic

institute: Duke University

summary: Advanced age impairs bone fracture healing; however, the underlying mechanisms remain unclear. We found that circulating levels of apolipoprotein E (ApoE) increase with age and contribute to impaired fracture healing. In vitro, ApoE treatment of aged bone marrow stromal cells (BMSCs) inhibited osteoblast differentiation. To investigate the mechanism by which ApoE inhibits osteoblast differentiation, we treated primary BMSCs isolated from the femurs and tibiae of 24-month-old C57BL6/J mice with recombinant ApoE.  For osteoblast differentiation, BMSCs were cultured in osteogenic medium. Recombinant ApoE (rApoE) was added at a concentration of 100 ng/mL starting two days after induction of differentiation and continued throughout the 10-day differentiation period. BMSCs treated with vehicle or rApoE were harvested on day 10. Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol for downstream transcriptomic analysis.

overall_design: RNA-seq profiling of bone marrow stromal cells (BMSCs) derived from 24-month-old wild-type (C57BL/6) mice during osteoblast differentiation. After 2 days of differentiation, cells were treated with either vehicle (n = 3) or recombinant ApoE (n = 3) for 8 additional days (total 10 days of differentiation) before RNA extraction and sequencing.

first: Mingjian

last: Huang

first: Abhinav

middle: R

last: Balu

first: Kristin

middle: H

last: Molitoris

first: Akshay

last: Bareja


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [RNA-seq]

first: Christopher

last: Hartl

last: Kumar

first: David


title: Childhood brain tumours instruct cranial haematopoiesis and immunotolerance [scRNAseqTCR postTx]

city: Cambridge

first: Elizabeth

last: Cooper

address: Li Ka Shing Centre, Robinson Way

institute: CRUK Cambridge Institute

summary: Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma–a childhood brain tumour–we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPCs lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T-regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma–all aggressive childhood brain tumours–disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

overall_design: Tumour/brain samples from age-matched 6-8 week-old EPZFTA-RELA  (NestinCreERT2;Fus1;RFPTdT) mice were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumour dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Supernatant was removed and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (CD45-PE and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [ATAC-seq]

first: Vijay

first: Rocio

last: Escarcega

first: Ellery

last: Wheeler

last: Tandon


title: Tubacin alleviate the reproductive toxicity of deoxynivalenol in mouse oocytes and zygotes via strengthening microtubule stability

city: Nanjing

first: Jianhua

last: Chen

state: Jiangsu

address: 101 Longmian Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: Deoxynivalenol (DON) is one of the most common food contaminants, widely present in grain products. Studies using murine and porcine models show deoxynivalenol exposure impairs oocyte maturation and mitochondrial function; however, the exact mechanisms remain unclear. In the present study, we found DON exposure markedly altered the microtubule nucleation-associated proteins expression pattern of oocytes, while supplementation of Tubacin recovered the progress of oocyte maturation, as well as the expression of KIF11 and TPX2, which are key factors for microtubule nucleation and spindle stabilization. More importantly, with the in vivo TUBB8 oocyte-specific knock-in model which introduced the human β-tubulin isotype into the most widely used mouse model, we found inhibition of HDAC6 activity reconstructed morphologically normal spindles and drastically recovered polar-body extrusion rate by culturing with the specific HDAC6 inhibitor Tubacin in DON-exposed oocytes. Mechanistically, DON represses mRNA translation and disrupts ribosomal function. In our investigation, DON interfered with fertilized egg cleavage by disrupting microtubule and microfilament networks, and Tubacin enhanced microtubule acetylation, stabilizing the network and rescuing developmental arrest. Taken together, these findings elucidated the rescue effects of Tubacin on DON-induced reproductive toxicity in oocytes,  and validated our TUBB8 oocyte-specific knock-in mouse model as a rapid evaluation of exposure and potential treatment of environmental pollutants to female reproductive health.

overall_design: Five oocytes per sample were collected from the Control, DON-treated, and DON+Tubacin for RNA-sequencing. Each sample was lysed with 1 µL lysis buffer, and immediately used for cDNA synthesis via the SMART-seq2 method.

first: Ruizhi

last: Feng

first: Hui

last: Luo


title: Childhood brain tumors instruct cranial haematopoiesis and immunotolerance [endpoint Fus1 GEX]

summary: Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site1–3. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma4–a childhood brain tumour–we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPCs lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T-regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma–all aggressive childhood brain tumours–disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

overall_design: Tumour/brain samples from age-matched 6-8 week-old EPZFTA-RELA (NestinCreERT2;Fus1) (n=5) and NestinCreERT2 (n=4) mice were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumour dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Supernatant was removed and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA3 Bulk RNA-Seq]

first: Yangzhenyu

last: Gao

overall_design: Bulk RNA-Seq was performed in MSKPCA3 AR-low patient-derived organoids with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane


title: Metabolic Reprogramming during Human Neuron Differentiation Identifies Glutaminase as a Key Determinant in Fragile X Syndrome

