title: Edited Filamin A in myeloid cells reduces intestinal inflammation and protects from colitis [RNA-Seq]

city: Wien

first: Cornelia

last: Vesely

state: Österreich

address: Schwarzspanierstr 17

department: Anatomy and Cell Biology

institute: Medical University of Vienna

summary: Patho-mechanistic origins and disease dynamics of ulcerative colitis are still poorly understood. The actin-crosslinker Filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. FLNA exists in two forms that differ only in one amino acid: genome-encoded FLNAQ and FLNAR - generated by post-transcriptional A-to-I editing. FLNA is edited in fibroblasts, smooth muscle- and endothelial cells in the colon. We identified the FLNA editing status as a key determinant of colitis severity. FLNA editing was highest in healthy colons and reduced during acute murine and human colitis. Mice that exclusively express edited FLNAR and do not downregulate editing upon challenge were highly resistant to DSS-induced colitis, whereas fully unedited FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and the microbiome composition, we found that FLNAR exerts protection specifically via its influence on myeloid cells, which are not edited under physiological conditions. Introducing fixed, fully edited FLNAR did not hamper normal cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. In conclusion, loss of FLNA editing correlates with colitis severity, and targeted FLNA editing of myeloid cells might serve as a novel therapeutic approach in intestinal inflammation.

overall_design: Bulk RNA-seq profiling of whole distal colon homogenates of DSS treated mice. The transcriptional profiles of distal colons of mice with unedited Filamin A (FLNA-Q) and fully edited FLNA (FLNA-R) were compared. Four-five biological replicates were analyzed per genotype.

first: Riem

last: Gawish

first: Florian

last: Deckert


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/NFE2L2]

status: Public on May 02 2025

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: First-line immune checkpoint inhibitor (ICI) combinations have shown responses in subsets of patients with advanced hepatocellular carcinoma (HCC). Nearly half of patients are Wnt active with mutations in CTNNB1 (encoding for beta-catenin), AXIN1/2, or APC, and demonstrate limited benefit to ICI due to an immunosuppressive tumor microenvironment. We investigated a novel siRNA encapsulated in lipid nanoparticle targeting CTNNB1 (LNP-CTNNB1) in multiple beta-catenin-mutated immunocompetent HCC mouse models, observing complete response. Integrated single-cell and spatial transcriptomics revealed complete cellular and zonal reprogramming of CTNNB1-mutated tumors, and a spatiotemporal shift in innate immune surveillance with intra-tumoral pro-inflammatory myeloid infiltration following LNP-CTNNB1 intervention. beta-catenin knockdown initiated tumor cell-intrinsic type I/II interferon signaling accompanied by IRF2 upregulation, which was suppressed in CTNNB1-mutated HCCs. IRF2 re-expression in beta-catenin-mutated HCC restored adaptive tumor immunity with increased CD4+ T cells and impaired recruitment of resident T regulatory cells. Finally, LNP-CTNNB1 synergized with ICI in advanced-stage disease through increasing intra-tumoral recruitment of cytotoxic T cells. In summary, RNAi-mediated inhibition of CTNNB1 is efficacious as monotherapy and in combination with ICI in CTNNB1-mutated HCCs through remodeling both tumor cell intrinsic signaling and global immune surveillance, thus providing rationale for clinical investigations.

overall_design: All these samples are FVB/NJ male mice. All these samples are from T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi. Treatment with LNP-CTRL/LNP-CTNNB1 began at 5-weeks post-HDTVi.

first: Brandon

last: Lehrich

first: Evan

last: Delgado

first: Tyler

last: Yasaka

first: Silvia

first: Catherine

last: Cao

first: Yuqing

first: Sucha

last: Singh

first: Anya

last: Singh-Varma

first: Yekaterina

last: Krutsenko

first: Minakshi

last: Poddar

first: T. Kevin

last: Hitchens

first: Lesley M.

last: Foley

first: Ravi P.

last: Rai

first: Panari

last: Patel

first: Madeline

last: Riley

first: Aaron

last: Bell

first: Reben

last: Raeman

first: Binyong

last: Liang

first: Tulin

last: Dadali

first: Jason J

last: Luke

first: Amaia

last: Lujambio

first: Xin

last: Chen

first: Martin

last: Maier

first: Wendy

last: Broom

first: Junyan

last: Tao

first: Satdarshan P.

last: Monga


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/hMet/POU2F1]

first: Shuchang

last: Liu

overall_design: All these samples are FVB/NJ male mice.TUMOR.CTRL.BLC409, TUMOR.CTRL.BLC410, and TUMOR.CTRL.BLC411 are S45Y-beta-catenin + hMET HCC model via SB-HDTVi. POU2F1.BLC413, POU2F1.BLC414,and  POU2F1.BLC415 are S45Y-beta-catenin + hMET + POU2F1 HCC model via SB-HDTVi.

first: Brandon

last: Lehrich

first: Evan

last: Delgado

first: Tyler

last: Yasaka

first: Silvia

first: Catherine

last: Cao

first: Yuqing

first: Sucha

last: Singh

first: Anya

last: Singh-Varma

first: Yekaterina

last: Krutsenko

first: Minakshi

last: Poddar


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Spatial Transcriptomics by 10X Visium CTNNB1/NFE2L2]

overall_design: BL-551 is LNP-CTRL. BL-584,BL-587 is LNP-CTNNB1 “NR” phenotype. BL-585, BL-586 is LNP-CTNNB1 “R” phenotype. All are from T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi. FVB/NJ male mice. Treatment with LNP-CTRL/LNP-CTNNB1 began at 8-weeks post-HDTVi.

first: T. Kevin

last: Hitchens

first: Lesley M.

last: Foley

first: Ravi P.

last: Rai

first: Panari

last: Patel

first: Madeline

last: Riley

first: Aaron

last: Bell

first: Reben

last: Raeman

first: Binyong

last: Liang

first: Tulin

last: Dadali

first: Jason J

first: Amaia


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Spatial Transcriptomics by 10X Visium]

first: Shuchang

last: Liu

overall_design:
BL-131 is LNP-CTRL
BL-146, BL-147 is LNP-CTNNB1 “NR” phenotype
BL-152 is LNP-CTNNB1 “R” phenotype
All are from S45Y-beta-catenin + hMET HCC model via SB-HDTVi.
FVB/NJ male mice, age 16wks old. Treatment with LNP-CTRL/LNP-CTNNB1 began at 6-weeks post-HDTVi.

first: Brandon

last: Lehrich

first: Evan

first: Tyler

first: Silvia

first: Cao

last: Catherine

first: T

middle: K

first: Lesley

middle: M

first: Ravi

middle: P

first: Liang

last: Binyong

first: Jason

middle: J

last: Luke

last: Lujambio

first: Xin

last: Chen

first: Martin

last: Maier

first: Wendy

last: Broom

first: Junyan

last: Tao

first: Satdarshan

last: Monga


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Single-cell RNA-seq hashtag immune]

overall_design:
“Control_” is LNP-CTRL and “Treated_” is LNP-CTNNB1. 3 tumor_control and 3 tumor_treat samples were pooled sequenced, but can be identified by hashtag.
Both are from T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi.
FVB/NJ male mice, age 11wks old. Treatment with LNP-CTRL/LNP-CTNNB1 began at 5-weeks post-HDTVi.

last: Delgado

last: Yasaka

first: Yuqing

first: Sucha

last: Singh

first: Anya

last: Singh-Varma

first: Yekaterina

last: Krutsenko

first: Minakshi

last: Poddar

last: Hitchens

last: Foley

last: Rai

first: Panari

last: Patel

first: Madeline

first: Aaron

first: Reben

first: Tulin

first: Amaia


title: Dmrt2 and Hmx2 direct intercalated cell diversity in the mammalian kidney through antagonistic and supporting regulatory processes.

status: Public on May 03 2025

city: Los Angeles

first: Riana

last: Parvez

state: CA

address: 1425 San Pablo St.

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: Intercalated cells (ICs) in the mammalian kidney regulate circulatory pH through IC subtype restricted actions of bicarbonate transcporters: pH is elevated by Slc4a1 restricted to type A-ICs (A-ICs) and depressed by Slc26a4 in type B-IC (B-ICs). nonA-nonB-ICs (nA/nB-ICs) also produce Slc26a4 though their function is unclear. Though both nephron and ureteric progenitor lineages generate A-ICs, the former also generates nA/nB-ICs and the latter B-ICs. Lineage and subtype restricted transporter gene expression in the mouse and human kidney is preceded by expression of the transcriptional regulators Dmrt2/DMRT2 in A-ICs, and either, or both Hmx2/HMX2 and Hmx3/HMX3 in B- and nA/nB ICs. CRISPR/CAS9-directed removal of Dmrt2 and the linked Hmx2/Hmx3 genes resulted in IC-subtype switching. A-ICs adopted an Hmx2+/Slc26a4+ B-IC cell fate on Dmrt2 removal while B-ICs initiated a Dmrt2+/Slc4a1+ A-IC program on Hmx2/Hmx3 removal. Triple knockout of Dmrt2, Hmx2, and Hmx3 resulted in hybrid ICs expressing both Slc4a1 and Slc26a4. Thus, restricted expression of these regulators is essential for specifying IC subtypes. These data support a model in which mutually repressive interactions between Dmrt2 and Hmx2/3 establish distinct IC-identities and activity of these factors supports gene regulatory programs specific to each IC sub-type.

overall_design: To understand the transcriptional profiles of human intercalated cells, we generated a snRNA-seq dataset of the ureteric lineage of two developing human kidneys (week 18; one female and one male sample)

first: Andrew

last: McMahon


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Single-cell RNA-seq GEX]

first: Shuchang

last: Liu

overall_design:
Both samples are from T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi.
FVB/NJ male mice, age 11wks old. Treatment with LNP-CTRL/LNP-CTNNB1 began at 5-weeks post-HDTVi.
Tumor_control is pooled from BL-1025, BL-1026 (LNP-CTRL)
Tumor_treat is pooled from BL-1028, BL-1029, BL-1030 (LNP-CTNNB1)

first: Brandon

last: Lehrich

first: Evan

first: Tyler

first: Silvia

first: Cao

last: Catherine

first: T

first: Lesley

first: Ravi

last: Riley

last: Bell

last: Raeman

first: Liang

last: Binyong

last: Dadali

first: Jason

last: Luke

last: Lujambio

first: Xin

last: Chen

first: Martin


title: Edited Filamin A in myeloid cells reduces intestinal inflammation and protects from colitis [scRNA-Seq]

first: Cornelia

last: Vesely

country: Austria

overall_design: Single cell RNA-seq profiling of  DSS treated and untreated mice. The transcriptional profiles of CD54+ and CD45- colon cells of mice with unedited Filamin A (FLNA-Q) and fully edited FLNA (FLNA-R) or FLNA -WT were analyzed. Cells of three-five colons were pooled into one sample and sequenced.

