title: Chromatin loops are an ancestral hallmark of the animal regulatory genome [DAP-seq]

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

institute: Centre for Genomic Regulation (CRG)

summary: We characterised the genome organization in non-bilaterian animals (sponge Ephydatia muelleri, ctenophores Mnemiopsis leidyi and Hormiphora californensis, placozoans Trichoplax adhaerens and Cladtertia collaboinventa, and cnidarian Nematostella vectensis) and close unicellular relatives (ichthyosporeans Sphaeroforma arctica, filasterean Capsaspora owczarzaki and choanoflagellate Salpingoeca rosetta) by combining high-resolution chromosome conformation capture (Micro-C) with profiling of chromatin marks (ChIP-seq), accessible genomic regions (ATAC-seq) and gene expression (MARS-seq).

overall_design: DAP-seq libraries were generated from native genomic DNA fragments or PCR-amplified DNA fragments lacking DNA methylation, which were bound by N-terminal HALO-tagged fusion proteins of CTEP1 and CTEP2.

first: Iana

middle: V

last: Kim

first: Ewa

last: Ksiezopolska


title: Clinical significance of p53 abnormal expression in low-grade endometrial cancer

status: Public on Mar 11 2025

city: Fukuoka

first: Kazuhisa

last: Hachisuga

address: 1-1, Maidashi 3-chome

country: Japan

institute: Kyushu University Hospital

type: Expression profiling by high throughput sequencing

summary: We conducted the present study to reveal the clinical significance of p53 abnormal immunohistochemical expression in low-grade endometrial cancer.

overall_design: We obtained nine frozen samples of endometrial cancer (low-grade endometrial cancer with p53 wild-type expression: n=3, low-grade endometrial cancer with p53 abnormal expression: n=3, and high-grade endometrial cancer: n=3). RNA-sequencing was performed for each sample.

first: Minoru

last: Kawakami

first: Hiroshi

last: Tomonobe

first: Shoji

last: Maenohara

first: Keisuke

last: Kodama

last: Yagi

first: Masafumi

last: Yasunaga

first: Ichiro

last: Onoyama

first: Kazuo

last: Asanoma

first: Hideaki

last: Yahata

first: Yoshinao

last: Oda

first: Kiyoko

last: Kato


title: Transcriptomic Analysis of the m6A Reader YTHDF2 in the Maintenance and Differentiation of Human Embryonic Stem Cells

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

country: China

institute: Zhejiang University

summary: As the most abundant internal modification on mRNAs, N6-methyladenosine (m6A) has been discovered to be involved in different biological processes. Mostly determined by m6A methyl-transferases (m6A writers) and demethylases (m6A erasers), different cell types possess differential m6A profiles of transcriptomes. However, the interpretation of the m6A-encoded epitranscriptomic information needs m6A readers to bind and recruit different machinery for regulating the target mRNAs, which in turn, may regulate cell fates. The functions of the m6A readers in the regulation of the maintenance and differentiation of human embryonic stem cells (hESCs) remain largely unknown. In this study, we deleted the whole genomic region of the m6A reader YTHDF2, and discovered that YTHDF2 is dispensible for the maintenance, but probably important for the differention of hESCs, especially for the differentiation towares ectoderm. Furthermore, we identified ROBO1 as a potential target gene by DF2 in regulating hESC to neuroectoderm differentiation. This study reveals the potential roles of the m6A reader DF2 in regulating the specification of neuroectodermal cell fate.

overall_design: hESCs (WT_hESCs and hESCs_DF2-KO) were cultured in Nuwacell® ncTarget hPSC Medium (Nuwacell, RP01020) on Matrigel-coated plates. Endoderm (WT_endoderm and endoderm_DF2-KO) and mesoderm (WT_mesoderm and mesoderm_DF2-KO) cells were induced from hESCs by culturing in STEMdiff™ Definitive Endoderm Medium (STEMCELL, 05110) or STEMdiff™ Definitive Mesoderm Medium (STEMCELL, 05220) for 4 days. Similarly, STEMdiffTM Neural induction medium supplemented with SMADi (STEMCELL, 8581) were used for induction and culture of ectoderm (WT_ectoderm and ectoderm_DF2-KO) cells, but a longer induction of around 13 days was applied.  hESCs with ADAR expression (hESC_ADAR and hESC_DF2-ADAR) were induced with doxcycyline for 24 hours before its RNA got extracted.

first: Boshi

last: Feng

first: Yanxi

last: Chen

first: Jin

last: Zhang

first: Lingling

last: Tong

first: Xiaohan

last: Lyu

first: Aaron

middle: T

last: Irving

first: Di


title: Chromatin loops are an ancestral hallmark of the animal regulatory genome [ChIP-seq]

first: Arnau

last: Sebé-Pedrós

country: Spain

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Ephydatia muelleri
Trichoplax adhaerens
Mnemiopsis leidyi
Nematostella vectensis
Sphaeroforma arctica
Capsaspora owczarzaki
Salpingoeca rosetta
Cladtertia collaboinventa

overall_design: ChIP-seq libraries were generated for histone H3, as well as histone modifications H3K4me2 and H3K4me3 for the non-bilaterian animal lineages (sponge Ephydatia muelleri, ctenophores Mnemiopsis leidyi, placozoans Trichoplax adhaerens and Cladtertia collaboinventa, and cnidarian Nematostella vectensis)  and close unicellular relative of animals (ichthyosporean Sphaeroforma arctica and choanoflagellate Salpingoeca rosetta).

first: Cristina

last: Navarrete

first: Iana

last: Kim


title: Chromatin loops are an ancestral hallmark of the animal regulatory genome [ATAC-seq]

sample_organism:
Ephydatia muelleri
Mnemiopsis leidyi

platform_organism:
Ephydatia muelleri
Mnemiopsis leidyi

overall_design: ATAC-seq libraries from Mnemiopsis leidyi and from FACS sorted choanocytes of Ephydatia muelleri

first: Marta

last: Iglesias


title: Enforced expression of miR-342 promotes an inflammatory phenotype in liver metastasis-associated macrophages [scRNA-seq]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Liver macrophages are crucial to maintain liver homeostasis. However, upon metastatic seeding, cancer cells co-opt these macrophages to act as tumor-associated macrophages (TAMs), facilitating tumor growth and invasiveness. MicroRNAs (miRNAs) are key regulators of TAM pro-tumoral functions, thus modulating their expression in liver macrophages may constitute a novel approach for liver metastasis immunotherapy. In this study, we identify a myeloid specific miRNA, miR-342-3p, and investigate its anti-tumoral function in liver macrophages in the context of colorectal cancer liver metastasis (CRLM). To this aim, we harnessed lentiviral vectors (LV) to infer and modulate miRNA activity in liver macrophages in vitro and in vivo. We found that miR-342-3p was highly active in macrophages in the healthy liver, but downregulated in proximity to CRLM. Rescuing miR-342-3p activity through enforced miRNA expression induced a pro-inflammatory phenotype in liver macrophages, which was associated to reduced CRLM growth. Transcriptomic analysis revealed Slc7a11, a cysteine-glutamate antiporter associated with TAM pro-tumoral functions, as a major miR-342-3p target. Overall, our findings highlight the potential of miR-342-3p in TAM reprogramming to enhance anti-tumoral immunity.

overall_design: mOrange+ positive cells were isolated from mouse liver and tumor by FACS and analysed for scRNAseq. These mice were bearing AKTPF liver metastases and were treated with Lentiviral vectors driving the expression of fluorescent marker mOrange together with miR-342-3p or its mutated version miR-mut (as control)

first: Chiara

last: Bresesti

first: Marco

last: Monti

first: Stefano

last: Beretta

first: Luigi

last: Naldini

first: Mario

middle: L

last: Squadrito


title: Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 [WGBS]

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

country: Canada

institute: IRCM

type: Methylation profiling by high throughput sequencing

summary: Pioneer transcription factors have the unique ability to open chromatin at enhancers to implement new cell fates. They also provide epigenetic memory through demethylation of enhancer DNA but the underlying mechanisms remain unclear. We now show that the pioneer PAX7 triggers DNA demethylation using two replication-dependent mechanisms, including direct PAX7 interaction with the UHRF1-DNMT1 complex that is responsible for DNA methylation maintenance. PAX7 binds to UHRF1 and prevents its interaction with DNMT1, thus blocking activation of its enzyme activity. The TET DNA demethylases also contribute to the replication-dependent loss of DNA methylation. Thus, PAX7 hijacks UHRF1 to block activation of DNMT1 after replication leading to loss of DNA methylation by dilution and the process is accelerated by the action of TET demethylases.

overall_design: Whole genome bisulfite sequencing (WGBS) in mouse corticotrope AtT-20 cells with ER-Pax7 ectopic expression. Treated with tamoxifen (tam, ER-Pax7 activation) or mimosine (mim, cell cycle arrest).

first: Alexandre

last: Mayran

first: Arthur

last: Gouhier

first: Yves

last: Gauthier

first: Nawal

last: Hajj Sleiman

first: Samir

last: Merabet

first: Micheal

last: Dukatz

first: Pavel

last: Bashtrykov

first: Albert

last: Jeltsch

first: Haig

last: Djambazian

first: Shu-Huang

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: CD301b+ monocyte-derived dendritic cells mediate resistance to radiotherapy

city: Stanford

first: Sirimuvva

last: Tadepalli

state: CA

address: 299 Campus Drive

country: USA

institute: Stanford University

summary: Monocytes infiltrating tumors acquire various states that distinctly impact cancer treatment. Here, we show that resistance of tumors to radiotherapy (RT) is controlled by the accumulation of monocyte-derived dendritic cells (moDCs). These moDCs are characterized by the expression of CD301b and have a superior capacity to generate regulatory T cells (Tregs). Accordingly, moDC depletion limits Treg generation and improves the therapeutic outcome of RT. Mechanistically, we demonstrate that granulocyte-macrophage colony-stimulating factor (GM-CSF) derived from radioresistant tumor cells following RT is necessary for the accumulation of moDCs. Our results unravel the immunosuppressive function of moDCs and identify GM-CSF as an immunotherapeutic target during RT.