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

summary: Metabolic homeostasis gone awry is a contributor to, if not an underlying cause of, several neurologic disorders. Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by a trinucleotide repeat expansion in FMR1 and consequent loss of the encoded protein FMRP, which results in downstream molecular, neurologic, and mitochondrial deficits that are linked to cognitive impairment. In human postmortem brain, many metabolites and solute carrier proteins are coordinately dysregulated, which also occurs during differentiation of human iPSCs into excitatory neurons. Metabolic tracing in FXS neurons demonstrates a dearth of glutamine deamidation to glutamate, which reduces anaplerosis into the TCA cycle, consequently hindering bioenergetic and biosynthetic functions of mitochondria. Mechanistically, aberrant expression of glutaminase isoforms in FXS is responsible for reduced glutaminolysis, thereby altering glutamate levels which may contribute to FXS.

overall_design: RNA-seq of age matched male post-mortem cortex tissues from 5 Typlically developing (TD) and FXS individuals.

first: Botao

last: Liu

first: Maurice

last: Swanson

first: Tenzin

last: Tseyang

first: Thang

last: Do

first: Jodi

last: Bubenik

first: Suna

last: Jung

first: Mina

middle: N

last: Anadolu

first: Verónica

last: Martínez-Cerdeño

last: Berry-Kravis

first: Jessica

middle: B

last: Spinelli

first: Joel

last: Richter


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCaP Bulk RNA-Seq]

overall_design: Bulk RNA-Seq was performed in LNCAP AR-high prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Erik

last: Ladewig

first: Taibo

last: Li


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [PC3 Bulk ATAC-seq]

first: Yangzhenyu

last: Gao

overall_design: Bulk ATAC-Seq was performed in PC3 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

last: Toska


title: Unique sequence features define epigenetic longevity of inflammatory memory

city: New York

first: Luis

last: Soto-Ugaldi

institute: The Rockefeller University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [H3K4me2 ChIP-Seq]

overall_design: H3K4me2 ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

first: Wouter

last: Karthaus

last: Kittane


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [PC3 Bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed in PC3 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Srushti


title: TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism.

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA36 sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application.

overall_design: A C57Bl/6J based mouse model with mKate2 fluorescence reporter for the expression of TREM2 was created. The experimental mice expressed the reporter heterozygous while AppSAA and the hTfR knock in were homozygous. 8-month-old Trem2-mKate2KI/wt APPSAA/SAA.hTfRKI/KI mice were injected with 1 mg/kg Trem2 agonist (4D9) coupeled with an antibody transport vehicle (ATV:4D9), monthly until 11 months. At 12 months, mice were injected with 30 mg/kg FDG, 641 perfused 1 hour later and the extracted microglia were then sorted into low, mid and high mKate2 expressing populations with FACS. The cells were stored in Trizol until RNA-Seq. The samples include longtime treated ATV:4D9 microglia and control treated miicroglia sorted into mKate2(Trem2) low, mid and high expressing cells.

first: Astrid

last: Feiten

first: Kilian

last: Dahm

first: Thomas

last: Ulas

first: Pia

last: Grundschoettel

first: Kathryn

last: Monroe

first: Christian

last: Haass


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [KMT2D ChIP-seq]

overall_design: KMT2D ChIP-Seq was performed in LNCaP AR-high cells treated with 1μM PI3K inhibitor.


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [FOXA1 ChIP-seq]

overall_design: FOXA1 ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [AR ChIP-Seq]

overall_design: AR ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D


title: Somatic deficiency of human CBL in leukocytes impairs B cell but not T cell development and function

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

summary: The casitas B lineage lymphoma (CBL) proto-oncogene promotes positive selection and antigen responses in murine T lymphocytes by ubiquitinating ZAP70. However, CBL and CBL-B are redundant for ubiquitination of SYK and regulation of B cell receptor (BCR) signaling in murine B cells. We studied lymphocyte development, maturation and function in patients with somatic homozygosity for CBL loss-of-function variants in leukocytes. Surprisingly, human CBL is largely redundant for the development and function of human T cells. Conversely, CBL is critical for B cell development and function. Patients with somatic, hematopoietic CBL deficiency have a 10-fold increase in transitional B cells during childhood and are susceptible to bacterial infections. CBL deficiency impairs B cell maturation in a cell-intrinsic manner through reduced apoptosis and dysregulated BCR signaling, thereby reducing the proportions and numbers of memory B cells. Overall, our findings demonstrate that CBL deficiency has two major effects on human B cells. First, B-cell development in the bone marrow is altered at the immature stage, resulting in enhanced survival and differentiation of autoreactive B cell clones and impaired B cell tolerance, manifested as the production of autoantibodies. Second, the generation of antigen-specific B cells is impaired, thereby disrupting the establishment of adaptive immune memory. Thus, our study reveals the critical role of human CBL in B cells and its redundancy in T cells.