first: Riem

last: Gawish

first: Florian

last: Deckert


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Spatial Transcriptomics by Resolve Biosciences Molecular Cartography]

overall_design:
Both slides are from T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi.
FVB/NJ male mice, age 11wks old. Treatment with LNP-CTRL/LNP-CTNNB1 began at 5-weeks post-HDTVi.
B1 is BL-568 (LNP-CTRL) with 6 slides;
B2 is BL-572 (LNP-CTNNB1) with 5 slides

last: Delgado

last: Yasaka

first: Yuqing

first: Sucha

last: Singh

first: Anya

last: Singh-Varma

first: Yekaterina

last: Krutsenko

first: Minakshi

last: Poddar

last: Hitchens

last: Foley

last: Rai

first: Panari

last: Patel

first: Madeline

first: Aaron

first: Reben

first: Tulin

first: Amaia

last: Maier

first: Wendy

last: Broom

first: Junyan

last: Tao

first: Satdarshan

last: Monga


title: The inflammatory micro-environment induced by targeted CNS radiotherapy is underpined by disruption of DNA methylation

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

summary: Although targeted radiotherapy (RT) is integral to the increasing survival of cancer patients, it has significant side-effects, the cellular and molecular mechanisms of which are not fully understood. During RT epigenetic changes occur in neoplastic tissue, but few studies have assessed these in non-neoplastic tissue and results are highly variable. Using bulk DNA methylation and RNA sequencing as well as spatial transcriptomics (ST) in a unique cohort of patient tissue samples, we show distinct differences in DNA methylation patterns in irradiated brain tissue, whilst ST characterisation identifies specific micro-environmental niches present after irradiation and highlights neuropeptides that could be propagating neuroinflammation. We also show that in a cerebral organoid (CO) model of early changes in neurons after irradiation there are similar DNA methylation alterations and disruption of the DNA methylation machinery, suggesting that early but persistent epigenetic dysregulation plays a role in neurotoxicity. We provide a link between radiotherapy induced neuroinflammation and disruption of DNA methylation for the first time and suggest possible driving mechanisms for this chronic neuroinflammation.

overall_design: Spatial transcriptomics was performed on brain tissue from surplus FFPE surgical material from patients who received radiotherapy for the treatment of cerebral lesions. The experimental samples comprised cases where neurosurgical removal of a brain lesion occurred following radiotherapy, and the control samples included peri-lesional CNS tissue that had not received radiotherapy.

first: Thomas

middle: O

last: Millner

first: James

middle: R

last: Boot


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/MET/IRF2]

first: Shuchang

last: Liu

overall_design:
All these samples are FVB/NJ male mice, age 13 wks old.
CTNNBT_MET_CTRL_1, CTNNBT_MET_CTRL_2 are S45Y-beta-catenin + hMET HCC model via SB-HDTVi.
CTNNBT_MET_IRF2_1, CTNNBT_MET_IRF2_2, CTNNBT_MET_IRF2_3, CTNNBT_MET_IRF2_4 are S45Y-beta-catenin + hMET + IRF2 HCC model via SB-HDTVi.

first: Brandon

last: Lehrich

first: Evan

last: Delgado

first: Tyler

first: Cao

last: Catherine

first: Yuqing

first: T

first: Lesley

first: Ravi

last: Riley

last: Bell

last: Raeman

first: Liang

last: Binyong

last: Dadali

first: Jason

last: Luke

last: Lujambio

first: Xin

last: Chen

first: Martin


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers

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

overall_design: Refer to individual Series


title: Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/hMet/NFE2L2]

overall_design:
All these samples are FVB/NJ male mice, age 9-11wks old.
BL-177, BL-179, BL-180, BL-181, BL-182, BL-183, BL-184 are S45Y-beta-catenin + hMET HCC model via SB-HDTVi.
BL-562, BL-563, BL-568, BL-566, BL-567, BL-572 are T41A-beta-catenin + G31A-NFE2L2 HCC model via SB-HDTVi.
BL-177, BL-179, BL-180 are LNP-CTRL treated. BL-562, BL-563, BL-568 are LNP-CTRL treated.
BL-181, BL-182, BL-183, BL-184 are LNP-CTNNB1 treated. BL-566, BL-567, BL-572 are LNP-CTNNB1 treated.
Treatment with LNP-CTRL/LNP-CTNNB1 began at 3-weeks post-HDTVi for beta-catenin + hMET model.
Treatment with LNP-CTRL/LNP-CTNNB1 began at 5-weeks post-HDTVi for beta-catenin + NFE2L2 model.

last: Yasaka

first: Sucha

last: Singh

first: Anya

last: Singh-Varma

first: Yekaterina

last: Krutsenko

first: Minakshi

last: Poddar

last: Hitchens

last: Foley

last: Rai

first: Panari

last: Patel

first: Madeline

first: Aaron

first: Reben

first: Tulin

first: Amaia

last: Maier

first: Wendy

last: Broom

first: Junyan

last: Tao

first: Satdarshan


title: Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications

city: Badalona

first: Cristina

last: Vilaplana

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n, IGTP - Edifici Mar - UTE

country: Spain

institute: IGTP

summary: The granuloma is a complex structure, contributing to the overall spectrum of tuberculosis (TB). We characterised 44 fresh human pulmonary TB lesion samples from 13 patients (drug-sensitive and multi-drug resistant TB) undergoing therapeutic surgery using RNA-Sequencing. We confirmed a clear separation between the granuloma and adjacent non-lesional tissue, with the granuloma samples consistently displaying an increased inflammatory profile despite heterogeneity. Using weighted correlation network analysis, we identified 17 transcriptional modules associated with granulomata and demonstrated a gradient of immune-related transcript abundance according to the granuloma’s spatial organization. Furthermore, we associated the modular transcriptional signature of the TB granuloma with clinical surrogates of treatment efficacy and TB severity. We show that in patients with severe disease, the IFN/cytokine signalling and neutrophil degranulation modules were overabundant, while tissue organization and metabolism modules were under-represented. Our findings provide evidence of a relationship between clinical parameters, treatment response and immune signatures at the infection site.

overall_design: A total of 48 total-RNA samples underwent RNA-seq from 14 patients undergoing therapeutic surgery from their pulmonary tuberculosis (TB) (Discovery Set). Total RNA was extracted from removed human tuberculosis granuloma biopsies (Center of the Lesion, Internal Wall, and External Wall) and surrounding non-lesional (NL) lung parenchyma tissue (as a control). Patients were matched according to sex (7 males and 7 females), and by their drug sensitivity to chemotherapy (6 drug-sensitive, 6 multi-drug resistant, and 2 extensively drug-resistant TB). Epidemiological, general clinical, TB-related and microbiological aspects are included.

first: Kaori

middle: L

last: Fonseca

first: Juan

last: Lozano

first: Albert

last: Despuig

first: Dominic

last: Habgood-Coote

first: Julia

last: Sidorova

first: Diego

last: Aznar

first: Lilibeth

last: Arias

first: Álvaro

last: Del Río-Álvarez

last: Carrillo-Reixach

last: Goff

first: Leticia

last: Wildner

first: Shota

last: Gogishvili

first: Keti

last: Nikolaishvili

first: Natalia

last: Shubladze

first: Zaza

last: Avaliani

first: Gustavo

last: Tapia

first: Paula

last: Rodríguez-Martínez

first: Pere-Joan

last: Cardona

first: Federico

last: Martinón-Torres

first: Antonio

last: Salas

first: Alberto

last: Gómez-Carballa

first: Carolina

last: Armengol

first: Simon

last: Waddell

first: Myrsini

last: Kaforou

first: Anne

last: O’Garra

first: Sergo

last: Vashakidze


title: Impact of Drp1 Loss on Organelle Interaction, Metabolism, and Inflammation in Mouse Liver

status: Public on May 01 2025

city: Fukuoka

first: Lixiang

last: Wang

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

summary: Dynamin-related protein 1 (Drp1) plays a critical role in mitochondrial fission and liver function. The interactions between mitochondria, endoplasmic reticulum (ER), and lipid droplets (LDs) are essential for lipid metabolism. In this study, liver-specific Drp1 knockout (Drp1LiKO) mice were utilized to investigate the impact of disrupted organelle interactions. Analysis revealed increased interactions between mitochondria and LDs, as well as among ER, mitochondria, and LDs in Drp1LiKO mice. As a result, impaired fatty acid metabolism was observed, leading to liver inflammation. In vitro studies using primary hepatocytes from Drp1LiKO mice further confirmed disrupted lipid metabolism and increased inflammation. These findings underscore the significance of Drp1 in maintaining organelle interactions for proper lipid metabolism and liver health. Tar-geting Drp1-mediated interactions may present a promising approach for the treatment of liver diseases associated with lipid metabolism dysregulation.

overall_design: Mice were  fasted for 17 hours  and then refed for 4 hours before sacrificed. Total RNA was isolated from mouse liver using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA, USA) and purified using a SV Total RNA Isolation System (Promega Corporation, Madison, WI, USA) according to the manufacturer’s instructions. Gene expression profiling was performed using the Whole Mouse Genome Microarray 4x44K v2 platform that contains 39,430 probes (Agilent Technologies).

first: Masatoshi

last: Nomura


summary: Dynamin-related protein 1 (Drp1) plays a critical role in mitochondrial fission and liver function. The interactions between mitochondria, endoplasmic reticulum (ER), and lipid droplets (LDs) are essential for lipid metabolism. In this study, liver-specific Drp1 knockout (Drp1LiKO) mice were utilized to investigate the impact of disrupted organelle interactions. Analysis revealed increased interactions between mitochondria and LDs, as well as among ER, mitochondria, and LDs in Drp1LiKO mice. As a result, impaired fatty acid metabolism was observed, leading to liver inflammation. In vitro studies using primary hepatocytes from Drp1LiKO mice further confirmed disrupted lipid metabolism and increased inflammation. These findings underscore the significance of Drp1 in maintaining organelle interactions for proper lipid metabolism and liver health. Targeting Drp1-mediated interactions may present a promising approach for the treatment of liver diseases associated with lipid metabolism dysregulation.

overall_design: We have reported that disruption of mitochondrial fission by deletion of Drp1 leads to an alteration in expression of the genes involved in the immune system in the liver and significant elevation of pro-inflammatory cytokines was detected in Drp1 knockout cells. To fully reveal the gene expression altered by Drp1 deletion, we conducted an independent microarray analysis with primary hepatocyte harvested 24 hours after seeding.


title: Single-Cell RNA-Seq uncovers lineage-specific regulatory alterations of fibroblasts and endothelial cells in ligamentum flavum hypertrophy

city: Nanjing

first: YONG

middle: XIN

last: CHEN

address: 167 Hushan Road

department: Department of Spine Surgery

country: China

institute: The Affiliated Jiangning Hospital of Nanjing Medical University

summary: Lumbar spinal stenosis (LSS) represents a major global healthcare burden resulting in back pain and disorders of the limbs among the elderly population. The hypertrophy of ligamentum flavum (HLF), marked by fibrosis and inflammation, significantly contributes to LSS. Fibroblasts and endothelial cells are two important cells in the pathological process of ligamentum flavum (LF) fibrosis and inflammation. These two cells exhibit heterogeneity in various fibrotic diseases, yet their heterogeneity in LF fibrosis remains poorly defined. Using single-cell RNA-seq, we examined the alterations of fibroblasts, endothelial cells, and key genes in the hypertrophic LF, aiming to establish a comprehensive single-cell atlas of LF to identify high-priority targets for pharmaceutical treatment of LSS. Here, we find there are five distinct subpopulations of LF fibroblasts: secretory-papillary, secretory-reticular, mesenchymal, pro-inflammatory, and unknown. Importantly, in HLF, the proportion of mesenchymal fibroblast subpopulations increases significantly compared to normal LF (NLF), reflecting their close association with the pathogenesis of HLF. Furthermore, critical target genes that might be involved in HLF and fibrosis, such as MGP, ASPN, OGN, LUM, and CTSK, are identified. In addition, we also investigate the heterogeneity of endothelial cells and highlight the critical role of AECs subpopulation in LF fibrosis. This study will contribute to our understanding of the pathogenesis of HLF and offer possible targets for the treatment of fibrotic diseases.

overall_design:
All LF specimens were obtained from the L4/5 segment during spinal decompression surgery. LF tissue was dissociated and cells were isolated. The suspended cells were processed through 10x Genomics and were analyzed as scRNAseq.