overall_design: CD45 positive, lineage (CD3, NK1.1, Ly6G, CD19) negative cells from tumor were sorted from either radiation (20 Gy) treated or non-treated B16F1 tumors.

first: Derek

last: Clements

first: Juliana

last: Idoyaga


title: Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

status: Public on Mar 10 2025

city: Xiamen

first: Mengjun

last: Zhang

address: State Key Laboratory of Cellular Stress Biology

department: Department of biochemistry

institute: Xiamen university

summary: Nuclear speckles (NSs) are viscoelastic network fluids formed via phase separation coupled to percolation (PSCP). Intermolecular cross-links of SRRM2, a key scaffold of NSs lead to the emergence of system-spanning networks, although the physiochemical grammar governing SRRM2 PSCP remains poorly decoded. Here, we demonstrate that SRRM2 is extensively phosphorylated within the intrinsically disordered domain (IDR) that are prominently positively charged. Rather than attaching phosphate groups to specific sites, the purpose of phosphorylation is to create alternating charge blocks. Employing a suite of biophysical approach, we show that in contrast to the leading theories that charge blocks lower condensation threshold of biopolymers, this specific charge pattern does not markedly alter the percolation threshold of SRRM2 in cells. Instead, SRRM2 charge blocks intensify intra-network molecular interactions to modulate the material properties of mesoscopic SRRM2 condensates. We further identify casein kinase 2 (CK2) as the upstream enzyme to catalyze SRRM2 phosphorylation. Phosphorylation of SRRM2 IDR by CK2 facilitates NS relaxation under physiological condition, but can be employed to safeguard genome stability in times of DNA damage. Our findings reveal important regulatory mechanisms of charge blocks and functionality in modulating the material properties of biomolecular condensates in cells. We interpretate our observation in the theoretical framework of stickers-and-spacers model. In addition to the chemistry- or sequence-specific associative interaction, spacers (e.g. SRRM2 IDR) can also engage in charge pattern-specific molecular interactions, which are spatiotemporally regulated, to dictate the biophysical properties of percolated macromolecular assemblies.

overall_design: Stable cell lines were generated by co-transfection of Piggybac transposon vector and Piggybac transposase (Supper Piggybac Transposase). After 48h transfection, clonal populations of each cell line were obtained by flow cytometric cell sorting.  Established cell lines were grown as described above in medium.RNA seq were used to detecte the splicing changes.The splicing differences of piggybac-WT, piggybac-SA and piggybac-SD cell lines were compared.


title: Redox Regulation of Lung Endothelial PERK, Unfolded Protein Response (UPR) and Proliferation via NOX1: Targeted Inhibition as a Potential Therapy for PAH

city: Pittsburgh

first: Christian

middle: Jeffrey

last: Goossen

state: PA

address: 200 Lothrop Street

department: Molecular Pharmacology

institute: University of Pittsburgh

summary: Aims: Reactive oxygen species (ROS) play an important role in the pathogenesis of pulmonary arterial hypertension (PAH) and NADPH oxidases (NOXs) as sources of ROS are implicated in the development of the disease. We previously showed that NOX isozyme 1 (NOX1)-derived ROS contributes to pulmonary vascular endothelial cell (EC) proliferation in response to PAH triggers in vitro. However, whether and how NOX1 is involved in PAH in vivo have not been explored nor has NOX1 been examined as a viable and effective therapeutic disease target.                                                          Methods and Results: Herein, infusion of mice exposed to Sugen/hypoxia (10% O2) with a specific NOX1 inhibitor, NOXA1ds, delivered via osmotic minipumps (i.p.), significantly suppressed pathological changes in hemodynamic parameters characteristic of PAH. Furthermore, lungs of human patients with idiopathic PAH (iPAH) and exploratory RNA-seq analysis of hypoxic human pulmonary ECs, in which NOX1 was suppressed, were probed. The findings showed a clear indication of NOX1 in the promotion of both protein disulfide isomerase (PDI) and the unfolded protein response (UPR; in particular, the PERK arm of the pathway including eIF2α and ATF4) leading to proliferation. In aggregate, these results are consistent with a causal role for NOX1 in the development of mouse and human PAH and reveal a novel and mechanistic pathway by which NOX1 activates the UPR response during EC proliferation.                                                                                Conclusion: NOX1 promotes phenotypic changes in ECs that are pivotal to proliferation and PAH through activation of the UPR. Taken together, our results are consistent with selective inhibition of NOX1 as a novel modality for attenuating PAH

overall_design: Human pulmonary artery endothelial cells (HPAECs) were transfected with scramble (Scr) or NOX1 (siNOX1) siRNA for 48 h before cells were exposed to Normoxia (Nx, 21% O2) or Hypoxia (Hx, 1% O2) for 24 h. At the end of treatment, cells were lysed for RNA isolation and purification (RNeasy MinElute cleanup kit, QIAGEN). Total RNA samples were sent to NovoGene (Sacramento, CA) for mRNA library preparation and sequencing. Unstranded and paired 150 bp sequencing data was filtered, trimmed, aligned to the human reference genome (GRCh38), and counted on the gene level.

middle: J

first: Alex

last: Kufner

first: Christopher

middle: M

last: Dustin

first: Imad

last: Al Ghouleh

first: Shuai

last: Yuan

first: Adam

middle: C

last: Straub

first: John

last: Sembrat

first: Jeffrey

last: Baust

first: Delphine

last: Gomez

first: Damir

last: Kračun

first: Patrick

last: Pagano


summary:
CD301b+ monocyte-derived dendritic cells mediate resistance to radiotherapy
The objective of this experiment was to evaluate the transcriptional changes in DC2s and TAMs cells following radiation in B16F1 tumors

overall_design: Two sorted cell populations run triplicate collected at 0 days post radiation (0 dpRT) or 5 days post radiation (5 dpRT). Radiation dosage was 20Gy. Control/nontreated samples are marked as 0dpRT.


title: Activated T cells break tumor immunosuppression by macrophage re-education

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49 box 912

department: Center for Cancer Biology

country: Belgium

institute: VIB - KULeuven

summary: Here, we observe that in human and murine melanomas, T-cell activation abates hematopoietic prostaglandin-D2 synthase (HPGDS) transcription in tumor-associated macrophages (TAMs) through TNFα signaling. Mechanistically, HPGDS installs a Prostaglandin-D2 (PGD2) autocrine loop in TAMs via DP1 and DP2 activation that sustains their pro-tumoral phenotype and promotes paracrine inhibition of CD8+ T cells via a PGD2-DP1 axis. Genetic or pharmacologic HPGDS targeting induces anti-tumoral features in TAMs and favors CD8+ T-cell recruitment, activation, and cytotoxicity, altogether sensitizing tumors to αPD1. Conversely, HPGDS overexpression in TAMs or systemic TNFα blockade sustains a pro-tumoral environment and αPD1-resistance, preventing the downregulation of HPGDS by T cells. Congruently, patients and mice resistant to αPD1 fail to suppress HPGDS in TAMs, reinforcing the evidence that circumventing HPGDS is necessary for efficient αPD1 treatment. Overall, we disclose a mechanism whereby T-cell activation controls the innate immune system, and we suggest HPGDS/PGD2 targeting to overcome immunotherapy resistance.

overall_design: Bulk RNA sequencing of in vivo sorted Hpgds KO and control tumor-associated macrophages from YUMM 1.7 tumor bearing mice.

first: Rosa

last: Trotta

first: Silvia

last: Rivis

first: Shikang

last: Zhao

first: Marie-Pauline

last: Orban

first: Sarah

last: Cafarello

first: Iris

last: Charatsidou

first: Joanna

last: Poźniak

first: Jonas

last: Dehairs

first: Lotte

last: Vanheer

first: Carlos

middle: A

last: Pulido-Vicuña

first: Veerle

last: Boecxstaens

first: Oliver

last: Bechter

first: Francesca

last: Bosisio

first: Johannes

last: Swinnen

first: Jean-Christophe

last: Marine


title: Light quantity impacts early response to cold and cold acclimation in young leaves of Arabidopsis

city: Gent

first: Marieke

last: Dubois

address: Technologiepark 71

institute: PSB, Vlaams Instituut voor Biotechnologie (VIB)

summary: Plant reactions to stress vary with development stage and fitness. This study assessed the relationship between light and chilling stress in Arabidopsis acclimation. By analyzing the transcriptome and proteome responses of expanding leaves subjected to varying light intensity and cold, 2251 and 2064 early response genes and proteins were identified, respectively. Many of these represent as yet unknown part of early response to cold, illustrating development-dependent response to stress and a duality in plant adaptations. While standard light promoted photosynthetic upregulation, plastid maintenance, and increased resilience, low light triggered a unique metabolic shift, prioritizing ribosome biogenesis and lipid metabolism and attenuating expression of genes associated with plant immunity. The comparison of early response in young leaves with that in expanded ones showed striking differences, suggesting a sacrifice of expanded leaves to support young ones. Validations of selected DEGs in mutant background confirmed a role of HSP90-1, transcription factor FLZ13, and Phospholipase A1 (PLIP) in response to cold, and the PLIP family emerged as crucial in promoting acclimation and freezing stress tolerance. The findings highlight the dynamic mechanisms that enable plants to adapt to challenging environments and pave the way for the development of genetically modified crops with enhanced freezing tolerance.

overall_design:
To examine the influence of low light intensity (20 µmol-2.s-1) on the chilling stress response, we utilized A. thaliana plants, which were grown under standard light conditions (100 µmol-2.s-1) until they obtained developmental stage L1.06, and subsequently subjected to the following conditions for 3 hours: (i) S-PPFD at 100 µmol.m-2.s-1, 21°C (S); (ii) low-PPFD at 20 µmol.m-2.s-1, 21°C (LL); (iii) S-PPFD at 4°C (C); and (iv) low-PPFD at 4°C (CLL). Next, we have performed RNA-seq analyses and comparative gene profiles of LL, C and CLL.