overall_design: Bulk RNASeq on healthy donor and CBL LOH naïve B cells RNA was extracted with the RNeasy Plus Micro Kit (Qiagen) from sorted naïve B cells (2 × 104 cells) sorted from the PBMCs of CBL LOH patients, and age-matched healthy children. Full-length cDNA was generated from 1 ng total RNA with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888), and 1 ng cDNA was then used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024). Libraries with unique barcodes were pooled at equal molar ratios and sequenced on an Illumina NovaSeq 6000 sequencer with V1.5 reagents and NovaSeq Control Software V1.7.0 to generate 100 bp paired-end reads, according to the manufacturer’s protocol. The FASTQ files generated were first inspected by fastqc to check sequencing quality. Sequences were aligned with the GENCODE reference genome (GRCh37.p13 and GRCm38.p6 for human and mouse, respectively) with STAR aligner v2.6. Gene-level features were quantified with featureCounts v1.6.0. Geneset enrichment analysis (GSEA) was conducted with the fgsea package by projecting genes ranked by their fold-changes in expression with effect-size shrinkage onto the Hallmark genesets retrieved from the MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/). Several of the healthy pediatric donor datasets are already published (68) and accessible on the NCBI Sequence Read Archive (accession no. PRJNA1141130).

first: Jonathan

last: Bohlen

first: Taja

last: Vatovec

first: Masato

last: Ogishi

first: Anna-Lena

last: Neehus


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer

first: Yangzhenyu

last: Gao


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA3 Bulk ATAC-seq]

overall_design: Bulk ATAC-Seq was performed in MSKPCA3 AR-low patient-derived organoids with doxycycline-inducible knockdown of KMT2D

last: Toska

first: Erik

last: Ladewig

first: Taibo

last: Li


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [DU145 Bulk ATAC-seq]

overall_design: Bulk ATAC-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

first: Wouter

last: Karthaus

last: Kittane


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [DU145 Bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Srushti


title: Single cell RNA sequencing of the steroidogenic lineage in the male adrenal cortex

first: Antonio

middle: Marcondes

last: Lerario

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary: To achieve single-cell characterization of the adrenal cortex transcriptome, we selectively labeled the steroidogenic adrenocortical cells using a transgenic Cre-LoxP approach. We combined Sf1-Crehigh mice with Rosa26mTmG animals to obtain mice expressing fluorescent reporter proteins at the cell membrane (mTmG) of cells that express or have expressed the transcription factor SF-1 (Steroidogenic Factor 1, also AdBP4, encoded by NR5A1). We prepared a single-cell suspension by combining mechanic and enzymatic dissociation at low temperatures to preserve the viability of steroid cells and their transcriptional states. Fluorescence-activated cell sorting (FACS) was then used to isolate GFP-positive cells representing the steroidogenic lineage. GFP-positive cells include the progenitor populations as well as differentiated cells (zona glomerulosa and zona fasciculata cells).

overall_design: A total of 26 male mouse adrenals (15 week-old) was harvested and dissociated into single cell suspension. Steroidogenic cells were isolated by FACS and analyzed by single cell RNAsequencing.

first: Typhanie

last: Dumontet


address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

overall_design: Single nuclei were harvested from MSKPCA3 patient-derived organoids upon KMT2D knockdown at 7 days post-doxycycline administration, with controls at day 0 and day 7 without KMT2D knockdown. Joint single-nucleus RNA and ATAC libraries were prepared using the 10x platform.


title: Transcription factor NKX2-1 cooperates with RUNX1 and protects T-cell acute lymphoblastic leukemia cells from DNA damage [RNA-seq]

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

institute: KULeuven / VIB

summary: T-cell acute lymphoblastic leukemia (T-ALL) is characterized by ectopic expression of transcription factors such as TAL1, TLX1/3 and NKX2-1. NKX2-1 is overexpressed in 5% of T-ALL patients, driving transcriptional induction and metabolic addiction to the serine/glycine synthesis pathway in cancer cells. However, a more complete picture of the transcriptional targets of NKX2-1 and its role in T-ALL pathogenesis is missing. We generated a CRISPR-Cas9 NKX2-1 knockout (KO) model in the NKX2-1 expressing RPMI-8402 (RPMI) T-ALL cell line. KO of NKX2-1 in RPMI cells induced apoptosis while not affecting cell cycle progression. RNA-seq on RPMI WT versus NKX2-1 KO cells showed significant downregulation of gene sets related to T-cell differentiation upon NKX2-1 KO. Additionally, we observed that NKX2-1 promoted a more mature phenotype in RPMI cells, by mildly decreasing CD34 and increasing CD2 expression. Furthermore, gene sets related to epigenetics and DNA damage were enriched in the RNA-seq data. Interestingly, DNA damage machinery related proteins, such as RPA1, appeared among the binding partners of NKX2-1 in IP-MS, and this interaction was confirmed in PDX cells. In agreement with this, we found significantly lower levels of DNA damage marks gH2AX and H3K27me3 in the presence of NKX2-1. NKX2-1 expression was associated with decreased sensitivity to topoisomerase inhibitor etoposide, and to HDAC inhibitors vorinostat and romidepsin. Furthermore, these agents resulted in lower induction of gH2AX and H3K27me3 in NKX2-1 expressing cells. Finally, NKX2-1 positive T-ALL patients showed overexpression of DNA repair genes in public RNA-seq data compared to NXK2-1 negative T-ALL, further supporting a critical role of NKX2-1 in protecting cells against DNA damage. Mechanistically,  we identified RUNX1 as NKX2-1 binding co-factor through motif analysis of NKX2-1 ChIP-seq peaks and in our NKX2-1 IP-MS experiment. NKX2-1/RUNX1 binding was confirmed in RPMI and in PDX cells. Interestingly, NKX2-1 and RUNX1 IP-MS experiments revealed that most NKX2-1 binding partners also bound to RUNX1, and that presence of NKX2-1 altered the co-factors of RUNX1. Moreover, iRegulon performed on T-ALL patients revealed that genes that are differentially expressed in NKX2-1+ T-ALL samples were regulated by RUNX1. Finally, we observed that RUNX1 inhibitor, Ro5-3335, provoked a significantly higher cell death in the presence of NKX2-1. Summing up, in addition to induction of metabolic serine/glycine synthesis addiction, our data indicate that NKX2-1 is essential to protect T-ALL cells against DNA damage. Furthermore, we observed that NKX2-1 is a co-factor of RUNX1, regulating its binding partners and activity.