Both LSS and LDH samples were derived from the ligamentum flavum of the human lumbar spine, so both are labeled as ligamentum flavum.
The ligamentum flavum of the LSS shows hypertrophy, whereas the LDH is a normal ligamentum flavum.
The main cell type of LSS is fibroblast. The main cell types of LDH are T cells, dendritic cells and fibroblasts.

first: Yongxin

last: Chen

first: Jue

last: Zhang

first: Xincheng

last: Feng

first: Qinghong

last: Ma

first: Chao

last: Sun


title: Conventional dendritic cells of lymphoid origin with a preferential distribution to barrier tissues [cDCs_scRNA-seq]

city: Bunkyo-ku

first: Masashi

last: Kanayama

state: Tokyo

address: 1-5-45 Yushima

department: Department of Biodefense Research

institute: Medical Research Laboratory, Institute of Science Tokyo

summary: Conventional dendritic cells (cDCs) regulate adaptive immunity. Although cDCs emerged with the evolution of adaptive immunity, it is considered that most cDCs are of myeloid origin (M-cDCs). Using a lymphoid progenitor-tracking system, we identify novel cDCs of lymphoid origin (L-cDCs) in a steady state. Notably, L-cDC2s are predominantly distributed in barrier tissues such as the lungs and skin. Single-cell RNA-sequencing analysis revealed that the distribution and gene expression patterns of L-cDC clusters are very similar to M-cDC clusters, except for the enrichment of lymphocyte-signature genes in L-cDCs. Importantly, we identified lymphoid-derived pre-DCs and lymphocyte-primed cDC precursors as sources of L-cDCs. Compared with M-cDC2s, L-cDC2s weakly primed T cells under low-dose antigen stimulation and preferentially promoted Th2 differentiation under sufficient antigenic stimulation. These results suggest the developmental diversity of cDCs and imply the contribution of L-cDCs to tolerance and hyper-responses to Th2-related antigens in barrier tissues.

overall_design: To examine gene expression profiles of M-cDC1s, M-cDC2s, L-cDC1s  and L-cDC2s, we sorted splenic L-cDCs and M-cDCs from Il7r-cre; Rosa26-lsl-tdTomato mice and performed scRNA-sequencing analysis for them.

first: Toshiaki

last: Ohteki


title: Conventional dendritic cells of lymphoid origin with a preferential distribution to barrier tissues [cDCs_RNA-seq]

summary: Conventional dendritic cells (cDCs) regulate adaptive immunity. Although cDCs emerged with  the evolution of adaptive immunity, it is considered that most cDCs are of myeloid origin (M-cDCs).  Using a lymphoid progenitor-tracking system, we identify novel cDCs of lymphoid origin (L-cDCs)  in a steady state. Notably, L-cDC2s are predominantly distributed in barrier tissues such as the  lungs and skin. Single-cell RNA-sequencing analysis revealed that the distribution and gene  expression patterns of L-cDC clusters are very similar to M-cDC clusters, except for the  enrichment of lymphocyte-signature genes in L-cDCs. Importantly, we identified lymphoid-derived  pre-DCs and lymphocyte-primed cDC precursors as sources of L-cDCs. Compared with M-cDC2s,  L-cDC2s weakly primed T cells under low-dose antigen stimulation and preferentially promoted  Th2 differentiation under sufficient antigenic stimulation. These results suggest the developmental  diversity of cDCs and imply the contribution of L-cDCs to tolerance and hyper-responses to  Th2-related antigens in barrier tissues.

overall_design: To examine gene expression profiles of M-cDC1s, M-cDC2s, L-cDC1s  and L-cDC2s, we sorted splenic  cDCs from naïve wild type C57BL/6J mice and performed RNA-sequencing analysis.


title: Conventional dendritic cells of lymphoid origin with a preferential distribution to barrier tissues [donor cDCs_RNA-seq]

overall_design: To examine similarlity of  CLP-derived cDC2s and L-cDC2s, we  transferred CLPs or CDPs from wild-type (WT) mice (CD45.2+) into the BM of B6.SJL mice (CD45.1+). Four days after LPS treatment, CLP-derived cDC2s (CLP-cDC2s) and CDP-derived cDC2s (CDP-cDC2s) were isolated from the spleens for transcriptome analysis. We also isolated L-cDC2s (tdTomato+) and M-cDC2s (tdTomato-) from the spleens of Il7r-Cre;Rosa26-lsl-tdTomato mice 4 days after LPS treatment to compare their gene expression profiles with CLP-cDC2s and CDP-cDC2s.


title: A bilaminar stem cell core governs tooth establishment.

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Establishment of human teeth relies on coordinated formation of dentin-pulp complex for nurturing and periodontal tissues for anchoring in alveolar bone. The exact cell origin of dentin-pulp complex and periodontal tissues, and the integrative developmental process remain elusive. Here, we identified a bilaminar core of Cd24a+ and Pax9+ stem cells that governs the tooth establishment and persists into adulthood. Specifically, Cd24a+ stem cells gave rise to the dentin-pulp complex while Pax9+ stem cells mainly generated periodontal tissues as well as partial dental pulp. DTA-mediated cell ablation of the Cd24a+/Pax9+ stem cells significantly compromised tooth establishment. Moreover, during development, the Cd24a+/Pax9+ bilaminar core concentrated on the apical region, collectively migrated and contributed to the newly formed dental root, potentially guided by PDGF-B derived from the alveolar bone. Integrated multi-omic analysis and spatial mapping further revealed lineage-associated key signaling pathways in Cd24a+/Pax9+ stem cells and the unique organization of different cell compositions. Finally, the CD24+/PAX9+ bilaminar core was also detected in human teeth at different stages, suggesting it a conserved developmental mechanism. Together, our work identified a unique bilaminar core of bona fide dental stem cells governing tooth establishment and might guide the future regenerative therapy to treat pulpitis, pulp necrosis and periodontal diseases.

overall_design: This study analyzed different types of dental stem cells using single-cell RNA sequencing (scRNA-seq) and H3K4me3 CUT&Tag epigenetic profiling.

first: Ce

last: Shan

first: Hui

last: Lu

first: Tianshu

first: Yongqiang

first: Kun

first: Mingxu

first: Haoyang

last: Cai

first: Yunqiu


title: Single-cell landscape of hematopoiesis and immunological responses in patients with severe aplastic anemia treated with immunosuppression and eltrombopag

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary: We performed single cell RNA sequencing, and VDJ sequencing of TCR and BCR of bone marrow samples (BMMMNCs and sorted CD34+ HSPCs) from 20 patients with severe aplastic anemia (SAA), pre- and post-treatment, to understand disease pathogenesis and response to treatment.

overall_design: RNA profiles of single bone marrow hematopoietic cells of 20 SAA patients and 4 healthy donors were generated by deep sequencing using Illumina NovaSeq.

first: Zhijie

last: Wu


title: Unraveling the Evolutionary Unique Glycoprotein Quality Control System and its Roles in Cellular Fitness and Extracellular Vesicle Transport in Cryptococcus neoformans

city: Seoul

first: Catia

last: Mota

state: Seoul

address: Heukseok-ro 84

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: This study focused on understanding the functional role of specific ERQC members of C. neoformans

first: Ye Ji

last: Son

first: Kiseung

last: Kim

first: Eun Jung

last: Thak

first: SuBin

last: Lee

first: Hyun Ah

last: Kang


title: Late gene regulation by the alternative sigma factors of Chlamydia trachomatis [sig54_ChIP-seq]

status: Public on Apr 30 2025

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

institute: University of California Irvine

summary: The pathogenic bacterium Chlamydia reproduces via two specialized forms inside a eukaryotic host cell. The dividing form called the reticulate body (RB) must convert at late times into the infectious elementary body (EB) for spread to a new host cell. Late genes are a temporal class of chlamydial genes believed to be responsible for RB-to-EB conversion, but late gene regulation is incompletely understood. In this study, we used chromatin immunoprecipitation (ChIP) to investigate two alternative sigma factors, σ28 and σ54, that alter the promoter specificity of C. trachomatis RNA-polymerase. σ28 ChIP-seq identified hctB and tsp as the only promoters bound by σ28, and binding only occurred late, around the time of RB-to-EB conversion. A σ28 overexpression strain confirmed that these genes are transcribed in a σ28-dependent manner. σ54 ChIP-seq showed that σ54 only bound ctl0021 and ctl0052, and only at late times. This σ54 regulon appears to be conserved as in silico analysis identified σ54 promoter sequences upstream of ctl0021 and ctl0052 homologs in all Chlamydia spp. The genes encoding σ28 and σ54 were only transcribed at late times, but ChIP analysis with the late regulator Euo showed that Euo only controls σ28 expression, and late transcription of σ54 is regulated in an Euo-dependent manner. Thus, multiple mechanisms regulate late genes, including Euo and different forms of RNA polymerase. The dedicated use of two alternative RNA polymerases to control just four late genes suggests that these genes and the independent control of their temporal expression are important for RB-to-EB conversion.

overall_design:
Samples collected at four timepoints (hours post infection). Each timepoint replicated twice. Sheared DNA from each sample divided into three parts: Ab (antibody coated bead added to immunoprecipitate)-450 µl, NoAb (bead without antibody for mock precipitation)- 450 µl, and wce (sheared input DNA)- 50 ul. Each sample eluted and decrosslinked in 150 ul sample volume and purified in 50 ul final volume for library preparation.
ChIP antibody: anti-sigma54 (ABClonal)

first: Syed Meraj

middle: A

first: Asha

last: Densi

first: Owais

last: Hakiem

first: Michael

last: McClelland

first: Ming

last: Tan


title: Edited Filamin A in myeloid cells reduces intestinal inflammation and protects from colitis

status: Public on Apr 29 2025

first: Cornelia

last: Vesely

summary: Patho-mechanistic origins and disease dynamics of ulcerative colitis are still poorly understood. The actin crosslinker Filamin A (FLNA) impacts cellular responses through interaction with numerous, cytosolic proteins. FLNA exists in two forms that differ only in a single amino acid: genome-encoded FLNAQ, and FLNAR - generated by post-transcriptional A-to-I editing. In the intestinal tract, FLNA is edited in fibroblasts, smooth muscle- and endothelial cells and we identified the FLNA editing status as a key determinant of colitis severity. FLNA editing was highest in healthy colons, and reduced during acute murine and human colitis. Mice that exclusively express edited FLNAR and do not downregulate editing upon challenge were highly resistant to DSS-induced colitis, whereas fully unedited FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced the transcriptional states of intestinal structural cells and microbiome composition, we found that edited FLNAR exerts protection specifically via its influence on myeloid immune cells, which are not edited under physiological conditions. The introduction of a fixed FLNAR editing state, did not hamper normal cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. We thus conclude that loss of FLNA editing correlates with colitis severity and targeted FLNA editing of myeloid cells might serve as novel therapeutic approach in intestinal inflammation.

