title: Targeting Polycomb for treatment of KMT2A-rearranged AML using AML-iPSCs as a model system [RNAseq]

first: Anna

last: Palau

summary: Pediatric and infant Acute myeloid leukemia (AML) often harbor chromosomal translocations involving the KMT2A gene, encoding theKMT2A lysine methyltransferase, and produce in-frame fusions of KMT2A to other chromatin-regulatory proteins. The KMT2A chromosomal rearrangements (KMT2A-r) are associated with bad prognosis, resistance to chemotherapy and high rates of relapse. Therefore, new therapeutic options are needed for this AML subtype. Here, we aim to identify epigenetic regulators involved in the development of KMT2A-r AML that can be exploited towards new treatments. Mutant and isogenic wild type iPSC lines generated from a KMT2A-r patient were differentiated into hematopoietic progenitor cells to investigate differences in gene expression and transcriptional regulation. KMT2A-r cells exhibited an aberrant gene expression signature with delayed or continuously repressed gene expression. The repressed genes display bivalent histone marks and become repressed by the Polycomb repressive complex (PRC). Targeted inhibition of the PRC2 member EZH2 restores the repressed signature to normal expression levels. Our results suggest that inhibition of PRC2 could be complement to treatment of KMT2A-r AML.

overall_design: control- and AML-iPSCs were differentiated into hematopoietic stem progenitor cells (HSPC) and treated with DMSO as vehicle (1:2000), UNC1999 (2 uM), or UNC1999 (2 uM) + 5-Azacytidine (1 uM).

first: Jonas

last: Thier

first: Andrew

last: Tae-Jun Kwon

first: David

last: Cabrerizo Granados

first: Bogumił

last: Kaczkowski

first: Erik

last: Arner

first: Vanessa

last: Lundin

first: Andreas

last: Lennartsson


title: Ralstonia pseudosolanacearum LOV domain protein regulates environmental stress tolerance, iron homeostasis and bacterial wilt virulence

status: Public on Dec 05 2025

city: Madison

first: Jose

middle: Alberto

last: Sanchez

state: WI

address: 1630 Linden Drive

country: USA

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

summary: Bacteria use diverse sensors to integrate environmental stimuli into physiological responses that ensure fitness and survival. Ralstonia pseudosolanacearum (Rps), a soil-borne plant pathogen that causes bacterial wilt disease, encodes a conserved LOV (light-oxygen-voltage) protein known to mediate photoreception across the tree of life. However, Rps had a minimal LOV-dependent transcriptional response to light. Using clues from functional domains, the lov genomic neighborhood, and in planta transcriptional analyses, we tested the hypothesis that LOV shapes Rps biology in response to stress. We discovered lov modulates Rps stress response and virulence independently of light cues, but in a plant-dependent fashion. A ∆lov mutant had reduced heat tolerance that required a conserved flavin mononucleotide-binding cysteine residue. Deleting lov caused broad metabolic dysregulation, leading to growth defects on several carbon sources. In contrast ∆lov grew better in ex vivo tomato xylem sap and in high-iron medium, a possible consequence of its increased siderophore production. However, LOV is essential for full virulence in the host, mediating attachment to the root surface, stem colonization, and overall symptom development. Together these findings reveal that LOV, which is highly conserved among plant pathogenic Ralstonia, regulates a myriad of functions required for plant fitness independently of light.

overall_design: RNAseq data of Ralstonia pseudosolanacearum strain GMI1000 wild-type compared to ∆lov both in vitro and in planta conditions. In vitro cells were subjected to blue light and dark conditions.

first: Bridget S.

last: O'Banion

first: Mariama D.

last: Carter

first: Jose A.

last: Sanchez-Gallego

first: Hanlei

last: Li

first: Stephanie

last: Hayes

first: Marlee

last: Strysick

first: Ja'Nyla

last: Holcomb

first: Caitilyn

last: Allen


title: Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation

status: Public on Dec 03 2025

city: Hamburg

first: Immo

last: Prinz

address: Martinistraße 52, Building N25

department: Institute of Systems Immunology

country: Germany

summary: Alloreactive T cells mediate graft-versus-leukemia (GvL) reactions and acute graft-versus-host disease (aGvHD) in AML patients following allogeneic hematopoietic stem cell transplantation. To investigate biomarkers that identify alloreactive T cells associated with either beneficial GvL or detrimental aGvHD, we collected graft samples and two post-transplant follow-up blood samples (day 30 and day 100) of ten AML patients undergoing hematopoietic stem cell transplantation and profiled over 777,000 CD45+ leukocytes in total by combinatorial barcoding-based mega-scale single-cell RNA sequencing. Using immune receptor sequences as intrinsic clonal barcodes, we observed that especially CD8+ graft-derived T cells persisted and displayed enhanced proliferation, clonal expansion, and likely alloreactivity. Notably, patient-derived peripheral leukocytes that survived the conditioning, as identified by sex-chromosome-related genes, were primarily CD4+ T helper cells. MDGA1 expression on T cells and NK cells emerged as a novel biomarker potentially associated with aGvHD. Additionally, we observed a significant deficiency of ADGRG1 expression, a marker of alloreactive cytotoxic T cells, by αβ and γδ T cells from relapsed patients. In conclusion, mega-scale single-cell monitoring of graft and hematopoietic immune cell reconstitution allowed us to demonstrate that MDGA1 and ADGRG1 may function as complementary biomarkers expressed by distinct circulating T cells that are associated with divergent outcomes in AML patients, enabling precise risk stratification of alloHSCT outcomes and presenting potential therapeutic targets.

overall_design: Ten adult ( > 18y) patients with AML in complete remission who underwent alloHSCT with peripheral blood stem cell grafts (matched unrelated, n = 8; matched related, n = 2) in the Department for Stem Cell Transplantation of University Cancer Center Hamburg-Eppendorf from December 2021 to May 2022 were included in this study (Table 1). The study was approved by ethics commission of the Medical Chamber of Hamburg and was performed according to the approved study protocol (version 1.1 from 01.11.2021). Written informed consent was obtained from all participants. The majority of patients received myeloablative conditioning (n = 7) with ATG-based immunoablation (n = 9). After a median follow-up of 20 months (18–22), three patients died (relapse, n = 2; NRM, n = 1). The relapses occurred on days +149 and +622. Five patients developed acute GvHD (II-IV) at a median of 57 days (19–136). The eight patients remained alive in complete remission at the last follow-up. Peripheral blood stem cell graft samples were collected at the time of transplantation and were cryopreserved on the next day. The PBMC samples of recipients were collected at day +30 (D30) and day +100 (D100) and were cryopreserved on the same or the following day. Mononuclear cells were isolated using a Ficoll gradient and cryopreserved in DMSO until they were used for single cell analysis. All DAPI− (Thermo Fisher Scientific Cat# D1306) (RRID:AB_2629482) live cells were sorted from frozen PBMC samples at the flow cytometry core facility of University Medical Center Hamburg-Eppendorf (RRID:SCR_017156). The sorted cells were fixed and permeabilized using Evercode™ Cell Fixation v2 (Parse Biosciences, Cat. ECF2001) following the manufacturer’s protocol. Fixed cells were stored at −80 °C. All samples were then processed together to prepare single-cell libraries using one Evercode™ WT Mega v2 Kit (Parse Biosciences, Cat. ECW02050), according to the manufacturer’s instructions. Fifteen sub-libraries were sequenced on the Illumina NovaSeq 6000 S4 flow cell platform (RRID:SCR_016387) using PE150 chemistry with a sequencing depth of 25,000 reads per cell.

first: Zheng

last: Song

first: Evgeny

last: Klyuchnikov

first: Anita

last: Badbaran

first: Nicolaus

last: Kröger


title: Influence of epigenetic modifications on gene expression in Fusarium oxysporum

status: Public on Dec 04 2025

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The influence of the heterochromatic marks H3K36me3 and H3K27me3 was elucidated by deletion and (cross-)complementation experiments. Gene expression was analyzed under axenic conditions and in planta by RNA-seq, and epigenetic profiles were assessed by ChIP-seq.

sample_organism:
Fusarium graminearum
Fusarium oxysporum f. sp. lycopersici

overall_design: Axenic cultivation F. oxysporum: NO3 2 days; in planta: 6 DPI. Axenic cultivation F. graminearum: ICI+60 mM glutamine 3 days. Material was subjected to RNA extraction for RNA-seq, and was crosslinked with formaldehyde prior to ChIP-seq using indicated antibodies.

first: Slavica

last: Janevska

first: Umer

last: Farooq

first: Antonio

last: Di Pietro

first: Manuel

last: Sánchez López-Berges


title: Targeting Polycomb for treatment of KMT2A-rearranged AML using AML-iPSCs as a model system [CAGEseq]

city: Huddinge

first: Anna

last: Palau

address: Hälsovägen 9

country: Sweden

institute: Karolinska Institutet

overall_design: control- and AML-iPSCs were differentiated into hematopoietic stem progenitor cells (HSPC) and collected for CAGEseq at day 0 (iPSC), day 8, day 10 and day 12 of HSPC differentiation.

first: Jonas

last: Thier

first: Andrew

last: Tae-Jun Kwon

first: David

last: Cabrerizo Granados

first: Bogumił

last: Kaczkowski

first: Erik

last: Arner

first: Vanessa

last: Lundin

first: Andreas

last: Lennartsson


title: STING activation induces cytotoxic and immune responses in meningiomas via inflammatory cell death pathways [scMulti-omics]

status: Public on Dec 02 2025

city: Chicago

first: Mark

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

institute: Northwestern University

summary: Up to one-quarter of meningiomas recur within five years of resection; however, there are currently no established adjuvant therapies for tumors that are intractable to surgery and radiation. Using integrated epigenetic and transcriptional profiling, we identify widespread expression of STING across multiple cell populations within the meningioma microenvironment, associated with increased chromatin accessibility in neoplastic cells and promoter hypomethylation. Ex vivo single-cell suspensions of resected human meningiomas treated with the STING agonist 8803 induced direct cytotoxicity within 72 hours, including even in the absence of CD45+ immune cells. Pharmacologic inhibitors and RNA-sequencing revealed the association of programmed necrotic cell death pathways that require reactive oxygen species production with STING agonist8803 efficacy, which also required reactive oxygen species production. Proteolytic maturation of the pore-forming protein gasdermin D (GSDMD) on meningioma cancer cells contributeds to 8803-induced cytotoxicity, and  the suggested release of pro-inflammatory damage-associated molecular pattern molecules that further upon 8803-induced cytotoxicity, which further potentiatedpotentiates STING activation of innate immune cell activation and responses through toll-like receptors activation.  Across four different preclinical murine meningioma models, 8803 reduced tumormeningioma volume, and survival significantly increased survival was significantly improved after treatment of across three orthotopic tumorsmodels. These therapeutic effects arewere Treatment with 8803 across multiple pre-clinical orthotopic meningioma models exhibited improved survival associated with marked immunological tumor infiltration and cytotoxicity, tumor stromal remodeling through macrophage elaborated metalloproteinases, and downregulation of the TIM3 and LAIR1 widespread cytotoxicity and immunologic infiltration during the therapeutic window, including down-regulation of severalthe dominant mechanisms of meningioma-mediated immune suppression. , such as TIM3 and LAIR1, alongside the LAIR ligand collagen through macrophage elaborated MMP production. Our results reveal widespread synergistic expression of STING in neoplastic and myeloid populations of meningiomas, identify novel mechanisms of STING signalingcytotoxicity inthrough tumor cells, andsuggest a role for STING activation in degradation of collagen-rich tumor microenvironments the impact on the extracellular matrix,  and clarify a new treatment indication for the STING agonist 8803.