overall_design: NKX2-1 was knocked out in RPMI-8402 cells resulting in 4 WT clones (WT10, WT13, WT28 and WT30) and 4 KO clones (C12, C15, S04, S36). RNA-sequencing was performed to assess the transcriptional changes upon NKX2-1 KO comparing WT to KO clones.

first: Linde

last: van Aerschot

first: Kalina

last: Timcheva

first: Kim

last: De Keersmaecker

first: Cabrerizo Granados

last: David


title: Transcription factor NKX2-1 cooperates with RUNX1 and protects T-cell acute lymphoblastic leukemia cells from DNA damage [ChIP-seq]

overall_design: NKX2-1 was knocked out in RPMI-8402 cells resulting in 4 WT clones (WT10, WT13, WT28 and WT30) and 4 KO clones (C12, C15, S04, S36). ChIP-seq was performed with a NKX2-1/TTF1 antibody (ab76013) to find out where this transcription factor binds.


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA2 Bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed in MSKPCA2 AR-high patient-derived organoids with doxycycline-inducible knockdown of KMT2D

first: Wanlu

last: Chen


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BCAP_KO_BMDM_Ribo-seq]

first: Xingxian

last: Liu

address: 30 Shuangqing Rd, Haidian District

institute: Tsinghua University

summary: Cytokine release syndrome (CRS) is a potentially life-threatening inflammatory condition. However, the defining features that distinguish it from self-resolving inflammation remain poorly understood. In this study, we identified monocyte/macrophage hyper-translation as a hallmark of CRS pathogenesis in patient samples. To uncover the molecular drivers of this phenomenon, a CRISPR screen followed by genetic validation pinpointed BCAP as a critical regulator of hyper-translation. Mechanistically, BCAP activated the RSK-EIF4B axis, fueling hyperactive translation in macrophages. Genetic ablation of RSK attenuated CRS-associated inflammation, and pharmacological inhibition of RSK alleviated CRS symptoms in a humanized mouse model. These findings establish hyper-translation as a key pathogenic feature of CRS and highlight protein translation as a druggable pathway, opening venues for therapeutic interventions of CRS and other inflammatory diseases.

overall_design: Ribo-seq and corresponding RNA-seq of KS (CRS model) stimulated WT and BCAP-deficient bone marrow derived macrophages (BMDM) at 0h and 24h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [CRISPR_screen]

overall_design: CRISPR screen of KS (CRS model) stimulated Cas9 transgenic marrow derived macrophages (BMDM) at 72h and isolation of IL-6 low population (top 5%) for sgRNA library construction and sequencing.


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [RSK1_KO_RNA-seq]

overall_design: RNA-seq of KS (CRS model) stimulated WT and RSK1 KO bone marrow derived macrophages (BMDM) at 0h and 24h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BMDM_RiboTag-seq]

overall_design: RiboTag-seq and corresponding RNA-seq of KS (CRS model) stimulated WT bone marrow derived macrophages (BMDM) at 0h , 24h and 72h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BMDM_Ribo-seq]

overall_design: Ribo-seq and corresponding RNA-seq of LPS stimulated WT bone marrow derived macrophages (BMDM) at 0h, 6h and 24h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [Monocytes_Ribo-seq]

overall_design: Ribo-seq and corresponding RNA-seq of KS (CRS model) stimulated human CD14-positive monocytes at 0h and 120h


title: Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy.

overall_design: Refer to individual Series


title: Transcriptomic analysis of spinal cord in day 35 experimental autoimmune encephalomyelitis (EAE) model

city: Sacramento

first: Hyun Kyu

last: Kim

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

summary: Experimental autoimmune encephalomyelitis (EAE) is a widely used model for studying multiple sclerosis (MS), characterized by inflammation and demyelination in the central nervous system. This study investigates the transcriptional changes in the spinal cord of mice at day 35 post-induction of EAE. Bulk RNA sequencing was performed on spinal cord samples from three groups: (1) naïve mice, (2) mice treated with complete Freund’s adjuvant (CFA) and pertussis toxin (CFA control group), and (3) EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin (MOG group). These findings provide insights into the spinal cord’s transcriptional response during EAE and advance our understanding of MS pathogenesis.

