title: Direct genetic transformation bypasses tumor-associated DNA methylation alterations (RRBS)

summary: Tumors represent dynamically evolving populations of mutant cells, and many advances have been made in understanding the biology of their progression. However, key unresolved questions remain about the conditions that support their initial transformation, which cannot be easily captured in patient populations but are instead modeled using transgenic cellular or animal systems. Here, we used extensive patient atlas data to define common features of the tumor DNA methylation landscape as they compare to healthy human cells and used this benchmark to screen 21 engineered human and mouse models for their ability to reproduce these patterns. Notably, we find that genetically induced cellular transformation can trigger global changes in DNA methylation levels that are consistent with extensive proliferation but rarely recapitulate the widespread de novo methylation of Polycomb targets as found in clinical samples. Our results raise pertinent questions about the relationship between genetic and epigenetic aspects of tumorigenesis and provide an important molecular reference for evaluating existing as well as newer tumor models.

overall_design: DNA methylation profiling of mouse models of cancer.

first: Eran

last: Hodis

first: Elena

last: Torlai Triglia

first: Alexander

last: Kovacsovics

first: Kathleen

last: Steinmann

first: Andreas

last: Gnirke

first: Meiying

last: Cui

first: Daniel

last: McQuaid

first: Raha

last: Weigert

first: Georg

last: Pohl

first: Mandar

last: Muzumdar

first: Serge

last: Leyvraz

first: Ulrich

last: Keilholz

first: Marie-Laure

last: Yaspo

first: Aviv

last: Regev

first: Helene

last: Kretzmer

first: Zachary

last: Smith

last: Meissner


title: Cellular Defense Mechanisms Show Stronger Response to Linear DNA Compared to Circular Plasmid [ChIP-seq]

status: Public on May 21 2025

city: Hong Kong

first: yicen

last: zhou

address: Block 2, To Yuen Building, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Low transfection efficiency poses a significant challenge to experimental success, making the improvement of gene-carrying plasmid delivery and expression essential across various research fields. The stability of transfected vector DNA or mRNA significantly impacts transgene expression, as the innate immune system may recognize plasmid DNA as foreign and initiate a degradation response. Currently, it is unclear whether RNA transcribed from plasmids can activate RNA sensors, affecting transfection efficiency. This study employed RNA sequencing to analyze cellular responses to various circular and linear DNAs across five cell lines—HEK293T, HCT116, HeLa, L02, and NCM460—revealing that the innate immune response is a primary contributor to low transfection efficiency. Additionally, we used ChIP-seq to detect H3K27ac histone marks to explore whether the immune response triggered by plasmid transfection is regulated by epigenetic mechanisms. Finally, we performed ChIP assays for IRF7 and p-IRF3 in HeLa cells transfected with the linear pcDNA3.1-neo plasmid to demonstrate that these two transcription factors can indeed bind to the RTV genes.

overall_design: We performed ChlP-seq for H3K27ac histone mark in HeLa and NCM460 cells transfected with the circular or linear pcDNA3.1-neo plasmids and circular or linear pre-gRNA plasmids, and the ChIP-seq for IRF7 and p-IRF3 in HeLa cells transfected with linear pcDNA3.1-neo plasmids. All ChIP-seq experiments were carried out with three independent biological samples.

first: Xiaoyu

last: Li

first: Yicen

last: Zhou

first: Jie

last: Wei

first: Wei

last: Sun

first: Ligang

last: Fan

first: Jian

last: Yan


title: Direct genetic transformation bypasses tumor-associated DNA methylation alterations (target enrichment)

status: Public on May 20 2025

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

first: Eran

last: Hodis

first: Elena

middle: T

last: Triglia

first: Alexander

last: Kovacsovics

first: Kathleen

last: Steinmann

first: Andreas

last: Gnirke

first: Meiying

last: Cui

first: Daniel

last: McQuaid

last: Weigert

middle: D


title: Multiplexed perturbation reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors

status: Public on May 19 2025

city: Stanford

first: Conor

middle: James

last: McClune

state: CA

address: 443 Via Ortega

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: Plants make complex and potent therapeutic molecules, but difficulties in sourcing from natural producers or chemical synthesis can challenge their use in the clinic. A prominent example is the anti-cancer therapeutic paclitaxel (Taxol®) from yew (Taxus) trees. Identification of the full paclitaxel biosynthetic pathway would enable heterologous drug production, but it has eluded discovery despite a half century of intensive research. Within the search space of Taxus' large, enzyme-rich genome, we suspected the complex paclitaxel pathway would be difficult to resolve using conventional gene co-expression analysis and small sample sets. To improve the resolution of gene set identification, we developed a multiplexed perturbation strategy to transcriptionally profile cell states spanning tissues, cell types, developmental stages, and elicitation conditions. This approach revealed a set of paclitaxel biosynthetic genes that segregate into expression modules that suggest consecutive biosynthetic sub-pathways. These modules resolved seven new genes that, when combined with previously known enzymes, are sufficient for the de novo biosynthesis and isolation of baccatin III, an industrial precursor for Taxol, in Nicotiana benthamiana leaves at levels comparable to the natural abundance in Taxus needles. Included are taxane 1β-hydroxylase (T1βH), taxane 9α-hydroxylase (T9αH), taxane 7β-O-acyltransferase (T7ΑΤ), taxane 7β-O-deacetylase (T7dA), taxane 9α-O-deacetylase (T9dA), and taxane 9-oxidase (T9ox). Importantly, the T9αH we discovered is distinct and independently evolved from those recently reported, which failed to yield baccatin III with downstream enzymes. Unexpectedly, we also found a nuclear transport factor 2 (NTF2)-like protein (FoTO1) crucial for high yields of taxanes; this protein promotes the formation of the desired product during the first taxane oxidation step, resolving a longstanding bottleneck in paclitaxel pathway reconstitution. Together with a new β-phenylalanine-CoA-ligase, the eight genes discovered in this study enables the complete reconstitution of 3’-N-debenzoyl-2’-deoxy-paclitaxel with a 20-enzyme pathway in Nicotiana plants. More broadly, we establish a generalizable approach for pathway discovery that scales the power of co-expression studies to match the complexity of specialized metabolism, enabling discovery of gene sets responsible for high-value biological functions.

overall_design: To improve the resolution of gene set identification, we developed a multiplexed perturbation strategy to transcriptionally profile cell states spanning tissues, cell types, developmental stages, and elicitation conditions. To maximize the probability of activating biosynthetic states, we compiled a panel of elicitors including plant hormones (associated with growth, abiotic stress, and biotic stress), pathogen associated molecular patterns (PAMPs), taxane pathway intermediates, and select bacterial and fungal species. This approach revealed a set of paclitaxel biosynthetic genes that segregate into expression modules that suggest consecutive biosynthetic sub-pathways.

first: Conor James

first: Polly M

last: Fordyce

first: Elizabeth S

last: Sattely


title: Proteasome dysfunction in T cells causes immunodeficiency via cell cycle disruption and apoptosis

city: Tokushima

first: Junko

last: Morimoto

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University

summary: Proteasomes are essential molecular complex that regulate intracellular protein homeostasis by selectively degrading ubiquitinated proteins. Genetic mutations in subunits of proteasomes leads to proteasome-associated autoinflammatory syndromes (PRAAS) characterized by autoinflammation, partial progressive lipodystrophy, and in certain mutations, immunodeficiency. However, the molecular mechanisms by which proteasome dysfunction results in these phenotypes remain unclear. Here, we established a mouse that carries a mutation in β5i (encoded by Psmb8) along with T cell specific β5 (encoded by Psmb5) deficiency (KIKO mice). The KIKO mice showed severe loss of mature T cells in the spleen but not in the thymus, with reduced proteasome activity leading to the accumulation of ubiquitinated proteins. The CD4+ T cells of KIKO mice showed impaired proliferative activity with cell cycle arrest in G0/G1 phase following TCR engagement. T cells of KIKO mice underwent rapid cell death through apoptosis, as treatment of T cells with a caspase inhibitor Z-VAD rescued cell viability. Moreover, proteasome dysfunction induced apoptosis in T cells without either affecting mitochondrial functions or ER stress responses. Thus, our data provide insight into the molecular mechanisms underlying not only for immunodeficiency in PRAAS but also for T cell deficiency associated other disorders.

overall_design: RNA-seq profiling of KI T cells (naïve and activated) and KIKO T cells (naïve and activated).

first: Erkhembayar

last: Shinebaatar

first: Rinna

last: Koga

first: Nam

last: Nguyen

first: Yuki

last: Sasaki

first: Shigenobu

last: Yonemura

first: Hidetaka

last: Kosako

first: Koji

last: Yasutomo


title: RNA sequencing of non-targetting ASOs on HEK293 and U2OS cells

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Non-targetting ASOs are commonly used as negative controls in vitro and in vivo. Here, we compare the transcriptomic profile of HEK293 and U2OS, following 3 days treatment with 3 different non-targetting ASOs. In those conditions, we did not find major transcriptomic changes following ASO treatment, confirming that they are appropriate negative controls.

overall_design: The experiment was performed using 2 different cell types (HEK293 and U2OS) and 3 non-targetting ASOS (CTRL1, CTRL2 and CTRL3). Splice switching ASO (SSO) does not have an endogeneous target in U2OS and is used as a fourth non-targetting ASO in this cell line. Untreated samples (both HEK293 and U2OS) are included in the analysis as well.  Each sample was prepared four times in total (2 replicates on 2 independent experiments). All ASO treatment were performed for 3 days at 1uM. 36 samples total. U2OS and HEK293 treated with control (non targetting ASOs called CTRL1, CTRL2, CTRL3 and SSO) ASOs or untreated. 4x HEKs -CTRL1, 4x HEKs -CTRL2, 4x HEKs- CTRL3, 4x HEKs untreated, 4x U2Os -CTRL1, 4x U2Os -CTRL2, 4x U2Os- CTRL3, 4x U2Os untreated, 4x U2OS- SSO.

first: Malong

last: Liza

first: Roskosch

last: Jessica

first: Roudnicky

last: Filip

first: Schmucki

last: Roland


title: RNA sequencing of AP1M1 KO HEK293 and U2OS

summary: AP1M1 is an obligatory member of the AP1 clatherin adaptor complex, important for cellular trafficking. In this study, we investigated the transcriptomic profiles of cells lines (HEK293 and U2OS) in presence and in absence of AP1M1.

