title: YAP targets TEAD4-NF-κB complex and inhibits ccRCC tumor growth II

status: Public on Apr 17 2025

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

summary: The prevalent understanding of Hippo signaling is one inhibitory pathway in tumor growth via deactivating the potential of YAP-TEAD transcriptional complex. The aberrant activation of YAP was observed in a series of human malignancies. However, recent studies implicate that in certain cancer types, YAP could be a tumor suppressor. Here, we reported a context-dependent function of YAP in clear cell renal carcinoma (ccRCC). Inhibition of Hippo kinase activity impeded ccRCC tumor growth and NF-κB transcriptional programs. Pharmacological blocking Hippo kinase activity or ectopic activation of YAP suppressed tumor growth in xenograft and PDX models. Mechanism studies revealed that TEAD could synchronize with P65 for NF-κB signaling activation, while YAP disrupted TEAD-NF-κB interactions and dissociated P65 from its target gene promoter, thereby inhibiting NF-κB transcriptional programs and ccRCC tumor growth. Our study identified a novel crosstalk between Hippo and NF-κB pathway, uncovered a non-canonical regulation of Hippo/YAP axis in renal cancer and suggested a novel strategy to ccRCC treatments by YAP activation.

overall_design: clear cell renal carcinoma mRNA samples were summarized in six samples, divided into two groups, Control and siTEAD4

first: Miao

last: YU

first: Jian

last: Zhu


title: Expression of Keratin-1 Predicts Recurrence and Treatment Response in Advanced Laryngeal Cancer: A Potential Therapeutic Target

status: Public on Apr 01 2025

city: Hwasun-gun

first: S. M. ABDUS

last: SALAM

state: Jeollanam-do

address: 322 Seoyang-ro

department: Pathology

country: South Korea

institute: Chonnam National University Hwasun Hospital

type: Expression profiling by high throughput sequencing

summary: RNA sequencing of 32 FFPE tissue samples, including 11 recurrent and 21 non-recurrent tumor specimens demonstrated higher KRT1 gene expression in the recurrence group than in non-recurrent cases. Patients with KRT1-positive immunostaining exhibited trends of worse overall survival (OS) and recurrence-free survival (RFS). In vitro studies showed that KRT1 knockdown suppressed tumor cell invasion, cell migration, and expression of epithelial-mesenchymal transition (EMT)-related genes in human head and neck squamous cell carcinoma (HNSCC) cell lines. Additionally, KRT1 knockdown enhanced tumor cell apoptosis and exhibited synergistic effects with conventional radiation and chemotherapy treatments. KRT1 may serve as a biomarker for predicting advanced laryngeal cancer recurrence and assist with selecting patients to receive concurrent chemoradiotherapy (CCRT).

overall_design: The RNA sequencing cohort comprised 32 FFPE tissue samples, including 11 recurrent and 21 non-recurrent tumor specimens.

first: Kyung-Hwa

last: Lee

first: Tae Mi

last: Yoon

last: Salam


title: Inverted chimeric RNAi molecules synergistically co-target MYC and KRAS

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

summary: Mutant KRAS has been implicated in driving a quarter of all cancer types. Although inhibition of the KRASG12C mutant protein has shown promise in the clinic, there is still a need for therapies that overcome clinical resistance and target non-KRASG12C mutations. Mutant KRAS activates downstream MYC, which is also a challenging-to-drug oncogene. We have developed a novel “inverted” RNAi molecule in which the passenger strand of the MYC-targeting siRNA is fused to the guide strand of the KRAS-targeting siRNA. The chimeric molecule simultaneously inhibits KRAS and MYC, showing marked improvements in efficacy beyond the individual siRNA components. This effect is mediated by 5’-dT overhangs following endosomal metabolism. The synergistic RNAi activity led to a >10-40-fold improvement in inhibiting cancer cell viability in vitro. When conjugated to an epidermal growth factor receptor (EGFR)-targeting ligand, the chimeric siRNA was co-delivered to and internalized by tumor cells. Notably, as compared with individual KRAS or MYC siRNAs, the chimeric design resulted in significantly improved metabolic stability in tumors, enhanced silencing of both oncogenes, and reduced tumor progression in lung cancer models. This inverted chimeric design establishes proof-of-concept for ligand-directed, dual-silencing of KRAS and MYC in cancer and constitutes a new molecular strategy for co-targeting any two genes of interest, which has broad implications.

overall_design: To understand the transcriptional effects of our siRNAs, we transfected A427 cells with MYC-targeting siRNA, KRAS-targeting siRNA, or MYC/KRAS co-targeting siRNA at 20nM for 24 hours.

first: Chad

middle: V

last: Pecot


title: Spatial Patterning and Transcriptomic Landscapes of Human Neural Organoids Derived by Local Delivery of Morphogens

status: Public on Mar 20 2025

city: BALTIMORE

first: Feiyu

last: Yang

state: Maryland

address: Ross Research Building

institute: Johns Hopkins University

summary: Positional patterning during human brain development is orchestrated through highly coordinated interplays of locally produced inductive signals. While animal models have elucidated general signaling pathways during early neurodevelopment, individual morphogens' effects underlying the proper human brain regionalization remain unclear. Current technologies are limited in generating stable, well-confined gradients in neural organoids for robust regionalization. Here, we report a Matrigel-free passive diffusion-based morphogen gradient generator (PdMG) that reliably established a steep exogenous spatial morphogen gradient in human neural organoids. We further established dorsal-ventral forebrain, rostral-caudal fore-midbrain-like, and rostral-caudal fore-hindbrain-like patterning by applying Sonic hedgehog/ WNT-inhibitor, WNT, and retinoic acid gradients, respectively. Spatial transcriptomics analysis revealed robust regionalization in early-stage patterned organoids, as well as active neurogenesis and GABAergic interneuron migrations in late-stage patterned organoids. Together, this study provides a framework for modeling the spatial-temporal morphogen dynamics that regulate key cell fate specifications and axis formations using patterned neural organoid models.

overall_design: Spatial transcriptomic analysis using 10X Visium assay

first: Narciso

last: Pavon

first: Tatsuya

last: Matsubara

first: Rebecca

last: Sebastian

first: Beatriz

middle: M

last: Martin

first: ChangHui

last: Pak

first: Yubing

last: Sun

first: Deok-Ho

last: Kim


title: DDX54 downregulation enhances anti-PD1 therapy in immune-desert lung tumors with high tumor mutational burden

status: Public on Mar 19 2025

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

institute: KAIST

summary: High tumor mutational burden (TMB) is a predictive biomarker for the responsiveness of cancer to immune checkpoint inhibitor therapy that indicates whether immune cells can sufficiently recognize cancer cells as non-self. However, about 30% of all cancers from The Cancer Genome Atlas are classified as immune-desert tumors lacking T cell infiltration despite high TMB. Since the underlying mechanism of these immune-desert tumors has yet to be unraveled, there is a pressing need to transform such immune-desert tumors into immune-inflamed tumors and thereby enhance their responsiveness to anti-PD1 therapy. Here, we present a systems framework for identifying immuno-oncotargets, based on analysis of gene regulatory networks, and validating the effect of these targets in transforming immune-desert into immune-inflamed tumors. In particular, we identify DEAD-box helicases 54 (DDX54) as a master regulator of immune escape in immune-desert lung cancer with high TMB, and show that knockdown of DDX54 can increase immune cell infiltration and lead to improved sensitivity to anti-PD1 therapy.

overall_design: After euthanizing the LLC1 xenograft mouse model, single cells were obtained from the mouse cancer tissues. From this population, CD45-positive immune cells were separated using Aria Fusion (Becton Dickinson) flow cytometry. A library for single-cell RNA sequencing was constructed using the 10x Genomics 5' single cell RNA-seq kit. This library was then sequenced using next-generation sequencing (NGS) on the Illumina HiSeq 2500 platform. Raw reads were mapped to the Mus musculus mm10 reference genome utilizing the CellRanger pipeline (20) v6.1.0 from 10X genomics.

first: Jungeun

first: Kwang-Hyun

last: Cho


title: IL22 supports Long-Term Expansion of Mouse and Human Hepatocytes in vitro.

status: Public on Mar 06 2025

city: Shanghai

first: shitong

last: wang

address: 上海市浦东张江祖冲之路555号

country: China

institute: 中国科学院上海药物研究所

summary: Hepatocytes have wide applications in drug development, disease modeling, and cell therapy. However, to expand hepatocytes in large quantities in vitro without losing their functions remains a challenging task. Here we report that IL22, a cytokine highly upregulated after partial hepatectomy or hepatocyte transplantation, could support long-term expansion (>30 passages, with theoretical expansion of ~1030 times within ~150 days) of mice hepatocytes in vitro by dedifferentiate hepatocytes into hepatocyte progenitor cells (HPCs), which maintain the capacity of differentiation into mature hepatocytes. With transcriptomic analysis and lineage-specific deletion, we uncover the critical involvement of STAT3 pathway in IL22-mediated hepatocyte to HPC conversion. Two key transcription factors (TFs) down-stream of STAT3 pathway, Bhlha15 and Arntl2, govern IL22-induced hepatic dedifferentiation. Expression of these two TFs directly initiates the dedifferentiation of hepatocytes into HPCs, which could be expanded in long-term without the supplement of IL22. IL22 also supports human hepatocyte growth in simple culture condition. Within 30 days, human hepatocytes could be expanded by more than 10,000-fold by dedifferentiation into HPCs, which maintain the full capacity of maturation. Collectively, this study provides a simple culture system enables large-scale expansion of both mice and human hepatocytes in vitro, and elucidates the critical pathways and TFs involved in these processes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We use RNA sequencing to analyze the following four aspects:(1) To characterize the differences and similarities between IL22-induced hepatic progenitor cells (IL22-iHPCs) and IL22-induced mature hepatocytes (IL22-iMHs), we compared the gene expression profiles of td-Hepa (D0), IL22-td-iHPCs (D14), IL22-td-iHPCs (P30), and IL22-td-iMHs (P30).(2) To elucidate the role of STAT3 signaling, a key pathway activated by IL22, in the early stages of IL22-mediated hepatocyte proliferation, we conducted RNA sequencing on HepaSTAT3f/f and HepaSTAT3-/- cells cultured in IL22-conditioned hepatocyte culture medium (IL22-HCM) for a period of 0-7 days.(3) To understand the crucial roles of transcription factors (TFs) in hepatocyte dedifferentiation downstream of the IL22-STAT3 pathway, we analyzed the gene expression profiles of primary hepatocytes (D0), IL22-td-iHPCs (D14), and hepatocytes infected with GFP or Bhlha15+Arntl2 and cultured in hepatocyte culture medium (HCM) for 14 days. (4) To characterize the differences and similarities between IL22-induced human hepatic progenitor cells (IL22-hiHPCs) and IL22-induced human mature hepatocytes (IL22-hiMHs), we compared the gene expression profiles of hHepa (D0), IL22-hiHPCs(P5) and IL22-hiMHs (P5).

