title: The genome of Pseudotaxus chienii, a relict conifer endemic  to China, provides insights into the origin and evolution of  taxane biosynthesis

status: Public on Jan 27 2025

city: Hangzhou City

first: M

last: Y

address: Hangzhou Normal University, Hangzhou City, Zhejiang Province

institute: Hangzhou Normal University

summary: As a sister genus to Taxus, Pseudotaxus holds significant importance for studying the origin and evolution of the taxane biosynthesis pathway. However, the reference genome of P. chienii, the sole species of Pseudotaxus, is not yet available. We have completed a chromosome-level genome assembly of P. chienii, with a total length of 15.6 Gb. P. chienii possesses only a partial pathway for Taxol biosynthesis, which terminates before the enzyme taxane 2α-O-benzoyl transferase (TBT), a crucial enzyme responsible for the production of 10-deacetylbaccatin III. With the emergence of the Taxus genus, the limitation posed by TBT is overcome, allowing for the extension of the existing taxane biosynthesis pathway into a complete Taxol biosynthesis pathway. Protein structure analysis revealed that the structure of metal ion catalysis sites in taxadiene synthase (TS) is conserved across the Pseudotaxus and Taxus genera, providing potential sites for enhancing TS activity through enzyme engineering. This comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis within the Taxaceae family.

overall_design: In this study, we successfully assembled the Pseudotaxus genome and presented a reference-grade genome sequence of P. chienii, which contains 16.79 giga-bases (Gb) of data, 15.45 Gb of which was assigned to 12 pseudochromosomes. Our comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis and provides insights into the genome structure and organization of the Taxaceae family.

first: Mingshuang

last: Wang

first: Ruoyun

last: Ma

first: Zijin

last: Fang

first: Lingxiao

first: Yibo

first: Mengyin

last: Zheng

first: Enhui

last: Bai

first: Wanting

last: Lin

first: Yanyan

last: Pei

first: Yue

last: Zang

first: Huijie

first: Shangguo

last: Feng

first: Xiaori

last: Zhan

first: Chunna

last: Yu

first: Shuling

first: Huizhong

first: Chenliang

first: Chenjia

last: Shen


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [ChIP]

status: Public on Jan 15 2025

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

country: USA

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mouse embryonic stem cells (mESCs) and other naïve pluripotent stem cells, under specific conditions, can reverse typical developmental trajectories and de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). We implemented a multipurpose allele for acute protein depletion and efficient immunoprecipitation to dissect the molecular functions of EHMT2 in mESCs. This approach allowed us to define different types of EHMT2 target genes and distinct modes of chromatin engagement and repression. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. Conversely, the loss of EHMT2 allows the recruitment of the activator DPPA2/4 to promoter-proximal ERVs in 2CLCs, thus facilitating the mESC-to-2CLC transition. Repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters in collaboration with ZFP462 and entails binding to non-repeat enhancers. Our data suggests that EHMT2 functions as an attenuator of the bidirectional differentiation potential of mouse naïve pluripotent stem cells and define molecular models for the gene-specific repressive activity of this essential histone methyltransferase.

overall_design: EHMT2-HA-dTAG lines were treated with DMSO  or dTAG13 for 24 hours. Cells were harvested using trypsin. CHIP-Seq using HA antibody performed to determine chromatin occupancy of EHMT2

first: Kaushiki

last: Chatterjee

middle: M

first: Kritika

last: Kasliwal

first: Effie

last: Apostolou

first: Matthias

last: Stadtfeld


title: Eosinophils in Lung Allograft

status: Public on Jan 14 2025

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: Eosinophils were isolated from the lungs of mice that were resting naïve or 7 or 30 days post-transplant with costimulatory blockade

overall_design: Lungs of 3 to 5 mice were pooled per sample. Lung eosinophils were isolated by flow cytometry sorting. RNA was prepared from Trizol and sequencing was performed at Genewiz (South Plainfield, NJ) using Ultra-Low Input RNA-Seq Service.

first: Elizabeth A.

first: Alexander

last: Krupnick


title: Eosinophils Restrain Humoral Alloimmunity after Lung Transplantation

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

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

overall_design: Refer to individual Series


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [Cut & Run]

overall_design: MERVL GFP- EHMT dTAG lines were treated with DMSO/dTAG for 72hrs , Sorted for gfp positive and negative population. Cut and Run performed using anti-DPPA4 antibody (AF3730)


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [RNA-seq]

overall_design: Transcriptional activity of EHMT-dTAG ESC's  treated with DMSO or dTAG for 24 hours, 7 days or 15days and  7 days of dTAG treatment followed by 8 days of recovery.  Transcriptional activity of MERVL GFP+ and GFP- population after 72 hours of dTAG treatment and post sorting was assesed using low input RNA-sequencing. Transcriptional activity of WT or Dppa4 KO ESC's  treated with DMSO or UNC0638 for 48 hrs.


title: Progenitor Effect in the spleen drives early recovery via Universal Hematopoietic Inflation [Bulk RNA-Seq]

status: Public on Jan 09 2025

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

summary: Hematopoietic stem cells (HSC) possess the capacity to regenerate the entire hematopoietic system. However, the precise HSC dynamics in the early post-transplantation phase remains an enigma. Clinically, the initial hematopoiesis in the post-transplantation period is critical, necessitating strategies to accelerate hematopoietic recovery. Here, we uncovered the spatiotemporal dynamics of early active hematopoiesis, “Hematopoietic Inflation”, using a highly sensitive in vivo imaging system and established universal HSPCs capable of immediately supplying vast numbers of blood cells. Hematopoietic Inflation occurs in three peaks in the spleen after transplantation, with common myeloid progenitors (CMPs), notably characterized by HSC-like signatures, playing a central role. Leveraging these findings, we developed expanded CMPs (exCMPs), characterized by a gene expression pattern that selectively proliferates in the spleen and promotes hematopoietic expansion. Moreover, universal exCMPs supported early hematopoiesis in allogeneic transplantation. Human universal exCMPs have the potential to be a viable therapeutic enhancement for all HSC transplant patients.

overall_design: RNA-seq profiling of fresh CMPs from bone marrow and expanded CMPs (exCMPs)

first: Takao

last: Yogo

first: Satoshi

last: Yamazaki


title: Integrated Multi-Omics Analysis Reveals Epigenetic and Sex-Specific Alterations in Colorectal Cancer Cachexia

status: Public on Jan 08 2025

city: Fayetteville

first: Ana

middle: Regina

last: Cabrera

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

summary: Cancer cachexia (CC) is experienced by 80% of cancer patients, representing up to 40% of cancer-related deaths. Evidence suggests biological sex dimorphism associated with CC. The initial triggering factors of muscle wasting, biological sex differences, and the epigenetic regulation during the onset and progression of cancer cachexia are not fully understood. The purpose of this study was to define the time course of C26-induced CC in males and females using transcriptomics, compare the transcriptomic changes with a more sever APC+/Min genetic model and identify the impact of epigenetic regulations associated to CC.

overall_design: At week-old Balb/c male and female mice (n=6-8/group) receivd 1x10^6 C26 cells injected bilateral, and tumors were developed for 10-, 20-, and 25-days, at endpoints, Tibialis Anterior (TA) muscle were collected.  The control mice received PBS injections  and TAs were colllected 25-days after PBS injections (controls). TA was also collected from 20-weeks-old APC+/Min mice (C57 black mice background) and their wild types (controls). RNA was extracted for RNA sequencing.

first: Nicholas

middle: P

last: Greene

first: Kevin

middle: A

last: Murach

middle: R


title: Progenitor Effect in the spleen drives early recovery via Universal Hematopoietic Inflation [scMultiome]

overall_design: Single-cell multiome analysis : Fresh CMPs, exCMPs and SPaCMPs were collected for single-cell RNA and ATAC sequencing.


title: Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing

status: Public on Jan 01 2025

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

country: China

institute: Peking University

summary: As the ancestor of CRISPR-Cas12 nucleases, TnpB represents the most compact gene editing tool currently available. Recent studies have identified multiple TnpB systems with gene editing activity in mammalian cells, and the potential of TnpB in treating diseases has been demonstrated in animal models. However, the editing characteristics of various TnpB systems, comparable to CRISPR tools, require more extensive investigation. Using a standardized evaluation framework, we conducted a thorough analysis of the editing properties of four TnpB variants alongside representative Cas12 and Cas9 tools. Overall, TnpBs exhibit intermediate editing activity and safety profiles among all tested systems, with ISYmu1 TnpB demonstrating a good performance in both editing activity and specificity. Considering its compact size, potent editing efficiency and high specificity, ISYmu1 TnpB represents a promising candidate for in vivo gene therapy applications.

overall_design: We employed primer-extension-mediated sequencing (PEM-seq) to study the gene-editing outcomes for various TnpB systems and CRISPR-Cas nuclease, including: SpCas9, Nme2-C.NR, AsCas12a, CasMINI, ISDra2, ISDge10, ISAam1, ISYmu1. Twelve different editing sites were targeted for each nuclease.

first: Guanghai

last: Xiang

first: Shiwei

last: Cui

first: Yuhong

last: Wang

first: Jiazhi

last: Hu

first: Haoyi


title: The regulatory RNA Ern0160 is involved in pathogenicity of Enterococcus faecium

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

summary: In this study, we aimed to further characterize Ern0160 functions and identify its targets. In silico prediction screen highlighted putative mRNA candidates. For two of them, homologous genes encoding for LysM-containing domain proteins (EFAU004_01059 and EFAU004_01150), we validated a direct and specific interaction to Ern0160. In addition, we found that Ern0160 overexpression was responsible for the repression of the target genes, emphasizing the mode of action of this sRNA. As a recent study provided the role of these genes in the virulence of E. faecium Aus0004 in a mouse model of systemic and urinary tract infections, we proposed that Ern0160 could be part of the regulatory network involved during colonization/infection by attenuating virulence. Furthermore, in vitro tests of antibiotic susceptibility profiles to vancomycin, teicoplanin, daptomycin, ciprofloxacin, and levofloxacin showed that a strain expressing Ern0160 presented lower MICs of fluoroquinolones compared to a ern0160-deleted strains. Very interestingly, we found that a gene implicated in fluoroquinolone resistance in E. faecium, Efmqnr was downregulated when Ern0160 was over-expressed, indicating a link between this sRNA and antibiotic resistance. For the first time, this study investigated throughout the identification of its cellular targets the regulation that could lead to virulence and fluoroquinolone resistance in E. faecium.

overall_design: Transcriptome analysis by RNA-seq to compare the levels of all transcripts in ern0160-deleted E. faecium Aus0004 mutant versus wild-type strain and in trans-complemented srn0160-deleted E. faecium Aus0004 mutant versus srn0160-deleted E. faecium Aus0004 mutant with empty plasmid

first: Loren

last: Dejoies

first: Valérie

last: Bordeau

first: Killian

last: Le Neindre

first: Sophie

last: Reissier

first: Brice

last: Felden

first: Svetlana

last: Chabelskaya

first: Charlotte

last: Michaux


status: Public on Jan 10 2025

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of ERpHER2n primary tumors (surgically resected) to target epigenetic regulation of FGFR4 in primary resectable (early-stage) ER-positive and HER2-negative tumors.

overall_design:
DNA methylation of tumor DNA was performed using Illumina MethylationEPIC V1 beadchips on 499 tumors according to manufacturer's instructions. No replicates.
Note from submitter:  Due to Swedish law we are not allowed to openly deposit (like in GEO) any data that can be considered personal patient information. The EPIC platform contains non CpGs, therefore we cannot deposit IDAT files.

last: Vallon-Christersson


title: Comparative analysis of chromatin accessibility during chondrogenesis and in osteoarthritis

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

country: United Kingdom

institute: Newcastle University

summary: To reveal the organisation of the cartilage cell chondrocyte genome and identify changes that occur within this organisation during development and due to osteoarthritis (OA).  Methods  Assay for Transposase -Accessible Chromatin using Sequencing (ATAC-seq) was performed on chondrocytes isolated from 16 patients undergoing total hip replacement because of OA (n=7) or due to a neck of femur fracture (NOF, n=9). ATAC-seq was similarly performed on bone-marrow mesenchymal stem cells (BM-MSC) and differentiated chondrocytes of two donors. DNA sequence reads (av. 50 million/sample) were aligned to human genome Hg38. Peaks were called using MACS2 and differential accessibility identified by DiffBind. Interexperiment comparisons and intersection with published gene expression changes, chondrogenesis ChIP-seq, knee ATAC-seq and human tissue scATAC-seq were performed in Galaxy and R. OA GWAS signal regions were overlapped with our defined chondrocyte ATAC-seq peaks.   Results  In BM-MSC and derived chondrocytes we mapped 138005 open chromatin regions, of which 20979 and 50699 significantly increased and decreased respectively during cell differentiation. In hip chondrocytes we identified 115295 open chromatin regions, 1383 and 573 were more or less differentially accessible respectively when comparing OA with NOF samples. In both data sets ‘newly accessible regions were enriched at enhancer regions (defined by ChIP-seq). Comparing the data with the ATAC-seq from the single cell ATLAS we identified 11866 open regions exclusive to chondrocytes. Genes associated with these regions were significantly enriched for cartilage-related gene ontology terms. Taking the 420 OA GWAS signals present in the GWAS catalogue, 313 of the OA regions (defined as lead SNP + proxy SNPs with r2 ≥ 0.8) overlapped with a chondrocyte ATAC-seq region.   Conclusions  Here we have mapped chromatin accessible region changes during chondrogenesis, showing that newly accessible regions are enriched at enhancer regions and positively correlate with gene expression. Open chromatin region changes between OA and NOF cartilage were fewer, and peak differences were subtle. Overall, we have associated OA GWAS loci with accessible regions and defined regions of the genome specific to cartilage and chondrogenesis.

overall_design: To reveal the organisation of the cartilage cell chondrocyte genome and identify changes that occur within this organisation during development and due to osteoarthritis (OA). Assay for Transposase -Accessible Chromatin using Sequencing (ATAC-seq) was performed on chondrocytes isolated from 16 patients undergoing total hip replacement because of OA (n=7) or due to a neck of femur fracture (NOF, n=9). ATAC-seq was similarly performed on bone-marrow mesenchymal stem cells (BM-MSC) and differentiated chondrocytes of two donors

first: David

last: Young

middle: J


title: DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: The dynamic balance of DNA methylation and demethylation is required for erythropoiesis. Our previous transcriptomic analyses revealed that DNA methyltransferase 1 (DNMT1) is abundantly expressed in erythroid cells at all developmental stages. However, the role and molecular mechanisms of DNMT1 in human erythropoiesis remain unknown. Here we found that DNMT1 deficiency led to cell cycle arrest of erythroid progenitors which was partially rescued by treatment with a p21 inhibitor UC2288. Mechanically, this is due to decreased DNA methylation of p21 promoter, leading to upregulation of p21 expression. In contrast, DNMT1 deficiency led to increased apoptosis during terminal stage by inducing endoplasmic reticulum (ER) stress in a p21 independent manner. ER stress was attributed to the upregulation of RPL15 expression due to the decreased DNA methylation at RPL15 promoter. The upregulated RPL15 expression subsequently caused a significant upregulation of core ribosomal proteins (RPs) and thus ultimately activated all branches of unfolded protein response (UPR)leading to the excessive ER stress, suggesting a role of DNMT1 in maintaining protein homeostasis during terminal erythroid differentiation. Furthermore, the increased apoptosis was significantly rescued by the treatment of ER stress inhibitor TUDCA. Our findings demonstrate the stage-specific role of DNMT1 in regulating human erythropoiesis and provide new insights into regulation of human erythropoiesis.

overall_design: To determine the molecular mechanism of for the DNMT1 deficiency-induced apoptosis, we performed RNA-seq analysis on the purified luciferase-shRNA and DNMT1-knockdown orthochromatic erythroblasts.

first: Qianqian

last: Yang

first: Lixiang

last: Chen

first: Ting


title: Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

status: Public on Dec 31 2024

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

state: CA

address: 515 LSA

department: Molecular and Cell Biology

institute: University of California Berkeley

summary: Even seemingly homogeneous populations of cells can express phenotypic diversity in response to environmental changes. Thus, the effects of X-ray irradiation on tissues composed of diverse cell types is likely to be complex. We have used single-cell RNA sequencing to study the effects of X-ray radiation on the wing-imaginal disc of Drosophila, a relatively simple tissue that is mostly composed of epithelial cells. Transcriptomic clustering of cells collected from the wing disc generates clusters that are mainly grouped based on cell location in the proximodistal axis. To quantify heterogeneity of gene expression among clusters, we adapted a metric used to study market concentration, the Herfindahl-Hirschman Index. We show that genes involved in DNA damage repair, alleviation of reactive oxygen species, cell-cycle progression, and apoptosis are expressed relatively uniformly. In contrast, genes encoding a subset of ligands, notably cytokines that activate the JAK/STAT pathway, transcription factors implicated in regeneration such as Ets21C, and some signaling proteins are expressed in more restricted territories. Several of these genes are still expressed in a p53-dependent manner indicating that regional and radiation-induced factors combine to regulate their expression. We similarly examined heterogeneity within territories by using a clustering approach based on cell-cycle gene expression. Using this method, we identified a subpopulation characterized by high levels of tribbles expression that is mostly found in irradiated discs. Remarkably, this subpopulation accounts for a considerable fraction of radiation-induced gene expression, indicating that cellular responses are non-uniform even within territories. Thus, both inter-regional and intra-regional heterogeneity are important features of tissue responses to X-ray radiation.

overall_design: Single-cell RNA-sequencing was performed on X-ray irradiated wing discs, an epithelial tissue found in Drosophila melanogaster larvae. Two wing disc samples were collected from larvae, and two wing disc samples collected from larvae exposed to 4000 rad.

first: Joyner

last: Cruz

first: William

middle: Y

last: Sun

first: Alexandra

last: Verbeke

middle: K


title: The Effects of Complement in a Chronic Murine Model of Inflammatory Erosive Arthritis and Pulmonary Vascular Disease

city: Rochester

first: Benjamin

last: Korman

address: 601 Elmwood Avenue, Box 695

institute: AIR

summary: Dysfunction of the complement pathway contributes to diseases such rheumatoid arthritis (RA) and pulmonary hypertension (PH). Here we aim to determine whether complement deficiency has a protective effect on joint and lung disease using the tumor necrosis factor-transgenic (TNF-Tg) mouse model with constitutive human TNF-ɑ expression characterized by spontaneous onset of inflammatory-erosive arthritis and PH.

overall_design: Cells were obtained from the lungs and synovium of TNF-Tg and WT mice and analyzed by using scRNAseq

first: Homaira

last: Rahimi

first: Kiana

middle: L

first: Gaochan

last: Wang


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (EC sorted)

city: Oklahoma City

first: Willard

last: Freeman

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

summary: Endothelial cells (ECs) display organ- and tissue-specific heterogeneity. In the eye, the retinal and choroidal vascular beds are distinct networks with different morphological and functional features with the former representing a tight barrier and the latter, a permeable fenestrated vasculature. Given that retinal health critically relies on the function of these vascular beds and that their dysfunction is implicated in a variety of retinal diseases, a molecular understanding of both physiological and pathophysiological characteristics of these distinct vasculatures is critical. Given their interspersed anatomic distribution among parenchymal cells, the study of EC gene expression, in vivo, has been hampered by the challenge of isolating pure populations of ocular ECs in sufficient quantities for large-scale transcriptomics. To address this challenge, we present a methodological and analytical workflow to facilitate inter-tissue comparisons of the in vivo EC translatome isolated from choroid, retina, and brain using the Cre-inducible NuTRAP flox construct and two widely-used endothelial cre mouse lines, constitutive Tie2-Cre and Tamoxifen-inducible Cdh5-CreERT2, which express EGFP and mCherry tags for cell-specific isolation of nuclei and ribosomes. Within each model, inter-tissue comparison of TRAP-RNAseq enrichment (TRAP translatome vs input transcriptome) showed tissue-specific gene enrichments with differential pathway representation. For each mouse model, inter-tissue comparison of the EC translatome (choroid vs brain, choroid vs retina, and brain vs retina) showed over 50% overlap of differentially expressed genes (DEGs) between the three paired comparisons, with differential pathway representation for each tissue. Pathway analysis of DEGs in the Cdh5-NT vs Tie2-NT comparison for retina, choroid, and brain predicted inhibition of processes related to myeloid cell function and activation, consistent with more specific targeting of ECs in the Cdh5-NT than in the Tie2-NT model. While TRAP enriches for EC transcripts in both models, it also captures myeloid transcripts in the Tie2-NT model. We confirmed these observations with a cell sorting approach. We suggest experimental/analytical considerations should be taken when selecting cre-lines to target ECs.

overall_design: Tie2-cre+; NuTRAP+ RNA from FACS sorted cells - Input and Positive Fractions; 3 biological replicates

first: Ana

last: Chucair-Elliott

first: Kevin

last: Pham

first: Audrey

last: Cleuren

first: Christopher

last: Schafer

first: Courtney

middle: T

last: Griffin

first: Sarah

last: Ocanas

first: Michael

middle: H

last: Elliott


title: Multi-omics Reveals Different Signatures of Obesity-Prone and Obesity-Resistant Mice

city: Hangzhou

first: Fei

last: Yang

address: 866 Yu-hang-tang Road

institute: Zhejiang University

summary: The expression profiles of mRNAs in colon were investigated by high-throughput RNA sequencing using HFD-induced C57BL/6J mice. Genes that play roles in obesity and related pathways were identified.

overall_design: The expression profiles of mRNAs in colons by high-throughput RNA sequencing using HFD-induced C57BL/6J mice.

first: Congcong

first: Jinhua

last: Lin

first: Shankuan

last: Zhu


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (Tie2)

overall_design: Tie2-cre+; NuTRAP+ RNA isolated via TRAP method - Input and Positive Fractions; 3 tissues with 3 biological replicates


title: Host-derived Interleukin 1α induces immune suppressive tumor microenvironment via regulation of monocyte-to-macrophage differentiation

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Tumor-associated macrophages exhibit high heterogeneity and contribute to the establishment of an immune-suppressive tumor microenvironment (TME). Although numerous studies have demonstrated that extracellular factors promote macrophage proliferation and polarization, the regulatory mechanisms governing the differentiation process to generate phenotypically, and functionally diverse macrophage subpopulations remain largely unexplored. In this study, we examined the influence of interleukin 1α (IL-1α) on the development of an immune-suppressive TME using syngeneic transplantation murine models of breast cancer. Deletion of IL-1α led to the rejection of syngeneic tumor challenges. Single-cell sequencing analysis revealed that Cx3cr1+ macrophage cells were the primary sources of IL-1α in the TME. The absence of IL-1α reprogrammed the monocyte-to-macrophage differentiation process within the TME, characterized by a notable decrease in the subset of Cx3cr+ ductal-like macrophages and an increase in iNos-expressing stress-responsive cells. Comparative analysis of gene signatures in both human and mouse macrophage subsets suggested that IL-1α deficiency shifted macrophage polarization from M2 to M1 phenotypes, leading to enhanced cytotoxic T lymphocyte activity in the TME. Importantly, elevated levels of IL-1α in human cancers were associated with improved prognosis following immunotherapy. These findings underscore the pivotal role of IL-1α in shaping an immune-suppressive TME through the regulation of macrophage differentiation and activity, highlighting IL-1α as a potential target for breast cancer immunotherapy.

overall_design: Freshly harvested HER2+ H605 tumors from transplanted WT and IL1α-/- mice, two pairs in total, were disaggregated into single cells two weeks after transplantation and subsequently subjected to single-cell sequencing.

first: Manikanda

last: Keerthi Raja

first: Hao

last: Ji

first: Hexin

last: Chen


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (Cdh5)

overall_design: Cdh5(PAC)-cre/ERT2+; NuTRAP+ RNA isolated via TRAP method - Input and Positive Fractions; 3 tissues with 3 biological replicates


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds

overall_design: Refer to individual Series


title: Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [ChIP-Seq]

status: Public on Dec 30 2024

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

summary: Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic metabolism of most other RCCs. The transcriptional program driven by TFE3 fusions sustains high NRF2 signaling and glutathione production, which offsets reactive oxygen species generated by OXPHOS but renders tRCC cells sensitive to reductive stress. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to maintaining this metabolic balance, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1compromises tRCC cell growth by stabilizing HIF-1a and promoting glycolytic reprogramming. Our study defines a distinctive tRCC-essential metabolic program driven by TFE3 fusions and nominates EGLN1inhibition as a therapeutic strategy to counteract fusion-induced metabolic rewiring.

overall_design: To investigate the epigenomics in tRCC, we performed H3K27ac ChIP-Seq in tRCC. And to investigate the role of TFE3 fusion in tRCC, we performed TFE3 ChIP-Seq in three tRCC cell lines.

first: Jiao

last: Li

first: Srinivas

last: Viswanathan


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus [RNA-Seq]

status: Public on Dec 18 2024

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

summary: MYT1L Syndrome mouse model displays obesity as observed in MYT1L patients. Utilizing this mouse model, ATAC-seq and RNA-seq on adult mouse hypothalamus reveals molecular alternations related to feeding behaviors, which might contribute to obesity phenotype.

overall_design: We have 3 biological replicates per genotype for ATAC-seq and 6(Het)/5(WT) replicates for RNA-seq on adult mouse hypothalamus

first: Jiayang


title: Clonorchis sinensis infection alters the methylation and hydroxymethylation of hepatocellular carcinoma

status: Public on Dec 20 2024

city: Nanning

first: Junxian

address: 71, Hedi Road, Qingxiu District

department: Department of Clinical Laboratory

institute: Guangxi Medical University Cancer Hospital

type: Methylation profiling by high throughput sequencing

summary: Clonorchis sinensis (Cs) infection is prevalent in Southeast Asia and has been classified as a Group I carcinogen by the International Agency for Research on Cancer, posing significant risks to the human liver and biliary system. While recent studies have linked Cs infection to poorer outcomes in hepatocellular carcinoma (HCC) patients, the precise molecular mechanisms underlying its effect on HCC remain to be fully elucidated. This study investigates the epigenetic changes in Cs-infected HCC using whole-genome bisulfite sequencing and whole-genome oxidative bisulfite sequencing to map 5-methylcytosine and 5-hydroxymethylcytosine profiles at single-nucleotide resolution. We identified 29 differentially methylated regions and 13 differentially hydroxymethylated regions in Cs-infected HCC, which were associated with 28 differentially methylated/hydroxymethylated-associated genes (DAGs/DhAGs). The methylation levels of four promoter Cytosine-phosphate-Guanine (CpG) sites of DAGs/DhAGs were found to correlate with prognosis in Cs-infected HCC, while two key DMR/DhMR-associated genes, DHDH and KCNQ3, were significantly linked to overall survival of HCC. Our study provides the first detailed epigenetic map of Cs-associated HCC, uncovering novel insights into potential biomarkers and therapeutic targets that could enhance prognostic predictions and inform treatment strategies for patients affected by this condition.

first: Weilong

first: Taijun

last: Huang

first: Caibiao

last: Wei

first: Lingling

last: Zhou

first: Yulong

last: Xu

first: Jie

last: Gao

first: Fengfei

last: Liu

first: Jian-Kang

first: Min

last: Fang


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus


title: Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders Fused to Tn5

status: Public on Dec 15 2024

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

summary:
Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration.
Keywords:
Antibody-Free CUT&Tag; Chromatin Binding; Epigenetic Profiling; Peptide-binder; Single-cell analysis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Af-CUT&Tag, an antibody-free and sensitive tool for epigenetic analysis, utilizes C-terminal peptide tagging of proteins of interest (POIs) and a Tn5 transposase fused to a peptide binder for precise chromatin profiling.

first: Yongyou

last: Zhang

first: Xindong

last: Wang

first: Xusheng

last: Deng


title: The transcriptional landscape of microspore embryogenesis induction in barley

status: Public on Dec 29 2024

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

summary: The effectiveness of microspore embryogenesis and plant formation from in vitro cultivated microspores is determined by a complex network of internal and environmental factors. Plant breeding and genetic engineering widely use haploids/doubled haploids (DHs) derived from in vitro-cultured microspores, but the mechanism of ME induction remains poorly defined. Here, RNA-sequencing was used to characterize the transcriptional landscapes of four early stages of ME in two barley cultivars (Golden Promise and Igri) that are contrastingly responsive in the microspore-derived plant formation. Our experimental setup revealed fundamental regulatory networks, key marker genes of ME (628 stage-specific markers), and 160 candidate genes crucial for genotype-dependent responsiveness/resistance to ME. We found that transcription factors probably give rise to embryo-like structure and callus formation at stage III and determine their further development. Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies aiming at unravelling the genetic control of microspore transition.

overall_design: Microspores isolated at four developmental stages of microspore embryogenesis; species barley (Hordeum vulgare) ; Microspores isolated from two cultivars: Golden Promise and Igri; each stage - four biological replicates

first: Anna

last: Nowicka

first: Martin

last: Kovacik

last: Maksylewicz

first: Przemysław

last: Kopeć

first: Ewa

last: Dubas

first: Monika

last: Krzewska

first: Agnieszka

last: Janas

first: Robert

middle: E

last: Hoffie

first: DiaaEldin

middle: S

last: Daghma

first: Jochen

last: Kumlehn

first: Iwona

last: Żur


title: Exacerbated Salmonellosis in poly(ADP-ribose) polymerase 14 deficient mice

status: Public on Dec 26 2024

city: Turku

first: Madhukar

last: Vedantham

address: Kiinamyllynkatu 10-D

country: Finland

institute: University of Turku

summary: Salmonella enterica serovar Typhimurium infection triggers a robust immune response in the host, but the molecular mechanisms regulating this response are not fully understood. Parp14 has been shown to enhance type I interferon responses and influence bacterial resistance, particularly in macrophages. To explore the role of Parp14 in immune regulation, we investigated Salmonella infection in Parp14 knockout mice over 5 days. On day 1 post-infection (p.i.), Parp14-deficient mice displayed elevated bacterial loads in the liver, but no differences in other tissues. By day 5, bacterial counts in the proximal colon were slightly lower in Parp14 knockout mice compared to wild-type controls, suggesting Parp14 regulates immune responses across multiple cell types, including epithelial cells. Histopathological analyses revealed increased immune cell infiltration, goblet cell loss, and tissue erosion in the proximal colon of Parp14-deficient mice on day 5 p.i. RNA-seq data from proximal colon tissue identified impaired expression of immune response genes, including Ccl2, Il1b, and Il6, which are critical for early-stage infection defense. Further analysis revealed downregulation of genes involved in cellular adhesion and cytoskeleton maintenance. These findings indicate that Parp14 is essential for an effective early innate immune response and for maintaining epithelial integrity during Salmonella infection, highlighting its potential as a therapeutic target for bacterial infections.

overall_design: To investigate the transcriptome changes in colon of Parp14-deficient mice when compared to wt mice in resting state and post Salmonella infection, we performed bulk tissue RNA-Seq analysis of the mouse colon proximal sections 1-day post-infection.

first: Arto

last: Pulliainen


title: ETVs dictate hPSC differentiation by tuning biophysical properties

status: Public on Dec 21 2024

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

summary: Stem cells maintain a dynamic dialogue with their niche, integrating biochemical and biophysical cues to modulate cellular behavior. Yet, the transcriptional networks that regulate cellular biophysical properties remain poorly defined. Here, we leverage human pluripotent stem cells (hPSCs) and two morphogenesis models – gastruloids and pancreatic differentiation – to establish ETV transcription factors as critical regulators of biophysical parameters and lineage commitment. Genetic ablation of ETV1 or ETV1/ETV4/ETV5 in hPSCs enhanced cell-cell and cell-ECM adhesion, leading to aberrant multilineage differentiation including disrupted germ-layer organization, ectoderm loss, and extraembryonic cell overgrowth in gastruloids. Furthermore, ETV1 loss abolished pancreatic progenitor formation. Single-cell RNA sequencing and follow-up assays revealed dysregulated mechanotransduction via the PI3K/AKT signaling. Our findings highlight the importance of transcriptional control over cell biophysical properties and suggest that manipulating these properties may improve in vitro cell and tissue engineering strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq, scRNA-seq and ATAC-seq data for hPSCs and its KO derivatives (KO=ETV1 KO and tKO=ETV1-, ETV4-, ETV5 KO) in pluripotency  (pluri) and pancreaatic progenitors stage.

first: Natalia

last: Ziojla

first: Magdalena

last: Socha

first: Cecilia

last: Guerra

first: Edyta

last: Urbaniak

first: Dorota

last: Kizewska

first: Sara

last: Henry

first: Malgorzata

last: Grabowska

first: Aryeh

last: Warmflash

last: Borowiak

first: Kathy

last: Niakan


title: A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing

status: Public on Dec 13 2024

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

summary: To assess the performance of our algorithm with real long-read data, we utilized VCaP cell lines with both direct RNA and direct cDNA sequencing approaches.

overall_design: Nanopore direct RNA long read sequencing of VCaP Cells using RNA002 and RNA004 kits.  Nanopore direct cDNA long read sequencing of VCaP Cells

first: Yangyang

last: Li

first: Ting-You

last: Wang

first: Qingxiang

last: Guo

first: Yannan

last: Ren

first: Xiaotong

last: Lu

first: Qi

last: Cao


title: PD-1 Mediated Regulation of Unique Activated CD8+ T Cells by NK Cells in the Submandibular Gland

status: Public on Dec 11 2024

first: Liang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: The increasing use of anti-PD-1 immune checkpoint blockade has led to the emergence of immune-related adverse events (irAEs), including dysfunction of the submandibular gland (SMG). In this study, we investigated the immunoregulatory mechanism contributing to the susceptibility of the SMG to irAEs. Here, we found that the SMG of PD-1 deficient mice and anti-PD-L1 treated mice harbor an expanded population of CD8+ T cells. We demonstrate that NK cells expressing PD-L1 tightly regulate CD8+ T cells in the SMG. When this immunoregulation is disrupted, CD8+ T cells clonally expand and acquire a unique transcriptional profile consistent with TCR activation. These clonally expanded cells phenotypically overlapped with cytotoxic GzmK+ CD8+ T autoimmune cells identified in primary Sjögren’s syndrome patients. Understanding how NK cells modulate CD8+ T cell activity in the SMG opens new avenues for preventing irAEs in patients undergoing checkpoint blockade therapies.

overall_design:
T cells were extracted from the submandibular glands of WT and PD-1KO mice, and the spleen of WT mice for transcriptomic, proteomic, and TCR repertoire analysis
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Sam

last: Borys

first: Shanelle

last: Reilly

first: Ian

last: Magill

first: David

last: Zemmour

first: Laurent

last: Brossay


title: Mechanism of pyroptosis of pancreatic cancer induced by arachidonic acid

status: Public on Dec 08 2024

city: Chang Chun

first: Tongjia

last: Chu

state: Jilin

address: The First Bethune Hospital of Jilin University, No. 1 Xinmin Street, Chaoyang District, Changchun , Jilin Province

summary: Pancreatic cancer is one of the most deadly malignant tumors, and its treatment is scarce. This study found that arachidonic acid can induce pyroptosis of pancreatic cancer both in vitro and in vivo, and can cause immune cell infiltration.  Arachidonic acid can be used as a tumor killing drug and an immunotherapy activator, which provides a new idea for the treatment of pancreatic cancer.

overall_design: We found that tumor cells could pyroptosis only under the condition of  high concentrations of arachidonic acid treatment, but not at low concentrations. Therefore, RNA-seq was performed on three groups of samples, including Control, 40μM AA treatment group and 120μM AA treatment group, to find out the specific mechanism of arachidonic acid-induced pyroptosis in tumor cells.

first: Feng

last: Wei

first: Ziyu

last: Liu

first: Huan


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus [ATAC-Seq]

first: Joseph

last: Dougherty

first: Jiayang

last: Chen


first: yongyou

last: zhang

first: Yongyou

last: Zhang

first: Xindong

first: Xusheng

last: Deng


title: Early Age Efferocytosis Directs Macrophage Arachidonic Acid Metabolism for Tissue Regeneration

first: Connor

last: Lantz

address: 303 E. Chicago Ave. Ward 4-075

summary: In response to organ injury in adults, macrophages often promote scarring, yet during early life are required for tissue regeneration. To elucidate mechanisms underlying age-associated regeneration, we compared the macrophage injury response in newborns versus adult hearts. Single cell analysis revealed an accumulation of tissue-resident macrophages in neonates that were selectively polarized for apoptotic cell recognition and uptake (efferocytosis). Ablation of the apoptotic cell recognition receptor Mertk in newborns prevented cardiac regeneration. These findings could be attributed to reprogramming of macrophage gene expression that was required for biosynthesis of the eicosanoid Thromboxane A2, which unexpectedly activated parenchymal cell proliferation. Markers of Thromboxane A2 production were suppressed in adult macrophages after efferocytosis. Moreover, macrophage-neighboring neonatal cardiomyocytes expressed the Thromboxane A2 receptor, whose activation induced a metabolic shift supporting cellular proliferation. Our data reveal a fundamental age-defined macrophage response in which lipid mitogens produced during efferocytosis support receptor-mediated tissue regeneration.

overall_design:
Single cell mRNA sequencing. Single cell suspensions were isolated as described in the method section “Flow Cytometry” by Collagenase Type II and DNase digestion of hearts. After RBC lysis, samples underwent dead cell removal (StemCell Technologies) by Annexin V staining. Next, samples underwent a CD45-positive selection (StemCell Technologies) to enrich cardiac leukocytes. Enriched cells and flow-through cells were both counted and recombined at a ratio of 2 CD45+ cells for every 1 non-CD45+ cell. Combined single cell suspensions were diluted to target a recovery of 5,000 cells per sample. The single cell RNA-sequencing libraries were prepared using the 10X Genomics Single Cell 3’ Gene Expression (v3 or v3.1 chemistry) pipeline. The prepared libraries were run on an Agilent Bioanalyzer High Sensitivity Chip and Kapa Biosystems Library Quantification Kit for Illumina platforms for quality control before sequencing. All libraries were sequenced on the Illumina NovaSeq 6000 platform with the following parameters: Read 1—26 cycles; i7 Index—8 cycles; Read 2—98 cycles.

Processing and analysis of scRNA-seq data.
Raw Sequencing Data Processing (Alignment, Barcode Assignment, and UMI Counting). The raw FASTQ files were first aligned to the murine transcriptome (GRCm38; mm10) using CellRanger (10X Genomics, v4.0.0). Aligned reads were then filtered for valid barcodes and UMIs to generate gene-cell matrices used for downstream analysis.

first: Edward

middle: B

last: Thorp


title: ISWI chromatin remodeler SMARCA5 is essential for meiotic gene expression and male fertility in mammals

status: Public on Dec 05 2024

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

institute: Yale University

summary: Regulation of the transcriptome to promote meiosis is important for sperm development and fertility. However, how chromatin remodeling directs the transcriptome during meiosis in male germ cells is largely unknown. Here, we demonstrate that the ISWI family ATP-dependent chromatin remodeling factor SMARCA5 (SNF2H) plays a critical role in regulating meiotic prophase progression during spermatogenesis. Males with germ cell-specific depletion of SMARCA5 are infertile and unable to form sperm. Loss of Smarca5 results in failure of meiotic progression with abnormal spermatocytes beginning at the pachytene stage and an aberrant global increase in chromatin accessibility, especially at genes important for meiotic prophase.

overall_design: ATAC-seq from sorted cKIT+ spermatogonia, scRNA-seq from whole testes

first: Shubhangini

last: Kataruka

first: Shannon

last: Rainsford


title: Development of Fit Epidermal Resident Memory T Cells Requires Antigen Encounter in the Skin.

status: Public on Dec 10 2024

first: Liang

last: Yang

summary: CD8+ tissue resident memory T cells (TRM) develop from effectors that are recruited into peripheral tissues by infection or inflammation where they persist and provide defense against subsequent challenges.  Long-term persistence of epidermal TRM requires autocrine TGFβ that is transactivated by integrins expressed on keratinocytes.  In response to inflammation, the availability of TGFβ transactivation is limited.  Antigen-experienced TRM that encountered antigen in the epidermis during their development are more fit and outcompete bystander TRM for TGFβ transactivation resulting in their enrichment in the epidermis.  Transcriptomic analysis of endogenous epidermal TRM revealed that antigen-experienced TRM were enriched for TRM signature genes while bystander TRM retained the transcriptome of an earlier developmental state.  Following antigen recall, antigen-experienced TRM displayed accelerated proliferation kinetics compared with bystanders that was determined by the TCR signal-strength during their differentiation the skin.  Finally, antigen experienced TRM expressed TGFβRIII, which increases avidity of the TGFβRI/II receptor complex.  Selective ablation of Tgfbr3 from antigen experienced TRM reduced their capacity to persist when TGFβ activation was limited thus rendering them phenotypically like bystander TRM.  In sum, antigen-driven TCR signaling in the epidermis during TRM differentiation represents a required final step in ontogeny resulting in a lowered requirement on TGFβ transactivation for persistence and increased proliferation during recall responses that together result in the enhanced fitness of antigen-experience epidermal TRM.

overall_design:
Cohorts of wildtype C57BL/6 mice were infected on the left flank with VV by skin scarification.  DNFB was applied to the right flank 5 days post infection to recruit into the skin circulating CD8 effectors expanded by infection.  Mice were then rested for 50+ days to allow for the formation of TRM. Cells were pooled from 10 mice, enriched by percoll gradient centrifugation and purified by double FACSorting based on expression of CD90 and CD8.
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Eric

last: Weiss

first: Toshiro

last: Hirai

first: Haiyue

last: Li

first: Andrew

last: Lui

last: Baker

first: Ian

first: Jingyu

last: Fan

first: David

last: Masopust

first: Niroshana

last: Anandasabapathy

first: Harinder

last: Singh

first: Laura

last: MacKay

first: Daniel

last: Kaplan


title: CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model [Single Cell Dataset]

status: Public on Dec 03 2024

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary:
Astrocytes promote neuroinflammation and neurodegeneration in multiple sclerosis (MS) through cell-intrinsic activities and their ability to recruit and activate other cell types. Here, in a genome-wide CRISPR-based forward genetic screen investigating regulators of astrocyte proinflammatory responses, we identified the C-type lectin domain-containing 16A gene (CLEC16A), linked to MS susceptibility, as a suppressor of nuclear factor-κB (NF-κB) signaling. Gene and small-molecule perturbation studies in mouse primary and human embryonic stem cell-derived astrocytes in combination with mitochodrial, metabolic and multiomic analyses established that CLEC16A promotes mitophagy, limiting mitochondrial dysfunction and the accumulation of mitochondrial products that activate NF-κB, the NLRP3 inflammasome and gasdermin D. Astrocyte-specific Clec16a inactivation increased NF-κB, NLRP3 and gasdermin D activation in vivo, worsening experimental autoimmune encephalomyelitis, a mouse model of MS. Moreover, we detected disrupted mitophagic capacity and gasdermin D activation in astrocytes in samples from individuals with MS. These findings identify CLEC16A as a suppressor of astrocyte pathological responses and a candidate therapeutic target in MS.
Scheduled for publication in Nature Neuroscience
DOI: 10.1038/s41593-025-01875-9

overall_design: For single cell RNA-sequencing, CNS cells from n=3 Control EAE and n=3 CLEC16AGFAP EAE (Day 23) were hashed before FACS sorting using multiplex 3’ Cell Plex Set Kit A (#100261, 10x Genomics).  After sorting and washing,  astrocytes from 6 samples were pooled and loaded into one well of a 10X Chromium Next GEM Chip G (10X Genomics). Single-cell libraries were further generated using the Single Cell 3’ Reagent Kit v3.1 chemistry (10x Genomics) using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) according to the manufacturer’s protocol. The generated scRNA-seq libraries were sequenced by NOVA-Seq S1 at the Broad Institute.

first: Atsushi

last: Kadowaki

first: Michael

last: Wheeler

first: Brian

last: Andersen

first: Hong-Gyun

last: Lee

first: Tomer

last: Illuz

first: Francisco

last: Quintana


title: Single Cell Profiling of Cotton Ovules Epidermis During Early Fiber Development [scRNA-Seq]

status: Public on Dec 02 2024

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Each cotton seed has approximately 25,000 singular fiber cells, which account for 25-30% epidermal cells. Understanding the basis of fiber cell initiation is critical for cotton yield improvement. However, it is difficult to separate and study fiber and non-fiber cells. Here we developed a reliable single-cell protocol to study transcriptome changes in Upland and Pima cotton and in a naked seed mutant. We analyzed over 40,000 single cells derived predominately from the epidermal layer of ovules during early stages of fiber development.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Whole ovules of Gossypium were collected and briefly digested using macerozyme and cellulase enzyme mix to release protoplasts from the epidermal surrface, including developing fiber cells. Ovules from Gossypium hirsutum TM1 at 0, 1 and 2 days post-anthesis, the N1N1 fiberless mutant at 0 and 2 DPA and Gossypium barbadense at 2 DPA processed this way and used for 10x single-cell RNAseq.

first: Ryan

middle: C

last: Kirkbride

first: Zenjian


title: Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets.

status: Public on Dec 01 2024

city: Brisbane

first: Robin

middle: William

last: Palfreyman

state: QLD

address: Old Cooper Road

department: AIBN

country: Australia

institute: The University of Queensland

summary: One of the greatest prospects of multimodal single-cell analysis is the ability to integrate single-cell transcriptomic and proteomic datasets to compare transcription and translation profiles to investigate regulation between phenotypes. However, the integration of these complex datasets remains challenging. In this study, we demonstrate the use of  pseudo-temporal cell orders as a mutual axis for integrating of scRNA-Seq and scp-MS data. We collected temporal samples of HEK293F cells undergoing hypoxia to isolate the variance of hypoxia from the tightly coupled variance of cell cycle. Markers for hypoxia were then used to construct pseudo-temporal orders in each dataset which were used to reveal transcription and translation dynamics of attenuated respiration in single cells. This approach allowed us to integrate  single-cell transcriptomics and proteomics methods to understand the regulatory mechanisms governing biological phenotypes.

overall_design: HEK293F cells undergoing hypoxia

first: Craig

last: Barry

first: Timothy

last: Mercer

first: Lars

last: Nielsen

first: Esteban

last: Marcellin


title: Clonorchis sinensis (C. sinensis) infection remodels the chromatin accessibility of hepatocellular carcinoma

status: Public on Nov 26 2024

first: Min

last: Fang

state: None Selected

address: Guangxi Medical University Cancer Hospital 71, Hedi Road, Qingxiu District

summary: Background: Liver cancer is the third deadliest type of cancer, posing a serious threat to human health. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. C. sinensis, classified as a definite group I carcinogen by the IARC (International Agency for Research on Cancer), is an important risk factor for HCC. Although many studies have shown that C. sinensis infection affects the prognosis of HCC patients, the specific mechanisms are still unclear, especially the dynamics and regulatory roles of chromatin accessibility. Results: In this study, we integrated ATAC-seq, RNA-seq, and ChIP-seq data to elucidate changes in the epigenetics of HCC after the C. sinensis infection. Many different accessibility regions (DARs) were identified both in tumors and adjacent tissue after the C. sinensis infection. Meanwhile, top TFs whose motifs were enriched in DAR were found, such as HNF4a, FOXI1, etc. Although there were slight deviations, epigenetic changes were found to be consistent with gene expression levels. We also revealed that H3K9ac, H3K4me2, H3K4me3, H3K27ac, and H3K4me1 were associated with chromatin accessibility. Importantly, we also found potential evidence that C. sinensis infection would alter the spatial structure of the HCC genome. Finally, both molecular experimental results and clinical data certified that C. sinensis infection would promote the metastasis of HCC. Conclusions: C. sinensis infection will remodel the chromatin accessibility of HCC, leading to changes in gene expression levels. This study provides conclusive evidence that C. sinensis infection alters the epigenetics of HCC.

overall_design: Comparatine gene expression profling analysis of ATAC‑seq data and RNA-seg data for Cs+ and Cs－ HCC

first: Weilong

last: Yang

first: Caibiao

last: Wei

first: Junxian


title: TGF-β protects dormant metastasis from immune mechanosurveillance

status: Public on Dec 04 2024

city: New York

first: Zhenghan

last: Wang

state: NY

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

summary: Cancer cells disseminated to distant sites enter a period of dormancy before generating overt metastases. The ability of these cells to elude immune surveillance determines their persistence as latent disease. We report that TGF-β promotes dormancy in lung adenocarcinoma (LUAD) mouse models by placing disseminated SOX2+ and NKX2-1+ progenitors in a quiescent state that biomechanically averts killing by cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. In these primitive progenitors, TGF-β induces an atypical epithelial-to-mesenchymal transition (EMT) lacking actin stress fibers. TGF-β drives expression of the actin-depolymerizing factor gelsolin that changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the stiffness of metastatic progenitors and their killing by mechanosensitive CTLs and NK cells. Thus, LUAD primitive progenitors activate a biomechanical process to evade immune-mediated elimination during prolonged dormancy periods. Inhibiting this process clears tissues of dormant metastatic cells.

overall_design: Expression profiling by high throughput sequencing of H2087-LCC, a dormant metastatic derivative from stage I LUAD cell line H2087,  treated with SB505124 for 3 days, TGF-b for 3 days and TGF-b for  7 days.

first: Joan

last: Massagué


title: Stem-cell-derived limb developmental cell type characterization.

city: Chavannes-près-Renens

first: Can

last: Aztekin

address: Swiss Federal Institute of Technology Lausanne (EPFL)

country: Switzerland

institute: EPFL

summary: Mouse embryonic stem cells were used to generate cell types of limb development and characterized using single-cell mRNA-sequencing.

overall_design: Time course in vitro differentiation samples.


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring [snMultiome sequencing]

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

summary: Kupffer cells (KCs) are tissue-resident macrophages which colonize the liver early during embryogenesis. KCs start to acquire a tissue-specific transcriptional signature immediately after colonizing the liver, mature together with the tissue, and adapt to the tissue’s functions. Throughout development and adulthood, KCs have distinct core functions that are essential for liver and organismal homeostasis, such as supporting fetal erythropoiesis as well as postnatal erythrocyte recycling and liver metabolism. However, whether perturbations of macrophage core functions during development contribute to or cause disease at postnatal stages is poorly understood. Here, we utilize a mouse model of maternal obesity to perturb KC functions during gestation. We show that offspring exposed to maternal obesity develop fatty liver disease, driven by aberrant developmental programming of KCs that persists into adulthood. Programmed KCs mediate lipid uptake by hepatocytes through apolipoprotein secretion. KC depletion in neonates born to obese mothers, followed by replenishment with exogenous monocytes, rescues the fatty liver disease. The transcriptional programming of KCs and the fatty liver disease phenotype are also rescued by genetic depletion of hypoxia-inducible factor alpha (Hif1a) in macrophages during gestation. These results establish developmental perturbation of KC functions as a cause for the development of fatty liver disease in adult life and, thereby, place fetal-derived macrophages as intergenerational messengers within the concept of developmental origins of health and diseases.

overall_design: Three-week-old female mice were initially fed with a control diet (CD) for two weeks and were thereafter divided into two groups: one continued on the CD while the other received a high-fat diet (HFD) for eight weeks. The homeostatic model for insulin resistance (HOMA-IR) was used to assess metabolic changes. Mice with higher HOMA-IR on the HFD were selected to create a maternal obesity model and mice fed with CD were used to generated maternal lean offspring. All females were mated with CD males. Offspring born to maternal obese were cross-fostered to generate both lactating groups and offspring born to maternal lean mothers were crossed-fostered by other maternal lean mothers. Male offspring were weaned into CD or HFD postweaning cages. Livers of offspring were harvested at 11-12 weeks. Nuclei were isolated from approximately 50 mg of flash-frozen adult liver tissue to enable simultaneous single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq), capturing both transcriptional profiles and chromatin accessibility.

first: Hao

last: Hunag

first: Nelli

last: Blank-Stein

first: Lea

last: Seep


title: Single-cell sequencing reveals cellular heterogeneity of nucleus pulposus in intervertebral disc degeneration

status: Public on Nov 14 2024

city: Jining

first: Shu

last: Jia

state: Shandong

address: No. 133, Hehua Road, Taibai Lake New District, Jining City

department: Clinical Research Team for Spinal Cord Disorders

institute: Affiliated Hospital of Jining Medical University

summary: Nucleus pulposus (NP) plays a vital role in intervertebral disc degeneration (IVDD). Previous studies have revealed cellular heterogeneity in the NP tissue during IVDD progression. Here, we used single cell RNA sequencing (scRNA-seq) to analyze the cellular and molecular alterations of diverse cell clusters during IVDD.

overall_design: NP tissues were obtained from patients diagnosed with lumbar disc herniation at L4/L5 or L5/S1 levels, who were undergoing endoscopic lumbar discectomy. The removed NP tissues were digested into single cell suspension and analyzed using scRNA-seq.

first: Tao

first: Chunyang

last: Meng


title: Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease

status: Public on Nov 13 2024

city: La Jolla

first: David

last: Brenner

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys

summary: Background and aims: Metabolic dysfunction-associated steatotic liver disease (MASLD) progresses from steatosis (Metabolic dysfunction-associated steatotic liver, MASL) to Metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis. Activation of Hepatic Stellate Cells (HSCs) into fibrogenic myofibroblasts plays a critical role in the pathogenesis of MASH liver fibrosis. Here we compared gene expression and chromatin accessibility profiles of human HSCs in NORMAL, MASL, and MASH livers at single cell resolution. Methods: 18 human livers were profiled using single-nucleus (sn) RNA-seq and snATAC-seq. High priority targets were identified and then tested in 2D human HSCs, 3D human liver spheroids, and HSC-specific gene knockout mice. Results: This study identified novel gene regulatory mechanisms underlying MASL- and MASH-associated HSC heterogeneity and outlined potential strategies for anti-fibrotic therapy. Specifically, MASH-enriched HSC-subcluster hA1, represented by highly fibrogenic population of myofibroblasts, served as a critical source of extracellular matrix protein (ECM) in MASH, and its activation was regulated via a cross-talk between lineage-specific (JUNB/AP1), cluster-specific (RUNX1/2) and signal-specific (FOXA1/2) transcription factors (TFs). Additionally, we identified a set of core genes (GAS7, SPON1, SERPINE1, LTBP2, KLF9, EFEMP1) that drive ECM production in hA1 HSCs. The pathological relevance of the selected hA1 targets, such as SERPINE1 and others, was demonstrated using siRNA-based HSC-specific gene knockdown or pharmacological inhibitor of SERPINE1 in 3D human MASH liver spheroids, and HSC-specific Serpine1 knockout mice with MASH. Conclusion: We identified potential targets for anti-fibrotic therapy of MASH in patients.

overall_design: 18 single nucleus ATACseq samples, 18 single nucleus RNAseq samples from human MASH, MASL, NORMAL livers.

first: Sara

last: Rosenthal

first: Hyun

last: Kim

first: Xiao

last: Liu

first: Charlene

last: Miciano

first: Xiaomeng

last: Hou

first: Michael

last: Miller

first: Justin

last: Buchanan

first: Olivier

last: Poiron

first: Daisy

last: Chilin-Fuentes

first: Cuijuan

last: Han

first: Mojgan

last: Hosseini

first: Raquel

last: Carvalho Gontijo Weber

first: Sadatsugu

last: Sakane

first: Huayi

last: Zhao

first: Karin

last: Diggle

first: Sebastian

last: Preissl

first: Christopher

last: Glass

first: Bing

last: Ren

first: Allen

first: Tatiana

last: Kisseleva


title: Small-Molecule-Induced ERBB4 Activation to Treat Heart Failure

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

summary: To determine the transcriptomic changes of small-molecule-induced activation of ERBB4 in heart failure, we tested the effects of the two small molecules (NRG1 and EF-1) of ERBB4 agonists on the HCF (human cardiac fibroblasts)  model.  The transcriptional profiles of mRNA in these samples will be measured with high throughput technology. Changes in transcriptional profiles between the activation of EF-1 and NRG1 will be compared.

overall_design: 9 HCF samples were analyzed. 3 from control, 3 from NRG1, and 3 from EF-1.

first: Julie

middle: M

last: Cools

first: Eline

last: Feyen

first: Siel

last: Van Den Bogaert

first: Bo

last: Goovaerts

first: Yile

last: Fu

first: Celine

last: Civati

first: Jens

last: Van fraeyenhove

first: Michiel

last: Tubeeckx

first: Jasper

last: Van Haver

first: B

last: van Berlo

first: Eike

last: Wülfers

first: Antoine

last: de Vries

first: Nele

last: Vandersickel

first: Daniel

last: Pijnappels

first: Dominique

last: Audenaert

first: H

first: Hans

last: De Winter

first: Gilles

middle: W

last: De Keulenaer

first: Vincent

middle: F

last: Segers


title: Transcriptomics profiling of the effect of inducible knock-down of the melanocyte inducing transcription factor (MITF) in melanoma cell lines

status: Public on Nov 08 2024

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: MITF plays critical role in development and differentiation of melanocytes and in the context of melanoma, as a lineage survival oncogene. Given its crucial role in melanoma biology, it is very difficult to generate complete knock-out (KO) of MITF and in our hands, those that were generated appear to behave differently than the effect observed using siRNA mediated knock-down, possibly indicative of selection. In order to overcome the limitation of the transient effect of siRNA and study the effect of MITF depletion over a longer period of time, we carried out transcriptomic analyses of Doxycycline inducible shMITF knock down after 8 days in 2 melanoma cell lines MeWo (CVCL_0445) and SkMel 28 (CVCL_0526)

overall_design: The cell line was a kind gift from Jiri Vachtenheim DOI: 10.1111/jcmm.13506. MeWo and SkMel28 were seeded on 6 cm dish overnight, the next day, fresh media with 1ug/ml Doxycycline were added. Media with or without Doxycycline were changed every other day. After 8 days, the media was aspirate and the plates snap frozen at -80 °C before total RNA extraction using RNeasy Mini Kit (QIAGEN #74106) as per manufacturer protocol. RNA quality were assessed on Bioanalzyer 2100 (Agilent) using Agilent RNA 6000 Nano Kit (#5067-1511). Only samples with RIN values of over 9.5 were subjected to library prep and sequencing using using the Wellcome Trust genomic service, Oxford. QuantSeq Forward kit (LEXOGEN #0.15.96) was used for library prep, using 500 ng starting material to minimize the PCR amplification step. Samples were sequenced on HiSeq 4000 (Illumina) as paired-end, however, only read 1 contain meaningful data.

first: Colin

middle: R

last: Goding


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression [ChIP-seq]

city: 上海

first: 润华

last: 杜

address: 上海市浦东新区

institute: 上海药物所

summary: Histone lysine lactylation is a physiologically relevant epigenetic pathway that can be stimulated by the Warburg effect and L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-CoA, the cofactor for the modification, and how this process is regulated remain unknown. Here we report identification of GTPSCS as a robust lactyl-CoA synthetase using biochemistry and cell biology approaches. The mechanism of this catalytic activity was elucidated using the crystallographic structure of GTPSCS in complex with L-lactate, followed by mutagenesis experiments. GTPSCS translocates into the nucleus and interacts with p300 to form a functional lactyltransferase to elevate histone lactylation, but not histone succinylation. This process is dependent on not only a nuclear localization signal in the GTPSCS G1 subunit, but also acetylation at G2 subunit residue K73 which mediates the interaction with p300. GTPSCS-p300 collaboration synergistically regulates histone H3K18la, subsequently enhancing the expression of GDF15. This process promotes the proliferation of glioma cells and facilitates tumor formation in mice. In addition, GTPSCS is upregulated in glioma and correlates with glioma malignancy, while histone H3K18la, and GDF15 levels are positively associated with glioma malignancy and poor prognosis in GBM patients. The GTPSCS-lactyltransferase-histone Kla axis thus represents an epigenetic pathway linking lactate metabolism with an oncogenic gene expression pattern in glioma.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for L-Lactyl-Histone H3 (Lys18) in shSUCLG1 rSUCLG1 WT and K192R UTSW63 cells.

first: Ruilong

last: Liu

first: He

last: Huang

first: Yingming

last: Zhao


title: LeuO fine-tunes the virulence attributable to Salmonella pathogenicity island-2 via repressing ssrA transcription in Salmonella Typhimurium

city: Suwon

first: Eunsuk

last: Kim

address: 206 World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University

summary: LeuO, initially identified as a leucine regulator in Escherichia coli, has since been identified as a global regulator required for bacterial pathogenicity in a broad range of bacteria, including gram-negative pathogens, such as Salmonella, Shigella, and Vibrio; and gram-positive bacteria, such as Streptococcus pneumoniae. However, the regulatory roles and targets of LeuO vary among species. In the Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), LeuO represses the transcription of Salmonella pathogenicity island (SPI)-1, thus diminishing the ability of the bacteria to invade host cells. However, its regulatory effect on SPI-2, essential for survival within macrophages, remains poorly understood. This study aimed to determine the regulatory role of LeuO in the intracellular persistence of S. Typhimurium. Overexpression of LeuO repressed the transcription of SPI-2 genes and accordingly decreased its protein levels. Chromatin immunoprecipitation sequencing revealed the genome-wide binding sites of LeuO in S. Typhimurium 14028 and identified a distinctive 23-nucleotide motif with high similarity to that previously discovered in E. coli. Notably, multiple LeuO-binding sites were predicted within SPI-2, primarily adjacent to the ssrA and ssrB loci. In vitro binding assays verified the high binding affinity between LeuO and three specific motifs located at positions -35 to -12 (ssrA1),+231 to +254 (ssrA2) near ssrA, and at positions -622 to -599 (ssrB3) near ssrB, relative to their transcription start sites. Furthermore, LeuO overexpression abolished the transcription of lacZ fused to the ssrA promoter containing ssrA1 and ssrA2, suggesting the direct repression of ssrA via LeuO-binding. The absence of LeuO increased the intracellular survival of S. Typhimurium within macrophages, whereas its overexpression attenuated bacterial persistence, which was presumably associated with the downregulation of SPI-2 by LeuO. This study reveals the versatile regulatory mechanisms of LeuO and underscores its pivotal role in modulating SPI-2 expression, thereby providing key insights into the fine tuning of virulence by Salmonella during systemic infection.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Chromatin immuniprecipitation DNA-sequencing (ChIP-seq) of LeuO in Salmonella Typhimurium 14028

first: Eumnsuk

first: Hyunjin

last: Yoon


title: Comparative characterization of human accelerated regions in neurons [HyPR-seq]

status: Public on Nov 12 2024

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

summary: Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here, we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem cell (iPSC)-induced excitatory neurons. Using genomic and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologs for functional characterization via single-cell CRISPRi, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPSC pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we use prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Characterization of the function of HARs in 2-week-old excitatory neurons derived from human and chimpanzee iPSCs.

first: Xiekui

last: Cui

first: Charles

last: Cai

first: Ian

last: Jones


title: Comparative characterization of human accelerated regions in neurons [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2-week excitatory neurons derived from human and chimpanzee iPSCs.

first: Han

last: Yang


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression [RNA-Seq]

overall_design: We carried out RNA-Seq analyses in either patient-derived SUCLG1-depleted rSUCLG1 WT UTSW63 cells or its rSUCLG1 K192R mutant counterpart.


title: SND1 is a novel regulator of endothelial function

status: Public on Oct 30 2024

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

summary: Staphylococcal nuclease and tudor domain containing protein 1 (SND1), which is also known as p100 or Tudor-SN, is a recently identified protein that is highly expressed in multiple cancers including breast cancer, liver cancer, and colon cancer. Endothelial function and vascular integrity are critical modulators in cancer metastasis and progression. Although much progress has been made in studying SND1’s oncogenic role, the involvement of SND1 in endothelial function has never been explored.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three lines of hiPSC-EC  transfected with either scramble shRNA or SND1 shRNA for 48 hours.

first: Zhenbo

last: Han

first: Sang-Ging

last: Ong


title: Analysis of expression profiles in miR-195 transduced Ebf1–/– Lin– cells

status: Public on Oct 28 2024

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary:
To further investigate whether miR-195 transduction lead  Ebf1–/– Lin– cells to develop into later stages than pro B, we have employed microarray expression profiling.
For the purpose, we compared B cell and other lineages (T cell, NK cell and myeloid) related gene expressions among these samples.

overall_design: miR-195 transduced or not Ebf1–/– Lin– cells were cultured with SCF, IL-7 and Flt-ligand containg medium.

first: Yuji

last: Miyatake

first: Ai

last: Kotani


title: Influence of Myrrh extract on gene expression in humen endometriotic cells.

status: Public on Oct 24 2024

city: Yangsan

first: Ki-Tae

last: Ha

address: Busandaehak-ro 49

institute: Pusan National University

summary: To investigate the anti-endometriotic a pathways of Myrrh extract.

overall_design: Total RNAs of 12Z cells were used to identify differential gene expression following Myrrh stimulation

first: Dongryeol

last: Ryu

first: Yunju

last: Jo

first: Bo-sung


first: Hywel

last: Roderick

summary: To determine the transcriptomic changes of small-molecule-induced activation of ERBB4 in heart failure, we tested the effects of the two small molecules (NRG1 and EF-1) of ERBB4 agonists on iAM (immortalized atrial cardiomyocytes)  model.  The transcriptional profiles of mRNA in these samples will be measured with high throughput technology. Changes in transcriptional profiles between the activation of EF-1 and NRG1 will be compared.

overall_design: 12 iAM samples were analyzed. 4 from control, 4 from NRG1, and 4 from EF-1.

first: Julie

last: Cools

first: Eline

last: Feyen

first: Siel

last: Van Den Bogaert

first: Bo

last: Goovaerts

first: Yile

last: Fu

first: Celine

last: Civati

first: Jens

last: Van fraeyenhove

first: Michiel

last: Tubeeckx

first: Jasper

last: Van Haver

first: B

last: van Berlo

first: Eike

last: Wülfers

first: Antoine

middle: A

last: de Vries

first: Nele

last: Vandersickel

first: Daniel

last: Pijnappels

first: Dominique

last: Audenaert

first: H

first: Hans

last: De Winter

first: Gilles

last: De Keulenaer

first: Vincent

last: Segers


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression

first: 润华

last: 杜

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

overall_design: Refer to individual Series


title: Comparative characterization of human accelerated regions in neurons [PIPseq]

first: Yin

last: Shen

overall_design: Single cell RNA-seq data for 2-week excitatory neurons derived from human and chimpanzee iPSCs.

first: Xiekui

last: Cui

first: Han

last: Yang


title: Single-Cell Transcriptomics Reveals the Molecular Basis of Human iPS Cell Differentiation into Ectodermal Ocular Lineages

status: Public on Oct 21 2024

city: Cardiff

first: Laura

last: Howard

address: Maindy Road

institute: Cardiff University

summary: The generation of a self-formed, ectodermal, autonomous multi-zone (SEAM) from human induced pluripotent stem cells (hiPSCs) offers a unique perspective to study the dynamics of ocular cell differentiation over time. Here, by utilising single-cell transcriptomics, we have (i) identified, (ii) molecularly characterised and (iii) ascertained the developmental trajectories of ectodermally-derived ocular cell populations which emerge within SEAMs as they form. Our analysis reveals interdependency between tissues of the early eye and delineates the sequential formation and maturation of distinct cell types over a 12-week period. We demonstrate a progression from pluripotency through to tissue specification and differentiation which encompasses both surface ectodermal and neuroectodermal ocular lineages and the generation of iPSC-derived components of the developing cornea, conjunctiva, lens, and retina.  Our findings not only advance the understanding of ocular development in a stem cell-based system of human origin, but also establish a robust methodological paradigm for exploring cellular and molecular dynamics during SEAM formation at single-cell resolution and highlight the potential of hiPSC-derived systems as powerful platforms for modelling human eye development and disease.

overall_design: Human iPSC cells (clone 201B7, RIKEN BioResource Center, Tsukuba, Japan) were maintained on LN511E8 (Nippi, Tokyo, Japan) coated culture dishes in serum-free StemFit medium (Ajinomoto, Tokyo, Japan) for at least 2 cell passages for stabilisation. Differentiation was initiated by culture in differentiation medium (DM) following established protocols. After culture for 4 weeks, DM was substituted for corneal DM (CDM) containing growth factors (KGF, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) and the ROCK inhibitor Y-27623 (FUJIFILM Wako Pure Chemical Corporation) to promote epithelial cell growth and survival.  After an additional 4 weeks of CDM culture (8 weeks in total), the medium was changed to corneal epithelial maintenance medium (CEM) consisting of DMEM/F12 (1:1; Life Technologies, Carlsbad, CA, USA) containing KGF, Y-27623 and B-27 supplement (Life Technologies). Cells were harvested at successive timepoints spanning 0 – 12 weeks and single cell suspensions were prepared according to current 10x Genomics guidelines.

first: Yuki

last: Ishikawa

first: Tomohiko

last: Katayama

first: Sung-Joon

last: Park

first: Matthew

middle: J

last: Hill

first: Derek

last: Blake

first: Kohji

last: Nishida

first: Ryuhei

last: Hayashi

first: Andrew

last: Quantock


title: BCR and TLR-induced IRF1 promotes T cell independent B cell responses by supporting Notch2 dependent Marginal Zone B cell development

status: Public on Nov 01 2024

first: Jessica

middle: N

last: Peel

address: 1230 York Ave

institute: The Rockefeller University

summary: The prototypic interferon (IFN)-inducible transcription factor, IRF1, not only controls expression of IFN genes but also regulates T cell and macrophage fate specification and function. We show that IRF1 expression in B cells is required for marginal zone B (MZB) cell development and T cell independent antibody responses [80% B6.129S2-Ighmtm1Cgn/J (MT) + B6.129S2-Irf1tm1Mak/J (Irf1-/-), B-Irf1-/- chimeras]. While IFNs can induce IRF1 expression in MZB precursors, IFN signaling is not required for MZB cell development [C57BL/6J (B6), B6.129S7-Ifngr1tm1Agt/J (Ifngr1-/-), B6(Cg)-Ifnar1tm1Agt/J (Ifnar1-/-)].  Instead, BCR and TLR signals, which influence MZB commitment, promote IRF1 expression and nuclear translocation in MZB cell precursors. In turn, IRF1 is required for Notch-dependent gene expression in transitional B cells and development of the MZB cell compartment.  Thus, T independent MZB-driven antibody responses are regulated by BCR and TLR signals that initiate IRF1-dependent Notch programming of transitional B cells and subsequent commitment of these cells to the MZB lineage.

overall_design: RNAseq was performed for the following (in triplicate for each sample type): 1. C57BL/6 mice 2. IRF1 KO uninfected mice; Transitional 1, Transitional 2, Follicular B, Marginal Zone B cells were isolated by FACS

first: Frances

last: Lund

first: Chris

last: Scharer

first: Alexander

last: Rosenberg


title: Comparative characterization of human accelerated regions in neurons [PLAC-Seq]

summary: Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees1,2. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation3. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here, we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem cell (iPSC)-induced excitatory neurons. Using genomic4 and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologs for functional characterization via single-cell CRISPRi, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPSC pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we use prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.

overall_design: Comparative genome interactions for 2-week excitatory neurons derived from human and chimpanzee iPSCs.


title: Comparative characterization of human accelerated regions in neurons [ATAC-seq]

overall_design: Comparative chromatin accessibility for 2-week excitatory neurons derived from human and chimpanzee iPSCs.


title: Expression profiles of human cumulus cells from patients with PCOS and non-PCOS

city: Zhongshan

first: Yuezhou

last: Chen

address: East 2 Sunwen Road

department: Center for Reproductive Medicine

institute: Zhongshan City People's Hospital

summary: To reveal mRNAs expression differences in cumulus cells between polycystic ovary syndrome (PCOS) and non-PCOS women. mRNAs expression profile of the cumulus cell samples with PCOS and non-PCOS were determined by  Illumina Novaseq 6000.

overall_design: 40 pooled RNAs from CC samples (23 PCOS and 17 non-PCOS pooled RNAs) were separately analyzed on Illumina Novaseq 6000

first: Minyu

last: Xie

first: Siyun

last: Wu

first: Zehua

last: Deng

first: Yan

last: Tang

first: Yiqing

last: Guan

first: Yun

last: Ye

first: Qiandong

last: He

first: Lei

last: Li


title: ATAC-seq data of miR-195 transduced Ebf1-KO FL-ProB-cells.

first: Ryo

last: Yanagiya

summary: EBF1 is crucial transcription factor in B cell lineage and Ebf1 -/- hematopoietic stem cells are arrest in early B cell development and disable to express CD19. miR-195 transduction is able to overcome Ebf1 deficiency and cause CD19 positive cells. ATAC-seq data of these cells provided a new insight into relationship between early B cell differentiation and micro-RNA regulation.

overall_design: ATAC-seq was performed on more than 5000 transplanted cells of from bonemarrow of NOG mouse in which miR-195 transduced or not EBF1 -/- FL cells were injected. Data was aligned to mouse reference genome mm10 and peak summits were determined using MACS3.

first: Y

last: Miyatake

first: R

last: Maruyama

first: A

last: Kotani


title: Genetic Insights into the Rheological Strength of Candida albicans Biofilms

city: ANN ARBOR

first: Anuj

last: Kumar

state: MI

address: 1105 N. University Avenue, BSB Room 3210

department: MCDB

institute: University of Michigan

summary: The principal opportunistic human fungal pathogen Candida albicans forms biofilms resistant to antifungal therapeutics. Biofilms are a class of soft matter with viscoelastic properties and response to flow, but little is known regarding the genes contributing to these rheological phenotypes in fungal biofilms. Here, we identify C. albicans genes with deletion phenotypes of altered biofilm viscoelasticity. We analyzed mutants deleted for genes contributing to cell wall structure or extracellular matrix (ECM) production, and we identified increased elastic moduli, indicative of higher viscoelasticity, in strains singly deleted for PMR1, KRE5, and ALG11. PMR1 encodes a secretory pathway calcium pump. KRE5 encodes a UDP-glucose:glycoprotein glucosyltransferase, and ALG11 encodes alpha-1,2-mannosyltransferase. These mutants form less biofilm ECM by weight relative to wild type when cultured on agar. For these strains, biofilm morphology is smooth, with reduced hyphal formation. The mutants exhibit decreased resistance to the antifungal agent fluconazole relative to wild type biofilm cultures. To identify intracellular changes underlying these altered rheological properties, we globally profiled transcript levels in the respective mutants. Genes encoding membrane proteins were enriched in the set of transcripts differentially abundant in the alg11 deletion mutant. RNA levels are altered for genes associated with translation in the pmr1 deletion mutant and protein catabolism in the kre5 deletion strain. Genes involved in lipid metabolism and filamentous development are differentially expressed in cells from alg11, kre5, and pmr1 deletion mutant biofilms. Collectively, the data indicate C. albicans biofilm rheology as a phenotype affected by ECM production and cell morphology, while identifying genes for the investigation of mechanisms underlying properties of fungal biofilm viscoelasticity.

overall_design: Wild-type and deletion mutant biofilms were grown from overnight cultures on polycarbonate membranes (nucleopore 0.8 micrometer pore size) placed on solid nutrient-limited Spider medium supplemented with uridine for seven days at 37 degrees C. Cell pellets were collected by centrifugation, and RNA was extracted from each sample using the RiboPure RNA purification kit according to suggested protocols and published methods. Approximately 10 to the seventh cells were lysed by agitation with cold Zirconia beads in a buffer containing SDS (1% final volume) and phenol:chloroform:isoamyl alcohol. The RNA was purified by ethanol washes and filtration using cartridges in the RiboPure kit. Prior to sequencing, approximately 3 micrograms of each RNA sample was treated with DNase I. The reaction was terminated with EDTA and incubation at 65 degrees C. The samples were subsequently precipitated with ethanol and washed with 70% cold ethanol. For sequencing, messenger RNA was purified from total RNA using poly-T oligonucleotide-attached magnetic beads. cDNA was generated using random hexamer primers for first-strand synthesis, and dUTP-priming for second-strand synthesis. The resulting cDNA library was quantified using fluorometry and real-time PCR. The size distribution of the synthesized cDNA was assessed using a bioanalyzer.

first: Joshua

last: Bauman


title: Consequences of the perivascular niche remodeling for tumoricidal T-cell trafficking into metastasis of ovarian cancer [Spatial Transciptomics]

status: Public on Oct 15 2024

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: We investigated the mechanisms by which inflammatory responses generated by tumor-specific T cells delivered to ovarian tumor-bearing mice alone or after oncolytic vaccinia virus-driven immunogenic cancer cell death affect antitumor efficacy using spatial transcriptomics.

overall_design: Changes in the perivascular tumor microenvironment within the ovarian cancer metastasis in MOVCAR 5009 tumor-bearing SCID mice were analyzed by Spatial Transcriptomic analysis using 10x Genomic Visium platform 10 days after the treatment.

first: Marta

last: Winkle

first: Danuta

last: Kozb


title: Consequences of the perivascular niche remodeling for tumoricidal T-cell trafficking into metastasis of ovarian cancer [scRNA-seq]

summary: We investigated the mechanisms by which inflammatory responses generated by tumor-specific T cells delivered to ovarian tumor-bearing mice alone or after oncolytic vaccinia virus-driven immunogenic cancer cell death affect antitumor efficacy using  scRNA-seq.

overall_design: Tumor draining lymph nodes  in MOVCAR 5009 tumor-bearing SCID mice were analyzed using 10 Genomics single cell RNASeq platfomr 10 days after the treatment.


title: Protocadherin 8 and transcription factor Dbx1 regulate the formation of developing cerebral cortex

status: Public on Oct 13 2024

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

institute: Inserm

summary: Normal development of the mammalian central nervous system requires correct tissue patterning, production of the appropriate cell types and establishment of functional neuronal circuits. Transcription factors (TFs) play essential roles in these processes, regulating the expression of target genes responsible for neuronal subtypes specific features. Cell adhesion molecules are key components of neuronal identities that control cell sorting, migration, neurite outgrowth/guidance and synaptogenesis. So far, the link between cell adhesion and cell fate is not known TFs are known to control neuronal adhesion but not the opposite.   Here, using acute gain- and loss-of-function experiments by in utero electroporation in the developing mouse telencephalon we demonstrate that ectopic expression of Dbx1, a homeodomain TF acting as a cell fate determinant, leads to increased expression of Protocadherin 8 (Pcdh8) and cell aggregation, together with the induction of neuronal fate markers Nr4a2 (Nurr1)   and Pax6. These effects were are modulated depending on the region and timing of electroporation. Furthermore, we found that Pcdh8 expression is required for Dbx1-induced fate specification. Surprisingly, Pcdh8 overexpression also proved sufficient to induce Dbx1 expression as well as a complete reorganisation of the apico-basal polarity and dorso-ventral patterning. Finally, we present evidence that these effects are mediated through regulation of the expression of Notch ligands and promotion of cell cycle exit. Altogether, our work therefore points to cell adhesion molecules as unexpectedimportant, yet unexpected important, players in the regulation of cell identity and, in particular, Pcdh8 through its bidirectional action crossregulation  with the Dbx1 transcription factor.

overall_design:
Explants encompassing the septum were dissected from eight PGKCre ; Rosa26YFP E11.5 mouse embryos originating from two distinct litters and four Dbx1Cre ; Rosa26tdTomato E12.5 embryos from two litters. Cells were dissociated, pooled and a Single Cell 3′ Kit v2 library was produced.
The telencephalic vesicle was dissected from three wild-type E12 mouse embryos originating from two distinct litters. Cells were dissociated, pooled and a Single Cell 3' Kit v3.1 library was produced.

first: Matthieu

middle: X

last: Moreau

first: Frédéric