overall_design: For this study, we generated the transcriptomic profiles of 2 cell lines (HEK293 and U2OS), either WT or KO for AP1M1. Each sample is a different clone. 32 samples total. 2x U2OS WT, 2xU2OS AP1M1 KO, 16x HEK293 WT, 12x HEK293 AP1M1 KO

first: Liza

last: Malong

first: Jessica

last: Roskosch

first: Filip

last: Roudnicky


title: Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues

city: philadelphia

first: Pengfei

last: Guo

state: PA

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

summary: Despite the extensive collection of formalin-fixed paraffin-embedded (FFPE) specimens, molecular tools for their in-depth analysis remain limited. Here, we introduce spatial FFPE-ATAC-seq, a technique that enables chromatin accessibility profiling in archival FFPE tissues with spatial resolution. Applied to both human and mouse samples, this method revealed the complex spatial organization and distinct cellular architectures, unlocking the potential of FFPE samples for comprehensive epigenomic studies and human disease research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Spatially resolved chromatin accessibility in FFPE samples.

first: Yanxiang

last: Deng

first: Liran

last: Mao

first: Yufan

last: Chen


title: DNA methylation protects cancer cells against non-canonical senescence

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

summary: Aberrant DNA methylation patterns are a hallmark of human cancers, prompting targeting of DNA methylation machinery to be explored as an anti-tumor strategy. DNA methyltransferase 1 (DNMT1) and ubiquitin like With PHD and Ring finger domains 1 (UHRF1) are crucial enzymes for DNA methylation maintenance. Unlike DNMT1, UHRF1 is overexpressed in most cancers and is a proven oncogene in vivo. Our previous work revealed that the degree of DNA methylation loss induced by UHRF1 depletion is more severe than DNMT1 depletion in colorectal cancer cells, indicating that targeting UHRF1 may be a more effective approach. Using an advanced chemical/genetic system, the auxin-inducible degron (AID) technology, we monitored the long-term effects of removing UHRF1 and/or DNMT1 in cancer cells, deciphering the mechanistic basis through bioinformatic tools. We found that chronic DNA demethylation triggers cancer cells to undergo cellular senescence. The loss of UHRF1 results in a more rapid and profound senescence phenotype than DNMT1 loss. Intriguingly, this senescence is not accompanied by DNA damage and functions independently of canonical senescence pathways such as p53 and p16/pRB. Non-canonical pathway investigations revealed that cytosolic p21 accumulation contributes to antiapoptosis during senescence. The suppression of cyclic GMP-AMP synthase (cGAS) also alleviates the senescence-associated secretory phenotype (SASP) and lysosomal activity, and this process is independent of stimulator of interferon genes (STING). Finally, xenograft experiments verified our findings in vivo. Our results highlight how DNA methylation protects cancer cells from non-canonical senescence and demonstrate the potential of targeting UHRF1 as a novel avenue for anticancer treatments.

overall_design: To elucidate the roles of UHRF1 and DNMT1 in the HCT116 cell line, we generated four distinct cell lines: wild-type (WT), UHRF1-AID, DNMT1-AID, and UHRF1-AID/DNMT1-AID. To analyze the kinetics of transcriptome, we treated these cell lines with auxin for 0, 2, 4, 6, and 8 days.

first: Kosuke

last: Yamaguchi

first: Xiaoying


title: DNA hypomethylation comprising transposable elements defines human regulatory T cells in cutaneous tissue and identifies their blood recirculating counterpart

city: Mainz

first: Niklas

last: Beumer

address: Langenbeckstrase 1

institute: University Medical Center Mainz

summary: Regulatory T cells (Treg cells) in tissues play crucial immunoregulatory and tissue-regenerative roles. Despite their significance, the epigenetic basis of human tissue-Treg cells, their differentiation as well as a migratory subset of tissue-Treg cells are incompletely understood. Here, we performed genome-wide DNA methylation analysis of human Treg cells from skin and blood and integrated these data into a multi-omic framework including chromatin accessibility and gene expression. This analysis revealed novel programs governing human skin Treg cell differentiation and delineated the presence of these programs across molecular levels. We discovered that subfamilies of transposable elements are a major constituent of the hypomethylated landscape of tissue-Treg cells. Based on DNA hypomethylation homologies, our data unveil that the population of blood CCR8+ Treg cells contains recirculating human skin Treg cells. Our findings provide novel insights into the biology of human tissue-Treg cells, which are essential to harness these cells for therapeutic purposes. This GEO record comprises the whole-geome bisulfite sequencing data used in the study.

overall_design:
Whole genome bisulfite sequencing of purified human skin Treg cells, skin Tconv cells, subcutaneous fat Treg cells, blood CCR8+ Treg cells, blood CD45RA+ Treg cells and blood CD45RA+ Tconv cells. Each cell type is represented by three biological replicates from individual donors.

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://ega-archive.org/datasets/EGAD50000001022) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Michael

last: Delacher

first: Markus

last: Feuerer


city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

overall_design: To elucidate the roles of UHRF1 and DNMT1 in the HCT116 cell line, we generated four distinct cell lines: wild-type (WT), UHRF1-AID, DNMT1-AID, and UHRF1-AID/DNMT1-AID. To analyze the kinetics of DNA methylation, we treated these cell lines with auxin for 0, 2, 4, 6, and 8 days.

first: Takashi

last: Ito


title: BLIMP1 negatively regulates IL-2 signaling in T cells

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: IL-2 signaling sustains immune homeostasis by fine-tuning the balance between effector and regulatory T cells. Our genome-wide CRISPR knockout screen using IL-2-dependent cells derived from a patient with Adult T-cell Leukemia (ATL) showed enriched sgRNAs targeting PRDM1 (encoding BLIMP1). BLIMP1 inhibits IL-2 production in T cells; however, its role in IL-2 signaling remains unknown. Here, we show that Prdm1 overexpression decreased IL-2 signaling in CD4+ T cells, while its deletion enhanced IL-2 signaling during influenza infection. Adoptive transfer of Prdm1 CKO Tregs into Rag2-/- mice elevated IL-2 signaling in T-cell induced colitis. Moreover, CRISPR/Cas9-mediated PRDM1 deletion augmented IL-2 signaling in human CD4+ T cells and natural Tregs with BLIMP1 binding to key genes affecting IL-2 signaling. Furthermore, ATL cells from acute patients exhibited increased IL-2 signaling but reduced BLIMP1 induction. Thus, BLIMP1 represses IL-2 signaling in T cells which is critical in orchestrating normal and pathophysiological immune responses.

overall_design: ChIP-seq were used to profile the binding sites of BLIMP1 in human Treg cells.

first: Suyasha

last: Roy

first: Min

last: Ren

first: Stephen

middle: M

last: Christensen

first: Peng

last: Li

first: Kairong

last: Cui

first: Bryan

last: Fisk

first: Tovah

middle: E

last: Markowitz

first: Neelam

last: Redekar

first: Keiko

last: Sakamoto

first: Keisuke

last: Nagao

first: Jangsuk

last: Oh

first: Rosanne

last: Spolski

first: Wei

last: Liao

first: Sigrid

middle: P

last: Dubois

first: Brian

middle: L

last: Kelsall

first: Keji

last: Zhao

first: James

last: Phelan

first: Warren

middle: J

last: Leonard


title: RIPK4 in Osteolineage cells regulate bone and bone marrow homeostasis via MFN2

city: Shanghai

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary: Human RIPK4 mutation leads to Bartsocas-Papas syndrome (BPS), characterized by severe craniofacial, skin and limb abnormalities. However, how RIPK4 regulates skeletal system development remains largely elusive. Herein, using global RIPK4 ablation mice model, we demonstrated that RIPK4 deficiency caused musculoskeletal disorders including severe osteoporosis, kyphosis, sarcopenia and induced myeloid-biased hematopoiesis and subsequently altered peripheral immune responses. Further detailed investigation confirmed that osteolineage RIPK4, not epidermal RIPK4, regulated the osteogenesis and bone marrow myelopoiesis via MFN2. These findings deciphered the essential role of RIPK4 in maintaining skeletal homeostasis and unveiled an unappreciated mechanism of RIPK4-MFN2 axis in regulating osteogenesis and bone marrow myelopoiesis.

overall_design: RNA sequencing was performed on cortical bones from UbcCre/ERT2 Ripk4fl/fl and Ripk4fl/fl mice mice.Selected osteogenesis related gene ontology (GO) analysis was performed.

first: Junjie

last: Gao

first: Chuan

first: Gan

first: Youshui

first: Changqing

last: Zhang


title: Specific oncogene activation of the cell of origin in mucosal melanoma

status: Public on May 18 2025

city: Brookline

first: Swathy

last: Babu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only develops from melanocytes lining internal organs, analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM-specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression, consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors, allowing this model to be used for MM therapeutic discovery. As this is a non-MAPK driven genetically engineered model of melanoma, our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK-driving mutations.

overall_design: single cell RNA sequencing of mucosal melanoma from patients

first: Jiajia

last: Chen

first: Chloé

middle: S

last: Baron

first: Kaiwen

last: Sun

first: Emily

last: Robitschek

first: Alicia

last: McConnell

first: Constance

last: Wu

first: Aikaterini

last: Dedeilia

first: Moshe

last: Sade-Feldman

first: Rodsy

last: Modhurima

first: Michael

last: Manos

first: Kevin

middle: Y

first: Anna

last: Cox

first: Calvin

middle: G

last: Ludwig

first: Manolis

last: Kellis

first: Elizabeth

middle: I

last: Buchbinder

first: Nir

last: Hacohen

first: Jiekun

last: Yang

first: Genevieve

last: Boland

last: Abraham

first: David

last: Liu

first: Leonard

last: Zon

first: Megan

last: Insco


title: Inhibition of integrin β1 activity support a naïve-like state in human induced  pluripotent stem cells

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

summary: Cell states are governed by cell-intrinsic properties and external cues that regulate cell shape and signaling via cell-cell junctions or adhesions. Integrin β1-mediated adhesion is dispensable in early mouse embryogenesis at pre-implantation but becomes indispensable post-implantation. This implies distinct roles for β1-integrins in the naïve pre-implantation and primed post-implantation pluripotent stem cells (PSC). These, however, remain poorly understood. We investigated integrin β1 control of naïve-like and primed human induced PSC (hiPSC) states. We find that integrin β1 is active in naïve and primed hiPSCs and the degree of activity varies in vitro on different extracellular matrices (ECMs). Integrin β1 inhibition in primed hiPSCs induces naïve-like colony features, reduces actomyosin contraction and ERK activity and alters gene expression, indicative of more naïve-like features. Reverting the primed state of pluripotency to naïve involves dramatic reorganization of colony morphology, actin and adhesions. Importantly, functional and single-cell transcriptomics analyses demonstrate that integrin β1 inhibition attenuates colony morphology transitions in cells exiting naïve pluripotency. These data reveal unprecedented integrin-dependent regulation of PSC states and demonstrate how integrin inhibitors may help to fine-tune hiPSC function and properties in vitro.

overall_design: Naïve hiPSCs (d0) were capacitated for 2 days (d2) with or without Mab13, and compared to primed hiPSCs (HEL24.3) with or without Mab13.