overall_design: FACS-sorted cells from DSS-colitis induced 8-10-week-old mice. Samples are defined by (1) tissue-of-origin, (2) cell type, (3) Duration of DSS-treatment. A variable number of biological replicates are included.

middle: F

last: Jantsch

first: Riem

last: Gawish

first: Martin

last: Pechhacker

first: Florian

last: Deckert


title: Measuring DNA replication timing of maize root tips using DNA copy number (S/G1) method

city: Raleigh

first: Emily

last: Markham

state: NC

address: 851 Main Campus Dr

institute: NCSU

summary: During the cell cycle, DNA replication is a highly regulated process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. We are using fluorescence activated nuclei sorting in combination with high throughput sequencing to characterize the patterns of DNA replication across the maize B73 genome using a DNA copy number based procedure.

overall_design: The terminal 0-1 mm root segments from B73 seedling roots were excised and separated into primary or seminal roots, fixed in 1% formaldehyde for 15 minutes, quenched with glycine, washed in 1x PBS, and snap frozen. Nuclei were isolated from the frozen, excised roots and total DNA was stained with DAPI. Nuclei were flow sorted based on DNA content only (DAPI fluorescence) for G1 and a broad S phase gate placed between the G1 and G2 DNA content peaks. Total genomic DNA was isolated from the G1 and S phase sorted nuclei, sheared and sequenced. The ratio of S phase to G1 genomic DNA provides a measure of the population average DNA copy number for each genomic loci, where earlier replicating genomic regions will have a greater copy number than later replicating genomic regions.

last: Wheeler

first: Leigh

last: Mickelson-Young

last: Wear

first: Mason

last: Burroughs

first: Hank

last: Bass

first: Lorenzo

last: Concia

first: William

last: Thompson

first: Linda

last: Hanley-Bowdoin


title: Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumour biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [DU145-SOX11overexpression_dataset]

city: Derio

first: Arkaitz

last: Carracedo

state: Biscay

address: Parque Científico Tecnológico de Bizkaia building 801A

department: Cancer Cell Signaling And Metabolism Lab

institute: CIC bioGUNE

summary: Metastatic hormone-naïve prostate cancer (mHNPC) is an infrequent form of this tumour type that is characterized by metastasis at the time of diagnosis and accounts for 50% of prostate cancer-related deaths. Despite the extensive characterization of localized and metastatic castration resistant prostate cancer (mCRPC), the molecular characteristics of mHNPC remain largely unexplored. To characterize the transcriptomic landscape of mHNPC, we generated discovery and validation bulk and single-cell RNA-Seq datasets. We performed integrative computational analysis in combination with experimental studies. Our results provide unprecedented evidence of the distinctive transcriptional profile of mHNPC and identify stroma remodelling as a predominant feature of these tumours. Importantly, we discover a central role for the transcription factor SOX11 in triggering a heterotypic communication that is associated to the acquisition of metastatic properties. Our study will constitute an invaluable resource for a profound understanding of mHNPC that can influence patient management.

overall_design: To characterize transcriptomic alterations emanating from SOX11 overexpression, we generated RNA-Seq in the DU145 cell line upon exogenous SOX11 expression and control cells.

first: Natalia

last: Martin-Martin

first: Saioa

last: Garcia-Longarte

first: Jon

last: Corres-Mendizabal

first: Uxue

last: Lazcano

first: Ianire

last: Astobiza

first: Laura

last: Bozal-Basterra

first: Nicolas

last: Herranz

first: Hielke

last: van Splunder

first: Onintza

last: Carlevaris

first: Mikel

last: Pujana-Vaquerizo

first: María

middle: T

last: Blasco

first: Ana

last: Aransay

first: Antonio

last: Rosino

first: Julian

last: Tudela

first: Daniel

last: Jimenez

first: Alberto

last: Martinez

first: Andrei

last: Salca

first: Aida

last: Santos-Martín

first: Sofía

last: Rey

first: Aitziber

last: Ugalde-Olano

first: David

last: Gonzalo

first: Mariona

last: Graupera

first: Roger

last: Gomis

first: Joaquin

last: Mateo

first: Miguel

last: Unda

first: Enrique

last: Gonzalez-Billalabeitia

last: Loizaga-Iriarte

first: Isabel

last: Mendizabal


title: miR-181a-5p mediates the effects of BMP4 on intestinal cell proliferation and differentiation

city: Lexington

first: Qingding

last: Wang

address: 760 Press Ave

institute: University of Kentucky

type: Non-coding RNA profiling by high throughput sequencing

summary: The intestinal mucosa undergoes a dynamic process of continual proliferation, differentiation and apoptosis. Delineating the mechanisms involved in intestinal epithelial cell (IEC) differentiation is crucial to our understanding of not only normal gut adaptation but also aberrant intestinal growth. BMP signaling is a crucial regulator of intestinal proliferation and differentiation. However, the molecular underpinnings of the BMP pathway in this context are not entirely known. Here we showed a key role for BMP4/miR-181/glycolysis signaling pathway in the maintenance of intestinal epithelial cell proliferation and differentiation. Treatment with BMP4 increased expression of enterocyte markers and decreased proliferation of IECs, and importantly, decreased the expression of miR-181a-5p in mouse and human intestinal organoids. Inhibition of miR-181a-5p, a member of miR-181 with highest expression in intestinal cells, significantly increased enterocyte differentiation as noted by increased expression of enterocyte markers in human and mouse intestinal organoids. In addition, miR-181a-5p miRCURY LNA inhibitor repressed the expression of endogenous miR-181a-5p and decreased intestinal stem cell self-renewal as noted by the decreased expression of Ki67, cyclin D1 and OLFM4 and organoid forming efficiency. In contrast, overexpression of miR-181a-5p mimics decreased the expression of enterocyte markers. Moreover, BMP4 treatment or inhibition of miR-181a-5p repressed HK1 expression and inhibited glycolysis. In line of this, knockdown of HK1 or inhibition of glycolysis using 2-DG promoted enterocyte maturation and inhibited proliferation of IECs. Together, we provide evidence showing that miR-181a-5p inhibits intestinal enterocyte differentiation and promotes IEC proliferation thorough HK1-dependent glycolysis. Importantly, our findings identified miR-181a-5p as downstream in mediating BMP4 induction of enterocyte differentiation and inhibition of proliferation in IECs.

overall_design: To determine downstream molecules in mediating the effects of BMP4 on intestinal cell proliferation and differentiation, we treated mouse intestinal organoids with BMP4 for 4 days. We performed miRNA expression profiling analysis using data obtained from miRNA-seq of mouse intestinal organoids treated with PBS control or BMP4.


title: Efficient generation of human retinal pigment epithelium cells via chemically induced pluripotency

city: Beijing

first: Ke

last: Zhang

address: Huayuan North Road

institute: Peking university

summary: The eye is an ideal target organ for Human induced pluripotent stem cells (hiPSCs)-based cellular therapies. However, the application of hiPSCs in ocular disease treatment is still challenging because the production of clinical-grade autologous hiPSCs via genetic techniques remains expensive, time-consuming, and subject to safety concerns. Addressing these challenges, our study utilized a recently reported chemical method to derive human chemically induced pluripotent stem cells (hCiPSCs), which simplified the reprogramming process by using small molecules, offering a more straightforward and potentially safer alternative to derive hiPSCs. Moreover, we demonstrate that hCiPSCs can be efficiently differentiated into functional retinal pigment epithelium (RPE) cells, showing promise for the treatment of age-related macular degeneration (AMD) and other retinal diseases. Our study provides a method for the efficient and safe production of autologous retinal cells, facilitating the advancement of personalized stem cell therapies for ocular diseases.

overall_design:
To reprogram the human adult adipose tissue-derived stromal cells (hADSCs) into human chemically induced pluripotent stem cells (hCiPSCs), and differentiate the latter into retinal pigment epithelial (RPE) cells.
We analyzed the transcriptomic data of hCiPSCs, hADSCs, and human embryonic stem cells to verify the pluripotency of  hCiPSCs.
We further analyzed the transcriptome differences among hCiPSCs-RPE, hCiPSCs and human primary RPE reported in GEO database (GSE210331).

first: Yan

middle: Q

first: Xuran

last: Dong

first: Chun


title: Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumour biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [Validation dataset]

first: Arkaitz

last: Carracedo

overall_design: We generated bulk RNA-Seq from a patient cohort comprising, 17 localized and 15 metastatic hormone-naïve prostate  tumours (Validation cohort).

first: Natalia

last: Martin-Martin

first: Saioa

last: Garcia-Longarte

first: Jon

last: Corres-Mendizabal

first: Uxue

last: Lazcano

first: Ianire

last: Astobiza

first: Laura

last: Bozal-Basterra

first: Nicolas

last: Herranz

first: Hielke

last: van Splunder

first: Onintza

last: Carlevaris

first: Mikel

last: Pujana-Vaquerizo

first: María

last: Blasco

first: Ana

last: Aransay

first: Antonio

last: Rosino

first: Julian

last: Tudela

first: Daniel

last: Jimenez

first: Alberto


title: Fat body-derived cytokine Upd2 regulates the polarity of Drosophila tracheal stem cells [ChIP-seq]

city: Hangzhou

first: qiang

last: zhao

address: 866 Yuhangtang Rd, Hangzhou

institute: Zhejiang University

summary: Adult stem cells are essential for maintaining tissue homeostasis. We employ Drosophila tracheal progenitors to understand the mechanism controlling the polarity of stem cell migration. Here, we show that polarity of tracheal progenitors depends on the function of fat body. Cytokine, Upd2, produced by fat body, signals to tracheal progenitors and activation JAK/STAT signal transduction. Perturbation of Upd2 production or loss-of-function of JAK/STAT signaling in the trachea cause aberrant bidirectional migration of tracheal progenitors. JAK/STAT signaling promotes the expression of a series of genes involved in planar cell polarity, which generates asymmetric localization of Fat and Pod1. Furthermore, the transport of Upd2 requires Rab5-, Rab7-mediated endocytic sorting and Lbm-dependent vesicle trafficking, where vesicular Upd2 functionally interacts with Rabs, Tetraspanin and Grasp65. These results reveal an inter-organ communication in which cytokines from fat body direct the polarity of ectodermal origin tracheal progenitors and suggest that Upd2-dependent JAK/STAT signaling regulates anterior-posterior polarity of tracheal progenitor movement.

overall_design: We performed RNA sequencing (RNA-seq) analysis of tracheal progenitors from aforementioned fat body defective flies to determine the signal between fat body and trachea.The tracheal progenitors were dissected and collected from 1hr APF pupae.  And third larvae trachea were collected for Chip-seq.

first: Pengzhen

last: Dong

first: Yue

last: Li

first: Yuying

last: Wang

first: Hai

last: Huang


title: Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumour biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [Discovery dataset]

first: Arkaitz

last: Carracedo

overall_design: We generated bulk RNA-Seq from a patient cohort comprising, 47 localized and 31 metastatic hormone-naïve prostate  tumours (Discovery cohort).