overall_design: Three-month-old C57BL/6 mice were received CFA and pertussis toxin (CFA control mice), or MOG peptide (35–55) emulsified in CFA and pertussis toxin to induce EAE. At day 35 post-induction, bulk RNA sequencing was performed from spinal cord of naïve mice, CFA control group and MOG group. Each group has 3 or 4 repeats.

first: Meina

last: Zhu

first: Yan

last: Wang

first: Fuzheng

last: Guo


title: Regulation of heterochromatin formation and tumor suppression in leukemia by IKAROS, HDAC1 and EZH2 [Molt4_RNA]

city: Hershey

first: Bing

last: He

state: PA

address: 500 University Dr

institute: Penn State University

summary: The IKZF1 gene encodes IKAROS – a DNA binding protein that acts as a tumor suppressor in  T-cell acute lymphoblastic leukemia (T-ALL). IKAROS can act as a transcriptional repressor via chromatin remodeling, however the mechanisms through which Ikaros exerts its tumor suppressor function via heterochromatin in T-ALL are largely unknown. We studied human and mouse T-ALL using loss-of-function and Ikzf1 re-expression approach, along with Ikzf1-wildtype primary human and mouse T-ALL and thymocytes to establish the role of  Ikaros and Ikaros-associated protein histone deacetylase 1 (HDAC1)  in global regulation of facultative heterochromatin and transcriptional repression in T-ALL.   Results identified novel Ikaros and HDAC1 functions in T-ALL: Ikaros and HDAC1 are essential for EZH2 histone methyltransferase activity, and formation of facultative heterochromatin; Recruitment of HDAC1 by Ikaros is critical for establishment of H3K27me3 and repression of active enhancers; and Ikaros-HDAC1 complexes promote formation and expansion of H3K27me3 large organized chromatin lysine domains (LOCKs) and broad genic repression domains (BGRDs) in T-ALL.  Our results establish that Ikaros’ tumor suppressor function in T-ALL occurs via activation of EZH2 and HDAC1 function, global regulation of the facultative heterochromatin landscape and silencing of active enhancers that regulate oncogene expression.

overall_design: The IKZF1 gene was deleted in human T-ALL cells MOLT4 using the CRISPR-Cas system to create MOLT-4 IKZF1-null cells

first: Sinisa

last: Dovat

first: Yali

last: Ding


title: In vivo Spatial Perturb-Seq in the mouse brain

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary: Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture and with spatial context, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment.

overall_design: We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed Stereo-seq. The 18 loci that are targeted are: mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3. The dataset here consists of 2 coronal hemisphere sections from 1 mouse.


title: The inflamed cauda epididymidis: a hub for ectopic lymphoid organ genesis

city: GLEN IRIS

first: Claire

last: Sun

state: VIC

address: 27-31 wright street

institute: hudson institute of medical research

summary: Infection and inflammation of the male reproductive tract are major factors leading to infertility. Insults targeting the epididymis are of concern as they can impair fertility. A considerable number of patients with epididymitis, even after antibiotic treatment, exhibit the presence of an epididymal infiltrate specifically in the cauda epididymidis and even suffer from infertility. For this reason, this study focused on investigating the cauda epididymidis at later time points from the infection in a well-established model of acute bacterial epididymitis as well as in an autoimmune model – experimental autoimmune epididymo-orchitis. We show that multiple elements associated with tertiary lymphoid organs formation, organization and maintenance are present in UPEC-infected as well as EAEO epididymidis compared to control cauda epididymidis.

overall_design: Induction of experimental autoimmune epididymo-orchitis (EAEO) was performed as previously described (Nicolas et al., 2017). In brief, the mice were actively immunised with testicular homogenate prepared from decapsulated testes obtained from adult syngeneic mice, combined with adjuvant. The testicular homogenate was administered subcutaneously, 3 times, two weeks apart, together with an intraperitoneal injection of 100 ng Bordetella pertussis toxin (Calbiochem, Darmstadt, Germany). Complete Freund’s adjuvant (Sigma-Aldrich, Saint Louis, USA) was used for the first immunisation, while incomplete Freund’s adjuvant (Sigma-Aldrich) was used for subsequent immunisations. Control animals received either the respective adjuvant injections instead of testicular homogenate, or were left untreated. Animals were euthanized using carbon dioxide overdose, and tissues were collected at 30 and 50 days after the first immunisation. For RNA sequencing, the cauda epididymis from 4 mice from the experimental autoimmune orchitis group (E), and 4 mice from the Adjuvant treated group (A), and 3 mice from the control group (C) were selected.