first: Ivaska

last: Johanna

first: Mikkola

last: Lea

first: Joshi

last: Shreya

first: Lönnberg

last: Tapio

first: Pasquier

last: Nicolas


title: Interleukin-27-Producing Cells in Gram-negative Neonatal Sepsis Display Diverse Phenotypes and Functions in the Liver

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

summary: Neonates have increased vulnerability to life-threatening infections due to the distinct immune landscape. Interleukin (IL)-27 is a key component of this immune profile that we have previously shown to be elevated in both newborn humans and mice. IL-27 continues to increase in the serum and tissues consistent with poor outcomes during gram-negative neonatal bacterial sepsis. Presently, we dissected the IL-27 producer profile at a single-cell level using IL 27p28eGFP reporter mice in our previously established model of sepsis with luciferase-expressing Escherichia coli. Whole animal imaging regionally highlighted the spleen, liver, and lungs as key infection sites by bacterial luminescence. Flow cytometry showed that IL-27 producers increased in the liver with infection and were predominantly F4/80+ and CD11b+. This information paired with single-cell RNA sequencing further identified the most robust populations as monocytes and derived cells, neutrophils, and Kupffer cells. The transcriptome demonstrated that some populations increased in bactericidal, metabolic, and inflammatory activities while others became less active. Sepsis is a disease characterized by extreme immune dysregulation similar to that shown in our cells. The phenotype and transcriptome of IL-27 producers from the livers of infected animals suggests suppressive activity, which contributes to the dysregulated immune environment observed in sepsis. Together, this work provides previously undescribed insight into the details of IL-27 producers during systemic early life infection. This further provides essential information to support IL-27 as a therapeutic target for neonatal bacterial sepsis.

overall_design: The livers of control or E. coli-infected neonatal mice were pooled and processed accordingly. The cells were gated for the live CD45+/CD3-/CD19-/GFP+ population and sorted using the BD FACSAria III available in the WVU FCSCCF. Downstream steps were performed according to the 10X Genomics manufacturer recommendations for the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (Product 1000269). Infected samples were compared to the control samples for analysis.

first: Jordan

middle: K

last: Vance

first: Nathalie

last: Lailler

first: Ashley

last: Divens

first: Jessica

last: Povroznik

first: Madhavi

last: Annamanedi

first: Kathleen

last: Brundage

first: Cory

last: Robinson


title: Specific oncogene activation of the cell of origin in mucosal melanoma [RNA-Seq]

first: Swathy

last: Babu

overall_design: Bulk RNA-sequencing data from mucosal melanoma and cutaneous melanoma zebrafish models

first: Jiajia

last: Chen

first: Chloé

last: Baron

first: Kaiwen

last: Sun

first: Emily

last: Robitschek

first: Alicia

last: McConnell

first: Constance

last: Wu

first: Aikaterini

last: Dedeilia

first: Moshe

last: Sade-Feldman

first: Rodsy

last: Modhurima

first: Michael

last: Manos

first: Kevin

first: Anna

last: Cox

first: Calvin

last: Ludwig

first: Manolis

last: Kellis

first: Elizabeth

last: Buchbinder

first: Nir

last: Hacohen

first: Jiekun

last: Yang

first: Genevieve

last: Boland

first: Brian

last: Abraham

first: David

last: Liu


title: Quiescent horizontal basal stem cells act as a niche for olfactory neurogenesis in a 3D organoid model

city: Boston

last: Lin

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

summary: The olfactory epithelium contains two basal stem cell populations that facilitate the normally life-long ability for neuronal regeneration that is required for maintaining our sense of smell over the long term. Horizontal basal cells (HBCs) are generally quiescent and only become active after direct injury to the epithelium that kills more than just the olfactory sensory neurons (OSNs). Globose basal cells (GBCs) lie apical to HBCs and are solely responsible for the ongoing generation of olfactory neurons in the undamaged epithelium. Understanding how these two neurogenic stem cell populations are regulated as OSNs are replenished is hampered by a lack of robust culture models. Here, we report the development of a 3-dimensional organoid model that recapitulates the neurogenic cascade while maintaining both HBCs and GBCs in culture. We use this model to demonstrate that despite their relative quiescence, HBCs form a critical niche for the emergence and composition of the organoid.

overall_design: We grew mouse olfactory epithelial organoids from single-cell dissociated tissue and subjected them to Parse single-cell RNAseq to characterize the cells contained within these organoids. Libraries were constructed following kit instructions and then sequenced on a NovaSeq6000 before processing using the provided computational pipeline.

first: Juliana

last: Gameiro

first: Marco

middle: A

last: Fornazieri


title: Cholinergic neuron-to-glioblastoma synapses in a human iPSC-derived co-culture model

status: Public on May 17 2025

city: Philadelphia

first: Yusha

last: Sun

address: 415 Curie Boulevard, Clinical Research Building, Room 105

institute: University of Pennsylvania Perelman School of Medicine

summary: This study examines a co-culture model of human iPSC-derived cholinergic neurons with glioblastoma (GBM) cells derived from GBM organoids (GBOs; UP-10072). To examine transcriptional regulation of GBM cells by cholinergic neurons, we performed scRNAseq of a set of distinct conditions: 1) cholinergic neurons only; 2) GBM cells only; 3) GBM cells treated with conditioned medium from neurons; 4) direct GBM cell-cholinergic neuron co-cultures.

overall_design: Cells from each of the 4 conditions listed previously were dissociated from coverslips. Whole cell scRNAseq libraries were performed via a modified Smart-seq3 protocol with cell barcodes. Therefore, cells could be pooled together and identified with a unique barcode. Gene expression data could be demultiplexed with a provided barcode whitelist.


title: Specific oncogene activation of the cell of origin in mucosal melanoma [SORT-seq]

first: Swathy

last: Babu

overall_design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT-seq platform.

first: Jiajia

last: Chen

first: Chloé

last: Baron

first: Kaiwen

first: Emily

last: Robitschek

first: Alicia

last: McConnell

first: Constance

last: Wu

first: Aikaterini

last: Dedeilia

first: Leonard

last: Zon

first: Megan

last: Insco


title: Specific oncogene activation of the cell of origin in mucosal melanoma [ATAC-Seq]

overall_design: Open chromatin profiling by ATAC-sequencing comparing cutaneous vs. mucosal zebrafish melanoma.

first: Moshe

last: Sade-Feldman

first: Rodsy

last: Modhurima

first: Michael

last: Manos

first: Kevin

first: Anna

last: Cox

first: Calvin

last: Ludwig

first: Manolis

last: Kellis

first: Elizabeth

last: Buchbinder

first: Nir

last: Hacohen

first: Jiekun

last: Yang


title: Total testosterone is not associated with muscle mass, function or exercise adaptations in pre-menopausal females

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

summary: Both circulating endogenous testosterone and muscle AR protein content are positively associated with muscle mass and strength in males, but there is no such evidence in females. Here, we tested whether circulating testosterone levels were associated with muscle mass, function, transcriptome or the muscle anabolic response to resistance training in pre-menopausal females.

overall_design:
Twenty-seven pre-menopausal, untrained females (aged 23.5 ± 4.8) underwent a 12-week resistance training program. Muscle strength, size, power and plasma and urine androgen hormone levels were measured. Skeletal muscle biopsies were collected before and after the training program to quantify the effect of resistance training on AR protein and mRNA content, and nuclear localisation. Primary muscle cell lines were cultured from a subset (n=6) of the participants’ biopsies and treated with testosterone to investigate its effect on myotube diameter, markers of muscle protein synthesis and AR cellular localisation.
Total testosterone was not associated with muscle mass or strength at baseline or with the changes in muscle mass and strength that occurred in response to resistance training. In vitro, supra-physiological doses of testosterone increased myocyte diameter, but this did not occur via the Akt/mTOR pathway as previously suggested. Instead, we show a marked increase in AR nuclear localisation with testosterone administration. In conclusion, we found that, bioavailable testosterone and the proportion of nuclear-localised AR, but not total testosterone, with skeletal muscle mass and strength in pre-menopausal females.

first: Briana

last: Gatto

first: Olivia

last: Knowles

first: Ross

last: Williams

first: Kinga

middle: N

last: Fiebig

first: Paul

last: Jansons

last: Gatta

first: Andrew

last: Garnham

last: Eynon

first: Glenn

last: Wadley

first: Brad

last: Aisbett

first: Séverine

last: Lamon


title: Multiplexed Self-Adaptable Janus Hydrogels Rescue Epithelial Malfunction to Shine Complete Trachea Repair

status: Public on May 16 2025

first: Boyu

last: Xu

address: 1239 Siping Road, Shanghai, P.R. China

institute: Tongji University

summary: To investigate the regenerative effects of the LA@PA-TA@C composite on tracheal reconstruction, comparative whole-transcriptome profiling was conducted between experimental cohorts and control groups.

overall_design: On day 14 post-intervention, tracheal tissues from both experimental and control groups (three biological replicates per group) were harvested and processed for whole-transcriptome RNA sequencing according to standardized protocols.

first: Yi

last: Chen

first: Hai

last: Tang

first: Yan

last: Zhang

first: Lei

last: Wang

first: Jun

last: Zhu

first: Lele

first: Anqi

last: Li

first: Xiang

last: Zeng

first: Binyu

last: Yin

first: Yu

last: Liang

first: Xiulin

last: Dong

first: Ziyin

last: Pan

first: Qingfeng

last: Bai

first: Long

first: Minglei

first: Yunlang

last: She

first: Weiyan

last: Sun

first: Kun

first: Chang


title: Lactate regulates cell differentiation of erythroid progenitor cells via histone lactylation modification [CUT&Tag]

city: zhengzhou

first: Hengchao

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: As a key metabolite of glycolysis, lactate plays important regulatory roles in a variety of biological events by regulating metabolic homeostasis and histone lactylation. However, the role of lactate and histone lactylation in human erythropoiesis remains unclear. Here, we explored the role of lactate in erythropoiesis by adding the glycolysis inhibitor 2-DG or exogenous lactate Na-La to decrease or increase intracellular lactate levels, respectively. The results showed that 2-DG treatment promoted erythroid progenitors differentiation, blocked cell cycle and reduced colony-forming ability of CFU-E. In contrast, Na-La delayed erythroid progenitors differentiation and promoted CFU-E colony formation. We also found that lactate levels directly regulated H3K14la and H3K18la intensity. Furthermore, CUT&Tag results showed that the lost H3K14la peaks after 2-DG treatment were mainly enriched in promoter region and were associated with cell cycle and division. RNA-seq results showed that gene expression pattern was dramatically altered after 2-DG treatment, and differentially expressed genes were enriched in cell cycle and division process. Integrated analysis of CUT&Tag and RNA-seq revealed that gene expression was regulated by H3K14la, and CCNB1, CFL1, CENPA, SKA2 and GNAI2 gene expression were verified by RT-qPCR. In conclusion, our study reveals that lactate affects the cell differentiation of early erythroid progenitors by regulating gene expression through histone lactylation.