overall_design: Single nucleus multiome (RNA-seq + ATAC-seq) profiling of frozen meningioma specimens post resection.

middle: W

first: Shashwat

last: Tripathi

first: Hinda

last: Najem

first: Harrshavasan

last: Congivaram

first: Mateo

last: Gomez

first: Amy

middle: B

last: Heimberger


title: Hfq orchestrates a robust RNA-RNA interaction network in Acinetobacter baumannii. [RIL-Seq]

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

summary: A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. We subjected cells of A. baumannii  strain AB5075 and a derivative of AB5075 harboring a C-terminal VSV-G epitope on Hfq to UV-irradiation, immune-precipitated the Hfq-RNA complexes, ligated neighboring RNA molecules together with RNA Ligase, and then purififed the resulting RNAs. These RNAs were converted into cDNA libraries and sequenced using the Illumina NextSeq platform and then subjected to RIL-seq analysis pipeline (version 0.78) to identify chimeric RNA molecules.

overall_design: Applying RIL-seq to WT AB5075 and a derivative thereof that carrys a chromosomally-encoded Hfq-VSVG for two different growth conditions

first: Simon

last: Dove


title: Lamin A/C-EZH2 interaction in modulating Epithelial-to-mesenchymal Transistion in breast cancer cells

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biology

country: India

institute: Indian Institute of Science Education and Research PUNE

summary: Epithelial-to-mesenchymal transition (EMT) is a developmentally conserved cell biological program adopted by cancer cells to metastasize to different organs. In this process, compact, cobblestone-shaped epithelial cells transform into more slender-shaped mesenchymal cells. Throughout metastasis, cells reside at various stages along the E-M spectrum. Epithelial cells are not necessarily converted to mesenchymal cells, as cells in the E-M continuum exhibit greater survival advantages and better metastatic ability than complete mesenchymal forms. During metastasis, epithelial cells traverse through narrow capillaries, inducing nucleus rupture. The nucleus is protected by type V intermediate filament proteins, Lamins, in the inner nuclear membrane, providing structural integrity, facilitating genome organization, and acting as an impediment to cell migration. Therefore, Lamin expression is downregulated to facilitate nuclear compliance during EMT, serving as a precursor for metastasis. Here, we aim to address the mechanism of Lamin downmodulation and its role in genome organization during EMT. We have attempted to address these questions in three independent and well-established breast cancer cell lines representing cells at specific stages of the EM spectrum, providing a paradigm to elucidate the role of Lamins in genome organization and function during EMT.

overall_design: RNA-Seq profiling of MCF10A cells upon Lamin A/C knockdown. siRNA for Lamin A/C was used and control non-targeting LacZ was used.

first: Balaji

last: AK

first: Santam

last: Saha


title: VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: Long noncoding RNAs (lncRNAs) have been found to play significant regulatory roles within antiviral and immune responses. We previously identified the novel lncRNA virus-inducible lncRNA modulator of interferon response (VILMIR), that was found to broadly regulate the host transcriptional response to interferon-beta (IFN-β) treatment in A549 human lung epithelial cells. Here, we investigated the mechanism by which VILMIR regulates the host interferon response in trans by identifying interacting proteins and gene regulatory networks of VILMIR. Through an RNA pull-down assay, we found that VILMIR interacted with both nuclear and cytoplasmic proteins in vitro, including the transcriptional regulators FUBP1 and PUF60 in the nucleus, as well as the antiviral proteins IFIT1 and IFIT3 and the aminoacyl-tRNA synthetases QARS1 and KARS1 in the cytoplasm. In addition, we found that overexpression of VILMIR in A549 cells resulted in an overall enhancement of host interferon response genes and identified a core set of interferon-stimulated genes that were consistently regulated by VILMIR knockdown and overexpression. Finally, we proposed several possible mechanisms by which VILMIR may interact with the identified proteins to regulate the interferon response, such as by interacting with FUBP1 and PUF60 in the nucleus to regulate host transcription in trans or by interacting with the IFIT proteins and aminoacyl-tRNA synthetases in the cytoplasm to regulate translation.

overall_design: To investigate the functional role of VILMIR during the human interferon response, we generated an A549 cell line overexpressing ectopic VILMIR as well as an empty vector control line. The control cell line as well as the VILMIR-overexpressing cell line were treated with or without human IFN-β at 1 ng/mL or 10 ng/mL for 6 hours in triplicate. RNA-sequencing and differential expression analysis was then performed to identify the impact of VILMIR overexpression on host transcription before and after IFN-β treatment.

first: Kristen

last: John

first: Ethan

last: Smith

first: Alexandra

last: Istishin

first: Nasif

last: Mahmood

first: Kayleigh

last: Diveley

first: Tammy

middle: S

last: Tollison

first: Susan

last: Carpenter


title: Canine morbillivirus infection of primary alveolar macrophages provides insights into mechanisms of viral interference with innate immune defense responses

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Morbillivirus canis (formerly: canine distemper virus, CDV) is a highly contagious pathogen with a broad host range among carnivore species. During respiratory infection, alveolar macrophages (AMs) are among the first cell types facing the virus, which has previously been shown for measles virus infection. While AMs contribute to pulmonary homeostasis, they likewise bear great potential in establishing a pro-inflammatory environment once confronted with viruses. This study aimed to investigate cellular defense responses by AMs, allowing assumptions on early pathogenesis of CDV.

overall_design: Primary canine AMs were obtained by post mortem bronchoalveolar lavage. Cells were subsequently infected with CDV Onderstepoort (Ond), a broadly used vaccine strain, and the virulent strain CDV R252. Samples from 1 day post infection were used for bulk RNA sequencing.

first: Pauline

last: Poepperl

first: Andreas

last: Beineke


title: LSD1 Performs Demethylase-Independent and Context-Specific Roles in Ewing Sarcoma

city: Columbus

first: Rachel

middle: D

last: Dreher

state: OH

address: 575 Children's Crossroad

institute: Nationwide Children's Hospital

summary: Lysine specific demethylase 1 (LSD1), encoded by the gene KDM1A, is overexpressed and correlates with poor patient prognosis in Ewing sarcoma. LSD1 colocalizes with the FET-fusion (EWSR::FLI1, EWS::ERG, etc) throughout the genome and has therefore been considered a critical co-regulator driving the progression of Ewing sarcoma. However therapeutic targeting of LSD1 by irreversible and noncompetitive inhibitors has yielded mixed results. Irreversible, enzymatic inhibition seems ineffective, but reversible noncompetitive inhibition has predominant off target mechanisms, leaving open the question of LSD1 function in Ewing sarcoma. Here we take a robust approach through multiple methods of depletion in multiple cell lines to define LSD1 function, both enzymatic and nonenzymatic, in Ewing sarcoma cell lines. We define a core set of 22 genes that are commonly repressed by LSD1 in all cell lines and that repression of these genes downregulates synapse functioning and e-cadherin target genes. De-repression of these genes with LSD1 loss is an early and sustained genotype in all cell lines tested. Furthermore, we define distinct gene sets in each cell line that are regulated by the enzymatic and nonenzymatic functions of LSD1 and find repression of e-cadherin target genes to be nonenzymatically regulated. This finding supports the growing body of evidence that in addition to their canonical catalytic activity, enzymes serve essential noncanonical roles as well. Lastly, we uncovered evidence through use of the irreversible inhibitor OG-L002 that 2D cytotoxicity and proliferation assays may be insufficient to determine how Ewing sarcoma responds to LSD1 inhibition.

overall_design: To evaluate the transcriptomic changes resulting from loss of LSD1 by CRISPR KO, UM171 degredation at 6hrs, 24hrs, and 96hrs, and OG-L002 inhibition in 3 Ewing sarcoma cell lines. In addition, we rescued LSD1 KO cell lines in A673 with empty vector, HA and twinstrep tagged full wild type LSD1 and HA and twinstrep tagged K661Q/A539 enzymatically dead mutant LSD1.

first: Cenny

middle: C

last: Taslim

first: Ira

last: Miller

first: John

last: Sherman

first: Emily

middle: R

last: Theisen


title: RELB Reprograms Exhausted Tumor-Infiltrating Lymphocytes for Improved Adoptive Cell Therapy [proliferation]

city: Durham

first: Charles

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

institute: Duke University

summary: Tumor-infiltrating lymphocytes (TILs) are a promising autologous cell therapy to treat solid tumors. TILs are manufactured by expanding and reinfusing tumor-reactive T cells from tumor biopsies. Efficacy of TIL therapies has been limited by the heterogeneity of expanded TIL products and the high prevalence of dysfunctional exhausted CD8+ T cells (TEX). A subset of CD8+ TILs that are double-positive (DP) for CD103 and CD39 is enriched for tumor-reactive TILs across multiple cancer types, but also is susceptible to the TEX state.  We screened overexpression of all human transcription factors (TFs) to discover master regulators of expansion in DP TILs from non-small cell lung cancer patients.  RELB emerged as the dominant hit driving proliferation of DP TILs despite exhaustion induced by repeat stimulation, with a skew towards CD8+ cells. TCR-seq showed maintenance of TCR diversity from the initial TCR repertoire after multiple days of in vitro expansion driven by RELB. Transcriptome profiling of multiple RELB-expressing TIL subtypes revealed a shift towards a memory/costimulatory-like phenotype. Using a HER2-targeting CAR and tumor co-culture model, RELB conferred improved persistence after multiple tumor challenges in vitro and improved solid tumor control in mouse xenografts in vivo. Finally, co-culture of RELB-overexpressing TILs with patient-matched tumor organoids showed an increase in TIL product polyfunctionality, tumor reactivity, and tumor killing.