first: Hiba

last: Hasan

first: Rukmali

last: Wijayarathna

first: Monika

last: Fijak


title: The impact of oligodendroglial Serpina3n depeletion on brain aging in mice

summary: This study investigates the role of oligodendroglial Serpina3n in brain aging by examining its depletion using Olig2-Cre Serpina3n flox/flox mice model. To assess the molecular impact of oligodendroglial Serpina3n depletion on brain aging, RNA-seq was performed on forebrain samples from three experimental groups: 1) Young Wild-Type Mice (2-month-old): Representing baseline gene expression in a young, healthy brain; 2) Aged Wild-Type Mice (22-month-old): Serving as a control group to analyze age-related changes in gene expression without genetic modifications. 3) Aged Olig2-Cre Serpina3n flox/flox mice (22-month-old): Assessing the effects of oligodendroglial Serpina3n depletion on the transcriptomic profile of aged brains. The experiment aims to identify gene expression changes associated with normal brain aging by comparing young and aged wild-type mice, determine the specific impact of oligodendroglial Serpina3n depletion on the aged brain by comparing aged wild-type mice to aged knockout mice, and highlight molecular mechanisms influenced by Serpina3n in the context of brain aging. This design allows for a comparative analysis of aging-related transcriptional changes and the specific contribution of Serpina3n depletion in this process.

overall_design: RNA-seq profiling of forebrains from 2-month-old young wild-type mice, 22-month-old aged wild-type mice, and 22-month-old aged oligodendroglial Serpina3n knockout mice.


title: PDX1 Phosphorylation Mediates Amino Acid-mTORC1 Signaling in Pancreatic β-Cells [RNA-seq]

city: New Brunswick

first: Jialin

last: Fan

state: NJ

address: 195 Little Albany St, Room 3527

institute: The Cancer Institute of New Jersey (CINJ)

summary: PDX1 is known as the insulin transcription factor that regulates insulin expression in pancreatic β-cells in response to circulating glucose levels. Our previous study showed PDX1 also acts as a downstream effector that mediates β-cell mTORC1 signaling in the control of whole-body glucose homeostasis in response to stimulation by amino acids (AAs). Here we report that PDX1 has a broad role in AA-mTORC1-regulated transcriptome in β-cells, especially in processes related to β-cell proliferation and function. Mechanistically, mTORC1 phosphorylates PDX1 at S61 in an AA-dependent and rapamycin-sensitive manner. S61 phosphorylation promotes PDX1 protein levels and transcriptional activity. Interestingly, S61 is located within the transactivation domain targeted by monogenic diabetes mutations, which interfere with S61 phosphorylation and PDX1's transcriptional activity. To help understand the role of S61 phosphorylation in vivo, we generated S61A and S61E genomic mutations in mice, mimicking the unphosphorylated and phosphorylated states, respectively. Our results indicate that S61 phosphorylation positively regulates insulin expression and β-cell proliferation, promoting Western diet-induced hyperinsulinemia, obesity, and liver steatosis. These findings reveal the mechanism and roles of AA-mTORC1-PDX1 signaling in the control of pancreatic β-cell proliferation and function under physiological and pathological conditions.

overall_design: RNA-seq for Pdx1 in MIN6 cells under different amino acid treatment.

first: Steven

last: Zheng


title: Sirt5 regulates chondrocyte metabolism and osteoarthritis development through protein lysine malonylation

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

summary: Chondrocyte metabolic dysfunction plays an important role in osteoarthritis (OA) development during aging and obesity. However, it is unknown how metabolic dysfunction occurs during these two conditions. Proteins post-translational modifications (PTMs) have recently emerged as an important regulator of cellular metabolism. We previously reported that one type of PTM, lysine malonylation (MaK) was increased in cartilage during obesity. Sirt5, the only known mammalian demalonylase, declines in cartilage during aging. To elucidate the interplay between Sirt5 deficiency and obesity in joint degeneration, we deploy systemic and cartilage-specific conditional knockout mouse models. Our findings reveal that the combination of Sirt5 deficiency and obesity exacerbates joint degeneration in mice. Through comprehensive proteomics analysis, we delineate the malonylome in chondrocytes, pinpointing MaK's predominant impact on various metabolic pathways such as carbon metabolism and glycolysis. Further biochemical investigation focuses on glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a target of MaK, confirming a reduction in its enzymatic activity and functionality by MaK. Lastly, we identified a rare coding mutation in SIRT5 that dominantly segregates in a family with hand OA. The mutation results in substitution of an evolutionally invariant phenylalanine (Phe–F) to leucine (Leu–L) (F101L), which is located in the catalytic domain. F101L mutant results in higher MaK level and decreased expression of cartilage ECM genes (e.g., Acan and Col2a1) and upregulation of inflammation associated genes (e.g., Il6 and Nos2). In conclusion, we found that Sirt5 mediated MaK is an important regulator of chondrocyte cellular metabolism and dysregulation of Sirt5-MaK could be an important mechanism underlying aging and obesity associated OA development.

overall_design: Primary mouse chondrocytes were transfected with either  Wildtype or SIRT5F101L mutant plasmids.