first: Natalia

last: Martin-Martin

first: Saioa

last: Garcia-Longarte

first: Jon

last: Corres-Mendizabal

first: Uxue

last: Lazcano

first: Ianire

last: Martinez

first: Andrei

last: Salca

first: Aida

last: Santos-Martín

first: Sofía

last: Rey

first: Aitziber

last: Ugalde-Olano

first: David

last: Gonzalo

first: Mariona

last: Graupera

first: Roger

last: Gomis

first: Joaquin

last: Mateo

first: Miguel

last: Unda

first: Enrique

last: Gonzalez-Billalabeitia

last: Loizaga-Iriarte

first: Isabel

last: Mendizabal


title: Nanopore long-reads sequencing of hepatitis A virus RNAs

city: CHAPEL HILL

first: Jason

last: Whitmire

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary: This experiment seeks to investigate the lengths and modifications of the poly(A) tails of hepatitis A virus (HAV) RNA by nanopore long-reads sequencing, and whether RG7834, an inhibitor of TENT4 noncanonical poly(A) polymerases, alters the poly(A) tails of HAV RNA. Poliovirus (PV) infected cells were analyzed in parallel for comparison.

overall_design: Huh7.5 cells were infected with cell culture adapted hepatitis A virus (HM175/18f) for 2 days and treated with DMSO control or RG7834 (500nM) for 3 days. For poliovirus infection, Huh7.5 cells were infected with poliovirus for 6 hours. Total RNAs were extracted and subjected to library preparation and nanopore sequencing to analyze the poly(A) tails of HAV and poliovirus RNAs as previously described (PMID 37085578).

first: You

last: Li

first: Stanley

last: Lemon


title: An RNA binding regulatory cascade controls the switch from proliferation to differentiation in the Drosophila male germ cell lineage

city: Stanford

first: Neuza

last: Reis Matias

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

summary: The switch from precursor cell proliferation to onset of differentiation in adult stem cell lineages must be carefully regulated to produce sufficient progeny to maintain and repair tissues, yet prevent overproliferation that may enable oncogenesis. In the Drosophila male germ cell lineage, spermatogonia produced by germ line stem cells undergo a limited number of transit amplifying mitotic divisions before switching to the spermatocyte program that sets up meiosis and eventual spermatid differentiation. The number of transit amplifying divisions is set by accumulation of the bag-of-marbles (Bam) protein to a critical threshold. In bam mutants, spermatogonia proliferate through several extra rounds of mitosis then die without becoming spermatocytes.  Here we show that a key role of Bam for the mitosis to differentiation switch is repressing expression of Held Out Wings (how), homolog of mammalian Quaking. Knock down of how in germ cells was sufficient to allow spermatogonia mutant for bam or its partner benign gonial cell neoplasm (bgcn) to differentiate, while forced expression of nuclear-targeted How protein in spermatogonia wild-type for bam resulted in continued proliferation at the expense of differentiation. Our findings suggest that Bam targets how RNA for degradation by acting as an adapter to recruit the CCR4-NOT deadenylation complex via binding its subunit, Caf40. As How is itself an RNA binding protein with roles in RNA processing, our findings reveal that the switch from proliferation to meiosis and differentiation in the Drosophila male germ line adult stem cell lineage is regulated by a cascade of RNA-binding proteins.

overall_design: RNA-seq from bam mutant testes were compared to RNA-seq from Caf40KD (under nosGAL4) testes.

last: Matias


title: Measuring DNA replication timing of maize root tips with Repli-seq method

status: Public on Apr 28 2025

first: Emily

last: Markham

summary: DNA replication is a highly regulated cell cycle process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. The overall goal of this project is to define such linkages in maize by exploiting the genetic and genomic resources of this species. We used an updated Repli-seq protocol to profile replication timing in Zea mays B73 root tips and compare it to other methods for profiling replication timing.

overall_design: B73 seedling roots were pulse-labeled with the thymidine analog 5-Ethynyl-2'-deoxyuridine (EdU) for 20 minutes to allow actively replicating DNA to incorporate the EdU. Then seedlings were rinsed and placed in 100 uM Thymidine to stop the label incorporation. The terminal 0-1 mm root segments from the primary and the first two emerging seminal roots were excised, fixed in 1% formaldehyde for 15 minutes, washed in PBS, and snap frozen. Nuclei were isolated from the frozen, excised roots, the incorporated EdU was "clicked" to Alexa Fluor-488 (AF-488), and total DNA was stained with DAPI. Nuclei were flow sorted based on EdU incorporation (AF-488 fluorescence) and DNA content (DAPI fluorescence) into various stages of the mitotic S phase. G1 nuclei were also sorted to use as a genomic DNA reference for sequencing. After DNA was isolated from the sorted nuclei, EdU/AF-488 labeled DNA was immunoprecipitated from each of the S-phase stages using an AF-488 antibody (Invitrogen # A-11094, lot 2551344). The resulting IP DNA from the S-phase stages, and the G1 reference genomic DNA were Illumina sequenced to generate whole-genome DNA replication timing profiles.

last: Wheeler

last: Wear

first: Leigh

last: Mickelson-Young

first: Hank

last: Bass

first: Lorenzo

last: Concia

first: William

last: Thompson

first: Linda

last: Hanley-Bowdoin


title: Early immune responses in the lung and blood following a randomized controlled human inhaled infection with aerosolized attenuated Mycobacterium Bovis BCG in healthy, BCG-naïve, UK adults

city: Oxford

first: Shuailin

address: Old Road Campus Research Building

institute: University of Oxford

summary: We utilise an aerosol mycobacterial human challenge model using attenuated M.bovis BCG, in BCG-naïve UK adult volunteers, to define the initial innate and adaptive immune events at the airway parenchymal interface, and in the blood. Blinded volunteers were randomised to inhale 1x10^7 CFU aerosolised BCG Danish or 0.9% saline (20:6); and sequentially allocated to bronchoscopy at day 2 or 7 post-inhalation (10 BCG, 3 saline each timepoint). scRNA-seq was conducted using the Bronchoalveolar lavage (BAL) samples collected 2 days and 7 days post-aerosol BCG infection and from the saline controls.

overall_design: Three BAL samples were collected from three volunteers 2 days post-aerosol BCG infection, three BAL samples were collected from another three volunteers 7 days post-aerosol BCG infection. Three BAL samples were collected from three volunteers 2 days post saline inhalation, three BAL samples were collected from another three volunteers 7 days post saline inhalation.

first: Julia

last: Marshall

first: Mirvat

last: Surakhy

first: Iman

last: Satti


title: Measuring DNA replication timing of maize root tips using DNA copy number (S/G1) method with an EdU lableing step for bivariate sorting of S and G1 phase

summary: DNA replication is a highly regulated cell cycle process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. We use both DAPI and 5-ethynyl-2'-deoxyuridine (EdU) labeling to perform fluorescence activated nuclei sorting (FANS) in combination with high throughput sequencing to characterize the patterns of DNA replication across the maize B73 genome using a DNA copy number based procedure.

overall_design: B73 seedling roots were pulse-labeled with the thymidine analog 5-Ethynyl-2'-deoxyuridine (EdU) for 20 minutes to allow actively replicating DNA to incorporate the EdU. Then seedlings were rinsed and placed in 100 uM Thymidine to stop the label incorporation. The terminal 1 mm root segments from primary and seminal roots were excised, fixed in 1% formaldehyde for 15 minutes, quenched with glycine, washed in 1x PBS, and snap frozen. Nuclei were isolated from the frozen, excised roots, the incorporated EdU was "clicked" to Alexa Fluor-488 (AF-488), and total DNA was stained with DAPI. Nuclei were flow sorted based on EdU incorporation (AF-488 fluorescence) and DNA content (DAPI fluorescence) from a broad EdU-labeled S phase gate. Unlabeled G1 nuclei were also sorted. Total genomic DNA was isolated from the G1 and EdU-S phase sorted nuclei, sheared and sequenced. The ratio of EdU-S to G1 genomic DNA provides a measure of the population average DNA copy number for each genomic loci, where earlier replicating genomic regions will have a greater copy number than later replicating genomic regions.

first: Mason

last: Burroughs


title: Efficacy of JAK1/2 inhibition in murine myeloproliferative neoplasms is mediated mainly by targeting pro-inflammatory cytokine signaling not oncogenic signaling

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: In this study, we evaluated the mechnasim of ruxolitinib action is directly on malignant cell or not. For this purpose, we evaluated whether the drug primarily blocks the proliferation of the malignant clone or exerts its effects also by targeting non-malignant cells. Therefore, we developed two JAK2-V617F-driven myeloproliferative neoplasm (MPN) mouse models harboring ruxolitinib resistance mutations. Mice carrying ruxolitinib-resistant JAK2-V617F-driven MPN responded to ruxolitinib treatment similar to mice with ruxolitinib-sensitive JAK2-V617F MPN with respect to reduction of spleen size, leukocyte count and pro-inflammatory cytokines in the serum. Ruxolitinib also reduced pro-inflammatory cytokines both in stromal cells and non-malignant hematopoietic cells. Using a rigorous ruxolitinib resistance mutation approach we can prove that ruxolitinib acts independent of oncogenic JAK2-V617F signaling and reduces the main features of MPN disease such as spleen size and leukocyte counts. Our findings characterize the mechanism of action for ruxolitinib in MPN.

overall_design: To prove our hypothesis, we developed MPN  model by transplanting JAK2-V617F bonemarrow into recipient Balb/c  and  measured the inflamatory cytokine land scape in different cellular origin of stromal cells after ruxolitinib treatment in these groups of mice.

first: Melanie

last: Boerries

first: Michael

last: Rassner

first: Sivahari

last: Gorantla


overall_design: To prove our hypothesis, we developed a ruxolitinib sensitive MPN variant (JAK2-V617F) and  resistant variant (JAK2-L902Q) and measured the inflamatory cytokine land scape in different cellular origin from spleen and bone marrow after ruxolitinib treatment in these groups of mice.


title: Late gene regulation by the alternative sigma factors of Chlamydia trachomatis [sig28_ChIP-seq]

first: Syed

last: Rizvi

overall_design:
Samples collected at four timepoints (hours post infection). Each timepoint replicated twice. Sheared DNA from each sample divided into three parts: Ab (antibody coated bead added to immunoprecipitate)-450 µl, NoAb (bead without antibody for mock precipitation)- 450 µl, and wce (sheared input DNA)- 50 ul. Each sample eluted and decrosslinked in 150 ul sample volume and purified in 50 ul final volume for library preparation.
ChIP antibody: anti-sigma28 (ABClonal)

first: Syed Meraj

first: Asha

last: Densi

first: Owais

last: Hakiem

last: McClelland

first: Ming

last: Tan


title: Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome

city: Montpellier

first: severine

last: chambeyron

address: 141 rue de la cardonille

country: France

institute: CNRS-Montpellier University

summary: Transposable elements (TEs) are genetic parasites that can potentially threaten the stability of the genomes they colonize. Nonetheless, TEs persist within genomes and are rarely fully eliminated, diverse TE families coexisting in various copy numbers. The TE replication strategies that enable host organisms to tolerate and accommodate the extensive diversity of TEs, while minimizing harm to the host and avoiding mutual competition among TEs, remain poorly understood. Here, by studying the spontaneous or experimental mobilization of four Drosophila LTR RetroTransposable Elements (LTR-RTEs), we reveal that each of them preferentially targets open chromatin regions characterized by specific epigenetic features. Among these, gtwin and ZAM are expressed in distinct cell types within female somatic gonadal tissues and inserted into the distinct accessible chromatin landscapes of the corresponding stages of embryogenesis. These findings suggest that individual LTR-RTEs exploit unique biological niches, enabling their coexistence within the tightly regulated ecosystem of the same host genome.