overall_design: CD8+ TILs were isolated using a TIL CD8+ magnetic isolation kit (REAlease® CD8 (TIL) MicroBead Kit, human, Miltenyi) and DP TILs were FACS sorted (n = 2 patient samples), activated with Transact (Miltenyi) according to manufacturer’s instructions, and transduced (n = 2 transduction replicates) with the MORF library at low MOI. Cells were expanded for 3 days, selected with puromycin at 1 µg/mL for 3 days, and then expanded for an additional 9 days. Cells were then re-activated at day 12 post-transduction with a 3:1 ratio of CD3/CD28 dynabeads (Invitrogen) to T cells, stained with CellTrace Violet (Invitrogen), and sorted for lower and upper 15% tails of CellTrace signal. All replicates were maintained and sorted at a minimum of 400x coverage. Cells were maintained at 1–2 × 106 cells ml−1 for all expansion steps unless otherwise indicated.

first: Christian

last: McRoberts Amador

middle: E

last: Conover

first: Pamela

middle: K

last: Noldner

first: Ying

last: Zhou


title: RELB Reprograms Exhausted Tumor-Infiltrating Lymphocytes for Improved Adoptive Cell Therapy [TCR-Seq]

overall_design: RNA was isolated from distinct TIL patient samples (n=4) that were transduced with either Thy1.1, RELB, or nothing using Norgen’s Total RNA Purification Plus Kit and Takara’s SMARTer Human TCR a/b Profiling Kit v1 was used to generate TCR-seq libraries. Library generation and purification methods were carried out according to manufacturer protocol. Initial data processing was performed using MiXCR using the present for the SMARTer Human TCR a/b kit. The R package immunarch  was used to analyze effective number of types for TCR diversity across samples to account for both number of clones and relative abundance.


title: Lamin A/C regulates lipid metabolism and inflammation: insights from models of familial partial lipodystrophy 2 sub 2

status: Public on Dec 01 2025

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

summary: Familial partial lipodystrophy 2 (FPLD2) is a rare disease characterized by adipose tissue loss and redistribution, and metabolic dysfunction. FPLD2 is caused by pathogenic variants in the LMNA gene, encoding nuclear lamins A/C, structural proteins that control nuclear function and gene expression. However, the mechanisms driving adipocyte loss in FPLD2 remain poorly defined. In this study, we recruited eight families with developing or established FPLD2 and performed clinical, histological, and transcriptomic analyses of subcutaneous adipose tissue biopsies. Bulk and single-nuclei RNA-sequencing revealed suppression of lipid metabolism and mitochondrial pathways, alongside increased inflammation. These signatures were mirrored in tamoxifen-inducible adipocyte-specific Lmna knockout mice, in which lamin A/C-deficient adipocytes shrank and disappeared. Lmna-deficient fibroblasts shared similar gene expression changes, linked to altered chromatin accessibility, underscoring lamin A/C’s potential regulatory role in lipid metabolism and inflammatory programs. By directly comparing atrophic and hypertrophic adipose depots in FPLD2, and integrating human, mouse, and in vitro models, this study provides new insights into disease progression and potential therapeutic targets.

overall_design: Bulk RNA-seq from mouse parametrial white adipose tissue, from control (Lmna fl/fl) or inducible Lmna adipocyte-specific KO (Lmna iADKO) mice. Mice were injected with tamoxifen at 12-14 weeks of age, and adipose tissue was analyzed two weeks post-tamoxifen administration.

first: Jessica

middle: N

last: Maung

first: Akira

last: Nishii


title: Basis for Lineage-Determining Pioneer Factors Targeting Distinct Repressed Chromatin States

city: Philadelphia

first: Kenneth

last: Zaret

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Pioneer transcription factors target compact, transcriptionally silent chromatin, thereby enabling gene activation in development, regeneration, and cell reprogramming.   However, silent chromatin is heterogenous, varying in nucleosome mobility, nucleosome compaction, and repressive histone modifications, and how pioneer factors may overcome these different chromatin barriers is unknown.  We systematically compared the chromatin targeting of 13 embryonic transcription factors and found that the DNA binding domain (DBD) type predicts whether a pioneer factor targets low-turnover nucleosomes in compact chromatin, dynamic nucleosomes in compact chromatin, or function as non-pioneer factors targeting accessible chromatin.  By contrast, non-DBD domains enable targeting of repressed chromatin marked by H3K9me3 or H3K27me3.  Fusions of different non-DBD segments of heterochromatin-targeting pioneer factors onto SOX2 can expand binding of Sox2 target motifs, including within heterochromatin, and improve cellular reprogramming.  Our study unveils how different forms of silent chromatin are coordinately targeted by lineage-specifying factors.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for V5-tagged transcription factors after 48 ectopic expression in hBJ fibroblasts

first: Andrew

last: Katznelson


title: Lamin A/C regulates lipid metabolism and inflammation: insights from models of familial partial lipodystrophy 2 sub1

overall_design: Bulk RNA-seq from human subcutaneous white adipose tissue, either from the upper neck or the abdominal depot. These samples are from control patients (Group C), patients with developing FPLD2 (Group A), or developed FPLD2 (Group B).


title: STING activation induces cytotoxic and immune responses in meningiomas via inflammatory cell death pathways

first: Mark

last: Youngblood

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

overall_design: Refer to individual Series


overall_design: Ex-vivo, patient derived meningiomas were processed as single cell suspensions post resection. RNA-seq profiling was applied to each patient sample with both a control treatment, and an 8803 STING-agoinst treatment

first: Shashwat

last: Tripathi

first: Hinda

last: Najem

first: Harrshavasan

last: Congivaram

first: Mateo

last: Gomez

first: Amy

last: Heimberger


title: Synthetic oleanane triterpenoids reduce tumor growth and promote an anti-tumor immune response independent of cancer KEAP1-mutational status

city: Indianapolis

first: Ana

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

institute: Indiana University

summary: KEAP1 negatively regulates the cytoprotective factor NRF2 and is commonly inactivated in lung cancer cells. Loss of function KEAP1 mutations in cancer cells contribute to NRF2 activation and tumor immune evasion through immunosuppression and drug resistance. Counterintuitively, treatment with synthetic oleanane triterpenoids, potent NRF2 activa-tors, reduces preclinical tumor burden. This suggests the functional target of these drugs in cancer models is not the cancer cells but another tumor immune microenvironment (TIME) cell population. The anti-tumor potential of cells within the TIME, particularly macrophages, is potentiated by triterpenoid treatment in cancers with wild-type KEAP1 status. As KEAP1-mutant cancers show reduced tumor immune responses, triterpenoid-mediated immune stimulation may particularly benefit these cases, but this has not been investigated. To characterize the immunomodulatory effects of triterpenoids in KEAP1-mutant lung cancer, we studied tumor-educated bone marrow-derived macrophages (TE-BMDMs) and lung cancer models treated with the triterpenoids CDDO-Me or omaveloxolone. RNA-sequencing of TE-BMDMs cultured in KEAP1 KO compared to WT cancer-conditioned media had enhanced tumor-promoting phenotypes which reversed with CDDO-Me treatment. Similarly, subcutaneous KEAP1 KO tumors were larger and more immune-suppressed compared to WT tumors. Both CDDO-Me and omaveloxolone reduced tumor burden and improved immune cell phenotypes within the TIME, independent of KEAP1 mutational status.

overall_design: RNA sequencing of bone marrow-derived macrophages treated for 24 hours with cancer conditioned media and 100nM CDDO-Me or vehicle control. Conditioned media was generated from LL2 cancer cells possessing different KEAP1 pathway mutations (WT, KEAP1 KO, and NRF2 KO).

first: Christopher

last: Occhiuto

last: Moerland

first: Karen

middle: T

last: Liby


title: Combining Spironolactone to Antiretroviral Therapy Accelerates HIV Decay in Humanized Mice

city: Jupiter

first: Susana

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Spironolactone (SP), a clinically used aldosterone antagonist, has been explored as an anti-HIV agent in models of HIV-1 latency for inducing transcriptional silencing of the viral reservoir. SP promotes the degradation of xeroderma pigmentosum group B (XPB) protein, a crucial component of transcription factor II H (TFIIH) required  for RNA polymerase II transcriptional initiation. This study evaluated the impact of a long-acting formulation of SP on HIV replication within the context of antiretroviral therapy (ART) in the humanized mice model of HIV infection. The findings demonstrate that adding SP to ART accelerates viral decline and reduces expression of inflammation-related genes in human immune cells - genes often upregulated in chronic viral infections. Although SP treatment did not alter levels of cell-associated viral DNA, it led to a significant 4.4-fold decrease in systemic cell-associated viral RNA. This supports the role of XPB in HIV transcriptional regulation and advocates for incorporating transcriptional inhibitors like SP into primary HIV therapy. Additionally, SP treatment diminished markers of immune activation and inflammation, critical factors contributing to morbidity and mortality in individuals with chronic HIV infection. These results highlight SP’s potential to enhance HIV treatment by mitigating key aspects of viral persistence and associated immune challenges.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A comparative RNA-seq analysis of mononuclear cells (MNCs) isolated from the liver, lung, spleen and lymph nodes of BLT humanized mice that were infected with HIV and then treated with ART or ART + Spironolactone (200 mg long-acting subcutaneous pellets) for 35 days. We compared gene expression of samples treated with ART alone or with the combination of ART + SP.

first: Lijun

last: Ling

first: Luisa

middle: P

last: Mori

first: Victor

last: Garcia-Martinez


title: Hfq orchestrates a robust RNA-RNA interaction network in Acinetobacter baumannii. [RNA-Seq]

first: Michael

last: Gebhardt

overall_design: Total RNA-seq data files to accompany the RIL-seq data on WT AB5075 and a derivative thereof that carrys a chromosomally-encoded Hfq-VSVG for two different growth conditions

first: Simon

last: Dove


title: RNA-sequencing reveals growth phase specific differences in global transcriptional thermoregulation in Pseudomonas aeruginosa

city: Atlanta

first: Rachel

middle: Evans

last: Robinson

state: GA

address: 1510 Clifton Road NE

department: Pediatrics

institute: Emory University

first: Joanna

last: Goldberg


title: RELB Reprograms Exhausted Tumor-Infiltrating Lymphocytes for Improved Adoptive Cell Therapy [RNA-Seq]

first: Charles

last: Gersbach

overall_design: RNA was isolated from distinct TIL patient samples (n=4) that were transduced with either Thy1.1, RELB, or nothing using Norgen’s Total RNA Purification Plus Kit and submitted to Azenta for standard RNA-seq with polyA selection

first: Christian

last: McRoberts Amador

first: Pamela

last: Noldner

first: Ying

last: Zhou


title: RNA-seq of PAO1 at two temperatures and at two growth phases

summary: Pseudomonas aeruginosa is a highly versatile bacterium capable of surviving and often thriving in stressful environmental conditions. Here we studied the effect of two environmental conditions, temperature and growth phase, on the P. aeruginosa PAO1 transcriptome. As P. aeruginosa is well-known for its growth-phase dependent phenotypes and gene regulation, our goal was to determine how temperature altered global gene expression at exponential versus stationary phase and to characterize how growth phase affects thermoregulation. To do this, we grew PAO1 in parallel at 25°C and 37°C and sampled the same populations first at exponential phase and then again at stationary phase and assessed gene expression by RNA-sequencing. We also grew PAO1 and an isogenic DlasR mutant at 25°C and 37°C and sampled populations at stationary phase to define LasR-regulated genes at each temperature by RNA-sequencing. This work provides a comprehensive thermoregulon for PAO1 at two distinct growth phases, as well as growth phase transcriptomics at two temperatures, and expands our understanding of quorum sensing regulation under different environmental conditions that P. aeruginosa encounters.