first: Huanhuan

first: Anupama

last: Binoy

first: Siqi

last: Ren

first: Thomas

middle: C

last: Martino

first: Anna

last: Miller

first: Craig

last: Willis

first: Shivakumar

last: Veerabhadraiah

first: Abhijit

last: Sukul

first: Martin

last: Lotz

first: Rachel

first: Anne-Marie

last: Malfait

first: Shouan


title: In vivo Perturb-Seq in the mouse brain

first: Kimberle

last: Shen

state: CA

summary: Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment.

overall_design:
We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed 10X 3' scRNA-seq. All 5 mice listed here are biological replicates, done across 3 batches (B1_1, B1_2, B2_1, B2_2, B3_1).
The 18 genes are:  mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3.


title: PDX1 Phosphorylation Mediates Amino Acid-mTORC1 Signaling in Pancreatic β-Cells [ChIP-seq]

overall_design: ChIP-seq for Pdx1 in MIN6 cells under different amino acid treatment.


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCAP Bulk ATAC-seq]

city: Baltimore

first: Yangzhenyu

last: Gao

address: 2917 Saint Paul

institute: johns hopkins university

summary: Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response.

overall_design: Bulk ATAC-Seq was performed in LNCAP AR-high prostate cancer cells treated with PI3K inhibitor, GDC0941

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li

first: Xinyu

last: Guo


title: Regulation of heterochromatin formation and tumor suppression in leukemia by IKAROS, HDAC1 and EZH2 [Molt4_CT]

first: Bing

last: He

first: Sinisa

last: Dovat

first: Yali

last: Ding


title: Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [EUseq]

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: DNA replication initiates at specific genomic regions known as initiation zones (IZs), which follow a defined spatiotemporal program partially dependent on cell type. Here, we examined the replication initiation patterns of pluripotent mouse embryonic stem cells (mESCs), which are characterized by a very short G1 phase and rapid entry into S phase. Using EdU-seq combined with cell cycle synchroni-zation and Repli-seq, we identified IZs, that are activated during S phase in mESCs and classified them as early, mid, or late, according to the replication timing (RT) domain to which they mapped. Remarka-bly, we found that some IZs mapping to mid or late RT domains were activated within 1–2 hours of entry into S phase. Chromatin and nascent transcriptome profiling revealed that these IZs were associated with regions of open chromatin structure that were bound by the pluripotency factor OCT4. Transient OCT4 depletion was associated with reduced chromatin accessibility and replication initiation efficiency at these sites. These results provide an example of a pioneer factor, OCT4, facilitating DNA replication initiation by promoting local chromatin accessibility.

overall_design: Monitor nascent transcription by EUseq

first: Eddie

last: Rodriguez-Carballo

first: Sotirios

middle: G

last: Ntallis

first: Lilia

last: Bernasconi

first: Ezgi

last: Keskin

first: Thanos

last: Halazonetis


title: CUT&RUN sequencing on wildtype HSCs, MPP3s, GMPs, and macrophages with four weeks M. avium infection

city: Houston

first: Brandon

middle: T

last: Tran

email: Brandon.Tran@bcm.edu, brttran@gmail.com

state: Texas

address: 1 Moursund St

institute: Baylor College of Medicine

summary: Purpose: Central trained immunity is a phenomenom in which reprogrammed HSPCs differentiate into innate immune cells with heightened immune responses. To determine whether histone modifications are conserved and passed down to downstream lineage cells, we performed CUT&RUN sequencing on various HSPC subpopulations and macrophages in both M. avium infected and naive states. This was done to determine if there were conserved changes across all subpopulations, which would imply to us if specific gene signatures and genomic loci  could be conserved for eliciting central trained immunity.