overall_design:
For ther ATAC-seq, Purified PGC cells and somatic cells by flow cytometry. ATAC-Seq experiments were performed using the ATAC-Seq kit from Diagenode (catalogue no. C01080002). Input material was between 100,000 to 130,000 cryopreserved PGCs (GFP positive) cells or somatic (GFP negative) cells isolated from whole embryos.
For Small-RNA sequencing, Small RNAs from ovaries collected at permissive (25°C) and non-permissive (20°C) temperature, for Piwi-sKD, were isolated using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08). The libraries were performed by MGX-Biocampus Montpellier plateform using the NEBNext® Small RNA Library Prep Set for Illumina® from NEB. 150 nt paired-end read (28 bp for R1 and 90 bp for R2) sequencing on NOVASEQ 6000 apparatus was performed by MGX. Only the R2 file contains informations.

first: Marion

last: Varoqui

first: Mourdas

last: Mohamed

first: Bruno

last: Mugat

first: Daniel

last: Gourion

first: Maëlys

last: Lemoine

first: Alain

last: Pélisson

first: Charlotte

last: Grimaud

first: Séverine

last: Chambeyron


title: PD-1 blockade mitigates surgery-induced immunosuppression and increases the efficacy of photodynamic therapy for malignant pleural mesothelioma

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Surgical resection can influence tissue behavior and immune interactions, leading to an altered inflammatory state. Our clinical trial delivers intraoperative photodynamic therapy (PDT) to the thoracic cavity after macroscopic complete resection of malignant pleural mesothelioma (MPM) tumors. We have previously published evidence of systemic inflammation via increases in circulating levels of IL-6 after surgical resection. Thus, we expect surgery to alter local signal transduction in the resection field by the time that PDT is delivered. To detect these signaling changes, RNA sequencing analysis was performed on tumor tissue isolated at different time intervals during the surgery (and prior to PDT) from 33 MPM patients. We discovered several pathways associated with tumor behavior and immune function were activated over the course of surgery.

overall_design: Malignant pleural mesothelioma tumor tissue was collected from patients at various timepoints throughout surgery and submitted for RNA sequencing.

first: Gwendolyn

last: Cramer

first: Richard

middle: W

last: Davis IV

first: Emmanouil

last: Papasavvas

first: Astero

last: Klampatsa

first: Sandy

last: Widura

first: Sonali

last: Majumdar

first: Sally

last: McNulty

first: Mary

last: Putt

first: Andrew

last: Kossenkov

first: Luis

last: Montaner

first: Sunil

last: Singhal

first: Edmund

last: Moon

first: Steven

last: Albelda

first: Keith

last: Cengel

first: Theresa

last: Busch


title: Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumour biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [scRNA-Seq]

first: Arkaitz

last: Carracedo

overall_design: Determine a comprehensive transcriptome sequencing profiling of 2 localized and 2 metastatic hormone naïve prostate cancer patients, 10X genomics single-cell RNA-sequencing analysis on human surgical specimen.

first: Natalia

last: Martin-Martin

first: Saioa

last: Garcia-Longarte

first: Jon

last: Corres-Mendizabal

first: Uxue

last: Lazcano

first: Ianire

last: Astobiza

first: Laura

last: Bozal-Basterra

first: Nicolas

last: Herranz

first: Hielke

last: van Splunder

first: Onintza

last: Carlevaris

first: Mikel

last: Pujana-Vaquerizo

first: María

last: Blasco

first: Ana

last: Aransay

first: Antonio

last: Rosino

first: Julian

last: Tudela

first: Daniel

last: Jimenez

first: Alberto

last: Martinez

first: Andrei

last: Salca

first: Aida

last: Santos-Martín

first: Sofía

last: Rey

first: Aitziber

last: Ugalde-Olano

first: David

last: Gonzalo

first: Mariona

last: Graupera

first: Roger

last: Gomis

first: Joaquin

last: Mateo

first: Miguel

last: Unda

first: Enrique

last: Gonzalez-Billalabeitia

last: Loizaga-Iriarte

first: Isabel

last: Mendizabal


title: Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome]

city: LA JOLLA

first: Maria Luisa

last: Amaral

address: 9500 GILMAN DR

institute: UCSD

summary: We performed single-nucleus ATAC-seq (snATAC-seq) to profile chromatin accessibility across eight brain regions from C57BL/6J male and female mice at 2, 9, and 18 months of age. Nuclei were isolated from frozen dissected brain regions, tagmented using barcoded Tn5, and sequenced using combinatorial barcoding or 10x Multiome (female samples). Our analysis reveals region- and age-dependent chromatin changes, highlighting regulatory programs associated with aging in specific brain cell types.

relation:
Reanalysis of: GSM7876941
Reanalysis of: GSM7876944
Reanalysis of: GSM7876911
Reanalysis of: GSM7876915
Reanalysis of: GSM7876920
Reanalysis of: GSM7876919
Reanalysis of: GSM7876951
Reanalysis of: GSM7876950
Reanalysis of: GSM7876899
Reanalysis of: GSM7876903
Reanalysis of: GSM7876889
Reanalysis of: GSM7876890
Reanalysis of: GSM7877041
Reanalysis of: GSM7877045
Reanalysis of: GSM7876980
Reanalysis of: GSM7876981
Reanalysis of: GSM7876894
Reanalysis of: GSM7876955
Reanalysis of: GSM7876940
Reanalysis of: GSM7876939
Reanalysis of: GSM7876901
Reanalysis of: GSM7876958
Reanalysis of: GSM7877006
Reanalysis of: GSM7877008
Reanalysis of: GSM7876907
Reanalysis of: GSM7876905
Reanalysis of: GSM7876924
Reanalysis of: GSM7876923
Reanalysis of: GSM7876960
Reanalysis of: GSM7876961
Reanalysis of: GSM7877023
Reanalysis of: GSM7876957
Reanalysis of: GSM7877039
Reanalysis of: GSM7877043
Reanalysis of: GSM7876912
Reanalysis of: GSM7877069
Reanalysis of: GSM7876904
Reanalysis of: GSM7876982
Reanalysis of: GSM7876902
Reanalysis of: GSM7876972

overall_design:
Single-nucleus ATAC-seq was performed on eight dissected brain regions (AMY, CP, ENT, RLP, NAC, AHC, PHC, FC) from male and female C57BL/6J mice at 2, 9, and 18 months of age. Male samples were processed using combinatorial indexing snATAC-seq; female samples were profiled using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit. For each brain region and age, 2–3 biological replicates consisting of pooled nuclei from 3–14 mice were used.

Please note that the sample extract protocol has been updated on May 21, 2025.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Sainath

last: Mamde

first: Bing

last: Ren


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Single Cell Dataset]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Glioblastoma (GBM) is the most lethal primary brain malignancy. Immunosuppression in the GBM tumor microenvironment (TME) presents a major barrier to immune-targeted therapies. However, our understanding of mechanisms of immunomodulation in the GBM TME is still limited. To address this challenge, we developed a viral barcode interaction tracing approach for the analysis of cell-cell communication in the TME in GBM samples and preclinical models with single-cell resolution, which we combined with single-cell and bulk RNA-seq analyses of GBM clinical samples and pre-clinical models, human organotypic GBM slice cultures, in vivocell-specific CRISPR/Cas9-driven genetic perturbations and human and mousein vitroexperimental systems to identify a novel bi-directional communication pathway between ANXA1 expressed inastrocytes and its receptor FPR1 expressed by GBM cells that limits anti-tumor immune responses. ANXA1 expression in astrocytes and FPR1 expression in cancer cells are associated with shorter survival and earlier recurrence in GBM patients. The inactivation of astrocyte-glioma ANXA1/FPR1-signaling enhanced tumor specific CD4+ and CD8+ T-cell responses, increasing tumor infiltration by neoantigen-specific CD8+ T cells while limiting transcriptional modules linked to T-cell exhaustion; ANXA1/FPR1-signaling inactivation also boosted tumor-associated macrophage responses. Using pre-clinical models and human GBMin vitroexperimental systems, we established that FPR1 inhibits immunogenic necroptosis in tumor cells, while ANXA1 retrograde signaling suppresses NF-kB and inflammasome activation within astrocytes. In summary, we developed a new barcoding approach to analyze TME cell-cell interactions with single-cell resolution in clinical samples and pre-clinical models, and used it to identify a novel pathway of bidirectional ANXA1–FPR1 astrocyte-GBM communication which promotes immunoevasion and cancer progression.

overall_design: Single Cell RNA-Seq dataset which includes 6 samples obtained from 6 Mice.

first: Brian

last: Andersen

first: Camilo

last: Akl

first: Francisco

last: Quintana


title: CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

country: Switzerland

institute: University of Geneva

summary: The SWI/SNF (or BAF) complex is an essential chromatin remodeler that regulates DNA accessibility at developmental genes and enhancers. SWI/SNF subunits are among the most frequently mutated genes in cancer and neurodevelopmental disorders. These mutations are often heterozygous loss-of-function alleles, indicating a dosage-sensitive role for SWI/SNF subunits in chromatin regulation. However, the molecular mechanisms that regulate SWI/SNF subunit dosage to ensure proper complex assembly remain largely unexplored. We performed a genome-wide CRISPR KO screen, using epigenome editing in mouse embryonic stem cells, and identified Mlf2 and Rbm15 as regulators of SWI/SNF complex activity. First, we show that MLF2, a poorly characterized chaperone protein, regulates a subset of SWI/SNF target genes by promoting chromatin remodeling activity. Next, we find that RBM15, part of the m6A RNA methylation writer complex, controls m6A modifications on specific SWI/SNF mRNAs to regulate protein levels of these subunits. Misregulation of m6A methylation causes overexpression of core SWI/SNF subunits leading to the assembly of incomplete complexes lacking the catalytic ATPase/ARP subunits. These data indicate that targeting modulators of SWI/SNF complex assembly may offer a potent therapeutic strategy for diseases associated with impaired chromatin remodeling.