For more details, see manuscript published in Plant Cell & Environment (Luklova et al., 2025).

first: Marketa

last: Luklova

first: Michaela

last: Kameniarova

first: Klara

last: Plackova

first: Jan

last: Novak

first: Romana

last: Kopecka

first: Michal

last: Karady

first: Jaroslav

last: Pavlu

last: Skalak

first: Sunita

last: Jindal

first: Ljiljana

last: Tubic

first: Zainab

last: Quddoos

first: Ondrej

first: Dirk

last: Inze

first: Martin

last: Cerny


title: Gene expression profile at single cell level of intraepithelial neutrophils (IENs) and lamina propria neutrophils (LPNs) of the colon from dextran sulfate sodium (DSS)-treated mice

city: Chicago

first: Ronen

last: Sumagin

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptional differences of spatially-separated populations of neutrophils in the inflamed colon.

overall_design: Colonic IENs and LPNs from DSS-treated C57BL/6J mice were isolated by fluorescence-activated cell sorting (FACS) based on cell surface neutrophil markers.

first: Lenore

middle: K

last: Yalom

first: Triet

last: Bui


title: Chromatin loops are an ancestral hallmark of the animal regulatory genome [MARS-seq]

first: Arnau

last: Sebé-Pedrós

overall_design: Single-cell transcriptome analysis (using MARS-seq) of Ephydatia muelleri choanocyte cells

first: Iana

last: Kim


title: Molecular mechanism of mutations in Microprocessor causing Wilms tumors [miRNA]

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: The Microprocessor complex, consisting of DROSHA and DGCR8, is essential for miRNA maturation and gene regulation. Mutations in these proteins are associated with Wilms tumor (WiT), a common pediatric kidney cancer. To explore the impact of these mutations on WiT pathogenesis, we developed the Microsensor system, a novel tool for dynamically monitoring Microprocessor activity in human cells. Using this system, we engineered HEK293T cells to express the DGCR8-E518K mutation, which was previously identified in WiT patients. Our results show that this mutation significantly impairs the Microprocessor's ability to process specific pri-miRNAs in vitro and alters the miRNA expression profiles. This study demonstrates the utility of the Microsensor system in investigating the molecular mechanisms underlying mutations related to the Microprocessor complex.

overall_design: RNA sequencing

first: Sheng

last: Bao

first: Cong-Truc

last: Le

first: Thi-Nhu-Y

first: Tuan-Anh

last: Nguyen


title: Molecular mechanism of mutations in Microprocessor causing Wilms tumors [mRNA]


title: Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and regulation of IL33 via Alu elements (part 3)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Idiopathic pulmonary fibrosis (IPF) causes remodelling of distal lung, leading to respiratory failure. Pulmonary remodelling is characterised histologically not only by fibrosis but by also appearance of basal cells, yet the involvement of basal cells to IPF pathogenesis remains unclear. Here, we focus on the long non-coding RNA MIR205HG highly expressed in basal cells by single-cell RNA sequencing, to elucidate their role in IPF. Through RNA sequencing of genetic manipulations using primary cells and IPF-derived airway organoids, we uncovered MIR205HG to regulate IL33 expression. Mechanistically, the AluJb element of MIR205HG plays a key role in IL33 expression. In addition, we successfully identified a small molecule that targets this AluJb element and decreases IL33 expression. IL33 is known to induce ILC2, and MIR205HG expression positively correlated with the number of ILC2 in IPF patients. Collectively, these findings provide insights into the contributing mechanisms of basal cells to IPF and potential therapeutic targets.

overall_design: To compare gene expression profiles between MIR205HG overexpressing alveolar organoids (#1_MIR205HG OE, #2_MIR205HG OE and #3_MIR205HG OE) and control cells (#1_NV, #2_NV and #3_NV), total RNA was extracted from the cells.

first: Tsuyoshi

last: Takashima

last: Okuzaki

first: Eiichi

last: Morii


title: Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and regulation of IL33 via Alu elements (part 2)

overall_design: To compare gene expression profiles between MIR205HG knock down NHBE cells (sgMIR205HG_#1, sgMIR205HG_#2) and control cells (NC and NV), total RNA was extracted from the cells.


title: Exploratory Transcriptomic Analysis of Choloepus didactylus

city: Shibuya-ku

first: David

middle: D

last: Ordinario

state: Tokyo

address: 26F Yebisu Garden Place Tower, 4-20-3 Ebisu

institute: Genesis Healthcare Co.

summary: Sloths, a group of xenarthran mammals comprised of 6 distinct species, have been the focus of much physiological animal research due to their extremely slow metabolisms, deliberate movements, and their status as a species relatively unchanged for over 26 million years. However, despite all the effort aimed at understanding these unique characteristics, the sloth genome remains largely unexplored. Due to the link between genetics and observed traits, such an investigation could potentially lead to insights regarding the genetic basis of sloth behaviors and characteristics. In this exploratory investigation, we performed genomic and transcriptomic analysis of a female Choloepus didactylus (Linnaeus’s Two-Toed Sloth). Transcriptome analysis of peripheral blood mononuclear cells (PBMCs) showed gene expression levels in two-toed sloths, which are conjectured to be responsible for many of the unique features of two-toed sloths and opens a path towards future exploratory research into specific gene and protein functions tied to the unique characteristics of the sloth species.

overall_design: To perform transcriptome analysis on the two-toed sloth, we extracted peripheral blood mononuclear cells (PBMCs) from sloth blood samples, fractionaed them by density gradient configuration, isolated the total RNA, prepared libraries, then performed sequencing.

first: Ozeki

last: Takeshi

first: Nakano

last: Yuka


title: Chromatin loops are an ancestral hallmark of the animal regulatory genome [Micro-C]

sample_organism:
Ephydatia muelleri
Trichoplax adhaerens
Mnemiopsis leidyi
Nematostella vectensis
Sphaeroforma arctica
Capsaspora owczarzaki
Salpingoeca rosetta
Hormiphora californensis
Cladtertia collaboinventa

overall_design: Micro-C chromosome conformation capture libraries were generated for the non-bilaterian animals (sponge Ephydatia muelleri, ctenophores Mnemiopsis leidyi and Hormiphora californensis, placozoans Trichoplax adhaerens and Cladtertia collaboinventa, and cnidarian Nematostella vectensis)  and close unicellular relative of animals (ichthyosporeans Sphaeroforma arctica, filasterean Capsaspora owczarzaki and choanoflagellate Salpingoeca rosetta).


title: Modeling PAX5P80R mutation reveals Hif2a as a common oncogenic relay in B-cell acute lymphoblastic leukemia

city: Toulouse

first: Bastien

last: Gerby

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

summary: The transcription factor PAX5 is a major target of genetic alterations in human B-cell precursor acute lymphoblastic leukemia (B-ALL). Among the alterations, the P80R mutation affecting the DNA-binding domain represents the most frequent PAX5 point mutation in B-ALL. In contrast to other somatic PAX5 mutations, PAX5P80R defines a distinct B-ALL subtype characterized by a unique transcriptional program. Here, we aimed to develop a model to elucidate the mechanism by which PAX5P80R perturbs normal B-cell differentiation and the oncogenic relays involved in PAX5P80R-driven malignant progression. A retroviral complementation approach of Pax5-deficient murine fetal liver cells demonstrated at the functional and molecular levels that PAX5P80R failed to rescue definitive B-cell commitment but maintained the repression of T-cell development. Moreover, PAX5P80R eventually led to clonal B-ALL transformation after transplantation through the acquisition of secondary mutations in genes involved in the JAK/STAT and RAS/MAPK pathways. Finally, transcriptomic analyses combined with pharmacological investigation revealed ectopic activation of HIF2α as a common feature of B-ALL and identified acriflavine as a potent drug against B-ALL. Hence, this study provides a strategy to model the multistep process of B-ALL and sheds light on the biological mechanism by which PAX5P80R mutation leads to leukemia.

overall_design: To characteize PAX5P80R-induced B-ALLs in vivo, we compared by RNA-sequencing the gene expression profiles of purified PAX5 P80R GFP+ B-ALL cells from four primary recipients (#1300, #1302, #1301, #1308) with purified CLP/pre-pro-B cells from Pax5-/- FLs (n=4) and with purified pro-B/pre-BI cells from Pax5+/+ FLs (n=4)

first: Gerby

last: Bastien

first: Bayet

last: Manon


title: Selective inhibition of matrix mechanosensing in stromal cells attenuates cardiovascular fibrosis

status: Public on Mar 08 2025

city: Palo Alto

first: Sangkyun

last: Cho

state: California

address: 240 Pasteur Dr, Room 3200, Biomedical Innovations Building

summary: Matrix-derived biophysical cues are known to regulate the activation of fibroblasts and their subsequent transdifferentiation into myofibroblasts, but whether modulation of these signals can suppress fibrosis in intact tissues remains unclear, particularly in the cardiovascular system. We have employed single-cell/nucleus RNA sequencing of myofibroblasts differentiated from induced pluripotent stem cell-derived cardiac fibroblasts (iPSC-CFs), as well as mouse transverse aortic constriction (TAC) hearts to investigate whether modulation of matrix mechanosensing, in concert with TGF-beta inhibition, can potentiate the de-activation of fibrosis-promoting cardiac stromal populations in vitro and in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In vitro samples (scRNA-seq): after 48h of treatment, aSMA-expressing myofibroblasts derived from iPSC-CFs were were harvested (n = 3 wells pooled into a single library per condition) for droplet-based scRNA-seq using the 10X Genomics platform. In vivo samples (snRNSA-seq): following 4 weeks of TAC and 2 weeks of subsequent drug treatment, apical tissue samples were harvested from male C57BL/6 mice (n = 3 animals pooled into a single sample per experimental group). Joint snRNA- and snATAC-seq libraries were prepared using the 10X scMultiome platform, but only the snRNA-seq (GEX) libraries were used for this study.