overall_design: PAO1 was grown in parallel at two temperatures, 37°C or 25°C, and cultures were sampled for RNA-seq first at exponential phase and then again at stationary phase.                          PAO1 and an isogenic ΔlasR mutant were also grown at 37°C and 25°C to stationary phase and sampled for RNA-seq.


title: Directed Functional Reinnervation to Curb Nociception and Enable Sensation

city: Boston

first: Lillian

last: Zhu

state: Massachusetts

address: 150 Western Avenue

department: Bioengineering

institute: Harvard University

summary: Peripheral nerve injuries lead to diminished function and pain via nociplastic phenomena. We propose a new strategy called Directed Functional Reinnervation, in which nerves are reassigned to new peripheral targets with the goal of altering circuit function. Here, we redirect pure sensory nerves into skeletal muscle grafts to curb nociplasticity and provide benign or useful inputs for prosthetic applications. Electrophysiological characterization of the functional signaling capabilities demonstrated robust afferent responses to mechanical stimuli. Immunofluorescence staining of the saphenous nerve graft indicated widespread innervation of various synapses within the muscle. With immediate graft placement, the injured nerves’ dorsal root ganglia revealed comparable levels of nociceptive markers to uninjured nerves, suggesting a molecular basis for the prevention of pain sensitization. These findings support the use of skeletal muscle grafts for the alleviation of neuropathic pain and use as a sensory transmitter in conjunction with neural interfaces.

overall_design: RNA seq profiling of dorsal root ganglia, comparing expression levels in unoperated controls with those upstream of saphenous nerve and skeletal muscle grafts

first: Benjamin

last: Johnston

first: Vlad

last: Tereshenko

first: Joshua

last: Bernstock

first: Sabrina

last: Liu

first: Alexander

last: Madinger

first: Patrick

last: Pariseau

first: Arriyan

last: Dowlatshahi

first: Kyle

last: Eberlin

first: Shriya

last: Srinivasan


title: Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT

city: Würzburg

last: Westermann

address: Josef-Schneider Straße 2

institute: HIRI

summary: Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular survival, respectively. There has been increasing evidence for post-transcriptional control of SPI gene expression by Hfq-dependent small RNAs (sRNAs) such as PinT. This 80-nucleotide sRNA is highly expressed after Salmonella enters host cells and modulates the transition from the SPI-1 to SPI-2 program by targeting different virulence factor mRNAs. It has been elusive, however, how PinT activity could be counteracted when virulence gene suppression were to be relieved. To identify putative inhibitors of PinT, we have mapped the RNA interactome of Salmonella recovered from infected macrophages, using an optimized version of the RIL-seq method. Next to offering an unprecedented view of Hfq-mediated RNA interactions during Salmonella’s intracellular infection stage, RIL-seq uncovered the 3’ end-derived sRNA InvS as a direct negative regulator of PinT. Biochemical and genetic experiments suggest a decoy mechanism whereby InvS lifts the PinT-mediated repression of virulence factors. Additionally, InvS acts as an mRNA repressor of the host cell adhesion protein, MipA, and PinT interaction with InvS relieves mipA repression. Together, our work identifies a unique pair of antagonistic sRNAs in a growing post-transcriptional network of virulence gene regulation.

sample_organism:
Mus musculus
Salmonella enterica

platform_organism:
Mus musculus
Salmonella enterica

overall_design: We have used the RIL-seq technique (Melamed et al. 2016) to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica under infection conditions (SPI-2 medium or mouse macrophage 20 h post infection).

first: Hoda

last: Kooshapour

first: Gianluca

last: Matera

first: Elisa

last: Venturini

first: Thorsten

last: Bischler

first: Jörg

last: Vogel


title: scRNA-seq, ULAC-seq and RNA-seq across mouse hematopoietic hierarchy

city: GuangZhou,GuangDong Province

first: Feng

last: Huang

state: China

country: China

institute: Guangzhou Laboratory


title: Induction of Senescence During Postpartum Mammary Gland Involution supports tissue remodeling and promotes postpartum tumorigenesis

city: Paris

first: Jérémy

last: Chantrel

state: Ile-de-France

address: 25-28 rue du Dr. Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

summary: Cellular senescence is an evolutionarily conserved stress response which contributes to tissue repair and tumor suppression, yet its accumulation is also linked to aging and disease. Whether physiological senescence can be exploited by oncogenic events to promote tumorigenesis is unknown. Postpartum mammary gland involution is a major adult tissue-remodeling event, resembling wound healing, and is closely associated with postpartum breast cancer (PPBC). Here, we show that during mammary gland involution in mice, a p16-dependent senescence response is induced in alveolar luminal cells. Eliminating senescent cells disrupts tissue remodeling and delays involution, demonstrating their physiological importance. However, in a PPBC model where oncogenic activation coincides with involution, removing involution-associated senescent cells extended tumor latency. Mechanistically, senescent cells enhance tumor cell plasticity via the senescence-associated secretory phenotype (SASP), fostering metastasis. Our findings reveal that senescence, while required for postpartum tissue remodelling, can be hijacked to facilitate tumorigenesis, defining senescence as a unifying mechanism linking tissue repair to tumorigenesis.

overall_design: Bulk RNAseq data include mammary gland from wild type females at different involution timepoints (Inv0, Inv1, Inv3, Inv7)

first: Aurélie

last: Chiche

first: Lamia

last: Djoual

first: Elsa

last: Charifou

first: Shuoyang

last: Wang

first: Laurianne

last: Temime

first: Marielle

last: Saclier

first: Shaoxiang

first: Han

last: Li


title: Global mRNA profiling (RNA-seq) across mouse hematopoietic hierarchy

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs) using RNA-seq and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To understand the role of epigenetic regulation in the establishment and maintenance of HSC fate decisions, we sorted distinct hematopoietic populations including long-term HSCs (LT-HSCs), short-term HSCs (ST-HSCs), multipotent progenitors (MPP), common myeloid progenitors (CMP), granulocyte-macrophage progenitor (GMP), megakaryocyte/erythroid progenitors (MEP), and the mature cells from the bone marrow (BM) using fluorescence-activated cell sorting (FACS), followed by RNA sequencing (RNA-seq) analysis.

first: Hengyou

last: Weng

first: Huilin

first: Yushuai


title: Dinutuximab beta effectively treats Ewing sarcoma when combined with chemotherapy

city: Rome

first: Probiomics

state: RM

address: via Montpellier 1

country: Italy

institute: Probiomics s.r.l

summary: Ewing sarcoma is a rare and aggressive cancer of the bone and soft tissues that mainly affects children and young adults. Despite intensive multimodal therapy, the prognosis of patients with metastatic or recurrent disease remains poor. Therefore, novel therapeutic approaches are needed to improve the outcomes of patients with Ewing sarcoma. The disialoganglioside GD2 is highly expressed on Ewing sarcoma cells, making this tumor eligible for treatment with Dinutuximab beta, a monoclonal antibody targeting this antigen.  Through in vitro and in vivo approaches, this study demonstrated that Dinutuximab beta effectively suppressed tumor growth by 60% (p=0.0135 vs vehicle) and improved survival rate by 68% (p=0.0006 vs vehicle) in a mouse model xenograft. The combination therapy with doxorubicin demonstrated superior efficacy compared to monotherapy, with enhanced tumor suppression (86%; p=0.0009 vs vehicle) and an extension of survival rate (146%; p=0.000025 vs vehicle). Overall, this study showed that Dinutuximab beta is effective against Ewing sarcoma, especially in combination with the standard induction chemotherapy regimen for this tumor. Integrating Dinutuximab beta into the standard chemotherapy regimen for Ewing sarcoma offers a promising new therapeutic approach that can potentially improve the prognosis for patients with high-risk disease, offering a more effective alternative to existing treatments.

overall_design: Human Ewing Sarcoma derived cells were subcutaneously injected into athymic nude mice. Animals were treated with either vehicle or Dinutuximab beta for 5 conscutive days. At day 5 (T1) and 11 (T2) tumor were collected and analysed. 4 tumors for each experimental group were analysed.

first: Roberta

last: Frapolli

first: Marina

last: Meroni

first: Ezia

last: Bello

first: Valentina

last: Kebede

first: Matteo

last: Malinverno


title: RNA-seq of PAO1 and ΔlasR grown at 37°C or 25°C at stationary phase

first: Rachel

last: Robinson

first: Michael

last: Gebhardt

first: Joanna

last: Goldberg


title: Post-transcriptional splicing of timeless drives ~24-hour circadian rhythms in Drosophila

first: Swathi

last: Yadlapalli

address: 109 Zina Pitcher Pl

summary: Circadian clocks drive ~24-hour rhythms in physiology and behavior through precisely timed gene expression cycles1-4. Here, we reveal an unexpected role for intron splicing in tuning the ~24-hour circadian period in Drosophila. Using RNA Fluorescent In Situ Hybridization and RNA-sequencing, we demonstrate that ~50% of timeless (tim) mRNAs—a core clock transcript—remain nuclear throughout the circadian cycle due to retention of a specific intron, termed intron P. Unlike other tim introns, spliced during transcription, intron P—lacking a canonical branch point—is spliced inefficiently post-transcriptionally near nuclear speckles, thereby limiting tim mRNA export and TIM protein synthesis. CRISPR deletion of intron P results in all tim mRNAs being fully spliced and exported, accelerating TIM production and shortening the circadian period to ~22.5 hours. Inserting intron P into reporter genes promotes their nuclear retention in both Drosophila neurons and human U2OS cells, which is reversed by adding a canonical branch point sequence. A genetic screen identified the KH-domain RNA-binding protein Qkr58E-2 (a Sam68 homolog5) as an intron P splicing activator, and HnRNP proteins Hrb27c and Squid6 as repressors. Together, these findings uncover a novel regulatory role for intron splicing dynamics in circadian timing and further suggest that introns have the potential to act as critical regulatory elements in other temporally regulated biological processes, including developmental transitions and stress responses.

overall_design: polyA RNA sequencing of Drosophila melanogaster clock neurons in control and Prp3-RNAi knockdown conditions. Cells were isolated by fluorescence-activated cell sorting (FACS) using Clk-GAL4>UAS-GFP-NLS line developed in the lab. GFP-positive and DAPI-negative cells were sorted to be clock neurons.

first: Ye

last: Yuan


title: Upper Airway Gene Expression in Hospitalized Children with Rhinovirus-induced Respiratory Illnesses

first: Marc

last: Hershenson

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

summary: In this study, we collected nasal swabs from infants and children hospitalized with RV infection and assessed gene expression by next generation sequencing, comparing profiles to swabs obtained from control subjects undergoing otolaryngologic procedures.  We also compared gene expression patterns to those obtained from children with respiratory syncytial virus (RSV) infection, another common respiratory virus well-studied in children.

overall_design:
Flocked nasal swab samples were obtained from children age 0-18 hospitalized with single-virus respiratory infections, as well as uninfected children for comparison.