overall_design:
m6A-RIP-seq in control, RBM15 KO and RBM15 deltaRRM1 mouse embryonic stem cells
ATAC-seq in MLF2-dTAG and SMARCA4-dTAG mouse embryonic stem cells
RNA-seq in MLF2-dTAG and SMARCA4-dTAG mouse embryonic stem cells
CUT&RUN in MLF2-dTAG mouse embryonic stem cells

first: Hanna

last: Schwaemmle


title: Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons identifies subsets of transcripts and RNA-binding proteins involved in synaptic plasticity and neurodegenerative  disorders [RNA-seq]

city: St Louis

first: Marianne

middle: Catherine

last: Kramer

state: MO

address: 975 N Warson Rd

institute: Danforth Plant Science Center

summary: Excitotoxicity and altered RNA regulation by RNA-binding proteins (RBPs) are two prevalent hallmarks in multiple neurodegenerative disorders. However, global analysis of RNA-protein interactions in primary neurons in the context of excitotoxicity has not been assessed. To address this, in this work we have applied the protein interaction profile sequencing (PIP-seq) method to primary neurons treated with NMDA to induce excitotoxicity. Our results reveal that NMDA dramatically changes RNA secondary structure at the UTR regions, and that specific RNA structure reduction at the 3’UTR correlates with increased mRNA abundance as assessed by mRNA-Seq. Protein binding sites increase in response to excitotoxicity and, interestingly, different RNA-protein binding in this context defines subsets of transcripts functionally associated with synaptic functions and neurodegenerative disorders. We also identify two RNA motifs enriched in protein binding in the context of excitotoxicity and a list of proteins binding to them in vitro. Accordingly, we observe that two of these RBPs, CELF6 and YBX3 alter their protein levels in response to NMDA treatment, suggesting their involvement in RNA regulation in the context of excitotoxicity. Overall, we describe for the first time the global RNA-protein interactions of primary cortical neurons in baseline conditions and in an in vitro model of excitotoxicity, providing extensive datasets that can be leveraged to bridge the mechanistic gap between two major hallmarks common in multiple neurodegenerative disorders: excitotoxicity and RNA regulation by RBPs

overall_design:
To examine the affect of excitotoxicity on RNA-protein interactions, RNA secondary structure and transcript abundance, we treated primary rat neuronal cultures with or without NMDA
To do this, we performed mRNA-seq and protein interaction profile sequencing (PIP-seq)

middle: C

first: Elena

last: Alvarez-Periel


title: Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons identifies subsets of transcripts and RNA-binding proteins involved in synaptic plasticity and neurodegenerative disorders [PIP-seq]


title: The Role of PD-1/PD-L1 in Overshooting Osteoclastogenesis in Periprosthetic Joint Infections

status: Public on Apr 27 2025

city: Berlin

first: Yi

state: Berlin

address: Charitéplatz 1 10117 Berlin

institute: Charité - Universitätsmedizin Berlin

summary: Periprosthetic joint infection (PJI) is a critical complication following arthroplasty, leading to increased prosthesis failure rates post-treatment. This study explores the role of PD-1/PD-L1 signaling in osteoclastogenesis associated with PJI. Peripheral blood, bone, and bone marrow of 65 patients (20 primary osteoarthritis, 21 PJI septic explantation, 24 PJI prosthesis reimplantation) were analyzed for their bone microstructure and cell composition. Immunocytochemistry, RT-qPCR, flow cytometry, bone resorption assay, ELISA, and RNA sequencing were performed to investigate the effects of PD-1 stimulation and blockade on osteoclast formation. PD-1 positive monocytes and sPD-L1 levels were elevated in PJI. Stimulation with PD-L1 enhanced osteoclastogenesis, while PD-1 inhibitor nivolumab reversed these effects. Impact of PD-1 and nivolumab was significantly more pronounced in PJI compared to the control. Our study suggests PD-1/PD-L1 signaling plays a significant role in PJI-related osteoclastogenesis. These findings highlight the potential of PD-1 inhibitors as a novel approach to manage this challenging clinical condition.

overall_design: Gene expression of cells induced by PD-1 stimulator and inhibitor was profiled with RNA-seq.

first: Denise

last: Jahn

first: Stefanie

last: Donner

first: Clemens

last: Gwinner

first: Weijie

last: Du

first: Dimitrios

last: Wagner

first: Serafeim

last: Tsitsilonis

first: Carsten

last: Perka

first: Georg

last: Duda

first: Arne

last: Kienzle


title: A deep lung cell atlas reveals cytokine-mediated lineage switching of a rare cell progenitor of the human airway epithelium: In-vitro ALI Data

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

summary: The human airway epithelium contains specialized rare cells, including ionocytes and tuft cells, that have been associated with  respiratory disease. Ionocytes express the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) whereas chemosensory tuft cells express asthma-associated alarmins. Surprisingly, exceedingly few mature tuft cells have been identified in human lung cell atlases.  To enable the identification of rare lung cells and define their lineage specification, we generated a deep lung cell atlas of 311,748 cell profiles with careful anatomical sampling of the large and small human airways from entire lungs declined for transplant. In contrast to prior reports, ionocytes were present in similar numbers in both the large and small airways, suggesting that they may contribute to both large and small airways pathologies in CF, a finding which has important implications for gene therapy. We also identify mature tuft cells in a patient who died from an asthma flare. Computational analysis identified rare, bipotent Tuft-Ionocyte Progenitor cells (TIP cells), which have a comparable/higher fraction of cycling cells in the large airways as basal cells (18% vs 11%)  and are predicted to give rise to either tuft cells or ionocytes based on the airway signaling milieu. Using an optimized in vitro system we show that the default pathway of TIP cell differentiation produces ionocytes, but in the presence of Type 2 and Type 17 cytokines, TIP cells are diverted to differentiate into tuft cells. Using scRNAseq and scATACseq we further predicted transcription factors and intermediate cell states that mark these rare cell lineages. Overall, our findings suggest that the immune signaling pathways that characterize asthma and CF may skew the composition of disease relevant rare cells and show how deep atlases are required to identify disease relevant but scarce cells and link them to molecular mechanisms driving pathology.

overall_design: We performed 10x based single-cell RNA sequencing on in-vitro, air-liquid interface cultures of primary bronchus and small airway basal cells, grown in pneumacult ALI media. We applied IL13 treatment and compared it to PBS controls

first: Avinash

last: Waghray

first: Isha

last: Monga

first: Alex

last: Tsankov

first: Jayaraj

last: Rajagopal

first: Aviv

last: Regev


title: DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [RNA-seq]

status: Public on Apr 26 2025

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

institute: DKFZ

summary: DNA methylation plays a fundamental role in regulating transcription during development, cell differentiation, and maintenance of cellular identity. However, the functional role of DNA methylation in the regulation of endothelial cell (EC) transcription during state transition, meaning the switch from an angiogenic to a quiescent cell state, has not been determined. Here, we conducted a DNA methylome analysis over a longitudinal postnatal timeline of EC in the murine pulmonary vasculature, revealing two significant observations. First, prominent alterations in DNA methylation patterns occurred during the transition from angiogenic to quiescent EC. Second, once a quiescent state is established, DNA methylation marks remain stable throughout further EC aging. These longitudinal differentially methylated regions correlated with endothelial gene expression and provided evidence for the recruitment of de novo DNA methyltransferase 3a (DNMT3A). Comprehensive loss-of-function studies in mice revealed that the absence of DNMT3A-dependent DNA methylation led to the loss of active enhancers, resulting in mild transcriptional changes, likely due to loss of active enhancer integrity. These results underline the importance of DNA methylation as a key epigenetic mechanism of EC function during state transition. Furthermore, we showed that DNMT3A-dependent DNA methylation appears to be involved in establishing the proper histone landscape required for accurate transcriptome regulation.

overall_design: Sequencing experiments were performed on FACS-sorted lung endothelial cells isolated from Dnmt3a KO and WT mice.

first: Hellmut

last: Augustin


title: DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [WGBS II]

type: Methylation profiling by high throughput sequencing

overall_design: Sequencing experiments were performed on FACS-sorted lung endothelial cells isolated from WT mice of different ages (8 months and 18 months).


title: DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [WGBS]


title: DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [ATAC-Seq]


title: A potent neuroepithelium-promoting activity of Otx2 during gastrulation as demonstrated by its exogenous epiblast-wide expression in chicken embryos

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

institute: Biohistory Research Hall

summary: Despite the history of Otx2 research over three decades, the role of Otx2 expressed in the brain-forming anterior epiblast during gastrulation stages has not been clarified. We paid attention to the fact epiblast regions exist where Otx2 expression is absent or downregulated, namely the posterior epiblast and tissue belts along the neural plate bending. Developmental events that follow filling these expression gaps with exogenous Otx2 expression would be informative concerning the roles of Otx2 during gastrulation. The effects were pleiotropic: (1) Development of open and flat midbrain and hindbrain, which occurred via unzippering of once closed neural tube; (2) Precocious neural tube development at the cervical level that gave rise to thick and unclosed neural tissue; (3) The absence of the sinus rhomboidalis where NMP stem cells multiply to provide a cell source for the trunk posterior extension, resulting in the trunk posterior extension; (4) Inhibition of somite development. To elucidate principles underlying these developmental abnormalities, the cellular events were analyzed using live imaging of epiblasts, cell states were characterized via transcriptome analysis, and spatial organization of transcription factor expression was determined by immunohistology. Common denominating Otx2 activities that account for these pleiotropic effects were identified: (1) Significant boosts of neuroepithelium development, which even overrides the bipotential nature of NMPs, resulting in the loss of paraxial mesoderm precursor and loss of multiplying NMP stem cell population, and (2) The development of bending-refractory neural tissues. By virtue of these Otx2 functions, Otx2-expressing anterior epiblasts develop into the vast brain tissue in advance of the trunk neurogenesis that occurs in much smaller scale. We did not observe the exogenous Otx2 expression affecting the CNS regional specification.

overall_design: RNA-seq profiling of two chicken embryo portions, the midbrain-hindbrain portion and the trunk sinus rhomboidalis-equivalent portion, at st. 10-11, which were electroporated with pCAGGS-mOtx2 and pCAGGS-EGFP on the epiblast side at st.4/5 and cultured ex ovo. Control embryos were electroporated with pCAGGS-EGFP only or without electroporation.


title: DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [ACT-Seq]


title: Hybrid hydrogel–extracellular matrix scaffolds identify biochemical and mechanical signatures of cardiac ageing

status: Public on Apr 25 2025

city: Singapore

first: Jennifer

last: Young

address: 5A Engineering Drive 1, Mechanobiology Insititute, T-Lab Lv 9, National University of Singapore

country: Singapore

institute: National University of S'pore

summary: Extracellular matrix remodelling of cardiac tissue is a key contributor to age-related cardiovascular disease and dysfunction. Such remodelling is multifaceted including changes to the biochemical composition, architecture and mechanics, clouding our understanding of how and which extracellular matrix properties contribute to a dysfunctional state. Here we describe a decellularized extracellular matrix-synthetic hydrogel hybrid scaffold that independently confers two distinct matrix properties-ligand presentation and stiffness-to cultured cells in vitro, allowing for the identification of their specific roles in cardiac ageing. The hybrid scaffold maintains native matrix composition and organization of young or aged murine cardiac tissue, whereas its mechanical properties can be independently tuned to mimic young or aged tissue stiffness. Seeding these scaffolds with murine primary cardiac fibroblasts, we identify distinct age- and matrix-dependent mechanisms of cardiac fibroblast activation, matrix remodelling and senescence. Importantly, we show that the ligand presentation of a young extracellular matrix can outweigh the profibrotic stiffness cues typically present in an aged extracellular matrix in maintaining or driving cardiac fibroblast quiescence. Ultimately, these tunable scaffolds can enable the discovery of specific extracellular targets to prevent ageing dysfunction and promote rejuvenation.

overall_design: RNA-seq profiling of freshly isolated cardiac fibroblasts (CFs) from young or aged mice, as well as in vitro culture of these cells on DECIPHER ECM-hydrogel substrates after 48 hours.