first: Bing

last: Li

first: Ren

last: Guo

first: Shitong

last: Wang

first: Xin

last: Xie


title: Exploring the Vestibulocerebellum- Vestibular Nuclei - Spinal Trigeminal Nucleus Causals communication and TRPV2 ion channel in vestibular migraine pathogenesis

status: Public on Mar 12 2025

city: Harbin

first: Qingling

last: Zhai

state: Heilongjiang

address: No. 23, Youzheng Street, Nangang District

department: Neurology

institute: Harbin medical university

summary: Background Vestibular migraine (VM) is a disorder characterized by recurrent episodes of dizziness or vertigo and is often accompanied by headache. The mechanisms underlying vestibular dysfunction and pain in VM remain unclear. Methods Chronic migraine (CM) and VM models were induced by NTG and kainic acid, respectively. Behavioral assessments were conducted to evaluate vestibular dysfunction and pain in the VM and CM models. Transmission electron microscopy (TEM) was used to examine peripheral receptor impairment. Immunofluorescence, including staining for Cellular Proto-oncogene (c-Fos), Neuronal Nuclei (NeuN), and calcitonin gene-related peptide (CGRP), identified activated brain regions such as the cortex, midbrain, and cerebellum. Multiplex immunohistochemistry and cholera toxin subunit B (CTB) tracing were performed to analyze nuclear heterogeneity and neural communication. Additionally, RNA sequencing (RNA-Seq) and Ionized calcium-binding adapter molecule 1 (IBA1) immunostaining were used to investigate ion channel expression in the spinal trigeminal nucleus caudalis (Sp5c). Results CM and VM-related behaviors, such as allodynia and balance disturbance, were successfully reproduced in mouse model. TEM revealed significant damage to peripheral sensory receptors, particularly in the trigeminal ganglion and cochlear cells. Distinct activation patterns of c-Fos and CGRP were observed in VMs and CMs. CTB tracing confirmed that signals are transmitted from the vestibulocerebellum (VbC) to the Sp5c via the vestibular nuclei (VN). Furthermore, RNA-Seq combined with coimmunostaining revealed an increased expression of transient receptor potential vanilloid 2 (TRPV2) ion channels in microglia within Sp5c, indicating their potential role in VM pathology. Conclusions This study preliminarily explored VbC-VN-Sp5c communication and identified TRPV2 ion channels in microglia as key players in neuron-glia crosstalk in VM. These findings provide new insights into the mechanisms underlying vestibular migraine and suggest potential therapeutic targets.

overall_design: Total RNA from the Sp5C nucleus was extracted to identify the most differentially expressed ion channels by comparing the data with the ion channel database.

first: Qihui

last: Chen

first: Ning

last: Zhang

first: Hongyan

first: Yonghui

last: Pan


title: Spatial transcriptomics signatures in COPD

status: Public on Mar 28 2025

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Human Stress Response Specificity through MAPK Bioresonance Selectivity

status: Public on Mar 04 2025

city: Riverside

first: Thomas

middle: Edward

last: Kuhlman

state: CA

address: 900 University Ave

department: Physics and Astronomy

institute: University of California Riverside

summary: In all eukaryotes, the mitogen activated protein kinase (MAPK) cascade, a multilayered interconnected network of enzymes, connects external stimuli to gene regulation, dictating cellular fate. However, mechanisms for information encoding, transmission, and decoding in this complex, fluctuating network to activate specific responses remain elusive. Here, we employ FRET to demonstrate that the central human stress regulator p38 MAPK encodes information regarding experienced stresses in oscillations of its activation state. We show that cells decode this information to drive specific responses through frequency-dependent resonance of oscillating biochemical phosphorylation reactions between p38 and downstream targets. Finally, we demonstrate how this understanding of bioresonance allows us to induce specific genetic responses simply by exposing cells to sugar to induce oscillations of p38 at predetermined frequencies.

overall_design: RNA-seq profiling of human HEK-293T cells that have been treated with different constant concentrations or frequency oscillations of sorbitol in order to drive p38 activation state oscillations and associated gene expression

middle: E


title: Single-nucleus multiomics of murine gonads reveals gene-regulatory networks underlying sex determination

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

address: 111 TW Alexander Drive

institute: NIEHS/NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sex determination in the mammalian gonad involves coordinated lineage decisions in both germ cells and gonadal supporting cells. To define the regulatory programs driving these processes, we generated a single-nucleus multiomics atlas of murine fetal gonads, integrating chromatin accessibility and gene expression from individual nuclei across sex determination timepoints in both XX and XY gonads. In primordial germ cells (PGCs), joint RNA- and ATAC-seq profiling identified transcriptional states and regulatory elements underlying germ cell sex determination. These data resolved previously uncharacterized PGC subpopulations, revealed that changes in chromatin accessibility often precede transcriptional activation during PGC lineage commitment, and showed that sexual dimorphism in gene expression and chromatin state increases over developmental time. Motif enrichment and gene-regulatory network analyses highlighted distinct cohorts of transcription factors associated with XX and XY germ cell differentiation, including TFAP2C, TCFL5, GATA2, MGA, NR6A1, TBX4, and ZFX in XX PGCs, and forkhead-box and POU6 factors in XY PGCs. The dataset also captured dynamic signaling pathways (WNT, BMP, and RA) and potential cell-cell communication interactions between PGCs and the surrounding somatic niche. In the supporting cell lineage, integrated snRNA- and snATAC-seq analyses revealed how precursor cells diverge to form Sertoli cells in testes and granulosa cells in ovaries. Sex-specific chromatin accessibility in supporting cells emerged shortly after sex determination, accompanied by activation-associated histone marks. Motif analyses identified regulatory networks associated with ovary-enriched transcription factors such as LEF1 and MSX1, which promote granulosa fate by activating key target genes including Foxl2 and Fst (bioRxiv 2025.02.24.639877). Together, this dataset provides a multimodal reference map of the chromatin landscapes, transcriptional programs, and regulatory networks that coordinately govern sex determination of germ cells and supporting cells during murine gonadal development.

overall_design: Single nuclei were extracted from embryonic gonads from E11.5-E13.5 male and female mice. Joint snRNA and snATAC-seq libraries were prepared using the 10x Genomics platform.

first: Adriana

middle: K

last: Alexander

first: Karina

middle: F

last: Rodriguez

first: Yu-Ying

first: Ciro

last: Amato

first: Martin

middle: A

last: Estermann

last: Xu

middle: H


title: Brain-infiltrating CD4 T cells drive inflammatory microglia proliferation during cryptococcal meningitis in mice

status: Public on Mar 01 2025

city: Birmingham

first: Rebecca

last: Drummond

state: Edgbaston

address: IBR 437, University of Birmingham

country: United Kingdom

institute: University of Birmingham

summary: An examination of the heterogeneity of myeloid cell subsets in the fungal-infected brain, comparing early and late time points post-infection. We focus on Cryptococcus neoformans infection for these studies, since this is the most common cause of fungal brain infection in humans.

overall_design: In this experiment, wild-type C57BL/6 mice were infected intravenously with the fungus Cryptococcus neoformans (strain H99). Brains were taken from uninfected controls or at day 3 and day 6 post-infection. Myeloid cells (defined as CD45+CD11b+) were FACS purified from brain samples, and the cells analysed by single-cell RNA sequencing using the 10X platform.


title: The role of TRAF1 in Helicobacter pylori infection

status: Public on Mar 05 2025

city: Changsha

first: Fen

state: Hunan

address: 138 Tongzipo Road

institute: The Third Xiangya Hospital, Central South University

summary: Our previous study has found the VacA virulence of Helicobacter pylori could induce the apoptosis of gastric epithelial cells and TRAF1 plays a crucial role in this process. In order to further investigate the detailed mechanism of TRAF1-related apoptosis, we constructed a TRAF1 knockdown model in MKN74 cells and TRAF1 overexpressing model in HGC27 cells.

overall_design: RNA-seq profiling of TRAF1-knockdown MKN74 cells and TRAF1-overexpressing HGC27 cells as well as corresponding controls.

first: Lingzhi

last: Yuan


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

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine


title: Gene expression profiles in rat alveolar macrophages exposure to cellulose nanocrystals

status: Public on Feb 16 2025

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: To evaluate the biological impact of cellulose nanocrystals (CNCs) at the transcriptional level, we conducted whole-genome microarray analyses on rat alveolar macrophages (NR8383) exposed to CNCs with different physicochemical properties.

overall_design: Rat alveolar macrophages (NR8383) were exposed for 24 hours to three types of cellulose nanocrystals (CNCs): sulfuric acid-hydrolyzed CNCs (CNC1), sulfuric acid-hydrolyzed CNCs with a high sulfonic group content (CNC2), and desulfated CNCs (CNC3), each at a concentration of 100 µg/mL. The experiments included a vehicle control group (n=4). Cyanine-3-labeled cRNA, generated from NR8383 exposed to CNCs was hybridized to a Whole Rat Genome Microarray. Subsequently, the scanned images of the hybridized microarray slides were subjected to numerical analysis to assess the transcriptional-level biological effects of CNCs on NR8383.