first: Siyeon

last: Rhee


title: Three-dimensional genome structures of single mammalian sperm [GAM]

status: Public on Mar 09 2025

city: Beijing

first: Heming

last: Xu

address: Yiheyuan Road

institute: Peking University

summary: The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is fundamentally different and not as well understood. In this study, we resolved the 3D whole-genome structures of a single mammalian sperm cell using an enhanced chromosome conformation capture assay. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discovered that sperm genomes are divided into chromosomal territories and A/B compartments, similarly as somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells.

overall_design: Use Genome Architecture Mapping (GAM) experiments o analyze the three-dimensional architecture of mammalian sperm nuclei

first: Yi

last: Chi

first: Changjian

last: Yin

first: Cheng

last: Li


title: An Affinity-based Depletion Strategy for Evaluating the Effects of Ergothioneine on Bacterial Physiology

city: West Haven

first: Anna

middle: B

last: Seminara

state: Connecticut

address: 840 West Campus Drive

department: MCDB

institute: Yale University

summary: Ergothioneine (EGT) is a thiol-based antioxidant synthesized by certain fungal and bacterial species that is prevalent in the human diet. Recently, an EGT-specific transporter, EgtUV, was discovered in bacteria that are incapable of EGT biosynthesis, including the gastric pathogen Helicobacter pylori. However, EGT is naturally abundant in the complex media required to culture H. pylori and many other host-associated microbes, complicating efforts to understand how this small molecule influences microbial physiology. Using the solute-binding domain of H. pylori EgtUV, we generated an EGT-chelating resin that depletes EGT from nutrient-rich media. We determined that wild-type H. pylori requires EGT to outcompete a transporter-deficient strain in vitro. Furthermore, EGT induces expression of outer-membrane proteins that regulate intracellular EGT content upstream of the inner-membrane-localized EgtUV transporter. Our work establishes a method for tuning exposure to an abundant antioxidant in vitro, enabling future studies of EGT in diverse bacterial strains and microbial communities.

overall_design: We investigated transcriptomic changes in WT H. pylori PMSS1 grown in EGT-depleted (EgtU-WT-resin-treated) vs. EGT-replete (EgtU-Y390A-resin-treated) culture media in biological triplicate to assess the effects of EGT on gene expression. We first used our EgtUWT- or EgtUY390A-resin to treat H. pylori culture media (Brucella Broth + 10% (v/v) heat-inactivated fetal bovine serum (FBS); "BB10") and verified EGT depletion from EgtUWT-treated BB10 using liquid-chromatography mass-spectrometry (LC-MS). WT PMSS1 H. pylori were then cultured in EgtU-WT-resin-treated and EgtU-Y390A-resin-treated BB10, and samples were collected at 8 h, 21 h, and 24 h for RNA extraction and transcriptomic analysis (RNA-seq).

first: Stavroula

last: Hatzios


title: Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation [scRNA-seq]

city: La Jolla

first: Maayan

last: Baron

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in >70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation.

overall_design: Melanoma tumors were collected post-operatively from two patients who consented and signed IRB. To obtain single-cell suspensions, samples were washed in PBS and cut into small pieces (4-5 mm3) followed by dissociation using the Miltenyi human tumor dissociation kit according to manufacturer instructions. Red blood cells were depleted using ACK lysis buffer for 3 minutes. Dead cells were removed, if needed, using the Milyenty dead cell separator. Single cell encapsulation and library preparation were performed using the inDrop platform followed by sequencing on an Illumina NextSeq.


title: Microglia activation orchestrates CXCL10-mediated CD8+ T cell recruitment to promote aging-related white matter degeneration (fixed scRNA-seq)

status: Public on Mar 07 2025

city: Munich

first: Ruoqing

last: Feng

address: Feodor-Lynen-Strasse 17

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Aging is the major risk factor for neurodegeneration and associated with structural and functional alterations in white matter. Myelin is particularly vulnerable to aging resulting in white matter-associated microglia activation. In this study, we employed pharmacological and genetic approaches to investigate microglial functions related to aging-associated changes in myelinated axons of mice. Our results reveal that maladaptive microglia activation promotes the accumulation of CD8+ T cells, leading to degeneration of myelinated axons and subsequent impairment of brain function and behavior. We characterize glial heterogeneity and aging-related changes in white matter by single-cell and spatial transcriptomics and reveal elaborate glial-immune interactions. Mechanistically, we show that the CXCL10-CXCR3 axis is crucial for the recruitment and retention of CD8+ T cells in aged white matter, where they exert pathogenic effects. Our results indicate that myelin-related microglia dysfunction promotes adaptive immune reactions in aging and identify putative targets to mitigate their detrimental impact.

overall_design: The optic nerve were collect from mouse (adult, aged and PLX5622 treated aged) and analyzed by 10X Chromium Fixed RNA Profiling Reagent Kits.

first: Janos

last: Groh


title: Three-dimensional genome structures of single mammalian sperm [scHi-C]

overall_design: Develop a new optimized Hi-C experimental approach to analyze the three-dimensional architecture of mouse and human sperm nuclei.


title: Microglia activation orchestrates CXCL10-mediated CD8+ T cell recruitment to promote aging-related white matter degeneration

summary: Aging is the major risk factor for neurodegeneration and associated with structural and functional alterations in white matter. Myelin is particularly vulnerable to aging resulting in white matter-associated microglia activation. In this study, we employed pharmacological and genetic approaches to investigate microglial functions related to aging-associated changes in myelinated axons of mice. Our results reveal that maladaptive microglia activation promotes the accumulation of CD8+ T cells, leading to degeneration of myelinated axons and subsequent impairment of brain function and behavior. We characterize glial heterogeneity and aging-related changes in white matter by single-cell and spatial transcriptomics and reveal elaborate glial-immune interactions. Mechanistically, we show that the CXCL10-CXCR3 axis is crucial for the recruitment and retention of CD8+ T cells in aged white matter, where they exert pathogenic effects.  Our results indicate that myelin-related microglia dysfunction promotes adaptive immune reactions in aging and identify putative targets to mitigate their detrimental impact.

overall_design: The optic nerve were collect from mouse (adult, aged and PLX5622 treated aged) and analyzed by MERFISH.


title: RNAseq analysis of the mouse aorta in response to Estradiol, Estetrol and Tamoxifen

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290

summary: Aim: To compare the transcriptional responses to estradiol, estetrol and tamoxifen in the mouse descending aorta

overall_design: Descending thoracic aortaes mRNA profiles of 3 weeks treated wild type mice with estradiol, estetrol or tamoxifen, were generated by deep sequencing using  Illumina NovaSeq sequencer

first: Rana

last: Zahreddine

first: Morgane

last: Davezac

first: Mélissa

last: Buscato

first: Françoise

last: Lenfant

first: Jean-François

last: Arnal

first: Coralie

last: Fontaine


title: Resolution of inflammation in imprinted fibroblast-like synoviocytes establishes a transcriptomic signature that promotes endothelial cell dysfunction.

status: Public on Mar 06 2025

city: Atlanta

first: Pallavi

last: Bhattaram

address: 21 Ortho Ln

institute: Emory University

summary: Purpose: We analyzed RNA-seq from fibroblast-like synoviocytes obtained from TNF induced inflammatory arthritis mice. Our goal was to evaluate the gene expression signatures after the cessation of inflammatory conditions. Methods: We analyzed bulk RNA-seq from fibroblast-like synoviocytes from TNF induced inflammatory arthritis mice in diferent conditions: homeostasis (5% sucrose water for 3 weeks), inflammation (1mg/ml Doxycycline + 5% sucrose water for 3 weeks), resolution (1mg/ml Doxycycline + 5% sucrose water for 3 weeks and then stopped for next 3 weeks). Samples were sequenced to determine transcriptional changes and regulated processes. Results: paired-end reads were mapped to the mus musculus GRCm38.p3 genome assembly. RNA levels were normalized by RPKM and student's t-test. Conclusion: Despite the resolution of the inflammatory phase of arthritis, fibroblast-like synoviocytes showed a clear persistence of inflammatory transcriptomic expression. Our study highlighted that the persistent aggressive phenotype of fibroblast-like synoviocytes not only promotes inflammation and exacerbates joint damage but also triggers impaired endothelial cell functioning.

overall_design: Investigation of the possible mechanisms underlying the endothelial cell dysfunction induced by activated fibroblast-like synoviocytes in the resolution phase of TNF-induced inflammatory arthritis.

first: Surabhi

last: Gautam


title: Omics of FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

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

overall_design: Refer to individual Series


title: Gestational Exposure to Air Pollutants Perturbs Metabolic and Placenta-Fetal Phenotype

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary:
Introduction: Air pollution is detrimental to a pregnancy with adverse effects in mother and child.
It is also known to increase pregnancy complications including risk factors of gestational diabetes.
Methods: We investigated the impact of intra-nasal instilled air pollutants upon gestational day 16-19 maternal mouse cardiovascular and metabolic status, placental nutrient transporters, and placental-fetal size and morphology. To further unravel mechanisms, we also examined placental total DNA 5’-hydroxymethylation and bulk RNA sequenced gene expression profiles.
Results: Air pollution exposed pregnant mice were tachycardic, hyperglycemic, glucose intolerant and insulin resistant, with no major placental glucose and fatty acid transporter changes, except for a spatial disruption of cells expressing GLUT10 that imports L-dehydroascorbic acid in protecting against oxidative stress. Placentas revealed inflammatory cellular infiltration with associated cellular edema and necrosis, with a paucity of vascularity and hemorrhage. While individual fetal body weights increased, they suffered a reduction in brain cortical thickness. Placental total DNA 5’-hydroxymethylation was 2.5-fold higher, with perturbed gene expression profiles involving key metabolic, inflammatory, transcriptional, cellular polarizing and processing genes and pathways.
Discussion: We conclude that gestational exposure to air pollutants incites a maternal inflammatory response resulting in features of maternal gestational diabetes mellitus with altered placental gene expression with associated injury to the placental-fetal unit. Thus, air pollutants adversely impact the health of mother and offspring.