first: Avery Rui

last: Sun


title: Innate immunity and Nfkb pathway control prostate stem cell plasticity, reprogramming and tumor initiation

status: Public on Apr 24 2025

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: Prostate epithelium develops from multipotent stem cells (SCs) which are replaced in adult life by different lineage-restricted basal and luminal unipotent SCs that sustain the homeostasis in a regionalized manner. Deletion of Pten re-induces multipotency in basal cells (BC). However, the molecular mechanisms regulating cell plasticity and tumor initiation are poorly understood. Here, we showed that Pten deletion in BCs led to distinct cell fate reprograming and tumor initiation in a regionalized manner. In anterior and dorsal prostates, BCs were reprogrammed into a Hillock like state that progressed into a basal-luminal hybrid state, which further transitioned into a proximal-like luminal state before progressing to tumorigenesis. In the ventral prostate, BC expressing Nkx3.1 gave rise to distal-like luminal state that are less plastic and progress more slowly to tumorigenesis. Single-cell sequencing and ATAC-seq analysis showed that the reprograming into hillock and proximal states induced activation of the innate immunity pathway during the cellular reprograming and tumor formation. Targeting Il-1, JAK/STAT and Nfkb inhibits Pten-induced cell plasticity and oncogenic reprograming, opening new opportunities in the prevention and treatment of prostate cancer.

overall_design: ATAC-seq of different lobes of murine prostate following 6W of PTEN deletion.

first: Chen

last: Jiang

first: Cédric

last: Blanpain


title: Histologic variants in bladder cancer share aggressive molecular features including a CA125+ cell state and targetable TM4SF1 expression

city: San Francisco

first: Hanbing

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

summary: Histologic variant (HV) subtypes of bladder cancer are clinically aggressive tumors that are more resistant to standard therapy compared to conventional urothelial carcinoma (UC). Little is known about the transcriptional programs that account for the morphological and biological differences in HV tumors. To investigate the tumor biology of HV bladder cancers, we generated a single cell RNA sequencing (scRNA-seq) atlas of nine HV tumors and three UC tumors. Our analyses revealed a tumor cell state specific to HVs that is characterized by expression of MUC16 (CA125), KRT24, and WISP2. This CA125+ cell state bears transcriptional hallmarks of epithelial-mesenchymal transition, is enriched in metastases, is predicted to be highly chemotherapy resistant, and is linked with poor survival, suggesting that this cell state plays an important role in the aggressive biology of HV tumors. Our analyses also provide evidence of transcriptional “mimicry” between HVs and histologically similar non-urothelial cell types. Lastly, we identified higher expression of TM4SF1, a cell surface protein associated with cancer metastasis, in HV tumor cells compared to UC tumor cells. Chimeric antigen receptor (CAR) T cells engineered against TM4SF1 protein demonstrated in vitro and in vivo activity against bladder cancer cell lines in a TM4SF1 expression-dependent manner, highlighting its potential as a therapeutic target in bladder cancer.

overall_design: cDNA library preparation was performed using the Seq-Well platform as previously described. Briefly, 10,000-20,000 cells were loaded onto a Seq-Well array containing 110,000 barcoded mRNA capture beads (ChemGenes, Ct: MACOSKO-2011-10(V+)). Arrays were sealed using a polycarbonate membrane (Sterlitech, Cat: PCT00162X22100) at 37 °C for 40 minutes. Cells were then lysed in lysis buffer (5 M guanidine thiocyanate, 1 mM EDTA, 0.5% sarkosyl, 1% BME) for 20 minutes at room temperature. Hybridization of mRNA to the beads was performed in hybridization buffer (2 M NaCL, 4% PEG8000) for 40 minutes. The beads were then collected and washed with 2 M NaCl, 3 mM MgCl2, 20 mM Tris-HCl pH 8.0, 4% PEG8000. Reverse transcription was then performed using Maxima H Minus Reverse Transcriptase (ThermoFisher, Cat: EP0753) in Maxima RT buffer, PEG8000, template switch Oligo dNTPs (NEB, Cat: No447L), and RNase inhibitor (Life Technologies, Cat: AM2696) at room temperature for 15 minutes and then 52 °C overnight. Second strand synthesis was performed using Klenow Exo- (NEB, Cat: M0212L) in Maxima RT buffer, PEG8000, dNTPs, and dN-SMRT oligo for 1 hr at 37 °C.  Whole transcriptome amplification was performed with KAPA HiFi Hotstart Readymix PCR kit (Kapa Biosystems, Cat: KK2602) and SMART PCR Primer. The reactions were purified using SPRI beads (Beckman Coulter) at 0.6X and then 0.8X volumetric ratio. Libraries were prepared using 800-1000 pg of DNA and the Nextera DNA Library Preparation Kit. Dual-indexing was performed using N700 and N500 oligonucleotides. Library products were purified using SPRI beads at 0.6X and then 1X volumetric ratio. A final 3 nM dilution was prepared for each library and sequenced on an Illumina NovaSeq S4 flow cell.

first: Heiko

last: Yang

first: Sima

last: Porten

first: Franklin

last: Huang


title: Transcriptomic Expression Profile Changes in Lung Tissue of Asthmatic Mice

city: Shenyang

first: Lishen

last: Shan

state: Liaoning

address: No. 36, Sanhao Street, Heping District

institute: Shengjing Hospital of China Medical University

summary: Asthma is a chronic inflammatory airway disease characterized by airway hyperresponsiveness and remodeling. In this study, we aimed to investigate the transcriptomic changes in the lung tissue of asthmatic mice using a well-established ovalbumin (OVA)-induced asthma model. Female BALB/c mice (6-8 weeks old) were randomly divided into two groups: sham (n=6) and OVA (n=5). The OVA group received intraperitoneal injections of 20 μg OVA and 2 mg Al(OH)₃ on days 0 and 14. Subsequently, from day 21 to day 23, the mice were exposed to 1% OVA aerosol for 30 minutes each day. The sham group received an equivalent volume of vehicle. After 24 hours of the last aerosol exposure, the mice were sacrificed, and lung tissues were collected for RNA sequencing. The sequencing data were analyzed to identify differentially expressed genes and pathways associated with asthma development and progression. The results provide valuable insights into the molecular mechanisms underlying OVA-induced asthma and may identify potential therapeutic targets.

overall_design: RNA-seq profiling of lung tissue from sham and OVA-challenged mice.


title: Aging and diet alter the protein ubiquitylation landscape in the mouse brain

city: Jena

first: Alessandro

last: Ori

address: Beutenbergstraße 11

institute: The Leibniz Institute on Aging – Fritz Lipmann Institute

summary: Post-translational modifications (PTMs) regulate protein homeostasis, but how aging impacts PTMs is unclear. Here, we used mass spectrometry to reveal changes in hundreds of protein ubiquitylation, acetylation, and phosphorylation sites in the mouse aging brain. We show that aging has a major impact on protein ubiquitylation. 29% of the ubiquitylation sites were affected independently of protein abundance, indicating altered PTM stoichiometry. Using iPSCs-derived neurons, we estimated that 35% of ubiquitylation changes observed in the aged brain can be recapitulated by reduced proteasome activity. Finally, we tested whether protein ubiquitylation in the brain can be influenced by dietary interventions. We found that one cycle of dietary restriction and re-feeding modifies the brain ubiquitylome, rescuing some but exacerbating other ubiquitylation changes observed in old brains. Our findings reveal an age-dependent ubiquitylation signature modifiable by dietary intervention providing insights into mechanisms of protein homeostasis impairment and highlighting new biomarkers of brain aging.

overall_design: We investigated which proteome and posttranslational modifications (phosphorylation, acetylation, and ubiquitylation) changes the mouse brain undergoes during aging. Additionally, we measured changes at the transcriptome level to understand if mRNA levels were explaining the data coming from the proteomic datasets. We used brains coming from five young (3 months old) and five old (33 months old) wild-type mice and generated RNA-seq data to analyze gene expression profiles.

first: Antonio

last: Marino


title: Innate immunity and Nfkb pathway control prostate stem cell plasticity, reprogramming and tumor initiation [II]

overall_design: To compare basal-derived luminal tumors and luminal-derived luminal tumors, we performed bulk RNA-seq on FACS-isolated basal-derived luminal cells (from K5-PTEN) and luminal-derived luminal cells (from K8-PTEN) from murine prostate tumors.


title: Gene expression of sorted synovial myeloid cells from wild type and Fas-/- mice with antigen-induced arthritis and immunized control mice without arthritis.

city: Zagreb

first: Nina

last: Lukač

address: Šalata 11

department: Department of Anatomy

country: Croatia

institute: University of Zagreb School of Medicine

summary: The aim of this experiment was to analyze differences in gene expression between synovial myeloid (CD11b+Gr-1+) cells from wild type (C57BL6; WT, B6) and Fas-/- mice with antigen-induced arthritis (AIA). Immunized control (CTRL) mice were used to asses the change in synovial myeloid cell trascriptome after arthritis induction in both genotypes.

overall_design: AIA was induced in wild-type (WT, B6) and Fas-/- mice by immunization with methylated bovine serum albumin (mBSA) and subsequent intra-articular injection of mBSA. Immunized control (CTRL) mice were intra-articulary injected with phosphate buffered saline (PBS). Ten days after intra-articular injection knee joints were harvested and synovial cells were released by collagenase and labeled with anti-mouse CD45-FITC, CD11b-PE, Gr1-PECy7, B220/CD3/NK1.1/CD31/TER119-APC, and CD51-APCeF780. CD11b+Gr-1+ population was sorted using BD FACSAria, RNA extracted by Trizol, and hybridized to Affymetrix Mouse Gene ST 2.0 arrays. Each experimental group contained 4 samples.

first: Nataša

last: Kovačić


title: Innate immunity and Nfkb pathway control prostate stem cell plasticity, reprogramming and tumor initiation [I]

overall_design: To assess the impact of innate immunity on cell fate changes following PTEN deletion in BC, we performed bulk RNA-seq on FACS-isolated BC cells at 6 weeks post-PTEN deletion and FACS-isolated BC cells from p65 knockout mice with 6 weeks of PTEN deletion induction.


title: Effect of EZH2 Inhibition on tumor infiltrating CART19 (day 11)

first: Marco

last: Ruella

address: 3400 Civic Center Blv

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

summary: Molecular carachterization of CART19-vehicle vs CART19-tazemetostat in tumor infiltrating CART cells

overall_design: OCI-Ly18 xenograft lymphoma model treated with vehicle or tazemetostat for 15 days and infused with CART19. Cell sorting and scRNA sequencing on 3 vs 3 animals infused with CART19 was performed 11 days post infusion of T cells.

first: Patrizia

last: Porazzi

first: Linhui

last: Chen

first: Ruchi

last: Patel

first: Puneeth

last: Guruprasad

first: Siena

last: Nason


title: Effect of EZH2 inhibition and CART19 on gene expression of a sub-cutaneous tumor model of B-NHL (OCI-ly18 cell line)

summary: The goas of this experiment were: 1) to assess the effect of CART19 killing on tumors dissected from xenograft models of B-NHL;  3) to assess the effect of combining tazemetostat/CART19 on tumors dissected from xenograft models of B-NHL.

overall_design: OCI-Ly18-GFP+ cells were sub-cutaneously implanted into NSG mice. 3 days later, mice were treated with tazemetostat (150 mg/kg/daily) or vehicle for 14 days. Mice were then infused with CART19 cells or UTD. 11 days post CART19 infusion, mice were sacrified, tumor were dissected and processed to prepare a single cell suspension. Cell sorting separated tumor-GFP+ cells from CART19 cells. Total RNA was extracted from tumor cells and submitted for bulk RNA sequencing.