overall_design: Here, we set 2.5mM 2-DG dosing which was an inhibitor of glycolysis to inhibit lactate level. After treated with 2.5mM 2-DG for 24h, we performed a H3K14la CUT&Tag of DMSO and 2-DG treated CFU-E cells.

first: Qianqian

last: Yang

first: Yan

last: Hou

first: Xiuyun

last: Wu


title: NEXN regulates vascular smooth muscle cells phenotypic switching and neointimal hyperplasia

city: Guangzhou

first: Hanyan

address: Zhujiang Hospital, Southern Medical University, Haizhu District, Guangzhou City, Guangdong Province

institute: Southern Medical University

summary: Vascular smooth muscle cells (VSMCs) exhibit significant heterogeneity and plasticity, enabling them to switch between contractile and synthetic states, which is crucial for vascular remodeling. NEXN has been identified as a high confidence gene associated with dilated cardiomyopathy (DCM). Existing evidence indicate NEXN is involved in phenotypic switching of VSMCs. However, a comprehensive understanding of the cell - specific roles and precise mechanisms of NEXN in vascular remodeling remains elusive. Using integrative transcriptomics analysis and smooth muscle specific lineage tracing mice, we demonstrate NEXN is highly expressed in VSMCs, and the expression of NEXN is significantly reduced during the phenotypic transformation of VSMCs and intimal hyperplasia induced by vascular injury. VSMC - specific NEXN deficiency promoted the phenotypic transition of VSMCs and exacerbated neointimal hyperplasia in mice following vascular injury. Mechanistically, we found NEXN primarily mediated VSMCs proliferation and phenotypic transition through endoplasmic reticulum (ER) stress and KLF4 signaling. Inhibiting ER stress ameliorated VSMCs phenotypic transition by reducing cell cycle activity and proliferation caused by NEXN deficiency. These findings indicate targeting NEXN could be explored as a promising therapeutic approach for proliferative arterial diseases.

overall_design: RNA-seq profiling of HASMCs pre-transfected with NC or si-NEXN followed by PDGF-BB stimulation for 24h.

first: Canzhao

last: Liu

first: Zexuan

last: Lin

first: Chaojie

first: Zhuohua

last: Wen

first: Wenjie

last: Guo

first: Zhaohui

last: Cai


title: Lactate regulates cell differentiation of erythroid progenitor cells via histone lactylation modification [RNA-seq]

last: Zhang

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

overall_design: Here, we set 2.5mM 2-DG dosing which was an inhibitor of glycolysis to inhibit lactate level. After treated with 2.5mM 2-DG for 24h, we performed a RNA-seq of DMSO and 2-DG treated CFU-E cells.


title: Physiological role and mechanisms of action for a long noncoding haplotype region [RNA-Seq]

city: Tucson

first: Yong

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

summary: Direct targeting of noncoding genomic regions harboring common sequence variants associated with human traits through in vivo animal model studies and precise genome editing in human cells is essential for closing the critical gap between genetic discoveries and physiological understanding. However, such investigation has been impractical for most of these variants as they have small effect sizes and are in haplotypes containing multiple single nucleotide polymorphisms (SNPs) spanning thousands of base pairs. We developed an integrated approach to address this challenge, combining an efficient two-step technique to precisely edit large haplotypes in human induced pluripotent stem cells and orthologous region deletion in phenotypically permissive animal models. As proof of principle, we applied this approach to examine a blood pressure associated locus with a noncoding haplotype containing 11 SNPs spanning 17.4 kbp. We found a robust blood pressure effect of nearly 10 mmHg and identified the physiological and molecular mechanisms involved.

overall_design: We identified a ~30.4-kbp region in the rat genome (rn7 chr2: 60,825,801-60,856,216) that was orthologous to the human rs1173771 LD region. We deleted the orthologous noncoding region in the Dahl salt-sensitive (SS) rat.RNA-seq of mesentery artery and kidney cortex were performed to identify any genes that might be influenced by the deletion of the rs1173771 LD orthologous region.

first: Hong

last: Xue

first: Manoj

last: Mishra

first: Pengyuan

first: Michael

last: Grzybowski

first: Rajan

last: Pandey

first: Kristie

last: Usa

first: Mark

last: Vanden Avond

first: Niharika

last: Bala

first: Abdel

last: Alli

first: Allen

middle: W

last: Cowley Jr

first: Qiongzi

last: Qiu

first: Andrew

last: Greene

first: Sridhar

last: Rao

first: Caitlin

middle: C

last: O'Meara

first: Aron

last: Geurts

first: Mingyu


title: Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [CUT&Tag]

first: Kei

last: Mizuno

state: MASSACHUSETTS

address: 450 Brookline Avenue

institute: Dana-Farber Cancer institute

summary: Prostate cancer is characterized as being histologically and molecularly heterogeneous. Additionally, epigenetic changes play an important role in regulating the progression of prostate cancer. However, epigenetic intraindividual heterogeneity is largely unknown in advanced prostate cancer. Hence, the epigenetic profiles of advanced prostate cancer, including autopsy cases, were investigated.

overall_design: CUT&Tag analysis for histone modifications on samples from advanced prostate cancer patients

first: Himisha

last: Beltran


title: Heterogeneity of IL-15-expressing mesenchymal stromal cells controls natural killer cell development and immune cell homeostasis

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

country: Austria

institute: Medical University of Vienna

summary: Bone marrow stromal cells have been shown to not only provide bone tissue structure, but guide hematopoiesis and lymphocyte differentiation. The role of Interleukin 15 (IL-15) expression in BM stromal cells and potential implication on immune cell homeostasis remains unknown. Here, we generated an IL15-IRES-EGFP knockin reporter mouse model to define and study IL15-expressing BM stromal cells.

overall_design: We profiled non-hematopoietic IL-15 expressing bone and bone marrow stromal cells from IL15-IRES-EGFP reporter mice. We enriched stromal and endothelial cells from eight 7 individual IL15-IRES-EGFP mice at the age of 8-12 weeks by FACS (Aqua Zombie- CD45- Ter119- and CD31- IL15-GFP+ for MSCs and CD31+ IL15-GFP+ for endothelial cells) and profiled them by scRNA-seq (10xGenomics, 3' chemistry)

first: Carmen

last: Stecher

first: Romana

last: Bischl

first: Matthias

last: Farlik


title: BLIMP1 negatively regulates IL-2 signaling in T cells

first: Peng

last: Li

state: MD

department: NHLBI

institute: NIH

overall_design: Purified CD4+ T cells from medLNs of influenza-infected WT or Prdm1 CKO mice were rested overnight in complete medium and restimulated with 200 IU/ml (influenza-infected) recombinant human IL-2 for 24 hours at 37°C. CD4+Foxp3+ Tregs from WT or Prdm1 CKO mice were pre-activated with anti-CD3 + anti-CD28, and cultured in complete RPMI media for 48 hours at 37°C.

first: Suyasha

last: Roy

first: Min

last: Ren

first: Stephen

last: Christensen

first: Kairong

last: Cui

first: Yaqiang

last: Cao

first: Bryan

last: Fisk

first: Tovah

last: Markowitz

first: Neelam

last: Redekar

first: Keiko

last: Sakamoto

first: Keisuke

last: Nagao

first: Jangsuk

last: Oh

first: Rosanne

last: Spolski

first: Wei

last: Liao

first: Sigrid

last: Dubois

first: Brian

last: Kelsall

first: Keji

last: Zhao

first: James

last: Phelan

first: Warren

last: Leonard


title: Physiological role and mechanisms of action for a long noncoding haplotype region [Hi-C]

first: Yong

last: Liu

overall_design: Human iPSC cells with homozygous BP-elevating or BP-lowering rs1173771 haplotypes were differentiated into endothelial (iEC) and vascular smooth muscle (iVSMC) cells. Region capture Micro-C with Dovetail Micro-C kit and Dovetail targeted enrichment panels plus customer designed probe panel targeting human chr5: 32,443,700-33,470,100 (hg38) to compare the chromatin conformation of the rs1173771 region.

first: Hong

last: Xue

first: Manoj

last: Mishra

first: Pengyuan

first: Michael

last: Grzybowski

first: Rajan

last: Pandey

first: Kristie

last: Usa

first: Mark

last: Vanden Avond

first: Niharika

last: Bala

first: Abdel

last: Alli

first: Allen

last: Cowley Jr

first: Qiongzi

last: Qiu

first: Andrew

last: Greene

first: Sridhar

last: Rao

first: Caitlin

last: O'Meara

first: Aron

last: Geurts

first: Mingyu

last: Liang


title: Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [eRRBS]

first: Kei

last: Mizuno

overall_design:
Reduced representation bisulfite sequencing (RRBS) analysis on samples from advanced prostate cancer patients

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

first: Himisha

last: Beltran


title: Preclinical and first-in-human of Purinostat Mesylate, a novel selective HDAC I/IIb inhibitor, in relapsed or refractory multiple myeloma and lymphoma [PDX]

status: Public on May 15 2025

city: Chengdu

first: Qiang

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

department: SKLB

institute: Sichuan university

summary: Purinostat Mesylate (PM), a highly selective HDAC I/IIb inhibitor, exhibits excellent antitumor activity in multiple MM and lymphoma cell lines and multiple mouse models, outperforming the pan-HDAC inhibitor panobinostat or first-line/second-line multi-drug combinations. Different from panobinostat, bulk RNA-seq analysis results revealed that PM targeted essential tumor survival factors, and triggered inflammation and interferon responses. ScRNA-seq of 5TMM models further indicated that PM enhanced antitumor immunity by boosting monocyte- and T cell-mediated immune responses.

overall_design: To investigate the effect of the I/IIb HDAC inhibitor Purostatin Mesylate (PM) on diffuse large B-cell lymphoma (DLBCL) gene expression, we treated the DLBCL PDX model mice with Vehicle or PM (10 mg/kg) for 24 hours. Tumor tissues were then collected and total RNA was extracted using Trizol. Gene expression profile changes were analyzed using RNA-seq.

first: Linyu

last: Yang

first: Yi

last: Wen

first: Yunyu

last: Feng

first: Ting

last: Niu

first: Lijuan

last: Chen


title: Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [RNA-seq]

overall_design: RNA-seq analysis on samples from advanced prostate cancer patients


title: Transcriptomic analysis of miAtxn2 knockdown effects on lumbar spinal cord in the TAR4/4 sporadic ALS mouse model

first: Ashley

middle: B

last: Robbins

address: 3501 Civic Center Blvd.