first: Amit

last: Ganguly

first: Bo-Chul

last: Shin

first: Marlin

last: Touma

first: Madhuri

last: Wadehra

first: Sherin

middle: U

last: Devaskar


title: CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines [ATAC-seq]

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

summary:
Introduction: Glioblastomas utilize malignant gene expression pathways to drive growth.  Many of these gene pathways are not directly accessible with molecularly targeted pharmacological agents. Chromatin-modifying compounds can alter gene expression and target glioblastoma growth pathways.  In this study, we utilize a systematic screen of chromatin-modifying compounds on a panel of patient-derived glioblastoma lines to identify promising compounds and their associated gene targets.
Methods: Five glioblastoma cell lines were subjected to a drug screen of 106 chromatin-modifying compounds representing 36 unique drug classes to determine the twelve most promising drug classes and the best candidate inhibitors in each class.  These twelve drugs were then tested with a panel of twelve patient-derived gliomasphere lines to identify growth inhibition and corresponding gene expression patterns.  Overlap analysis and weighted co-expression network analysis (WCGNA) were utilized to determine potential target genes and gene pathways.
Results: The initial drug screen identified twelve candidate pharmacologic agents for further testing.  Drug sensitivity testing indicated an overall high degree of variability between gliomasphere lines. However, CPI203 was the most consistently effective compound, and the BET inhibitor class was the most consistently effective class of compounds across the gliomasphere panel.  Correspondingly, most of the compounds tested had highly variable effects on gene expression between gliomasphere lines.  CPI203 stood out as the only compound to induce a consistent effect on gene expression across different gliomasphere lines, specifically down-regulation of DNA-synthesis genes.  Amongst the twelve tested cell lines, high expression of CDKN2A and CDKN2B distinguished more drug sensitive from more drug resistant lines.  WCGNA identified two oncogenic gene modules (FBXO5 and MELK) that were effectively downregulated by CPI203 (FBXO5) and ML228 (FBXO5 and MELK).
Conclusions: The bromodomain inhibitor CPI203 induced relatively consistent effects on gene expression and growth across a variety of glioblastoma lines, specifically down-regulating genes associated with DNA replication.  We propose that clinically effective BET inhibitors have the potential to induce consistent beneficial effects across a spectrum of glioblastomas.

overall_design: 156 samples (12 cell lines × 12 drugs + controls), single condition per sample

first: Troy

last: Carnwath

first: Rebecca

last: Albano

first: Yonghua

last: Zhuang

first: Catherine

last: Behrmann

first: Merissa

last: Pemberton

first: Farah

last: Barakat

first: Robert

last: Lober

first: Mark

last: Hoeprich

first: Anthony

last: Paravati

first: Marilyn

last: Reed

first: Hailey

last: Spry

first: Daniel

last: Woo

first: Eric

last: O'Brien

first: Brett

last: VanCauwenbergh

first: John

last: Perenthesis

first: Rani

last: Nasser

first: Mario

last: Medvedovic

first: David

middle: R

last: Plas


title: Atherosclerotic Plaque Macrophages Drive Abdominal Aortic Aneurysm Formation [bulkRNA-Seq]

city: Toronto

first: Clinton

last: Robbins

state: ON

address: 101 College Street

institute: UHN

summary: There is no effective pharmacotherapy to prevent the growth and rupture of abdominal aortic aneurysms (AAA), a leading cause of death. We developed a novel preclinical model showing that the interaction of bona fide risk factors (i.e., cigarette smoke (CS) and hypercholesterolemia) induced AAA formation, rupture, and death. Elastin fragmentation resulted from CS-induced exacerbation of the atherosclerotic process, significant given atherosclerosis is a disease of the inner intimal layer of the artery, with the media remaining largely intact. Importantly, arterial injury was driven by CSF-1-dependent macrophages (Mφ) accumulating within developing atherosclerotic plaques that exhibited tissue degrading proteolytic activity in vivo. Single-cell RNA sequencing further demonstrated conservation of Mφ responses in atherosclerotic plaque from murine and human AAA. Our findings advance understanding of the pathological sequelae of atherosclerosis, establishing plaque Mφ as important mediators of tissue damage and a potential target for prevention of AAA growth and rupture.

overall_design: Differential expression analysis was performed on bulk RNA sequencing data generated from the abdominal aortas of room air (n=5) and cigarette smoke (n=8) exposed animals

first: Danya

last: Thayaparan

first: Takuo

last: Emoto

first: Aniqa

last: Khan

first: Rickvinder

last: Besla

first: Homaira

last: Hamidzada

first: Mahmoud

last: El-Maklizi

first: Shabana

last: Vohra

first: Tharini

last: Sivasubramaniyam

first: Ash

last: Hagerman

first: Sara

last: Nejat

first: Charlotte

middle: E

last: Needham-Robbins

first: Moritz

last: Lindquist

first: Steven

last: Botts

first: Stephanie

last: Schroer

first: Tao

last: Wang

first: Masayuki

last: Taniguchi

first: Taishi

last: Inoue

first: Aja

last: Michalski

first: Katsuhiro

last: Yamanaka

first: Haotian

last: Cui

first: Hangjun

last: Zhang

first: Marwan

middle: G

last: Althagafi

first: Joshua

last: McGrath

middle: P

last: Cass

last: Luong

first: Yuya

last: Suzuki

first: Angela

last: Li

first: Amina

last: Abow

first: Rachel

last: Heo

first: Shaun

last: Pacheco

first: Edouard

last: Al-Chami

first: Emily

last: Chen

first: Felix

last: Chiu

last: Byrne

first: Tomoyuki

last: Furuyashiki

first: Mansoor

last: Husain

first: Peter

last: Libby

first: Kenji

last: Okada

first: Kathryn

last: Howe

first: Scott

last: Heximer

first: Tomoya

last: Yamashita

first: Bo


title: Atherosclerotic Plaque Macrophages Drive Abdominal Aortic Aneurysm Formation

first: Clinton

last: Robbins

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed to define macrophage heterogeneity in aortic lesions

first: Danya

last: Thayaparan

first: Takuo

last: Emoto

first: Aniqa

last: Khan

first: Rickvinder

last: Besla

first: Homaira

last: Hamidzada

first: Mahmoud

last: El-Maklizi

first: Shabana

last: Vohra

first: Tharini

last: Sivasubramaniyam

first: Ash

last: Hagerman

first: Sara

last: Nejat

first: Charlotte

last: Needham-Robbins

first: Moritz

last: Lindquist

first: Steven

last: Botts

first: Stephanie

last: Schroer

first: Tao

last: Wang

first: Masayuki

last: Taniguchi

first: Taishi

last: Inoue

first: Aja

last: Michalski

first: Katsuhiro

last: Yamanaka

first: Haotian

last: Cui

first: Hangjun

last: Zhang

first: Marwan

last: Althagafi

first: Joshua

last: McGrath

last: Cass

first: David

last: Luong

first: John


title: Three-dimensional genome structures of single mammalian sperm

first: Heming

last: Xu


title: Atherosclerotic Plaque Macrophages Drive Abdominal Aortic Aneurysm Formation [snRNAseq]

first: Clinton

last: Robbins

overall_design: Single nucleus RNA sequencing (snRNAseq) was performed on abdominal aortae from ApoE-/- mice exposed to room air and cigarette smoke for 20 weeks.

first: Danya

last: Thayaparan

first: Takuo

last: Emoto

first: Aniqa

last: Khan

first: Rickvinder

last: Besla

first: Homaira

last: Hamidzada

first: Mahmoud

last: El-Maklizi

first: Shabana

last: Vohra

first: Tharini

last: Sivasubramaniyam

first: Ash

last: Hagerman

first: Sara

last: Nejat

first: Yuya

last: Suzuki

first: Angela

last: Li

first: Amina

last: Abow

first: Rachel

last: Heo

first: Shaun

last: Pacheco

first: Edouard

last: Al-Chami

first: Emily

last: Chen

first: Felix

last: Chiu

last: Byrne

first: Tomoyuki

last: Furuyashiki

first: Mansoor

last: Husain

first: Peter

last: Libby

first: Kenji

last: Okada

first: Kathryn

last: Howe

first: Scott

last: Heximer

first: Tomoya

last: Yamashita

first: Bo


title: Transcriptome profiling of developing choroid plexus and FoxJ1-/- choroid plexus

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

summary: We report the transcription profiling of choroid plexus at 4 developmental stages, E12,5, P0, P14 and 6 month. We also compared wildtype and Foxj1-/- choroid plexus transcriptome at P0.

overall_design: We collected 3 or 4 independent specimens for each datapoint and performed RNA-seq experiments on the samples to generate 100bp-PE sequencing data.

first: Xuan

last: Zhenyu

first: He

last: Lin


title: NRF2 deficiency leads to inadequate beta cell adaptation during pregnancy and gestational diabetes

city: Duarte

first: Sharon

last: Baumel Alterzon

address: 1500 East Duarte road

department: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute

institute: City of Hope

summary: The late stages of mammalian pregnancy are accompanied by a mild increase in insulin resistance likely due to enhanced glucose demand of the growing fetus. Therefore, as an adaptive process to maintain euglycemia during pregnancy, maternal β-cell mass expands leading to increased insulin release. Defects in functional β-cell adaptive expansion during pregnancy can lead to gestational diabetes mellitus (GDM). While the exact mechanisms that promote GDM are poorly understood, GDM is associated with inadequate functional β-cell mass expansion and with a systematic increase of oxidative stress. Here, we show that NRF2 levels are upregulated in mouse β-cells at gestational day 15 (GD15). Inducible β-cell-specific Nrf2 deleted (βNrf2KO) mice display reduced β-cell proliferation, increased β-cell oxidative stress and lipid peroxidation, compromised β-cell function, and elevated β-cell death, leading to impaired β-cell mass expansion and dysregulated glucose homeostasis towards the end of pregnancy. Importantly, the gestational hormone 17-β-estradiol (E2) increases NRF2 levels, and downregulation of NRF2 suppresses E2-induced protection of β-cells against oxidative stress, suggesting that E2 exerts its antioxidant effects through activation of NRF2 signaling in β-cells. Collectively, these data highlight the critical role of NRF2 in regulating oxidative stress during the adaptive response of β-cells in pregnancy and identify NRF2 as a potential therapeutic target for GDM treatment.