first: Sawae

last: Obara


title: Automated denudation of bovine oocytes prior to in vitro culture does not impact the blastocyst transcriptome.

status: Public on Jan 27 2025

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

summary: The new use of automated tools in assisted reproductive techniques rises the concern of a posible detrimental effect on development. In the current study there are no meaningful differences between the transcriptomes of bovine blastocysts produced in vitro following manual or automatic denudation of the presumptive zygotes after in vitro fertilization.

overall_design: Five D7 blastocysts per experimental group.

first: Guerrero-Sánchez

last: Javier

first: González-Brusi

last: Leopoldo

first: Bermejo-Álvarez

last: Pablo


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [GLORI m6A-seq II]

status: Public on Jan 25 2025

city: ANN ARBOR

first: Yuanhao

last: Huang

state: MI

address: 1418 McIntyre st

institute: University of Michigan

summary: METTL3 catalyzes N6-methyladenosine (m6A) on mRNA, regulating RNA metabolism, but its role in early retinal development remains virtually unstudied. Using stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation, we found that loss of METTL3 nuclear m6A enzymatic activity impairs formation of the Rx+ retinal anlage in vitro. Through dCas13b-FTO m6A engineering, we demonstrate that m6A modifications at the Six3 3'UTR control its stability. While Mettl3 loss altered histone modifications, direct METTL3 chromatin targets were not transcriptionally functional. Integration of transcriptome-wide m6A and protein-RNA mapping with a degron-based strategy revealed immediate effects of METTL3 degradation in RPCs, uncovering a regulatory interaction between METTL3 and its RNA target Ythdf1. We demonstrate uncoupling of chromatin accessibility from changes in retinal transcription and m6A modifications. In vivo studies of Mettl3-deficient RPCs showed altered cell cycle and impaired retinal ganglion cell generation. Our findings establish METTL3-dependent m6A modifications as an essential post-transcriptional layer that drives retinal development.

overall_design: GLORI m6A-seq profiling of dTAG13 induced acute degradation of METTL3 in day 6 retinal organoids of Rx:GFP harboring FKBP12F36V-HA knocking into c-termincal of endogenous Mettl3.

first: Jing

first: Rajesh

last: Rao


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [Nanopore-seq]

overall_design: Nanopore-seq profiling of day 6 retinal organoids of WT Rx:GFP. Direct RNA libraries were made by RNA002 kit.


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [ATAC-seq]

overall_design: ATAC-seq profiling of time point assay (0hr, 1hr, 8hr and 24hr dTAG-13 treatment) at day 6 retinal organoids of Rx:GFP harboring FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles .

first: Qiang

last: Li


title: Chromatin accessibility mapping for functional GWAS risk variants of neuropsychiatric and neurodegenerative disorders in hiPSC-derived neural cells

status: Public on Jan 30 2025

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Despite genome-wide association studies (GWAS) of late-onset Alzheimer’s disease (LOAD) have identified 75 genetic risk loci 2-7, the disease causal mechanism underlying most GWAS risk loci remains largely unknown.  A major challenge is how to identify a putative causal disease variant among multiple risk variants at individual GWAS risk locus and functionally link the risk allele to LOAD-relevant cellular phenotypes. Leveraging our recent approach for identifying functional noncoding GWAS risk variants that show allele-specific open chromatin (ASoC), we systematically identified putative causal LOAD risk variants in human iPSC-derived neurons and glia cells, and established a causal link between PICALM risk allele to unappreciated microglia (MG)-specific role of PICALM in lipid droplet (LD) accumulation and phagocytosis.  Our ASoC mapping identified functional risk variants for 26 AD risk loci, most of which are MG-specific. At the PICALM locus, the LOAD risk allele of the ASoC SNP rs10792832 altered chromatin accessibility to PU.1 binding and reduced PICALM expression in MG, thereby leading to impaired phagocytosis of Amyloid beta (Aβ) and myelin debris. Interestingly, transcriptomic profiling of MG carrying PICALM risk allele not only supported abnormal phagocytosis but also revealed enrichment of gene pathways related to cholesterol synthesis and LD formation. Further genetic and pharmacological perturbations in MG established the causal link of the PICALM risk allele with PICALM reduction, LD accumulation and phagocytosis deficits. Our work elucidates an MG-specific role of PICALM in regulating lipid/cholesterol accumulation that is potentially linked to AD pathophysiology, providing a functional neurobiological basis for developing novel clinical interventions.

overall_design: We systematically identified putative causal LOAD risk variants in human iPSC-derived neurons and glia cells and established a causal link between the PICALM risk allele and the unappreciated microglia (MG)- specific role of PICALM in lipid droplet (LD) accumulation and phagocytosis. Our ASoC mapping identified functional risk variants for 26 AD risk loci, most of which are MG-specific.

first: Siwei

last: Zhang

first: Zhiping

middle: P

last: Pang

first: Alena

last: Kozlova


title: scRNA-seq analysis of human peripheral blood mononuclear cells collected from donors on ART

status: Public on Jan 29 2025

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: To identify host factors restricting HIV-1 infection, single cell gene expression profiles of immune cells at different timepoints in the course of HIV-1 infection were examined

overall_design: Single cell gene expression profiles of immune cells at different timepoints in the course of HIV-1 infection

first: Aviva

last: Geretz

first: Robert

last: Clifford


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [GLORI m6A-seq I]

overall_design: GLORI m6A-seq profiling of day 4 retinal organoids of  WT Rx:GFP and Mettl3 KO line.

last: Xu


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [ChIP-seq]

overall_design: CHIP-seq of day 6 retinal organoids of Rx:GFP line and Mettl3 KO line harboring Dox inducible HA-METTL3 treated with or without Dox. METTL3 antibody (Bethyl) was used for Rx:GFP line; HA antibody (Abcam) was used for Mettl3 KO line treated with or without Dox.


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [mRNA-seq]

overall_design: mRNA-seq profiling of time point assay (day 0, day 2, day 4 and day 6) retinal organoids of WT Rx:GFP, Mettl3 KO, reintroduced cytosolic GRBD-METTL3 (No Dex treatment) and nucleus-translocated GRBD-METTL3 (Dex treatment).


title: Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity

status: Public on Jan 23 2025

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

country: Sweden

institute: Karolinska Institute

summary: To understand the cross-lineage transition of neuroblastoma. We performed RNA sequencing for bulk tissue of tumor xenografts

overall_design: RNA sequencing for bulk tissue of neuroblastoma cell xenografts

first: Daohua

last: Lou

first: Dimtry

last: Usoskin

first: Patrik

last: Ernfors


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [delSBD-ChIP-Rx]

status: Public on Jan 13 2025

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

state: New York

address: 1230 York ave

institute: Rockefeller University

summary: Polycomb group proteins maintain gene expression patterns established during early development, with Polycomb Repressive Complex 2 (PRC2) methyltransferase a key regulator of cell differentiation, identity and plasticity. Consequently, extensive somatic mutations in PRC2, including gain- or loss- of function (GOF or LOF), are observed in human cancers. The regulation of chromatin structure by PRC2 is critically dependent on its EZH2 (Enhancer of Zeste Homolog 2) subunit, which catalyzes the methylation of histone H3 lysine 27 (H3K27). Recent structural studies of PRC2 revealed extensive conformational changes in the non-catalytic EZH2 N-terminal SANT-Binding Domain (SBD) during PRC2 activation, though the functional significance remains unclear. Here, we investigate how the SBD regulates PRC2 function. The domain is highly conserved in metazoans, dispensable for PRC2 assembly and chromatin localization, yet required for genome-wide histone H3K27 methylation. Further, we show that an intact SBD is necessary for the proliferation of EZH2-addicted lymphomas, and its deletion in the presence of EZH2 GOF mutations inhibits cancer cell growth. These observations provide new insights to the regulation of PRC2 activity in normal development and malignancy.

overall_design:
EZH2, SUZ12, H3K27me3, H3K27me2, H3K27ac ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
MTF2, JARID2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 Î?SBD.
Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF)
RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF), 72 hours after EZH2-KO induction.
H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of  EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF)

middle: L

first: Douglas

middle: W

last: Barrows

first: C. David

last: Allis


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [RNA-seq]

status: Public on Jan 21 2025

first: Yuanhao

last: Huang

overall_design: mRNA-seq profiling of day 6 retinal organoids of Mettl3 KO line harboring Dox inducible HA-METTL3 were treated with or without Dox. .

first: Jing

last: Rao


title: Microglial Prrc2a regulates microglia-neuron interaction in cerebellum and motor functions in mice

status: Public on Jan 16 2025

city: Beijing

first: Zengqiang

last: yuan

address: No. 27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

summary: The crosstalk between microglia and neuron has been recognized as a crucial process in the development and disorders of the central nervous system. The present study probes into the role of Prrc2a—a post-transcriptional regulator that binds and stabilizes transcripts pivotal for microglial development—specifically within cerebellar microglia using a microglia-targeted conditional knockout model, identifying it as a crucial regulator of microglial function. Single-cell RNA sequencing underscored a transcriptomic shift in Prrc2a-ablated microglia, revealing an abnormally activated state. Prrc2a deficiency and the consequent alteration of cerebellar microglia were associated with reduced mutual interactions, altered Purkinje cell morphology and electrophysiological activity, decreased molecular layer width, and subsequently defects in motor balance and coordination. Collectively, this study provides insights into the molecular mechanisms underlying microglia-neuron interaction within the cerebellum.