institute: Children's Hospital of Philadephia

summary: Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron death due to nuclear loss and cytoplasmic aggregation of the splice factor TDP-43. Pathologic TDP-43 associates with stress granules (SGs) and downregulating the SG-associated protein Ataxin-2 (Atxn2) using antisense oligonucleotides (ASOs) prolongs survival in the TAR4/4 sporadic ALS mouse model, a strategy that failed in clinical trials, likely due to inadequate target engagement. Here, we used an AAV with potent motor neuron transduction to deliver optimized Atxn2-targeting miRNAs. Atxn2 knockdown was achieved throughout the central nervous system (CNS) at a dose 40x lower than used in other work. In TAR4/4 mice, miAtxn2 treatment increased mean (54%) and median (45%) survival and robustly improved strength-related measures. There was a corresponding reduction of lower motor neuron death as well as reduced inflammatory markers in both motor cortex and spinal cord, and phosphorylated TDP-43 was reduced to wildtype levels. Transcriptome-wide dysregulation in the TAR4/4 model recapitulated ALS-associated gene signatures that were rescued after Atxn2 reduction, identifying therapeutic mechanisms and potential biomarkers for translation. Additionally, in slow progressing hemizygous mice, treatment slowed disease progression and in ALS patient-derived lower motor neurons, our vector transduced >95% of cells at an MOI 4 logs lower than previously reported for AAV and reduced human ATXN2 in a dose-dependent manner. Cumulatively these data support the utility of AAV-mediated RNAi against Atxn2 as a robust and translatable treatment strategy for sporadic ALS.

overall_design: PolyA mRNA profiles were generated from lumbar spinal cords of P19 TAR4/4 mice (n = 5  mice/treatment) and wild-type littermates (n = 6 mice). All mice received intravenous injections at P1 with either AAV9-miAtxn2 (TAR4/4 only) or vehicle control. Libraries were indexed and pooled for sequencing at a depth of 60M paired-end reads per sample using an Illumina NovaSeq 6000.

first: Defne

last: Amado

first: Alicia

middle: R

last: Smith

first: Beverly

last: Davidson


title: Epigenetic modulation of γ-globin expression as a new therapeutic approach for sickle cell disease

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Sickle cell disease (SCD) is a severe genetic disease caused by a mutation affecting the production of the β-globin chain. Its clinical severity is mitigated by the co-inheritance of mutations that reactivate the production of fetal hemoglobin (HbF) in adults. Here, we investigated the epigenetic regulation of the HBG genes and developed a novel approach based on programmable epigenome editing. Analysis of epigenetic marks at the HBG promoters revealed a distinct pattern of modifications in adult versus fetal erythroid cells. Our studies showed efficient HBG reactivation in the HEK293T cell line and in the progeny of hematopoietic stem and progenitor cells (HSPCs) when using activating epigenome editors targeting the HBG promoters, reaching up to 50% of HbF production and a substantial correction of the sickling phenotype. Our findings highlight the pivotal role of epigenetic modifications in the regulation of the β-globin locus and demonstrate that epigenome reprogramming represents a promising alternative to DNA-cleaving enzymes. This approach mitigates the risks associated with genotoxicity, providing a safe and effective strategy for treating SCD.

overall_design: We performed RNA-seq analysis in SCD and HD CD34+ HSPCs (4 donors) that were preactivated for 2 days, then electroporated with a combination of epigenome editors mRNA and sgRNA targeting the HBG promoters, and then cultured for 3 additional days. Cells electroporated with TE buffer only or with epigenome editors mRNA only were used as controls.

first: Simone

last: Amistadi

first: Annarita

last: Miccio

first: Letizia

last: Fontana


title: Analyzing gene expression profiles in the brain of miR-137 knockout mice versus wild-type mice

city: Taipei

first: Keng-Mao

last: Liao

state: Taipei

address: Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
We conducted this experiment using mice with a systemic knockout of miR-137. At 14 days post-birth, we sacrificed the mice and extracted key organs, including the brain.
To assess the impact of miR-137 knockout on brain gene expression, we extracted RNA from the livers of both wild-type and knockout mice and analyzed it using microarray.

overall_design: We collected RNA samples from two groups, consisting of miR-137 knockout mice and wild-type mice, each comprising three individuals.

first: Kang-Yi

last: Su


title: MicroRNA expression profling from 14 adult whole blood samples with flow cytometry cell fractions

first: Zhen

address: 131 Dongan Road

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Cellular heterogeneity represents one of the foremost confounding factors currently facing omics study, including miRNAome. Statistical methods leveraging the cell-specificity of miRNA expression for deconvoluting the cellular mixture of heterogeneous biospecimens, may provide a solution. The objective of this study is to develop and validate an algorithm for the deconvolution of heterogeneous samples such as whole blood based on miRNA expression profiling data.

overall_design: Fourteen adult blood donors were included in the study. From each individual, global miRNA expression levels were analyzed in the whole blood. In addition, cell fractions for eight immune cell types (CD4+ T cell, CD8+ T cell, B cell, NK cell, Monocytes, Neutrophil, Eosinophils and Basophil) were determined by flow cytometry.


title: Analyzing gene expression profiles in the liver of miR-137 knockout mice versus wild-type mice

summary:
We conducted this experiment using mice with a systemic knockout of miR-137. At 14 days post-birth, we sacrificed the mice and extracted key organs, including the liver.
To assess the impact of miR-137 knockout on liver gene expression, we extracted RNA from the livers of both wild-type and knockout mice and analyzed it using microarray.


title: An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Treg cells

status: Public on May 14 2025

city: New York

first: Nicholas

last: Arpaia

state: NY

department: Microbiology & Immunology

institute: Columbia University

summary: Treg cells play critical roles in tissue repair processes, certain of which are mediated by production of the growth factor amphiregulin (Areg). We developed a knock-in mouse model for detection of Areg production in live Treg cells, inserting a Thy1a (Thy1.1) construct into the endogenous Areg locus, such that for every transcript of Areg that is translated, a Thy1.1 transcript is also translated and trafficked separately to the cell surface. We used this mouse model to sort for Thy1.1- or Thy1.1+ (Areg-producing or -non-producing) lung Treg cells in models of lung damage (influenza A virus infection and bleomycin acute lung injury), and used them for assessment of gene expression and clonal expansion of these populations.

overall_design: Foxp3GFP mice were administered bleomycin (1 mg/kg). At 15 days post-instillation (dpi) (bleomycin), lung Treg cells were sorted into 4 separate pools (from 2-4 mice each), each pool was split between 2 wells, then paired wells were treated with IL-2, IL-7, and either IgG control or 4-1BB agonistic antibody (clone 3H3) (10 μg/ml) for 4h. Treg cells were then washed out of wells and lysed in Trizol for bulk RNA-seq.

first: Lucas

middle: F

last: Loffredo

first: Katherine

last: Kaiser

first: Adam

last: Kornberg

first: Samhita

last: Rao

first: Kenia

last: de los Santos-Alexis

first: Arnold

last: Han


title: STAT5 and STAT3 balance shapes dendritic cell function and tumor immunity

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

summary: Immune checkpoint blockade (ICB) has transformed cancer therapy. Therapeutic efficacy of ICB depends on dendritic cell (DC)-mediated tumor antigen presentation, T-cell priming and activation. However, the relationship between the key transcription factors in DCs and ICB efficacy remains unknown. Here, we discover that ICB reprogramed the interplay between the STAT3 and STAT5 transcriptional pathways in DCs, thereby activating T-cell immunity, and enabling ICB efficacy in cancer patients and tumor bearing mice. Mechanistically, STAT3 competed with STAT5 for JAK interaction, determining the fate of DC function. As STAT3 is often activated in the tumor microenvironment (TME), we designed specific PROTAC degraders of STAT3, SD-36 and SD-2301. Low doses of SD-36 selectively and preferentially degraded STAT3 in DCs and reprogramed the DC transcriptional network toward immunogenicity. Furthermore, SD-36 monotherapy efficiently treated mice bearing large, advanced tumors and ICB resistant tumors without any signs of toxicity. Notably, SD2301 exhibits superior therapeutic efficacy compared to SD-36. Thus, the crosstalk between STAT3 and STAT5 determines DC phenotype in the TME and STAT3-degradation holds promise for cancer immunotherapy.

overall_design: BMDC derivation protocol: Bone marrow was collected from the femurs and tibias of mice, and red blood cells were lysed using ACK lysis buffer. Dendritic cells were generated with bone marrow cells cultured with GM-CSF (20 ng/ml) and Flt3L (100 ng/ml) in IMDM (Gibco, 12440-053) supplemented with 10% FBS, 1% penicillin-streptomycin and 55 μΜ β-meraptoethanol for 7-10 days. BMDCs were either sorted as DC1 (CD11c+ Xcr1+) using a FACSAria flow cytometry sorter (BD Biosciences) or purified using biotin anti-mouse XCR1 antibody (BioLegend,148212) and anti-biotin microbeads (Miltenyi Biotec, 130-090-485) following the manufacturer’s protocols for subsequent experiments. Primary cell cultures were tested to be mycoplasma-free by MycoAlert Mycoplasma Detection kit. The RNA was isolated using the miRNeasy Micro Kit (Qiagen, 217084). 150PE RNA-seq was conducted by BGI Genomics via the DNBSEQ platform with a target of 30 million reads per sample.

first: Jiajia

last: Zhou

first: Kole

last: Tison

first: Michael

last: Pitter


title: Hippocampal epitranscriptomic (m6A) in IA-KA mouse model of Temporal Lobe Epilepsy

city: Dublin 4

first: Justine

last: Mathoux

address: Belfield

country: Ireland

institute: FutureNeuro Research Center

summary: RNA is subject to extensive processing and modification. N6-methyladenosine (m6A) is the most abundant internal modification and regulates RNA fate in several ways including stability and translational efficiency. Here, we provide a detailed analysis of the m6A-ome in hippocampus of a mouse model of temporal lobe epilepsy during epileptogenesis and into the epilepsy stage of the disease. Our results suggest that m6A represents a novel layer of complexity in gene regulation in epilepsy.

overall_design: m6A-RNA-sequencing of hippocampi of IA-KA mouse model of temporal lobe epilepsy

first: Gary

last: Brennan


title: Synaptotagmin-7 deficit causes insulin hypoactivity and contributes to behavioral alterations in mice

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

summary: Synaptotagmin-7 (Syt7) KO mice show diurnal fluctuations of mania- and depression-like behavioral abnormalities. Although GluN2B-NMDAR hypoactivity has been shown to be involved in the induction of mania-like behaviors of the Syt7 KO mice in the dark phase, the reasons for the depression-like behaviors in the light phase and behavioral fluctuation remain unknown. Here, we show that bipolar I disorder (BDI)-patient-induced pluripotent stem cell (iPSC)-derived islet-like organoids exhibited Syt7-dependent insulin secretion defects; moreover, Syt7-deficiency-induced insulin hyposecretion generated depression-like behaviors in Syt7 KO mice in the light phase. Furthermore, pancreatic insulin secretion and neuronal activity showed opposite diurnal patterns, in which the Syt7-deficiency-induced disequilibrium induced periodic antagonistic shifts in the mania- and depression-like behaviors. Finally, using RNA sequencing (RNA-seq) analysis, we explored downstream pathways that might underlie the diurnal fluctuation of behaviors. Therefore, Syt7-deficiency-induced insulin hypoactivity contributed to light-phase depression-like behaviors and diurnal behavioral fluctuations in the mice.