overall_design: Bulk RNA-seq profiling of pancreatic islets from non-pregnant and pregnant (gestational day 15) wildtype and beta-cell specific Nrf2-KO female mice generated by crossing MIP-CreERTAM mice85 (RRID: IMSR_JAX:024709) with Nrf2lox/lox mice (RRID: IMSR_JAX:025433).

last: Baumel-Alterzon

first: Luca

last: Lambertini


title: BAT Transcriptomics in DIO Vehicle or Cotadutide Mice

city: Gaithersburg

first: Rhianna

last: Laker

address: One Medimmune Way

department: eCVRM

institute: AstraZeneca

summary: Early drivers of Type 2 diabetes mellitus (T2D) include ectopic fat accumulation, especially in the liver, that significantly impairs insulin sensitivity. In a T2D setting, GLP-1R/GCGR dual agonists have been shown to reduce glycaemia, body weight and hepatic steatosis. We utilized cotadutide, a well characterized GLP-1R/GCGR dual-agonist, to demonstrate improved insulin sensitivity during hyperinsulinemic euglycemic clamp following sub-chronic dosing in male, diet-induced obese mice. Cotadutide or GCGR monoagonist treatment resulted in specific increased brown adipose tissue (BAT) insulin-stimulated glucose uptake, while GLP-1R monoagonist only showed a weak effect. BAT from cotadutide treated mice had induction of UCP-1 protein, increased mitochondrial area and a transcriptomic profile of increased fat oxidation and mitochondrial activity. Thus, GLP-1R/GCGR dual agonism provides multimodal efficacy to decrease hepatic steatosis and consequently improve insulin sensitivity, in concert with recovery of endogenous β-cell function and reduced insulin demand. This substantiates GLP-1R/GCGR dual-agonism as a novel and effective T2D treatment.

overall_design: To investiagate the mechanistic impact of cotadutide treatment on brown adipose tissue (BAT), we condcuted RNA-sequencing on BAT from diet-induced obese (DIO) mice treated with vehicle or cotadutide (n=4-5 mice per group) to determine differentially expressed genes.

first: Xidan

last: Li

first: Shaun

last: Egolf

first: Christopher J.

last: Rhodes


title: Effect of GATA2 depletion on Ark1 endometrial serous carcinoma cells.

city: Madison

first: Daniel

middle: Rusch

last: Matson

state: WI

address: WIMR Room 1761 - 1111 Highland Avenue

department: Pathology and Laboratory Medicine

institute: University of Wisconsin - Madison

summary: GATA2 expression in endometrial serous carcinoma cells correlates with patient outcome. Depletion of GATA2 in patient-derived endometrial serous carcinoma cell lines correlates with invasive potential. As GATA2 is a transcription factor, we hypothesize that GATA2-dependent target genes normally suppress invasion in endometrial serous carcinoma.

overall_design: Ark1 patient-derived endometrial serous carcinoma cell lines were depleted of either GATA2 or scramble control and RNA transcript differences measured after 48 hours using RNA-seq.

first: Apoorva

middle: T

last: Patil


title: CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines [RNA-seq]

first: Matthew

last: Garrett

first: Troy

last: Carnwath

first: Rebecca

last: Albano

first: Yonghua

last: Zhuang

first: Catherine

last: Behrmann

first: Merissa

last: Pemberton

first: Farah

last: Barakat

first: Robert

last: Lober

first: Mark

last: Hoeprich

first: Anthony

last: Paravati

first: Marilyn

last: Reed

first: Hailey

last: Spry

last: Woo

first: Eric

last: O'Brien

first: Brett

last: VanCauwenbergh

first: John

last: Perenthesis

first: Rani

last: Nasser

first: Mario

last: Medvedovic

first: David

last: Plas


title: Three-dimensional genome structures of single mammalian sperm [bulk Hi-C]

first: Heming

last: Xu

overall_design: Validation of an Optimized Single-Cell Hi-C Protocol for Sperm Cells in Mouse Embryonic Stem Cells (ESCs)

first: Yi

last: Chi

first: Changjian

last: Yin

first: Cheng

last: Li


title: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances [Hi-C]

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

summary: Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. However, it remains unclear how widespread such functional conservation might be.

overall_design: Hi-C  data generated from embryonic chicken heart at HH22 in 2 biological replicates

first: Mai

last: Phan


title: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances [RNA-seq]

overall_design: RNA-seq from embryonic chicken heart at HH22 and HH24, with 2 biological replicates


title: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances [ATAC-seq]

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: ATAC-seq from embryonic mouse heart (E10.5 & E11.5), and chicken heart + forelimb (HH22 & HH24) in 2 biological replicates


title: GA-CFP data for the manuscript "Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model"

first: Ali

last: Rezaei

institute: LMU

summary: These sequences support the following paper abstract: Clinical and genetic research links altered cholesterol metabolism with ALS development and progression, yet pinpointing specific pathomechanisms remain challenging. We investigated how cholesterol dysmetabolism interacts with protein aggregation, demyelination, and neuronal loss in ALS. Bulk RNAseq transcriptomics showed decreased cholesterol biosynthesis and increased cholesterol export in ALS mouse models (GA-Nes, GA-CFP, rNLS8) and patient samples (spinal cord), suggesting an adaptive response to cholesterol overload. Consequently, we assessed the efficacy of the cholesterol-binding drug 2-hydroxypropyl-β-cyclodextrin (CD) in a fast-progressing C9orf72 ALS mouse model with extensive poly-GA expression and myelination deficits. CD treatment normalized cholesteryl ester levels, lowered neurofilament light chain levels, and prolonged lifespan in female but not male GA-Nes mice, without impacting poly-GA aggregates. Single nucleus transcriptomics indicated that CD primarily affected oligodendrocytes, significantly restored myelin gene expression, increased density of myelinated axons, inhibited the disease-associated oligodendrocyte response, and downregulated the lipid-associated genes Plin4 and ApoD. These results suggest that reducing excess free cholesterol in the CNS could be a viable ALS treatment strategy.

overall_design: Aged GA-CFP mice (Schludi et al) were used to validate the cholesterol effect seen in GA-Nes mice of the manuscript mentioned in the title. Spinal cord was dissected, and RNA was isolated. DESeq2 library was used to analyze differentially expressed genes.

first: Virág

last: Kocsis-Jutka

first: Qihui

last: Zhou

first: Dieter

last: Edbauer


title: ATG5 suppresses type I interferon-dependent neutrophil swarming and NET release

city: St. Louis

first: Christina

last: Stallings

state: MO

address: 425 South Euclid ave

institute: Washington University in Saint Louis

summary: Inflammation is critical for controlling infections but can cause disease when unchecked. For tuberculosis, the leading cause of death by infection, neutrophil-dominated inflammation is associated with disease progression, emphasizing the need to understand how neutrophil functions are regulated during Mycobacterium tuberculosis infection. Atg5 was the first gene shown to specifically function within neutrophils to promote control of M. tuberculosis. ATG5 is best studied for its role in autophagy, however, the protective activity of ATG5 in neutrophils was unexpectedly independent of other autophagy proteins and remained elusive. We report that ATG5 is required in neutrophils to suppress type I interferon-induced neutrophil extracellular trap (NET) release and swarming during M. tuberculosis infection. Elevated NET release contributes to the early susceptibility of Atg5fl/fl-LysM-Cre mice during infection. These findings identify ATG5 as a master regulator of how type I interferon influences neutrophil responses during infection, revealing a new potential target for host-directed therapies.

overall_design: Mice were infected with 100 CFUs of aerosolized M. tuberculosis per lung using an Inhalation Exposure System (Glas-Col). Neutrophils were isolated from the lung at 14dpi by Ly6G enrichment according to themanufacturer’s instructions (Miltenyi, 130-120-337).

first: Rachel

middle: L

last: Kinsella

first: Jacqueline

last: Kimmey

first: Ekaterina

last: Esaulova

first: Maxim

middle: N

last: Artyomov

first: Yassin

last: Mreyoud


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [HiChIP]

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

summary: Enhancer-promoter communication in the context of the three-dimensional (3D) nucleus is critical for the regulation of transcriptional programs specific for cell identity. Here, we profile the 3D enhancer-promoter networks of primary patient-derived human glioma spheres (GSCs) in comparison with neuronal stem cells to identify candidate central nodes of GSC tumorigenic programs. We have identified highly interacting 3D enhancer-promoter “hubs” which strongly associate with robust and coordinated expression of tumor-associated genes, suggesting potentially central roles in the regulation of oncogenic programs. Integration of whole-genome sequencing (WGS) data from The Cancer Genome Atlas showed that 3D regulatory hubs are strongly enriched for recurrent point mutations in the larger cohort of glioblastoma patients. In a proof-of-concept experiment, epigenetic perturbation of a highly interacting and recurrent 3D enhancer hub in the GOLIM4 locus led to significant downregulation of multiple hub-connected genes and reduced clonogenicity along with a global shift in the transcriptional states. Finally, integration of published H3K27ac HiChIP from other cancer types enabled the identification of both “universal” and cancer type-specific 3D regulatory hubs which enrich for different oncogenic programs and potential regulators, and often associate with a worse prognosis. Overall, our study identifies complex 3D regulatory hubs in glioblastoma and provides computational and experimental support for their potential role in driving oncogenic programs and promoting tumorigenic properties.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in lt-NSC and four patient-derived glioma stem cell lines (all samples in duplicates)
bedpe format of loops from merged replicates

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


title: Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation

city: Montreal

first: Anna

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

institute: McGill University

summary:
Background: Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs), which represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored.