overall_design: To investigate the role of Prrc2a in microglia, we utilized microglia-specific knockout mice and ablated Prrc2a at postnatal day1. In order to gain a more comprehensive understanding of Prrc2a deficiency on microglial transcriptome characteristics and subsequent neuronal changes in cerebellum, we performed single-cell RNA-sequencing of 18658 murine cerebellar cells from Prrc2a cKO (specific deletion of Prrc2a in microglia) and Prrc2a flox/flox (control) mice at postnatal day7.

first: Xiaoheng

last: Li

first: Pin

last: Yang

first: Binbin

last: Dong

first: Lingling

last: Jiang

first: Ruilian

last: Xiu

first: Jia

last: Guo

first: Shuoshuo

first: Ping

first: Runze

last: Gu

first: Ao

first: Jinyu

first: Rong

last: Wu

first: Fengchao

last: Wang

first: Ying

last: Shen

first: Ningsheng

last: Shao

first: Jinbo

last: Cheng

last: Yuan


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [MTF2-JARID2]

first: Agata

last: Patriotis

overall_design:
EZH2, SUZ12, H3K27me3, H3K27me2 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
MTF2, JARID2, EPOP, AEBP2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)
RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF), 72 hours after EZH2-KO induction.
H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of  EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)

first: Douglas

last: Barrows

first: C. David

last: Allis


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

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


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [eCLIP]

city: Ann Arbor

first: Zhaowei

last: Han

state: Michigan

address: 1000 Wall St

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

overall_design: METTL3 eCLIP assay of day 6 retinal organoids of WT Rx:GFP and Mettl3 KO line. METTL3 antibody (Abcam, Ab195352) was used for this eCLIP assay.

first: Jing

last: Xu

first: Yuanhao

last: Huang

first: Rajesh

last: Rao


title: Exploring the Molecular Basis and Mechanism of Rougan Keli in Alleviating Portal Hypertension in Liver Cirrhosis

status: Public on Dec 30 2024

city: jiangsu

first: tianle

last: ma

institute: nanjing university of chinese medicine

summary: Our study aimed to elucidate the molecular basis and mechanism underlying the efficacy of Rgkl in PH treatment.

overall_design: we performed gene expression profiling analysis using data obtained from RNA-seq of different cells at two tine points.

first: huihua

last: fang

first: yiheng

last: zhang

first: li

last: wu


title: Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway [5hmC]

status: Public on Dec 18 2024

city: Bethesda

first: Kan

last: Jiang

address: 9000 Rockville Pike

institute: NIAMS/NIH

summary: By satisfying bioenergetic demands, generating biomass, and providing metabolites serving as cofactors for chromatin modifiers, metabolism regulates adult stem cell biology. Here, we report that, branching off from glycolysis, the serine biosynthesis pathway (SBP) is activated in regenerating muscle stem cells (MuSCs). Gene inactivation and metabolomics revealed that Psat1, one of the three SBP enzymes, controls MuSCs activation and expansion of myogenic progenitors through production of the metabolite a-ketoglutarate (a-KG) and the a-KG-generated amino acid glutamine. Genetic ablation of Psat1 in MuSCs resulted in defective expansion of MuSCs and impaired regeneration. Psat1, a-KG, and glutamine were reduced in MuSCs of old mice and myoblasts of old individuals. a-KG or glutamine re-established appropriate muscle regeneration of adult Psat1-/- mice, old mice, and improved proliferation of old human myoblasts. These findings contribute insights into the metabolic role of Psat1 during muscle regeneration and suggest a-KG and glutamine as potential therapeutic interventions to ameliorate muscle regeneration during aging.

overall_design: Genomic DNA was extracted from Ctrl or Psat1cKO myoblasts, sonicated to generate 300bp fragment size. 5 mg DNA was used for 5hmC immunoprecipitation. 10% of DNA was used as input.

first: Ciuffoli

last: Veronica

first: Feng

last: Xuesong

first: Jiang

last: Kan

first: Dell'Orso

last: Stefania

first: Sartorelli

last: Vittorio


title: Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway

overall_design: Refer to individual Series


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [RNA-Seq]

overall_design: mRNA-seq profiling of time point assay (0hr, 1hr, 8hr and 24hr dTAG-13 treatment) at day 6 retinal organoids of Rx:GFP harboring FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles .


title: Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Half of all amyotrophic lateral sclerosis (ALS) patients demonstrate a spectrum of cognitive and behavioral changes over the course of the disease, but the mechanisms underlying this heterogeneity remain unclear. We assemble a high-resolution cellular map of prefrontal cortex regions of the ALS brain by integrating spatial and single-nucleus transcriptomic profiles of a cognitively stratified ALS patient cohort that includes non-neuropathological controls. We find cellular programs characteristic of ALS, including a frequent gliotic response. We also find that executive and language cognitive impairments differ from ALS without cognitive impairment, and from each other, in the extent and pattern of neuronal dysregulation and neuron-glial interactions across different brain regions. These findings reveal a relationship between cognitive phenotype and prefrontal cortex dysfunction in ALS.

overall_design: Single cell multiomic (transcriptomic and ATAC) libraries generated from 48 human donor prefrontal cortex samples (24 from BA44/45 and 24 from BA46), across a range of non-neuropathological sudden-death controls, ALS patients, and ALS patients who exhibit cognitive impairment on a standardized screening exam

first: Aidan

last: Daly

first: Cláudio

last: Roque

first: Joana

last: Petrescu

first: Hemali

last: Phatnani


title: TSLP acts on regulatory T cells to maintain their identity and limit allergic inflammation

status: Public on Dec 25 2024

first: Peng

last: Li

department: NHLBI

institute: NIH

summary: Thymic stromal lymphopoietin (TSLP) is a type I cytokine that promotes allergic responses and mediates type 2 immunity. A balance between effector T cells (Teff), which drive the immune response, and regulatory T cells (Tregs), which suppress the response, is required for proper immune homeostasis. Here, we report that TSLP differentially acts on Teff versus Tregs to balance type 2 immunity. As expected, deletion of TSLPR on all T cells (Cd4CreCrlf2fl/fl mice) resulted in lower numbers of Th2 cells and diminished ovalbumin-induced airway inflammation, but selective deletion of TSLPR on Tregs (Foxp3YFP-Cre/YCrlf2fl/fl mice) resulted in increased IL-5- and IL-13-secreting Th2 cells and lung eosinophilia. Moreover, TSLP augmented the expression of factors that stabilize Tregs. During type 2 immune responses, TSLPR-deficient Tregs acquired Th2-like properties, with augmented GATA3 expression and secretion of IL-13. TSLP is not only a driver of Th2 effector cells  but also acts in a negative feedback loop, thus promoting the ability of Tregs to limit allergic inflammation.

overall_design: RNA-sequencing was performed using total RNA from nTregs with TCR in the absence versus presence of TSLP and also Tregs from Foxp3YFP-Cre/YCrlf2fl/fl and Foxp3YFP-Cre isolated from allergic lung tissue.

first: Rama

last: Gurram

first: Jangsuk

last: Oh

first: Xi

last: Chen

first: Rosanne

last: Spolski

first: Xianglan

last: Yao

first: Jian-Xin

last: Lin

first: Suyasha

last: Roy

first: Matthew

middle: J

last: Liao

first: Chengyu

last: Liu

first: Zu-Xi

last: Yu

first: Stewart

last: Levine

first: Jinfang

last: Zhu

first: Warren

last: Leonard


title: Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana [RNA-seq]

status: Public on Dec 16 2024

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

country: Austria

institute: GMI

summary: DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7α) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7α and its paralog, CDCA7β, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7α/β selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7α expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7α alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.

overall_design: 3' tag RNA-seq profiling of cdca7α/β and ddm1 mutants (batch A) and cdca7α/β-3 mutants complemented with various constructs (batch B).


title: Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway [3dpiRNA]

first: Kan

last: Jiang

summary: By satisfying bioenergetic demands, generating biomass, and providing metabolites serving as cofactors for chromatin modifiers, metabolism regulates adult stem cell biology. Here, we report that, branching off from glycolysis, the serine biosynthesis pathway (SBP) is activated in regenerating muscle stem cells (MuSCs). Gene inactivation and metabolomics revealed that Psat1, one of the three SBP enzymes, controls MuSCs activation and expansion of myogenic progenitors through production of the metabolite a-ketoglutarate (a-KG) and the a-KG-generated amino acid glutamine. Genetic ablation of Psat1 in MuSCs resulted in defective expansion of MuSCs and impaired regeneration. Psat1, a-KG, and glutamine were reduced in MuSCs of old mice and myoblasts of old individuals. a-KG or glutamine re-established appropriate muscle regeneration of adult Psat1-/- mice, old mice, and improved proliferation of old human myoblasts. These findings contribute insights into the metabolic role of Psat1 during muscle regeneration and suggest a-KG and glutamine as potential therapeutic interventions to ameliorate muscle regeneration during aging

overall_design: total RNA was extracted with Trizol from 3 days post injury (dpi) TA/EDL of  Ctrl and Psat1iKO. 250ng of RNA was enriched for poly(A)+ mRNA and used for library construction using NEBNext Ultra II Library preparation kit

first: Ciuffoli

last: Veronica

first: Feng

last: Xuesong

first: Jiang

last: Kan

first: Dell'Orso

last: Stefania

first: Sartorelli

last: Vittorio


title: Asymmetrical end structures of leading and lagging telomeres in Saccharomyces cerevisiae dictate the nature of the end replication problem

status: Public on Dec 09 2024

city: Shanghai

first: Qingqing

last: Yuan

address: 320 Yueyang Road

department: SIBCB

institute: CEMCS, CAS

summary: The end replication problem refers to the incomplete replication of parental DNA at telomeres, a process whose molecular depiction is hampered by the complex nature of telomere ends. Here we recapitulate this process using a synthetic de novo telomere in Saccharomyces cerevisiae and delineate distinct molecular fates of telomere ends in vivo. We show that the lagging-strand telomeres carry a ~10-nucleotide 3’ overhang, while the leading-strand telomeres have a Yku-protected blunt end, a feature that is common to native telomeres. Additionally, RNase H2 is primarily responsible for removing the terminal RNA primer. Consistently, the absence of RNase H2 activity results in the retention of the RNA primer on the lagging-strand telomere, which attenuates telomere erosion and delays senescence in telomerase-null cells. These findings highlight incongruent end structures on yeast telomeres and clarify that the primary culprit behind the end replication problem is the incompletely replicated lagging-strand telomere.