overall_design: CUT&RUN-sequencing protocol was performed with slight modifications previously published work from the lab and others (Skene and Henikoff et al., Elife 2017 and Le et al., iScience 2023). Bone marrow from M. avium infected or sham-treated mice was isolated from tibias, femurs, and pelvic bones and pooled per group. After red blood cell lysis, cells were separated by cKit-enrichment and stained for specific cell surface markers. From cKit+ postivie fractions, 30,000 HSCs (Lin-,cKit-enriched, CD150+, CD48-), 200,000 MPP3s (Lin-, cKit-enriched, CD150-+, CD48+, Flk2-, CD34+), 200,000 GMPs (Lin-, cKit-enriched) were sorted per sample. 200,000 macrophages (CD3-, B220-, NK1.1-, CD11b+, Ly6g-, Ly6c+) were sorted per sample from the cKit- fractions. Samples were counted and washed with wash buffer (50 mL H2O with 20 mM HEPES (GIBCO 15630080)  three times. Cells were then incubated with activated concanavalin a beads (Bang Laboratories L2007231C) for fifteen minutes at room temperature. Sample slurries were then washed one more time and resuspended in wash buffer supplemented with 0.5% Digitonin (Dig-wash buffer). Dig-wash buffer was used for the remainder of the experimental method, with samples and buffers were kept on ice or at 4°C.  Samples were then incubated with histone modification antibodies overnight at 4°C on a rotator. Depending on the sample, the antibodies used were targeted for Rabbit anti-H3K27ac (Cell Signaling Technologies 8173, 1:50 concentration), Rabbit anti-H3K427me3 (Cell Signaling Technologies 9733, 1:50 concentration), and Rabbit-antimouse IgG (Jackson ImmunoResearch 315-005-003, 1:50 concentration) for negative controls. Samples were washed once again three times and incubated with pAG-MNase (Epicypher SKU:15-016 ) on a rotator for one hour in 4°C. After, samples were washed three times and then resuspended in 150uL Dig-wash buffer and 2uL of 100mM CaCl2 was added to catalyze MNase activity and cutting. Cell-bead homogenates were kept in 4°C for 40 minutes while the reaction occured. The reaction was quenched with 2X stopping buffer (5 mL total, H2O, NaCl 340mM, EDTA 20 mM, EGTA, 4 mM, Digitonin 0.05%, RNAse A 100ug/mL, Glycogen 50 ug/mL, and Spike-in DNA 1ng/mL), and samples were heated to 37 C for 20 minutes for MNase/Histone/DNA complex release from cells and out into the supernatant. Samples were placed on magnetic stands to separate the DNA supernatant from the bead slurry, and DNA purification was completed via phenol chloroform and ethanol precipitation extraction. Libraries were generated with the services of Admerahealth. Quantified DNA by Qubit 2.0 HS DNA (ThermoFisher, Massachusetts, USA) was assessed by Tapestation High on a D1000 High sensitivity DNA Assay (Agilent Technologies, California, USA). Library preparation was completed using the KAPA HyperPrep kit (Roche, Basel, Switzerland) per the manufacturer’s instructions. Library quality was assessed with Qubit 2.0 (ThermoFisher, Massachusetts, USA), Tapestation (Agilent Technologies, California, USA), and QuantStudio 5 System (Applied Biosystems, California, USA). Illumina 8-nt dual indices were used. Libraries were pooled equimolarly based on quality and sequenced on an Illumina NovaSeq (Illumina, California, USA) with a 150 paired-end (PE) read length.

first: Katherine

middle: Y

last: King


title: Temporal gene expression profiling analysis of Clostridium boutlinum strain ATCC 19397.

city: Helsinki

first: Miia

last: Lindström

address: Agnes Sjöbergin katu 2

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

summary: Clostridium botulinum is a Gram-positive bacterium that produces highly potent botulinum neurotoxins causing botulism. The study examines the temporal gene expression profile of C. botulinum ATCC 19397 over time. Using these data, we aimed developping new transcriptomic analytical tools as understanding the regulation of neurotoxin production. The research contributes to unraveling the complexities of controlling C. botulinum and its neurotoxin in the food industry.

overall_design: Temporal gene expression profiling analysis of RNA-seq from Clostridium boutlinum strain ATCC 19397 grown in laboratory conditions.

first: François

middle: P

last: Douillard

first: Katja

last: Selby

first: Elio

last: Nushi

first: Antti

last: Honkela


title: Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [Repli-seq]

overall_design: Monitor DNA replication by Repli-seq


title: Heterobifunctional proteomimetic polymers for targeted degradation of MYC and KRAS

city: Chicago

first: Mihai

middle: Ioan

last: Truica

state: Illinois

address: 303 E Superior

department: Urology

institute: Northwestern University

summary: Targeted protein degradation has unlocked new strategies for modulating previously undruggable proteins; however, existing small molecule approaches are challenging to optimize and largely limited to targets with ligandable pockets. To overcome these challenges, we introduce the HYbrid DegRAding Copolymer (HYDRAC), a polymer-based platform that integrates target-binding peptides with peptide or small-molecule degrons for the selective degradation of disease-relevant proteins. HYDRACs are synthesized easily, exhibit structural tunability, and facilitate the attachment of multivalent payloads. The modular payload capability accommodates diverse target-binding motifs and E3 ligase recruiters—such as VHL, KEAP1, and CRBN—broadening the design space. We apply HYDRACs against two historically intractable targets, MYC and KRAS, achieving robust degradation in vitro and sustained tumor inhibition in murine models. Notably, HYDRACs containing consensus RAS-binding motifs effectively degrade KRAS in cells harboring different alleles, suggesting pan-KRAS potential. We envision the HYDRAC platform as a generalizable approach, greatly expanding the armamentarium for TPD.

overall_design:
To investigate effects of MYC-degrading HYDRACs, as well as scrambled sequence (non-targeting) controls, on cellular transcriptional programs in order to ascertain target-engagement and selectivity, we performed gene expression profilling analysis using data obtained from RNA sequencing of PC3 cell line treated for 24 hours with Vehicle (DMSO) or 5 uM of HYDRAC or scrambled negative control.
RNAseq profiling of wild-type PC3, A549 and MycCaP cells treated with HYDRAC and negative control (nontargeting polymer, denoted as sHR) for 24 hours treatment. As well as PC3 cells treated with genetic knockdown of MYC (siMYC and siCNT).

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