overall_design: The experimental conditions and variables under investigation, replicates are included, we used hippocampal samples from wild-type (WT) mice that were not treated with any drugs as the control group.

first: Yao-Nan

last: Liu

first: Qiu-Wen

last: Wang

first: Si-Yao

last: Lu

first: Wei

last: Shen

first: Chongye

last: Guo

first: Zhikai

last: Xing

first: Chang

last: Li

first: Shan

last: Sun

first: Sen-Fang

last: Sui

first: Shuangli

last: Mi

first: Fred H

last: Gage

first: Jun

last: Yao


title: An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Treg cells [scRNA-Seq]

first: Nicholas

last: Arpaia

overall_design: AregThy1.1/Thy1.1 mice were administered saline (control), influenza A virus (IAV) (275 TCID50) or bleomycin (1 mg/kg). For experiment 1, timepoints used were 5 days post-instillation (dpi) for saline (control), 5 dpi for IAV, and 12 dpi for bleomycin. For experiment 2, timepoints used were 21 dpi for saline (control) and 21 dpi for bleomycin. Lung Treg cells were sorted for Thy1.1- (Areg-non-producing) and Thy1.1+ (Areg-producing) populations, then sorted populations were prepared for single cell RNA-seq using 10x Genomics protocols. GEX: gene expression; TCR: T cell receptor; HTO: hash tag oligos.

first: Lucas

last: Loffredo

first: Katherine

last: Kaiser

first: Adam

last: Kornberg

first: Samhita

last: Rao

first: Kenia

last: de los Santos-Alexis

first: Arnold

last: Han


title: An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Treg cells [RNA-Seq]

overall_design: AregThy1.1/Thy1.1 mice were administered influenza A virus (IAV) (275 TCID50) or bleomycin (1 mg/kg). At 8 days post-instillation (dpi) (IAV) or 12 dpi (bleomycin), lung Treg cells were sorted for Thy1.1- (Areg-non-producing) and Thy1.1+ (Areg-producing) populations, then sorted populations were lysed for total mRNA for bulk RNA-seq.


title: RNAseq analysis of human neutrophils from people with DMARD-refractory rheumatoid arthritis

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

summary: We report gene expression profiles of blood neutrophils from (1) people with DMARD-refractory RA before commencement of anti-TNF therapy and (2) healthy controls.

overall_design: Neutrophils (purity >97%) were isolated from peripheral blood by centrifugation through density-gradient reagent (Ficoll-Paque). RNA was isolated using Trizol:chloroform, cleaned up by Qiagen RNeasy kit including on-column DNase digest and sequenced on the DNBseq platform.


title: Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [ChIP-seq]

first: Kei

last: Mizuno

overall_design: ChIP-seq analysis for histone modifications on samples from advanced prostate cancer patients

first: Himisha

last: Beltran


title: RNAseq analysis of human neutrophils from people with rheumatoid arthritis

summary: We report gene expression profiles of blood neutrophils from (1) people newly-diagnosed with rheumatoid arthritis (early RA) before commencement of disease-modifying anti-rheumatic drug therapy, (2) DMARD-refractory RA (severe RA) before commencement of anti-TNF therapy and (3) healthy controls.

overall_design: Neutrophils (purity >97%) were isolated from peripheral blood by centrifugation through density-gradient reagent (Polymorphprep or Ficoll-Paque). RNA was isolated using Trizol:chloroform, cleaned up by Qiagen RNeasy kit including on-column DNase digest and sequenced on the Illumina HiSeq 2000 platform.


title: Preclinical and first-in-human of Purinostat Mesylate, a novel selective HDAC I/IIb inhibitor, in relapsed or refractory multiple myeloma and lymphoma

first: Qiang

last: Qiu

overall_design: To investigate the effect of the I/IIb HDAC inhibitor Purostatin Mesylate (PM) on Multiple Myeloma (MM) gene expression, we treated MM.1S CDX model mice with Vehicle or PM (10 mg/kg) for 24 hours. Tumor tissues were then collected and total RNA was extracted using Trizol. Gene expression profile changes were analyzed using RNA-seq.

first: Linyu

last: Yang

first: Yi

last: Wen

first: Yunyu

last: Feng

first: Ting

last: Niu

first: Lijuan

last: Chen


title: Gene expression changes of CRISPR/Cas13d-mediated HoxB13 knockdown in 293FT cells and LNCaP95 mouse liver metastasis

city: Durham

first: Qianben

last: Wang

address: 905 S. Lasalle Street

institute: Duke University

summary: To examine the potential off-target effects by CRISPR/Cas13d-mediated HoxB13 knockdown in 293FT cells. To analyze differentially expressed genes upon CRISPR/Cas13d-mediated HoxB13 knockdown in LNCaP95 mouse liver metastasis.

overall_design: 293FT cells were transfected with non-targeting pre-gRNA control(gCtrl) or pre-gRNA targeting HoxB13(gHoxB13) expression plasmid in combination with Cas13d expression plasmid for 24h. LNCaP95 mouse liver metastasis samples were collected after mice treated with LNP-Cas13d-pre-gControl or SCORT LNP-Cas13d-pre-gHoxB13 for 72h in the final treatment.RNA-seq was performed to characterize the differentially expressed genes between gCtrl and gHoxB13 groups.

first: Zhifen

last: Cui

first: Furong

last: Huang

first: Kun

last: Fang

first: Yufan

last: Zhou


title: Aging modulates the immunosuppressive, polarizing and metabolic functions of blood-derived myeloid-derived suppressor cells (MDSCs)

status: Public on May 13 2025

city: Ulm

first: Emma

last: Keltsch

address: Eythstr. 24

department: Department of Pediatrics and Adolescent Medicine

institute: University Medical Center Ulm

summary: With aging, the immune system undergoes immunosenescence, accompanied by chronic low-grade inflammation (inflammaging). Balanced immunity relies on effector and regulatory cells, with myeloid-derived suppressor cells (MDSCs) playing a key regulatory role. MDSCs, a heterogeneous population of immature myeloid cells, develop under inflammatory conditions and primarily suppress T cell activity. The age-dependent increase in myelopoiesis and inflammation, along with reduced immune reactivity, suggests that changes in the number and function of regulatory cells, such as MDSCs, might strongly contribute to age-related modifications of immune responses. While studies in mice have demonstrated an age-related increase in MDSC numbers, human studies have predominantly focused on cancer patients, making it challenging to separate the effects of aging and cancer on MDSC induction. Therefore, we analyzed MDSC increases in older individuals without a history of cancer. Furthermore, we excluded patients with neurodegenerative, cardiovascular or autoimmune diseases. We found a significant increase in circulating MDSCs in old donors. In addition, in vitro generated, blood-derived MDSCs from old donors exhibited enhanced immunosuppressive and Th2 polarizing capacity. RNA sequencing indicated age-related metabolic changes. These findings highlight that age-related changes in MDSCs contribute to dysregulated immune functions during aging.

overall_design: This study investigates age-related transcriptional changes in isolated CD14+ and CD14+-derived MDSCs (myeloid-derived suppressor cells) using RNA-seq. Blood was collected from young (20-35 years) and old (70+ years) donors. CD14+ cells from each donor were isolated and used for RNA isolation and/or in vitro-induction of MDSCs. The dataset consists of 7 RNA-seq samples from CD14+ cells (3 young, 4 old) and 9 from CD14+-derived MDSCs (4 young, 5 old). The goal is to assess age-related transcriptional changes within CD14+ cells, differentiated MDSCs, and during the monocyte-to-MDSC differentiation process.

first: Gudrun

last: Strauss


title: YTHDF2-KIF26B-Wnt signaling forms a positive-feedback regulatory loop to maintain ISC stemness

status: Public on May 12 2025

city: Beijing

first: Ye-guang

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: m6A modification plays a regulatory role in the stemness of small intestinal epithelial stem cells (ISCs), which is crucial for the renewal of intestinal epithelium and the maintenance of homeostasis. Although existing research has demonstrated that METTL3, as an m6A ‘writer’, is a crucial protein in the regulation of the stemness of ISCs, the mechanism by which the function of downstream ‘reader’ proteins is regulated has not been fully elucidated. In this study, we found that the knockout of Ythdf2 could significantly down-regulate the expression of the stemness marker gene Lgr5, suggesting that this ‘reader’ protein plays an important role in the regulation of the stemness of ISCs. Upon exploring the specific downstream mechanisms, we discovered that YTHDF2 promoted the Wnt signaling pathway by regulating the expression of KIF26B. This helps maintain the expression of Lgr5 in stem cells, thus preserving the stemness of these cells. Meanwhile, the expression of YTHDF2 itself is also regulated by the Wnt signaling pathway. Overall, YTHDF2 forms a positive-feedback regulatory loop centered around the Wnt signaling pathway. This loop ensures that ISCs remain in a stem-cell state, enabling the intestinal epithelium to function stably and properly.

overall_design: Cultivate the small intestinal epithelial organoids of Villin-CreERT2; Lgr5-EGFP-IRES-CreERT2; Ythdf2fl/fl mice in vitro. The Lgr5-GFP+ cells are sorted on the 4th or 6th day after the treatment with 0.5 μM EtOH/4-OHT.  Then their RNA was collected and performed RNA sequencing.

first: Zinan

last: Liu

first: Chunlin

last: Li

first: Meimei

first: Yuan

first: Ye-Guang


title: MLL3/4 Direct a Gene-expression Program Required for Efficient Platelet Production [CUT&RUN]

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: MLL3 and MLL4 are the mjor histone lysine methyltransferases for the active enhance mark H3K4me1. We observed that platelet counts are dramatically decreased in the MLL3/4 SET-deletion mice. Cultured megakaryocytes from MLL3/4 SET-deletion fetal liver were used for RNA-seq analysis to investigate the changes in gene expression. We also performed CUT&RUN analysis to examine the changes in enhncers that may regulate those gene expression. We included PTIP in this study, because it is an important co-factor of the MLL3/4 complex, and knockout of PTIP also leads to decreased platelet production.

overall_design: 3 samples for each genotype were used for CUT&RUN using IgG control, anti-H3K4me1, anti-H3K27ac and anti-H3K4me3 antibodies.

first: Guozhen

last: Gao

first: Kevin

last: Lin

first: Margarida

last: Santos


title: MLL3/4 Direct a Gene-expression Program Required for Efficient Platelet Production [RNA-seq]

overall_design: 3 samples for each genotype (WT, PTIP-KO, MLL3/4 DKO) were used for RNA-seq


title: B cell-derived nociceptin/orphanin FQ contributes to impaired glucose tolerance and insulin resistance in obesity