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

first: Jordan

last: Kreger

first: Alex

middle: L

last: Sliwicki

first: Saly

last: Essoh

first: Yiran

first: Chaandini

last: Jayachandran

first: Jessica

last: Czapla

first: Toby

last: Lewis

first: Erin

middle: M

last: Kirkham

first: Rodney

last: Vergotine

first: Antonia

last: Popova

first: Heidi

last: Flori


title: single-cell transcriptomic analysis of mouse haematopoietic stem cells upon Nat10 deletion

first: Feng

last: Huang

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs)  tracked by single-cell transcriptomic analysis and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To  investigate the role of Nat10-mediated ac4C in HSC maintenance and differentiation, we performed 10×Genomics single-cell RNA sequencing (scRNA-seq) on sorted lineage-negative cells (HSPCs) from the bone marrow (BM) of five independent WT or Nat10 cKO mice.

first: Hengyou

last: Weng

first: Huilin

first: Yushuai

last: Wang


title: Dynamic ac4C landscape across mouse hematopoietic stem and progenitor hierarchy using the ultra-low input acRIP-seq (ULAC-seq)

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs) using  the ultra-low input acRIP-seq (ULAC-seq) and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To further investigate the role of Nat10-mediated ac4C in HSC maintenance and differentiation, we developed an ultra-low input acRIP-seq (ULAC-seq) method, capable of handling varying amounts of input, as low as 500 ng of total RNA. We subsequently profiled ac4C modification in six distinct sorted hematopoietic populations, including HSCs, MPP, CMP, GMP, MEP, and CLP from wild-type (WT) mouse BM using ULAC-seq. We also applied ULAC-seq in Nat10 knockout BM lin- cells and control BM lin- cells to characterize Nat10 targets.


title: Derepression of a single microRNA target causes female infertility in mice [smallRNA-Seq]

city: Cambridge

first: David

last: Bartel

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute / MIT

type: Non-coding RNA profiling by high throughput sequencing

summary: The miR-200a and miR-200b families control mouse ovulation and are essential for female fertility. The ZEB1  transcription factor is a conserved target of both families and has been implicated as a key player in female fertility at multiple levels. Using gene-edited mice that express a miR-200a/b-resistant form of Zeb1, we found that derepression of Zeb1 in the female pituitary caused decreased production of luteinizing hormone and anovulatory infertility. These phenotypes were accompanied by widespread changes in pituitary gene expression characterized by decreased levels of ZEB1 targets, which include the miR-200a/b miRNAs, as expected from the miR-200a/b–ZEB1 double-negative feedback loop. Also observed were increased levels of mesenchymal genes, neuronal genes, and miR-200a/b targets. These results show that a double-negative feedback loop centered on the miRNA regulation of a single transcription factor can significantly influence the expression of thousands of genes and have dramatic phenotypic consequences.

overall_design: To investigate the physiological importance of the miR-200a/b–ZEB1 double-negative feedback loop, we generated miR-200a/b-resistant Zeb1 mice. We performed miRNA expression profiling analyses using data obtained from small RNA-seq of pituitary tissue from adult female wild-type (WT), heterozygous (Zeb1_200H), and homozygous (Zeb1_200M) mice.

first: Benjamin

last: Kleaveland

first: Lara E

last: Elcavage


title: Epidermal cell fusion promotes the transition from an embryonic to a larval transcriptome in C. elegans

city: Laramie

first: Owen

last: Funk

address: 1000 E. University Ave

institute: University of Wyoming

summary: Cell fusion is a fundamental process in the development of multicellular organisms, but its precise influence on gene regulation during critical developmental stages remains largely unknown. The Caenorhabditis elegans epidermis, a powerful model for studying cell fusion, forms 8–10 syncytial cells. The largest of these, hyp7, integrates 139 individual nuclei via cell–cell fusion mediated by the fusogenic protein EFF-1. To explore the effects of cell fusion on developmental progression and associated gene expression changes, we conducted transcriptomic analyses of eff-1 knockout and fusion-deficient C. elegans mutants. Our RNAseq findings showed widespread transcriptomic changes including enrichment for epidermal genes and key molecular pathways involved in epidermal function during larval development. Subsequent single-molecule fluorescence in situ hybridization validated the altered expression of mRNA transcripts, confirming quantifiable changes in gene expression in the absence of embryonic epidermal fusion. These results underscore the significance of cell–cell fusion in shaping transcriptional programs during development and raise questions regarding the precise identities and specialized functions of different subclasses of nuclei within developing syncytial cells and tissues.

overall_design: RNAseq of L1 wildtype and mutant larva

first: Funk

last: Owen


title: Single nucleus RNA-seq of late embryonic and early postnatal mouse kidney.

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: We are interested in changes to cell type composition of the developing kidney and so performed single nucleus RNA sequencing of whole kidney at E18.5 and P3.

overall_design: Nuclei were obtained from digestion of whole kidneys and analyzed with snRNA-seq.

first: Alexandria N.

last: Fusco

first: Jane N.

last: Warshaw

first: Denise K.

last: Marciano

first: Thomas J.


title: Derepression of a single microRNA target causes female infertility in mice [RNA-Seq]

overall_design: To investigate the physiological importance of the miR-200a/b–ZEB1 double-negative feedback loop, we generated miR-200a/b-resistant Zeb1 mice. We performed gene expression profiling analyses using data obtained from RNA-seq of pituitary, hypothalamus, and ovary tissue from adult female wild-type (WT), heterozygous (Zeb1_200H), and homozygous (Zeb1_200M) mice.


title: Arabidopsis thaliana gene expression in seedlings of mutants in exocyst subunits exo70B1, exo70B2 and exo70B1xexo70B2

status: Public on Nov 30 2025

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: Several mutants in plant exocyst vesicle-tethering complex have various phenotypes. We decided to look into the differential gene expression for subunits exo70B1, B2 and double B1xB2 mutant, which were found before to be mores susceptible toward Pseudomonas in young developmental stages. We uncovered both the quantitative and qualitative changes in gene expressions among the analysed mutant lines in comparison to WT. We discovered several interesting candidate genes involved in cell wall function, that would be worth of further more focused studies.

overall_design: The seven-day-old whole seedlings (ca 50 seedlings) grown on vertical plates (23oC, 16/8 light/dark) were used as a source of RNA, always as three replicates for each mutant line and WT.

last: Müller

first: Tamara

last: Pečenková

first: Matěj

last: Drs


title: SAMHD1 depletion restricts SARS-CoV-2 infection by suppressing HNF1-dependent ACE2 expression in lung epithelial cells

city: Iowa City

first: Pak Hin Hinson

last: Cheung

state: Iowa

address: 51 Newton Raod

department: Department of Microbiology and Immunology

institute: University of Iowa

summary: SAMHD1 protein is a restriction factor against broad spectrum of viruses through dNTPase- and dNTPase-independent mechanisms. Moreover, it limits spontaneous- and virus-induced innate immune responses by suppressing proinflammatory cytokine and IFN-I production. Some viruses that escape the restriction functions of SAMHD1 may utilize SAMHD1-mediated innate immune suppression to establish effective infection by better IFN antagonism. Previously, we found that, instead of being a restriction factor, SAMHD1 was a proviral factor facilitating SARS-CoV-2 replication in human macrophages and immortalized human kidney cells HEK293T by suppressing IFN response. However, it is unclear about the function of SAMHD1 to the primary target and producer cells of SARS-CoV-2. In the current study, we found that SAMHD1 was a proviral factor to facilitate SARS-CoV-2 replication in Calu-3 cells, which were lung epithelial cells endogenously expressing viral entry factors such as ACE2 and TMPRSS2. Unlike human macrophages and HEK293T cells, inhibition of IFN antiviral response by baricitinib, a JAK1/2 inhibitor, did not revert the suppression of SARS-CoV-2 in SAMHD1 knockout Calu-3 cells. Through the experiments with pseudotyped viruses, we found that spike-protein mediated viral entry was suppressed in SAMHD1 knockout Calu-3 cells. Through mRNA-seq, we found that SAMHD1 knockout repressed ACE2 expression of Calu-3 cells at mRNA and protein levels. Knockdown experiments revealed that HNF1α and HNF1β were crucial for the endogenous expression of ACE2 in Calu-3 cells. Additionally, SAMHD1 knockout led to a reduction in the expression levels and ACE2-promoting function of HNF1α and HNF1β. This suggested that SAMHD1 facilitates HNF1-mediated ACE2 expression and SARS-CoV-2 replication in ACE2-expressing cells via a mechanism independent of its IFN- suppressive function

overall_design: To gain mechanistic insight, mRNA-seq was performed to profile the transcriptome of SAMHD1 knockout Calu3 cells (KO) and compared with that of the control Calu-3 cells (Ctrl). Two clones of KO cells were generated through CRISPR/Cas9 with one single guide RNA having different target sequences. Ctrl cells were mock control treated similarly as the KO cells but were transduced with empty vector. 8 x 105 Calu-3 Ctrl, KO1 and KO2 cells were seeded in 6 well plates in biological triplicate. Cells were cultured in 2mL DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. At 20 hours after seeding, cells were washed once with DPBS and lysed with RLT plus lysis buffer. Cellular RNA was purified with RNeasy Plus kit following manufacturer’s instructions. All RNA samples got RNA integrity Number (RIN) scores equal to or more than 9.9 as determined by Agilent BioAnalyzer by Genomics Division of Iowa Institute of Human Genetics (University of Iowa). RNA samples were processed through Illumina Stranded mRNA Prep (illumina) and sequenced by Element Aviti24 using Cloudbreak FS-High output flow cell at 150 cycle (2x75) by the Genomics Division.