overall_design: END-seq analysis of blunt ends on native telomeres

first: Tiantian

last: Ye

first: Shuheng

last: Wu

first: Jingtong

last: Zhao

first: Zhijing

first: Jiacheng

first: Wei

first: Jinqiu

last: Zhou


title: Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway [bulkRNA]

overall_design: total RNA was extracted with Trizol from Ctrl and Psat1cKO myoblasts. 500ng of RNA was used to generate poly (A)+ mRNA libraries using NEBNext Ultra II Library preparation kit


title: Gene expression profiles of nasal epithelium in long COVID and post-COVID

status: Public on Jan 31 2025

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: Recent studies suggest that chronic inflammation and immune dysregulation in the local tissues and systemically play a critical role in the pathophysiology of long COVID. Here, we report a role for nasal epithelium in mediating inflammation in a subset of long COVID patients. We demonstrate impaired barrier function of nasal epithelial cells, inadequate wound healing potential, and nasal cell hypersensitivity along with a persistent inflammatory state in long COVID. These inflamed structural cells activate type 1 innate lymphoid cells in the blood of long COVID patients and propagate systemic inflammation. We demonstrated the importance of understanding the immunological mechanisms driving long COVID to develop effective treatments. We highlight the critical role of the nasal epithelial barrier and the interplay between epithelial cells and ILCs in maintaining mucosal homeostasis and contributing to chronic inflammation in long COVID.

overall_design: In this study, we examined whether the crosstalk between the nasal epithelium and pro-inflammatory innate lymphoid cells plays a role in modulating the pathophysiology of long COVID. Considering the transcriptome, we studied the functional and phenotypic consequences of dysregulated gene expression patterns, we performed bulk RNA-sequencing on the collected nasal epithelium from long COVID (N=3) and post-COVID (N=3) individuals at baseline and after exposure to poly(I:C) and IFN-γ

first: Nadia

last: Baalbaki

first: Danielle

last: van Egmond

first: Patricia

last: Jaeger

first: Merel

last: Cornelissen

first: Sien

middle: T

last: Verbeek

first: Cornelis

last: van Drunen

first: Anke

last: Maitland

first: Korneliusz

last: Golebski


title: (p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms

status: Public on Dec 06 2024

city: Braunschweig

first: Florian

last: Engelhardt

address: Inhoffenstraße 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Centre for Infection Research

summary: Transcriptomic analysis of Pseudomonas aeruginosa PA14 in liquid minimal medium with serine hydroxamate.

overall_design: Liquid cultures of Pseudomonas aeruginosa in exponential growth phase (OD 0.5) were treated with increasing concentrations of serine hydroxamate (SHX) for 30 minutes to induce elevated cellular levels of (p)ppGpp. Experiment was performed in three biological replicates.

first: Engelhardt

last: Florian

first: Turnbull

last: Kathryn

first: Müsken

last: Mathias

first: Preuße

last: Matthias

first: Häussler

last: Susanne

first: Roghanian

last: Mohammad


title: SOX10 regulates multiple genes to direct eumelanin vs. pheomelanin production in domestic rock pigeon

status: Public on Nov 10 2024

city: Orem

first: Eric

last: Domyan

state: UT

address: 800 W University Parkway

department: Department of Biology

institute: Utah Valley University

summary: The domesticated rock pigeon (Columba livia) has been bred for hundreds of years to display an immense variety of ornamental attributes such as feather color and color patterns. Color is influenced by multiple loci that impact the type and amount of melanin deposited on the feathers. Pigeons homozygous for the “recessive red” mutation, which causes downregulation of Sox10, display brilliant red feathers instead of blue/black feathers. Sox10 encodes a transcription factor important for melanocyte differentiation and function, but the genes that mediate its promotion of black vs. red pigment are unknown. Here, we present a transcriptomic comparison of regenerating feathers from wild-type and recessive red pigeons to identify candidate SOX10 targets. Our results identify both known and novel targets, including many genes not previously implicated in pigmentation. These data highlight the value of using novel, emerging model organisms to gain insight into the genetic basis of pigment variation.

overall_design: RNA-seq data was generated from regenerating feathers of  wild-type and  recessive red (Sox10 mutant) pigeons. Samples in Batch 1 were sequenced in 2017, and were utilized in the manuscript (Domyan et al. PCMR 2019). Samples in Batch 2 were collected in 2020 and are unpublished.

first: Jonathon

last: Hill


title: Investigating genome occupancy of SOX10 in avian melanocytes

summary: Domestic rock pigeons (Columba livia) homozygous for either of two “recessive red” mutations, which are partially-overlapping deletions causing downregulation of Sox10, display brilliant red colors instead of blue/black feathers. Sox10 encodes a transcription factor important for melanocyte differentiation and function, but the precise role that it plays in promoting eumelanin over pheomelanin pigment production in pigeons are unknown. In this study, we perform ChIPseq for SOX10, H3K27ac, and H3K27me3 to better understand the genome occupancy of SOX10 in avian melanocytes.

overall_design: Chromatin-immunoprecipitation DNA sequencing (ChIPseq) for SOX10, as well as chromatin modifications H3K27ac and H3K27me3 in primary lines of pigeon melanocytes.

first: Whitney

last: Brownlee

first: Brittney

last: Burton

first: Max

last: Ellsworth

first: Samuel

last: Perez

first: Nathan

last: Walker


title: Php|NF-Y transcription factor infiltrates repressive heterochromatin to generate transcripts crucial for spliceosome-dependent small RNA production

first: Shiv

last: Grewal

department: National Cancer Institute

institute: National Institutes of Health

type: Non-coding RNA profiling by high throughput sequencing

summary: The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA- based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) Php|NF-Y complex, which includes histone fold domain proteins, can infiltrate constitutive heterochromatin to transcribe repeat elements. Php|NF-Y collaborates with a Zn-finger containing TF to bind repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, Php|NF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain cryptic introns that are processed via a mechanism requiring the spliceosome to generate small interfering RNAs (siRNAs) by the RNAi machinery. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for heterochromatin nucleation at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.


title: Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana [WGBS]

first: Pierre

last: Bourguet

type: Methylation profiling by high throughput sequencing

overall_design: Tagmentation whole genome bisulfite-sequencing (TWGBS) of cdca7α/β and ddm1 mutants (batch A), cdca7α/β-3 mutants complemented with various constructs (batch B), inbred cdca7α/β-1 and ddm1 mutants (batch C).


title: ACSS2 drives drinking indulgence in male mice by coordinating a gene expression program in the ventral striatum

status: Public on Oct 31 2024

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: We recently established ACSS2 as a potential candidate for therapeutic interventions in alcohol use disorders (AUD), in which memory of alcohol-associated environmental cues is a primary driver of craving and relapse. Prior research, however, has been limited to passive exposure to ethanol and the importance of this pathway in models of voluntary drinking that better approximate human alcohol consumption remains unknown. Therefore, we assessed the effect of genetic ACSS2 inhibition on voluntary alcohol intake and simultaneously assayed the epigenetic and transcriptional changes that accompany alcohol consumption.

overall_design: This study tests the effect of knocking out ACSS2 (an enzyme involved in alcohol metabolism in the brain) on alcohol drinking behavior in rodents. This series contains RNA-seq from WT or ACSS2 KO mice, including both males and females, who were subjected to the "drinking in the dark" experimental model for chronic alcohol use (see treatment protocol, below). Samples are from seven dissected portions of the brain: amygdala, cortex, dorsal & ventral hippocampus, prefrontal cortex, and dorsal & ventral striatum. The replicate structure is as follows. For female mice, there are three ACSS2 KO biological replicates each for all brain regions, while the number of WT biological replicates is either two or three depending on the brain region (amygdala, cortex, and prefrontal cortex have two replicates each while dorsal and ventral hippcampus and dorsal and ventral striatum have three replicates each). For male mice, there are three biological replicates each of ACSS2 KO and WT for all tissues except prefrontal cortex, which has one ACSS2 KO and two WT.

first: Gabor

last: Egervari

first: Natalia

last: Quijano-Cardé

first: Connor

last: Hogan

first: Erica

middle: M

last: Periandri

first: Desi

middle: C

last: Alexander

first: Mariella

last: De Biasi

first: Shelley

last: Berger


title: Single-Cell Profiling of Diabetic Nephropathy in a Murine Model Reveals Novel CellChat Signatures, Podocyte-to-Parietal Epithelial Cells Crosstalk

city: Shenzhen

first: Tingfei

last: Xie

state: Guangdong

address: Longjing 2nd Road, Xin'an Street

institute: Southern Medical University

summary: We used scRNA-seq to confirm the rich cellular interactions between podocytes and glomerular parietal epithelial cells in early diabetic nephropathy and to construct a global view of early diabetic nephropathy.