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

summary: Immune-derived opioid peptides have been implicated in immune regulation and inflammatory processes. Here, we investigate the effects of nociceptin/orphanin FQ (N/OFQ) on metabolic function and inflammation in obesity. Selectively targeting N/OFQ, encoded by the Pnoc gene, in B cells mitigates the adverse metabolic effects of diet-induced obesity and enhances insulin sensitivity and glucose tolerance. Notably, B cell-specific Pnoc knockout mice display a marked reduction in markers of immune cell migration and diminished macrophage recruitment in adipose tissue and liver. Mechanistically, we identify that N/OFQ promotes macrophage recruitment and metabolic inflammation, exacerbating glucose intolerance and insulin resistance during obesity. Overall, the immunomodulatory properties exhibited by the N/OFQ-NOP system render it a promising therapeutic target for mitigating metabolic inflammation.

overall_design: Gene expression profiling analysis of RNA-seq data of PMA-differentiated THP-1 cells (Vehicle vs. 10 ng/ml N/OFQ)


overall_design: Gene expression profiling analysis of RNA-seq data from visceral adipose tissue (eWAT) of Pnoc∆CD19 and littermate control animals (CD19-Cre). Organs were collected after 17 weeks of high-fat diet feeding.


overall_design: Gene expression profiling analysis of RNA-seq data from liver tissue of Pnoc∆CD19 and littermate control animals (CD19-Cre). Organs were collected after 17 weeks of high-fat diet feeding.


title: Histone ChIP-Seq of B16-F10 melanoma cell lines (mouse)

city: Little Rock

first: Michael

middle: Anton

last: Bauer

state: United States

address: 4301 W Markham  Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Unleashing the immune anti-tumor response through immune checkpoint blockade (ICB) has been successful in treating many solid-tumor malignancies, including metastatic melanoma. When successful, the ICB response can be potent; however, half of patients fail to respond. ICB responsiveness is impacted by the harsh solid tumor microenvironment (TME), which is characterized by metabolic stress. The TME impacts tumor antigenicity, with ICB-responsive melanomas exhibiting increased major histocompatibility complex class I (MHC-I) expression. Further investigation of tumor immunogenicity in the context of the TME may improve cellular therapies. Here, we define and characterize an epigenetic mechanism regulating melanoma antigen presentation driven by prolonged metabolic stress. Murine and human melanoma cell lines were cultured under prolonged metabolic stress, forcing cells to adapt to the absence of glucose. Melanoma cells adapted to the absence of glucose have IFN-γ-independent increases in MHC-I and an increased sensitivity to T cell-mediated killing. Proteomic analysis revealed dysregulation of histone epigenetic modifiers under prolonged metabolic stress, specifically loss of histone methyltransferase EZH2 (Enhancer of Zeste Homolog 2). EZH2 directly silences gene transcription via catalyzing H3K27me3. Following metabolic adaptation, ChIP-sequencing and ChIP-PCR revealed H3K27me3 loss at genes specific to MHC-I antigen presentation. Prolonged metabolic stress in melanoma cells blunt EZH2 levels and H3K27me3 levels at promoters of genes regulating MHC-I presentation, resulting in elevated MHC-I antigenicity and increased CD8+ T cell killing. This demonstrates potential for EZH2 abundance and mutational status as a prognostic indicators of ICB-responsiveness in metastatic melanoma and supports EZH2 inhibition as adjuvant for immunotherapies.

overall_design: In this study, we examine the impact of metabolic adaptation induced by prolonged glucose deprivation, as found in the TME, on MHC-I presentation and overall immunogenicity of melanoma cells. ChIP sequencing reveals H3K27me3 reduction at MHC-I genes during prolonged metabolic stress. We find that metabolic adaptation of melanoma cells results in loss of EZH2, restoration of MHC-I expression and antigen presentation, and an increase in T cell mediated tumor killing. Here we provide H3K27me3 ChIP-Seq for B16-F10 melanoma mouse cell line cultured under 2 conditions; normal glucose and no glucose replaced with galactose.

first: Jacob

last: Edmondson

first: Megan

last: Reed

first: Daniel

last: Fil

first: Billie

last: Heflin

first: Alyson

last: McKinnon

first: Nathan

last: Avaritt

first: Mary

last: Phillips

first: Sean

middle: D

last: Taverna

first: Alan

last: Tackett

first: Brian

last: Koss


title: The CXCL16/CXCR6 axis is linked to immune effector cell-associated neurotoxicity in chimeric antigen receptor (CAR) T cell therapy

city: Muenster

first: I-Na

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

summary: Immune effector cell-associated neurotoxicity syndrome (ICANS) is a significant complication of CAR T-cell therapy, affecting 20% to 70% of patients. Unraveling the mechanisms underlying ICANS is crucial for improving patient outcomes. This study employed single-cell RNA sequencing (scRNA-seq) to analyze cerebrospinal fluid (CSF) cells from ICANS patients, uncovering a ICANS-specific increase in proliferating T cells compared to controls that contained both CAR  and non-CAR expressing cells indicating bystander activation. These ICANS-specific proliferating T cells showed elevated expression of cytotoxic genes and the chemokine receptor gene CXCR6. Spatial transcriptomic mapping of postmortem choroid plexus and brain parenchyma of a patient with lethal ICANS revealed widespread myeloid cell infiltration and the spatial association of CXCR6+ T cells to CXCL16-expressing myeloid cells. These findings suggest that the CXCL16/CXCR6 axis may drive the recruitment of cytotoxic CAR CD4 T cells to the central nervous system during ICANS, potentially contributing to its pathogenesis and suggesting diagnostic and therapeutic potential.

overall_design: We analyzed scRNA-seq data of cerebrospinal fluid (CSF) samples from CAR T cell–treated patients who developed ICANS (n=5) within 5–21 days post-infusion. ICANS severity was graded as follows: grade 1 (n=1), grade 2 (n=2), grade 3 (n=1), and grade 4 (n=1). Control samples were obtained from patients with idiopathic intracranial hypertension and functional neurological disorders. We performed spatial transcriptomics (Visium HD) on postmortem choroid plexus and brain tissue from a patient with fatal grade 4 ICANS.

first: Louisa

last: Müller-Miny

first: Oliver

middle: M

last: Grauer

first: Gerd

last: Meyer zu Horste


title: Mechanism of cytarabine-induced neurotoxicity

city: Bethesda

first: Chuanyuan

last: Chen

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution

city: Shanghai

first: Yuanbo

last: Liu

address: 100 Hai Ke Rd.

institute: Shanghai Institute of Organic Chemistry

summary: Recent studies have revealed that nucleotide-containing metabolites, including nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), 3′-dephospho-coenzyme A (dpCoA), uridine diphosphate glucose (UDP-Glc), and uridine diphosphate N-acetyl glucosamine (UDP-GlcNAc), can be incorporated into the RNA 5′-terminus as noncanonical initiating nucleotides (NCIN), resulting in NCIN-capped RNA (NCIN-RNA).

overall_design: We subjected 20 μg total RNA from mouse liver mixed with 0.014 ng spike-in RNAs with ascending ratios of NAD-capped forms 0% (i.e., 100% m7G-capped), 1%, 5%, 10%, and 20% to CompasSeq, followed by CompassAnalyzer analysis of NCIN-RNA profiles.

first: Dean

last: Li

first: Xueting

last: Wang

first: Kongyan

last: Niu

first: Jun

last: Bai

first: Lefeng

last: Qu


title: Sickle cell disease induces chromatin introversion and ferroptosis in CD8+ T cells to suppress anti-tumor immunity

first: Benxia

last: Hu

state: Texas

address: 431 Fannin

institute: University of Texas Health Science Center at Houston

summary: Understanding how genetic disorders affect CD8+ T cells in the tumor microenvironment is key to improving cancer immunotherapy. Individuals with sickle cell disease (SCD), the most prevalent inherited blood disorder, have a higher risk of developing certain cancers than the general population, but the mechanisms driving this increased risk remain unclear. Our study revealed that SCD altered CD8+ T cell 3D genome architecture, triggering ferroptosis and weakening anti-tumor immunity, thereby promoting tumor growth. Using murine and humanized SCD models, we found that disrupted chromosomal interactions in CD8+ T cells reduced the expression of anti-ferroptotic genes, including SLC7A11 and hydrogen sulfide (H2S) biogenesis genes, thereby increasing susceptibility to ferroptosis. Therapeutic restoration of H2S concentration in SCD mice rescued SLC7A11 expression, mitigated ferroptosis, and enhanced immune and anti-tumor responses. These findings highlight the impact of inherited disorders on cancer immunity and suggest precision immunotherapy strategies for affected individuals.

overall_design: We utlizied in situe Hi-C to map the alterations of 3D genome between CD8+ T cells from Health and sickle cell disease (SCD).

first: Wenbo

first: Zilong

last: Zhao

first: Chunru

last: Lin

first: Liuqing

last: Yang


title: Autophagy controls DNA accessibility to immunoglobulin variable regions and centroblast dynamics

city: London

first: Marta

last: Crespi-Sallan

address: Charterhouse Square

department: Haemato-Oncology

institute: Barts Cancer Institute


title: Autophagy controls DNA accessibility to immunoglobulin variable regions and centroblast dynamics [scATAC-seq]

summary: Nuclear lamina dynamic changes influence chromatin landscape. Mechanisms governing nuclear lamina behavior have not been studied within the adaptive immune context. Here, we show autophagy regulates withdrawal of nuclear lamina protein, Lamin B1, in B cells transiting germinal centers (GCs). Autophagy inhibition was sufficient to keep Lamin B1 nuclear integrity preventing NP-CGG immunisation-induced nucleotide substitution during the somatic hypermutation process resulting in compromised B cell capacity to build up a competitive high-affinity antibodies. Atg7 loss-of-function in GC B cells resolved in decreased chromatin accessibility. Single-cell RNAseq revealed centroblasts accumulate in dark zone upon autophagy impairment due to inefficient signals to finish GC reaction. Hence, GC B cells rely on autophagy for Lamin B1 disassembly, becoming autophagy key part of somatic hypermutation process and centroblast dynamics.

overall_design: Splenocytes were isolated from NP-CGG immunised for 10- and 21- days Cγ1Cre+/- and  Cγ1ATG7fl/fl mouse models. To increase the proportion of Germinal Center B cells (GC B) up to 25%  from total splenocyte population, PNA+ cells were MACS separated and then cell sorted (FACS) according to : Viability Dye -; B220+; GL7+, CD95+. After that GC B cells were mixed in 1/4 proportion to total splenocytes

last: Crespi Sallan

first: Andrejs

last: Braun


title: Autophagy controls DNA accessibility to immunoglobulin variable regions and centroblast dynamics [scRNA-seq]


title: Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [bulk RNA-Seq]

status: Public on May 11 2025

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

summary: recision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis.