first: Pearl

last: Chan

first: Hua

last: Yang

first: Krisztina

last: Ambrus

first: Shravya

last: Honne

first: Baek

last: Kim

first: Stanley

last: Perlman

first: Li

last: Wu


title: Bypass of blocking lesions by RNAPII reveals a novel stress induced by DNA damage [PRO-seq]

city: Miami

first: Carolina

middle: Paula

last: Banuelos

state: Florida

address: 1580 NW 10th Ave

department: Medicine

institute: University of Miami

summary: Platinum-based compounds and ultraviolet (UV) irradiation produce bulky DNA lesions that stall RNA polymerase II (RNAPII), activating transcription-coupled nucleotide excision repair (TC-NER), RNAPII degradation, and global transcriptional shutdown. However, the consequences of RNAPII bypassing such lesions remain unclear. We identified the acetyltransferase p300 as a key regulator of TC-NER-dependent RNAPII removal from damaged chromatin via a USP7-dependent mechanism. Loss of p300 permits RNAPII to bypass transcription-blocking lesions, sustaining transcription and full-length mRNA production despite DNA damage. This leads to continued translation, endoplasmic reticulum (ER) stress, and activation of the unfolded protein response (UPR), compromising cell viability. Notably, this stress response resensitizes tumors resistant to platinum-based chemotherapy. Our findings reveal a vulnerability in tumor cells that evade transcriptional shutdown and define a synthetic lethal interaction between p300 inhibition and platinum-induced DNA damage, offering a targeted strategy to overcome chemoresistance.

overall_design: To characterize the impact of p300 deficiency on transcription control post DNA damage, Precision Run-On Sequencing (PRO-Seq) was conducted in both WT and p300-deficient cells. PRO-Seq maps the location of actively engaged, non-arrested, or paused RNA polymerases with base-pair resolution


title: Extracellular matrix-driven antagonism: Bacillus ECM components modulate Botrytis physiology and counterdefence

city: Malaga

first: Alicia

last: Pérez Lorente

address: Av Louis Pasteur 49. IHSM

country: Spain

institute: University of Malaga

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of Bacillus subtilis growing in the presence of Botrytis cinerea. In addition, we study  the transcriptomic response of Botrytis cinerea when cocultured with Bacillus subtilis and also the transcriptomic response of Botrytis treated with purified TasA and Fengycin after 6h

sample_organism:
Bacillus subtilis
Botrytis cinerea

platform_organism:
Bacillus subtilis
Botrytis cinerea

overall_design: Botrytis-Bacillus coculture for 6h and Botrytis treated with TasA and Fengycin for 6h. All in liquid media, PDB cultured at 28 °C

first: Alicia Isabel

first: Carlos

last: Molina Santiago

first: David

last: Vela

first: Paolo

last: Stincone

first: Abzer

last: Pakkir Shah

first: Jesus

last: Hierrezuelo

first: Daniel

last: Petras

first: Diego

last: Romero


title: Infusible Extracellular Matrix Biomaterial Enhances and Expedites Cell-Specific Pro-Repair Following Acute Myocardial Infarction

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Myocardial infarctions (MI) affect 805,000 people per year in the United States. To mitigate the pathological effects of MI, we have developed and investigated pro-reparative decellularized extracellular matrix (ECM) biomaterials: an intravascularly infusible ECM (iECM). However, no one has ever utilized single cell and spatially resolved transcriptomics to further probe how systemically administered infusible ECM can elicit pro-repair in an MI model. Thus, we utilize spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) to further measure pro-repair in various cell types, and thus validate these findings with spectral flow cytometry.With iECM, we found pro-reparative macrophage activation, fibroblast remodeling, increased vasculature development, and cardioprotection. Thus, we depict the pro-reparative nature of decellularized ECM biomaterials on cardiac cell types and elucidate previously undiscovered therapeutic pathways, further demonstrating infusible ECM’s potential as an MI therapy.

overall_design: Gene expression profiling of 10x Genomic Chromium single nucleus RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium short axis sections  on injured Sprague Dawley female rats (225-250 g). Injuries include I/R (45 minutes of ischemia followed by reperfusion).

first: Joshua

last: Mesfin

first: Alexander

last: Chen

first: Maria

last: Karkanitsa

first: Justin

last: Yu

first: Quincy

last: Lyons

first: Van

last: Ninh

first: Emily

last: Gardner

first: Elyse

last: Wong

first: Sriya

last: Paleti

first: Colin

last: Luo

first: Zhenxing

last: Fu

first: Kevin

last: King


title: Arabidopsis thaliana gene expression in adult leaf tissue of mutants in exocyst subunits exo70B1, exo70B2 and exo70B1xexo70B2

first: Karel

last: Muller

summary: Several mutants in plant exocyst vesicle-tethering complex have various phenotypes. We decided to look into the differential gene expression for subunits exo70B1, B2 and double B1xB2 mutant, which were found before to be mores susceptible toward Pseudomonas in young developmental stages, but may develop enhanced resistance in later stages of development (especially exo70B1). We uncovered both the quantitative and qualitative changes in gene expressions among the analysed mutant lines in comparison to WT. We discovered several interesting candidate genes involved in stomatal and cell wall function, that would be worth of further more focused studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from A. thaliana leaf tissue from WT and mutants. exo70B1, exo70B2 and double exo70B1xB2

last: Müller

first: Tamara

last: Pečenková

first: Matěj

last: Drs


title: Pou5f3 and Nanog organize active chromatin in three dimensions

first: Aleksandra

last: Galitsyna

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

summary: Zygotic genome in zebrafish embryogenesis is activated by transcription factors Pou5f3, Sox19b and Nanog. While it  was previously demonstrated, that these factors displace nucleosomes and create the regions of open chromatin, their role in three-dimensional genome organisation was not studied. Here we show, that large-scale chromatin structures, TADs and compartments, form independently of Pou5f3, Sox19b and Nanog. However, Pou5f3 and Nanog are required for formation of small-scale 3D active chromatin structures which we call "fountains".

overall_design: To investigate if Pou5f3, Sox19b and Nanog play a role in 3D organization of chromatin , we compared 3D chromatin maps using Hi-C method in the wild-type, single, double and triple mutants by these factors. Hi-C was performed shortly before zygotic genome activation ( 2.75 hours post-fertilization, or hpf), and after zygotic genome activation, at late blastula stage ( 5.3 hpf). To characterize the developmental  changes of 3D chromatin , we also performed Hi-C on the wild-type at 11 hpf and 25 hpf.

first: Sergey

middle: V

last: Ulianov

first: Daria

last: Onichtchouk


title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding [Spatial Transcriptomics]

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

institute: Karolinska Institutet

summary: Dietary modification by consuming plant-based food with high fiber content is a primary strategy to induce weight loss in obese individuals. However, long-term usage of such fiber-enriched dieting is challenging and rapid weight regain often occurs once the high-fat dietary habit resumes. Currently, how do adipose and intestinal tissues respond to a switch between high-fiber and high-fat diet remains unknown. Here, we applied C57BL/6J mice to chow diet (CD)/high-fiber diet (HfiD)-to-high-fat diet (HFD) switching paradigms and collected mesenteric white adipose tissue (mWAT), duodenum and colon tissue sections at different time points for single-nucleus profiling and spatially resolved transcriptomic analysis, respectively. We show that the progenitors and adipocytes of HfiD-fed mWAT are more sensitive to HFD-induced molecular changes. In addition, HfiD feeding prevents the subsequent HFD-induced expansion of immune-related enterocytes in duodenum and reverses the HFD-induced enterocyte-to-goblet cell conversion in colon. Moreover, HfiD-induced microbiome changes are mostly abrogated upon HFD feeding. Our results indicate that prior HfiD feeding can alter the cellular response of adipose and intestinal tissues to subsequent HFD feeding, which highlights the impact of dietary interventions with fiber-rich food for obesity treatment from a different perspective. Our data provide a spatiotemporal resource for future hypothesis-driven studies on the mechanisms of adipose and intestinal tissue plasticity in response to diet switches.

overall_design: To investigate how switch between HfiD and HFD shapes the intestinal and adipose tissues, we applied freshly weaned C57BL/6J male mice to either a control diet (CD) (AIN93G) or an HfiD (AIN93G supplemented with inulin for 5 weeks, before switching both groups to an HFD (AIN93G supplemented with 60 kcal% fat) and collected different cohorts of mice right before, 4 and 8 weeks after switching to HFD for analysis.

first: Meng

last: Xie


title: Comprehensive transcriptome analysis of the skin in epidermis-specific Nampt cKO mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Nicotinamide adenine dinucleotide (NAD⁺) is essential for cellular metabolism, DNA repair, and stress response. NAD+ is synthesized from nicotinamide, nicotinic acid (collectively termed niacin), and tryptophan. In humans, deficiencies in these nutrients result in pellagra, marked by dermatitis, diarrhea, and dementia. The dermatitis associated with pellagra typically manifests as photodermatosis in sun-exposed areas. This study examined the effects of NAD+ deficiency on skin homeostasis using epidermis-specific Nampt conditional knockout (cKO) mice. These mice displayed substantial NAD⁺ depletion, reduced poly (ADP-ribose) polymerase (PARP) activity, and increased DNA damage, indicated by γH2AX accumulation. Nampt cKO mice also developed spontaneous skin inflammation and epidermal hyperplasia. Here, we provide gene expression profiling of skin tissues using the RNA sequencing for identifying changes in gene expression of Nampt-cKO mice.

overall_design: The mRNA profile of  skin tissues was generated by RNA sequencing using the Illumina NovaSeq 6000  (Illumina).