overall_design: Isolation of kidney tissue from diabetic nephropathy mice (n=3) and control mice (n=2) for single-cell sequencing analysis

first: Jihong

last: Chen

first: Xiaolu

last: Sui


title: Single nuclei RNA-sequencing of normal and diseased liver

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: Gene expression profile at single nucleus level of liver cells from the healthy and diseased donors

overall_design: Single nucleus RNA-sequencing of normal and diseased liver

first: Raza

last: Ur Rahman

first: Liat

last: Amir-Zilberstein

first: Jacques

last: Deguine

first: Ramnik

last: Xavier


title: Mechanical regulation of the glucocorticoid-sensitive transcriptome in young and aged skeletal muscle

status: Public on Oct 28 2024

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Elevated glucocorticoids alter the skeletal muscle transcriptome to induce a myopathy characterized by muscle atrophy, muscle weakness, and decreased metabolic function. These effects are more likely to occur and be more severe in aged muscle. Resistance exercise can blunt development of glucocorticoid myopathy in young muscle, but the potential to blunt the signals initiating myopathy in aged muscle is unknown. To answer this, young (4-month-old) and aged (24-25-month-old) male C57BL/6 mice were randomized to receive either an intraperitoneal (IP) injection of dexamethasone (DEX; 2 mg/kg) or saline as a control. Two hours post-injections, tibialis anterior (TA) muscles of mice were subjected to unilateral high force contractions. Muscles were harvested four hours later. The glucocorticoid- and contraction-sensitive genes were determined by RNA sequencing. The number of glucocorticoid sensitive genes was similar between young and aged muscle. Contractions altered more glucocorticoid-sensitive genes in aged muscle, with this outcome primarily occurring when hormone levels   were elevated. Glucocorticoid-sensitive gene programs altered by contractions were primarily related to metabolism in young mice and muscle size regulation and inflammation in aged mice. In silico analysis implied Peroxisome proliferator-activated receptor gamma-1 (PPARG) contributed to the contraction-induced changes in glucocorticoid-sensitive genes in aged muscle. Increasing PPARG expression in the TA of aged mice using Adeno-associated virus serotype 9 partially counteracted the glucocorticoid-induced reduction in Runt-related transcription factor 1 (Runx1) mRNA content, recapitulating the effects observed by contractions. Overall, these data contribute to our understanding of the mechanical regulation of the glucocorticoid transcriptome in aged skeletal muscle.

overall_design: 4-mo-old male mice (Young) and 24-25-mo-old male mice (Aged) were randomized to receive an intraperitoneal (IP) injection of dexamethasone at 2 mg/kg (DEX) diluted in saline or an IP injection of saline only as a control (Vehicle). The mice were given 2 h recovery after the injection to allow for full activation of the glucocorticoid receptor in the DEX treated group. Mice were then subjected to unilateral high force eccentric contractions by electrical stimulation of the sciatic nerve under deep isoflurane (3%) anesthesia. Following the contractions, all mice received a 500 µL subcutaneous injection of warm saline before returning to their cages. During the recovery, all mice had access to water but not food. Four hours after completing the contractions protocol (6.5 h post-DEX or saline injection), both tibialis anterior (TA) muscles (Non-Stim and Stim leg) were extracted under deep isoflurane (3%) anesthesia, snap-frozen in liquid nitrogen, and stored at -80°C. Total RNA extracted from the TA muscles generated was subjected to RNA sequencing to determine acute glucocortocoid- and contraction-sensitive genes (Young-Vehicle: n=6 mice; Young-DEX: n=6 mice; Aged-Vehicle: n=4 mice; Aged-DEX: n=6 mice).

first: Grant

middle: R

last: Laskin

first: David

middle: S

last: Waddell

first: Bradley

last: Gordon


title: Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana

first: Pierre

last: Bourguet

overall_design: Whole genome bisulfite sequencing of cdca7α-2, smp2, and AT4G37130 mutants.

first: Eriko

last: Sasaki


title: Investigating the function of Sox10 in avian melanogenesis

first: Eric

last: Domyan

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

overall_design: Refer to individual Series


title: Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway [Cut & Run]

first: Kan

last: Jiang

summary: By satisfying bioenergetic demands, generating biomass, and providing metabolites serving as cofactors for chromatin modifiers, metabolism regulates adult stem cell biology. Here, we report that, branching off from glycolysis, the serine biosynthesis pathway (SBP) is activated in regenerating muscle stem cells (MuSCs). Gene inactivation and metabolomics revealed that Psat1, one of the three SBP enzymes, controls MuSCs activation and expansion of myogenic progenitors through production of the metabolite -ketoglutarate (-KG) and the -KG-generated amino acid glutamine. Genetic ablation of Psat1 in MuSCs resulted in defective expansion of MuSCs and impaired regeneration. Psat1, -KG, and glutamine were reduced in MuSCs of old mice and myoblasts of old individuals. -KG or glutamine re-established appropriate muscle regeneration of adult Psat1-/- mice, old mice, and improved proliferation of old human myoblasts. These findings contribute insights into the metabolic role of Psat1 during muscle regeneration and suggest -KG and glutamine as potential therapeutic interventions to ameliorate muscle regeneration during aging.

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN)for H3K27me3 cell signaling #C36B11 in Ctrl and Psat1cKO myoblasts

first: Ciuffoli

last: Veronica

first: Feng

last: Xuesong

first: Jiang

last: Kan

first: Dell'Orso

last: Stefania

first: Sartorelli

last: Vittorio


title: RNA-binding proteins control the G2-M checkpoint of the germinal center B cell [iCLIP]

status: Public on Oct 24 2024

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: The germinal center (GC) reaction drives the production of high-affinity antibodies by iterative cycles of B cell somatic hypermutation, selection, and proliferation. How GC B cells undergo rapid cell division while maintaining genome stability is poorly understood. Here, we show that the RNA binding proteins ZFP36L1 and ZFP36L2 act downstream of antigen sensing and protect GC B cells from replication stress by controlling a cell cycle-related posttranscriptional regulon. They safeguard the successful completion of mitosis by balancing CDK1 and p21-mediated regulation of cell-cycle progression. In their absence, GC B cells are prone to arrest in the G2-M phase and die by apoptosis, resulting in curtailed GC responses. DNA replication forks stalled at active replication initiation zones, causing replication stress and increased activity of the ATR-CHK1 DNA damage response. Thus, RNA binding proteins guide posttranscriptional gene regulation and maintain a functional G2-M checkpoint in GC B cells.

overall_design: iCLIP for mCherry-ZFP36L1 in induced germinal center B cells, with 3 replicates each of mCherry-ZFP36L1 transgenic and WT (negative control) cells

first: Fiamma

last: Salerno

first: Martin

last: Turner


title: RNA-binding proteins control the G2-M checkpoint of the germinal center B cell [TrAEL-seq]

overall_design: Naive B cells isolated from peripheral lymph nodes of Zfp36l1 fl/fl Zfp36l2 fl/fl and Zfp36l1 fl/fl Zfp36l2 fl/fl CD23cre mice (2 replicates each), were activated in vitro for 7 days in iGCB culture conditions. Agarose-embedded DNA from 2x10^6 iGCB cells were taken and processed into TrAEL-seq libraries, to track replication fork sites and profile replication origin usage genome-wide

first: Alex

last: Whale

first: William

last: Foster

first: Sarah

middle: E

last: Bell

first: Daniel

last: Hodson

first: Michelle

last: Linterman

first: Jonathan

last: Houseley


title: RNA-binding proteins control the G2-M checkpoint of the germinal center B cell [RNAseq]

overall_design: RNA-seq from induced germinal center B cells, with 3 replicates each of control and Zfp36l1/Zfp36l2-deficient cells.


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

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: Upregulation of olfactory receptors and neuronal-associated genes highlights complex immune and neuronal dysregulation in Long COVID patients

status: Public on Oct 15 2024

city: Edmonton

first: Hussain

last: Syed

state: Alberta

address: 116 Street and 85th Ave

department: Medicine

country: Canada

institute: University of Alberta

summary: In this study, we isolated RNA from the whole blood of 19 patients who developed myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) following acute SARS-CoV-2 infection. We also isolated RNA from the whole blood of 17 healthy controls (HCs). We analyzed the genes that had differential expression between patients with ME/CFS and HCs.

overall_design: To investigate the differential gene expression pattern of long COVID patients with chronic fatigue syndrome vs healthy controls

first: Shima

last: Shahbaz

first: Shokrollah

last: Elahi

first: Mohammed

last: Osman

first: Charmaine

last: van Eeden

first: Andrew

last: Mason

first: Maryam

last: Rezaeifar


title: Whole-genome bisulfite sequencing in the whole blood of three dog breeds

status: Public on Oct 18 2024

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

institute: KDDI research Inc

summary: DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment in mammals.  This experiment addressed the DNA methylation landscape in the dog genome across three breeds: Shiba, Dachshund (Miniature), and Poodle (Toy).  A comprehensive profile of whole-genome DNA methylation from the whole blood of three dog breeds was generated using whole-genome bisulfite sequencing.

overall_design: Whole-genome bisulfite sequencing was performed with whole blood obtained from nineteen individual dogs across three breeds: Shiba, Dachshund (Miniature), and Poodle (Toy).


title: Single Cell Multiomics Profiling for the Mouse Polycystic Kidney Disease

status: Public on Oct 02 2024

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: We performed multiomics analysis; single nucleus RNA-seq (snRNA-seq) combined with ATAC (snATAC-seq) with 10XGenomics Multiome platform to generate cell-type-specific gene expression and chromatin accessibility atlas of the mouse polycystic kidney disease on a time course.

overall_design: We inducedPkd1deletion in the tubular cells of Pkd1fl/fl; Pax8rtTA; TetO-Cremale mice from postnatal day 27 (P27) to 57 (P57) with doxycycline injection. The littermate male controls lacked either thePax8rtTA(P66) ortheTetOCremodule (P100, P130) but were treated with doxycycline in the same manner. The kidneys were harvested and snap-frozen at postnatal day 66 (P66), 100 (P100) or 130 (P130).

first: Benjamin

middle: D

last: Humphreys


title: Chromatin accessibility mapping for functional GWAS risk variants of neuropsychiatric and neurodegenerative disorders in hiPSC-derived neural cells

status: Public on Sep 05 2024

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Chromatin accessibility (ATAC-seq) data from additional 41 lines of hiPSC-derived neurons.

first: Siwei

last: Zhang

first: Zhiping

last: Pang

first: Alena

last: Kozlova


title: Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana [ChIP-Seq]

first: Pierre

last: Bourguet

summary: DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7α) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7α and its paralog, CDCA7β, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7α/β selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7α expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7α alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.