Results: We report a survey of gene, lncRNA, and TE expression in four organs from mice with different combinations of gonadal and genetic sex. The data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in the liver. In contrast, the X-chromosome dosage alone had a modest influence on sex-biased transcription across organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y-chromosome influences TE, but not gene or lncRNA, expression in the liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside less than 100 kb from sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We test the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals finding no evidence to support it.

Conclusions: Our data show that sex-biased expression of TEs varies among organs with the highest numbers of sDETEs found in the liver following trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.

overall_design: Mice with different combinations of sex-chromosome complement and gonadal sex were generated using crosses between B6.YTIR males and C57BL/6J females (B6.YTIR cross) as well as B6.C3H/HeSn-Paf males with C57BL/6J females (XPaf cross). Liver, lung parenchyma, heart, and whole brain were collected from 8-week old mice and used for RNA extraction. Gonadal sex was confirmed at the time of organ collection.

first: Qinwei

last: Zhuang

first: Klara

last: Bauermeister

first: Jose

middle: H

last: Galvez

first: Najla

last: AlOgayil

first: Enkhjin

last: Batdorj

first: Fernando

last: Pardo Manuel de Villena

first: Teruko

last: Taketo

first: Guillaume

last: Bourque


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in lt-NSC and four patient-derived glioma stem cell lines (all samples in duplicates)
raw counts per sample in a 2 column tab delimited file with Ensemble gene ID and raw counts


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [ChIP-seq]

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in lt-NSC and four patient-derived glioma stem cell lines (all samples in duplicates)
bed format files for H3k27a peaks that are shared among replicates


title: Epigenetic Mapping of Cis-Regulatory Elements in the Developing Mouse and Pig Forelimbs.

city: Seville

first: Ismael

last: Sospedra-Arrufat

address: Carretera de Utrera km1, UPO

institute: CABD

summary: Cis-regulatory elements (CREs) orchestrate the spatio-temporal regulation of key transcriptional programs. These elements - including promoters, enhancers, and insulators - play a crucial role in embryonic development and in morphological evolution. We performed ChIP-seq for histone modifications (H3K4me3, H3K27ac, and H3K4me1) from equivalent stages of mouse (E11.5) and pig (day 23; D23) forelimb development to catalog the limb bud regulome in both species. The overlap of these epigenomic signatures with the pattern of open chromatin during limb development previously described for both species allowed us to classify these putative regulatory regions into different chromatin states. Our studies offer a valuable resource in the evo-devo field for exploring mechanisms underlying the morphological evolution of the tetrapod limb.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: Mouse (E11.5) or pig (D23) embryonic forelimbs were collected from littermates to generate biological replicates. Nuclei homogenization was performed mechanically, and chromatin was crosslinked with 1% formaldehyde. Material from each biological replicate was split in half to generate technical replicates for ChIP-seq. Due to technical limitations, only one biological replicate (with two technical replicates) was generated for the pig H3K4me1 mark. All libraries were generated by ChIPmentation (Schmidl et al., 2015; PMID: 26280331), using 1 μg of the following antibodies: anti-H3K4me3 (Abcam ab8580), anti-H3K27ac (Abcam ab4729), and anti-H3K4me1 (Abcam ab8895). All pig libraries were sequenced 50bp paired-end, except for H3K4me1. This sample, together with all mouse libraries, was sequenced using 100bp paired-end reads, and subsequently cropped to 50bp. Reads were aligned to the corresponding assemblies: mouse GRCm38/mm10 or pig SusScrofa11.1/susScr11. BigWigs were normalized to RPKM. Peak calling was performed using a broad IDR <0.01.

first: Javier

last: Lopez-Rios

first: Gretel

last: Nusspaumer

first: Tena

middle: J

last: Juan


title: Presurgical ablative radiation downstages high-risk features and alters immune response in pancreatic cancer

city: Dallas

first: Todd

last: Aguilera

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

summary: Neoadjuvant (NA) stereotactic ablative radiotherapy (SAbR) may improve outcomes in pancreatic cancer. We compared outcomes and molecular characteristics of patients who had surgery after neoadjuvant chemotherapy, with and without SAbR. We compared clinical data from surgically resected patients treated with either NA chemotherapy or NA chemotherapy plus SAbR. Recurrence-free and overall survival (RFS/OS) were analyzed using stepwise-AIC-optimized multivariable Cox modeling and log-rank tests. When available, we used transcriptomic analyses (GSEA, CIBERSORTx, and SCISSOR) to link clinical outcomes to gene expression patterns. We reviewed 133 patients treated with NA chemotherapy and 48 with NA chemotherapy + SAbR, including RNA sequencing data from 29 and 14 patients, respectively. Before surgery, the SAbR group had more advanced disease with arterial involvement, yet still achieved similar OS and RFS. Patients treated with SAbR had better post-treatment pathology linked to improved OS and RFS. RNA sequencing showed that patients with nodal involvement had enriched MYC targets and worse distant RFS. Those with arterial involvement had worse locoregional RFS with chemotherapy alone, but not in the SAbR group. GSEA highlighted immune-related changes in myeloid and T cell activation, suggesting treatment-related functional changes. SCISSOR analysis revealed cytotoxic CD8 and NK/NKT cell signatures correlating with better local control, while Treg signatures were linked to worse LRFS. Patients treated with NA chemotherapy + SAbR showed better pathologic outcomes, improved local control, and comparable survival, along with a distinct immune response. Further evaluation of SAbR in the neoadjuvant setting, combined with enhanced chemotherapy and novel treatment combinations, may lead to even greater clinical benefits.

overall_design: To investigate the transcriptomic differences of PDAC patients treated with either neoadjuvant chemotherapy or neoadjuvant chemotherapy plus SAbR. Surgically resected samples were used. Performed bulk-RNAseq from resected tissues to link clinical outcomes to gene expression patterns.

first: Peter

middle: Q

last: Leung

first: Eslam

middle: A

last: Elghonaimy

first: Ahmed

middle: M

last: Elamir

first: Megan

last: Wachsmann

first: Song

last: Zhang

first: Neha

last: Barrows

first: Hollis

last: Notgrass

first: Ethan

last: Johnson

first: Cheryl

last: Lewis

first: Rachel

last: von Ebers

first: Cassandra

last: Hamilton

first: Grace

last: Josephson

first: Zhikai

last: Chi

first: Salwan

last: Al Mutar

first: Patricio

last: Polanco

first: Nina

last: Sanford

first: Syed

last: Kazmi

first: Mathew

last: Porembka

first: David

last: Hsiehchen

first: Adam

middle: C

last: Yopp

first: John

last: Mansour

first: Muhammed

middle: S

last: Beg

first: Herbert

last: Zeh III


title: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances [ChIP-seq]

first: Daniel

last: Ibrahim

overall_design: Histone ChIPmentation for H3K27ac, K3K4me1, and K3K4m3 at for embryonic chicken heart and forelimb 2 stages HH22 and HH24

first: Mai

last: Phan


title: Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A [ATAC]

city: Oxford

first: Charlotte

last: Brierley

address: University of Oxford, Headley Way

country: United Kingdom

institute: MRC WIMM

summary: Investigating the impact of chr21 amplification in primary patient Lin-Cd34+ cells

overall_design: ATAC-sequencing was performed in 5 primary patient chr21amp cells, 4 non-chr21amp primary patient cells and 5 age-matched controls

first: Giulia

last: Orlando

last: Mead

first: Beth

last: Psaila


title: Neutrophil Transcriptomics During Pneumonia

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

overall_design: Refer to individual Series


title: Transcription in peripheral and alveolar neutrophils during pneumococcal pneumonia

summary: The goal of this study is to investigate changes in gene transcription during pneumonia by neutrophils migrating to the lung, compared with those remaining in the peripheral circulation.

overall_design: C57BL/6 mice were infected with S. pneumoniae or saline control for 24 hours. Flow cytometry assisted cell sorting was used to isolate neutrophils from peripheral blood in infected and uninfected mice, and bronchoalveolar lavage fluid (BALF) in infected mice. Three mice were used per group, noting that peripheral blood and BALF from infected mice were harvested from the same mouse. Experiments were repeated on two separate days.

first: Katrina

last: Traber

first: Lee

last: Quinton


title: Identification of Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma [HiC]

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

institute: University of Michigan Medical School

summary: High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC-intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer (BCL6-SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6-SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3’ enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3’ rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene.

overall_design:
Hi-C chromatin topology mapping in four GCB-DLBCL patient biopsies
***Raw data have not been deposited in GEO due to patient privacy concerns.****

first: Aishwarya

last: Gurumurthy

first: Ashwin

last: Iyer


title: MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut III

status: Public on Mar 05 2025

city: Hershey

first: Marina

last: Chulkina

state: Pennsylvania

address: 500 University dr department of medicine

department: Medicine

institute: Penn State Health Medical Center

summary: Fibroblasts that reside in the gut mucosa are among the key regulators of innate immune cells, but their role in the regulation of the defense functions of macrophages remains unknown. MyD88 is suggested to shape fibroblast responses in the intestinal microenvironment. We found that mice lacking MyD88 in fibroblasts showed a decrease in the colonic antimicrobial defense, developing dysbiosis and aggravated DSS-induced colitis. These pathological changes were associated with accumulation of Arginase 1+ macrophages with low antimicrobial defense capability. Mechanistically, production of IL-6 and CCL2 downstream of MyD88 was critically involved in fibroblast-mediated support of macrophage antimicrobial function, and IL-6/CCL2 neutralization resulted in the generation of macrophages with decreased production of antimicrobial peptide cathelicidin and impaired bacterial clearance. Collectively, these findings revealed a critical role of fibroblast-intrinsic MyD88 signaling in regulating macrophage antimicrobial defense under colonic homeostasis, and its disruption results in dysbiosis, predisposing host to the development of intestinal inflammation.

overall_design: Gene expression profiling based on RNA-seq data from enriched colonic mucosal tissue of mice with or without conditional fibroblast-specific MyD88 knockout in DSS colitis.