first: Taiki

last: Seki

first: Takashi

last: Nakagawa


title: Glycolytic heterogeneity drives metabolic-targeted therapy in PDAC

status: Public on Nov 28 2025

city: Naples

first: Ugo

last: Chianese

address: via Luigi De Crecchio

department: Department of Precision Medicine

institute: Universita degli Studi della Campania Luigi Vanvitelli

summary: Background: Pancreatic ductal adenocarcinoma is classically characterized as a glycolytic tumor. However, the extent and implications of metabolic heterogeneity within PDAC remain poorly defined. This study aimed to determine whether glycolytic activity follows a consistent expression pattern across PDAC patients and to explore how metabolic diversity influences therapeutic vulnerability. Methods: We employed spatial transcriptomics in six, ex vivo, primary human PDAC specimens, complemented by single-cell and bulk RNA sequencing, to map glycolytic heterogeneity in PDAC. Patient-derived cell models, representative of distinct glycolytic phenotypes, were used to assess metabolic and antiproliferative responses to glycolytic pathway inhibition. A comprehensive multi-omics strategy—including metabolomics, proteomics, and lipidomics—was integrated through a robust bioinformatics pipeline to dissect pathway-specific variations and integromics. Results: PDAC tumors displayed marked glycolytic heterogeneity, with distinct transcriptional profiles that preserved cell identity and spatial organization. These glycolytic patterns correlated with clinical outcomes, highlighting their potential prognostic value. Functional studies strengthen differential sensitivity to metabolic inhibitors in models with opposite glycolytic activity, demonstrating both the therapeutic relevance of PDAC glycolytic stratification and highlighting the potential of metabolic targeting. Conclusions: Our findings uncover a clinically relevant metabolic heterogeneity in PDAC, offering a novel stratification framework based on glycolytic profiling. This approach may allow the selection of patients for tailored metabolic therapies, advancing precision oncology in pancreatic cancer.

overall_design: Pancreas samples have been acquired from patients with pancreatic ductal adenocarcinoma diagnosis, having a grade between 2-3, T and N, respectively, between 2-3 and 0-1.

first: Chiara

last: Papulino

first: Gerardo

last: Saggese

first: Ahmad

last: Ali

first: Marianna

last: Ciotola

first: Enza

last: Lonardo

first: Mirko

last: Cortese

first: Gregorio

last: Favale

first: Annabella

last: Di Mauro

first: Danila

last: La Gioia

first: Valentina

last: Golino

first: Eduardo

last: Sommella

first: Pietro

last: Campiglia

first: Renato

last: Franco

first: Fortunato

last: Ciardiello

first: Ferdinando

last: De Vita

first: Vincenzo

last: Carafa

first: Lucia

last: Altucci

first: Rosaria

last: Benedetti


title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding

first: Zhi

last: Peng

first: Meng

last: Xie


title: Effect of CA3 overexpression on signalling pathways in different cell lines

status: Public on Nov 29 2025

city: Nathan

first: Yezhou

last: Yu

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

country: Australia

institute: Griffith University

summary: Carbonic Anhydrase 3 (CA3) was an understudied member of the carbonic anhydrase family. It is highly expressed in muscle tissue and contains two surface-exposed cysteine residues, which can undergo glutathionylation. The redox modification protects cells under oxidative stress. Recent studies have shown that CA3 interacts with Bcl-2–Associated Athanogene 3 (BAG3) and squalene epoxidase (SQLE), implicating CA3 in the pathogenesis of myasthenia gravis and non-alcoholic fatty liver disease. CA3 overexpression has also been reported to reduce hypoxia-induced apoptosis in cardiomyocytes. In this study, we performed RNA-seq profiling on HEK293T, MDA-MB-231, and SVCT cell lines following CA3 overexpression. HEK293T cells were analyzed only under normoxic conditions, whereas MDA-MB-231 and SVCT cells were cultured under both normoxia and hypoxia.

first: Giovanna

last: Trapani

first: Kathryn

last: Tonissen


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [CUT&Tag]

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: Transposons, or transposable elements (TEs) have extensively reshaped the cis-regulatory landscape of mammalian genomes, yet the mechanisms that govern their context-specific activity remain incompletely understood. KRAB zinc finger proteins (KZFPs), a large family of transcription factors specialized in TE recognition, are known repressors of TE-derived regulatory activity through TRIM28-mediated H3K9me3 deposition. Here, we expand this paradigm by uncovering noncanonical relationships between TEs and KZFPs. By generating a comprehensive epigenomic map of KZFP-bound TEs, we find that the regulatory activity of ancient mammalian L2/MIR elements is broadly delineated by KZFP binding patterns, despite low H3K9me3 enrichment. We further dissect this relationship by investigating the function of ZNF436, a non-canonical KZFP, highly expressed during in vivo human fetal heart development. Using loss-of-function approaches, we show that ZNF436 preserves cardiomyocyte function by promoting cardiac gene expression while restricting the activation of alternative lineage programs. Mechanistically, ZNF436 recruits specialized SWI/SNF chromatin remodeling complexes to limit the accessibility of L2/MIR-derived enhancers, many of which are active in non-cardiac tissues. These findings reveal a noncanonical, TRIM28-independent role for KZFPs in shaping cell-type-specific regulatory landscapes and emphasize the importance of repressing alternative regulatory programs alongside activating lineage-specific ones to safeguard cell identity.

overall_design: Profiling the gene expression, histone mark and accessibility changes in d15 hESC-derived cardiomyocytes in control and ZNF436 KD condition.

first: Danica

last: Milovanovic


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [RNA-Seq]


title: A shear stress-responsive pathway in monocytes drives cardiopulmonary bypass-induced inflammation via spectrin/RAF1/store-operated calcium entry

city: Seattle

first: Weiming

last: Li

state: WA

address: 4032 8th ave ne

department: Center for developmental biology and regenerative medicine

institute: Seattle children's research institute

summary: Patients undergoing cardiac surgery face significant inflammation induced by exposure to cardiopulmonary bypass (CPB), contributing to heightened morbidity and mortality. The molecular and cellular mechanisms that underpin this inflammatory process remain unknown. To address this knowledge gap, we conducted snRNA/ATAC sequencing to profile transcriptional and chromatin changes on circulating leukocytes from neonatal CPB patients. Classical monocytes become more prevalent after CPB, showing dysregulation of numerous inflammatory genes and significant changes in chromatin accessibility, highlighting their role in CPB-associated inflammation. The proinflammatory cytokine Interleukin 8 (IL8 or CXCL8),  is significantly induced by CPB, with its promoter accessibility to the AP-1 transcription factor significantly increased. A genome-wide CRISPR screen using IL8 gene as a readout in non-adherent monocytic cells identified two genes, non-erythroid spectrin (SPTAN1) and RAF1, as novel effectors of hemodynamic stress. We further found that SPTAN1 and RAF1 activate store-operated calcium entry (SOCE) under CPB conditions, leading to elevated IL8 expression. We propose a novel shear stress-responsive pathway consisting of SPTAN1/RAF1/SOCE signaling. Drug treatment experiments offer a potential therapeutic approach to alleviate CPB-induced inflammation. Together, these findings provide novel insights into the pathogenesis of CPB-associated inflammation, enhancing our understanding of sterile inflammation and how non-adherent cells sense shear stress at molecular level.

overall_design:
Sorafenib, BVD-523, CM-4620 drugs treat PBMCs from three donors.
single cell RNA sequencing using 10x Flex kit.

first: Lan N.

last: Tu

first: Lance

last: Hsieh

first: Julian R.

last: Smith

first: Yi-Ting

last: Yeh

first: Anothony

last: Sinyagin

first: Majid

last: Ghassemian

first: Andrew

last: Timms

first: Lyubomyr

last: Bohuta

first: Christina

last: Greene

first: Juan Carlos

last: del Alamo

first: Ram

last: Savan

first: Vishal

last: Nigam


title: Differential gene expression between the hippocampus of WT and SNAT3 (Slc38a3)-conditional knockout mice

city: Haifa

first: Inna

last: Radzishevsky

address: Oren 13

department: Biochemistry

country: Israel

institute: Inna Radzishevsky

summary: The main goal of this study was how the brain obtains glutamine during the early postnatal period, when the expression of glutamine synthetase is low. We found that early postnatal mice maintain their brain glutamine levels by importing glutamine from the blood. We identified the Slc38a3 transporter as a primary transendothelial glutamine transporter at brain capillaries. Mice with selective knockout of Slc38a3 (Slc38a3-cKO) in endothelial cells exhibit a significant decrease in the influx of glutamine and histidine through the BBB at postnatal day 11 (P11). This is accompanied by a significant decrease in brain glutamine and histidine levels, along with secondary reductions in essential amino acids that are not substrates of Slc38a3. Slc38a3-cKO mice also exhibit postnatal/progressive microcephaly, similar to that observed in patients with mutations in Slc38a3. Slc38a3-cKO mice exhibit behavioral deficits, metabolic impairments, and synaptic alterations at P11.

overall_design: RNA-seq profiling of hippocampi isolated from 11-day-old wild-type mice and mice with selective knockout of Slc38a3 (Slc38a3-cKO) in endothelial cells

first: Herman

last: Wolosker


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [ATAC-seq]

first: Evarist

last: Planet


title: MHC II-restricted neoantigen vaccine reverses immune microenvironment and overcomes resistance to immune checkpoint inhibitors in cold tumors

city: Nanjing

first: Chun

last: Lu

address: No. 8 Xuefu Road, Pukou

institute: Nanjing University

summary: Cold tumors are resistant to immune checkpoint inhibitors (ICIs) due to their poor T cell infiltration and immunosuppressive tumor microenvironment (TME). While the role of CD4+ T cell response in anti-tumor immunity has been emphasized, it remains unclear whether the MHC II-restricted neoantigen vaccines targeting CD4+ T cell can reverse the immune microenvironment and overcome resistance to ICIs. Here we observed an enrichment of immune inflammation-related signaling pathways in TME following administration of MHC II-restricted neoantigen vaccines, indicating their potent role in reversing immunosuppressive TME. An increase in the tumor infiltration of CD4+ T cells and CD8+ T cells, an enhancement of their effector functions, and a tendency towards exhaustion were observed, providing prerequisites for the effectiveness of ICI treatment. Furthermore, NicheNet analysis indicated an enrichment of the inhibitory immune checkpoint signaling axis PVR-TIGIT following vaccination. The combination of the vaccines and TIGIT blockade exhibited synergistic anti-tumor efficacy. Mechanistically, the combination therapy promoted the differentiation of CD8+ T cells into effector memory phenotypes while delaying their exhaustion. Our study demonstrates that MHC II-restricted neoantigen vaccines can remodel the inhibitory TME with insufficient T cell infiltration and synergistically inhibit tumor growth with TIGIT antibody, providing a novel strategy for treating cold tumors.

overall_design: B16F10 tumor bearing mice were subcutaneously injected with two doses of saline, M44 vaccine (50 µg M44 peptide formulated with 20 μg CpG) or M44 vaccine and TIGIT antibody on day 2 and 8, and tumors were collected by euthanizing on day 10. CD45 (TIL) MicroBeads (Miltenyi Biotec, #130-110-618, DE) were used for isolating the CD45+ immune cells for scRNA-seq (n=6 mice per group, mixed sample detection).

first: Xueru

last: Song


title: CDK9 is a Dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas [RNA-seq]

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

summary: The transcription factor GATA-3 is a proto-oncogene in subsets of mature T cell lymphomas (TCL). CDK9 is a transcriptional regulator that, by phosphorylating paused RNA polymerase II (RNAPII), enables efficient transcriptional elongation. Therefore, we were motivated to examine the extent to which CDK9 is required for controlling transcription and expression of GATA-3 and its target genes. A pharmacologic strategy, using the selective CDK9 inhibitor AZD4573, was utilized to identify CDK9 dependent transcripts. Traveling ratios, defined as the ratio of RNAPII bound at promoter to RNAPII bound within the gene body, were determined by RNAPII ChIP-seq in cell treated with AZD4573 (or vehicle control). CDK9 dependent genes were defined as those with increased traveling ratio and decreased transcripts. MCL-1 dependency was determined in these cell lines by BH3 profiling. The extent to which CDK9 inhibition transcriptionally reprograms TCL was further examined in complementary ex vivo and in vivo studies using primary TCL specimens and GEM and PDX models

overall_design: ChIP-seq and RNA-seq of human T cell lymphoma cells treated with CDK9 inhibitor AZD4573

first: Ryan

last: Wilcox


title: CDK9 is a Dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas [ChIP-seq]


title: Boron deficiency stress treatment in sweet orange

city: kunming

first: xiuyao

last: yang

state: yunnan

address: Southwest Forestry University, 300 Bailong Road, Qingyun Street, Panlong District, Kunming, Yunnan Province, China

institute: Southwest Forestry University

summary: Transcriptome sequencing of boron deficiency stress treatment in sweet orange

overall_design:
Sweet orange histocultures were transferred to MS nutrient solution with adequate boron concentration of
0.25 mg/L as control and set boron stress concentration of 0.01 mg/L, respectively
control and treated histocultures were placed in the histoculture chamber at 25°C for 25 days and sweet orange leaves were collected in three biological replicates


title: Extensive remodelling of XIST regulatory networks during primate evolution [WGS]

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

institute: Université Paris Cité

type: Genome variation profiling by high throughput sequencing

summary: Unravelling how gene regulatory networks are remodelled during evolution is crucial to understand how species adapt to environmental changes. We addressed this question for X-chromosome inactivation, a process essential to female development that is governed, in eutherians, by the XIST lncRNA and its cis-regulators. To reach high resolution, we studied closely related primate species, spanning 55 million years of evolution. We show that the XIST regulatory circuitry has diversified extensively over such evolutionary timeframe. The insertion of a HERVK transposon has reshuffled XIST 3D interaction network in macaque embryonic stem cells (ESC) and XIST expression is maintained by the additive effects of the JPX lncRNA gene and a macaque specific enhancer. In contrast, JPX is the main contributor to XIST expression in human ESCs but is not significantly involved in XIST regulation in marmoset ESCs. None of these entities are however under purifying selection, which suggests that neutrally evolving non-coding elements harbour high adaptive potentials.

sample_organism:
Callithrix jacchus
Macaca mulatta

platform_organism:
Callithrix jacchus
Macaca mulatta

overall_design:
Whole genome sequencing of two female embryonic stem cell lines from macaque (rhESC-LYON1) and marmoset (CMES-40)

Re-analyzed Sample GSM4610404 was submitted to GEO previously in GSE152259.

first: Cazottes

last: Emmanuel


title: Prostaglandin E2-EP2/EP4 signaling induces the tumor-infiltrating Treg phenotype for tumor growth [nTreg]

city: Kyoto

first: Ryuma

last: Matsuura

address: 53 Kawara-cho, Shogoin, Sakyo-ku, Kyoto City,

institute: Kyoto University

summary: Foxp3+ regulatory T cells (Tregs) heavily infiltrate malignant tumors and restrict anti-tumor immunity. These tumor-infiltrating Tregs (TI-Tregs) adopt a distinct phenotype by expressing a unique set of genes including those encoding various co-stimulatory and co-inhibitory molecules. This TI-Treg gene expression signature is conserved in TI-Tregs across species and the types and stages of tumors, suggesting the presence of a common inducing mechanism or mechanisms in tumor microenvironment (TME). However, identity of such a mechanism remains elusive. Here, we show that prostaglandin E2 (PGE2) produced in TME directly acts on its receptor EP2/EP4 on Tregs to induce the TI-Treg phenotype. Indeed, PGE2 added to TCR-activated Tregs induces a set of genes, many of which are included in the reported TI-Treg signature genes, in both induced Tregs (iTregs) and naturally occurring Tregs (nTregs), in a manner dependent on EP2 and EP4 via cAMP-PKA pathway. This is not limited to phenotypic changes, as EP4 agonist-treated Tregs exhibit potent suppressive activity to CD8+ T cells and strongly inhibit their proliferation and survival. Consistently, selective loss of EP2 and EP4 in mouse Tregs and pharmacological inhibition of EP2 and EP4 reduce expression of those genes in Tregs infiltrating LLC1 mouse syngeneic tumor, and significantly delay the tumor progression. In human FOXP3+iTregs, the expression of Treg signature genes, FOXP3, CD25 and CTLA4 as well as a typical TI-Treg signature gene, 4-1BB are significantly upregulated by PGE2-EP4 signaling. Furthermore, analysis of scRNA-seq of nasopharyngeal cancer patients demonstrates preferential expression of the TI-Treg signature genes in Tregs infiltrating the PTGS2hi tumor group compared to the PTGS2lo tumor group. These findings suggest that PGE2-EP2/EP4 signaling is one of the molecular mechanisms inducing the TI-Treg phenotype in TME.

overall_design: mRNA profiles of Foxp3+ iTreg and nTreg treated in vitro with PGE2 and an EP4 agonist, respectively, and tumor-infiltrating Treg sorted ex vivo from LLC1 tumor-bearing control mice and Treg-specific EP2/EP4 KO mice.

first: Shuh

last: Narumiya


title: Extensive remodelling of XIST regulatory networks during primate evolution [Capture Hi-C]

sample_organism:
Macaca mulatta
Pan troglodytes

platform_organism:
Macaca mulatta
Pan troglodytes

overall_design: capture HiC in primed rhesus ESCs and chimpanzee iPSC. Two independent replicates were analysed.

first: Villacorta

last: Laura


title: Innate immune and metabolic signaling retain damaged mitochondria at cell membranes for mitoxyperilysis

city: Memphis

first: Thirumala-Devi

last: Kanneganti

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Innate immune activation coupled with metabolic disruptions play critical roles in many diseases, often leading to mitochondrial dysfunction and oxidative stress that drive pathogenesis. However, mechanistic regulation under these conditions remains poorly defined. Here, we report a distinct lytic cell death mechanism induced by innate immune signaling and metabolic disruption, independent of caspase activity and previously described pyroptosis, PANoptosis, necroptosis, ferroptosis, and oxeiptosis. Instead, mitochondria undergoing BAX/BAK1/BID-dependent oxidative stress maintained prolonged plasma membrane contact, leading to local oxidative damage, a process we termed mitoxyperiosis. This process then caused membrane lysis and cell death, mitoxyperilysis. mTORC2 regulated the cell death, and mTOR inhibition restored cytoskeletal activity for lamellipodia retractions to mobilize mitochondria away from the membrane, preserving integrity. Activating this pathway in vivo regressed tumors in an mTORC2-dependent manner. Overall, our results identify a lytic cell death modality in response to the synergism of innate immune signaling and metabolic disruption.

overall_design: To evaluate the expression profiles in bone marrow derived macrophages under different stimulations (media, CS, LPS, LPS+CS and LPS+CS+Torin), BMDMs were stimulated as indicated for 9hours and RNA was extracted by trizol and subject to sequencing.

first: Yaqiu


title: Extensive remodelling of XIST regulatory networks during primate evolution [Cut & Run]

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: CUT&RUN for H3K4me3, H3K4me1 and H3K27ac histone modifications and for CTCF in primed rhesus ESCs and for H3K4me1 and H3K27ac histone modifications in primed human ESCs. Two independent replicates were analysed.

first: Charbel

last: Alfeghaly


title: RNA sequencing of fresh tumor tissues from B16F10 tumor bearing mice treated with saline or M44 vaccine

summary: To further reveal the immune regulatory effects of MHC II-restricted vaccines on TME, bulk RNA sequencing (bulk RNA-seq) was performed to analyze the overall immune signal transformation. Differential gene expression analysis recognized a total of 1695 upregulated and 343 downregulated genes on the M44 vaccination. Specifically, a higher expression of CD74, H2-Ab1, H2-Eb1, H2-Aa was observed in the vaccinated group, indicating the active MHC class II antigen processing and presentation in tumors. The ssGSEA method was used to quantify RNA-seq data of each sample and the GO_BP (Biological Process of Gene Ontology) term scores were calculated. The results indicated that the majority of the terms within high ssGSEA scores were related to both adaptive and innate immune-related processes.We then sorted the top 300 differently upregulated genes to generated pathway enrichment analysis and clustered the pathways into 20 categories based on functional relevance. Interestingly, the majority of categories were related to the activation of antitumor immune response, such as “inflammatory response” “leukocyte activation” “antigen processing and presentation” “leukocyte migration” and “phagocytosis”. Moreover, immune infiltration estimations showed increased infiltration levels of T cells, CD8+ T cells, NK cells, memory B cells and monocytes/macrophages.

overall_design: B16F10 tumor bearing mice were subcutaneously injected with two doses of saline or M44 vaccine (50 µg M44 peptide formulated with 20 μg CpG) on day 2 and 8, and tumors were collected by euthanizing on day 10 (n=5 mice per group) . Fresh tumor tissues were processed for bulk RNA-seq to reveal the immune regulatory effects of MHC II-restricted vaccines on tumor microenvironment.


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

status: Public on Nov 27 2025

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To identify potential contaminating gRNAs, we adapted a gRNA sequencing assay based on an established SMARTer smRNA sequencing technology. We evaluated five research-grade gRNAs from three synthetic gRNA manufacturer suppliers (A, B and C). We detected the presence of contaminating gRNAs in CBLB and CIITA gRNAs from supplier A (batch 1), with frequency ranging from 0.09% to 2.71%.

overall_design: guide-RNA (gRNA) sequencing of commerically synthesized gRNAs from multiple manufacturers (suppliers A, B, and C) using modified SMARTer smRNA-seq technology.

first: Varun

last: Katta

first: Yichao

last: Li


title: Extensive remodelling of XIST regulatory networks during primate evolution [ATAC-Seq]

overall_design: Chromatin accessibility in primed rhesus ESCs studied by ATAC-seq on primed rhESCs replicates.