overall_design: RNA was extracted using ARCTURUS® PicoPure® RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturers’ instructions. Library prep was completed using Novogene NGS RNA Library Prep Set and sequenced on a NovaSeq 6000 or NovaSeq X Plus using Illumina PE-150 strategy. Sequenced reads were aligned to the GRCh38 human genome using Bowtie2 (v2.4.4). PCR duplicates were removed using SMAtools (v1.15.1). Count matrices were generated using Subread (v2.0.1).

first: Chris

last: Mahony

middle: P


title: UBE2F inhibits Natural Killer cell tumor immunity by activating the ARIH2-CRL5 complex to degrade interleukin 15 receptors

city: Moonee Ponds

first: Nicholas

last: Huntington

state: VIC

address: 27 Norwood Cres

institute: oNKo-innate Pty Ltd

summary: Interleukin-15 receptor (IL-15R) agonists induce anti-tumor immunity in pre-clinical models, however, dose-limiting toxicity has hampered their clinical development. An alternative is to target pathways downstream of the IL-15R to access different therapeutic profiles. We performed genome-wide CRISPR screens to reveal the complete IL15R signaling mechanism in NK cells and discovered ubiquitin-dependent IL15R degradation as the dominant mechanism restraining IL-15R signaling. Top hits included the NEDD8 E2conjugating enzyme UBE2F & ubiquitin E3-ligase ARIH2, along with Cullin-5 RING E3 Ligase (CRL5) members. UBE2F was required for CUL5 neddylation/activation whereas ARIH2 contributed to CRL5-mediated IL-15RB degradation. Ablation of ARIH2 or UBE2F enhanced IL-15RB surface expression/signaling & proinflammatory cytokine production, and augmented natural & CAR-mediated cytotoxicity. In mice lacking Arih2, Rnf7 or Ube2f, IL-15R hyperresponsive NK cells resulted in superior in vivo anti-tumor immunity against primary and disseminated metastatic tumors. Thus, we have identified the enzymes UBE2F and ARIH2 as tractable immunotherapy drug targets.

overall_design: Primary human NK cells from 3 donors (B77, B78, & B80). For each donor there AAVS1-edited control cells, ARIH2-edited cells and UBE2F-edited cells. All edits were performed using CRISPR (please see the corresponding manuscript for details on gRNAs etc).

first: Iva

last: Nikolic

first: Joseph

last: Cursons


status: Public on May 10 2025

city: Fuzhou

first: zhaofeng

last: zhang

address: No. 29 Xinquan Road

institute: Fujian Medical University Union Hospital

summary: The farnesoid X receptor (FXR) is a nuclear receptor mainly expressed in the liver and intestine. In the intestine, FXR plays a crucial role in regulating lipid metabolism, bile acid homeostasis, and intestinal barrier function.Activation of FXR can lead to the regulation of a variety of genes involved in these processes. For example, it can affect the absorption and transport of lipids and bile acids through the intestine,in this paper,we Ursodeoxycholic acid alleviates aortic aneurysm and dissection through the intestinal farnesoid X receptor/ceramide synthesis 2 axis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FXR in mice intestine.

first: Zhaofeng

last: Zhang

first: Linfeng

last: Xie

first: Xinfan

first: Liangwan

last: Chen


title: Effect of fasting-refeeding on gene expression in young and old killifsh adipose tissue.

city: Cologne

first: Kazuto

last: Kawamura

address: Joseph-Stelzmann-Str. 9b

department: Molecular Genetics of Ageing

institute: Max Planck Institute for Biology of Ageing

summary: Fasting-refeeding paradigms result in drastic shifts in metabolism and gene expression patterns. The effect of fasting-refeeding changes between young and old individuals. We sought to decipher the changes in response to fasting-refeeding in young and old animals by profiling gene expression in adipose tissue of killifish Nothobranchius furzeri.

overall_design: Wild-type killifish N. furzeri GRZ-AD were fasted for 3 days and refed for 1 day at either young or old age. Young killifish were 7 weeks old compared to 18 weeks for the older time point.

first: Roberto

last: Ripa


title: A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment [scRNA-seq]

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Vitamin A/Retinoic Acid (Vit A/RA) signaling is essential for heart development.  In cardiac progenitor cells (CPCs), RA signaling induces the expression of atrial lineage genes while repressing ventricular genes, thereby promoting the acquisition of an atrial cardiomyocyte cell fate. To achieve this, RA coordinates a complex regulatory network of downstream effectors that is not fully identified. To address this gap, we applied a functional genomics approach (scRNAseq, scATACseq and ChIP-seq) to untreated and RA-treated human embryonic stem cells (hESCs)-derived CPCs. Unbiased analysis revealed that the Hippo effectors YAP and TEAD4 are integrated with the atrial transcription factor enhancer network, and that YAP1 is necessary for activation of RA-enhancers in CPCs. Furthermore, scRNAseq analysis of control and conditionally YAP KO mouse E7.75 embryos (Sox2cre) revealed that the expression of atrial lineage genes such as NR2F2 is compromised by YAP deletion in the CPCs of the second heart field.  Accordingly, we found that YAP is required for the formation of an atrial chamber but is dispensable for the formation of a ventricle, in hESC-derived patterned cardiac organoids. Overall, our findings revealed that YAP1 is a non-canonical effector of RA signaling essential for the acquisition of atrial lineages during cardiogenesis.

overall_design: H1 hESCs WT and YAP KO were plated in 24well plates.  Cells were treated with GSK3i (XV 50nM) in mTeSR1 for 24h (Day 0 to Day 1). After that, media was changed and RPMI/B27- media was applied for 48h. At day 3, half of the media was replaced and IWP2 7.5uM was added for 48h. At D4, Retinoic Acid 1uM was added to the media for 3 days. Cells were collected at Day 5 or Day 30 of differentiation. For CPC experiments, cells were collected 24h after RA addition (or untreated control), at Day 5,for single-cell RNAseq. For CMs analysis, untreated or RA-treated CMs were collected at Day 30 of differentiation.   Two to three differentiation experiments performed at the same time were pooled for library prep and downstream sequencing analysis.

first: Conchi

last: Estaras

first: Elizabeth

last: Abraham

first: Ling

last: Huang

first: April

last: Williams


title: Regulation of Redox Homeostasis by ATF4-MTHFD2 Axis during White Adipose Tissue Browning

city: Cheonan-si, Chungcheongnam-do

first: Ahyeon

last: Son

address: 25 Bongjeong-ro, Dongnam-gu

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science

summary: Maintaining redox balance is crucial for mitochondrial homeostasis. During browning of white adipocytes, both the quality and quantity of mitochondria undergo dramatic changes. However, the mechanisms controlling the redox balance in the mitochondria during this process remain unclear. In this study, we demonstrate that thermogenic activation occurs before mitochondrial biogenesis during cold-induced browning of inguinal white adipose tissue (iWAT) and is accompanied by increased mitochondrial stress and integrated stress response (ISR) signaling. Specifically, cold exposure enhances the expression of ATF4, an ISR effector. Adipocyte-specific deletion of ATF4 results in increased energy expenditure, but paradoxically leads to a lower core body temperature, and heightened pro-inflammation in iWAT after cold exposure, which is restored by the antioxidant, MitoQ. Mechanistically, ATF4 regulates the redox balance through MTHFD2, an enzyme involved in mitochondrial redox homeostasis by NADPH generation. Cold exposure upregulates MTHFD2 expression in an ATF4-dependent manner, and its inhibition by DS18561882 in vivo leads to impaired cold- induced mitochondrial respiration similar to the effects of ATF4 loss. These findings suggest that ATF4 is essential for redox balance via MTHFD2, thereby affecting tissue homeostasis during iWAT browning.

overall_design: RNA-seq analysis on iWAT from Atf4WT and Atf4AKO mice housed in temperature or exposed to cold for 24 hours.

first: Rehna Paula

last: Ginting

first: Hoang-Anh

last: Pham-Bui

first: Choijamts

last: Munkhzul

first: Siti Aisyah

last: Fuad

first: Jong-Seok

last: Moon

first: Jaeseok

last: Han

first: Mihye

last: Lee

first: Min-Woo


title: A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment [scATAC-seq]

overall_design: H1 hESCs WT and YAP KO were plated in 24well plates.  Cells were treated with GSK3i (XV 50nM) in mTeSR1 for 24h (Day 0 to Day 1). After that, media was changed and RPMI/B27- media was applied for 48h. At day 3, half of the media was replaced and IWP2 7.5uM was added for 48h. At D4, Retinoic Acid 1uM was added to the media for 3 days. Cells were collected at Day 5 for single-nuclei ATACseq. Two to three differentiation experiments performed at the same time were pooled for library prep and downstream sequencing analysis.


title: A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment [ChIP-Seq]

overall_design: H1 WT hESCs   were plated in 6 well plates.  Cells were treated with GSK3i (XV 50nM) in mTeSR1 for 24h (Day 0 to Day 1). After that, media was changed and RPMI/B27- media was applied for 48h. At day 3, half of the media was replaced and IWP2 7.5uM was added for 48h. At D4, Retinoic Acid 1uM was added to the media for 3 days. Cells were processed at Day 5 of differentiation 24h after RA addition for ChIP-analysis.


title: Spatial and Single Cell Mapping of Human Lymph Node Disease

status: Public on May 09 2025

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

summary: To determine the cellular and molecular basis of Castleman Disease (CD), we analyze the spatial proteome of spatial proteome and transcriptome of 22 cases of Unicentric CD, idiopathic Multicentric CD, HHV8-associated MCD, and reactive lymph nodes. CD shows increased stromal cells that form unique microenvironments. Interaction of activated follicular dendritic cell (FDC) cytoplasmic meshworks with mantle-zone B cells is associated with B-cell activation and differentiation. CXCL13+ FDCs, PDGFRA+ T-zone reticular cells (TRC), and ACTA2-positive perivascular reticular cells (PRC) were the predominant source of increased VEGF expression and IL-6 signaling.  MCD is characterized by increased TRC while UCD shows increased B-reticular cells (BRC). VEGF expression by FDCs is associated with peri-follicular neovascularization. FDC, TRC and PRC of CD activates JAK-STAT, TGFβ, and MAPK pathways via specific ligand-receptor interactions. Here, we show that stromal-cell activation and associated B-cell activation and differentiation, neovascularization and stromal remodeling underlie CD.

overall_design: Lymph node bioposies were otained from patients diagnosed with Kikuchi-Fujimoto disease, castleman disease, or experiencing an immune reaction. The objective to identify how cell interactions vary between the states was undertaken using multiplexed imaging technologies (PhenoCycler, RNAscope) and single-cell sequencing.

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