first: Iryna

middle: V

last: Pinchuk


title: Identification of Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma [4C-seq]

overall_design: 4C-Seq chromatin topology mapping for the MYC promoter and BCL6 promoter and super-enhancer in three DLBCL cell lines


title: Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma

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


title: Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [scRNA-seq]

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

summary: Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett’s esophagus have not been resolved in humans. Here, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis unexpectedly revealed that the squamous esophagus and gastric cardia contained cells belonging to common lineages that also included transitional basal progenitor cells; both esophageal and gastric tissues were also related to Barrett's esophagus. Barrett’s esophagus biopsies consisted of multiple clones, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic lesions were initiated by the expansion of a single molecularly aberrant Barrett’s esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the disease trajectory, from its origin to cancer.

overall_design: Performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue.

first: Rodrigo

last: Gier

first: Raúl

last: Reyes Hueros

first: Jiazhen

last: Rong

first: Maureen

last: DeMarshall

last: Bracht

first: Tatiana

last: Karakasheva

first: Amanda

middle: B

last: Muir

first: Gary

middle: W

last: Falk

first: Nancy

middle: R

last: Zhang


title: MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut I


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [scRNA-seq]

first: Effie

last: Apostolou

overall_design: Glioma stem cell lines expressing doxycycline-inducible dCas9-KRAB-GFP with guides targeting a negative control region and the GOLIM4 enhancer were co-cultured with 4.5 month old brain cerebral organoids (GLICO). After co-culture and doxycycline induction for 7 days, cells were harvested, sorted as single cells for GFP+/DAPI- cells and submitted for scRNA-seq (10X Genomics)


title: Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation [Spatial transcriptomics]

city: La Jolla

first: Maayan

last: Baron

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in >70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation.

overall_design: Formalin-fixed paraffin-embedded (FFPE) samples of 8 primary melanomas were chosen and sectioned (clinical information provided in Supplementary Table 2). One section was retained for the digital spatial profiling workflow to determine desmosome expression. Digital spatial profiling was performed using the GeoMX system as previously described (Merritt et al. 2020). Immunofluorescent visualization markers for keratinocytes (PanCK), melanoma cells (S100B, PMEL) and immune cells (CD45) were used to guide the selection of regions of interest (ROIs) containing either pure or mixed areas of each cell type (keratinocyte, melanocyte) followed by RNA profiling using the GeoMx human whole assay.


title: Transcription in vascular, interstitial, alveolar and BALF neutrophils during pneumococcal pneumonia

first: Boston University

last: Microarray and Sequencing Resource

summary: The goal of this study is to investigate changes in gene transcription during pneumonia in neutrophils in various locations in the lung (vasculature, intersitium, alveolus and lavageate).

overall_design: C57BL/6 mice were infected with S. pneumoniae or saline control for 24 hours. Flow cytometry assisted cell sorting (FACS) and intravascular (IV) and intratracheal (IT) dyes were used to identify and isolate neutrophils from lung vasculature, interstitium, alveolus and bronchoalveolar lavage fluid (BALF).

first: Katrina

last: Traber


title: Cancer-Associated Fibroblasts Shape a High-Lactate Microenvironment to Drive Perineural Invasion in Pancreatic Cancer via Histone Lactylation [RNA-seq]

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

summary: Perineural invasion (PNI) is a pivotal prognostic factor in pancreatic cancer, associated with aggressive tumor behavior and adverse patient outcomes. Despite its recognized clinical impact, the molecular mechanisms underlying PNI are not well understood. In this study, we isolated perineural invasion-associated cancer-associated fibroblasts (pCAFs), which demonstrated a markedly enhanced capacity to promote neural invasion in pancreatic cancer compared to non-perineural invasion-associated CAFs (npCAFs). Utilizing single-cell, high-throughput sequencing, and metabolomics, we identified a significant upregulation of glycolysis in pCAFs, fostering a high-lactate tumor microenvironment conducive to cancer progression. pCAFs-derived lactate is absorbed by tumor cells, facilitating histone H3K18 lactylation. This epigenetic modification activates the transcription of neural invasion-associated genes such as L1CAM and SLIT1, thereby driving PNI in pancreatic cancer. Further exploration of metabolic reprogramming in pCAFs revealed enhanced acetylation of the glycolytic enzyme GAPDH, correlated with increased enzymatic activity and glycolytic flux. Targeting of GAPDH and lactylation modifications significantly inhibits neural invasion in a KPC mouse model. Clinical data suggested that high levels of H3K18 lactylation correlate with severe PNI and poorer patient prognosis. Our findings provide critical insights into the role of pCAFs in the PNI of pancreatic cancer, highlighting glycolytic reprogramming and lactate-driven histone modifications as potential therapeutic targets for PDAC.

overall_design: Using anti- H3K18la antibodies to delineate the regulatory role of H3K18la in gene expression in PANC-1 cells treated with lactic acid.

first: Tingting

last: Li

first: Chonghui

last: Hu

first: Tianhao

last: Huang

first: Yu

last: Zhou


title: Phenotypic complexities of rare heterozygous neurexin-1 deletions [shNEG_ASO_rnaseq]

first: GANG

last: FANG

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1+/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. For NRXN1 deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration of NRXN1 isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.

overall_design: RNA-Seq of three indepenent experiments assessing the impact of shRNAs, ASOs or beta-estradiol on NRXN1 gene expression and splicing under control or patient genotypes. shRNA condition represents four experiments across two cell-types and genotypes; shRNA targeting wildtype isoforms (WT) were performed in control healthy donors, shRNA condition targeting mutant isoforms (MT) were performed in 3'-Del genotype compared to a non-targeting control shRNA (shNEG). ASO experiments were performed in 3'-Del genotype(s) and compared to a non-targeting ASO. Beta-estradiol experiments were performed in 5'-Del genotype(s) and compared to the vehicle.

first: Michael

last: Fernando

last: Fan

first: Yanchun

first: Alex

last: Tokolyi

first: Aleta

last: Murphy

first: Sarah

middle: K

last: Kammourh

first: Peter

last: Deans

first: Sadaf

last: Ghorbani

first: Ryan

last: Onatzevitch

first: Adriana

last: Pero

first: Christopher

last: Padilla

last: Williams

first: Erin

last: Flaherty

first: Iya

last: Prytkova

first: Lei

last: Cao

first: David

last: Knowles

first: Gang

last: Fang

first: Paul

last: Slesinger

first: Kristen

last: Brennand


title: Phenotypic complexities of rare heterozygous neurexin-1 deletions [nrxn1_bulk_rnaseq]

first: GANG

last: FANG

first: Michael

last: Fernando

first: Yu

last: Fan

last: Zhang


title: MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut IV

first: Marina

last: Chulkina

overall_design: Gene expression profiling analysis of RNA-seq data from colonic enriched tissue of mice with or without conditional fibroblast-specific MyD88 knokout under DSS colitis condition.

first: Iryna

last: Pinchuk


title: Intracellular metabolic gradients dictate dependence on exogenous pyruvate

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-sequencing of S/L and S/L+2i-cultured mouse embryonic stem cells with either CRISPR-directed editing of Slc16a1 or chr8 control. RNA-sequencing of S/L-cultured ESCs with expression of the bacterial NADH oxidase LbNOX or vector control.

overall_design: Cells generated as above were cultured in medium containing 0.2 mM pyruvate for 48h.

first: Benjamin

middle: T

last: Jackson

first: Angela

last: Montero


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [ATAC-seq]

first: Effie

last: Apostolou

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in lt-NSC and four patient-derived glioma stem cell lines (all samples in duplicates)
bed format files for H3k27a peaks that are shared among replicates


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [CUT&Tag]

city: GuangZhou

first: meijun

last: ye

state: -- Please Select --

address: Room 418, Science and Technology Building, North Campus, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, Guangdong, China.

institute: SUN YAT-SEN UNIVERSITY

summary: Interaction between the m6A methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. It is still intriguing whether there is spatial control of m6A deposition on different types of RNAs. Here, through genome-wide CRISPR/Cas9 screening, we find H3K27ac acetylase p300-mediated METTL3 acetylation suppresses the binding of METTL3 on H3K27ac-marked chromatin by inhibiting its interaction with METTL14. Consistently, p300 catalyzing the acetylation of METTL3 specifically occurs on H3K27ac marked chromatin. Disruptive mutations on METTL3 acetylation sites selectively promote the m6A of chromatin-associated RNAs from p300-bound enhancers and promoters marked by H3K27ac, resulting in transcription inhibition of ferroptosis-inhibition related genes. In addition, PAK2 promotes METTL3 acetylation by phosphorylating METTL3. Inhibition of PAK2 promotes the ferroptosis in a manner that depends on the acetylation of METTL3. Our study reveals a spatial-selective way to specifically regulate the deposition of m6A on enhancer and promoter RNAs.

overall_design: CUT&Tag in METTL3-WT or METTL3-3KR A549 cells by using METTL3 and H3K27ac antibodies, respectlly.

first: Xiang

last: Huang

first: Jinkai

last: Wang

first: Zhijun

last: Ren

first: Meijun

last: Ye


title: Identification of Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma [PCR-amplified sgRNA]

first: Russell

last: Ryan

overall_design: 2-4 replicates of KRAB-dCas9-expressing, sgRNA library-transduced cell lines, harvested at two time points, T0 and T14

first: Aishwarya

last: Gurumurthy

first: Ashwin

last: Iyer


title: Identification of Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. [ATAC-Seq]

overall_design: ATAC-Seq datasets were aligned to hg19


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [RNA-seq]

overall_design: The mRNA expression profile of METTL3-WT or METTL3-3KR A549 cells was generated by deep sequencing, in diplicate, using MGISEQ-2000RS platform on PE150 mode.


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [caRNA-seq]

overall_design: Chromatin-associated RNA m6A profiles of METTL3-WT or METTL3-3KR A549 cells were generated by deep sequencing using MGISEQ-2000RS on PE150.