overall_design: ChIP-seq of histone modifications (H3K27me1, H3K9me2) and histone variants (H2A.W.6/7, H2A.Z.9/11) in cdca7α/β and ddm1 mutants.


title: Profiling of gene expression during aging in isolated bodies of wild type vs Cdk5a-mutant Drosophila melanogaster.

status: Public on Aug 23 2024

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: To provide a consistent background for studies of the link between neurodegeneration and aging, we performed microarray-based expression profiling (Affymetrix) of RNA isolated from the bodies of adult male Drosophila at various ages from either wild type flies (Oregon R), or flies bearing a null mutation of the gene encoding the Cdk5 activator (Cdk5a). Note that all flies were wild type for the chromosomal white locus due to the pleiotropic effects of the w locus on many neuronal and physiological functions of the adult fly. In order to match samples by ‘physiological age’ in the two populations, WT flies were collected at 10 days, 20 days, 41 days and 58 days after eclosion and Cdk5a flies were collected at 10, 23, and 31 days (NOTE: 41 days for WT and 23 days for Cdk5a corresponded to <10% population mortality; 58 days (WT) and 31 days (Cdk5a) corresponded to ~50% population mortality in this experiment). These samples provide a well-matched basis for identification of genes with age-dependent expression level in each of the two genotypes and for comparison of differences in expression between the genotypes.

overall_design: Gene expression for 42 samples representing male Drosophila melanogaster body collected at 4 different ages across two different genotypes.

last: Scott

last: Wodrich

first: Edward

last: Giniger


title: Integrative genome-wide DNA methylome and transcriptome data reveals key genes involved in the dysregulation of adipose-stem cells linked to Crohn’s disease [RNA-seq]

status: Public on Sep 03 2024

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Creeping fat, also known as mesenteric fat, which is connected to the inflamed segments of the intestine and is a hallmark of Crohn's disease (CD), appears to be correlated with disease activity. Adipose-stem cells isolated from the creeping fat of CD subjects were found to be dysfunctional (exhibiting a high inflammatory profile, high invasive and phagocytic capacities, and worse immunosuppressive properties), and this dysfunction persisted in hASCs taken from CD subjects who were in remission of the disease. We hypothesized that the abnormal behavior of adipose stem cells is caused by the accumulation of epigenetic modifications due to the inflammatory environment underlying active CD. DNA methylation and transcriptomics were performed in adipose-derived stem cells (ASCs) isolated from visceral adipose tissue biopsies of active and inactive CD patients and non-IBD patients. An integrative analysis of both omics was performed to obtain the best gene candidates.

overall_design: Total RNA extracted from human adipocyte stem cells (hASCs) derived 21 Crohn’s disease (CD) patients samples and 7 healthy individual samples were processed using the TruSeq mRNA library preparation kit (Illumna) and sequenced using 1x50 single reads. CD samples were derived from different tissues and disease states: 7 creeping fat samples from active Crohn’s disease (CF_aCD), 7 mesenteric samples from active Crohn’s disease (hMES_aCD), and 7 mesenteric samples from inactive Crohn’s disease (hMES_iCD).

first: Diandra

last: Monfort-Ferré

first: Albert

last: Boronat-Toscano

first: Jose-Francisco

last: Sánchez-Herrero

first: Aleidis

last: Caro

first: Margarita

last: Menacho

first: Maria-José

last: Mañas

first: Beatriz

last: Espina

first: Raquel

last: Pluvinet

first: Lidia

last: Cabrinety

first: Carme

last: Abadia

first: Marc

last: Marti

first: Carolina

last: Serena


title: Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes

status: Public on Aug 15 2024

first: Min

last: Dai

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

summary: The mammalian cerebral cortex comprises a complex neuronal network that maintains a delicate balance between excitatory neurons and inhibitory interneurons. Previous studies, including our own research, have shown that specific interneuron subtypes are closely associated with particular pyramidal neuron types, forming stereotyped local inhibitory microcircuits. However, the developmental processes that establish these precise networks are not well understood. Here we show that pyramidal neuron types are instrumental in maintaining the terminal differentiation and survival of specific associated interneuron subtypes. In a wild-type cortex, the relative abundance of different interneuron subtypes aligns precisely with the pyramidal neuron types with which they synaptically target. In Fezf2 mutant cortex, characterized by the absence of layer 5 pyramidal tract neurons and an expansion of layer 6 intratelencephalic neurons, we observed a corresponding decrease in associated layer 5b interneurons and an increase in layer 6 subtypes. Interestingly, these shifts in composition are achieved through mechanisms that are specific to different interneuron types.  While SST interneurons adjust their abundance to the change in pyramidal neuron prevalence through the regulation of programmed cell death, parvalbumin cells alter their identity. These findings illustrate two key strategies by which the dynamic interplay between pyramidal neurons and interneurons allows local microcircuits to be sculpted precisely. These insights underscored the precise roles of extrinsic signals from pyramidal cells in the establishment of interneuron diversity and their subsequent integration into local cortical microcircuits.

overall_design: To directly test the influence of pyramidal neurons (PNs) on interneuron development, we used genetic strategies to selectively alter the identity of specific PN types and demonstrated that the quantity and position of particular PVALB and SST interneuron subtypes change in accordance with this shift. Importantly, these changes occur through distinct mechanisms: PNs promote the survival of their partner SST interneuron subtypes, while inducing fate changes in PVALB interneuron population towards their preferred subtypes.

first: Sherry

last: Wu


title: A convenient single-cell newly synthesized transcriptome assay reveals FLI1 regulon downregulation during T-cell activation

city: Bethesda

first: Jun

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

summary: We invented NOTE-seq, a method for simultaneous profiling of regular and newly synthesized transcriptomes in single cells with high cellular throughput. NOTE-seq integrates 4-thiouridine labeling of newly synthesized RNA, thiol-alkylation-based chemical conversion, and a streamlined 10X Genomics workflow, making it accessible and convenient for biologists without extensive single-cell expertise. Using NOTE-seq, we investigated the temporal dynamics of gene expression during early-stage T-cell activation, identified transcription factors and regulons in Jurkat and naïve T cells, and uncovered the down-regulation of FLI1 as a master transcription factor upon T-cell stimulation. Notably, topoisomerase inhibition led to the depletion of both topoisomerases and FLI1 in T cells through a proteasome-dependent mechanism. This degradation was driven by topoisomerase cleavage complexes rather than topoisomerase catalytic inhibition, highlighting potential complications topoisomerase-targeting cancer chemotherapies could pose to the immune system.

overall_design:
eHAP cells were cultivated and subjected to NOTE-seq and 10xGenomics 3' expression v3.1 kit. Jurkat T cells were cultivated and subjected to PMA/ION treatment versus DMSO treatment, followed by NOTE-seq profiling. Mouse naïve T cells were subjected to antiCD3 and antiCD28 stimulation, followed by NOTE-seq profiling.  For the barnyard experiment, Jurkart T cells and NIH3T3 cells were mixed at a 1:1 ratio, followed by the NOTE-seq workflow without T-to-C conversion.

newly synthesized transcriptome profiling at single cell level for eHAP1 cells fixed with formaldehyde (NOTE-seq) or methanol (MeOH-4sU-10X). NOTE-seq profiling of K562 cells with or without chemical conversion. NOTE-seq profiling of Jurkat cells with or without PMA/ION stimulation

first: Xiaoyan

last: Xu

first: Chongyi

last: Chen


title: Transcriptome analysis of patient derived induced pluripotent stem cell derived cardiomyocytes with severe, early onset hypertrophic cardiomyopathy due to biallelic MYBPC3 variants c.442G>A and c.506-1G>A

status: Public on Aug 11 2024

city: Ann Arbor

first: Joshua

last: Meisner

address: 1540 E. Hospital Drive

department: Pediatrics

institute: University of Michigan

summary: Induced pluripotent stem cells (iPSCs) were generated from a patient with severe, early onset hypertrophic cardiomyopathy due to pathogenic (c.506-1G>A) and low penetrance pathogenic (c.442G>A) variants in MYBPC3 in trans (i.e. MYBPC3 biallelic patient). Healthy control (WTC11, Coriell repository) iPSCs were used as reference. iPSCs were differentiated into cardiomyocytes for transcriptome analysis and assessment of the c.442G>A variant on MYBPC3 splicing.

overall_design: The biallelic patient derived iPSCs (iPSC31 cell line) and control iPSCs were differentiated into cardiomyocytes in monolayers then purified through lactate metabolic selection. Purified iPSC derived cardiomyocytes were then collected at ~day 24 after differentiation. 3 samples from 3 differentiation batches were collected for bulk RNA sequencing.

first: Adam

last: Helms


title: Bisulfite sequencing of medaka

status: Public on Nov 03 2024

city: Columbia

first: Ramji

middle: Kumar

last: Bhandari

address: 1200 University Avenue Lefevre Hall 114

department: Biological Sciences

institute: University of Missouri


title: Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease

status: Public on Aug 01 2024

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

state: CO

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

summary: Growing evidence implicates transposable elements (TEs) in aging and Alzheimer’s disease (AD). To evaluate potential transcriptional and epigenetic differences related to TE expression in this context, we generated whole blood total RNA-seq, and peripheral blood cell whole-genome bisulfite sequencing (WGBS), and transposase-accessible chromatin sequencing (ATAC-seq) on samples from healthy middle-aged/older adults, mild cognitive impairment (MCI), and AD patients.

overall_design: Total RNA-seq was performed on whole blood from 45 older adults including healthy, asymptomatic middle-aged/older adults (ASM, n = 11), older asymptomatic adults (ASO, n = 14), symptomatic older adults with MCI (n = 10), and older adults with AD dementia (n = 10). WGBS and ATAC-seq data were generated using buffy coat samples from these same subjects.

first: Thomas

last: LaRocca


title: RNA-binding proteins control the G2-M checkpoint of the germinal center B cell

first: Louise

last: Matheson


title: Mild hyperuricemia and salt-sensitive hypertension

status: Public on Jul 10 2024

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: Increased plasma uric acid (hyperuricemia) has been associated with worse outcomes for chronic kidney disease (CKD). But some attempts to control uric acid (UA) in large-cohort clinical trials did not produce clinically meaningful benefits for CKD. Some studies suggest that only hyperuricemia with crystals, but not asymptomatic hyperuricemia promotes the progression of CKD. Salt-sensitivity (SS) in blood pressure is a prevalent trait that is sexually dimorphic and results in kidney damage. But the connection between hyperuricemia and SS hypertension (HTN) is still unclear. Here we tested the connection between the two using both male and female Dahl SS rats, a well-establish model of SS HTN. We hypothesized that mild asymptomatic hyperuricemia is beneficial in controlling the progression of SS HTN. A uricase inhibitor, oxonic acid (2%) (Oxo) was used to induce hyperuricemia and high-salt (HS) (4% NaCl) diet was used to induce SS HTN. After 3 weeks, in response to oxonic acid supplementation, both sexes showed a significant increase of UA in plasma compared to their respective HS-only controls (Males: 0.63 ±0.07 vs. 2.17 ±0.34; Females: 0.78 ±0.15 vs. 2.04 ±0.35 mg/dl, HS vs. HS/oxo). Interestingly, only male HS/oxo rats showed a significant increase in uricosuria (Males: 0.23 ±0.03 vs. 0.45 ±0.06; Femaels: 0.26 ±0.06 vs. 0.26 ±0.001 UA/Cre, HS vs. HS/oxo). Moreover, the mild hyperuricemia was associated with a significant attenuation of the progression and magnitude of the mean arterial pressure in male but not female rats (Males: 157 ±3 vs. 136 ±3; Females: 155 ±6 vs. 154 ±5 mmHg, HS vs. HS/oxo). Xanthine oxidase (XO) is one of the enzymes that produce UA, and its activity has been shown to affect HTN as well. Therefore, we examined the level of XO activity in the plasma after the treatment. While there was no difference in the activity based on the diet within each sex, females had significantly lower levels of XO activity compared to males in each of the diets. To further investigate the beneficial phenotype seen in male rats, we evaluate changes in the progression of renal pathology. The HS/oxo group compared to the HS group had a lower kidney weight/body weight ratio and lower protein cast accumulation, indicating lower kidney damage. Furthermore, the HS/Oxo treated males had less oxidative damage in their tubules than the HS-only males. Bulk-RNA seq done on the male kidneys revealed that attenuated HTN phenotype was associated with an increased expression in Mas1 (MAS receptor), Klk-1 (Kallikrein-1), and Pcsk6 (PCSK6 enzyme) which can all lead to the activation of different vasodilatory pathways. Our study showed that in male but not female Dahl SS rats, asymptomatic mild hyperuricemia accompanied by hyperuricosuria ameliorates the progression of SS HTN and protects kidneys from further damage. Thus, our findings challenge the notion of hyperuricemia being inherently detrimental to health and highlight that this is an oversimplified view of UA’s role in disease.

overall_design: Male and female rats from the Dahl salt-sensitive (SS/JrHsdMcwi) strain were used. Rats were kept on a normal salt (0.4% NaCl/NS) diet and water ad libitum. The rats were implanted with telemeters at 8-9 weeks of age. After recovery, blood pressure measurements were collected for 4 days on the NS diet and switched to either a 4% NaCl diet (HS) or  a HS + 2% oxonic acid diet for 3 weeks. These custom diets were purchased from Dyets, Inc. At the endpoint before euthanasia, under anesthesia kidneys were perfused with PBS and harvested. One kidney was fixed in 10% formalin for histology and the other was snap-frozen in liquid nitrogen for other analyses including RNA seq.

last: Staruschenko


title: Chromatin plasticity contributes to neuronal selection during memory allocation

status: Public on Jul 26 2024

city: Lausanne

first: Johannes

last: Graeff

address: Station 19

department: SV

country: Switzerland

institute: EPFL

summary: Memory allocation refers to the process by which neurons are recruited into the encoding ensemble to store learned information. This recruitment is regulated by neuronal selection based on differences in intrinsic excitability (IE) and the expression of the transcription factor CREB. However, whether other forms of plasticity influence memory allocation remains unknown. Here, we found that chromatin compaction and histone acetylation in the mouse lateral amygdala display a high degree of heterogeneity, a prerequisite for neuronal selection. Consequently, when we increased histone acetylation by overexpressing histone acetyl transferases (HATs), neurons with elevated histone acetylation were preferentially recruited into the encoding ensemble and memory retention was enhanced, while optogenetic silencing of the epigenetically altered neurons prevented memory expression. Mechanistically, using patch-clamp recordings and single-nucleus multi-ome sequencing, we observed that HAT overexpression increased IE and epitranscriptomic changes favoring synaptic plasticity. Lastly, by merging FRET-based epigenetic beacons with calcium indicators to simultaneously record histone acetylation and neuronal dynamics in real time, we found that epigenetic heterogeneity underlies IE in cell-autonomous manner. These results identify chromatin plasticity as a key factor catalyzing memory allocation.

overall_design: Single-nuclear sequencing of mouse brain lateral amigdala.

first: Giulia

last: Santoni

first: Marion

last: Leleu

last: Gräff


title: Ex vivo imaging reveals the spatiotemporal control of ovulation

status: Public on Jul 08 2024

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

institute: Max Planck Institute for Multidisciplinary Sciences

summary: To investigate the transcriptomic profile of in vivo and ex vivo ovulation systems

overall_design: Expression profiling through single-cell RNA sequencing of ovulating follicles at 0,3,6,9,12 hours post-hCG addition

first: Chris

last: Thomas

first: Tabea

last: Marx

first: Sarah

first: Melina

last: Schuh


title: Inhibiting macrophage-derived lactate transport restores cGAS-STING signaling and enhances anti-tumour immunity in glioblastoma

status: Public on Jun 01 2024

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

summary: Glioblastoma (GBM) is a malignancy with a complex tumour microenvironment (TME) dominated by glioblastoma stem cells (GSCs) and infiltrated by tumour-associated macrophages (TAMs), and exhibits aberrant metabolic pathways. Lactate is a critical glycolytic metabolite that promotes tumour progression; however, the mechanisms of lactate transport and lactylation in the TME of GBM remain elusive. Here we show that lactate is transported from TAMs to GSCs via MCT4/MCT1. TAMs provide lactate to GSCs, promoting GSC proliferation and inducing lactylation of the non-homologous end joining (NHEJ) protein KU70 at lysine 317 (K317), which inhibits cGAS-STING signaling and remodels the immunosuppressive TME. Inhibition of lactate transport or targeting the lactylation of KU70, in combination with the immune checkpoint blockade, demonstrates additive therapeutic benefits in immunocompetent xenograft models. This study unveils TAM-derived lactate and lactylation as critical regulators in GSCs to enforce an immunosuppressive microenvironment, opening avenues for developing combinatorial therapy for GBM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MES28 cell and its KD and rescued derivatives (shMCT1/shKU70/KU70-WT/KU70-MU).

first: Gaoyuan

last: Cui

first: Kailin

last: Yang

first: Chenfei

last: Lu

first: Yuhan

last: Jiang

first: Le

last: Zhang

first: Qiulian

last: Wu

first: Deobrat

last: Dixit

first: Zhe

last: Zhu

first: Ryan

last: Gimple

first: Danling

last: Gu

first: Jiancheng

last: Gao

first: Qiankun

last: Lin

first: Hang

last: Yu

first: Zhumei

last: Shi

first: Yun

last: Chen

first: Qianghu

last: Wang

first: Guangfu

last: Jin

first: Fan

first: Junfei

last: Shao

first: Qigang

last: Zhou

first: Chong

last: Liu

first: Chaojun

first: Yongping

last: You

first: Nu

first: Junxia

first: Xu

last: Qian

first: Qian

first: Jeremy

last: Rich

first: Xiuxing


title: Uniform dynamics of cohesin-mediated loop extrusion in living human cells

status: Public on Jul 28 2024

city: PARIS

first: Christophe

last: Zimmer

address: 25-28 rue du docteur Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: Most animal genomes are partitioned into Topologically Associating Domains (TADs), created by cohesin-mediated loop extrusion and defined by convergently oriented CCCTC-binding factor (CTCF) sites. The dynamics of loop extrusion and its regulation remain poorly characterized in vivo. Here, we tracked the motion of TAD anchors in living human cells to visualize and quantify cohesin-dependent loop extrusion across multiple endogenous genomic regions. We show that TADs are dynamic structures whose anchors are brought in proximity about once per hour and for 6-19 min (~16% of the time). Moreover, TADs are continuously subjected to extrusion by multiple cohesin complexes. Remarkably, despite strong differences of Hi-C patterns between the chromatin regions, their dynamics is consistent with the same density, residence time and speed of cohesin. Our results suggest that TAD dynamics is governed primarily by the location and affinity of CTCF binding sites, which allows genome-wide predictive models of cohesin-dependent chromatin interactions.

overall_design: We performed Capture Micro-C in HCT116 cells treated or not with 500 𝞵M auxin (leading to RAD21 depletion) for 3 hours. We used cell lines with TetO and CuO repeats inserted in the genome at the L1, L2, T1 and No Loop genomic regions.

first: Thomas

last: Sabaté

first: Benoît

last: Lelandais

first: Marie-Cécile

last: Robert

first: Michael

last: Szalay

first: Jean-Yves

last: Tinevez

first: Edouard

last: Bertrand


title: Integrative genome-wide DNA methylome and transcriptome data reveals key genes involved in the dysregulation of adipose-stem cells linked to Crohn’s disease

first: Lauro

last: Sumoy

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: MPRA from K562 (ENCSR820RPI)

status: Public on May 07 2024

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf